# Date 2008-01-16 Time 05:43:22 PST -0800 (1200491002.25 s)
#phil __OFF__

Command line arguments: "../856.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 13008
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 856

-------------------------------------------------------------------------------
  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: (70.9525, 45.7567, 88.1178, 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: (70.9525, 45.7567, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1841 1.95412
Completeness in resolution range: 0.916316
Completeness with d_max=infinity: 0.913709

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1841
                             d_min =   1.9541

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: (70.9525, 45.7567, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1841 1.95412
Completeness in resolution range: 0.916316
Completeness with d_max=infinity: 0.913709

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1846 -  4.1834 [2241/2267]  2018   223  10.0%
  bin  2:  4.1834 -  3.3321 [2169/2189]  1955   214   9.9%
  bin  3:  3.3321 -  2.9142 [2116/2135]  1902   214  10.1%
  bin  4:  2.9142 -  2.6493 [2118/2148]  1897   221  10.4%
  bin  5:  2.6493 -  2.4603 [2105/2124]  1898   207   9.8%
  bin  6:  2.4603 -  2.3158 [2073/2098]  1867   206   9.9%
  bin  7:  2.3158 -  2.2002 [2094/2122]  1886   208   9.9%
  bin  8:  2.2002 -  2.1046 [2065/2101]  1854   211  10.2%
  bin  9:  2.1046 -  2.0238 [2010/2094]  1818   192   9.6%
  bin 10:  2.0238 -  1.9541 [ 598/2100]   535    63  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_856/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.68 -     2.32: 32
        2.32 -     2.97: 1774
        2.97 -     3.61: 4564
        3.61 -     4.26: 9146
        4.26 -     4.90: 12752
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 324 " - " O   HOH Z 374 "  1.869 3.040 -x,y-1/2,-z+1/2
  ... (remaining 28263 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_856/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_856/model_refine_001.geo

CPU time processing inputs: 9.18


============================ 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 = 70.9525 45.75675 88.1178 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: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4797   r_free= 0.4826   ksol= 0.00   Bsol= 0.00   scale= 0.876    |
|                                                                             |
| 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:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.294769                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1846 -  4.6670 0.99   1455  163 0.3982 0.3826      6.6199       6.589|
|  2:  4.6670 -  3.7223 0.99   1399  154 0.4246 0.4257      6.8439      6.8237|
|  3:  3.7223 -  3.2571 0.99   1378  154 0.4514 0.4302      6.6808      6.6749|
|  4:  3.2571 -  2.9617 0.99   1380  153 0.4834 0.5107      6.5407      6.5398|
|  5:  2.9617 -  2.7507 0.99   1346  150 0.5116 0.5150      6.3648      6.3915|
|  6:  2.7507 -  2.5894 0.99   1368  150 0.5114 0.5325       6.278      6.2235|
|  7:  2.5894 -  2.4603 0.99   1344  155 0.5098 0.5318      6.2319      6.1739|
|  8:  2.4603 -  2.3536 0.98   1332  147 0.5263 0.5286       6.169      6.1521|
|  9:  2.3536 -  2.2633 0.98   1335  145 0.5150 0.5455      6.1276      6.2086|
| 10:  2.2633 -  2.1854 1.00   1352  157 0.5301 0.5567      6.0591      6.0681|
| 11:  2.1854 -  2.1173 0.98   1313  142 0.5093 0.4761      6.0191      6.0384|
| 12:  2.1173 -  2.0569 0.98   1336  143 0.5148 0.5120      5.9274      5.9326|
| 13:  2.0569 -  2.0029 0.79   1051  118 0.5251 0.5100      5.8861      5.7932|
| 14:  2.0029 -  1.9541 0.18    241   28 0.5188 0.4991      5.8476      5.8932|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1846 -  4.6670  1455   163  0.70  33.89   0.80     0.76      73086.23|
|  2:  4.6670 -  3.7223  1399   154  0.67  37.98   0.88     0.78     124059.01|
|  3:  3.7223 -  3.2571  1378   154  0.51  51.10   0.90     0.70     137633.27|
|  4:  3.2571 -  2.9617  1380   153  0.38  61.14   0.88     0.56     130122.18|
|  5:  2.9617 -  2.7507  1346   150  0.33  65.39   0.86     0.49      95908.40|
|  6:  2.7507 -  2.5894  1368   150  0.31  67.05   0.88     0.45      80198.43|
|  7:  2.5894 -  2.4603  1344   155  0.32  66.34   0.90     0.45      69280.05|
|  8:  2.4603 -  2.3536  1332   147  0.29  68.64   0.89     0.42      63729.30|
|  9:  2.3536 -  2.2633  1335   145  0.27  69.65   0.92     0.41      61082.09|
| 10:  2.2633 -  2.1854  1352   157  0.26  70.51   0.90     0.40      54164.04|
| 11:  2.1854 -  2.1173  1313   142  0.25  71.48   0.96     0.39      52162.36|
| 12:  2.1173 -  2.0569  1336   143  0.26  70.42   0.91     0.42      45478.92|
| 13:  2.0569 -  2.0029  1051   118  0.28  68.97   0.94     0.48      39266.65|
| 14:  2.0029 -  1.9541   241    28  0.41  59.74   1.01     0.58      28367.38|
|alpha:            min =        0.39 max =            0.78 mean =         0.52|
|beta:             min =    28367.38 max =       137633.27 mean =     79300.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.38|
|phase err.(work): min =        0.00 max =           89.99 mean =        61.30|
|phase err.(test): min =        0.00 max =           89.76 mean =        61.77|
|-----------------------------------------------------------------------------|

