# Date 2008-01-16 Time 04:44:18 PST -0800 (1200487458.24 s)
#phil __OFF__

Command line arguments: "../442.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 10811
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 442

-------------------------------------------------------------------------------
  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: (69.5475, 47.3993, 85.0941, 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: 3.26, 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: (69.5475, 47.3993, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8236 1.97128
Completeness in resolution range: 0.958929
Completeness with d_max=infinity: 0.955934

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8236
                             d_min =   1.9713

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: (69.5475, 47.3993, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8236 1.97128
Completeness in resolution range: 0.958929
Completeness with d_max=infinity: 0.955934

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8240 -  4.2174 [2148/2176]  1933   215  10.0%
  bin  2:  4.2174 -  3.3603 [2049/2072]  1845   204  10.0%
  bin  3:  3.3603 -  2.9393 [2039/2061]  1833   206  10.1%
  bin  4:  2.9393 -  2.6723 [2008/2027]  1814   194   9.7%
  bin  5:  2.6723 -  2.4817 [2013/2042]  1803   210  10.4%
  bin  6:  2.4817 -  2.3360 [1970/2011]  1780   190   9.6%
  bin  7:  2.3360 -  2.2194 [1982/2017]  1780   202  10.2%
  bin  8:  2.2194 -  2.1231 [1978/2017]  1778   200  10.1%
  bin  9:  2.1231 -  2.0416 [1952/1983]  1762   190   9.7%
  bin 10:  2.0416 -  1.9713 [1450/2022]  1302   148  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_442/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:
        1.81 -     2.42: 40
        2.42 -     3.04: 2209
        3.04 -     3.66: 4728
        3.66 -     4.28: 9089
        4.28 -     4.90: 12438
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.806 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.817 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.941 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.942 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28499 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_442/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_442/model_refine_001.geo

CPU time processing inputs: 9.09


============================ 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 = 69.5475 47.3993 85.09415 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: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3680   r_free= 0.3619   ksol= 0.00   Bsol= 0.00   scale= 0.960    |
|                                                                             |
| 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:   0.44 A                  |
| x-ray target function (ml) for work reflections: 6.129654                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8240 -  4.7036 0.99   1388  156 0.3029 0.3158      6.3953      6.4167|
|  2:  4.7036 -  3.7533 0.99   1348  146 0.2964 0.2806      6.5425      6.5168|
|  3:  3.7533 -  3.2848 0.99   1313  153 0.3134 0.3006      6.4261      6.4881|
|  4:  3.2848 -  2.9871 0.99   1312  137 0.3400 0.3313      6.3069       6.267|
|  5:  2.9871 -  2.7745 0.98   1278  143 0.3682 0.3232      6.1904      6.1181|
|  6:  2.7745 -  2.6119 0.98   1292  144 0.3945 0.3862      6.1259      6.0243|
|  7:  2.6119 -  2.4817 0.99   1297  150 0.3945 0.3394      6.1176      5.9819|
|  8:  2.4817 -  2.3741 0.99   1279  134 0.3999 0.4497      6.0527      6.1333|
|  9:  2.3741 -  2.2831 0.98   1289  145 0.4325 0.4285      6.0271      6.0547|
| 10:  2.2831 -  2.2046 0.97   1249  144 0.4165 0.4664      6.0004      6.0584|
| 11:  2.2046 -  2.1358 0.98   1266  143 0.4347 0.4352      5.9466      6.0049|
| 12:  2.1358 -  2.0749 0.99   1270  135 0.4258 0.4360      5.8917      5.9304|
| 13:  2.0749 -  2.0205 0.97   1259  137 0.4428 0.4267      5.8107      5.7979|
| 14:  2.0205 -  1.9713 0.62    790   92 0.4608 0.4226      5.7795      5.6594|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8240 -  4.7036  1388   156  0.76  29.21   0.86     0.77      52011.00|
|  2:  4.7036 -  3.7533  1348   146  0.81  25.25   0.97     0.89      57212.39|
|  3:  3.7533 -  3.2848  1313   153  0.77  29.09   0.98     0.94      55402.96|
|  4:  3.2848 -  2.9871  1312   137  0.74  32.27   0.99     0.93      47589.09|
|  5:  2.9871 -  2.7745  1278   143  0.69  35.88   0.97     0.90      38709.76|
|  6:  2.7745 -  2.6119  1292   144  0.68  37.61   0.98     0.90      33737.48|
|  7:  2.6119 -  2.4817  1297   150  0.69  36.62   0.97     0.89      31299.78|
|  8:  2.4817 -  2.3741  1279   134  0.64  41.10   1.00     0.85      33062.52|
|  9:  2.3741 -  2.2831  1289   145  0.58  45.66   1.00     0.80      32889.05|
| 10:  2.2831 -  2.2046  1249   144  0.56  47.67   1.02     0.76      33823.60|
| 11:  2.2046 -  2.1358  1266   143  0.54  48.76   1.02     0.78      31464.66|
| 12:  2.1358 -  2.0749  1270   135  0.56  47.66   1.04     0.81      28655.66|
| 13:  2.0749 -  2.0205  1259   137  0.57  47.10   1.00     0.82      23729.54|
| 14:  2.0205 -  1.9713   790    92  0.59  45.44   0.99     0.82      19306.26|
|alpha:            min =        0.76 max =            0.94 mean =         0.85|
|beta:             min =    19306.26 max =        57212.39 mean =     37800.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.66|
|phase err.(work): min =        0.00 max =           89.96 mean =        38.88|
|phase err.(test): min =        0.00 max =           89.58 mean =        38.60|
|-----------------------------------------------------------------------------|

