# Date 2008-01-16 Time 04:09:12 PST -0800 (1200485352.82 s)
#phil __OFF__

Command line arguments: "../201.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 24753
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 201

-------------------------------------------------------------------------------
  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: (68.845, 47.3993, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 47.3993, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8205 1.96066
Completeness in resolution range: 0.949401
Completeness with d_max=infinity: 0.946466

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8205
                             d_min =   1.9607

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: (68.845, 47.3993, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8205 1.96066
Completeness in resolution range: 0.949401
Completeness with d_max=infinity: 0.946466

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8210 -  4.1952 [2178/2206]  1959   219  10.1%
  bin  2:  4.1952 -  3.3424 [2066/2089]  1859   207  10.0%
  bin  3:  3.3424 -  2.9236 [2057/2082]  1852   205  10.0%
  bin  4:  2.9236 -  2.6579 [2033/2049]  1828   205  10.1%
  bin  5:  2.6579 -  2.4684 [2011/2050]  1806   205  10.2%
  bin  6:  2.4684 -  2.3234 [2032/2064]  1837   195   9.6%
  bin  7:  2.3234 -  2.2075 [1993/2030]  1790   203  10.2%
  bin  8:  2.2075 -  2.1116 [1991/2033]  1795   196   9.8%
  bin  9:  2.1116 -  2.0306 [1979/2018]  1784   195   9.9%
  bin 10:  2.0306 -  1.9607 [1249/2012]  1120   129  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_201/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:
        1.29 -     2.01: 12
        2.01 -     2.73: 239
        2.73 -     3.45: 4686
        3.45 -     4.18: 9468
        4.18 -     4.90: 14215
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.287 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.554 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.600 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.672 3.040 -x+1,y-1/2,-z+1/2
  " C   GLY A  91 " - " O   HOH Z 401 "  1.805 3.270 -x+1,y-1/2,-z+1/2
  ... (remaining 28615 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_201/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_201/model_refine_001.geo

CPU time processing inputs: 9.33


============================ 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 = 68.845 47.3993 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3895   r_free= 0.3864   ksol= 0.00   Bsol= 0.00   scale= 0.951    |
|                                                                             |
| 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:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.167265                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8210 -  4.6790 0.99   1408  158 0.3186 0.3270      6.4326      6.4883|
|  2:  4.6790 -  3.7334 0.99   1356  149 0.3131 0.2979      6.5893      6.5803|
|  3:  3.7334 -  3.2672 0.99   1330  150 0.3389 0.3189      6.4771      6.5421|
|  4:  3.2672 -  2.9711 0.99   1311  138 0.3631 0.3779        6.35       6.342|
|  5:  2.9711 -  2.7596 0.98   1312  148 0.3949 0.3601      6.2253      6.1794|
|  6:  2.7596 -  2.5978 0.99   1298  144 0.4169 0.4149      6.1705      6.0478|
|  7:  2.5978 -  2.4684 0.99   1289  154 0.4183 0.3974      6.1478      6.0592|
|  8:  2.4684 -  2.3614 0.99   1328  135 0.4310 0.4564      6.0861       6.104|
|  9:  2.3614 -  2.2708 0.99   1278  146 0.4604 0.4646      6.0507      6.1196|
| 10:  2.2708 -  2.1927 0.98   1277  140 0.4360 0.4754      6.0237      6.0676|
| 11:  2.1927 -  2.1243 0.98   1282  149 0.4558 0.4862      5.9686      5.9952|
| 12:  2.1243 -  2.0638 1.00   1284  142 0.4568 0.4331      5.9086      5.9303|
| 13:  2.0638 -  2.0096 0.96   1276  130 0.4620 0.4754      5.8357      5.8323|
| 14:  2.0096 -  1.9607 0.48    601   76 0.4838 0.4496        5.83      5.6589|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8210 -  4.6790  1408   158  0.74  30.69   0.86     0.75      55666.13|
|  2:  4.6790 -  3.7334  1356   149  0.79  27.41   0.97     0.88      67207.70|
|  3:  3.7334 -  3.2672  1330   150  0.74  31.90   0.98     0.92      66526.16|
|  4:  3.2672 -  2.9711  1311   138  0.70  35.77   0.98     0.90      56739.20|
|  5:  2.9711 -  2.7596  1312   148  0.65  39.47   0.95     0.87      45417.50|
|  6:  2.7596 -  2.5978  1298   144  0.64  40.88   0.96     0.85      39637.61|
