# Date 2008-01-16 Time 03:52:01 PST -0800 (1200484321.21 s)
#phil __OFF__

Command line arguments: "../83.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 17290
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 83

-------------------------------------------------------------------------------
  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, 47.3993, 86.822, 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, 47.3993, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.847 1.95085
Completeness in resolution range: 0.925363
Completeness with d_max=infinity: 0.922573

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8470
                             d_min =   1.9509

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 47.3993, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.847 1.95085
Completeness in resolution range: 0.925363
Completeness with d_max=infinity: 0.922573

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8474 -  4.1748 [2223/2251]  1998   225  10.1%
  bin  2:  4.1748 -  3.3259 [2130/2153]  1915   215  10.1%
  bin  3:  3.3259 -  2.9091 [2100/2125]  1893   207   9.9%
  bin  4:  2.9091 -  2.6447 [2089/2105]  1879   210  10.1%
  bin  5:  2.6447 -  2.4561 [2055/2099]  1846   209  10.2%
  bin  6:  2.4561 -  2.3118 [2072/2100]  1869   203   9.8%
  bin  7:  2.3118 -  2.1964 [2049/2085]  1850   199   9.7%
  bin  8:  2.1964 -  2.1011 [2061/2103]  1853   208  10.1%
  bin  9:  2.1011 -  2.0204 [2014/2061]  1812   202  10.0%
  bin 10:  2.0204 -  1.9509 [ 796/2087]   715    81  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_83/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: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.15 -     1.90: 14
        1.90 -     2.65: 96
        2.65 -     3.40: 4410
        3.40 -     4.15: 9453
        4.15 -     4.90: 14572
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.154 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.154 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.412 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.508 3.040 -x+1,y+1/2,-z+1/2
  " N   TRP A  92 " - " O   HOH Z 401 "  1.588 3.120 -x+1,y-1/2,-z+1/2
  ... (remaining 28540 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_83/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_83/model_refine_001.geo

CPU time processing inputs: 9.01


============================ 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 47.3993 86.82195 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 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3945   r_free= 0.3907   ksol= 0.00   Bsol= 0.00   scale= 0.942    |
|                                                                             |
| 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:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.186096                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8474 -  4.6565 0.99   1444  159 0.3189 0.3266      6.4477      6.5061|
|  2:  4.6565 -  3.7151 0.99   1399  155 0.3171 0.2945       6.604      6.5913|
|  3:  3.7151 -  3.2511 0.99   1352  151 0.3546 0.3457      6.5077      6.5636|
|  4:  3.2511 -  2.9564 0.99   1359  146 0.3774 0.3733      6.3689      6.3828|
|  5:  2.9564 -  2.7459 0.98   1321  153 0.4098 0.4011      6.2524       6.264|
|  6:  2.7459 -  2.5849 0.99   1362  148 0.4137 0.4684      6.1714      6.1088|
|  7:  2.5849 -  2.4561 0.98   1294  154 0.4280 0.3635      6.1395      6.0261|
|  8:  2.4561 -  2.3496 0.99   1340  134 0.4422 0.4296      6.0982      6.1074|
|  9:  2.3496 -  2.2595 0.99   1343  152 0.4505 0.4327      6.0633      6.0843|
| 10:  2.2595 -  2.1817 0.98   1324  146 0.4472 0.4334      6.0287      6.0034|
| 11:  2.1817 -  2.1137 0.97   1273  151 0.4702 0.4892      5.9842      6.0041|
| 12:  2.1137 -  2.0535 0.99   1327  149 0.4568 0.4568      5.8946      5.9087|
| 13:  2.0535 -  1.9995 0.88   1190  123 0.4622 0.5057      5.8247      5.8137|
| 14:  1.9995 -  1.9509 0.23    302   38 0.4973 0.4906      5.8946      5.7353|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8474 -  4.6565  1444   159  0.74  31.04   0.86     0.75      57807.46|
|  2:  4.6565 -  3.7151  1399   155  0.78  28.28   0.96     0.87      72177.73|
|  3:  3.7151 -  3.2511  1352   151  0.71  34.55   0.96     0.88      74106.71|
|  4:  3.2511 -  2.9564  1359   146  0.65  39.86   0.96     0.83      65126.98|
|  5:  2.9564 -  2.7459  1321   153  0.59  44.69   0.95     0.80      54230.51|
|  6:  2.7459 -  2.5849  1362   148  0.59  44.74   0.94     0.79      45723.62|
|  7:  2.5849 -  2.4561  1294   154  0.59  44.49   0.97     0.80      40748.15|
|  8:  2.4561 -  2.3496  1340   134  0.58  45.53   0.97     0.80      36953.99|
|  9:  2.3496 -  2.2595  1343   152  0.58  45.55   0.95     0.83      35209.55|
| 10:  2.2595 -  2.1817  1324   146  0.56  47.26   0.99     0.80      33145.31|
| 11:  2.1817 -  2.1137  1273   151  0.52  50.61   0.97     0.78      34106.85|
| 12:  2.1137 -  2.0535  1327   149  0.46  55.28   1.00     0.72      33998.82|
| 13:  2.0535 -  1.9995  1190   123  0.43  57.90   0.98     0.68      31456.75|
| 14:  1.9995 -  1.9509   302    38  0.47  54.01   0.97     0.63      25276.14|
|alpha:            min =        0.63 max =            0.88 mean =         0.79|
|beta:             min =    25276.14 max =        74106.71 mean =     47310.45|
|figures of merit: min =        0.00 max =            1.00 mean =         0.60|
|phase err.(work): min =        0.00 max =           90.00 mean =        43.71|
|phase err.(test): min =        0.00 max =           89.94 mean =        43.99|
|-----------------------------------------------------------------------------|

