# Date 2008-01-16 Time 05:05:05 PST -0800 (1200488705.02 s)
#phil __OFF__

Command line arguments: "../584.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 6866
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 584

-------------------------------------------------------------------------------
  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: (69.8988, 47.8686, 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: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.8686, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9307 1.96149
Completeness in resolution range: 0.935974
Completeness with d_max=infinity: 0.933165

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9307
                             d_min =   1.9615

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: (69.8988, 47.8686, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9307 1.96149
Completeness in resolution range: 0.935974
Completeness with d_max=infinity: 0.933165

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9311 -  4.1975 [2201/2230]  1979   222  10.1%
  bin  2:  4.1975 -  3.3440 [2102/2125]  1893   209   9.9%
  bin  3:  3.3440 -  2.9249 [2072/2097]  1865   207  10.0%
  bin  4:  2.9249 -  2.6591 [2068/2085]  1868   200   9.7%
  bin  5:  2.6591 -  2.4695 [2045/2088]  1833   212  10.4%
  bin  6:  2.4695 -  2.3244 [2049/2077]  1852   197   9.6%
  bin  7:  2.3244 -  2.2084 [2019/2055]  1815   204  10.1%
  bin  8:  2.2084 -  2.1125 [2014/2056]  1810   204  10.1%
  bin  9:  2.1125 -  2.0314 [2009/2066]  1809   200  10.0%
  bin 10:  2.0314 -  1.9615 [1010/2050]   906   104  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_584/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:
        1.59 -     2.26: 25
        2.26 -     2.92: 1491
        2.92 -     3.58: 4472
        3.58 -     4.24: 9233
        4.24 -     4.90: 13222
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.594 3.040 -x+1/2,-y+1,z+1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.672 3.040 -x+1/2,-y+1,z-1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.706 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.721 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.743 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28438 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_584/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_584/model_refine_001.geo

CPU time processing inputs: 9.71


============================ 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 = 69.89875 47.8686 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 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4461   r_free= 0.4388   ksol= 0.00   Bsol= 0.00   scale= 0.908    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.258442                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9311 -  4.6819 0.99   1426  160 0.3550 0.3705      6.5233      6.5398|
|  2:  4.6819 -  3.7353 0.99   1374  149 0.3807 0.3742      6.7793      6.7419|
|  3:  3.7353 -  3.2688 0.99   1340  152 0.4093 0.3923      6.6277      6.6705|
|  4:  3.2688 -  2.9725 0.99   1336  146 0.4221 0.3952      6.4697      6.4311|
|  5:  2.9725 -  2.7609 0.99   1337  147 0.4608 0.4235      6.3375      6.2814|
|  6:  2.7609 -  2.5990 0.99   1318  148 0.4780 0.4555      6.2576      6.1498|
|  7:  2.5990 -  2.4695 0.98   1307  148 0.4818 0.4252      6.2286      6.1553|
|  8:  2.4695 -  2.3624 0.98   1309  143 0.4932 0.5447       6.148      6.2064|
|  9:  2.3624 -  2.2718 0.99   1322  147 0.5186 0.5040      6.1302      6.1179|
| 10:  2.2718 -  2.1936 0.98   1307  140 0.4936 0.5181      6.0844      6.1372|
| 11:  2.1936 -  2.1252 0.97   1286  147 0.5131 0.5100      6.0288       5.999|
| 12:  2.1252 -  2.0646 0.98   1281  145 0.4872 0.5396      5.9373       6.005|
| 13:  2.0646 -  2.0104 0.92   1213  138 0.5063 0.4835      5.8563      5.8348|
| 14:  2.0104 -  1.9615 0.35    474   49 0.5432 0.4482      5.8368      5.6814|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9311 -  4.6819  1426   160  0.70  34.65   0.84     0.72      71786.85|
|  2:  4.6819 -  3.7353  1374   149  0.73  32.83   0.92     0.82      91628.52|
|  3:  3.7353 -  3.2688  1340   152  0.65  39.39   0.93     0.83      94045.85|
|  4:  3.2688 -  2.9725  1336   146  0.59  44.58   0.94     0.80      81224.21|
|  5:  2.9725 -  2.7609  1337   147  0.54  48.88   0.89     0.75      65870.80|
|  6:  2.7609 -  2.5990  1318   148  0.51  51.46   0.92     0.70      56599.31|
|  7:  2.5990 -  2.4695  1307   148  0.49  52.87   0.92     0.66      53242.11|
|  8:  2.4695 -  2.3624  1309   143  0.41  59.32   0.90     0.59      54723.18|
|  9:  2.3624 -  2.2718  1322   147  0.36  62.85   0.92     0.54      52956.58|
| 10:  2.2718 -  2.1936  1307   140  0.33  65.51   0.96     0.48      51991.22|
| 11:  2.1936 -  2.1252  1286   147  0.30  67.45   0.95     0.46      47732.18|
| 12:  2.1252 -  2.0646  1281   145  0.30  67.71   0.96     0.47      44795.16|
| 13:  2.0646 -  2.0104  1213   138  0.32  66.29   0.96     0.50      36337.02|
| 14:  2.0104 -  1.9615   474    49  0.39  61.06   0.92     0.57      27909.39|
|alpha:            min =        0.46 max =            0.83 mean =         0.64|
|beta:             min =    27909.39 max =        94045.85 mean =     61300.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           89.99 mean =        53.22|
|phase err.(test): min =        0.00 max =           89.98 mean =        53.30|
|-----------------------------------------------------------------------------|