|  7:  2.5978 -  2.4684  1289   154  0.64  40.49   0.97     0.84      36807.21|
|  8:  2.4684 -  2.3614  1328   135  0.59  44.78   0.99     0.81      37377.41|
|  9:  2.3614 -  2.2708  1278   146  0.55  48.43   0.96     0.77      36938.14|
| 10:  2.2708 -  2.1927  1277   140  0.52  50.48   1.02     0.74      36771.27|
| 11:  2.1927 -  2.1243  1282   149  0.51  51.75   0.99     0.74      34946.37|
| 12:  2.1243 -  2.0638  1284   142  0.50  52.45   1.01     0.76      32572.26|
| 13:  2.0638 -  2.0096  1276   130  0.50  52.59   0.99     0.74      27390.56|
| 14:  2.0096 -  1.9607   601    76  0.53  49.82   0.98     0.69      21097.66|
|alpha:            min =        0.69 max =            0.92 mean =         0.81|
|beta:             min =    21097.66 max =        67207.70 mean =     43613.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.62|
|phase err.(work): min =        0.00 max =           90.00 mean =        42.16|
|phase err.(test): min =        0.00 max =           89.91 mean =        42.16|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.063464              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.642   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.104012              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.278   (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 |  1.287 -  1.648:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.648 -  2.009:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.009 -  2.371:       25 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.371 -  2.732:      214 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.732 -  3.093:     2338 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.093 -  3.455:     2348 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.455 -  3.816:     4224 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.816 -  4.177:     5244 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.177 -  4.539:     6385 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.539 -  4.900:     7830 |
|-----------------------------------------------------------------------------|
|-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 |        0.191 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.287 |       0.628 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.601)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3895   r_free= 0.3864   ksol= 0.00   Bsol= 0.00   scale= 0.951    |
|                                                                             |
| 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:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.167265                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3801   r_free= 0.3758   ksol= 0.31   Bsol= 25.81   scale= 0.976   |
|                                                                             |
| 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:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.154785                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.521321              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.443   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.590258              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.014   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3801      final r-factor (work) = 0.2329          |
| start r-factor (free) = 0.3758      final r-factor (free) = 0.2522          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.1161 = 4.52 * 0.50 * 6.1595 + 1.00 * 0.1915                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.4701 = 4.52 * 0.50 * 5.9231 + 1.00 * 0.0800                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2329      final r-factor (work) = 0.2123          |
| start r-factor (free) = 0.2522      final r-factor (free) = 0.2594          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5024 = 0.59 * 1.00 * 5.9231 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3664 = 0.59 * 1.00 * 5.6734 + 1.00 * 0.0176                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.601)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    66.44   17.27    None  None   None       |
|    all(noH): 2823   0      0.00    66.44   17.27    None  None   None       |
|    Sol.    : 438    0      7.28    66.44   38.48    None  None   None       |
|    Mac.    : 2385   0      0.00    58.20   13.38    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.644:  423   |   5:    33.222 -  39.867:  122        |