============================== 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 = 16.827679             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.671   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.785142              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.626   (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 |  1.681 -  2.003:       12 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.003 -  2.325:       20 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.325 -  2.647:       78 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.647 -  2.969:     1696 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.969 -  3.290:     1910 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.290 -  3.612:     2654 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.612 -  3.934:     4742 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.934 -  4.256:     4404 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.256 -  4.578:     5800 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.578 -  4.900:     6952 |
|-----------------------------------------------------------------------------|
|-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 |        0.185 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.681 |       0.510 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.858)------------------------------------------|
|    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: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4797   r_free= 0.4826   ksol= 0.00   Bsol= 0.00   scale= 0.876    |
|                                                                             |
| 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:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.294769                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4711   r_free= 0.4779   ksol= 0.30   Bsol= 50.00   scale= 0.910   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,1.32,2.31,0.00,0.00,0.00); trace/3= 0.41                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.292150                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.032774             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.487   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.694012              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.310   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4711      final r-factor (work) = 0.3989          |
| start r-factor (free) = 0.4779      final r-factor (free) = 0.4411          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.1467 = 13.03 * 0.50 * 6.2859 + 1.00 * 0.1853                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.6343 = 13.03 * 0.50 * 6.2159 + 1.00 * 0.1292                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3989      final r-factor (work) = 0.3672          |
| start r-factor (free) = 0.4411      final r-factor (free) = 0.4501          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.5358 = 1.69 * 1.00 * 6.2159 + 1.00 * 0.0061                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.4395 = 1.69 * 1.00 * 6.1496 + 1.00 * 0.0221                              |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.858)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.16   19.89    None  None   None       |
|    all(noH): 2823   0      0.00    89.16   19.89    None  None   None       |
|    Sol.    : 438    0      0.00    89.16   36.07    None  None   None       |
|    Mac.    : 2385   0      0.00    71.75   16.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.916:  707   |   5:    44.580 -  53.497:  108        |
|      1:     8.916 -  17.832:  789   |   6:    53.497 -  62.413:   68        |
|      2:    17.832 -  26.748:  594   |   7:    62.413 -  71.329:   26        |
|      3:    26.748 -  35.664:  351   |   8:    71.329 -  80.245:   13        |
|      4:    35.664 -  44.580:  164   |   9:    80.245 -  89.161:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3672 r_free = 0.4501             target_work(ml) = 6.154         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3669 r_free = 0.4513             target_work(ml) = 6.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3669   r_free= 0.4513   ksol= 0.30   Bsol= 50.00   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,1.32,2.31,0.00,0.00,0.00); trace/3= 0.41                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.153929                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3671   r_free= 0.4501   ksol= 0.36   Bsol= 82.66   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.99,0.13,1.37,0.00,0.00,0.00); trace/3= 0.17                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.157328                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.867299             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.552  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.675216              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.489  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3671      final r-factor (work) = 0.3081          |
| start r-factor (free) = 0.4501      final r-factor (free) = 0.3959          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 45.8579 = 14.87 * 0.50 * 6.1516 + 1.00 * 0.1292                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 45.4787 = 14.87 * 0.50 * 6.1037 + 1.00 * 0.1059                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3081      final r-factor (work) = 0.2940          |
| start r-factor (free) = 0.3959      final r-factor (free) = 0.3820          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1432 = 0.68 * 1.00 * 6.1037 + 1.00 * 0.0219                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0759 = 0.68 * 1.00 * 6.0173 + 1.00 * 0.0129                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.858)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.38   19.14    None  None   None       |
|    all(noH): 2823   0      0.00    87.38   19.14    None  None   None       |
|    Sol.    : 438    0      0.00    87.38   36.04    None  None   None       |
|    Mac.    : 2385   0      0.00    75.05   16.04    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.738:  642   |   5:    43.691 -  52.429:  101        |
|      1:     8.738 -  17.476:  934   |   6:    52.429 -  61.167:   54        |
|      2:    17.476 -  26.215:  573   |   7:    61.167 -  69.905:   24        |
|      3:    26.215 -  34.953:  331   |   8:    69.905 -  78.643:    9        |
|      4:    34.953 -  43.691:  152   |   9:    78.643 -  87.382:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2940 r_free = 0.3820             target_work(ml) = 6.003         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2938 r_free = 0.3819             target_work(ml) = 6.003         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2938   r_free= 0.3819   ksol= 0.36   Bsol= 82.66   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.99,0.13,1.37,0.00,0.00,0.00); trace/3= 0.17                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.002652                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2942   r_free= 0.3811   ksol= 0.36   Bsol= 88.29   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.19,-0.85,0.47,-0.00,0.00,0.00); trace/3= -0.52                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.002022                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.993066              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.513  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.472794              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.310  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2942      final r-factor (work) = 0.2373          |
| start r-factor (free) = 0.3811      final r-factor (free) = 0.3117          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.1718 = 9.99 * 0.50 * 6.0173 + 1.00 * 0.1059                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.7296 = 9.99 * 0.50 * 5.9318 + 1.00 * 0.0911                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2373      final r-factor (work) = 0.2119          |
| start r-factor (free) = 0.3117      final r-factor (free) = 0.2957          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7492 = 1.47 * 1.00 * 5.9318 + 1.00 * 0.0128                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.5086 = 1.47 * 1.00 * 5.7657 + 1.00 * 0.0170                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.858)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.39   19.92    None  None   None       |
|    all(noH): 2823   0      0.00    98.39   19.92    None  None   None       |
|    Sol.    : 438    0      3.34    98.39   46.89    None  None   None       |
|    Mac.    : 2385   0      0.00    91.78   14.96    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.839:  925   |   5:    49.193 -  59.031:  102        |
|      1:     9.839 -  19.677:  953   |   6:    59.031 -  68.870:   72        |
|      2:    19.677 -  29.516:  378   |   7:    68.870 -  78.708:   42        |
|      3:    29.516 -  39.354:  192   |   8:    78.708 -  88.547:   25        |
|      4:    39.354 -  49.193:  127   |   9:    88.547 -  98.385:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2119 r_free = 0.2957             target_work(ml) = 5.738         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2119 r_free = 0.2956             target_work(ml) = 5.738         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2119   r_free= 0.2956   ksol= 0.36   Bsol= 88.29   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.19,-0.85,0.47,-0.00,0.00,0.00); trace/3= -0.52                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.737627                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2117   r_free= 0.2954   ksol= 0.34   Bsol= 80.29   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.66,-1.73,0.09,-0.00,0.00,0.00); trace/3= -1.10                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.735620                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.452144              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.627   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.580196              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.280  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2117      final r-factor (work) = 0.1735          |
| start r-factor (free) = 0.2954      final r-factor (free) = 0.2367          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.9263 = 4.45 * 0.50 * 5.7659 + 1.00 * 0.0911                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.6690 = 4.45 * 0.50 * 5.6622 + 1.00 * 0.0645                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1735      final r-factor (work) = 0.1578          |
