# Date 2008-01-16 Time 05:20:15 PST -0800 (1200489615.72 s)
#phil __OFF__

Command line arguments: "../696.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 14541
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 696

-------------------------------------------------------------------------------
  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: (70.25, 47.6339, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.6339, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9529 1.98129
Completeness in resolution range: 0.955188
Completeness with d_max=infinity: 0.952217

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9529
                             d_min =   1.9813

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: (70.25, 47.6339, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9529 1.98129
Completeness in resolution range: 0.955188
Completeness with d_max=infinity: 0.952217

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9533 -  4.2392 [2154/2182]  1939   215  10.0%
  bin  2:  4.2392 -  3.3775 [2063/2086]  1855   208  10.1%
  bin  3:  3.3775 -  2.9543 [2047/2069]  1842   205  10.0%
  bin  4:  2.9543 -  2.6859 [2021/2040]  1826   195   9.6%
  bin  5:  2.6859 -  2.4943 [2019/2048]  1809   210  10.4%
  bin  6:  2.4943 -  2.3479 [1976/2017]  1789   187   9.5%
  bin  7:  2.3479 -  2.2307 [1987/2022]  1783   204  10.3%
  bin  8:  2.2307 -  2.1339 [1996/2035]  1795   201  10.1%
  bin  9:  2.1339 -  2.0519 [1985/2016]  1791   194   9.8%
  bin 10:  2.0519 -  1.9813 [1341/1993]  1201   140  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_696/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: 21
        2.42 -     3.04: 2186
        3.04 -     3.66: 4685
        3.66 -     4.28: 8979
        4.28 -     4.90: 12404
  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 206 " - " O   HOH Z 342 "  1.988 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  2.006 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.060 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  2.104 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28270 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_696/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_696/model_refine_001.geo

