# Date 2008-01-16 Time 05:30:56 PST -0800 (1200490256.31 s)
#phil __OFF__

Command line arguments: "../764.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 23994
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 764

-------------------------------------------------------------------------------
  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: (70.6012, 46.4607, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.32, per 1000 atoms: 1.18


================================== 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: (70.6012, 46.4607, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0485 1.9825
Completeness in resolution range: 0.965451
Completeness with d_max=infinity: 0.962463

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0485
                             d_min =   1.9825

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: (70.6012, 46.4607, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0485 1.9825
Completeness in resolution range: 0.965451
Completeness with d_max=infinity: 0.962463

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0489 -  4.2423 [2126/2150]  1913   213  10.0%
  bin  2:  4.2423 -  3.3798 [2042/2062]  1838   204  10.0%
  bin  3:  3.3798 -  2.9562 [2028/2047]  1825   203  10.0%
  bin  4:  2.9562 -  2.6876 [2005/2035]  1808   197   9.8%
  bin  5:  2.6876 -  2.4959 [2002/2021]  1803   199   9.9%
  bin  6:  2.4959 -  2.3493 [1965/1990]  1763   202  10.3%
  bin  7:  2.3493 -  2.2321 [1966/1994]  1766   200  10.2%
  bin  8:  2.2321 -  2.1352 [1975/2011]  1780   195   9.9%
  bin  9:  2.1352 -  2.0532 [1958/2000]  1765   193   9.9%
  bin 10:  2.0532 -  1.9825 [1522/1980]  1369   153  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_764/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 15
        2.42 -     3.04: 2196
        3.04 -     3.66: 4693
        3.66 -     4.28: 9094
        4.28 -     4.90: 12323
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.305 3.040 x,y+1,z
  " O   HOH Z 280 " - " O   HOH Z 438 "  2.318 3.040 -x,y-1/2,-z+1/2
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.330 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28316 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_764/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_764/model_refine_001.geo

CPU time processing inputs: 8.96


============================ 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 = 70.60125 46.4607 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


