# Date 2008-01-16 Time 04:20:17 PST -0800 (1200486017.78 s)
#phil __OFF__

Command line arguments: "../271.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 30312
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 271

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 46.2261, 87.2539, 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: (69.1963, 46.2261, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8679 1.97041
Completeness in resolution range: 0.961471
Completeness with d_max=infinity: 0.958507

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8679
                             d_min =   1.9704

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 46.2261, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8679 1.97041
Completeness in resolution range: 0.961471
Completeness with d_max=infinity: 0.958507

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8683 -  4.2159 [2144/2168]  1925   219  10.2%
  bin  2:  4.2159 -  3.3590 [2049/2069]  1847   202   9.9%
  bin  3:  3.3590 -  2.9381 [2033/2052]  1834   199   9.8%
  bin  4:  2.9381 -  2.6712 [1995/2025]  1791   204  10.2%
  bin  5:  2.6712 -  2.4806 [2002/2021]  1801   201  10.0%
  bin  6:  2.4806 -  2.3350 [1996/2021]  1795   201  10.1%
  bin  7:  2.3350 -  2.2184 [1985/2013]  1788   197   9.9%
  bin  8:  2.2184 -  2.1222 [1954/1990]  1758   196  10.0%
  bin  9:  2.1222 -  2.0407 [1963/2005]  1769   194   9.9%
  bin 10:  2.0407 -  1.9704 [1468/2010]  1322   146   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_271/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.59 -     2.25: 25
        2.25 -     2.91: 1473
        2.91 -     3.57: 4555
        3.57 -     4.24: 9292
        4.24 -     4.90: 13287
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.585 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.835 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.851 3.040 -x+1/2,-y+1,z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.858 3.120 -x+1,y+1/2,-z+1/2
  ... (remaining 28627 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_271/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_271/model_refine_001.geo

CPU time processing inputs: 9.17


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 46.22605 87.2539 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: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4065   r_free= 0.4013   ksol= 0.00   Bsol= 0.00   scale= 0.940    |
|                                                                             |
| 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:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.201580                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8683 -  4.7020 0.99   1394  152 0.3221 0.3092      6.4547      6.3901|
|  2:  4.7020 -  3.7519 0.99   1329  154 0.3209 0.3020      6.6152      6.5984|
|  3:  3.7519 -  3.2834 0.99   1307  143 0.3629 0.3482      6.5617      6.5769|
|  4:  3.2834 -  2.9859 0.99   1304  140 0.3867 0.4389      6.4222      6.5208|
|  5:  2.9859 -  2.7733 0.99   1292  147 0.4269 0.3374      6.2769      6.1727|
|  6:  2.7733 -  2.6108 0.99   1301  145 0.4311 0.4676      6.1946      6.1449|
|  7:  2.6108 -  2.4806 0.99   1271  144 0.4398 0.4047      6.1674      6.0595|
|  8:  2.4806 -  2.3731 0.98   1270  136 0.4589 0.4769      6.1336      6.1826|
|  9:  2.3731 -  2.2821 0.98   1281  148 0.4533 0.4651      6.0725      6.1204|
| 10:  2.2821 -  2.2036 1.00   1276  139 0.4704 0.4360      6.0733      5.9848|
| 11:  2.2036 -  2.1349 0.97   1267  134 0.4638 0.5068      5.9947      6.0366|
| 12:  2.1349 -  2.0740 0.98   1250  145 0.4852 0.4560      5.9527      5.9799|
| 13:  2.0740 -  2.0196 1.00   1270  138 0.4680 0.4716      5.8564      5.8001|
| 14:  2.0196 -  1.9704 0.63    818   94 0.4937 0.4837      5.8608      5.7466|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8683 -  4.7020  1394   152  0.77  27.69   0.85     0.81      48026.56|
|  2:  4.7020 -  3.7519  1329   154  0.79  27.33   0.95     0.89      69212.80|
|  3:  3.7519 -  3.2834  1307   143  0.72  33.60   0.97     0.89      74685.71|
|  4:  3.2834 -  2.9859  1304   140  0.66  39.14   0.96     0.84      68651.42|
|  5:  2.9859 -  2.7733  1292   147  0.59  44.32   0.95     0.79      53193.37|
|  6:  2.7733 -  2.6108  1301   145  0.59  45.01   0.94     0.77      46263.15|
|  7:  2.6108 -  2.4806  1271   144  0.57  46.76   0.97     0.76      43406.76|
|  8:  2.4806 -  2.3731  1270   136  0.54  48.86   0.95     0.73      42132.30|
|  9:  2.3731 -  2.2821  1281   148  0.53  49.70   0.97     0.73      39926.46|
| 10:  2.2821 -  2.2036  1276   139  0.52  50.72   0.97     0.74      36693.07|
| 11:  2.2036 -  2.1349  1267   134  0.51  51.64   0.98     0.77      36616.01|
| 12:  2.1349 -  2.0740  1250   145  0.48  54.21   0.98     0.74      34158.65|
| 13:  2.0740 -  2.0196  1270   138  0.46  55.66   0.99     0.68      30548.78|
| 14:  2.0196 -  1.9704   818    94  0.45  56.24   0.99     0.61      25073.99|
|alpha:            min =        0.61 max =            0.89 mean =         0.77|
|beta:             min =    25073.99 max =        74685.71 mean =     47080.27|
|figures of merit: min =        0.00 max =            1.00 mean =         0.59|
|phase err.(work): min =        0.00 max =           90.00 mean =        44.55|
|phase err.(test): min =        0.00 max =           89.84 mean =        44.57|
|-----------------------------------------------------------------------------|

