# Date 2008-01-16 Time 05:50:06 PST -0800 (1200491406.19 s)
#phil __OFF__

Command line arguments: "../899.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 16986
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 899

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 46.6953, 87.6859, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.6953, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1641 1.99267
Completeness in resolution range: 0.955934
Completeness with d_max=infinity: 0.953004

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1641
                             d_min =   1.9927

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.6953, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1641 1.99267
Completeness in resolution range: 0.955934
Completeness with d_max=infinity: 0.953004

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1646 -  4.2643 [2155/2179]  1937   218  10.1%
  bin  2:  4.2643 -  3.3972 [2057/2077]  1853   204   9.9%
  bin  3:  3.3972 -  2.9714 [2048/2067]  1842   206  10.1%
  bin  4:  2.9714 -  2.7014 [2025/2055]  1825   200   9.9%
  bin  5:  2.7014 -  2.5087 [2003/2022]  1805   198   9.9%
  bin  6:  2.5087 -  2.3614 [1993/2018]  1790   203  10.2%
  bin  7:  2.3614 -  2.2435 [1998/2026]  1794   204  10.2%
  bin  8:  2.2435 -  2.1461 [1983/2019]  1788   195   9.8%
  bin  9:  2.1461 -  2.0637 [1971/2013]  1777   194   9.8%
  bin 10:  2.0637 -  1.9927 [1356/2016]  1219   137  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_899/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 14
        2.42 -     3.04: 2166
        3.04 -     3.66: 4643
        3.66 -     4.28: 8911
        4.28 -     4.90: 12294
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.113 3.040 -x+1,y+1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.246 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  2.246 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28023 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_899/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_899/model_refine_001.geo

CPU time processing inputs: 9.05


============================ Non-default parameters ===========================

A complete record of all parameters was written to the .eff file above.
Below are only the non-defaults.

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 46.69535 87.68585 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: 1.99 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3330   r_free= 0.3216   ksol= 0.00   Bsol= 0.00   scale= 0.960    |
|                                                                             |
| 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:   0.39 A                  |
| x-ray target function (ml) for work reflections: 6.057946                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1646 -  4.7563 0.99   1400  155 0.2870 0.2631      6.3614      6.2509|
|  2:  4.7563 -  3.7947 0.99   1343  151 0.2586 0.2580      6.4426      6.4237|
|  3:  3.7947 -  3.3208 0.99   1317  143 0.2832 0.2569      6.3428      6.3451|
|  4:  3.3208 -  3.0198 0.99   1319  151 0.3066 0.3162      6.2348      6.2417|
|  5:  3.0198 -  2.8048 0.99   1299  145 0.3529 0.3081      6.1325      6.0786|
|  6:  2.8048 -  2.6403 0.99   1299  140 0.3371 0.3496      6.0186      5.9625|
|  7:  2.6403 -  2.5087 0.99   1285  141 0.3579 0.3590      6.0181      6.0723|
|  8:  2.5087 -  2.4000 0.98   1276  146 0.3712 0.3350      6.0053      5.9639|
|  9:  2.4000 -  2.3079 0.98   1277  142 0.3758 0.3451       5.943      5.8927|
| 10:  2.3079 -  2.2285 1.00   1293  147 0.3905 0.3858      5.9507      5.8827|
| 11:  2.2285 -  2.1590 0.97   1268  135 0.4047 0.4016      5.8931      5.9493|
| 12:  2.1590 -  2.0975 0.98   1262  146 0.3814 0.3730      5.8191      5.8648|
| 13:  2.0975 -  2.0424 0.99   1291  135 0.3974 0.3813      5.7221      5.6683|
| 14:  2.0424 -  1.9927 0.54    701   82 0.3742 0.4348      5.7043      5.7072|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1646 -  4.7563  1400   155  0.81  23.99   0.86     0.83      36665.13|
|  2:  4.7563 -  3.7947  1343   151  0.86  20.74   0.96     0.92      42783.99|
|  3:  3.7947 -  3.3208  1317   143  0.81  25.29   0.98     0.94      43140.44|
|  4:  3.3208 -  3.0198  1319   151  0.78  28.39   0.98     0.91      38263.87|
|  5:  3.0198 -  2.8048  1299   145  0.72  33.62   0.99     0.88      32146.35|
|  6:  2.8048 -  2.6403  1299   140  0.71  34.66   0.98     0.86      28906.03|
|  7:  2.6403 -  2.5087  1285   141  0.70  35.72   1.00     0.86      27544.88|
|  8:  2.5087 -  2.4000  1276   146  0.69  36.39   0.99     0.87      25589.52|
|  9:  2.4000 -  2.3079  1277   142  0.70  35.88   1.00     0.89      23469.57|
| 10:  2.3079 -  2.2285  1293   147  0.68  37.58   1.03     0.88      22344.42|
| 11:  2.2285 -  2.1590  1268   135  0.66  39.39   1.01     0.88      22696.60|
| 12:  2.1590 -  2.0975  1262   146  0.65  39.98   1.03     0.87      21799.20|
| 13:  2.0975 -  2.0424  1291   135  0.62  42.52   1.00     0.87      19015.61|
| 14:  2.0424 -  1.9927   701    82  0.68  38.02   1.04     0.87      15160.68|
|alpha:            min =        0.83 max =            0.94 mean =         0.88|
|beta:             min =    15160.68 max =        43140.44 mean =     29141.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.72|
|phase err.(work): min =        0.00 max =           89.99 mean =        33.44|
|phase err.(test): min =        0.00 max =           89.87 mean =        32.87|
|-----------------------------------------------------------------------------|