| start r-factor (free) = 0.2367      final r-factor (free) = 0.2151          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3022 = 0.58 * 1.00 * 5.6622 + 1.00 * 0.0170                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2046 = 0.58 * 1.00 * 5.5010 + 1.00 * 0.0129                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.858)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.31   19.08    None  None   None       |
|    all(noH): 2823   0      0.00    99.31   19.08    None  None   None       |
|    Sol.    : 438    0      5.84    99.31   47.96    None  None   None       |
|    Mac.    : 2385   0      0.00    94.89   13.78    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.931:  975   |   5:    49.654 -  59.585:  109        |
|      1:     9.931 -  19.862: 1105   |   6:    59.585 -  69.516:   73        |
|      2:    19.862 -  29.793:  256   |   7:    69.516 -  79.447:   48        |
|      3:    29.793 -  39.723:  131   |   8:    79.447 -  89.378:   19        |
|      4:    39.723 -  49.654:   99   |   9:    89.378 -  99.308:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1578 r_free = 0.2151             target_work(ml) = 5.453         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1576 r_free = 0.2149             target_work(ml) = 5.452         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1576   r_free= 0.2149   ksol= 0.34   Bsol= 80.29   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.66,-1.73,0.09,-0.00,0.00,0.00); trace/3= -1.10                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.451916                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1575   r_free= 0.2143   ksol= 0.33   Bsol= 66.28   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-2.54,-0.34,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.449227                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.322073              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.615  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.955631              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.300  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1575      final r-factor (work) = 0.1407          |
| start r-factor (free) = 0.2143      final r-factor (free) = 0.1946          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4523 = 2.32 * 0.50 * 5.5017 + 1.00 * 0.0645                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3287 = 2.32 * 0.50 * 5.4038 + 1.00 * 0.0546                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1407      final r-factor (work) = 0.1358          |
| start r-factor (free) = 0.1946      final r-factor (free) = 0.1888          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1768 = 0.96 * 1.00 * 5.4038 + 1.00 * 0.0127                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1083 = 0.96 * 1.00 * 5.3321 + 1.00 * 0.0128                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.858)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.24  18.87    None  None   None       |
|    all(noH): 2823   0      0.00    101.24  18.87    None  None   None       |
|    Sol.    : 438    0      4.78    101.24  48.82    None  None   None       |
|    Mac.    : 2385   0      0.00    100.99  13.37    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.124: 1050   |   5:    50.618 -  60.741:   86        |
|      1:    10.124 -  20.247: 1084   |   6:    60.741 -  70.865:   73        |
|      2:    20.247 -  30.371:  233   |   7:    70.865 -  80.988:   53        |
|      3:    30.371 -  40.494:  119   |   8:    80.988 -  91.112:   22        |
|      4:    40.494 -  50.618:   91   |   9:    91.112 - 101.235:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1358 r_free = 0.1888             target_work(ml) = 5.320         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1358 r_free = 0.1887             target_work(ml) = 5.320         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1358   r_free= 0.1887   ksol= 0.33   Bsol= 66.28   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-2.54,-0.34,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.319579                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1846 -  4.6670 0.99   1455  163 0.0987 0.1378      5.4128      5.6427|
|  2:  4.6670 -  3.7223 0.99   1399  154 0.0915 0.1270      5.5104      5.7578|
|  3:  3.7223 -  3.2571 0.99   1378  154 0.1244 0.1783      5.5969      5.9291|
|  4:  3.2571 -  2.9617 0.99   1380  153 0.1611 0.2144      5.6543      5.8391|
|  5:  2.9617 -  2.7507 0.99   1346  150 0.1639 0.2115      5.5233      5.7355|
|  6:  2.7507 -  2.5894 0.99   1368  150 0.1598 0.2293      5.3942      5.5976|
|  7:  2.5894 -  2.4603 0.99   1344  155 0.1515 0.2071      5.3262      5.4922|
|  8:  2.4603 -  2.3536 0.98   1332  147 0.1534 0.2141      5.2791      5.5448|
|  9:  2.3536 -  2.2633 0.98   1335  145 0.1522 0.2094      5.2401      5.4663|
| 10:  2.2633 -  2.1854 1.00   1352  157 0.1409 0.1930      5.1237      5.3147|
| 11:  2.1854 -  2.1173 0.98   1313  142 0.1371 0.2135      5.0926      5.4603|
| 12:  2.1173 -  2.0569 0.98   1336  143 0.1406 0.2159       5.022      5.2707|
| 13:  2.0569 -  2.0029 0.79   1051  118 0.1379 0.1954      4.9448       5.126|
| 14:  2.0029 -  1.9541 0.18    241   28 0.1224 0.1853      4.8319      5.1353|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1846 -  4.6670  1455   163  0.93  10.04   0.96     0.93       8276.93|
|  2:  4.6670 -  3.7223  1399   154  0.95   8.85   1.03     1.01      10478.13|
|  3:  3.7223 -  3.2571  1378   154  0.91  14.11   1.05     1.05      13429.57|
|  4:  3.2571 -  2.9617  1380   153  0.88  18.63   1.03     0.99      15665.94|
|  5:  2.9617 -  2.7507  1346   150  0.86  20.27   1.01     0.98      12956.63|
|  6:  2.7507 -  2.5894  1368   150  0.86  20.60   1.00     0.95      10114.30|
|  7:  2.5894 -  2.4603  1344   155  0.87  19.56   1.01     0.97       8850.38|
|  8:  2.4603 -  2.3536  1332   147  0.86  20.19   1.01     0.98       8230.11|
|  9:  2.3536 -  2.2633  1335   145  0.86  20.79   1.01     0.95       7697.04|
| 10:  2.2633 -  2.1854  1352   157  0.87  19.86   1.02     0.98       6391.51|
| 11:  2.1854 -  2.1173  1313   142  0.87  19.93   1.00     0.94       6067.93|
| 12:  2.1173 -  2.0569  1336   143  0.87  19.90   1.01     0.99       5402.65|
| 13:  2.0569 -  2.0029  1051   118  0.86  20.36   1.00     0.99       4758.55|
| 14:  2.0029 -  1.9541   241    28  0.91  15.74   0.99     0.96       3491.14|
|alpha:            min =        0.93 max =            1.05 mean =         0.98|
|beta:             min =     3491.14 max =        15665.94 mean =      9126.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.95 mean =        17.77|
|phase err.(test): min =        0.00 max =           89.81 mean =        17.04|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1358   r_free= 0.1888   ksol= 0.32   Bsol= 62.27   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-2.81,-0.60,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.319374                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1358   r_free= 0.1888   ksol= 0.32   Bsol= 62.27   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-2.81,-0.60,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.319374                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1846 -  4.6670 0.99   1455  163 0.0986 0.1374      5.4116      5.6402|
|  2:  4.6670 -  3.7223 0.99   1399  154 0.0913 0.1268      5.5088      5.7555|
|  3:  3.7223 -  3.2571 0.99   1378  154 0.1243 0.1781      5.5962      5.9284|
|  4:  3.2571 -  2.9617 0.99   1380  153 0.1612 0.2146      5.6542      5.8391|
|  5:  2.9617 -  2.7507 0.99   1346  150 0.1640 0.2116      5.5235      5.7365|
|  6:  2.7507 -  2.5894 0.99   1368  150 0.1598 0.2293      5.3943      5.5977|
|  7:  2.5894 -  2.4603 0.99   1344  155 0.1516 0.2074      5.3265      5.4928|
|  8:  2.4603 -  2.3536 0.98   1332  147 0.1534 0.2142      5.2795      5.5458|
|  9:  2.3536 -  2.2633 0.98   1335  145 0.1522 0.2093      5.2401      5.4659|
| 10:  2.2633 -  2.1854 1.00   1352  157 0.1409 0.1930      5.1238      5.3152|
| 11:  2.1854 -  2.1173 0.98   1313  142 0.1371 0.2135      5.0923      5.4603|
| 12:  2.1173 -  2.0569 0.98   1336  143 0.1406 0.2159      5.0223      5.2711|
| 13:  2.0569 -  2.0029 0.79   1051  118 0.1379 0.1954       4.945      5.1262|
| 14:  2.0029 -  1.9541 0.18    241   28 0.1225 0.1851      4.8315      5.1343|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1846 -  4.6670  1455   163  0.93  10.04   0.96     0.93       8263.86|
|  2:  4.6670 -  3.7223  1399   154  0.95   8.84   1.02     1.01      10452.24|
|  3:  3.7223 -  3.2571  1378   154  0.91  14.08   1.05     1.04      13391.96|
|  4:  3.2571 -  2.9617  1380   153  0.88  18.62   1.02     0.99      15643.83|
|  5:  2.9617 -  2.7507  1346   150  0.86  20.27   1.00     0.97      12962.33|
|  6:  2.7507 -  2.5894  1368   150  0.86  20.60   0.99     0.94      10122.94|
|  7:  2.5894 -  2.4603  1344   155  0.87  19.57   1.00     0.96       8860.37|
|  8:  2.4603 -  2.3536  1332   147  0.86  20.20   1.00     0.97       8239.19|
|  9:  2.3536 -  2.2633  1335   145  0.86  20.79   1.00     0.93       7703.62|
| 10:  2.2633 -  2.1854  1352   157  0.87  19.85   1.00     0.97       6392.68|
| 11:  2.1854 -  2.1173  1313   142  0.87  19.93   0.99     0.93       6069.08|
| 12:  2.1173 -  2.0569  1336   143  0.87  19.90   0.99     0.98       5404.06|
| 13:  2.0569 -  2.0029  1051   118  0.86  20.35   0.99     0.97       4759.26|
| 14:  2.0029 -  1.9541   241    28  0.91  15.73   0.97     0.94       3487.64|
|alpha:            min =        0.93 max =            1.04 mean =         0.97|
|beta:             min =     3487.64 max =        15643.83 mean =      9122.29|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.84 mean =        17.77|
|phase err.(test): min =        0.00 max =           89.95 mean =        17.03|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.858)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.24  18.88    None  None   None       |
|    all(noH): 2823   0      0.00    101.24  18.88    None  None   None       |
|    Sol.    : 438    0      4.78    101.24  48.82    None  None   None       |
|    Mac.    : 2385   0      0.00    100.99  13.38    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:     0.003 -  10.127: 1050   |   5:    50.621 -  60.744:   86        |
|      1:    10.127 -  20.250: 1084   |   6:    60.744 -  70.868:   73        |
|      2:    20.250 -  30.374:  233   |   7:    70.868 -  80.991:   53        |
|      3:    30.374 -  40.497:  119   |   8:    80.991 -  91.115:   22        |
|      4:    40.497 -  50.621:   91   |   9:    91.115 - 101.238:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 343         
Filter by distance & map next to the model:
   mapped sites are within: 0.626 - 4.267
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 339 from: 343
   mapped sites are within: 0.724 - 4.267