============================== 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 = 4.664839              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.761   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.965532              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.147   (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 |  1.806 -  2.115:       10 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       30 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      188 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2021 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1898 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2830 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4655 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4434 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5678 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6760 |
|-----------------------------------------------------------------------------|
|-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 |        0.171 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.806 |       0.311 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.714)------------------------------------------|
|    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: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3680   r_free= 0.3619   ksol= 0.00   Bsol= 0.00   scale= 0.960    |
|                                                                             |
| 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:   0.44 A                  |
| x-ray target function (ml) for work reflections: 6.129654                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3569   r_free= 0.3491   ksol= 0.31   Bsol= 26.94   scale= 0.974   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,0.28,0.89,0.00,0.00,0.00); trace/3= -0.41                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 6.113261                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.175445              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.596   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.524797              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.059   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3569      final r-factor (work) = 0.2067          |
| start r-factor (free) = 0.3491      final r-factor (free) = 0.2241          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.9456 = 4.18 * 0.50 * 6.1191 + 1.00 * 0.1706                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.2783 = 4.18 * 0.50 * 5.8449 + 1.00 * 0.0759                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2067      final r-factor (work) = 0.1882          |
| start r-factor (free) = 0.2241      final r-factor (free) = 0.2345          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0734 = 0.52 * 1.00 * 5.8449 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9295 = 0.52 * 1.00 * 5.5624 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.714)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.94   17.52    None  None   None       |
|    all(noH): 2823   0      0.00    80.94   17.52    None  None   None       |
|    Sol.    : 438    0      7.70    75.32   39.62    None  None   None       |
|    Mac.    : 2385   0      0.00    80.94   13.47    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.094:  602   |   5:    40.468 -  48.561:  128        |
|      1:     8.094 -  16.187: 1252   |   6:    48.561 -  56.655:   74        |
|      2:    16.187 -  24.281:  416   |   7:    56.655 -  64.748:   55        |
|      3:    24.281 -  32.374:  137   |   8:    64.748 -  72.842:   22        |
|      4:    32.374 -  40.468:  131   |   9:    72.842 -  80.935:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1882 r_free = 0.2345             target_work(ml) = 5.577         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1878 r_free = 0.2350             target_work(ml) = 5.577         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1878   r_free= 0.2350   ksol= 0.31   Bsol= 26.94   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,0.28,0.89,0.00,0.00,0.00); trace/3= -0.41                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.576530                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1851   r_free= 0.2333   ksol= 0.31   Bsol= 38.16   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-1.38,-1.12,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.571167                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.612382              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.492   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.171305              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.928  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1851      final r-factor (work) = 0.1322          |
| start r-factor (free) = 0.2333      final r-factor (free) = 0.1785          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1448 = 3.61 * 0.50 * 5.5747 + 1.00 * 0.0759                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8693 = 3.61 * 0.50 * 5.4312 + 1.00 * 0.0595                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1322      final r-factor (work) = 0.1246          |
| start r-factor (free) = 0.1785      final r-factor (free) = 0.1672          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9407 = 0.17 * 1.00 * 5.4312 + 1.00 * 0.0103                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9114 = 0.17 * 1.00 * 5.2514 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.714)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.09   17.07    None  None   None       |
|    all(noH): 2823   0      0.00    80.09   17.07    None  None   None       |
|    Sol.    : 438    0      6.25    73.08   38.64    None  None   None       |
|    Mac.    : 2385   0      0.00    80.09   13.11    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.009:  519   |   5:    40.044 -  48.052:  125        |
|      1:     8.009 -  16.018: 1417   |   6:    48.052 -  56.061:   73        |
|      2:    16.018 -  24.026:  355   |   7:    56.061 -  64.070:   44        |
|      3:    24.026 -  32.035:  140   |   8:    64.070 -  72.079:   20        |
|      4:    32.035 -  40.044:  125   |   9:    72.079 -  80.087:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1246 r_free = 0.1672             target_work(ml) = 5.218         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1244 r_free = 0.1669             target_work(ml) = 5.217         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1244   r_free= 0.1669   ksol= 0.31   Bsol= 38.16   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-1.38,-1.12,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.216996                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1248   r_free= 0.1660   ksol= 0.31   Bsol= 42.15   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-1.78,-1.53,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.216259                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.095500              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 122.535  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.245515              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.359   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1248      final r-factor (work) = 0.1143          |
| start r-factor (free) = 0.1660      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5624 = 2.10 * 0.50 * 5.2522 + 1.00 * 0.0594                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4844 = 2.10 * 0.50 * 5.1801 + 1.00 * 0.0569                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1143      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1561      final r-factor (free) = 0.1546          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3010 = 0.25 * 1.00 * 5.1801 + 1.00 * 0.0292                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2699 = 0.25 * 1.00 * 5.1410 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.714)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.32    81.87   16.89    None  None   None       |
|    all(noH): 2823   0      2.32    81.87   16.89    None  None   None       |
|    Sol.    : 438    0      5.82    71.90   38.47    None  None   None       |
|    Mac.    : 2385   0      2.32    81.87   12.92    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:     2.319 -  10.274: 1058   |   5:    42.095 -  50.050:  107        |
|      1:    10.274 -  18.229: 1056   |   6:    50.050 -  58.005:   81        |
|      2:    18.229 -  26.184:  233   |   7:    58.005 -  65.960:   27        |
|      3:    26.184 -  34.139:  123   |   8:    65.960 -  73.915:   14        |
|      4:    34.139 -  42.095:  121   |   9:    73.915 -  81.870:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1121 r_free = 0.1546             target_work(ml) = 5.135         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1121 r_free = 0.1545             target_work(ml) = 5.135         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1545   ksol= 0.31   Bsol= 42.15   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-1.78,-1.53,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.134695                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1545   ksol= 0.32   Bsol= 42.92   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,-1.87,-1.60,-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: 5.134694                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.852651              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 151.767  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.953381              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.475  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1120      final r-factor (work) = 0.1066          |
| start r-factor (free) = 0.1545      final r-factor (free) = 0.1533          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3895 = 2.85 * 0.50 * 5.1409 + 1.00 * 0.0569                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3619 = 2.85 * 0.50 * 5.1135 + 1.00 * 0.0685                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1066      final r-factor (work) = 0.1055          |
| start r-factor (free) = 0.1533      final r-factor (free) = 0.1543          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8827 = 0.95 * 1.00 * 5.1135 + 1.00 * 0.0076                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8716 = 0.95 * 1.00 * 5.1005 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.714)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.23    91.97   16.93    None  None   None       |
