# Date 2008-01-16 Time 05:10:11 PST -0800 (1200489011.90 s)
#phil __OFF__

Command line arguments: "../620.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 9550
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 620

-------------------------------------------------------------------------------
  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, 45.9914, 85.9581, 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: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 45.9914, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9735 1.96285
Completeness in resolution range: 0.955981
Completeness with d_max=infinity: 0.953097

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9735
                             d_min =   1.9628

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, 45.9914, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9735 1.96285
Completeness in resolution range: 0.955981
Completeness with d_max=infinity: 0.953097

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9740 -  4.2006 [2154/2179]  1939   215  10.0%
  bin  2:  4.2006 -  3.3464 [2052/2072]  1847   205  10.0%
  bin  3:  3.3464 -  2.9270 [2060/2079]  1851   209  10.1%
  bin  4:  2.9270 -  2.6610 [2008/2038]  1811   197   9.8%
  bin  5:  2.6610 -  2.4712 [2023/2042]  1824   199   9.8%
  bin  6:  2.4712 -  2.3260 [1999/2024]  1792   207  10.4%
  bin  7:  2.3260 -  2.2099 [1980/2008]  1783   197   9.9%
  bin  8:  2.2099 -  2.1140 [1993/2029]  1797   196   9.8%
  bin  9:  2.1140 -  2.0328 [1961/2003]  1761   200  10.2%
  bin 10:  2.0328 -  1.9628 [1359/2017]  1225   134   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_620/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: 0.15 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: 37
        2.42 -     3.04: 2239
        3.04 -     3.66: 4758
        3.66 -     4.28: 9138
        4.28 -     4.90: 12450
  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
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.883 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 302 " - " O   HOH Z  70 "  1.883 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  ... (remaining 28617 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_620/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_620/model_refine_001.geo

CPU time processing inputs: 9.63


============================ 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 45.9914 85.95805 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: 1.96 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3860   r_free= 0.3821   ksol= 0.00   Bsol= 0.00   scale= 0.944    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.194014                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9740 -  4.6854 0.99   1397  155 0.3290 0.3283      6.4712      6.4596|
|  2:  4.6854 -  3.7380 0.99   1346  152 0.3209 0.2997      6.6705        6.58|
|  3:  3.7380 -  3.2711 0.99   1319  141 0.3477 0.3236      6.5636      6.6296|
|  4:  3.2711 -  2.9746 0.99   1314  152 0.3617 0.3818      6.4197      6.4227|
|  5:  2.9746 -  2.7628 0.99   1307  147 0.4069 0.3697      6.2804      6.2478|
|  6:  2.7628 -  2.6008 0.99   1301  136 0.4058 0.4330      6.1881      6.1524|
|  7:  2.6008 -  2.4712 0.99   1288  142 0.4075 0.4229      6.1568      6.1309|
|  8:  2.4712 -  2.3640 0.98   1270  145 0.4280 0.4295      6.1059      6.1151|
|  9:  2.3640 -  2.2734 0.98   1266  147 0.4208 0.4434      6.0567      6.0971|
| 10:  2.2734 -  2.1952 1.00   1301  146 0.4192 0.4156      6.0191      5.9973|
| 11:  2.1952 -  2.1267 0.98   1272  136 0.4193 0.4404      5.9635      6.0218|
| 12:  2.1267 -  2.0661 0.98   1256  139 0.4263 0.4097      5.9236       5.939|
| 13:  2.0661 -  2.0118 0.99   1280  140 0.4394 0.4274      5.8126      5.7614|
| 14:  2.0118 -  1.9628 0.55    713   81 0.4775 0.4431      5.8638      5.7657|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9740 -  4.6854  1397   155  0.75  29.85   0.85     0.79      56809.15|
|  2:  4.6854 -  3.7380  1346   152  0.78  27.82   0.94     0.89      72753.92|
|  3:  3.7380 -  3.2711  1319   141  0.72  34.11   0.97     0.90      75648.77|
|  4:  3.2711 -  2.9746  1314   152  0.66  39.00   0.98     0.85      69361.20|
|  5:  2.9746 -  2.7628  1307   147  0.59  44.99   0.94     0.80      56419.00|
|  6:  2.7628 -  2.6008  1301   136  0.57  46.41   0.94     0.76      50320.86|
|  7:  2.6008 -  2.4712  1288   142  0.55  48.19   0.98     0.74      46964.50|
|  8:  2.4712 -  2.3640  1270   145  0.53  49.62   0.97     0.74      43554.44|
|  9:  2.3640 -  2.2734  1266   147  0.55  48.35   0.98     0.76      38929.26|
| 10:  2.2734 -  2.1952  1301   146  0.56  47.30   1.00     0.79      33859.64|
| 11:  2.1952 -  2.1267  1272   136  0.55  48.24   1.03     0.81      32705.08|
| 12:  2.1267 -  2.0661  1256   139  0.55  48.18   1.02     0.80      29432.92|
| 13:  2.0661 -  2.0118  1280   140  0.52  51.05   1.00     0.78      25457.98|
| 14:  2.0118 -  1.9628   713    81  0.58  46.30   1.01     0.80      20075.38|
|alpha:            min =        0.74 max =            0.90 mean =         0.80|
|beta:             min =    20075.38 max =        75648.77 mean =     47761.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.61|
|phase err.(work): min =        0.00 max =           89.99 mean =        43.26|
|phase err.(test): min =        0.00 max =           89.94 mean =        43.48|
|-----------------------------------------------------------------------------|