peak=    8.080 closest distance to " O   HOH Z 390 " =    1.325
peak=    7.013 closest distance to " O   HOH Z 385 " =    1.824
peak=    6.935 closest distance to " O   HOH Z 245 " =    1.468
peak=    6.493 closest distance to " O   HOH Z 103 " =    1.113
peak=    5.798 closest distance to " O   HOH Z 381 " =    1.291
peak=    5.584 closest distance to " CG  PRO A  90 " =    1.414
peak=    5.558 closest distance to " O   HOH Z 431 " =    1.859
peak=    5.496 closest distance to " O   HOH Z 222 " =    1.596
peak=    5.469 closest distance to " O   HOH Z  77 " =    1.222
peak=    5.238 closest distance to " O   HOH Z  46 " =    1.291
peak=    5.203 closest distance to " O  BHOH Z  74 " =    1.167
peak=    5.195 closest distance to " O   HOH Z  65 " =    1.658
peak=    5.195 closest distance to " O   HOH Z 417 " =    2.794
peak=    5.181 closest distance to " O   HOH Z  29 " =    1.551
peak=    5.139 closest distance to " O   HOH Z 130 " =    0.942
peak=    5.132 closest distance to " O   HOH Z 278 " =    1.279
peak=    5.056 closest distance to " O   HOH Z 287 " =    2.270
peak=    5.010 closest distance to " O   HOH Z  66 " =    1.228
peak=    5.005 closest distance to " O   HOH Z 424 " =    1.986
peak=    4.960 closest distance to " O   HOH Z 105 " =    1.379
peak=    4.916 closest distance to " NE2 GLN A  11 " =    1.354
peak=    4.906 closest distance to " O   HOH Z 126 " =    2.022
peak=    4.844 closest distance to " O   HOH Z  11 " =    1.362
peak=    4.793 closest distance to " O   HOH Z 295 " =    1.389
peak=    4.778 closest distance to " O   HOH Z 293 " =    1.528
peak=    4.706 closest distance to " CB  SER A 216 " =    1.065
peak=    4.703 closest distance to " CG  PRO A  54 " =    1.482
peak=    4.690 closest distance to " O   HOH Z 422 " =    1.029
peak=    4.677 closest distance to " O   HOH Z 359 " =    1.658
peak=    4.674 closest distance to " O   HOH Z 145 " =    2.220
peak=    4.650 closest distance to " O   HOH Z 403 " =    1.574
peak=    4.641 closest distance to " O   HOH Z 427 " =    2.285
peak=    4.586 closest distance to " NH1AARG A 145 " =    1.210
peak=    4.575 closest distance to " O   HOH Z  63 " =    1.736
peak=    4.572 closest distance to " O   HOH Z 375 " =    1.084
peak=    4.565 closest distance to " CB  GLN A 223 " =    1.589
peak=    4.552 closest distance to " O   HOH Z 142 " =    2.073
peak=    4.548 closest distance to " O   HOH Z  92 " =    1.367
peak=    4.524 closest distance to " O   HOH Z  69 " =    2.019
peak=    4.465 closest distance to " O   HOH Z 232 " =    2.224
peak=    4.464 closest distance to " CB  SER A  63 " =    1.429
peak=    4.456 closest distance to " CG2 ILE A 120 " =    1.157
peak=    4.406 closest distance to " CB  PRO A  54 " =    1.219
peak=    4.390 closest distance to " O   HOH Z 427 " =    1.197
peak=    4.387 closest distance to " O   HOH Z 139 " =    1.256
peak=    4.383 closest distance to " O   HOH Z 418 " =    1.193
peak=    4.377 closest distance to " CE3 TRP A 274 " =    1.414
peak=    4.365 closest distance to " O   HOH Z   9 " =    1.922
peak=    4.308 closest distance to " O   HOH Z 419 " =    2.426
peak=    4.273 closest distance to " O   HOH Z 158 " =    1.424
peak=    4.268 closest distance to " O   HOH Z 316 " =    3.066
peak=    4.261 closest distance to " O   HOH Z 147 " =    1.327
peak=    4.260 closest distance to " CA  ALA A  51 " =    1.078
peak=    4.234 closest distance to " O   HOH Z  67 " =    1.378
peak=    4.213 closest distance to " O   PRO A 198 " =    1.274
peak=    4.211 closest distance to " O   HOH Z 361 " =    1.582
peak=    4.206 closest distance to " O   HOH Z 414 " =    1.546
peak=    4.192 closest distance to " CZ3 TRP A 266 " =    1.118
peak=    4.185 closest distance to " O   HOH Z 380 " =    2.190
peak=    4.135 closest distance to " N   GLN A 278 " =    1.110
peak=    4.118 closest distance to " CB  ALA A 114 " =    0.928
peak=    4.091 closest distance to " O   HOH Z  57 " =    1.481
peak=    4.083 closest distance to " O   HOH Z 424 " =    1.327
peak=    4.068 closest distance to " CB  ASP A 124 " =    0.911
peak=    4.053 closest distance to " O   HOH Z 133 " =    1.099
peak=    4.044 closest distance to " CA  TYR A  30 " =    1.150
peak=    3.988 closest distance to " O   HOH Z  39 " =    1.233
peak=    3.978 closest distance to " O   HOH Z 298 " =    1.996
peak=    3.977 closest distance to " CB  PRO A  90 " =    1.088
peak=    3.976 closest distance to " O   HOH Z 425 " =    1.352
peak=    3.974 closest distance to " O   HOH Z 225 " =    1.817
peak=    3.968 closest distance to " CG  LEU A 167 " =    1.353
peak=    3.965 closest distance to " CG  TRP A 179 " =    2.170
peak=    3.963 closest distance to " CB  GLU A 128 " =    1.083
peak=    3.955 closest distance to " O   HOH Z  27 " =    1.078
peak=    3.951 closest distance to " NZ BLYS A 290 " =    1.018
peak=    3.949 closest distance to " CG  PRO A 198 " =    1.246
peak=    3.945 closest distance to " O   HOH Z 414 " =    2.168
peak=    3.935 closest distance to " O   HOH Z 126 " =    1.449
peak=    3.929 closest distance to " O   HOH Z  30 " =    1.785
peak=    3.929 closest distance to " N   TYR A  15 " =    1.150
peak=    3.918 closest distance to " O   HOH Z 276 " =    1.326
peak=    3.905 closest distance to " CB  TRP A 266 " =    0.974
peak=    3.904 closest distance to " CB  ASN A 148 " =    1.372
peak=    3.897 closest distance to " C   GLN A  73 " =    1.046
peak=    3.874 closest distance to " CB  LYS A 290 " =    0.913
peak=    3.855 closest distance to " O   HOH Z  97 " =    1.491
peak=    3.848 closest distance to " O   HOH Z 426 " =    1.132
peak=    3.843 closest distance to " O   HOH Z 368 " =    3.635
peak=    3.840 closest distance to " CG2BVAL A  41 " =    1.145
peak=    3.836 closest distance to " ND2BASN A 224 " =    0.937
peak=    3.831 closest distance to " C   VAL A  72 " =    0.972
peak=    3.825 closest distance to " NZ  LYS A 119 " =    2.276
peak=    3.822 closest distance to " O   HOH Z 211 " =    1.314
peak=    3.815 closest distance to " CA  ALA A 160 " =    0.996
peak=    3.815 closest distance to " CE  MET A  93 " =    1.465
peak=    3.799 closest distance to " CB  ARG A 275 " =    1.122
peak=    3.794 closest distance to " O   HOH Z 393 " =    1.346
peak=    3.781 closest distance to " O   HOH Z  61 " =    1.758
peak=    3.777 closest distance to " O   HOH Z 392 " =    1.315
peak=    3.773 closest distance to " O   HOH Z  59 " =    1.873
peak=    3.761 closest distance to " CG2 THR A 221 " =    1.220
peak=    3.758 closest distance to " CB  ASN A  39 " =    0.871
peak=    3.751 closest distance to " O   HOH Z 369 " =    1.918
peak=    3.744 closest distance to " CB  SER A   3 " =    1.463
peak=    3.743 closest distance to " CB  SER A 276 " =    1.190
peak=    3.740 closest distance to " O   HOH Z 193 " =    1.830
peak=    3.739 closest distance to " O   HOH Z 135 " =    1.467
peak=    3.738 closest distance to " CB  SER A  99 " =    0.861
peak=    3.737 closest distance to " CZ  PHE A  38 " =    1.291
peak=    3.736 closest distance to " O   HOH Z 217 " =    3.187
peak=    3.716 closest distance to " O   HOH Z 352 " =    1.698
peak=    3.714 closest distance to " OE1 GLN A 240 " =    1.532