============================= ml refinement start =============================


   ----------structure factors based statistics (before refinement)----------  


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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2782   r_free= 0.2727   ksol= 0.00   Bsol= 0.00   scale= 0.990    |
|                                                                             |
| 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:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.934343                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0489 -  4.7317 0.99   1385  155 0.2704 0.2601      6.3078      6.2509|
|  2:  4.7317 -  3.7752 0.99   1334  147 0.2195 0.2094      6.3092      6.2319|
|  3:  3.7752 -  3.3037 0.99   1306  143 0.2256 0.2222      6.1789      6.2924|
|  4:  3.3037 -  3.0043 0.99   1293  146 0.2479 0.2654      6.1045       6.153|
|  5:  3.0043 -  2.7904 0.99   1288  145 0.2824 0.2372      5.9887      5.8811|
|  6:  2.7904 -  2.6268 0.99   1297  139 0.2771 0.2813       5.902      5.8305|
|  7:  2.6268 -  2.4959 0.99   1284  141 0.2881 0.2654      5.8777      5.8516|
|  8:  2.4959 -  2.3877 0.98   1261  145 0.2966 0.2950      5.8567      5.8828|
|  9:  2.3877 -  2.2961 0.98   1269  140 0.2962 0.3103      5.7983      5.7936|
| 10:  2.2961 -  2.2171 1.00   1261  142 0.3125 0.2795      5.8106      5.6863|
| 11:  2.2171 -  2.1480 0.98   1269  139 0.3143 0.3383      5.7739      5.8228|
| 12:  2.1480 -  2.0868 0.98   1245  142 0.3165 0.3017      5.7247      5.7319|
| 13:  2.0868 -  2.0320 0.99   1284  138 0.3247 0.3334      5.6246      5.6019|
| 14:  2.0320 -  1.9825 0.67    854   97 0.3549 0.3458      5.6732      5.5741|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0489 -  4.7317  1385   155  0.81  23.74   0.87     0.83      36024.30|
|  2:  4.7317 -  3.7752  1334   147  0.87  19.06   0.98     0.94      34972.08|
|  3:  3.7752 -  3.3037  1306   143  0.85  21.60   1.02     0.99      32635.44|
|  4:  3.3037 -  3.0043  1293   146  0.84  23.03   1.01     0.99      27743.86|
|  5:  3.0043 -  2.7904  1288   145  0.80  26.53   1.01     0.97      22521.77|
|  6:  2.7904 -  2.6268  1297   139  0.81  26.00   1.01     0.97      18644.52|
|  7:  2.6268 -  2.4959  1284   141  0.79  27.56   1.03     0.97      17743.57|
|  8:  2.4959 -  2.3877  1261   145  0.79  28.03   1.04     0.97      16927.13|
|  9:  2.3877 -  2.2961  1269   140  0.79  28.24   1.05     0.99      16228.72|
| 10:  2.2961 -  2.2171  1261   142  0.77  29.25   1.07     1.00      15150.59|
| 11:  2.2171 -  2.1480  1269   139  0.76  30.89   1.07     1.01      15370.70|
| 12:  2.1480 -  2.0868  1245   142  0.75  31.46   1.08     0.99      14837.14|
| 13:  2.0868 -  2.0320  1284   138  0.71  34.82   1.07     0.97      13517.58|
| 14:  2.0320 -  1.9825   854    97  0.74  32.72   1.06     0.94      10978.52|
|alpha:            min =        0.83 max =            1.01 mean =         0.97|
|beta:             min =    10978.52 max =        36024.30 mean =     21370.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.79|
|phase err.(work): min =        0.00 max =           89.97 mean =        27.15|
|phase err.(test): min =        0.00 max =           89.99 mean =        26.79|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.209424              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.141   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.529858              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.002   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       14 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      204 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1992 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1865 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2828 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4680 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4414 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5620 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6703 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.161 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.806 |       0.155 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.861)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2782   r_free= 0.2727   ksol= 0.00   Bsol= 0.00   scale= 0.990    |
|                                                                             |
| 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:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.934343                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2621   r_free= 0.2580   ksol= 0.34   Bsol= 51.79   scale= 0.983   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,0.22,-1.69,0.00,-0.00,-0.00); trace/3= -1.32                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.907881                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.889862              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.306   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.263896              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.928   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2621      final r-factor (work) = 0.1590          |
| start r-factor (free) = 0.2580      final r-factor (free) = 0.1808          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7230 = 2.89 * 0.50 * 5.9257 + 1.00 * 0.1608                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1334 = 2.89 * 0.50 * 5.5883 + 1.00 * 0.0587                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1590      final r-factor (work) = 0.1449          |
| start r-factor (free) = 0.1808      final r-factor (free) = 0.1872          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4807 = 0.26 * 1.00 * 5.5883 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4168 = 0.26 * 1.00 * 5.3384 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.861)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.69    68.54   16.85    None  None   None       |
|    all(noH): 2823   0      1.69    68.54   16.85    None  None   None       |
|    Sol.    : 438    0      7.06    68.54   38.30    None  None   None       |
|    Mac.    : 2385   0      1.69    65.61   12.91    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.695 -   8.379:  578   |   5:    35.116 -  41.801:  112        |
|      1:     8.379 -  15.063: 1266   |   6:    41.801 -  48.485:   83        |
|      2:    15.063 -  21.748:  411   |   7:    48.485 -  55.169:   72        |
|      3:    21.748 -  28.432:  133   |   8:    55.169 -  61.854:   40        |
|      4:    28.432 -  35.116:  108   |   9:    61.854 -  68.538:   20        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1449 r_free = 0.1872             target_work(ml) = 5.354         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1446 r_free = 0.1872             target_work(ml) = 5.353         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1446   r_free= 0.1872   ksol= 0.34   Bsol= 51.79   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,0.22,-1.69,0.00,-0.00,-0.00); trace/3= -1.32                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.353022                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1436   r_free= 0.1851   ksol= 0.33   Bsol= 51.79   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-2.04,-1.69,-0.00,-0.00,-0.00); trace/3= -2.16                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.344787                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.567132              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.175  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.131027              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.708  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1436      final r-factor (work) = 0.1213          |
| start r-factor (free) = 0.1851      final r-factor (free) = 0.1621          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2456 = 1.57 * 0.50 * 5.3434 + 1.00 * 0.0587                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1762 = 1.57 * 0.50 * 5.2674 + 1.00 * 0.0489                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1213      final r-factor (work) = 0.1191          |
| start r-factor (free) = 0.1621      final r-factor (free) = 0.1568          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6981 = 0.13 * 1.00 * 5.2674 + 1.00 * 0.0079                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6870 = 0.13 * 1.00 * 5.1902 + 1.00 * 0.0069                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.861)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.03    67.45   16.73    None  None   None       |
|    all(noH): 2823   0      2.03    67.45   16.73    None  None   None       |
|    Sol.    : 438    0      6.12    67.45   37.73    None  None   None       |
|    Mac.    : 2385   0      2.03    66.26   12.88    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.027 -   8.569:  591   |   5:    34.738 -  41.280:  113        |
|      1:     8.569 -  15.111: 1277   |   6:    41.280 -  47.822:   75        |
|      2:    15.111 -  21.653:  394   |   7:    47.822 -  54.365:   77        |
|      3:    21.653 -  28.196:  132   |   8:    54.365 -  60.907:   40        |
|      4:    28.196 -  34.738:  104   |   9:    60.907 -  67.449:   20        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1191 r_free = 0.1568             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1189 r_free = 0.1569             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1189   r_free= 0.1569   ksol= 0.33   Bsol= 51.79   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-2.04,-1.69,-0.00,-0.00,-0.00); trace/3= -2.16                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.173984                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1188   r_free= 0.1566   ksol= 0.33   Bsol= 51.79   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-2.42,-1.38,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.172499                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.822300              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.966  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.701907              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.117  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1188      final r-factor (work) = 0.1116          |
| start r-factor (free) = 0.1566      final r-factor (free) = 0.1525          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7770 = 1.82 * 0.50 * 5.1892 + 1.00 * 0.0489                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7424 = 1.82 * 0.50 * 5.1426 + 1.00 * 0.0568                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1116      final r-factor (work) = 0.1092          |
| start r-factor (free) = 0.1525      final r-factor (free) = 0.1532          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 19.0442 = 3.70 * 1.00 * 5.1426 + 1.00 * 0.0069                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.9491 = 3.70 * 1.00 * 5.1162 + 1.00 * 0.0095                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.861)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.57    84.57   17.25    None  None   None       |
|    all(noH): 2823   0      0.57    84.57   17.25    None  None   None       |
|    Sol.    : 438    0      6.30    78.12   40.39    None  None   None       |
|    Mac.    : 2385   0      0.57    84.57   13.00    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:     0.572 -   8.972:  777   |   5:    42.573 -  50.973:  103        |
|      1:     8.972 -  17.372: 1271   |   6:    50.973 -  59.373:   76        |
|      2:    17.372 -  25.772:  289   |   7:    59.373 -  67.773:   46        |
|      3:    25.772 -  34.173:  125   |   8:    67.773 -  76.174:   21        |