============================== 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 = 12.935942             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.504   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.327777              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.952   (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 |  1.594 -  1.924:       10 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.924 -  2.255:       15 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.255 -  2.586:       48 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.586 -  2.916:     1443 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.916 -  3.247:     1908 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.247 -  3.578:     2564 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.578 -  3.908:     4734 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.908 -  4.239:     4499 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.239 -  4.569:     6036 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.569 -  4.900:     7186 |
|-----------------------------------------------------------------------------|
|-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 |        0.183 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.594 |       0.488 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4461   r_free= 0.4388   ksol= 0.00   Bsol= 0.00   scale= 0.908    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.258442                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4349   r_free= 0.4270   ksol= 0.30   Bsol= 21.53   scale= 0.944   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.41,4.02,1.26,0.00,0.00,0.00); trace/3= 0.62                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.247763                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.172967             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.210   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.077209              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.759   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4349      final r-factor (work) = 0.3078          |
| start r-factor (free) = 0.4270      final r-factor (free) = 0.3384          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.0849 = 11.17 * 0.50 * 6.2476 + 1.00 * 0.1829                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.1412 = 11.17 * 0.50 * 6.0861 + 1.00 * 0.1413                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3078      final r-factor (work) = 0.2792          |
| start r-factor (free) = 0.3384      final r-factor (free) = 0.3504          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5624 = 1.08 * 1.00 * 6.0861 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4037 = 1.08 * 1.00 * 5.9231 + 1.00 * 0.0232                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.12  18.46    None  None   None       |
|    all(noH): 2823   0      0.00    101.12  18.46    None  None   None       |
|    Sol.    : 438    0      1.09    101.12  39.56    None  None   None       |
|    Mac.    : 2385   0      0.00    99.03   14.58    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.112: 1001   |   5:    50.559 -  60.671:   83        |
|      1:    10.112 -  20.224:  936   |   6:    60.671 -  70.783:   35        |
|      2:    20.224 -  30.335:  383   |   7:    70.783 -  80.895:   26        |
|      3:    30.335 -  40.447:  231   |   8:    80.895 -  91.006:    8        |
|      4:    40.447 -  50.559:  115   |   9:    91.006 - 101.118:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2792 r_free = 0.3504             target_work(ml) = 5.933         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2787 r_free = 0.3505             target_work(ml) = 5.933         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2787   r_free= 0.3505   ksol= 0.30   Bsol= 21.53   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.41,4.02,1.26,0.00,0.00,0.00); trace/3= 0.62                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.932568                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2757   r_free= 0.3463   ksol= 0.32   Bsol= 47.01   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,1.43,-0.31,0.00,-0.00,-0.00); trace/3= -0.40                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.927937                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.912837              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.272   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.579911              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.229   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2757      final r-factor (work) = 0.2174          |
| start r-factor (free) = 0.3463      final r-factor (free) = 0.2709          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7259 = 3.91 * 0.50 * 5.9213 + 1.00 * 0.1413                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.4856 = 3.91 * 0.50 * 5.8373 + 1.00 * 0.0653                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2174      final r-factor (work) = 0.2028          |
| start r-factor (free) = 0.2709      final r-factor (free) = 0.2575          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4050 = 0.58 * 1.00 * 5.8373 + 1.00 * 0.0199                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3087 = 0.58 * 1.00 * 5.6841 + 1.00 * 0.0125                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.81   17.99    None  None   None       |
|    all(noH): 2823   0      0.00    98.81   17.99    None  None   None       |
|    Sol.    : 438    0      5.79    98.81   40.75    None  None   None       |
|    Mac.    : 2385   0      0.00    97.88   13.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.881: 1059   |   5:    49.404 -  59.285:   83        |
|      1:     9.881 -  19.762:  975   |   6:    59.285 -  69.165:   40        |
|      2:    19.762 -  29.642:  301   |   7:    69.165 -  79.046:   28        |
|      3:    29.642 -  39.523:  172   |   8:    79.046 -  88.927:   12        |
|      4:    39.523 -  49.404:  149   |   9:    88.927 -  98.808:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2028 r_free = 0.2575             target_work(ml) = 5.664         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2027 r_free = 0.2576             target_work(ml) = 5.664         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2027   r_free= 0.2576   ksol= 0.32   Bsol= 47.01   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,1.43,-0.31,0.00,-0.00,-0.00); trace/3= -0.40                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.663643                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2026   r_free= 0.2574   ksol= 0.32   Bsol= 50.66   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,0.46,-0.82,0.00,-0.00,-0.00); trace/3= -0.83                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.663012                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.629637              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.448  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 20.113548             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.412  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2026      final r-factor (work) = 0.1551          |
| start r-factor (free) = 0.2574      final r-factor (free) = 0.2027          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.3811 = 3.63 * 0.50 * 5.6842 + 1.00 * 0.0653                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1412 = 3.63 * 0.50 * 5.5534 + 1.00 * 0.0627                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1551      final r-factor (work) = 0.1410          |
| start r-factor (free) = 0.2027      final r-factor (free) = 0.1920          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 111.7113 = 20.11 * 1.00 * 5.5534 + 1.00 * 0.0126                            |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 108.1805 = 20.11 * 1.00 * 5.3778 + 1.00 * 0.0145                            |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.50  18.32    None  None   None       |
|    all(noH): 2823   0      0.00    108.50  18.32    None  None   None       |
|    Sol.    : 438    0      6.04    107.40  45.90    None  None   None       |
|    Mac.    : 2385   0      0.00    108.50  13.26    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.850: 1280   |   5:    54.250 -  65.100:   82        |
|      1:    10.850 -  21.700:  908   |   6:    65.100 -  75.951:   52        |
|      2:    21.700 -  32.550:  209   |   7:    75.951 -  86.801:   32        |
|      3:    32.550 -  43.400:  121   |   8:    86.801 -  97.651:   17        |
|      4:    43.400 -  54.250:  115   |   9:    97.651 - 108.501:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1410 r_free = 0.1920             target_work(ml) = 5.348         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1409 r_free = 0.1920             target_work(ml) = 5.348         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1409   r_free= 0.1920   ksol= 0.32   Bsol= 50.66   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,0.46,-0.82,0.00,-0.00,-0.00); trace/3= -0.83                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.347545                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1411   r_free= 0.1917   ksol= 0.32   Bsol= 60.69   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-0.46,-1.13,-0.00,-0.00,-0.00); trace/3= -1.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.348897                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.643380              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.356  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.822768              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.432  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1411      final r-factor (work) = 0.1234          |
| start r-factor (free) = 0.1917      final r-factor (free) = 0.1751          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8646 = 3.64 * 0.50 * 5.3806 + 1.00 * 0.0627                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7099 = 3.64 * 0.50 * 5.2931 + 1.00 * 0.0675                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1234      final r-factor (work) = 0.1189          |