============================== 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 = 5.997061              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.837   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.071124              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.609   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.154 -  1.528:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.528 -  1.903:       10 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.903 -  2.278:       15 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.278 -  2.652:       81 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.652 -  3.027:     2060 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.027 -  3.401:     2350 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.401 -  3.776:     3996 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.776 -  4.151:     5457 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.151 -  4.525:     6498 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.525 -  4.900:     8074 |
|-----------------------------------------------------------------------------|
|-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 |        0.216 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.154 |       0.978 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.661)------------------------------------------|
|    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 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3945   r_free= 0.3907   ksol= 0.00   Bsol= 0.00   scale= 0.942    |
|                                                                             |
| 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:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.186096                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3850   r_free= 0.3809   ksol= 0.31   Bsol= 35.86   scale= 0.968   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.04,-0.05,-0.93,-0.00,-0.00,-0.00); trace/3= 0.02                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.173319                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.351867              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.601   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.581034              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.363   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3850      final r-factor (work) = 0.2520          |
| start r-factor (free) = 0.3809      final r-factor (free) = 0.2783          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.7492 = 5.35 * 0.50 * 6.1786 + 1.00 * 0.2156                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.0631 = 5.35 * 0.50 * 5.9676 + 1.00 * 0.0941                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2520      final r-factor (work) = 0.2306          |
| start r-factor (free) = 0.2783      final r-factor (free) = 0.2799          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4738 = 0.58 * 1.00 * 5.9676 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3931 = 0.58 * 1.00 * 5.7594 + 1.00 * 0.0467                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.661)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.88   17.27    None  None   None       |
|    all(noH): 2823   0      0.00    90.88   17.27    None  None   None       |
|    Sol.    : 438    0      6.26    64.40   38.05    None  None   None       |
|    Mac.    : 2385   0      0.00    90.88   13.45    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 -   9.088:  813   |   5:    45.441 -  54.529:  110        |
|      1:     9.088 -  18.176: 1100   |   6:    54.529 -  63.617:   43        |
|      2:    18.176 -  27.264:  407   |   7:    63.617 -  72.705:    1        |
|      3:    27.264 -  36.353:  198   |   8:    72.705 -  81.793:    0        |
|      4:    36.353 -  45.441:  150   |   9:    81.793 -  90.881:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2306 r_free = 0.2799             target_work(ml) = 5.764         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2303 r_free = 0.2797             target_work(ml) = 5.763         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2303   r_free= 0.2797   ksol= 0.31   Bsol= 35.86   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.04,-0.05,-0.93,-0.00,-0.00,-0.00); trace/3= 0.02                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.763200                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2258   r_free= 0.2747   ksol= 0.33   Bsol= 49.09   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-1.53,-1.46,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.752077                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.269937              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.251   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.397285              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.033   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2258      final r-factor (work) = 0.1562          |
| start r-factor (free) = 0.2747      final r-factor (free) = 0.1971          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.4022 = 4.27 * 0.50 * 5.7650 + 1.00 * 0.0940                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0350 = 4.27 * 0.50 * 5.6073 + 1.00 * 0.0637                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1562      final r-factor (work) = 0.1390          |
| start r-factor (free) = 0.1971      final r-factor (free) = 0.1854          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2523 = 0.40 * 1.00 * 5.6073 + 1.00 * 0.0246                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1399 = 0.40 * 1.00 * 5.3626 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.661)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.11   17.75    None  None   None       |
|    all(noH): 2823   0      0.00    91.11   17.75    None  None   None       |
|    Sol.    : 438    0      5.95    73.23   40.94    None  None   None       |
|    Mac.    : 2385   0      0.00    91.11   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:     0.000 -   9.111:  777   |   5:    45.556 -  54.667:  113        |
|      1:     9.111 -  18.222: 1281   |   6:    54.667 -  63.778:   76        |
|      2:    18.222 -  27.334:  286   |   7:    63.778 -  72.889:   36        |
|      3:    27.334 -  36.445:  128   |   8:    72.889 -  82.001:    4        |
|      4:    36.445 -  45.556:  119   |   9:    82.001 -  91.112:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1390 r_free = 0.1854             target_work(ml) = 5.327         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1388 r_free = 0.1854             target_work(ml) = 5.327         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1388   r_free= 0.1854   ksol= 0.33   Bsol= 49.09   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-1.53,-1.46,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.326531                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1386   r_free= 0.1848   ksol= 0.32   Bsol= 49.09   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.09,-1.93,-1.36,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.323069                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.472115              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.759  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.201618              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.149  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1386      final r-factor (work) = 0.1210          |
| start r-factor (free) = 0.1848      final r-factor (free) = 0.1642          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6931 = 2.47 * 0.50 * 5.3633 + 1.00 * 0.0638                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5655 = 2.47 * 0.50 * 5.2651 + 1.00 * 0.0575                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1210      final r-factor (work) = 0.1188          |
| start r-factor (free) = 0.1642      final r-factor (free) = 0.1611          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0708 = 0.20 * 1.00 * 5.2651 + 1.00 * 0.0093                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0565 = 0.20 * 1.00 * 5.2017 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.661)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.81    88.97   17.20    None  None   None       |
|    all(noH): 2823   0      1.81    88.97   17.20    None  None   None       |
|    Sol.    : 438    0      6.02    73.94   39.17    None  None   None       |
|    Mac.    : 2385   0      1.81    88.97   13.16    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:     1.815 -  10.530: 1073   |   5:    45.392 -  54.107:  105        |
|      1:    10.530 -  19.245: 1084   |   6:    54.107 -  62.822:   55        |
|      2:    19.245 -  27.961:  212   |   7:    62.822 -  71.538:   21        |
|      3:    27.961 -  36.676:  133   |   8:    71.538 -  80.253:    6        |
|      4:    36.676 -  45.392:  131   |   9:    80.253 -  88.969:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1188 r_free = 0.1611             target_work(ml) = 5.191         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1187 r_free = 0.1611             target_work(ml) = 5.191         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1187   r_free= 0.1611   ksol= 0.32   Bsol= 49.09   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.09,-1.93,-1.36,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.190702                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1187   r_free= 0.1612   ksol= 0.33   Bsol= 49.09   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.32,-2.10,-1.32,-0.00,-0.00,-0.00); trace/3= -2.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.190636                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.414402              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 140.346  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.127831              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 159.719  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1187      final r-factor (work) = 0.1124          |
| start r-factor (free) = 0.1612      final r-factor (free) = 0.1556          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3365 = 2.41 * 0.50 * 5.2013 + 1.00 * 0.0575                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3020 = 2.41 * 0.50 * 5.1677 + 1.00 * 0.0635                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1124      final r-factor (work) = 0.1123          |
| start r-factor (free) = 0.1556      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6683 = 0.13 * 1.00 * 5.1677 + 1.00 * 0.0078                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6655 = 0.13 * 1.00 * 5.1475 + 1.00 * 0.0075                               |