CPU time processing inputs: 9.37


============================ 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 = 70.25 47.63395 85.5261 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: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3567   r_free= 0.3482   ksol= 0.00   Bsol= 0.00   scale= 0.953    |
|                                                                             |
| 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: 6.126431                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.7280 0.99   1395  154 0.2986 0.3149      6.3892      6.3798|
|  2:  4.7280 -  3.7726 0.99   1356  148 0.2863 0.2937      6.5456      6.5446|
|  3:  3.7726 -  3.3016 0.99   1319  155 0.3072 0.2892      6.4375      6.4161|
|  4:  3.3016 -  3.0024 0.99   1316  138 0.3296 0.3084      6.3136      6.2091|
|  5:  3.0024 -  2.7887 0.99   1292  147 0.3507 0.3054      6.1807       6.145|
|  6:  2.7887 -  2.6252 0.98   1296  149 0.3817 0.3565      6.1316      6.0245|
|  7:  2.6252 -  2.4943 0.99   1297  142 0.3798 0.3253      6.1026      5.9916|
|  8:  2.4943 -  2.3862 0.99   1283  143 0.3948 0.4351      6.0488      6.0872|
|  9:  2.3862 -  2.2947 0.98   1298  137 0.4181 0.3910       6.027       6.043|
| 10:  2.2947 -  2.2158 0.98   1264  147 0.4121 0.4503      5.9937      6.0535|
| 11:  2.2158 -  2.1467 0.98   1273  139 0.4113 0.3677      5.9373       5.921|
| 12:  2.1467 -  2.0855 0.99   1261  141 0.4075 0.4380      5.8816      5.9312|
| 13:  2.0855 -  2.0307 0.97   1267  138 0.4350 0.4261      5.8032      5.7922|
| 14:  2.0307 -  1.9813 0.56    713   81 0.4121 0.3862      5.7312      5.6586|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9533 -  4.7280  1395   154  0.76  28.44   0.86     0.78      50543.13|
|  2:  4.7280 -  3.7726  1356   148  0.82  24.65   0.96     0.89      55337.03|
|  3:  3.7726 -  3.3016  1319   155  0.78  28.22   0.97     0.92      53151.66|
|  4:  3.3016 -  3.0024  1316   138  0.75  31.16   0.98     0.92      45039.23|
|  5:  3.0024 -  2.7887  1292   147  0.71  34.75   0.97     0.89      37046.14|
|  6:  2.7887 -  2.6252  1296   149  0.69  36.43   0.97     0.88      32569.37|
|  7:  2.6252 -  2.4943  1297   142  0.69  36.87   0.98     0.87      30735.90|
|  8:  2.4943 -  2.3862  1283   143  0.63  41.65   0.98     0.84      32454.94|
|  9:  2.3862 -  2.2947  1298   137  0.60  44.10   0.98     0.80      32184.50|
| 10:  2.2947 -  2.2158  1264   147  0.58  45.88   1.00     0.79      31788.95|
| 11:  2.2158 -  2.1467  1273   139  0.58  45.81   1.01     0.81      29248.42|
| 12:  2.1467 -  2.0855  1261   141  0.58  45.85   1.03     0.83      27095.23|
| 13:  2.0855 -  2.0307  1267   138  0.57  47.03   0.99     0.82      23209.29|
| 14:  2.0307 -  1.9813   713    81  0.59  44.83   1.01     0.80      18991.23|
|alpha:            min =        0.78 max =            0.92 mean =         0.85|
|beta:             min =    18991.23 max =        55337.03 mean =     36460.86|
|figures of merit: min =        0.00 max =            1.00 mean =         0.67|
|phase err.(work): min =        0.00 max =           89.97 mean =        37.87|
|phase err.(test): min =        0.00 max =           89.98 mean =        37.97|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.800251              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.462   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.890407              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.497   (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:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       14 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      187 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1999 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1868 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2817 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4608 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4371 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5651 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6753 |
|-----------------------------------------------------------------------------|
|-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 |        0.164 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.806 |       0.197 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.950)------------------------------------------|
|    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: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3567   r_free= 0.3482   ksol= 0.00   Bsol= 0.00   scale= 0.953    |
|                                                                             |
| 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: 6.126431                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3426   r_free= 0.3321   ksol= 0.31   Bsol= 38.71   scale= 0.973   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.27,3.41,-0.56,0.00,-0.00,-0.00); trace/3= -0.14                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 6.105220                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.212656              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.361   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.477371              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.282   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3426      final r-factor (work) = 0.2030          |
| start r-factor (free) = 0.3321      final r-factor (free) = 0.2263          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.1435 = 6.21 * 0.50 * 6.1100 + 1.00 * 0.1638                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.1882 = 6.21 * 0.50 * 5.8283 + 1.00 * 0.0835                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2030      final r-factor (work) = 0.1840          |
| start r-factor (free) = 0.2263      final r-factor (free) = 0.2316          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7883 = 0.48 * 1.00 * 5.8283 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6651 = 0.48 * 1.00 * 5.5613 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.950)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.25   17.24    None  None   None       |
|    all(noH): 2823   0      0.00    81.25   17.24    None  None   None       |
|    Sol.    : 438    0      6.65    79.75   39.26    None  None   None       |
|    Mac.    : 2385   0      0.00    81.25   13.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.125:  674   |   5:    40.623 -  48.747:  112        |
|      1:     8.125 -  16.249: 1196   |   6:    48.747 -  56.872:   82        |
|      2:    16.249 -  24.374:  403   |   7:    56.872 -  64.996:   52        |
|      3:    24.374 -  32.498:  158   |   8:    64.996 -  73.121:   16        |
|      4:    32.498 -  40.623:  124   |   9:    73.121 -  81.245:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1840 r_free = 0.2316             target_work(ml) = 5.571         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1836 r_free = 0.2317             target_work(ml) = 5.570         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1836   r_free= 0.2317   ksol= 0.31   Bsol= 38.71   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.27,3.41,-0.56,0.00,-0.00,-0.00); trace/3= -0.14                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.569940                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1809   r_free= 0.2293   ksol= 0.32   Bsol= 55.89   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.00,-0.12,-1.31,-0.00,-0.00,-0.00); trace/3= -1.48                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.559704                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.910709              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.257   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.170044              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.736  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1809      final r-factor (work) = 0.1367          |
| start r-factor (free) = 0.2293      final r-factor (free) = 0.1774          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1829 = 2.91 * 0.50 * 5.5652 + 1.00 * 0.0835                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9884 = 2.91 * 0.50 * 5.4450 + 1.00 * 0.0640                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1367      final r-factor (work) = 0.1302          |
| start r-factor (free) = 0.1774      final r-factor (free) = 0.1686          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9362 = 0.17 * 1.00 * 5.4450 + 1.00 * 0.0103                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9053 = 0.17 * 1.00 * 5.2779 + 1.00 * 0.0079                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.950)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.06    80.88   16.80    None  None   None       |
|    all(noH): 2823   0      2.06    80.88   16.80    None  None   None       |
|    Sol.    : 438    0      3.87    77.06   38.53    None  None   None       |
|    Mac.    : 2385   0      2.06    80.88   12.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.059 -   9.941: 1034   |   5:    41.467 -  49.349:  106        |
|      1:     9.941 -  17.822: 1037   |   6:    49.349 -  57.231:   74        |
|      2:    17.822 -  25.704:  266   |   7:    57.231 -  65.112:   41        |
|      3:    25.704 -  33.586:  122   |   8:    65.112 -  72.994:   14        |
|      4:    33.586 -  41.467:  125   |   9:    72.994 -  80.876:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1302 r_free = 0.1686             target_work(ml) = 5.254         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1300 r_free = 0.1685             target_work(ml) = 5.254         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1300   r_free= 0.1685   ksol= 0.32   Bsol= 55.89   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.00,-0.12,-1.31,-0.00,-0.00,-0.00); trace/3= -1.48                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.253501                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1300   r_free= 0.1682   ksol= 0.32   Bsol= 53.85   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-1.10,-1.32,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.252682                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.451007              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.241  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.063639              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.040  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1300      final r-factor (work) = 0.1203          |
| start r-factor (free) = 0.1682      final r-factor (free) = 0.1598          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8927 = 1.45 * 0.50 * 5.2773 + 1.00 * 0.0640                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8380 = 1.45 * 0.50 * 5.2181 + 1.00 * 0.0522                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1203      final r-factor (work) = 0.1172          |
| start r-factor (free) = 0.1598      final r-factor (free) = 0.1602          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5581 = 1.06 * 1.00 * 5.2181 + 1.00 * 0.0079                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5172 = 1.06 * 1.00 * 5.1780 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.950)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.10    91.36   16.98    None  None   None       |
|    all(noH): 2823   0      1.10    91.36   16.98    None  None   None       |
|    Sol.    : 438    0      3.22    79.36   40.30    None  None   None       |
|    Mac.    : 2385   0      1.10    91.36   12.69    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:     1.097 -  10.123: 1123   |   5:    46.228 -  55.254:  112        |
|      1:    10.123 -  19.149: 1032   |   6:    55.254 -  64.280:   64        |
|      2:    19.149 -  28.175:  215   |   7:    64.280 -  73.306:   28        |
|      3:    28.175 -  37.201:  131   |   8:    73.306 -  82.332:    7        |
