# Date 2008-01-16 Time 05:13:18 PST -0800 (1200489198.27 s)
#phil __OFF__

Command line arguments: "../643.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29999
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 643

-------------------------------------------------------------------------------
  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, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.4607, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.994 1.98222
Completeness in resolution range: 0.969512
Completeness with d_max=infinity: 0.966499

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9940
                             d_min =   1.9822

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, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.994 1.98222
Completeness in resolution range: 0.969512
Completeness with d_max=infinity: 0.966499

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9944 -  4.2414 [2118/2142]  1905   213  10.1%
  bin  2:  4.2414 -  3.3792 [2038/2058]  1835   203  10.0%
  bin  3:  3.3792 -  2.9557 [2012/2031]  1812   200   9.9%
  bin  4:  2.9557 -  2.6872 [2002/2032]  1802   200  10.0%
  bin  5:  2.6872 -  2.4955 [1985/2004]  1785   200  10.1%
  bin  6:  2.4955 -  2.3490 [1957/1982]  1759   198  10.1%
  bin  7:  2.3490 -  2.2317 [1959/1987]  1765   194   9.9%
  bin  8:  2.2317 -  2.1349 [1963/1999]  1769   194   9.9%
  bin  9:  2.1349 -  2.0529 [1944/1986]  1749   195  10.0%
  bin 10:  2.0529 -  1.9822 [1611/1984]  1449   162  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_643/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: 15
        2.42 -     3.04: 2211
        3.04 -     3.66: 4706
        3.66 -     4.28: 9097
        4.28 -     4.90: 12387
  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  70 " - " O   HOH Z 302 "  2.253 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.305 3.040 x,y+1,z
  " O   HOH Z 280 " - " O   HOH Z 438 "  2.318 3.040 -x,y-1/2,-z+1/2
  ... (remaining 28411 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_643/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_643/model_refine_001.geo

CPU time processing inputs: 9.14


============================ 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 86.39 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 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2667   r_free= 0.2615   ksol= 0.00   Bsol= 0.00   scale= 0.995    |
|                                                                             |
| 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:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.906880                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7305 0.99   1381  153 0.2660 0.2576      6.2987      6.2409|
|  2:  4.7305 -  3.7745 0.99   1324  149 0.2099 0.1966       6.275      6.1991|
|  3:  3.7745 -  3.3032 0.99   1298  142 0.2172 0.2167      6.1614      6.2776|
|  4:  3.3032 -  3.0038 0.99   1289  145 0.2344 0.2564      6.0698      6.1358|
|  5:  3.0038 -  2.7900 0.99   1280  143 0.2635 0.2211      5.9552      5.8164|
|  6:  2.7900 -  2.6264 0.99   1298  140 0.2653 0.2759      5.8838      5.8202|
|  7:  2.6264 -  2.4955 0.99   1269  144 0.2735 0.2492      5.8449      5.7811|
|  8:  2.4955 -  2.3873 0.98   1258  138 0.2815 0.2934      5.8295      5.8971|
|  9:  2.3873 -  2.2958 0.98   1263  143 0.2782 0.2909      5.7654      5.7593|
| 10:  2.2958 -  2.2168 1.00   1263  142 0.2944 0.2553      5.7847      5.6402|
| 11:  2.2168 -  2.1477 0.97   1264  136 0.2989 0.3017      5.7406      5.7521|
| 12:  2.1477 -  2.0865 0.98   1238  140 0.3041 0.2926      5.7069      5.7024|
| 13:  2.0865 -  2.0317 0.99   1287  141 0.3079 0.3106      5.6029      5.6096|
| 14:  2.0317 -  1.9822 0.73    918  103 0.3318 0.3115      5.6426      5.5167|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9944 -  4.7305  1381   153  0.81  23.66   0.87     0.83      35737.93|
|  2:  4.7305 -  3.7745  1324   149  0.87  18.85   0.99     0.95      33899.51|
|  3:  3.7745 -  3.3032  1298   142  0.86  20.71   1.02     1.00      30778.63|
|  4:  3.3032 -  3.0038  1289   145  0.85  21.90   1.01     1.00      25742.89|
|  5:  3.0038 -  2.7900  1280   143  0.82  24.94   1.02     0.98      20443.51|
|  6:  2.7900 -  2.6264  1298   140  0.82  24.89   1.02     0.98      17097.80|
|  7:  2.6264 -  2.4955  1269   144  0.80  26.50   1.04     0.99      16302.25|
|  8:  2.4955 -  2.3873  1258   138  0.80  26.73   1.05     0.99      15909.78|
|  9:  2.3873 -  2.2958  1263   143  0.80  27.06   1.06     1.00      15142.58|
| 10:  2.2958 -  2.2168  1263   142  0.79  27.95   1.08     1.02      14067.71|
| 11:  2.2168 -  2.1477  1264   136  0.77  29.49   1.08     1.03      13940.93|
| 12:  2.1477 -  2.0865  1238   140  0.77  29.98   1.09     1.01      13379.93|
| 13:  2.0865 -  2.0317  1287   141  0.74  32.31   1.08     0.99      12090.61|
| 14:  2.0317 -  1.9822   918   103  0.77  30.34   1.09     0.96       9663.73|
|alpha:            min =        0.83 max =            1.03 mean =         0.98|
|beta:             min =     9663.73 max =        35737.93 mean =     19962.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.81|
|phase err.(work): min =        0.00 max =           89.97 mean =        25.95|
|phase err.(test): min =        0.00 max =           89.74 mean =        25.74|
|-----------------------------------------------------------------------------|