|-----------------------------------------------------------------------------|
| number of iterations = 3       |    number of function evaluations = 5      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.661)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.87    88.86   17.18    None  None   None       |
|    all(noH): 2823   0      2.87    88.86   17.18    None  None   None       |
|    Sol.    : 438    0      5.15    73.87   39.02    None  None   None       |
|    Mac.    : 2385   0      2.87    88.86   13.17    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:     2.872 -  11.471: 1284   |   5:    45.868 -  54.468:  100        |
|      1:    11.471 -  20.070:  911   |   6:    54.468 -  63.067:   52        |
|      2:    20.070 -  28.670:  189   |   7:    63.067 -  71.666:   21        |
|      3:    28.670 -  37.269:  132   |   8:    71.666 -  80.266:    5        |
|      4:    37.269 -  45.868:  126   |   9:    80.266 -  88.865:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1123 r_free = 0.1549             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1122 r_free = 0.1548             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1122   r_free= 0.1548   ksol= 0.33   Bsol= 49.09   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.32,-2.10,-1.32,-0.00,-0.00,-0.00); trace/3= -2.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.144818                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1546   ksol= 0.33   Bsol= 49.09   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.32,-2.10,-1.32,-0.00,-0.00,-0.00); trace/3= -2.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.143770                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.622479              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 155.947  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.559913              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.966  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1120      final r-factor (work) = 0.1127          |
| start r-factor (free) = 0.1546      final r-factor (free) = 0.1554          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2386 = 1.62 * 0.50 * 5.1465 + 1.00 * 0.0635                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2305 = 1.62 * 0.50 * 5.1481 + 1.00 * 0.0542                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1127      final r-factor (work) = 0.1112          |
| start r-factor (free) = 0.1554      final r-factor (free) = 0.1574          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.1861 = 2.56 * 1.00 * 5.1481 + 1.00 * 0.0074                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.1791 = 2.56 * 1.00 * 5.1445 + 1.00 * 0.0095                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.661)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.98    96.08   17.52    None  None   None       |
|    all(noH): 2823   0      0.98    96.08   17.52    None  None   None       |
|    Sol.    : 438    0      5.06    84.15   40.91    None  None   None       |
|    Mac.    : 2385   0      0.98    96.08   13.22    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:     0.977 -  10.487: 1079   |   5:    48.529 -  58.039:  108        |
|      1:    10.487 -  19.998: 1112   |   6:    58.039 -  67.550:   57        |
|      2:    19.998 -  29.508:  196   |   7:    67.550 -  77.060:   22        |
|      3:    29.508 -  39.019:  121   |   8:    77.060 -  86.571:    6        |
|      4:    39.019 -  48.529:  119   |   9:    86.571 -  96.081:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1112 r_free = 0.1574             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1112 r_free = 0.1574             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1574   ksol= 0.33   Bsol= 49.09   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.32,-2.10,-1.32,-0.00,-0.00,-0.00); trace/3= -2.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.150932                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8474 -  4.6565 0.99   1444  159 0.0970 0.1282      5.3787      5.5384|
|  2:  4.6565 -  3.7151 0.99   1399  155 0.0836 0.1075      5.4084       5.603|
|  3:  3.7151 -  3.2511 0.99   1352  151 0.1065 0.1487      5.4513      5.8009|
|  4:  3.2511 -  2.9564 0.99   1359  146 0.1224 0.1575      5.4386      5.6056|
|  5:  2.9564 -  2.7459 0.98   1321  153 0.1277 0.1566      5.3033      5.4796|
|  6:  2.7459 -  2.5849 0.99   1362  148 0.1250 0.2144      5.2103      5.5163|
|  7:  2.5849 -  2.4561 0.98   1294  154 0.1238 0.1623      5.1616      5.3616|
|  8:  2.4561 -  2.3496 0.99   1340  134 0.1169 0.1601      5.0824      5.2522|
|  9:  2.3496 -  2.2595 0.99   1343  152 0.1157 0.1814      5.0158      5.3258|
| 10:  2.2595 -  2.1817 0.98   1324  146 0.1101 0.1754      4.9386      5.1984|
| 11:  2.1817 -  2.1137 0.97   1273  151 0.1147 0.1784      4.9091       5.232|
| 12:  2.1137 -  2.0535 0.99   1327  149 0.1141 0.1675      4.8613      5.1029|
| 13:  2.0535 -  1.9995 0.88   1190  123 0.1128 0.1978       4.798      5.0913|
| 14:  1.9995 -  1.9509 0.23    302   38 0.1051 0.1680      4.7682      4.9213|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8474 -  4.6565  1444   159  0.94   9.20   0.98     0.95       7215.34|
|  2:  4.6565 -  3.7151  1399   155  0.95   7.71   1.02     1.00       8537.78|
|  3:  3.7151 -  3.2511  1352   151  0.94  11.18   1.03     1.02       9742.09|
|  4:  3.2511 -  2.9564  1359   146  0.92  13.88   1.02     1.01      10177.29|
|  5:  2.9564 -  2.7459  1321   153  0.90  15.68   1.00     0.97       8163.04|
|  6:  2.7459 -  2.5849  1362   148  0.90  16.49   0.98     0.96       7066.86|
|  7:  2.5849 -  2.4561  1294   154  0.91  15.55   0.99     0.95       6194.87|
|  8:  2.4561 -  2.3496  1340   134  0.90  15.87   1.00     0.97       5615.07|
|  9:  2.3496 -  2.2595  1343   152  0.91  15.72   1.00     0.96       4929.75|
| 10:  2.2595 -  2.1817  1324   146  0.90  15.70   1.00     0.96       4368.02|
| 11:  2.1817 -  2.1137  1273   151  0.90  16.02   0.99     0.96       4163.82|
| 12:  2.1137 -  2.0535  1327   149  0.91  15.90   1.00     1.00       3866.92|
| 13:  2.0535 -  1.9995  1190   123  0.90  16.97   0.99     0.97       3548.25|
| 14:  1.9995 -  1.9509   302    38  0.91  15.38   0.97     0.92       3097.55|
|alpha:            min =        0.92 max =            1.02 mean =         0.98|
|beta:             min =     3097.55 max =        10177.29 mean =      6427.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.77 mean =        14.23|
|phase err.(test): min =        0.00 max =           88.70 mean =        13.85|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1574   ksol= 0.32   Bsol= 49.06   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.22,-1.97,-1.12,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.150838                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1574   ksol= 0.32   Bsol= 49.06   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.22,-1.97,-1.12,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.150838                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8474 -  4.6565 0.99   1444  159 0.0969 0.1282      5.3778      5.5383|
|  2:  4.6565 -  3.7151 0.99   1399  155 0.0837 0.1075      5.4088      5.6032|
|  3:  3.7151 -  3.2511 0.99   1352  151 0.1065 0.1486      5.4512      5.8005|
|  4:  3.2511 -  2.9564 0.99   1359  146 0.1223 0.1573      5.4383       5.605|
|  5:  2.9564 -  2.7459 0.98   1321  153 0.1277 0.1565      5.3032      5.4795|
|  6:  2.7459 -  2.5849 0.99   1362  148 0.1250 0.2143      5.2101      5.5158|
|  7:  2.5849 -  2.4561 0.98   1294  154 0.1238 0.1624      5.1614      5.3616|
|  8:  2.4561 -  2.3496 0.99   1340  134 0.1169 0.1600      5.0822      5.2515|
|  9:  2.3496 -  2.2595 0.99   1343  152 0.1157 0.1814      5.0159      5.3256|
| 10:  2.2595 -  2.1817 0.98   1324  146 0.1101 0.1755       4.939      5.1991|
| 11:  2.1817 -  2.1137 0.97   1273  151 0.1147 0.1785      4.9094      5.2325|
| 12:  2.1137 -  2.0535 0.99   1327  149 0.1141 0.1675      4.8611      5.1026|
| 13:  2.0535 -  1.9995 0.88   1190  123 0.1129 0.1979      4.7981      5.0913|
| 14:  1.9995 -  1.9509 0.23    302   38 0.1052 0.1682      4.7674      4.9206|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8474 -  4.6565  1444   159  0.94   9.19   0.98     0.95       7196.42|
|  2:  4.6565 -  3.7151  1399   155  0.95   7.72   1.02     1.01       8533.95|
|  3:  3.7151 -  3.2511  1352   151  0.94  11.18   1.03     1.03       9742.09|
|  4:  3.2511 -  2.9564  1359   146  0.92  13.88   1.02     1.01      10172.45|
|  5:  2.9564 -  2.7459  1321   153  0.90  15.68   1.00     0.98       8157.62|
|  6:  2.7459 -  2.5849  1362   148  0.90  16.49   0.98     0.96       7065.53|
|  7:  2.5849 -  2.4561  1294   154  0.91  15.55   0.99     0.96       6190.01|
|  8:  2.4561 -  2.3496  1340   134  0.90  15.87   1.01     0.98       5610.38|
|  9:  2.3496 -  2.2595  1343   152  0.91  15.71   1.00     0.96       4927.06|
| 10:  2.2595 -  2.1817  1324   146  0.90  15.71   1.00     0.97       4371.38|
| 11:  2.1817 -  2.1137  1273   151  0.90  16.04   1.00     0.96       4169.17|
| 12:  2.1137 -  2.0535  1327   149  0.91  15.91   1.01     1.01       3868.79|
| 13:  2.0535 -  1.9995  1190   123  0.90  16.97   1.00     0.98       3549.26|
| 14:  1.9995 -  1.9509   302    38  0.91  15.37   0.98     0.92       3097.62|
|alpha:            min =        0.92 max =            1.03 mean =         0.98|
|beta:             min =     3097.62 max =        10172.45 mean =      6424.20|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.88 mean =        14.23|
|phase err.(test): min =        0.00 max =           88.83 mean =        13.85|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.661)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.94    96.05   17.48    None  None   None       |
|    all(noH): 2823   0      0.94    96.05   17.48    None  None   None       |
|    Sol.    : 438    0      5.02    84.12   40.88    None  None   None       |
|    Mac.    : 2385   0      0.94    96.05   13.19    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:     0.943 -  10.454: 1079   |   5:    48.495 -  58.006:  108        |
|      1:    10.454 -  19.964: 1112   |   6:    58.006 -  67.516:   57        |
|      2:    19.964 -  29.474:  196   |   7:    67.516 -  77.026:   22        |
|      3:    29.474 -  38.985:  121   |   8:    77.026 -  86.537:    6        |
|      4:    38.985 -  48.495:  119   |   9:    86.537 -  96.047:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 282         
Filter by distance & map next to the model:
   mapped sites are within: 0.702 - 3.982
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 281 from: 282
   mapped sites are within: 0.702 - 3.982