| start r-factor (free) = 0.1751      final r-factor (free) = 0.1698          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.6625 = 1.82 * 1.00 * 5.2931 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.5394 = 1.82 * 1.00 * 5.2264 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    116.51  17.80    None  None   None       |
|    all(noH): 2823   0      0.00    116.51  17.80    None  None   None       |
|    Sol.    : 438    0      5.28    107.12  45.05    None  None   None       |
|    Mac.    : 2385   0      0.00    116.51  12.80    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 -  11.651: 1475   |   5:    58.255 -  69.906:   74        |
|      1:    11.651 -  23.302:  807   |   6:    69.906 -  81.557:   39        |
|      2:    23.302 -  34.953:  168   |   7:    81.557 -  93.208:   24        |
|      3:    34.953 -  46.604:  116   |   8:    93.208 - 104.859:    6        |
|      4:    46.604 -  58.255:  109   |   9:   104.859 - 116.510:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1189 r_free = 0.1698             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1188 r_free = 0.1698             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1188   r_free= 0.1698   ksol= 0.32   Bsol= 60.69   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-0.46,-1.13,-0.00,-0.00,-0.00); trace/3= -1.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.206341                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1188   r_free= 0.1697   ksol= 0.33   Bsol= 58.78   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.97,-0.67,-1.06,-0.00,-0.00,-0.00); trace/3= -1.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.206288                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.384816              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.786  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.201618              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.762  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1188      final r-factor (work) = 0.1154          |
| start r-factor (free) = 0.1697      final r-factor (free) = 0.1657          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2994 = 2.38 * 0.50 * 5.2263 + 1.00 * 0.0675                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2565 = 2.38 * 0.50 * 5.1977 + 1.00 * 0.0588                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1154      final r-factor (work) = 0.1157          |
| start r-factor (free) = 0.1657      final r-factor (free) = 0.1614          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0608 = 0.20 * 1.00 * 5.1977 + 1.00 * 0.0129                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0548 = 0.20 * 1.00 * 5.1874 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.26    108.03  16.60    None  None   None       |
|    all(noH): 2823   0      1.26    108.03  16.60    None  None   None       |
|    Sol.    : 438    0      4.68    96.17   40.06    None  None   None       |
|    Mac.    : 2385   0      1.26    108.03  12.29    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.263 -  11.939: 1592   |   5:    54.644 -  65.320:   53        |
|      1:    11.939 -  22.615:  710   |   6:    65.320 -  75.997:   29        |
|      2:    22.615 -  33.291:  168   |   7:    75.997 -  86.673:   14        |
|      3:    33.291 -  43.968:  141   |   8:    86.673 -  97.349:    9        |
|      4:    43.968 -  54.644:  103   |   9:    97.349 - 108.025:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1157 r_free = 0.1614             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1155 r_free = 0.1615             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1615   ksol= 0.33   Bsol= 58.78   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.97,-0.67,-1.06,-0.00,-0.00,-0.00); trace/3= -1.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.173925                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9311 -  4.6819 0.99   1426  160 0.0990 0.1280      5.3699      5.5215|
|  2:  4.6819 -  3.7353 0.99   1374  149 0.0849 0.1098      5.4253      5.6391|
|  3:  3.7353 -  3.2688 0.99   1340  152 0.1061 0.1551      5.4748      5.8477|
|  4:  3.2688 -  2.9725 0.99   1336  146 0.1312 0.1636       5.495      5.6578|
|  5:  2.9725 -  2.7609 0.99   1337  147 0.1373 0.1835      5.3595       5.532|
|  6:  2.7609 -  2.5990 0.99   1318  148 0.1319 0.2052      5.2618      5.4955|
|  7:  2.5990 -  2.4695 0.98   1307  148 0.1290 0.1717      5.1899      5.4092|
|  8:  2.4695 -  2.3624 0.98   1309  143 0.1236 0.1689       5.111      5.3004|
|  9:  2.3624 -  2.2718 0.99   1322  147 0.1218 0.1913      5.0552      5.3338|
| 10:  2.2718 -  2.1936 0.98   1307  140 0.1200 0.1759           5      5.2395|
| 11:  2.1936 -  2.1252 0.97   1286  147 0.1143 0.1785      4.9348      5.2184|
| 12:  2.1252 -  2.0646 0.98   1281  145 0.1194 0.1627      4.8785      5.1029|
| 13:  2.0646 -  2.0104 0.92   1213  138 0.1159 0.1905       4.793      5.0798|
| 14:  2.0104 -  1.9615 0.35    474   49 0.1141 0.1697      4.6947      4.9107|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9311 -  4.6819  1426   160  0.94   8.91   0.97     0.96       6932.86|
|  2:  4.6819 -  3.7353  1374   149  0.95   7.89   1.02     1.00       8786.42|
|  3:  3.7353 -  3.2688  1340   152  0.93  11.60   1.02     1.02      10467.36|
|  4:  3.2688 -  2.9725  1336   146  0.91  14.64   1.01     0.98      11009.67|
|  5:  2.9725 -  2.7609  1337   147  0.89  17.04   1.00     0.97       8955.85|
|  6:  2.7609 -  2.5990  1318   148  0.89  16.80   0.99     0.96       7663.69|
|  7:  2.5990 -  2.4695  1307   148  0.90  16.04   0.99     0.96       6510.33|
|  8:  2.4695 -  2.3624  1309   143  0.90  16.38   1.00     0.97       5897.46|
|  9:  2.3624 -  2.2718  1322   147  0.90  16.28   1.00     0.97       5206.55|
| 10:  2.2718 -  2.1936  1307   140  0.90  16.07   1.00     0.96       4748.89|
| 11:  2.1936 -  2.1252  1286   147  0.90  16.35   1.00     0.96       4322.59|
| 12:  2.1252 -  2.0646  1281   145  0.91  15.46   1.00     0.98       3816.29|
| 13:  2.0646 -  2.0104  1213   138  0.90  16.13   1.00     1.00       3325.86|
| 14:  2.0104 -  1.9615   474    49  0.90  16.21   0.98     0.95       2710.22|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2710.22 max =        11009.67 mean =      6684.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.55|
|phase err.(test): min =        0.00 max =           89.87 mean =        14.03|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1611   ksol= 0.32   Bsol= 51.52   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-0.75,-0.99,-0.00,-0.00,-0.00); trace/3= -1.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.174726                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1611   ksol= 0.32   Bsol= 51.52   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-0.75,-0.99,-0.00,-0.00,-0.00); trace/3= -1.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.174726                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9311 -  4.6819 0.99   1426  160 0.0996 0.1258      5.3717      5.5122|
|  2:  4.6819 -  3.7353 0.99   1374  149 0.0853 0.1090      5.4272      5.6472|
|  3:  3.7353 -  3.2688 0.99   1340  152 0.1055 0.1541      5.4747      5.8375|
|  4:  3.2688 -  2.9725 0.99   1336  146 0.1320 0.1629      5.4952      5.6534|
|  5:  2.9725 -  2.7609 0.99   1337  147 0.1376 0.1841        5.36      5.5327|
|  6:  2.7609 -  2.5990 0.99   1318  148 0.1320 0.2053      5.2621       5.496|
|  7:  2.5990 -  2.4695 0.98   1307  148 0.1291 0.1724      5.1908      5.4124|
|  8:  2.4695 -  2.3624 0.98   1309  143 0.1236 0.1692      5.1125      5.2998|
|  9:  2.3624 -  2.2718 0.99   1322  147 0.1216 0.1911      5.0551      5.3343|
| 10:  2.2718 -  2.1936 0.98   1307  140 0.1201 0.1761      5.0002      5.2403|
| 11:  2.1936 -  2.1252 0.97   1286  147 0.1144 0.1786      4.9354      5.2191|
| 12:  2.1252 -  2.0646 0.98   1281  145 0.1195 0.1635        4.88      5.1065|
| 13:  2.0646 -  2.0104 0.92   1213  138 0.1158 0.1904      4.7944      5.0802|
| 14:  2.0104 -  1.9615 0.35    474   49 0.1145 0.1690      4.6953      4.9078|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9311 -  4.6819  1426   160  0.94   8.82   0.97     0.95       6811.79|
|  2:  4.6819 -  3.7353  1374   149  0.95   7.97   1.02     1.00       8783.94|
|  3:  3.7353 -  3.2688  1340   152  0.93  11.59   1.02     1.02      10545.82|
|  4:  3.2688 -  2.9725  1336   146  0.91  14.58   1.01     0.98      10919.74|
|  5:  2.9725 -  2.7609  1337   147  0.89  17.00   1.00     0.97       8924.72|
|  6:  2.7609 -  2.5990  1318   148  0.89  16.81   0.99     0.96       7684.91|
|  7:  2.5990 -  2.4695  1307   148  0.90  16.06   0.99     0.96       6531.57|
|  8:  2.4695 -  2.3624  1309   143  0.90  16.39   1.00     0.97       5912.36|
|  9:  2.3624 -  2.2718  1322   147  0.90  16.30   1.00     0.97       5214.05|
| 10:  2.2718 -  2.1936  1307   140  0.90  16.07   0.99     0.96       4748.94|
| 11:  2.1936 -  2.1252  1286   147  0.90  16.37   1.00     0.96       4331.16|
| 12:  2.1252 -  2.0646  1281   145  0.91  15.50   1.00     0.98       3832.99|
| 13:  2.0646 -  2.0104  1213   138  0.90  16.16   1.00     0.99       3336.23|
| 14:  2.0104 -  1.9615   474    49  0.90  16.21   0.98     0.94       2707.30|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2707.30 max =        10919.74 mean =      6678.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.56|
|phase err.(test): min =        0.00 max =           89.46 mean =        14.03|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.22    107.98  16.56    None  None   None       |
|    all(noH): 2823   0      1.22    107.98  16.56    None  None   None       |
|    Sol.    : 438    0      4.63    96.13   40.01    None  None   None       |
|    Mac.    : 2385   0      1.22    107.98  12.25    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.218 -  11.895: 1592   |   5:    54.600 -  65.276:   53        |
|      1:    11.895 -  22.571:  710   |   6:    65.276 -  75.952:   29        |
|      2:    22.571 -  33.247:  168   |   7:    75.952 -  86.628:   14        |
|      3:    33.247 -  43.923:  141   |   8:    86.628 -  97.305:    9        |
|      4:    43.923 -  54.600:  103   |   9:    97.305 - 107.981:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 324         
Filter by distance & map next to the model:
   mapped sites are within: 0.422 - 4.515
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 320 from: 324
   mapped sites are within: 0.705 - 4.515