|      4:    37.201 -  46.228:  109   |   9:    82.332 -  91.358:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1172 r_free = 0.1602             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1172 r_free = 0.1601             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1172   r_free= 0.1601   ksol= 0.32   Bsol= 53.85   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-1.10,-1.32,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.179008                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1171   r_free= 0.1600   ksol= 0.32   Bsol= 53.85   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-1.29,-1.22,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.178727                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.251871              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 138.269  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.188377              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 110.556  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1171      final r-factor (work) = 0.1108          |
| start r-factor (free) = 0.1600      final r-factor (free) = 0.1582          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8820 = 2.25 * 0.50 * 5.1777 + 1.00 * 0.0522                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8657 = 2.25 * 0.50 * 5.1540 + 1.00 * 0.0626                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1108      final r-factor (work) = 0.1102          |
| start r-factor (free) = 0.1582      final r-factor (free) = 0.1587          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1346 = 1.19 * 1.00 * 5.1540 + 1.00 * 0.0097                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1171 = 1.19 * 1.00 * 5.1389 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.950)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.42    100.27  16.84    None  None   None       |
|    all(noH): 2823   0      0.42    100.27  16.84    None  None   None       |
|    Sol.    : 438    0      4.08    78.48   40.25    None  None   None       |
|    Mac.    : 2385   0      0.42    100.27  12.54    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:     0.418 -  10.403: 1222   |   5:    50.343 -  60.328:   93        |
|      1:    10.403 -  20.388:  996   |   6:    60.328 -  70.313:   46        |
|      2:    20.388 -  30.373:  202   |   7:    70.313 -  80.298:   13        |
|      3:    30.373 -  40.358:  120   |   8:    80.298 -  90.282:    4        |
|      4:    40.358 -  50.343:  125   |   9:    90.282 - 100.267:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1102 r_free = 0.1587             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1101 r_free = 0.1587             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1101   r_free= 0.1587   ksol= 0.32   Bsol= 53.85   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-1.29,-1.22,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.141137                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1100   r_free= 0.1587   ksol= 0.32   Bsol= 53.85   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-1.16,-0.97,-0.00,-0.00,-0.00); trace/3= -1.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.141215                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.073764              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 162.982  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.448173              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.851  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1100      final r-factor (work) = 0.1098          |
| start r-factor (free) = 0.1587      final r-factor (free) = 0.1588          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3921 = 2.07 * 0.50 * 5.1399 + 1.00 * 0.0626                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3901 = 2.07 * 0.50 * 5.1415 + 1.00 * 0.0590                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1098      final r-factor (work) = 0.1097          |
| start r-factor (free) = 0.1588      final r-factor (free) = 0.1586          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4558 = 1.45 * 1.00 * 5.1415 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4564 = 1.45 * 1.00 * 5.1416 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.950)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.09    109.08  16.66    None  None   None       |
|    all(noH): 2823   0      0.09    109.08  16.66    None  None   None       |
|    Sol.    : 438    0      5.17    84.71   40.06    None  None   None       |
|    Mac.    : 2385   0      0.09    109.08  12.36    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:     0.086 -  10.986: 1402   |   5:    54.584 -  65.483:   81        |
|      1:    10.986 -  21.885:  855   |   6:    65.483 -  76.383:   24        |
|      2:    21.885 -  32.785:  198   |   7:    76.383 -  87.282:   12        |
|      3:    32.785 -  43.684:  130   |   8:    87.282 -  98.182:    2        |
|      4:    43.684 -  54.584:  117   |   9:    98.182 - 109.081:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1097 r_free = 0.1586             target_work(ml) = 5.143         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1097 r_free = 0.1586             target_work(ml) = 5.143         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1097   r_free= 0.1586   ksol= 0.32   Bsol= 53.85   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-1.16,-0.97,-0.00,-0.00,-0.00); trace/3= -1.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.142857                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.7280 0.99   1395  154 0.0958 0.1272      5.3517       5.512|
|  2:  4.7280 -  3.7726 0.99   1356  148 0.0825 0.1083      5.4054      5.6151|
|  3:  3.7726 -  3.3016 0.99   1319  155 0.1021 0.1485      5.4513      5.8288|
|  4:  3.3016 -  3.0024 0.99   1316  138 0.1223 0.1568      5.4556      5.6184|
|  5:  3.0024 -  2.7887 0.99   1292  147 0.1301 0.1742       5.326      5.5279|
|  6:  2.7887 -  2.6252 0.98   1296  149 0.1222 0.1908       5.222      5.4535|
|  7:  2.6252 -  2.4943 0.99   1297  142 0.1205 0.1609      5.1437      5.3862|
|  8:  2.4943 -  2.3862 0.99   1283  143 0.1129 0.1773      5.0635      5.2985|
|  9:  2.3862 -  2.2947 0.98   1298  137 0.1148 0.1789      5.0205      5.3364|
| 10:  2.2947 -  2.2158 0.98   1264  147 0.1107 0.1851      4.9723      5.2424|
| 11:  2.2158 -  2.1467 0.98   1273  139 0.1137 0.1777      4.9382      5.2646|
| 12:  2.1467 -  2.0855 0.99   1261  141 0.1080 0.1654      4.8773      5.1385|
| 13:  2.0855 -  2.0307 0.97   1267  138 0.1136 0.1815      4.8039      5.1262|
| 14:  2.0307 -  1.9813 0.56    713   81 0.1079 0.1762      4.7155      4.9135|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9533 -  4.7280  1395   154  0.94   8.76   0.97     0.95       6718.65|
|  2:  4.7280 -  3.7726  1356   148  0.95   7.76   1.01     1.00       8522.84|
|  3:  3.7726 -  3.3016  1319   155  0.94  10.94   1.02     1.02      10077.39|
|  4:  3.3016 -  3.0024  1316   138  0.92  13.97   1.01     0.99      10447.67|
|  5:  3.0024 -  2.7887  1292   147  0.90  16.18   0.99     0.97       8436.44|
|  6:  2.7887 -  2.6252  1296   149  0.90  16.20   0.98     0.95       7333.67|
|  7:  2.6252 -  2.4943  1297   142  0.91  15.28   0.98     0.96       6015.25|
|  8:  2.4943 -  2.3862  1283   143  0.91  15.53   0.99     0.96       5514.97|
|  9:  2.3862 -  2.2947  1298   137  0.91  15.43   0.99     0.95       4921.68|
| 10:  2.2947 -  2.2158  1264   147  0.90  15.84   0.98     0.95       4604.75|
| 11:  2.2158 -  2.1467  1273   139  0.90  16.38   0.99     0.94       4361.70|
| 12:  2.1467 -  2.0855  1261   141  0.91  15.18   0.99     0.98       4010.98|
| 13:  2.0855 -  2.0307  1267   138  0.89  16.87   0.98     0.98       3569.29|
| 14:  2.0307 -  1.9813   713    81  0.91  15.72   0.96     0.92       2888.90|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2888.90 max =        10447.67 mean =      6389.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.17|
|phase err.(test): min =        0.00 max =           89.53 mean =        13.65|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1096   r_free= 0.1586   ksol= 0.32   Bsol= 54.42   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.85,-1.01,-0.77,-0.00,-0.00,-0.00); trace/3= -1.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.142958                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1096   r_free= 0.1586   ksol= 0.32   Bsol= 54.42   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.85,-1.01,-0.77,-0.00,-0.00,-0.00); trace/3= -1.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.142958                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.7280 0.99   1395  154 0.0958 0.1273      5.3528      5.5136|
|  2:  4.7280 -  3.7726 0.99   1356  148 0.0826 0.1084      5.4064      5.6154|
|  3:  3.7726 -  3.3016 0.99   1319  155 0.1021 0.1486      5.4516      5.8291|
|  4:  3.3016 -  3.0024 0.99   1316  138 0.1222 0.1568      5.4555      5.6184|
|  5:  3.0024 -  2.7887 0.99   1292  147 0.1300 0.1742      5.3255      5.5273|
|  6:  2.7887 -  2.6252 0.98   1296  149 0.1222 0.1907      5.2216      5.4528|
|  7:  2.6252 -  2.4943 0.99   1297  142 0.1205 0.1610      5.1435      5.3866|
|  8:  2.4943 -  2.3862 0.99   1283  143 0.1129 0.1774      5.0635      5.2982|
|  9:  2.3862 -  2.2947 0.98   1298  137 0.1148 0.1789      5.0206      5.3366|
| 10:  2.2947 -  2.2158 0.98   1264  147 0.1107 0.1852      4.9724      5.2426|
| 11:  2.2158 -  2.1467 0.98   1273  139 0.1137 0.1776      4.9381      5.2646|
| 12:  2.1467 -  2.0855 0.99   1261  141 0.1079 0.1654      4.8771      5.1387|
| 13:  2.0855 -  2.0307 0.97   1267  138 0.1136 0.1814      4.8038      5.1255|
| 14:  2.0307 -  1.9813 0.56    713   81 0.1079 0.1760      4.7153      4.9132|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9533 -  4.7280  1395   154  0.94   8.78   0.97     0.95       6737.04|
|  2:  4.7280 -  3.7726  1356   148  0.95   7.77   1.01     1.00       8539.25|
|  3:  3.7726 -  3.3016  1319   155  0.94  10.94   1.03     1.02      10088.21|
|  4:  3.3016 -  3.0024  1316   138  0.92  13.97   1.01     0.99      10445.85|
|  5:  3.0024 -  2.7887  1292   147  0.90  16.17   1.00     0.97       8428.13|
|  6:  2.7887 -  2.6252  1296   149  0.90  16.20   0.99     0.96       7325.68|
|  7:  2.6252 -  2.4943  1297   142  0.91  15.27   0.99     0.96       6012.40|
|  8:  2.4943 -  2.3862  1283   143  0.91  15.53   1.00     0.97       5515.03|
|  9:  2.3862 -  2.2947  1298   137  0.91  15.43   1.00     0.96       4924.05|
| 10:  2.2947 -  2.2158  1264   147  0.90  15.84   0.99     0.95       4604.50|
| 11:  2.2158 -  2.1467  1273   139  0.90  16.38   0.99     0.95       4360.55|
| 12:  2.1467 -  2.0855  1261   141  0.91  15.18   1.00     0.99       4009.62|
| 13:  2.0855 -  2.0307  1267   138  0.89  16.87   1.00     0.99       3567.28|
| 14:  2.0307 -  1.9813   713    81  0.91  15.71   0.97     0.93       2886.53|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2886.53 max =        10445.85 mean =      6391.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.17|
|phase err.(test): min =        0.00 max =           89.59 mean =        13.65|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.950)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.09    109.08  16.66    None  None   None       |
|    all(noH): 2823   0      0.09    109.08  16.66    None  None   None       |
|    Sol.    : 438    0      5.17    84.71   40.06    None  None   None       |
|    Mac.    : 2385   0      0.09    109.08  12.36    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:     0.086 -  10.985: 1402   |   5:    54.583 -  65.483:   81        |
|      1:    10.985 -  21.885:  855   |   6:    65.483 -  76.383:   24        |
|      2:    21.885 -  32.784:  198   |   7:    76.383 -  87.282:   12        |
|      3:    32.784 -  43.684:  130   |   8:    87.282 -  98.182:    2        |
|      4:    43.684 -  54.583:  117   |   9:    98.182 - 109.081:    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)= 285         
Filter by distance & map next to the model:
   mapped sites are within: 0.536 - 4.556
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 282 from: 285
   mapped sites are within: 0.711 - 4.556