============================== 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 = 5.173254              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.935   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.671525              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.947   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       12 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      193 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1973 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1833 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2810 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4579 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4332 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5631 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6663 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.161 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.806 |       0.145 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.126)------------------------------------------|
|    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: 1.99 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3330   r_free= 0.3216   ksol= 0.00   Bsol= 0.00   scale= 0.960    |
|                                                                             |
| 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:   0.39 A                  |
| x-ray target function (ml) for work reflections: 6.057946                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3201   r_free= 0.3115   ksol= 0.33   Bsol= 63.69   scale= 0.971   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.79,-2.56,2.35,-0.00,0.00,0.00); trace/3= -0.67                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 6.035199                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.537764              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.882   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.363358              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.654   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3201      final r-factor (work) = 0.1753          |
| start r-factor (free) = 0.3115      final r-factor (free) = 0.2008          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.8594 = 4.54 * 0.50 * 6.0373 + 1.00 * 0.1614                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.0696 = 4.54 * 0.50 * 5.7301 + 1.00 * 0.0688                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1753      final r-factor (work) = 0.1623          |
| start r-factor (free) = 0.2008      final r-factor (free) = 0.2054          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0884 = 0.36 * 1.00 * 5.7301 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0130 = 0.36 * 1.00 * 5.4341 + 1.00 * 0.0385                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 5      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.126)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    65.87   16.48    None  None   None       |
|    all(noH): 2823   0      0.00    65.87   16.48    None  None   None       |
|    Sol.    : 438    0      5.04    63.34   37.57    None  None   None       |
|    Mac.    : 2385   0      0.00    65.87   12.61    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 -   6.587:  261   |   5:    32.935 -  39.522:   99        |
|      1:     6.587 -  13.174: 1295   |   6:    39.522 -  46.108:   99        |
|      2:    13.174 -  19.761:  631   |   7:    46.108 -  52.695:   76        |
|      3:    19.761 -  26.348:  196   |   8:    52.695 -  59.282:   46        |
|      4:    26.348 -  32.935:  111   |   9:    59.282 -  65.869:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1623 r_free = 0.2054             target_work(ml) = 5.445         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1619 r_free = 0.2049             target_work(ml) = 5.442         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1619   r_free= 0.2049   ksol= 0.33   Bsol= 63.69   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.79,-2.56,2.35,-0.00,0.00,0.00); trace/3= -0.67                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.442339                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1602   r_free= 0.2023   ksol= 0.34   Bsol= 66.71   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.54,-2.85,-0.28,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.438748                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.007933              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.968  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.281273              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.425   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1602      final r-factor (work) = 0.1310          |
| start r-factor (free) = 0.2023      final r-factor (free) = 0.1685          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5387 = 2.01 * 0.50 * 5.4483 + 1.00 * 0.0688                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4246 = 2.01 * 0.50 * 5.3480 + 1.00 * 0.0555                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1310      final r-factor (work) = 0.1237          |
| start r-factor (free) = 0.1685      final r-factor (free) = 0.1655          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5308 = 0.28 * 1.00 * 5.3480 + 1.00 * 0.0265                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4795 = 0.28 * 1.00 * 5.2302 + 1.00 * 0.0084                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.126)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.16    72.10   16.98    None  None   None       |
|    all(noH): 2823   0      1.16    72.10   16.98    None  None   None       |
|    Sol.    : 438    0      6.02    72.10   39.40    None  None   None       |
|    Mac.    : 2385   0      1.16    70.06   12.86    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:     1.160 -   8.254:  579   |   5:    36.631 -  43.725:   94        |
|      1:     8.254 -  15.348: 1302   |   6:    43.725 -  50.819:   83        |
|      2:    15.348 -  22.443:  394   |   7:    50.819 -  57.913:   87        |
|      3:    22.443 -  29.537:  133   |   8:    57.913 -  65.008:   34        |
|      4:    29.537 -  36.631:   99   |   9:    65.008 -  72.102:   18        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1237 r_free = 0.1655             target_work(ml) = 5.218         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1236 r_free = 0.1654             target_work(ml) = 5.217         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1236   r_free= 0.1654   ksol= 0.34   Bsol= 66.71   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.54,-2.85,-0.28,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.217433                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1235   r_free= 0.1650   ksol= 0.34   Bsol= 66.71   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-2.61,-0.61,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.216446                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.406645              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.707  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.187063              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.534  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1235      final r-factor (work) = 0.1180          |
| start r-factor (free) = 0.1650      final r-factor (free) = 0.1603          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7334 = 1.41 * 0.50 * 5.2295 + 1.00 * 0.0555                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7074 = 1.41 * 0.50 * 5.1968 + 1.00 * 0.0524                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1180      final r-factor (work) = 0.1175          |
| start r-factor (free) = 0.1603      final r-factor (free) = 0.1590          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9805 = 0.19 * 1.00 * 5.1968 + 1.00 * 0.0084                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9774 = 0.19 * 1.00 * 5.1828 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.126)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.22    72.47   16.73    None  None   None       |
|    all(noH): 2823   0      1.22    72.47   16.73    None  None   None       |
|    Sol.    : 438    0      2.93    72.47   38.54    None  None   None       |
|    Mac.    : 2385   0      1.22    71.03   12.72    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:     1.223 -   8.347:  620   |   5:    36.844 -  43.968:  103        |
|      1:     8.347 -  15.471: 1300   |   6:    43.968 -  51.092:   79        |
|      2:    15.471 -  22.596:  363   |   7:    51.092 -  58.217:   77        |
|      3:    22.596 -  29.720:  138   |   8:    58.217 -  65.341:   31        |
|      4:    29.720 -  36.844:   99   |   9:    65.341 -  72.465:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1175 r_free = 0.1590             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1174 r_free = 0.1590             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1174   r_free= 0.1590   ksol= 0.34   Bsol= 66.71   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-2.61,-0.61,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.178794                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1174   r_free= 0.1589   ksol= 0.34   Bsol= 66.71   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-2.46,-0.68,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.178766                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.233585              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 153.249  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.523810              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.353  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1174      final r-factor (work) = 0.1100          |
| start r-factor (free) = 0.1589      final r-factor (free) = 0.1573          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4319 = 3.23 * 0.50 * 5.1828 + 1.00 * 0.0524                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4011 = 3.23 * 0.50 * 5.1485 + 1.00 * 0.0772                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1100      final r-factor (work) = 0.1090          |
| start r-factor (free) = 0.1573      final r-factor (free) = 0.1574          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7046 = 0.52 * 1.00 * 5.1485 + 1.00 * 0.0078                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6977 = 0.52 * 1.00 * 5.1335 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.126)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.59    75.97   16.76    None  None   None       |
