# Date 2008-01-16 Time 05:13:05 PST -0800 (1200489185.26 s)
#phil __OFF__

Command line arguments: "../641.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29635
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 641

-------------------------------------------------------------------------------
  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, 46.4607, 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: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.4607, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9529 1.98037
Completeness in resolution range: 0.976423
Completeness with d_max=infinity: 0.973415

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9529
                             d_min =   1.9804

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, 46.4607, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9529 1.98037
Completeness in resolution range: 0.976423
Completeness with d_max=infinity: 0.973415

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9533 -  4.2373 [2099/2124]  1889   210  10.0%
  bin  2:  4.2373 -  3.3760 [2031/2051]  1828   203  10.0%
  bin  3:  3.3760 -  2.9530 [1998/2017]  1796   202  10.1%
  bin  4:  2.9530 -  2.6847 [1971/2001]  1777   194   9.8%
  bin  5:  2.6847 -  2.4932 [1980/1999]  1783   197   9.9%
  bin  6:  2.4932 -  2.3468 [1957/1982]  1762   195  10.0%
  bin  7:  2.3468 -  2.2297 [1943/1971]  1743   200  10.3%
  bin  8:  2.2297 -  2.1329 [1945/1981]  1752   193   9.9%
  bin  9:  2.1329 -  2.0510 [1933/1975]  1745   188   9.7%
  bin 10:  2.0510 -  1.9804 [1732/1961]  1555   177  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_641/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: 0.13 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: 23
        2.42 -     3.04: 2218
        3.04 -     3.66: 4757
        3.66 -     4.28: 9118
        4.28 -     4.90: 12448
  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
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 110 " - " O   HOH Z 355 "  2.221 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 204 " - " O   HOH Z 296 "  2.223 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  2.256 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28559 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_641/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_641/model_refine_001.geo