============================== 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 = 6.211434              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.257   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.232484              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.898   (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 |  1.585 -  1.917:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.917 -  2.248:       20 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.248 -  2.580:       54 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.580 -  2.911:     1419 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.911 -  3.243:     1922 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.243 -  3.574:     2633 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.574 -  3.906:     4737 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.906 -  4.237:     4555 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.237 -  4.568:     6076 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.568 -  4.900:     7211 |
|-----------------------------------------------------------------------------|
|-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 |        0.175 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.585 |       0.386 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.597)------------------------------------------|
|    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: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4065   r_free= 0.4013   ksol= 0.00   Bsol= 0.00   scale= 0.940    |
|                                                                             |
| 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:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.201580                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3958   r_free= 0.3917   ksol= 0.33   Bsol= 30.58   scale= 0.971   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.41,1.79,0.12,0.00,0.00,0.00); trace/3= 0.17                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.192891                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.979346              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.018   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.671680              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.634   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3958      final r-factor (work) = 0.2535          |
| start r-factor (free) = 0.3917      final r-factor (free) = 0.2842          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.5785 = 4.98 * 0.50 * 6.1869 + 1.00 * 0.1750                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.9580 = 4.98 * 0.50 * 5.9695 + 1.00 * 0.0960                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2535      final r-factor (work) = 0.2302          |
| start r-factor (free) = 0.2842      final r-factor (free) = 0.2957          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0156 = 0.67 * 1.00 * 5.9695 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8807 = 0.67 * 1.00 * 5.7586 + 1.00 * 0.0128                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.597)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.89   17.80    None  None   None       |
|    all(noH): 2823   0      0.00    86.89   17.80    None  None   None       |
|    Sol.    : 438    0      2.41    86.89   39.73    None  None   None       |
|    Mac.    : 2385   0      0.00    72.00   13.77    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.689:  735   |   5:    43.445 -  52.134:  108        |
|      1:     8.689 -  17.378: 1112   |   6:    52.134 -  60.824:   59        |
|      2:    17.378 -  26.067:  413   |   7:    60.824 -  69.513:   33        |
|      3:    26.067 -  34.756:  197   |   8:    69.513 -  78.202:   13        |
|      4:    34.756 -  43.445:  152   |   9:    78.202 -  86.891:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2302 r_free = 0.2957             target_work(ml) = 5.776         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2300 r_free = 0.2958             target_work(ml) = 5.776         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2300   r_free= 0.2958   ksol= 0.33   Bsol= 30.58   scale= 1.045   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.41,1.79,0.12,0.00,0.00,0.00); trace/3= 0.17                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.776121                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2283   r_free= 0.2939   ksol= 0.34   Bsol= 55.98   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-0.90,-0.58,-0.00,-0.00,-0.00); trace/3= -1.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.772205                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.500984              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.565   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.175093              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.882  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2283      final r-factor (work) = 0.1678          |
| start r-factor (free) = 0.2939      final r-factor (free) = 0.2185          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1896 = 3.50 * 0.50 * 5.7664 + 1.00 * 0.0955                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9447 = 3.50 * 0.50 * 5.6462 + 1.00 * 0.0610                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1678      final r-factor (work) = 0.1556          |
| start r-factor (free) = 0.2185      final r-factor (free) = 0.2018          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0013 = 0.18 * 1.00 * 5.6462 + 1.00 * 0.0127                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9620 = 0.18 * 1.00 * 5.4530 + 1.00 * 0.0072                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.597)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.98    77.99   16.98    None  None   None       |
|    all(noH): 2823   0      0.98    77.99   16.98    None  None   None       |
|    Sol.    : 438    0      6.17    77.99   38.26    None  None   None       |
|    Mac.    : 2385   0      0.98    75.92   13.07    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.981 -   8.683:  664   |   5:    39.488 -  47.189:  114        |
|      1:     8.683 -  16.384: 1264   |   6:    47.189 -  54.891:   87        |
|      2:    16.384 -  24.085:  368   |   7:    54.891 -  62.592:   39        |
|      3:    24.085 -  31.787:  133   |   8:    62.592 -  70.293:    8        |
|      4:    31.787 -  39.488:  139   |   9:    70.293 -  77.995:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1556 r_free = 0.2018             target_work(ml) = 5.414         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1553 r_free = 0.2012             target_work(ml) = 5.412         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1553   r_free= 0.2012   ksol= 0.34   Bsol= 55.98   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-0.90,-0.58,-0.00,-0.00,-0.00); trace/3= -1.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.412477                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1552   r_free= 0.2005   ksol= 0.34   Bsol= 55.98   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.95,-2.02,-0.65,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.408381                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.921976              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.031  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.188653              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.901  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1552      final r-factor (work) = 0.1283          |
| start r-factor (free) = 0.2005      final r-factor (free) = 0.1703          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3013 = 1.92 * 0.50 * 5.4530 + 1.00 * 0.0610                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1646 = 1.92 * 0.50 * 5.3207 + 1.00 * 0.0515                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1283      final r-factor (work) = 0.1234          |
| start r-factor (free) = 0.1703      final r-factor (free) = 0.1658          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0110 = 0.19 * 1.00 * 5.3207 + 1.00 * 0.0072                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9926 = 0.19 * 1.00 * 5.2229 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.597)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.01    79.75   16.84    None  None   None       |
|    all(noH): 2823   0      1.01    79.75   16.84    None  None   None       |
|    Sol.    : 438    0      3.63    76.27   38.65    None  None   None       |
|    Mac.    : 2385   0      1.01    79.75   12.84    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:     1.012 -   8.886:  713   |   5:    40.380 -  48.254:  114        |
|      1:     8.886 -  16.759: 1306   |   6:    48.254 -  56.127:   92        |
|      2:    16.759 -  24.633:  307   |   7:    56.127 -  64.001:   31        |
|      3:    24.633 -  32.506:  121   |   8:    64.001 -  71.875:   14        |
|      4:    32.506 -  40.380:  121   |   9:    71.875 -  79.748:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1234 r_free = 0.1658             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1232 r_free = 0.1659             target_work(ml) = 5.210         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1232   r_free= 0.1659   ksol= 0.34   Bsol= 55.98   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.95,-2.02,-0.65,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.210220                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1233   r_free= 0.1657   ksol= 0.34   Bsol= 55.98   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-2.46,-0.86,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.208998                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.530861              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 121.686  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.324784              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.562  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1233      final r-factor (work) = 0.1162          |
| start r-factor (free) = 0.1657      final r-factor (free) = 0.1577          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0494 = 1.53 * 0.50 * 5.2231 + 1.00 * 0.0515                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0164 = 1.53 * 0.50 * 5.1814 + 1.00 * 0.0504                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1162      final r-factor (work) = 0.1143          |