peak=    5.873 closest distance to " CB  ARG A 275 " =    0.965
peak=    5.425 closest distance to " CG  PRO A  54 " =    1.271
peak=    5.198 closest distance to " NH2 ARG A  56 " =    2.208
peak=    5.013 closest distance to " CG  PRO A  90 " =    1.185
peak=    4.950 closest distance to " CA  TYR A  30 " =    0.905
peak=    4.928 closest distance to " CB  GLN A 223 " =    1.427
peak=    4.847 closest distance to " CG  PRO A 198 " =    1.235
peak=    4.754 closest distance to " O   HOH Z 417 " =    1.884
peak=    4.681 closest distance to " O   HOH Z 232 " =    2.324
peak=    4.647 closest distance to " O   HOH Z 126 " =    1.798
peak=    4.614 closest distance to " CG  PRO A 213 " =    1.272
peak=    4.600 closest distance to " O   HOH Z  97 " =    2.051
peak=    4.576 closest distance to " CB  SER A  63 " =    1.129
peak=    4.554 closest distance to " O   HOH Z 142 " =    1.587
peak=    4.529 closest distance to " O   HOH Z 234 " =    3.550
peak=    4.529 closest distance to " NE2 GLN A  11 " =    1.039
peak=    4.502 closest distance to " O   HOH Z 298 " =    1.764
peak=    4.492 closest distance to " CB  GLN A 183 " =    1.291
peak=    4.491 closest distance to " O   HOH Z 193 " =    1.742
peak=    4.480 closest distance to " NZ  LYS A 117 " =    2.920
peak=    4.461 closest distance to " O   HOH Z 402 " =    1.413
peak=    4.416 closest distance to " C   PRO A 198 " =    1.509
peak=    4.405 closest distance to " CB  PRO A  54 " =    1.070
peak=    4.400 closest distance to " O   HOH Z 109 " =    2.423
peak=    4.381 closest distance to " O   HOH Z 209 " =    2.249
peak=    4.369 closest distance to " O   HOH Z 272 " =    1.880
peak=    4.361 closest distance to " O   HOH Z 369 " =    2.421
peak=    4.358 closest distance to " CB  ARG A  79 " =    1.334
peak=    4.355 closest distance to " CG  PRO A 243 " =    1.073
peak=    4.301 closest distance to " CD2 TRP A 179 " =    1.368
peak=    4.272 closest distance to " CB  ARG A 190 " =    1.696
peak=    4.254 closest distance to " O  BHOH Z  74 " =    1.300
peak=    4.251 closest distance to " O   HOH Z 287 " =    1.780
peak=    4.244 closest distance to " O   HOH Z  43 " =    2.316
peak=    4.232 closest distance to " O   SER A  87 " =    2.236
peak=    4.202 closest distance to " O   HOH Z 189 " =    2.386
peak=    4.200 closest distance to " O   HOH Z 327 " =    1.657
peak=    4.193 closest distance to " O   HOH Z 250 " =    1.463
peak=    4.191 closest distance to " O   HOH Z 102 " =    1.288
peak=    4.172 closest distance to " NH2BARG A 145 " =    2.062
peak=    4.159 closest distance to " CB  ASN A 148 " =    1.416
peak=    4.153 closest distance to " O   HOH Z  40 " =    2.011
peak=    4.150 closest distance to " O   HOH Z 406 " =    1.528
peak=    4.135 closest distance to " CG  ARG A  66 " =    2.691
peak=    4.115 closest distance to " O   HOH Z 346 " =    1.690
peak=    4.110 closest distance to " CG2 VAL A 257 " =    0.827
peak=    4.110 closest distance to " CA  ARG A  36 " =    0.989
peak=    4.107 closest distance to " O   HOH Z 265 " =    2.208
peak=    4.104 closest distance to " ND2 ASN A 187 " =    1.418
peak=    4.101 closest distance to " O   HOH Z 128 " =    2.219
peak=    4.087 closest distance to " O   HOH Z  15 " =    2.152
peak=    4.065 closest distance to " CB  GLU A 152 " =    1.199
peak=    4.053 closest distance to " O   HOH Z  85 " =    1.459
peak=    4.044 closest distance to " O   HOH Z  44 " =    2.007
peak=    4.041 closest distance to " OE1 GLU A   2 " =    2.334
peak=    4.031 closest distance to " O   HOH Z 389 " =    1.837
peak=    4.013 closest distance to " CB  VAL A 265 " =    1.193
peak=    4.006 closest distance to " O   HOH Z 403 " =    1.715
peak=    3.948 closest distance to " CG1 ILE A  33 " =    1.218
peak=    3.925 closest distance to " O   HOH Z 203 " =    1.731
peak=    3.906 closest distance to " O   HOH Z  63 " =    1.912
peak=    3.895 closest distance to " O   HOH Z 368 " =    2.043
peak=    3.894 closest distance to " O   HOH Z 357 " =    1.923
peak=    3.894 closest distance to " CA  ALA A  84 " =    1.148
peak=    3.879 closest distance to " N   ASN A  39 " =    1.201
peak=    3.875 closest distance to " O   HOH Z 245 " =    1.362
peak=    3.874 closest distance to " O   HOH Z 227 " =    1.771
peak=    3.851 closest distance to " O   HOH Z  78 " =    1.683
peak=    3.847 closest distance to " O   HOH Z  54 " =    1.686
peak=    3.841 closest distance to " O   HOH Z 128 " =    1.932
peak=    3.841 closest distance to " CZ  PHE A 218 " =    1.132
peak=    3.831 closest distance to " O   HOH Z 132 " =    2.462
peak=    3.831 closest distance to " CD  ARG A 269 " =    1.051
peak=    3.821 closest distance to " O   HOH Z 361 " =    3.558
peak=    3.820 closest distance to " O   HOH Z 427 " =    2.877
peak=    3.817 closest distance to " O   HOH Z 126 " =    1.916
peak=    3.815 closest distance to " CB  TRP A 266 " =    1.079
peak=    3.805 closest distance to " O   HOH Z  59 " =    2.124
peak=    3.801 closest distance to " CA  ALA A  51 " =    0.956
peak=    3.790 closest distance to " O   HOH Z  43 " =    1.420
peak=    3.788 closest distance to " O   HOH Z 316 " =    3.068
peak=    3.784 closest distance to " CG2 ILE A 120 " =    1.252
peak=    3.779 closest distance to " O   HOH Z 173 " =    2.105
peak=    3.774 closest distance to " CG AARG A 275 " =    1.102
peak=    3.773 closest distance to " CE  LYS A 119 " =    1.130
peak=    3.758 closest distance to " O   HOH Z  97 " =    2.216
peak=    3.743 closest distance to " CA  ASN A 176 " =    1.178
peak=    3.725 closest distance to " CB  GLU A 277 " =    3.545
peak=    3.718 closest distance to " CB  VAL A 202 " =    1.488
peak=    3.715 closest distance to " O   HOH Z 345 " =    2.810
peak=    3.709 closest distance to " O   HOH Z 158 " =    2.932
peak=    3.704 closest distance to " CB  ASP A 140 " =    1.121
peak=    3.689 closest distance to " CB  THR A  31 " =    1.526
peak=    3.687 closest distance to " CA  ARG A 195 " =    1.228
peak=    3.676 closest distance to " O   THR A 220 " =    1.168
peak=    3.676 closest distance to " O   HOH Z 423 " =    1.902
peak=    3.676 closest distance to " O   HOH Z 280 " =    2.960
peak=    3.674 closest distance to " O   HOH Z  80 " =    1.692
peak=    3.672 closest distance to " N   ARG A 156 " =    1.449
peak=    3.671 closest distance to " CB  SER A 141 " =    1.062
peak=    3.656 closest distance to " O   HOH Z 214 " =    2.238
peak=    3.655 closest distance to " CD  ARG A 159 " =    0.779
peak=    3.653 closest distance to " CB  SER A   3 " =    1.216
peak=    3.652 closest distance to " O   HOH Z 325 " =    2.308
peak=    3.630 closest distance to " CB  HIS A 108 " =    0.886
peak=    3.623 closest distance to " CB  SER A  62 " =    0.966
peak=    3.623 closest distance to " O   HOH Z 261 " =    1.944
peak=    3.615 closest distance to " CB  TRP A 179 " =    1.208
peak=    3.613 closest distance to " O   HOH Z 298 " =    2.304
peak=    3.609 closest distance to " O   HOH Z 421 " =    1.849
peak=    3.608 closest distance to " CB  ASN A  39 " =    0.816
peak=    3.600 closest distance to " O   HOH Z  61 " =    1.567
peak=    3.600 closest distance to " CG2 ILE A  20 " =    1.428
peak=    3.599 closest distance to " N   CYS A 260 " =    0.954
peak=    3.598 closest distance to " OG BSER A 164 " =    2.102
peak=    3.594 closest distance to " O   HOH Z 247 " =    1.388
peak=    3.588 closest distance to " CA  ASN A 215 " =    1.030
peak=    3.586 closest distance to " CD2 LEU A 297 " =    0.933
peak=    3.586 closest distance to " O   HOH Z 303 " =    2.056
peak=    3.585 closest distance to " N   TYR A 116 " =    1.604
peak=    3.580 closest distance to " O   HOH Z 185 " =    1.775
peak=    3.580 closest distance to " O   HOH Z 180 " =    2.316
peak=    3.567 closest distance to " O   HOH Z 365 " =    2.698
peak=    3.560 closest distance to " CG2AVAL A 121 " =    2.170
peak=    3.554 closest distance to " CB  SER A  26 " =    1.781
peak=    3.549 closest distance to " O   ALA A 165 " =    1.447
peak=    3.544 closest distance to " CB  THR A  52 " =    0.702
peak=    3.529 closest distance to " O   ASN A  74 " =    1.569
peak=    3.527 closest distance to " O   HOH Z  47 " =    1.675
peak=    3.527 closest distance to " O   HOH Z 344 " =    3.021
peak=    3.524 closest distance to " CB  ILE A 120 " =    1.311
peak=    3.522 closest distance to " CZ  PHE A  38 " =    1.254
peak=    3.520 closest distance to " O   HOH Z 392 " =    2.555
peak=    3.519 closest distance to " CG  MET A 185 " =    1.145
peak=    3.518 closest distance to " CA  MET A  40 " =    1.077
peak=    3.515 closest distance to " CG2BVAL A  41 " =    0.781
peak=    3.505 closest distance to " CB  ASN A 148 " =    1.961
peak=    3.497 closest distance to " CA  VAL A 125 " =    1.114
peak=    3.484 closest distance to " O   HOH Z  21 " =    1.852
peak=    3.474 closest distance to " O   HOH Z 380 " =    1.942
peak=    3.473 closest distance to " N   HIS A 108 " =    1.796