|      4:    34.173 -  42.573:  108   |   9:    76.174 -  84.574:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1092 r_free = 0.1532             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1091 r_free = 0.1533             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1533   ksol= 0.33   Bsol= 51.79   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-2.42,-1.38,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.120366                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1532   ksol= 0.32   Bsol= 51.79   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,-2.42,-1.25,-0.00,-0.00,-0.00); trace/3= -2.03                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.120051                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.007118              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 146.596  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.358387              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.966  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1091      final r-factor (work) = 0.1052          |
| start r-factor (free) = 0.1532      final r-factor (free) = 0.1539          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7484 = 3.01 * 0.50 * 5.1159 + 1.00 * 0.0563                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7410 = 3.01 * 0.50 * 5.1032 + 1.00 * 0.0680                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1052      final r-factor (work) = 0.1049          |
| start r-factor (free) = 0.1539      final r-factor (free) = 0.1542          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9416 = 1.36 * 1.00 * 5.1032 + 1.00 * 0.0094                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9409 = 1.36 * 1.00 * 5.1025 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.861)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.40    86.11   17.07    None  None   None       |
|    all(noH): 2823   0      0.40    86.11   17.07    None  None   None       |
|    Sol.    : 438    0      6.25    78.94   40.28    None  None   None       |
|    Mac.    : 2385   0      0.40    86.11   12.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.396 -   8.967:  839   |   5:    43.251 -  51.822:   99        |
|      1:     8.967 -  17.538: 1233   |   6:    51.822 -  60.393:   74        |
|      2:    17.538 -  26.109:  272   |   7:    60.393 -  68.964:   40        |
|      3:    26.109 -  34.680:  127   |   8:    68.964 -  77.535:   21        |
|      4:    34.680 -  43.251:  112   |   9:    77.535 -  86.106:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1049 r_free = 0.1542             target_work(ml) = 5.104         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1048 r_free = 0.1542             target_work(ml) = 5.105         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1048   r_free= 0.1542   ksol= 0.32   Bsol= 51.79   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,-2.42,-1.25,-0.00,-0.00,-0.00); trace/3= -2.03                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.104506                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1047   r_free= 0.1542   ksol= 0.32   Bsol= 51.79   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-2.23,-0.98,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.104609                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.248257              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 165.983  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.142392              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.273  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1047      final r-factor (work) = 0.1094          |
| start r-factor (free) = 0.1542      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.2534 = 1.25 * 0.50 * 5.1037 + 1.00 * 0.0680                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.2461 = 1.25 * 0.50 * 5.1237 + 1.00 * 0.0482                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1094      final r-factor (work) = 0.1111          |
| start r-factor (free) = 0.1561      final r-factor (free) = 0.1548          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7393 = 0.14 * 1.00 * 5.1237 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7391 = 0.14 * 1.00 * 5.1404 + 1.00 * 0.0071                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.861)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.95    82.00   16.26    None  None   None       |
|    all(noH): 2823   0      1.95    82.00   16.26    None  None   None       |
|    Sol.    : 438    0      6.23    78.53   36.80    None  None   None       |
|    Mac.    : 2385   0      1.95    82.00   12.49    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.951 -   9.956: 1083   |   5:    41.977 -  49.983:   86        |
|      1:     9.956 -  17.962: 1043   |   6:    49.983 -  57.988:   62        |
|      2:    17.962 -  25.967:  237   |   7:    57.988 -  65.993:   22        |
|      3:    25.967 -  33.972:  143   |   8:    65.993 -  73.999:   14        |
|      4:    33.972 -  41.977:  129   |   9:    73.999 -  82.004:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1111 r_free = 0.1548             target_work(ml) = 5.135         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1111 r_free = 0.1548             target_work(ml) = 5.135         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1111   r_free= 0.1548   ksol= 0.32   Bsol= 51.79   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-2.23,-0.98,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.135097                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0489 -  4.7317 0.99   1385  155 0.0993 0.1257       5.385      5.5173|
|  2:  4.7317 -  3.7752 0.99   1334  147 0.0871 0.1128       5.448      5.6287|
|  3:  3.7752 -  3.3037 0.99   1306  143 0.1054 0.1492      5.4688      5.8634|
|  4:  3.3037 -  3.0043 0.99   1293  146 0.1196 0.1582      5.4487      5.5756|
|  5:  3.0043 -  2.7904 0.99   1288  145 0.1317 0.1713      5.3251      5.5602|
|  6:  2.7904 -  2.6268 0.99   1297  139 0.1181 0.1868       5.205      5.4454|
|  7:  2.6268 -  2.4959 0.99   1284  141 0.1278 0.1543      5.1671      5.3394|
|  8:  2.4959 -  2.3877 0.98   1261  145 0.1147 0.1751      5.0418      5.3316|
|  9:  2.3877 -  2.2961 0.98   1269  140 0.1146 0.1688      5.0124      5.2475|
| 10:  2.2961 -  2.2171 1.00   1261  142 0.1125 0.1689      4.9392      5.2421|
| 11:  2.2171 -  2.1480 0.98   1269  139 0.1128 0.1756      4.9324      5.2639|
| 12:  2.1480 -  2.0868 0.98   1245  142 0.1101 0.1569      4.8661      5.1098|
| 13:  2.0868 -  2.0320 0.99   1284  138 0.1126 0.1740       4.771      5.0514|
| 14:  2.0320 -  1.9825 0.67    854   97 0.1070 0.1609      4.6653      4.8694|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0489 -  4.7317  1385   155  0.94   9.13   0.98     0.95       7042.37|
|  2:  4.7317 -  3.7752  1334   147  0.95   7.82   1.01     1.00       8996.55|
|  3:  3.7752 -  3.3037  1306   143  0.94  10.96   1.02     1.01      10071.87|
|  4:  3.3037 -  3.0043  1293   146  0.92  13.57   1.00     0.98      10224.92|
|  5:  3.0043 -  2.7904  1288   145  0.90  15.72   0.99     0.96       8231.56|
|  6:  2.7904 -  2.6268  1297   139  0.90  15.61   0.98     0.96       6983.73|
|  7:  2.6268 -  2.4959  1284   141  0.91  15.45   0.99     0.96       6108.21|
|  8:  2.4959 -  2.3877  1261   145  0.91  14.50   0.99     0.97       4894.11|
|  9:  2.3877 -  2.2961  1269   140  0.92  14.49   1.00     0.97       4662.68|
| 10:  2.2961 -  2.2171  1261   142  0.91  14.89   1.00     0.97       4134.32|
| 11:  2.2171 -  2.1480  1269   139  0.90  15.84   0.99     0.95       4158.92|
| 12:  2.1480 -  2.0868  1245   142  0.92  14.48   1.01     1.00       3795.09|
| 13:  2.0868 -  2.0320  1284   138  0.91  15.49   0.99     0.98       3152.15|
| 14:  2.0320 -  1.9825   854    97  0.92  13.73   0.98     0.95       2451.34|
|alpha:            min =        0.95 max =            1.01 mean =         0.97|
|beta:             min =     2451.34 max =        10224.92 mean =      6187.07|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.64|
|phase err.(test): min =        0.00 max =           89.43 mean =        13.20|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1111   r_free= 0.1550   ksol= 0.32   Bsol= 45.48   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-2.13,-0.82,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.135562                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1111   r_free= 0.1550   ksol= 0.32   Bsol= 45.48   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-2.13,-0.82,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.135562                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0489 -  4.7317 0.99   1385  155 0.0990 0.1256      5.3835      5.5155|
|  2:  4.7317 -  3.7752 0.99   1334  147 0.0864 0.1123      5.4432       5.625|
|  3:  3.7752 -  3.3037 0.99   1306  143 0.1051 0.1490      5.4665      5.8622|
|  4:  3.3037 -  3.0043 0.99   1293  146 0.1197 0.1586      5.4496      5.5773|
|  5:  3.0043 -  2.7904 0.99   1288  145 0.1321 0.1720      5.3275      5.5633|
|  6:  2.7904 -  2.6268 0.99   1297  139 0.1184 0.1872      5.2075      5.4475|
|  7:  2.6268 -  2.4959 0.99   1284  141 0.1279 0.1548      5.1694      5.3415|
|  8:  2.4959 -  2.3877 0.98   1261  145 0.1149 0.1758      5.0437      5.3352|
|  9:  2.3877 -  2.2961 0.98   1269  140 0.1147 0.1684      5.0136      5.2462|
| 10:  2.2961 -  2.2171 1.00   1261  142 0.1126 0.1697      4.9404      5.2458|
| 11:  2.2171 -  2.1480 0.98   1269  139 0.1129 0.1759      4.9338      5.2653|
| 12:  2.1480 -  2.0868 0.98   1245  142 0.1101 0.1572      4.8669      5.1106|
| 13:  2.0868 -  2.0320 0.99   1284  138 0.1126 0.1739      4.7715      5.0521|
| 14:  2.0320 -  1.9825 0.67    854   97 0.1071 0.1607      4.6657      4.8695|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0489 -  4.7317  1385   155  0.94   9.12   0.98     0.95       7014.44|
|  2:  4.7317 -  3.7752  1334   147  0.95   7.79   1.01     1.00       8955.44|
|  3:  3.7752 -  3.3037  1306   143  0.94  10.93   1.02     1.01      10036.43|
|  4:  3.3037 -  3.0043  1293   146  0.92  13.58   1.00     0.98      10242.36|
|  5:  3.0043 -  2.7904  1288   145  0.90  15.76   0.99     0.97       8266.32|
|  6:  2.7904 -  2.6268  1297   139  0.90  15.66   0.99     0.96       7021.70|
|  7:  2.6268 -  2.4959  1284   141  0.91  15.49   0.99     0.96       6144.42|
|  8:  2.4959 -  2.3877  1261   145  0.91  14.53   0.99     0.97       4913.60|
|  9:  2.3877 -  2.2961  1269   140  0.92  14.51   1.00     0.98       4676.82|
| 10:  2.2961 -  2.2171  1261   142  0.91  14.92   1.01     0.97       4146.75|
| 11:  2.2171 -  2.1480  1269   139  0.90  15.88   0.99     0.95       4173.50|
| 12:  2.1480 -  2.0868  1245   142  0.92  14.51   1.01     1.00       3806.01|
| 13:  2.0868 -  2.0320  1284   138  0.91  15.50   1.00     0.99       3158.02|
| 14:  2.0320 -  1.9825   854    97  0.92  13.74   0.98     0.95       2452.98|
|alpha:            min =        0.95 max =            1.01 mean =         0.98|
|beta:             min =     2452.98 max =        10242.36 mean =      6194.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.66|
|phase err.(test): min =        0.00 max =           89.58 mean =        13.22|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.861)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.88    81.93   16.19    None  None   None       |
|    all(noH): 2823   0      1.88    81.93   16.19    None  None   None       |
|    Sol.    : 438    0      6.16    78.46   36.73    None  None   None       |
|    Mac.    : 2385   0      1.88    81.93   12.42    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.881 -   9.886: 1083   |   5:    41.907 -  49.912:   86        |
|      1:     9.886 -  17.891: 1043   |   6:    49.912 -  57.918:   62        |
|      2:    17.891 -  25.897:  237   |   7:    57.918 -  65.923:   22        |
|      3:    25.897 -  33.902:  143   |   8:    65.923 -  73.928:   14        |
|      4:    33.902 -  41.907:  129   |   9:    73.928 -  81.934:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 300         
Filter by distance & map next to the model:
   mapped sites are within: 0.549 - 4.634
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 292 from: 300
   mapped sites are within: 0.704 - 4.634