peak=    5.788 closest distance to " NH2 ARG A  56 " =    2.340
peak=    5.672 closest distance to " CB  GLN A 223 " =    1.406
peak=    5.221 closest distance to " CB  ARG A 275 " =    0.909
peak=    5.218 closest distance to " CB  SER A  63 " =    1.208
peak=    5.007 closest distance to " CG  PRO A 213 " =    1.223
peak=    4.854 closest distance to " CB  GLN A 183 " =    1.302
peak=    4.755 closest distance to " CA  TYR A  30 " =    0.943
peak=    4.644 closest distance to " O   HOH Z 403 " =    1.745
peak=    4.629 closest distance to " O   HOH Z 232 " =    2.338
peak=    4.619 closest distance to " O   HOH Z 298 " =    1.921
peak=    4.602 closest distance to " CG  PRO A 198 " =    1.226
peak=    4.590 closest distance to " C   PRO A 198 " =    1.481
peak=    4.515 closest distance to " CG  PRO A  90 " =    1.108
peak=    4.505 closest distance to " CB  GLU A 128 " =    1.179
peak=    4.467 closest distance to " OD1 ASN A  69 " =    2.557
peak=    4.427 closest distance to " CA  ALA A  21 " =    1.344
peak=    4.380 closest distance to " O   HOH Z 234 " =    3.774
peak=    4.349 closest distance to " O   HOH Z  78 " =    1.740
peak=    4.347 closest distance to " O   HOH Z  15 " =    2.110
peak=    4.321 closest distance to " CG1 ILE A  33 " =    1.238
peak=    4.318 closest distance to " CB  TYR A 169 " =    0.841
peak=    4.259 closest distance to " CB  ARG A 190 " =    1.723
peak=    4.246 closest distance to " CB  GLU A 277 " =    3.602
peak=    4.194 closest distance to " CB  GLU A 152 " =    1.140
peak=    4.192 closest distance to " O   HOH Z 193 " =    1.842
peak=    4.188 closest distance to " NZ  LYS A 117 " =    3.191
peak=    4.184 closest distance to " O   HOH Z  97 " =    1.938
peak=    4.172 closest distance to " O   HOH Z  59 " =    2.385
peak=    4.169 closest distance to " O   HOH Z  43 " =    2.111
peak=    4.147 closest distance to " NH2 ARG A 156 " =    1.151
peak=    4.146 closest distance to " O   HOH Z  40 " =    1.914
peak=    4.146 closest distance to " O   HOH Z 369 " =    2.176
peak=    4.145 closest distance to " O   HOH Z 132 " =    2.461
peak=    4.145 closest distance to " CG  PRO A 243 " =    1.134
peak=    4.133 closest distance to " CB  ARG A  79 " =    1.363
peak=    4.118 closest distance to " NH2BARG A 145 " =    2.178
peak=    4.117 closest distance to " O   HOH Z 287 " =    1.986
peak=    4.100 closest distance to " O   HOH Z 142 " =    1.588
peak=    4.095 closest distance to " CD  ARG A 269 " =    0.989
peak=    4.093 closest distance to " CB  SER A   3 " =    1.272
peak=    4.066 closest distance to " O   SER A  87 " =    2.263
peak=    4.058 closest distance to " CB  ASN A 148 " =    1.456
peak=    4.053 closest distance to " O   HOH Z 352 " =    1.862
peak=    4.042 closest distance to " NE2 GLN A  11 " =    0.974
peak=    4.030 closest distance to " CG  ARG A  66 " =    2.581
peak=    4.024 closest distance to " O   HOH Z 126 " =    1.880
peak=    3.980 closest distance to " O   HOH Z 279 " =    2.205
peak=    3.963 closest distance to " CB  LEU A 228 " =    1.142
peak=    3.957 closest distance to " O   HOH Z 368 " =    2.109
peak=    3.952 closest distance to " O   HOH Z 316 " =    3.040
peak=    3.950 closest distance to " OD2 ASP A 286 " =    2.843
peak=    3.949 closest distance to " O   HOH Z 209 " =    2.245
peak=    3.946 closest distance to " CA  ASN A 176 " =    1.239
peak=    3.942 closest distance to " O   HOH Z 423 " =    1.963
peak=    3.939 closest distance to " O   HOH Z 134 " =    1.369
peak=    3.931 closest distance to " O   HOH Z 402 " =    1.479
peak=    3.899 closest distance to " CZ  PHE A 218 " =    1.072
peak=    3.893 closest distance to " CA  THR A 221 " =    0.947
peak=    3.891 closest distance to " O   HOH Z 284 " =    3.003
peak=    3.882 closest distance to " CA  ARG A 195 " =    1.267
peak=    3.882 closest distance to " O   HOH Z 346 " =    1.595
peak=    3.867 closest distance to " O   HOH Z 158 " =    2.935
peak=    3.867 closest distance to " CB  TRP A 179 " =    1.341
peak=    3.864 closest distance to " CD2 LEU A 297 " =    0.883
peak=    3.850 closest distance to " O   HOH Z  68 " =    1.888
peak=    3.846 closest distance to " O   HOH Z  44 " =    1.947
peak=    3.841 closest distance to " O   HOH Z 357 " =    1.987
peak=    3.834 closest distance to " O   HOH Z 426 " =    1.554
peak=    3.826 closest distance to " O   HOH Z  80 " =    1.614
peak=    3.826 closest distance to " CG2 ILE A 120 " =    1.095
peak=    3.822 closest distance to " CA  ARG A  36 " =    1.089
peak=    3.820 closest distance to " CG2 THR A 221 " =    1.158
peak=    3.818 closest distance to " CG  GLN A  58 " =    2.641
peak=    3.816 closest distance to " CB  VAL A 265 " =    1.208
peak=    3.812 closest distance to " O   HOH Z 132 " =    2.769
peak=    3.811 closest distance to " O   HOH Z 411 " =    3.695
peak=    3.809 closest distance to " O   HOH Z 427 " =    2.952
peak=    3.799 closest distance to " O   HOH Z  20 " =    1.485
peak=    3.787 closest distance to " CB  SER A  62 " =    0.776
peak=    3.787 closest distance to " O   THR A 251 " =    1.192
peak=    3.784 closest distance to " O   HOH Z 189 " =    2.233
peak=    3.781 closest distance to " O   HOH Z  21 " =    1.762
peak=    3.781 closest distance to " CB  SER A 141 " =    0.995
peak=    3.775 closest distance to " O   HOH Z 245 " =    1.351
peak=    3.759 closest distance to " O   HOH Z 371 " =    3.381
peak=    3.756 closest distance to " CB  TRP A 266 " =    0.952
peak=    3.753 closest distance to " O   HOH Z  61 " =    1.550
peak=    3.736 closest distance to " O   HOH Z 250 " =    1.438
peak=    3.724 closest distance to " CB  ASN A  39 " =    0.834
peak=    3.720 closest distance to " O   HOH Z 261 " =    1.917
peak=    3.719 closest distance to " O   MET A 105 " =    1.913
peak=    3.719 closest distance to " O   HOH Z 303 " =    2.097
peak=    3.717 closest distance to " ND2 ASN A 187 " =    1.531
peak=    3.709 closest distance to " CG1BVAL A  72 " =    1.693
peak=    3.706 closest distance to " O   HOH Z 214 " =    2.283
peak=    3.706 closest distance to " O   HOH Z 108 " =    2.622
peak=    3.706 closest distance to " CB  ASP A 140 " =    0.930
peak=    3.704 closest distance to " O   HOH Z 247 " =    1.375
peak=    3.698 closest distance to " O   HOH Z 345 " =    3.078
peak=    3.697 closest distance to " O   HOH Z 147 " =    1.774
peak=    3.695 closest distance to " OD2 ASP A 298 " =    3.960
peak=    3.693 closest distance to " OE1 GLU A   2 " =    2.219
peak=    3.689 closest distance to " CB  VAL A 202 " =    1.512
peak=    3.673 closest distance to " CA  ASP A 140 " =    1.154
peak=    3.671 closest distance to " O   TRP A 274 " =    1.922
peak=    3.664 closest distance to " O   HOH Z 406 " =    1.558
peak=    3.663 closest distance to " CD2 TRP A 179 " =    1.410
peak=    3.658 closest distance to " O   HOH Z 128 " =    2.146
peak=    3.654 closest distance to " O   HOH Z 374 " =    2.720
peak=    3.652 closest distance to " O   HOH Z 389 " =    1.921
peak=    3.651 closest distance to " CD1 LEU A 300 " =    1.183
peak=    3.651 closest distance to " CD1 LEU A  96 " =    0.763
peak=    3.645 closest distance to " CB  ALA A 291 " =    1.337
peak=    3.645 closest distance to " O   HOH Z 180 " =    2.253
peak=    3.638 closest distance to " O   HOH Z 163 " =    1.499
peak=    3.634 closest distance to " CA  ASN A 215 " =    1.165
peak=    3.619 closest distance to " CA  ALA A  51 " =    0.949
peak=    3.618 closest distance to " O   HOH Z 102 " =    1.241
peak=    3.616 closest distance to " O   HOH Z 344 " =    3.154
peak=    3.586 closest distance to " OG BSER A 164 " =    2.350
peak=    3.583 closest distance to " O   HOH Z  63 " =    1.903
peak=    3.583 closest distance to " CG2 VAL A 257 " =    0.871
peak=    3.581 closest distance to " O   HOH Z  19 " =    1.811
peak=    3.581 closest distance to " O   HOH Z  54 " =    2.290
peak=    3.573 closest distance to " O   HOH Z 421 " =    1.703
peak=    3.573 closest distance to " CG2BVAL A  41 " =    0.830
peak=    3.567 closest distance to " CG2 VAL A 197 " =    1.108
peak=    3.557 closest distance to " O   HOH Z 291 " =    1.491
peak=    3.553 closest distance to " O   HOH Z 361 " =    3.598
peak=    3.547 closest distance to " O   HOH Z 295 " =    1.496
peak=    3.540 closest distance to " CA  LYS A 117 " =    1.261
peak=    3.539 closest distance to " O   HOH Z  49 " =    2.311
peak=    3.527 closest distance to " CD  LYS A 166 " =    1.354
peak=    3.524 closest distance to " O   HOH Z 383 " =    2.064
peak=    3.520 closest distance to " CB  ARG A 139 " =    0.802
peak=    3.519 closest distance to " CA  ALA A 160 " =    0.835
peak=    3.517 closest distance to " O   HOH Z 126 " =    1.565
peak=    3.504 closest distance to " CD  ARG A 159 " =    0.793
peak=    3.502 closest distance to " OG  SER A  62 " =    2.878
peak=    3.501 closest distance to " N   ASN A  39 " =    1.347
peak=    3.493 closest distance to " CB  PRO A 198 " =    1.104