CPU time processing inputs: 9.19


============================ 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 46.4607 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= 0.3145   r_free= 0.3131   ksol= 0.00   Bsol= 0.00   scale= 0.984    |
|                                                                             |
| 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:   0.34 A                  |
| x-ray target function (ml) for work reflections: 6.018368                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.7259 0.99   1372  152 0.2834 0.2787       6.344      6.2894|
|  2:  4.7259 -  3.7709 0.99   1316  146 0.2489 0.2349      6.4095      6.3666|
|  3:  3.7709 -  3.3001 0.99   1286  144 0.2629 0.2625      6.2972      6.4021|
|  4:  3.3001 -  3.0010 0.99   1279  144 0.2792 0.3105      6.1948      6.2219|
|  5:  3.0010 -  2.7874 0.99   1279  141 0.3159 0.2935      6.0775       6.033|
|  6:  2.7874 -  2.6240 0.99   1270  139 0.3218 0.3490      6.0178      6.0134|
|  7:  2.6240 -  2.4932 0.99   1271  140 0.3349 0.2923      5.9772      5.9067|
|  8:  2.4932 -  2.3851 0.98   1253  143 0.3456 0.3615      5.9637      6.0012|
|  9:  2.3851 -  2.2936 0.98   1245  134 0.3397 0.3467      5.8962      5.8617|
| 10:  2.2936 -  2.2147 1.00   1248  144 0.3447 0.3272      5.8734      5.8428|
| 11:  2.2147 -  2.1457 0.97   1259  136 0.3695 0.3608      5.8554       5.882|
| 12:  2.1457 -  2.0845 0.98   1231  138 0.3655 0.3836      5.8107      5.8353|
| 13:  2.0845 -  2.0298 0.99   1247  142 0.3691 0.3496      5.7171      5.6881|
| 14:  2.0298 -  1.9804 0.84   1074  116 0.3834 0.3664      5.7108      5.5802|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 -  4.7259  1372   152  0.79  25.59   0.87     0.82      40966.17|
|  2:  4.7259 -  3.7709  1316   146  0.85  21.47   0.98     0.93      44150.29|
|  3:  3.7709 -  3.3001  1286   144  0.82  24.70   1.01     0.98      43214.89|
|  4:  3.3001 -  3.0010  1279   144  0.79  27.53   1.01     0.96      38321.47|
|  5:  3.0010 -  2.7874  1279   141  0.75  31.13   1.00     0.94      30984.22|
|  6:  2.7874 -  2.6240  1270   139  0.75  31.16   1.01     0.94      26628.05|
|  7:  2.6240 -  2.4932  1271   140  0.74  32.01   1.01     0.96      23875.80|
|  8:  2.4932 -  2.3851  1253   143  0.73  33.21   1.03     0.95      22986.63|
|  9:  2.3851 -  2.2936  1245   134  0.74  32.86   1.03     0.94      21364.36|
| 10:  2.2936 -  2.2147  1248   144  0.71  34.96   1.06     0.95      21017.65|
| 11:  2.2147 -  2.1457  1259   136  0.69  36.94   1.06     0.96      20418.78|
| 12:  2.1457 -  2.0845  1231   138  0.69  36.85   1.07     0.95      19127.15|
| 13:  2.0845 -  2.0298  1247   142  0.68  37.72   1.06     0.93      16218.78|
| 14:  2.0298 -  1.9804  1074   116  0.71  34.89   1.05     0.91      12355.02|
|alpha:            min =        0.82 max =            0.98 mean =         0.94|
|beta:             min =    12355.02 max =        44150.29 mean =     27627.07|
|figures of merit: min =        0.00 max =            1.00 mean =         0.75|
|phase err.(work): min =        0.00 max =           89.99 mean =        31.36|
|phase err.(test): min =        0.00 max =           89.99 mean =        31.52|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.400442              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.477   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.651857              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.827   (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:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       22 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      212 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2006 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1881 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2876 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4683 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4435 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5660 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6788 |
|-----------------------------------------------------------------------------|
|-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 |        0.161 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.806 |       0.179 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    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= 0.3145   r_free= 0.3131   ksol= 0.00   Bsol= 0.00   scale= 0.984    |
|                                                                             |
| 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:   0.34 A                  |
| x-ray target function (ml) for work reflections: 6.018368                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2988   r_free= 0.2958   ksol= 0.33   Bsol= 38.30   scale= 0.983   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,0.15,-0.39,0.00,-0.00,-0.00); trace/3= -1.10                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.998812                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.708945              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.567   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.319052              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.747   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2988      final r-factor (work) = 0.1585          |
| start r-factor (free) = 0.2958      final r-factor (free) = 0.1821          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.3032 = 4.71 * 0.50 * 6.0064 + 1.00 * 0.1613                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.3953 = 4.71 * 0.50 * 5.6624 + 1.00 * 0.0634                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1585      final r-factor (work) = 0.1475          |
| start r-factor (free) = 0.1821      final r-factor (free) = 0.1877          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8128 = 0.32 * 1.00 * 5.6624 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7334 = 0.32 * 1.00 * 5.3422 + 1.00 * 0.0290                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    62.44   16.55    None  None   None       |
|    all(noH): 2823   0      0.00    62.44   16.55    None  None   None       |
|    Sol.    : 438    0      7.56    62.44   37.56    None  None   None       |
|    Mac.    : 2385   0      0.00    58.21   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:     0.000 -   6.244:  188   |   5:    31.222 -  37.466:   96        |
|      1:     6.244 -  12.489: 1265   |   6:    37.466 -  43.710:  110        |
|      2:    12.489 -  18.733:  683   |   7:    43.710 -  49.955:   71        |
|      3:    18.733 -  24.977:  212   |   8:    49.955 -  56.199:   52        |
|      4:    24.977 -  31.222:  113   |   9:    56.199 -  62.443:   33        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1475 r_free = 0.1877             target_work(ml) = 5.356         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1471 r_free = 0.1877             target_work(ml) = 5.354         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1471   r_free= 0.1877   ksol= 0.33   Bsol= 38.30   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,0.15,-0.39,0.00,-0.00,-0.00); trace/3= -1.10                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.353703                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1457   r_free= 0.1844   ksol= 0.32   Bsol= 43.00   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.12,-2.18,-1.63,-0.00,-0.00,-0.00); trace/3= -2.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.345431                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.315870              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.918  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.216021              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.901   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1457      final r-factor (work) = 0.1196          |
| start r-factor (free) = 0.1844      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2708 = 2.32 * 0.50 * 5.3614 + 1.00 * 0.0626                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1396 = 2.32 * 0.50 * 5.2551 + 1.00 * 0.0545                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1196      final r-factor (work) = 0.1145          |
| start r-factor (free) = 0.1596      final r-factor (free) = 0.1542          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2002 = 0.22 * 1.00 * 5.2551 + 1.00 * 0.0649                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1201 = 0.22 * 1.00 * 5.1521 + 1.00 * 0.0072                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.68    70.60   16.78    None  None   None       |
|    all(noH): 2823   0      1.68    70.60   16.78    None  None   None       |
|    Sol.    : 438    0      6.59    70.60   37.97    None  None   None       |
|    Mac.    : 2385   0      1.68    65.82   12.89    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:     1.676 -   8.568:  592   |   5:    36.138 -  43.030:  115        |
|      1:     8.568 -  15.461: 1301   |   6:    43.030 -  49.923:   76        |
|      2:    15.461 -  22.353:  378   |   7:    49.923 -  56.815:   88        |
|      3:    22.353 -  29.245:  131   |   8:    56.815 -  63.707:   27        |
|      4:    29.245 -  36.138:  109   |   9:    63.707 -  70.600:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1145 r_free = 0.1542             target_work(ml) = 5.137         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1144 r_free = 0.1543             target_work(ml) = 5.136         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1144   r_free= 0.1543   ksol= 0.32   Bsol= 43.00   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.12,-2.18,-1.63,-0.00,-0.00,-0.00); trace/3= -2.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.136242                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1142   r_free= 0.1542   ksol= 0.32   Bsol= 43.00   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-2.41,-1.55,-0.00,-0.00,-0.00); trace/3= -2.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.135014                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.418406              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 140.129  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.506126              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.111  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1142      final r-factor (work) = 0.1079          |
| start r-factor (free) = 0.1542      final r-factor (free) = 0.1507          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2837 = 2.42 * 0.50 * 5.1515 + 1.00 * 0.0545                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2404 = 2.42 * 0.50 * 5.1099 + 1.00 * 0.0615                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1079      final r-factor (work) = 0.1064          |
| start r-factor (free) = 0.1507      final r-factor (free) = 0.1510          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5934 = 0.51 * 1.00 * 5.1099 + 1.00 * 0.0072                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5853 = 0.51 * 1.00 * 5.0921 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.10    76.23   16.88    None  None   None       |
|    all(noH): 2823   0      1.10    76.23   16.88    None  None   None       |
|    Sol.    : 438    0      6.11    76.23   38.71    None  None   None       |
|    Mac.    : 2385   0      1.10    75.88   12.86    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:     1.098 -   8.612:  656   |   5:    38.666 -  46.179:  118        |
|      1:     8.612 -  16.125: 1297   |   6:    46.179 -  53.693:   83        |
|      2:    16.125 -  23.639:  349   |   7:    53.693 -  61.206:   60        |
|      3:    23.639 -  31.152:  132   |   8:    61.206 -  68.720:   23        |