peak=    5.807 closest distance to " NH2 ARG A  56 " =    2.188
peak=    5.635 closest distance to " NE2 GLN A  11 " =    1.189
peak=    5.574 closest distance to " CG  PRO A  54 " =    1.363
peak=    5.326 closest distance to " CG  PRO A 213 " =    1.241
peak=    5.285 closest distance to " O   HOH Z 126 " =    1.971
peak=    5.144 closest distance to " CB  GLN A 223 " =    1.424
peak=    5.143 closest distance to " CB  ARG A 275 " =    0.891
peak=    4.976 closest distance to " CB  PRO A  54 " =    0.996
peak=    4.853 closest distance to " O   HOH Z 144 " =    1.791
peak=    4.736 closest distance to " O   HOH Z 232 " =    2.309
peak=    4.712 closest distance to " CB  GLN A 183 " =    1.182
peak=    4.711 closest distance to " CB  SER A  63 " =    1.199
peak=    4.679 closest distance to " ND2 ASN A 187 " =    1.529
peak=    4.569 closest distance to " O   HOH Z 369 " =    2.039
peak=    4.550 closest distance to " CB  ASN A 187 " =    1.250
peak=    4.523 closest distance to " O   HOH Z 236 " =    2.149
peak=    4.442 closest distance to " CB  GLU A 128 " =    0.961
peak=    4.434 closest distance to " C   PRO A 198 " =    1.509
peak=    4.434 closest distance to " CB  LEU A 228 " =    1.095
peak=    4.408 closest distance to " CG  PRO A 198 " =    1.275
peak=    4.402 closest distance to " CB  ASN A 148 " =    1.411
peak=    4.377 closest distance to " O   HOH Z 298 " =    1.930
peak=    4.364 closest distance to " O   HOH Z 303 " =    2.105
peak=    4.362 closest distance to " CG  PRO A 243 " =    1.097
peak=    4.355 closest distance to " O   HOH Z  78 " =    1.718
peak=    4.335 closest distance to " CG2 VAL A 257 " =    0.950
peak=    4.332 closest distance to " O   HOH Z  15 " =    2.284
peak=    4.211 closest distance to " CB  ARG A 190 " =    1.627
peak=    4.208 closest distance to " CB  GLU A 152 " =    1.215
peak=    4.197 closest distance to " CB  ARG A  79 " =    1.356
peak=    4.189 closest distance to " O   HOH Z 234 " =    3.745
peak=    4.188 closest distance to " O   HOH Z 250 " =    1.498
peak=    4.184 closest distance to " CB  VAL A 265 " =    1.270
peak=    4.171 closest distance to " O   HOH Z 427 " =    2.906
peak=    4.120 closest distance to " CB  SER A 216 " =    0.802
peak=    4.113 closest distance to " CD  ARG A 159 " =    0.743
peak=    4.096 closest distance to " O   HOH Z 189 " =    2.394
peak=    4.077 closest distance to " CA  TYR A  30 " =    0.955
peak=    4.067 closest distance to " CE  LYS A  76 " =    0.895
peak=    4.048 closest distance to " OD1 ASN A  69 " =    2.566
peak=    4.040 closest distance to " CB  SER A   3 " =    1.301
peak=    4.016 closest distance to " O   HOH Z 419 " =    2.070
peak=    4.013 closest distance to " CA  ASN A 215 " =    1.128
peak=    3.995 closest distance to " CZ  PHE A 218 " =    1.018
peak=    3.985 closest distance to " O   HOH Z 261 " =    2.144
peak=    3.969 closest distance to " O   HOH Z 158 " =    3.147
peak=    3.962 closest distance to " O   HOH Z 272 " =    1.814
peak=    3.960 closest distance to " CA  THR A 264 " =    0.862
peak=    3.946 closest distance to " CB  TRP A 266 " =    0.975
peak=    3.942 closest distance to " O   HOH Z  61 " =    1.628
peak=    3.916 closest distance to " O   HOH Z 368 " =    1.879
peak=    3.895 closest distance to " O   HOH Z 352 " =    1.841
peak=    3.880 closest distance to " CB  ASP A 124 " =    0.704
peak=    3.877 closest distance to " O   HOH Z 193 " =    1.858
peak=    3.875 closest distance to " O   HOH Z 346 " =    1.637
peak=    3.861 closest distance to " CB  ASN A  39 " =    0.887
peak=    3.858 closest distance to " CA  SER A  87 " =    0.995
peak=    3.853 closest distance to " CG  LEU A 167 " =    1.234
peak=    3.837 closest distance to " O   HOH Z 234 " =    1.776
peak=    3.826 closest distance to " CB  ASN A 142 " =    0.984
peak=    3.822 closest distance to " O   HOH Z 316 " =    3.126
peak=    3.821 closest distance to " O   HOH Z 132 " =    2.442
peak=    3.817 closest distance to " O   HOH Z   9 " =    2.000
peak=    3.817 closest distance to " CD1 LEU A 300 " =    1.235
peak=    3.809 closest distance to " CB  SER A 212 " =    1.212
peak=    3.803 closest distance to " NH1AARG A 145 " =    1.218
peak=    3.802 closest distance to " CB  ALA A  34 " =    1.052
peak=    3.802 closest distance to " O   HOH Z   1 " =    1.937
peak=    3.757 closest distance to " O   SER A  87 " =    2.140
peak=    3.748 closest distance to " O   HOH Z  68 " =    2.154
peak=    3.742 closest distance to " CB  LEU A 143 " =    1.113
peak=    3.731 closest distance to " CD  ARG A 269 " =    0.965
peak=    3.717 closest distance to " O   HOH Z  40 " =    1.932
peak=    3.714 closest distance to " O   HOH Z  21 " =    1.736
peak=    3.710 closest distance to " CB  SER A  62 " =    1.156
peak=    3.709 closest distance to " NZ  LYS A 117 " =    3.279
peak=    3.702 closest distance to " CG1 ILE A  33 " =    1.288
peak=    3.701 closest distance to " O   HOH Z 423 " =    1.536
peak=    3.697 closest distance to " O   HOH Z 353 " =    2.575
peak=    3.697 closest distance to " CB  ARG A  79 " =    0.882
peak=    3.694 closest distance to " O   HOH Z 214 " =    2.109
peak=    3.685 closest distance to " O   HOH Z 406 " =    1.671
peak=    3.679 closest distance to " O   HOH Z  78 " =    2.136
peak=    3.671 closest distance to " O   HOH Z 193 " =    1.678
peak=    3.670 closest distance to " O   HOH Z 389 " =    1.889
peak=    3.669 closest distance to " O   HOH Z 368 " =    3.619
peak=    3.667 closest distance to " CD  ARG A  66 " =    2.299
peak=    3.666 closest distance to " CB  VAL A 202 " =    1.593
peak=    3.663 closest distance to " CG2 ILE A 120 " =    1.213
peak=    3.663 closest distance to " O   HOH Z 128 " =    2.242
peak=    3.662 closest distance to " OD1BASN A 224 " =    2.277
peak=    3.659 closest distance to " N   PHE A 130 " =    1.221
peak=    3.650 closest distance to " CG2 THR A 221 " =    1.011
peak=    3.647 closest distance to " O   HOH Z 291 " =    1.549
peak=    3.632 closest distance to " ND1 HIS A  86 " =    1.663
peak=    3.622 closest distance to " O   HOH Z 371 " =    1.724
peak=    3.622 closest distance to " O   HOH Z  40 " =    1.743
peak=    3.619 closest distance to " CG  MET A 113 " =    1.138
peak=    3.616 closest distance to " O   HOH Z  10 " =    1.861
peak=    3.614 closest distance to " O   HOH Z 180 " =    2.126
peak=    3.612 closest distance to " CD  LYS A 166 " =    1.273
peak=    3.609 closest distance to " CD2 TRP A 179 " =    1.291
peak=    3.607 closest distance to " OD2 ASP A 286 " =    2.834
peak=    3.602 closest distance to " CA  ALA A 233 " =    1.278
peak=    3.596 closest distance to " O   HOH Z 371 " =    2.896
peak=    3.589 closest distance to " O   HOH Z 261 " =    2.292
peak=    3.588 closest distance to " O   HOH Z 213 " =    1.988
peak=    3.588 closest distance to " CB  TYR A 116 " =    0.832
peak=    3.576 closest distance to " O   HOH Z 133 " =    2.365
peak=    3.569 closest distance to " N   ASN A  39 " =    1.257
peak=    3.567 closest distance to " O   HOH Z 344 " =    3.136
peak=    3.563 closest distance to " O   ASN A 209 " =    1.286
peak=    3.561 closest distance to " O   HOH Z  44 " =    1.688
peak=    3.557 closest distance to " CG1BVAL A  72 " =    1.567
peak=    3.552 closest distance to " O   HOH Z 402 " =    1.437
peak=    3.551 closest distance to " O   HOH Z 219 " =    2.131
peak=    3.550 closest distance to " CB  MET A  40 " =    0.794
peak=    3.546 closest distance to " CB  ASP A 140 " =    0.867
peak=    3.546 closest distance to " O   HOH Z 273 " =    2.710
peak=    3.537 closest distance to " CG1 VAL A 153 " =    0.867
peak=    3.536 closest distance to " CB  GLU A  46 " =    0.933
peak=    3.532 closest distance to " O   HOH Z 403 " =    1.660
peak=    3.529 closest distance to " CB  ILE A 120 " =    1.161
peak=    3.524 closest distance to " O   HOH Z  61 " =    1.491
peak=    3.521 closest distance to " O   HOH Z 265 " =    2.452
peak=    3.515 closest distance to " O   HOH Z 128 " =    2.082
peak=    3.513 closest distance to " CB  THR A 157 " =    1.124
peak=    3.510 closest distance to " CB  GLN A  88 " =    1.196
peak=    3.508 closest distance to " O   HOH Z 305 " =    3.675
peak=    3.499 closest distance to " CD1 ILE A 106 " =    0.834
peak=    3.497 closest distance to " O   HOH Z 207 " =    1.796
peak=    3.496 closest distance to " O   TYR A 116 " =    1.292
peak=    3.492 closest distance to " NH2BARG A 145 " =    2.062
peak=    3.487 closest distance to " O   HOH Z   3 " =    1.875
peak=    3.486 closest distance to " CB  TRP A 179 " =    1.381
peak=    3.484 closest distance to " CA  ILE A 234 " =    0.935
peak=    3.471 closest distance to " N   ARG A 156 " =    1.326
peak=    3.469 closest distance to " O   HOH Z 193 " =    1.959
peak=    3.463 closest distance to " O   HOH Z 437 " =    1.526
peak=    3.463 closest distance to " O   HOH Z 411 " =    3.797
peak=    3.462 closest distance to " O   HOH Z 426 " =    1.868
peak=    3.462 closest distance to " O   HOH Z 209 " =    2.266
peak=    3.457 closest distance to " CD BLYS A 290 " =    1.130
peak=    3.456 closest distance to " CA  THR A 221 " =    0.976
peak=    3.447 closest distance to " O   HOH Z  93 " =    2.485
peak=    3.445 closest distance to " CB  LYS A 117 " =    1.226