|      1:     6.644 -  13.289: 1034   |   6:    39.867 -  46.511:  104        |
|      2:    13.289 -  19.933:  590   |   7:    46.511 -  53.155:   95        |
|      3:    19.933 -  26.578:  265   |   8:    53.155 -  59.800:   53        |
|      4:    26.578 -  33.222:  128   |   9:    59.800 -  66.444:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2123 r_free = 0.2594             target_work(ml) = 5.685         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2119 r_free = 0.2595             target_work(ml) = 5.684         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2119   r_free= 0.2595   ksol= 0.31   Bsol= 25.81   scale= 1.043   |
|                                                                             |
| 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:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.684312                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2082   r_free= 0.2562   ksol= 0.32   Bsol= 36.86   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-1.44,-1.41,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.676546                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.219471              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.216   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.247581              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.988   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2082      final r-factor (work) = 0.1518          |
| start r-factor (free) = 0.2562      final r-factor (free) = 0.1956          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3899 = 2.22 * 0.50 * 5.6859 + 1.00 * 0.0800                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2101 = 2.22 * 0.50 * 5.5449 + 1.00 * 0.0566                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1518      final r-factor (work) = 0.1412          |
| start r-factor (free) = 0.1956      final r-factor (free) = 0.1830          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3915 = 0.25 * 1.00 * 5.5449 + 1.00 * 0.0187                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3348 = 0.25 * 1.00 * 5.3592 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.601)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.92    78.12   17.17    None  None   None       |
|    all(noH): 2823   0      0.92    78.12   17.17    None  None   None       |
|    Sol.    : 438    0      5.57    69.69   38.74    None  None   None       |
|    Mac.    : 2385   0      0.92    78.12   13.21    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:     0.922 -   8.642:  659   |   5:    39.521 -  47.241:  122        |
|      1:     8.642 -  16.362: 1266   |   6:    47.241 -  54.961:   94        |
|      2:    16.362 -  24.081:  361   |   7:    54.961 -  62.680:   43        |
|      3:    24.081 -  31.801:  135   |   8:    62.680 -  70.400:   18        |
|      4:    31.801 -  39.521:  122   |   9:    70.400 -  78.120:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1412 r_free = 0.1830             target_work(ml) = 5.328         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1410 r_free = 0.1829             target_work(ml) = 5.327         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1410   r_free= 0.1829   ksol= 0.32   Bsol= 36.86   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-1.44,-1.41,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.327347                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1415   r_free= 0.1824   ksol= 0.32   Bsol= 36.86   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-1.69,-1.54,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.327957                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.875827              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.455   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.200200              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.776  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1415      final r-factor (work) = 0.1203          |
| start r-factor (free) = 0.1824      final r-factor (free) = 0.1623          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0844 = 1.88 * 0.50 * 5.3606 + 1.00 * 0.0566                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9816 = 1.88 * 0.50 * 5.2542 + 1.00 * 0.0537                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1203      final r-factor (work) = 0.1176          |