|    all(noH): 2823   0      1.23    91.97   16.93    None  None   None       |
|    Sol.    : 438    0      5.66    75.71   39.33    None  None   None       |
|    Mac.    : 2385   0      1.23    91.97   12.82    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.226 -  10.300: 1120   |   5:    46.600 -  55.675:  111        |
|      1:    10.300 -  19.375: 1052   |   6:    55.675 -  64.750:   59        |
|      2:    19.375 -  28.450:  208   |   7:    64.750 -  73.825:   14        |
|      3:    28.450 -  37.525:  131   |   8:    73.825 -  82.900:    8        |
|      4:    37.525 -  46.600:  118   |   9:    82.900 -  91.975:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1055 r_free = 0.1543             target_work(ml) = 5.107         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1055 r_free = 0.1543             target_work(ml) = 5.107         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1055   r_free= 0.1543   ksol= 0.32   Bsol= 42.92   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,-1.87,-1.60,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.106711                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1054   r_free= 0.1543   ksol= 0.32   Bsol= 44.24   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-1.70,-1.41,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.106760                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.509592              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 161.763  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.973841              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.602  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1054      final r-factor (work) = 0.1084          |
| start r-factor (free) = 0.1543      final r-factor (free) = 0.1556          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9189 = 1.51 * 0.50 * 5.1013 + 1.00 * 0.0685                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9169 = 1.51 * 0.50 * 5.1202 + 1.00 * 0.0522                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1084      final r-factor (work) = 0.1083          |
| start r-factor (free) = 0.1556      final r-factor (free) = 0.1562          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9951 = 0.97 * 1.00 * 5.1202 + 1.00 * 0.0089                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0001 = 0.97 * 1.00 * 5.1250 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.714)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.63    93.93   16.81    None  None   None       |
|    all(noH): 2823   0      0.63    93.93   16.81    None  None   None       |
|    Sol.    : 438    0      5.32    76.57   39.30    None  None   None       |
|    Mac.    : 2385   0      0.63    93.93   12.68    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.625 -   9.956: 1069   |   5:    47.277 -  56.608:  110        |
|      1:     9.956 -  19.286: 1103   |   6:    56.608 -  65.938:   52        |
|      2:    19.286 -  28.616:  214   |   7:    65.938 -  75.268:   14        |
|      3:    28.616 -  37.947:  129   |   8:    75.268 -  84.599:    6        |
|      4:    37.947 -  47.277:  124   |   9:    84.599 -  93.929:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1083 r_free = 0.1562             target_work(ml) = 5.128         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1083 r_free = 0.1562             target_work(ml) = 5.128         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1562   ksol= 0.32   Bsol= 44.24   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-1.70,-1.41,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.128025                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8240 -  4.7036 0.99   1388  156 0.0975 0.1245      5.3589      5.5096|
|  2:  4.7036 -  3.7533 0.99   1348  146 0.0828 0.1086      5.4042      5.6008|
|  3:  3.7533 -  3.2848 0.99   1313  153 0.1011 0.1494      5.4404      5.8333|
|  4:  3.2848 -  2.9871 0.99   1312  137 0.1190 0.1544      5.4393      5.6106|
|  5:  2.9871 -  2.7745 0.98   1278  143 0.1261 0.1652      5.3085      5.4981|
|  6:  2.7745 -  2.6119 0.98   1292  144 0.1208 0.1895      5.2039      5.4308|
|  7:  2.6119 -  2.4817 0.99   1297  150 0.1160 0.1616      5.1187      5.3659|
|  8:  2.4817 -  2.3741 0.99   1279  134 0.1122 0.1757      5.0589      5.3116|
|  9:  2.3741 -  2.2831 0.98   1289  145 0.1156 0.1825      5.0142      5.3226|
| 10:  2.2831 -  2.2046 0.97   1249  144 0.1084 0.1758      4.9632      5.1948|
| 11:  2.2046 -  2.1358 0.98   1266  143 0.1120 0.1748      4.9154      5.2555|
| 12:  2.1358 -  2.0749 0.99   1270  135 0.1057 0.1672      4.8527      5.1474|
| 13:  2.0749 -  2.0205 0.97   1259  137 0.1098 0.1738      4.7839      5.0565|
| 14:  2.0205 -  1.9713 0.62    790   92 0.1074 0.1734      4.7044       4.932|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8240 -  4.7036  1388   156  0.94   8.70   0.98     0.96       6645.03|
|  2:  4.7036 -  3.7533  1348   146  0.95   7.71   1.02     1.00       8385.24|
|  3:  3.7533 -  3.2848  1313   153  0.94  10.70   1.03     1.02       9785.03|
|  4:  3.2848 -  2.9871  1312   137  0.92  13.44   1.01     1.00      10163.81|
|  5:  2.9871 -  2.7745  1278   143  0.90  15.59   1.00     0.97       8150.16|
|  6:  2.7745 -  2.6119  1292   144  0.90  15.93   0.98     0.95       6978.53|
|  7:  2.6119 -  2.4817  1297   150  0.91  14.90   0.98     0.96       5737.04|
|  8:  2.4817 -  2.3741  1279   134  0.91  14.79   1.00     0.97       5373.52|
|  9:  2.3741 -  2.2831  1289   145  0.91  15.51   1.00     0.96       4827.92|
| 10:  2.2831 -  2.2046  1249   144  0.90  15.52   0.99     0.96       4538.11|
| 11:  2.2046 -  2.1358  1266   143  0.90  15.74   1.00     0.96       4125.58|
| 12:  2.1358 -  2.0749  1270   135  0.92  14.68   1.00     0.99       3785.47|
| 13:  2.0749 -  2.0205  1259   137  0.90  15.96   0.99     0.99       3385.02|
| 14:  2.0205 -  1.9713   790    92  0.91  15.48   0.98     0.94       2808.95|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2808.95 max =        10163.81 mean =      6174.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.79|
|phase err.(test): min =        0.00 max =           89.21 mean =        13.40|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1562   ksol= 0.32   Bsol= 44.90   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.42,-1.51,-1.23,-0.00,-0.00,-0.00); trace/3= -1.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.128062                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1562   ksol= 0.32   Bsol= 44.90   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.42,-1.51,-1.23,-0.00,-0.00,-0.00); trace/3= -1.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.128062                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8240 -  4.7036 0.99   1388  156 0.0975 0.1247      5.3599       5.511|
|  2:  4.7036 -  3.7533 0.99   1348  146 0.0829 0.1086      5.4051      5.6008|
|  3:  3.7533 -  3.2848 0.99   1313  153 0.1012 0.1494      5.4406      5.8334|
|  4:  3.2848 -  2.9871 0.99   1312  137 0.1189 0.1544      5.4391      5.6104|
|  5:  2.9871 -  2.7745 0.98   1278  143 0.1260 0.1652      5.3082      5.4978|
|  6:  2.7745 -  2.6119 0.98   1292  144 0.1208 0.1894      5.2036      5.4304|
|  7:  2.6119 -  2.4817 0.99   1297  150 0.1160 0.1616      5.1185      5.3658|
|  8:  2.4817 -  2.3741 0.99   1279  134 0.1122 0.1757      5.0587      5.3111|
|  9:  2.3741 -  2.2831 0.98   1289  145 0.1155 0.1826      5.0142       5.323|
| 10:  2.2831 -  2.2046 0.97   1249  144 0.1084 0.1758      4.9632      5.1947|
| 11:  2.2046 -  2.1358 0.98   1266  143 0.1120 0.1748      4.9154      5.2556|
| 12:  2.1358 -  2.0749 0.99   1270  135 0.1057 0.1672      4.8525      5.1472|
| 13:  2.0749 -  2.0205 0.97   1259  137 0.1097 0.1737      4.7837      5.0562|
| 14:  2.0205 -  1.9713 0.62    790   92 0.1074 0.1734      4.7043       4.932|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8240 -  4.7036  1388   156  0.94   8.72   0.98     0.96       6660.99|
|  2:  4.7036 -  3.7533  1348   146  0.95   7.72   1.02     1.00       8397.74|
|  3:  3.7533 -  3.2848  1313   153  0.94  10.71   1.03     1.03       9789.40|
|  4:  3.2848 -  2.9871  1312   137  0.92  13.44   1.02     1.00      10161.16|
|  5:  2.9871 -  2.7745  1278   143  0.90  15.58   1.00     0.97       8146.34|
|  6:  2.7745 -  2.6119  1292   144  0.90  15.93   0.99     0.96       6973.98|
|  7:  2.6119 -  2.4817  1297   150  0.91  14.89   0.99     0.96       5733.24|
|  8:  2.4817 -  2.3741  1279   134  0.91  14.79   1.00     0.98       5370.81|
|  9:  2.3741 -  2.2831  1289   145  0.91  15.51   1.00     0.97       4826.99|
| 10:  2.2831 -  2.2046  1249   144  0.90  15.52   1.00     0.97       4537.20|
| 11:  2.2046 -  2.1358  1266   143  0.90  15.74   1.00     0.96       4124.19|
| 12:  2.1358 -  2.0749  1270   135  0.92  14.68   1.01     1.00       3783.29|
| 13:  2.0749 -  2.0205  1259   137  0.90  15.96   1.00     1.00       3383.40|
| 14:  2.0205 -  1.9713   790    92  0.91  15.48   0.99     0.95       2808.08|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2808.08 max =        10161.16 mean =      6175.28|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.90 mean =        13.80|
|phase err.(test): min =        0.00 max =           89.19 mean =        13.40|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.714)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.60    93.91   16.79    None  None   None       |
|    all(noH): 2823   0      0.60    93.91   16.79    None  None   None       |
|    Sol.    : 438    0      5.30    76.55   39.28    None  None   None       |
|    Mac.    : 2385   0      0.60    93.91   12.66    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:     0.605 -   9.935: 1069   |   5:    47.257 -  56.587:  110        |
|      1:     9.935 -  19.265: 1103   |   6:    56.587 -  65.917:   52        |
|      2:    19.265 -  28.596:  214   |   7:    65.917 -  75.248:   14        |
|      3:    28.596 -  37.926:  129   |   8:    75.248 -  84.578:    6        |
|      4:    37.926 -  47.257:  124   |   9:    84.578 -  93.909:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 281         
Filter by distance & map next to the model:
   mapped sites are within: 0.624 - 4.455
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 279 from: 281
   mapped sites are within: 0.735 - 4.455