peak=    5.698 closest distance to " O   HOH Z 113 " =    2.286
peak=    5.532 closest distance to " CB  SER A  63 " =    1.140
peak=    5.470 closest distance to " O   HOH Z 124 " =    1.537
peak=    5.308 closest distance to " CG  PRO A  54 " =    1.282
peak=    5.104 closest distance to " CB  GLN A 223 " =    1.418
peak=    5.026 closest distance to " O   HOH Z 210 " =    1.198
peak=    4.858 closest distance to " CG  PRO A 213 " =    1.250
peak=    4.849 closest distance to " C   PRO A 198 " =    1.543
peak=    4.813 closest distance to " O   HOH Z 403 " =    1.865
peak=    4.790 closest distance to " CA  TYR A  30 " =    0.996
peak=    4.771 closest distance to " O   HOH Z  15 " =    2.130
peak=    4.744 closest distance to " CG  PRO A 198 " =    1.188
peak=    4.707 closest distance to " CG  PRO A  90 " =    1.197
peak=    4.691 closest distance to " O   HOH Z 134 " =    1.877
peak=    4.667 closest distance to " O   HOH Z  63 " =    1.938
peak=    4.635 closest distance to " O   HOH Z 189 " =    1.980
peak=    4.629 closest distance to " O   HOH Z 402 " =    1.548
peak=    4.629 closest distance to " O   HOH Z  80 " =    1.724
peak=    4.509 closest distance to " O   HOH Z 389 " =    1.979
peak=    4.502 closest distance to " O   HOH Z 209 " =    2.408
peak=    4.470 closest distance to " CG  PRO A 280 " =    0.705
peak=    4.443 closest distance to " O   HOH Z 234 " =    3.786
peak=    4.436 closest distance to " O   HOH Z  97 " =    1.883
peak=    4.431 closest distance to " O   HOH Z 132 " =    1.199
peak=    4.429 closest distance to " CB  ARG A 275 " =    0.862
peak=    4.404 closest distance to " CG1 ILE A  33 " =    1.288
peak=    4.396 closest distance to " CB  PRO A  54 " =    0.881
peak=    4.396 closest distance to " O   HOH Z 193 " =    1.790
peak=    4.361 closest distance to " CB  GLU A 277 " =    3.606
peak=    4.345 closest distance to " O   HOH Z 133 " =    1.541
peak=    4.344 closest distance to " CB  SER A 141 " =    1.040
peak=    4.322 closest distance to " O   HOH Z 368 " =    2.030
peak=    4.318 closest distance to " CB  SER A   3 " =    1.363
peak=    4.306 closest distance to " NH2 ARG A 156 " =    1.175
peak=    4.299 closest distance to " O   HOH Z 433 " =    1.587
peak=    4.284 closest distance to " O   HOH Z 426 " =    1.441
peak=    4.265 closest distance to " O   SER A  87 " =    2.157
peak=    4.253 closest distance to " O   HOH Z 130 " =    2.842
peak=    4.227 closest distance to " CB  GLN A 183 " =    1.276
peak=    4.219 closest distance to " O   HOH Z 232 " =    2.324
peak=    4.200 closest distance to " O   HOH Z  43 " =    1.630
peak=    4.200 closest distance to " O   HOH Z  39 " =    1.216
peak=    4.178 closest distance to " O   HOH Z  40 " =    1.772
peak=    4.167 closest distance to " CG  PRO A 243 " =    1.200
peak=    4.152 closest distance to " O   HOH Z 214 " =    1.007
peak=    4.143 closest distance to " NH2BARG A 145 " =    2.113
peak=    4.136 closest distance to " O   HOH Z 227 " =    1.789
peak=    4.125 closest distance to " O   HOH Z 298 " =    1.900
peak=    4.109 closest distance to " OE1 GLN A  11 " =    1.879
peak=    4.105 closest distance to " O   HOH Z 316 " =    2.946
peak=    4.104 closest distance to " NZ  LYS A 117 " =    3.085
peak=    4.100 closest distance to " O   HOH Z 154 " =    1.469
peak=    4.099 closest distance to " CB  ARG A  79 " =    1.398
peak=    4.096 closest distance to " O   HOH Z 142 " =    1.540
peak=    4.094 closest distance to " O   HOH Z  59 " =    2.442
peak=    4.091 closest distance to " CB  GLU A 152 " =    1.164
peak=    4.063 closest distance to " OD2 ASP A 286 " =    2.836
peak=    4.061 closest distance to " CB  GLU A 128 " =    1.152
peak=    4.055 closest distance to " O   HOH Z 406 " =    1.576
peak=    4.047 closest distance to " O   HOH Z 291 " =    1.537
peak=    4.044 closest distance to " O   HOH Z  61 " =    1.554
peak=    4.044 closest distance to " CB  ARG A 190 " =    1.705
peak=    4.026 closest distance to " O   HOH Z 247 " =    1.461
peak=    4.024 closest distance to " CB  TRP A 179 " =    1.236
peak=    4.003 closest distance to " O   HOH Z  43 " =    2.339
peak=    3.999 closest distance to " CB  TYR A 169 " =    0.887
peak=    3.994 closest distance to " O   HOH Z 126 " =    1.664
peak=    3.981 closest distance to " O   HOH Z 272 " =    1.908
peak=    3.963 closest distance to " O   HOH Z  20 " =    1.483
peak=    3.959 closest distance to " O   HOH Z 374 " =    2.596
peak=    3.958 closest distance to " O   HOH Z  11 " =    1.330
peak=    3.956 closest distance to " O   HOH Z 313 " =    1.908
peak=    3.950 closest distance to " O   HOH Z 412 " =    3.454
peak=    3.948 closest distance to " CB  VAL A 202 " =    1.497
peak=    3.943 closest distance to " N   ASN A  39 " =    1.282
peak=    3.934 closest distance to " ND2 ASN A 187 " =    1.652
peak=    3.930 closest distance to " O   HOH Z 132 " =    2.058
peak=    3.921 closest distance to " O   HOH Z 423 " =    1.881
peak=    3.919 closest distance to " O   HOH Z 345 " =    1.708
peak=    3.917 closest distance to " O   HOH Z 422 " =    0.789
peak=    3.907 closest distance to " O   HOH Z 173 " =    2.116
peak=    3.903 closest distance to " O   HOH Z 371 " =    3.256
peak=    3.900 closest distance to " O   HOH Z 132 " =    2.573
peak=    3.892 closest distance to " O   HOH Z 369 " =    2.200
peak=    3.883 closest distance to " CG  ARG A  66 " =    0.951
peak=    3.873 closest distance to " CA  ALA A  21 " =    1.343
peak=    3.861 closest distance to " O   HOH Z 196 " =    1.232
peak=    3.861 closest distance to " O   HOH Z 163 " =    1.546
peak=    3.844 closest distance to " CA  ASP A 191 " =    0.911
peak=    3.827 closest distance to " NZ  LYS A  76 " =    1.178
peak=    3.809 closest distance to " O   HOH Z 352 " =    1.833
peak=    3.797 closest distance to " OE1 GLU A   2 " =    2.174
peak=    3.796 closest distance to " OD1 ASN A  69 " =    2.493
peak=    3.790 closest distance to " CD  ARG A 269 " =    1.036
peak=    3.789 closest distance to " CA  ARG A  36 " =    1.118
peak=    3.781 closest distance to " O   HOH Z 279 " =    2.107
peak=    3.776 closest distance to " CB  LEU A 228 " =    1.154
peak=    3.774 closest distance to " O   HOH Z  67 " =    1.921
peak=    3.772 closest distance to " CD  LYS A 166 " =    1.376
peak=    3.768 closest distance to " CB  SER A  62 " =    0.754
peak=    3.766 closest distance to " O   HOH Z  44 " =    1.891
peak=    3.762 closest distance to " O   HOH Z 126 " =    1.874
peak=    3.758 closest distance to " CA  ASN A 176 " =    1.448
peak=    3.751 closest distance to " O   HOH Z  30 " =    1.343
peak=    3.749 closest distance to " O   HOH Z 421 " =    1.590
peak=    3.740 closest distance to " O   HOH Z 362 " =    3.535
peak=    3.739 closest distance to " O   HOH Z 128 " =    2.127
peak=    3.736 closest distance to " NH2AARG A 145 " =    2.217
peak=    3.726 closest distance to " O   HOH Z 236 " =    1.996
peak=    3.721 closest distance to " O   HOH Z 260 " =    1.340
peak=    3.711 closest distance to " O   HOH Z 394 " =    1.652
peak=    3.696 closest distance to " CB  ASN A 187 " =    1.177
peak=    3.694 closest distance to " O   HOH Z  78 " =    1.670
peak=    3.688 closest distance to " O   HOH Z 358 " =    2.014
peak=    3.677 closest distance to " CG2BVAL A  41 " =    0.870
peak=    3.667 closest distance to " CG AARG A 275 " =    0.840
peak=    3.667 closest distance to " CB  ASN A 285 " =    0.928
peak=    3.660 closest distance to " O   HOH Z 145 " =    2.151
peak=    3.659 closest distance to " O   HOH Z 147 " =    1.793
peak=    3.653 closest distance to " O   HOH Z 255 " =    1.755
peak=    3.648 closest distance to " CA  ARG A 195 " =    1.215
peak=    3.645 closest distance to " O   HOH Z 344 " =    2.969
peak=    3.637 closest distance to " O   HOH Z 427 " =    2.994
peak=    3.636 closest distance to " OG BSER A 164 " =    2.626
peak=    3.631 closest distance to " NZ  LYS A 117 " =    1.120
peak=    3.622 closest distance to " O   HOH Z 386 " =    2.215
peak=    3.619 closest distance to " O   HOH Z 334 " =    1.458
peak=    3.618 closest distance to " O   HOH Z 408 " =    1.602
peak=    3.594 closest distance to " OG  SER A  62 " =    3.011
peak=    3.594 closest distance to " CA  THR A 221 " =    0.956
peak=    3.593 closest distance to " O   HOH Z 128 " =    2.197
peak=    3.592 closest distance to " O   HOH Z  88 " =    3.388
peak=    3.584 closest distance to " CE  LYS A 119 " =    1.097
peak=    3.582 closest distance to " O   HOH Z 326 " =    1.523
peak=    3.580 closest distance to " CA  ASP A 162 " =    1.203
peak=    3.578 closest distance to " OG1 THR A 294 " =    2.389
peak=    3.575 closest distance to " O   HOH Z  54 " =    1.624
peak=    3.572 closest distance to " CD  PRO A  54 " =    1.133
peak=    3.569 closest distance to " CG1BVAL A  72 " =    1.642
peak=    3.563 closest distance to " CG2 VAL A 197 " =    1.110
peak=    3.562 closest distance to " O   HOH Z 345 " =    2.799
peak=    3.548 closest distance to " O   HOH Z 434 " =    1.461
peak=    3.546 closest distance to " CD  ARG A 195 " =    1.002
peak=    3.544 closest distance to " O   HOH Z 357 " =    1.992
peak=    3.541 closest distance to " CB  PRO A 198 " =    1.040
peak=    3.539 closest distance to " CD2 LEU A 297 " =    0.916
peak=    3.536 closest distance to " O   ALA A 165 " =    1.242
peak=    3.536 closest distance to " NE2 GLN A  11 " =    1.088
peak=    3.532 closest distance to " O   HOH Z 261 " =    1.634
peak=    3.529 closest distance to " O   HOH Z  54 " =    2.279
peak=    3.528 closest distance to " O   HOH Z 427 " =    2.717
peak=    3.525 closest distance to " O   HOH Z 336 " =    1.609
peak=    3.522 closest distance to " O   HOH Z 245 " =    1.403
peak=    3.520 closest distance to " CB  ASN A 148 " =    1.173
peak=    3.519 closest distance to " CD2 TRP A 179 " =    1.295
peak=    3.517 closest distance to " O   HOH Z 234 " =    1.853
peak=    3.510 closest distance to " CA  ASP A 140 " =    1.155
peak=    3.506 closest distance to " CD2 HIS A  81 " =    1.186
peak=    3.503 closest distance to " CA  ALA A  51 " =    0.885
peak=    3.499 closest distance to " CB  ALA A 100 " =    1.300