| start r-factor (free) = 0.1623      final r-factor (free) = 0.1600          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0598 = 0.20 * 1.00 * 5.2542 + 1.00 * 0.0079                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0454 = 0.20 * 1.00 * 5.1848 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.601)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.91    81.04   16.94    None  None   None       |
|    all(noH): 2823   0      1.91    81.04   16.94    None  None   None       |
|    Sol.    : 438    0      2.37    72.69   38.38    None  None   None       |
|    Mac.    : 2385   0      1.91    81.04   13.00    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:     1.911 -   9.823:  938   |   5:    41.473 -  49.386:  120        |
|      1:     9.823 -  17.736: 1133   |   6:    49.386 -  57.298:   86        |
|      2:    17.736 -  25.648:  266   |   7:    57.298 -  65.211:   28        |
|      3:    25.648 -  33.561:  119   |   8:    65.211 -  73.124:    9        |
|      4:    33.561 -  41.473:  121   |   9:    73.124 -  81.036:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1176 r_free = 0.1600             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1175 r_free = 0.1599             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1175   r_free= 0.1599   ksol= 0.32   Bsol= 36.86   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-1.69,-1.54,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.174285                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1175   r_free= 0.1599   ksol= 0.32   Bsol= 40.15   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-1.69,-1.54,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.174176                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.279615              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 137.259  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.437763              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.837  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1175      final r-factor (work) = 0.1105          |
| start r-factor (free) = 0.1599      final r-factor (free) = 0.1550          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9629 = 2.28 * 0.50 * 5.1844 + 1.00 * 0.0537                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9275 = 2.28 * 0.50 * 5.1477 + 1.00 * 0.0601                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1105      final r-factor (work) = 0.1092          |
| start r-factor (free) = 0.1550      final r-factor (free) = 0.1554          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2609 = 0.44 * 1.00 * 5.1477 + 1.00 * 0.0074                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2516 = 0.44 * 1.00 * 5.1249 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.601)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.56    85.11   16.91    None  None   None       |
|    all(noH): 2823   0      1.56    85.11   16.91    None  None   None       |
|    Sol.    : 438    0      3.46    75.81   38.84    None  None   None       |
|    Mac.    : 2385   0      1.56    85.11   12.89    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:     1.564 -   9.919:  987   |   5:    43.337 -  51.691:  116        |
|      1:     9.919 -  18.273: 1124   |   6:    51.691 -  60.046:   78        |
|      2:    18.273 -  26.628:  245   |   7:    60.046 -  68.400:   24        |
|      3:    26.628 -  34.982:  127   |   8:    68.400 -  76.755:    8        |
|      4:    34.982 -  43.337:  109   |   9:    76.755 -  85.109:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1092 r_free = 0.1554             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1092 r_free = 0.1554             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1092   r_free= 0.1554   ksol= 0.32   Bsol= 40.15   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-1.69,-1.54,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.126824                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1092   r_free= 0.1544   ksol= 0.32   Bsol= 42.56   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-1.69,-1.54,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.125088                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.215932              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 145.388  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.886350              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.573  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1092      final r-factor (work) = 0.1051          |