============================== 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 = 3.089906              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.369   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.480217              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.133   (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:       14 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      207 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2004 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1857 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2849 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4686 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4411 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5659 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6728 |
|-----------------------------------------------------------------------------|
|-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 |   4.112    4.900  1.806 |       0.158 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    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 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2667   r_free= 0.2615   ksol= 0.00   Bsol= 0.00   scale= 0.995    |
|                                                                             |
| 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:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.906880                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2485   r_free= 0.2439   ksol= 0.33   Bsol= 47.56   scale= 0.983   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.13,0.31,-1.78,0.00,-0.00,-0.00); trace/3= -1.53                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.877957                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.773249              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.448   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.242153              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.088   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2485      final r-factor (work) = 0.1539          |
| start r-factor (free) = 0.2439      final r-factor (free) = 0.1761          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3430 = 2.77 * 0.50 * 5.9010 + 1.00 * 0.1605                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7550 = 2.77 * 0.50 * 5.5507 + 1.00 * 0.0582                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1539      final r-factor (work) = 0.1405          |
| start r-factor (free) = 0.1761      final r-factor (free) = 0.1826          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3501 = 0.24 * 1.00 * 5.5507 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2938 = 0.24 * 1.00 * 5.3114 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.50    66.36   16.78    None  None   None       |
|    all(noH): 2823   0      1.50    66.36   16.78    None  None   None       |
|    Sol.    : 438    0      7.20    66.36   38.02    None  None   None       |
|    Mac.    : 2385   0      1.50    63.28   12.87    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:     1.496 -   7.983:  475   |   5:    33.930 -  40.416:  108        |
|      1:     7.983 -  14.469: 1310   |   6:    40.416 -  46.903:   89        |
|      2:    14.469 -  20.956:  437   |   7:    46.903 -  53.390:   78        |
|      3:    20.956 -  27.443:  152   |   8:    53.390 -  59.877:   51        |
|      4:    27.443 -  33.930:  103   |   9:    59.877 -  66.363:   20        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1405 r_free = 0.1826             target_work(ml) = 5.327         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1403 r_free = 0.1825             target_work(ml) = 5.325         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1403   r_free= 0.1825   ksol= 0.33   Bsol= 47.56   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.13,0.31,-1.78,0.00,-0.00,-0.00); trace/3= -1.53                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.325300                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1390   r_free= 0.1797   ksol= 0.32   Bsol= 48.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.99,-1.98,-1.66,-0.00,-0.00,-0.00); trace/3= -2.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.314076                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.922156              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.991  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.116479              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.469  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1390      final r-factor (work) = 0.1152          |
| start r-factor (free) = 0.1797      final r-factor (free) = 0.1575          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8188 = 2.92 * 0.50 * 5.3116 + 1.00 * 0.0582                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6987 = 2.92 * 0.50 * 5.2280 + 1.00 * 0.0602                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1152      final r-factor (work) = 0.1129          |
| start r-factor (free) = 0.1575      final r-factor (free) = 0.1528          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6166 = 0.12 * 1.00 * 5.2280 + 1.00 * 0.0076                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7205 = 0.12 * 1.00 * 5.1453 + 1.00 * 0.1211                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 7      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    66.93   16.65    None  None   None       |
|    all(noH): 2823   0      0.00    66.93   16.65    None  None   None       |
|    Sol.    : 438    0      6.16    66.93   37.45    None  None   None       |
|    Mac.    : 2385   0      0.00    63.94   12.83    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 -   6.693:  193   |   5:    33.466 -  40.159:  121        |
|      1:     6.693 -  13.386: 1480   |   6:    40.159 -  46.852:   82        |
|      2:    13.386 -  20.079:  532   |   7:    46.852 -  53.545:   85        |
|      3:    20.079 -  26.773:  163   |   8:    53.545 -  60.238:   44        |
|      4:    26.773 -  33.466:  105   |   9:    60.238 -  66.931:   18        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1129 r_free = 0.1528             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1128 r_free = 0.1528             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1128   r_free= 0.1528   ksol= 0.32   Bsol= 48.00   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.99,-1.98,-1.66,-0.00,-0.00,-0.00); trace/3= -2.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.129934                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1126   r_free= 0.1526   ksol= 0.32   Bsol= 48.00   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-2.33,-1.34,-0.00,-0.00,-0.00); trace/3= -2.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.128159                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.112385              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 146.328  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.113375              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.435   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1126      final r-factor (work) = 0.1075          |
| start r-factor (free) = 0.1526      final r-factor (free) = 0.1514          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0658 = 3.11 * 0.50 * 5.1444 + 1.00 * 0.0602                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0184 = 3.11 * 0.50 * 5.1072 + 1.00 * 0.0705                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1075      final r-factor (work) = 0.1051          |
| start r-factor (free) = 0.1514      final r-factor (free) = 0.1516          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7044 = 1.11 * 1.00 * 5.1072 + 1.00 * 0.0182                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6778 = 1.11 * 1.00 * 5.0920 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.26    76.85   16.93    None  None   None       |
|    all(noH): 2823   0      1.26    76.85   16.93    None  None   None       |
|    Sol.    : 438    0      6.55    74.48   39.16    None  None   None       |
|    Mac.    : 2385   0      1.26    76.85   12.84    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:     1.260 -   8.818:  733   |   5:    39.052 -  46.611:  108        |
|      1:     8.818 -  16.377: 1239   |   6:    46.611 -  54.170:   75        |
|      2:    16.377 -  23.935:  331   |   7:    54.170 -  61.728:   68        |
|      3:    23.935 -  31.494:  122   |   8:    61.728 -  69.287:   23        |
|      4:    31.494 -  39.052:  113   |   9:    69.287 -  76.845:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1051 r_free = 0.1516             target_work(ml) = 5.095         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1051 r_free = 0.1517             target_work(ml) = 5.095         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1051   r_free= 0.1517   ksol= 0.32   Bsol= 48.00   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-2.33,-1.34,-0.00,-0.00,-0.00); trace/3= -2.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.095388                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1050   r_free= 0.1518   ksol= 0.32   Bsol= 48.00   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-2.35,-1.17,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.095132                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.778898              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 159.111  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.157434              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.532  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1050      final r-factor (work) = 0.1071          |
| start r-factor (free) = 0.1518      final r-factor (free) = 0.1530          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5991 = 1.78 * 0.50 * 5.0921 + 1.00 * 0.0699                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5944 = 1.78 * 0.50 * 5.1040 + 1.00 * 0.0547                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1071      final r-factor (work) = 0.1081          |