|    all(noH): 2823   0      0.59    75.97   16.76    None  None   None       |
|    Sol.    : 438    0      3.53    74.49   39.19    None  None   None       |
|    Mac.    : 2385   0      0.59    75.97   12.64    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:     0.592 -   8.130:  617   |   5:    38.279 -  45.817:  106        |
|      1:     8.130 -  15.667: 1317   |   6:    45.817 -  53.354:   84        |
|      2:    15.667 -  23.205:  354   |   7:    53.354 -  60.892:   67        |
|      3:    23.205 -  30.742:  139   |   8:    60.892 -  68.429:   30        |
|      4:    30.742 -  38.279:   99   |   9:    68.429 -  75.967:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1090 r_free = 0.1574             target_work(ml) = 5.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1090 r_free = 0.1574             target_work(ml) = 5.134         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1090   r_free= 0.1574   ksol= 0.34   Bsol= 66.71   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-2.46,-0.68,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.134413                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1089   r_free= 0.1573   ksol= 0.34   Bsol= 66.71   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-2.23,-0.50,-0.00,-0.00,-0.00); trace/3= -1.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.134497                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.323720              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 163.918  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.528043              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.209  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1089      final r-factor (work) = 0.1105          |
| start r-factor (free) = 0.1573      final r-factor (free) = 0.1581          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0427 = 2.32 * 0.50 * 5.1345 + 1.00 * 0.0772                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0380 = 2.32 * 0.50 * 5.1413 + 1.00 * 0.0646                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1105      final r-factor (work) = 0.1105          |
| start r-factor (free) = 0.1581      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7236 = 0.53 * 1.00 * 5.1413 + 1.00 * 0.0088                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7257 = 0.53 * 1.00 * 5.1449 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.126)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.47    76.68   16.60    None  None   None       |
|    all(noH): 2823   0      0.47    76.68   16.60    None  None   None       |
|    Sol.    : 438    0      5.46    74.59   39.14    None  None   None       |
|    Mac.    : 2385   0      0.47    76.68   12.46    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:     0.465 -   8.086:  664   |   5:    38.571 -  46.192:  105        |
|      1:     8.086 -  15.708: 1283   |   6:    46.192 -  53.814:   83        |
|      2:    15.708 -  23.329:  343   |   7:    53.814 -  61.435:   66        |
|      3:    23.329 -  30.950:  141   |   8:    61.435 -  69.056:   28        |
|      4:    30.950 -  38.571:  101   |   9:    69.056 -  76.677:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1105 r_free = 0.1584             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1105 r_free = 0.1584             target_work(ml) = 5.147         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1105   r_free= 0.1584   ksol= 0.34   Bsol= 66.71   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-2.23,-0.50,-0.00,-0.00,-0.00); trace/3= -1.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.146574                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1646 -  4.7563 0.99   1400  155 0.1008 0.1330      5.4145      5.5648|
|  2:  4.7563 -  3.7947 0.99   1343  151 0.0859 0.1138      5.4484      5.6391|
|  3:  3.7947 -  3.3208 0.99   1317  143 0.1046 0.1478      5.4735      5.8459|
|  4:  3.3208 -  3.0198 0.99   1319  151 0.1186 0.1659      5.4393      5.5967|
|  5:  3.0198 -  2.8048 0.99   1299  145 0.1329 0.1733      5.3293       5.586|
|  6:  2.8048 -  2.6403 0.99   1299  140 0.1192 0.1996      5.2116      5.4876|
|  7:  2.6403 -  2.5087 0.99   1285  141 0.1268 0.1534      5.1744      5.3234|
|  8:  2.5087 -  2.4000 0.98   1276  146 0.1107 0.1633      5.0508      5.3069|
|  9:  2.4000 -  2.3079 0.98   1277  142 0.1162 0.1721      5.0295      5.2811|
| 10:  2.3079 -  2.2285 1.00   1293  147 0.1099 0.1780       4.943      5.2413|
| 11:  2.2285 -  2.1590 0.97   1268  135 0.1119 0.1757      4.9364      5.2663|
| 12:  2.1590 -  2.0975 0.98   1262  146 0.1086 0.1729      4.8723      5.1881|
| 13:  2.0975 -  2.0424 0.99   1291  135 0.1111 0.1717       4.779      5.0345|
| 14:  2.0424 -  1.9927 0.54    701   82 0.0987 0.1592       4.672      4.8887|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1646 -  4.7563  1400   155  0.94   9.63   0.97     0.94       7762.10|
|  2:  4.7563 -  3.7947  1343   151  0.95   8.04   1.00     0.99       9416.92|
|  3:  3.7947 -  3.3208  1317   143  0.93  11.23   1.02     1.01      10335.25|
|  4:  3.3208 -  3.0198  1319   151  0.92  13.67   1.00     0.98      10189.13|
|  5:  3.0198 -  2.8048  1299   145  0.90  16.11   0.99     0.97       8514.50|
|  6:  2.8048 -  2.6403  1299   140  0.90  16.35   0.98     0.95       7236.63|
|  7:  2.6403 -  2.5087  1285   141  0.90  15.74   0.98     0.95       6370.49|
|  8:  2.5087 -  2.4000  1276   146  0.91  15.08   0.98     0.96       5236.32|
|  9:  2.4000 -  2.3079  1277   142  0.91  15.11   0.99     0.95       4923.61|
| 10:  2.3079 -  2.2285  1293   147  0.90  15.72   0.99     0.96       4363.94|
| 11:  2.2285 -  2.1590  1268   135  0.90  16.14   0.97     0.93       4287.21|
| 12:  2.1590 -  2.0975  1262   146  0.91  15.12   1.00     0.99       3971.22|
| 13:  2.0975 -  2.0424  1291   135  0.90  16.49   0.98     0.95       3362.02|
| 14:  2.0424 -  1.9927   701    82  0.92  14.21   0.96     0.93       2673.52|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     2673.52 max =        10335.25 mean =      6493.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.90 mean =        14.13|
|phase err.(test): min =        0.00 max =           89.83 mean =        13.63|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1583   ksol= 0.32   Bsol= 59.14   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-2.02,-0.32,-0.00,-0.00,-0.00); trace/3= -1.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.146531                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1583   ksol= 0.32   Bsol= 59.14   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-2.02,-0.32,-0.00,-0.00,-0.00); trace/3= -1.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.146531                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1646 -  4.7563 0.99   1400  155 0.1002 0.1324      5.4079      5.5604|
|  2:  4.7563 -  3.7947 0.99   1343  151 0.0856 0.1137      5.4454      5.6368|
|  3:  3.7947 -  3.3208 0.99   1317  143 0.1045 0.1478      5.4725      5.8467|
|  4:  3.3208 -  3.0198 0.99   1319  151 0.1188 0.1661       5.441      5.5982|
|  5:  3.0198 -  2.8048 0.99   1299  145 0.1332 0.1736      5.3314      5.5878|
|  6:  2.8048 -  2.6403 0.99   1299  140 0.1194 0.2001      5.2135      5.4896|
|  7:  2.6403 -  2.5087 0.99   1285  141 0.1270 0.1536       5.176      5.3248|
|  8:  2.5087 -  2.4000 0.98   1276  146 0.1108 0.1634      5.0518      5.3075|
|  9:  2.4000 -  2.3079 0.98   1277  142 0.1162 0.1719        5.03      5.2807|
| 10:  2.3079 -  2.2285 1.00   1293  147 0.1100 0.1783      4.9435       5.242|
| 11:  2.2285 -  2.1590 0.97   1268  135 0.1119 0.1757      4.9369      5.2668|
| 12:  2.1590 -  2.0975 0.98   1262  146 0.1086 0.1731      4.8724      5.1884|
| 13:  2.0975 -  2.0424 0.99   1291  135 0.1112 0.1718      4.7795      5.0345|
| 14:  2.0424 -  1.9927 0.54    701   82 0.0987 0.1593      4.6727      4.8898|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1646 -  4.7563  1400   155  0.94   9.58   0.97     0.94       7660.53|
|  2:  4.7563 -  3.7947  1343   151  0.95   8.00   1.01     0.99       9364.85|
|  3:  3.7947 -  3.3208  1317   143  0.93  11.22   1.02     1.01      10326.08|
|  4:  3.3208 -  3.0198  1319   151  0.92  13.69   1.00     0.98      10212.40|
|  5:  3.0198 -  2.8048  1299   145  0.90  16.13   1.00     0.97       8544.11|
|  6:  2.8048 -  2.6403  1299   140  0.90  16.39   0.98     0.95       7263.03|
|  7:  2.6403 -  2.5087  1285   141  0.90  15.77   0.99     0.96       6392.49|
|  8:  2.5087 -  2.4000  1276   146  0.91  15.10   0.99     0.97       5245.57|
|  9:  2.4000 -  2.3079  1277   142  0.91  15.11   1.00     0.96       4928.92|
| 10:  2.3079 -  2.2285  1293   147  0.90  15.73   1.00     0.97       4365.29|
| 11:  2.2285 -  2.1590  1268   135  0.90  16.15   0.98     0.93       4290.96|
| 12:  2.1590 -  2.0975  1262   146  0.91  15.13   1.01     1.00       3973.82|
| 13:  2.0975 -  2.0424  1291   135  0.90  16.50   0.99     0.96       3366.08|
| 14:  2.0424 -  1.9927   701    82  0.92  14.23   0.97     0.94       2677.66|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2677.66 max =        10326.08 mean =      6490.62|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.75 mean =        14.14|
|phase err.(test): min =        0.00 max =           89.65 mean =        13.64|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.126)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.45    76.66   16.59    None  None   None       |
|    all(noH): 2823   0      0.45    76.66   16.59    None  None   None       |
|    Sol.    : 438    0      5.45    74.57   39.12    None  None   None       |
|    Mac.    : 2385   0      0.45    76.66   12.45    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:     0.451 -   8.072:  664   |   5:    38.557 -  46.178:  105        |
|      1:     8.072 -  15.693: 1283   |   6:    46.178 -  53.799:   83        |
|      2:    15.693 -  23.314:  343   |   7:    53.799 -  61.420:   66        |
|      3:    23.314 -  30.936:  141   |   8:    61.420 -  69.042:   28        |
|      4:    30.936 -  38.557:  101   |   9:    69.042 -  76.663:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 286         
Filter by distance & map next to the model:
   mapped sites are within: 0.482 - 4.794
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 279 from: 286
   mapped sites are within: 0.707 - 4.794