| start r-factor (free) = 0.1577      final r-factor (free) = 0.1564          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6901 = 0.32 * 1.00 * 5.1814 + 1.00 * 0.0073                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6800 = 0.32 * 1.00 * 5.1478 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.597)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.93    83.81   16.88    None  None   None       |
|    all(noH): 2823   0      0.93    83.81   16.88    None  None   None       |
|    Sol.    : 438    0      3.18    76.85   39.23    None  None   None       |
|    Mac.    : 2385   0      0.93    83.81   12.77    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.927 -   9.215:  847   |   5:    42.367 -  50.656:  109        |
|      1:     9.215 -  17.503: 1223   |   6:    50.656 -  58.944:   81        |
|      2:    17.503 -  25.791:  276   |   7:    58.944 -  67.232:   33        |
|      3:    25.791 -  34.079:  120   |   8:    67.232 -  75.520:    9        |
|      4:    34.079 -  42.367:  121   |   9:    75.520 -  83.808:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1143 r_free = 0.1564             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1143 r_free = 0.1564             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1143   r_free= 0.1564   ksol= 0.34   Bsol= 55.98   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-2.46,-0.86,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.146198                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1142   r_free= 0.1564   ksol= 0.33   Bsol= 55.98   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-2.41,-0.74,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.145913                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.096775              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.446  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.342360              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.410  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1142      final r-factor (work) = 0.1093          |
| start r-factor (free) = 0.1564      final r-factor (free) = 0.1538          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4473 = 2.10 * 0.50 * 5.1479 + 1.00 * 0.0504                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4326 = 2.10 * 0.50 * 5.1260 + 1.00 * 0.0586                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1093      final r-factor (work) = 0.1085          |
| start r-factor (free) = 0.1538      final r-factor (free) = 0.1544          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8890 = 1.34 * 1.00 * 5.1260 + 1.00 * 0.0081                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8766 = 1.34 * 1.00 * 5.1158 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.597)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.17   16.97    None  None   None       |
|    all(noH): 2823   0      0.00    88.17   16.97    None  None   None       |
|    Sol.    : 438    0      4.66    79.51   40.21    None  None   None       |
|    Mac.    : 2385   0      0.00    88.17   12.70    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.817:  786   |   5:    44.086 -  52.903:  100        |
|      1:     8.817 -  17.634: 1293   |   6:    52.903 -  61.720:   79        |
|      2:    17.634 -  26.452:  272   |   7:    61.720 -  70.538:   33        |
|      3:    26.452 -  35.269:  130   |   8:    70.538 -  79.355:   12        |
|      4:    35.269 -  44.086:  115   |   9:    79.355 -  88.172:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1085 r_free = 0.1544             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1084 r_free = 0.1544             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1084   r_free= 0.1544   ksol= 0.33   Bsol= 55.98   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-2.41,-0.74,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.119556                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8683 -  4.7020 0.99   1394  152 0.0971 0.1232      5.3582      5.5025|
|  2:  4.7020 -  3.7519 0.99   1329  154 0.0831 0.1119      5.4162      5.6221|
|  3:  3.7519 -  3.2834 0.99   1307  143 0.1050 0.1496      5.4652      5.8364|
|  4:  3.2834 -  2.9859 0.99   1304  140 0.1176 0.1610      5.4246      5.5874|
|  5:  2.9859 -  2.7733 0.99   1292  147 0.1255 0.1655       5.294      5.5257|
|  6:  2.7733 -  2.6108 0.99   1301  145 0.1166 0.1865      5.1796      5.4642|
|  7:  2.6108 -  2.4806 0.99   1271  144 0.1241 0.1527      5.1508      5.2876|
|  8:  2.4806 -  2.3731 0.98   1270  136 0.1120 0.1563      5.0465      5.3134|
|  9:  2.3731 -  2.2821 0.98   1281  148 0.1136 0.1788      4.9991      5.2853|
| 10:  2.2821 -  2.2036 1.00   1276  139 0.1081 0.1639      4.9238      5.1468|
| 11:  2.2036 -  2.1349 0.97   1267  134 0.1086 0.1763      4.9192      5.2505|
| 12:  2.1349 -  2.0740 0.98   1250  145 0.1131 0.1633      4.8732       5.221|
| 13:  2.0740 -  2.0196 1.00   1270  138 0.1058 0.1755      4.7674      5.0401|
| 14:  2.0196 -  1.9704 0.63    818   94 0.0910 0.1676      4.6138      4.8866|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8683 -  4.7020  1394   152  0.94   8.77   0.98     0.95       6629.94|
|  2:  4.7020 -  3.7519  1329   154  0.95   7.68   1.02     1.01       8710.02|
|  3:  3.7519 -  3.2834  1307   143  0.94  10.94   1.03     1.02       9973.74|
|  4:  3.2834 -  2.9859  1304   140  0.93  12.97   1.01     1.00       9724.17|
|  5:  2.9859 -  2.7733  1292   147  0.91  15.11   1.00     0.98       7845.45|
|  6:  2.7733 -  2.6108  1301   145  0.90  15.62   0.98     0.96       6682.58|
|  7:  2.6108 -  2.4806  1271   144  0.91  15.38   0.99     0.96       5989.72|
|  8:  2.4806 -  2.3731  1270   136  0.91  14.57   0.99     0.97       5059.32|
|  9:  2.3731 -  2.2821  1281   148  0.92  14.56   1.00     0.96       4669.02|
| 10:  2.2821 -  2.2036  1276   139  0.90  15.52   1.00     0.97       4167.47|
| 11:  2.2036 -  2.1349  1267   134  0.90  15.68   0.99     0.95       4271.66|
| 12:  2.1349 -  2.0740  1250   145  0.90  15.99   1.01     1.00       3980.85|
| 13:  2.0740 -  2.0196  1270   138  0.91  15.25   0.99     0.97       3240.49|
| 14:  2.0196 -  1.9704   818    94  0.92  13.50   0.98     0.95       2413.17|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2413.17 max =         9973.74 mean =      6079.34|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.63|
|phase err.(test): min =        0.00 max =           89.97 mean =        13.16|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1543   ksol= 0.33   Bsol= 55.98   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.68,-2.27,-0.56,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.119530                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1543   ksol= 0.33   Bsol= 55.98   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.68,-2.27,-0.56,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.119530                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8683 -  4.7020 0.99   1394  152 0.0970 0.1233      5.3578      5.5028|
|  2:  4.7020 -  3.7519 0.99   1329  154 0.0832 0.1120       5.417      5.6226|
|  3:  3.7519 -  3.2834 0.99   1307  143 0.1050 0.1496      5.4656      5.8369|
|  4:  3.2834 -  2.9859 0.99   1304  140 0.1176 0.1610      5.4246      5.5873|
|  5:  2.9859 -  2.7733 0.99   1292  147 0.1255 0.1654      5.2938      5.5252|
|  6:  2.7733 -  2.6108 0.99   1301  145 0.1165 0.1865      5.1792      5.4637|
|  7:  2.6108 -  2.4806 0.99   1271  144 0.1241 0.1528      5.1508      5.2878|
|  8:  2.4806 -  2.3731 0.98   1270  136 0.1120 0.1563      5.0465      5.3134|
|  9:  2.3731 -  2.2821 0.98   1281  148 0.1136 0.1787      4.9992      5.2849|
| 10:  2.2821 -  2.2036 1.00   1276  139 0.1080 0.1641      4.9238      5.1478|
| 11:  2.2036 -  2.1349 0.97   1267  134 0.1085 0.1763      4.9194      5.2505|
| 12:  2.1349 -  2.0740 0.98   1250  145 0.1130 0.1632      4.8731      5.2207|
| 13:  2.0740 -  2.0196 1.00   1270  138 0.1058 0.1754       4.767      5.0395|
| 14:  2.0196 -  1.9704 0.63    818   94 0.0910 0.1674      4.6132      4.8856|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8683 -  4.7020  1394   152  0.94   8.76   0.98     0.95       6628.52|
|  2:  4.7020 -  3.7519  1329   154  0.95   7.69   1.02     1.02       8716.93|
|  3:  3.7519 -  3.2834  1307   143  0.94  10.94   1.04     1.03       9982.61|
|  4:  3.2834 -  2.9859  1304   140  0.93  12.97   1.02     1.00       9723.53|
|  5:  2.9859 -  2.7733  1292   147  0.91  15.10   1.01     0.98       7840.26|
|  6:  2.7733 -  2.6108  1301   145  0.90  15.62   0.99     0.97       6678.52|
|  7:  2.6108 -  2.4806  1271   144  0.91  15.38   0.99     0.96       5989.42|
|  8:  2.4806 -  2.3731  1270   136  0.91  14.57   1.00     0.98       5057.91|
|  9:  2.3731 -  2.2821  1281   148  0.92  14.56   1.01     0.97       4669.36|
| 10:  2.2821 -  2.2036  1276   139  0.90  15.53   1.01     0.98       4168.71|
| 11:  2.2036 -  2.1349  1267   134  0.90  15.68   1.00     0.96       4274.02|
| 12:  2.1349 -  2.0740  1250   145  0.90  16.00   1.02     1.01       3981.27|
| 13:  2.0740 -  2.0196  1270   138  0.91  15.24   1.00     0.98       3236.97|
| 14:  2.0196 -  1.9704   818    94  0.92  13.49   0.99     0.96       2407.98|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2407.98 max =         9982.61 mean =      6079.37|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.63|
|phase err.(test): min =        0.00 max =           89.98 mean =        13.16|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.597)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.17   16.97    None  None   None       |
|    all(noH): 2823   0      0.00    88.17   16.97    None  None   None       |
|    Sol.    : 438    0      4.67    79.51   40.21    None  None   None       |
|    Mac.    : 2385   0      0.00    88.17   12.70    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   8.820:  786   |   5:    44.089 -  52.906:  100        |
|      1:     8.820 -  17.637: 1293   |   6:    52.906 -  61.723:   79        |
|      2:    17.637 -  26.455:  272   |   7:    61.723 -  70.541:   33        |
|      3:    26.455 -  35.272:  130   |   8:    70.541 -  79.358:   12        |
|      4:    35.272 -  44.089:  115   |   9:    79.358 -  88.175:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 295         
Filter by distance & map next to the model:
   mapped sites are within: 0.426 - 4.746
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 292 from: 295
   mapped sites are within: 0.714 - 4.746