| start r-factor (free) = 0.1530      final r-factor (free) = 0.1526          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8121 = 0.16 * 1.00 * 5.1040 + 1.00 * 0.0085                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8120 = 0.16 * 1.00 * 5.1129 + 1.00 * 0.0071                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.76    76.30   16.38    None  None   None       |
|    all(noH): 2823   0      1.76    76.30   16.38    None  None   None       |
|    Sol.    : 438    0      6.43    74.70   36.88    None  None   None       |
|    Mac.    : 2385   0      1.76    76.30   12.61    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:     1.758 -   9.213:  851   |   5:    39.031 -  46.486:   89        |
|      1:     9.213 -  16.668: 1166   |   6:    46.486 -  53.940:   87        |
|      2:    16.668 -  24.122:  309   |   7:    53.940 -  61.395:   36        |
|      3:    24.122 -  31.577:  130   |   8:    61.395 -  68.850:   17        |
|      4:    31.577 -  39.031:  133   |   9:    68.850 -  76.304:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1081 r_free = 0.1526             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1081 r_free = 0.1526             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1526   ksol= 0.32   Bsol= 48.00   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-2.35,-1.17,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.111765                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1527   ksol= 0.32   Bsol= 44.64   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.41,-2.30,-1.03,-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: 5.112069                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.427900              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 162.850  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.392780              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.159  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1081      final r-factor (work) = 0.1089          |
| start r-factor (free) = 0.1527      final r-factor (free) = 0.1535          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7053 = 1.43 * 0.50 * 5.1132 + 1.00 * 0.0547                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7026 = 1.43 * 0.50 * 5.1155 + 1.00 * 0.0504                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1089      final r-factor (work) = 0.1081          |
| start r-factor (free) = 0.1535      final r-factor (free) = 0.1546          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1319 = 1.39 * 1.00 * 5.1155 + 1.00 * 0.0071                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1309 = 1.39 * 1.00 * 5.1137 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.66    80.84   16.57    None  None   None       |
|    all(noH): 2823   0      0.66    80.84   16.57    None  None   None       |
|    Sol.    : 438    0      6.28    75.30   38.40    None  None   None       |
|    Mac.    : 2385   0      0.66    80.84   12.56    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:     0.656 -   8.674:  779   |   5:    40.748 -  48.766:  106        |
|      1:     8.674 -  16.692: 1245   |   6:    48.766 -  56.785:   84        |
|      2:    16.692 -  24.711:  301   |   7:    56.785 -  64.803:   38        |
|      3:    24.711 -  32.729:  132   |   8:    64.803 -  72.822:   16        |
|      4:    32.729 -  40.748:  118   |   9:    72.822 -  80.840:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1081 r_free = 0.1546             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1081 r_free = 0.1546             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1546   ksol= 0.32   Bsol= 44.64   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.41,-2.30,-1.03,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.120049                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7305 0.99   1381  153 0.0985 0.1271      5.3797      5.5124|
|  2:  4.7305 -  3.7745 0.99   1324  149 0.0843 0.1134      5.4287      5.6278|
|  3:  3.7745 -  3.3032 0.99   1298  142 0.1038 0.1470       5.464      5.8446|
|  4:  3.3032 -  3.0038 0.99   1289  145 0.1186 0.1564       5.437      5.5715|
|  5:  3.0038 -  2.7900 0.99   1280  143 0.1275 0.1686       5.311      5.5506|
|  6:  2.7900 -  2.6264 0.99   1298  140 0.1149 0.1874       5.189      5.4474|
|  7:  2.6264 -  2.4955 0.99   1269  144 0.1248 0.1524       5.148       5.334|
|  8:  2.4955 -  2.3873 0.98   1258  138 0.1111 0.1724      5.0371      5.3341|
|  9:  2.3873 -  2.2958 0.98   1263  143 0.1109 0.1668      5.0011      5.2386|
| 10:  2.2958 -  2.2168 1.00   1263  142 0.1065 0.1678      4.9316      5.2249|
| 11:  2.2168 -  2.1477 0.97   1264  136 0.1084 0.1707       4.909      5.2296|
| 12:  2.1477 -  2.0865 0.98   1238  140 0.1074 0.1652      4.8575      5.1879|
| 13:  2.0865 -  2.0317 0.99   1287  141 0.1043 0.1778      4.7604      5.0716|
| 14:  2.0317 -  1.9822 0.73    918  103 0.0977 0.1688      4.6358      4.8972|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9944 -  4.7305  1381   153  0.94   8.94   0.98     0.95       6883.99|
|  2:  4.7305 -  3.7745  1324   149  0.95   7.68   1.02     1.01       8836.19|
|  3:  3.7745 -  3.3032  1298   142  0.94  10.89   1.02     1.02      10072.83|
|  4:  3.3032 -  3.0038  1289   145  0.92  13.39   1.01     0.99      10035.38|
|  5:  3.0038 -  2.7900  1280   143  0.91  15.31   0.99     0.96       8094.79|
|  6:  2.7900 -  2.6264  1298   140  0.90  15.54   0.98     0.96       6910.15|
|  7:  2.6264 -  2.4955  1269   144  0.91  15.51   0.99     0.96       6016.04|
|  8:  2.4955 -  2.3873  1258   138  0.91  14.47   0.99     0.97       4984.82|
|  9:  2.3873 -  2.2958  1263   143  0.92  14.48   1.00     0.96       4706.02|
| 10:  2.2958 -  2.2168  1263   142  0.91  14.88   1.00     0.96       4175.92|
| 11:  2.2168 -  2.1477  1264   136  0.90  15.92   0.99     0.95       4174.05|
| 12:  2.1477 -  2.0865  1238   140  0.91  14.81   1.00     0.99       3821.82|
| 13:  2.0865 -  2.0317  1287   141  0.91  15.46   0.99     0.97       3231.92|
| 14:  2.0317 -  1.9822   918   103  0.92  13.74   0.97     0.94       2466.65|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2466.65 max =        10072.83 mean =      6131.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.59|
|phase err.(test): min =        0.00 max =           89.95 mean =        13.20|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1080   r_free= 0.1546   ksol= 0.32   Bsol= 45.85   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-2.13,-0.83,-0.00,-0.00,-0.00); trace/3= -1.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.119875                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1080   r_free= 0.1546   ksol= 0.32   Bsol= 45.85   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-2.13,-0.83,-0.00,-0.00,-0.00); trace/3= -1.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.119875                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7305 0.99   1381  153 0.0985 0.1272      5.3797      5.5131|
|  2:  4.7305 -  3.7745 0.99   1324  149 0.0845 0.1135        5.43      5.6285|
|  3:  3.7745 -  3.3032 0.99   1298  142 0.1039 0.1471      5.4645      5.8454|
|  4:  3.3032 -  3.0038 0.99   1289  145 0.1185 0.1563      5.4367      5.5709|
|  5:  3.0038 -  2.7900 0.99   1280  143 0.1274 0.1684      5.3101      5.5494|
|  6:  2.7900 -  2.6264 0.99   1298  140 0.1148 0.1872      5.1882      5.4466|
|  7:  2.6264 -  2.4955 0.99   1269  144 0.1248 0.1524      5.1475      5.3341|
|  8:  2.4955 -  2.3873 0.98   1258  138 0.1111 0.1722      5.0368      5.3327|
|  9:  2.3873 -  2.2958 0.98   1263  143 0.1108 0.1669      5.0009      5.2388|
| 10:  2.2958 -  2.2168 1.00   1263  142 0.1065 0.1677      4.9315      5.2249|
| 11:  2.2168 -  2.1477 0.97   1264  136 0.1084 0.1706      4.9088      5.2293|
| 12:  2.1477 -  2.0865 0.98   1238  140 0.1074 0.1651      4.8572      5.1876|
| 13:  2.0865 -  2.0317 0.99   1287  141 0.1043 0.1777      4.7601      5.0709|
| 14:  2.0317 -  1.9822 0.73    918  103 0.0977 0.1687      4.6354      4.8967|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9944 -  4.7305  1381   153  0.94   8.94   0.98     0.95       6884.72|
|  2:  4.7305 -  3.7745  1324   149  0.95   7.69   1.02     1.01       8847.52|
|  3:  3.7745 -  3.3032  1298   142  0.94  10.90   1.03     1.02      10083.09|
|  4:  3.3032 -  3.0038  1289   145  0.92  13.38   1.01     0.99      10028.22|
|  5:  3.0038 -  2.7900  1280   143  0.91  15.30   1.00     0.97       8080.22|
|  6:  2.7900 -  2.6264  1298   140  0.90  15.53   0.99     0.97       6897.98|
|  7:  2.6264 -  2.4955  1269   144  0.91  15.50   0.99     0.96       6006.86|
|  8:  2.4955 -  2.3873  1258   138  0.91  14.46   1.00     0.98       4979.83|
|  9:  2.3873 -  2.2958  1263   143  0.92  14.48   1.01     0.97       4704.51|
| 10:  2.2958 -  2.2168  1263   142  0.91  14.87   1.01     0.97       4174.20|
| 11:  2.2168 -  2.1477  1264   136  0.90  15.92   1.00     0.96       4172.22|
| 12:  2.1477 -  2.0865  1238   140  0.92  14.79   1.01     1.00       3818.84|
| 13:  2.0865 -  2.0317  1287   141  0.91  15.46   1.00     0.98       3228.34|
| 14:  2.0317 -  1.9822   918   103  0.92  13.73   0.98     0.95       2462.92|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2462.92 max =        10083.09 mean =      6128.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.59|
|phase err.(test): min =        0.00 max =           89.98 mean =        13.20|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.63    80.82   16.55    None  None   None       |
|    all(noH): 2823   0      0.63    80.82   16.55    None  None   None       |
|    Sol.    : 438    0      6.26    75.28   38.38    None  None   None       |
|    Mac.    : 2385   0      0.63    80.82   12.54    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.634 -   8.652:  779   |   5:    40.726 -  48.745:  106        |
|      1:     8.652 -  16.671: 1245   |   6:    48.745 -  56.763:   84        |
|      2:    16.671 -  24.689:  301   |   7:    56.763 -  64.781:   38        |
|      3:    24.689 -  32.708:  132   |   8:    64.781 -  72.800:   16        |
|      4:    32.708 -  40.726:  118   |   9:    72.800 -  80.818:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 299         
Filter by distance & map next to the model:
   mapped sites are within: 0.522 - 4.634
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 294 from: 299
   mapped sites are within: 0.712 - 4.634