peak=    5.693 closest distance to " NH2 ARG A  56 " =    2.215
peak=    5.335 closest distance to " CG  PRO A  54 " =    1.343
peak=    5.133 closest distance to " CB  GLN A 223 " =    1.437
peak=    5.097 closest distance to " O   HOH Z 232 " =    2.321
peak=    5.068 closest distance to " NE2 GLN A  11 " =    1.138
peak=    4.938 closest distance to " O   HOH Z 144 " =    1.796
peak=    4.827 closest distance to " O   HOH Z 126 " =    1.868
peak=    4.768 closest distance to " CB  ARG A  79 " =    1.383
peak=    4.718 closest distance to " O   HOH Z 298 " =    2.000
peak=    4.710 closest distance to " CB  ARG A 275 " =    0.921
peak=    4.647 closest distance to " CB  SER A  63 " =    1.213
peak=    4.647 closest distance to " CB  GLN A 183 " =    1.230
peak=    4.626 closest distance to " CG  PRO A 213 " =    1.219
peak=    4.583 closest distance to " CB  ARG A 190 " =    1.659
peak=    4.578 closest distance to " CB  PRO A  54 " =    0.979
peak=    4.545 closest distance to " CG  PRO A 198 " =    1.243
peak=    4.493 closest distance to " CB  LEU A 228 " =    1.107
peak=    4.484 closest distance to " O   HOH Z  78 " =    1.677
peak=    4.478 closest distance to " CZ  PHE A 218 " =    1.059
peak=    4.448 closest distance to " O   HOH Z 287 " =    2.184
peak=    4.438 closest distance to " O   HOH Z 369 " =    2.129
peak=    4.389 closest distance to " CB  ASN A 148 " =    1.430
peak=    4.387 closest distance to " O   HOH Z  15 " =    2.205
peak=    4.349 closest distance to " CA  TYR A  30 " =    0.979
peak=    4.297 closest distance to " CD  ARG A 159 " =    0.780
peak=    4.251 closest distance to " O   HOH Z 250 " =    1.540
peak=    4.225 closest distance to " ND2 ASN A 187 " =    1.491
peak=    4.218 closest distance to " O   HOH Z 303 " =    2.140
peak=    4.191 closest distance to " C   PRO A 198 " =    1.495
peak=    4.176 closest distance to " O   HOH Z 189 " =    2.806
peak=    4.171 closest distance to " CE  LYS A  76 " =    0.858
peak=    4.149 closest distance to " NH1AARG A 145 " =    1.309
peak=    4.139 closest distance to " CG2 VAL A 257 " =    0.909
peak=    4.107 closest distance to " CB  TRP A 266 " =    1.020
peak=    4.075 closest distance to " O   HOH Z 234 " =    3.830
peak=    4.059 closest distance to " CB  GLU A 152 " =    1.245
peak=    4.033 closest distance to " O   HOH Z 427 " =    3.019
peak=    4.008 closest distance to " O   HOH Z 158 " =    3.090
peak=    3.997 closest distance to " CB  VAL A 265 " =    1.254
peak=    3.989 closest distance to " O   HOH Z 193 " =    1.913
peak=    3.972 closest distance to " CG  LEU A 167 " =    1.262
peak=    3.959 closest distance to " O   HOH Z  21 " =    1.786
peak=    3.922 closest distance to " CB  ASN A 187 " =    1.229
peak=    3.919 closest distance to " O   HOH Z  53 " =    2.539
peak=    3.911 closest distance to " CB  GLU A 128 " =    0.965
peak=    3.911 closest distance to " NZ  LYS A 117 " =    3.252
peak=    3.910 closest distance to " CA  ASN A 215 " =    1.109
peak=    3.902 closest distance to " O   HOH Z 346 " =    1.672
peak=    3.896 closest distance to " CB  TYR A 169 " =    0.731
peak=    3.891 closest distance to " CB  ASN A  39 " =    0.917
peak=    3.890 closest distance to " O   HOH Z 316 " =    3.126
peak=    3.886 closest distance to " CG  PRO A 243 " =    1.075
peak=    3.885 closest distance to " CB  SER A 212 " =    1.171
peak=    3.884 closest distance to " CB  ASP A 124 " =    0.809
peak=    3.881 closest distance to " CB  ASN A 142 " =    1.002
peak=    3.880 closest distance to " O   HOH Z  40 " =    1.909
peak=    3.871 closest distance to " OD1 ASN A  69 " =    2.643
peak=    3.862 closest distance to " O   HOH Z 265 " =    2.338
peak=    3.861 closest distance to " O   HOH Z 214 " =    2.155
peak=    3.855 closest distance to " O   HOH Z 272 " =    1.808
peak=    3.847 closest distance to " CD2 TRP A 179 " =    1.314
peak=    3.840 closest distance to " CA  ARG A 195 " =    1.233
peak=    3.840 closest distance to " O   HOH Z  61 " =    1.591
peak=    3.835 closest distance to " O   HOH Z 180 " =    2.121
peak=    3.832 closest distance to " CB  GLU A 277 " =    3.691
peak=    3.830 closest distance to " CD1 LEU A 300 " =    1.170
peak=    3.826 closest distance to " CA  ALA A  51 " =    0.943
peak=    3.810 closest distance to " O   HOH Z 313 " =    1.935
peak=    3.799 closest distance to " O   HOH Z 368 " =    2.113
peak=    3.796 closest distance to " CD  ARG A  66 " =    2.253
peak=    3.785 closest distance to " CB  GLU A  46 " =    0.948
peak=    3.778 closest distance to " CA  SER A  87 " =    0.985
peak=    3.772 closest distance to " O   HOH Z  10 " =    1.841
peak=    3.771 closest distance to " O   HOH Z 386 " =    3.070
peak=    3.766 closest distance to " CA  THR A 264 " =    0.881
peak=    3.754 closest distance to " O   HOH Z   1 " =    2.024
peak=    3.746 closest distance to " CB  ASP A 140 " =    1.028
peak=    3.745 closest distance to " O   HOH Z 406 " =    1.647
peak=    3.733 closest distance to " O   HOH Z 389 " =    1.938
peak=    3.730 closest distance to " O   HOH Z 285 " =    2.447
peak=    3.729 closest distance to " CD  LYS A 166 " =    1.246
peak=    3.718 closest distance to " CD  ARG A 269 " =    0.934
peak=    3.694 closest distance to " O   HOH Z 133 " =    2.496
peak=    3.693 closest distance to " CZ3 TRP A 266 " =    1.151
peak=    3.681 closest distance to " ND2 ASN A 249 " =    0.884
peak=    3.670 closest distance to " CB  TYR A 116 " =    0.813
peak=    3.669 closest distance to " O   HOH Z 368 " =    3.637
peak=    3.668 closest distance to " O   SER A  87 " =    2.250
peak=    3.662 closest distance to " CE1 PHE A 218 " =    0.992
peak=    3.645 closest distance to " O  BHOH Z 338 " =    2.362
peak=    3.642 closest distance to " CB  SER A   3 " =    1.355
peak=    3.637 closest distance to " O   HOH Z 172 " =    3.216
peak=    3.630 closest distance to " O   HOH Z 261 " =    1.921
peak=    3.619 closest distance to " CB  ASN A 110 " =    1.091
peak=    3.613 closest distance to " CB  GLN A  88 " =    1.216
peak=    3.603 closest distance to " O   HOH Z 371 " =    2.966
peak=    3.602 closest distance to " CB  SER A 210 " =    0.742
peak=    3.598 closest distance to " CB  PRO A  90 " =    1.118
peak=    3.593 closest distance to " O   HOH Z 193 " =    1.724
peak=    3.590 closest distance to " CA  ARG A  36 " =    1.094
peak=    3.589 closest distance to " N   ASN A 127 " =    1.302
peak=    3.588 closest distance to " O   HOH Z 291 " =    1.607
peak=    3.580 closest distance to " CG2AVAL A  72 " =    1.616
peak=    3.577 closest distance to " O   HOH Z  43 " =    1.907
peak=    3.568 closest distance to " CB  VAL A 202 " =    1.636
peak=    3.567 closest distance to " O   HOH Z 353 " =    2.627
peak=    3.552 closest distance to " N   ARG A 156 " =    1.365
peak=    3.548 closest distance to " CG1 VAL A 153 " =    0.979
peak=    3.545 closest distance to " CB  MET A  40 " =    0.803
peak=    3.543 closest distance to " O   HOH Z 280 " =    3.018
peak=    3.541 closest distance to " O   HOH Z 419 " =    2.134
peak=    3.536 closest distance to " CB  ALA A  34 " =    0.907
peak=    3.532 closest distance to " NE2 HIS A 207 " =    1.255
peak=    3.526 closest distance to " CB  SER A 216 " =    0.862
peak=    3.523 closest distance to " CD2 LEU A 297 " =    0.875
peak=    3.517 closest distance to " CD BLYS A 290 " =    0.975
peak=    3.511 closest distance to " O   HOH Z 329 " =    4.066
peak=    3.502 closest distance to " O   HOH Z 185 " =    1.899
peak=    3.500 closest distance to " CA  ALA A 158 " =    1.220
peak=    3.496 closest distance to " N   ASN A  39 " =    1.318
peak=    3.494 closest distance to " O   HOH Z  88 " =    3.927
peak=    3.494 closest distance to " O   HOH Z  68 " =    2.183
peak=    3.494 closest distance to " O   HOH Z 426 " =    1.922
peak=    3.494 closest distance to " O   HOH Z 411 " =    3.801
peak=    3.493 closest distance to " O   HOH Z 166 " =    3.933
peak=    3.492 closest distance to " O   TYR A 116 " =    1.331
peak=    3.486 closest distance to " O   HOH Z 148 " =    3.437
peak=    3.483 closest distance to " O   HOH Z 209 " =    2.301
peak=    3.482 closest distance to " N   PHE A 130 " =    1.215
peak=    3.477 closest distance to " O   HOH Z 132 " =    2.659
peak=    3.474 closest distance to " O   HOH Z   9 " =    1.941
peak=    3.474 closest distance to " CE1 PHE A  38 " =    1.228
peak=    3.460 closest distance to " O   HOH Z  88 " =    3.497
peak=    3.457 closest distance to " CA  THR A 221 " =    1.064
peak=    3.453 closest distance to " CB  ALA A   1 " =    4.794
peak=    3.447 closest distance to " CA  TYR A 116 " =    1.342
peak=    3.445 closest distance to " O   HOH Z 391 " =    2.900
peak=    3.443 closest distance to " O   HOH Z 218 " =    4.616
peak=    3.441 closest distance to " CG2 ILE A 120 " =    1.227
peak=    3.440 closest distance to " O   HOH Z 234 " =    1.832