peak=    5.714 closest distance to " CB  ARG A 275 " =    0.957
peak=    5.622 closest distance to " NH2 ARG A  56 " =    2.271
peak=    5.589 closest distance to " CB  GLN A 223 " =    1.402
peak=    5.583 closest distance to " CG  PRO A  54 " =    1.266
peak=    5.121 closest distance to " CB  SER A  63 " =    1.136
peak=    5.047 closest distance to " CG  PRO A 213 " =    1.255
peak=    4.900 closest distance to " O   HOH Z 126 " =    1.840
peak=    4.809 closest distance to " CA  TYR A  30 " =    0.937
peak=    4.711 closest distance to " CG  PRO A  90 " =    1.182
peak=    4.711 closest distance to " O   HOH Z 298 " =    1.842
peak=    4.640 closest distance to " CB  GLN A 183 " =    1.309
peak=    4.585 closest distance to " O   HOH Z 234 " =    3.737
peak=    4.580 closest distance to " O   HOH Z 142 " =    1.641
peak=    4.493 closest distance to " O   HOH Z 232 " =    2.359
peak=    4.484 closest distance to " CB  GLU A 152 " =    1.146
peak=    4.469 closest distance to " C   PRO A 198 " =    1.480
peak=    4.454 closest distance to " O   HOH Z 403 " =    1.802
peak=    4.428 closest distance to " O   HOH Z  44 " =    2.058
peak=    4.421 closest distance to " CB  PRO A  54 " =    0.921
peak=    4.414 closest distance to " CB  TYR A 169 " =    0.824
peak=    4.392 closest distance to " CG  PRO A 198 " =    1.201
peak=    4.369 closest distance to " CA  ALA A  21 " =    1.222
peak=    4.354 closest distance to " NZ  LYS A 117 " =    3.168
peak=    4.352 closest distance to " O   HOH Z 193 " =    1.709
peak=    4.341 closest distance to " O   HOH Z  15 " =    2.126
peak=    4.337 closest distance to " O   HOH Z  78 " =    1.688
peak=    4.315 closest distance to " NE2 GLN A  11 " =    0.994
peak=    4.313 closest distance to " OD1 ASN A  69 " =    2.544
peak=    4.286 closest distance to " O   HOH Z 236 " =    1.994
peak=    4.284 closest distance to " CB  GLU A 128 " =    1.181
peak=    4.250 closest distance to " O   HOH Z 272 " =    1.822
peak=    4.248 closest distance to " O   HOH Z  97 " =    1.879
peak=    4.197 closest distance to " O   HOH Z 402 " =    1.458
peak=    4.195 closest distance to " O   HOH Z 316 " =    2.926
peak=    4.193 closest distance to " OD2 ASP A 286 " =    2.782
peak=    4.191 closest distance to " CB  SER A   3 " =    1.251
peak=    4.184 closest distance to " NH2BARG A 145 " =    2.137
peak=    4.177 closest distance to " CB  ASN A 148 " =    1.458
peak=    4.157 closest distance to " CB  ARG A  79 " =    1.363
peak=    4.154 closest distance to " CG  PRO A 243 " =    1.091
peak=    4.147 closest distance to " O   HOH Z 203 " =    1.814
peak=    4.143 closest distance to " CB  GLU A 277 " =    3.531
peak=    4.086 closest distance to " O   HOH Z 144 " =    2.090
peak=    4.086 closest distance to " O   SER A  87 " =    2.220
peak=    4.083 closest distance to " CA  ASN A 176 " =    1.118
peak=    4.067 closest distance to " O   HOH Z 368 " =    2.011
peak=    4.049 closest distance to " CG2 ILE A 120 " =    1.152
peak=    4.046 closest distance to " O   HOH Z 427 " =    2.833
peak=    4.039 closest distance to " O   HOH Z 426 " =    1.503
peak=    4.020 closest distance to " CG1 ILE A  33 " =    1.266
peak=    4.019 closest distance to " O   HOH Z 369 " =    2.261
peak=    4.014 closest distance to " O   HOH Z 209 " =    2.240
peak=    4.011 closest distance to " O   HOH Z 389 " =    1.854
peak=    3.993 closest distance to " O   HOH Z  97 " =    2.584
peak=    3.987 closest distance to " O   HOH Z  40 " =    1.808
peak=    3.982 closest distance to " CG  ARG A  66 " =    2.596
peak=    3.978 closest distance to " O   HOH Z  54 " =    1.756
peak=    3.973 closest distance to " CB  TRP A 179 " =    1.192
peak=    3.955 closest distance to " CB  VAL A 265 " =    1.219
peak=    3.937 closest distance to " ND2 ASN A 187 " =    1.500
peak=    3.931 closest distance to " CG1BVAL A  72 " =    1.602
peak=    3.929 closest distance to " CB  ARG A 190 " =    1.715
peak=    3.928 closest distance to " CD2 TRP A 179 " =    1.410
peak=    3.919 closest distance to " O   HOH Z 346 " =    1.663
peak=    3.917 closest distance to " O   HOH Z  43 " =    2.071
peak=    3.909 closest distance to " O   HOH Z 124 " =    1.365
peak=    3.898 closest distance to " O   HOH Z 284 " =    2.919
peak=    3.893 closest distance to " O   HOH Z 344 " =    3.018
peak=    3.881 closest distance to " N   ASN A  39 " =    1.262
peak=    3.878 closest distance to " OE1 GLU A   2 " =    2.205
peak=    3.875 closest distance to " CD  ARG A 269 " =    1.001
peak=    3.866 closest distance to " CA  ARG A  36 " =    1.075
peak=    3.860 closest distance to " O   HOH Z 371 " =    3.323
peak=    3.857 closest distance to " CA  ASN A 215 " =    1.183
peak=    3.855 closest distance to " O   HOH Z 250 " =    1.408
peak=    3.851 closest distance to " O   HOH Z  59 " =    2.231
peak=    3.850 closest distance to " OG BSER A 164 " =    2.361
peak=    3.848 closest distance to " O   HOH Z 158 " =    2.951
peak=    3.844 closest distance to " CB  LEU A 228 " =    1.102
peak=    3.833 closest distance to " OD2 ASP A 298 " =    3.933
peak=    3.819 closest distance to " O   HOH Z 245 " =    1.313
peak=    3.816 closest distance to " O   HOH Z 327 " =    1.678
peak=    3.810 closest distance to " CD2 LEU A 297 " =    0.913
peak=    3.805 closest distance to " O   HOH Z 279 " =    2.105
peak=    3.789 closest distance to " CA  ASP A 140 " =    1.115
peak=    3.783 closest distance to " CA  THR A 221 " =    0.948
peak=    3.778 closest distance to " O   HOH Z 128 " =    1.950
peak=    3.778 closest distance to " O   HOH Z 416 " =    2.787
peak=    3.774 closest distance to " O   HOH Z 303 " =    1.982
peak=    3.769 closest distance to " O   HOH Z 247 " =    1.320
peak=    3.764 closest distance to " O   HOH Z 128 " =    2.174
peak=    3.762 closest distance to " O   HOH Z 132 " =    2.444
peak=    3.742 closest distance to " O   HOH Z 345 " =    2.959
peak=    3.741 closest distance to " O   HOH Z 214 " =    2.237
peak=    3.740 closest distance to " O   HOH Z  61 " =    1.587
peak=    3.733 closest distance to " O   HOH Z 132 " =    2.577
peak=    3.727 closest distance to " O   HOH Z  19 " =    1.973
peak=    3.725 closest distance to " CB  ALA A 291 " =    1.306
peak=    3.714 closest distance to " CG2 VAL A 257 " =    0.860
peak=    3.710 closest distance to " CG  GLN A  58 " =    2.575
peak=    3.703 closest distance to " O   HOH Z 147 " =    1.748
peak=    3.701 closest distance to " O   HOH Z 183 " =    1.506
peak=    3.693 closest distance to " O   HOH Z 108 " =    2.385
peak=    3.690 closest distance to " CG2 ILE A  20 " =    1.380
peak=    3.687 closest distance to " CE  LYS A  76 " =    0.911
peak=    3.684 closest distance to " O   HOH Z 180 " =    2.280
peak=    3.672 closest distance to " CB  TYR A 169 " =    0.902
peak=    3.669 closest distance to " O   HOH Z 173 " =    1.987
peak=    3.665 closest distance to " NH2 ARG A 156 " =    1.150
peak=    3.655 closest distance to " O   HOH Z 185 " =    1.676
peak=    3.655 closest distance to " CB  SER A 141 " =    1.045
peak=    3.652 closest distance to " O   HOH Z  21 " =    1.748
peak=    3.648 closest distance to " O   HOH Z 227 " =    1.626
peak=    3.642 closest distance to " CA  GLY A  80 " =    0.946
peak=    3.639 closest distance to " CB  TRP A 266 " =    0.969
peak=    3.629 closest distance to " CA  LYS A 117 " =    1.235
peak=    3.623 closest distance to " CG  ARG A  66 " =    0.941
peak=    3.616 closest distance to " O   HOH Z  68 " =    1.759
peak=    3.612 closest distance to " O   HOH Z 134 " =    1.299
peak=    3.611 closest distance to " O   MET A 105 " =    1.904
peak=    3.609 closest distance to " O   HOH Z 423 " =    1.942
peak=    3.607 closest distance to " CB  ASN A  39 " =    0.858
peak=    3.603 closest distance to " O   HOH Z 411 " =    3.648
peak=    3.597 closest distance to " CZ  PHE A 218 " =    1.046
peak=    3.595 closest distance to " O   HOH Z 189 " =    2.002
peak=    3.594 closest distance to " O   HOH Z 357 " =    1.867
peak=    3.591 closest distance to " O   HOH Z  49 " =    2.120
peak=    3.589 closest distance to " CB  SER A  26 " =    1.636
peak=    3.586 closest distance to " O   HOH Z 197 " =    2.799
peak=    3.579 closest distance to " O   HOH Z 374 " =    2.575
peak=    3.577 closest distance to " NZ  LYS A 119 " =    1.549
peak=    3.559 closest distance to " O   HOH Z  63 " =    1.991
peak=    3.559 closest distance to " CG2BVAL A  41 " =    0.818
peak=    3.557 closest distance to " CB  ARG A 139 " =    0.828
peak=    3.555 closest distance to " CB  ALA A 248 " =    1.402
peak=    3.552 closest distance to " CG2 VAL A  78 " =    0.899
peak=    3.547 closest distance to " O   HOH Z 214 " =    2.268
peak=    3.541 closest distance to " O   TRP A 274 " =    1.930
peak=    3.540 closest distance to " CD  ARG A 159 " =    0.752
peak=    3.540 closest distance to " CB  SER A  62 " =    0.823