============================== 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 = 8.678335              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.182   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.261207              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.186   (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:       11 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       26 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      205 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2034 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1894 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2864 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4697 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4441 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5688 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6762 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.171 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.806 |       0.326 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.602)------------------------------------------|
|    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: 1.96 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3860   r_free= 0.3821   ksol= 0.00   Bsol= 0.00   scale= 0.944    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.194014                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3702   r_free= 0.3693   ksol= 0.36   Bsol= 50.00   scale= 0.957   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.29,3.62,-1.72,0.00,-0.00,-0.00); trace/3= -0.46                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.176820                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.569970              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.178   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.672891              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.151   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3702      final r-factor (work) = 0.2602          |
| start r-factor (free) = 0.3693      final r-factor (free) = 0.2959          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.5533 = 7.57 * 0.50 * 6.1777 + 1.00 * 0.1710                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.7411 = 7.57 * 0.50 * 5.9764 + 1.00 * 0.1205                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2602      final r-factor (work) = 0.2371          |
| start r-factor (free) = 0.2959      final r-factor (free) = 0.3096          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0275 = 0.67 * 1.00 * 5.9764 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9190 = 0.67 * 1.00 * 5.8051 + 1.00 * 0.0128                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.602)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.21   17.61    None  None   None       |
|    all(noH): 2823   0      0.00    89.21   17.61    None  None   None       |
|    Sol.    : 438    0      4.27    89.21   39.86    None  None   None       |
|    Mac.    : 2385   0      0.00    71.77   13.52    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.922:  806   |   5:    44.608 -  53.529:  115        |
|      1:     8.922 -  17.843: 1102   |   6:    53.529 -  62.450:   68        |
|      2:    17.843 -  26.765:  399   |   7:    62.450 -  71.372:   21        |
|      3:    26.765 -  35.686:  170   |   8:    71.372 -  80.293:    5        |
|      4:    35.686 -  44.608:  136   |   9:    80.293 -  89.215:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2371 r_free = 0.3096             target_work(ml) = 5.821         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2369 r_free = 0.3091             target_work(ml) = 5.820         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2369   r_free= 0.3091   ksol= 0.36   Bsol= 50.00   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.29,3.62,-1.72,0.00,-0.00,-0.00); trace/3= -0.46                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.819953                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2340   r_free= 0.3030   ksol= 0.34   Bsol= 50.27   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,-0.24,-1.15,-0.00,-0.00,-0.00); trace/3= -1.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.806224                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.611133              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.220   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.211786              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.692  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2340      final r-factor (work) = 0.1682          |
| start r-factor (free) = 0.3030      final r-factor (free) = 0.2158          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.4936 = 4.61 * 0.50 * 5.8003 + 1.00 * 0.1205                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.1627 = 4.61 * 0.50 * 5.6805 + 1.00 * 0.0659                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1682      final r-factor (work) = 0.1510          |
| start r-factor (free) = 0.2158      final r-factor (free) = 0.1964          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2157 = 0.21 * 1.00 * 5.6805 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1600 = 0.21 * 1.00 * 5.4406 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.602)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.12   17.03    None  None   None       |
|    all(noH): 2823   0      0.00    83.12   17.03    None  None   None       |
|    Sol.    : 438    0      6.67    83.12   39.15    None  None   None       |
|    Mac.    : 2385   0      0.00    74.27   12.97    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.312:  609   |   5:    41.561 -  49.873:  123        |
|      1:     8.312 -  16.624: 1364   |   6:    49.873 -  58.185:   82        |
|      2:    16.624 -  24.937:  344   |   7:    58.185 -  66.497:   33        |
|      3:    24.937 -  33.249:  143   |   8:    66.497 -  74.810:    8        |
|      4:    33.249 -  41.561:  116   |   9:    74.810 -  83.122:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1510 r_free = 0.1964             target_work(ml) = 5.396         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1508 r_free = 0.1963             target_work(ml) = 5.396         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1508   r_free= 0.1963   ksol= 0.34   Bsol= 50.27   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,-0.24,-1.15,-0.00,-0.00,-0.00); trace/3= -1.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.395622                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1500   r_free= 0.1947   ksol= 0.34   Bsol= 50.27   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-1.79,-1.10,-0.00,-0.00,-0.00); trace/3= -1.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.387812                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.794238              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.040   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.241976              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.195  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1500      final r-factor (work) = 0.1238          |
| start r-factor (free) = 0.1947      final r-factor (free) = 0.1690          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6650 = 2.79 * 0.50 * 5.4391 + 1.00 * 0.0659                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4654 = 2.79 * 0.50 * 5.3023 + 1.00 * 0.0575                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1238      final r-factor (work) = 0.1187          |
| start r-factor (free) = 0.1690      final r-factor (free) = 0.1642          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2907 = 0.24 * 1.00 * 5.3023 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2667 = 0.24 * 1.00 * 5.2027 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.602)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.58    81.81   16.90    None  None   None       |
|    all(noH): 2823   0      0.58    81.81   16.90    None  None   None       |
|    Sol.    : 438    0      4.93    81.81   39.50    None  None   None       |
|    Mac.    : 2385   0      0.58    79.01   12.75    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:     0.579 -   8.702:  689   |   5:    41.196 -  49.319:  101        |
|      1:     8.702 -  16.826: 1330   |   6:    49.319 -  57.443:   92        |
|      2:    16.826 -  24.949:  307   |   7:    57.443 -  65.566:   41        |
|      3:    24.949 -  33.073:  136   |   8:    65.566 -  73.690:   14        |
|      4:    33.073 -  41.196:  108   |   9:    73.690 -  81.813:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1187 r_free = 0.1642             target_work(ml) = 5.187         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1186 r_free = 0.1642             target_work(ml) = 5.187         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1186   r_free= 0.1642   ksol= 0.34   Bsol= 50.27   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-1.79,-1.10,-0.00,-0.00,-0.00); trace/3= -1.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.186990                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1189   r_free= 0.1643   ksol= 0.34   Bsol= 50.27   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.54,-2.41,-1.34,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.187692                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.397449              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.265  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.408542              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.119  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1189      final r-factor (work) = 0.1097          |
| start r-factor (free) = 0.1643      final r-factor (free) = 0.1560          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8991 = 3.40 * 0.50 * 5.2049 + 1.00 * 0.0575                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8218 = 3.40 * 0.50 * 5.1535 + 1.00 * 0.0673                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1097      final r-factor (work) = 0.1080          |