peak=    5.893 closest distance to " NH2 ARG A  56 " =    2.193
peak=    5.632 closest distance to " NE2 GLN A  11 " =    1.182
peak=    5.565 closest distance to " CG  PRO A  54 " =    1.294
peak=    5.281 closest distance to " CB  GLN A 223 " =    1.437
peak=    5.275 closest distance to " O   HOH Z 126 " =    1.944
peak=    5.250 closest distance to " CG  PRO A 213 " =    1.243
peak=    5.213 closest distance to " CB  ARG A 275 " =    0.923
peak=    5.038 closest distance to " O   HOH Z 144 " =    1.743
peak=    4.985 closest distance to " O   HOH Z 232 " =    2.395
peak=    4.876 closest distance to " CB  PRO A  54 " =    0.980
peak=    4.783 closest distance to " CB  SER A  63 " =    1.215
peak=    4.700 closest distance to " CB  GLN A 183 " =    1.236
peak=    4.668 closest distance to " CG2 VAL A 257 " =    0.923
peak=    4.608 closest distance to " O   HOH Z 303 " =    2.099
peak=    4.543 closest distance to " O   HOH Z  78 " =    1.741
peak=    4.470 closest distance to " O   HOH Z 287 " =    2.227
peak=    4.465 closest distance to " CG  PRO A 198 " =    1.231
peak=    4.439 closest distance to " O   HOH Z 369 " =    2.152
peak=    4.437 closest distance to " O   HOH Z 427 " =    2.918
peak=    4.416 closest distance to " O   HOH Z 298 " =    1.886
peak=    4.407 closest distance to " O   HOH Z  15 " =    2.338
peak=    4.399 closest distance to " CB  ARG A  79 " =    1.377
peak=    4.393 closest distance to " CA  ASN A 215 " =    1.082
peak=    4.344 closest distance to " CA  TYR A  30 " =    0.937
peak=    4.315 closest distance to " CB  ASN A 148 " =    1.366
peak=    4.300 closest distance to " CB  VAL A 265 " =    1.262
peak=    4.290 closest distance to " CB  GLU A 152 " =    1.271
peak=    4.273 closest distance to " CG  PRO A 243 " =    1.048
peak=    4.251 closest distance to " CB  ARG A 190 " =    1.641
peak=    4.246 closest distance to " CB  LEU A 228 " =    1.110
peak=    4.240 closest distance to " ND2 ASN A 187 " =    1.463
peak=    4.198 closest distance to " C   PRO A 198 " =    1.497
peak=    4.188 closest distance to " O   HOH Z 193 " =    1.829
peak=    4.186 closest distance to " CB  GLU A 128 " =    0.984
peak=    4.152 closest distance to " O   HOH Z 158 " =    3.081
peak=    4.143 closest distance to " O   HOH Z 272 " =    1.819
peak=    4.141 closest distance to " O   HOH Z 250 " =    1.503
peak=    4.120 closest distance to " O   HOH Z 234 " =    3.688
peak=    4.115 closest distance to " O   HOH Z 419 " =    2.111
peak=    4.108 closest distance to " O   HOH Z  61 " =    1.626
peak=    4.098 closest distance to " O   HOH Z 189 " =    2.354
peak=    4.084 closest distance to " O   HOH Z 203 " =    1.774
peak=    4.083 closest distance to " CB  SER A   3 " =    1.264
peak=    4.075 closest distance to " OD1 ASN A  69 " =    2.575
peak=    4.066 closest distance to " CZ  PHE A 218 " =    1.035
peak=    4.065 closest distance to " O   HOH Z 144 " =    2.275
peak=    4.045 closest distance to " NZ  LYS A 117 " =    3.211
peak=    4.027 closest distance to " CE  LYS A  76 " =    0.883
peak=    3.965 closest distance to " O   HOH Z  78 " =    2.128
peak=    3.940 closest distance to " CB  TRP A 266 " =    1.024
peak=    3.923 closest distance to " O   HOH Z  66 " =    2.237
peak=    3.913 closest distance to " CD  ARG A 159 " =    0.732
peak=    3.910 closest distance to " O   HOH Z 316 " =    3.088
peak=    3.909 closest distance to " O   HOH Z   9 " =    2.013
peak=    3.904 closest distance to " O   HOH Z 346 " =    1.680
peak=    3.899 closest distance to " CG1 ILE A  33 " =    1.236
peak=    3.875 closest distance to " CD  ARG A  66 " =    2.429
peak=    3.829 closest distance to " O   HOH Z   1 " =    1.987
peak=    3.815 closest distance to " O   HOH Z 389 " =    1.874
peak=    3.808 closest distance to " O   HOH Z  44 " =    1.755
peak=    3.781 closest distance to " O   HOH Z 344 " =    3.178
peak=    3.772 closest distance to " O   SER A  87 " =    2.138
peak=    3.763 closest distance to " O   HOH Z 368 " =    2.031
peak=    3.756 closest distance to " O   HOH Z 245 " =    1.281
peak=    3.753 closest distance to " O   HOH Z 132 " =    2.461
peak=    3.739 closest distance to " O   HOH Z 402 " =    1.421
peak=    3.728 closest distance to " CB  SER A 212 " =    1.080
peak=    3.725 closest distance to " O   HOH Z 133 " =    2.431
peak=    3.725 closest distance to " O   HOH Z 209 " =    2.244
peak=    3.712 closest distance to " CB  VAL A 202 " =    1.604
peak=    3.711 closest distance to " CD2 TRP A 179 " =    1.340
peak=    3.707 closest distance to " ND1 HIS A  86 " =    1.720
peak=    3.689 closest distance to " O   HOH Z 371 " =    3.034
peak=    3.685 closest distance to " O   HOH Z  43 " =    1.831
peak=    3.685 closest distance to " NH1AARG A 145 " =    1.162
peak=    3.685 closest distance to " CB  SER A 216 " =    0.822
peak=    3.684 closest distance to " O   HOH Z 368 " =    3.596
peak=    3.680 closest distance to " CB  ALA A  34 " =    1.052
peak=    3.676 closest distance to " O   HOH Z  10 " =    1.827
peak=    3.672 closest distance to " O   HOH Z 403 " =    1.633
peak=    3.672 closest distance to " CB  TYR A 116 " =    0.768
peak=    3.665 closest distance to " O   HOH Z  40 " =    1.664
peak=    3.663 closest distance to " O   HOH Z 371 " =    1.757
peak=    3.652 closest distance to " CA  THR A 264 " =    0.846
peak=    3.648 closest distance to " CB  ASP A 140 " =    0.949
peak=    3.648 closest distance to " O   HOH Z 265 " =    2.480
peak=    3.634 closest distance to " CD BLYS A 290 " =    1.122
peak=    3.628 closest distance to " CB  ARG A 139 " =    0.941
peak=    3.625 closest distance to " O   HOH Z 327 " =    1.651
peak=    3.620 closest distance to " CG  LEU A 167 " =    1.234
peak=    3.618 closest distance to " O   HOH Z 392 " =    3.182
peak=    3.606 closest distance to " O   HOH Z 291 " =    1.508
peak=    3.606 closest distance to " O   HOH Z  93 " =    2.479
peak=    3.605 closest distance to " O   HOH Z 172 " =    3.061
peak=    3.602 closest distance to " N   PHE A 130 " =    1.217
peak=    3.596 closest distance to " O   HOH Z 128 " =    2.260
peak=    3.594 closest distance to " CB  ASN A 142 " =    0.998
peak=    3.587 closest distance to " O   HOH Z   1 " =    1.724
peak=    3.587 closest distance to " OD2 ASP A 286 " =    2.778
peak=    3.585 closest distance to " CB  LYS A 117 " =    1.230
peak=    3.584 closest distance to " CD  ARG A  66 " =    2.285
peak=    3.583 closest distance to " O   HOH Z 248 " =    1.582
peak=    3.583 closest distance to " O   HOH Z   3 " =    1.922
peak=    3.564 closest distance to " O   HOH Z 214 " =    2.107
peak=    3.563 closest distance to " O   HOH Z  21 " =    1.752
peak=    3.563 closest distance to " CB  GLU A 277 " =    3.573
peak=    3.557 closest distance to " CD1 ILE A 106 " =    0.768
peak=    3.557 closest distance to " OG BSER A 164 " =    2.275
peak=    3.546 closest distance to " CB  ILE A 120 " =    1.307
peak=    3.545 closest distance to " O   HOH Z 425 " =    2.093
peak=    3.542 closest distance to " CD1 LEU A  96 " =    0.857
peak=    3.539 closest distance to " O   HOH Z  64 " =    2.227
peak=    3.536 closest distance to " O   HOH Z 261 " =    2.264
peak=    3.530 closest distance to " O   HOH Z 193 " =    1.665
peak=    3.520 closest distance to " O   HOH Z 433 " =    1.780
peak=    3.515 closest distance to " CG2 ILE A 120 " =    1.092
peak=    3.515 closest distance to " CB  SER A  62 " =    1.213
peak=    3.514 closest distance to " O   HOH Z 353 " =    2.641
peak=    3.503 closest distance to " CB  ALA A 291 " =    1.298
peak=    3.502 closest distance to " NH1BARG A 145 " =    1.198
peak=    3.502 closest distance to " O   HOH Z 313 " =    1.892
peak=    3.501 closest distance to " CB  ASN A  39 " =    0.846
peak=    3.499 closest distance to " N   ARG A 156 " =    1.312
peak=    3.498 closest distance to " CB  TRP A 179 " =    1.368
peak=    3.497 closest distance to " CG1BVAL A  72 " =    1.554
peak=    3.493 closest distance to " CA  ARG A  36 " =    1.034
peak=    3.488 closest distance to " O   HOH Z 305 " =    3.601
peak=    3.474 closest distance to " CB  THR A 157 " =    1.127
peak=    3.473 closest distance to " CA  ILE A 234 " =    0.956
peak=    3.472 closest distance to " CA  ALA A 233 " =    1.263
peak=    3.471 closest distance to " N   ASN A  39 " =    1.208
peak=    3.466 closest distance to " CB  HIS A 108 " =    0.797
peak=    3.462 closest distance to " CA  THR A 221 " =    0.992
peak=    3.460 closest distance to " O   MET A 105 " =    1.859
peak=    3.458 closest distance to " CG  MET A 113 " =    1.136
peak=    3.458 closest distance to " CA  ALA A 291 " =    0.870
peak=    3.452 closest distance to " CB  ASN A 110 " =    1.105
peak=    3.449 closest distance to " O   HOH Z  88 " =    2.671
peak=    3.448 closest distance to " O   HOH Z  40 " =    2.036
peak=    3.448 closest distance to " O   HOH Z 219 " =    2.133
peak=    3.446 closest distance to " CA  GLY A 241 " =    3.846
peak=    3.445 closest distance to " CA  ALA A  21 " =    1.132
peak=    3.442 closest distance to " CD  LYS A 166 " =    1.241
peak=    3.441 closest distance to " O   HOH Z 213 " =    2.007
peak=    3.438 closest distance to " NH2BARG A 145 " =    2.042
peak=    3.429 closest distance to " O   HOH Z 423 " =    1.783
peak=    3.426 closest distance to " CE1 TYR A 186 " =    1.343