peak=    3.537 closest distance to " NH1AARG A 145 " =    1.200
peak=    3.536 closest distance to " CB  VAL A 202 " =    1.496
peak=    3.530 closest distance to " CG  LYS A  76 " =    1.065
peak=    3.521 closest distance to " O   HOH Z 421 " =    1.629
peak=    3.511 closest distance to " O   HOH Z 337 " =    3.683
peak=    3.501 closest distance to " CZ2 TRP A 179 " =    1.701
peak=    3.496 closest distance to " O   HOH Z  80 " =    1.638
peak=    3.492 closest distance to " CA  ARG A 195 " =    1.234
peak=    3.491 closest distance to " O   HOH Z 368 " =    3.687
peak=    3.490 closest distance to " CG2 THR A 221 " =    1.149
peak=    3.484 closest distance to " O   HOH Z  71 " =    2.282
peak=    3.483 closest distance to " O   HOH Z 406 " =    1.668
peak=    3.482 closest distance to " O   HOH Z  68 " =    1.960
peak=    3.480 closest distance to " CD  LYS A 166 " =    1.328
peak=    3.468 closest distance to " ND2 ASN A 110 " =    1.711
peak=    3.459 closest distance to " CA  ALA A  51 " =    0.928
peak=    3.455 closest distance to " O   HOH Z 427 " =    3.061
peak=    3.446 closest distance to " O   HOH Z  61 " =    1.528
peak=    3.442 closest distance to " CD1 LEU A 300 " =    1.276
peak=    3.441 closest distance to " CD1 ILE A 106 " =    0.867
peak=    3.440 closest distance to " O   HOH Z 365 " =    2.833
peak=    3.440 closest distance to " O   HOH Z 148 " =    3.162
peak=    3.430 closest distance to " O   HOH Z 145 " =    2.330
peak=    3.424 closest distance to " O   HOH Z 291 " =    1.481
peak=    3.410 closest distance to " CD1 LEU A  96 " =    0.767
peak=    3.407 closest distance to " CB  SER A 273 " =    0.805
peak=    3.405 closest distance to " CG2 VAL A 202 " =    1.171
peak=    3.402 closest distance to " CB  ASP A 140 " =    0.974
peak=    3.402 closest distance to " O   HOH Z 193 " =    2.134
peak=    3.399 closest distance to " CG AARG A 275 " =    1.075
peak=    3.399 closest distance to " CB  ILE A 120 " =    1.309
peak=    3.397 closest distance to " CA  MET A  40 " =    1.049
peak=    3.393 closest distance to " O   HOH Z  66 " =    2.113
peak=    3.387 closest distance to " CE  LYS A 119 " =    1.127
peak=    3.380 closest distance to " O   HOH Z  85 " =    1.377
peak=    3.380 closest distance to " O   HOH Z  89 " =    2.227
peak=    3.378 closest distance to " O   HOH Z 286 " =    2.186
peak=    3.378 closest distance to " O   HOH Z 305 " =    3.634
peak=    3.377 closest distance to " O   HOH Z 411 " =    1.684
peak=    3.365 closest distance to " O   HOH Z 281 " =    4.455
peak=    3.364 closest distance to " O   HOH Z 264 " =    1.549
peak=    3.364 closest distance to " CD2 HIS A  81 " =    1.181
peak=    3.363 closest distance to " CG  GLN A  77 " =    2.236
peak=    3.361 closest distance to " O   HOH Z 261 " =    1.552
peak=    3.356 closest distance to " CA  ALA A 291 " =    0.856
peak=    3.352 closest distance to " O   HOH Z 423 " =    3.344
peak=    3.350 closest distance to " CA  ALA A  84 " =    1.266
peak=    3.347 closest distance to " O   HOH Z 368 " =    2.573
peak=    3.347 closest distance to " O   HOH Z 299 " =    2.399
peak=    3.345 closest distance to " ND1 HIS A  81 " =    1.611
peak=    3.345 closest distance to " NH2 ARG A 219 " =    1.934
peak=    3.340 closest distance to " O   HOH Z 380 " =    2.045
peak=    3.340 closest distance to " CD BLYS A 290 " =    1.150
peak=    3.333 closest distance to " OG  SER A  62 " =    2.868
peak=    3.332 closest distance to " CD2 LEU A 255 " =    1.231
peak=    3.329 closest distance to " O   HOH Z  88 " =    3.054
peak=    3.328 closest distance to " CB  MET A  47 " =    0.969
peak=    3.314 closest distance to " O   HOH Z 417 " =    3.040
peak=    3.313 closest distance to " CE1 TYR A 186 " =    1.251
peak=    3.312 closest distance to " CB  SER A 216 " =    0.794
peak=    3.308 closest distance to " O   HOH Z 425 " =    2.077
peak=    3.307 closest distance to " O   HOH Z   1 " =    2.134
peak=    3.303 closest distance to " O   HOH Z 408 " =    1.465
peak=    3.301 closest distance to " C   SER A  32 " =    1.057
peak=    3.299 closest distance to " O   HOH Z  35 " =    2.398
peak=    3.298 closest distance to " N   ARG A 156 " =    1.372
peak=    3.297 closest distance to " CA  MET A 105 " =    1.066
peak=    3.295 closest distance to " CA  ASP A 162 " =    1.143
peak=    3.293 closest distance to " CB  ALA A 295 " =    1.155
peak=    3.290 closest distance to " O   HOH Z  10 " =    1.745
peak=    3.283 closest distance to " O   HOH Z 435 " =    1.864
peak=    3.278 closest distance to " CG1 VAL A 153 " =    1.001
peak=    3.271 closest distance to " O   SER A  26 " =    1.697
peak=    3.271 closest distance to " CA  VAL A  41 " =    0.913
peak=    3.266 closest distance to " CB  GLN A 278 " =    0.903
peak=    3.265 closest distance to " OG1 THR A 294 " =    2.331
peak=    3.257 closest distance to " O   HOH Z 325 " =    2.284
peak=    3.256 closest distance to " O   THR A 251 " =    1.129
peak=    3.255 closest distance to " O   HOH Z 334 " =    1.461
peak=    3.252 closest distance to " CG  GLU A 277 " =    2.133
peak=    3.247 closest distance to " O   HOH Z  64 " =    2.267
peak=    3.246 closest distance to " O   HOH Z  54 " =    2.369
peak=    3.239 closest distance to " CB  TYR A 116 " =    0.826
peak=    3.238 closest distance to " O   HOH Z 299 " =    4.392
peak=    3.236 closest distance to " CB  ARG A 269 " =    0.735
peak=    3.234 closest distance to " CG2 VAL A 197 " =    1.129
peak=    3.233 closest distance to " CB  ASN A 215 " =    1.137
peak=    3.232 closest distance to " CB  PHE A  16 " =    1.036
peak=    3.231 closest distance to " O   HOH Z 353 " =    2.736
peak=    3.231 closest distance to " CB  THR A 157 " =    1.020
peak=    3.230 closest distance to " CB  ALA A   9 " =    1.589
peak=    3.227 closest distance to " O   HOH Z 250 " =    1.653
peak=    3.220 closest distance to " CB  ALA A 242 " =    1.002
peak=    3.219 closest distance to " O   HOH Z 102 " =    1.233
peak=    3.214 closest distance to " O   HOH Z 313 " =    1.706
peak=    3.213 closest distance to " O   HOH Z 163 " =    1.790
peak=    3.211 closest distance to " O   HOH Z 257 " =    2.319
peak=    3.208 closest distance to " CA  ASN A 217 " =    1.263
peak=    3.207 closest distance to " O   HOH Z 261 " =    2.116
peak=    3.204 closest distance to " CB  GLN A 103 " =    0.840
peak=    3.200 closest distance to " O   HOH Z 152 " =    2.000
peak=    3.196 closest distance to " O   ALA A 165 " =    1.422
peak=    3.188 closest distance to " CA  THR A 264 " =    0.862
peak=    3.188 closest distance to " CD  LYS A 119 " =    1.226
peak=    3.187 closest distance to " O   THR A 220 " =    1.252
peak=    3.184 closest distance to " CB  ASN A 127 " =    0.896
peak=    3.180 closest distance to " O   HOH Z 367 " =    3.554
peak=    3.178 closest distance to " O   HOH Z 234 " =    1.771
peak=    3.177 closest distance to " O   HOH Z 211 " =    2.766
peak=    3.174 closest distance to " O   HOH Z  85 " =    2.087
peak=    3.172 closest distance to " O   HOH Z 189 " =    2.680
peak=    3.163 closest distance to " O   HOH Z 345 " =    1.550
peak=    3.160 closest distance to " O   HOH Z 438 " =    1.861
peak=    3.159 closest distance to " O   HOH Z 273 " =    2.757
peak=    3.158 closest distance to " O   HOH Z 359 " =    1.403
peak=    3.158 closest distance to " O   HOH Z 417 " =    2.245
peak=    3.155 closest distance to " O   HOH Z 341 " =    1.827
peak=    3.147 closest distance to " O   HOH Z  50 " =    1.976
peak=    3.140 closest distance to " CB  SER A 212 " =    1.030
peak=    3.137 closest distance to " N   TYR A 116 " =    1.525
peak=    3.134 closest distance to " N   ARG A 190 " =    0.973
peak=    3.132 closest distance to " O   HOH Z 336 " =    1.697
peak=    3.130 closest distance to " CA  ILE A  33 " =    1.426
peak=    3.129 closest distance to " CB  ALA A  71 " =    1.277
peak=    3.129 closest distance to " O   HOH Z 163 " =    1.378
peak=    3.127 closest distance to " CG  GLN A  11 " =    1.165
peak=    3.119 closest distance to " CD1AILE A 234 " =    0.949
peak=    3.116 closest distance to " NZ  LYS A  76 " =    1.343
peak=    3.110 closest distance to " O   HOH Z 403 " =    1.247
peak=    3.101 closest distance to " CA  ASP A 191 " =    0.815
peak=    3.097 closest distance to " CD1 LEU A 228 " =    1.630
peak=    3.091 closest distance to " O   HOH Z 135 " =    1.624
peak=    3.090 closest distance to " OH  TYR A 116 " =    1.036
peak=    3.090 closest distance to " O   HOH Z 217 " =    2.267
peak=    3.078 closest distance to " CG  MET A 113 " =    1.136
peak=    3.067 closest distance to " O   HOH Z 251 " =    1.630
peak=    3.061 closest distance to " CE  LYS A  48 " =    1.115
peak=    3.047 closest distance to " CB  LEU A 255 " =    0.752
peak=    3.037 closest distance to " CA  SER A  87 " =    1.014