peak=    6.010 closest distance to " NE2 GLN A  11 " =    1.205
peak=    5.960 closest distance to " O   HOH Z 142 " =    1.908
peak=    5.598 closest distance to " NH2 ARG A  56 " =    2.104
peak=    5.454 closest distance to " CG  PRO A  54 " =    1.263
peak=    5.376 closest distance to " O   HOH Z 126 " =    2.006
peak=    5.296 closest distance to " O   HOH Z 417 " =    1.696
peak=    5.243 closest distance to " CB  ARG A 275 " =    0.943
peak=    4.964 closest distance to " O   HOH Z 232 " =    2.354
peak=    4.829 closest distance to " O   HOH Z 427 " =    2.741
peak=    4.685 closest distance to " O   HOH Z 371 " =    2.255
peak=    4.641 closest distance to " CB  PRO A  54 " =    0.968
peak=    4.604 closest distance to " CG  PRO A 213 " =    1.241
peak=    4.532 closest distance to " CB  GLN A 223 " =    1.471
peak=    4.519 closest distance to " O   HOH Z 287 " =    1.984
peak=    4.497 closest distance to " O   HOH Z 112 " =    1.228
peak=    4.460 closest distance to " CB  GLN A 183 " =    1.226
peak=    4.459 closest distance to " O   HOH Z  78 " =    1.742
peak=    4.455 closest distance to " ND2 ASN A 187 " =    1.517
peak=    4.390 closest distance to " CG2 VAL A 257 " =    0.819
peak=    4.375 closest distance to " O   HOH Z 419 " =    2.326
peak=    4.374 closest distance to " CB  SER A  63 " =    1.210
peak=    4.328 closest distance to " CB  ASN A 148 " =    1.430
peak=    4.308 closest distance to " CB  ARG A 190 " =    1.659
peak=    4.300 closest distance to " CG  TRP A 179 " =    2.134
peak=    4.288 closest distance to " O   HOH Z   9 " =    1.252
peak=    4.283 closest distance to " O   HOH Z 236 " =    1.404
peak=    4.263 closest distance to " CB  ARG A  79 " =    1.414
peak=    4.257 closest distance to " O   HOH Z 371 " =    1.951
peak=    4.246 closest distance to " O   HOH Z 158 " =    3.024
peak=    4.229 closest distance to " O   SER A  87 " =    2.147
peak=    4.199 closest distance to " CA  TYR A  30 " =    0.939
peak=    4.191 closest distance to " NZ  LYS A 119 " =    2.543
peak=    4.157 closest distance to " CG  ARG A  66 " =    2.556
peak=    4.151 closest distance to " CB  GLU A 152 " =    1.303
peak=    4.133 closest distance to " OG ASER A 258 " =    3.022
peak=    4.120 closest distance to " O   HOH Z 402 " =    1.423
peak=    4.118 closest distance to " C   PRO A 198 " =    1.438
peak=    4.118 closest distance to " O   HOH Z 380 " =    1.740
peak=    4.115 closest distance to " CD2 TRP A 179 " =    1.318
peak=    4.088 closest distance to " O   HOH Z  61 " =    1.633
peak=    4.081 closest distance to " O   HOH Z 365 " =    2.656
peak=    4.064 closest distance to " O   HOH Z 375 " =    1.012
peak=    4.055 closest distance to " O   HOH Z 209 " =    2.235
peak=    4.055 closest distance to " O   HOH Z 423 " =    1.410
peak=    4.052 closest distance to " CB  VAL A 265 " =    1.287
peak=    4.042 closest distance to " O   HOH Z   1 " =    1.716
peak=    4.021 closest distance to " CB  TRP A 266 " =    1.116
peak=    4.020 closest distance to " O   HOH Z 327 " =    1.620
peak=    4.012 closest distance to " O   HOH Z 298 " =    1.832
peak=    3.996 closest distance to " CG  PRO A  90 " =    1.185
peak=    3.985 closest distance to " O   HOH Z   9 " =    2.079
peak=    3.982 closest distance to " O   HOH Z 346 " =    1.646
peak=    3.979 closest distance to " CG  PRO A 198 " =    1.280
peak=    3.962 closest distance to " CZ  PHE A 218 " =    1.072
peak=    3.962 closest distance to " O   HOH Z 272 " =    1.800
peak=    3.956 closest distance to " O   HOH Z 250 " =    1.507
peak=    3.953 closest distance to " NZ  LYS A 117 " =    3.122
peak=    3.952 closest distance to " O   HOH Z 425 " =    2.042
peak=    3.943 closest distance to " O   HOH Z  61 " =    1.496
peak=    3.935 closest distance to " OG BSER A 164 " =    2.222
peak=    3.911 closest distance to " O   HOH Z 353 " =    2.566
peak=    3.909 closest distance to " CB  THR A  31 " =    1.609
peak=    3.907 closest distance to " CB  SER A   3 " =    1.274
peak=    3.895 closest distance to " CA  ASN A 215 " =    1.027
peak=    3.887 closest distance to " O   HOH Z 132 " =    2.304
peak=    3.867 closest distance to " O   HOH Z   1 " =    1.962
peak=    3.863 closest distance to " O   HOH Z 403 " =    1.688
peak=    3.839 closest distance to " O   HOH Z  44 " =    1.777
peak=    3.838 closest distance to " CD  ARG A 159 " =    0.714
peak=    3.808 closest distance to " CB  GLU A 277 " =    3.516
peak=    3.807 closest distance to " CB  ARG A  79 " =    0.880
peak=    3.806 closest distance to " O   HOH Z 234 " =    3.580
peak=    3.805 closest distance to " O   HOH Z 189 " =    2.688
peak=    3.786 closest distance to " O   HOH Z 203 " =    1.776
peak=    3.769 closest distance to " O   HOH Z  40 " =    1.794
peak=    3.767 closest distance to " O   HOH Z 357 " =    1.933
peak=    3.763 closest distance to " CE  LYS A  76 " =    0.888
peak=    3.758 closest distance to " O   HOH Z 248 " =    1.538
peak=    3.757 closest distance to " N   PHE A 130 " =    1.283
peak=    3.746 closest distance to " CG1BVAL A  72 " =    1.524
peak=    3.743 closest distance to " O   HOH Z 193 " =    1.667
peak=    3.741 closest distance to " NH1AARG A 145 " =    1.196
peak=    3.737 closest distance to " CB  ASN A 187 " =    1.281
peak=    3.735 closest distance to " CB  VAL A 202 " =    1.598
peak=    3.720 closest distance to " NH2AARG A 190 " =    1.873
peak=    3.717 closest distance to " OD1 ASN A  69 " =    2.518
peak=    3.716 closest distance to " O   HOH Z 368 " =    3.482
peak=    3.714 closest distance to " CG  PRO A 243 " =    1.057
peak=    3.709 closest distance to " N   ASN A  39 " =    1.202
peak=    3.704 closest distance to " CB  ARG A 139 " =    1.068
peak=    3.700 closest distance to " CB  SER A  26 " =    1.742
peak=    3.691 closest distance to " CA  ARG A 195 " =    1.214
peak=    3.690 closest distance to " O   HOH Z 425 " =    1.276
peak=    3.688 closest distance to " O   HOH Z  10 " =    1.753
peak=    3.686 closest distance to " CB  TYR A 169 " =    0.970
peak=    3.673 closest distance to " N   TYR A 116 " =    1.554
peak=    3.650 closest distance to " O   HOH Z 405 " =    1.287
peak=    3.647 closest distance to " O   HOH Z 124 " =    2.210
peak=    3.644 closest distance to " CB  LYS A 117 " =    1.211
peak=    3.643 closest distance to " CB  ASN A  39 " =    0.898
peak=    3.639 closest distance to " O   HOH Z 359 " =    1.498
peak=    3.634 closest distance to " O   HOH Z 128 " =    2.001
peak=    3.625 closest distance to " O   HOH Z 336 " =    1.781
peak=    3.624 closest distance to " O   HOH Z  59 " =    1.548
peak=    3.610 closest distance to " O   HOH Z 406 " =    1.568
peak=    3.606 closest distance to " O   HOH Z 214 " =    2.431
peak=    3.603 closest distance to " CE  LYS A 119 " =    1.224
peak=    3.592 closest distance to " O   HOH Z 116 " =    2.813
peak=    3.592 closest distance to " O   HOH Z 344 " =    3.226
peak=    3.590 closest distance to " O   HOH Z 193 " =    2.005
peak=    3.580 closest distance to " O   HOH Z 394 " =    1.717
peak=    3.579 closest distance to " O   HOH Z 126 " =    1.515
peak=    3.578 closest distance to " CA  ALA A 233 " =    0.979
peak=    3.574 closest distance to " CD2 LEU A 297 " =    0.972
peak=    3.574 closest distance to " NE2 GLN A  73 " =    3.745
peak=    3.572 closest distance to " O   HOH Z  88 " =    2.417
peak=    3.571 closest distance to " O   HOH Z 128 " =    2.032
peak=    3.569 closest distance to " ND2 ASN A 249 " =    0.822
peak=    3.565 closest distance to " O   HOH Z 394 " =    3.845
peak=    3.562 closest distance to " CB  ASN A 142 " =    1.034
peak=    3.559 closest distance to " O   HOH Z 421 " =    2.160
peak=    3.550 closest distance to " O   HOH Z 286 " =    2.336
peak=    3.547 closest distance to " CB  LEU A 228 " =    1.125
peak=    3.543 closest distance to " O   HOH Z 305 " =    3.526
peak=    3.538 closest distance to " CG2 ILE A 120 " =    1.070
peak=    3.536 closest distance to " CB  ASP A 140 " =    0.942
peak=    3.533 closest distance to " O   HOH Z 415 " =    3.683
peak=    3.524 closest distance to " O   HOH Z 148 " =    3.446
peak=    3.521 closest distance to " NH2BARG A 145 " =    2.018
peak=    3.511 closest distance to " O   HOH Z  66 " =    2.113
peak=    3.511 closest distance to " O   HOH Z 257 " =    2.175
peak=    3.510 closest distance to " O   HOH Z 325 " =    2.267
peak=    3.503 closest distance to " O   ASN A  74 " =    1.513
peak=    3.502 closest distance to " O   HOH Z 422 " =    2.558
peak=    3.501 closest distance to " O   HOH Z  93 " =    2.354
peak=    3.499 closest distance to " CB  GLU A  46 " =    1.068
peak=    3.498 closest distance to " O   HOH Z 213 " =    2.198
peak=    3.496 closest distance to " O   HOH Z  63 " =    1.297
peak=    3.494 closest distance to " CB  GLU A 128 " =    1.000
peak=    3.486 closest distance to " O   HOH Z 285 " =    2.419
peak=    3.482 closest distance to " O   HOH Z 173 " =    2.004
peak=    3.479 closest distance to " O   HOH Z  44 " =    2.793
peak=    3.470 closest distance to " CB  ILE A 120 " =    1.399
peak=    3.469 closest distance to " O   HOH Z 371 " =    3.002
peak=    3.463 closest distance to " O   HOH Z 437 " =    1.521
peak=    3.462 closest distance to " N   GLN A 278 " =    1.288