peak=    3.423 closest distance to " O   HOH Z 406 " =    1.546
peak=    3.422 closest distance to " O   HOH Z 147 " =    1.755
peak=    3.419 closest distance to " O   HOH Z  59 " =    1.693
peak=    3.419 closest distance to " CA  ALA A  51 " =    0.876
peak=    3.418 closest distance to " O   HOH Z 180 " =    2.183
peak=    3.416 closest distance to " O   HOH Z 407 " =    2.339
peak=    3.414 closest distance to " CG  LYS A  76 " =    0.988
peak=    3.411 closest distance to " O   ASN A  74 " =    1.578
peak=    3.409 closest distance to " O   THR A 220 " =    1.313
peak=    3.396 closest distance to " OD1BASN A 224 " =    2.306
peak=    3.394 closest distance to " O   HOH Z 280 " =    3.071
peak=    3.392 closest distance to " O   HOH Z 337 " =    3.620
peak=    3.387 closest distance to " CA  SER A  87 " =    1.077
peak=    3.386 closest distance to " O   HOH Z 437 " =    1.502
peak=    3.386 closest distance to " CA  MET A  40 " =    1.070
peak=    3.382 closest distance to " OG  SER A  62 " =    2.875
peak=    3.381 closest distance to " O   HOH Z 148 " =    3.388
peak=    3.377 closest distance to " CB  TYR A 169 " =    1.211
peak=    3.360 closest distance to " O   HOH Z   6 " =    1.994
peak=    3.358 closest distance to " O   HOH Z 128 " =    2.060
peak=    3.357 closest distance to " N   TYR A 116 " =    1.529
peak=    3.356 closest distance to " CG2 THR A 221 " =    1.155
peak=    3.356 closest distance to " CB  GLN A  89 " =    1.386
peak=    3.351 closest distance to " O   HOH Z  53 " =    2.541
peak=    3.349 closest distance to " O   HOH Z 426 " =    1.890
peak=    3.348 closest distance to " CD  ARG A 269 " =    0.963
peak=    3.347 closest distance to " O  BHOH Z 338 " =    2.328
peak=    3.342 closest distance to " CA  ALA A  84 " =    1.339
peak=    3.340 closest distance to " O   HOH Z  97 " =    2.035
peak=    3.339 closest distance to " CA  ARG A 195 " =    1.210
peak=    3.335 closest distance to " CD1 LEU A 300 " =    1.239
peak=    3.333 closest distance to " O   HOH Z 403 " =    1.404
peak=    3.331 closest distance to " CG1 VAL A 153 " =    0.894
peak=    3.323 closest distance to " O   HOH Z 207 " =    1.778
peak=    3.322 closest distance to " O   HOH Z 417 " =    3.125
peak=    3.316 closest distance to " CA  ASN A 217 " =    1.208
peak=    3.309 closest distance to " C   TYR A 214 " =    1.528
peak=    3.309 closest distance to " O   HOH Z 329 " =    3.830
peak=    3.307 closest distance to " O   HOH Z 175 " =    2.121
peak=    3.303 closest distance to " CB  GLU A  46 " =    0.973
peak=    3.301 closest distance to " O   HOH Z 234 " =    1.842
peak=    3.296 closest distance to " NE2 HIS A 207 " =    1.351
peak=    3.291 closest distance to " CA  ALA A 158 " =    1.225
peak=    3.290 closest distance to " O   HOH Z  85 " =    2.237
peak=    3.288 closest distance to " CB  SER A  26 " =    1.622
peak=    3.287 closest distance to " O   HOH Z  61 " =    1.435
peak=    3.287 closest distance to " N   ASN A 127 " =    1.271
peak=    3.287 closest distance to " CB  MET A  40 " =    0.850
peak=    3.287 closest distance to " O   HOH Z 391 " =    2.899
peak=    3.284 closest distance to " O   HOH Z 409 " =    2.662
peak=    3.282 closest distance to " CB  GLN A  88 " =    1.228
peak=    3.280 closest distance to " CB  ALA A 248 " =    1.351
peak=    3.278 closest distance to " CG  ARG A 159 " =    0.840
peak=    3.275 closest distance to " O   HOH Z  44 " =    3.014
peak=    3.273 closest distance to " CB  THR A  31 " =    1.643
peak=    3.272 closest distance to " O   HOH Z 405 " =    1.106
peak=    3.270 closest distance to " O   HOH Z 271 " =    2.347
peak=    3.269 closest distance to " O   HOH Z 286 " =    2.305
peak=    3.267 closest distance to " O   HOH Z 411 " =    1.654
peak=    3.266 closest distance to " NE2 GLN A  73 " =    3.687
peak=    3.264 closest distance to " CB  MET A  47 " =    1.057
peak=    3.264 closest distance to " O   HOH Z 193 " =    1.946
peak=    3.261 closest distance to " OG  SER A  22 " =    2.694
peak=    3.260 closest distance to " CA  GLY A  80 " =    0.777
peak=    3.260 closest distance to " O   HOH Z  96 " =    2.141
peak=    3.254 closest distance to " O   HOH Z 357 " =    1.877
peak=    3.247 closest distance to " CB  SER A 273 " =    0.852
peak=    3.242 closest distance to " O   THR A 251 " =    1.146
peak=    3.236 closest distance to " O   HOH Z 336 " =    1.913
peak=    3.236 closest distance to " CB  SER A 141 " =    1.009
peak=    3.229 closest distance to " CG2BVAL A  41 " =    0.883
peak=    3.229 closest distance to " O   HOH Z 128 " =    2.050
peak=    3.227 closest distance to " O   HOH Z 345 " =    3.430
peak=    3.224 closest distance to " CZ2 TRP A 179 " =    1.754
peak=    3.221 closest distance to " CD  PRO A 243 " =    1.531
peak=    3.213 closest distance to " O   HOH Z  88 " =    2.464
peak=    3.211 closest distance to " CB  ALA A 114 " =    0.798
peak=    3.211 closest distance to " O   HOH Z 273 " =    2.728
peak=    3.208 closest distance to " CE1 PHE A  38 " =    1.295
peak=    3.207 closest distance to " O   HOH Z 325 " =    3.815
peak=    3.206 closest distance to " N   GLN A 278 " =    1.254
peak=    3.204 closest distance to " O   HOH Z 285 " =    2.727
peak=    3.202 closest distance to " O   HOH Z 359 " =    1.411
peak=    3.189 closest distance to " CD1 ILE A 263 " =    1.323
peak=    3.189 closest distance to " O   HOH Z 257 " =    2.212
peak=    3.188 closest distance to " CD1AILE A 234 " =    0.906
peak=    3.188 closest distance to " O   HOH Z 133 " =    1.562
peak=    3.185 closest distance to " ND2 ASN A 249 " =    0.857
peak=    3.183 closest distance to " O   HOH Z 203 " =    1.221
peak=    3.181 closest distance to " CB  LYS A 290 " =    1.004
peak=    3.181 closest distance to " N   ALA A 154 " =    0.881
peak=    3.181 closest distance to " CD2 LEU A 255 " =    1.362
peak=    3.179 closest distance to " O   HOH Z 173 " =    1.861
peak=    3.178 closest distance to " N   TYR A  15 " =    0.741
peak=    3.178 closest distance to " CB  ARG A 138 " =    0.939
peak=    3.178 closest distance to " CA  MET A 105 " =    0.971
peak=    3.177 closest distance to " O   HOH Z 422 " =    2.639
peak=    3.174 closest distance to " O   HOH Z  66 " =    2.001
peak=    3.173 closest distance to " O   HOH Z 298 " =    2.472
peak=    3.173 closest distance to " O   HOH Z 135 " =    1.578
peak=    3.172 closest distance to " O   PRO A  90 " =    1.434
peak=    3.170 closest distance to " CG  MET A 185 " =    1.162
peak=    3.163 closest distance to " O   HOH Z 365 " =    2.851
peak=    3.161 closest distance to " CB  ASN A 215 " =    1.089
peak=    3.157 closest distance to " CB  ALA A   1 " =    4.634
peak=    3.156 closest distance to " CG2 VAL A 197 " =    1.114
peak=    3.152 closest distance to " CA  GLY A 136 " =    1.084
peak=    3.152 closest distance to " CA  LYS A 290 " =    1.272
peak=    3.150 closest distance to " O   HOH Z  62 " =    2.077
peak=    3.147 closest distance to " CB  LEU A 255 " =    0.794
peak=    3.140 closest distance to " O   HOH Z 258 " =    1.610
peak=    3.136 closest distance to " CE AMET A  47 " =    1.356
peak=    3.135 closest distance to " CA  ARG A 102 " =    1.075
peak=    3.134 closest distance to " CB  SER A 210 " =    0.712
peak=    3.132 closest distance to " CG  GLN A  89 " =    1.513
peak=    3.132 closest distance to " O  BHOH Z  74 " =    1.328
peak=    3.131 closest distance to " O   HOH Z 423 " =    1.469
peak=    3.129 closest distance to " O   HOH Z 227 " =    2.078
peak=    3.126 closest distance to " CG2 VAL A  78 " =    0.917
peak=    3.123 closest distance to " O   HOH Z 183 " =    1.287
peak=    3.120 closest distance to " CA  VAL A 125 " =    1.024
peak=    3.117 closest distance to " CD  ARG A  36 " =    1.017
peak=    3.117 closest distance to " CA  GLY A 267 " =    1.249
peak=    3.117 closest distance to " CB  VAL A 268 " =    0.859
peak=    3.115 closest distance to " O   HOH Z 152 " =    1.777
peak=    3.109 closest distance to " O   HOH Z 163 " =    1.642
peak=    3.108 closest distance to " O   HOH Z 380 " =    1.646
peak=    3.103 closest distance to " OG1 THR A 294 " =    1.690
peak=    3.103 closest distance to " O   HOH Z 417 " =    2.022
peak=    3.097 closest distance to " O   HOH Z 124 " =    2.151
peak=    3.091 closest distance to " O   HOH Z 371 " =    3.414
peak=    3.090 closest distance to " O   HOH Z 163 " =    1.815
peak=    3.084 closest distance to " CB  VAL A 126 " =    1.037
peak=    3.083 closest distance to " CB  LEU A 300 " =    0.884
peak=    3.082 closest distance to " CB  ASN A 224 " =    0.936
peak=    3.079 closest distance to " CB  ALA A   9 " =    1.567
peak=    3.070 closest distance to " O   HOH Z 319 " =    2.352
peak=    3.070 closest distance to " O   HOH Z 130 " =    3.801
peak=    3.068 closest distance to " CA  ALA A 248 " =    1.184
peak=    3.067 closest distance to " CG BARG A 102 " =    1.799
peak=    3.061 closest distance to " OG BSER A  99 " =    2.148
peak=    3.060 closest distance to " O   ALA A   1 " =    1.710
peak=    3.052 closest distance to " CA  ALA A 299 " =    0.947
peak=    3.042 closest distance to " O   HOH Z 153 " =    3.843
peak=    3.040 closest distance to " O   HOH Z 342 " =    0.798
peak=    3.030 closest distance to " O   HOH Z 153 " =    1.576
peak=    3.004 closest distance to " CG  LYS A  76 " =    0.941