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.880 - 5.744
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 210 from: 211
   mapped sites are within: 0.880 - 5.744

peak=   -5.024 closest distance to " O   HOH Z 266 " =    4.461
peak=   -4.407 closest distance to " C   HIS A 108 " =    1.074
peak=   -4.247 closest distance to " OXT GLY A 302 " =    2.745
peak=   -4.218 closest distance to " O   HOH Z 372 " =    2.290
peak=   -4.218 closest distance to " CD  ARG A 156 " =    2.052
peak=   -4.197 closest distance to " CB  PRO A 243 " =    2.637
peak=   -4.151 closest distance to " O   ILE A 109 " =    2.582
peak=   -4.146 closest distance to " SG  CYS A 254 " =    3.273
peak=   -4.110 closest distance to " O   HOH Z 377 " =    1.942
peak=   -4.100 closest distance to " O   VAL A  67 " =    2.674
peak=   -4.090 closest distance to " O   HOH Z  13 " =    1.611
peak=   -3.989 closest distance to " CD1 LEU A 101 " =    2.424
peak=   -3.976 closest distance to " OG  SER A  97 " =    2.142
peak=   -3.974 closest distance to " O   HOH Z 165 " =    1.974
peak=   -3.964 closest distance to " CG  GLN A 223 " =    2.027
peak=   -3.954 closest distance to " O   SER A 210 " =    1.936
peak=   -3.951 closest distance to " CD1 PHE A 130 " =    2.285
peak=   -3.939 closest distance to " N   ALA A 248 " =    1.730
peak=   -3.936 closest distance to " CG  ASP A 231 " =    0.880
peak=   -3.936 closest distance to " O   HOH Z 353 " =    2.194
peak=   -3.932 closest distance to " ND2 ASN A  45 " =    0.960
peak=   -3.930 closest distance to " OG BSER A 134 " =    1.276
peak=   -3.926 closest distance to " N   GLN A  58 " =    1.619
peak=   -3.918 closest distance to " O   PRO A 163 " =    2.061
peak=   -3.889 closest distance to " O   HOH Z 290 " =    1.019
peak=   -3.880 closest distance to " CE2 TYR A  30 " =    2.770
peak=   -3.871 closest distance to " CD1 LEU A  25 " =    2.467
peak=   -3.862 closest distance to " CA  VAL A  67 " =    2.748
peak=   -3.829 closest distance to " CZ3 TRP A 179 " =    1.306
peak=   -3.821 closest distance to " O   HOH Z 407 " =    2.954
peak=   -3.815 closest distance to " O   HOH Z 166 " =    1.557
peak=   -3.814 closest distance to " OD1 ASN A  39 " =    2.242
peak=   -3.811 closest distance to " CZ  TYR A 169 " =    1.789
peak=   -3.804 closest distance to " O   HOH Z 126 " =    1.867
peak=   -3.802 closest distance to " CD1 LEU A 228 " =    2.180
peak=   -3.784 closest distance to " O   HOH Z 198 " =    2.040
peak=   -3.764 closest distance to " O   HOH Z  11 " =    2.025
peak=   -3.755 closest distance to " O   HOH Z 196 " =    1.962
peak=   -3.752 closest distance to " CD  ARG A 139 " =    1.547
peak=   -3.743 closest distance to " CG  ASP A 132 " =    2.307
peak=   -3.738 closest distance to " CD  GLN A  58 " =    1.190
peak=   -3.735 closest distance to " O   HOH Z 292 " =    4.435
peak=   -3.732 closest distance to " O   MET A  40 " =    2.614
peak=   -3.728 closest distance to " CD1 PHE A  59 " =    1.921
peak=   -3.727 closest distance to " O   PRO A 198 " =    1.264
peak=   -3.716 closest distance to " O   HOH Z  10 " =    1.511
peak=   -3.704 closest distance to " CZ  PHE A  59 " =    1.630
peak=   -3.704 closest distance to " CA  ASP A 298 " =    1.047
peak=   -3.695 closest distance to " OG  SER A  62 " =    1.479
peak=   -3.685 closest distance to " O   HOH Z 185 " =    2.311
peak=   -3.685 closest distance to " OG  SER A   3 " =    1.698
peak=   -3.667 closest distance to " O   HOH Z 118 " =    3.279
peak=   -3.650 closest distance to " NH1 ARG A 195 " =    2.556
peak=   -3.646 closest distance to " O   HOH Z 234 " =    4.118
peak=   -3.643 closest distance to " O   PHE A 218 " =    1.579
peak=   -3.642 closest distance to " CB  ASN A  39 " =    2.270
peak=   -3.632 closest distance to " O   HOH Z  52 " =    1.446
peak=   -3.628 closest distance to " CB  ALA A 291 " =    2.329
peak=   -3.626 closest distance to " O   ALA A 256 " =    1.491
peak=   -3.599 closest distance to " ND2 ASN A 187 " =    1.480
peak=   -3.587 closest distance to " N   ALA A  43 " =    2.620
peak=   -3.584 closest distance to " O   GLY A  80 " =    2.419
peak=   -3.581 closest distance to " O   HOH Z 102 " =    1.629
peak=   -3.575 closest distance to " CG1 VAL A 112 " =    2.750
peak=   -3.574 closest distance to " CB  PHE A 192 " =    1.972
peak=   -3.569 closest distance to " CE  MET A 105 " =    2.129
peak=   -3.563 closest distance to " O   TRP A  92 " =    1.824
peak=   -3.560 closest distance to " CD  ARG A 195 " =    5.120
peak=   -3.549 closest distance to " O   HOH Z 389 " =    1.710
peak=   -3.549 closest distance to " O   HOH Z 166 " =    1.905
peak=   -3.536 closest distance to " OG BSER A 134 " =    1.726
peak=   -3.531 closest distance to " O   HOH Z 388 " =    2.048
peak=   -3.506 closest distance to " C   LEU A 143 " =    1.048
peak=   -3.503 closest distance to " OD2 ASP A 171 " =    2.361
peak=   -3.494 closest distance to " O   ALA A 160 " =    1.482
peak=   -3.486 closest distance to " O   HOH Z 351 " =    1.463
peak=   -3.482 closest distance to " O   LEU A 167 " =    1.521
peak=   -3.476 closest distance to " O   ALA A  34 " =    2.314
peak=   -3.475 closest distance to " O   HOH Z 311 " =    3.510
peak=   -3.459 closest distance to " OD1 ASP A 191 " =    1.609
peak=   -3.456 closest distance to " CB  PHE A 208 " =    2.231
peak=   -3.452 closest distance to " CD2 LEU A 300 " =    2.854
peak=   -3.447 closest distance to " C   THR A 279 " =    1.176
peak=   -3.445 closest distance to " N   VAL A 189 " =    1.642
peak=   -3.439 closest distance to " N   ALA A 248 " =    2.238
peak=   -3.435 closest distance to " N   THR A 235 " =    1.346
peak=   -3.432 closest distance to " CG2 THR A 178 " =    2.183
peak=   -3.426 closest distance to " C   ALA A 158 " =    1.263
peak=   -3.426 closest distance to " NH2 ARG A 159 " =    2.311
peak=   -3.418 closest distance to " CG  GLU A 277 " =    1.161
peak=   -3.408 closest distance to " NH2 ARG A  66 " =    5.079
peak=   -3.407 closest distance to " O   HOH Z 361 " =    3.426
peak=   -3.400 closest distance to " CG  GLU A  53 " =    1.352
peak=   -3.396 closest distance to " O   HOH Z 369 " =    2.234
peak=   -3.392 closest distance to " OD1 ASN A 148 " =    1.595
peak=   -3.389 closest distance to " OD2 ASP A 191 " =    1.567
peak=   -3.381 closest distance to " O   HOH Z  71 " =    1.540
peak=   -3.374 closest distance to " NH2AARG A 275 " =    5.106
peak=   -3.370 closest distance to " O   VAL A 174 " =    2.041
peak=   -3.366 closest distance to " O   HOH Z 250 " =    1.406
peak=   -3.364 closest distance to " N   GLY A 133 " =    1.913
peak=   -3.363 closest distance to " OE2 GLU A   2 " =    1.740
peak=   -3.363 closest distance to " CB  ALA A 248 " =    1.986
peak=   -3.362 closest distance to " CZ  PHE A 130 " =    0.917
