# Date 2008-01-16 Time 05:58:52 PST -0800 (1200491932.42 s)
#phil __OFF__

Command line arguments: "../958.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 2479
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 958

-------------------------------------------------------------------------------
  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, 48.1033, 84.6622, 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: 3.31, per 1000 atoms: 1.17


================================== 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, 48.1033, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.96157
Completeness in resolution range: 0.917647
Completeness with d_max=infinity: 0.914946

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0179
                             d_min =   1.9616

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, 48.1033, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.96157
Completeness in resolution range: 0.917647
Completeness with d_max=infinity: 0.914946

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0183 -  4.1982 [2246/2275]  2023   223   9.9%
  bin  2:  4.1982 -  3.3443 [2144/2167]  1931   213   9.9%
  bin  3:  3.3443 -  2.9251 [2111/2136]  1896   215  10.2%
  bin  4:  2.9251 -  2.6593 [2106/2132]  1901   205   9.7%
  bin  5:  2.6593 -  2.4696 [2096/2130]  1884   212  10.1%
  bin  6:  2.4696 -  2.3246 [2072/2100]  1869   203   9.8%
  bin  7:  2.3246 -  2.2085 [2069/2105]  1859   210  10.1%
  bin  8:  2.2085 -  2.1126 [2061/2103]  1854   207  10.0%
  bin  9:  2.1126 -  2.0315 [1990/2085]  1791   199  10.0%
  bin 10:  2.0315 -  1.9616 [ 694/2114]   622    72  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_958/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:
        1.35 -     2.06: 13
        2.06 -     2.77: 494
        2.77 -     3.48: 4504
        3.48 -     4.19: 9334
        4.19 -     4.90: 13834
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.346 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.357 3.040 -x+1/2,-y+1,z+1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.461 3.040 -x+1/2,-y+1,z-1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.524 3.120 -x+1/2,-y+1,z-1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.742 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28174 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_958/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_958/model_refine_001.geo

CPU time processing inputs: 9.40


============================ 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 48.10325 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4706   r_free= 0.4573   ksol= 0.00   Bsol= 0.00   scale= 0.883    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.284059                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6829 0.99   1457  164 0.3770 0.3954      6.5756      6.5816|
|  2:  4.6829 -  3.7358 0.99   1390  151 0.4135 0.4098       6.843      6.8348|
|  3:  3.7358 -  3.2691 0.99   1382  151 0.4471 0.3989       6.666      6.6361|
|  4:  3.2691 -  2.9727 0.98   1341  157 0.4650 0.4666      6.5175      6.4924|
|  5:  2.9727 -  2.7611 0.99   1370  149 0.4910 0.4651      6.3575      6.3255|
|  6:  2.7611 -  2.5992 0.99   1344  153 0.5117 0.4595      6.2759      6.1531|
|  7:  2.5992 -  2.4696 0.98   1351  143 0.4933 0.4546      6.2384      6.1817|
|  8:  2.4696 -  2.3625 0.98   1320  142 0.5209 0.5279      6.1409      6.2115|
|  9:  2.3625 -  2.2719 0.99   1341  151 0.5366 0.5082      6.1389      6.0889|
| 10:  2.2719 -  2.1937 0.99   1335  155 0.5034 0.5296      6.0762      6.0982|
| 11:  2.1937 -  2.1253 0.97   1320  142 0.5259 0.5284      6.0208      6.0118|
| 12:  2.1253 -  2.0647 0.98   1315  143 0.4970 0.5341      5.9188       5.986|
| 13:  2.0647 -  2.0105 0.81   1079  129 0.5153 0.4103      5.8648      5.8104|
| 14:  2.0105 -  1.9616 0.21    285   29 0.5736 0.4998      5.8305      5.7388|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.6829  1457   164  0.68  36.17   0.82     0.71      79378.29|
|  2:  4.6829 -  3.7358  1390   151  0.69  36.17   0.89     0.78     106113.07|
|  3:  3.7358 -  3.2691  1382   151  0.59  44.51   0.90     0.77     112332.62|
|  4:  3.2691 -  2.9727  1341   157  0.52  50.50   0.90     0.71      97973.02|
|  5:  2.9727 -  2.7611  1370   149  0.46  55.08   0.86     0.66      76781.01|
|  6:  2.7611 -  2.5992  1344   153  0.45  55.68   0.88     0.63      62347.52|
|  7:  2.5992 -  2.4696  1351   143  0.45  55.82   0.92     0.61      56528.22|
|  8:  2.4696 -  2.3625  1320   142  0.39  60.80   0.87     0.58      55853.73|
|  9:  2.3625 -  2.2719  1341   151  0.37  61.95   0.90     0.56      52508.77|
| 10:  2.2719 -  2.1937  1335   155  0.36  62.82   0.94     0.54      49945.14|
| 11:  2.1937 -  2.1253  1320   142  0.34  64.65   0.91     0.51      45787.80|
| 12:  2.1253 -  2.0647  1315   143  0.31  67.27   0.94     0.49      43440.68|
| 13:  2.0647 -  2.0105  1079   129  0.33  65.62   0.93     0.51      36165.95|
| 14:  2.0105 -  1.9616   285    29  0.37  61.97   0.89     0.59      28504.47|
|alpha:            min =        0.49 max =            0.78 mean =         0.62|
|beta:             min =    28504.47 max =       112332.62 mean =     67536.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.46|
|phase err.(work): min =        0.00 max =           90.00 mean =        54.87|
|phase err.(test): min =        0.00 max =           89.89 mean =        54.91|
|-----------------------------------------------------------------------------|