peak=    3.442 closest distance to " CD2 LEU A 255 " =    1.699
peak=    3.442 closest distance to " CD  PRO A 243 " =    1.448
peak=    3.441 closest distance to " CB  ARG A 139 " =    0.912
peak=    3.440 closest distance to " O   HOH Z  43 " =    1.774
peak=    3.437 closest distance to " O   HOH Z 329 " =    3.739
peak=    3.435 closest distance to " CB  ALA A   1 " =    4.634
peak=    3.431 closest distance to " CB  ASN A 110 " =    1.020
peak=    3.431 closest distance to " OG BSER A 164 " =    2.335
peak=    3.430 closest distance to " O   HOH Z 285 " =    2.693
peak=    3.426 closest distance to " CB  GLU A 277 " =    3.588
peak=    3.418 closest distance to " CB  HIS A 108 " =    0.777
peak=    3.409 closest distance to " CA  ALA A  21 " =    1.152
peak=    3.404 closest distance to " O   HOH Z 327 " =    1.724
peak=    3.401 closest distance to " CG  ARG A 159 " =    0.856
peak=    3.398 closest distance to " O   HOH Z   1 " =    1.756
peak=    3.398 closest distance to " O   HOH Z 135 " =    1.661
peak=    3.397 closest distance to " O   HOH Z 245 " =    1.341
peak=    3.386 closest distance to " O   HOH Z 386 " =    3.163
peak=    3.384 closest distance to " N   ASN A 127 " =    1.247
peak=    3.383 closest distance to " CA  ALA A 291 " =    0.857
peak=    3.378 closest distance to " O   HOH Z 294 " =    1.472
peak=    3.377 closest distance to " O   HOH Z 280 " =    3.095
peak=    3.376 closest distance to " O   HOH Z 425 " =    1.914
peak=    3.372 closest distance to " CA  ALA A  51 " =    0.883
peak=    3.372 closest distance to " O   HOH Z 172 " =    3.066
peak=    3.368 closest distance to " CA  ASN A 127 " =    1.053
peak=    3.367 closest distance to " NH1BARG A 145 " =    1.227
peak=    3.365 closest distance to " O   HOH Z 435 " =    1.967
peak=    3.364 closest distance to " NE2 HIS A 207 " =    1.315
peak=    3.358 closest distance to " O   HOH Z 146 " =    1.726
peak=    3.356 closest distance to " CZ  PHE A 208 " =    1.093
peak=    3.355 closest distance to " O   HOH Z 147 " =    1.758
peak=    3.351 closest distance to " CB  MET A  47 " =    1.023
peak=    3.350 closest distance to " CB  ALA A 291 " =    1.256
peak=    3.347 closest distance to " O   HOH Z 227 " =    2.093
peak=    3.344 closest distance to " O   HOH Z 313 " =    1.932
peak=    3.342 closest distance to " ND2 ASN A 249 " =    0.901
peak=    3.341 closest distance to " O  BHOH Z  74 " =    1.271
peak=    3.337 closest distance to " O   HOH Z 213 " =    1.892
peak=    3.329 closest distance to " OE1 GLU A 236 " =    1.210
peak=    3.329 closest distance to " O   HOH Z 133 " =    1.624
peak=    3.328 closest distance to " NZ  LYS A  76 " =    1.566
peak=    3.325 closest distance to " NH2 ARG A 156 " =    1.211
peak=    3.317 closest distance to " O   HOH Z  88 " =    2.862
peak=    3.311 closest distance to " O   HOH Z 337 " =    3.714
peak=    3.308 closest distance to " CA  ARG A  36 " =    1.045
peak=    3.308 closest distance to " CA  ALA A 158 " =    1.149
peak=    3.306 closest distance to " O   HOH Z 409 " =    2.529
peak=    3.306 closest distance to " CB  PRO A 243 " =    1.333
peak=    3.305 closest distance to " OG  SER A  22 " =    2.730
peak=    3.303 closest distance to " O   HOH Z  97 " =    1.985
peak=    3.298 closest distance to " O   HOH Z 128 " =    2.015
peak=    3.294 closest distance to " O   THR A 251 " =    1.140
peak=    3.292 closest distance to " CD1 ILE A 263 " =    1.347
peak=    3.290 closest distance to " N   GLN A 278 " =    1.173
peak=    3.287 closest distance to " CD2 LEU A 297 " =    0.904
peak=    3.287 closest distance to " O   HOH Z 257 " =    2.219
peak=    3.286 closest distance to " O   HOH Z 345 " =    3.457
peak=    3.283 closest distance to " O   HOH Z 336 " =    1.967
peak=    3.280 closest distance to " O   HOH Z 325 " =    3.873
peak=    3.280 closest distance to " O   HOH Z 425 " =    1.287
peak=    3.277 closest distance to " O  BHOH Z 338 " =    2.395
peak=    3.276 closest distance to " CB  SER A 141 " =    1.007
peak=    3.270 closest distance to " CZ  PHE A  38 " =    1.287
peak=    3.267 closest distance to " CA  ALA A  84 " =    1.338
peak=    3.264 closest distance to " O   HOH Z  66 " =    2.063
peak=    3.259 closest distance to " N   CYS A 260 " =    0.769
peak=    3.258 closest distance to " CB  LEU A 255 " =    0.846
peak=    3.258 closest distance to " O   HOH Z 391 " =    2.857
peak=    3.253 closest distance to " O   HOH Z  44 " =    3.002
peak=    3.247 closest distance to " CG1 ILE A 151 " =    1.012
peak=    3.242 closest distance to " O   HOH Z 188 " =    1.990
peak=    3.241 closest distance to " NE2 GLN A  73 " =    3.748
peak=    3.239 closest distance to " CB  ALA A 248 " =    0.947
peak=    3.237 closest distance to " CA  ARG A 195 " =    1.209
peak=    3.237 closest distance to " O   HOH Z 162 " =    2.044
peak=    3.237 closest distance to " CG  GLN A 144 " =    0.938
peak=    3.236 closest distance to " O   HOH Z 183 " =    1.416
peak=    3.236 closest distance to " O   HOH Z  88 " =    1.925
peak=    3.235 closest distance to " CB  ALA A 248 " =    1.339
peak=    3.234 closest distance to " CA  ASN A 217 " =    1.265
peak=    3.232 closest distance to " O   HOH Z  96 " =    2.165
peak=    3.230 closest distance to " CB  ASN A 224 " =    1.023
peak=    3.227 closest distance to " O   HOH Z 407 " =    2.319
peak=    3.227 closest distance to " CB  SER A  26 " =    1.644
peak=    3.223 closest distance to " O   HOH Z 163 " =    1.843
peak=    3.222 closest distance to " O   HOH Z 411 " =    1.728
peak=    3.221 closest distance to " O   HOH Z 433 " =    1.827
peak=    3.219 closest distance to " N   VAL A 296 " =    1.696
peak=    3.218 closest distance to " CB  ALA A   9 " =    1.586
peak=    3.217 closest distance to " O   HOH Z  59 " =    1.889
peak=    3.216 closest distance to " O   HOH Z 295 " =    1.534
peak=    3.211 closest distance to " O   HOH Z 422 " =    2.695
peak=    3.210 closest distance to " O   HOH Z 148 " =    3.362
peak=    3.205 closest distance to " ND1 HIS A  81 " =    1.651
peak=    3.205 closest distance to " CB  ALA A 242 " =    0.796
peak=    3.205 closest distance to " CB  ARG A 138 " =    0.993
peak=    3.205 closest distance to " O   HOH Z 359 " =    4.056
peak=    3.202 closest distance to " CG  GLN A 278 " =    1.315
peak=    3.200 closest distance to " O   ASP A 124 " =    1.128
peak=    3.199 closest distance to " CA  ALA A 154 " =    0.929
peak=    3.198 closest distance to " CA  MET A  40 " =    1.084
peak=    3.193 closest distance to " O   HOH Z 175 " =    2.147
peak=    3.193 closest distance to " O   HOH Z 357 " =    1.886
peak=    3.190 closest distance to " O   HOH Z 332 " =    1.519
peak=    3.189 closest distance to " O   HOH Z 248 " =    1.650
peak=    3.187 closest distance to " CB  LYS A 193 " =    0.988
peak=    3.184 closest distance to " CG  GLN A  89 " =    1.523
peak=    3.182 closest distance to " O   MET A 105 " =    1.729
peak=    3.179 closest distance to " CG BARG A 102 " =    1.839
peak=    3.178 closest distance to " O   HOH Z  62 " =    1.964
peak=    3.177 closest distance to " O   HOH Z 173 " =    1.812
peak=    3.174 closest distance to " O   HOH Z  64 " =    2.137
peak=    3.169 closest distance to " CZ2 TRP A 179 " =    1.702
peak=    3.168 closest distance to " C   TYR A 214 " =    1.518
peak=    3.167 closest distance to " CG  GLN A 240 " =    3.556
peak=    3.163 closest distance to " CB  LEU A  83 " =    0.717
peak=    3.158 closest distance to " CA  ARG A 102 " =    1.108
peak=    3.156 closest distance to " CA  LYS A 290 " =    1.267
peak=    3.156 closest distance to " O   HOH Z 319 " =    2.276
peak=    3.156 closest distance to " OD1 ASP A 238 " =    1.016
peak=    3.153 closest distance to " O   HOH Z 417 " =    1.979
peak=    3.149 closest distance to " CB  ALA A 114 " =    1.085
peak=    3.149 closest distance to " CD  ARG A 219 " =    1.122
peak=    3.149 closest distance to " OG1 THR A 294 " =    1.716
peak=    3.148 closest distance to " CB  ASN A 215 " =    1.020
peak=    3.147 closest distance to " N   SER A 135 " =    1.239
peak=    3.146 closest distance to " NH1 ARG A 138 " =    1.135
peak=    3.146 closest distance to " O   HOH Z  85 " =    2.191
peak=    3.140 closest distance to " OG  SER A 206 " =    1.251
peak=    3.137 closest distance to " O   HOH Z 263 " =    1.695
peak=    3.132 closest distance to " CA  GLY A 267 " =    1.165
peak=    3.129 closest distance to " CB  TRP A 150 " =    1.415
peak=    3.126 closest distance to " O   HOH Z 109 " =    2.590
peak=    3.123 closest distance to " O   HOH Z 302 " =    1.899
peak=    3.108 closest distance to " CB  ALA A 291 " =    0.839
peak=    3.106 closest distance to " CB  VAL A 268 " =    0.814
peak=    3.085 closest distance to " O   HOH Z 423 " =    2.666
peak=    3.081 closest distance to " CG  MET A 185 " =    1.182
peak=    3.080 closest distance to " CG  LYS A  76 " =    0.948
peak=    3.079 closest distance to " CA  ASP A 140 " =    1.259
peak=    3.073 closest distance to " CD1 LEU A  96 " =    0.773
peak=    3.053 closest distance to " CA  ALA A 299 " =    0.917
peak=    3.043 closest distance to " CA  MET A 105 " =    0.911
peak=    3.025 closest distance to " N   GLY A  98 " =    1.012
peak=    3.004 closest distance to " CD2 LEU A 255 " =    1.117