peak=    3.711 closest distance to " NZ  LYS A 117 " =    1.208
peak=    3.706 closest distance to " CB  SER A 210 " =    1.006
peak=    3.695 closest distance to " O   HOH Z 284 " =    1.416
peak=    3.692 closest distance to " O   HOH Z 411 " =    3.205
peak=    3.689 closest distance to " CB  ALA A  43 " =    0.893
peak=    3.685 closest distance to " O   HOH Z  58 " =    1.791
peak=    3.681 closest distance to " CD  ARG A 195 " =    3.577
peak=    3.681 closest distance to " O   HOH Z 119 " =    1.490
peak=    3.677 closest distance to " CE3 TRP A 150 " =    1.127
peak=    3.669 closest distance to " O   HOH Z 218 " =    1.911
peak=    3.667 closest distance to " CB  TRP A 179 " =    1.460
peak=    3.661 closest distance to " NH2 ARG A  56 " =    2.016
peak=    3.654 closest distance to " O   HOH Z 410 " =    1.462
peak=    3.650 closest distance to " CA  VAL A 125 " =    1.103
peak=    3.645 closest distance to " ND2 ASN A  60 " =    2.777
peak=    3.643 closest distance to " NH2AARG A 145 " =    2.339
peak=    3.636 closest distance to " CB  MET A  40 " =    0.829
peak=    3.635 closest distance to " CE  LYS A 119 " =    1.228
peak=    3.634 closest distance to " CB  ARG A 219 " =    0.780
peak=    3.634 closest distance to " NH2AARG A 145 " =    1.270
peak=    3.632 closest distance to " CG  GLN A  58 " =    1.104
peak=    3.630 closest distance to " O   HOH Z  88 " =    3.145
peak=    3.630 closest distance to " O   HOH Z 349 " =    2.088
peak=    3.627 closest distance to " O   HOH Z   6 " =    1.625
peak=    3.627 closest distance to " CB  TYR A 116 " =    1.300
peak=    3.622 closest distance to " O   HOH Z 437 " =    2.048
peak=    3.616 closest distance to " O   HOH Z 280 " =    1.397
peak=    3.615 closest distance to " CZ  PHE A 218 " =    1.209
peak=    3.612 closest distance to " CA  ARG A 102 " =    1.113
peak=    3.609 closest distance to " CG2 VAL A 257 " =    0.867
peak=    3.602 closest distance to " CB  GLU A 152 " =    1.126
peak=    3.602 closest distance to " O   HOH Z 272 " =    1.888
peak=    3.600 closest distance to " O   HOH Z 143 " =    1.322
peak=    3.598 closest distance to " N   GLU A   2 " =    1.445
peak=    3.597 closest distance to " O   HOH Z  17 " =    1.986
peak=    3.596 closest distance to " OE2 GLU A  53 " =    2.053
peak=    3.594 closest distance to " O   HOH Z  78 " =    1.794
peak=    3.589 closest distance to " O   HOH Z 358 " =    1.271
peak=    3.586 closest distance to " NE2 HIS A 207 " =    1.046
peak=    3.584 closest distance to " OG ASER A 212 " =    1.438
peak=    3.584 closest distance to " CB  VAL A 296 " =    1.448
peak=    3.581 closest distance to " CD  GLN A  77 " =    1.337
peak=    3.568 closest distance to " CD  ARG A  66 " =    2.115
peak=    3.565 closest distance to " NH2 ARG A 269 " =    1.163
peak=    3.558 closest distance to " OD1 ASP A 238 " =    1.066
peak=    3.555 closest distance to " O   HOH Z 127 " =    1.028
peak=    3.551 closest distance to " CB  PHE A 225 " =    1.446
peak=    3.551 closest distance to " CG  ARG A 159 " =    0.904
peak=    3.548 closest distance to " O   HOH Z 327 " =    1.771
peak=    3.542 closest distance to " CB  SER A 141 " =    1.154
peak=    3.541 closest distance to " O   HOH Z 153 " =    3.567
peak=    3.539 closest distance to " CA  ARG A  36 " =    1.207
peak=    3.539 closest distance to " N   VAL A 296 " =    1.856
peak=    3.538 closest distance to " CG2 ILE A  20 " =    1.563
peak=    3.537 closest distance to " O   HOH Z 258 " =    1.956
peak=    3.535 closest distance to " O   HOH Z  90 " =    2.285
peak=    3.534 closest distance to " O   HOH Z 220 " =    1.437
peak=    3.534 closest distance to " CA  LEU A 282 " =    1.088
peak=    3.533 closest distance to " CG  GLN A  89 " =    1.574
peak=    3.528 closest distance to " N   CYS A 260 " =    0.965
peak=    3.525 closest distance to " CA  ARG A 195 " =    1.409
peak=    3.519 closest distance to " O   HOH Z  43 " =    1.243
peak=    3.508 closest distance to " O   HOH Z 244 " =    1.565
peak=    3.502 closest distance to " O   HOH Z 368 " =    1.829
peak=    3.500 closest distance to " O   HOH Z 371 " =    3.200
peak=    3.497 closest distance to " O   HOH Z 207 " =    0.910
peak=    3.495 closest distance to " CB  PHE A  61 " =    1.254
peak=    3.489 closest distance to " OG  SER A 276 " =    1.020
peak=    3.485 closest distance to " O   HOH Z  44 " =    2.087
peak=    3.484 closest distance to " O   HOH Z   7 " =    2.724
peak=    3.483 closest distance to " O   HOH Z 170 " =    1.004
peak=    3.472 closest distance to " O   HOH Z  40 " =    2.297
peak=    3.472 closest distance to " CG  LYS A  76 " =    1.841
peak=    3.469 closest distance to " O   HOH Z  91 " =    2.437
peak=    3.465 closest distance to " CA  ARG A 159 " =    1.216
peak=    3.465 closest distance to " O   HOH Z 405 " =    1.753
peak=    3.461 closest distance to " O   HOH Z 104 " =    1.771
peak=    3.456 closest distance to " N   ALA A   1 " =    1.570
peak=    3.449 closest distance to " CG  PRO A 243 " =    1.167
peak=    3.447 closest distance to " O   HOH Z 365 " =    2.601
peak=    3.445 closest distance to " CE3 TRP A  85 " =    1.081
peak=    3.439 closest distance to " O   HOH Z 106 " =    4.025
peak=    3.438 closest distance to " O   HOH Z 303 " =    1.232
peak=    3.437 closest distance to " O   HOH Z 357 " =    2.096
peak=    3.437 closest distance to " O   HOH Z 422 " =    2.244
peak=    3.435 closest distance to " ND2 ASN A 249 " =    0.748
peak=    3.434 closest distance to " CB  VAL A 202 " =    1.607
peak=    3.434 closest distance to " CG2 ILE A 239 " =    1.003
peak=    3.433 closest distance to " NH2AARG A 190 " =    1.790
peak=    3.430 closest distance to " CD  ARG A 159 " =    0.848
peak=    3.423 closest distance to " O   HOH Z 434 " =    1.565
peak=    3.422 closest distance to " CG  GLU A 277 " =    2.057
peak=    3.418 closest distance to " O   ALA A 165 " =    1.494
peak=    3.415 closest distance to " NE2 GLN A  73 " =    1.704
peak=    3.413 closest distance to " C   HIS A 115 " =    0.992
peak=    3.410 closest distance to " CA  GLU A 152 " =    1.004
peak=    3.409 closest distance to " CA  MET A 105 " =    0.909
peak=    3.407 closest distance to " O   TYR A 116 " =    1.312
peak=    3.406 closest distance to " CB  TRP A 150 " =    0.856
peak=    3.404 closest distance to " CB  ASN A 187 " =    0.952
peak=    3.389 closest distance to " CB  PHE A 130 " =    1.135
peak=    3.387 closest distance to " O   HOH Z 296 " =    1.130
peak=    3.384 closest distance to " O   HOH Z 424 " =    3.140
peak=    3.380 closest distance to " O   HOH Z   1 " =    1.658
peak=    3.377 closest distance to " CA  PHE A 283 " =    1.275
peak=    3.374 closest distance to " CG1 VAL A 296 " =    1.245
peak=    3.370 closest distance to " O   HOH Z 400 " =    0.724
peak=    3.367 closest distance to " NZ  LYS A 166 " =    1.025
peak=    3.359 closest distance to " O   HOH Z 389 " =    1.778
peak=    3.356 closest distance to " O   HOH Z 214 " =    2.279
peak=    3.353 closest distance to " O   HOH Z  51 " =    1.962
peak=    3.350 closest distance to " CA  SER A  87 " =    1.028
peak=    3.350 closest distance to " CB  LEU A 300 " =    0.931