============================== 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 = 14.483887             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.598   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.698337              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.259   (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 |  1.346 -  1.701:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.701 -  2.057:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.057 -  2.412:       26 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.412 -  2.768:      468 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.768 -  3.123:     2210 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.123 -  3.478:     2294 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.478 -  3.834:     4419 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.834 -  4.189:     4915 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.189 -  4.545:     6229 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.545 -  4.900:     7605 |
|-----------------------------------------------------------------------------|
|-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 |        0.192 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.346 |       0.606 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.030)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4706   r_free= 0.4573   ksol= 0.00   Bsol= 0.00   scale= 0.883    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.284059                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4619   r_free= 0.4480   ksol= 0.29   Bsol= 19.45   scale= 0.923   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,4.05,0.53,0.00,0.00,0.00); trace/3= 0.77                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.277968                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.164872             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.323   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.226719              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.080   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4619      final r-factor (work) = 0.3656          |
| start r-factor (free) = 0.4480      final r-factor (free) = 0.4065          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.3633 = 12.16 * 0.50 * 6.2756 + 1.00 * 0.1923                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.6273 = 12.16 * 0.50 * 6.1605 + 1.00 * 0.1567                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3656      final r-factor (work) = 0.3351          |
| start r-factor (free) = 0.4065      final r-factor (free) = 0.4149          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5634 = 1.23 * 1.00 * 6.1605 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4888 = 1.23 * 1.00 * 6.0857 + 1.00 * 0.0234                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.030)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.11   18.80    None  None   None       |
|    all(noH): 2823   0      0.00    89.11   18.80    None  None   None       |
|    Sol.    : 438    0      1.60    89.11   36.47    None  None   None       |
|    Mac.    : 2385   0      0.00    83.07   15.55    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 -   8.911:  794   |   5:    44.557 -  53.468:  101        |
|      1:     8.911 -  17.823:  866   |   6:    53.468 -  62.379:   60        |
|      2:    17.823 -  26.734:  514   |   7:    62.379 -  71.291:   27        |
|      3:    26.734 -  35.645:  276   |   8:    71.291 -  80.202:    8        |
|      4:    35.645 -  44.557:  172   |   9:    80.202 -  89.113:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3351 r_free = 0.4149             target_work(ml) = 6.090         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3349 r_free = 0.4157             target_work(ml) = 6.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3349   r_free= 0.4157   ksol= 0.29   Bsol= 19.45   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,4.05,0.53,0.00,0.00,0.00); trace/3= 0.77                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.090191                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3342   r_free= 0.4113   ksol= 0.32   Bsol= 52.80   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.33,2.17,-0.27,0.00,-0.00,-0.00); trace/3= 0.19                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.090259                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.379245              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.434   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.316597              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.096  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3342      final r-factor (work) = 0.2875          |
| start r-factor (free) = 0.4113      final r-factor (free) = 0.3551          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.6145 = 7.38 * 0.50 * 6.0868 + 1.00 * 0.1567                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.3484 = 7.38 * 0.50 * 6.0351 + 1.00 * 0.0810                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2875      final r-factor (work) = 0.2743          |
| start r-factor (free) = 0.3551      final r-factor (free) = 0.3559          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9688 = 1.32 * 1.00 * 6.0351 + 1.00 * 0.0230                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.8514 = 1.32 * 1.00 * 5.9483 + 1.00 * 0.0199                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.030)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.55   19.38    None  None   None       |
|    all(noH): 2823   0      0.00    93.55   19.38    None  None   None       |
|    Sol.    : 438    0      1.04    93.55   39.02    None  None   None       |
|    Mac.    : 2385   0      0.00    90.75   15.77    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 -   9.355:  899   |   5:    46.773 -  56.127:  106        |
|      1:     9.355 -  18.709:  858   |   6:    56.127 -  65.482:   68        |
|      2:    18.709 -  28.064:  428   |   7:    65.482 -  74.836:   26        |
|      3:    28.064 -  37.418:  239   |   8:    74.836 -  84.191:   18        |
|      4:    37.418 -  46.773:  169   |   9:    84.191 -  93.545:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2743 r_free = 0.3559             target_work(ml) = 5.952         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2742 r_free = 0.3558             target_work(ml) = 5.952         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2742   r_free= 0.3558   ksol= 0.32   Bsol= 52.80   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.33,2.17,-0.27,0.00,-0.00,-0.00); trace/3= 0.19                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 5.951513                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2744   r_free= 0.3557   ksol= 0.32   Bsol= 59.96   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.67,2.13,-0.07,0.00,-0.00,-0.00); trace/3= 0.47                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 5.952250                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.108371              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.404  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.207768              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.506  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2744      final r-factor (work) = 0.2345          |
| start r-factor (free) = 0.3557      final r-factor (free) = 0.3094          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.2512 = 6.11 * 0.50 * 5.9493 + 1.00 * 0.0810                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.0615 = 6.11 * 0.50 * 5.8901 + 1.00 * 0.0719                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2345      final r-factor (work) = 0.2195          |
| start r-factor (free) = 0.3094      final r-factor (free) = 0.2961          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 24.8045 = 4.21 * 1.00 * 5.8901 + 1.00 * 0.0201                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 24.3377 = 4.21 * 1.00 * 5.7782 + 1.00 * 0.0244                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.030)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    122.47  19.95    None  None   None       |
|    all(noH): 2823   0      0.00    122.47  19.95    None  None   None       |
|    Sol.    : 438    0      1.83    117.70  46.50    None  None   None       |
|    Mac.    : 2385   0      0.00    122.47  15.08    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 -  12.247: 1344   |   5:    61.237 -  73.484:   81        |
|      1:    12.247 -  24.495:  776   |   6:    73.484 -  85.731:   39        |
|      2:    24.495 -  36.742:  250   |   7:    85.731 -  97.979:   31        |
|      3:    36.742 -  48.989:  181   |   8:    97.979 - 110.226:   13        |
|      4:    48.989 -  61.237:   98   |   9:   110.226 - 122.473:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2195 r_free = 0.2961             target_work(ml) = 5.762         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2194 r_free = 0.2959             target_work(ml) = 5.762         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2194   r_free= 0.2959   ksol= 0.32   Bsol= 59.96   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.67,2.13,-0.07,0.00,-0.00,-0.00); trace/3= 0.47                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.761914                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2197   r_free= 0.2959   ksol= 0.32   Bsol= 73.86   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.46,1.43,-0.19,0.00,-0.00,-0.00); trace/3= 0.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.762444                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.087456              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.059  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.651655              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.860  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2197      final r-factor (work) = 0.1817          |
| start r-factor (free) = 0.2959      final r-factor (free) = 0.2386          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.7721 = 5.09 * 0.50 * 5.7790 + 1.00 * 0.0719                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.5525 = 5.09 * 0.50 * 5.6921 + 1.00 * 0.0733                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1817      final r-factor (work) = 0.1629          |