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 199         
Filter by distance & map next to the model:
   mapped sites are within: 0.513 - 5.546
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 199
   mapped sites are within: 0.749 - 5.546

peak=   -4.799 closest distance to " O   HOH Z 290 " =    1.091
peak=   -4.628 closest distance to " CB  PRO A 243 " =    2.663
peak=   -4.432 closest distance to " CD  ARG A 156 " =    2.052
peak=   -4.329 closest distance to " O   HOH Z 435 " =    2.822
peak=   -4.303 closest distance to " O   HOH Z 266 " =    5.042
peak=   -4.237 closest distance to " O   PRO A 198 " =    1.209
peak=   -4.227 closest distance to " CG  GLN A 223 " =    1.788
peak=   -4.199 closest distance to " O   VAL A  67 " =    2.629
peak=   -4.181 closest distance to " CD  ARG A  14 " =    3.444
peak=   -4.180 closest distance to " O   HOH Z 377 " =    1.979
peak=   -4.092 closest distance to " O   HOH Z 351 " =    1.464
peak=   -4.092 closest distance to " O   HOH Z 231 " =    2.246
peak=   -4.050 closest distance to " CZ3 TRP A 179 " =    1.160
peak=   -4.040 closest distance to " OG BSER A 134 " =    1.256
peak=   -3.954 closest distance to " CG1 VAL A 112 " =    2.929
peak=   -3.934 closest distance to " CD  GLN A  58 " =    0.997
peak=   -3.927 closest distance to " C   HIS A 108 " =    1.139
peak=   -3.912 closest distance to " CE2 TYR A  30 " =    2.809
peak=   -3.891 closest distance to " O   VAL A  67 " =    2.833
peak=   -3.869 closest distance to " O   HOH Z 313 " =    1.884
peak=   -3.862 closest distance to " ND2 ASN A  45 " =    1.724
peak=   -3.841 closest distance to " O   HOH Z 389 " =    1.986
peak=   -3.829 closest distance to " CE  MET A 105 " =    2.332
peak=   -3.812 closest distance to " O   HOH Z 372 " =    2.491
peak=   -3.807 closest distance to " N   ALA A  43 " =    2.509
peak=   -3.806 closest distance to " CD1 ILE A 263 " =    3.151
peak=   -3.773 closest distance to " O   HOH Z 185 " =    2.313
peak=   -3.756 closest distance to " CE2 PHE A 218 " =    2.494
peak=   -3.737 closest distance to " CZ  TYR A 169 " =    1.648
peak=   -3.730 closest distance to " CB  ALA A 161 " =    2.608
peak=   -3.702 closest distance to " CB  ASN A  39 " =    2.183
peak=   -3.697 closest distance to " CB  ALA A 291 " =    2.227
peak=   -3.687 closest distance to " CB  ALA A  43 " =    2.555
peak=   -3.684 closest distance to " CD1 PHE A  59 " =    1.839
peak=   -3.683 closest distance to " ND2 ASN A  45 " =    1.092
peak=   -3.678 closest distance to " CG  ASP A 231 " =    0.749
peak=   -3.651 closest distance to " O   HOH Z 114 " =    2.984
peak=   -3.633 closest distance to " O   HOH Z 407 " =    3.172
peak=   -3.629 closest distance to " CA  GLY A  98 " =    1.839
peak=   -3.625 closest distance to " CG  MET A 105 " =    0.957
peak=   -3.620 closest distance to " O   HOH Z 198 " =    2.067
peak=   -3.612 closest distance to " CG  PHE A 283 " =    2.682
peak=   -3.610 closest distance to " CD2 PHE A 192 " =    2.037
peak=   -3.609 closest distance to " O   VAL A 189 " =    2.518
peak=   -3.602 closest distance to " CA  GLY A 241 " =    2.312
peak=   -3.592 closest distance to " O   HOH Z 395 " =    5.173
peak=   -3.588 closest distance to " C   ALA A 158 " =    1.504
peak=   -3.582 closest distance to " CB  ALA A 248 " =    2.060
peak=   -3.579 closest distance to " O   HOH Z  60 " =    2.424
peak=   -3.577 closest distance to " OE1 GLN A  88 " =    1.153
peak=   -3.575 closest distance to " N   THR A 157 " =    1.510
peak=   -3.570 closest distance to " O   HOH Z 394 " =    1.379
peak=   -3.558 closest distance to " CD  ARG A 139 " =    1.595
peak=   -3.552 closest distance to " O   ARG A 145 " =    1.590
peak=   -3.548 closest distance to " O   HOH Z 198 " =    1.377
peak=   -3.547 closest distance to " NH2AARG A 275 " =    5.333
peak=   -3.545 closest distance to " CD1 ILE A 239 " =    2.574
peak=   -3.540 closest distance to " O   HOH Z  38 " =    1.509
peak=   -3.537 closest distance to " CG2 ILE A 263 " =    2.304
peak=   -3.537 closest distance to " N   ASP A 286 " =    2.451
peak=   -3.525 closest distance to " O   SER A  95 " =    1.554
peak=   -3.519 closest distance to " O   HOH Z 359 " =    3.321
peak=   -3.517 closest distance to " CB  ALA A 248 " =    2.431
peak=   -3.511 closest distance to " O   HOH Z 282 " =    1.053
peak=   -3.510 closest distance to " ND2 ASN A 249 " =    2.336
peak=   -3.508 closest distance to " N   GLN A  58 " =    1.853
peak=   -3.493 closest distance to " OXT GLY A 302 " =    2.873
peak=   -3.484 closest distance to " O   HOH Z  10 " =    1.472
peak=   -3.484 closest distance to " OD1 ASP A 171 " =    1.603
peak=   -3.482 closest distance to " O   HOH Z  52 " =    1.127
peak=   -3.482 closest distance to " O   HOH Z  51 " =    1.202
peak=   -3.469 closest distance to " CZ  PHE A  59 " =    1.495
peak=   -3.469 closest distance to " OD1 ASN A 148 " =    1.588
peak=   -3.468 closest distance to " CB  PHE A 208 " =    2.247
peak=   -3.461 closest distance to " O   HOH Z 211 " =    1.620
peak=   -3.459 closest distance to " O   PRO A 163 " =    1.983
peak=   -3.454 closest distance to " O   HOH Z 126 " =    1.890
peak=   -3.444 closest distance to " O   HOH Z  73 " =    2.225
peak=   -3.444 closest distance to " O   HOH Z 353 " =    2.187
peak=   -3.441 closest distance to " O   HOH Z  63 " =    1.683
peak=   -3.436 closest distance to " CB  PRO A 163 " =    2.561
peak=   -3.433 closest distance to " NE2 GLN A 278 " =    1.740
peak=   -3.427 closest distance to " CB  ALA A 131 " =    2.085
peak=   -3.423 closest distance to " O   GLN A 240 " =    2.168
peak=   -3.421 closest distance to " CB  TRP A  85 " =    2.482
peak=   -3.419 closest distance to " O   HOH Z 140 " =    1.582
peak=   -3.417 closest distance to " CE3 TRP A 274 " =    1.079
peak=   -3.415 closest distance to " CG2 THR A 178 " =    2.257
peak=   -3.415 closest distance to " OD2 ASP A 171 " =    2.164
peak=   -3.413 closest distance to " OG  SER A  97 " =    2.195
peak=   -3.413 closest distance to " O   HOH Z  11 " =    1.825
peak=   -3.409 closest distance to " C   LEU A 222 " =    0.767
peak=   -3.409 closest distance to " O   HOH Z  43 " =    1.711
peak=   -3.405 closest distance to " CG  GLU A 277 " =    1.242
peak=   -3.404 closest distance to " CA  GLY A 203 " =    2.308
peak=   -3.396 closest distance to " CD2 LEU A 237 " =    2.816