|      4:    31.152 -  38.666:   99   |   9:    68.720 -  76.233:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1064 r_free = 0.1510             target_work(ml) = 5.095         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1063 r_free = 0.1509             target_work(ml) = 5.095         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1063   r_free= 0.1509   ksol= 0.32   Bsol= 43.00   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-2.41,-1.55,-0.00,-0.00,-0.00); trace/3= -2.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.094736                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1064   r_free= 0.1510   ksol= 0.32   Bsol= 43.26   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-2.42,-1.49,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.094914                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.259886              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 159.357  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.125975              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.444  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1064      final r-factor (work) = 0.1091          |
| start r-factor (free) = 0.1510      final r-factor (free) = 0.1524          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.2690 = 1.26 * 0.50 * 5.0918 + 1.00 * 0.0615                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.2645 = 1.26 * 0.50 * 5.1071 + 1.00 * 0.0473                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1091      final r-factor (work) = 0.1105          |
| start r-factor (free) = 0.1524      final r-factor (free) = 0.1519          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6514 = 0.13 * 1.00 * 5.1071 + 1.00 * 0.0081                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6513 = 0.13 * 1.00 * 5.1185 + 1.00 * 0.0065                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.84    76.47   16.34    None  None   None       |
|    all(noH): 2823   0      1.84    76.47   16.34    None  None   None       |
|    Sol.    : 438    0      6.62    76.47   36.37    None  None   None       |
|    Mac.    : 2385   0      1.84    74.71   12.67    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:     1.839 -   9.302:  838   |   5:    39.155 -  46.618:  100        |
|      1:     9.302 -  16.766: 1188   |   6:    46.618 -  54.081:   81        |
|      2:    16.766 -  24.229:  308   |   7:    54.081 -  61.545:   29        |
|      3:    24.229 -  31.692:  130   |   8:    61.545 -  69.008:   12        |
|      4:    31.692 -  39.155:  133   |   9:    69.008 -  76.471:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1105 r_free = 0.1519             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1105 r_free = 0.1519             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1105   r_free= 0.1519   ksol= 0.32   Bsol= 43.26   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-2.42,-1.49,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.116593                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1519   ksol= 0.32   Bsol= 43.26   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,-2.40,-1.40,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.116553                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.377537              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 160.903  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.141024              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 160.673  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1104      final r-factor (work) = 0.1088          |
| start r-factor (free) = 0.1519      final r-factor (free) = 0.1516          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5729 = 1.38 * 0.50 * 5.1186 + 1.00 * 0.0473                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5692 = 1.38 * 0.50 * 5.1089 + 1.00 * 0.0504                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1074          |
| start r-factor (free) = 0.1516      final r-factor (free) = 0.1527          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8359 = 1.14 * 1.00 * 5.1089 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8282 = 1.14 * 1.00 * 5.1003 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.48    85.36   16.77    None  None   None       |
|    all(noH): 2823   0      0.48    85.36   16.77    None  None   None       |
|    Sol.    : 438    0      6.44    79.28   38.82    None  None   None       |
|    Mac.    : 2385   0      0.48    85.36   12.72    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:     0.478 -   8.967:  821   |   5:    42.921 -  51.410:  104        |
|      1:     8.967 -  17.455: 1253   |   6:    51.410 -  59.898:   79        |
|      2:    17.455 -  25.944:  270   |   7:    59.898 -  68.387:   24        |
|      3:    25.944 -  34.433:  141   |   8:    68.387 -  76.875:   13        |
|      4:    34.433 -  42.921:  113   |   9:    76.875 -  85.364:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1074 r_free = 0.1527             target_work(ml) = 5.106         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1073 r_free = 0.1527             target_work(ml) = 5.106         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1073   r_free= 0.1527   ksol= 0.32   Bsol= 43.26   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,-2.40,-1.40,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.105796                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.7259 0.99   1372  152 0.0986 0.1240      5.3694      5.4846|
|  2:  4.7259 -  3.7709 0.99   1316  146 0.0842 0.1106      5.4204      5.6145|
|  3:  3.7709 -  3.3001 0.99   1286  144 0.1040 0.1481      5.4627      5.8331|
|  4:  3.3001 -  3.0010 0.99   1279  144 0.1184 0.1530      5.4377      5.5837|
|  5:  3.0010 -  2.7874 0.99   1279  141 0.1259 0.1716      5.2914      5.5267|
|  6:  2.7874 -  2.6240 0.99   1270  139 0.1126 0.1656      5.1688      5.3524|
|  7:  2.6240 -  2.4932 0.99   1271  140 0.1220 0.1572      5.1247      5.3692|
|  8:  2.4932 -  2.3851 0.98   1253  143 0.1093 0.1708      5.0186      5.3215|
|  9:  2.3851 -  2.2936 0.98   1245  134 0.1099 0.1581      4.9859      5.1948|
| 10:  2.2936 -  2.2147 1.00   1248  144 0.1042 0.1762      4.9171      5.2569|
| 11:  2.2147 -  2.1457 0.97   1259  136 0.1094 0.1618      4.9124      5.2133|
| 12:  2.1457 -  2.0845 0.98   1231  138 0.1071 0.1711       4.846      5.2158|
| 13:  2.0845 -  2.0298 0.99   1247  142 0.1037 0.1644      4.7604      5.0431|
| 14:  2.0298 -  1.9804 0.84   1074  116 0.0987 0.1692      4.6285      4.8884|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 -  4.7259  1372   152  0.94   8.67   0.98     0.96       6570.41|
|  2:  4.7259 -  3.7709  1316   146  0.95   7.63   1.02     1.01       8561.96|
|  3:  3.7709 -  3.3001  1286   144  0.94  10.83   1.03     1.02       9956.38|
|  4:  3.3001 -  3.0010  1279   144  0.92  13.04   1.01     1.00       9933.67|
|  5:  3.0010 -  2.7874  1279   141  0.91  15.03   0.99     0.96       7692.85|
|  6:  2.7874 -  2.6240  1270   139  0.91  14.79   0.99     0.96       6534.20|
|  7:  2.6240 -  2.4932  1271   140  0.91  15.07   0.99     0.96       5703.13|
|  8:  2.4932 -  2.3851  1253   143  0.92  14.03   0.99     0.97       4749.81|
|  9:  2.3851 -  2.2936  1245   134  0.92  14.19   1.00     0.98       4550.19|
| 10:  2.2936 -  2.2147  1248   144  0.92  14.11   1.00     0.96       3950.83|
| 11:  2.2147 -  2.1457  1259   136  0.90  16.06   1.00     0.96       4192.16|
| 12:  2.1457 -  2.0845  1231   138  0.92  14.25   1.00     0.98       3654.87|
| 13:  2.0845 -  2.0298  1247   142  0.91  14.92   1.01     1.00       3200.64|
| 14:  2.0298 -  1.9804  1074   116  0.92  13.94   0.98     0.94       2403.31|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2403.31 max =         9956.38 mean =      5903.24|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.93 mean =        13.27|
|phase err.(test): min =        0.00 max =           89.82 mean =        12.91|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1073   r_free= 0.1527   ksol= 0.32   Bsol= 43.42   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,-2.22,-1.23,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.105805                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1073   r_free= 0.1527   ksol= 0.32   Bsol= 43.42   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,-2.22,-1.23,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.105805                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.7259 0.99   1372  152 0.0987 0.1241      5.3699      5.4854|
|  2:  4.7259 -  3.7709 0.99   1316  146 0.0842 0.1107       5.421      5.6147|
|  3:  3.7709 -  3.3001 0.99   1286  144 0.1041 0.1481      5.4629      5.8336|
|  4:  3.3001 -  3.0010 0.99   1279  144 0.1184 0.1530      5.4376      5.5836|
|  5:  3.0010 -  2.7874 0.99   1279  141 0.1258 0.1715      5.2911      5.5261|
|  6:  2.7874 -  2.6240 0.99   1270  139 0.1126 0.1656      5.1685      5.3522|
|  7:  2.6240 -  2.4932 0.99   1271  140 0.1220 0.1573      5.1247      5.3697|
|  8:  2.4932 -  2.3851 0.98   1253  143 0.1093 0.1707      5.0186      5.3209|
|  9:  2.3851 -  2.2936 0.98   1245  134 0.1099 0.1581      4.9859      5.1948|
| 10:  2.2936 -  2.2147 1.00   1248  144 0.1042 0.1762      4.9171      5.2574|
| 11:  2.2147 -  2.1457 0.97   1259  136 0.1094 0.1617      4.9123      5.2128|
| 12:  2.1457 -  2.0845 0.98   1231  138 0.1070 0.1711      4.8458      5.2155|
| 13:  2.0845 -  2.0298 0.99   1247  142 0.1036 0.1642      4.7602      5.0424|
| 14:  2.0298 -  1.9804 0.84   1074  116 0.0987 0.1691      4.6284      4.8883|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 -  4.7259  1372   152  0.94   8.68   0.98     0.96       6579.80|
|  2:  4.7259 -  3.7709  1316   146  0.95   7.64   1.02     1.01       8572.36|
|  3:  3.7709 -  3.3001  1286   144  0.94  10.83   1.03     1.02       9961.77|
|  4:  3.3001 -  3.0010  1279   144  0.92  13.04   1.02     1.00       9929.85|
|  5:  3.0010 -  2.7874  1279   141  0.91  15.03   1.00     0.97       7689.40|
|  6:  2.7874 -  2.6240  1270   139  0.91  14.78   0.99     0.97       6530.85|
|  7:  2.6240 -  2.4932  1271   140  0.91  15.07   0.99     0.97       5703.30|
|  8:  2.4932 -  2.3851  1253   143  0.92  14.03   1.00     0.98       4748.32|
|  9:  2.3851 -  2.2936  1245   134  0.92  14.19   1.01     0.98       4551.13|
| 10:  2.2936 -  2.2147  1248   144  0.92  14.11   1.01     0.97       3949.45|
| 11:  2.2147 -  2.1457  1259   136  0.90  16.05   1.00     0.97       4190.72|
| 12:  2.1457 -  2.0845  1231   138  0.92  14.25   1.01     0.99       3651.98|
| 13:  2.0845 -  2.0298  1247   142  0.91  14.91   1.02     1.01       3198.67|
| 14:  2.0298 -  1.9804  1074   116  0.92  13.93   0.99     0.95       2402.44|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2402.44 max =         9961.77 mean =      5903.75|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.93 mean =        13.27|
|phase err.(test): min =        0.00 max =           89.85 mean =        12.91|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.46    85.35   16.75    None  None   None       |
|    all(noH): 2823   0      0.46    85.35   16.75    None  None   None       |
|    Sol.    : 438    0      6.43    79.26   38.81    None  None   None       |
|    Mac.    : 2385   0      0.46    85.35   12.70    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:     0.463 -   8.952:  821   |   5:    42.906 -  51.395:  104        |
|      1:     8.952 -  17.440: 1253   |   6:    51.395 -  59.883:   79        |
|      2:    17.440 -  25.929:  270   |   7:    59.883 -  68.372:   24        |
|      3:    25.929 -  34.418:  141   |   8:    68.372 -  76.860:   13        |
|      4:    34.418 -  42.906:  113   |   9:    76.860 -  85.349:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 298         
Filter by distance & map next to the model:
   mapped sites are within: 0.482 - 4.615
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 295 from: 298
   mapped sites are within: 0.717 - 4.615