| start r-factor (free) = 0.2386      final r-factor (free) = 0.2116          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7336 = 0.65 * 1.00 * 5.6921 + 1.00 * 0.0243                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6148 = 0.65 * 1.00 * 5.5243 + 1.00 * 0.0149                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.030)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    124.17  18.16    None  None   None       |
|    all(noH): 2823   0      0.00    124.17  18.16    None  None   None       |
|    Sol.    : 438    0      4.96    115.47  46.35    None  None   None       |
|    Mac.    : 2385   0      0.00    124.17  12.98    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 -  12.417: 1562   |   5:    62.083 -  74.499:   53        |
|      1:    12.417 -  24.833:  707   |   6:    74.499 -  86.916:   37        |
|      2:    24.833 -  37.250:  179   |   7:    86.916 -  99.332:   20        |
|      3:    37.250 -  49.666:  139   |   8:    99.332 - 111.749:    6        |
|      4:    49.666 -  62.083:  113   |   9:   111.749 - 124.165:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1629 r_free = 0.2116             target_work(ml) = 5.464         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1627 r_free = 0.2115             target_work(ml) = 5.464         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1627   r_free= 0.2115   ksol= 0.32   Bsol= 73.86   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.46,1.43,-0.19,0.00,-0.00,-0.00); trace/3= 0.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.463765                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1627   r_free= 0.2116   ksol= 0.33   Bsol= 69.50   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.94,0.42,-0.48,0.00,-0.00,-0.00); trace/3= -0.33                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.464454                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.522757              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.968  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.146538              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.439  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1627      final r-factor (work) = 0.1377          |
| start r-factor (free) = 0.2116      final r-factor (free) = 0.1865          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8070 = 3.52 * 0.50 * 5.5262 + 1.00 * 0.0733                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5729 = 3.52 * 0.50 * 5.3934 + 1.00 * 0.0731                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1377      final r-factor (work) = 0.1342          |
| start r-factor (free) = 0.1865      final r-factor (free) = 0.1765          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8052 = 0.15 * 1.00 * 5.3934 + 1.00 * 0.0149                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8065 = 0.15 * 1.00 * 5.3193 + 1.00 * 0.0271                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.030)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.05  16.47    None  None   None       |
|    all(noH): 2823   0      0.00    110.05  16.47    None  None   None       |
|    Sol.    : 438    0      4.85    110.05  40.45    None  None   None       |
|    Mac.    : 2385   0      0.00    109.17  12.06    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 -  11.006: 1449   |   5:    55.028 -  66.033:   52        |
|      1:    11.006 -  22.011:  831   |   6:    66.033 -  77.038:   33        |
|      2:    22.011 -  33.017:  185   |   7:    77.038 -  88.044:   12        |
|      3:    33.017 -  44.022:  145   |   8:    88.044 -  99.049:    5        |
|      4:    44.022 -  55.028:  106   |   9:    99.049 - 110.055:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1342 r_free = 0.1765             target_work(ml) = 5.293         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1340 r_free = 0.1765             target_work(ml) = 5.292         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1340   r_free= 0.1765   ksol= 0.33   Bsol= 69.50   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.94,0.42,-0.48,0.00,-0.00,-0.00); trace/3= -0.33                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.292055                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6829 0.99   1457  164 0.1003 0.1386      5.4104      5.6367|
|  2:  4.6829 -  3.7358 0.99   1390  151 0.0944 0.1134      5.5122      5.7123|
|  3:  3.7358 -  3.2691 0.99   1382  151 0.1244 0.1832      5.6025      5.9618|
|  4:  3.2691 -  2.9727 0.98   1341  157 0.1569 0.1788      5.6213      5.7425|
|  5:  2.9727 -  2.7611 0.99   1370  149 0.1657 0.1911      5.4951      5.6295|
|  6:  2.7611 -  2.5992 0.99   1344  153 0.1510 0.2273      5.3694      5.5775|
|  7:  2.5992 -  2.4696 0.98   1351  143 0.1499 0.1934       5.318       5.505|
|  8:  2.4696 -  2.3625 0.98   1320  142 0.1537 0.1967      5.2389      5.4412|
|  9:  2.3625 -  2.2719 0.99   1341  151 0.1446 0.1954      5.1673      5.3584|
| 10:  2.2719 -  2.1937 0.99   1335  155 0.1381 0.1922      5.1114      5.3468|
| 11:  2.1937 -  2.1253 0.97   1320  142 0.1350 0.1915      5.0318      5.2697|
| 12:  2.1253 -  2.0647 0.98   1315  143 0.1383 0.2047      4.9863      5.2338|
| 13:  2.0647 -  2.0105 0.81   1079  129 0.1417 0.1807      4.9153      5.1099|
| 14:  2.0105 -  1.9616 0.21    285   29 0.1423 0.1699      4.8175      4.9893|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.6829  1457   164  0.93   9.84   0.96     0.94       8037.48|
|  2:  4.6829 -  3.7358  1390   151  0.94   9.35   1.01     1.00      10637.86|
|  3:  3.7358 -  3.2691  1382   151  0.91  13.84   1.03     1.02      13273.55|
|  4:  3.2691 -  2.9727  1341   157  0.89  16.85   1.02     0.98      13605.49|
|  5:  2.9727 -  2.7611  1370   149  0.86  19.87   1.02     0.99      11523.77|
|  6:  2.7611 -  2.5992  1344   153  0.88  18.98   1.00     0.97       9399.72|
|  7:  2.5992 -  2.4696  1351   143  0.88  18.39   1.00     0.96       8181.19|
|  8:  2.4696 -  2.3625  1320   142  0.87  19.32   1.02     0.98       7366.70|
|  9:  2.3625 -  2.2719  1341   151  0.88  18.55   1.01     0.96       6327.12|
| 10:  2.2719 -  2.1937  1335   155  0.88  18.04   1.01     0.96       5740.00|
| 11:  2.1937 -  2.1253  1320   142  0.88  18.21   1.01     0.97       5119.50|
| 12:  2.1253 -  2.0647  1315   143  0.88  18.47   1.01     0.99       4796.59|
| 13:  2.0647 -  2.0105  1079   129  0.88  18.71   1.01     1.01       4075.91|
| 14:  2.0105 -  1.9616   285    29  0.87  18.59   1.00     0.97       3255.59|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     3255.59 max =        13605.49 mean =      8327.99|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.79 mean =        16.73|
|phase err.(test): min =        0.00 max =           89.65 mean =        16.06|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1344   r_free= 0.1764   ksol= 0.32   Bsol= 61.86   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.41,-0.32,-0.87,-0.00,-0.00,-0.00); trace/3= -0.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.294569                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1344   r_free= 0.1764   ksol= 0.32   Bsol= 61.86   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.41,-0.32,-0.87,-0.00,-0.00,-0.00); trace/3= -0.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.294569                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6829 0.99   1457  164 0.1028 0.1389       5.435      5.6331|
|  2:  4.6829 -  3.7358 0.99   1390  151 0.0948 0.1126       5.516      5.7117|
|  3:  3.7358 -  3.2691 0.99   1382  151 0.1247 0.1825      5.6035      5.9603|
|  4:  3.2691 -  2.9727 0.98   1341  157 0.1573 0.1786      5.6217      5.7409|
|  5:  2.9727 -  2.7611 0.99   1370  149 0.1660 0.1912      5.4962      5.6316|
|  6:  2.7611 -  2.5992 0.99   1344  153 0.1511 0.2265        5.37      5.5764|
|  7:  2.5992 -  2.4696 0.98   1351  143 0.1498 0.1935      5.3177      5.5048|
|  8:  2.4696 -  2.3625 0.98   1320  142 0.1535 0.1970      5.2391      5.4424|
|  9:  2.3625 -  2.2719 0.99   1341  151 0.1443 0.1957      5.1659      5.3577|
| 10:  2.2719 -  2.1937 0.99   1335  155 0.1381 0.1926      5.1109      5.3487|
| 11:  2.1937 -  2.1253 0.97   1320  142 0.1348 0.1914      5.0312      5.2686|
| 12:  2.1253 -  2.0647 0.98   1315  143 0.1385 0.2052      4.9882      5.2366|
| 13:  2.0647 -  2.0105 0.81   1079  129 0.1415 0.1803      4.9153      5.1086|
| 14:  2.0105 -  1.9616 0.21    285   29 0.1426 0.1696      4.8169       4.985|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.6829  1457   164  0.93  10.05   0.96     0.94       8205.40|
|  2:  4.6829 -  3.7358  1390   151  0.94   9.39   1.01     0.99      10698.25|
|  3:  3.7358 -  3.2691  1382   151  0.92  13.82   1.02     1.01      13237.39|
|  4:  3.2691 -  2.9727  1341   157  0.89  16.81   1.00     0.97      13569.66|
|  5:  2.9727 -  2.7611  1370   149  0.86  19.83   1.00     0.98      11499.09|
|  6:  2.7611 -  2.5992  1344   153  0.88  18.96   0.98     0.96       9400.12|
|  7:  2.5992 -  2.4696  1351   143  0.88  18.37   0.98     0.94       8181.62|
|  8:  2.4696 -  2.3625  1320   142  0.87  19.33   0.99     0.96       7375.02|
|  9:  2.3625 -  2.2719  1341   151  0.88  18.53   0.99     0.94       6332.15|
| 10:  2.2719 -  2.1937  1335   155  0.88  18.04   0.98     0.94       5745.19|
| 11:  2.1937 -  2.1253  1320   142  0.88  18.20   0.98     0.95       5124.59|
| 12:  2.1253 -  2.0647  1315   143  0.88  18.49   0.98     0.96       4815.92|
| 13:  2.0647 -  2.0105  1079   129  0.88  18.69   0.98     0.98       4073.32|
| 14:  2.0105 -  1.9616   285    29  0.87  18.54   0.98     0.95       3233.83|
|alpha:            min =        0.94 max =            1.01 mean =         0.96|
|beta:             min =     3233.83 max =        13569.66 mean =      8341.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.73 mean =        16.73|
|phase err.(test): min =        0.00 max =           89.48 mean =        16.05|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.030)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.06  16.47    None  None   None       |
|    all(noH): 2823   0      0.00    110.06  16.47    None  None   None       |
|    Sol.    : 438    0      4.85    110.06  40.45    None  None   None       |
|    Mac.    : 2385   0      0.00    109.17  12.07    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 -  11.009: 1449   |   5:    55.030 -  66.036:   52        |
|      1:    11.009 -  22.014:  831   |   6:    66.036 -  77.041:   33        |
|      2:    22.014 -  33.019:  185   |   7:    77.041 -  88.047:   12        |
|      3:    33.019 -  44.025:  145   |   8:    88.047 -  99.052:    5        |
|      4:    44.025 -  55.030:  106   |   9:    99.052 - 110.058:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 346         
Filter by distance & map next to the model:
   mapped sites are within: 0.583 - 5.597
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 342 from: 346
   mapped sites are within: 0.730 - 5.597