peak=    3.460 closest distance to " O   HOH Z 291 " =    1.492
peak=    3.449 closest distance to " O   HOH Z 386 " =    3.033
peak=    3.448 closest distance to " CG  LEU A 167 " =    1.254
peak=    3.443 closest distance to " O   HOH Z 407 " =    2.223
peak=    3.443 closest distance to " CB  LEU A 300 " =    0.921
peak=    3.440 closest distance to " CB  ALA A 114 " =    1.436
peak=    3.439 closest distance to " O   HOH Z 391 " =    2.894
peak=    3.436 closest distance to " O   HOH Z 180 " =    2.265
peak=    3.434 closest distance to " O   HOH Z 261 " =    1.623
peak=    3.431 closest distance to " O   HOH Z 411 " =    3.811
peak=    3.430 closest distance to " CB  THR A 157 " =    1.142
peak=    3.429 closest distance to " CA  ASP A 162 " =    1.031
peak=    3.419 closest distance to " CA  PHE A 283 " =    1.283
peak=    3.418 closest distance to " N   GLU A   2 " =    1.491
peak=    3.415 closest distance to " O   HOH Z 337 " =    3.534
peak=    3.415 closest distance to " CB  GLN A  89 " =    1.398
peak=    3.410 closest distance to " CB  GLN A  88 " =    1.205
peak=    3.410 closest distance to " O   HOH Z  40 " =    2.117
peak=    3.409 closest distance to " O   HOH Z   2 " =    1.404
peak=    3.407 closest distance to " CA  ALA A 299 " =    0.911
peak=    3.407 closest distance to " CB  SER A 212 " =    1.115
peak=    3.406 closest distance to " O   HOH Z 233 " =    2.010
peak=    3.406 closest distance to " CD  LYS A  76 " =    1.765
peak=    3.399 closest distance to " O   HOH Z 261 " =    2.164
peak=    3.394 closest distance to " CD  PRO A 243 " =    1.549
peak=    3.382 closest distance to " O   HOH Z   3 " =    1.938
peak=    3.381 closest distance to " OG  SER A  62 " =    2.822
peak=    3.371 closest distance to " CG1 ILE A  33 " =    1.203
peak=    3.371 closest distance to " OG BSER A  99 " =    2.439
peak=    3.370 closest distance to " O   HOH Z 390 " =    2.525
peak=    3.367 closest distance to " CA  SER A  87 " =    1.036
peak=    3.367 closest distance to " O   HOH Z 368 " =    2.010
peak=    3.362 closest distance to " O   HOH Z  21 " =    1.780
peak=    3.358 closest distance to " O   HOH Z 389 " =    1.731
peak=    3.353 closest distance to " CA  ALA A  84 " =    1.292
peak=    3.350 closest distance to " CG1 VAL A 189 " =    1.973
peak=    3.345 closest distance to " CG AARG A 275 " =    1.113
peak=    3.344 closest distance to " O   HOH Z 219 " =    2.141
peak=    3.337 closest distance to " O   HOH Z 147 " =    1.734
peak=    3.337 closest distance to " O   HOH Z 345 " =    3.245
peak=    3.335 closest distance to " CB  ALA A 114 " =    0.935
peak=    3.332 closest distance to " O   HOH Z 426 " =    1.929
peak=    3.328 closest distance to " O   HOH Z 119 " =    4.374
peak=    3.326 closest distance to " CB  PRO A  90 " =    1.135
peak=    3.325 closest distance to " CZ3 TRP A 266 " =    1.103
peak=    3.325 closest distance to " CB  HIS A 108 " =    0.806
peak=    3.314 closest distance to " NH1BARG A 145 " =    1.254
peak=    3.311 closest distance to " O   HOH Z 423 " =    2.361
peak=    3.311 closest distance to " CA  ASN A 217 " =    1.102
peak=    3.310 closest distance to " O   HOH Z 329 " =    4.008
peak=    3.308 closest distance to " CB  TRP A 179 " =    1.332
peak=    3.308 closest distance to " CG  LYS A 119 " =    1.113
peak=    3.303 closest distance to " CE1 TYR A 186 " =    1.339
peak=    3.303 closest distance to " O   HOH Z 294 " =    1.436
peak=    3.301 closest distance to " ND1 HIS A  86 " =    1.817
peak=    3.300 closest distance to " CA  THR A 221 " =    1.081
peak=    3.299 closest distance to " OE1 GLN A  11 " =    2.102
peak=    3.294 closest distance to " CB  ASN A 110 " =    1.032
peak=    3.291 closest distance to " CG2 THR A 221 " =    1.127
peak=    3.285 closest distance to " O   ARG A 145 " =    1.781
peak=    3.285 closest distance to " O   HOH Z 193 " =    1.653
peak=    3.284 closest distance to " N   ASP A 162 " =    1.099
peak=    3.282 closest distance to " O   HOH Z 435 " =    1.966
peak=    3.276 closest distance to " O   HOH Z   6 " =    2.075
peak=    3.275 closest distance to " O   HOH Z  88 " =    2.459
peak=    3.271 closest distance to " O   HOH Z 109 " =    2.396
peak=    3.271 closest distance to " N   ARG A 156 " =    1.267
peak=    3.270 closest distance to " O   HOH Z 266 " =    3.408
peak=    3.270 closest distance to " CD  ARG A  79 " =    2.262
peak=    3.269 closest distance to " O   HOH Z 172 " =    2.934
peak=    3.268 closest distance to " O   HOH Z 175 " =    2.052
peak=    3.263 closest distance to " O  BHOH Z 338 " =    2.343
peak=    3.262 closest distance to " CG  MET A 185 " =    1.356
peak=    3.261 closest distance to " O   HOH Z 265 " =    2.166
peak=    3.261 closest distance to " CD1 ILE A 263 " =    1.365
peak=    3.260 closest distance to " CG2 VAL A 197 " =    1.042
peak=    3.257 closest distance to " O   HOH Z  85 " =    2.333
peak=    3.250 closest distance to " N   ASN A 127 " =    1.308
peak=    3.250 closest distance to " O   HOH Z 146 " =    1.584
peak=    3.242 closest distance to " CB  MET A 188 " =    1.620
peak=    3.242 closest distance to " CA  LEU A 300 " =    1.023
peak=    3.242 closest distance to " CB  SER A  62 " =    1.324
peak=    3.238 closest distance to " OD1BASN A 224 " =    2.263
peak=    3.233 closest distance to " CA  ILE A 234 " =    0.996
peak=    3.233 closest distance to " CD  LYS A 166 " =    1.287
peak=    3.231 closest distance to " O   HOH Z 373 " =    1.425
peak=    3.229 closest distance to " C   PHE A  59 " =    0.787
peak=    3.226 closest distance to " O   HOH Z 298 " =    2.497
peak=    3.226 closest distance to " OD2 ASP A 286 " =    3.196
peak=    3.222 closest distance to " O   HOH Z 261 " =    2.438
peak=    3.221 closest distance to " O   HOH Z 432 " =    1.718
peak=    3.216 closest distance to " O   THR A 220 " =    1.277
peak=    3.215 closest distance to " O   HOH Z 302 " =    1.720
peak=    3.215 closest distance to " CB  ASN A 215 " =    1.042
peak=    3.215 closest distance to " CE AMET A  47 " =    1.421
peak=    3.215 closest distance to " O   HOH Z 175 " =    2.103
peak=    3.213 closest distance to " NE  ARG A  24 " =    1.957
peak=    3.211 closest distance to " CG2 ILE A  20 " =    1.546
peak=    3.210 closest distance to " CD BLYS A 290 " =    1.259
peak=    3.210 closest distance to " O   HOH Z 153 " =    1.625
peak=    3.205 closest distance to " O   PRO A  90 " =    1.688
peak=    3.201 closest distance to " CB  LYS A 290 " =    0.929
peak=    3.199 closest distance to " CA  TYR A 116 " =    1.305
peak=    3.191 closest distance to " CD1 LEU A  96 " =    0.772
peak=    3.188 closest distance to " O   HOH Z  53 " =    2.488
peak=    3.186 closest distance to " CA  VAL A 125 " =    1.113
peak=    3.186 closest distance to " CA  ASN A 127 " =    1.088
peak=    3.182 closest distance to " CB  ALA A   1 " =    4.746
peak=    3.180 closest distance to " CA  ALA A 158 " =    1.243
peak=    3.177 closest distance to " CD2 LEU A 255 " =    1.326
peak=    3.177 closest distance to " N   CYS A 260 " =    0.822
peak=    3.171 closest distance to " O   HOH Z  66 " =    2.217
peak=    3.160 closest distance to " O   HOH Z 245 " =    1.352
peak=    3.159 closest distance to " O   HOH Z  88 " =    3.019
peak=    3.158 closest distance to " O   HOH Z 280 " =    2.985
peak=    3.155 closest distance to " CA  ALA A 233 " =    1.007
peak=    3.154 closest distance to " CG  LYS A  76 " =    0.944
peak=    3.152 closest distance to " CA  ALA A 291 " =    0.809
peak=    3.151 closest distance to " O   HOH Z 371 " =    3.165
peak=    3.150 closest distance to " CB  TYR A 116 " =    0.836
peak=    3.150 closest distance to " O   HOH Z 271 " =    2.364
peak=    3.145 closest distance to " CA  ALA A  51 " =    0.932
peak=    3.142 closest distance to " NZ  LYS A 119 " =    1.378
peak=    3.139 closest distance to " CB  SER A 273 " =    0.830
peak=    3.139 closest distance to " CA  ARG A  36 " =    0.984
peak=    3.129 closest distance to " O   HOH Z 409 " =    2.600
peak=    3.126 closest distance to " O  BHOH Z  74 " =    1.272
peak=    3.125 closest distance to " O   HOH Z  30 " =    1.635
peak=    3.120 closest distance to " CB  PHE A 204 " =    0.773
peak=    3.103 closest distance to " CB  ALA A 291 " =    1.280
peak=    3.100 closest distance to " NH1 ARG A 138 " =    1.087
peak=    3.097 closest distance to " CD1 ILE A 106 " =    0.871
peak=    3.096 closest distance to " OE2 GLU A  53 " =    1.978
peak=    3.095 closest distance to " CB  SER A 216 " =    0.781
peak=    3.093 closest distance to " CG  MET A 113 " =    0.856
peak=    3.086 closest distance to " CA  SER A  95 " =    1.006
peak=    3.082 closest distance to " CA  MET A 105 " =    0.945
peak=    3.078 closest distance to " O   HOH Z 433 " =    1.933
peak=    3.071 closest distance to " CD1AILE A 234 " =    0.864
peak=    3.067 closest distance to " NE2 HIS A 207 " =    1.300
peak=    3.067 closest distance to " CB  MET A  47 " =    1.181
peak=    3.057 closest distance to " O   HOH Z 153 " =    3.822
peak=    3.055 closest distance to " N   SER A 135 " =    1.208
peak=    3.053 closest distance to " O   ALA A   1 " =    1.695
peak=    3.044 closest distance to " O   HOH Z  89 " =    2.045
peak=    3.041 closest distance to " CA  LYS A 290 " =    1.411