peak=    5.708 closest distance to " NE2 GLN A  11 " =    1.177
peak=    5.605 closest distance to " CG  PRO A  54 " =    1.253
peak=    5.583 closest distance to " O   HOH Z 126 " =    1.923
peak=    5.579 closest distance to " NH2 ARG A  56 " =    2.144
peak=    5.333 closest distance to " CB  ARG A 275 " =    0.913
peak=    5.285 closest distance to " CG  PRO A 213 " =    1.252
peak=    5.187 closest distance to " CB  GLN A 223 " =    1.454
peak=    5.142 closest distance to " CB  SER A  63 " =    1.217
peak=    5.017 closest distance to " O   HOH Z 144 " =    1.732
peak=    4.842 closest distance to " O   HOH Z 232 " =    2.412
peak=    4.802 closest distance to " CB  GLN A 183 " =    1.221
peak=    4.792 closest distance to " CG  PRO A  90 " =    1.088
peak=    4.756 closest distance to " O   HOH Z  78 " =    1.830
peak=    4.693 closest distance to " CB  PRO A  54 " =    0.977
peak=    4.617 closest distance to " C   PRO A 198 " =    1.495
peak=    4.558 closest distance to " CG2 VAL A 257 " =    0.906
peak=    4.526 closest distance to " O   HOH Z 427 " =    2.812
peak=    4.490 closest distance to " CA  TYR A  30 " =    0.934
peak=    4.479 closest distance to " O   HOH Z 303 " =    2.068
peak=    4.454 closest distance to " O   HOH Z 209 " =    2.258
peak=    4.436 closest distance to " O   HOH Z 236 " =    2.043
peak=    4.426 closest distance to " O   HOH Z  15 " =    2.351
peak=    4.421 closest distance to " O   HOH Z 203 " =    1.729
peak=    4.415 closest distance to " CB  GLU A 152 " =    1.244
peak=    4.410 closest distance to " CB  SER A   3 " =    1.289
peak=    4.394 closest distance to " O   HOH Z 298 " =    1.879
peak=    4.337 closest distance to " CG  PRO A 198 " =    1.229
peak=    4.337 closest distance to " CB  ASN A 148 " =    1.386
peak=    4.333 closest distance to " O   HOH Z 193 " =    1.785
peak=    4.331 closest distance to " OD1 ASN A  69 " =    2.607
peak=    4.329 closest distance to " O   HOH Z  61 " =    1.684
peak=    4.280 closest distance to " O   HOH Z  78 " =    2.111
peak=    4.275 closest distance to " O   HOH Z 369 " =    2.161
peak=    4.251 closest distance to " CB  ARG A  79 " =    1.340
peak=    4.191 closest distance to " CG  PRO A 243 " =    1.067
peak=    4.173 closest distance to " O   HOH Z 158 " =    2.983
peak=    4.164 closest distance to " OG ASER A 258 " =    3.100
peak=    4.150 closest distance to " CB  LEU A 228 " =    1.102
peak=    4.150 closest distance to " CB  TYR A 169 " =    0.717
peak=    4.119 closest distance to " O   HOH Z 234 " =    3.651
peak=    4.113 closest distance to " ND2 ASN A 187 " =    1.423
peak=    4.111 closest distance to " CB  GLU A 128 " =    1.041
peak=    4.096 closest distance to " O   HOH Z 144 " =    2.219
peak=    4.065 closest distance to " O   HOH Z 272 " =    1.813
peak=    4.059 closest distance to " O   HOH Z 344 " =    3.174
peak=    4.052 closest distance to " O   HOH Z 289 " =    1.713
peak=    4.046 closest distance to " CB  VAL A 265 " =    1.289
peak=    4.029 closest distance to " NZ  LYS A 117 " =    3.232
peak=    4.028 closest distance to " O   HOH Z 419 " =    2.087
peak=    4.002 closest distance to " CA  ASN A 215 " =    1.106
peak=    3.979 closest distance to " O   HOH Z  66 " =    2.173
peak=    3.978 closest distance to " CG  ARG A  66 " =    2.402
peak=    3.972 closest distance to " CG1 ILE A  33 " =    1.229
peak=    3.945 closest distance to " O   HOH Z  44 " =    1.827
peak=    3.906 closest distance to " O   HOH Z   1 " =    1.996
peak=    3.899 closest distance to " O   HOH Z 250 " =    1.482
peak=    3.884 closest distance to " CE  LYS A  76 " =    0.893
peak=    3.873 closest distance to " O   HOH Z 132 " =    2.409
peak=    3.858 closest distance to " O   HOH Z 189 " =    2.119
peak=    3.853 closest distance to " O   HOH Z 403 " =    1.675
peak=    3.845 closest distance to " OD2 ASP A 286 " =    2.809
peak=    3.841 closest distance to " CB  ARG A 139 " =    0.941
peak=    3.840 closest distance to " O   HOH Z 386 " =    3.232
peak=    3.833 closest distance to " O   HOH Z  43 " =    1.915
peak=    3.826 closest distance to " CB  TRP A 266 " =    0.994
peak=    3.817 closest distance to " CB  ARG A 190 " =    1.647
peak=    3.816 closest distance to " CB  SER A 216 " =    0.828
peak=    3.816 closest distance to " CD BLYS A 290 " =    1.253
peak=    3.800 closest distance to " O   SER A  87 " =    2.238
peak=    3.789 closest distance to " O   HOH Z 402 " =    1.439
peak=    3.774 closest distance to " O   HOH Z   9 " =    2.016
peak=    3.750 closest distance to " CB  TYR A 169 " =    0.747
peak=    3.725 closest distance to " O   HOH Z 368 " =    3.558
peak=    3.724 closest distance to " O   HOH Z 327 " =    1.674
peak=    3.720 closest distance to " O   HOH Z 389 " =    1.793
peak=    3.711 closest distance to " CB  TRP A 179 " =    1.325
peak=    3.706 closest distance to " O   HOH Z  40 " =    1.661
peak=    3.701 closest distance to " O   HOH Z 193 " =    1.695
peak=    3.701 closest distance to " O   HOH Z 425 " =    2.043
peak=    3.697 closest distance to " O   HOH Z  59 " =    1.711
peak=    3.697 closest distance to " O   HOH Z 245 " =    1.277
peak=    3.694 closest distance to " O   HOH Z 371 " =    3.037
peak=    3.687 closest distance to " NH1BARG A 145 " =    1.249
peak=    3.682 closest distance to " O   HOH Z  21 " =    1.735
peak=    3.677 closest distance to " CZ  PHE A 218 " =    1.007
peak=    3.660 closest distance to " CB  ALA A 291 " =    1.386
peak=    3.659 closest distance to " CA  THR A 264 " =    0.854
peak=    3.654 closest distance to " O   HOH Z 207 " =    1.772
peak=    3.651 closest distance to " O   HOH Z  10 " =    1.820
peak=    3.647 closest distance to " O   HOH Z 128 " =    2.189
peak=    3.645 closest distance to " CD2 TRP A 179 " =    1.343
peak=    3.644 closest distance to " O   HOH Z 368 " =    1.982
peak=    3.643 closest distance to " N   ARG A 156 " =    1.262
peak=    3.643 closest distance to " O   HOH Z 371 " =    1.669
peak=    3.636 closest distance to " O   HOH Z 248 " =    1.611
peak=    3.636 closest distance to " O   HOH Z 407 " =    2.337
peak=    3.633 closest distance to " CB  ALA A  34 " =    1.174
peak=    3.625 closest distance to " OG BSER A 164 " =    2.351
peak=    3.622 closest distance to " O   HOH Z 305 " =    3.532
peak=    3.616 closest distance to " N   PHE A 130 " =    1.262
peak=    3.615 closest distance to " O   HOH Z 219 " =    2.264
peak=    3.614 closest distance to " NH2BARG A 145 " =    2.020
peak=    3.604 closest distance to " CB  VAL A 202 " =    1.590
peak=    3.598 closest distance to " CG2 THR A 221 " =    1.141
peak=    3.593 closest distance to " O   HOH Z  97 " =    1.975
peak=    3.591 closest distance to " CG  LEU A 167 " =    1.216
peak=    3.591 closest distance to " O   HOH Z  40 " =    2.345
peak=    3.591 closest distance to " O   HOH Z 437 " =    1.502
peak=    3.588 closest distance to " O   HOH Z   3 " =    1.921
peak=    3.587 closest distance to " CB  SER A 212 " =    1.045
peak=    3.584 closest distance to " O   HOH Z 214 " =    2.079
peak=    3.584 closest distance to " CD  ARG A 159 " =    0.721
peak=    3.568 closest distance to " O   HOH Z  64 " =    2.273
peak=    3.551 closest distance to " O   HOH Z  93 " =    2.372
peak=    3.550 closest distance to " O   HOH Z   1 " =    1.692
peak=    3.548 closest distance to " CB  THR A 157 " =    1.118
peak=    3.529 closest distance to " O   HOH Z 236 " =    1.431
peak=    3.526 closest distance to " O   HOH Z  53 " =    2.546
peak=    3.522 closest distance to " CB  ASP A 140 " =    0.873
peak=    3.509 closest distance to " CD1 ILE A 106 " =    0.818
peak=    3.503 closest distance to " O   HOH Z 128 " =    2.035
peak=    3.502 closest distance to " CA  ALA A  21 " =    1.123
peak=    3.501 closest distance to " O   HOH Z  54 " =    1.670
peak=    3.497 closest distance to " O   HOH Z 147 " =    1.725
peak=    3.496 closest distance to " CG2AVAL A 121 " =    2.353
peak=    3.490 closest distance to " O   HOH Z 180 " =    2.172
peak=    3.488 closest distance to " NH1AARG A 145 " =    1.117
peak=    3.485 closest distance to " CD1 LEU A  96 " =    0.823
peak=    3.480 closest distance to " O   HOH Z 172 " =    3.242
peak=    3.479 closest distance to " O   HOH Z 280 " =    3.036
peak=    3.478 closest distance to " O   MET A 105 " =    1.799
peak=    3.477 closest distance to " O   HOH Z  61 " =    1.498
peak=    3.469 closest distance to " CB  TYR A 116 " =    0.798
peak=    3.468 closest distance to " CB  GLU A 277 " =    3.510
peak=    3.465 closest distance to " O   HOH Z 133 " =    1.523
peak=    3.457 closest distance to " O   HOH Z 345 " =    3.402
peak=    3.456 closest distance to " O   HOH Z  88 " =    2.727
peak=    3.444 closest distance to " ND1 HIS A  86 " =    1.724
peak=    3.435 closest distance to " N   GLN A 278 " =    1.175
peak=    3.433 closest distance to " NE2 GLN A  73 " =    3.674
peak=    3.431 closest distance to " CB  SER A  62 " =    1.197
peak=    3.430 closest distance to " CG  LYS A  76 " =    1.032
peak=    3.429 closest distance to " CA  PHE A 283 " =    1.233
peak=    3.426 closest distance to " CB  HIS A 108 " =    0.815
peak=    3.425 closest distance to " O   HOH Z 353 " =    2.664
peak=    3.423 closest distance to " OD1BASN A 224 " =    2.320
peak=    3.422 closest distance to " CA  THR A 221 " =    0.974
peak=    3.420 closest distance to " O   HOH Z 108 " =    2.180