peak=    3.440 closest distance to " CE1 TYR A 186 " =    1.366
peak=    3.436 closest distance to " CG2 THR A 221 " =    1.020
peak=    3.434 closest distance to " ND1 HIS A  86 " =    1.722
peak=    3.433 closest distance to " CB  LYS A 117 " =    1.204
peak=    3.428 closest distance to " O   HOH Z 128 " =    2.306
peak=    3.425 closest distance to " O   ASN A  74 " =    1.466
peak=    3.423 closest distance to " CB  ILE A 120 " =    1.268
peak=    3.413 closest distance to " CG1 ILE A  33 " =    1.238
peak=    3.407 closest distance to " CA  ASN A 217 " =    1.221
peak=    3.406 closest distance to " CG1 VAL A 189 " =    2.050
peak=    3.401 closest distance to " CD2 LEU A 255 " =    1.688
peak=    3.400 closest distance to " NH2BARG A 145 " =    2.167
peak=    3.400 closest distance to " CA  ALA A 233 " =    1.340
peak=    3.397 closest distance to " O   HOH Z 325 " =    4.036
peak=    3.393 closest distance to " CB  ALA A 291 " =    1.239
peak=    3.389 closest distance to " O   HOH Z 213 " =    2.066
peak=    3.387 closest distance to " O   HOH Z 294 " =    1.535
peak=    3.383 closest distance to " CA  ALA A 160 " =    0.995
peak=    3.380 closest distance to " CG  GLN A  11 " =    1.650
peak=    3.375 closest distance to " OD2 ASP A 286 " =    2.912
peak=    3.373 closest distance to " CA  VAL A 125 " =    1.099
peak=    3.369 closest distance to " CD1 LEU A  96 " =    0.743
peak=    3.369 closest distance to " O   THR A 251 " =    1.120
peak=    3.366 closest distance to " NH2AARG A 275 " =    3.641
peak=    3.364 closest distance to " OG BSER A 164 " =    2.386
peak=    3.364 closest distance to " CA  ALA A 154 " =    1.020
peak=    3.364 closest distance to " NH2 ARG A 156 " =    1.202
peak=    3.363 closest distance to " CA  MET A 105 " =    1.005
peak=    3.362 closest distance to " O   THR A 220 " =    1.290
peak=    3.359 closest distance to " O   HOH Z 248 " =    1.641
peak=    3.359 closest distance to " O   HOH Z 116 " =    3.099
peak=    3.351 closest distance to " O   HOH Z 403 " =    1.495
peak=    3.349 closest distance to " CB  LEU A  83 " =    0.753
peak=    3.345 closest distance to " O   MET A 105 " =    1.883
peak=    3.341 closest distance to " CB  ARG A 138 " =    1.014
peak=    3.332 closest distance to " CB  MET A  47 " =    0.989
peak=    3.329 closest distance to " O   HOH Z 273 " =    2.873
peak=    3.329 closest distance to " CA  MET A  40 " =    1.206
peak=    3.327 closest distance to " CB  ARG A 139 " =    1.001
peak=    3.325 closest distance to " CB  TRP A 179 " =    1.520
peak=    3.320 closest distance to " CB  THR A  82 " =    1.433
peak=    3.319 closest distance to " OG  SER A  22 " =    2.780
peak=    3.318 closest distance to " O   HOH Z 305 " =    3.571
peak=    3.312 closest distance to " O   HOH Z 421 " =    2.067
peak=    3.311 closest distance to " O   HOH Z 371 " =    1.843
peak=    3.308 closest distance to " O   HOH Z 409 " =    2.780
peak=    3.304 closest distance to " O   HOH Z 422 " =    2.745
peak=    3.301 closest distance to " O   HOH Z 345 " =    1.781
peak=    3.299 closest distance to " CG  MET A 185 " =    1.176
peak=    3.297 closest distance to " CD1 ILE A 106 " =    0.761
peak=    3.293 closest distance to " O   HOH Z  59 " =    1.907
peak=    3.291 closest distance to " O   HOH Z   1 " =    1.672
peak=    3.290 closest distance to " O   HOH Z 171 " =    4.097
peak=    3.285 closest distance to " O   HOH Z 365 " =    2.936
peak=    3.284 closest distance to " CB  GLN A  89 " =    1.303
peak=    3.280 closest distance to " O   HOH Z 147 " =    1.839
peak=    3.280 closest distance to " CA  ALA A 291 " =    0.825
peak=    3.279 closest distance to " O   HOH Z 193 " =    2.039
peak=    3.279 closest distance to " CB  ALA A 248 " =    0.940
peak=    3.270 closest distance to " CG2 ILE A  20 " =    1.464
peak=    3.265 closest distance to " CB  ALA A 242 " =    0.875
peak=    3.264 closest distance to " CB  LEU A 143 " =    1.122
peak=    3.264 closest distance to " CB  THR A 235 " =    1.218
peak=    3.261 closest distance to " O   HOH Z 425 " =    1.232
peak=    3.251 closest distance to " CB  ALA A 114 " =    0.767
peak=    3.250 closest distance to " O   HOH Z 344 " =    3.207
peak=    3.250 closest distance to " O   HOH Z 359 " =    1.421
peak=    3.248 closest distance to " CD  ARG A 219 " =    1.128
peak=    3.243 closest distance to " CB  LYS A 193 " =    1.032
peak=    3.234 closest distance to " CA  ARG A 102 " =    1.124
peak=    3.234 closest distance to " CZ2 TRP A 179 " =    1.747
peak=    3.232 closest distance to " CB  LEU A  96 " =    1.296
peak=    3.231 closest distance to " OD1BASN A 224 " =    2.359
peak=    3.220 closest distance to " CA  ALA A 100 " =    1.144
peak=    3.218 closest distance to " O   HOH Z 325 " =    2.502
peak=    3.217 closest distance to " O   HOH Z 384 " =    3.089
peak=    3.216 closest distance to " O   HOH Z 135 " =    1.693
peak=    3.214 closest distance to " O   HOH Z 287 " =    2.295
peak=    3.214 closest distance to " O   HOH Z 282 " =    1.864
peak=    3.212 closest distance to " CA  ALA A  21 " =    1.187
peak=    3.208 closest distance to " CA  ILE A 234 " =    0.981
peak=    3.208 closest distance to " O   HOH Z 126 " =    1.607
peak=    3.207 closest distance to " O   HOH Z 132 " =    3.268
peak=    3.207 closest distance to " CB  ALA A   9 " =    1.596
peak=    3.207 closest distance to " O   HOH Z 245 " =    1.237
peak=    3.203 closest distance to " O   HOH Z 423 " =    1.737
peak=    3.200 closest distance to " O   HOH Z 403 " =    1.627
peak=    3.199 closest distance to " O   HOH Z 188 " =    1.935
peak=    3.199 closest distance to " O   HOH Z 163 " =    1.827
peak=    3.192 closest distance to " O   ASN A 209 " =    1.245
peak=    3.190 closest distance to " NZ  LYS A  48 " =    1.334
peak=    3.185 closest distance to " O   HOH Z  61 " =    1.456
peak=    3.178 closest distance to " O   HOH Z 285 " =    1.916
peak=    3.176 closest distance to " CG1 ILE A 151 " =    1.072
peak=    3.171 closest distance to " O   HOH Z 213 " =    2.617
peak=    3.169 closest distance to " CB  SER A  26 " =    1.739
peak=    3.168 closest distance to " O   HOH Z 248 " =    1.615
peak=    3.164 closest distance to " NE  ARG A  79 " =    1.124
peak=    3.163 closest distance to " O   HOH Z 407 " =    2.444
peak=    3.160 closest distance to " O   HOH Z 124 " =    1.835
peak=    3.160 closest distance to " O   PHE A 192 " =    1.373
peak=    3.156 closest distance to " O   HOH Z 417 " =    3.427
peak=    3.155 closest distance to " CA  GLU A  46 " =    0.823
peak=    3.155 closest distance to " O   HOH Z 203 " =    1.818
peak=    3.153 closest distance to " CB  ASP A 298 " =    1.157
peak=    3.152 closest distance to " CB  ASN A 215 " =    1.136
peak=    3.150 closest distance to " O   ALA A 158 " =    1.319
peak=    3.149 closest distance to " CG  GLU A  37 " =    0.843
peak=    3.140 closest distance to " O   HOH Z 128 " =    2.200
peak=    3.139 closest distance to " CB  VAL A 265 " =    1.980
peak=    3.138 closest distance to " ND2 ASN A 110 " =    1.623
peak=    3.138 closest distance to " OG BSER A 134 " =    2.934
peak=    3.137 closest distance to " O   SER A 164 " =    1.447
peak=    3.137 closest distance to " CB  ASN A 224 " =    0.980
peak=    3.136 closest distance to " CG  GLN A  89 " =    1.517
peak=    3.127 closest distance to " CB  GLN A 103 " =    0.855
peak=    3.126 closest distance to " O   HOH Z 332 " =    1.525
peak=    3.126 closest distance to " CB  PHE A 204 " =    0.707
peak=    3.121 closest distance to " O   HOH Z 227 " =    1.803
peak=    3.117 closest distance to " O   HOH Z 383 " =    2.140
peak=    3.109 closest distance to " N   GLY A  98 " =    1.104
peak=    3.104 closest distance to " CA  ARG A 159 " =    1.253
peak=    3.101 closest distance to " O   PHE A  61 " =    1.347
peak=    3.100 closest distance to " CD1 ILE A 263 " =    1.333
peak=    3.099 closest distance to " OG BSER A  99 " =    2.243
peak=    3.098 closest distance to " O   HOH Z 327 " =    1.750
peak=    3.096 closest distance to " O   HOH Z 271 " =    2.834
peak=    3.095 closest distance to " O   HOH Z 152 " =    2.301
peak=    3.089 closest distance to " CG  ARG A 159 " =    0.870
peak=    3.083 closest distance to " CB  ALA A 291 " =    0.776
peak=    3.081 closest distance to " O   HOH Z 116 " =    1.786
peak=    3.071 closest distance to " O   HOH Z 345 " =    3.527
peak=    3.059 closest distance to " O   HOH Z 261 " =    1.706
peak=    3.052 closest distance to " CA  ALA A 299 " =    0.955
peak=    3.052 closest distance to " CG BARG A 102 " =    1.850
peak=    3.051 closest distance to " NH1 ARG A 138 " =    1.045
peak=    3.050 closest distance to " O   HOH Z 175 " =    2.178
peak=    3.049 closest distance to " CG2 ILE A 234 " =    0.824
peak=    3.010 closest distance to " O   GLN A 278 " =    1.531