peak=    3.489 closest distance to " O   HOH Z 346 " =    1.506
peak=    3.487 closest distance to " O   HOH Z 402 " =    2.884
peak=    3.485 closest distance to " O   HOH Z 261 " =    2.065
peak=    3.480 closest distance to " CB  ARG A 139 " =    0.942
peak=    3.475 closest distance to " O   HOH Z 263 " =    2.230
peak=    3.471 closest distance to " O   HOH Z 377 " =    1.247
peak=    3.465 closest distance to " OG BSER A 210 " =    1.172
peak=    3.465 closest distance to " O   HOH Z 227 " =    1.717
peak=    3.459 closest distance to " CG  GLN A  58 " =    2.345
peak=    3.454 closest distance to " NE1 TRP A 274 " =    0.906
peak=    3.451 closest distance to " O   HOH Z 108 " =    1.160
peak=    3.442 closest distance to " CB  PHE A  16 " =    1.027
peak=    3.441 closest distance to " O   HOH Z 108 " =    2.535
peak=    3.436 closest distance to " CG2 THR A 221 " =    1.116
peak=    3.435 closest distance to " O   HOH Z 214 " =    2.455
peak=    3.432 closest distance to " O   HOH Z  21 " =    1.790
peak=    3.431 closest distance to " O   HOH Z  18 " =    1.744
peak=    3.430 closest distance to " CB  ALA A  71 " =    1.233
peak=    3.428 closest distance to " O   HOH Z 250 " =    1.414
peak=    3.425 closest distance to " O   HOH Z 419 " =    1.590
peak=    3.421 closest distance to " O   HOH Z  66 " =    2.194
peak=    3.416 closest distance to " CB  ALA A 291 " =    1.260
peak=    3.415 closest distance to " O   HOH Z 261 " =    1.920
peak=    3.415 closest distance to " OD1 ASP A 238 " =    0.951
peak=    3.414 closest distance to " O   HOH Z 409 " =    3.286
peak=    3.406 closest distance to " O   HOH Z  35 " =    2.429
peak=    3.404 closest distance to " O   GLY A  91 " =    1.210
peak=    3.390 closest distance to " O   HOH Z  49 " =    1.868
peak=    3.389 closest distance to " O   HOH Z 303 " =    2.061
peak=    3.384 closest distance to " CD  ARG A 139 " =    1.370
peak=    3.371 closest distance to " CD  LYS A 119 " =    1.695
peak=    3.370 closest distance to " CG2 ILE A 120 " =    1.183
peak=    3.369 closest distance to " O   HOH Z 112 " =    1.505
peak=    3.369 closest distance to " O   HOH Z 197 " =    1.927
peak=    3.368 closest distance to " CB  ASN A  39 " =    0.909
peak=    3.367 closest distance to " O   HOH Z 280 " =    2.457
peak=    3.365 closest distance to " O   HOH Z 284 " =    2.921
peak=    3.364 closest distance to " O   GLY A  57 " =    2.599
peak=    3.357 closest distance to " O   HOH Z 150 " =    1.633
peak=    3.355 closest distance to " O   HOH Z 166 " =    1.382
peak=    3.350 closest distance to " O   HOH Z 365 " =    2.727
peak=    3.345 closest distance to " O   TRP A 274 " =    1.803
peak=    3.339 closest distance to " OG BSER A 258 " =    3.404
peak=    3.336 closest distance to " CA  ILE A 263 " =    0.974
peak=    3.332 closest distance to " O   HOH Z  78 " =    2.408
peak=    3.329 closest distance to " O   SER A  26 " =    1.729
peak=    3.322 closest distance to " O   HOH Z 327 " =    2.045
peak=    3.320 closest distance to " O   HOH Z 387 " =    2.375
peak=    3.318 closest distance to " O   HOH Z 144 " =    1.767
peak=    3.314 closest distance to " CB  ALA A 256 " =    1.020
peak=    3.311 closest distance to " O   HOH Z   1 " =    2.687
peak=    3.311 closest distance to " CD  ARG A 159 " =    0.854
peak=    3.311 closest distance to " CD1 LEU A 300 " =    1.195
peak=    3.310 closest distance to " CG2AVAL A 121 " =    2.132
peak=    3.308 closest distance to " O   HOH Z 166 " =    3.374
peak=    3.307 closest distance to " CA  ARG A  66 " =    1.249
peak=    3.301 closest distance to " O   HOH Z 162 " =    1.804
peak=    3.298 closest distance to " CG2 THR A 220 " =    0.821
peak=    3.295 closest distance to " O   HOH Z 217 " =    1.984
peak=    3.292 closest distance to " NH2AARG A 190 " =    1.291
peak=    3.289 closest distance to " CG1 VAL A 153 " =    1.049
peak=    3.289 closest distance to " CB  ARG A 269 " =    1.025
peak=    3.288 closest distance to " CG2 ILE A  20 " =    1.391
peak=    3.286 closest distance to " O   HOH Z   4 " =    1.895
peak=    3.285 closest distance to " O   GLY A 211 " =    1.291
peak=    3.283 closest distance to " O   HOH Z  97 " =    2.495
peak=    3.281 closest distance to " O   HOH Z 368 " =    4.515
peak=    3.280 closest distance to " CA  GLU A 152 " =    0.817
peak=    3.278 closest distance to " C   ILE A 106 " =    1.916
peak=    3.277 closest distance to " CD BLYS A 290 " =    1.200
peak=    3.273 closest distance to " OD1 ASN A  60 " =    1.158
peak=    3.270 closest distance to " CG  GLN A  11 " =    1.084
peak=    3.268 closest distance to " O   HOH Z 438 " =    2.373
peak=    3.266 closest distance to " O   HOH Z 118 " =    1.203
peak=    3.265 closest distance to " CG2 VAL A  78 " =    0.991
peak=    3.264 closest distance to " CA  LEU A  83 " =    1.378
peak=    3.258 closest distance to " CA  VAL A  41 " =    0.815
peak=    3.258 closest distance to " O   HOH Z 128 " =    1.655
peak=    3.253 closest distance to " NZ  LYS A 119 " =    1.612
peak=    3.252 closest distance to " CB  GLN A  58 " =    0.810
peak=    3.246 closest distance to " CB  GLN A 194 " =    0.893
peak=    3.242 closest distance to " O   HOH Z 123 " =    2.030
peak=    3.242 closest distance to " CG  MET A 185 " =    1.140
peak=    3.237 closest distance to " CA  ALA A  84 " =    1.241
peak=    3.236 closest distance to " O   HOH Z 334 " =    1.307
peak=    3.236 closest distance to " CZ  PHE A 218 " =    1.048
peak=    3.234 closest distance to " O   HOH Z 339 " =    1.328
peak=    3.232 closest distance to " OH  TYR A  30 " =    1.226
peak=    3.231 closest distance to " CB  THR A  52 " =    1.111
peak=    3.229 closest distance to " CA  ALA A 160 " =    0.862
peak=    3.227 closest distance to " O   HOH Z 383 " =    2.013
peak=    3.225 closest distance to " O   HOH Z 250 " =    1.818
peak=    3.224 closest distance to " O   HOH Z 102 " =    1.218
peak=    3.223 closest distance to " O   HOH Z 130 " =    2.335
peak=    3.221 closest distance to " N   ARG A 156 " =    1.432
peak=    3.220 closest distance to " OG  SER A 245 " =    1.529
peak=    3.218 closest distance to " CA  ALA A 295 " =    1.130
peak=    3.218 closest distance to " O   HOH Z  19 " =    1.553
peak=    3.218 closest distance to " CB  THR A 157 " =    1.043
peak=    3.212 closest distance to " CB  GLN A 103 " =    0.845
peak=    3.207 closest distance to " O   HOH Z  48 " =    1.467
peak=    3.205 closest distance to " CB  MET A 105 " =    1.213
peak=    3.205 closest distance to " CA  ALA A 248 " =    1.231
peak=    3.204 closest distance to " O   THR A 251 " =    1.212
peak=    3.201 closest distance to " CA  ASP A 124 " =    0.735
peak=    3.199 closest distance to " CB  GLN A  88 " =    1.092
peak=    3.199 closest distance to " O   HOH Z 155 " =    2.954
peak=    3.198 closest distance to " CB  ASN A 127 " =    1.131
peak=    3.197 closest distance to " O   HOH Z 194 " =    1.821
peak=    3.188 closest distance to " CB  LEU A 261 " =    1.213
peak=    3.186 closest distance to " CZ  PHE A  38 " =    1.428
peak=    3.185 closest distance to " O   HOH Z 185 " =    1.616
peak=    3.183 closest distance to " O   HOH Z  63 " =    2.087
peak=    3.183 closest distance to " O   ALA A 158 " =    1.228
peak=    3.183 closest distance to " CA  GLY A  80 " =    1.141
peak=    3.182 closest distance to " O   HOH Z 380 " =    1.905
peak=    3.179 closest distance to " CE1 TYR A 186 " =    1.289
peak=    3.177 closest distance to " O   VAL A  72 " =    3.203
peak=    3.176 closest distance to " O   HOH Z 281 " =    4.283
peak=    3.174 closest distance to " O   HOH Z 282 " =    2.067
peak=    3.174 closest distance to " CB  TRP A 266 " =    0.960
peak=    3.168 closest distance to " O   HOH Z 171 " =    1.826
peak=    3.166 closest distance to " NH1 ARG A 269 " =    0.768
peak=    3.166 closest distance to " ND2 ASN A 209 " =    3.739
peak=    3.165 closest distance to " O   HOH Z 285 " =    2.045
peak=    3.165 closest distance to " CB  ALA A   9 " =    1.505
peak=    3.163 closest distance to " O   HOH Z  51 " =    1.541
peak=    3.161 closest distance to " CG  GLN A  89 " =    1.400
peak=    3.160 closest distance to " CB  SER A 273 " =    0.797
peak=    3.160 closest distance to " CB  LEU A 143 " =    1.083
peak=    3.158 closest distance to " O   HOH Z 432 " =    1.824
peak=    3.158 closest distance to " CA  GLU A  46 " =    0.775
peak=    3.157 closest distance to " C   SER A  32 " =    1.048
peak=    3.156 closest distance to " NH1BARG A 145 " =    1.015
peak=    3.155 closest distance to " CB  ASN A 148 " =    1.605
peak=    3.153 closest distance to " O   HOH Z 195 " =    1.987
peak=    3.144 closest distance to " CG  MET A 185 " =    1.057
peak=    3.142 closest distance to " O   HOH Z 287 " =    1.782
peak=    3.140 closest distance to " O   HOH Z 336 " =    1.619
peak=    3.125 closest distance to " ND1 HIS A  81 " =    1.502
peak=    3.117 closest distance to " O   HOH Z 368 " =    2.531
peak=    3.113 closest distance to " O   HOH Z 425 " =    1.338
peak=    3.108 closest distance to " O   HOH Z 189 " =    1.263
peak=    3.102 closest distance to " O   HOH Z 211 " =    2.666
peak=    3.101 closest distance to " CB  PHE A 283 " =    0.709
peak=    3.095 closest distance to " OD1 ASP A 286 " =    1.515
peak=    3.095 closest distance to " CB  GLN A 278 " =    0.770
peak=    3.092 closest distance to " CH2 TRP A 274 " =    1.982
peak=    3.085 closest distance to " CA  LYS A 117 " =    1.213
peak=    3.077 closest distance to " O   HOH Z  89 " =    2.109
peak=    3.077 closest distance to " NE AARG A 275 " =    1.333
peak=    3.070 closest distance to " O   HOH Z 273 " =    2.731
peak=    3.066 closest distance to " CA  MET A  40 " =    1.025
peak=    3.061 closest distance to " CB  LEU A  83 " =    0.765
peak=    3.061 closest distance to " CA  GLY A 241 " =    0.970
peak=    3.058 closest distance to " O   HOH Z 417 " =    3.149
peak=    3.058 closest distance to " CB  LYS A 289 " =    0.948
peak=    3.052 closest distance to " O   HOH Z 420 " =    1.938
peak=    3.051 closest distance to " CA  ALA A 158 " =    1.164
peak=    3.051 closest distance to " O   HOH Z 104 " =    3.082