peak=    3.468 closest distance to " N   PHE A 130 " =    1.294
peak=    3.467 closest distance to " O   HOH Z 411 " =    3.873
peak=    3.462 closest distance to " CE  LYS A  76 " =    0.820
peak=    3.462 closest distance to " CA  ALA A 160 " =    0.844
peak=    3.462 closest distance to " O   HOH Z 375 " =    2.129
peak=    3.457 closest distance to " O   HOH Z  19 " =    1.617
peak=    3.454 closest distance to " CB  TYR A 169 " =    0.712
peak=    3.452 closest distance to " CB  ALA A 248 " =    1.346
peak=    3.452 closest distance to " O   HOH Z 371 " =    3.144
peak=    3.451 closest distance to " O   HOH Z 248 " =    1.548
peak=    3.449 closest distance to " CB  GLU A 128 " =    1.188
peak=    3.444 closest distance to " CD  LYS A 166 " =    1.273
peak=    3.438 closest distance to " CB  ALA A 291 " =    1.238
peak=    3.426 closest distance to " CA  ALA A  21 " =    1.137
peak=    3.426 closest distance to " CB  ALA A 114 " =    1.046
peak=    3.423 closest distance to " O   HOH Z 337 " =    3.546
peak=    3.417 closest distance to " O   HOH Z 426 " =    1.498
peak=    3.415 closest distance to " CG  ARG A  66 " =    0.971
peak=    3.415 closest distance to " NH1AARG A 145 " =    1.279
peak=    3.410 closest distance to " O   HOH Z 305 " =    3.605
peak=    3.404 closest distance to " CA  ALA A 248 " =    1.218
peak=    3.398 closest distance to " CB  PRO A 198 " =    1.137
peak=    3.393 closest distance to " CG1BVAL A  72 " =    1.733
peak=    3.392 closest distance to " O   HOH Z 313 " =    1.901
peak=    3.391 closest distance to " O   HOH Z  88 " =    2.761
peak=    3.385 closest distance to " O   HOH Z 415 " =    3.511
peak=    3.385 closest distance to " OG  SER A 276 " =    1.398
peak=    3.378 closest distance to " O   HOH Z 291 " =    1.429
peak=    3.366 closest distance to " O   HOH Z 282 " =    1.912
peak=    3.365 closest distance to " O   HOH Z 359 " =    1.481
peak=    3.365 closest distance to " CG  LEU A 167 " =    1.230
peak=    3.364 closest distance to " O   HOH Z 407 " =    1.342
peak=    3.362 closest distance to " O   HOH Z 353 " =    2.669
peak=    3.360 closest distance to " NE2 GLN A  77 " =    3.099
peak=    3.355 closest distance to " O   HOH Z 345 " =    1.645
peak=    3.353 closest distance to " O   HOH Z 416 " =    2.770
peak=    3.353 closest distance to " O   HOH Z  88 " =    2.877
peak=    3.352 closest distance to " O   HOH Z 422 " =    2.542
peak=    3.344 closest distance to " O   HOH Z  48 " =    1.551
peak=    3.338 closest distance to " O   HOH Z 234 " =    1.936
peak=    3.337 closest distance to " O   HOH Z   1 " =    2.135
peak=    3.332 closest distance to " CD  GLN A 194 " =    1.565
peak=    3.331 closest distance to " CA  ASP A 162 " =    1.153
peak=    3.329 closest distance to " O   HOH Z 183 " =    1.784
peak=    3.328 closest distance to " O   HOH Z 250 " =    1.641
peak=    3.326 closest distance to " CG  GLN A  11 " =    1.562
peak=    3.322 closest distance to " CB  GLU A  46 " =    1.062
peak=    3.322 closest distance to " OD2 ASP A 298 " =    3.923
peak=    3.321 closest distance to " N   TRP A 150 " =    1.166
peak=    3.319 closest distance to " O   HOH Z 425 " =    1.986
peak=    3.316 closest distance to " CB  ASN A 110 " =    1.111
peak=    3.313 closest distance to " CG2 VAL A 197 " =    1.066
peak=    3.310 closest distance to " O   HOH Z  63 " =    2.318
peak=    3.306 closest distance to " CB  ASN A  45 " =    1.109
peak=    3.301 closest distance to " O   ALA A   1 " =    1.638
peak=    3.298 closest distance to " OH  TYR A 116 " =    1.058
peak=    3.295 closest distance to " CB  ASN A 215 " =    1.147
peak=    3.292 closest distance to " ND2 ASN A 249 " =    0.922
peak=    3.288 closest distance to " O   THR A 182 " =    1.463
peak=    3.288 closest distance to " O   HOH Z 380 " =    1.888
peak=    3.286 closest distance to " O   HOH Z 163 " =    1.448
peak=    3.283 closest distance to " O   HOH Z 148 " =    3.313
peak=    3.282 closest distance to " O   GLY A  91 " =    1.503
peak=    3.274 closest distance to " O   HOH Z  68 " =    2.014
peak=    3.272 closest distance to " CA  ALA A 291 " =    0.776
peak=    3.272 closest distance to " CB  LYS A 290 " =    1.132
peak=    3.271 closest distance to " O   HOH Z 132 " =    2.453
peak=    3.269 closest distance to " O   HOH Z 427 " =    3.105
peak=    3.267 closest distance to " CA  SER A  32 " =    1.647
peak=    3.267 closest distance to " CA  SER A  87 " =    1.068
peak=    3.252 closest distance to " O   HOH Z  63 " =    2.240
peak=    3.245 closest distance to " CD1AILE A 234 " =    0.902
peak=    3.241 closest distance to " CB  ASP A 191 " =    1.212
peak=    3.237 closest distance to " CA  GLU A 152 " =    0.872
peak=    3.236 closest distance to " CB  GLN A 278 " =    0.858
peak=    3.236 closest distance to " O   HOH Z 303 " =    1.714
peak=    3.235 closest distance to " CB  PRO A 163 " =    3.982
peak=    3.234 closest distance to " NH2 ARG A 219 " =    1.835
peak=    3.231 closest distance to " CA  ILE A 234 " =    0.968
peak=    3.226 closest distance to " O   HOH Z 126 " =    1.494
peak=    3.221 closest distance to " O   HOH Z 383 " =    1.923
peak=    3.219 closest distance to " CB  ASN A 285 " =    0.966
peak=    3.217 closest distance to " O   HOH Z 257 " =    2.233
peak=    3.214 closest distance to " O   HOH Z 423 " =    3.322
peak=    3.210 closest distance to " OG1 THR A 221 " =    1.284
peak=    3.210 closest distance to " O   HOH Z  61 " =    1.479
peak=    3.209 closest distance to " O   HOH Z 124 " =    1.245
peak=    3.209 closest distance to " CB  SER A  99 " =    1.384
peak=    3.209 closest distance to " O   HOH Z 310 " =    3.630
peak=    3.207 closest distance to " CA  LYS A 117 " =    1.239
peak=    3.207 closest distance to " O   HOH Z 147 " =    1.815
peak=    3.204 closest distance to " OG  SER A  62 " =    2.757
peak=    3.199 closest distance to " NH2BARG A 190 " =    1.779
peak=    3.198 closest distance to " NE2 GLN A  73 " =    3.949
peak=    3.196 closest distance to " CA  THR A  82 " =    1.773
peak=    3.194 closest distance to " O   HOH Z  10 " =    1.755
peak=    3.192 closest distance to " CB  ARG A 269 " =    0.758
peak=    3.189 closest distance to " O   HOH Z  35 " =    2.383
peak=    3.187 closest distance to " OD2 ASP A 286 " =    2.769
peak=    3.185 closest distance to " NZ  LYS A 119 " =    1.656
peak=    3.180 closest distance to " OD1 ASN A  69 " =    2.480
peak=    3.179 closest distance to " O   HOH Z 134 " =    1.133
peak=    3.174 closest distance to " CA  ASP A 140 " =    1.162
peak=    3.170 closest distance to " CG  GLU A  37 " =    0.943
peak=    3.164 closest distance to " O   HOH Z 342 " =    0.919
peak=    3.164 closest distance to " CE3 TRP A  85 " =    1.416
peak=    3.157 closest distance to " CD1 LEU A  96 " =    0.722
peak=    3.155 closest distance to " CB  LEU A 228 " =    1.148
peak=    3.155 closest distance to " O   HOH Z 116 " =    2.626
peak=    3.151 closest distance to " CB  GLU A 175 " =    1.453
peak=    3.149 closest distance to " OG1 THR A 294 " =    1.621
peak=    3.149 closest distance to " CB  PRO A 243 " =    1.398
peak=    3.149 closest distance to " O   HOH Z 234 " =    2.231
peak=    3.148 closest distance to " O   HOH Z 371 " =    1.478
peak=    3.148 closest distance to " CB  ALA A 242 " =    1.037
peak=    3.147 closest distance to " CD  LYS A 119 " =    1.667
peak=    3.146 closest distance to " CA  SER A 146 " =    1.890
peak=    3.145 closest distance to " CB  ARG A 139 " =    1.078
peak=    3.140 closest distance to " CB  MET A  47 " =    1.233
peak=    3.135 closest distance to " O   HOH Z  49 " =    2.164
peak=    3.134 closest distance to " CA  MET A 105 " =    1.081
peak=    3.124 closest distance to " CA  ARG A 156 " =    1.096
peak=    3.122 closest distance to " CG2 VAL A  78 " =    0.862
peak=    3.121 closest distance to " CG  ARG A  66 " =    2.811
peak=    3.120 closest distance to " O   HOH Z 293 " =    1.936
peak=    3.118 closest distance to " CB  LYS A 289 " =    1.060
peak=    3.111 closest distance to " O   HOH Z 109 " =    2.081
peak=    3.110 closest distance to " OG1 THR A 264 " =    0.841
peak=    3.103 closest distance to " N   LYS A 119 " =    1.500
peak=    3.099 closest distance to " O   HOH Z 193 " =    2.127
peak=    3.097 closest distance to " O   HOH Z  88 " =    3.058
peak=    3.094 closest distance to " O   HOH Z 298 " =    2.080
peak=    3.089 closest distance to " CB  VAL A 126 " =    1.104
peak=    3.089 closest distance to " O   HOH Z 433 " =    2.026
peak=    3.081 closest distance to " CG1 ILE A 120 " =    1.027
peak=    3.079 closest distance to " O   HOH Z 182 " =    1.984
peak=    3.068 closest distance to " O   HOH Z 156 " =    3.378
peak=    3.059 closest distance to " O   HOH Z 128 " =    1.605
peak=    3.059 closest distance to " O   HOH Z  68 " =    1.730
peak=    3.043 closest distance to " O   HOH Z 123 " =    2.207