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 196         
Filter by distance & map next to the model:
   mapped sites are within: 0.746 - 5.979
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 196
   mapped sites are within: 0.746 - 5.979

peak=   -4.608 closest distance to " O   HOH Z 377 " =    2.146
peak=   -4.495 closest distance to " OG BSER A 134 " =    1.295
peak=   -4.488 closest distance to " CD  ARG A 156 " =    2.121
peak=   -4.416 closest distance to " CB  PRO A 243 " =    2.632
peak=   -4.349 closest distance to " SG  CYS A 254 " =    3.380
peak=   -4.316 closest distance to " O   HOH Z 266 " =    5.083
peak=   -4.304 closest distance to " CB  PHE A 192 " =    1.959
peak=   -4.293 closest distance to " CG  GLN A  58 " =    0.999
peak=   -4.280 closest distance to " O   PRO A 198 " =    1.249
peak=   -4.217 closest distance to " C   HIS A 108 " =    1.143
peak=   -4.125 closest distance to " CG  GLN A 223 " =    1.895
peak=   -4.071 closest distance to " O   HOH Z 351 " =    1.478
peak=   -4.054 closest distance to " CD1 LEU A 255 " =    2.797
peak=   -4.039 closest distance to " OD2 ASP A 191 " =    1.356
peak=   -4.037 closest distance to " CB  ALA A  43 " =    2.414
peak=   -4.034 closest distance to " O   HOH Z 372 " =    2.404
peak=   -4.023 closest distance to " O   VAL A  67 " =    2.612
peak=   -4.004 closest distance to " CA  VAL A  67 " =    2.902
peak=   -3.982 closest distance to " CE  MET A 105 " =    2.365
peak=   -3.955 closest distance to " O   HOH Z 231 " =    2.210
peak=   -3.934 closest distance to " OD1 ASP A 171 " =    1.572
peak=   -3.922 closest distance to " CG1 VAL A 112 " =    2.875
peak=   -3.882 closest distance to " CB  ALA A 291 " =    2.176
peak=   -3.882 closest distance to " CB  ASN A  39 " =    2.349
peak=   -3.860 closest distance to " O   HOH Z 429 " =    1.996
peak=   -3.839 closest distance to " O   HOH Z 290 " =    1.136
peak=   -3.833 closest distance to " O   HOH Z 185 " =    2.193
peak=   -3.831 closest distance to " O   HOH Z 389 " =    2.015
peak=   -3.793 closest distance to " O   HOH Z 407 " =    2.833
peak=   -3.789 closest distance to " ND2 ASN A  45 " =    1.964
peak=   -3.768 closest distance to " O   PRO A 198 " =    1.290
peak=   -3.759 closest distance to " CZ3 TRP A 179 " =    1.220
peak=   -3.754 closest distance to " O   HOH Z 395 " =    5.086
peak=   -3.744 closest distance to " CD2 LEU A 237 " =    2.755
peak=   -3.719 closest distance to " O   HOH Z 313 " =    1.737
peak=   -3.714 closest distance to " CG2 ILE A 263 " =    2.251
peak=   -3.693 closest distance to " CE BMET A  47 " =    1.170
peak=   -3.690 closest distance to " CG  PHE A 283 " =    2.612
peak=   -3.688 closest distance to " O   HOH Z 211 " =    1.562
peak=   -3.684 closest distance to " OD1 ASN A 187 " =    1.676
peak=   -3.676 closest distance to " N   ALA A  43 " =    2.551
peak=   -3.661 closest distance to " O   HOH Z  13 " =    1.748
peak=   -3.641 closest distance to " CB  ALA A 291 " =    2.140
peak=   -3.640 closest distance to " N   THR A 157 " =    1.546
peak=   -3.631 closest distance to " CD2 PHE A 225 " =    1.193
peak=   -3.626 closest distance to " CA  GLY A  98 " =    1.798
peak=   -3.615 closest distance to " O   HOH Z 385 " =    1.875
peak=   -3.615 closest distance to " O   HOH Z 198 " =    1.567
peak=   -3.606 closest distance to " O   HOH Z 131 " =    4.090
peak=   -3.606 closest distance to " OD1 ASN A 148 " =    1.519
peak=   -3.602 closest distance to " CD1 LEU A 101 " =    2.203
peak=   -3.592 closest distance to " ND2 ASN A 249 " =    2.364
peak=   -3.592 closest distance to " CB  ALA A 248 " =    2.268
peak=   -3.589 closest distance to " CZ2 TRP A 274 " =    0.877
peak=   -3.585 closest distance to " O   ALA A 161 " =    1.601
peak=   -3.572 closest distance to " O   HOH Z 348 " =    2.224
peak=   -3.569 closest distance to " O   PRO A 243 " =    2.566
peak=   -3.562 closest distance to " O   SER A 210 " =    1.992
peak=   -3.556 closest distance to " ND2 ASN A  60 " =    4.095
peak=   -3.553 closest distance to " N   GLN A  58 " =    1.711
peak=   -3.552 closest distance to " O   ALA A  10 " =    1.602
peak=   -3.548 closest distance to " O   HOH Z 362 " =    5.979
peak=   -3.545 closest distance to " O   PHE A 218 " =    1.437
peak=   -3.542 closest distance to " CD2 TYR A 293 " =    1.924
peak=   -3.535 closest distance to " CB  TYR A  15 " =    2.191
peak=   -3.534 closest distance to " O   HOH Z 102 " =    1.578
peak=   -3.533 closest distance to " CG2 THR A  18 " =    2.730
peak=   -3.528 closest distance to " O   SER A 135 " =    1.452
peak=   -3.523 closest distance to " OXT GLY A 302 " =    2.990
peak=   -3.514 closest distance to " N   ALA A 248 " =    1.615
peak=   -3.511 closest distance to " O   HOH Z 165 " =    2.245
peak=   -3.497 closest distance to " O   TRP A  70 " =    1.441
peak=   -3.487 closest distance to " CZ  TYR A 169 " =    1.764
peak=   -3.483 closest distance to " O   VAL A 189 " =    2.596
peak=   -3.479 closest distance to " O   SER A  22 " =    2.491
peak=   -3.474 closest distance to " OD1 ASP A 191 " =    1.899
peak=   -3.470 closest distance to " CA  GLY A 133 " =    1.952
peak=   -3.455 closest distance to " O   HOH Z 339 " =    1.826
peak=   -3.452 closest distance to " O   HOH Z  43 " =    1.764
peak=   -3.443 closest distance to " O   HOH Z  63 " =    1.812
peak=   -3.435 closest distance to " O   HOH Z 317 " =    1.459
peak=   -3.432 closest distance to " CB  ALA A 161 " =    2.419
peak=   -3.429 closest distance to " CE1 PHE A  59 " =    2.158
peak=   -3.427 closest distance to " OG  SER A  97 " =    2.139
peak=   -3.425 closest distance to " CB  TRP A  85 " =    2.405
peak=   -3.417 closest distance to " O   HOH Z 298 " =    1.248
peak=   -3.408 closest distance to " OE2 GLU A 152 " =    1.178
peak=   -3.408 closest distance to " CE3 TRP A 274 " =    2.259
peak=   -3.401 closest distance to " ND2 ASN A  45 " =    1.135
peak=   -3.399 closest distance to " O   SER A  95 " =    1.445
peak=   -3.398 closest distance to " O   ALA A 292 " =    2.060
peak=   -3.395 closest distance to " O   PRO A 163 " =    1.908
peak=   -3.387 closest distance to " O   HOH Z  38 " =    1.978
peak=   -3.382 closest distance to " O   HOH Z 421 " =    2.968
peak=   -3.378 closest distance to " CA  ASP A 298 " =    1.071
peak=   -3.374 closest distance to " ND2 ASN A 187 " =    1.465