peak=    3.415 closest distance to " CA  MET A  40 " =    1.078
peak=    3.409 closest distance to " O   HOH Z 163 " =    1.762
peak=    3.408 closest distance to " O   HOH Z  44 " =    3.159
peak=    3.407 closest distance to " O   HOH Z 175 " =    2.154
peak=    3.405 closest distance to " CB  ASN A  39 " =    0.882
peak=    3.405 closest distance to " O   HOH Z 148 " =    3.325
peak=    3.404 closest distance to " CD2 LEU A 255 " =    1.362
peak=    3.400 closest distance to " O   HOH Z  40 " =    1.928
peak=    3.396 closest distance to " O   HOH Z 133 " =    2.500
peak=    3.393 closest distance to " O   HOH Z 417 " =    3.175
peak=    3.392 closest distance to " O   HOH Z 193 " =    1.968
peak=    3.390 closest distance to " O   HOH Z 365 " =    2.944
peak=    3.385 closest distance to " NH2AARG A 190 " =    1.929
peak=    3.385 closest distance to " O   HOH Z 433 " =    1.760
peak=    3.383 closest distance to " CA  ALA A  43 " =    1.195
peak=    3.381 closest distance to " O   HOH Z 426 " =    1.673
peak=    3.380 closest distance to " CA  ALA A  84 " =    1.306
peak=    3.378 closest distance to " CD1 LEU A 300 " =    1.280
peak=    3.375 closest distance to " CB  VAL A 126 " =    1.066
peak=    3.375 closest distance to " CB  LEU A 143 " =    1.104
peak=    3.369 closest distance to " CG2 ILE A 120 " =    1.141
peak=    3.369 closest distance to " CB  ILE A 120 " =    1.256
peak=    3.366 closest distance to " CA  GLY A 241 " =    3.828
peak=    3.363 closest distance to " CA  ALA A  51 " =    0.929
peak=    3.358 closest distance to " CG1BVAL A  72 " =    1.469
peak=    3.357 closest distance to " CA  ILE A 234 " =    0.971
peak=    3.357 closest distance to " CB  SER A 273 " =    0.851
peak=    3.354 closest distance to " O   HOH Z 258 " =    1.707
peak=    3.346 closest distance to " CG1 VAL A 153 " =    0.929
peak=    3.346 closest distance to " CA  ALA A 291 " =    0.892
peak=    3.344 closest distance to " O   HOH Z 173 " =    1.889
peak=    3.342 closest distance to " O  BHOH Z 338 " =    2.327
peak=    3.341 closest distance to " CA  ASP A 162 " =    1.085
peak=    3.338 closest distance to " CG  MET A 113 " =    1.145
peak=    3.328 closest distance to " O   HOH Z 357 " =    1.788
peak=    3.328 closest distance to " O   HOH Z  71 " =    2.230
peak=    3.325 closest distance to " O   HOH Z 261 " =    2.198
peak=    3.321 closest distance to " O   HOH Z 423 " =    1.805
peak=    3.319 closest distance to " CB  LEU A 255 " =    0.808
peak=    3.319 closest distance to " O   HOH Z 409 " =    2.721
peak=    3.317 closest distance to " O   HOH Z 271 " =    2.315
peak=    3.317 closest distance to " CB  LYS A 117 " =    1.183
peak=    3.315 closest distance to " O   HOH Z 291 " =    1.630
peak=    3.306 closest distance to " N   TYR A  15 " =    0.782
peak=    3.301 closest distance to " CD2 LEU A 297 " =    0.908
peak=    3.301 closest distance to " CA  ARG A  36 " =    1.010
peak=    3.300 closest distance to " CA  ALA A 233 " =    1.237
peak=    3.299 closest distance to " O  BHOH Z  74 " =    1.328
peak=    3.299 closest distance to " CE1 TYR A 186 " =    1.337
peak=    3.297 closest distance to " OG  SER A  22 " =    2.692
peak=    3.296 closest distance to " NZ  LYS A  76 " =    1.502
peak=    3.289 closest distance to " O   HOH Z 273 " =    2.714
peak=    3.281 closest distance to " O   HOH Z 227 " =    1.700
peak=    3.277 closest distance to " CB  THR A  31 " =    1.721
peak=    3.275 closest distance to " CA  ALA A 158 " =    1.181
peak=    3.269 closest distance to " O   HOH Z 163 " =    1.866
peak=    3.269 closest distance to " O   HOH Z 403 " =    1.357
peak=    3.263 closest distance to " CE AMET A  47 " =    1.393
peak=    3.262 closest distance to " O   HOH Z 183 " =    1.339
peak=    3.261 closest distance to " O   HOH Z 213 " =    2.000
peak=    3.256 closest distance to " O   HOH Z  89 " =    2.157
peak=    3.251 closest distance to " CB  ALA A 248 " =    1.376
peak=    3.250 closest distance to " CB  ASN A 224 " =    0.991
peak=    3.249 closest distance to " O   HOH Z 391 " =    2.953
peak=    3.245 closest distance to " CD1AILE A 234 " =    0.954
peak=    3.241 closest distance to " O   HOH Z 135 " =    1.608
peak=    3.237 closest distance to " CA  ARG A 195 " =    1.170
peak=    3.228 closest distance to " O   ALA A 165 " =    1.468
peak=    3.228 closest distance to " CG1 ILE A 151 " =    0.940
peak=    3.224 closest distance to " N   ASN A  39 " =    1.179
peak=    3.223 closest distance to " CB  PRO A 198 " =    0.996
peak=    3.217 closest distance to " O   HOH Z 435 " =    1.918
peak=    3.217 closest distance to " CA  GLY A  80 " =    0.781
peak=    3.212 closest distance to " ND1 HIS A  81 " =    1.610
peak=    3.211 closest distance to " O   HOH Z 128 " =    2.076
peak=    3.210 closest distance to " CA  ALA A 248 " =    1.233
peak=    3.207 closest distance to " CB  ALA A   1 " =    4.615
peak=    3.206 closest distance to " CG2 VAL A  78 " =    0.889
peak=    3.204 closest distance to " CA  SER A  87 " =    1.039
peak=    3.204 closest distance to " O   GLN A 278 " =    1.395
peak=    3.203 closest distance to " O   HOH Z 257 " =    2.170
peak=    3.203 closest distance to " O   HOH Z 337 " =    3.637
peak=    3.198 closest distance to " CA  LYS A 290 " =    1.262
peak=    3.196 closest distance to " CA  LEU A 101 " =    1.538
peak=    3.196 closest distance to " O   HOH Z 144 " =    1.875
peak=    3.196 closest distance to " O   HOH Z 263 " =    1.602
peak=    3.194 closest distance to " O   HOH Z 329 " =    3.769
peak=    3.191 closest distance to " CB  ASN A 142 " =    0.970
peak=    3.190 closest distance to " CB  MET A  40 " =    0.848
peak=    3.190 closest distance to " CB  SER A  26 " =    1.577
peak=    3.189 closest distance to " N   ASN A 127 " =    1.236
peak=    3.186 closest distance to " CG1 ILE A 120 " =    1.131
peak=    3.185 closest distance to " O   HOH Z 291 " =    1.846
peak=    3.181 closest distance to " CA  ASN A 127 " =    1.087
peak=    3.178 closest distance to " OG BSER A 134 " =    2.821
peak=    3.177 closest distance to " O   HOH Z 298 " =    2.607
peak=    3.175 closest distance to " O   HOH Z  96 " =    2.123
peak=    3.175 closest distance to " O   THR A 220 " =    1.324
peak=    3.169 closest distance to " O   HOH Z 124 " =    1.330
peak=    3.168 closest distance to " OG  SER A 206 " =    1.255
peak=    3.166 closest distance to " O   HOH Z 371 " =    3.394
peak=    3.157 closest distance to " CG2 ILE A  20 " =    1.444
peak=    3.154 closest distance to " OE1 GLU A   2 " =    2.184
peak=    3.153 closest distance to " O   HOH Z 185 " =    1.766
peak=    3.152 closest distance to " O   HOH Z 295 " =    1.541
peak=    3.150 closest distance to " CB  SER A  62 " =    0.825
peak=    3.150 closest distance to " O   HOH Z  88 " =    2.441
peak=    3.146 closest distance to " CA  VAL A 125 " =    1.044
peak=    3.144 closest distance to " CB  GLN A 278 " =    0.853
peak=    3.142 closest distance to " CD  LYS A 119 " =    1.174
peak=    3.141 closest distance to " O   HOH Z  85 " =    2.165
peak=    3.139 closest distance to " O   HOH Z 261 " =    1.426
peak=    3.132 closest distance to " CB  LYS A 290 " =    1.075
peak=    3.132 closest distance to " O   HOH Z 411 " =    1.748
peak=    3.132 closest distance to " CZ2 TRP A 179 " =    1.686
peak=    3.129 closest distance to " N   ALA A 154 " =    0.871
peak=    3.128 closest distance to " NH1 ARG A 138 " =    1.167
peak=    3.128 closest distance to " OG  SER A  62 " =    2.851
peak=    3.126 closest distance to " CG  ARG A 159 " =    0.798
peak=    3.122 closest distance to " CA  ARG A 102 " =    1.087
peak=    3.122 closest distance to " CG2BVAL A  41 " =    0.831
peak=    3.122 closest distance to " CG BARG A 102 " =    1.765
peak=    3.122 closest distance to " N   SER A 135 " =    1.164
peak=    3.118 closest distance to " CD  ARG A  36 " =    1.037
peak=    3.116 closest distance to " CG  GLN A  89 " =    1.532
peak=    3.114 closest distance to " CA  MET A 105 " =    0.966
peak=    3.108 closest distance to " CB  MET A  47 " =    1.204
peak=    3.106 closest distance to " CB  ASN A 110 " =    1.126
peak=    3.101 closest distance to " CA  GLU A  46 " =    0.724
peak=    3.097 closest distance to " O   HOH Z 359 " =    1.333
peak=    3.093 closest distance to " CG2 VAL A 197 " =    1.092
peak=    3.091 closest distance to " O   HOH Z 374 " =    2.577
peak=    3.082 closest distance to " CB  LEU A 300 " =    0.907
peak=    3.080 closest distance to " O   PRO A  90 " =    1.420
peak=    3.079 closest distance to " CG  ARG A 269 " =    1.289
peak=    3.072 closest distance to " O   HOH Z 152 " =    1.736
peak=    3.071 closest distance to " O   HOH Z 271 " =    2.493
peak=    3.069 closest distance to " CA  SER A 146 " =    1.730
peak=    3.055 closest distance to " O   HOH Z  20 " =    3.802
peak=    3.051 closest distance to " O   HOH Z 303 " =    1.628
peak=    3.045 closest distance to " O   ALA A   1 " =    1.703
peak=    3.042 closest distance to " O   HOH Z 423 " =    2.790
peak=    3.035 closest distance to " O   HOH Z 342 " =    0.743
peak=    3.031 closest distance to " O   HOH Z 153 " =    1.595
peak=    3.029 closest distance to " OG BSER A  99 " =    2.184
peak=    3.024 closest distance to " O   HOH Z 383 " =    1.703
peak=    3.019 closest distance to " O   HOH Z 156 " =    2.858