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.902 - 5.997
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 204
   mapped sites are within: 0.902 - 5.997

peak=   -4.602 closest distance to " C   HIS A 108 " =    1.090
peak=   -4.565 closest distance to " O   HOH Z 266 " =    5.051
peak=   -4.558 closest distance to " OG BSER A 134 " =    1.343
peak=   -4.460 closest distance to " CG  GLN A  58 " =    1.070
peak=   -4.252 closest distance to " CD  ARG A  14 " =    3.391
peak=   -4.214 closest distance to " O   HOH Z 165 " =    1.877
peak=   -4.202 closest distance to " O   HOH Z 377 " =    2.110
peak=   -4.179 closest distance to " OXT GLY A 302 " =    2.862
peak=   -4.141 closest distance to " CG1 VAL A 112 " =    2.813
peak=   -4.069 closest distance to " CG  GLN A 223 " =    2.145
peak=   -4.064 closest distance to " O   HOH Z 198 " =    1.513
peak=   -4.064 closest distance to " CB  ALA A   7 " =    2.136
peak=   -4.043 closest distance to " O   HOH Z  13 " =    1.718
peak=   -4.038 closest distance to " CD  ARG A 156 " =    2.053
peak=   -4.000 closest distance to " CA  VAL A  67 " =    2.952
peak=   -3.996 closest distance to " N   ALA A 248 " =    1.745
peak=   -3.976 closest distance to " CZ3 TRP A 179 " =    1.292
peak=   -3.975 closest distance to " CB  ALA A 184 " =    2.310
peak=   -3.948 closest distance to " ND2 ASN A  45 " =    1.024
peak=   -3.937 closest distance to " CB  PRO A 243 " =    2.680
peak=   -3.933 closest distance to " CG  MET A  93 " =    2.423
peak=   -3.903 closest distance to " CB  ALA A 161 " =    2.463
peak=   -3.895 closest distance to " O   HOH Z 351 " =    1.435
peak=   -3.882 closest distance to " CZ  ARG A  66 " =    1.089
peak=   -3.846 closest distance to " O   HOH Z 372 " =    2.184
peak=   -3.844 closest distance to " O   PHE A 218 " =    1.597
peak=   -3.821 closest distance to " CZ  TYR A 169 " =    1.861
peak=   -3.794 closest distance to " O   PRO A 198 " =    1.272
peak=   -3.788 closest distance to " O   VAL A  67 " =    2.600
peak=   -3.783 closest distance to " O   VAL A 174 " =    2.194
peak=   -3.757 closest distance to " O   GLY A 241 " =    2.324
peak=   -3.754 closest distance to " CE2 TYR A  30 " =    2.753
peak=   -3.734 closest distance to " O   HOH Z 348 " =    2.280
peak=   -3.715 closest distance to " O   PRO A 163 " =    2.104
peak=   -3.710 closest distance to " OD2 ASP A 171 " =    2.375
peak=   -3.698 closest distance to " CB  ASN A  39 " =    2.306
peak=   -3.697 closest distance to " O   HOH Z 102 " =    1.837
peak=   -3.696 closest distance to " O   ALA A  34 " =    2.266
peak=   -3.677 closest distance to " O   HOH Z 369 " =    2.289
peak=   -3.667 closest distance to " CB  PHE A 192 " =    2.053
peak=   -3.663 closest distance to " CE  MET A 105 " =    2.358
peak=   -3.647 closest distance to " O   HOH Z 377 " =    1.667
peak=   -3.644 closest distance to " CG1 VAL A  78 " =    3.170
peak=   -3.643 closest distance to " CG  ASP A 132 " =    2.279
peak=   -3.639 closest distance to " ND2 ASN A 187 " =    1.547
peak=   -3.637 closest distance to " CA  ASP A 298 " =    1.066
peak=   -3.629 closest distance to " CA  GLY A 203 " =    2.353
peak=   -3.619 closest distance to " CD1 LEU A  25 " =    2.549
peak=   -3.601 closest distance to " O   HOH Z 394 " =    1.495
peak=   -3.592 closest distance to " OD2 ASP A 191 " =    1.397
peak=   -3.590 closest distance to " O   GLY A  80 " =    2.483
peak=   -3.587 closest distance to " O   HOH Z 301 " =    2.291
peak=   -3.578 closest distance to " CD2 TYR A 247 " =    2.408
peak=   -3.570 closest distance to " O   HOH Z 353 " =    2.234
peak=   -3.555 closest distance to " NE2 GLN A 194 " =    1.888
peak=   -3.554 closest distance to " O   HOH Z 183 " =    1.508
peak=   -3.552 closest distance to " ND2 ASN A  39 " =    1.106
peak=   -3.539 closest distance to " N   GLN A  58 " =    1.705
peak=   -3.538 closest distance to " CD1 ILE A 106 " =    2.189
peak=   -3.529 closest distance to " N   SER A 206 " =    1.782
peak=   -3.521 closest distance to " CB  ALA A 291 " =    2.302
peak=   -3.514 closest distance to " CG1AVAL A  41 " =    2.640
peak=   -3.514 closest distance to " O   HOH Z 435 " =    2.542
peak=   -3.512 closest distance to " O   GLN A  11 " =    1.266
peak=   -3.509 closest distance to " CG  GLU A  53 " =    1.431
peak=   -3.501 closest distance to " CB  ALA A 248 " =    2.198
peak=   -3.500 closest distance to " CD2 LEU A 237 " =    2.373
peak=   -3.498 closest distance to " C   THR A 279 " =    1.156
peak=   -3.495 closest distance to " CD  ARG A 139 " =    1.521
peak=   -3.487 closest distance to " O   TRP A  92 " =    1.945
peak=   -3.486 closest distance to " OD1 ASP A 171 " =    1.449
peak=   -3.485 closest distance to " O   HOH Z  88 " =    4.340
peak=   -3.482 closest distance to " O   SER A   3 " =    1.013
peak=   -3.480 closest distance to " O   HOH Z 395 " =    5.111
peak=   -3.478 closest distance to " O   HOH Z 389 " =    1.770
peak=   -3.476 closest distance to " CG  PHE A 283 " =    2.553
peak=   -3.476 closest distance to " N   ALA A 226 " =    1.833
peak=   -3.471 closest distance to " O   SER A 210 " =    1.980
peak=   -3.465 closest distance to " N   THR A 235 " =    1.269
peak=   -3.458 closest distance to " NE2 GLN A  88 " =    1.115
peak=   -3.457 closest distance to " OD1 ASP A 191 " =    1.393
peak=   -3.457 closest distance to " CB  ALA A 131 " =    2.122
peak=   -3.456 closest distance to " CD2 TYR A 293 " =    1.915
peak=   -3.452 closest distance to " O   HOH Z 191 " =    5.997
peak=   -3.427 closest distance to " O   HOH Z 166 " =    1.899
peak=   -3.422 closest distance to " O   HOH Z 114 " =    3.391
peak=   -3.421 closest distance to " CG  PRO A 243 " =    1.736
peak=   -3.419 closest distance to " O   HOH Z 290 " =    1.106
peak=   -3.419 closest distance to " OE1 GLN A 183 " =    1.423
peak=   -3.415 closest distance to " O   HOH Z 422 " =    1.584
peak=   -3.415 closest distance to " NE2 GLN A  88 " =    1.714
peak=   -3.409 closest distance to " ND2 ASN A  69 " =    1.679
peak=   -3.404 closest distance to " O   HOH Z 234 " =    3.841
peak=   -3.401 closest distance to " O   HOH Z 109 " =    2.106
peak=   -3.396 closest distance to " CA  GLY A 133 " =    1.924
peak=   -3.395 closest distance to " O   HOH Z 185 " =    2.379
peak=   -3.388 closest distance to " OD1 ASN A 148 " =    1.504
peak=   -3.386 closest distance to " CG2 ILE A  49 " =    2.690
peak=   -3.376 closest distance to " OG  SER A  97 " =    2.203
peak=   -3.375 closest distance to " CB  ALA A 248 " =    2.125