peak=    7.079 closest distance to " O   HOH Z 120 " =    1.365
peak=    6.616 closest distance to " O   HOH Z  41 " =    1.111
peak=    5.405 closest distance to " CG  GLN A  77 " =    0.961
peak=    5.329 closest distance to " O   HOH Z 210 " =    1.669
peak=    5.239 closest distance to " O   HOH Z 130 " =    1.033
peak=    5.192 closest distance to " O   HOH Z 352 " =    1.371
peak=    5.157 closest distance to " CB  SER A  63 " =    1.328
peak=    5.137 closest distance to " O   HOH Z  61 " =    1.627
peak=    4.944 closest distance to " CG  PRO A  54 " =    1.244
peak=    4.875 closest distance to " OE1 GLN A  77 " =    1.110
peak=    4.810 closest distance to " CA  TYR A  30 " =    1.044
peak=    4.802 closest distance to " O   HOH Z 111 " =    2.253
peak=    4.781 closest distance to " O   HOH Z 389 " =    1.969
peak=    4.734 closest distance to " O   HOH Z 433 " =    1.832
peak=    4.726 closest distance to " O   HOH Z  15 " =    2.025
peak=    4.661 closest distance to " O   HOH Z 142 " =    1.784
peak=    4.660 closest distance to " O   HOH Z 350 " =    1.184
peak=    4.655 closest distance to " O   HOH Z  80 " =    2.211
peak=    4.653 closest distance to " O   PRO A 198 " =    1.627
peak=    4.649 closest distance to " O   HOH Z 124 " =    1.444
peak=    4.647 closest distance to " O   HOH Z 272 " =    1.317
peak=    4.642 closest distance to " O   HOH Z 134 " =    2.116
peak=    4.601 closest distance to " OE1 GLN A  11 " =    2.085
peak=    4.583 closest distance to " O   HOH Z  44 " =    2.468
peak=    4.524 closest distance to " O   HOH Z 400 " =    0.882
peak=    4.496 closest distance to " CB  ARG A 275 " =    0.997
peak=    4.485 closest distance to " O   HOH Z 154 " =    1.658
peak=    4.452 closest distance to " O   HOH Z 404 " =    1.596
peak=    4.412 closest distance to " CB  GLN A 223 " =    1.419
peak=    4.385 closest distance to " O   ARG A 275 " =    0.771
peak=    4.355 closest distance to " O   HOH Z 133 " =    1.876
peak=    4.352 closest distance to " CG  PRO A 213 " =    1.322
peak=    4.342 closest distance to " O   HOH Z  47 " =    1.781
peak=    4.336 closest distance to " O   HOH Z 126 " =    1.907
peak=    4.274 closest distance to " CB  SER A  62 " =    0.933
peak=    4.271 closest distance to " O   HOH Z 221 " =    1.384
peak=    4.250 closest distance to " O   HOH Z 234 " =    3.875
peak=    4.240 closest distance to " NE2 HIS A 115 " =    1.059
peak=    4.239 closest distance to " O   HOH Z  97 " =    1.936
peak=    4.237 closest distance to " CB  GLN A  73 " =    1.026
peak=    4.233 closest distance to " O   HOH Z  11 " =    1.311
peak=    4.226 closest distance to " O   HOH Z 132 " =    1.451
peak=    4.166 closest distance to " O   HOH Z 247 " =    1.516
peak=    4.159 closest distance to " CB  PRO A  54 " =    0.808
peak=    4.139 closest distance to " O   HOH Z  48 " =    1.966
peak=    4.121 closest distance to " CB  ALA A   1 " =    1.242
peak=    4.121 closest distance to " CG  PRO A  90 " =    1.261
peak=    4.114 closest distance to " O   HOH Z 422 " =    1.161
peak=    4.107 closest distance to " CB  ASN A 285 " =    0.867
peak=    4.097 closest distance to " CG2 THR A 221 " =    1.068
peak=    4.097 closest distance to " O   HOH Z  43 " =    1.962
peak=    4.091 closest distance to " O   HOH Z 132 " =    1.967
peak=    4.088 closest distance to " O   HOH Z 271 " =    2.275
peak=    4.083 closest distance to " O   HOH Z 211 " =    1.358
peak=    4.082 closest distance to " CG2BVAL A  41 " =    1.118
peak=    4.079 closest distance to " O   HOH Z 250 " =    2.252
peak=    4.077 closest distance to " NH2BARG A 102 " =    1.013
peak=    4.049 closest distance to " O   HOH Z 142 " =    1.532
peak=    4.004 closest distance to " O   HOH Z 189 " =    2.065
peak=    4.001 closest distance to " CB  GLN A 194 " =    0.862
peak=    3.982 closest distance to " CB  GLU A 152 " =    1.166
peak=    3.978 closest distance to " CB  TRP A 179 " =    1.378
peak=    3.971 closest distance to " O   HOH Z 193 " =    1.925
peak=    3.966 closest distance to " O   HOH Z 403 " =    1.807
peak=    3.952 closest distance to " CB  GLN A  88 " =    1.055
peak=    3.949 closest distance to " CG AARG A 275 " =    1.068
peak=    3.943 closest distance to " O   HOH Z  47 " =    1.787
peak=    3.941 closest distance to " O   HOH Z 406 " =    1.611
peak=    3.936 closest distance to " CB  ARG A 190 " =    1.714
peak=    3.935 closest distance to " O   HOH Z 163 " =    1.887
peak=    3.927 closest distance to " O   HOH Z 214 " =    1.220
peak=    3.901 closest distance to " CB  GLN A 183 " =    1.232
peak=    3.900 closest distance to " O   HOH Z 108 " =    1.390
peak=    3.899 closest distance to " N   ASN A  39 " =    1.179
peak=    3.893 closest distance to " O   HOH Z 324 " =    1.517
peak=    3.887 closest distance to " O   HOH Z  59 " =    1.840
peak=    3.862 closest distance to " CA  ARG A 195 " =    1.104
peak=    3.857 closest distance to " O   HOH Z  39 " =    2.014
peak=    3.830 closest distance to " CB  SER A 141 " =    0.996
peak=    3.830 closest distance to " CD  LYS A 166 " =    1.471
peak=    3.821 closest distance to " O   HOH Z  44 " =    1.691
peak=    3.813 closest distance to " O   HOH Z 196 " =    2.176
peak=    3.812 closest distance to " O   HOH Z  54 " =    1.279
peak=    3.807 closest distance to " O   HOH Z   7 " =    1.143
peak=    3.805 closest distance to " O   HOH Z  49 " =    1.177
peak=    3.805 closest distance to " CE  LYS A 119 " =    1.236
peak=    3.798 closest distance to " O   HOH Z 265 " =    2.219
peak=    3.796 closest distance to " O   HOH Z 369 " =    2.085
peak=    3.788 closest distance to " O   HOH Z 411 " =    3.117
peak=    3.788 closest distance to " CB  PRO A 198 " =    0.970
peak=    3.787 closest distance to " O   HOH Z 127 " =    1.144
peak=    3.780 closest distance to " O   HOH Z 428 " =    1.278
peak=    3.769 closest distance to " O   HOH Z 128 " =    2.307
peak=    3.768 closest distance to " O   HOH Z 118 " =    1.967
peak=    3.763 closest distance to " O   HOH Z 402 " =    1.543
peak=    3.759 closest distance to " CB  ALA A 256 " =    1.188
peak=    3.757 closest distance to " O   HOH Z 362 " =    3.312
peak=    3.749 closest distance to " CB  TRP A 266 " =    0.986
peak=    3.748 closest distance to " CB  MET A  47 " =    0.986
peak=    3.745 closest distance to " CB  GLU A 277 " =    0.944
peak=    3.745 closest distance to " O   HOH Z 357 " =    2.101
peak=    3.744 closest distance to " CG  PRO A 198 " =    1.378
peak=    3.743 closest distance to " CD2 LEU A 297 " =    1.001
peak=    3.734 closest distance to " O   HOH Z 431 " =    1.387
peak=    3.729 closest distance to " CB  VAL A 202 " =    1.502
peak=    3.723 closest distance to " CG2 VAL A  78 " =    1.055
peak=    3.722 closest distance to " CB  GLN A  58 " =    0.898
peak=    3.720 closest distance to " CA  ASP A 191 " =    0.861
peak=    3.719 closest distance to " O   HOH Z 203 " =    1.726
peak=    3.718 closest distance to " O   HOH Z 437 " =    1.960
peak=    3.717 closest distance to " O   HOH Z 363 " =    1.282
peak=    3.714 closest distance to " O   HOH Z  68 " =    1.947
peak=    3.707 closest distance to " O   THR A 251 " =    1.346
peak=    3.697 closest distance to " O   HOH Z 394 " =    1.752