| start r-factor (free) = 0.1560      final r-factor (free) = 0.1552          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1132 = 0.41 * 1.00 * 5.1535 + 1.00 * 0.0078                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0997 = 0.41 * 1.00 * 5.1192 + 1.00 * 0.0083                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.602)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.61    84.80   16.87    None  None   None       |
|    all(noH): 2823   0      0.61    84.80   16.87    None  None   None       |
|    Sol.    : 438    0      5.92    82.98   39.55    None  None   None       |
|    Mac.    : 2385   0      0.61    84.80   12.71    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:     0.607 -   9.026:  815   |   5:    42.702 -  51.121:   90        |
|      1:     9.026 -  17.445: 1242   |   6:    51.121 -  59.540:   81        |
|      2:    17.445 -  25.864:  287   |   7:    59.540 -  67.959:   37        |
|      3:    25.864 -  34.283:  139   |   8:    67.959 -  76.378:   12        |
|      4:    34.283 -  42.702:  114   |   9:    76.378 -  84.797:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1080 r_free = 0.1552             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1079 r_free = 0.1552             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1079   r_free= 0.1552   ksol= 0.34   Bsol= 50.27   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.54,-2.41,-1.34,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.118066                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1079   r_free= 0.1552   ksol= 0.34   Bsol= 50.27   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-2.43,-1.19,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.117797                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.016785              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 154.082  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.185834              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.315  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1079      final r-factor (work) = 0.1088          |
| start r-factor (free) = 0.1552      final r-factor (free) = 0.1547          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2296 = 2.02 * 0.50 * 5.1193 + 1.00 * 0.0673                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2199 = 2.02 * 0.50 * 5.1224 + 1.00 * 0.0545                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1093          |
| start r-factor (free) = 0.1547      final r-factor (free) = 0.1538          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9602 = 0.19 * 1.00 * 5.1224 + 1.00 * 0.0083                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9594 = 0.19 * 1.00 * 5.1230 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.602)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.92    84.38   16.50    None  None   None       |
|    all(noH): 2823   0      0.92    84.38   16.50    None  None   None       |
|    Sol.    : 438    0      6.20    79.84   37.92    None  None   None       |
|    Mac.    : 2385   0      0.92    84.38   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:     0.915 -   9.262:  873   |   5:    42.650 -  50.997:   91        |
|      1:     9.262 -  17.609: 1220   |   6:    50.997 -  59.343:   65        |
|      2:    17.609 -  25.956:  262   |   7:    59.343 -  67.690:   28        |
|      3:    25.956 -  34.303:  142   |   8:    67.690 -  76.037:    7        |
|      4:    34.303 -  42.650:  129   |   9:    76.037 -  84.384:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1093 r_free = 0.1538             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1092 r_free = 0.1538             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1092   r_free= 0.1538   ksol= 0.34   Bsol= 50.27   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-2.43,-1.19,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.119556                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9740 -  4.6854 0.99   1397  155 0.0966 0.1212      5.3545      5.5073|
|  2:  4.6854 -  3.7380 0.99   1346  152 0.0852 0.1149       5.435      5.6232|
|  3:  3.7380 -  3.2711 0.99   1319  141 0.1069 0.1505      5.4737      5.8579|
|  4:  3.2711 -  2.9746 0.99   1314  152 0.1197 0.1584      5.4421        5.57|
|  5:  2.9746 -  2.7628 0.99   1307  147 0.1304 0.1786      5.3082      5.5639|
|  6:  2.7628 -  2.6008 0.99   1301  136 0.1163 0.1702      5.1794      5.3915|
|  7:  2.6008 -  2.4712 0.99   1288  142 0.1230 0.1582      5.1428       5.358|
|  8:  2.4712 -  2.3640 0.98   1270  145 0.1136 0.1664      5.0256      5.2912|
|  9:  2.3640 -  2.2734 0.98   1266  147 0.1125 0.1658      4.9911       5.249|
| 10:  2.2734 -  2.1952 1.00   1301  146 0.1078 0.1677      4.9088      5.1797|
| 11:  2.1952 -  2.1267 0.98   1272  136 0.1110 0.1728      4.9163      5.2579|
| 12:  2.1267 -  2.0661 0.98   1256  139 0.1086 0.1627      4.8516      5.1353|
| 13:  2.0661 -  2.0118 0.99   1280  140 0.1089 0.1723      4.7404       5.028|
| 14:  2.0118 -  1.9628 0.55    713   81 0.0968 0.1443      4.6125      4.8017|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9740 -  4.6854  1397   155  0.94   8.53   0.99     0.96       6564.40|
|  2:  4.6854 -  3.7380  1346   152  0.95   7.71   1.02     1.02       8822.64|
|  3:  3.7380 -  3.2711  1319   141  0.93  11.24   1.03     1.02      10254.11|
|  4:  3.2711 -  2.9746  1314   152  0.92  13.58   1.01     0.99      10160.22|
|  5:  2.9746 -  2.7628  1307   147  0.90  15.53   1.00     0.97       7984.82|
|  6:  2.7628 -  2.6008  1301   136  0.90  15.67   0.99     0.97       6713.26|
|  7:  2.6008 -  2.4712  1288   142  0.91  15.15   0.99     0.96       5861.33|
|  8:  2.4712 -  2.3640  1270   145  0.91  14.46   0.99     0.98       4769.74|
|  9:  2.3640 -  2.2734  1266   147  0.92  14.28   1.01     0.98       4510.96|
| 10:  2.2734 -  2.1952  1301   146  0.91  14.72   1.00     0.98       3964.19|
| 11:  2.1952 -  2.1267  1272   136  0.90  15.58   1.00     0.96       4073.34|
| 12:  2.1267 -  2.0661  1256   139  0.92  14.61   1.02     1.01       3756.07|
| 13:  2.0661 -  2.0118  1280   140  0.91  15.54   1.01     0.99       3049.25|
| 14:  2.0118 -  1.9628   713    81  0.93  12.83   0.99     0.97       2289.80|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2289.80 max =        10254.11 mean =      6069.28|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.89 mean =        13.50|
|phase err.(test): min =        0.00 max =           89.82 mean =        13.05|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1092   r_free= 0.1538   ksol= 0.34   Bsol= 50.24   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.25,-2.39,-1.05,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.119469                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1092   r_free= 0.1538   ksol= 0.34   Bsol= 50.24   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.25,-2.39,-1.05,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.119469                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9740 -  4.6854 0.99   1397  155 0.0966 0.1213       5.355      5.5081|
|  2:  4.6854 -  3.7380 0.99   1346  152 0.0852 0.1148      5.4353      5.6231|
|  3:  3.7380 -  3.2711 0.99   1319  141 0.1069 0.1505      5.4738       5.858|
|  4:  3.2711 -  2.9746 0.99   1314  152 0.1197 0.1584      5.4421        5.57|
|  5:  2.9746 -  2.7628 0.99   1307  147 0.1304 0.1785       5.308      5.5636|
|  6:  2.7628 -  2.6008 0.99   1301  136 0.1162 0.1699      5.1791      5.3907|
|  7:  2.6008 -  2.4712 0.99   1288  142 0.1230 0.1583      5.1427      5.3584|
|  8:  2.4712 -  2.3640 0.98   1270  145 0.1136 0.1664      5.0254      5.2907|
|  9:  2.3640 -  2.2734 0.98   1266  147 0.1126 0.1657       4.991      5.2486|
| 10:  2.2734 -  2.1952 1.00   1301  146 0.1078 0.1678      4.9089       5.181|
| 11:  2.1952 -  2.1267 0.98   1272  136 0.1110 0.1729      4.9165      5.2582|
| 12:  2.1267 -  2.0661 0.98   1256  139 0.1085 0.1627      4.8514      5.1354|
| 13:  2.0661 -  2.0118 0.99   1280  140 0.1089 0.1721      4.7398      5.0267|
| 14:  2.0118 -  1.9628 0.55    713   81 0.0967 0.1440      4.6112      4.7997|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9740 -  4.6854  1397   155  0.94   8.53   0.99     0.96       6571.08|
|  2:  4.6854 -  3.7380  1346   152  0.95   7.72   1.02     1.02       8829.15|
|  3:  3.7380 -  3.2711  1319   141  0.93  11.24   1.03     1.02      10257.38|
|  4:  3.2711 -  2.9746  1314   152  0.92  13.58   1.01     0.99      10157.38|
|  5:  2.9746 -  2.7628  1307   147  0.90  15.52   1.00     0.98       7976.92|
|  6:  2.7628 -  2.6008  1301   136  0.90  15.66   0.99     0.97       6708.66|
|  7:  2.6008 -  2.4712  1288   142  0.91  15.15   1.00     0.96       5858.19|
|  8:  2.4712 -  2.3640  1270   145  0.91  14.45   1.00     0.98       4766.46|
|  9:  2.3640 -  2.2734  1266   147  0.92  14.27   1.01     0.98       4509.00|
| 10:  2.2734 -  2.1952  1301   146  0.91  14.73   1.01     0.98       3967.29|
| 11:  2.1952 -  2.1267  1272   136  0.90  15.60   1.00     0.96       4078.46|
| 12:  2.1267 -  2.0661  1256   139  0.92  14.61   1.02     1.01       3757.45|
| 13:  2.0661 -  2.0118  1280   140  0.91  15.52   1.01     0.99       3044.10|
| 14:  2.0118 -  1.9628   713    81  0.93  12.81   1.00     0.97       2281.65|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2281.65 max =        10257.38 mean =      6068.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.89 mean =        13.50|
|phase err.(test): min =        0.00 max =           89.82 mean =        13.05|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.602)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.88    84.35   16.47    None  None   None       |
|    all(noH): 2823   0      0.88    84.35   16.47    None  None   None       |
|    Sol.    : 438    0      6.17    79.81   37.89    None  None   None       |
|    Mac.    : 2385   0      0.88    84.35   12.53    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:     0.884 -   9.231:  873   |   5:    42.618 -  50.965:   91        |
|      1:     9.231 -  17.578: 1220   |   6:    50.965 -  59.312:   65        |
|      2:    17.578 -  25.925:  262   |   7:    59.312 -  67.659:   28        |
|      3:    25.925 -  34.271:  142   |   8:    67.659 -  76.006:    7        |
|      4:    34.271 -  42.618:  129   |   9:    76.006 -  84.353:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 297         
Filter by distance & map next to the model:
   mapped sites are within: 0.560 - 4.622
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 292 from: 297
   mapped sites are within: 0.736 - 4.622