peak=    3.349 closest distance to " O   HOH Z 394 " =    1.602
peak=    3.346 closest distance to " O   HOH Z 146 " =    1.538
peak=    3.342 closest distance to " N   GLN A  73 " =    0.928
peak=    3.341 closest distance to " CE2 PHE A  16 " =    0.803
peak=    3.340 closest distance to " CA  LEU A  83 " =    1.690
peak=    3.340 closest distance to " O   HOH Z 236 " =    1.552
peak=    3.338 closest distance to " OG1 THR A 221 " =    1.333
peak=    3.333 closest distance to " O   HOH Z 180 " =    2.253
peak=    3.333 closest distance to " CB  GLU A 277 " =    3.707
peak=    3.327 closest distance to " O   HOH Z  22 " =    1.449
peak=    3.326 closest distance to " CA  ILE A 106 " =    0.747
peak=    3.321 closest distance to " O   HOH Z 219 " =    3.928
peak=    3.318 closest distance to " O   ASN A  69 " =    1.599
peak=    3.316 closest distance to " CA  ALA A 160 " =    1.363
peak=    3.315 closest distance to " CB  TYR A  30 " =    1.663
peak=    3.313 closest distance to " CA  TYR A 116 " =    1.490
peak=    3.312 closest distance to " CA  SER A  95 " =    0.946
peak=    3.309 closest distance to " O   HOH Z 378 " =    1.162
peak=    3.309 closest distance to " CB  ARG A  79 " =    0.913
peak=    3.301 closest distance to " O   HOH Z 132 " =    1.038
peak=    3.298 closest distance to " N   SER A 210 " =    1.019
peak=    3.292 closest distance to " CA  ILE A 234 " =    1.100
peak=    3.287 closest distance to " CB  ALA A 242 " =    1.148
peak=    3.286 closest distance to " O   HOH Z  28 " =    1.009
peak=    3.283 closest distance to " O   HOH Z 112 " =    1.293
peak=    3.281 closest distance to " O   HOH Z 158 " =    2.700
peak=    3.279 closest distance to " O   HOH Z 415 " =    0.991
peak=    3.277 closest distance to " O   HOH Z  53 " =    2.273
peak=    3.275 closest distance to " CA  ALA A 129 " =    1.223
peak=    3.274 closest distance to " O   HOH Z 239 " =    1.573
peak=    3.273 closest distance to " O   THR A 294 " =    1.078
peak=    3.269 closest distance to " CA  ALA A 180 " =    1.232
peak=    3.269 closest distance to " CB  ARG A 138 " =    0.923
peak=    3.269 closest distance to " CE  LYS A  76 " =    0.885
peak=    3.267 closest distance to " O   GLY A 211 " =    1.098
peak=    3.267 closest distance to " CB  TRP A 274 " =    1.138
peak=    3.263 closest distance to " O   HOH Z 407 " =    1.674
peak=    3.262 closest distance to " CD  ARG A 138 " =    0.963
peak=    3.261 closest distance to " CD1 LEU A 300 " =    1.056
peak=    3.257 closest distance to " OG BSER A 212 " =    2.685
peak=    3.255 closest distance to " CB  ASN A 215 " =    1.222
peak=    3.242 closest distance to " CB  ALA A  10 " =    0.983
peak=    3.241 closest distance to " CB  THR A  31 " =    1.568
peak=    3.239 closest distance to " O   HOH Z 423 " =    1.578
peak=    3.235 closest distance to " O   HOH Z  42 " =    1.579
peak=    3.228 closest distance to " CD  LYS A 166 " =    1.573
peak=    3.226 closest distance to " O   HOH Z 130 " =    1.890
peak=    3.225 closest distance to " O   ASN A 142 " =    1.077
peak=    3.222 closest distance to " CB  GLN A 183 " =    1.216
peak=    3.218 closest distance to " C   GLU A 277 " =    1.312
peak=    3.213 closest distance to " CA  SER A  12 " =    1.627
peak=    3.211 closest distance to " O   HOH Z  47 " =    2.284
peak=    3.210 closest distance to " O   HOH Z 248 " =    1.705
peak=    3.209 closest distance to " O   HOH Z 280 " =    2.518
peak=    3.209 closest distance to " O   HOH Z 387 " =    2.505
peak=    3.207 closest distance to " CB  ALA A 114 " =    1.474
peak=    3.205 closest distance to " N   GLU A 152 " =    1.431
peak=    3.203 closest distance to " OG BSER A  99 " =    2.351
peak=    3.202 closest distance to " CB  ASN A 285 " =    0.992
peak=    3.201 closest distance to " CG2 ILE A 151 " =    1.037
peak=    3.200 closest distance to " O   HOH Z 171 " =    1.582
peak=    3.198 closest distance to " O   HOH Z 215 " =    1.677
peak=    3.198 closest distance to " N   VAL A 125 " =    1.460
peak=    3.195 closest distance to " CA  ASP A 124 " =    0.788
peak=    3.195 closest distance to " CD1 ILE A  33 " =    1.789
peak=    3.193 closest distance to " O   HOH Z 171 " =    2.199
peak=    3.190 closest distance to " O   HOH Z 140 " =    2.071
peak=    3.189 closest distance to " CG  LYS A 119 " =    1.088
peak=    3.187 closest distance to " O   HOH Z 350 " =    1.540
peak=    3.186 closest distance to " O   HOH Z 260 " =    2.424
peak=    3.185 closest distance to " CD2 LEU A   5 " =    1.333
peak=    3.185 closest distance to " O   HOH Z  57 " =    2.458
peak=    3.183 closest distance to " CA  TRP A  92 " =    1.224
peak=    3.182 closest distance to " O   HOH Z 356 " =    1.451
peak=    3.180 closest distance to " N   ALA A 165 " =    1.331
peak=    3.177 closest distance to " CG1AVAL A 121 " =    0.948
peak=    3.172 closest distance to " CA  ASN A  74 " =    1.363
peak=    3.171 closest distance to " O   HOH Z  21 " =    1.483
peak=    3.171 closest distance to " O   HOH Z 116 " =    1.152
peak=    3.168 closest distance to " O   HOH Z 157 " =    1.663
peak=    3.167 closest distance to " N   SER A  97 " =    0.826
peak=    3.164 closest distance to " CB  ALA A 248 " =    1.131
peak=    3.161 closest distance to " N   ALA A 292 " =    1.163
peak=    3.158 closest distance to " CB  SER A  62 " =    1.078
peak=    3.158 closest distance to " O   HOH Z 189 " =    2.906
peak=    3.155 closest distance to " O   HOH Z 394 " =    3.640
peak=    3.154 closest distance to " CA  VAL A 121 " =    1.004
peak=    3.152 closest distance to " O   MET A 105 " =    1.664
peak=    3.150 closest distance to " O   HOH Z 425 " =    2.139
peak=    3.149 closest distance to " CG AARG A 275 " =    1.322
peak=    3.139 closest distance to " ND2 ASN A  60 " =    3.684
peak=    3.134 closest distance to " O   HOH Z   2 " =    1.789
peak=    3.133 closest distance to " CB  VAL A 265 " =    1.291
peak=    3.131 closest distance to " N   PHE A 155 " =    1.448
peak=    3.131 closest distance to " C   ASN A 209 " =    1.831
peak=    3.130 closest distance to " OG BSER A 164 " =    2.332
peak=    3.128 closest distance to " OD2 ASP A 286 " =    2.449
peak=    3.122 closest distance to " CB  LEU A 237 " =    0.811
peak=    3.121 closest distance to " O   HOH Z 213 " =    2.076
peak=    3.107 closest distance to " O   HOH Z 119 " =    4.267
peak=    3.106 closest distance to " O   HOH Z 124 " =    1.376
peak=    3.101 closest distance to " O   HOH Z 362 " =    1.813
peak=    3.099 closest distance to " CD1 LEU A 228 " =    1.702
peak=    3.091 closest distance to " O   HOH Z 189 " =    3.284
peak=    3.086 closest distance to " CG1 ILE A 151 " =    1.167
peak=    3.086 closest distance to " O   HOH Z 425 " =    2.119
peak=    3.084 closest distance to " O   HOH Z  78 " =    1.961
peak=    3.082 closest distance to " CA  CYS A 260 " =    1.311
peak=    3.070 closest distance to " CA  ALA A 161 " =    1.042
peak=    3.067 closest distance to " O   HOH Z  32 " =    2.294
peak=    3.051 closest distance to " CB  ASN A 142 " =    0.919
peak=    3.044 closest distance to " N   PHE A  59 " =    0.890
peak=    3.043 closest distance to " O   TRP A  70 " =    1.321