peak=    3.490 closest distance to " O   HOH Z 193 " =    2.201
peak=    3.488 closest distance to " O   ALA A 165 " =    1.421
peak=    3.486 closest distance to " CB  TYR A 169 " =    0.923
peak=    3.484 closest distance to " CG2 ILE A  20 " =    1.372
peak=    3.475 closest distance to " O   HOH Z  97 " =    2.597
peak=    3.474 closest distance to " NH1AARG A 145 " =    1.171
peak=    3.465 closest distance to " OG1 THR A 294 " =    2.362
peak=    3.462 closest distance to " O   HOH Z 227 " =    1.685
peak=    3.460 closest distance to " O   HOH Z 391 " =    3.008
peak=    3.459 closest distance to " CG2 VAL A  78 " =    0.912
peak=    3.459 closest distance to " ND2 ASN A 110 " =    1.624
peak=    3.456 closest distance to " CA  ASP A 124 " =    0.711
peak=    3.456 closest distance to " C   SER A  32 " =    1.074
peak=    3.456 closest distance to " O   HOH Z 281 " =    4.556
peak=    3.453 closest distance to " O   HOH Z 427 " =    3.103
peak=    3.449 closest distance to " O   HOH Z  54 " =    1.703
peak=    3.445 closest distance to " NZ  LYS A 166 " =    3.077
peak=    3.441 closest distance to " CG AARG A 275 " =    1.120
peak=    3.439 closest distance to " O   HOH Z 423 " =    3.441
peak=    3.436 closest distance to " O   HOH Z 437 " =    1.452
peak=    3.434 closest distance to " O   HOH Z 197 " =    2.770
peak=    3.430 closest distance to " CD1 ILE A 106 " =    0.847
peak=    3.430 closest distance to " CG1 VAL A 153 " =    0.969
peak=    3.430 closest distance to " CB  MET A  47 " =    0.963
peak=    3.422 closest distance to " O   HOH Z 155 " =    3.248
peak=    3.414 closest distance to " ND1 HIS A  81 " =    1.594
peak=    3.412 closest distance to " CA  ALA A 248 " =    1.205
peak=    3.412 closest distance to " CA  GLY A  80 " =    1.110
peak=    3.411 closest distance to " O   HOH Z 425 " =    2.062
peak=    3.410 closest distance to " O   HOH Z 185 " =    1.690
peak=    3.406 closest distance to " O   GLY A  57 " =    2.636
peak=    3.404 closest distance to " O   HOH Z 258 " =    2.237
peak=    3.398 closest distance to " O   THR A 220 " =    1.223
peak=    3.392 closest distance to " CB  SER A 212 " =    1.092
peak=    3.392 closest distance to " CE  LYS A  76 " =    0.822
peak=    3.388 closest distance to " CA  ASP A 191 " =    0.819
peak=    3.385 closest distance to " O   HOH Z 214 " =    2.294
peak=    3.385 closest distance to " O   HOH Z 345 " =    1.584
peak=    3.372 closest distance to " CB  MET A  40 " =    0.878
peak=    3.371 closest distance to " CB  ILE A 120 " =    1.319
peak=    3.370 closest distance to " O   HOH Z  61 " =    1.539
peak=    3.369 closest distance to " O   HOH Z 250 " =    1.655
peak=    3.367 closest distance to " O   HOH Z 327 " =    1.699
peak=    3.366 closest distance to " O   HOH Z 416 " =    2.928
peak=    3.366 closest distance to " O   HOH Z 272 " =    1.851
peak=    3.362 closest distance to " O   HOH Z  88 " =    3.378
peak=    3.360 closest distance to " O   HOH Z 133 " =    1.479
peak=    3.354 closest distance to " O   HOH Z 299 " =    2.437
peak=    3.351 closest distance to " NH2AARG A 275 " =    3.679
peak=    3.351 closest distance to " O   HOH Z 313 " =    1.875
peak=    3.349 closest distance to " O   HOH Z 130 " =    2.300
peak=    3.348 closest distance to " O   HOH Z 135 " =    1.826
peak=    3.347 closest distance to " O   HOH Z 173 " =    2.131
peak=    3.347 closest distance to " CB  SER A 273 " =    0.842
peak=    3.344 closest distance to " CA  ALA A 291 " =    0.848
peak=    3.342 closest distance to " O   HOH Z 183 " =    1.459
peak=    3.341 closest distance to " O   HOH Z  66 " =    2.144
peak=    3.337 closest distance to " O   HOH Z 365 " =    2.898
peak=    3.333 closest distance to " CA  ALA A 295 " =    1.184
peak=    3.317 closest distance to " O   HOH Z 368 " =    2.652
peak=    3.313 closest distance to " O   SER A  26 " =    1.679
peak=    3.313 closest distance to " O   HOH Z 305 " =    3.662
peak=    3.304 closest distance to " CG1 ILE A 151 " =    0.888
peak=    3.297 closest distance to " CG  ARG A 219 " =    1.228
peak=    3.296 closest distance to " O   HOH Z  89 " =    2.193
peak=    3.292 closest distance to " CG  LYS A  76 " =    1.066
peak=    3.291 closest distance to " O   HOH Z 124 " =    1.309
peak=    3.280 closest distance to " N   ARG A 156 " =    1.422
peak=    3.278 closest distance to " O   HOH Z 403 " =    1.357
peak=    3.269 closest distance to " CA  MET A  40 " =    1.059
peak=    3.265 closest distance to " O   HOH Z 193 " =    1.549
peak=    3.256 closest distance to " O   HOH Z  35 " =    2.419
peak=    3.255 closest distance to " CD BLYS A 290 " =    1.082
peak=    3.255 closest distance to " O   HOH Z 166 " =    3.691
peak=    3.254 closest distance to " CB  SER A 216 " =    0.855
peak=    3.253 closest distance to " NZ  LYS A  76 " =    1.513
peak=    3.247 closest distance to " CB  THR A 157 " =    1.033
peak=    3.245 closest distance to " CG2AVAL A 121 " =    2.247
peak=    3.237 closest distance to " CA  MET A 105 " =    1.097
peak=    3.236 closest distance to " O   HOH Z 156 " =    2.573
peak=    3.233 closest distance to " CB  ALA A 242 " =    0.970
peak=    3.232 closest distance to " CA  ASP A 162 " =    1.168
peak=    3.232 closest distance to " O   HOH Z 299 " =    4.530
peak=    3.226 closest distance to " O   ALA A 158 " =    1.204
peak=    3.223 closest distance to " OG  SER A 245 " =    1.615
peak=    3.222 closest distance to " CB  ALA A   9 " =    1.568
peak=    3.215 closest distance to " CB  ASN A 215 " =    1.167
peak=    3.213 closest distance to " NZ  LYS A 117 " =    1.717
peak=    3.212 closest distance to " CB  ALA A 295 " =    1.160
peak=    3.211 closest distance to " O   HOH Z 393 " =    3.401
peak=    3.211 closest distance to " O   HOH Z 148 " =    3.240
peak=    3.202 closest distance to " CA  VAL A  41 " =    0.898
peak=    3.200 closest distance to " CG2 THR A 220 " =    0.787
peak=    3.197 closest distance to " CB  PHE A  16 " =    1.022
peak=    3.197 closest distance to " O   HOH Z 387 " =    2.720
peak=    3.197 closest distance to " CB  TYR A 116 " =    0.913
peak=    3.193 closest distance to " O   HOH Z 109 " =    2.512
peak=    3.192 closest distance to " CB  PRO A  54 " =    1.047
peak=    3.189 closest distance to " CA  LEU A  83 " =    1.338
peak=    3.180 closest distance to " CD  LYS A 119 " =    1.305
peak=    3.179 closest distance to " NZ ALYS A 290 " =    1.096
peak=    3.178 closest distance to " O   HOH Z 411 " =    1.730
peak=    3.178 closest distance to " O   HOH Z 425 " =    1.231
peak=    3.178 closest distance to " O   HOH Z   1 " =    2.260
peak=    3.175 closest distance to " O   HOH Z 353 " =    2.804
peak=    3.173 closest distance to " CB  HIS A 108 " =    0.813
peak=    3.172 closest distance to " O   HOH Z 273 " =    2.848
peak=    3.170 closest distance to " CZ  PHE A  38 " =    1.359
peak=    3.169 closest distance to " CA  ALA A  84 " =    1.276
peak=    3.165 closest distance to " O   HOH Z 422 " =    2.638
peak=    3.163 closest distance to " CG  ARG A  66 " =    0.963
peak=    3.163 closest distance to " CB  ALA A  71 " =    1.278
peak=    3.163 closest distance to " O   HOH Z 255 " =    1.655
peak=    3.162 closest distance to " O   HOH Z 359 " =    1.377
peak=    3.161 closest distance to " O   HOH Z 128 " =    2.182
peak=    3.160 closest distance to " OH  TYR A 116 " =    1.083
peak=    3.150 closest distance to " O   HOH Z 417 " =    3.063
peak=    3.149 closest distance to " O   HOH Z 234 " =    1.778
peak=    3.147 closest distance to " CA  SER A  87 " =    1.055
peak=    3.145 closest distance to " CG  GLN A  11 " =    1.318
peak=    3.145 closest distance to " O   HOH Z  10 " =    1.759
peak=    3.142 closest distance to " CG2 VAL A 296 " =    1.022
peak=    3.140 closest distance to " O   HOH Z 271 " =    2.219
peak=    3.135 closest distance to " CD  GLU A 152 " =    0.841
peak=    3.130 closest distance to " O   HOH Z  85 " =    2.118
peak=    3.129 closest distance to " CA  LEU A 101 " =    1.441
peak=    3.124 closest distance to " CB  SER A  28 " =    1.058
peak=    3.122 closest distance to " NE2 GLN A  58 " =    2.986
peak=    3.120 closest distance to " O   HOH Z 261 " =    1.523
peak=    3.116 closest distance to " O   HOH Z 438 " =    1.988
peak=    3.105 closest distance to " NE2 HIS A 115 " =    0.991
peak=    3.104 closest distance to " O   HOH Z   4 " =    1.817
peak=    3.102 closest distance to " O   HOH Z 329 " =    3.668
peak=    3.097 closest distance to " ND1 HIS A  86 " =    1.783
peak=    3.091 closest distance to " O   HOH Z 334 " =    1.554
peak=    3.090 closest distance to " CD1AILE A 234 " =    0.910
peak=    3.086 closest distance to " OG  SER A  22 " =    2.684
peak=    3.084 closest distance to " CB  PRO A  54 " =    1.175
peak=    3.082 closest distance to " CA  ALA A 158 " =    1.153
peak=    3.078 closest distance to " CB  GLN A 103 " =    0.828
peak=    3.056 closest distance to " CB  ALA A 100 " =    1.263