| start r-factor (free) = 0.1544      final r-factor (free) = 0.1544          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3004 = 3.22 * 0.50 * 5.1247 + 1.00 * 0.0601                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2868 = 3.22 * 0.50 * 5.1096 + 1.00 * 0.0708                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1051      final r-factor (work) = 0.1047          |
| start r-factor (free) = 0.1544      final r-factor (free) = 0.1548          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5370 = 0.89 * 1.00 * 5.1096 + 1.00 * 0.0082                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5327 = 0.89 * 1.00 * 5.1039 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.601)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.98    87.32   16.85    None  None   None       |
|    all(noH): 2823   0      0.98    87.32   16.85    None  None   None       |
|    Sol.    : 438    0      5.31    79.45   39.13    None  None   None       |
|    Mac.    : 2385   0      0.98    87.32   12.76    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:     0.983 -   9.616:  968   |   5:    44.149 -  52.782:  103        |
|      1:     9.616 -  18.249: 1146   |   6:    52.782 -  61.415:   77        |
|      2:    18.249 -  26.882:  249   |   7:    61.415 -  70.049:   22        |
|      3:    26.882 -  35.516:  124   |   8:    70.049 -  78.682:    7        |
|      4:    35.516 -  44.149:  121   |   9:    78.682 -  87.315:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1047 r_free = 0.1548             target_work(ml) = 5.107         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1047 r_free = 0.1548             target_work(ml) = 5.107         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1047   r_free= 0.1548   ksol= 0.32   Bsol= 42.56   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-1.69,-1.54,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.106517                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8210 -  4.6790 0.99   1408  158 0.0934 0.1257      5.3354      5.5142|
|  2:  4.6790 -  3.7334 0.99   1356  149 0.0798 0.1088      5.3898      5.6123|
|  3:  3.7334 -  3.2672 0.99   1330  150 0.1002 0.1483      5.4252      5.8063|
|  4:  3.2672 -  2.9711 0.99   1311  138 0.1130 0.1513      5.4026      5.5917|
|  5:  2.9711 -  2.7596 0.98   1312  148 0.1224 0.1680      5.2755      5.4916|
|  6:  2.7596 -  2.5978 0.99   1298  144 0.1166 0.1870      5.1831      5.4194|
|  7:  2.5978 -  2.4684 0.99   1289  154 0.1110 0.1622      5.1037      5.3659|
|  8:  2.4684 -  2.3614 0.99   1328  135 0.1100 0.1640       5.042      5.2687|
|  9:  2.3614 -  2.2708 0.99   1278  146 0.1092 0.1793      4.9812      5.3104|
| 10:  2.2708 -  2.1927 0.98   1277  140 0.1046 0.1692       4.924      5.1635|
| 11:  2.1927 -  2.1243 0.98   1282  149 0.1071 0.1808      4.8952      5.2152|
| 12:  2.1243 -  2.0638 1.00   1284  142 0.1023 0.1628      4.8161      5.1325|
| 13:  2.0638 -  2.0096 0.96   1276  130 0.1055 0.1673      4.7507      5.0053|
| 14:  2.0096 -  1.9607 0.48    601   76 0.1006 0.1843      4.6752      4.9298|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8210 -  4.6790  1408   158  0.94   8.72   0.98     0.96       6579.11|
|  2:  4.6790 -  3.7334  1356   149  0.96   7.60   1.02     1.01       8479.47|
|  3:  3.7334 -  3.2672  1330   150  0.94  10.79   1.03     1.02       9677.24|
|  4:  3.2672 -  2.9711  1311   138  0.92  13.23   1.01     1.01       9752.27|
|  5:  2.9711 -  2.7596  1312   148  0.90  15.47   1.00     0.98       7820.78|
|  6:  2.7596 -  2.5978  1298   144  0.90  15.96   0.98     0.94       6784.43|
|  7:  2.5978 -  2.4684  1289   154  0.91  14.63   0.99     0.96       5711.71|
|  8:  2.4684 -  2.3614  1328   135  0.91  14.80   1.00     0.98       5224.93|
|  9:  2.3614 -  2.2708  1278   146  0.91  15.16   1.00     0.96       4643.66|
| 10:  2.2708 -  2.1927  1277   140  0.90  15.48   0.99     0.96       4276.74|
| 11:  2.1927 -  2.1243  1282   149  0.91  15.50   1.00     0.97       4151.62|
| 12:  2.1243 -  2.0638  1284   142  0.92  14.69   1.01     1.00       3598.32|
| 13:  2.0638 -  2.0096  1276   130  0.90  15.83   1.00     0.98       3212.20|
| 14:  2.0096 -  1.9607   601    76  0.91  14.87   0.97     0.93       2670.03|