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.719 - 5.725
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 204
   mapped sites are within: 0.719 - 5.725

peak=   -4.537 closest distance to " CD  ARG A  14 " =    3.478
peak=   -4.533 closest distance to " CB  PRO A 243 " =    2.631
peak=   -4.513 closest distance to " CG1 VAL A 112 " =    2.682
peak=   -4.411 closest distance to " CD  GLN A  58 " =    0.916
peak=   -4.365 closest distance to " O   HOH Z 231 " =    2.255
peak=   -4.335 closest distance to " O   HOH Z 377 " =    2.062
peak=   -4.266 closest distance to " O   VAL A  67 " =    2.722
peak=   -4.252 closest distance to " CZ3 TRP A 179 " =    1.173
peak=   -4.246 closest distance to " CD  ARG A 156 " =    2.078
peak=   -4.209 closest distance to " O   PRO A 198 " =    1.287
peak=   -4.174 closest distance to " O   HOH Z 266 " =    5.415
peak=   -4.130 closest distance to " O   HOH Z  73 " =    2.169
peak=   -4.117 closest distance to " OG BSER A 134 " =    1.296
peak=   -4.089 closest distance to " N   ALA A  43 " =    2.614
peak=   -4.074 closest distance to " CG  GLN A 223 " =    2.078
peak=   -3.999 closest distance to " CG1 VAL A 112 " =    2.919
peak=   -3.997 closest distance to " O   HOH Z 389 " =    2.107
peak=   -3.961 closest distance to " C   HIS A 108 " =    1.126
peak=   -3.933 closest distance to " CE2 TYR A  30 " =    2.768
peak=   -3.915 closest distance to " CB  ALA A  43 " =    2.603
peak=   -3.893 closest distance to " O   HOH Z 290 " =    1.221
peak=   -3.890 closest distance to " O   HOH Z 351 " =    1.480
peak=   -3.887 closest distance to " OG  SER A  97 " =    2.270
peak=   -3.881 closest distance to " CD1 PHE A  59 " =    1.892
peak=   -3.846 closest distance to " O   HOH Z 372 " =    2.431
peak=   -3.821 closest distance to " O   HOH Z 394 " =    1.500
peak=   -3.820 closest distance to " CD2 TYR A 293 " =    1.999
peak=   -3.809 closest distance to " CD2 PHE A 192 " =    2.077
peak=   -3.800 closest distance to " O   HOH Z 185 " =    2.289
peak=   -3.779 closest distance to " NH2AARG A 275 " =    5.501
peak=   -3.775 closest distance to " O   HOH Z  38 " =    1.414
peak=   -3.766 closest distance to " CE BMET A  47 " =    1.484
peak=   -3.766 closest distance to " CE2 PHE A  61 " =    2.650
peak=   -3.739 closest distance to " OXT GLY A 302 " =    3.005
peak=   -3.728 closest distance to " CG2 ILE A  49 " =    2.782
peak=   -3.711 closest distance to " O   HOH Z 198 " =    2.037
peak=   -3.711 closest distance to " CE  MET A 105 " =    2.459
peak=   -3.709 closest distance to " O   HOH Z 435 " =    2.888
peak=   -3.698 closest distance to " O   HOH Z  10 " =    1.493
peak=   -3.695 closest distance to " CG1 VAL A 250 " =    2.673
peak=   -3.692 closest distance to " CB  ALA A 291 " =    2.271
peak=   -3.659 closest distance to " O   HOH Z 407 " =    3.247
peak=   -3.655 closest distance to " OD1 ASP A 171 " =    1.675
peak=   -3.655 closest distance to " CA  GLY A 241 " =    2.325
peak=   -3.654 closest distance to " CB  ASN A  39 " =    2.271
peak=   -3.639 closest distance to " O   TYR A 247 " =    2.865
peak=   -3.639 closest distance to " CA  VAL A  67 " =    2.901
peak=   -3.629 closest distance to " O   HOH Z 313 " =    1.904
peak=   -3.620 closest distance to " O   HOH Z  52 " =    1.437
peak=   -3.594 closest distance to " O   HOH Z 196 " =    2.066
peak=   -3.579 closest distance to " OD1 ASN A 148 " =    1.500
peak=   -3.577 closest distance to " CB  TRP A  85 " =    2.490
peak=   -3.576 closest distance to " ND2 ASN A  45 " =    1.175
peak=   -3.572 closest distance to " CG2 THR A 178 " =    2.331
peak=   -3.572 closest distance to " O   HOH Z  51 " =    1.571
peak=   -3.571 closest distance to " O   HOH Z 114 " =    3.096
peak=   -3.562 closest distance to " N   THR A 157 " =    1.582
peak=   -3.560 closest distance to " O   VAL A 189 " =    2.607
peak=   -3.559 closest distance to " CG  ARG A 269 " =    2.382
peak=   -3.555 closest distance to " ND2 ASN A  45 " =    1.856
peak=   -3.549 closest distance to " CA  GLY A 203 " =    2.435
peak=   -3.546 closest distance to " CE3 TRP A 150 " =    2.151
peak=   -3.545 closest distance to " CG2 ILE A 263 " =    2.334
peak=   -3.539 closest distance to " O   HOH Z  60 " =    2.357
peak=   -3.531 closest distance to " O   ALA A  10 " =    1.682
peak=   -3.516 closest distance to " C   LEU A 222 " =    0.773
peak=   -3.504 closest distance to " C   ASN A 285 " =    2.445
peak=   -3.504 closest distance to " CA  ASP A 298 " =    1.071
peak=   -3.501 closest distance to " O   PRO A 163 " =    2.086
peak=   -3.498 closest distance to " ND2 ASN A  60 " =    1.576
peak=   -3.492 closest distance to " ND2 ASN A 249 " =    2.377
peak=   -3.480 closest distance to " O   PHE A 218 " =    1.560
peak=   -3.476 closest distance to " CG1 VAL A 125 " =    1.940
peak=   -3.467 closest distance to " CD1 LEU A 101 " =    2.360
peak=   -3.465 closest distance to " CG  PHE A 283 " =    2.665
peak=   -3.460 closest distance to " O   HOH Z 211 " =    1.477
peak=   -3.459 closest distance to " O   HOH Z 359 " =    3.167
peak=   -3.447 closest distance to " C   GLY A  17 " =    1.195
peak=   -3.445 closest distance to " C   MET A 188 " =    1.408
peak=   -3.444 closest distance to " CB  ASP A 286 " =    2.104
peak=   -3.429 closest distance to " CA  GLY A 241 " =    3.310
peak=   -3.420 closest distance to " CD  ARG A 139 " =    1.575
peak=   -3.418 closest distance to " NE2 GLN A 194 " =    1.847
peak=   -3.417 closest distance to " NH2 ARG A  79 " =    1.532
peak=   -3.408 closest distance to " CD2 PHE A  61 " =    2.077
peak=   -3.401 closest distance to " CB  ALA A 291 " =    2.211
peak=   -3.398 closest distance to " OE1 GLN A  88 " =    1.068
peak=   -3.397 closest distance to " CA  SER A 135 " =    1.309
peak=   -3.394 closest distance to " O   ARG A 145 " =    1.615
peak=   -3.388 closest distance to " CB  GLN A  11 " =    1.738
peak=   -3.385 closest distance to " O   HOH Z 253 " =    3.998
peak=   -3.381 closest distance to " CG  GLU A 277 " =    1.187
peak=   -3.379 closest distance to " CD  ARG A 195 " =    5.169
peak=   -3.375 closest distance to " OD1 ASP A 191 " =    1.831
peak=   -3.369 closest distance to " CG  MET A 105 " =    0.961
peak=   -3.363 closest distance to " O   HOH Z   6 " =    1.409
peak=   -3.362 closest distance to " NH2 ARG A 159 " =    2.391
peak=   -3.361 closest distance to " O   HOH Z 128 " =    2.632
peak=   -3.360 closest distance to " O   HOH Z 174 " =    2.619
peak=   -3.358 closest distance to " O   HOH Z 198 " =    1.474
peak=   -3.357 closest distance to " O   HOH Z 353 " =    2.158