peak=   -3.373 closest distance to " CA  GLY A 241 " =    2.189
peak=   -3.368 closest distance to " O   HOH Z 123 " =    2.379
peak=   -3.358 closest distance to " O   HOH Z 359 " =    3.222
peak=   -3.358 closest distance to " OE1 GLN A 183 " =    1.534
peak=   -3.355 closest distance to " O   HOH Z  15 " =    1.496
peak=   -3.349 closest distance to " O   HOH Z  11 " =    1.776
peak=   -3.349 closest distance to " CZ  PHE A  59 " =    1.486
peak=   -3.348 closest distance to " CB  ASP A 132 " =    2.389
peak=   -3.345 closest distance to " O   HOH Z 191 " =    5.621
peak=   -3.343 closest distance to " CE2 TYR A  30 " =    2.646
peak=   -3.339 closest distance to " CB  ASP A 286 " =    2.293
peak=   -3.338 closest distance to " O   HOH Z 166 " =    2.159
peak=   -3.332 closest distance to " O   HOH Z 140 " =    1.544
peak=   -3.323 closest distance to " CE2 PHE A 218 " =    2.349
peak=   -3.321 closest distance to " NE2 GLN A 278 " =    1.578
peak=   -3.307 closest distance to " O   HOH Z  90 " =    2.324
peak=   -3.306 closest distance to " O   GLN A 240 " =    1.737
peak=   -3.305 closest distance to " OD2 ASP A 171 " =    2.265
peak=   -3.304 closest distance to " O   HOH Z  24 " =    1.277
peak=   -3.291 closest distance to " OG  SER A  87 " =    1.309
peak=   -3.291 closest distance to " O   HOH Z 298 " =    2.449
peak=   -3.288 closest distance to " CB  GLN A  11 " =    1.885
peak=   -3.283 closest distance to " CD  ARG A 139 " =    1.552
peak=   -3.279 closest distance to " O   HOH Z 393 " =    3.258
peak=   -3.278 closest distance to " N   MET A 188 " =    1.896
peak=   -3.273 closest distance to " CB  PRO A 163 " =    2.427
peak=   -3.273 closest distance to " CE  LYS A  76 " =    2.711
peak=   -3.272 closest distance to " CG  ASP A 231 " =    0.746
peak=   -3.272 closest distance to " O   HOH Z  60 " =    1.813
peak=   -3.271 closest distance to " CG2 ILE A  49 " =    2.745
peak=   -3.271 closest distance to " O   HOH Z 256 " =    1.282
peak=   -3.271 closest distance to " O   HOH Z 369 " =    2.271
peak=   -3.267 closest distance to " N   PHE A  59 " =    1.861
peak=   -3.266 closest distance to " CE2 PHE A  61 " =    2.594
peak=   -3.265 closest distance to " NE2 GLN A 194 " =    1.795
peak=   -3.262 closest distance to " O   GLU A 152 " =    1.411
peak=   -3.262 closest distance to " CG1 VAL A 197 " =    2.121
peak=   -3.261 closest distance to " CD2 PHE A  61 " =    2.010
peak=   -3.257 closest distance to " O   ARG A 145 " =    1.432
peak=   -3.257 closest distance to " O   HOH Z 281 " =    2.758
peak=   -3.256 closest distance to " C   ALA A 158 " =    1.481
peak=   -3.254 closest distance to " O   HOH Z   9 " =    1.622
peak=   -3.254 closest distance to " CD  GLU A 277 " =    1.287
peak=   -3.254 closest distance to " NH2BARG A 275 " =    1.816
peak=   -3.251 closest distance to " O   ALA A  34 " =    2.227
peak=   -3.251 closest distance to " OH  TYR A 172 " =    1.772
peak=   -3.246 closest distance to " O   ILE A  49 " =    1.744
peak=   -3.235 closest distance to " O   HOH Z 253 " =    3.786
peak=   -3.229 closest distance to " CB  ALA A   7 " =    2.082
peak=   -3.228 closest distance to " NH2AARG A 275 " =    5.182
peak=   -3.221 closest distance to " O   VAL A 125 " =    2.150
peak=   -3.220 closest distance to " CB  ALA A 100 " =    2.188
peak=   -3.219 closest distance to " O   HOH Z  49 " =    1.200
peak=   -3.218 closest distance to " O   HOH Z 198 " =    2.007
peak=   -3.218 closest distance to " O   HOH Z  60 " =    1.924
peak=   -3.213 closest distance to " O   HOH Z   6 " =    1.411
peak=   -3.209 closest distance to " CA  GLY A 241 " =    3.124
peak=   -3.208 closest distance to " O   ASP A 162 " =    2.121
peak=   -3.208 closest distance to " N   ASN A 127 " =    1.469
peak=   -3.208 closest distance to " OG  SER A  63 " =    1.227
peak=   -3.206 closest distance to " CB  CYS A 201 " =    2.540
peak=   -3.200 closest distance to " NH1AARG A 275 " =    1.886
peak=   -3.192 closest distance to " CA  GLY A  57 " =    2.170
peak=   -3.189 closest distance to " NE  ARG A  36 " =    1.874
peak=   -3.189 closest distance to " O   HOH Z 187 " =    1.818
peak=   -3.177 closest distance to " C   ASP A 272 " =    2.187
peak=   -3.172 closest distance to " CB  ALA A 244 " =    2.124
peak=   -3.171 closest distance to " O   HOH Z 414 " =    2.397
peak=   -3.169 closest distance to " CG  ARG A 269 " =    2.181
peak=   -3.162 closest distance to " O   ALA A 180 " =    1.027
peak=   -3.162 closest distance to " O   VAL A 174 " =    2.203
peak=   -3.158 closest distance to " CE1 TYR A 247 " =    2.776
peak=   -3.154 closest distance to " CB  ASP A 132 " =    2.255
peak=   -3.154 closest distance to " OD1AASN A 224 " =    1.805
peak=   -3.152 closest distance to " O   HOH Z 137 " =    1.393
peak=   -3.149 closest distance to " CD2 HIS A 207 " =    2.317
peak=   -3.147 closest distance to " CB  SER A 210 " =    1.180
peak=   -3.141 closest distance to " O   HOH Z 166 " =    1.307
peak=   -3.128 closest distance to " C   ALA A 114 " =    2.244
peak=   -3.121 closest distance to " O   LYS A  76 " =    1.797
peak=   -3.116 closest distance to " O   HOH Z 423 " =    2.234
peak=   -3.116 closest distance to " OD1 ASN A 301 " =    1.800
peak=   -3.112 closest distance to " CG2 THR A 178 " =    2.205
peak=   -3.103 closest distance to " OE1 GLN A 223 " =    1.904
peak=   -3.095 closest distance to " CG1 VAL A 197 " =    2.238
peak=   -3.089 closest distance to " O   HOH Z 288 " =    1.298
peak=   -3.088 closest distance to " O   HOH Z 189 " =    1.886
peak=   -3.087 closest distance to " C   LYS A  76 " =    1.665
peak=   -3.086 closest distance to " O   HOH Z 213 " =    1.624
peak=   -3.085 closest distance to " N   SER A 276 " =    1.241
peak=   -3.080 closest distance to " NH1 ARG A 195 " =    2.663
peak=   -3.075 closest distance to " O   HOH Z 412 " =    3.877
peak=   -3.074 closest distance to " CG2 VAL A 189 " =    1.969
peak=   -3.068 closest distance to " CG2BVAL A  41 " =    1.112
peak=   -3.061 closest distance to " O   HOH Z 250 " =    1.298
peak=   -3.055 closest distance to " OE1 GLN A 223 " =    1.467
peak=   -3.053 closest distance to " OG  SER A 245 " =    1.391
peak=   -3.051 closest distance to " O   SER A 276 " =    1.637
peak=   -3.028 closest distance to " OD1 ASP A 200 " =    1.476
peak=   -3.015 closest distance to " O   GLY A  57 " =    2.139