peak=    3.693 closest distance to " CA  ARG A  66 " =    1.018
peak=    3.687 closest distance to " O   ALA A 165 " =    1.269
peak=    3.685 closest distance to " O   HOH Z 215 " =    1.378
peak=    3.684 closest distance to " O   HOH Z 183 " =    1.530
peak=    3.675 closest distance to " CB  TYR A 116 " =    1.387
peak=    3.674 closest distance to " N   SER A 164 " =    0.956
peak=    3.668 closest distance to " CH2 TRP A 274 " =    2.130
peak=    3.666 closest distance to " O   HOH Z 426 " =    1.280
peak=    3.665 closest distance to " O   HOH Z  63 " =    1.668
peak=    3.654 closest distance to " CG  ARG A  66 " =    2.876
peak=    3.650 closest distance to " CG1 VAL A 153 " =    1.144
peak=    3.644 closest distance to " O   HOH Z  22 " =    2.210
peak=    3.644 closest distance to " CA  ASN A 176 " =    1.705
peak=    3.644 closest distance to " O   HOH Z 408 " =    1.913
peak=    3.636 closest distance to " O   HOH Z 174 " =    1.995
peak=    3.628 closest distance to " CG2 VAL A 197 " =    1.352
peak=    3.626 closest distance to " NH1 ARG A  36 " =    1.272
peak=    3.621 closest distance to " CD  PRO A  54 " =    1.002
peak=    3.621 closest distance to " ND2 ASN A  45 " =    1.187
peak=    3.612 closest distance to " O   VAL A  72 " =    1.254
peak=    3.612 closest distance to " OD1 ASP A 238 " =    0.933
peak=    3.610 closest distance to " CA  ALA A  21 " =    1.461
peak=    3.608 closest distance to " NH2 ARG A 156 " =    1.244
peak=    3.607 closest distance to " NH1 ARG A 269 " =    0.891
peak=    3.598 closest distance to " CG1 ILE A 120 " =    1.116
peak=    3.596 closest distance to " O   HOH Z  88 " =    3.682
peak=    3.584 closest distance to " O   HOH Z   4 " =    1.254
peak=    3.581 closest distance to " OG  SER A  62 " =    3.179
peak=    3.563 closest distance to " O   HOH Z 139 " =    4.411
peak=    3.563 closest distance to " CA  GLY A 196 " =    0.940
peak=    3.561 closest distance to " NE AARG A 275 " =    1.527
peak=    3.557 closest distance to " CG1 ILE A  33 " =    1.316
peak=    3.556 closest distance to " CD BLYS A 290 " =    1.011
peak=    3.553 closest distance to " CB  ALA A 100 " =    1.471
peak=    3.553 closest distance to " O   HOH Z 250 " =    1.304
peak=    3.545 closest distance to " O   HOH Z 162 " =    2.006
peak=    3.545 closest distance to " O   HOH Z 139 " =    3.490
peak=    3.544 closest distance to " O   GLY A  91 " =    1.190
peak=    3.542 closest distance to " O   HOH Z 377 " =    1.571
peak=    3.542 closest distance to " CD1 LEU A 222 " =    0.963
peak=    3.539 closest distance to " O   HOH Z 128 " =    1.558
peak=    3.537 closest distance to " CA  ILE A 106 " =    0.766
peak=    3.536 closest distance to " CB  GLU A 128 " =    1.094
peak=    3.532 closest distance to " CD1 TRP A 274 " =    1.077
peak=    3.526 closest distance to " CE BMET A  47 " =    1.361
peak=    3.524 closest distance to " O   HOH Z 387 " =    2.395
peak=    3.523 closest distance to " CG  PRO A 243 " =    1.172
peak=    3.520 closest distance to " O   HOH Z 420 " =    2.314
peak=    3.514 closest distance to " CG2 THR A 220 " =    0.757
peak=    3.504 closest distance to " O   HOH Z  88 " =    1.605
peak=    3.503 closest distance to " O   HOH Z  38 " =    3.448
peak=    3.497 closest distance to " CB  LEU A  83 " =    0.783
peak=    3.490 closest distance to " N   LYS A 166 " =    0.861
peak=    3.490 closest distance to " O   HOH Z 192 " =    1.554
peak=    3.484 closest distance to " CB  ASN A 148 " =    2.044
peak=    3.483 closest distance to " O   HOH Z   1 " =    3.194
peak=    3.482 closest distance to " NZ  LYS A 117 " =    0.853
peak=    3.482 closest distance to " CB  ARG A 275 " =    1.488
peak=    3.480 closest distance to " O   HOH Z 272 " =    1.994
peak=    3.476 closest distance to " CD  LYS A 119 " =    1.498
peak=    3.470 closest distance to " O   SER A 276 " =    1.144
peak=    3.457 closest distance to " O   HOH Z 418 " =    1.626
peak=    3.456 closest distance to " O   HOH Z 336 " =    1.494
peak=    3.456 closest distance to " O   HOH Z  26 " =    1.508
peak=    3.450 closest distance to " CB  MET A 105 " =    1.148
peak=    3.449 closest distance to " O   HOH Z 316 " =    3.086
peak=    3.448 closest distance to " O   SER A  87 " =    2.312
peak=    3.443 closest distance to " O   HOH Z  66 " =    2.193
peak=    3.443 closest distance to " CD2 TRP A 179 " =    1.237
peak=    3.442 closest distance to " O   HOH Z  78 " =    2.241
peak=    3.437 closest distance to " CB  LEU A 228 " =    1.148
peak=    3.436 closest distance to " O   HOH Z 142 " =    1.992
peak=    3.435 closest distance to " CB  GLU A 152 " =    1.676
peak=    3.430 closest distance to " CD1 LEU A  96 " =    0.825
peak=    3.428 closest distance to " CA  ALA A 160 " =    1.053
peak=    3.426 closest distance to " O   HOH Z 435 " =    2.011
peak=    3.423 closest distance to " OH  TYR A  30 " =    1.434
peak=    3.423 closest distance to " CA  VAL A  41 " =    0.834
peak=    3.419 closest distance to " ND2 ASN A 187 " =    1.480
peak=    3.418 closest distance to " CB  SER A  26 " =    0.930
peak=    3.418 closest distance to " O   HOH Z 432 " =    2.015
peak=    3.416 closest distance to " OD2 ASP A 162 " =    1.154
peak=    3.416 closest distance to " NZ  LYS A 117 " =    3.079
peak=    3.408 closest distance to " O  BHOH Z 338 " =    1.105
peak=    3.403 closest distance to " O   HOH Z 374 " =    2.713
peak=    3.402 closest distance to " CB  SER A 276 " =    1.298
peak=    3.402 closest distance to " O   HOH Z 183 " =    1.455
peak=    3.397 closest distance to " CA  SER A  12 " =    1.319
peak=    3.392 closest distance to " OG1 THR A 294 " =    2.538
peak=    3.391 closest distance to " O   HOH Z  83 " =    1.515
peak=    3.389 closest distance to " O   HOH Z 409 " =    3.152
peak=    3.387 closest distance to " CB  TYR A 169 " =    0.931
peak=    3.387 closest distance to " O   HOH Z 271 " =    1.280
peak=    3.385 closest distance to " CA  ASP A 124 " =    0.849
peak=    3.383 closest distance to " NZ  LYS A 193 " =    1.559
peak=    3.383 closest distance to " CA  GLN A 223 " =    0.790
peak=    3.382 closest distance to " O   HOH Z 417 " =    3.176
peak=    3.380 closest distance to " O   HOH Z 261 " =    2.118
peak=    3.380 closest distance to " O  BHOH Z 338 " =    2.290
peak=    3.373 closest distance to " O   HOH Z 102 " =    1.373
peak=    3.364 closest distance to " O   HOH Z 200 " =    1.439
peak=    3.363 closest distance to " O   HOH Z   2 " =    1.943
peak=    3.361 closest distance to " O   HOH Z 426 " =    3.243
peak=    3.360 closest distance to " O   HOH Z 287 " =    1.879
peak=    3.356 closest distance to " O   HOH Z 132 " =    2.364
peak=    3.355 closest distance to " O   HOH Z 292 " =    1.537
peak=    3.352 closest distance to " O   GLY A  23 " =    2.465
peak=    3.348 closest distance to " OG  SER A  97 " =    3.423
peak=    3.343 closest distance to " O   HOH Z  20 " =    1.847
peak=    3.343 closest distance to " O   HOH Z 380 " =    2.006
peak=    3.343 closest distance to " O   HOH Z 112 " =    1.590
peak=    3.342 closest distance to " O   HOH Z 371 " =    3.162
peak=    3.342 closest distance to " CA  ALA A 100 " =    1.208
peak=    3.340 closest distance to " O   HOH Z 287 " =    1.844