peak=    6.575 closest distance to " NE2 GLN A  11 " =    1.301
peak=    5.691 closest distance to " O   HOH Z 126 " =    1.930
peak=    5.666 closest distance to " O   HOH Z 144 " =    1.755
peak=    5.541 closest distance to " CG  PRO A  54 " =    1.292
peak=    5.398 closest distance to " NH2 ARG A  56 " =    2.072
peak=    5.161 closest distance to " O   HOH Z 423 " =    1.781
peak=    5.095 closest distance to " CG  PRO A 213 " =    1.291
peak=    5.092 closest distance to " O   HOH Z  63 " =    1.696
peak=    4.936 closest distance to " CB  ARG A 275 " =    0.901
peak=    4.918 closest distance to " O   HOH Z 232 " =    2.308
peak=    4.902 closest distance to " CB  SER A  63 " =    1.217
peak=    4.893 closest distance to " O   HOH Z 417 " =    1.537
peak=    4.878 closest distance to " CB  PRO A  54 " =    0.996
peak=    4.805 closest distance to " O   HOH Z 427 " =    2.551
peak=    4.805 closest distance to " CB  GLN A 223 " =    1.477
peak=    4.799 closest distance to " O   HOH Z 287 " =    2.009
peak=    4.680 closest distance to " O   HOH Z  78 " =    1.724
peak=    4.679 closest distance to " O   HOH Z 236 " =    1.515
peak=    4.679 closest distance to " O   HOH Z 298 " =    1.940
peak=    4.627 closest distance to " CG  TRP A 179 " =    2.183
peak=    4.619 closest distance to " O   HOH Z 369 " =    2.147
peak=    4.608 closest distance to " ND2 ASN A 187 " =    1.523
peak=    4.508 closest distance to " CB  ASN A 187 " =    1.159
peak=    4.497 closest distance to " O   HOH Z 209 " =    2.226
peak=    4.474 closest distance to " O   HOH Z 419 " =    2.391
peak=    4.428 closest distance to " O   HOH Z 380 " =    1.770
peak=    4.418 closest distance to " O   HOH Z 193 " =    1.858
peak=    4.400 closest distance to " CB  ASN A 148 " =    1.384
peak=    4.357 closest distance to " O   HOH Z   1 " =    1.849
peak=    4.350 closest distance to " CB  GLN A 183 " =    1.165
peak=    4.329 closest distance to " CB  GLU A 152 " =    1.298
peak=    4.302 closest distance to " CG2 VAL A 257 " =    0.860
peak=    4.299 closest distance to " CB  GLU A 128 " =    0.983
peak=    4.272 closest distance to " CD  ARG A  66 " =    2.285
peak=    4.270 closest distance to " CG  PRO A 198 " =    1.266
peak=    4.262 closest distance to " CB  ARG A  79 " =    1.367
peak=    4.244 closest distance to " CB  SER A   3 " =    1.345
peak=    4.228 closest distance to " O   HOH Z 272 " =    1.790
peak=    4.223 closest distance to " O   HOH Z  78 " =    2.097
peak=    4.218 closest distance to " CG  PRO A 243 " =    1.116
peak=    4.207 closest distance to " O   HOH Z   7 " =    1.312
peak=    4.191 closest distance to " O   HOH Z 368 " =    3.631
peak=    4.185 closest distance to " CA  TYR A  30 " =    0.958
peak=    4.163 closest distance to " C   PRO A 198 " =    1.456
peak=    4.123 closest distance to " O   HOH Z 234 " =    3.701
peak=    4.116 closest distance to " O   HOH Z   2 " =    1.559
peak=    4.095 closest distance to " CB  LEU A 228 " =    1.062
peak=    4.091 closest distance to " CD  ARG A 159 " =    0.778
peak=    4.065 closest distance to " O   HOH Z 425 " =    1.355
peak=    4.064 closest distance to " O   HOH Z 371 " =    1.955
peak=    4.063 closest distance to " CB  VAL A 265 " =    1.307
peak=    4.054 closest distance to " O   HOH Z 261 " =    2.045
peak=    4.054 closest distance to " CB  ARG A 190 " =    1.629
peak=    4.053 closest distance to " O   HOH Z 158 " =    2.931
peak=    4.050 closest distance to " O   HOH Z 217 " =    2.938
peak=    4.031 closest distance to " CG  PRO A  90 " =    1.213
peak=    4.025 closest distance to " O   HOH Z   9 " =    2.011
peak=    4.013 closest distance to " O   HOH Z  61 " =    1.637
peak=    4.008 closest distance to " CB  SER A 216 " =    0.781
peak=    3.998 closest distance to " O   HOH Z 128 " =    2.081
peak=    3.996 closest distance to " CB  ARG A 139 " =    0.999
peak=    3.992 closest distance to " O   HOH Z 362 " =    2.129
peak=    3.972 closest distance to " CE  LYS A  76 " =    0.869
peak=    3.966 closest distance to " O   HOH Z 132 " =    2.395
peak=    3.942 closest distance to " O   HOH Z   1 " =    1.741
peak=    3.932 closest distance to " O   HOH Z 316 " =    3.043
peak=    3.931 closest distance to " CA  ASN A 215 " =    1.091
peak=    3.931 closest distance to " O   HOH Z 352 " =    1.862
peak=    3.927 closest distance to " O   HOH Z  40 " =    2.222
peak=    3.922 closest distance to " O   HOH Z  61 " =    1.493
peak=    3.921 closest distance to " OD1BASN A 224 " =    2.238
peak=    3.904 closest distance to " O   HOH Z 146 " =    1.829
peak=    3.900 closest distance to " O   HOH Z 214 " =    2.169
peak=    3.877 closest distance to " OD1 ASN A  69 " =    2.679
peak=    3.864 closest distance to " O   HOH Z 389 " =    1.838
peak=    3.862 closest distance to " OG BSER A 164 " =    2.293
peak=    3.859 closest distance to " O   HOH Z 327 " =    1.626
peak=    3.828 closest distance to " O   HOH Z   3 " =    1.951
peak=    3.796 closest distance to " O   SER A  87 " =    2.153
peak=    3.796 closest distance to " O   HOH Z 425 " =    1.972
peak=    3.777 closest distance to " CB  ASN A  39 " =    0.873
peak=    3.774 closest distance to " N   PHE A 130 " =    1.197
peak=    3.771 closest distance to " O   HOH Z  10 " =    1.785
peak=    3.757 closest distance to " O   HOH Z 175 " =    2.103
peak=    3.749 closest distance to " O   HOH Z 346 " =    1.716
peak=    3.745 closest distance to " O   HOH Z 250 " =    1.522
peak=    3.744 closest distance to " O   HOH Z 128 " =    1.958
peak=    3.743 closest distance to " NH2BARG A 145 " =    2.022
peak=    3.727 closest distance to " ND1 HIS A  86 " =    1.728
peak=    3.721 closest distance to " CB  TRP A 266 " =    1.041
peak=    3.719 closest distance to " CD  PRO A 243 " =    1.555
peak=    3.717 closest distance to " CB  TRP A 179 " =    1.374
peak=    3.714 closest distance to " CB  SER A 212 " =    1.176
peak=    3.713 closest distance to " O   HOH Z 133 " =    2.577
peak=    3.678 closest distance to " O   HOH Z 344 " =    3.092
peak=    3.672 closest distance to " CB  GLU A 277 " =    3.516
peak=    3.668 closest distance to " O   HOH Z   9 " =    1.213
peak=    3.665 closest distance to " CB  ILE A 120 " =    1.260
peak=    3.659 closest distance to " O   HOH Z 213 " =    2.160
peak=    3.657 closest distance to " O   HOH Z  44 " =    1.659
peak=    3.647 closest distance to " O   HOH Z 365 " =    2.706
peak=    3.645 closest distance to " O   HOH Z 219 " =    2.356
peak=    3.642 closest distance to " CG2 THR A 221 " =    1.089
peak=    3.641 closest distance to " NH1BARG A 145 " =    1.295
peak=    3.638 closest distance to " CB  ASN A 142 " =    0.908
peak=    3.633 closest distance to " O   HOH Z  59 " =    2.014
peak=    3.622 closest distance to " O   HOH Z  66 " =    2.199
peak=    3.621 closest distance to " O   HOH Z 128 " =    2.034
peak=    3.614 closest distance to " O   HOH Z 257 " =    2.154
peak=    3.604 closest distance to " CD2 TRP A 179 " =    1.268
peak=    3.603 closest distance to " O   HOH Z 222 " =    2.485
peak=    3.602 closest distance to " CA  ALA A 299 " =    0.842
peak=    3.595 closest distance to " CA  ALA A 233 " =    1.150
peak=    3.594 closest distance to " O   HOH Z 368 " =    1.879
peak=    3.593 closest distance to " O   HOH Z 386 " =    3.028
peak=    3.588 closest distance to " O   HOH Z 437 " =    1.930
peak=    3.576 closest distance to " O   HOH Z 405 " =    1.396
peak=    3.573 closest distance to " CB  ALA A 114 " =    1.094
peak=    3.571 closest distance to " N   ALA A   1 " =    2.246
peak=    3.566 closest distance to " N   GLN A 278 " =    1.111
peak=    3.565 closest distance to " CB  LEU A 143 " =    1.087
peak=    3.564 closest distance to " O   HOH Z 147 " =    1.758
peak=    3.562 closest distance to " CA  SER A  87 " =    1.016
peak=    3.562 closest distance to " CG1 ILE A  33 " =    1.293
peak=    3.559 closest distance to " O   HOH Z 426 " =    1.938
peak=    3.555 closest distance to " O   HOH Z 305 " =    3.598
peak=    3.547 closest distance to " NH1AARG A 145 " =    1.182
peak=    3.543 closest distance to " OG  SER A  62 " =    2.958
peak=    3.537 closest distance to " CB  ALA A   1 " =    4.622
peak=    3.536 closest distance to " CA  ALA A  84 " =    1.373
peak=    3.534 closest distance to " CB  ALA A  34 " =    1.087
peak=    3.532 closest distance to " O   HOH Z 423 " =    1.984
peak=    3.529 closest distance to " O   HOH Z  21 " =    1.698
peak=    3.523 closest distance to " O   HOH Z 298 " =    2.480
peak=    3.519 closest distance to " O   HOH Z 286 " =    2.286
peak=    3.516 closest distance to " O   HOH Z 390 " =    2.348
peak=    3.515 closest distance to " OD2 ASP A 286 " =    2.774
peak=    3.513 closest distance to " CB  SER A  62 " =    1.260
peak=    3.512 closest distance to " CA  THR A 264 " =    0.855
peak=    3.510 closest distance to " O   HOH Z 291 " =    1.521
peak=    3.502 closest distance to " CD BLYS A 290 " =    1.196
peak=    3.500 closest distance to " CB  THR A 157 " =    1.144
peak=    3.493 closest distance to " O   HOH Z 116 " =    2.858
peak=    3.485 closest distance to " CD  ARG A 138 " =    0.736
peak=    3.485 closest distance to " O   HOH Z 245 " =    1.363
peak=    3.477 closest distance to " O   HOH Z 371 " =    2.948