peak=   -3.362 closest distance to " CB  GLN A  11 " =    1.776
peak=   -3.360 closest distance to " O   HOH Z 298 " =    1.237
peak=   -3.359 closest distance to " CG1 VAL A 125 " =    2.339
peak=   -3.359 closest distance to " C   SER A 206 " =    1.625
peak=   -3.357 closest distance to " OG BSER A 210 " =    2.046
peak=   -3.354 closest distance to " NH2 ARG A  79 " =    1.992
peak=   -3.343 closest distance to " CE  MET A  93 " =    1.162
peak=   -3.341 closest distance to " O   HOH Z 283 " =    1.913
peak=   -3.337 closest distance to " O   HOH Z  11 " =    1.774
peak=   -3.337 closest distance to " CG2 ILE A 263 " =    2.267
peak=   -3.336 closest distance to " O   HOH Z 243 " =    2.122
peak=   -3.335 closest distance to " O   HOH Z 427 " =    1.407
peak=   -3.335 closest distance to " O   HOH Z  37 " =    1.822
peak=   -3.333 closest distance to " CB  ASP A 286 " =    1.928
peak=   -3.329 closest distance to " O   HOH Z  43 " =    1.575
peak=   -3.319 closest distance to " CD1 ILE A 239 " =    2.196
peak=   -3.318 closest distance to " O   HOH Z 148 " =    3.745
peak=   -3.314 closest distance to " CA  GLY A 133 " =    2.308
peak=   -3.309 closest distance to " O   HOH Z 422 " =    1.495
peak=   -3.307 closest distance to " O   ALA A 161 " =    1.514
peak=   -3.304 closest distance to " CG  PHE A 283 " =    2.585
peak=   -3.298 closest distance to " O   HOH Z  38 " =    1.593
peak=   -3.297 closest distance to " CA  TYR A  68 " =    2.924
peak=   -3.296 closest distance to " CA  PRO A 243 " =    2.384
peak=   -3.292 closest distance to " CG1 VAL A 250 " =    2.625
peak=   -3.289 closest distance to " NE2 GLN A  58 " =    1.186
peak=   -3.287 closest distance to " N   ASP A 286 " =    2.421
peak=   -3.284 closest distance to " O   HOH Z 252 " =    3.558
peak=   -3.284 closest distance to " O   GLY A 196 " =    0.957
peak=   -3.276 closest distance to " N   GLN A 122 " =    1.444
peak=   -3.274 closest distance to " O   HOH Z  90 " =    2.894
peak=   -3.273 closest distance to " CG1 VAL A 112 " =    2.915
peak=   -3.269 closest distance to " O   ALA A   1 " =    1.818
peak=   -3.268 closest distance to " O   HOH Z   6 " =    1.725
peak=   -3.264 closest distance to " O   HOH Z 262 " =    2.466
peak=   -3.263 closest distance to " CD1 TYR A 247 " =    2.435
peak=   -3.262 closest distance to " O   HOH Z 377 " =    1.755
peak=   -3.260 closest distance to " O   HOH Z  61 " =    1.611
peak=   -3.260 closest distance to " CB  ALA A 291 " =    2.265
peak=   -3.254 closest distance to " NE2 GLN A  88 " =    1.810
peak=   -3.252 closest distance to " O   HOH Z 191 " =    5.744
peak=   -3.245 closest distance to " O   HOH Z 213 " =    1.410
peak=   -3.244 closest distance to " N   SER A 206 " =    1.859
peak=   -3.241 closest distance to " CG1AVAL A  41 " =    2.654
peak=   -3.239 closest distance to " N   ALA A 226 " =    1.981
peak=   -3.236 closest distance to " CD2 LEU A 237 " =    2.549
peak=   -3.233 closest distance to " O   SER A 146 " =    1.049
peak=   -3.227 closest distance to " O   HOH Z 377 " =    1.753
peak=   -3.224 closest distance to " N   SER A 276 " =    1.311
peak=   -3.224 closest distance to " O   VAL A 189 " =    2.545
peak=   -3.224 closest distance to " OD1 ASP A 171 " =    1.511
peak=   -3.221 closest distance to " O   HOH Z   9 " =    2.014
peak=   -3.219 closest distance to " O   ASN A  45 " =    1.840
peak=   -3.217 closest distance to " O   HOH Z 417 " =    2.508
peak=   -3.213 closest distance to " O   HOH Z 414 " =    1.510
peak=   -3.213 closest distance to " O   GLY A  80 " =    2.510
peak=   -3.212 closest distance to " O   SER A 135 " =    1.534
peak=   -3.209 closest distance to " CG  PRO A 243 " =    1.678
peak=   -3.202 closest distance to " O   ALA A  10 " =    1.778
peak=   -3.200 closest distance to " O   GLY A 111 " =    1.174
peak=   -3.197 closest distance to " O   HOH Z  41 " =    2.361
peak=   -3.195 closest distance to " N   SER A  12 " =    1.397
peak=   -3.195 closest distance to " CA  SER A 245 " =    2.379
peak=   -3.194 closest distance to " NE2 GLN A  88 " =    1.085
peak=   -3.186 closest distance to " O   HOH Z 123 " =    2.212
peak=   -3.184 closest distance to " O   SER A  95 " =    1.535
peak=   -3.184 closest distance to " OG ASER A 134 " =    1.236
peak=   -3.183 closest distance to " O   ILE A 106 " =    1.716
peak=   -3.180 closest distance to " OH  TYR A 169 " =    0.972
peak=   -3.178 closest distance to " O   HOH Z 385 " =    1.946
peak=   -3.172 closest distance to " CB  CYS A 201 " =    2.574
peak=   -3.170 closest distance to " CG1 VAL A  78 " =    2.565
peak=   -3.169 closest distance to " O   HOH Z 423 " =    2.285
peak=   -3.169 closest distance to " ND2 ASN A  69 " =    1.483
peak=   -3.159 closest distance to " O   HOH Z 436 " =    1.563
peak=   -3.159 closest distance to " O   HOH Z 265 " =    2.107
peak=   -3.157 closest distance to " N   THR A  52 " =    1.659
peak=   -3.155 closest distance to " O   HOH Z 211 " =    1.642
peak=   -3.154 closest distance to " CG  GLN A  58 " =    1.102
peak=   -3.152 closest distance to " O   HOH Z 297 " =    2.784
peak=   -3.144 closest distance to " O   HOH Z 326 " =    1.664
peak=   -3.141 closest distance to " OG  SER A  26 " =    1.301
peak=   -3.140 closest distance to " SG ACYS A 201 " =    2.098
peak=   -3.139 closest distance to " O   ALA A  51 " =    1.448
peak=   -3.136 closest distance to " O   PRO A 198 " =    1.308
peak=   -3.135 closest distance to " CG2 VAL A 189 " =    2.230
peak=   -3.122 closest distance to " CD2 LEU A 237 " =    2.237
peak=   -3.119 closest distance to " O   GLU A 152 " =    1.487
peak=   -3.118 closest distance to " O   SER A   3 " =    1.125
peak=   -3.116 closest distance to " CG  ASP A  50 " =    2.379
peak=   -3.113 closest distance to " NH2 ARG A  66 " =    1.929
peak=   -3.111 closest distance to " OD2 ASP A 171 " =    1.760
peak=   -3.111 closest distance to " O   LYS A 117 " =    1.632
peak=   -3.108 closest distance to " OE1 GLN A 183 " =    1.496
peak=   -3.105 closest distance to " CZ3 TRP A 274 " =    2.425
peak=   -3.101 closest distance to " O   GLY A  75 " =    1.771
peak=   -3.100 closest distance to " O   HOH Z 309 " =    2.472
peak=   -3.098 closest distance to " NH1 ARG A  66 " =    1.048
peak=   -3.097 closest distance to " O   HOH Z  19 " =    2.033
peak=   -3.092 closest distance to " OE1 GLN A  88 " =    1.103
peak=   -3.086 closest distance to " CD2 PHE A 192 " =    2.276
peak=   -3.080 closest distance to " O   HOH Z 193 " =    1.701
peak=   -3.062 closest distance to " O   HOH Z 280 " =    2.379
peak=   -3.060 closest distance to " O   HOH Z 263 " =    2.895
peak=   -3.056 closest distance to " CE  LYS A 166 " =    2.924
peak=   -3.010 closest distance to " CE1 TYR A 247 " =    2.659