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 218         
Filter by distance & map next to the model:
   mapped sites are within: 0.452 - 5.119
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 215 from: 218
   mapped sites are within: 0.793 - 5.119

peak=   -4.600 closest distance to " O   HOH Z 377 " =    0.957
peak=   -4.515 closest distance to " CA  SER A 164 " =    2.072
peak=   -4.488 closest distance to " CD  ARG A 156 " =    1.999
peak=   -4.451 closest distance to " O   HOH Z 266 " =    4.322
peak=   -4.440 closest distance to " OXT GLY A 302 " =    2.722
peak=   -4.199 closest distance to " O   VAL A  67 " =    2.654
peak=   -4.182 closest distance to " CA  SER A 276 " =    1.490
peak=   -4.123 closest distance to " O   HOH Z 290 " =    0.864
peak=   -4.084 closest distance to " O   PRO A 198 " =    1.297
peak=   -4.075 closest distance to " O   HOH Z 221 " =    1.085
peak=   -4.042 closest distance to " O   TRP A  92 " =    1.906
peak=   -4.036 closest distance to " O   HOH Z 210 " =    0.849
peak=   -4.025 closest distance to " C   HIS A 108 " =    1.067
peak=   -4.024 closest distance to " O   HOH Z  13 " =    1.520
peak=   -3.966 closest distance to " O   HOH Z 196 " =    1.989
peak=   -3.925 closest distance to " CD1 LEU A 101 " =    2.531
peak=   -3.919 closest distance to " O   HOH Z  52 " =    1.853
peak=   -3.906 closest distance to " CE2 TYR A  30 " =    2.698
peak=   -3.868 closest distance to " O   HOH Z 372 " =    2.564
peak=   -3.844 closest distance to " O   HOH Z  71 " =    1.431
peak=   -3.813 closest distance to " CA  VAL A  67 " =    2.963
peak=   -3.809 closest distance to " O   HOH Z 196 " =    2.063
peak=   -3.779 closest distance to " O   HOH Z  11 " =    1.538
peak=   -3.770 closest distance to " ND2 ASN A  45 " =    1.009
peak=   -3.767 closest distance to " O   HOH Z  10 " =    1.566
peak=   -3.764 closest distance to " N   ALA A  43 " =    2.646
peak=   -3.761 closest distance to " C   THR A 279 " =    1.183
peak=   -3.760 closest distance to " CD2 LEU A 300 " =    2.842
peak=   -3.759 closest distance to " O   HOH Z 292 " =    4.517
peak=   -3.757 closest distance to " O   HOH Z 313 " =    1.064
peak=   -3.756 closest distance to " OG  SER A  62 " =    1.399
peak=   -3.753 closest distance to " OG  SER A  97 " =    2.137
peak=   -3.752 closest distance to " O   HOH Z 377 " =    2.170
peak=   -3.739 closest distance to " O   HOH Z 165 " =    2.008
peak=   -3.737 closest distance to " CD1 PHE A  59 " =    1.879
peak=   -3.735 closest distance to " NH2 ARG A  66 " =    1.558
peak=   -3.735 closest distance to " O   HOH Z 407 " =    3.485
peak=   -3.710 closest distance to " O   HOH Z  93 " =    1.340
peak=   -3.696 closest distance to " C   SER A 206 " =    1.671
peak=   -3.693 closest distance to " O   HOH Z 150 " =    1.545
peak=   -3.680 closest distance to " CD2 LEU A 237 " =    2.508
peak=   -3.674 closest distance to " OD1 ASP A 191 " =    1.718
peak=   -3.671 closest distance to " CE  MET A 105 " =    1.858
peak=   -3.668 closest distance to " N   ASP A 286 " =    2.261
peak=   -3.653 closest distance to " CB  PHE A 208 " =    2.302
peak=   -3.648 closest distance to " OE2 GLU A   2 " =    1.521
peak=   -3.647 closest distance to " SG  CYS A 254 " =    3.329
peak=   -3.645 closest distance to " O   HOH Z 418 " =    1.208
peak=   -3.645 closest distance to " O   HOH Z 234 " =    4.266
peak=   -3.637 closest distance to " OG ASER A 134 " =    1.314
peak=   -3.625 closest distance to " CG2 THR A   4 " =    1.853
peak=   -3.625 closest distance to " CB  PRO A 243 " =    2.582
peak=   -3.621 closest distance to " CD1 TYR A 247 " =    2.249
peak=   -3.620 closest distance to " CZ  TYR A 169 " =    1.832
peak=   -3.613 closest distance to " O   HOH Z 423 " =    2.339
peak=   -3.609 closest distance to " OG BSER A 134 " =    1.776
peak=   -3.607 closest distance to " N   GLN A  58 " =    1.610
peak=   -3.606 closest distance to " ND2 ASN A  45 " =    1.428
peak=   -3.596 closest distance to " C   ALA A 158 " =    1.217
peak=   -3.583 closest distance to " O   ASN A 187 " =    1.516
peak=   -3.582 closest distance to " CD  GLN A  58 " =    1.304
peak=   -3.579 closest distance to " CG  GLN A  58 " =    1.292
peak=   -3.573 closest distance to " O   HOH Z  19 " =    2.219
peak=   -3.563 closest distance to " CG  GLU A  53 " =    1.393
peak=   -3.561 closest distance to " O   HOH Z 422 " =    1.371
peak=   -3.561 closest distance to " O  BHOH Z 338 " =    1.331
peak=   -3.561 closest distance to " O   HOH Z 353 " =    2.369
peak=   -3.555 closest distance to " O   ALA A 161 " =    1.635
peak=   -3.551 closest distance to " O   HOH Z 118 " =    3.353
peak=   -3.549 closest distance to " O   HOH Z 185 " =    2.400
peak=   -3.542 closest distance to " O   HOH Z 151 " =    1.531
peak=   -3.541 closest distance to " CD1 LEU A 228 " =    2.308
peak=   -3.537 closest distance to " OD1 ASN A 148 " =    1.704
peak=   -3.526 closest distance to " O   GLY A 196 " =    0.970
peak=   -3.525 closest distance to " N   MET A 188 " =    1.994
peak=   -3.518 closest distance to " O   SER A 210 " =    1.839
peak=   -3.518 closest distance to " CG  ASP A  50 " =    2.419
peak=   -3.518 closest distance to " O   HOH Z 283 " =    1.677
peak=   -3.511 closest distance to " O   HOH Z 136 " =    1.657
peak=   -3.510 closest distance to " NH2 ARG A  66 " =    5.029
peak=   -3.504 closest distance to " NE2 GLN A 103 " =    1.680
peak=   -3.496 closest distance to " CD  GLN A  88 " =    0.856
peak=   -3.491 closest distance to " OD2 ASP A 171 " =    2.295
peak=   -3.477 closest distance to " O   HOH Z 102 " =    1.612
peak=   -3.464 closest distance to " CG2 VAL A 189 " =    2.214
peak=   -3.457 closest distance to " O   HOH Z 392 " =    1.532
peak=   -3.445 closest distance to " O   ALA A   1 " =    2.081
peak=   -3.445 closest distance to " O   ALA A 256 " =    1.533
peak=   -3.441 closest distance to " CA  ASP A 298 " =    1.116
peak=   -3.431 closest distance to " CH2 TRP A 179 " =    1.200
peak=   -3.431 closest distance to " O   ALA A 160 " =    1.435
peak=   -3.428 closest distance to " CB  SER A 210 " =    1.333
peak=   -3.425 closest distance to " O   HOH Z  17 " =    1.185
peak=   -3.422 closest distance to " O   HOH Z   6 " =    1.757
peak=   -3.421 closest distance to " O   SER A 146 " =    0.897
peak=   -3.419 closest distance to " C   LEU A 143 " =    1.188
peak=   -3.419 closest distance to " CB  ALA A 161 " =    2.536
peak=   -3.418 closest distance to " O   HOH Z 396 " =    1.910
peak=   -3.416 closest distance to " O   PRO A 198 " =    1.297
peak=   -3.409 closest distance to " O   HOH Z 311 " =    3.508
peak=   -3.409 closest distance to " CG  ASP A 231 " =    0.828
peak=   -3.407 closest distance to " CB  ALA A 248 " =    1.976
peak=   -3.406 closest distance to " O   PHE A 218 " =    1.452
peak=   -3.404 closest distance to " CD2 LEU A 237 " =    2.752
peak=   -3.402 closest distance to " CB  LEU A 167 " =    2.104