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.581 - 5.559
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 204
   mapped sites are within: 0.769 - 5.559

peak=   -4.608 closest distance to " O   PRO A 198 " =    1.159
peak=   -4.436 closest distance to " O   HOH Z  28 " =    1.010
peak=   -4.353 closest distance to " O   HOH Z  60 " =    1.546
peak=   -4.218 closest distance to " O   HOH Z 216 " =    1.399
peak=   -4.183 closest distance to " OE1 GLU A  44 " =    1.892
peak=   -4.169 closest distance to " O   HOH Z 231 " =    0.965
peak=   -4.168 closest distance to " OD1 ASP A 191 " =    1.920
peak=   -4.142 closest distance to " CD  LYS A 166 " =    2.617
peak=   -4.099 closest distance to " O   HOH Z  39 " =    0.769
peak=   -4.090 closest distance to " O   HOH Z 313 " =    1.191
peak=   -4.039 closest distance to " O   HOH Z 100 " =    1.012
peak=   -4.021 closest distance to " N   THR A 157 " =    1.664
peak=   -4.005 closest distance to " CD1 TRP A 179 " =    1.174
peak=   -3.990 closest distance to " O   ALA A  10 " =    1.578
peak=   -3.977 closest distance to " OG  SER A  32 " =    0.943
peak=   -3.962 closest distance to " O   HOH Z 415 " =    0.991
peak=   -3.958 closest distance to " CG2 ILE A  49 " =    2.832
peak=   -3.940 closest distance to " CB  ALA A 160 " =    2.156
peak=   -3.936 closest distance to " CG  MET A 105 " =    0.954
peak=   -3.933 closest distance to " CB  GLN A  55 " =    1.284
peak=   -3.931 closest distance to " O   HOH Z 242 " =    1.539
peak=   -3.926 closest distance to " O   HOH Z 111 " =    1.621
peak=   -3.914 closest distance to " O   HOH Z 385 " =    1.355
peak=   -3.910 closest distance to " CB  PRO A 243 " =    2.575
peak=   -3.869 closest distance to " O   HOH Z 381 " =    1.211
peak=   -3.865 closest distance to " CD  ARG A  14 " =    3.257
peak=   -3.859 closest distance to " CB  ALA A 131 " =    1.842
peak=   -3.854 closest distance to " O   SER A  22 " =    2.741
peak=   -3.837 closest distance to " O   PRO A 163 " =    1.464
peak=   -3.833 closest distance to " OG  SER A  97 " =    2.116
peak=   -3.831 closest distance to " O   GLY A 203 " =    2.599
peak=   -3.817 closest distance to " CB  ASP A  27 " =    2.506
peak=   -3.808 closest distance to " O   GLN A 240 " =    3.176
peak=   -3.784 closest distance to " C   VAL A  72 " =    0.922
peak=   -3.761 closest distance to " N   ALA A  43 " =    2.701
peak=   -3.756 closest distance to " CB  ALA A 291 " =    2.103
peak=   -3.749 closest distance to " NZ  LYS A 166 " =    1.445
peak=   -3.735 closest distance to " CD  ARG A 156 " =    2.002
peak=   -3.728 closest distance to " NE2 GLN A  55 " =    0.987
peak=   -3.728 closest distance to " OG BSER A 134 " =    1.688
peak=   -3.727 closest distance to " O   HOH Z 298 " =    2.596
peak=   -3.719 closest distance to " OG  SER A  63 " =    1.497
peak=   -3.695 closest distance to " O   GLY A  80 " =    2.457
peak=   -3.685 closest distance to " CG  TRP A 266 " =    1.824
peak=   -3.678 closest distance to " CG1 VAL A 265 " =    2.395
peak=   -3.678 closest distance to " O   HOH Z 143 " =    0.989
peak=   -3.662 closest distance to " CG1BVAL A  41 " =    2.685
peak=   -3.660 closest distance to " CD2 TYR A 293 " =    1.861
peak=   -3.654 closest distance to " O   HOH Z 404 " =    1.256
peak=   -3.648 closest distance to " CD2 PHE A  61 " =    1.970
peak=   -3.642 closest distance to " CB  ASN A  45 " =    2.192
peak=   -3.637 closest distance to " CZ2 TRP A 274 " =    0.968
peak=   -3.631 closest distance to " CZ  TYR A 169 " =    1.960
peak=   -3.629 closest distance to " CB  ALA A   9 " =    2.468
peak=   -3.619 closest distance to " CD2 TYR A 116 " =    2.150
peak=   -3.617 closest distance to " O   HOH Z 389 " =    2.430
peak=   -3.613 closest distance to " O   HOH Z 129 " =    3.755
peak=   -3.612 closest distance to " CG2 ILE A 120 " =    0.861
peak=   -3.605 closest distance to " O   HOH Z  24 " =    0.860
peak=   -3.600 closest distance to " O   HOH Z 163 " =    1.800
peak=   -3.599 closest distance to " O   HOH Z 198 " =    1.748
peak=   -3.575 closest distance to " C   ILE A 239 " =    2.022
peak=   -3.565 closest distance to " NH2 ARG A 219 " =    2.108
peak=   -3.562 closest distance to " O   HOH Z 200 " =    3.438
peak=   -3.562 closest distance to " O   HOH Z 185 " =    2.014
peak=   -3.551 closest distance to " CA  GLY A 241 " =    2.263
peak=   -3.551 closest distance to " O   HOH Z  69 " =    1.487
peak=   -3.545 closest distance to " CD2 HIS A 207 " =    1.412
peak=   -3.542 closest distance to " C   HIS A 207 " =    1.193
peak=   -3.539 closest distance to " O   PHE A 218 " =    1.601
peak=   -3.532 closest distance to " CE3 TRP A 179 " =    1.358
peak=   -3.529 closest distance to " OD2 ASP A 272 " =    1.500
peak=   -3.521 closest distance to " O   GLU A 152 " =    1.383
peak=   -3.520 closest distance to " O   HOH Z 139 " =    3.078
peak=   -3.520 closest distance to " CG2 VAL A 202 " =    1.976
peak=   -3.507 closest distance to " O   HOH Z 275 " =    1.721
peak=   -3.503 closest distance to " CG1 VAL A 125 " =    2.334
peak=   -3.494 closest distance to " CG  ARG A 219 " =    2.404
peak=   -3.492 closest distance to " O   HOH Z 131 " =    3.822
peak=   -3.490 closest distance to " CA  ASN A 110 " =    0.923
peak=   -3.489 closest distance to " N   GLN A  58 " =    1.357
peak=   -3.489 closest distance to " CE2 TYR A  30 " =    2.555
peak=   -3.486 closest distance to " O   HOH Z  52 " =    1.045
peak=   -3.486 closest distance to " CB  PHE A 130 " =    1.130
peak=   -3.485 closest distance to " O   HOH Z 390 " =    2.533
peak=   -3.480 closest distance to " NE2 GLN A  77 " =    1.581
peak=   -3.475 closest distance to " O   LEU A 261 " =    1.131
peak=   -3.472 closest distance to " C   PHE A  59 " =    1.078
peak=   -3.468 closest distance to " CB  ASP A 171 " =    2.324
peak=   -3.463 closest distance to " CA  GLY A 133 " =    2.113
peak=   -3.448 closest distance to " CG  GLN A  88 " =    0.846
peak=   -3.446 closest distance to " O   HOH Z   5 " =    1.208
peak=   -3.440 closest distance to " NE2 GLN A 122 " =    1.013
peak=   -3.439 closest distance to " O   HOH Z 130 " =    0.984
peak=   -3.438 closest distance to " O   HOH Z 275 " =    1.611
peak=   -3.437 closest distance to " ND2 ASN A 209 " =    1.851
peak=   -3.435 closest distance to " NE2 GLN A 223 " =    1.633
peak=   -3.429 closest distance to " O   ILE A  49 " =    1.613
peak=   -3.428 closest distance to " OE1 GLU A 277 " =    2.354
peak=   -3.428 closest distance to " O   HOH Z 348 " =    1.999
peak=   -3.427 closest distance to " O   HOH Z  49 " =    1.309
peak=   -3.415 closest distance to " O   HOH Z 351 " =    1.659
peak=   -3.409 closest distance to " OE1 GLN A  88 " =    0.958
peak=   -3.394 closest distance to " O   ASP A 253 " =    1.734
peak=   -3.394 closest distance to " CB  TRP A  85 " =    2.034
peak=   -3.393 closest distance to " OG  SER A 245 " =    1.589
peak=   -3.383 closest distance to " O   HOH Z 412 " =    3.966
peak=   -3.379 closest distance to " CD1 TYR A 214 " =    1.481
peak=   -3.371 closest distance to " O   HOH Z  22 " =    2.546
peak=   -3.368 closest distance to " C   ALA A 299 " =    1.337
peak=   -3.363 closest distance to " CG1 VAL A 197 " =    2.443
peak=   -3.362 closest distance to " NH2AARG A 275 " =    5.559
peak=   -3.342 closest distance to " CZ  PHE A 130 " =    1.010
peak=   -3.334 closest distance to " CB  SER A 210 " =    1.141
peak=   -3.331 closest distance to " O   HOH Z 231 " =    1.887
peak=   -3.327 closest distance to " OG  SER A  87 " =    1.970
peak=   -3.321 closest distance to " CG2 ILE A 151 " =    2.538
peak=   -3.315 closest distance to " O   HOH Z 276 " =    1.094
peak=   -3.315 closest distance to " CA  GLY A  35 " =    2.068
peak=   -3.311 closest distance to " O   HOH Z 411 " =    5.176
peak=   -3.310 closest distance to " O   HOH Z  70 " =    2.067
peak=   -3.307 closest distance to " CB  ALA A 158 " =    1.722
peak=   -3.303 closest distance to " O   HOH Z 126 " =    1.857
peak=   -3.300 closest distance to " CB  ALA A  43 " =    2.508
peak=   -3.300 closest distance to " O   HOH Z 324 " =    0.923
peak=   -3.298 closest distance to " C   GLU A   2 " =    1.876
peak=   -3.294 closest distance to " CG  ARG A 219 " =    2.209
peak=   -3.293 closest distance to " O   HOH Z 211 " =    0.828
peak=   -3.291 closest distance to " O   LEU A 300 " =    2.257
peak=   -3.291 closest distance to " O   HOH Z 181 " =    1.052
peak=   -3.288 closest distance to " O   HOH Z 165 " =    2.388
peak=   -3.285 closest distance to " O   HOH Z 359 " =    1.421
peak=   -3.280 closest distance to " NE2 GLN A 194 " =    1.920
peak=   -3.275 closest distance to " O   HOH Z 238 " =    0.969
peak=   -3.274 closest distance to " O   HOH Z 251 " =    0.988
peak=   -3.271 closest distance to " O   HOH Z  88 " =    1.973
peak=   -3.267 closest distance to " N   LEU A 282 " =    2.186
peak=   -3.262 closest distance to " CG2 THR A 178 " =    2.129
peak=   -3.260 closest distance to " O   HOH Z 323 " =    2.097
peak=   -3.255 closest distance to " O   HOH Z 425 " =    0.801
peak=   -3.250 closest distance to " ND2 ASN A 285 " =    2.192
peak=   -3.249 closest distance to " O   HOH Z  37 " =    1.626
peak=   -3.248 closest distance to " CG  LEU A  83 " =    2.193
peak=   -3.246 closest distance to " CA  GLY A  98 " =    1.699
peak=   -3.241 closest distance to " CB  ALA A 100 " =    2.101
peak=   -3.237 closest distance to " N   ARG A 138 " =    1.777
peak=   -3.237 closest distance to " O   HOH Z 389 " =    0.992
peak=   -3.225 closest distance to " C   LEU A 101 " =    1.564
peak=   -3.225 closest distance to " O   ASP A  27 " =    1.893
peak=   -3.222 closest distance to " O   HOH Z  68 " =    1.442
peak=   -3.222 closest distance to " CD2 LEU A  25 " =    2.254
peak=   -3.221 closest distance to " O   HOH Z 286 " =    1.466
peak=   -3.221 closest distance to " CG1 ILE A 234 " =    2.062
peak=   -3.220 closest distance to " O   ALA A  84 " =    1.643
peak=   -3.220 closest distance to " O   HOH Z  60 " =    1.452
peak=   -3.220 closest distance to " CB  ALA A   7 " =    1.921
peak=   -3.219 closest distance to " O   HOH Z 300 " =    2.405
peak=   -3.212 closest distance to " CD  GLU A 236 " =    1.136
peak=   -3.212 closest distance to " O   ARG A 145 " =    1.322
peak=   -3.210 closest distance to " O   HOH Z 403 " =    1.477
peak=   -3.209 closest distance to " N   ARG A 159 " =    2.105
peak=   -3.203 closest distance to " OH  TYR A 247 " =    1.524
peak=   -3.203 closest distance to " CA  ILE A 120 " =    1.158
peak=   -3.202 closest distance to " CG2 THR A 221 " =    2.324
peak=   -3.200 closest distance to " NE2 GLN A  58 " =    3.366
peak=   -3.200 closest distance to " C   ASN A 285 " =    2.198
peak=   -3.197 closest distance to " CA  GLY A 203 " =    2.520
peak=   -3.196 closest distance to " O   ALA A   1 " =    1.785
peak=   -3.193 closest distance to " CG2 THR A  52 " =    3.183
peak=   -3.192 closest distance to " CG  PRO A 163 " =    2.711
peak=   -3.186 closest distance to " CG  GLN A  88 " =    0.953
peak=   -3.185 closest distance to " CB  ASP A 132 " =    2.512
peak=   -3.183 closest distance to " O   HOH Z 337 " =    1.616
peak=   -3.178 closest distance to " CE1 TYR A  15 " =    2.405
peak=   -3.178 closest distance to " N   GLN A 223 " =    1.982
peak=   -3.167 closest distance to " O   HOH Z 128 " =    2.490
peak=   -3.163 closest distance to " CZ  ARG A  36 " =    1.510
peak=   -3.150 closest distance to " O   HOH Z 371 " =    2.379
peak=   -3.144 closest distance to " CG  GLN A  58 " =    1.254
peak=   -3.142 closest distance to " O   HOH Z  27 " =    1.165
peak=   -3.138 closest distance to " O   HOH Z 427 " =    1.978
peak=   -3.134 closest distance to " O   HOH Z 134 " =    4.193
peak=   -3.130 closest distance to " CB  ASP A 132 " =    2.623
peak=   -3.129 closest distance to " OE2 GLU A 175 " =    1.315
peak=   -3.126 closest distance to " N   ASP A 270 " =    1.292
peak=   -3.125 closest distance to " CE  LYS A  76 " =    2.961
peak=   -3.125 closest distance to " O   VAL A 174 " =    2.427
peak=   -3.125 closest distance to " O   HOH Z 155 " =    0.925
peak=   -3.123 closest distance to " CE BMET A  47 " =    1.358
peak=   -3.120 closest distance to " CD  GLU A  44 " =    1.156
peak=   -3.116 closest distance to " CG  ARG A 259 " =    2.374
peak=   -3.109 closest distance to " C   HIS A 108 " =    1.274
peak=   -3.105 closest distance to " CE  MET A  93 " =    2.051
peak=   -3.103 closest distance to " CB  CYS A 254 " =    1.941
peak=   -3.101 closest distance to " CB  TYR A  15 " =    2.164
peak=   -3.099 closest distance to " O   LYS A  76 " =    1.699
peak=   -3.087 closest distance to " CD2 LEU A 297 " =    2.178
peak=   -3.082 closest distance to " CB  TYR A  68 " =    1.059
peak=   -3.063 closest distance to " SG BCYS A 201 " =    2.507
peak=   -3.051 closest distance to " CE3 TRP A 274 " =    2.439
peak=   -3.039 closest distance to " N   LYS A 166 " =    1.827
peak=   -3.030 closest distance to " CB  PRO A  54 " =    2.312