================= 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    :  0.3680 0.3619   6.129654e+00   6.120408e+00
   1_bss:  0.3569 0.3491   6.113261e+00   6.093651e+00
   1_xyz:  0.2067 0.2241   5.630610e+00   5.710579e+00
   1_adp:  0.1882 0.2345   5.577205e+00   5.748243e+00
   1_occ:  0.1878 0.2350   5.576530e+00   5.748195e+00
   2_bss:  0.1851 0.2333   5.571167e+00   5.741973e+00
   2_xyz:  0.1322 0.1785   5.277867e+00   5.496974e+00
   2_adp:  0.1246 0.1672   5.218093e+00   5.432422e+00
   2_occ:  0.1244 0.1669   5.216996e+00   5.431287e+00
   3_bss:  0.1248 0.1660   5.216259e+00   5.428570e+00
   3_xyz:  0.1143 0.1561   5.151005e+00   5.376011e+00
   3_adp:  0.1121 0.1546   5.134890e+00   5.364717e+00
   3_occ:  0.1121 0.1545   5.134695e+00   5.364729e+00
   4_bss:  0.1120 0.1545   5.134694e+00   5.364781e+00
   4_xyz:  0.1066 0.1533   5.106556e+00   5.354388e+00
   4_adp:  0.1055 0.1543   5.106635e+00   5.362108e+00
   4_occ:  0.1055 0.1543   5.106711e+00   5.362418e+00
   5_bss:  0.1054 0.1543   5.106760e+00   5.362454e+00
   5_xyz:  0.1084 0.1556   5.126727e+00   5.374007e+00
   5_adp:  0.1083 0.1562   5.128002e+00   5.378082e+00
   5_occ:  0.1083 0.1562   5.128025e+00   5.378261e+00
   5_bss:  0.1083 0.1562   5.128062e+00   5.378278e+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:  0.305  26.940  -2.399   0.278   0.886   0.000   0.000   0.000
   1_xyz:  0.305  26.940  -2.399   0.278   0.886   0.000   0.000   0.000
   1_adp:  0.305  26.940  -2.399   0.278   0.886   0.000   0.000   0.000
   1_occ:  0.305  26.940  -2.399   0.278   0.886   0.000   0.000   0.000
   2_bss:  0.311  38.157  -3.058  -1.385  -1.122  -0.000  -0.000  -0.000
   2_xyz:  0.311  38.157  -3.058  -1.385  -1.122  -0.000  -0.000  -0.000
   2_adp:  0.311  38.157  -3.058  -1.385  -1.122  -0.000  -0.000  -0.000
   2_occ:  0.311  38.157  -3.058  -1.385  -1.122  -0.000  -0.000  -0.000
   3_bss:  0.310  42.148  -2.919  -1.780  -1.531  -0.000  -0.000  -0.000
   3_xyz:  0.310  42.148  -2.919  -1.780  -1.531  -0.000  -0.000  -0.000
   3_adp:  0.310  42.148  -2.919  -1.780  -1.531  -0.000  -0.000  -0.000
   3_occ:  0.310  42.148  -2.919  -1.780  -1.531  -0.000  -0.000  -0.000
   4_bss:  0.320  42.924  -2.850  -1.869  -1.596  -0.000  -0.000  -0.000
   4_xyz:  0.320  42.924  -2.850  -1.869  -1.596  -0.000  -0.000  -0.000
   4_adp:  0.320  42.924  -2.850  -1.869  -1.596  -0.000  -0.000  -0.000
   4_occ:  0.320  42.924  -2.850  -1.869  -1.596  -0.000  -0.000  -0.000
   5_bss:  0.323  44.237  -2.622  -1.703  -1.411  -0.000  -0.000  -0.000
   5_xyz:  0.323  44.237  -2.622  -1.703  -1.411  -0.000  -0.000  -0.000
   5_adp:  0.323  44.237  -2.622  -1.703  -1.411  -0.000  -0.000  -0.000
   5_occ:  0.323  44.237  -2.622  -1.703  -1.411  -0.000  -0.000  -0.000
   5_bss:  0.323  44.898  -2.423  -1.513  -1.228  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  38.853 0.6587  0.8473    37799.172
   1_bss:  37.501 0.6727  0.8516    34012.852
   1_xyz:  21.452 0.8487  1.0087    12625.841
   1_adp:  22.717 0.8350  0.9984    13713.521
   1_occ:  22.724 0.8349  0.9981    13723.158
   2_bss:  22.453 0.8375  0.9510    13444.875
   2_xyz:  16.608 0.8922  0.9859     7874.388
   2_adp:  15.124 0.9055  0.9878     6976.297
   2_occ:  15.099 0.9056  0.9878     6950.924
   3_bss:  15.018 0.9063  0.9805     6895.820
   3_xyz:  13.878 0.9158  0.9849     6196.863
   3_adp:  13.606 0.9181  0.9822     6082.464
   3_occ:  13.602 0.9182  0.9821     6078.424
   4_bss:  13.605 0.9182  0.9814     6084.060
   4_xyz:  13.381 0.9198  0.9808     5934.776
   4_adp:  13.510 0.9189  0.9739     6001.149
   4_occ:  13.516 0.9189  0.9737     6003.184
   5_bss:  13.514 0.9189  0.9807     6005.082
   5_xyz:  13.677 0.9178  0.9804     6129.376
   5_adp:  13.753 0.9172  0.9742     6172.412
   5_occ:  13.754 0.9172  0.9742     6173.661
   5_bss:  13.756 0.9172  0.9803     6174.374
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.7056e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.7056e-01
   1_xyz:   1.171  0.009  0.072 15.223  0.004  4.111   7.5881e-02
   1_adp:   1.171  0.009  0.072 15.223  0.004  4.111   7.5881e-02
   1_occ:   1.171  0.009  0.072 15.223  0.004  4.111   7.5881e-02
   2_bss:   1.171  0.009  0.072 15.223  0.004  4.111   7.5881e-02
   2_xyz:   1.021  0.007  0.071 14.618  0.004  4.116   5.9513e-02
   2_adp:   1.021  0.007  0.071 14.618  0.004  4.116   5.9513e-02
   2_occ:   1.021  0.007  0.071 14.618  0.004  4.116   5.9513e-02
   3_bss:   1.021  0.007  0.071 14.618  0.004  4.116   5.9513e-02
   3_xyz:   0.989  0.006  0.071 14.691  0.004  4.112   5.6937e-02
   3_adp:   0.989  0.006  0.071 14.691  0.004  4.112   5.6937e-02
   3_occ:   0.989  0.006  0.071 14.691  0.004  4.112   5.6937e-02
   4_bss:   0.989  0.006  0.071 14.691  0.004  4.112   5.6937e-02
   4_xyz:   1.097  0.008  0.080 14.940  0.005  4.114   6.8468e-02
   4_adp:   1.097  0.008  0.080 14.940  0.005  4.114   6.8468e-02
   4_occ:   1.097  0.008  0.080 14.940  0.005  4.114   6.8468e-02
   5_bss:   1.097  0.008  0.080 14.940  0.005  4.114   6.8468e-02
   5_xyz:   0.931  0.006  0.070 14.552  0.004  4.113   5.2195e-02
   5_adp:   0.931  0.006  0.070 14.552  0.004  4.113   5.2195e-02
   5_occ:   0.931  0.006  0.070 14.552  0.004  4.113   5.2195e-02
   5_bss:   0.931  0.006  0.070 14.552  0.004  4.113   5.2195e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3992e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3992e-01
   1_xyz:   7.607  0.057  0.286 86.035  0.032  2.219   1.0239e-01
   1_adp:   7.607  0.057  0.286 86.035  0.032  2.219   1.0239e-01
   1_occ:   7.607  0.057  0.286 86.035  0.032  2.219   1.0239e-01
   2_bss:   7.607  0.057  0.286 86.035  0.032  2.219   1.0239e-01
   2_xyz:   6.584  0.046  0.216 82.976  0.036  2.324   5.0141e-02
   2_adp:   6.584  0.046  0.216 82.976  0.036  2.324   5.0141e-02
   2_occ:   6.584  0.046  0.216 82.976  0.036  2.324   5.0141e-02
   3_bss:   6.584  0.046  0.216 82.976  0.036  2.324   5.0141e-02
   3_xyz:   7.183  0.040  0.227 82.966  0.038  2.375   3.8473e-02
   3_adp:   7.183  0.040  0.227 82.966  0.038  2.375   3.8473e-02
   3_occ:   7.183  0.040  0.227 82.966  0.038  2.375   3.8473e-02
   4_bss:   7.183  0.040  0.227 82.966  0.038  2.375   3.8473e-02
   4_xyz:   7.797  0.048  0.256 81.913  0.041  2.287   5.1617e-02
   4_adp:   7.797  0.048  0.256 81.913  0.041  2.287   5.1617e-02
   4_occ:   7.797  0.048  0.256 81.913  0.041  2.287   5.1617e-02
   5_bss:   7.797  0.048  0.256 81.913  0.041  2.287   5.1617e-02
   5_xyz:   6.670  0.041  0.230 82.063  0.037  2.379   3.2985e-02
   5_adp:   6.670  0.041  0.230 82.063  0.037  2.379   3.2985e-02
   5_occ:   6.670  0.041  0.230 82.063  0.037  2.379   3.2985e-02
   5_bss:   6.670  0.041  0.230 82.063  0.037  2.379   3.2985e-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:  80.94   0.00  17.52  80.94   0.00  13.47  75.32   7.70  39.62
   1_occ:  80.94   0.00  17.52  80.94   0.00  13.47  75.32   7.70  39.62
   2_bss:  80.94   0.00  17.52  80.94   0.00  13.47  75.32   7.70  39.62
   2_xyz:  80.94   0.00  17.52  80.94   0.00  13.47  75.32   7.70  39.62
   2_adp:  80.09   0.00  17.07  80.09   0.00  13.11  73.08   6.25  38.64
   2_occ:  80.09   0.00  17.07  80.09   0.00  13.11  73.08   6.25  38.64
   3_bss:  80.09   0.00  17.07  80.09   0.00  13.11  73.08   6.25  38.64
   3_xyz:  80.09   0.00  17.07  80.09   0.00  13.11  73.08   6.25  38.64
   3_adp:  81.87   2.32  16.89  81.87   2.32  12.92  71.90   5.82  38.47
   3_occ:  81.87   2.32  16.89  81.87   2.32  12.92  71.90   5.82  38.47
   4_bss:  81.87   2.32  16.89  81.87   2.32  12.92  71.90   5.82  38.47
   4_xyz:  81.87   2.32  16.89  81.87   2.32  12.92  71.90   5.82  38.47
   4_adp:  91.97   1.23  16.93  91.97   1.23  12.82  75.71   5.66  39.33
   4_occ:  91.97   1.23  16.93  91.97   1.23  12.82  75.71   5.66  39.33
   5_bss:  91.97   1.23  16.93  91.97   1.23  12.82  75.71   5.66  39.33
   5_xyz:  91.97   1.23  16.93  91.97   1.23  12.82  75.71   5.66  39.33
   5_adp:  93.93   0.63  16.81  93.93   0.63  12.68  76.57   5.32  39.30
   5_occ:  93.93   0.63  16.81  93.93   0.63  12.68  76.57   5.32  39.30
   5_bss:  93.91   0.60  16.79  93.91   0.60  12.66  76.55   5.30  39.28
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.715    0.013    0.359
   1_adp:    1.715    0.013    0.359
   1_occ:    1.715    0.013    0.359
   2_bss:    1.715    0.013    0.359
   2_xyz:    1.001    0.031    0.434
   2_adp:    1.001    0.031    0.434
   2_occ:    1.001    0.031    0.434
   3_bss:    1.001    0.031    0.434
   3_xyz:    1.181    0.026    0.467
   3_adp:    1.181    0.026    0.467
   3_occ:    1.181    0.026    0.467
   4_bss:    1.181    0.026    0.467
   4_xyz:    1.179    0.032    0.485
   4_adp:    1.179    0.032    0.485
   4_occ:    1.179    0.032    0.485
   5_bss:    1.179    0.032    0.485
   5_xyz:    1.282    0.058    0.488
   5_adp:    1.282    0.058    0.488
   5_occ:    1.282    0.058    0.488
   5_bss:    1.282    0.058    0.488
------------------------------------------------------------------------

CPU time actual refinement: 340.78


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_442/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_442/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_442/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_442/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_442/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 340.63 
  Macro-tasks:
    bulk solvent and scale       = 36.87  
    individual site refinement   = 142.92 
    weights calculation          = 30.01  
    collect and process          = 6.67   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 216.57 
  Micro-tasks:
    mask                            = 1.21   
    f_calc                          = 111.04 
    alpha_beta                      = 8.44   
    target                          = 1.25   
    gradients_wrt_atomic_parameters = 120.45 
    fmodel                         = 6.68   
    r_factors                      = 0.18   
    phase_errors                   = 11.07  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 260.60 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.779 micro seconds
Total CPU time: 5.90 minutes
from_scatterers_fft:    665 calls, 110.76 s
gradients_fft:          610 calls, 106.32 s

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

# Date 2008-01-16 Time 04:50:11 PST -0800 (1200487811.96 s)
Start R-work = 0.3680, R-free = 0.3619 (no bulk solvent and anisotropic scale)
Final R-work = 0.1319, R-free = 0.1755 (no bulk solvent and anisotropic scale)

Start R-work = 0.3569, R-free = 0.3491
Final R-work = 0.1083, R-free = 0.1562