================= 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    :  0.4065 0.4013   6.201580e+00   6.180162e+00
   1_bss:  0.3958 0.3917   6.192891e+00   6.162835e+00
   1_xyz:  0.2535 0.2842   5.829057e+00   5.904132e+00
   1_adp:  0.2302 0.2957   5.776480e+00   5.944975e+00
   1_occ:  0.2300 0.2958   5.776121e+00   5.944995e+00
   2_bss:  0.2283 0.2939   5.772205e+00   5.940889e+00
   2_xyz:  0.1678 0.2185   5.486729e+00   5.691558e+00
   2_adp:  0.1556 0.2018   5.414305e+00   5.611047e+00
   2_occ:  0.1553 0.2012   5.412477e+00   5.608952e+00
   3_bss:  0.1552 0.2005   5.408381e+00   5.603683e+00
   3_xyz:  0.1283 0.1703   5.242779e+00   5.451127e+00
   3_adp:  0.1234 0.1658   5.210618e+00   5.426570e+00
   3_occ:  0.1232 0.1659   5.210220e+00   5.426113e+00
   4_bss:  0.1233 0.1657   5.208998e+00   5.424542e+00
   4_xyz:  0.1162 0.1577   5.156274e+00   5.380376e+00
   4_adp:  0.1143 0.1564   5.146416e+00   5.376257e+00
   4_occ:  0.1143 0.1564   5.146198e+00   5.376069e+00
   5_bss:  0.1142 0.1564   5.145913e+00   5.375877e+00
   5_xyz:  0.1093 0.1538   5.120591e+00   5.365590e+00
   5_adp:  0.1085 0.1544   5.119686e+00   5.370554e+00
   5_occ:  0.1084 0.1544   5.119556e+00   5.370475e+00
   5_bss:  0.1083 0.1543   5.119530e+00   5.370443e+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:  0.331  30.578  -1.414   1.790   0.124   0.000   0.000   0.000
   1_xyz:  0.331  30.578  -1.414   1.790   0.124   0.000   0.000   0.000
   1_adp:  0.331  30.578  -1.414   1.790   0.124   0.000   0.000   0.000
   1_occ:  0.331  30.578  -1.414   1.790   0.124   0.000   0.000   0.000
   2_bss:  0.339  55.976  -2.617  -0.899  -0.577  -0.000  -0.000  -0.000
   2_xyz:  0.339  55.976  -2.617  -0.899  -0.577  -0.000  -0.000  -0.000
   2_adp:  0.339  55.976  -2.617  -0.899  -0.577  -0.000  -0.000  -0.000
   2_occ:  0.339  55.976  -2.617  -0.899  -0.577  -0.000  -0.000  -0.000
   3_bss:  0.339  55.976  -2.954  -2.020  -0.655  -0.000  -0.000  -0.000
   3_xyz:  0.339  55.976  -2.954  -2.020  -0.655  -0.000  -0.000  -0.000
   3_adp:  0.339  55.976  -2.954  -2.020  -0.655  -0.000  -0.000  -0.000
   3_occ:  0.339  55.976  -2.954  -2.020  -0.655  -0.000  -0.000  -0.000
   4_bss:  0.339  55.976  -3.057  -2.459  -0.859  -0.000  -0.000  -0.000
   4_xyz:  0.339  55.976  -3.057  -2.459  -0.859  -0.000  -0.000  -0.000
   4_adp:  0.339  55.976  -3.057  -2.459  -0.859  -0.000  -0.000  -0.000
   4_occ:  0.339  55.976  -3.057  -2.459  -0.859  -0.000  -0.000  -0.000
   5_bss:  0.332  55.976  -2.884  -2.406  -0.742  -0.000  -0.000  -0.000
   5_xyz:  0.332  55.976  -2.884  -2.406  -0.742  -0.000  -0.000  -0.000
   5_adp:  0.332  55.976  -2.884  -2.406  -0.742  -0.000  -0.000  -0.000
   5_occ:  0.332  55.976  -2.884  -2.406  -0.742  -0.000  -0.000  -0.000
   5_bss:  0.328  55.979  -2.683  -2.275  -0.556  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  44.553 0.5893  0.7735    47078.721
   1_bss:  43.429 0.6008  0.7944    43745.092
   1_xyz:  27.606 0.7851  0.9870    20433.131
   1_adp:  29.480 0.7635  0.9687    22644.258
   1_occ:  29.522 0.7630  0.9676    22637.814
   2_bss:  29.180 0.7666  0.9216    22214.473
   2_xyz:  21.019 0.8514  0.9880    11982.397
   2_adp:  18.681 0.8748  0.9971    10168.428
   2_occ:  18.626 0.8753  0.9971    10097.999
   3_bss:  18.452 0.8767  0.9793     9908.085
   3_xyz:  15.453 0.9026  0.9900     7302.619
   3_adp:  14.832 0.9082  0.9866     6973.118
   3_occ:  14.823 0.9083  0.9864     6962.767
   4_bss:  14.783 0.9086  0.9779     6931.672
   4_xyz:  13.812 0.9163  0.9821     6227.647
   4_adp:  13.694 0.9175  0.9781     6169.249
   4_occ:  13.692 0.9175  0.9781     6165.513
   5_bss:  13.685 0.9175  0.9822     6162.068
   5_xyz:  13.507 0.9190  0.9828     6057.013
   5_adp:  13.581 0.9185  0.9763     6079.526
   5_occ:  13.580 0.9185  0.9762     6079.037
   5_bss:  13.580 0.9185  0.9825     6079.070
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.7502e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.7502e-01
   1_xyz:   1.314  0.010  0.086 15.312  0.006  4.107   9.5964e-02
   1_adp:   1.314  0.010  0.086 15.312  0.006  4.107   9.5964e-02
   1_occ:   1.314  0.010  0.086 15.312  0.006  4.107   9.5964e-02
   2_bss:   1.314  0.010  0.086 15.312  0.006  4.107   9.5964e-02
   2_xyz:   1.045  0.006  0.074 14.712  0.004  4.109   6.1007e-02
   2_adp:   1.045  0.006  0.074 14.712  0.004  4.109   6.1007e-02
   2_occ:   1.045  0.006  0.074 14.712  0.004  4.109   6.1007e-02
   3_bss:   1.045  0.006  0.074 14.712  0.004  4.109   6.1007e-02
   3_xyz:   0.920  0.006  0.067 14.629  0.003  4.111   5.1524e-02
   3_adp:   0.920  0.006  0.067 14.629  0.003  4.111   5.1524e-02
   3_occ:   0.920  0.006  0.067 14.629  0.003  4.111   5.1524e-02
   4_bss:   0.920  0.006  0.067 14.629  0.003  4.111   5.1524e-02
   4_xyz:   0.910  0.005  0.069 14.492  0.004  4.114   5.0353e-02
   4_adp:   0.910  0.005  0.069 14.492  0.004  4.114   5.0353e-02
   4_occ:   0.910  0.005  0.069 14.492  0.004  4.114   5.0353e-02
   5_bss:   0.910  0.005  0.069 14.492  0.004  4.114   5.0353e-02
   5_xyz:   0.988  0.007  0.075 14.713  0.004  4.108   5.8579e-02
   5_adp:   0.988  0.007  0.075 14.713  0.004  4.108   5.8579e-02
   5_occ:   0.988  0.007  0.075 14.713  0.004  4.108   5.8579e-02
   5_bss:   0.988  0.007  0.075 14.713  0.004  4.108   5.8579e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.585   2.3916e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.585   2.3916e-01
   1_xyz:   9.621  0.045  0.306 87.760  0.067  2.048   1.0120e-01
   1_adp:   9.621  0.045  0.306 87.760  0.067  2.048   1.0120e-01
   1_occ:   9.621  0.045  0.306 87.760  0.067  2.048   1.0120e-01
   2_bss:   9.621  0.045  0.306 87.760  0.067  2.048   1.0120e-01
   2_xyz:   6.518  0.043  0.247 86.010  0.041  2.393   6.6944e-02
   2_adp:   6.518  0.043  0.247 86.010  0.041  2.393   6.6944e-02
   2_occ:   6.518  0.043  0.247 86.010  0.041  2.393   6.6944e-02
   3_bss:   6.518  0.043  0.247 86.010  0.041  2.393   6.6944e-02
   3_xyz:   6.665  0.049  0.212 82.591  0.031  2.342   3.9381e-02
   3_adp:   6.665  0.049  0.212 82.591  0.031  2.342   3.9381e-02
   3_occ:   6.665  0.049  0.212 82.591  0.031  2.342   3.9381e-02
   4_bss:   6.665  0.049  0.212 82.591  0.031  2.342   3.9381e-02
   4_xyz:   6.611  0.042  0.217 83.599  0.034  2.354   3.2281e-02
   4_adp:   6.611  0.042  0.217 83.599  0.034  2.354   3.2281e-02
   4_occ:   6.611  0.042  0.217 83.599  0.034  2.354   3.2281e-02
   5_bss:   6.611  0.042  0.217 83.599  0.034  2.354   3.2281e-02
   5_xyz:   6.586  0.050  0.262 84.615  0.035  2.323   4.3706e-02
   5_adp:   6.586  0.050  0.262 84.615  0.035  2.323   4.3706e-02
   5_occ:   6.586  0.050  0.262 84.615  0.035  2.323   4.3706e-02
   5_bss:   6.586  0.050  0.262 84.615  0.035  2.323   4.3706e-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:  86.89   0.00  17.80  72.00   0.00  13.77  86.89   2.41  39.73
   1_occ:  86.89   0.00  17.80  72.00   0.00  13.77  86.89   2.41  39.73
   2_bss:  86.89   0.00  17.80  72.00   0.00  13.77  86.89   2.41  39.73
   2_xyz:  86.89   0.00  17.80  72.00   0.00  13.77  86.89   2.41  39.73
   2_adp:  77.99   0.98  16.98  75.92   0.98  13.07  77.99   6.17  38.26
   2_occ:  77.99   0.98  16.98  75.92   0.98  13.07  77.99   6.17  38.26
   3_bss:  77.99   0.98  16.98  75.92   0.98  13.07  77.99   6.17  38.26
   3_xyz:  77.99   0.98  16.98  75.92   0.98  13.07  77.99   6.17  38.26
   3_adp:  79.75   1.01  16.84  79.75   1.01  12.84  76.27   3.63  38.65
   3_occ:  79.75   1.01  16.84  79.75   1.01  12.84  76.27   3.63  38.65
   4_bss:  79.75   1.01  16.84  79.75   1.01  12.84  76.27   3.63  38.65
   4_xyz:  79.75   1.01  16.84  79.75   1.01  12.84  76.27   3.63  38.65
   4_adp:  83.81   0.93  16.88  83.81   0.93  12.77  76.85   3.18  39.23
   4_occ:  83.81   0.93  16.88  83.81   0.93  12.77  76.85   3.18  39.23
   5_bss:  83.81   0.93  16.88  83.81   0.93  12.77  76.85   3.18  39.23
   5_xyz:  83.81   0.93  16.88  83.81   0.93  12.77  76.85   3.18  39.23
   5_adp:  88.17   0.00  16.97  88.17   0.00  12.70  79.51   4.66  40.21
   5_occ:  88.17   0.00  16.97  88.17   0.00  12.70  79.51   4.66  40.21
   5_bss:  88.17   0.00  16.97  88.17   0.00  12.70  79.51   4.67  40.21
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.675    0.032    0.372
   1_adp:    1.675    0.032    0.372
   1_occ:    1.675    0.032    0.372
   2_bss:    1.675    0.032    0.372
   2_xyz:    1.418    0.016    0.477
   2_adp:    1.418    0.016    0.477
   2_occ:    1.418    0.016    0.477
   3_bss:    1.418    0.016    0.477
   3_xyz:    1.291    0.026    0.550
   3_adp:    1.291    0.026    0.550
   3_occ:    1.291    0.026    0.550
   4_bss:    1.291    0.026    0.550
   4_xyz:    1.316    0.054    0.569
   4_adp:    1.316    0.054    0.569
   4_occ:    1.316    0.054    0.569
   5_bss:    1.316    0.054    0.569
   5_xyz:    1.427    0.088    0.586
   5_adp:    1.427    0.088    0.586
   5_occ:    1.427    0.088    0.586
   5_bss:    1.427    0.088    0.586
------------------------------------------------------------------------

CPU time actual refinement: 322.30


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_271/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_271/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_271/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_271/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_271/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 322.15 
  Macro-tasks:
    bulk solvent and scale       = 38.56  
    individual site refinement   = 128.48 
    weights calculation          = 30.08  
    collect and process          = 6.64   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 203.89 
  Micro-tasks:
    mask                            = 1.76   
    f_calc                          = 101.07 
    alpha_beta                      = 8.25   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 108.68 
    fmodel                         = 6.55   
    r_factors                      = 0.17   
    phase_errors                   = 10.88  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 238.80 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.642 micro seconds
Total CPU time: 5.59 minutes
from_scatterers_fft:    628 calls, 100.70 s
gradients_fft:          573 calls,  95.75 s

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

# Date 2008-01-16 Time 04:25:52 PST -0800 (1200486352.44 s)
Start R-work = 0.4065, R-free = 0.4013 (no bulk solvent and anisotropic scale)
Final R-work = 0.1328, R-free = 0.1739 (no bulk solvent and anisotropic scale)

Start R-work = 0.3958, R-free = 0.3917
Final R-work = 0.1083, R-free = 0.1543