peak=   -3.356 closest distance to " O   TRP A  70 " =    1.414
peak=   -3.354 closest distance to " O   HOH Z 295 " =    1.641
peak=   -3.350 closest distance to " N   ALA A 248 " =    1.584
peak=   -3.349 closest distance to " OD1AASN A 224 " =    1.765
peak=   -3.348 closest distance to " C   LEU A 143 " =    1.187
peak=   -3.337 closest distance to " O   HOH Z 357 " =    2.081
peak=   -3.336 closest distance to " ND2BASN A 224 " =    1.780
peak=   -3.335 closest distance to " O   HOH Z 426 " =    1.603
peak=   -3.332 closest distance to " O   HOH Z  43 " =    1.676
peak=   -3.326 closest distance to " O   HOH Z  11 " =    1.704
peak=   -3.324 closest distance to " NH2BARG A 275 " =    1.885
peak=   -3.322 closest distance to " CA  GLY A 241 " =    2.865
peak=   -3.314 closest distance to " CG1BVAL A  41 " =    2.780
peak=   -3.312 closest distance to " O   HOH Z 243 " =    1.950
peak=   -3.309 closest distance to " ND2 ASN A  60 " =    4.136
peak=   -3.307 closest distance to " O   HOH Z 166 " =    1.941
peak=   -3.299 closest distance to " C   ALA A 158 " =    1.499
peak=   -3.298 closest distance to " NE2 GLN A  88 " =    1.904
peak=   -3.288 closest distance to " CB  ALA A 248 " =    2.181
peak=   -3.287 closest distance to " O   VAL A 189 " =    1.572
peak=   -3.285 closest distance to " CB  ALA A 248 " =    2.473
peak=   -3.285 closest distance to " CD1 LEU A   5 " =    2.633
peak=   -3.280 closest distance to " O   HOH Z 176 " =    0.838
peak=   -3.273 closest distance to " N   ASP A 171 " =    2.339
peak=   -3.272 closest distance to " O   HOH Z 103 " =    1.864
peak=   -3.271 closest distance to " O   HOH Z 298 " =    1.262
peak=   -3.267 closest distance to " O   ALA A  34 " =    2.555
peak=   -3.264 closest distance to " CB  ASP A 132 " =    2.272
peak=   -3.260 closest distance to " CD1 LEU A 228 " =    2.372
peak=   -3.259 closest distance to " CD  GLN A 223 " =    0.719
peak=   -3.259 closest distance to " O   HOH Z 311 " =    3.799
peak=   -3.259 closest distance to " CG1 VAL A 197 " =    2.278
peak=   -3.258 closest distance to " O   HOH Z 348 " =    2.252
peak=   -3.258 closest distance to " CG  HIS A  86 " =    1.103
peak=   -3.255 closest distance to " CE3 TRP A 274 " =    2.414
peak=   -3.254 closest distance to " O   HOH Z 281 " =    2.722
peak=   -3.252 closest distance to " O   HOH Z 191 " =    5.725
peak=   -3.249 closest distance to " OD1 ASN A 187 " =    1.563
peak=   -3.247 closest distance to " CB  PRO A 163 " =    2.493
peak=   -3.247 closest distance to " CB  PRO A  54 " =    2.508
peak=   -3.243 closest distance to " CB  ALA A 100 " =    2.195
peak=   -3.241 closest distance to " N   THR A  52 " =    1.716
peak=   -3.236 closest distance to " O   HOH Z 126 " =    1.921
peak=   -3.235 closest distance to " CZ  PHE A 155 " =    1.232
peak=   -3.231 closest distance to " CB  ALA A   9 " =    2.450
peak=   -3.230 closest distance to " CG2 ILE A  20 " =    2.902
peak=   -3.226 closest distance to " O   GLY A 211 " =    1.388
peak=   -3.224 closest distance to " O   HOH Z 298 " =    2.509
peak=   -3.220 closest distance to " O   HOH Z 232 " =    1.682
peak=   -3.217 closest distance to " OH  TYR A 247 " =    2.107
peak=   -3.216 closest distance to " O   HOH Z 275 " =    1.780
peak=   -3.206 closest distance to " O   PRO A 198 " =    1.354
peak=   -3.205 closest distance to " CG  TRP A 266 " =    1.792
peak=   -3.204 closest distance to " NE2 GLN A 278 " =    1.639
peak=   -3.203 closest distance to " CD1 LEU A 297 " =    2.501
peak=   -3.203 closest distance to " O   HOH Z 134 " =    3.039
peak=   -3.201 closest distance to " CZ  PHE A  38 " =    2.063
peak=   -3.201 closest distance to " O   HOH Z 421 " =    3.039
peak=   -3.200 closest distance to " N   SER A 212 " =    1.946
peak=   -3.191 closest distance to " OD2 ASP A 191 " =    1.508
peak=   -3.187 closest distance to " O   HOH Z 106 " =    1.910
peak=   -3.187 closest distance to " CA  ASN A 110 " =    2.435
peak=   -3.183 closest distance to " O   GLN A 240 " =    2.124
peak=   -3.182 closest distance to " CD2 TYR A 247 " =    2.465
peak=   -3.181 closest distance to " O   HOH Z 241 " =    1.406
peak=   -3.180 closest distance to " O   SER A 135 " =    1.414
peak=   -3.179 closest distance to " CG2 VAL A 189 " =    2.073
peak=   -3.178 closest distance to " O   HOH Z  71 " =    2.024
peak=   -3.176 closest distance to " ND2 ASN A 187 " =    1.524
peak=   -3.172 closest distance to " C   SER A 206 " =    1.512
peak=   -3.165 closest distance to " O   HOH Z 262 " =    2.931
peak=   -3.164 closest distance to " CB  ALA A 129 " =    2.420
peak=   -3.163 closest distance to " O   HOH Z  22 " =    2.497
peak=   -3.163 closest distance to " CZ  TYR A 169 " =    1.700
peak=   -3.163 closest distance to " CE2 PHE A 218 " =    2.437
peak=   -3.160 closest distance to " SD  MET A 188 " =    2.290
peak=   -3.158 closest distance to " O   HOH Z 114 " =    1.480
peak=   -3.153 closest distance to " CB  ASN A 252 " =    1.618
peak=   -3.151 closest distance to " CD  ARG A  79 " =    1.153
peak=   -3.143 closest distance to " CE  LYS A  76 " =    2.579
peak=   -3.134 closest distance to " O   HOH Z 266 " =    5.102
peak=   -3.133 closest distance to " O   HOH Z 189 " =    2.000
peak=   -3.128 closest distance to " O   GLN A 240 " =    2.543
peak=   -3.127 closest distance to " O   HOH Z 111 " =    1.458
peak=   -3.122 closest distance to " OG BSER A 134 " =    1.779
peak=   -3.113 closest distance to " O   HOH Z 140 " =    1.687
peak=   -3.112 closest distance to " O   HOH Z 111 " =    2.136
peak=   -3.109 closest distance to " CB  TYR A  15 " =    2.237
peak=   -3.099 closest distance to " OH  TYR A 247 " =    1.871
peak=   -3.097 closest distance to " O   HOH Z 278 " =    1.652
peak=   -3.094 closest distance to " CD1 ILE A 199 " =    2.585
peak=   -3.090 closest distance to " N   SER A 276 " =    1.276
peak=   -3.076 closest distance to " O   HOH Z 409 " =    4.667
peak=   -3.075 closest distance to " O   HOH Z 123 " =    2.579
peak=   -3.069 closest distance to " NH1 ARG A  36 " =    2.020
peak=   -3.068 closest distance to " N   LYS A 166 " =    1.984
peak=   -3.065 closest distance to " OG  SER A 206 " =    1.859
peak=   -3.059 closest distance to " SG ACYS A 201 " =    1.949
peak=   -3.056 closest distance to " O   HOH Z 247 " =    2.011
peak=   -3.053 closest distance to " O   HOH Z 216 " =    1.613
peak=   -3.034 closest distance to " O   HOH Z 350 " =    1.998
peak=   -3.032 closest distance to " O   HOH Z 412 " =    4.398
peak=   -3.008 closest distance to " CG  ARG A 269 " =    2.035