peak=   -3.374 closest distance to " CD  PRO A 198 " =    1.270
peak=   -3.372 closest distance to " O   ALA A 161 " =    1.666
peak=   -3.371 closest distance to " N   THR A  52 " =    1.733
peak=   -3.369 closest distance to " O   HOH Z  11 " =    1.829
peak=   -3.360 closest distance to " O   SER A  95 " =    1.553
peak=   -3.356 closest distance to " CG2 ILE A 263 " =    2.243
peak=   -3.353 closest distance to " N   ALA A  43 " =    2.714
peak=   -3.352 closest distance to " CD2 LEU A 237 " =    2.394
peak=   -3.351 closest distance to " CA  GLY A 241 " =    3.209
peak=   -3.351 closest distance to " O   LEU A 167 " =    1.632
peak=   -3.340 closest distance to " NH1 ARG A 195 " =    2.633
peak=   -3.338 closest distance to " O   GLU A 152 " =    1.445
peak=   -3.330 closest distance to " OD1 ASN A  39 " =    2.194
peak=   -3.321 closest distance to " CB  GLN A  11 " =    1.859
peak=   -3.316 closest distance to " O   HOH Z 139 " =    3.246
peak=   -3.315 closest distance to " OD1 ASN A 301 " =    1.936
peak=   -3.313 closest distance to " CD1 PHE A  59 " =    2.008
peak=   -3.309 closest distance to " OD1 ASN A 187 " =    1.769
peak=   -3.307 closest distance to " O   ALA A  10 " =    1.793
peak=   -3.300 closest distance to " O   HOH Z 313 " =    1.929
peak=   -3.296 closest distance to " O   HOH Z 196 " =    1.925
peak=   -3.294 closest distance to " O   HOH Z 174 " =    3.822
peak=   -3.293 closest distance to " O   HOH Z 362 " =    5.849
peak=   -3.293 closest distance to " O   MET A  40 " =    2.756
peak=   -3.292 closest distance to " O   HOH Z 326 " =    1.716
peak=   -3.288 closest distance to " CB  PRO A 163 " =    2.465
peak=   -3.281 closest distance to " CG  GLN A  58 " =    1.344
peak=   -3.281 closest distance to " O   HOH Z 418 " =    1.518
peak=   -3.281 closest distance to " O   HOH Z 251 " =    1.540
peak=   -3.276 closest distance to " CG  GLU A 277 " =    1.284
peak=   -3.272 closest distance to " CD  GLN A 223 " =    1.758
peak=   -3.268 closest distance to " CD  LYS A 289 " =    2.417
peak=   -3.266 closest distance to " CG  ARG A 219 " =    2.555
peak=   -3.264 closest distance to " O   HOH Z 197 " =    5.202
peak=   -3.263 closest distance to " CB  ALA A 291 " =    2.342
peak=   -3.255 closest distance to " CG  TRP A 266 " =    2.127
peak=   -3.252 closest distance to " CE1 TYR A 247 " =    2.618
peak=   -3.251 closest distance to " OG BSER A 134 " =    1.833
peak=   -3.251 closest distance to " OG  SER A  63 " =    1.098
peak=   -3.243 closest distance to " O   HOH Z 171 " =    2.245
peak=   -3.242 closest distance to " O   HOH Z  38 " =    1.597
peak=   -3.238 closest distance to " O   HOH Z 198 " =    1.446
peak=   -3.238 closest distance to " OH  TYR A 169 " =    0.960
peak=   -3.226 closest distance to " O   HOH Z 126 " =    1.916
peak=   -3.225 closest distance to " CE1 TYR A 169 " =    2.296
peak=   -3.223 closest distance to " O   HOH Z  19 " =    2.431
peak=   -3.223 closest distance to " NE  ARG A  66 " =    4.288
peak=   -3.221 closest distance to " O   HOH Z 423 " =    2.275
peak=   -3.218 closest distance to " O   ASN A  45 " =    1.822
peak=   -3.214 closest distance to " NH2AARG A 275 " =    4.890
peak=   -3.213 closest distance to " O   ILE A 106 " =    1.796
peak=   -3.207 closest distance to " CZ3 TRP A 274 " =    2.281
peak=   -3.199 closest distance to " O   HOH Z  15 " =    1.607
peak=   -3.199 closest distance to " CD2 PHE A  61 " =    2.241
peak=   -3.198 closest distance to " O   VAL A  67 " =    2.079
peak=   -3.198 closest distance to " O   HOH Z 283 " =    2.441
peak=   -3.192 closest distance to " O   HOH Z   6 " =    1.660
peak=   -3.189 closest distance to " O   ASP A 298 " =    1.757
peak=   -3.184 closest distance to " C   SER A 206 " =    1.619
peak=   -3.180 closest distance to " N   SER A 276 " =    1.252
peak=   -3.179 closest distance to " CZ2 TRP A 274 " =    1.063
peak=   -3.172 closest distance to " O   PRO A 198 " =    1.260
peak=   -3.170 closest distance to " O   HOH Z 421 " =    3.834
peak=   -3.169 closest distance to " O   HOH Z 174 " =    2.328
peak=   -3.167 closest distance to " CB  ASP A 286 " =    1.798
peak=   -3.161 closest distance to " O   HOH Z  59 " =    3.979
peak=   -3.160 closest distance to " CE3 TRP A 150 " =    2.210
peak=   -3.159 closest distance to " O  BHOH Z 338 " =    1.335
peak=   -3.154 closest distance to " OG  SER A  26 " =    1.229
peak=   -3.153 closest distance to " O   HOH Z 414 " =    1.434
peak=   -3.151 closest distance to " O   SER A  26 " =    1.252
peak=   -3.150 closest distance to " CB  TRP A  85 " =    2.452
peak=   -3.149 closest distance to " O   ALA A 292 " =    2.219
peak=   -3.140 closest distance to " CB  SER A 210 " =    1.198
peak=   -3.137 closest distance to " O   GLN A  94 " =    2.182
peak=   -3.134 closest distance to " O   HOH Z 265 " =    2.345
peak=   -3.129 closest distance to " O   HOH Z 280 " =    2.349
peak=   -3.127 closest distance to " OE1 GLN A 223 " =    1.996
peak=   -3.127 closest distance to " O   HOH Z 111 " =    3.683
peak=   -3.122 closest distance to " O   HOH Z 193 " =    1.620
peak=   -3.116 closest distance to " C   ALA A 158 " =    1.366
peak=   -3.113 closest distance to " C   GLY A  17 " =    0.902
peak=   -3.108 closest distance to " NE2 GLN A 278 " =    1.885
peak=   -3.107 closest distance to " O   LYS A  76 " =    1.898
peak=   -3.107 closest distance to " O   HOH Z  43 " =    1.753
peak=   -3.106 closest distance to " NE2 GLN A 223 " =    1.542
peak=   -3.098 closest distance to " O   HOH Z  71 " =    2.008
peak=   -3.097 closest distance to " O   HOH Z 256 " =    1.398
peak=   -3.097 closest distance to " O   HOH Z 384 " =    2.353
peak=   -3.094 closest distance to " OXT GLY A 302 " =    3.272
peak=   -3.093 closest distance to " O   HOH Z 113 " =    2.125
peak=   -3.092 closest distance to " O   GLU A 152 " =    1.392
peak=   -3.089 closest distance to " O   HOH Z 401 " =    0.943
peak=   -3.087 closest distance to " N   PHE A  59 " =    1.741
peak=   -3.084 closest distance to " NH2 ARG A  66 " =    5.156
peak=   -3.084 closest distance to " CD1 LEU A 228 " =    2.081
peak=   -3.074 closest distance to " CB  ASN A  39 " =    2.137
peak=   -3.052 closest distance to " O   ALA A   1 " =    1.836
peak=   -3.045 closest distance to " O   HOH Z 111 " =    3.687
peak=   -3.041 closest distance to " O   HOH Z 166 " =    1.807
peak=   -3.037 closest distance to " CG  GLU A   2 " =    1.889
peak=   -3.028 closest distance to " CD2 LEU A 300 " =    2.668
peak=   -3.028 closest distance to " CE BMET A  47 " =    1.535