peak=   -3.397 closest distance to " O   HOH Z  78 " =    1.785
peak=   -3.393 closest distance to " CE3 TRP A 150 " =    2.227
peak=   -3.387 closest distance to " ND2 ASN A 187 " =    1.669
peak=   -3.386 closest distance to " CB  ALA A 291 " =    2.447
peak=   -3.383 closest distance to " O   HOH Z 210 " =    2.729
peak=   -3.378 closest distance to " ND2 ASN A  69 " =    1.474
peak=   -3.372 closest distance to " CA  VAL A 197 " =    0.956
peak=   -3.371 closest distance to " O   HOH Z 417 " =    2.692
peak=   -3.370 closest distance to " CB  TYR A  15 " =    2.239
peak=   -3.369 closest distance to " CD1 LEU A  25 " =    2.449
peak=   -3.364 closest distance to " CA  GLY A  98 " =    2.197
peak=   -3.358 closest distance to " N   ALA A 248 " =    1.836
peak=   -3.354 closest distance to " CA  GLY A 203 " =    2.219
peak=   -3.353 closest distance to " O   HOH Z 388 " =    2.145
peak=   -3.353 closest distance to " NH2 ARG A  79 " =    1.924
peak=   -3.352 closest distance to " CD1 PHE A 130 " =    2.263
peak=   -3.351 closest distance to " O   HOH Z 166 " =    2.124
peak=   -3.351 closest distance to " O   HOH Z 360 " =    2.496
peak=   -3.350 closest distance to " CD  GLU A 152 " =    1.017
peak=   -3.348 closest distance to " CE2 TRP A 274 " =    1.135
peak=   -3.344 closest distance to " CG2 ILE A 263 " =    2.252
peak=   -3.340 closest distance to " O   HOH Z 413 " =    4.953
peak=   -3.337 closest distance to " CH2 TRP A 274 " =    1.027
peak=   -3.333 closest distance to " O   VAL A 174 " =    2.061
peak=   -3.325 closest distance to " CD  ARG A 195 " =    5.119
peak=   -3.312 closest distance to " OD2 ASP A 171 " =    1.747
peak=   -3.312 closest distance to " CG  ARG A 219 " =    2.341
peak=   -3.312 closest distance to " OG BSER A 134 " =    1.327
peak=   -3.309 closest distance to " NE2 GLN A 194 " =    1.653
peak=   -3.306 closest distance to " C   ASP A 191 " =    1.358
peak=   -3.300 closest distance to " NE2 GLN A  88 " =    1.850
peak=   -3.296 closest distance to " O   HOH Z  38 " =    1.421
peak=   -3.294 closest distance to " O   HOH Z 423 " =    1.118
peak=   -3.289 closest distance to " O   HOH Z 150 " =    2.264
peak=   -3.287 closest distance to " NH2AARG A 275 " =    5.000
peak=   -3.274 closest distance to " CG1 VAL A 112 " =    2.571
peak=   -3.274 closest distance to " CE  MET A  93 " =    1.261
peak=   -3.271 closest distance to " NH1 ARG A 195 " =    2.592
peak=   -3.270 closest distance to " O   GLN A  11 " =    1.288
peak=   -3.267 closest distance to " CG  ASP A 132 " =    2.361
peak=   -3.267 closest distance to " O   HOH Z 222 " =    1.140
peak=   -3.266 closest distance to " CD  GLN A  58 " =    0.970
peak=   -3.265 closest distance to " CB  ALA A 248 " =    2.297
peak=   -3.257 closest distance to " O   HOH Z 385 " =    3.666
peak=   -3.247 closest distance to " N   ALA A 226 " =    2.041
peak=   -3.246 closest distance to " CB  TRP A  85 " =    2.421
peak=   -3.245 closest distance to " O   HOH Z 198 " =    2.274
peak=   -3.243 closest distance to " O   HOH Z  90 " =    2.114
peak=   -3.238 closest distance to " NZ  LYS A 117 " =    1.643
peak=   -3.237 closest distance to " CB  ALA A 291 " =    2.067
peak=   -3.236 closest distance to " O   HOH Z 424 " =    3.051
peak=   -3.236 closest distance to " CG  LYS A 119 " =    2.964
peak=   -3.233 closest distance to " CG  TRP A 266 " =    1.793
peak=   -3.229 closest distance to " O   HOH Z 140 " =    0.815
peak=   -3.227 closest distance to " CD2 PHE A  59 " =    2.425
peak=   -3.227 closest distance to " CD  ARG A 139 " =    1.595
peak=   -3.222 closest distance to " CG  PRO A 243 " =    1.579
peak=   -3.221 closest distance to " N   VAL A 189 " =    1.855
peak=   -3.218 closest distance to " OH  TYR A 169 " =    1.010
peak=   -3.215 closest distance to " CD  GLN A 223 " =    0.994
peak=   -3.211 closest distance to " O   HOH Z  15 " =    1.544
peak=   -3.206 closest distance to " CA  GLY A 133 " =    1.866
peak=   -3.205 closest distance to " NE1 TRP A 177 " =    1.930
peak=   -3.201 closest distance to " CB  ALA A  10 " =    2.110
peak=   -3.194 closest distance to " CD1 TRP A 179 " =    1.103
peak=   -3.194 closest distance to " ND2 ASN A 249 " =    2.032
peak=   -3.193 closest distance to " O   SER A   3 " =    1.140
peak=   -3.191 closest distance to " CB  PRO A 163 " =    2.771
peak=   -3.187 closest distance to " O   ASN A  45 " =    1.894
peak=   -3.184 closest distance to " NH1 ARG A 195 " =    2.244
peak=   -3.183 closest distance to " O   HOH Z  39 " =    1.604
peak=   -3.182 closest distance to " CG  ARG A 269 " =    2.284
peak=   -3.179 closest distance to " CD2 LEU A 167 " =    1.705
peak=   -3.179 closest distance to " CG1AVAL A  41 " =    2.622
peak=   -3.176 closest distance to " O   LYS A 117 " =    1.700
peak=   -3.175 closest distance to " O   HOH Z 145 " =    1.872
peak=   -3.174 closest distance to " O   HOH Z 380 " =    4.672
peak=   -3.173 closest distance to " OE1 GLN A 223 " =    2.287
peak=   -3.172 closest distance to " O   HOH Z  43 " =    1.635
peak=   -3.168 closest distance to " CD2 TYR A 293 " =    2.031
peak=   -3.165 closest distance to " C   GLY A  80 " =    2.451
peak=   -3.161 closest distance to " O   HOH Z 361 " =    3.461
peak=   -3.157 closest distance to " O   HOH Z 384 " =    1.895
peak=   -3.156 closest distance to " O   HOH Z 100 " =    0.793
peak=   -3.150 closest distance to " CB  CYS A 254 " =    2.473
peak=   -3.148 closest distance to " O   HOH Z 422 " =    1.432
peak=   -3.142 closest distance to " O   HOH Z 252 " =    4.201
peak=   -3.139 closest distance to " O   ALA A  34 " =    2.483
peak=   -3.136 closest distance to " O   VAL A 197 " =    1.195
peak=   -3.131 closest distance to " CA  TRP A 274 " =    1.534
peak=   -3.129 closest distance to " O   HOH Z  91 " =    2.123
peak=   -3.124 closest distance to " OD1 ASN A 187 " =    1.509
peak=   -3.103 closest distance to " O   ALA A  34 " =    1.987
peak=   -3.100 closest distance to " CE3 TRP A 274 " =    2.493
peak=   -3.098 closest distance to " CB  ALA A 131 " =    2.363
peak=   -3.097 closest distance to " CG  ASN A 301 " =    2.045
peak=   -3.083 closest distance to " O   HOH Z 264 " =    1.756
peak=   -3.081 closest distance to " N   GLN A  77 " =    1.455
peak=   -3.074 closest distance to " O   HOH Z 414 " =    1.484
peak=   -3.072 closest distance to " O   ALA A  10 " =    1.647
peak=   -3.069 closest distance to " O   HOH Z 111 " =    3.482
peak=   -3.068 closest distance to " O   HOH Z  97 " =    1.534
peak=   -3.062 closest distance to " C   ALA A 242 " =    1.994
peak=   -3.059 closest distance to " O   HOH Z 265 " =    2.055
peak=   -3.057 closest distance to " O   HOH Z 411 " =    3.355
peak=   -3.056 closest distance to " CH2 TRP A 177 " =    1.891
peak=   -3.049 closest distance to " ND2 ASN A  60 " =    1.481
peak=   -3.046 closest distance to " O   HOH Z 427 " =    1.369
peak=   -3.015 closest distance to " O   HOH Z  40 " =    3.070
peak=   -3.001 closest distance to " CD1 ILE A 263 " =    2.378