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 193         
Filter by distance & map next to the model:
   mapped sites are within: 0.788 - 5.664
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 192 from: 193
   mapped sites are within: 0.788 - 5.664

peak=   -4.654 closest distance to " CB  PRO A 243 " =    2.579
peak=   -4.571 closest distance to " CD  ARG A 156 " =    1.975
peak=   -4.570 closest distance to " O   HOH Z 266 " =    4.774
peak=   -4.376 closest distance to " CG  GLN A 223 " =    1.743
peak=   -4.315 closest distance to " OG BSER A 134 " =    1.219
peak=   -4.259 closest distance to " CB  PRO A 280 " =    2.072
peak=   -4.246 closest distance to " CG1 VAL A 112 " =    2.827
peak=   -4.197 closest distance to " C   HIS A 108 " =    1.068
peak=   -4.166 closest distance to " O   VAL A  67 " =    2.642
peak=   -4.114 closest distance to " O   HOH Z 372 " =    2.392
peak=   -4.080 closest distance to " CE  MET A 105 " =    2.263
peak=   -4.067 closest distance to " O   PRO A 198 " =    1.264
peak=   -4.056 closest distance to " CA  VAL A  67 " =    2.706
peak=   -4.054 closest distance to " CG  ASP A 231 " =    0.788
peak=   -4.038 closest distance to " SG  CYS A 254 " =    3.473
peak=   -4.027 closest distance to " O   HOH Z 290 " =    1.229
peak=   -4.021 closest distance to " O   HOH Z 231 " =    2.124
peak=   -4.001 closest distance to " ND2 ASN A  45 " =    1.440
peak=   -3.995 closest distance to " O   HOH Z 389 " =    1.869
peak=   -3.970 closest distance to " O   HOH Z 435 " =    2.833
peak=   -3.960 closest distance to " OD1 ASN A 187 " =    1.600
peak=   -3.902 closest distance to " O   HOH Z 198 " =    1.942
peak=   -3.893 closest distance to " O   HOH Z 313 " =    1.881
peak=   -3.890 closest distance to " N   GLN A  58 " =    1.762
peak=   -3.885 closest distance to " CZ3 TRP A 179 " =    1.170
peak=   -3.883 closest distance to " O   ILE A 109 " =    2.512
peak=   -3.874 closest distance to " CE2 PHE A 218 " =    2.453
peak=   -3.854 closest distance to " O   ARG A 145 " =    1.492
peak=   -3.847 closest distance to " O   HOH Z 407 " =    3.055
peak=   -3.837 closest distance to " CE2 TYR A  30 " =    2.809
peak=   -3.818 closest distance to " CB  ALA A 291 " =    2.188
peak=   -3.818 closest distance to " CD  GLN A  58 " =    1.052
peak=   -3.788 closest distance to " O   HOH Z 114 " =    3.024
peak=   -3.781 closest distance to " CB  PHE A 192 " =    1.957
peak=   -3.762 closest distance to " CB  ASN A  39 " =    2.244
peak=   -3.759 closest distance to " ND2 ASN A  45 " =    1.038
peak=   -3.756 closest distance to " CD  ARG A 139 " =    1.473
peak=   -3.753 closest distance to " CG  PHE A 283 " =    2.709
peak=   -3.748 closest distance to " O   HOH Z  43 " =    1.704
peak=   -3.744 closest distance to " N   ALA A  43 " =    2.562
peak=   -3.739 closest distance to " O   SER A 135 " =    1.469
peak=   -3.739 closest distance to " CA  GLY A 203 " =    2.204
peak=   -3.732 closest distance to " O   PRO A 163 " =    1.978
peak=   -3.705 closest distance to " CZ  PHE A  59 " =    1.484
peak=   -3.704 closest distance to " O   HOH Z 185 " =    2.191
peak=   -3.701 closest distance to " OXT GLY A 302 " =    2.794
peak=   -3.688 closest distance to " CZ  TYR A 169 " =    1.707
peak=   -3.687 closest distance to " O   HOH Z 353 " =    2.074
peak=   -3.686 closest distance to " O   HOH Z 102 " =    1.586
peak=   -3.685 closest distance to " O   HOH Z 351 " =    1.571
peak=   -3.674 closest distance to " OD1 ASP A 171 " =    1.598
peak=   -3.665 closest distance to " CB  ALA A 248 " =    1.998
peak=   -3.651 closest distance to " OD2 ASP A 191 " =    1.428
peak=   -3.639 closest distance to " CB  ALA A 291 " =    2.341
peak=   -3.638 closest distance to " CD  ARG A 195 " =    5.184
peak=   -3.624 closest distance to " CB  TYR A  15 " =    2.138
peak=   -3.620 closest distance to " O   HOH Z 198 " =    1.503
peak=   -3.619 closest distance to " O   HOH Z 126 " =    1.852
peak=   -3.613 closest distance to " C   ALA A 158 " =    1.312
peak=   -3.596 closest distance to " O   HOH Z  13 " =    1.532
peak=   -3.595 closest distance to " O   HOH Z 211 " =    1.673
peak=   -3.565 closest distance to " NH1 ARG A 195 " =    2.586
peak=   -3.532 closest distance to " CD1 PHE A  59 " =    1.847
peak=   -3.532 closest distance to " N   ASP A 286 " =    2.454
peak=   -3.515 closest distance to " NH2AARG A 275 " =    5.256
peak=   -3.508 closest distance to " O   HOH Z  44 " =    2.247
peak=   -3.507 closest distance to " CG2 ILE A 263 " =    2.306
peak=   -3.502 closest distance to " O   HOH Z 385 " =    1.909
peak=   -3.502 closest distance to " N   ALA A 248 " =    1.530
peak=   -3.501 closest distance to " C   LEU A 143 " =    1.098
peak=   -3.498 closest distance to " CA  GLY A  98 " =    1.883
peak=   -3.497 closest distance to " O   HOH Z 298 " =    1.256
peak=   -3.490 closest distance to " NH2BARG A 275 " =    1.827
peak=   -3.481 closest distance to " OD1 ASN A 148 " =    1.583
peak=   -3.477 closest distance to " O   ALA A 161 " =    1.554
peak=   -3.475 closest distance to " OD2 ASP A 171 " =    2.436
peak=   -3.458 closest distance to " O   HOH Z  11 " =    1.820
peak=   -3.457 closest distance to " ND2 ASN A 249 " =    2.055
peak=   -3.451 closest distance to " O   HOH Z  10 " =    1.466
peak=   -3.443 closest distance to " CD1 LEU A 228 " =    2.147
peak=   -3.436 closest distance to " O   HOH Z 322 " =    1.624
peak=   -3.435 closest distance to " NH2 ARG A  79 " =    1.977
peak=   -3.433 closest distance to " OG  SER A  97 " =    2.090
peak=   -3.432 closest distance to " O   HOH Z  60 " =    2.401
peak=   -3.432 closest distance to " CD1 ILE A 239 " =    2.577
peak=   -3.427 closest distance to " OG BSER A 134 " =    1.637
peak=   -3.413 closest distance to " OXT GLY A 302 " =    3.410
peak=   -3.404 closest distance to " O   PHE A 218 " =    1.515
peak=   -3.402 closest distance to " O   HOH Z  24 " =    1.368
peak=   -3.401 closest distance to " O   VAL A 189 " =    2.534
peak=   -3.395 closest distance to " CB  PRO A 163 " =    2.484
peak=   -3.382 closest distance to " OD1 ASP A 191 " =    1.494
peak=   -3.381 closest distance to " CD1 LEU A 101 " =    2.273
peak=   -3.376 closest distance to " CA  GLY A 133 " =    1.975