peak=    3.338 closest distance to " O   HOH Z 315 " =    1.906
peak=    3.335 closest distance to " O   HOH Z 395 " =    1.453
peak=    3.334 closest distance to " O   HOH Z 150 " =    1.908
peak=    3.328 closest distance to " O   HOH Z 358 " =    1.588
peak=    3.328 closest distance to " O   HOH Z 197 " =    1.902
peak=    3.328 closest distance to " O   HOH Z  54 " =    2.265
peak=    3.327 closest distance to " CB  ARG A  79 " =    1.372
peak=    3.326 closest distance to " CG  GLN A  89 " =    1.309
peak=    3.326 closest distance to " CB  ILE A 199 " =    1.127
peak=    3.321 closest distance to " CA  ASN A 127 " =    1.161
peak=    3.319 closest distance to " O   HOH Z  50 " =    3.355
peak=    3.318 closest distance to " NH2BARG A 145 " =    1.878
peak=    3.317 closest distance to " O   HOH Z   6 " =    1.231
peak=    3.314 closest distance to " O   HOH Z  39 " =    2.035
peak=    3.312 closest distance to " O   HOH Z 298 " =    1.937
peak=    3.308 closest distance to " CB  PHE A  16 " =    1.445
peak=    3.308 closest distance to " NZ  LYS A 166 " =    3.162
peak=    3.306 closest distance to " CB  PHE A 283 " =    0.907
peak=    3.302 closest distance to " O   HOH Z 299 " =    1.605
peak=    3.301 closest distance to " CB  PHE A  61 " =    0.773
peak=    3.298 closest distance to " CB  ASN A 187 " =    1.159
peak=    3.293 closest distance to " O   HOH Z 260 " =    1.390
peak=    3.283 closest distance to " CB  TRP A 123 " =    1.339
peak=    3.283 closest distance to " N   HIS A 108 " =    1.881
peak=    3.282 closest distance to " CB  ARG A 139 " =    1.021
peak=    3.276 closest distance to " O   HOH Z 145 " =    1.959
peak=    3.275 closest distance to " CD  GLN A  73 " =    1.027
peak=    3.273 closest distance to " CA  THR A 221 " =    0.924
peak=    3.271 closest distance to " CG2AVAL A 121 " =    1.915
peak=    3.269 closest distance to " CB  SER A   3 " =    1.523
peak=    3.266 closest distance to " O   ALA A  71 " =    0.946
peak=    3.263 closest distance to " CG2 THR A  42 " =    0.838
peak=    3.263 closest distance to " CD1 TRP A 266 " =    1.209
peak=    3.262 closest distance to " O   HOH Z 345 " =    2.810
peak=    3.259 closest distance to " CD ALYS A 290 " =    1.250
peak=    3.258 closest distance to " CG  GLN A  11 " =    1.282
peak=    3.257 closest distance to " CA  LYS A  48 " =    1.517
peak=    3.254 closest distance to " N   GLU A 277 " =    1.091
peak=    3.253 closest distance to " CA  ALA A 295 " =    1.015
peak=    3.253 closest distance to " CB  PRO A 213 " =    1.862
peak=    3.251 closest distance to " NH1BARG A 145 " =    0.730
peak=    3.251 closest distance to " NH1 ARG A  14 " =    1.263
peak=    3.246 closest distance to " O   HOH Z 215 " =    2.130
peak=    3.246 closest distance to " CD2 HIS A  86 " =    1.278
peak=    3.244 closest distance to " NH2AARG A 190 " =    1.303
peak=    3.241 closest distance to " CA  LEU A  83 " =    1.401
peak=    3.238 closest distance to " N   TYR A  15 " =    0.808
peak=    3.237 closest distance to " CA  GLU A 152 " =    0.967
peak=    3.233 closest distance to " O   HOH Z 326 " =    1.445
peak=    3.233 closest distance to " O   HOH Z 245 " =    1.437
peak=    3.232 closest distance to " CE1 TYR A 186 " =    1.097
peak=    3.232 closest distance to " NE2 GLN A  11 " =    1.116
peak=    3.231 closest distance to " O   HOH Z 208 " =    1.782
peak=    3.229 closest distance to " OG ASER A 164 " =    0.834
peak=    3.228 closest distance to " OG BSER A 210 " =    1.122
peak=    3.228 closest distance to " CB  SER A  28 " =    0.977
peak=    3.226 closest distance to " CG1BVAL A  72 " =    1.760
peak=    3.226 closest distance to " CA  SER A  87 " =    0.860
peak=    3.222 closest distance to " O   HOH Z 214 " =    1.651
peak=    3.218 closest distance to " O   HOH Z 272 " =    1.138
peak=    3.216 closest distance to " O   HOH Z 379 " =    1.596
peak=    3.216 closest distance to " CA  ALA A 248 " =    1.197
peak=    3.215 closest distance to " O   HOH Z 227 " =    1.806
peak=    3.213 closest distance to " O   HOH Z 174 " =    1.269
peak=    3.211 closest distance to " NE1 TRP A 274 " =    0.817
peak=    3.207 closest distance to " CA  THR A 221 " =    1.205
peak=    3.206 closest distance to " O   HOH Z 238 " =    5.597
peak=    3.203 closest distance to " SD  MET A 185 " =    1.466
peak=    3.197 closest distance to " CB  ASN A 148 " =    1.358
peak=    3.197 closest distance to " CA  HIS A 115 " =    0.991
peak=    3.197 closest distance to " O   HOH Z 213 " =    1.836
peak=    3.195 closest distance to " NH1BARG A 145 " =    1.571
peak=    3.188 closest distance to " CA  ASP A 162 " =    1.091
peak=    3.181 closest distance to " O   HOH Z 303 " =    1.807
peak=    3.180 closest distance to " CG2 VAL A 112 " =    1.439
peak=    3.179 closest distance to " CB  ILE A 120 " =    1.399
peak=    3.179 closest distance to " O   HOH Z 257 " =    2.318
peak=    3.173 closest distance to " O   HOH Z  52 " =    1.370
peak=    3.165 closest distance to " CA  GLY A 241 " =    0.808
peak=    3.163 closest distance to " CB  LEU A 261 " =    1.306
peak=    3.160 closest distance to " O   HOH Z 200 " =    3.724
peak=    3.159 closest distance to " O   HOH Z 343 " =    2.420
peak=    3.157 closest distance to " CD1 PHE A  59 " =    1.715
peak=    3.153 closest distance to " CD1 LEU A 300 " =    1.235
peak=    3.150 closest distance to " O   HOH Z 373 " =    1.704
peak=    3.147 closest distance to " CE3 TRP A  85 " =    1.124
peak=    3.144 closest distance to " OD1 ASN A  69 " =    2.284
peak=    3.141 closest distance to " CD  ARG A 269 " =    0.880
peak=    3.137 closest distance to " CE3 TRP A 274 " =    3.468
peak=    3.135 closest distance to " O   HOH Z 353 " =    2.479
peak=    3.131 closest distance to " CG2 THR A 251 " =    1.108
peak=    3.131 closest distance to " O   HOH Z 293 " =    1.905
peak=    3.129 closest distance to " OE1 GLN A  58 " =    0.890
peak=    3.129 closest distance to " O   HOH Z 151 " =    1.773
peak=    3.125 closest distance to " O   HOH Z 109 " =    2.119
peak=    3.124 closest distance to " CZ3 TRP A 274 " =    4.686
peak=    3.123 closest distance to " CZ  PHE A 218 " =    1.078
peak=    3.122 closest distance to " O   HOH Z 334 " =    1.625
peak=    3.121 closest distance to " O   HOH Z 135 " =    1.766
peak=    3.121 closest distance to " N   TYR A 116 " =    1.900
peak=    3.119 closest distance to " O   HOH Z 196 " =    2.126
peak=    3.111 closest distance to " O   HOH Z 402 " =    2.892
peak=    3.105 closest distance to " O   HOH Z 425 " =    1.528
peak=    3.104 closest distance to " CA  LEU A 282 " =    1.085
peak=    3.102 closest distance to " O   HOH Z 386 " =    2.337
peak=    3.100 closest distance to " O   HOH Z 403 " =    1.557
peak=    3.099 closest distance to " O   HOH Z  64 " =    2.128
peak=    3.087 closest distance to " O   HOH Z 301 " =    1.749
peak=    3.081 closest distance to " O   HOH Z 128 " =    1.970
peak=    3.068 closest distance to " CA  LYS A 117 " =    1.266
peak=    3.064 closest distance to " CB  THR A  31 " =    1.701
peak=    3.059 closest distance to " O   HOH Z 279 " =    2.336
peak=    3.019 closest distance to " CA  ALA A 100 " =    2.197
peak=    3.003 closest distance to " O   HOH Z 261 " =    1.885