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 199         
Filter by distance & map next to the model:
   mapped sites are within: 0.865 - 5.887
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 199
   mapped sites are within: 0.865 - 5.887

peak=   -4.961 closest distance to " O   HOH Z 266 " =    4.582
peak=   -4.322 closest distance to " CD  ARG A 156 " =    2.064
peak=   -4.299 closest distance to " C   HIS A 108 " =    1.112
peak=   -4.127 closest distance to " OXT GLY A 302 " =    2.853
peak=   -4.100 closest distance to " O   ILE A 109 " =    2.636
peak=   -4.072 closest distance to " O   HOH Z  13 " =    1.715
peak=   -4.071 closest distance to " O   PRO A 163 " =    2.114
peak=   -4.060 closest distance to " OE1 GLN A 223 " =    1.965
peak=   -4.011 closest distance to " CE2 TYR A  30 " =    2.721
peak=   -4.006 closest distance to " O   HOH Z 196 " =    1.966
peak=   -3.991 closest distance to " OG  SER A  97 " =    2.181
peak=   -3.988 closest distance to " O   VAL A  67 " =    2.692
peak=   -3.987 closest distance to " N   ALA A  43 " =    2.631
peak=   -3.985 closest distance to " O   HOH Z  10 " =    1.596
peak=   -3.976 closest distance to " O   HOH Z 292 " =    4.494
peak=   -3.963 closest distance to " CD1 LEU A 101 " =    2.478
peak=   -3.941 closest distance to " CB  PRO A 243 " =    2.714
peak=   -3.941 closest distance to " SG  CYS A 254 " =    3.435
peak=   -3.925 closest distance to " O   HOH Z 377 " =    2.028
peak=   -3.916 closest distance to " ND2 ASN A  45 " =    0.998
peak=   -3.899 closest distance to " O   HOH Z 394 " =    1.577
peak=   -3.897 closest distance to " O   HOH Z 353 " =    2.242
peak=   -3.859 closest distance to " CG  ASP A 132 " =    2.355
peak=   -3.857 closest distance to " O   HOH Z 372 " =    2.355
peak=   -3.854 closest distance to " O   HOH Z 165 " =    1.962
peak=   -3.815 closest distance to " O   HOH Z 231 " =    2.335
peak=   -3.789 closest distance to " O   HOH Z 126 " =    1.940
peak=   -3.789 closest distance to " CA  ASP A 298 " =    1.049
peak=   -3.736 closest distance to " CB  ASN A  39 " =    2.303
peak=   -3.727 closest distance to " N   GLN A  58 " =    1.497
peak=   -3.727 closest distance to " O   HOH Z 198 " =    2.161
peak=   -3.727 closest distance to " CG1 VAL A 250 " =    2.677
peak=   -3.718 closest distance to " CD1 LEU A  25 " =    2.483
peak=   -3.711 closest distance to " O   HOH Z 407 " =    3.238
peak=   -3.709 closest distance to " CD1 PHE A  59 " =    1.884
peak=   -3.707 closest distance to " O   SER A 210 " =    1.991
peak=   -3.704 closest distance to " CB  ALA A 291 " =    2.268
peak=   -3.703 closest distance to " O   HOH Z 118 " =    3.313
peak=   -3.702 closest distance to " O   HOH Z  11 " =    2.037
peak=   -3.699 closest distance to " CZ  PHE A  59 " =    1.742
peak=   -3.692 closest distance to " O   HOH Z 166 " =    1.797
peak=   -3.690 closest distance to " NH2 ARG A  66 " =    1.811
peak=   -3.676 closest distance to " N   ALA A 248 " =    1.725
peak=   -3.665 closest distance to " CD2 LEU A 300 " =    2.835
peak=   -3.660 closest distance to " OD1 ASN A 187 " =    1.693
peak=   -3.659 closest distance to " O   HOH Z  52 " =    1.569
peak=   -3.658 closest distance to " CD  GLN A  58 " =    1.142
peak=   -3.651 closest distance to " OG  SER A  62 " =    1.575
peak=   -3.645 closest distance to " O   HOH Z 283 " =    2.144
peak=   -3.643 closest distance to " CD  ARG A 139 " =    1.604
peak=   -3.639 closest distance to " OG BSER A 134 " =    1.232
peak=   -3.627 closest distance to " O   HOH Z 234 " =    4.201
peak=   -3.623 closest distance to " O   HOH Z 377 " =    1.523
peak=   -3.622 closest distance to " O   PRO A 198 " =    1.284
peak=   -3.615 closest distance to " CA  GLY A 133 " =    2.355
peak=   -3.609 closest distance to " CG2 ILE A 263 " =    2.321
peak=   -3.604 closest distance to " OD1 ASN A 148 " =    1.591
peak=   -3.586 closest distance to " CD1 LEU A 228 " =    2.242
peak=   -3.585 closest distance to " CG  ASP A 231 " =    0.865
peak=   -3.582 closest distance to " O   HOH Z 290 " =    1.127
peak=   -3.579 closest distance to " NE2 GLN A  88 " =    1.848
peak=   -3.569 closest distance to " CZ  TYR A 169 " =    1.858
peak=   -3.558 closest distance to " NH1 ARG A 195 " =    2.583
peak=   -3.555 closest distance to " O   HOH Z  71 " =    1.652
peak=   -3.551 closest distance to " OG BSER A 210 " =    2.085
peak=   -3.546 closest distance to " O   TRP A  92 " =    1.887
peak=   -3.521 closest distance to " O   HOH Z 185 " =    2.437
peak=   -3.518 closest distance to " CB  PHE A 208 " =    2.306
peak=   -3.517 closest distance to " CB  ASP A 286 " =    1.969
peak=   -3.512 closest distance to " O   ALA A 160 " =    1.467
peak=   -3.511 closest distance to " CH2 TRP A 179 " =    1.271
peak=   -3.509 closest distance to " CG  GLU A  53 " =    1.401
peak=   -3.506 closest distance to " CB  TYR A  15 " =    2.276
peak=   -3.488 closest distance to " C   ASN A 285 " =    2.368
peak=   -3.474 closest distance to " O   HOH Z 389 " =    1.685
peak=   -3.474 closest distance to " N   THR A 235 " =    1.316
peak=   -3.472 closest distance to " C   SER A 206 " =    1.603
peak=   -3.470 closest distance to " O   HOH Z 252 " =    3.680
peak=   -3.468 closest distance to " OD1 ASP A 191 " =    1.569
peak=   -3.461 closest distance to " O   HOH Z 166 " =    1.607
peak=   -3.457 closest distance to " CB  PHE A 192 " =    1.943
peak=   -3.455 closest distance to " O   HOH Z 351 " =    1.470
peak=   -3.453 closest distance to " O   PHE A 218 " =    1.621
peak=   -3.446 closest distance to " CE  MET A 105 " =    2.095
peak=   -3.432 closest distance to " C   THR A 279 " =    1.173
peak=   -3.431 closest distance to " O   HOH Z  43 " =    1.523
peak=   -3.431 closest distance to " N   THR A 157 " =    1.650
peak=   -3.402 closest distance to " OD2 ASP A 171 " =    1.793
peak=   -3.402 closest distance to " CA  TYR A  68 " =    2.874
peak=   -3.402 closest distance to " O   GLY A 196 " =    1.062
peak=   -3.398 closest distance to " OG BSER A 134 " =    1.809
peak=   -3.396 closest distance to " O   LEU A 167 " =    1.574
peak=   -3.396 closest distance to " C   ALA A 158 " =    1.251
peak=   -3.395 closest distance to " OE2 GLU A   2 " =    1.631
peak=   -3.392 closest distance to " O   VAL A  67 " =    2.889
peak=   -3.384 closest distance to " CD  LYS A 289 " =    2.443
peak=   -3.380 closest distance to " ND2 ASN A 187 " =    1.627
peak=   -3.379 closest distance to " O   HOH Z 384 " =    2.288