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 194         
Filter by distance & map next to the model:
   mapped sites are within: 0.736 - 5.657
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 194
   mapped sites are within: 0.736 - 5.657

peak=   -4.589 closest distance to " CB  PRO A 243 " =    2.629
peak=   -4.512 closest distance to " O   HOH Z 266 " =    4.997
peak=   -4.477 closest distance to " CD  ARG A 156 " =    2.028
peak=   -4.333 closest distance to " O   HOH Z 377 " =    2.084
peak=   -4.330 closest distance to " CG  GLN A 223 " =    1.931
peak=   -4.261 closest distance to " OG BSER A 134 " =    1.234
peak=   -4.195 closest distance to " C   HIS A 108 " =    1.075
peak=   -4.188 closest distance to " CG1 VAL A 112 " =    2.894
peak=   -4.188 closest distance to " SG  CYS A 254 " =    3.471
peak=   -4.168 closest distance to " O   PRO A 198 " =    1.235
peak=   -4.124 closest distance to " O   VAL A  67 " =    2.684
peak=   -4.077 closest distance to " O   HOH Z 231 " =    2.209
peak=   -4.063 closest distance to " CZ3 TRP A 179 " =    1.195
peak=   -4.023 closest distance to " O   HOH Z 435 " =    2.866
peak=   -3.994 closest distance to " O   HOH Z 290 " =    1.156
peak=   -3.989 closest distance to " O   HOH Z 313 " =    1.883
peak=   -3.981 closest distance to " N   ALA A  43 " =    2.470
peak=   -3.978 closest distance to " O   VAL A  67 " =    2.913
peak=   -3.973 closest distance to " CD  GLN A  58 " =    1.040
peak=   -3.968 closest distance to " O   HOH Z 389 " =    1.921
peak=   -3.958 closest distance to " CE  MET A 105 " =    2.288
peak=   -3.945 closest distance to " O   HOH Z 372 " =    2.369
peak=   -3.944 closest distance to " CD2 PHE A 192 " =    2.001
peak=   -3.944 closest distance to " CE2 TYR A  30 " =    2.776
peak=   -3.894 closest distance to " ND2 ASN A  45 " =    1.645
peak=   -3.858 closest distance to " CA  GLY A 203 " =    2.309
peak=   -3.855 closest distance to " O   HOH Z 351 " =    1.507
peak=   -3.842 closest distance to " CD  ARG A 139 " =    1.504
peak=   -3.812 closest distance to " O   HOH Z 185 " =    2.208
peak=   -3.795 closest distance to " OD1 ASN A 187 " =    1.581
peak=   -3.764 closest distance to " O   ARG A 145 " =    1.548
peak=   -3.761 closest distance to " CB  ASN A  39 " =    2.263
peak=   -3.750 closest distance to " CZ  TYR A 169 " =    1.609
peak=   -3.746 closest distance to " CB  ALA A 291 " =    2.238
peak=   -3.740 closest distance to " OG  SER A  97 " =    2.157
peak=   -3.738 closest distance to " O   HOH Z 198 " =    1.946
peak=   -3.732 closest distance to " CB  ALA A 161 " =    2.510
peak=   -3.691 closest distance to " ND2 ASN A  45 " =    1.072
peak=   -3.688 closest distance to " CB  ALA A  43 " =    2.549
peak=   -3.679 closest distance to " O   HOH Z 407 " =    3.060
peak=   -3.678 closest distance to " O   HOH Z  13 " =    1.588
peak=   -3.666 closest distance to " CD1 PHE A  59 " =    1.823
peak=   -3.665 closest distance to " CZ  PHE A  59 " =    1.502
peak=   -3.661 closest distance to " OD1 ASN A 148 " =    1.526
peak=   -3.655 closest distance to " O   HOH Z 114 " =    2.986
peak=   -3.633 closest distance to " CG  ASP A 231 " =    0.790
peak=   -3.629 closest distance to " CD2 TYR A 247 " =    2.556
peak=   -3.620 closest distance to " OD2 ASP A 191 " =    1.399
peak=   -3.620 closest distance to " OD1 ASP A 171 " =    1.607
peak=   -3.605 closest distance to " CB  PHE A 208 " =    2.232
peak=   -3.598 closest distance to " O   HOH Z 102 " =    1.555
peak=   -3.590 closest distance to " O   HOH Z  43 " =    1.769
peak=   -3.582 closest distance to " CB  ALA A 291 " =    2.183
peak=   -3.579 closest distance to " N   GLN A  58 " =    1.683
peak=   -3.579 closest distance to " CD2 LEU A 237 " =    2.786
peak=   -3.576 closest distance to " CB  ALA A 248 " =    2.066
peak=   -3.574 closest distance to " CE2 PHE A 218 " =    2.406
peak=   -3.568 closest distance to " O   HOH Z 126 " =    1.877
peak=   -3.564 closest distance to " N   THR A 157 " =    1.488
peak=   -3.556 closest distance to " N   ALA A 248 " =    1.622
peak=   -3.551 closest distance to " CG  PHE A 283 " =    2.704
peak=   -3.551 closest distance to " O   HOH Z 198 " =    1.492
peak=   -3.542 closest distance to " OXT GLY A 302 " =    2.826
peak=   -3.537 closest distance to " CA  GLY A  98 " =    1.844
peak=   -3.520 closest distance to " O   HOH Z 395 " =    5.168
peak=   -3.520 closest distance to " O   HOH Z 353 " =    2.109
peak=   -3.519 closest distance to " O   HOH Z  60 " =    2.221
peak=   -3.510 closest distance to " CG2 ILE A 263 " =    2.303
peak=   -3.504 closest distance to " OD2 ASP A 171 " =    2.306
peak=   -3.492 closest distance to " NH2AARG A 275 " =    5.261
peak=   -3.491 closest distance to " O   MET A  40 " =    2.767
peak=   -3.486 closest distance to " O   SER A 135 " =    1.461
peak=   -3.486 closest distance to " O   HOH Z 211 " =    1.692
peak=   -3.483 closest distance to " O   HOH Z 298 " =    1.247
peak=   -3.469 closest distance to " O   HOH Z  10 " =    1.497
peak=   -3.452 closest distance to " O   HOH Z  63 " =    1.697
peak=   -3.448 closest distance to " NH2BARG A 275 " =    1.825
peak=   -3.442 closest distance to " CB  TYR A  15 " =    2.191
peak=   -3.421 closest distance to " O   HOH Z 317 " =    1.519
peak=   -3.414 closest distance to " OE1 GLN A  88 " =    1.093
peak=   -3.411 closest distance to " O   PHE A 218 " =    1.603
peak=   -3.408 closest distance to " O   HOH Z  38 " =    1.570
peak=   -3.404 closest distance to " O   VAL A 189 " =    2.543
peak=   -3.392 closest distance to " C   LEU A 222 " =    0.736
peak=   -3.385 closest distance to " O   HOH Z 244 " =    2.037
peak=   -3.380 closest distance to " C   LEU A 143 " =    1.099
peak=   -3.378 closest distance to " O   HOH Z 385 " =    1.994
peak=   -3.374 closest distance to " O   HOH Z  11 " =    1.785
peak=   -3.374 closest distance to " CB  PRO A 163 " =    2.468
peak=   -3.369 closest distance to " CB  ALA A 248 " =    2.382
peak=   -3.367 closest distance to " O   ALA A 180 " =    1.126
peak=   -3.366 closest distance to " CB  ASP A 132 " =    2.263
peak=   -3.364 closest distance to " CD2 PHE A 225 " =    1.073
peak=   -3.362 closest distance to " O   PRO A 163 " =    1.994
peak=   -3.360 closest distance to " O   ALA A 161 " =    1.609