peak=    3.477 closest distance to " O   HOH Z 261 " =    2.276
peak=    3.466 closest distance to " O   HOH Z  88 " =    2.845
peak=    3.463 closest distance to " CG1BVAL A  72 " =    1.409
peak=    3.460 closest distance to " O   HOH Z 244 " =    1.695
peak=    3.455 closest distance to " CZ  PHE A 218 " =    1.019
peak=    3.452 closest distance to " O   HOH Z  97 " =    1.966
peak=    3.440 closest distance to " O   HOH Z 357 " =    1.929
peak=    3.426 closest distance to " CG  LEU A 167 " =    1.216
peak=    3.420 closest distance to " O   HOH Z  44 " =    2.934
peak=    3.412 closest distance to " O   HOH Z 345 " =    1.796
peak=    3.412 closest distance to " O   HOH Z 189 " =    2.180
peak=    3.411 closest distance to " CD2 LEU A 255 " =    1.516
peak=    3.407 closest distance to " CB  ASP A 140 " =    0.848
peak=    3.407 closest distance to " O   HOH Z 394 " =    1.644
peak=    3.404 closest distance to " N   ARG A 156 " =    1.311
peak=    3.399 closest distance to " O   HOH Z 422 " =    2.623
peak=    3.397 closest distance to " O   HOH Z 391 " =    2.897
peak=    3.396 closest distance to " O   HOH Z 329 " =    3.739
peak=    3.391 closest distance to " O   HOH Z 343 " =    3.322
peak=    3.386 closest distance to " CB  LYS A 117 " =    1.188
peak=    3.385 closest distance to " O   HOH Z  64 " =    2.429
peak=    3.382 closest distance to " CB  ALA A 114 " =    1.431
peak=    3.380 closest distance to " NH2BARG A 190 " =    1.497
peak=    3.377 closest distance to " O   HOH Z  88 " =    2.731
peak=    3.376 closest distance to " NZ  LYS A  76 " =    1.551
peak=    3.375 closest distance to " O   HOH Z 272 " =    2.012
peak=    3.373 closest distance to " O   HOH Z  93 " =    2.227
peak=    3.367 closest distance to " CE1 TYR A 186 " =    1.366
peak=    3.365 closest distance to " CG  MET A 113 " =    1.115
peak=    3.362 closest distance to " CB  LEU A 300 " =    0.920
peak=    3.361 closest distance to " O   HOH Z 227 " =    1.807
peak=    3.355 closest distance to " O   HOH Z 193 " =    1.644
peak=    3.351 closest distance to " O   HOH Z 213 " =    1.722
peak=    3.343 closest distance to " O   HOH Z 403 " =    1.366
peak=    3.341 closest distance to " CD1 ILE A 263 " =    1.388
peak=    3.336 closest distance to " CA  GLY A 241 " =    3.759
peak=    3.334 closest distance to " O   HOH Z  88 " =    3.912
peak=    3.331 closest distance to " CD1 LEU A 300 " =    1.183
peak=    3.330 closest distance to " N   SER A 134 " =    1.335
peak=    3.326 closest distance to " O   HOH Z 403 " =    1.567
peak=    3.325 closest distance to " O   HOH Z 336 " =    1.988
peak=    3.324 closest distance to " NE2 GLN A  73 " =    3.677
peak=    3.321 closest distance to " O   HOH Z 313 " =    1.759
peak=    3.320 closest distance to " CD2 LEU A 297 " =    0.967
peak=    3.320 closest distance to " CB  ASP A 124 " =    0.850
peak=    3.319 closest distance to " N   SER A  97 " =    0.891
peak=    3.318 closest distance to " CA  TYR A 116 " =    1.297
peak=    3.309 closest distance to " O   HOH Z 126 " =    1.456
peak=    3.306 closest distance to " O   HOH Z 217 " =    1.658
peak=    3.304 closest distance to " CA  MET A  40 " =    1.117
peak=    3.304 closest distance to " CG1 ILE A 151 " =    1.093
peak=    3.302 closest distance to " O   HOH Z 172 " =    2.693
peak=    3.301 closest distance to " O   HOH Z 154 " =    1.967
peak=    3.298 closest distance to " N   ASN A 127 " =    1.362
peak=    3.298 closest distance to " O   HOH Z 133 " =    1.517
peak=    3.297 closest distance to " O   HOH Z 359 " =    1.474
peak=    3.297 closest distance to " O   HOH Z 392 " =    1.317
peak=    3.291 closest distance to " O   HOH Z 435 " =    1.950
peak=    3.291 closest distance to " CA  ILE A 234 " =    0.948
peak=    3.289 closest distance to " O   HOH Z  43 " =    2.261
peak=    3.279 closest distance to " CB  GLN A  88 " =    1.247
peak=    3.277 closest distance to " O   HOH Z 325 " =    3.718
peak=    3.275 closest distance to " O   HOH Z  90 " =    2.036
peak=    3.274 closest distance to " O   ARG A 145 " =    1.655
peak=    3.273 closest distance to " NH2AARG A 275 " =    3.568
peak=    3.273 closest distance to " O   HOH Z 302 " =    1.668
peak=    3.269 closest distance to " O   HOH Z  17 " =    1.967
peak=    3.268 closest distance to " O   HOH Z  66 " =    2.091
peak=    3.263 closest distance to " CG  GLN A  89 " =    1.470
peak=    3.259 closest distance to " CB  LYS A 290 " =    1.401
peak=    3.258 closest distance to " NE AARG A 275 " =    1.327
peak=    3.255 closest distance to " OG BSER A  99 " =    2.211
peak=    3.253 closest distance to " O   HOH Z 193 " =    1.966
peak=    3.250 closest distance to " O   HOH Z 271 " =    2.321
peak=    3.250 closest distance to " O   ASN A 209 " =    1.341
peak=    3.249 closest distance to " CG2 ILE A 120 " =    1.068
peak=    3.247 closest distance to " CG  GLN A 278 " =    1.266
peak=    3.247 closest distance to " CA  ALA A  21 " =    1.161
peak=    3.247 closest distance to " O   HOH Z 139 " =    2.453
peak=    3.245 closest distance to " O   HOH Z 109 " =    2.494
peak=    3.238 closest distance to " O   HOH Z 280 " =    2.993
peak=    3.237 closest distance to " CD1 ILE A 106 " =    0.854
peak=    3.231 closest distance to " O   HOH Z 266 " =    3.287
peak=    3.229 closest distance to " O   HOH Z 265 " =    2.093
peak=    3.226 closest distance to " CB  ALA A  21 " =    1.933
peak=    3.219 closest distance to " CB  THR A  31 " =    1.726
peak=    3.217 closest distance to " O   HOH Z 124 " =    1.324
peak=    3.216 closest distance to " O   HOH Z 180 " =    2.112
peak=    3.214 closest distance to " NH2AARG A 190 " =    1.807
peak=    3.213 closest distance to " O  BHOH Z 338 " =    2.426
peak=    3.213 closest distance to " O   HOH Z 152 " =    1.900
peak=    3.213 closest distance to " NZ  LYS A 117 " =    1.329
peak=    3.209 closest distance to " N   ASN A  39 " =    1.233
peak=    3.209 closest distance to " O   PRO A  90 " =    1.506
peak=    3.207 closest distance to " CG  GLU A 277 " =    2.075
peak=    3.205 closest distance to " CB  SER A  26 " =    1.642
peak=    3.205 closest distance to " O   HOH Z 148 " =    3.420
peak=    3.203 closest distance to " O   HOH Z  50 " =    1.643
peak=    3.202 closest distance to " O   HOH Z  32 " =    1.836
peak=    3.202 closest distance to " O   HOH Z 153 " =    1.813
peak=    3.202 closest distance to " O   HOH Z 195 " =    1.289
peak=    3.199 closest distance to " O   HOH Z 263 " =    1.731
peak=    3.199 closest distance to " O   HOH Z  85 " =    2.144
peak=    3.188 closest distance to " O   HOH Z 207 " =    1.659
peak=    3.187 closest distance to " O   HOH Z 238 " =    3.695
peak=    3.185 closest distance to " O   HOH Z  47 " =    1.843
peak=    3.176 closest distance to " CH2 TRP A  92 " =    2.024
peak=    3.174 closest distance to " O   HOH Z  71 " =    2.227
peak=    3.172 closest distance to " NE2 GLN A  58 " =    3.691
peak=    3.170 closest distance to " CA  ALA A 158 " =    1.067
peak=    3.165 closest distance to " CG BARG A 102 " =    1.793
peak=    3.165 closest distance to " O   HOH Z 421 " =    2.139
peak=    3.161 closest distance to " O   HOH Z 407 " =    2.105
peak=    3.160 closest distance to " O   HOH Z 432 " =    1.876
peak=    3.158 closest distance to " N   GLU A   2 " =    1.406
peak=    3.155 closest distance to " O   HOH Z 183 " =    1.367
peak=    3.149 closest distance to " O   HOH Z 389 " =    1.897
peak=    3.149 closest distance to " O   HOH Z 188 " =    2.041
peak=    3.148 closest distance to " CB  PRO A 243 " =    1.181
peak=    3.145 closest distance to " CA  LEU A 101 " =    1.670
peak=    3.140 closest distance to " O   HOH Z 375 " =    1.066
peak=    3.139 closest distance to " CA  ARG A 102 " =    1.138
peak=    3.137 closest distance to " O   HOH Z  89 " =    2.073
peak=    3.134 closest distance to " CB  MET A  47 " =    1.114
peak=    3.133 closest distance to " O   HOH Z 130 " =    3.720
peak=    3.128 closest distance to " CB  ARG A 138 " =    0.929
peak=    3.127 closest distance to " CA  GLY A 302 " =    1.038
peak=    3.124 closest distance to " CB  SER A 276 " =    1.263
peak=    3.118 closest distance to " CB  MET A 188 " =    1.664
peak=    3.115 closest distance to " O   HOH Z 409 " =    2.244
peak=    3.114 closest distance to " CB  TRP A 150 " =    1.435
peak=    3.109 closest distance to " CB  TYR A 116 " =    0.887
peak=    3.109 closest distance to " CD  LYS A 166 " =    1.272
peak=    3.107 closest distance to " O   HOH Z 248 " =    1.563
peak=    3.103 closest distance to " O   HOH Z 130 " =    2.172
peak=    3.101 closest distance to " CG  LYS A  76 " =    0.968
peak=    3.096 closest distance to " O   HOH Z 402 " =    1.476
peak=    3.096 closest distance to " O   HOH Z  88 " =    2.307
peak=    3.088 closest distance to " O  BHOH Z  74 " =    1.390
peak=    3.085 closest distance to " CB  VAL A  72 " =    1.539
peak=    3.082 closest distance to " O   HOH Z  40 " =    2.992
peak=    3.065 closest distance to " O   PHE A 192 " =    1.424
peak=    3.050 closest distance to " CG1 VAL A 189 " =    1.788
peak=    3.036 closest distance to " O   HOH Z  30 " =    1.712
peak=    3.029 closest distance to " CA  ALA A  51 " =    0.960
peak=    3.017 closest distance to " CA  SER A  95 " =    1.054