================= 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    :  0.4797 0.4826   6.294769e+00   6.286026e+00
   1_bss:  0.4711 0.4779   6.292150e+00   6.281560e+00
   1_xyz:  0.3989 0.4411   6.186717e+00   6.240172e+00
   1_adp:  0.3672 0.4501   6.154023e+00   6.248416e+00
   1_occ:  0.3669 0.4513   6.153929e+00   6.248802e+00
   2_bss:  0.3671 0.4501   6.157328e+00   6.249695e+00
   2_xyz:  0.3081 0.3959   6.028699e+00   6.170206e+00
   2_adp:  0.2940 0.3820   6.003058e+00   6.148763e+00
   2_occ:  0.2938 0.3819   6.002652e+00   6.148789e+00
   3_bss:  0.2942 0.3811   6.002022e+00   6.147668e+00
   3_xyz:  0.2373 0.3117   5.813029e+00   5.992317e+00
   3_adp:  0.2119 0.2957   5.738073e+00   5.947302e+00
   3_occ:  0.2119 0.2956   5.737627e+00   5.947014e+00
   4_bss:  0.2117 0.2954   5.735620e+00   5.944995e+00
   4_xyz:  0.1735 0.2367   5.534178e+00   5.764667e+00
   4_adp:  0.1578 0.2151   5.452758e+00   5.681673e+00
   4_occ:  0.1576 0.2149   5.451916e+00   5.680773e+00
   5_bss:  0.1575 0.2143   5.449227e+00   5.677592e+00
   5_xyz:  0.1407 0.1946   5.345370e+00   5.581232e+00
   5_adp:  0.1358 0.1888   5.319813e+00   5.556125e+00
   5_occ:  0.1358 0.1887   5.319579e+00   5.555914e+00
   5_bss:  0.1358 0.1888   5.319374e+00   5.555701e+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:  0.300  50.000  -2.388   1.324   2.307   0.000   0.000   0.000
   1_xyz:  0.300  50.000  -2.388   1.324   2.307   0.000   0.000   0.000
   1_adp:  0.300  50.000  -2.388   1.324   2.307   0.000   0.000   0.000
   1_occ:  0.300  50.000  -2.388   1.324   2.307   0.000   0.000   0.000
   2_bss:  0.361  82.663  -0.992   0.126   1.367   0.000   0.000   0.000
   2_xyz:  0.361  82.663  -0.992   0.126   1.367   0.000   0.000   0.000
   2_adp:  0.361  82.663  -0.992   0.126   1.367   0.000   0.000   0.000
   2_occ:  0.361  82.663  -0.992   0.126   1.367   0.000   0.000   0.000
   3_bss:  0.364  88.292  -1.193  -0.847   0.467  -0.000   0.000   0.000
   3_xyz:  0.364  88.292  -1.193  -0.847   0.467  -0.000   0.000   0.000
   3_adp:  0.364  88.292  -1.193  -0.847   0.467  -0.000   0.000   0.000
   3_occ:  0.364  88.292  -1.193  -0.847   0.467  -0.000   0.000   0.000
   4_bss:  0.344  80.292  -1.661  -1.726   0.088  -0.000   0.000   0.000
   4_xyz:  0.344  80.292  -1.661  -1.726   0.088  -0.000   0.000   0.000
   4_adp:  0.344  80.292  -1.661  -1.726   0.088  -0.000   0.000   0.000
   4_occ:  0.344  80.292  -1.661  -1.726   0.088  -0.000   0.000   0.000
   5_bss:  0.325  66.280  -2.032  -2.542  -0.339  -0.000  -0.000  -0.000
   5_xyz:  0.325  66.280  -2.032  -2.542  -0.339  -0.000  -0.000  -0.000
   5_adp:  0.325  66.280  -2.032  -2.542  -0.339  -0.000  -0.000  -0.000
   5_occ:  0.325  66.280  -2.032  -2.542  -0.339  -0.000  -0.000  -0.000
   5_bss:  0.321  62.275  -2.265  -2.807  -0.597  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.346 0.3760  0.5201    79299.778
   1_bss:  60.743 0.3827  0.5419    77583.461
   1_xyz:  52.436 0.4890  0.6795    61588.418
   1_adp:  53.738 0.4719  0.6720    63989.482
   1_occ:  53.807 0.4710  0.6702    64155.951
   2_bss:  53.884 0.4700  0.6646    64409.114
   2_xyz:  44.847 0.5823  0.8153    46201.532
   2_adp:  42.621 0.6101  0.8405    43282.088
   2_occ:  42.622 0.6101  0.8405    43254.742
   3_bss:  42.481 0.6116  0.8224    42943.094
   3_xyz:  32.661 0.7270  0.9433    26574.548
   3_adp:  30.439 0.7520  0.9468    23328.199
   3_occ:  30.424 0.7521  0.9467    23301.810
   4_bss:  30.322 0.7531  0.9289    23131.842
   4_xyz:  23.698 0.8230  0.9806    14315.883
   4_adp:  21.085 0.8505  0.9887    12034.163
   4_occ:  21.057 0.8507  0.9884    11995.062
   5_bss:  20.963 0.8514  0.9701    11858.645
   5_xyz:  18.413 0.8760  0.9818     9575.707
   5_adp:  17.710 0.8831  0.9770     9135.078
   5_occ:  17.701 0.8832  0.9769     9126.954
   5_bss:  17.695 0.8832  0.9684     9122.479
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.8530e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.8530e-01
   1_xyz:   1.514  0.011  0.103 16.011  0.006  4.105   1.2924e-01
   1_adp:   1.514  0.011  0.103 16.011  0.006  4.105   1.2924e-01
   1_occ:   1.514  0.011  0.103 16.011  0.006  4.105   1.2924e-01
   2_bss:   1.514  0.011  0.103 16.011  0.006  4.105   1.2924e-01
   2_xyz:   1.361  0.010  0.091 15.689  0.005  4.106   1.0595e-01
   2_adp:   1.361  0.010  0.091 15.689  0.005  4.106   1.0595e-01
   2_occ:   1.361  0.010  0.091 15.689  0.005  4.106   1.0595e-01
   3_bss:   1.361  0.010  0.091 15.689  0.005  4.106   1.0595e-01
   3_xyz:   1.239  0.010  0.090 15.226  0.005  4.108   9.1119e-02
   3_adp:   1.239  0.010  0.090 15.226  0.005  4.108   9.1119e-02
   3_occ:   1.239  0.010  0.090 15.226  0.005  4.108   9.1119e-02
   4_bss:   1.239  0.010  0.090 15.226  0.005  4.108   9.1119e-02
   4_xyz:   1.060  0.007  0.077 14.568  0.004  4.122   6.4536e-02
   4_adp:   1.060  0.007  0.077 14.568  0.004  4.122   6.4536e-02
   4_occ:   1.060  0.007  0.077 14.568  0.004  4.122   6.4536e-02
   5_bss:   1.060  0.007  0.077 14.568  0.004  4.122   6.4536e-02
   5_xyz:   0.932  0.006  0.069 14.444  0.003  4.113   5.4614e-02
   5_adp:   0.932  0.006  0.069 14.444  0.003  4.113   5.4614e-02
   5_occ:   0.932  0.006  0.069 14.444  0.003  4.113   5.4614e-02
   5_bss:   0.932  0.006  0.069 14.444  0.003  4.113   5.4614e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.681   2.4200e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.681   2.4200e-01
   1_xyz:   8.828  0.056  0.344 82.490  0.045  2.053   1.0052e-01
   1_adp:   8.828  0.056  0.344 82.490  0.045  2.053   1.0052e-01
   1_occ:   8.828  0.056  0.344 82.490  0.045  2.053   1.0052e-01
   2_bss:   8.828  0.056  0.344 82.490  0.045  2.053   1.0052e-01
   2_xyz:   9.041  0.057  0.308 78.507  0.044  1.998   1.0231e-01
   2_adp:   9.041  0.057  0.308 78.507  0.044  1.998   1.0231e-01
   2_occ:   9.041  0.057  0.308 78.507  0.044  1.998   1.0231e-01
   3_bss:   9.041  0.057  0.308 78.507  0.044  1.998   1.0231e-01
   3_xyz:   8.881  0.052  0.308 80.966  0.019  2.223   1.0259e-01
   3_adp:   8.881  0.052  0.308 80.966  0.019  2.223   1.0259e-01
   3_occ:   8.881  0.052  0.308 80.966  0.019  2.223   1.0259e-01
   4_bss:   8.881  0.052  0.308 80.966  0.019  2.223   1.0259e-01
   4_xyz:   6.318  0.041  0.214 81.459  0.038  2.322   5.7968e-02
   4_adp:   6.318  0.041  0.214 81.459  0.038  2.322   5.7968e-02
   4_occ:   6.318  0.041  0.214 81.459  0.038  2.322   5.7968e-02
   5_bss:   6.318  0.041  0.214 81.459  0.038  2.322   5.7968e-02
   5_xyz:   7.828  0.039  0.212 80.355  0.030  2.347   6.2954e-02
   5_adp:   7.828  0.039  0.212 80.355  0.030  2.347   6.2954e-02
   5_occ:   7.828  0.039  0.212 80.355  0.030  2.347   6.2954e-02
   5_bss:   7.828  0.039  0.212 80.355  0.030  2.347   6.2954e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  89.16   0.00  19.89  71.75   0.00  16.92  89.16   0.00  36.07
   1_occ:  89.16   0.00  19.89  71.75   0.00  16.92  89.16   0.00  36.07
   2_bss:  89.16   0.00  19.89  71.75   0.00  16.92  89.16   0.00  36.07
   2_xyz:  89.16   0.00  19.89  71.75   0.00  16.92  89.16   0.00  36.07
   2_adp:  87.38   0.00  19.14  75.05   0.00  16.04  87.38   0.00  36.04
   2_occ:  87.38   0.00  19.14  75.05   0.00  16.04  87.38   0.00  36.04
   3_bss:  87.38   0.00  19.14  75.05   0.00  16.04  87.38   0.00  36.04
   3_xyz:  87.38   0.00  19.14  75.05   0.00  16.04  87.38   0.00  36.04
   3_adp:  98.39   0.00  19.92  91.78   0.00  14.96  98.39   3.34  46.89
   3_occ:  98.39   0.00  19.92  91.78   0.00  14.96  98.39   3.34  46.89
   4_bss:  98.39   0.00  19.92  91.78   0.00  14.96  98.39   3.34  46.89
   4_xyz:  98.39   0.00  19.92  91.78   0.00  14.96  98.39   3.34  46.89
   4_adp:  99.31   0.00  19.08  94.89   0.00  13.78  99.31   5.84  47.96
   4_occ:  99.31   0.00  19.08  94.89   0.00  13.78  99.31   5.84  47.96
   5_bss:  99.31   0.00  19.08  94.89   0.00  13.78  99.31   5.84  47.96
   5_xyz:  99.31   0.00  19.08  94.89   0.00  13.78  99.31   5.84  47.96
   5_adp: 101.24   0.00  18.87 100.99   0.00  13.37 101.24   4.78  48.82
   5_occ: 101.24   0.00  18.87 100.99   0.00  13.37 101.24   4.78  48.82
   5_bss: 101.24   0.00  18.88 100.99   0.00  13.38 101.24   4.78  48.82
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.740    0.015    0.329
   1_adp:    1.740    0.015    0.329
   1_occ:    1.740    0.015    0.329
   2_bss:    1.740    0.015    0.329
   2_xyz:    1.511    0.033    0.543
   2_adp:    1.511    0.033    0.543
   2_occ:    1.511    0.033    0.543
   3_bss:    1.511    0.033    0.543
   3_xyz:    1.814    0.059    0.740
   3_adp:    1.814    0.059    0.740
   3_occ:    1.814    0.059    0.740
   4_bss:    1.814    0.059    0.740
   4_xyz:    1.618    0.073    0.826
   4_adp:    1.618    0.073    0.826
   4_occ:    1.618    0.073    0.826
   5_bss:    1.618    0.073    0.826
   5_xyz:    1.671    0.084    0.861
   5_adp:    1.671    0.084    0.861
   5_occ:    1.671    0.084    0.861
   5_bss:    1.671    0.084    0.861
------------------------------------------------------------------------

CPU time actual refinement: 377.70


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_856/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_856/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_856/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_856/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_856/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 377.56 
  Macro-tasks:
    bulk solvent and scale       = 55.60  
    individual site refinement   = 160.48 
    weights calculation          = 29.97  
    collect and process          = 6.38   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 252.57 
  Micro-tasks:
    mask                            = 2.50   
    f_calc                          = 119.39 
    alpha_beta                      = 8.30   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 128.89 
    fmodel                         = 9.12   
    r_factors                      = 0.34   
    phase_errors                   = 10.15  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 280.18 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.231 micro seconds
Total CPU time: 6.52 minutes
from_scatterers_fft:    648 calls, 118.96 s
gradients_fft:          593 calls, 114.95 s

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

# Date 2008-01-16 Time 05:49:53 PST -0800 (1200491393.05 s)
Start R-work = 0.4797, R-free = 0.4826 (no bulk solvent and anisotropic scale)
Final R-work = 0.1570, R-free = 0.2053 (no bulk solvent and anisotropic scale)

Start R-work = 0.4711, R-free = 0.4779
Final R-work = 0.1358, R-free = 0.1888