peak=   -3.357 closest distance to " O   GLY A 211 " =    1.290
peak=   -3.351 closest distance to " CA  GLY A 133 " =    1.996
peak=   -3.345 closest distance to " CB  ALA A 131 " =    2.102
peak=   -3.341 closest distance to " O   HOH Z 253 " =    3.835
peak=   -3.339 closest distance to " O   HOH Z  51 " =    1.485
peak=   -3.336 closest distance to " C   ALA A 158 " =    1.378
peak=   -3.334 closest distance to " CG  ARG A 269 " =    2.405
peak=   -3.330 closest distance to " CG2 THR A 178 " =    2.215
peak=   -3.325 closest distance to " CG  GLU A 277 " =    1.248
peak=   -3.325 closest distance to " CB  ASP A 286 " =    1.723
peak=   -3.321 closest distance to " O   GLN A 240 " =    2.041
peak=   -3.321 closest distance to " CA  GLY A 241 " =    2.239
peak=   -3.321 closest distance to " ND2 ASN A 249 " =    2.131
peak=   -3.317 closest distance to " O   HOH Z 322 " =    1.588
peak=   -3.316 closest distance to " CB  ASP A 286 " =    2.078
peak=   -3.316 closest distance to " O   HOH Z  73 " =    2.242
peak=   -3.316 closest distance to " OG BSER A 134 " =    1.679
peak=   -3.315 closest distance to " OD2 ASP A 171 " =    1.756
peak=   -3.312 closest distance to " CG  MET A 105 " =    0.937
peak=   -3.311 closest distance to " ND2 ASN A 187 " =    1.509
peak=   -3.302 closest distance to " O   HOH Z 394 " =    1.439
peak=   -3.301 closest distance to " N   ASP A 286 " =    2.395
peak=   -3.298 closest distance to " O   HOH Z 359 " =    3.327
peak=   -3.293 closest distance to " O   HOH Z 339 " =    1.846
peak=   -3.291 closest distance to " O   SER A  95 " =    1.557
peak=   -3.286 closest distance to " O   HOH Z  52 " =    1.322
peak=   -3.282 closest distance to " O   ALA A  10 " =    1.572
peak=   -3.280 closest distance to " O   SER A  22 " =    2.398
peak=   -3.276 closest distance to " OD2 ASP A  50 " =    1.653
peak=   -3.276 closest distance to " O   TRP A  70 " =    1.423
peak=   -3.272 closest distance to " CB  CYS A 201 " =    2.432
peak=   -3.271 closest distance to " O   ALA A  34 " =    2.511
peak=   -3.266 closest distance to " O   HOH Z 191 " =    5.657
peak=   -3.266 closest distance to " O   VAL A 174 " =    2.115
peak=   -3.263 closest distance to " O   HOH Z 165 " =    2.104
peak=   -3.254 closest distance to " CA  ASP A 298 " =    1.066
peak=   -3.251 closest distance to " N   ASN A  60 " =    1.389
peak=   -3.250 closest distance to " CD1 LEU A 297 " =    2.467
peak=   -3.249 closest distance to " O   PRO A 198 " =    1.288
peak=   -3.247 closest distance to " O   HOH Z 426 " =    1.567
peak=   -3.243 closest distance to " O   GLY A  17 " =    1.164
peak=   -3.242 closest distance to " CD2 PHE A  61 " =    2.605
peak=   -3.241 closest distance to " O   GLY A  80 " =    2.425
peak=   -3.239 closest distance to " O   ALA A 292 " =    2.066
peak=   -3.237 closest distance to " CD  GLU A 236 " =    1.061
peak=   -3.236 closest distance to " NH2 ARG A  79 " =    2.019
peak=   -3.233 closest distance to " CG1 VAL A 112 " =    2.591
peak=   -3.229 closest distance to " CE3 TRP A 150 " =    2.125
peak=   -3.216 closest distance to " O   HOH Z 298 " =    2.421
peak=   -3.216 closest distance to " CB  TRP A  85 " =    2.413
peak=   -3.214 closest distance to " OH  TYR A 214 " =    1.211
peak=   -3.212 closest distance to " O   HOH Z 140 " =    1.712
peak=   -3.206 closest distance to " CD1 LEU A 228 " =    2.183
peak=   -3.202 closest distance to " N   SER A 212 " =    1.932
peak=   -3.202 closest distance to " NE  ARG A  36 " =    1.990
peak=   -3.196 closest distance to " CA  TRP A 274 " =    1.464
peak=   -3.195 closest distance to " O   HOH Z 357 " =    2.062
peak=   -3.193 closest distance to " O   HOH Z 266 " =    4.754
peak=   -3.191 closest distance to " O   VAL A 189 " =    1.597
peak=   -3.191 closest distance to " N   THR A  52 " =    1.741
peak=   -3.187 closest distance to " OG  SER A 206 " =    1.749
peak=   -3.183 closest distance to " CB  ASP A 132 " =    2.353
peak=   -3.180 closest distance to " O   HOH Z   6 " =    1.453
peak=   -3.176 closest distance to " CG  LEU A  83 " =    1.884
peak=   -3.176 closest distance to " CA  GLY A 241 " =    3.223
peak=   -3.171 closest distance to " O   HOH Z 282 " =    1.304
peak=   -3.170 closest distance to " CA  TYR A  30 " =    2.934
peak=   -3.168 closest distance to " OG  SER A  87 " =    1.354
peak=   -3.162 closest distance to " NH1 ARG A 195 " =    2.591
peak=   -3.161 closest distance to " C   MET A 188 " =    1.372
peak=   -3.159 closest distance to " O   HOH Z  51 " =    1.336
peak=   -3.148 closest distance to " CA  ILE A 263 " =    0.965
peak=   -3.147 closest distance to " O   HOH Z 281 " =    2.715
peak=   -3.145 closest distance to " O   HOH Z  93 " =    2.362
peak=   -3.141 closest distance to " O   HOH Z 263 " =    3.035
peak=   -3.139 closest distance to " CG1 VAL A 125 " =    1.913
peak=   -3.135 closest distance to " CG  TRP A 266 " =    1.965
peak=   -3.130 closest distance to " CB  GLN A  11 " =    1.712
peak=   -3.127 closest distance to " N   TYR A  68 " =    3.184
peak=   -3.125 closest distance to " OD1AASN A 224 " =    1.821
peak=   -3.125 closest distance to " CG1 VAL A 250 " =    2.642
peak=   -3.120 closest distance to " O   HOH Z 134 " =    3.051
peak=   -3.117 closest distance to " O   HOH Z 423 " =    1.181
peak=   -3.115 closest distance to " OXT GLY A 302 " =    3.456
peak=   -3.112 closest distance to " O   HOH Z 311 " =    3.614
peak=   -3.106 closest distance to " CD2 TYR A 293 " =    1.923
peak=   -3.106 closest distance to " OG1 THR A 246 " =    1.379
peak=   -3.104 closest distance to " O   GLU A 152 " =    1.373
peak=   -3.103 closest distance to " CG  GLU A 152 " =    1.223
peak=   -3.087 closest distance to " OD1 ASP A 200 " =    1.407
peak=   -3.085 closest distance to " O   HOH Z 417 " =    2.664
peak=   -3.080 closest distance to " NE2 GLN A  58 " =    2.505
peak=   -3.079 closest distance to " O   HOH Z 137 " =    1.513
peak=   -3.074 closest distance to " NH2 ARG A  79 " =    1.581
peak=   -3.066 closest distance to " O   HOH Z 365 " =    1.940
peak=   -3.060 closest distance to " CA  GLY A  57 " =    2.070
peak=   -3.057 closest distance to " CG  PHE A 283 " =    2.679
peak=   -3.007 closest distance to " O   HOH Z 283 " =    5.641