peak=   -3.375 closest distance to " CB  ASP A 286 " =    1.734
peak=   -3.373 closest distance to " O   HOH Z 388 " =    2.117
peak=   -3.365 closest distance to " O   GLY A  80 " =    2.399
peak=   -3.363 closest distance to " CG1 VAL A 230 " =    2.005
peak=   -3.349 closest distance to " SG ACYS A 201 " =    1.839
peak=   -3.338 closest distance to " O   HOH Z  63 " =    1.702
peak=   -3.337 closest distance to " O   PRO A 198 " =    1.254
peak=   -3.333 closest distance to " CD2 LEU A 237 " =    2.772
peak=   -3.331 closest distance to " O   HOH Z 311 " =    3.504
peak=   -3.324 closest distance to " ND2 ASN A 187 " =    1.575
peak=   -3.322 closest distance to " N   SER A 212 " =    1.867
peak=   -3.317 closest distance to " O   GLY A 211 " =    1.288
peak=   -3.314 closest distance to " N   THR A 235 " =    1.339
peak=   -3.314 closest distance to " CB  ASP A 286 " =    2.121
peak=   -3.313 closest distance to " NE2 GLN A 278 " =    1.736
peak=   -3.313 closest distance to " O   HOH Z 196 " =    2.133
peak=   -3.302 closest distance to " OD2 ASP A  50 " =    1.523
peak=   -3.300 closest distance to " CB  PHE A 208 " =    2.239
peak=   -3.297 closest distance to " CB  CYS A 201 " =    2.559
peak=   -3.293 closest distance to " O   HOH Z 417 " =    2.462
peak=   -3.290 closest distance to " CB  ASP A 132 " =    2.219
peak=   -3.289 closest distance to " NE  ARG A  36 " =    1.910
peak=   -3.280 closest distance to " CB  ALA A   7 " =    2.059
peak=   -3.264 closest distance to " OG  SER A  62 " =    1.645
peak=   -3.261 closest distance to " CD2 LEU A 300 " =    2.895
peak=   -3.255 closest distance to " O   SER A  95 " =    1.490
peak=   -3.254 closest distance to " O   SER A  22 " =    2.362
peak=   -3.254 closest distance to " O   ALA A  51 " =    1.392
peak=   -3.252 closest distance to " C   PRO A  90 " =    1.509
peak=   -3.247 closest distance to " O   ALA A  34 " =    2.492
peak=   -3.245 closest distance to " CB  ALA A 248 " =    2.344
peak=   -3.245 closest distance to " CB  ASP A 132 " =    2.324
peak=   -3.243 closest distance to " CB  CYS A 254 " =    2.365
peak=   -3.237 closest distance to " OD2 ASP A 171 " =    1.728
peak=   -3.232 closest distance to " O   ALA A 180 " =    1.098
peak=   -3.231 closest distance to " CB  ILE A  33 " =    2.916
peak=   -3.228 closest distance to " O   HOH Z 266 " =    4.553
peak=   -3.228 closest distance to " O   HOH Z 250 " =    1.433
peak=   -3.221 closest distance to " CD1 ILE A 151 " =    2.189
peak=   -3.221 closest distance to " OD1 ASP A 200 " =    1.348
peak=   -3.219 closest distance to " CG  MET A 105 " =    0.922
peak=   -3.218 closest distance to " O   HOH Z 339 " =    1.858
peak=   -3.217 closest distance to " CG  GLU A 277 " =    1.254
peak=   -3.212 closest distance to " O   VAL A 174 " =    2.101
peak=   -3.209 closest distance to " OD1 ASN A 176 " =    1.247
peak=   -3.208 closest distance to " O   HOH Z 253 " =    3.800
peak=   -3.207 closest distance to " CA  ASP A 298 " =    1.049
peak=   -3.206 closest distance to " CG1 VAL A 112 " =    2.548
peak=   -3.204 closest distance to " O   TRP A  70 " =    1.473
peak=   -3.202 closest distance to " O   VAL A 189 " =    1.596
peak=   -3.195 closest distance to " OH  TYR A 214 " =    1.213
peak=   -3.194 closest distance to " OE1 GLN A 223 " =    1.927
peak=   -3.190 closest distance to " O   HOH Z  37 " =    1.710
peak=   -3.187 closest distance to " O   HOH Z 234 " =    3.981
peak=   -3.185 closest distance to " CA  GLY A 241 " =    3.234
peak=   -3.182 closest distance to " O   HOH Z  93 " =    2.114
peak=   -3.182 closest distance to " O   HOH Z 316 " =    1.761
peak=   -3.177 closest distance to " O   HOH Z 263 " =    2.900
peak=   -3.177 closest distance to " CG  LEU A  83 " =    1.850
peak=   -3.175 closest distance to " O   HOH Z 281 " =    2.738
peak=   -3.168 closest distance to " CD  GLU A 236 " =    1.041
peak=   -3.167 closest distance to " N   ALA A 226 " =    2.000
peak=   -3.163 closest distance to " O   HOH Z 351 " =    1.674
peak=   -3.161 closest distance to " CA  GLY A  57 " =    2.099
peak=   -3.158 closest distance to " O   ASN A 249 " =    1.419
peak=   -3.156 closest distance to " OE1 GLN A  88 " =    1.255
peak=   -3.153 closest distance to " O   HOH Z 166 " =    1.498
peak=   -3.145 closest distance to " OG  SER A 206 " =    1.737
peak=   -3.145 closest distance to " O   HOH Z 137 " =    1.458
peak=   -3.143 closest distance to " O   HOH Z 191 " =    5.664
peak=   -3.141 closest distance to " CD2 PHE A  61 " =    2.476
peak=   -3.137 closest distance to " CG  TRP A 266 " =    1.896
peak=   -3.136 closest distance to " OD1AASN A 224 " =    1.813
peak=   -3.131 closest distance to " CZ  PHE A 155 " =    1.323
peak=   -3.125 closest distance to " CG  GLU A 152 " =    1.173
peak=   -3.124 closest distance to " C   MET A 188 " =    1.441
peak=   -3.123 closest distance to " O   HOH Z 417 " =    2.595
peak=   -3.123 closest distance to " O   ALA A 292 " =    1.972
peak=   -3.121 closest distance to " O   HOH Z 324 " =    2.027
peak=   -3.120 closest distance to " CD1 LEU A 297 " =    2.443
peak=   -3.117 closest distance to " O   LEU A 167 " =    1.388
peak=   -3.116 closest distance to " O   HOH Z 137 " =    1.441
peak=   -3.115 closest distance to " O   HOH Z  60 " =    1.937
peak=   -3.114 closest distance to " O   HOH Z 359 " =    3.278
peak=   -3.109 closest distance to " O   HOH Z 426 " =    1.581
peak=   -3.103 closest distance to " O   HOH Z  51 " =    1.687
peak=   -3.094 closest distance to " CG  ARG A 269 " =    2.555
peak=   -3.087 closest distance to " O   GLN A 144 " =    1.398
peak=   -3.082 closest distance to " O   HOH Z 423 " =    1.162
peak=   -3.079 closest distance to " O   HOH Z 111 " =    2.443
peak=   -3.076 closest distance to " O   HOH Z 281 " =    3.140
peak=   -3.075 closest distance to " OE2 GLU A 152 " =    1.074
peak=   -3.075 closest distance to " NH2 ARG A  79 " =    1.581
peak=   -3.066 closest distance to " O   LYS A 289 " =    2.974
peak=   -3.056 closest distance to " O   HOH Z 298 " =    2.429
peak=   -3.052 closest distance to " O   HOH Z 288 " =    1.433
peak=   -3.042 closest distance to " OG1 THR A 246 " =    1.396
peak=   -3.027 closest distance to " CD2 TYR A 293 " =    1.975