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.549 - 5.776
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 203
   mapped sites are within: 0.716 - 5.776

peak=   -4.750 closest distance to " CB  PRO A 243 " =    2.583
peak=   -4.587 closest distance to " O   HOH Z 377 " =    2.021
peak=   -4.481 closest distance to " O   HOH Z 290 " =    1.092
peak=   -4.320 closest distance to " C   HIS A 108 " =    1.226
peak=   -4.226 closest distance to " CD1 LEU A 255 " =    2.926
peak=   -4.219 closest distance to " O   HOH Z 266 " =    4.673
peak=   -4.197 closest distance to " CD  ARG A 156 " =    2.054
peak=   -4.116 closest distance to " O   PRO A 198 " =    1.241
peak=   -4.082 closest distance to " CG1 VAL A 112 " =    2.847
peak=   -4.075 closest distance to " O   HOH Z 185 " =    2.084
peak=   -4.052 closest distance to " CA  GLY A  98 " =    1.776
peak=   -4.042 closest distance to " CD  ARG A  14 " =    3.320
peak=   -4.040 closest distance to " O   HOH Z 372 " =    2.528
peak=   -3.990 closest distance to " CG  GLN A 223 " =    1.597
peak=   -3.987 closest distance to " CG  PHE A 283 " =    2.635
peak=   -3.973 closest distance to " O   VAL A  67 " =    2.531
peak=   -3.965 closest distance to " N   GLN A  58 " =    1.715
peak=   -3.941 closest distance to " O   HOH Z 231 " =    2.076
peak=   -3.940 closest distance to " O   HOH Z 351 " =    1.592
peak=   -3.922 closest distance to " O   HOH Z 389 " =    1.916
peak=   -3.898 closest distance to " CB  ALA A 291 " =    2.149
peak=   -3.868 closest distance to " O   ARG A 145 " =    1.476
peak=   -3.852 closest distance to " O   VAL A  67 " =    2.789
peak=   -3.834 closest distance to " OG BSER A 134 " =    1.360
peak=   -3.829 closest distance to " CZ3 TRP A 179 " =    1.225
peak=   -3.828 closest distance to " O   SER A 135 " =    1.436
peak=   -3.807 closest distance to " O   HOH Z 407 " =    3.118
peak=   -3.804 closest distance to " O   PRO A 243 " =    2.481
peak=   -3.802 closest distance to " O   HOH Z 313 " =    1.930
peak=   -3.780 closest distance to " CE2 PHE A 218 " =    2.437
peak=   -3.775 closest distance to " O   HOH Z 317 " =    1.477
peak=   -3.738 closest distance to " O   HOH Z 152 " =    4.943
peak=   -3.734 closest distance to " CZ  PHE A  59 " =    1.450
peak=   -3.716 closest distance to " O   HOH Z 377 " =    0.739
peak=   -3.692 closest distance to " O   PRO A 198 " =    1.256
peak=   -3.690 closest distance to " CB  ALA A 248 " =    2.020
peak=   -3.690 closest distance to " CB  CYS A 254 " =    2.228
peak=   -3.681 closest distance to " CD  GLN A  58 " =    1.068
peak=   -3.675 closest distance to " ND2 ASN A  45 " =    1.092
peak=   -3.660 closest distance to " OG  SER A  87 " =    1.269
peak=   -3.650 closest distance to " O   VAL A 189 " =    2.523
peak=   -3.649 closest distance to " O   HOH Z  60 " =    2.397
peak=   -3.643 closest distance to " N   THR A 157 " =    1.470
peak=   -3.624 closest distance to " O   SER A  22 " =    2.488
peak=   -3.607 closest distance to " C   ALA A 158 " =    1.502
peak=   -3.602 closest distance to " OD1 ASP A 171 " =    1.601
peak=   -3.596 closest distance to " O   HOH Z 131 " =    4.118
peak=   -3.594 closest distance to " O   HOH Z  13 " =    1.487
peak=   -3.592 closest distance to " CG  ASP A 231 " =    0.716
peak=   -3.589 closest distance to " OG  SER A   3 " =    1.548
peak=   -3.582 closest distance to " O   SER A  95 " =    1.435
peak=   -3.568 closest distance to " CB  ALA A 161 " =    2.547
peak=   -3.563 closest distance to " O   HOH Z 140 " =    1.513
peak=   -3.558 closest distance to " OD2 ASP A 191 " =    1.411
peak=   -3.552 closest distance to " ND2 ASN A  45 " =    1.903
peak=   -3.551 closest distance to " O   HOH Z 385 " =    2.041
peak=   -3.548 closest distance to " O   HOH Z 298 " =    1.135
peak=   -3.536 closest distance to " CD2 PHE A 225 " =    1.128
peak=   -3.523 closest distance to " OD2 ASP A 171 " =    1.971
peak=   -3.522 closest distance to " CB  ASN A  39 " =    2.245
peak=   -3.515 closest distance to " OD1 ASP A 191 " =    1.871
peak=   -3.499 closest distance to " NE2 GLN A 278 " =    1.682
peak=   -3.498 closest distance to " N   ALA A  43 " =    2.519
peak=   -3.496 closest distance to " CB  PHE A 192 " =    1.913
peak=   -3.495 closest distance to " CD1 LEU A 101 " =    2.237
peak=   -3.494 closest distance to " NH2AARG A 275 " =    5.259
peak=   -3.493 closest distance to " O   HOH Z  52 " =    1.236
peak=   -3.493 closest distance to " O   HOH Z 282 " =    0.995
peak=   -3.492 closest distance to " OD1 ASN A 148 " =    1.656
peak=   -3.477 closest distance to " O   HOH Z  43 " =    1.783
peak=   -3.465 closest distance to " O   HOH Z  63 " =    2.375
peak=   -3.464 closest distance to " CB  TRP A  85 " =    2.375
peak=   -3.464 closest distance to " OE1 GLN A  88 " =    1.138
peak=   -3.460 closest distance to " CD2 LEU A 237 " =    2.819
peak=   -3.460 closest distance to " NH1AARG A 275 " =    1.831
peak=   -3.459 closest distance to " O   HOH Z 250 " =    1.407
peak=   -3.452 closest distance to " CB  PRO A 163 " =    2.481
peak=   -3.444 closest distance to " ND2 ASN A  45 " =    1.359
peak=   -3.441 closest distance to " CD1 PHE A  59 " =    1.927
peak=   -3.437 closest distance to " CB  ALA A 248 " =    2.384
peak=   -3.437 closest distance to " CB  ALA A 291 " =    2.129
peak=   -3.435 closest distance to " N   HIS A 115 " =    2.166
peak=   -3.434 closest distance to " O   HOH Z 198 " =    1.890
peak=   -3.433 closest distance to " NE  ARG A  36 " =    1.957
peak=   -3.430 closest distance to " O   HOH Z 359 " =    3.301
peak=   -3.412 closest distance to " O   HOH Z 384 " =    2.792
peak=   -3.408 closest distance to " CA  GLY A 133 " =    2.008
peak=   -3.407 closest distance to " O   HOH Z 409 " =    5.776
peak=   -3.404 closest distance to " CG  GLU A 152 " =    0.997
peak=   -3.404 closest distance to " OG  SER A  97 " =    2.191
peak=   -3.404 closest distance to " CD  GLU A 277 " =    1.093
peak=   -3.398 closest distance to " CG  MET A 105 " =    0.957
peak=   -3.397 closest distance to " CE  LYS A  76 " =    2.802
peak=   -3.393 closest distance to " NH2 ARG A  79 " =    2.012
peak=   -3.389 closest distance to " O   HOH Z 351 " =    1.705
peak=   -3.388 closest distance to " O   HOH Z 166 " =    1.257
peak=   -3.376 closest distance to " O   HOH Z 345 " =    2.031
peak=   -3.372 closest distance to " CE3 TRP A 274 " =    2.354
peak=   -3.372 closest distance to " CA  GLY A 203 " =    2.247
peak=   -3.371 closest distance to " N   ASP A 286 " =    2.284