peak=   -3.393 closest distance to " CG  GLU A 152 " =    0.799
peak=   -3.368 closest distance to " CD1 LEU A 101 " =    2.255
peak=   -3.364 closest distance to " O   SER A  22 " =    2.500
peak=   -3.346 closest distance to " O   HOH Z 176 " =    0.841
peak=   -3.343 closest distance to " N   MET A 105 " =    2.614
peak=   -3.338 closest distance to " CG1 VAL A 112 " =    2.647
peak=   -3.335 closest distance to " CB  CYS A 254 " =    2.349
peak=   -3.334 closest distance to " O   HOH Z 114 " =    1.654
peak=   -3.332 closest distance to " O   HOH Z 423 " =    1.135
peak=   -3.332 closest distance to " O   PRO A 198 " =    1.243
peak=   -3.331 closest distance to " O   GLY A 211 " =    1.287
peak=   -3.330 closest distance to " O   SER A 135 " =    1.422
peak=   -3.328 closest distance to " CB  ALA A 291 " =    2.030
peak=   -3.312 closest distance to " O   HOH Z 298 " =    1.204
peak=   -3.309 closest distance to " NH1 ARG A 195 " =    2.574
peak=   -3.309 closest distance to " O   ALA A 161 " =    1.600
peak=   -3.306 closest distance to " CE BMET A  47 " =    1.721
peak=   -3.306 closest distance to " CE1 TYR A 169 " =    2.532
peak=   -3.306 closest distance to " N   SER A 212 " =    1.892
peak=   -3.305 closest distance to " ND2 ASN A 187 " =    1.610
peak=   -3.297 closest distance to " O   HOH Z 174 " =    2.672
peak=   -3.295 closest distance to " O   HOH Z  98 " =    2.279
peak=   -3.292 closest distance to " O   GLY A  17 " =    1.321
peak=   -3.292 closest distance to " CG1 VAL A 197 " =    2.195
peak=   -3.290 closest distance to " NH2BARG A 275 " =    1.824
peak=   -3.288 closest distance to " O   HOH Z 385 " =    2.091
peak=   -3.287 closest distance to " OG  SER A   3 " =    1.657
peak=   -3.287 closest distance to " NH2 ARG A  79 " =    1.574
peak=   -3.284 closest distance to " OG BSER A 134 " =    1.744
peak=   -3.284 closest distance to " CD  GLU A 236 " =    1.049
peak=   -3.281 closest distance to " O   PHE A 218 " =    1.487
peak=   -3.281 closest distance to " CD1 LEU A 228 " =    2.287
peak=   -3.273 closest distance to " NH2 ARG A  79 " =    2.011
peak=   -3.272 closest distance to " CB  TYR A  15 " =    2.228
peak=   -3.268 closest distance to " C   PHE A  59 " =    1.352
peak=   -3.267 closest distance to " CE2 PHE A  61 " =    2.625
peak=   -3.266 closest distance to " OH  TYR A 172 " =    1.847
peak=   -3.263 closest distance to " CB  ASP A 132 " =    2.370
peak=   -3.262 closest distance to " O   ALA A 180 " =    1.228
peak=   -3.258 closest distance to " CB  ASP A 286 " =    2.035
peak=   -3.257 closest distance to " C   MET A 188 " =    1.457
peak=   -3.251 closest distance to " CA  TRP A 274 " =    1.339
peak=   -3.249 closest distance to " C   LEU A 143 " =    1.245
peak=   -3.247 closest distance to " CB  GLN A  11 " =    1.676
peak=   -3.246 closest distance to " O   HOH Z 298 " =    2.424
peak=   -3.246 closest distance to " CG  ARG A 269 " =    2.427
peak=   -3.242 closest distance to " O   HOH Z 222 " =    1.086
peak=   -3.241 closest distance to " N   ASP A 171 " =    2.349
peak=   -3.233 closest distance to " O   HOH Z  13 " =    1.486
peak=   -3.233 closest distance to " CG  LEU A  83 " =    1.833
peak=   -3.227 closest distance to " CA  GLY A 133 " =    2.028
peak=   -3.225 closest distance to " ND2BASN A 224 " =    1.757
peak=   -3.218 closest distance to " O   HOH Z 253 " =    3.923
peak=   -3.218 closest distance to " O   VAL A 189 " =    1.585
peak=   -3.214 closest distance to " CE3 TRP A 274 " =    2.432
peak=   -3.211 closest distance to " O   HOH Z 244 " =    1.943
peak=   -3.209 closest distance to " O   HOH Z 198 " =    0.755
peak=   -3.208 closest distance to " CD  GLN A  88 " =    0.815
peak=   -3.208 closest distance to " O   HOH Z 210 " =    0.892
peak=   -3.208 closest distance to " O   HOH Z 317 " =    1.435
peak=   -3.206 closest distance to " CB  CYS A 201 " =    2.580
peak=   -3.197 closest distance to " O   TRP A  70 " =    1.430
peak=   -3.196 closest distance to " CD1 LEU A 297 " =    2.502
peak=   -3.185 closest distance to " O   HOH Z 102 " =    1.567
peak=   -3.181 closest distance to " OD2 ASP A  50 " =    1.758
peak=   -3.176 closest distance to " O   HOH Z 281 " =    2.689
peak=   -3.175 closest distance to " O   HOH Z 417 " =    2.507
peak=   -3.174 closest distance to " N   SER A 276 " =    1.219
peak=   -3.169 closest distance to " OG1 THR A 246 " =    1.455
peak=   -3.169 closest distance to " CA  GLY A 241 " =    3.297
peak=   -3.168 closest distance to " O   HOH Z 100 " =    1.363
peak=   -3.168 closest distance to " OD1 ASP A 191 " =    1.628
peak=   -3.167 closest distance to " CZ  ARG A 259 " =    0.830
peak=   -3.160 closest distance to " CE  LYS A  76 " =    2.765
peak=   -3.158 closest distance to " CA  ASP A  27 " =    2.444
peak=   -3.155 closest distance to " CH2 TRP A 179 " =    2.074
peak=   -3.149 closest distance to " O   HOH Z  93 " =    2.397
peak=   -3.148 closest distance to " CG1 VAL A 250 " =    2.689
peak=   -3.148 closest distance to " O   HOH Z 426 " =    1.614
peak=   -3.137 closest distance to " N   ALA A 248 " =    1.575
peak=   -3.137 closest distance to " O   HOH Z 390 " =    2.458
peak=   -3.135 closest distance to " CD1 TYR A 247 " =    2.797
peak=   -3.134 closest distance to " CG1 VAL A 125 " =    1.910
peak=   -3.131 closest distance to " CE3 TRP A 150 " =    2.090
peak=   -3.131 closest distance to " CG  TRP A 266 " =    1.899
peak=   -3.128 closest distance to " O   HOH Z 357 " =    2.004
peak=   -3.127 closest distance to " O   HOH Z 282 " =    4.961
peak=   -3.126 closest distance to " O   HOH Z 283 " =    5.546
peak=   -3.125 closest distance to " OD2 ASP A 171 " =    1.769
peak=   -3.120 closest distance to " CD2 TYR A 293 " =    1.952
peak=   -3.100 closest distance to " N   ALA A 226 " =    2.135
peak=   -3.099 closest distance to " CA  ILE A 263 " =    1.022
peak=   -3.098 closest distance to " O   HOH Z 111 " =    2.065
peak=   -3.093 closest distance to " O   HOH Z 429 " =    2.106
peak=   -3.091 closest distance to " O   HOH Z 200 " =    4.477
peak=   -3.074 closest distance to " O   HOH Z 323 " =    1.281
peak=   -3.074 closest distance to " O   ALA A 292 " =    2.010
peak=   -3.054 closest distance to " N   ASP A 270 " =    1.369
peak=   -3.042 closest distance to " O   HOH Z 137 " =    1.565
peak=   -3.004 closest distance to " ND2 ASN A  60 " =    1.341