================= 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    :  0.3330 0.3216   6.057946e+00   6.036714e+00
   1_bss:  0.3201 0.3115   6.035199e+00   6.011146e+00
   1_xyz:  0.1753 0.2008   5.489467e+00   5.588426e+00
   1_adp:  0.1623 0.2054   5.444604e+00   5.616067e+00
   1_occ:  0.1619 0.2049   5.442339e+00   5.614654e+00
   2_bss:  0.1602 0.2023   5.438748e+00   5.611339e+00
   2_xyz:  0.1310 0.1685   5.258446e+00   5.455067e+00
   2_adp:  0.1237 0.1655   5.217710e+00   5.430249e+00
   2_occ:  0.1236 0.1654   5.217433e+00   5.430371e+00
   3_bss:  0.1235 0.1650   5.216446e+00   5.428461e+00
   3_xyz:  0.1180 0.1603   5.184610e+00   5.405287e+00
   3_adp:  0.1175 0.1590   5.178831e+00   5.397784e+00
   3_occ:  0.1174 0.1590   5.178794e+00   5.397996e+00
   4_bss:  0.1174 0.1589   5.178766e+00   5.398036e+00
   4_xyz:  0.1100 0.1573   5.138731e+00   5.383738e+00
   4_adp:  0.1090 0.1574   5.134261e+00   5.383346e+00
   4_occ:  0.1090 0.1574   5.134413e+00   5.383644e+00
   5_bss:  0.1089 0.1573   5.134497e+00   5.383662e+00
   5_xyz:  0.1105 0.1581   5.146506e+00   5.392848e+00
   5_adp:  0.1105 0.1584   5.146381e+00   5.394249e+00
   5_occ:  0.1105 0.1584   5.146574e+00   5.394635e+00
   5_bss:  0.1104 0.1583   5.146531e+00   5.394834e+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:  0.329  63.693  -1.788  -2.559   2.347  -0.000   0.000   0.000
   1_xyz:  0.329  63.693  -1.788  -2.559   2.347  -0.000   0.000   0.000
   1_adp:  0.329  63.693  -1.788  -2.559   2.347  -0.000   0.000   0.000
   1_occ:  0.329  63.693  -1.788  -2.559   2.347  -0.000   0.000   0.000
   2_bss:  0.336  66.713  -2.537  -2.846  -0.281  -0.000  -0.000  -0.000
   2_xyz:  0.336  66.713  -2.537  -2.846  -0.281  -0.000  -0.000  -0.000
   2_adp:  0.336  66.713  -2.537  -2.846  -0.281  -0.000  -0.000  -0.000
   2_occ:  0.336  66.713  -2.537  -2.846  -0.281  -0.000  -0.000  -0.000
   3_bss:  0.336  66.713  -2.462  -2.615  -0.610  -0.000  -0.000  -0.000
   3_xyz:  0.336  66.713  -2.462  -2.615  -0.610  -0.000  -0.000  -0.000
   3_adp:  0.336  66.713  -2.462  -2.615  -0.610  -0.000  -0.000  -0.000
   3_occ:  0.336  66.713  -2.462  -2.615  -0.610  -0.000  -0.000  -0.000
   4_bss:  0.336  66.713  -2.349  -2.464  -0.682  -0.000  -0.000  -0.000
   4_xyz:  0.336  66.713  -2.349  -2.464  -0.682  -0.000  -0.000  -0.000
   4_adp:  0.336  66.713  -2.349  -2.464  -0.682  -0.000  -0.000  -0.000
   4_occ:  0.336  66.713  -2.349  -2.464  -0.682  -0.000  -0.000  -0.000
   5_bss:  0.336  66.713  -2.120  -2.226  -0.504  -0.000  -0.000  -0.000
   5_xyz:  0.336  66.713  -2.120  -2.226  -0.504  -0.000  -0.000  -0.000
   5_adp:  0.336  66.713  -2.120  -2.226  -0.504  -0.000  -0.000  -0.000
   5_occ:  0.336  66.713  -2.120  -2.226  -0.504  -0.000  -0.000  -0.000
   5_bss:  0.321  59.145  -1.924  -2.022  -0.321  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  33.385 0.7230  0.8821    29141.450
   1_bss:  32.263 0.7341  0.8795    26618.898
   1_xyz:  18.491 0.8769  1.0004     9901.554
   1_adp:  19.241 0.8693  0.9943    10386.290
   1_occ:  19.201 0.8696  0.9941    10331.920
   2_bss:  19.030 0.8716  0.9542    10315.737
   2_xyz:  15.480 0.9027  0.9700     7309.890
   2_adp:  14.926 0.9075  0.9679     6952.968
   2_occ:  14.925 0.9075  0.9678     6952.857
   3_bss:  14.893 0.9078  0.9674     6919.481
   3_xyz:  14.358 0.9124  0.9683     6602.052
   3_adp:  14.176 0.9140  0.9640     6515.175
   3_occ:  14.182 0.9139  0.9639     6517.977
   4_bss:  14.181 0.9139  0.9661     6518.821
   4_xyz:  13.922 0.9158  0.9690     6372.684
   4_adp:  13.912 0.9159  0.9633     6344.688
   4_occ:  13.917 0.9159  0.9632     6349.139
   5_bss:  13.920 0.9159  0.9705     6350.559
   5_xyz:  14.055 0.9149  0.9693     6480.557
   5_adp:  14.074 0.9148  0.9623     6489.271
   5_occ:  14.082 0.9147  0.9622     6493.949
   5_bss:  14.088 0.9147  0.9682     6490.772
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6144e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6144e-01
   1_xyz:   1.102  0.009  0.075 15.416  0.004  4.115   6.8778e-02
   1_adp:   1.102  0.009  0.075 15.416  0.004  4.115   6.8778e-02
   1_occ:   1.102  0.009  0.075 15.416  0.004  4.115   6.8778e-02
   2_bss:   1.102  0.009  0.075 15.416  0.004  4.115   6.8778e-02
   2_xyz:   0.958  0.007  0.072 14.866  0.003  4.125   5.5451e-02
   2_adp:   0.958  0.007  0.072 14.866  0.003  4.125   5.5451e-02
   2_occ:   0.958  0.007  0.072 14.866  0.003  4.125   5.5451e-02
   3_bss:   0.958  0.007  0.072 14.866  0.003  4.125   5.5451e-02
   3_xyz:   0.917  0.007  0.071 14.674  0.003  4.114   5.2363e-02
   3_adp:   0.917  0.007  0.071 14.674  0.003  4.114   5.2363e-02
   3_occ:   0.917  0.007  0.071 14.674  0.003  4.114   5.2363e-02
   4_bss:   0.917  0.007  0.071 14.674  0.003  4.114   5.2363e-02
   4_xyz:   1.116  0.011  0.086 15.033  0.004  4.119   7.7154e-02
   4_adp:   1.116  0.011  0.086 15.033  0.004  4.119   7.7154e-02
   4_occ:   1.116  0.011  0.086 15.033  0.004  4.119   7.7154e-02
   5_bss:   1.116  0.011  0.086 15.033  0.004  4.119   7.7154e-02
   5_xyz:   1.016  0.009  0.079 14.811  0.004  4.119   6.4587e-02
   5_adp:   1.016  0.009  0.079 14.811  0.004  4.119   6.4587e-02
   5_occ:   1.016  0.009  0.079 14.811  0.004  4.119   6.4587e-02
   5_bss:   1.016  0.009  0.079 14.811  0.004  4.119   6.4587e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4269e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4269e-01
   1_xyz:   8.447  0.048  0.251 83.086  0.042  2.299   5.3487e-02
   1_adp:   8.447  0.048  0.251 83.086  0.042  2.299   5.3487e-02
   1_occ:   8.447  0.048  0.251 83.086  0.042  2.299   5.3487e-02
   2_bss:   8.447  0.048  0.251 83.086  0.042  2.299   5.3487e-02
   2_xyz:   7.260  0.035  0.224 81.475  0.031  2.345   4.4178e-02
   2_adp:   7.260  0.035  0.224 81.475  0.031  2.345   4.4178e-02
   2_occ:   7.260  0.035  0.224 81.475  0.031  2.345   4.4178e-02
   3_bss:   7.260  0.035  0.224 81.475  0.031  2.345   4.4178e-02
   3_xyz:   7.357  0.040  0.214 83.453  0.035  2.412   3.0343e-02
   3_adp:   7.357  0.040  0.214 83.453  0.035  2.412   3.0343e-02
   3_occ:   7.357  0.040  0.214 83.453  0.035  2.412   3.0343e-02
   4_bss:   7.357  0.040  0.214 83.453  0.035  2.412   3.0343e-02
   4_xyz:   7.170  0.054  0.286 83.503  0.036  2.246   5.9003e-02
   4_adp:   7.170  0.054  0.286 83.503  0.036  2.246   5.9003e-02
   4_occ:   7.170  0.054  0.286 83.503  0.036  2.246   5.9003e-02
   5_bss:   7.170  0.054  0.286 83.503  0.036  2.246   5.9003e-02
   5_xyz:   7.152  0.049  0.250 83.244  0.036  2.376   4.8242e-02
   5_adp:   7.152  0.049  0.250 83.244  0.036  2.376   4.8242e-02
   5_occ:   7.152  0.049  0.250 83.244  0.036  2.376   4.8242e-02
   5_bss:   7.152  0.049  0.250 83.244  0.036  2.376   4.8242e-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:  65.87   0.00  16.48  65.87   0.00  12.61  63.34   5.04  37.57
   1_occ:  65.87   0.00  16.48  65.87   0.00  12.61  63.34   5.04  37.57
   2_bss:  65.87   0.00  16.48  65.87   0.00  12.61  63.34   5.04  37.57
   2_xyz:  65.87   0.00  16.48  65.87   0.00  12.61  63.34   5.04  37.57
   2_adp:  72.10   1.16  16.98  70.06   1.16  12.86  72.10   6.02  39.40
   2_occ:  72.10   1.16  16.98  70.06   1.16  12.86  72.10   6.02  39.40
   3_bss:  72.10   1.16  16.98  70.06   1.16  12.86  72.10   6.02  39.40
   3_xyz:  72.10   1.16  16.98  70.06   1.16  12.86  72.10   6.02  39.40
   3_adp:  72.47   1.22  16.73  71.03   1.22  12.72  72.47   2.93  38.54
   3_occ:  72.47   1.22  16.73  71.03   1.22  12.72  72.47   2.93  38.54
   4_bss:  72.47   1.22  16.73  71.03   1.22  12.72  72.47   2.93  38.54
   4_xyz:  72.47   1.22  16.73  71.03   1.22  12.72  72.47   2.93  38.54
   4_adp:  75.97   0.59  16.76  75.97   0.59  12.64  74.49   3.53  39.19
   4_occ:  75.97   0.59  16.76  75.97   0.59  12.64  74.49   3.53  39.19
   5_bss:  75.97   0.59  16.76  75.97   0.59  12.64  74.49   3.53  39.19
   5_xyz:  75.97   0.59  16.76  75.97   0.59  12.64  74.49   3.53  39.19
   5_adp:  76.68   0.47  16.60  76.68   0.47  12.46  74.59   5.46  39.14
   5_occ:  76.68   0.47  16.60  76.68   0.47  12.46  74.59   5.46  39.14
   5_bss:  76.66   0.45  16.59  76.66   0.45  12.45  74.57   5.45  39.12
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    0.905    0.011    0.318
   1_adp:    0.905    0.011    0.318
   1_occ:    0.905    0.011    0.318
   2_bss:    0.905    0.011    0.318
   2_xyz:    0.879    0.010    0.352
   2_adp:    0.879    0.010    0.352
   2_occ:    0.879    0.010    0.352
   3_bss:    0.879    0.010    0.352
   3_xyz:    0.995    0.032    0.382
   3_adp:    0.995    0.032    0.382
   3_occ:    0.995    0.032    0.382
   4_bss:    0.995    0.032    0.382
   4_xyz:    1.222    0.055    0.394
   4_adp:    1.222    0.055    0.394
   4_occ:    1.222    0.055    0.394
   5_bss:    1.222    0.055    0.394
   5_xyz:    1.329    0.036    0.399
   5_adp:    1.329    0.036    0.399
   5_occ:    1.329    0.036    0.399
   5_bss:    1.329    0.036    0.399
------------------------------------------------------------------------

CPU time actual refinement: 313.59


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_899/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_899/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_899/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_899/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_899/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 313.45 
  Macro-tasks:
    bulk solvent and scale       = 36.49  
    individual site refinement   = 125.28 
    weights calculation          = 28.33  
    collect and process          = 6.47   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 196.67 
  Micro-tasks:
    mask                            = 1.16   
    f_calc                          = 99.37  
    alpha_beta                      = 7.87   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 107.86 
    fmodel                         = 6.65   
    r_factors                      = 0.13   
    phase_errors                   = 11.27  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 235.73 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.491 micro seconds
Total CPU time: 5.44 minutes
from_scatterers_fft:    645 calls, 99.10 s
gradients_fft:          590 calls, 94.81 s

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

# Date 2008-01-16 Time 05:55:31 PST -0800 (1200491731.85 s)
Start R-work = 0.3330, R-free = 0.3216 (no bulk solvent and anisotropic scale)
Final R-work = 0.1324, R-free = 0.1759 (no bulk solvent and anisotropic scale)

Start R-work = 0.3201, R-free = 0.3115
Final R-work = 0.1104, R-free = 0.1583