peak=   -3.370 closest distance to " C   LEU A 222 " =    0.716
peak=   -3.369 closest distance to " O   PHE A 218 " =    1.555
peak=   -3.363 closest distance to " O   LEU A 101 " =    2.419
peak=   -3.363 closest distance to " O   ALA A 161 " =    1.519
peak=   -3.361 closest distance to " OG  SER A 245 " =    1.184
peak=   -3.361 closest distance to " O   HOH Z  11 " =    1.838
peak=   -3.359 closest distance to " CG1 VAL A 197 " =    2.099
peak=   -3.359 closest distance to " CZ  TYR A 169 " =    1.583
peak=   -3.359 closest distance to " ND2 ASN A 187 " =    1.410
peak=   -3.355 closest distance to " O   HOH Z 298 " =    2.454
peak=   -3.355 closest distance to " CE3 TRP A 123 " =    1.312
peak=   -3.355 closest distance to " O   HOH Z  65 " =    1.095
peak=   -3.352 closest distance to " OG BSER A 134 " =    1.558
peak=   -3.347 closest distance to " CE2 TYR A  30 " =    2.633
peak=   -3.347 closest distance to " O   ALA A  34 " =    2.525
peak=   -3.345 closest distance to " O   HOH Z  90 " =    2.474
peak=   -3.344 closest distance to " CG2 THR A  18 " =    2.773
peak=   -3.340 closest distance to " CB  ASP A 132 " =    2.313
peak=   -3.338 closest distance to " O   VAL A 197 " =    1.664
peak=   -3.329 closest distance to " O   HOH Z 266 " =    4.501
peak=   -3.328 closest distance to " CB  ILE A  33 " =    2.878
peak=   -3.318 closest distance to " C   LEU A 143 " =    1.216
peak=   -3.317 closest distance to " O   TRP A  70 " =    1.456
peak=   -3.316 closest distance to " O   HOH Z 348 " =    1.826
peak=   -3.309 closest distance to " CG1 VAL A 230 " =    2.005
peak=   -3.309 closest distance to " O   PRO A 163 " =    1.956
peak=   -3.299 closest distance to " CE  MET A 105 " =    2.271
peak=   -3.287 closest distance to " O   HOH Z  93 " =    2.328
peak=   -3.286 closest distance to " ND2 ASN A 249 " =    2.373
peak=   -3.286 closest distance to " CA  GLY A 241 " =    2.202
peak=   -3.285 closest distance to " O   HOH Z  51 " =    1.130
peak=   -3.282 closest distance to " CB  TYR A  15 " =    2.162
peak=   -3.282 closest distance to " NE2 GLN A  58 " =    2.966
peak=   -3.282 closest distance to " O   HOH Z 126 " =    1.896
peak=   -3.278 closest distance to " CD2 TYR A 293 " =    1.914
peak=   -3.273 closest distance to " CD  ARG A 139 " =    1.526
peak=   -3.271 closest distance to " O   HOH Z 211 " =    1.525
peak=   -3.264 closest distance to " O   HOH Z 438 " =    1.177
peak=   -3.262 closest distance to " O   ALA A  10 " =    1.697
peak=   -3.262 closest distance to " O   HOH Z 198 " =    1.536
peak=   -3.258 closest distance to " N   GLN A 122 " =    1.413
peak=   -3.253 closest distance to " O   HOH Z  38 " =    1.706
peak=   -3.253 closest distance to " O   HOH Z 134 " =    3.078
peak=   -3.250 closest distance to " CG2 ILE A 263 " =    2.265
peak=   -3.249 closest distance to " O   HOH Z 388 " =    2.123
peak=   -3.248 closest distance to " N   SER A 212 " =    1.729
peak=   -3.246 closest distance to " O   HOH Z 247 " =    0.921
peak=   -3.244 closest distance to " O   HOH Z 102 " =    1.526
peak=   -3.237 closest distance to " CG2 THR A 178 " =    2.140
peak=   -3.236 closest distance to " O   HOH Z 282 " =    4.662
peak=   -3.226 closest distance to " CB  ALA A 131 " =    1.956
peak=   -3.224 closest distance to " O   HOH Z  24 " =    1.250
peak=   -3.224 closest distance to " O   HOH Z 281 " =    2.756
peak=   -3.217 closest distance to " OXT GLY A 302 " =    2.985
peak=   -3.215 closest distance to " CB  ASP A 132 " =    2.168
peak=   -3.214 closest distance to " O   HOH Z  28 " =    1.865
peak=   -3.214 closest distance to " CA  ASP A  27 " =    2.388
peak=   -3.213 closest distance to " CB  CYS A 201 " =    2.519
peak=   -3.209 closest distance to " O   HOH Z  15 " =    1.643
peak=   -3.208 closest distance to " CG  GLN A  88 " =    0.790
peak=   -3.208 closest distance to " O   ILE A  49 " =    1.720
peak=   -3.208 closest distance to " CD2 PHE A  61 " =    1.980
peak=   -3.206 closest distance to " O   HOH Z 369 " =    2.117
peak=   -3.202 closest distance to " CG  PRO A 243 " =    1.684
peak=   -3.198 closest distance to " O   HOH Z 423 " =    2.393
peak=   -3.198 closest distance to " ND2 ASN A 285 " =    2.061
peak=   -3.198 closest distance to " CB  ALA A   7 " =    2.009
peak=   -3.196 closest distance to " O   HOH Z   9 " =    1.627
peak=   -3.196 closest distance to " O   VAL A 174 " =    2.207
peak=   -3.195 closest distance to " O   HOH Z 253 " =    3.797
peak=   -3.190 closest distance to " O   HOH Z 191 " =    5.467
peak=   -3.187 closest distance to " CA  GLY A  57 " =    2.107
peak=   -3.180 closest distance to " O   HOH Z 210 " =    0.819
peak=   -3.179 closest distance to " CZ BARG A 275 " =    1.641
peak=   -3.172 closest distance to " CD1 LEU A 228 " =    2.142
peak=   -3.170 closest distance to " N   ALA A 248 " =    1.506
peak=   -3.163 closest distance to " O   HOH Z  60 " =    1.924
peak=   -3.160 closest distance to " O   HOH Z 414 " =    2.198
peak=   -3.157 closest distance to " O   ASP A 270 " =    1.848
peak=   -3.155 closest distance to " OD2 ASP A  27 " =    1.565
peak=   -3.152 closest distance to " O   GLY A  80 " =    2.450
peak=   -3.151 closest distance to " O   HOH Z 103 " =    1.712
peak=   -3.139 closest distance to " O   SER A   3 " =    1.179
peak=   -3.137 closest distance to " ND2 ASN A  39 " =    1.511
peak=   -3.134 closest distance to " ND2BASN A 224 " =    1.741
peak=   -3.130 closest distance to " O   HOH Z 281 " =    3.055
peak=   -3.128 closest distance to " O   HOH Z 111 " =    2.104
peak=   -3.128 closest distance to " O   GLY A  17 " =    1.182
peak=   -3.113 closest distance to " O   SER A 146 " =    1.119
peak=   -3.107 closest distance to " O   ASP A 162 " =    2.176
peak=   -3.102 closest distance to " C   MET A 188 " =    1.555
peak=   -3.101 closest distance to " CH2 TRP A 179 " =    2.150
peak=   -3.100 closest distance to " CZ3 TRP A 123 " =    1.770
peak=   -3.096 closest distance to " CD1 TRP A 179 " =    1.028
peak=   -3.087 closest distance to " O   ALA A 292 " =    2.058
peak=   -3.085 closest distance to " CA  GLY A  57 " =    1.949
peak=   -3.084 closest distance to " O   HOH Z 137 " =    1.420
peak=   -3.083 closest distance to " CG  TRP A 266 " =    1.829
peak=   -3.079 closest distance to " CB  GLN A  55 " =    1.343
peak=   -3.066 closest distance to " N   ASP A 270 " =    1.377
peak=   -3.065 closest distance to " CG  PRO A 163 " =    2.605
peak=   -3.040 closest distance to " CB  PHE A 208 " =    2.192