================= 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    :  0.3145 0.3131   6.018368e+00   6.004107e+00
   1_bss:  0.2988 0.2958   5.998812e+00   5.968764e+00
   1_xyz:  0.1585 0.1821   5.399997e+00   5.514861e+00
   1_adp:  0.1475 0.1877   5.355747e+00   5.550777e+00
   1_occ:  0.1471 0.1877   5.353703e+00   5.549437e+00
   2_bss:  0.1457 0.1844   5.345431e+00   5.537924e+00
   2_xyz:  0.1196 0.1596   5.174293e+00   5.395523e+00
   2_adp:  0.1145 0.1542   5.136542e+00   5.364620e+00
   2_occ:  0.1144 0.1543   5.136242e+00   5.364712e+00
   3_bss:  0.1142 0.1542   5.135014e+00   5.363837e+00
   3_xyz:  0.1079 0.1507   5.099189e+00   5.344425e+00
   3_adp:  0.1064 0.1510   5.094736e+00   5.345827e+00
   3_occ:  0.1063 0.1509   5.094736e+00   5.345939e+00
   4_bss:  0.1064 0.1510   5.094914e+00   5.345949e+00
   4_xyz:  0.1091 0.1524   5.112173e+00   5.355545e+00
   4_adp:  0.1105 0.1519   5.116565e+00   5.353333e+00
   4_occ:  0.1105 0.1519   5.116593e+00   5.353611e+00
   5_bss:  0.1104 0.1519   5.116553e+00   5.353587e+00
   5_xyz:  0.1088 0.1516   5.108090e+00   5.352734e+00
   5_adp:  0.1074 0.1527   5.105841e+00   5.359015e+00
   5_occ:  0.1073 0.1527   5.105796e+00   5.359034e+00
   5_bss:  0.1073 0.1527   5.105805e+00   5.359014e+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:  0.333  38.298  -3.056   0.153  -0.387   0.000  -0.000  -0.000
   1_xyz:  0.333  38.298  -3.056   0.153  -0.387   0.000  -0.000  -0.000
   1_adp:  0.333  38.298  -3.056   0.153  -0.387   0.000  -0.000  -0.000
   1_occ:  0.333  38.298  -3.056   0.153  -0.387   0.000  -0.000  -0.000
   2_bss:  0.325  43.000  -3.123  -2.184  -1.629  -0.000  -0.000  -0.000
   2_xyz:  0.325  43.000  -3.123  -2.184  -1.629  -0.000  -0.000  -0.000
   2_adp:  0.325  43.000  -3.123  -2.184  -1.629  -0.000  -0.000  -0.000
   2_occ:  0.325  43.000  -3.123  -2.184  -1.629  -0.000  -0.000  -0.000
   3_bss:  0.325  43.000  -2.786  -2.406  -1.550  -0.000  -0.000  -0.000
   3_xyz:  0.325  43.000  -2.786  -2.406  -1.550  -0.000  -0.000  -0.000
   3_adp:  0.325  43.000  -2.786  -2.406  -1.550  -0.000  -0.000  -0.000
   3_occ:  0.325  43.000  -2.786  -2.406  -1.550  -0.000  -0.000  -0.000
   4_bss:  0.321  43.264  -2.592  -2.421  -1.485  -0.000  -0.000  -0.000
   4_xyz:  0.321  43.264  -2.592  -2.421  -1.485  -0.000  -0.000  -0.000
   4_adp:  0.321  43.264  -2.592  -2.421  -1.485  -0.000  -0.000  -0.000
   4_occ:  0.321  43.264  -2.592  -2.421  -1.485  -0.000  -0.000  -0.000
   5_bss:  0.321  43.264  -2.500  -2.404  -1.403  -0.000  -0.000  -0.000
   5_xyz:  0.321  43.264  -2.500  -2.404  -1.403  -0.000  -0.000  -0.000
   5_adp:  0.321  43.264  -2.500  -2.404  -1.403  -0.000  -0.000  -0.000
   5_occ:  0.321  43.264  -2.500  -2.404  -1.403  -0.000  -0.000  -0.000
   5_bss:  0.320  43.419  -2.272  -2.224  -1.228  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  31.379 0.7465  0.9380    27628.830
   1_bss:  29.869 0.7608  0.9171    23861.559
   1_xyz:  16.432 0.8958  1.0158     8413.221
   1_adp:  17.271 0.8881  1.0126     8939.652
   1_occ:  17.243 0.8883  1.0126     8890.614
   2_bss:  16.908 0.8911  0.9723     8619.074
   2_xyz:  13.977 0.9151  0.9834     6340.547
   2_adp:  13.410 0.9195  0.9828     6002.516
   2_occ:  13.413 0.9195  0.9827     6002.062
   3_bss:  13.385 0.9197  0.9855     5993.234
   3_xyz:  12.970 0.9231  0.9861     5743.263
   3_adp:  13.000 0.9229  0.9806     5746.364
   3_occ:  13.005 0.9229  0.9805     5748.655
   4_bss:  13.019 0.9227  0.9836     5752.597
   4_xyz:  13.165 0.9218  0.9827     5871.007
   4_adp:  13.101 0.9223  0.9795     5868.621
   4_occ:  13.109 0.9222  0.9794     5872.282
   5_bss:  13.107 0.9222  0.9818     5872.382
   5_xyz:  13.087 0.9223  0.9820     5861.056
   5_adp:  13.230 0.9213  0.9762     5901.717
   5_occ:  13.231 0.9213  0.9761     5903.517
   5_bss:  13.231 0.9213  0.9826     5904.026
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6132e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6132e-01
   1_xyz:   1.032  0.007  0.072 15.026  0.005  4.106   6.3354e-02
   1_adp:   1.032  0.007  0.072 15.026  0.005  4.106   6.3354e-02
   1_occ:   1.032  0.007  0.072 15.026  0.005  4.106   6.3354e-02
   2_bss:   1.032  0.007  0.072 15.026  0.005  4.106   6.3354e-02
   2_xyz:   0.952  0.006  0.072 14.754  0.004  4.116   5.4467e-02
   2_adp:   0.952  0.006  0.072 14.754  0.004  4.116   5.4467e-02
   2_occ:   0.952  0.006  0.072 14.754  0.004  4.116   5.4467e-02
   3_bss:   0.952  0.006  0.072 14.754  0.004  4.116   5.4467e-02
   3_xyz:   1.010  0.007  0.076 14.916  0.004  4.117   6.1477e-02
   3_adp:   1.010  0.007  0.076 14.916  0.004  4.117   6.1477e-02
   3_occ:   1.010  0.007  0.076 14.916  0.004  4.117   6.1477e-02
   4_bss:   1.010  0.007  0.076 14.916  0.004  4.117   6.1477e-02
   4_xyz:   0.857  0.005  0.066 14.461  0.004  4.116   4.7344e-02
   4_adp:   0.857  0.005  0.066 14.461  0.004  4.116   4.7344e-02
   4_occ:   0.857  0.005  0.066 14.461  0.004  4.116   4.7344e-02
   5_bss:   0.857  0.005  0.066 14.461  0.004  4.116   4.7344e-02
   5_xyz:   0.898  0.005  0.069 14.463  0.004  4.117   5.0395e-02
   5_adp:   0.898  0.005  0.069 14.463  0.004  4.117   5.0395e-02
   5_occ:   0.898  0.005  0.069 14.463  0.004  4.117   5.0395e-02
   5_bss:   0.898  0.005  0.069 14.463  0.004  4.117   5.0395e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3910e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3910e-01
   1_xyz:   6.994  0.047  0.350 86.217  0.044  2.232   7.3158e-02
   1_adp:   6.994  0.047  0.350 86.217  0.044  2.232   7.3158e-02
   1_occ:   6.994  0.047  0.350 86.217  0.044  2.232   7.3158e-02
   2_bss:   6.994  0.047  0.350 86.217  0.044  2.232   7.3158e-02
   2_xyz:   7.242  0.037  0.205 83.886  0.041  2.318   3.9104e-02
   2_adp:   7.242  0.037  0.205 83.886  0.041  2.318   3.9104e-02
   2_occ:   7.242  0.037  0.205 83.886  0.041  2.318   3.9104e-02
   3_bss:   7.242  0.037  0.205 83.886  0.041  2.318   3.9104e-02
   3_xyz:   6.566  0.039  0.246 84.234  0.037  2.273   4.7023e-02
   3_adp:   6.566  0.039  0.246 84.234  0.037  2.273   4.7023e-02
   3_occ:   6.566  0.039  0.246 84.234  0.037  2.273   4.7023e-02
   4_bss:   6.566  0.039  0.246 84.234  0.037  2.273   4.7023e-02
   4_xyz:   6.417  0.037  0.208 83.558  0.040  2.381   2.8807e-02
   4_adp:   6.417  0.037  0.208 83.558  0.040  2.381   2.8807e-02
   4_occ:   6.417  0.037  0.208 83.558  0.040  2.381   2.8807e-02
   5_bss:   6.417  0.037  0.208 83.558  0.040  2.381   2.8807e-02
   5_xyz:   6.455  0.037  0.219 84.335  0.035  2.310   2.9931e-02
   5_adp:   6.455  0.037  0.219 84.335  0.035  2.310   2.9931e-02
   5_occ:   6.455  0.037  0.219 84.335  0.035  2.310   2.9931e-02
   5_bss:   6.455  0.037  0.219 84.335  0.035  2.310   2.9931e-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:  62.44   0.00  16.55  58.21   0.00  12.69  62.44   7.56  37.56
   1_occ:  62.44   0.00  16.55  58.21   0.00  12.69  62.44   7.56  37.56
   2_bss:  62.44   0.00  16.55  58.21   0.00  12.69  62.44   7.56  37.56
   2_xyz:  62.44   0.00  16.55  58.21   0.00  12.69  62.44   7.56  37.56
   2_adp:  70.60   1.68  16.78  65.82   1.68  12.89  70.60   6.59  37.97
   2_occ:  70.60   1.68  16.78  65.82   1.68  12.89  70.60   6.59  37.97
   3_bss:  70.60   1.68  16.78  65.82   1.68  12.89  70.60   6.59  37.97
   3_xyz:  70.60   1.68  16.78  65.82   1.68  12.89  70.60   6.59  37.97
   3_adp:  76.23   1.10  16.88  75.88   1.10  12.86  76.23   6.11  38.71
   3_occ:  76.23   1.10  16.88  75.88   1.10  12.86  76.23   6.11  38.71
   4_bss:  76.23   1.10  16.88  75.88   1.10  12.86  76.23   6.11  38.71
   4_xyz:  76.23   1.10  16.88  75.88   1.10  12.86  76.23   6.11  38.71
   4_adp:  76.47   1.84  16.34  74.71   1.84  12.67  76.47   6.62  36.37
   4_occ:  76.47   1.84  16.34  74.71   1.84  12.67  76.47   6.62  36.37
   5_bss:  76.47   1.84  16.34  74.71   1.84  12.67  76.47   6.62  36.37
   5_xyz:  76.47   1.84  16.34  74.71   1.84  12.67  76.47   6.62  36.37
   5_adp:  85.36   0.48  16.77  85.36   0.48  12.72  79.28   6.44  38.82
   5_occ:  85.36   0.48  16.77  85.36   0.48  12.72  79.28   6.44  38.82
   5_bss:  85.35   0.46  16.75  85.35   0.46  12.70  79.26   6.43  38.81
------------------------------------------------------------------------
 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:    0.883    0.018    0.319
   1_adp:    0.883    0.018    0.319
   1_occ:    0.883    0.018    0.319
   2_bss:    0.883    0.018    0.319
   2_xyz:    0.750    0.029    0.354
   2_adp:    0.750    0.029    0.354
   2_occ:    0.750    0.029    0.354
   3_bss:    0.750    0.029    0.354
   3_xyz:    0.800    0.029    0.379
   3_adp:    0.800    0.029    0.379
   3_occ:    0.800    0.029    0.379
   4_bss:    0.800    0.029    0.379
   4_xyz:    0.902    0.037    0.383
   4_adp:    0.902    0.037    0.383
   4_occ:    0.902    0.037    0.383
   5_bss:    0.902    0.037    0.383
   5_xyz:    0.995    0.055    0.389
   5_adp:    0.995    0.055    0.389
   5_occ:    0.995    0.055    0.389
   5_bss:    0.995    0.055    0.389
------------------------------------------------------------------------

CPU time actual refinement: 319.43


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_641/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_641/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_641/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_641/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_641/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 319.27 
  Macro-tasks:
    bulk solvent and scale       = 38.08  
    individual site refinement   = 128.76 
    weights calculation          = 30.05  
    collect and process          = 6.62   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 203.64 
  Micro-tasks:
    mask                            = 1.18   
    f_calc                          = 100.91 
    alpha_beta                      = 8.04   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 108.76 
    fmodel                         = 6.62   
    r_factors                      = 0.19   
    phase_errors                   = 11.18  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 238.36 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.565 micro seconds
Total CPU time: 5.55 minutes
from_scatterers_fft:    633 calls, 100.58 s
gradients_fft:          578 calls,  95.66 s

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

# Date 2008-01-16 Time 05:18:37 PST -0800 (1200489517.06 s)
Start R-work = 0.3145, R-free = 0.3131 (no bulk solvent and anisotropic scale)
Final R-work = 0.1320, R-free = 0.1731 (no bulk solvent and anisotropic scale)

Start R-work = 0.2988, R-free = 0.2958
Final R-work = 0.1073, R-free = 0.1527