================= 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    :  0.4461 0.4388   6.258442e+00   6.243236e+00
   1_bss:  0.4349 0.4270   6.247763e+00   6.226303e+00
   1_xyz:  0.3078 0.3384   5.984058e+00   6.054976e+00
   1_adp:  0.2792 0.3504   5.933494e+00   6.076947e+00
   1_occ:  0.2787 0.3505   5.932568e+00   6.076308e+00
   2_bss:  0.2757 0.3463   5.927937e+00   6.072498e+00
   2_xyz:  0.2174 0.2709   5.713419e+00   5.887050e+00
   2_adp:  0.2028 0.2575   5.663865e+00   5.848690e+00
   2_occ:  0.2027 0.2576   5.663643e+00   5.848953e+00
   3_bss:  0.2026 0.2574   5.663012e+00   5.848294e+00
   3_xyz:  0.1551 0.2027   5.421012e+00   5.630841e+00
   3_adp:  0.1410 0.1920   5.347632e+00   5.571355e+00
   3_occ:  0.1409 0.1920   5.347545e+00   5.571265e+00
   4_bss:  0.1411 0.1917   5.348897e+00   5.572245e+00
   4_xyz:  0.1234 0.1751   5.239873e+00   5.483280e+00
   4_adp:  0.1189 0.1698   5.206520e+00   5.448901e+00
   4_occ:  0.1188 0.1698   5.206341e+00   5.448888e+00
   5_bss:  0.1188 0.1697   5.206288e+00   5.448807e+00
   5_xyz:  0.1154 0.1657   5.183818e+00   5.427112e+00
   5_adp:  0.1157 0.1614   5.174544e+00   5.405661e+00
   5_occ:  0.1155 0.1615   5.173925e+00   5.405751e+00
   5_bss:  0.1158 0.1611   5.174726e+00   5.405146e+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:  0.298  21.530  -3.414   4.017   1.259   0.000   0.000   0.000
   1_xyz:  0.298  21.530  -3.414   4.017   1.259   0.000   0.000   0.000
   1_adp:  0.298  21.530  -3.414   4.017   1.259   0.000   0.000   0.000
   1_occ:  0.298  21.530  -3.414   4.017   1.259   0.000   0.000   0.000
   2_bss:  0.316  47.009  -2.324   1.434  -0.313   0.000  -0.000  -0.000
   2_xyz:  0.316  47.009  -2.324   1.434  -0.313   0.000  -0.000  -0.000
   2_adp:  0.316  47.009  -2.324   1.434  -0.313   0.000  -0.000  -0.000
   2_occ:  0.316  47.009  -2.324   1.434  -0.313   0.000  -0.000  -0.000
   3_bss:  0.319  50.665  -2.116   0.455  -0.816   0.000  -0.000  -0.000
   3_xyz:  0.319  50.665  -2.116   0.455  -0.816   0.000  -0.000  -0.000
   3_adp:  0.319  50.665  -2.116   0.455  -0.816   0.000  -0.000  -0.000
   3_occ:  0.319  50.665  -2.116   0.455  -0.816   0.000  -0.000  -0.000
   4_bss:  0.324  60.686  -2.170  -0.463  -1.127  -0.000  -0.000  -0.000
   4_xyz:  0.324  60.686  -2.170  -0.463  -1.127  -0.000  -0.000  -0.000
   4_adp:  0.324  60.686  -2.170  -0.463  -1.127  -0.000  -0.000  -0.000
   4_occ:  0.324  60.686  -2.170  -0.463  -1.127  -0.000  -0.000  -0.000
   5_bss:  0.326  58.775  -1.974  -0.666  -1.057  -0.000  -0.000  -0.000
   5_xyz:  0.326  58.775  -1.974  -0.666  -1.057  -0.000  -0.000  -0.000
   5_adp:  0.326  58.775  -1.974  -0.666  -1.057  -0.000  -0.000  -0.000
   5_occ:  0.326  58.775  -1.974  -0.666  -1.057  -0.000  -0.000  -0.000
   5_bss:  0.323  51.520  -1.938  -0.747  -0.994  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.230 0.4801  0.6413    61296.522
   1_bss:  51.673 0.4982  0.6775    56914.480
   1_xyz:  36.320 0.6858  0.8970    31350.994
   1_adp:  37.721 0.6685  0.8750    33371.019
   1_occ:  37.701 0.6687  0.8743    33312.509
   2_bss:  37.185 0.6748  0.8557    32696.971
   2_xyz:  27.966 0.7788  0.9534    19546.089
   2_adp:  26.082 0.7999  0.9587    17686.418
   2_occ:  26.084 0.7999  0.9586    17688.144
   3_bss:  25.999 0.8008  0.9458    17607.433
   3_xyz:  19.831 0.8624  0.9893    10639.895
   3_adp:  18.304 0.8772  0.9860     9424.521
   3_occ:  18.303 0.8773  0.9859     9422.807
   4_bss:  18.295 0.8774  0.9720     9443.762
   4_xyz:  16.352 0.8948  0.9819     7822.850
   4_adp:  15.539 0.9021  0.9781     7323.703
   4_occ:  15.535 0.9022  0.9781     7325.271
   5_bss:  15.531 0.9022  0.9793     7323.586
   5_xyz:  14.970 0.9070  0.9795     6921.233
   5_adp:  14.504 0.9111  0.9754     6681.734
   5_occ:  14.502 0.9111  0.9754     6684.314
   5_bss:  14.503 0.9111  0.9740     6678.448
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.8290e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.8290e-01
   1_xyz:   1.631  0.014  0.098 16.197  0.006  4.115   1.4131e-01
   1_adp:   1.631  0.014  0.098 16.197  0.006  4.115   1.4131e-01
   1_occ:   1.631  0.014  0.098 16.197  0.006  4.115   1.4131e-01
   2_bss:   1.631  0.014  0.098 16.197  0.006  4.115   1.4131e-01
   2_xyz:   1.125  0.008  0.076 14.292  0.004  4.111   6.5330e-02
   2_adp:   1.125  0.008  0.076 14.292  0.004  4.111   6.5330e-02
   2_occ:   1.125  0.008  0.076 14.292  0.004  4.111   6.5330e-02
   3_bss:   1.125  0.008  0.076 14.292  0.004  4.111   6.5330e-02
   3_xyz:   1.032  0.007  0.069 14.505  0.004  4.120   6.2734e-02
   3_adp:   1.032  0.007  0.069 14.505  0.004  4.120   6.2734e-02
   3_occ:   1.032  0.007  0.069 14.505  0.004  4.120   6.2734e-02
   4_bss:   1.032  0.007  0.069 14.505  0.004  4.120   6.2734e-02
   4_xyz:   1.089  0.008  0.076 14.771  0.004  4.112   6.7538e-02
   4_adp:   1.089  0.008  0.076 14.771  0.004  4.112   6.7538e-02
   4_occ:   1.089  0.008  0.076 14.771  0.004  4.112   6.7538e-02
   5_bss:   1.089  0.008  0.076 14.771  0.004  4.112   6.7538e-02
   5_xyz:   1.008  0.007  0.072 14.604  0.004  4.114   5.8776e-02
   5_adp:   1.008  0.007  0.072 14.604  0.004  4.114   5.8776e-02
   5_occ:   1.008  0.007  0.072 14.604  0.004  4.114   5.8776e-02
   5_bss:   1.008  0.007  0.072 14.604  0.004  4.114   5.8776e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.594   2.4106e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.594   2.4106e-01
   1_xyz:  10.369  0.114  0.488 89.151  0.024  2.062   1.0775e-01
   1_adp:  10.369  0.114  0.488 89.151  0.024  2.062   1.0775e-01
   1_occ:  10.369  0.114  0.488 89.151  0.024  2.062   1.0775e-01
   2_bss:  10.369  0.114  0.488 89.151  0.024  2.062   1.0775e-01
   2_xyz:   7.643  0.048  0.278 87.511  0.044  2.336   6.5997e-02
   2_adp:   7.643  0.048  0.278 87.511  0.044  2.336   6.5997e-02
   2_occ:   7.643  0.048  0.278 87.511  0.044  2.336   6.5997e-02
   3_bss:   7.643  0.048  0.278 87.511  0.044  2.336   6.5997e-02
   3_xyz:   7.402  0.062  0.240 81.774  0.032  2.297   5.4473e-02
   3_adp:   7.402  0.062  0.240 81.774  0.032  2.297   5.4473e-02
   3_occ:   7.402  0.062  0.240 81.774  0.032  2.297   5.4473e-02
   4_bss:   7.402  0.062  0.240 81.774  0.032  2.297   5.4473e-02
   4_xyz:   7.247  0.050  0.234 82.168  0.032  2.313   6.3334e-02
   4_adp:   7.247  0.050  0.234 82.168  0.032  2.313   6.3334e-02
   4_occ:   7.247  0.050  0.234 82.168  0.032  2.313   6.3334e-02
   5_bss:   7.247  0.050  0.234 82.168  0.032  2.313   6.3334e-02
   5_xyz:   7.318  0.040  0.236 81.129  0.034  2.340   4.5353e-02
   5_adp:   7.318  0.040  0.236 81.129  0.034  2.340   4.5353e-02
   5_occ:   7.318  0.040  0.236 81.129  0.034  2.340   4.5353e-02
   5_bss:   7.318  0.040  0.236 81.129  0.034  2.340   4.5353e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp: 101.12   0.00  18.46  99.03   0.00  14.58 101.12   1.09  39.56
   1_occ: 101.12   0.00  18.46  99.03   0.00  14.58 101.12   1.09  39.56
   2_bss: 101.12   0.00  18.46  99.03   0.00  14.58 101.12   1.09  39.56
   2_xyz: 101.12   0.00  18.46  99.03   0.00  14.58 101.12   1.09  39.56
   2_adp:  98.81   0.00  17.99  97.88   0.00  13.81  98.81   5.79  40.75
   2_occ:  98.81   0.00  17.99  97.88   0.00  13.81  98.81   5.79  40.75
   3_bss:  98.81   0.00  17.99  97.88   0.00  13.81  98.81   5.79  40.75
   3_xyz:  98.81   0.00  17.99  97.88   0.00  13.81  98.81   5.79  40.75
   3_adp: 108.50   0.00  18.32 108.50   0.00  13.26 107.40   6.04  45.90
   3_occ: 108.50   0.00  18.32 108.50   0.00  13.26 107.40   6.04  45.90
   4_bss: 108.50   0.00  18.32 108.50   0.00  13.26 107.40   6.04  45.90
   4_xyz: 108.50   0.00  18.32 108.50   0.00  13.26 107.40   6.04  45.90
   4_adp: 116.51   0.00  17.80 116.51   0.00  12.80 107.12   5.28  45.05
   4_occ: 116.51   0.00  17.80 116.51   0.00  12.80 107.12   5.28  45.05
   5_bss: 116.51   0.00  17.80 116.51   0.00  12.80 107.12   5.28  45.05
   5_xyz: 116.51   0.00  17.80 116.51   0.00  12.80 107.12   5.28  45.05
   5_adp: 108.03   1.26  16.60 108.03   1.26  12.29  96.17   4.68  40.06
   5_occ: 108.03   1.26  16.60 108.03   1.26  12.29  96.17   4.68  40.06
   5_bss: 107.98   1.22  16.56 107.98   1.22  12.25  96.13   4.63  40.01
------------------------------------------------------------------------
 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:    2.021    0.007    0.456
   1_adp:    2.021    0.007    0.456
   1_occ:    2.021    0.007    0.456
   2_bss:    2.021    0.007    0.456
   2_xyz:    1.414    0.057    0.548
   2_adp:    1.414    0.057    0.548
   2_occ:    1.414    0.057    0.548
   3_bss:    1.414    0.057    0.548
   3_xyz:    1.343    0.027    0.681
   3_adp:    1.343    0.027    0.681
   3_occ:    1.343    0.027    0.681
   4_bss:    1.343    0.027    0.681
   4_xyz:    1.396    0.041    0.728
   4_adp:    1.396    0.041    0.728
   4_occ:    1.396    0.041    0.728
   5_bss:    1.396    0.041    0.728
   5_xyz:    1.457    0.148    0.745
   5_adp:    1.457    0.148    0.745
   5_occ:    1.457    0.148    0.745
   5_bss:    1.457    0.148    0.745
------------------------------------------------------------------------

CPU time actual refinement: 335.37


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_584/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_584/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_584/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_584/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_584/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 335.22 
  Macro-tasks:
    bulk solvent and scale       = 44.07  
    individual site refinement   = 131.34 
    weights calculation          = 29.76  
    collect and process          = 6.52   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 211.79 
  Micro-tasks:
    mask                            = 2.51   
    f_calc                          = 105.87 
    alpha_beta                      = 8.40   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 112.81 
    fmodel                         = 6.94   
    r_factors                      = 0.26   
    phase_errors                   = 10.49  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 248.74 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.843 micro seconds
Total CPU time: 5.82 minutes
from_scatterers_fft:    623 calls, 105.47 s
gradients_fft:          568 calls, 100.45 s

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

# Date 2008-01-16 Time 05:10:52 PST -0800 (1200489052.75 s)
Start R-work = 0.4461, R-free = 0.4388 (no bulk solvent and anisotropic scale)
Final R-work = 0.1358, R-free = 0.1792 (no bulk solvent and anisotropic scale)

Start R-work = 0.4349, R-free = 0.4270
Final R-work = 0.1158, R-free = 0.1611