================= 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    :  0.3945 0.3907   6.186096e+00   6.181410e+00
   1_bss:  0.3850 0.3809   6.173319e+00   6.168600e+00
   1_xyz:  0.2520 0.2783   5.819911e+00   5.903195e+00
   1_adp:  0.2306 0.2799   5.763838e+00   5.919049e+00
   1_occ:  0.2303 0.2797   5.763200e+00   5.919028e+00
   2_bss:  0.2258 0.2747   5.752077e+00   5.907611e+00
   2_xyz:  0.1562 0.1971   5.418613e+00   5.606072e+00
   2_adp:  0.1390 0.1854   5.327154e+00   5.538176e+00
   2_occ:  0.1388 0.1854   5.326531e+00   5.538058e+00
   3_bss:  0.1386 0.1848   5.323069e+00   5.532034e+00
   3_xyz:  0.1210 0.1642   5.209327e+00   5.430964e+00
   3_adp:  0.1188 0.1611   5.191167e+00   5.411133e+00
   3_occ:  0.1187 0.1611   5.190702e+00   5.411044e+00
   4_bss:  0.1187 0.1612   5.190636e+00   5.410909e+00
   4_xyz:  0.1124 0.1556   5.147503e+00   5.377780e+00
   4_adp:  0.1123 0.1549   5.145506e+00   5.374265e+00
   4_occ:  0.1122 0.1548   5.144818e+00   5.374019e+00
   5_bss:  0.1120 0.1546   5.143770e+00   5.371795e+00
   5_xyz:  0.1127 0.1554   5.152230e+00   5.380436e+00
   5_adp:  0.1112 0.1574   5.150911e+00   5.390155e+00
   5_occ:  0.1112 0.1574   5.150932e+00   5.390394e+00
   5_bss:  0.1112 0.1574   5.150838e+00   5.390266e+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:  0.314  35.860   1.039  -0.047  -0.933  -0.000  -0.000  -0.000
   1_xyz:  0.314  35.860   1.039  -0.047  -0.933  -0.000  -0.000  -0.000
   1_adp:  0.314  35.860   1.039  -0.047  -0.933  -0.000  -0.000  -0.000
   1_occ:  0.314  35.860   1.039  -0.047  -0.933  -0.000  -0.000  -0.000
   2_bss:  0.326  49.093  -2.135  -1.530  -1.463  -0.000  -0.000  -0.000
   2_xyz:  0.326  49.093  -2.135  -1.530  -1.463  -0.000  -0.000  -0.000
   2_adp:  0.326  49.093  -2.135  -1.530  -1.463  -0.000  -0.000  -0.000
   2_occ:  0.326  49.093  -2.135  -1.530  -1.463  -0.000  -0.000  -0.000
   3_bss:  0.321  49.093  -3.089  -1.930  -1.359  -0.000  -0.000  -0.000
   3_xyz:  0.321  49.093  -3.089  -1.930  -1.359  -0.000  -0.000  -0.000
   3_adp:  0.321  49.093  -3.089  -1.930  -1.359  -0.000  -0.000  -0.000
   3_occ:  0.321  49.093  -3.089  -1.930  -1.359  -0.000  -0.000  -0.000
   4_bss:  0.326  49.093  -3.319  -2.099  -1.324  -0.000  -0.000  -0.000
   4_xyz:  0.326  49.093  -3.319  -2.099  -1.324  -0.000  -0.000  -0.000
   4_adp:  0.326  49.093  -3.319  -2.099  -1.324  -0.000  -0.000  -0.000
   4_occ:  0.326  49.093  -3.319  -2.099  -1.324  -0.000  -0.000  -0.000
   5_bss:  0.326  49.093  -3.319  -2.099  -1.324  -0.000  -0.000  -0.000
   5_xyz:  0.326  49.093  -3.319  -2.099  -1.324  -0.000  -0.000  -0.000
   5_adp:  0.326  49.093  -3.319  -2.099  -1.324  -0.000  -0.000  -0.000
   5_occ:  0.326  49.093  -3.319  -2.099  -1.324  -0.000  -0.000  -0.000
   5_bss:  0.322  49.060  -3.220  -1.969  -1.122  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  43.735 0.5998  0.7927    47306.593
   1_bss:  42.769 0.6099  0.8130    44321.508
   1_xyz:  28.023 0.7805  0.9797    20526.832
   1_adp:  28.629 0.7731  0.9766    20969.769
   1_occ:  28.640 0.7731  0.9761    20977.643
   2_bss:  28.124 0.7782  0.9222    20168.232
   2_xyz:  19.217 0.8681  0.9878     9926.672
   2_adp:  17.444 0.8853  0.9924     8725.240
   2_occ:  17.435 0.8854  0.9925     8718.660
   3_bss:  17.310 0.8863  0.9769     8554.934
   3_xyz:  15.211 0.9045  0.9840     6967.176
   3_adp:  14.771 0.9085  0.9826     6766.469
   3_occ:  14.764 0.9086  0.9824     6753.751
   4_bss:  14.763 0.9086  0.9782     6754.023
   4_xyz:  14.021 0.9147  0.9808     6289.224
   4_adp:  13.936 0.9155  0.9814     6255.488
   4_occ:  13.928 0.9155  0.9813     6248.459
   5_bss:  13.901 0.9157  0.9813     6213.573
   5_xyz:  14.006 0.9150  0.9814     6324.162
   5_adp:  14.190 0.9136  0.9765     6425.774
   5_occ:  14.190 0.9136  0.9764     6426.208
   5_bss:  14.192 0.9136  0.9801     6423.408
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   2.1560e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   2.1560e-01
   1_xyz:   1.297  0.010  0.081 15.156  0.004  4.107   9.4147e-02
   1_adp:   1.297  0.010  0.081 15.156  0.004  4.107   9.4147e-02
   1_occ:   1.297  0.010  0.081 15.156  0.004  4.107   9.4147e-02
   2_bss:   1.297  0.010  0.081 15.156  0.004  4.107   9.4147e-02
   2_xyz:   1.066  0.007  0.074 14.533  0.004  4.124   6.3666e-02
   2_adp:   1.066  0.007  0.074 14.533  0.004  4.124   6.3666e-02
   2_occ:   1.066  0.007  0.074 14.533  0.004  4.124   6.3666e-02
   3_bss:   1.066  0.007  0.074 14.533  0.004  4.124   6.3666e-02
   3_xyz:   1.002  0.006  0.073 14.614  0.004  4.117   5.7519e-02
   3_adp:   1.002  0.006  0.073 14.614  0.004  4.117   5.7519e-02
   3_occ:   1.002  0.006  0.073 14.614  0.004  4.117   5.7519e-02
   4_bss:   1.002  0.006  0.073 14.614  0.004  4.117   5.7519e-02
   4_xyz:   1.057  0.007  0.077 14.678  0.004  4.109   6.3529e-02
   4_adp:   1.057  0.007  0.077 14.678  0.004  4.109   6.3529e-02
   4_occ:   1.057  0.007  0.077 14.678  0.004  4.109   6.3529e-02
   5_bss:   1.057  0.007  0.077 14.678  0.004  4.109   6.3529e-02
   5_xyz:   0.961  0.006  0.072 14.430  0.004  4.110   5.4154e-02
   5_adp:   0.961  0.006  0.072 14.430  0.004  4.110   5.4154e-02
   5_occ:   0.961  0.006  0.072 14.430  0.004  4.110   5.4154e-02
   5_bss:   0.961  0.006  0.072 14.430  0.004  4.110   5.4154e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.154   2.4337e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.154   2.4337e-01
   1_xyz:   8.625  0.092  0.309 85.340  0.022  2.123   1.0179e-01
   1_adp:   8.625  0.092  0.309 85.340  0.022  2.123   1.0179e-01
   1_occ:   8.625  0.092  0.309 85.340  0.022  2.123   1.0179e-01
   2_bss:   8.625  0.092  0.309 85.340  0.022  2.123   1.0179e-01
   2_xyz:   7.438  0.039  0.211 80.718  0.031  2.204   6.5623e-02
   2_adp:   7.438  0.039  0.211 80.718  0.031  2.204   6.5623e-02
   2_occ:   7.438  0.039  0.211 80.718  0.031  2.204   6.5623e-02
   3_bss:   7.438  0.039  0.211 80.718  0.031  2.204   6.5623e-02
   3_xyz:   6.970  0.046  0.226 81.797  0.038  2.293   4.0401e-02
   3_adp:   6.970  0.046  0.226 81.797  0.038  2.293   4.0401e-02
   3_occ:   6.970  0.046  0.226 81.797  0.038  2.293   4.0401e-02
   4_bss:   6.970  0.046  0.226 81.797  0.038  2.293   4.0401e-02
   4_xyz:   7.491  0.044  0.253 82.591  0.038  2.336   4.3919e-02
   4_adp:   7.491  0.044  0.253 82.591  0.038  2.336   4.3919e-02
   4_occ:   7.491  0.044  0.253 82.591  0.038  2.336   4.3919e-02
   5_bss:   7.491  0.044  0.253 82.591  0.038  2.336   4.3919e-02
   5_xyz:   6.801  0.045  0.230 82.688  0.038  2.379   3.3335e-02
   5_adp:   6.801  0.045  0.230 82.688  0.038  2.379   3.3335e-02
   5_occ:   6.801  0.045  0.230 82.688  0.038  2.379   3.3335e-02
   5_bss:   6.801  0.045  0.230 82.688  0.038  2.379   3.3335e-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:  90.88   0.00  17.27  90.88   0.00  13.45  64.40   6.26  38.05
   1_occ:  90.88   0.00  17.27  90.88   0.00  13.45  64.40   6.26  38.05
   2_bss:  90.88   0.00  17.27  90.88   0.00  13.45  64.40   6.26  38.05
   2_xyz:  90.88   0.00  17.27  90.88   0.00  13.45  64.40   6.26  38.05
   2_adp:  91.11   0.00  17.75  91.11   0.00  13.49  73.23   5.95  40.94
   2_occ:  91.11   0.00  17.75  91.11   0.00  13.49  73.23   5.95  40.94
   3_bss:  91.11   0.00  17.75  91.11   0.00  13.49  73.23   5.95  40.94
   3_xyz:  91.11   0.00  17.75  91.11   0.00  13.49  73.23   5.95  40.94
   3_adp:  88.97   1.81  17.20  88.97   1.81  13.16  73.94   6.02  39.17
   3_occ:  88.97   1.81  17.20  88.97   1.81  13.16  73.94   6.02  39.17
   4_bss:  88.97   1.81  17.20  88.97   1.81  13.16  73.94   6.02  39.17
   4_xyz:  88.97   1.81  17.20  88.97   1.81  13.16  73.94   6.02  39.17
   4_adp:  88.86   2.87  17.18  88.86   2.87  13.17  73.87   5.15  39.02
   4_occ:  88.86   2.87  17.18  88.86   2.87  13.17  73.87   5.15  39.02
   5_bss:  88.86   2.87  17.18  88.86   2.87  13.17  73.87   5.15  39.02
   5_xyz:  88.86   2.87  17.18  88.86   2.87  13.17  73.87   5.15  39.02
   5_adp:  96.08   0.98  17.52  96.08   0.98  13.22  84.15   5.06  40.91
   5_occ:  96.08   0.98  17.52  96.08   0.98  13.22  84.15   5.06  40.91
   5_bss:  96.05   0.94  17.48  96.05   0.94  13.19  84.12   5.02  40.88
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    2.592    0.011    0.368
   1_adp:    2.592    0.011    0.368
   1_occ:    2.592    0.011    0.368
   2_bss:    2.592    0.011    0.368
   2_xyz:    2.548    0.033    0.490
   2_adp:    2.548    0.033    0.490
   2_occ:    2.548    0.033    0.490
   3_bss:    2.548    0.033    0.490
   3_xyz:    2.558    0.032    0.538
   3_adp:    2.558    0.032    0.538
   3_occ:    2.558    0.032    0.538
   4_bss:    2.558    0.032    0.538
   4_xyz:    2.582    0.062    0.554
   4_adp:    2.582    0.062    0.554
   4_occ:    2.582    0.062    0.554
   5_bss:    2.582    0.062    0.554
   5_xyz:    2.617    0.054    0.561
   5_adp:    2.617    0.054    0.561
   5_occ:    2.617    0.054    0.561
   5_bss:    2.617    0.054    0.561
------------------------------------------------------------------------

CPU time actual refinement: 319.29


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_83/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_83/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_83/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_83/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_83/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 319.14 
  Macro-tasks:
    bulk solvent and scale       = 36.13  
    individual site refinement   = 128.84 
    weights calculation          = 30.70  
    collect and process          = 6.59   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 202.40 
  Micro-tasks:
    mask                            = 1.83   
    f_calc                          = 101.37 
    alpha_beta                      = 8.25   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 108.54 
    fmodel                         = 6.17   
    r_factors                      = 0.16   
    phase_errors                   = 10.87  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 238.59 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.632 micro seconds
Total CPU time: 5.54 minutes
from_scatterers_fft:    611 calls, 100.99 s
gradients_fft:          556 calls,  95.92 s

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

# Date 2008-01-16 Time 03:57:33 PST -0800 (1200484653.13 s)
Start R-work = 0.3945, R-free = 0.3907 (no bulk solvent and anisotropic scale)
Final R-work = 0.1373, R-free = 0.1780 (no bulk solvent and anisotropic scale)

Start R-work = 0.3850, R-free = 0.3809
Final R-work = 0.1112, R-free = 0.1574