================= 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    :  0.2667 0.2615   5.906880e+00   5.878911e+00
   1_bss:  0.2485 0.2439   5.877957e+00   5.840136e+00
   1_xyz:  0.1539 0.1761   5.378813e+00   5.490147e+00
   1_adp:  0.1405 0.1826   5.326699e+00   5.525204e+00
   1_occ:  0.1403 0.1825   5.325300e+00   5.524118e+00
   2_bss:  0.1390 0.1797   5.314076e+00   5.510734e+00
   2_xyz:  0.1152 0.1575   5.153753e+00   5.385112e+00
   2_adp:  0.1129 0.1528   5.130378e+00   5.357456e+00
   2_occ:  0.1128 0.1528   5.129934e+00   5.357425e+00
   3_bss:  0.1126 0.1526   5.128159e+00   5.356012e+00
   3_xyz:  0.1075 0.1514   5.103182e+00   5.352123e+00
   3_adp:  0.1051 0.1516   5.095427e+00   5.354038e+00
   3_occ:  0.1051 0.1517   5.095388e+00   5.354193e+00
   4_bss:  0.1050 0.1518   5.095132e+00   5.352496e+00
   4_xyz:  0.1071 0.1530   5.108762e+00   5.361324e+00
   4_adp:  0.1081 0.1526   5.111806e+00   5.359697e+00
   4_occ:  0.1081 0.1526   5.111765e+00   5.359763e+00
   5_bss:  0.1081 0.1527   5.112069e+00   5.360262e+00
   5_xyz:  0.1089 0.1535   5.118923e+00   5.366322e+00
   5_adp:  0.1081 0.1546   5.120155e+00   5.374460e+00
   5_occ:  0.1081 0.1546   5.120049e+00   5.374370e+00
   5_bss:  0.1080 0.1546   5.119875e+00   5.374153e+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:  0.334  47.563  -3.132   0.307  -1.778   0.000  -0.000  -0.000
   1_xyz:  0.334  47.563  -3.132   0.307  -1.778   0.000  -0.000  -0.000
   1_adp:  0.334  47.563  -3.132   0.307  -1.778   0.000  -0.000  -0.000
   1_occ:  0.334  47.563  -3.132   0.307  -1.778   0.000  -0.000  -0.000
   2_bss:  0.324  48.001  -2.995  -1.981  -1.659  -0.000  -0.000  -0.000
   2_xyz:  0.324  48.001  -2.995  -1.981  -1.659  -0.000  -0.000  -0.000
   2_adp:  0.324  48.001  -2.995  -1.981  -1.659  -0.000  -0.000  -0.000
   2_occ:  0.324  48.001  -2.995  -1.981  -1.659  -0.000  -0.000  -0.000
   3_bss:  0.325  48.001  -2.744  -2.326  -1.343  -0.000  -0.000  -0.000
   3_xyz:  0.325  48.001  -2.744  -2.326  -1.343  -0.000  -0.000  -0.000
   3_adp:  0.325  48.001  -2.744  -2.326  -1.343  -0.000  -0.000  -0.000
   3_occ:  0.325  48.001  -2.744  -2.326  -1.343  -0.000  -0.000  -0.000
   4_bss:  0.323  48.000  -2.535  -2.347  -1.167  -0.000  -0.000  -0.000
   4_xyz:  0.323  48.000  -2.535  -2.347  -1.167  -0.000  -0.000  -0.000
   4_adp:  0.323  48.000  -2.535  -2.347  -1.167  -0.000  -0.000  -0.000
   4_occ:  0.323  48.000  -2.535  -2.347  -1.167  -0.000  -0.000  -0.000
   5_bss:  0.321  44.641  -2.412  -2.298  -1.027  -0.000  -0.000  -0.000
   5_xyz:  0.321  44.641  -2.412  -2.298  -1.027  -0.000  -0.000  -0.000
   5_adp:  0.321  44.641  -2.412  -2.298  -1.027  -0.000  -0.000  -0.000
   5_occ:  0.321  44.641  -2.412  -2.298  -1.027  -0.000  -0.000  -0.000
   5_bss:  0.319  45.846  -2.190  -2.126  -0.833  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  25.931 0.8063  0.9798    19963.137
   1_bss:  24.583 0.8181  0.9396    16873.594
   1_xyz:  15.986 0.8994  0.9943     7898.984
   1_adp:  16.828 0.8916  0.9895     8415.228
   1_occ:  16.811 0.8917  0.9893     8387.098
   2_bss:  16.442 0.8949  0.9696     8128.052
   2_xyz:  13.946 0.9151  0.9797     6246.239
   2_adp:  13.378 0.9196  0.9786     5961.219
   2_occ:  13.380 0.9196  0.9785     5956.549
   3_bss:  13.344 0.9199  0.9817     5940.779
   3_xyz:  13.139 0.9218  0.9820     5901.206
   3_adp:  13.201 0.9214  0.9759     5890.132
   3_occ:  13.203 0.9214  0.9758     5892.595
   4_bss:  13.188 0.9214  0.9802     5865.624
   4_xyz:  13.321 0.9206  0.9791     5980.764
   4_adp:  13.279 0.9209  0.9747     5979.564
   4_occ:  13.283 0.9208  0.9746     5979.729
   5_bss:  13.294 0.9208  0.9782     5984.409
   5_xyz:  13.389 0.9202  0.9781     6063.541
   5_adp:  13.555 0.9189  0.9713     6132.001
   5_occ:  13.553 0.9189  0.9712     6131.713
   5_bss:  13.548 0.9189  0.9775     6128.855
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6051e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6051e-01
   1_xyz:   0.967  0.007  0.069 15.123  0.004  4.109   5.8221e-02
   1_adp:   0.967  0.007  0.069 15.123  0.004  4.109   5.8221e-02
   1_occ:   0.967  0.007  0.069 15.123  0.004  4.109   5.8221e-02
   2_bss:   0.967  0.007  0.069 15.123  0.004  4.109   5.8221e-02
   2_xyz:   0.998  0.007  0.075 15.029  0.004  4.108   6.0159e-02
   2_adp:   0.998  0.007  0.075 15.029  0.004  4.108   6.0159e-02
   2_occ:   0.998  0.007  0.075 15.029  0.004  4.108   6.0159e-02
   3_bss:   0.998  0.007  0.075 15.029  0.004  4.108   6.0159e-02
   3_xyz:   1.066  0.009  0.083 15.177  0.004  4.109   7.0546e-02
   3_adp:   1.066  0.009  0.083 15.177  0.004  4.109   7.0546e-02
   3_occ:   1.066  0.009  0.083 15.177  0.004  4.109   7.0546e-02
   4_bss:   1.066  0.009  0.083 15.177  0.004  4.109   7.0546e-02
   4_xyz:   0.929  0.006  0.072 14.841  0.004  4.113   5.4663e-02
   4_adp:   0.929  0.006  0.072 14.841  0.004  4.113   5.4663e-02
   4_occ:   0.929  0.006  0.072 14.841  0.004  4.113   5.4663e-02
   5_bss:   0.929  0.006  0.072 14.841  0.004  4.113   5.4663e-02
   5_xyz:   0.886  0.005  0.070 14.687  0.003  4.113   5.0380e-02
   5_adp:   0.886  0.005  0.070 14.687  0.003  4.113   5.0380e-02
   5_occ:   0.886  0.005  0.070 14.687  0.003  4.113   5.0380e-02
   5_bss:   0.886  0.005  0.070 14.687  0.003  4.113   5.0380e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4005e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4005e-01
   1_xyz:   7.226  0.049  0.251 85.019  0.042  2.282   5.5233e-02
   1_adp:   7.226  0.049  0.251 85.019  0.042  2.282   5.5233e-02
   1_occ:   7.226  0.049  0.251 85.019  0.042  2.282   5.5233e-02
   2_bss:   7.226  0.049  0.251 85.019  0.042  2.282   5.5233e-02
   2_xyz:   7.103  0.042  0.237 84.386  0.029  2.323   4.5594e-02
   2_adp:   7.103  0.042  0.237 84.386  0.029  2.323   4.5594e-02
   2_occ:   7.103  0.042  0.237 84.386  0.029  2.323   4.5594e-02
   3_bss:   7.103  0.042  0.237 84.386  0.029  2.323   4.5594e-02
   3_xyz:   6.524  0.048  0.276 84.495  0.037  2.249   5.9291e-02
   3_adp:   6.524  0.048  0.276 84.495  0.037  2.249   5.9291e-02
   3_occ:   6.524  0.048  0.276 84.495  0.037  2.249   5.9291e-02
   4_bss:   6.524  0.048  0.276 84.495  0.037  2.249   5.9291e-02
   4_xyz:   6.586  0.041  0.224 84.032  0.034  2.366   3.7797e-02
   4_adp:   6.586  0.041  0.224 84.032  0.034  2.366   3.7797e-02
   4_occ:   6.586  0.041  0.224 84.032  0.034  2.366   3.7797e-02
   5_bss:   6.586  0.041  0.224 84.032  0.034  2.366   3.7797e-02
   5_xyz:   6.591  0.040  0.223 84.165  0.032  2.332   2.9934e-02
   5_adp:   6.591  0.040  0.223 84.165  0.032  2.332   2.9934e-02
   5_occ:   6.591  0.040  0.223 84.165  0.032  2.332   2.9934e-02
   5_bss:   6.591  0.040  0.223 84.165  0.032  2.332   2.9934e-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:  66.36   1.50  16.78  63.28   1.50  12.87  66.36   7.20  38.02
   1_occ:  66.36   1.50  16.78  63.28   1.50  12.87  66.36   7.20  38.02
   2_bss:  66.36   1.50  16.78  63.28   1.50  12.87  66.36   7.20  38.02
   2_xyz:  66.36   1.50  16.78  63.28   1.50  12.87  66.36   7.20  38.02
   2_adp:  66.93   0.00  16.65  63.94   0.00  12.83  66.93   6.16  37.45
   2_occ:  66.93   0.00  16.65  63.94   0.00  12.83  66.93   6.16  37.45
   3_bss:  66.93   0.00  16.65  63.94   0.00  12.83  66.93   6.16  37.45
   3_xyz:  66.93   0.00  16.65  63.94   0.00  12.83  66.93   6.16  37.45
   3_adp:  76.85   1.26  16.93  76.85   1.26  12.84  74.48   6.55  39.16
   3_occ:  76.85   1.26  16.93  76.85   1.26  12.84  74.48   6.55  39.16
   4_bss:  76.85   1.26  16.93  76.85   1.26  12.84  74.48   6.55  39.16
   4_xyz:  76.85   1.26  16.93  76.85   1.26  12.84  74.48   6.55  39.16
   4_adp:  76.30   1.76  16.38  76.30   1.76  12.61  74.70   6.43  36.88
   4_occ:  76.30   1.76  16.38  76.30   1.76  12.61  74.70   6.43  36.88
   5_bss:  76.30   1.76  16.38  76.30   1.76  12.61  74.70   6.43  36.88
   5_xyz:  76.30   1.76  16.38  76.30   1.76  12.61  74.70   6.43  36.88
   5_adp:  80.84   0.66  16.57  80.84   0.66  12.56  75.30   6.28  38.40
   5_occ:  80.84   0.66  16.57  80.84   0.66  12.56  75.30   6.28  38.40
   5_bss:  80.82   0.63  16.55  80.82   0.63  12.54  75.28   6.26  38.38
------------------------------------------------------------------------
 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:    0.811    0.010    0.249
   1_adp:    0.811    0.010    0.249
   1_occ:    0.811    0.010    0.249
   2_bss:    0.811    0.010    0.249
   2_xyz:    0.687    0.013    0.291
   2_adp:    0.687    0.013    0.291
   2_occ:    0.687    0.013    0.291
   3_bss:    0.687    0.013    0.291
   3_xyz:    0.943    0.020    0.312
   3_adp:    0.943    0.020    0.312
   3_occ:    0.943    0.020    0.312
   4_bss:    0.943    0.020    0.312
   4_xyz:    1.056    0.039    0.317
   4_adp:    1.056    0.039    0.317
   4_occ:    1.056    0.039    0.317
   5_bss:    1.056    0.039    0.317
   5_xyz:    1.147    0.043    0.321
   5_adp:    1.147    0.043    0.321
   5_occ:    1.147    0.043    0.321
   5_bss:    1.147    0.043    0.321
------------------------------------------------------------------------

CPU time actual refinement: 314.70


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_643/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_643/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_643/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_643/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_643/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 314.55 
  Macro-tasks:
    bulk solvent and scale       = 36.59  
    individual site refinement   = 124.62 
    weights calculation          = 29.45  
    collect and process          = 6.70   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 197.46 
  Micro-tasks:
    mask                            = 1.17   
    f_calc                          = 99.85  
    alpha_beta                      = 8.16   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 107.76 
    fmodel                         = 6.52   
    r_factors                      = 0.12   
    phase_errors                   = 11.32  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 236.39 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.535 micro seconds
Total CPU time: 5.47 minutes
from_scatterers_fft:    628 calls, 99.52 s
gradients_fft:          573 calls, 94.82 s

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

# Date 2008-01-16 Time 05:18:47 PST -0800 (1200489527.69 s)
Start R-work = 0.2667, R-free = 0.2615 (no bulk solvent and anisotropic scale)
Final R-work = 0.1320, R-free = 0.1739 (no bulk solvent and anisotropic scale)

Start R-work = 0.2485, R-free = 0.2439
Final R-work = 0.1080, R-free = 0.1546