peak=   -3.378 closest distance to " NH2 ARG A  66 " =    5.446
peak=   -3.373 closest distance to " CB  ALA A 291 " =    2.304
peak=   -3.370 closest distance to " NH2AARG A 275 " =    5.206
peak=   -3.360 closest distance to " CD  ARG A 195 " =    5.050
peak=   -3.358 closest distance to " C   LEU A 143 " =    1.108
peak=   -3.356 closest distance to " O   HOH Z 252 " =    4.171
peak=   -3.355 closest distance to " O   HOH Z  93 " =    1.752
peak=   -3.347 closest distance to " CA  GLY A 203 " =    2.290
peak=   -3.346 closest distance to " O   ALA A  34 " =    2.339
peak=   -3.345 closest distance to " O   HOH Z  37 " =    1.833
peak=   -3.340 closest distance to " O   HOH Z  19 " =    2.023
peak=   -3.340 closest distance to " O   GLY A  80 " =    2.483
peak=   -3.335 closest distance to " CA  SER A 276 " =    1.472
peak=   -3.335 closest distance to " CD2 PHE A 225 " =    1.294
peak=   -3.328 closest distance to " O   VAL A 125 " =    2.301
peak=   -3.324 closest distance to " C   MET A 188 " =    1.716
peak=   -3.324 closest distance to " CG1 VAL A 112 " =    2.745
peak=   -3.324 closest distance to " CB  ALA A   9 " =    2.611
peak=   -3.324 closest distance to " CE  MET A  93 " =    1.198
peak=   -3.319 closest distance to " NH2 ARG A 159 " =    2.323
peak=   -3.319 closest distance to " O   HOH Z 311 " =    3.685
peak=   -3.310 closest distance to " CB  ALA A 248 " =    1.969
peak=   -3.308 closest distance to " O   HOH Z 418 " =    1.380
peak=   -3.304 closest distance to " O   HOH Z 426 " =    1.638
peak=   -3.300 closest distance to " O   HOH Z   6 " =    1.704
peak=   -3.296 closest distance to " O   HOH Z 388 " =    2.044
peak=   -3.293 closest distance to " CE3 TRP A 150 " =    2.078
peak=   -3.290 closest distance to " NH2 ARG A  79 " =    2.037
peak=   -3.288 closest distance to " CB  ALA A  10 " =    2.173
peak=   -3.287 closest distance to " O   HOH Z 414 " =    1.588
peak=   -3.285 closest distance to " CD1 ILE A 239 " =    2.061
peak=   -3.284 closest distance to " CG1 VAL A 112 " =    2.571
peak=   -3.280 closest distance to " SG ACYS A 201 " =    2.075
peak=   -3.276 closest distance to " O   VAL A 189 " =    2.587
peak=   -3.265 closest distance to " CG  GLU A 277 " =    1.145
peak=   -3.264 closest distance to " N   ALA A 226 " =    2.041
peak=   -3.261 closest distance to " C   ALA A   8 " =    1.604
peak=   -3.259 closest distance to " O   HOH Z 123 " =    2.303
peak=   -3.259 closest distance to " ND2BASN A 224 " =    1.751
peak=   -3.258 closest distance to " O   HOH Z  97 " =    1.600
peak=   -3.257 closest distance to " O   HOH Z  11 " =    1.838
peak=   -3.256 closest distance to " CG  PRO A 243 " =    1.746
peak=   -3.251 closest distance to " O   ALA A  10 " =    1.778
peak=   -3.243 closest distance to " OE1 GLN A 223 " =    2.080
peak=   -3.243 closest distance to " N   THR A  52 " =    1.654
peak=   -3.233 closest distance to " O   HOH Z 283 " =    5.887
peak=   -3.230 closest distance to " O   HOH Z 361 " =    3.368
peak=   -3.225 closest distance to " CG2 VAL A 189 " =    2.215
peak=   -3.224 closest distance to " CB  ALA A 248 " =    2.267
peak=   -3.223 closest distance to " CG  PHE A 283 " =    2.580
peak=   -3.222 closest distance to " O   HOH Z 102 " =    1.588
peak=   -3.218 closest distance to " O   HOH Z 422 " =    1.490
peak=   -3.215 closest distance to " CA  VAL A 197 " =    0.984
peak=   -3.213 closest distance to " O   HOH Z 393 " =    1.505
peak=   -3.212 closest distance to " OD1 ASP A 171 " =    1.513
peak=   -3.211 closest distance to " ND2 ASN A 249 " =    2.322
peak=   -3.211 closest distance to " OG ASER A 134 " =    1.259
peak=   -3.204 closest distance to " O   HOH Z  38 " =    1.582
peak=   -3.202 closest distance to " O   HOH Z  61 " =    1.622
peak=   -3.200 closest distance to " OD2 ASP A 191 " =    1.625
peak=   -3.196 closest distance to " O   HOH Z 222 " =    1.301
peak=   -3.192 closest distance to " CB  GLN A  11 " =    1.732
peak=   -3.189 closest distance to " O   HOH Z 145 " =    2.003
peak=   -3.181 closest distance to " OH  TYR A 169 " =    1.024
peak=   -3.180 closest distance to " O   ALA A   1 " =    1.917
peak=   -3.178 closest distance to " O   HOH Z 111 " =    1.552
peak=   -3.175 closest distance to " CB  PRO A 163 " =    2.653
peak=   -3.173 closest distance to " CD2 TYR A 293 " =    2.034
peak=   -3.168 closest distance to " CD2 LEU A 237 " =    2.426
peak=   -3.166 closest distance to " CD2 PHE A  61 " =    2.568
peak=   -3.164 closest distance to " CG2 THR A 221 " =    2.352
peak=   -3.164 closest distance to " O   HOH Z 213 " =    1.502
peak=   -3.163 closest distance to " O   HOH Z  17 " =    1.496
peak=   -3.155 closest distance to " O   HOH Z 280 " =    2.327
peak=   -3.154 closest distance to " OD2 ASP A 171 " =    2.315
peak=   -3.154 closest distance to " O   TYR A 186 " =    1.627
peak=   -3.150 closest distance to " O   HOH Z 211 " =    1.675
peak=   -3.145 closest distance to " O   HOH Z  90 " =    1.959
peak=   -3.144 closest distance to " CE BMET A  47 " =    2.140
peak=   -3.142 closest distance to " CB  TRP A  85 " =    2.392
peak=   -3.137 closest distance to " CZ  PHE A  38 " =    1.946
peak=   -3.130 closest distance to " CG1 VAL A 112 " =    2.896
peak=   -3.129 closest distance to " O   HOH Z 298 " =    2.651
peak=   -3.125 closest distance to " O   HOH Z 171 " =    2.090
peak=   -3.124 closest distance to " O   HOH Z 262 " =    2.516
peak=   -3.116 closest distance to " O   HOH Z 191 " =    5.822
peak=   -3.112 closest distance to " CG  PRO A 163 " =    2.570
peak=   -3.109 closest distance to " N   SER A  12 " =    1.417
peak=   -3.104 closest distance to " O   HOH Z 324 " =    2.290
peak=   -3.100 closest distance to " CG  LYS A 119 " =    2.895
peak=   -3.088 closest distance to " O   HOH Z 149 " =    1.995
peak=   -3.085 closest distance to " CD2 TYR A 247 " =    2.423
peak=   -3.084 closest distance to " NE2 GLN A  58 " =    1.149
peak=   -3.081 closest distance to " NH1BARG A 275 " =    2.305
peak=   -3.059 closest distance to " CE3 TRP A 274 " =    2.487
peak=   -3.053 closest distance to " O   SER A 135 " =    1.576
peak=   -3.051 closest distance to " CZ  PHE A 130 " =    0.992
peak=   -3.033 closest distance to " O   HOH Z  91 " =    2.026
peak=   -3.033 closest distance to " CB  PHE A  16 " =    2.614
peak=   -3.032 closest distance to " O   GLU A 152 " =    1.467
peak=   -3.019 closest distance to " O   HOH Z 193 " =    1.762