================= 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    :  0.3860 0.3821   6.194014e+00   6.184200e+00
   1_bss:  0.3702 0.3693   6.176820e+00   6.163180e+00
   1_xyz:  0.2602 0.2959   5.866131e+00   5.953451e+00
   1_adp:  0.2371 0.3096   5.821255e+00   5.986668e+00
   1_occ:  0.2369 0.3091   5.819953e+00   5.985482e+00
   2_bss:  0.2340 0.3030   5.806224e+00   5.971323e+00
   2_xyz:  0.1682 0.2158   5.489943e+00   5.683893e+00
   2_adp:  0.1510 0.1964   5.395887e+00   5.601009e+00
   2_occ:  0.1508 0.1963   5.395622e+00   5.601642e+00
   3_bss:  0.1500 0.1947   5.387812e+00   5.592485e+00
   3_xyz:  0.1238 0.1690   5.221848e+00   5.451538e+00
   3_adp:  0.1187 0.1642   5.187094e+00   5.420423e+00
   3_occ:  0.1186 0.1642   5.186990e+00   5.420376e+00
   4_bss:  0.1189 0.1643   5.187692e+00   5.420629e+00
   4_xyz:  0.1097 0.1560   5.126071e+00   5.374875e+00
   4_adp:  0.1080 0.1552   5.118148e+00   5.370954e+00
   4_occ:  0.1079 0.1552   5.118066e+00   5.370929e+00
   5_bss:  0.1079 0.1552   5.117797e+00   5.370628e+00
   5_xyz:  0.1088 0.1547   5.120984e+00   5.369130e+00
   5_adp:  0.1093 0.1538   5.119760e+00   5.365055e+00
   5_occ:  0.1092 0.1538   5.119556e+00   5.364857e+00
   5_bss:  0.1092 0.1538   5.119469e+00   5.364728e+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:  0.361  50.000  -3.291   3.623  -1.717   0.000  -0.000  -0.000
   1_xyz:  0.361  50.000  -3.291   3.623  -1.717   0.000  -0.000  -0.000
   1_adp:  0.361  50.000  -3.291   3.623  -1.717   0.000  -0.000  -0.000
   1_occ:  0.361  50.000  -3.291   3.623  -1.717   0.000  -0.000  -0.000
   2_bss:  0.335  50.272  -2.387  -0.237  -1.154  -0.000  -0.000  -0.000
   2_xyz:  0.335  50.272  -2.387  -0.237  -1.154  -0.000  -0.000  -0.000
   2_adp:  0.335  50.272  -2.387  -0.237  -1.154  -0.000  -0.000  -0.000
   2_occ:  0.335  50.272  -2.387  -0.237  -1.154  -0.000  -0.000  -0.000
   3_bss:  0.335  50.272  -2.322  -1.792  -1.100  -0.000  -0.000  -0.000
   3_xyz:  0.335  50.272  -2.322  -1.792  -1.100  -0.000  -0.000  -0.000
   3_adp:  0.335  50.272  -2.322  -1.792  -1.100  -0.000  -0.000  -0.000
   3_occ:  0.335  50.272  -2.322  -1.792  -1.100  -0.000  -0.000  -0.000
   4_bss:  0.335  50.272  -2.537  -2.411  -1.337  -0.000  -0.000  -0.000
   4_xyz:  0.335  50.272  -2.537  -2.411  -1.337  -0.000  -0.000  -0.000
   4_adp:  0.335  50.272  -2.537  -2.411  -1.337  -0.000  -0.000  -0.000
   4_occ:  0.335  50.272  -2.537  -2.411  -1.337  -0.000  -0.000  -0.000
   5_bss:  0.335  50.272  -2.378  -2.434  -1.195  -0.000  -0.000  -0.000
   5_xyz:  0.335  50.272  -2.378  -2.434  -1.195  -0.000  -0.000  -0.000
   5_adp:  0.335  50.272  -2.378  -2.434  -1.195  -0.000  -0.000  -0.000
   5_occ:  0.335  50.272  -2.378  -2.434  -1.195  -0.000  -0.000  -0.000
   5_bss:  0.335  50.241  -2.248  -2.390  -1.051  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  43.279 0.6059  0.8018    47762.355
   1_bss:  42.319 0.6158  0.7990    44304.142
   1_xyz:  30.086 0.7583  0.9401    23518.008
   1_adp:  31.872 0.7372  0.9178    25624.598
   1_occ:  31.838 0.7376  0.9177    25544.123
   2_bss:  30.875 0.7482  0.9072    24283.512
   2_xyz:  21.104 0.8502  0.9915    11822.654
   2_adp:  18.682 0.8744  1.0031     9965.586
   2_occ:  18.692 0.8742  1.0026     9963.850
   3_bss:  18.427 0.8765  0.9871     9691.333
   3_xyz:  15.408 0.9028  0.9973     7211.470
   3_adp:  14.705 0.9091  0.9950     6848.194
   3_occ:  14.706 0.9091  0.9949     6844.436
   4_bss:  14.716 0.9090  0.9826     6880.272
   4_xyz:  13.762 0.9166  0.9865     6188.525
   4_adp:  13.654 0.9177  0.9826     6124.657
   4_occ:  13.654 0.9177  0.9825     6123.408
   5_bss:  13.649 0.9177  0.9860     6121.690
   5_xyz:  13.576 0.9185  0.9856     6120.583
   5_adp:  13.456 0.9194  0.9821     6073.413
   5_occ:  13.453 0.9195  0.9821     6069.280
   5_bss:  13.451 0.9195  0.9848     6068.798
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.7100e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.7100e-01
   1_xyz:   1.484  0.012  0.099 15.515  0.007  4.104   1.2051e-01
   1_adp:   1.484  0.012  0.099 15.515  0.007  4.104   1.2051e-01
   1_occ:   1.484  0.012  0.099 15.515  0.007  4.104   1.2051e-01
   2_bss:   1.484  0.012  0.099 15.515  0.007  4.104   1.2051e-01
   2_xyz:   1.071  0.007  0.073 14.645  0.004  4.108   6.5929e-02
   2_adp:   1.071  0.007  0.073 14.645  0.004  4.108   6.5929e-02
   2_occ:   1.071  0.007  0.073 14.645  0.004  4.108   6.5929e-02
   3_bss:   1.071  0.007  0.073 14.645  0.004  4.108   6.5929e-02
   3_xyz:   0.972  0.006  0.070 14.695  0.004  4.109   5.7464e-02
   3_adp:   0.972  0.006  0.070 14.695  0.004  4.109   5.7464e-02
   3_occ:   0.972  0.006  0.070 14.695  0.004  4.109   5.7464e-02
   4_bss:   0.972  0.006  0.070 14.695  0.004  4.109   5.7464e-02
   4_xyz:   1.065  0.008  0.079 14.979  0.005  4.108   6.7311e-02
   4_adp:   1.065  0.008  0.079 14.979  0.005  4.108   6.7311e-02
   4_occ:   1.065  0.008  0.079 14.979  0.005  4.108   6.7311e-02
   5_bss:   1.065  0.008  0.079 14.979  0.005  4.108   6.7311e-02
   5_xyz:   0.940  0.006  0.071 14.573  0.004  4.108   5.4546e-02
   5_adp:   0.940  0.006  0.071 14.573  0.004  4.108   5.4546e-02
   5_occ:   0.940  0.006  0.071 14.573  0.004  4.108   5.4546e-02
   5_bss:   0.940  0.006  0.071 14.573  0.004  4.108   5.4546e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3899e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3899e-01
   1_xyz:   8.000  0.079  0.426 84.083  0.041  2.103   1.0063e-01
   1_adp:   8.000  0.079  0.426 84.083  0.041  2.103   1.0063e-01
   1_occ:   8.000  0.079  0.426 84.083  0.041  2.103   1.0063e-01
   2_bss:   8.000  0.079  0.426 84.083  0.041  2.103   1.0063e-01
   2_xyz:   7.756  0.041  0.219 82.813  0.033  2.314   1.1071e-01
   2_adp:   7.756  0.041  0.219 82.813  0.033  2.314   1.1071e-01
   2_occ:   7.756  0.041  0.219 82.813  0.033  2.314   1.1071e-01
   3_bss:   7.756  0.041  0.219 82.813  0.033  2.314   1.1071e-01
   3_xyz:   6.993  0.044  0.204 84.547  0.034  2.302   4.4576e-02
   3_adp:   6.993  0.044  0.204 84.547  0.034  2.302   4.4576e-02
   3_occ:   6.993  0.044  0.204 84.547  0.034  2.302   4.4576e-02
   4_bss:   6.993  0.044  0.204 84.547  0.034  2.302   4.4576e-02
   4_xyz:   6.660  0.043  0.242 84.855  0.041  2.265   5.7781e-02
   4_adp:   6.660  0.043  0.242 84.855  0.041  2.265   5.7781e-02
   4_occ:   6.660  0.043  0.242 84.855  0.041  2.265   5.7781e-02
   5_bss:   6.660  0.043  0.242 84.855  0.041  2.265   5.7781e-02
   5_xyz:   6.533  0.043  0.216 85.084  0.040  2.333   4.2786e-02
   5_adp:   6.533  0.043  0.216 85.084  0.040  2.333   4.2786e-02
   5_occ:   6.533  0.043  0.216 85.084  0.040  2.333   4.2786e-02
   5_bss:   6.533  0.043  0.216 85.084  0.040  2.333   4.2786e-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:  89.21   0.00  17.61  71.77   0.00  13.52  89.21   4.27  39.86
   1_occ:  89.21   0.00  17.61  71.77   0.00  13.52  89.21   4.27  39.86
   2_bss:  89.21   0.00  17.61  71.77   0.00  13.52  89.21   4.27  39.86
   2_xyz:  89.21   0.00  17.61  71.77   0.00  13.52  89.21   4.27  39.86
   2_adp:  83.12   0.00  17.03  74.27   0.00  12.97  83.12   6.67  39.15
   2_occ:  83.12   0.00  17.03  74.27   0.00  12.97  83.12   6.67  39.15
   3_bss:  83.12   0.00  17.03  74.27   0.00  12.97  83.12   6.67  39.15
   3_xyz:  83.12   0.00  17.03  74.27   0.00  12.97  83.12   6.67  39.15
   3_adp:  81.81   0.58  16.90  79.01   0.58  12.75  81.81   4.93  39.50
   3_occ:  81.81   0.58  16.90  79.01   0.58  12.75  81.81   4.93  39.50
   4_bss:  81.81   0.58  16.90  79.01   0.58  12.75  81.81   4.93  39.50
   4_xyz:  81.81   0.58  16.90  79.01   0.58  12.75  81.81   4.93  39.50
   4_adp:  84.80   0.61  16.87  84.80   0.61  12.71  82.98   5.92  39.55
   4_occ:  84.80   0.61  16.87  84.80   0.61  12.71  82.98   5.92  39.55
   5_bss:  84.80   0.61  16.87  84.80   0.61  12.71  82.98   5.92  39.55
   5_xyz:  84.80   0.61  16.87  84.80   0.61  12.71  82.98   5.92  39.55
   5_adp:  84.38   0.92  16.50  84.38   0.92  12.56  79.84   6.20  37.92
   5_occ:  84.38   0.92  16.50  84.38   0.92  12.56  79.84   6.20  37.92
   5_bss:  84.35   0.88  16.47  84.35   0.88  12.53  79.81   6.17  37.89
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.587    0.030    0.409
   1_adp:    1.587    0.030    0.409
   1_occ:    1.587    0.030    0.409
   2_bss:    1.587    0.030    0.409
   2_xyz:    1.328    0.034    0.527
   2_adp:    1.328    0.034    0.527
   2_occ:    1.328    0.034    0.527
   3_bss:    1.328    0.034    0.527
   3_xyz:    1.200    0.051    0.588
   3_adp:    1.200    0.051    0.588
   3_occ:    1.200    0.051    0.588
   4_bss:    1.200    0.051    0.588
   4_xyz:    1.315    0.054    0.612
   4_adp:    1.315    0.054    0.612
   4_occ:    1.315    0.054    0.612
   5_bss:    1.315    0.054    0.612
   5_xyz:    1.434    0.061    0.618
   5_adp:    1.434    0.061    0.618
   5_occ:    1.434    0.061    0.618
   5_bss:    1.434    0.061    0.618
------------------------------------------------------------------------

CPU time actual refinement: 341.18


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_620/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_620/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_620/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_620/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_620/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 341.02 
  Macro-tasks:
    bulk solvent and scale       = 37.50  
    individual site refinement   = 151.43 
    weights calculation          = 28.93  
    collect and process          = 6.51   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 224.46 
  Micro-tasks:
    mask                            = 1.81   
    f_calc                          = 109.47 
    alpha_beta                      = 7.99   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 121.13 
    fmodel                         = 6.68   
    r_factors                      = 0.21   
    phase_errors                   = 10.58  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 259.32 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.685 micro seconds
Total CPU time: 5.91 minutes
from_scatterers_fft:    676 calls, 109.01 s
gradients_fft:          621 calls, 106.07 s

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

# Date 2008-01-16 Time 05:16:05 PST -0800 (1200489365.53 s)
Start R-work = 0.3860, R-free = 0.3821 (no bulk solvent and anisotropic scale)
Final R-work = 0.1340, R-free = 0.1740 (no bulk solvent and anisotropic scale)

Start R-work = 0.3702, R-free = 0.3693
Final R-work = 0.1092, R-free = 0.1538