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 213         
Filter by distance & map next to the model:
   mapped sites are within: 0.209 - 5.489
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 213
   mapped sites are within: 0.702 - 5.489

peak=   -5.171 closest distance to " O   HOH Z 221 " =    0.891
peak=   -4.984 closest distance to " O   HOH Z 290 " =    0.741
peak=   -4.525 closest distance to " N   ARG A 275 " =    0.885
peak=   -4.368 closest distance to " O   HOH Z 120 " =    0.702
peak=   -4.346 closest distance to " C   ASN A 285 " =    2.604
peak=   -4.319 closest distance to " O   HOH Z 266 " =    4.675
peak=   -4.252 closest distance to " CB  LEU A 167 " =    2.058
peak=   -4.235 closest distance to " CD2 HIS A 115 " =    1.037
peak=   -4.199 closest distance to " O   HOH Z 166 " =    1.803
peak=   -4.187 closest distance to " O  BHOH Z 338 " =    1.453
peak=   -4.157 closest distance to " O   HOH Z 423 " =    0.919
peak=   -4.137 closest distance to " O   HOH Z  52 " =    1.911
peak=   -4.101 closest distance to " CG2BVAL A  41 " =    2.479
peak=   -4.068 closest distance to " O   HOH Z  93 " =    1.364
peak=   -4.058 closest distance to " NH2 ARG A  66 " =    0.952
peak=   -4.033 closest distance to " O   HOH Z 350 " =    0.762
peak=   -4.020 closest distance to " N   ARG A 275 " =    1.279
peak=   -4.008 closest distance to " NE2 GLN A 223 " =    1.024
peak=   -3.985 closest distance to " O   HOH Z 155 " =    1.526
peak=   -3.947 closest distance to " N   ALA A  43 " =    2.725
peak=   -3.933 closest distance to " CG2 ILE A  49 " =    2.589
peak=   -3.932 closest distance to " O   HOH Z   7 " =    1.177
peak=   -3.917 closest distance to " CD1 PHE A  59 " =    1.837
peak=   -3.913 closest distance to " O   HOH Z 130 " =    1.126
peak=   -3.906 closest distance to " O   GLN A  11 " =    1.093
peak=   -3.896 closest distance to " OG  SER A  97 " =    2.261
peak=   -3.871 closest distance to " CB  SER A 146 " =    2.022
peak=   -3.838 closest distance to " O   HOH Z 422 " =    0.902
peak=   -3.828 closest distance to " O   PRO A 198 " =    1.348
peak=   -3.824 closest distance to " OXT GLY A 302 " =    2.886
peak=   -3.818 closest distance to " NH2 ARG A  66 " =    1.070
peak=   -3.818 closest distance to " O   HOH Z 151 " =    1.412
peak=   -3.815 closest distance to " O   HOH Z 407 " =    0.754
peak=   -3.813 closest distance to " O   HOH Z  11 " =    1.149
peak=   -3.805 closest distance to " C   GLY A 133 " =    1.259
peak=   -3.797 closest distance to " CA  VAL A 197 " =    0.920
peak=   -3.737 closest distance to " CG1 VAL A 112 " =    2.578
peak=   -3.724 closest distance to " O   ALA A   1 " =    2.072
peak=   -3.707 closest distance to " CG  ASP A 231 " =    0.707
peak=   -3.703 closest distance to " CE  MET A 105 " =    2.113
peak=   -3.696 closest distance to " O   HOH Z 140 " =    0.895
peak=   -3.695 closest distance to " O   HOH Z  37 " =    1.574
peak=   -3.683 closest distance to " CB  GLN A  73 " =    1.020
peak=   -3.683 closest distance to " O   HOH Z  71 " =    1.343
peak=   -3.679 closest distance to " O   HOH Z 401 " =    1.193
peak=   -3.657 closest distance to " CD1 TRP A 179 " =    0.973
peak=   -3.650 closest distance to " OH  TYR A 169 " =    0.876
peak=   -3.627 closest distance to " CA  SER A 164 " =    2.057
peak=   -3.624 closest distance to " OD2 ASP A 298 " =    0.937
peak=   -3.614 closest distance to " O   HOH Z 127 " =    1.288
peak=   -3.614 closest distance to " N   GLN A  58 " =    1.705
peak=   -3.614 closest distance to " CA  GLY A 203 " =    2.276
peak=   -3.605 closest distance to " CD  GLN A  77 " =    0.898
peak=   -3.605 closest distance to " CG2 THR A 221 " =    2.384
peak=   -3.594 closest distance to " O   HOH Z 185 " =    2.443
peak=   -3.594 closest distance to " CD  GLN A  88 " =    0.754
peak=   -3.573 closest distance to " CD2 LEU A 237 " =    2.447
peak=   -3.563 closest distance to " O   ALA A  34 " =    1.874
peak=   -3.559 closest distance to " O   HOH Z  52 " =    1.194
peak=   -3.558 closest distance to " OD1 ASN A 148 " =    1.534
peak=   -3.557 closest distance to " C   THR A 279 " =    1.110
peak=   -3.552 closest distance to " CD2 TYR A  30 " =    2.766
peak=   -3.550 closest distance to " OD2 ASP A 171 " =    2.298
peak=   -3.549 closest distance to " O   HOH Z 428 " =    0.992
peak=   -3.537 closest distance to " CG  PRO A 243 " =    1.615
peak=   -3.533 closest distance to " CG  ARG A 269 " =    2.354
peak=   -3.528 closest distance to " CA  VAL A  67 " =    2.946
peak=   -3.525 closest distance to " C   ASN A 187 " =    2.056
peak=   -3.520 closest distance to " OE1 GLN A  73 " =    0.808
peak=   -3.517 closest distance to " CA  GLU A 277 " =    1.229
peak=   -3.504 closest distance to " O   HOH Z 422 " =    1.687
peak=   -3.497 closest distance to " CD2 LEU A 300 " =    2.658
peak=   -3.489 closest distance to " CB  SER A 276 " =    0.754
peak=   -3.484 closest distance to " O   HOH Z 348 " =    2.280
peak=   -3.475 closest distance to " OE2 GLU A   2 " =    1.141
peak=   -3.473 closest distance to " NE2 GLN A  88 " =    0.860
peak=   -3.471 closest distance to " CD1 LEU A  25 " =    2.588
peak=   -3.464 closest distance to " O   HOH Z 339 " =    0.900
peak=   -3.459 closest distance to " O   HOH Z  91 " =    2.311
peak=   -3.459 closest distance to " O   HOH Z 198 " =    1.301
peak=   -3.454 closest distance to " O   HOH Z 222 " =    1.285
peak=   -3.451 closest distance to " C   SER A 271 " =    1.305
peak=   -3.450 closest distance to " O   HOH Z  60 " =    1.342
peak=   -3.441 closest distance to " O   HOH Z 407 " =    1.552
peak=   -3.438 closest distance to " CE  MET A  93 " =    1.197
peak=   -3.438 closest distance to " OG BSER A 210 " =    1.112
peak=   -3.427 closest distance to " O   HOH Z 308 " =    1.746
peak=   -3.426 closest distance to " C   HIS A 108 " =    1.072
peak=   -3.420 closest distance to " O   HOH Z 313 " =    1.184
peak=   -3.419 closest distance to " O   HOH Z 426 " =    2.107
peak=   -3.417 closest distance to " OD2 ASP A 171 " =    1.914
peak=   -3.405 closest distance to " O   HOH Z 148 " =    3.065
peak=   -3.401 closest distance to " O   HOH Z 426 " =    2.497
peak=   -3.400 closest distance to " O   HOH Z  15 " =    1.613
peak=   -3.399 closest distance to " O   HOH Z 418 " =    1.481
peak=   -3.399 closest distance to " O   HOH Z   7 " =    1.440
peak=   -3.392 closest distance to " ND2 ASN A  60 " =    1.215
peak=   -3.389 closest distance to " CD2 PHE A  59 " =    2.227
peak=   -3.388 closest distance to " O   HOH Z 128 " =    4.392
peak=   -3.378 closest distance to " O   HOH Z  17 " =    1.002
peak=   -3.375 closest distance to " ND2 ASN A  60 " =    5.489
peak=   -3.374 closest distance to " ND2 ASN A  60 " =    1.453
peak=   -3.361 closest distance to " O   HOH Z  10 " =    1.626
peak=   -3.359 closest distance to " O   HOH Z 109 " =    3.563
peak=   -3.357 closest distance to " CB  ALA A 161 " =    2.565
peak=   -3.355 closest distance to " O   HOH Z 396 " =    1.225
peak=   -3.341 closest distance to " CG  GLN A  58 " =    1.215
peak=   -3.325 closest distance to " O   TYR A  15 " =    1.347
peak=   -3.320 closest distance to " O   HOH Z 184 " =    1.114
peak=   -3.315 closest distance to " O   HOH Z 231 " =    0.945
peak=   -3.315 closest distance to " O   HOH Z  19 " =    2.187
peak=   -3.308 closest distance to " CA  TYR A  68 " =    2.670
peak=   -3.308 closest distance to " O   GLY A 118 " =    2.404
peak=   -3.308 closest distance to " CB  ASP A  50 " =    2.428
peak=   -3.308 closest distance to " CB  PRO A 280 " =    2.238
peak=   -3.306 closest distance to " N   GLY A 262 " =    2.058
peak=   -3.305 closest distance to " CD  GLN A  11 " =    0.840
peak=   -3.304 closest distance to " OG1 THR A  82 " =    2.041
peak=   -3.304 closest distance to " CE2 TRP A  85 " =    1.088
peak=   -3.303 closest distance to " NH2AARG A 275 " =    5.044
peak=   -3.300 closest distance to " O   HOH Z  47 " =    1.016
peak=   -3.293 closest distance to " CD  ARG A 156 " =    1.887
peak=   -3.293 closest distance to " O   HOH Z 436 " =    1.350
peak=   -3.292 closest distance to " O   HOH Z 368 " =    2.186
peak=   -3.291 closest distance to " N   GLY A  75 " =    1.315
peak=   -3.288 closest distance to " O   GLY A 196 " =    1.080
peak=   -3.287 closest distance to " O   ARG A 275 " =    1.838
peak=   -3.285 closest distance to " O   HOH Z 423 " =    2.458
peak=   -3.283 closest distance to " O   HOH Z  24 " =    0.746
peak=   -3.278 closest distance to " CB  ALA A 291 " =    2.170
peak=   -3.276 closest distance to " NH2 ARG A  36 " =    0.994
peak=   -3.268 closest distance to " N   VAL A  72 " =    1.218
peak=   -3.267 closest distance to " C   SER A 206 " =    1.397
peak=   -3.259 closest distance to " SG  CYS A 254 " =    3.221
peak=   -3.244 closest distance to " O   HOH Z  64 " =    1.621
peak=   -3.243 closest distance to " CA  VAL A 232 " =    2.292
peak=   -3.239 closest distance to " OD2 ASP A 270 " =    2.234
peak=   -3.238 closest distance to " OD1 ASP A 298 " =    1.916
peak=   -3.237 closest distance to " OD1 ASP A 191 " =    1.964
peak=   -3.233 closest distance to " O   HOH Z 182 " =    0.888
peak=   -3.233 closest distance to " C   ALA A 165 " =    2.049
peak=   -3.228 closest distance to " OG ASER A 134 " =    1.272
peak=   -3.226 closest distance to " O   HOH Z 298 " =    3.021
peak=   -3.223 closest distance to " O   HOH Z 408 " =    1.007
peak=   -3.223 closest distance to " CA  PRO A 198 " =    1.266
peak=   -3.223 closest distance to " OG  SER A  32 " =    1.275
peak=   -3.222 closest distance to " O   HOH Z  23 " =    1.194
peak=   -3.221 closest distance to " CG  PHE A 225 " =    1.241
peak=   -3.218 closest distance to " O   HOH Z 428 " =    1.449
peak=   -3.217 closest distance to " O   ALA A 256 " =    1.611
peak=   -3.217 closest distance to " O   VAL A 174 " =    1.961
peak=   -3.216 closest distance to " CG  GLU A  53 " =    1.305
peak=   -3.213 closest distance to " O   HOH Z 378 " =    1.128
peak=   -3.213 closest distance to " O   PHE A 218 " =    1.556
peak=   -3.207 closest distance to " NH2 ARG A  79 " =    1.724
peak=   -3.204 closest distance to " CD  LYS A 119 " =    0.863
peak=   -3.202 closest distance to " CA  GLY A 241 " =    2.295
peak=   -3.202 closest distance to " O   VAL A 197 " =    1.343
peak=   -3.200 closest distance to " O   HOH Z  29 " =    1.216
peak=   -3.196 closest distance to " CH2 TRP A 177 " =    2.071
peak=   -3.196 closest distance to " CD  PRO A 213 " =    2.226
peak=   -3.193 closest distance to " NE2 GLN A 103 " =    1.571
peak=   -3.184 closest distance to " O   HOH Z 193 " =    1.152
peak=   -3.180 closest distance to " CD2 PHE A  61 " =    1.902
peak=   -3.179 closest distance to " O   HOH Z 136 " =    1.491
peak=   -3.179 closest distance to " CD1 LEU A 228 " =    2.620
peak=   -3.178 closest distance to " ND2 ASN A  39 " =    1.415
peak=   -3.178 closest distance to " O   HOH Z 137 " =    1.377
peak=   -3.171 closest distance to " O   HOH Z 281 " =    4.550
peak=   -3.171 closest distance to " O   HOH Z 234 " =    4.311
peak=   -3.170 closest distance to " CG2 VAL A 296 " =    1.876
peak=   -3.167 closest distance to " O   THR A  52 " =    2.107
peak=   -3.166 closest distance to " CD2 LEU A 237 " =    2.544
peak=   -3.157 closest distance to " CD  GLN A 223 " =    1.635
peak=   -3.153 closest distance to " OD2 ASP A 171 " =    2.859
peak=   -3.145 closest distance to " CA  SER A 276 " =    1.407
peak=   -3.144 closest distance to " CA  GLY A  23 " =    2.245
peak=   -3.140 closest distance to " CB  GLN A  55 " =    1.566
peak=   -3.132 closest distance to " OE1 GLN A  88 " =    0.982
peak=   -3.129 closest distance to " CD  PRO A 198 " =    1.107
peak=   -3.126 closest distance to " N   GLY A  17 " =    1.703
peak=   -3.126 closest distance to " CA  ASP A 298 " =    1.042
peak=   -3.119 closest distance to " CB  SER A  26 " =    1.126
peak=   -3.109 closest distance to " O   HOH Z  38 " =    1.188
peak=   -3.107 closest distance to " CD2 TRP A 274 " =    2.329
peak=   -3.105 closest distance to " O   HOH Z 141 " =    0.835
peak=   -3.102 closest distance to " O   ALA A 161 " =    2.651
peak=   -3.101 closest distance to " O   HOH Z 109 " =    1.209
peak=   -3.099 closest distance to " NE2 GLN A  58 " =    0.956
peak=   -3.091 closest distance to " O   HOH Z 119 " =    2.994
peak=   -3.084 closest distance to " O   HOH Z   5 " =    1.113
peak=   -3.075 closest distance to " O   HOH Z 130 " =    0.824
peak=   -3.052 closest distance to " SG  CYS A 168 " =    0.942
peak=   -3.051 closest distance to " O   VAL A 125 " =    1.954
peak=   -3.032 closest distance to " O   HOH Z 166 " =    2.171
peak=   -3.028 closest distance to " O   HOH Z 351 " =    1.215
peak=   -3.011 closest distance to " CD  ARG A  14 " =    3.400