================= 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    :  0.3567 0.3482   6.126431e+00   6.104857e+00
   1_bss:  0.3426 0.3321   6.105220e+00   6.075645e+00
   1_xyz:  0.2030 0.2263   5.626614e+00   5.727644e+00
   1_adp:  0.1840 0.2316   5.570850e+00   5.751688e+00
   1_occ:  0.1836 0.2317   5.569940e+00   5.750948e+00
   2_bss:  0.1809 0.2293   5.559704e+00   5.740785e+00
   2_xyz:  0.1367 0.1774   5.299298e+00   5.507354e+00
   2_adp:  0.1302 0.1686   5.254130e+00   5.458554e+00
   2_occ:  0.1300 0.1685   5.253501e+00   5.457930e+00
   3_bss:  0.1300 0.1682   5.252682e+00   5.456026e+00
   3_xyz:  0.1203 0.1598   5.192151e+00   5.408450e+00
   3_adp:  0.1172 0.1602   5.179331e+00   5.407621e+00
   3_occ:  0.1172 0.1601   5.179008e+00   5.407383e+00
   4_bss:  0.1171 0.1600   5.178727e+00   5.407159e+00
   4_xyz:  0.1108 0.1582   5.142678e+00   5.388228e+00
   4_adp:  0.1102 0.1587   5.141140e+00   5.390532e+00
   4_occ:  0.1101 0.1587   5.141137e+00   5.390767e+00
   5_bss:  0.1100 0.1587   5.141215e+00   5.390813e+00
   5_xyz:  0.1098 0.1588   5.143337e+00   5.394755e+00
   5_adp:  0.1097 0.1586   5.142900e+00   5.395388e+00
   5_occ:  0.1097 0.1586   5.142857e+00   5.395506e+00
   5_bss:  0.1096 0.1586   5.142958e+00   5.395577e+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:  0.307  38.713  -3.269   3.412  -0.556   0.000  -0.000  -0.000
   1_xyz:  0.307  38.713  -3.269   3.412  -0.556   0.000  -0.000  -0.000
   1_adp:  0.307  38.713  -3.269   3.412  -0.556   0.000  -0.000  -0.000
   1_occ:  0.307  38.713  -3.269   3.412  -0.556   0.000  -0.000  -0.000
   2_bss:  0.322  55.888  -3.000  -0.123  -1.315  -0.000  -0.000  -0.000
   2_xyz:  0.322  55.888  -3.000  -0.123  -1.315  -0.000  -0.000  -0.000
   2_adp:  0.322  55.888  -3.000  -0.123  -1.315  -0.000  -0.000  -0.000
   2_occ:  0.322  55.888  -3.000  -0.123  -1.315  -0.000  -0.000  -0.000
   3_bss:  0.321  53.851  -2.595  -1.097  -1.323  -0.000  -0.000  -0.000
   3_xyz:  0.321  53.851  -2.595  -1.097  -1.323  -0.000  -0.000  -0.000
   3_adp:  0.321  53.851  -2.595  -1.097  -1.323  -0.000  -0.000  -0.000
   3_occ:  0.321  53.851  -2.595  -1.097  -1.323  -0.000  -0.000  -0.000
   4_bss:  0.321  53.851  -2.372  -1.293  -1.222  -0.000  -0.000  -0.000
   4_xyz:  0.321  53.851  -2.372  -1.293  -1.222  -0.000  -0.000  -0.000
   4_adp:  0.321  53.851  -2.372  -1.293  -1.222  -0.000  -0.000  -0.000
   4_occ:  0.321  53.851  -2.372  -1.293  -1.222  -0.000  -0.000  -0.000
   5_bss:  0.321  53.851  -2.064  -1.158  -0.966  -0.000  -0.000  -0.000
   5_xyz:  0.321  53.851  -2.064  -1.158  -0.966  -0.000  -0.000  -0.000
   5_adp:  0.321  53.851  -2.064  -1.158  -0.966  -0.000  -0.000  -0.000
   5_occ:  0.321  53.851  -2.064  -1.158  -0.966  -0.000  -0.000  -0.000
   5_bss:  0.321  54.425  -1.848  -1.012  -0.771  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  37.879 0.6704  0.8472    36461.584
   1_bss:  36.639 0.6829  0.8551    32664.515
   1_xyz:  22.390 0.8390  0.9932    13297.657
   1_adp:  23.204 0.8298  0.9768    13942.128
   1_occ:  23.203 0.8298  0.9765    13921.557
   2_bss:  22.708 0.8349  0.9405    13512.329
   2_xyz:  16.738 0.8912  0.9773     7985.885
   2_adp:  15.543 0.9022  0.9779     7304.056
   2_occ:  15.530 0.9023  0.9779     7294.685
   3_bss:  15.478 0.9028  0.9722     7295.195
   3_xyz:  14.417 0.9118  0.9756     6601.973
   3_adp:  14.385 0.9121  0.9688     6584.413
   3_occ:  14.379 0.9122  0.9688     6580.551
   4_bss:  14.371 0.9123  0.9707     6579.317
   4_xyz:  14.040 0.9147  0.9727     6332.260
   4_adp:  14.070 0.9146  0.9662     6356.912
   4_occ:  14.072 0.9145  0.9661     6359.728
   5_bss:  14.073 0.9145  0.9743     6361.574
   5_xyz:  14.108 0.9143  0.9736     6388.699
   5_adp:  14.115 0.9142  0.9664     6390.058
   5_occ:  14.117 0.9142  0.9663     6390.254
   5_bss:  14.119 0.9142  0.9728     6391.977
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6383e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6383e-01
   1_xyz:   1.281  0.010  0.079 15.463  0.005  4.115   8.3470e-02
   1_adp:   1.281  0.010  0.079 15.463  0.005  4.115   8.3470e-02
   1_occ:   1.281  0.010  0.079 15.463  0.005  4.115   8.3470e-02
   2_bss:   1.281  0.010  0.079 15.463  0.005  4.115   8.3470e-02
   2_xyz:   1.019  0.007  0.072 14.818  0.004  4.125   6.3975e-02
   2_adp:   1.019  0.007  0.072 14.818  0.004  4.125   6.3975e-02
   2_occ:   1.019  0.007  0.072 14.818  0.004  4.125   6.3975e-02
   3_bss:   1.019  0.007  0.072 14.818  0.004  4.125   6.3975e-02
   3_xyz:   0.923  0.006  0.068 14.758  0.004  4.128   5.2237e-02
   3_adp:   0.923  0.006  0.068 14.758  0.004  4.128   5.2237e-02
   3_occ:   0.923  0.006  0.068 14.758  0.004  4.128   5.2237e-02
   4_bss:   0.923  0.006  0.068 14.758  0.004  4.128   5.2237e-02
   4_xyz:   1.025  0.008  0.077 14.959  0.004  4.131   6.2639e-02
   4_adp:   1.025  0.008  0.077 14.959  0.004  4.131   6.2639e-02
   4_occ:   1.025  0.008  0.077 14.959  0.004  4.131   6.2639e-02
   5_bss:   1.025  0.008  0.077 14.959  0.004  4.131   6.2639e-02
   5_xyz:   0.982  0.007  0.074 14.835  0.004  4.112   5.8993e-02
   5_adp:   0.982  0.007  0.074 14.835  0.004  4.112   5.8993e-02
   5_occ:   0.982  0.007  0.074 14.835  0.004  4.112   5.8993e-02
   5_bss:   0.982  0.007  0.074 14.835  0.004  4.112   5.8993e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4116e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4116e-01
   1_xyz:   7.427  0.048  0.322 88.126  0.027  2.291   8.7297e-02
   1_adp:   7.427  0.048  0.322 88.126  0.027  2.291   8.7297e-02
   1_occ:   7.427  0.048  0.322 88.126  0.027  2.291   8.7297e-02
   2_bss:   7.427  0.048  0.322 88.126  0.027  2.291   8.7297e-02
   2_xyz:   6.968  0.064  0.234 82.010  0.039  2.326   1.3461e-01
   2_adp:   6.968  0.064  0.234 82.010  0.039  2.326   1.3461e-01
   2_occ:   6.968  0.064  0.234 82.010  0.039  2.326   1.3461e-01
   3_bss:   6.968  0.064  0.234 82.010  0.039  2.326   1.3461e-01
   3_xyz:   6.756  0.046  0.216 83.516  0.037  2.380   3.3336e-02
   3_adp:   6.756  0.046  0.216 83.516  0.037  2.380   3.3336e-02
   3_occ:   6.756  0.046  0.216 83.516  0.037  2.380   3.3336e-02
   4_bss:   6.756  0.046  0.216 83.516  0.037  2.380   3.3336e-02
   4_xyz:   7.625  0.048  0.252 82.130  0.036  2.310   4.3139e-02
   4_adp:   7.625  0.048  0.252 82.130  0.036  2.310   4.3139e-02
   4_occ:   7.625  0.048  0.252 82.130  0.036  2.310   4.3139e-02
   5_bss:   7.625  0.048  0.252 82.130  0.036  2.310   4.3139e-02
   5_xyz:   7.387  0.045  0.242 81.827  0.035  2.363   4.0929e-02
   5_adp:   7.387  0.045  0.242 81.827  0.035  2.363   4.0929e-02
   5_occ:   7.387  0.045  0.242 81.827  0.035  2.363   4.0929e-02
   5_bss:   7.387  0.045  0.242 81.827  0.035  2.363   4.0929e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  81.25   0.00  17.24  81.25   0.00  13.19  79.75   6.65  39.26
   1_occ:  81.25   0.00  17.24  81.25   0.00  13.19  79.75   6.65  39.26
   2_bss:  81.25   0.00  17.24  81.25   0.00  13.19  79.75   6.65  39.26
   2_xyz:  81.25   0.00  17.24  81.25   0.00  13.19  79.75   6.65  39.26
   2_adp:  80.88   2.06  16.80  80.88   2.06  12.81  77.06   3.87  38.53
   2_occ:  80.88   2.06  16.80  80.88   2.06  12.81  77.06   3.87  38.53
   3_bss:  80.88   2.06  16.80  80.88   2.06  12.81  77.06   3.87  38.53
   3_xyz:  80.88   2.06  16.80  80.88   2.06  12.81  77.06   3.87  38.53
   3_adp:  91.36   1.10  16.98  91.36   1.10  12.69  79.36   3.22  40.30
   3_occ:  91.36   1.10  16.98  91.36   1.10  12.69  79.36   3.22  40.30
   4_bss:  91.36   1.10  16.98  91.36   1.10  12.69  79.36   3.22  40.30
   4_xyz:  91.36   1.10  16.98  91.36   1.10  12.69  79.36   3.22  40.30
   4_adp: 100.27   0.42  16.84 100.27   0.42  12.54  78.48   4.08  40.25
   4_occ: 100.27   0.42  16.84 100.27   0.42  12.54  78.48   4.08  40.25
   5_bss: 100.27   0.42  16.84 100.27   0.42  12.54  78.48   4.08  40.25
   5_xyz: 100.27   0.42  16.84 100.27   0.42  12.54  78.48   4.08  40.25
   5_adp: 109.08   0.09  16.66 109.08   0.09  12.36  84.71   5.17  40.06
   5_occ: 109.08   0.09  16.66 109.08   0.09  12.36  84.71   5.17  40.06
   5_bss: 109.08   0.09  16.66 109.08   0.09  12.36  84.71   5.17  40.06
------------------------------------------------------------------------
 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:    1.360    0.027    0.387
   1_adp:    1.360    0.027    0.387
   1_occ:    1.360    0.027    0.387
   2_bss:    1.360    0.027    0.387
   2_xyz:    0.961    0.025    0.446
   2_adp:    0.961    0.025    0.446
   2_occ:    0.961    0.025    0.446
   3_bss:    0.961    0.025    0.446
   3_xyz:    1.047    0.029    0.488
   3_adp:    1.047    0.029    0.488
   3_occ:    1.047    0.029    0.488
   4_bss:    1.047    0.029    0.488
   4_xyz:    1.016    0.008    0.505
   4_adp:    1.016    0.008    0.505
   4_occ:    1.016    0.008    0.505
   5_bss:    1.016    0.008    0.505
   5_xyz:    1.139    0.077    0.511
   5_adp:    1.139    0.077    0.511
   5_occ:    1.139    0.077    0.511
   5_bss:    1.139    0.077    0.511
------------------------------------------------------------------------

CPU time actual refinement: 344.82


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_696/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_696/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_696/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_696/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_696/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 344.67 
  Macro-tasks:
    bulk solvent and scale       = 41.18  
    individual site refinement   = 145.28 
    weights calculation          = 29.88  
    collect and process          = 6.68   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 223.12 
  Micro-tasks:
    mask                            = 1.25   
    f_calc                          = 110.18 
    alpha_beta                      = 8.16   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 120.13 
    fmodel                         = 6.84   
    r_factors                      = 0.24   
    phase_errors                   = 10.90  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 259.15 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.817 micro seconds
Total CPU time: 5.97 minutes
from_scatterers_fft:    661 calls, 109.73 s
gradients_fft:          606 calls, 106.02 s

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

# Date 2008-01-16 Time 05:26:13 PST -0800 (1200489973.29 s)
Start R-work = 0.3567, R-free = 0.3482 (no bulk solvent and anisotropic scale)
Final R-work = 0.1300, R-free = 0.1755 (no bulk solvent and anisotropic scale)

Start R-work = 0.3426, R-free = 0.3321
Final R-work = 0.1096, R-free = 0.1586