================= 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    :  0.2782 0.2727   5.934343e+00   5.911193e+00
   1_bss:  0.2621 0.2580   5.907881e+00   5.877574e+00
   1_xyz:  0.1590 0.1808   5.406854e+00   5.513553e+00
   1_adp:  0.1449 0.1872   5.354499e+00   5.548163e+00
   1_occ:  0.1446 0.1872   5.353022e+00   5.546977e+00
   2_bss:  0.1436 0.1851   5.344787e+00   5.536558e+00
   2_xyz:  0.1213 0.1621   5.197884e+00   5.415394e+00
   2_adp:  0.1191 0.1568   5.174216e+00   5.385023e+00
   2_occ:  0.1189 0.1569   5.173984e+00   5.385303e+00
   3_bss:  0.1188 0.1566   5.172499e+00   5.383954e+00
   3_xyz:  0.1116 0.1525   5.128282e+00   5.358773e+00
   3_adp:  0.1092 0.1532   5.120305e+00   5.362743e+00
   3_occ:  0.1091 0.1533   5.120366e+00   5.363119e+00
   4_bss:  0.1091 0.1532   5.120051e+00   5.361340e+00
   4_xyz:  0.1052 0.1539   5.105013e+00   5.366035e+00
   4_adp:  0.1049 0.1542   5.104439e+00   5.367351e+00
   4_occ:  0.1048 0.1542   5.104506e+00   5.367548e+00
   5_bss:  0.1047 0.1542   5.104609e+00   5.367629e+00
   5_xyz:  0.1094 0.1561   5.132575e+00   5.381742e+00
   5_adp:  0.1111 0.1548   5.135207e+00   5.375075e+00
   5_occ:  0.1111 0.1548   5.135097e+00   5.375154e+00
   5_bss:  0.1111 0.1550   5.135562e+00   5.375938e+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:  0.337  51.789  -2.497   0.224  -1.687   0.000  -0.000  -0.000
   1_xyz:  0.337  51.789  -2.497   0.224  -1.687   0.000  -0.000  -0.000
   1_adp:  0.337  51.789  -2.497   0.224  -1.687   0.000  -0.000  -0.000
   1_occ:  0.337  51.789  -2.497   0.224  -1.687   0.000  -0.000  -0.000
   2_bss:  0.328  51.789  -2.739  -2.041  -1.688  -0.000  -0.000  -0.000
   2_xyz:  0.328  51.789  -2.739  -2.041  -1.688  -0.000  -0.000  -0.000
   2_adp:  0.328  51.789  -2.739  -2.041  -1.688  -0.000  -0.000  -0.000
   2_occ:  0.328  51.789  -2.739  -2.041  -1.688  -0.000  -0.000  -0.000
   3_bss:  0.328  51.789  -2.596  -2.415  -1.381  -0.000  -0.000  -0.000
   3_xyz:  0.328  51.789  -2.596  -2.415  -1.381  -0.000  -0.000  -0.000
   3_adp:  0.328  51.789  -2.596  -2.415  -1.381  -0.000  -0.000  -0.000
   3_occ:  0.328  51.789  -2.596  -2.415  -1.381  -0.000  -0.000  -0.000
   4_bss:  0.322  51.789  -2.434  -2.424  -1.246  -0.000  -0.000  -0.000
   4_xyz:  0.322  51.789  -2.434  -2.424  -1.246  -0.000  -0.000  -0.000
   4_adp:  0.322  51.789  -2.434  -2.424  -1.246  -0.000  -0.000  -0.000
   4_occ:  0.322  51.789  -2.434  -2.424  -1.246  -0.000  -0.000  -0.000
   5_bss:  0.322  51.789  -2.172  -2.230  -0.985  -0.000  -0.000  -0.000
   5_xyz:  0.322  51.789  -2.172  -2.230  -0.985  -0.000  -0.000  -0.000
   5_adp:  0.322  51.789  -2.172  -2.230  -0.985  -0.000  -0.000  -0.000
   5_occ:  0.322  51.789  -2.172  -2.230  -0.985  -0.000  -0.000  -0.000
   5_bss:  0.319  45.477  -2.059  -2.128  -0.822  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  27.115 0.7936  0.9674    21370.198
   1_bss:  25.906 0.8043  0.9360    18529.575
   1_xyz:  16.484 0.8952  0.9982     8324.216
   1_adp:  17.379 0.8868  0.9926     8885.313
   1_occ:  17.361 0.8869  0.9924     8854.383
   2_bss:  17.075 0.8894  0.9663     8649.415
   2_xyz:  14.556 0.9104  0.9776     6672.920
   2_adp:  13.900 0.9159  0.9781     6332.272
   2_occ:  13.907 0.9159  0.9779     6329.994
   3_bss:  13.878 0.9161  0.9793     6314.564
   3_xyz:  13.349 0.9202  0.9806     6004.171
   3_adp:  13.427 0.9197  0.9744     6004.116
   3_occ:  13.432 0.9197  0.9743     6009.038
   4_bss:  13.409 0.9198  0.9774     5973.445
   4_xyz:  13.469 0.9194  0.9772     6048.716
   4_adp:  13.498 0.9191  0.9705     6049.992
   4_occ:  13.503 0.9191  0.9704     6052.340
   5_bss:  13.506 0.9191  0.9789     6054.649
   5_xyz:  13.747 0.9174  0.9776     6234.490
   5_adp:  13.591 0.9186  0.9735     6188.144
   5_occ:  13.596 0.9186  0.9734     6186.637
   5_bss:  13.614 0.9185  0.9752     6193.585
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6076e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6076e-01
   1_xyz:   0.973  0.007  0.069 15.145  0.004  4.111   5.8694e-02
   1_adp:   0.973  0.007  0.069 15.145  0.004  4.111   5.8694e-02
   1_occ:   0.973  0.007  0.069 15.145  0.004  4.111   5.8694e-02
   2_bss:   0.973  0.007  0.069 15.145  0.004  4.111   5.8694e-02
   2_xyz:   0.880  0.005  0.069 14.713  0.003  4.111   4.8858e-02
   2_adp:   0.880  0.005  0.069 14.713  0.003  4.111   4.8858e-02
   2_occ:   0.880  0.005  0.069 14.713  0.003  4.111   4.8858e-02
   3_bss:   0.880  0.005  0.069 14.713  0.003  4.111   4.8858e-02
   3_xyz:   0.954  0.007  0.074 14.867  0.003  4.112   5.6755e-02
   3_adp:   0.954  0.007  0.074 14.867  0.003  4.112   5.6755e-02
   3_occ:   0.954  0.007  0.074 14.867  0.003  4.112   5.6755e-02
   4_bss:   0.954  0.007  0.074 14.867  0.003  4.112   5.6755e-02
   4_xyz:   1.050  0.009  0.081 15.101  0.004  4.119   6.8005e-02
   4_adp:   1.050  0.009  0.081 15.101  0.004  4.119   6.8005e-02
   4_occ:   1.050  0.009  0.081 15.101  0.004  4.119   6.8005e-02
   5_bss:   1.050  0.009  0.081 15.101  0.004  4.119   6.8005e-02
   5_xyz:   0.863  0.005  0.068 14.703  0.003  4.117   4.8218e-02
   5_adp:   0.863  0.005  0.068 14.703  0.003  4.117   4.8218e-02
   5_occ:   0.863  0.005  0.068 14.703  0.003  4.117   4.8218e-02
   5_bss:   0.863  0.005  0.068 14.703  0.003  4.117   4.8218e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4069e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4069e-01
   1_xyz:   7.891  0.044  0.255 84.962  0.042  2.329   5.1519e-02
   1_adp:   7.891  0.044  0.255 84.962  0.042  2.329   5.1519e-02
   1_occ:   7.891  0.044  0.255 84.962  0.042  2.329   5.1519e-02
   2_bss:   7.891  0.044  0.255 84.962  0.042  2.329   5.1519e-02
   2_xyz:   7.424  0.040  0.198 83.526  0.027  2.382   3.1958e-02
   2_adp:   7.424  0.040  0.198 83.526  0.027  2.382   3.1958e-02
   2_occ:   7.424  0.040  0.198 83.526  0.027  2.382   3.1958e-02
   3_bss:   7.424  0.040  0.198 83.526  0.027  2.382   3.1958e-02
   3_xyz:   7.113  0.041  0.241 84.694  0.032  2.334   4.0528e-02
   3_adp:   7.113  0.041  0.241 84.694  0.032  2.334   4.0528e-02
   3_occ:   7.113  0.041  0.241 84.694  0.032  2.334   4.0528e-02
   4_bss:   7.113  0.041  0.241 84.694  0.032  2.334   4.0528e-02
   4_xyz:   6.689  0.047  0.265 84.114  0.038  2.298   5.5198e-02
   4_adp:   6.689  0.047  0.265 84.114  0.038  2.298   5.5198e-02
   4_occ:   6.689  0.047  0.265 84.114  0.038  2.298   5.5198e-02
   5_bss:   6.689  0.047  0.265 84.114  0.038  2.298   5.5198e-02
   5_xyz:   7.032  0.038  0.210 83.925  0.032  2.387   2.7113e-02
   5_adp:   7.032  0.038  0.210 83.925  0.032  2.387   2.7113e-02
   5_occ:   7.032  0.038  0.210 83.925  0.032  2.387   2.7113e-02
   5_bss:   7.032  0.038  0.210 83.925  0.032  2.387   2.7113e-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:  68.54   1.69  16.85  65.61   1.69  12.91  68.54   7.06  38.30
   1_occ:  68.54   1.69  16.85  65.61   1.69  12.91  68.54   7.06  38.30
   2_bss:  68.54   1.69  16.85  65.61   1.69  12.91  68.54   7.06  38.30
   2_xyz:  68.54   1.69  16.85  65.61   1.69  12.91  68.54   7.06  38.30
   2_adp:  67.45   2.03  16.73  66.26   2.03  12.88  67.45   6.12  37.73
   2_occ:  67.45   2.03  16.73  66.26   2.03  12.88  67.45   6.12  37.73
   3_bss:  67.45   2.03  16.73  66.26   2.03  12.88  67.45   6.12  37.73
   3_xyz:  67.45   2.03  16.73  66.26   2.03  12.88  67.45   6.12  37.73
   3_adp:  84.57   0.57  17.25  84.57   0.57  13.00  78.12   6.30  40.39
   3_occ:  84.57   0.57  17.25  84.57   0.57  13.00  78.12   6.30  40.39
   4_bss:  84.57   0.57  17.25  84.57   0.57  13.00  78.12   6.30  40.39
   4_xyz:  84.57   0.57  17.25  84.57   0.57  13.00  78.12   6.30  40.39
   4_adp:  86.11   0.40  17.07  86.11   0.40  12.81  78.94   6.25  40.28
   4_occ:  86.11   0.40  17.07  86.11   0.40  12.81  78.94   6.25  40.28
   5_bss:  86.11   0.40  17.07  86.11   0.40  12.81  78.94   6.25  40.28
   5_xyz:  86.11   0.40  17.07  86.11   0.40  12.81  78.94   6.25  40.28
   5_adp:  82.00   1.95  16.26  82.00   1.95  12.49  78.53   6.23  36.80
   5_occ:  82.00   1.95  16.26  82.00   1.95  12.49  78.53   6.23  36.80
   5_bss:  81.93   1.88  16.19  81.93   1.88  12.42  78.46   6.16  36.73
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    0.850    0.022    0.258
   1_adp:    0.850    0.022    0.258
   1_occ:    0.850    0.022    0.258
   2_bss:    0.850    0.022    0.258
   2_xyz:    0.691    0.023    0.291
   2_adp:    0.691    0.023    0.291
   2_occ:    0.691    0.023    0.291
   3_bss:    0.691    0.023    0.291
   3_xyz:    0.807    0.043    0.321
   3_adp:    0.807    0.043    0.321
   3_occ:    0.807    0.043    0.321
   4_bss:    0.807    0.043    0.321
   4_xyz:    0.957    0.043    0.331
   4_adp:    0.957    0.043    0.331
   4_occ:    0.957    0.043    0.331
   5_bss:    0.957    0.043    0.331
   5_xyz:    1.053    0.051    0.334
   5_adp:    1.053    0.051    0.334
   5_occ:    1.053    0.051    0.334
   5_bss:    1.053    0.051    0.334
------------------------------------------------------------------------

CPU time actual refinement: 326.03


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_764/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_764/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_764/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_764/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_764/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 325.89 
  Macro-tasks:
    bulk solvent and scale       = 38.53  
    individual site refinement   = 132.28 
    weights calculation          = 29.84  
    collect and process          = 6.73   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 207.47 
  Micro-tasks:
    mask                            = 1.12   
    f_calc                          = 105.16 
    alpha_beta                      = 7.98   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 109.38 
    fmodel                         = 6.61   
    r_factors                      = 0.25   
    phase_errors                   = 12.37  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 244.23 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.605 micro seconds
Total CPU time: 5.65 minutes
from_scatterers_fft:    654 calls, 104.78 s
gradients_fft:          599 calls,  97.48 s

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

# Date 2008-01-16 Time 05:36:35 PST -0800 (1200490595.47 s)
Start R-work = 0.2782, R-free = 0.2727 (no bulk solvent and anisotropic scale)
Final R-work = 0.1345, R-free = 0.1746 (no bulk solvent and anisotropic scale)

Start R-work = 0.2621, R-free = 0.2580
Final R-work = 0.1111, R-free = 0.1550