================= 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    :  0.4706 0.4573   6.284059e+00   6.264952e+00
   1_bss:  0.4619 0.4480   6.277968e+00   6.252993e+00
   1_xyz:  0.3656 0.4065   6.130216e+00   6.189089e+00
   1_adp:  0.3351 0.4149   6.090443e+00   6.196514e+00
   1_occ:  0.3349 0.4157   6.090191e+00   6.197193e+00
   2_bss:  0.3342 0.4113   6.090259e+00   6.195402e+00
   2_xyz:  0.2875 0.3551   5.967042e+00   6.107817e+00
   2_adp:  0.2743 0.3559   5.951622e+00   6.107580e+00
   2_occ:  0.2742 0.3558   5.951513e+00   6.107510e+00
   3_bss:  0.2744 0.3557   5.952250e+00   6.108067e+00
   3_xyz:  0.2345 0.3094   5.804428e+00   5.989722e+00
   3_adp:  0.2195 0.2961   5.762331e+00   5.962641e+00
   3_occ:  0.2194 0.2959   5.761914e+00   5.962184e+00
   4_bss:  0.2197 0.2959   5.762444e+00   5.962510e+00
   4_xyz:  0.1817 0.2386   5.566789e+00   5.783343e+00
   4_adp:  0.1629 0.2116   5.464317e+00   5.671492e+00
   4_occ:  0.1627 0.2115   5.463765e+00   5.670906e+00
   5_bss:  0.1627 0.2116   5.464454e+00   5.670758e+00
   5_xyz:  0.1377 0.1865   5.324979e+00   5.551487e+00
   5_adp:  0.1342 0.1765   5.292508e+00   5.502302e+00
   5_occ:  0.1340 0.1765   5.292055e+00   5.502429e+00
   5_bss:  0.1344 0.1764   5.294569e+00   5.502066e+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:  0.286  19.454  -2.263   4.051   0.532   0.000   0.000   0.000
   1_xyz:  0.286  19.454  -2.263   4.051   0.532   0.000   0.000   0.000
   1_adp:  0.286  19.454  -2.263   4.051   0.532   0.000   0.000   0.000
   1_occ:  0.286  19.454  -2.263   4.051   0.532   0.000   0.000   0.000
   2_bss:  0.318  52.805  -1.331   2.167  -0.267   0.000  -0.000  -0.000
   2_xyz:  0.318  52.805  -1.331   2.167  -0.267   0.000  -0.000  -0.000
   2_adp:  0.318  52.805  -1.331   2.167  -0.267   0.000  -0.000  -0.000
   2_occ:  0.318  52.805  -1.331   2.167  -0.267   0.000  -0.000  -0.000
   3_bss:  0.318  59.961  -0.665   2.134  -0.069   0.000  -0.000  -0.000
   3_xyz:  0.318  59.961  -0.665   2.134  -0.069   0.000  -0.000  -0.000
   3_adp:  0.318  59.961  -0.665   2.134  -0.069   0.000  -0.000  -0.000
   3_occ:  0.318  59.961  -0.665   2.134  -0.069   0.000  -0.000  -0.000
   4_bss:  0.324  73.862  -0.456   1.425  -0.187   0.000  -0.000  -0.000
   4_xyz:  0.324  73.862  -0.456   1.425  -0.187   0.000  -0.000  -0.000
   4_adp:  0.324  73.862  -0.456   1.425  -0.187   0.000  -0.000  -0.000
   4_occ:  0.324  73.862  -0.456   1.425  -0.187   0.000  -0.000  -0.000
   5_bss:  0.328  69.496  -0.942   0.422  -0.475   0.000  -0.000  -0.000
   5_xyz:  0.328  69.496  -0.942   0.422  -0.475   0.000  -0.000  -0.000
   5_adp:  0.328  69.496  -0.942   0.422  -0.475   0.000  -0.000  -0.000
   5_occ:  0.328  69.496  -0.942   0.422  -0.475   0.000  -0.000  -0.000
   5_bss:  0.323  61.861  -1.413  -0.320  -0.867  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.874 0.4603  0.6231    67533.633
   1_bss:  53.815 0.4722  0.6551    64024.369
   1_xyz:  46.546 0.5628  0.7687    49479.572
   1_adp:  47.569 0.5494  0.7549    50570.668
   1_occ:  47.625 0.5487  0.7527    50689.723
   2_bss:  47.284 0.5529  0.7474    50113.812
   2_xyz:  39.514 0.6473  0.8544    36369.188
   2_adp:  39.609 0.6461  0.8372    36714.236
   2_occ:  39.633 0.6459  0.8363    36725.388
   3_bss:  39.610 0.6462  0.8446    36724.991
   3_xyz:  32.943 0.7235  0.9260    25984.696
   3_adp:  31.217 0.7436  0.9184    24108.660
   3_occ:  31.192 0.7438  0.9185    24068.393
   4_bss:  31.140 0.7444  0.9130    24024.694
   4_xyz:  24.303 0.8170  0.9715    14925.851
   4_adp:  20.739 0.8540  0.9832    11776.210
   4_occ:  20.726 0.8541  0.9833    11772.959
   5_bss:  20.708 0.8543  0.9640    11752.460
   5_xyz:  17.826 0.8815  0.9792     9001.871
   5_adp:  16.660 0.8927  0.9804     8312.225
   5_occ:  16.661 0.8927  0.9806     8327.972
   5_bss:  16.667 0.8927  0.9626     8341.907
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.9233e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.9233e-01
   1_xyz:   1.724  0.013  0.102 16.263  0.006  4.108   1.5669e-01
   1_adp:   1.724  0.013  0.102 16.263  0.006  4.108   1.5669e-01
   1_occ:   1.724  0.013  0.102 16.263  0.006  4.108   1.5669e-01
   2_bss:   1.724  0.013  0.102 16.263  0.006  4.108   1.5669e-01
   2_xyz:   1.247  0.008  0.080 14.627  0.006  4.109   8.1029e-02
   2_adp:   1.247  0.008  0.080 14.627  0.006  4.109   8.1029e-02
   2_occ:   1.247  0.008  0.080 14.627  0.006  4.109   8.1029e-02
   3_bss:   1.247  0.008  0.080 14.627  0.006  4.109   8.1029e-02
   3_xyz:   1.144  0.008  0.069 14.661  0.004  4.117   7.1934e-02
   3_adp:   1.144  0.008  0.069 14.661  0.004  4.117   7.1934e-02
   3_occ:   1.144  0.008  0.069 14.661  0.004  4.117   7.1934e-02
   4_bss:   1.144  0.008  0.069 14.661  0.004  4.117   7.1934e-02
   4_xyz:   1.154  0.008  0.079 14.672  0.004  4.112   7.3311e-02
   4_adp:   1.154  0.008  0.079 14.672  0.004  4.112   7.3311e-02
   4_occ:   1.154  0.008  0.079 14.672  0.004  4.112   7.3311e-02
   5_bss:   1.154  0.008  0.079 14.672  0.004  4.112   7.3311e-02
   5_xyz:   1.113  0.009  0.078 14.714  0.004  4.123   7.3115e-02
   5_adp:   1.113  0.009  0.078 14.714  0.004  4.123   7.3115e-02
   5_occ:   1.113  0.009  0.078 14.714  0.004  4.123   7.3115e-02
   5_bss:   1.113  0.009  0.078 14.714  0.004  4.123   7.3115e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.346   2.4376e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.346   2.4376e-01
   1_xyz:  11.777  0.093  0.388 87.383  0.019  1.821   1.3486e-01
   1_adp:  11.777  0.093  0.388 87.383  0.019  1.821   1.3486e-01
   1_occ:  11.777  0.093  0.388 87.383  0.019  1.821   1.3486e-01
   2_bss:  11.777  0.093  0.388 87.383  0.019  1.821   1.3486e-01
   2_xyz:   7.314  0.049  0.218 79.301  0.059  2.253   7.6218e-02
   2_adp:   7.314  0.049  0.218 79.301  0.059  2.253   7.6218e-02
   2_occ:   7.314  0.049  0.218 79.301  0.059  2.253   7.6218e-02
   3_bss:   7.314  0.049  0.218 79.301  0.059  2.253   7.6218e-02
   3_xyz:   7.335  0.045  0.299 84.842  0.027  2.249   6.5495e-02
   3_adp:   7.335  0.045  0.299 84.842  0.027  2.249   6.5495e-02
   3_occ:   7.335  0.045  0.299 84.842  0.027  2.249   6.5495e-02
   4_bss:   7.335  0.045  0.299 84.842  0.027  2.249   6.5495e-02
   4_xyz:   7.966  0.052  0.220 87.363  0.046  2.280   4.5060e-02
   4_adp:   7.966  0.052  0.220 87.363  0.046  2.280   4.5060e-02
   4_occ:   7.966  0.052  0.220 87.363  0.046  2.280   4.5060e-02
   5_bss:   7.966  0.052  0.220 87.363  0.046  2.280   4.5060e-02
   5_xyz:   7.471  0.054  0.243 81.161  0.039  2.310   1.1190e-01
   5_adp:   7.471  0.054  0.243 81.161  0.039  2.310   1.1190e-01
   5_occ:   7.471  0.054  0.243 81.161  0.039  2.310   1.1190e-01
   5_bss:   7.471  0.054  0.243 81.161  0.039  2.310   1.1190e-01
------------------------------------------------------------------------
           |-----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:  89.11   0.00  18.80  83.07   0.00  15.55  89.11   1.60  36.47
   1_occ:  89.11   0.00  18.80  83.07   0.00  15.55  89.11   1.60  36.47
   2_bss:  89.11   0.00  18.80  83.07   0.00  15.55  89.11   1.60  36.47
   2_xyz:  89.11   0.00  18.80  83.07   0.00  15.55  89.11   1.60  36.47
   2_adp:  93.55   0.00  19.38  90.75   0.00  15.77  93.55   1.04  39.02
   2_occ:  93.55   0.00  19.38  90.75   0.00  15.77  93.55   1.04  39.02
   3_bss:  93.55   0.00  19.38  90.75   0.00  15.77  93.55   1.04  39.02
   3_xyz:  93.55   0.00  19.38  90.75   0.00  15.77  93.55   1.04  39.02
   3_adp: 122.47   0.00  19.95 122.47   0.00  15.08 117.70   1.83  46.50
   3_occ: 122.47   0.00  19.95 122.47   0.00  15.08 117.70   1.83  46.50
   4_bss: 122.47   0.00  19.95 122.47   0.00  15.08 117.70   1.83  46.50
   4_xyz: 122.47   0.00  19.95 122.47   0.00  15.08 117.70   1.83  46.50
   4_adp: 124.17   0.00  18.16 124.17   0.00  12.98 115.47   4.96  46.35
   4_occ: 124.17   0.00  18.16 124.17   0.00  12.98 115.47   4.96  46.35
   5_bss: 124.17   0.00  18.16 124.17   0.00  12.98 115.47   4.96  46.35
   5_xyz: 124.17   0.00  18.16 124.17   0.00  12.98 115.47   4.96  46.35
   5_adp: 110.05   0.00  16.47 109.17   0.00  12.06 110.05   4.85  40.45
   5_occ: 110.05   0.00  16.47 109.17   0.00  12.06 110.05   4.85  40.45
   5_bss: 110.06   0.00  16.47 109.17   0.00  12.07 110.06   4.85  40.45
------------------------------------------------------------------------
 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:    2.569    0.027    0.407
   1_adp:    2.569    0.027    0.407
   1_occ:    2.569    0.027    0.407
   2_bss:    2.569    0.027    0.407
   2_xyz:    2.269    0.030    0.521
   2_adp:    2.269    0.030    0.521
   2_occ:    2.269    0.030    0.521
   3_bss:    2.269    0.030    0.521
   3_xyz:    2.121    0.051    0.668
   3_adp:    2.121    0.051    0.668
   3_occ:    2.121    0.051    0.668
   4_bss:    2.121    0.051    0.668
   4_xyz:    1.942    0.103    0.800
   4_adp:    1.942    0.103    0.800
   4_occ:    1.942    0.103    0.800
   5_bss:    1.942    0.103    0.800
   5_xyz:    1.840    0.054    0.859
   5_adp:    1.840    0.054    0.859
   5_occ:    1.840    0.054    0.859
   5_bss:    1.840    0.054    0.859
------------------------------------------------------------------------

CPU time actual refinement: 387.12


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_958/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_958/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_958/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_958/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_958/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 386.97 
  Macro-tasks:
    bulk solvent and scale       = 47.36  
    individual site refinement   = 160.25 
    weights calculation          = 30.90  
    collect and process          = 6.55   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 245.17 
  Micro-tasks:
    mask                            = 3.27   
    f_calc                          = 128.27 
    alpha_beta                      = 8.89   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 136.13 
    fmodel                         = 7.44   
    r_factors                      = 0.20   
    phase_errors                   = 10.11  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 295.74 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.442 micro seconds
Total CPU time: 6.68 minutes
from_scatterers_fft:    662 calls, 127.83 s
gradients_fft:          607 calls, 122.76 s

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

# Date 2008-01-16 Time 06:05:33 PST -0800 (1200492333.86 s)
Start R-work = 0.4706, R-free = 0.4573 (no bulk solvent and anisotropic scale)
Final R-work = 0.1512, R-free = 0.1938 (no bulk solvent and anisotropic scale)

Start R-work = 0.4619, R-free = 0.4480
Final R-work = 0.1344, R-free = 0.1764