|alpha:            min =        0.93 max =            1.02 mean =         0.98|
|beta:             min =     2670.03 max =         9752.27 mean =      6059.43|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.66|
|phase err.(test): min =        0.00 max =           89.93 mean =        13.25|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1046   r_free= 0.1548   ksol= 0.32   Bsol= 42.70   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-1.56,-1.23,-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: 5.106709                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.82 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1046   r_free= 0.1548   ksol= 0.32   Bsol= 42.70   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-1.56,-1.23,-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: 5.106709                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8210 -  4.6790 0.99   1408  158 0.0935 0.1260      5.3377      5.5167|
|  2:  4.6790 -  3.7334 0.99   1356  149 0.0798 0.1088      5.3905      5.6119|
|  3:  3.7334 -  3.2672 0.99   1330  150 0.1001 0.1483       5.425      5.8066|
|  4:  3.2672 -  2.9711 0.99   1311  138 0.1130 0.1512      5.4025      5.5914|
|  5:  2.9711 -  2.7596 0.98   1312  148 0.1225 0.1680      5.2752      5.4913|
|  6:  2.7596 -  2.5978 0.99   1298  144 0.1166 0.1866      5.1827      5.4179|
|  7:  2.5978 -  2.4684 0.99   1289  154 0.1110 0.1622      5.1032      5.3658|
|  8:  2.4684 -  2.3614 0.99   1328  135 0.1099 0.1640      5.0417      5.2683|
|  9:  2.3614 -  2.2708 0.99   1278  146 0.1093 0.1793      4.9814      5.3106|
| 10:  2.2708 -  2.1927 0.98   1277  140 0.1046 0.1695      4.9246       5.165|
| 11:  2.1927 -  2.1243 0.98   1282  149 0.1071 0.1808      4.8954      5.2155|
| 12:  2.1243 -  2.0638 1.00   1284  142 0.1022 0.1630      4.8164      5.1339|
| 13:  2.0638 -  2.0096 0.96   1276  130 0.1055 0.1671      4.7508      5.0049|
| 14:  2.0096 -  1.9607 0.48    601   76 0.1007 0.1842      4.6747      4.9287|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8210 -  4.6790  1408   158  0.94   8.75   0.98     0.96       6616.21|
|  2:  4.6790 -  3.7334  1356   149  0.96   7.61   1.02     1.01       8498.02|
|  3:  3.7334 -  3.2672  1330   150  0.94  10.79   1.04     1.03       9673.83|
|  4:  3.2672 -  2.9711  1311   138  0.92  13.24   1.02     1.01       9752.06|
|  5:  2.9711 -  2.7596  1312   148  0.90  15.46   1.01     0.98       7807.70|
|  6:  2.7596 -  2.5978  1298   144  0.90  15.95   0.98     0.95       6777.42|
|  7:  2.5978 -  2.4684  1289   154  0.91  14.62   0.99     0.96       5703.51|
|  8:  2.4684 -  2.3614  1328   135  0.91  14.80   1.01     0.98       5223.65|
|  9:  2.3614 -  2.2708  1278   146  0.91  15.17   1.01     0.97       4644.83|
| 10:  2.2708 -  2.1927  1277   140  0.90  15.49   1.00     0.97       4282.60|
| 11:  2.1927 -  2.1243  1282   149  0.91  15.52   1.01     0.98       4157.82|
| 12:  2.1243 -  2.0638  1284   142  0.91  14.70   1.02     1.01       3602.79|
| 13:  2.0638 -  2.0096  1276   130  0.90  15.83   1.01     0.99       3210.69|
| 14:  2.0096 -  1.9607   601    76  0.91  14.84   0.99     0.94       2664.41|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2664.41 max =         9752.06 mean =      6062.34|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.66|
|phase err.(test): min =        0.00 max =           89.93 mean =        13.26|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.601)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.95    87.28   16.82    None  None   None       |
|    all(noH): 2823   0      0.95    87.28   16.82    None  None   None       |
|    Sol.    : 438    0      5.27    79.41   39.10    None  None   None       |
|    Mac.    : 2385   0      0.95    87.28   12.73    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:     0.949 -   9.582:  968   |   5:    44.115 -  52.748:  103        |
|      1:     9.582 -  18.215: 1146   |   6:    52.748 -  61.382:   77        |
|      2:    18.215 -  26.849:  249   |   7:    61.382 -  70.015:   22        |
|      3:    26.849 -  35.482:  124   |   8:    70.015 -  78.648:    7        |
|      4:    35.482 -  44.115:  121   |   9:    78.648 -  87.281:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 281         
Filter by distance & map next to the model:
   mapped sites are within: 0.525 - 4.225
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 279 from: 281
   mapped sites are within: 0.725 - 4.225

peak=    5.653 closest distance to " CB  ARG A 275 " =    0.955
peak=    5.448 closest distance to " NH2 ARG A  56 " =    2.233
peak=    5.237 closest distance to " O   HOH Z 142 " =    1.644
peak=    5.093 closest distance to " CB  SER A  63 " =    1.098
peak=    5.032 closest distance to " CB  GLN A 183 " =    1.317
peak=    4.912 closest distance to " CG  PRO A  54 " =    1.202
peak=    4.884 closest distance to " NE2 GLN A  11 " =    1.026
peak=    4.788 closest distance to " O   HOH Z 232 " =    2.349
peak=    4.767 closest distance to " O   HOH Z 272 " =    1.832
peak=    4.718 closest distance to " CB  GLN A 223 " =    1.434
peak=    4.717 closest distance to " CA  TYR A  30 " =    0.906
peak=    4.709 closest distance to " O   HOH Z 298 " =    1.774
peak=    4.703 closest distance to " O   HOH Z 126 " =    1.832
peak=    4.648 closest distance to " O   HOH Z 193 " =    1.756
peak=    4.610 closest distance to " O   HOH Z 209 " =    2.250
peak=    4.557 closest distance to " CB  ARG A  79 " =    1.367
peak=    4.547 closest distance to " CB  GLU A 152 " =    1.199
peak=    4.529 closest distance to " O   HOH Z 403 " =    1.846
peak=    4.523 closest distance to " C   PRO A 198 " =    1.449
peak=    4.515 closest distance to " O   SER A  87 " =    2.183
peak=    4.496 closest distance to " O   HOH Z  97 " =    1.897
peak=    4.471 closest distance to " CG  PRO A 213 " =    1.194
peak=    4.448 closest distance to " O   HOH Z 234 " =    3.615
peak=    4.441 closest distance to " O   HOH Z  15 " =    2.089
peak=    4.372 closest distance to " O   HOH Z 236 " =    2.083
peak=    4.317 closest distance to " O   HOH Z 327 " =    1.720
peak=    4.297 closest distance to " O   HOH Z 402 " =    1.449
peak=    4.288 closest distance to " NZ  LYS A 117 " =    3.138
peak=    4.270 closest distance to " O   HOH Z  78 " =    1.655
peak=    4.250 closest distance to " O   HOH Z  44 " =    1.981
peak=    4.249 closest distance to " O   HOH Z 368 " =    2.012
peak=    4.246 closest distance to " CD2 TRP A 179 " =    1.414
peak=    4.244 closest distance to " O   HOH Z  54 " =    1.721
peak=    4.190 closest distance to " O   HOH Z 369 " =    2.277
peak=    4.182 closest distance to " CG1 ILE A  33 " =    1.227
peak=    4.154 closest distance to " NH2BARG A 145 " =    2.028
peak=    4.153 closest distance to " CG  ARG A  66 " =    2.764
peak=    4.150 closest distance to " CB  ASN A 148 " =    1.452
peak=    4.135 closest distance to " OE1 GLU A   2 " =    2.266
peak=    4.121 closest distance to " O   HOH Z  43 " =    2.022
peak=    4.103 closest distance to " CB  TYR A 169 " =    0.885
peak=    4.102 closest distance to " O   HOH Z 203 " =    1.740
peak=    4.088 closest distance to " CB  ARG A 190 " =    1.705
peak=    4.076 closest distance to " ND2 ASN A 187 " =    1.463
peak=    4.044 closest distance to " CB  SER A   3 " =    1.202
peak=    4.037 closest distance to " CB  GLU A 277 " =    3.485
peak=    4.028 closest distance to " CA  ALA A  21 " =    1.208
peak=    4.021 closest distance to " O   HOH Z  63 " =    1.932
peak=    4.012 closest distance to " O   HOH Z 346 " =    1.602
peak=    4.011 closest distance to " O   HOH Z 128 " =    1.877
peak=    4.009 closest distance to " O   HOH Z 128 " =    2.142
peak=    4.004 closest distance to " O   HOH Z 316 " =    2.938
peak=    4.003 closest distance to " O   HOH Z 227 " =    1.585
peak=    3.990 closest distance to " O   HOH Z 124 " =    1.297
peak=    3.982 closest distance to " O   HOH Z  40 " =    1.812
peak=    3.955 closest distance to " CB  VAL A 265 " =    1.289
peak=    3.947 closest distance to " O   HOH Z 144 " =    2.118
peak=    3.943 closest distance to " O   HOH Z  59 " =    2.183
peak=    3.942 closest distance to " CG2 ILE A  20 " =    1.386
peak=    3.928 closest distance to " CD  ARG A 269 " =    0.998
peak=    3.924 closest distance to " CB  SER A  26 " =    1.643
peak=    3.907 closest distance to " O   HOH Z 284 " =    2.882
peak=    3.905 closest distance to " O   HOH Z 265 " =    2.268
peak=    3.902 closest distance to " OD1 ASN A  69 " =    2.560
peak=    3.899 closest distance to " O   HOH Z 132 " =    2.415
peak=    3.895 closest distance to " O   HOH Z 245 " =    1.363
peak=    3.883 closest distance to " O   HOH Z 427 " =    2.753
peak=    3.880 closest distance to " O   HOH Z 197 " =    2.778
peak=    3.879 closest distance to " O   HOH Z 389 " =    1.902
peak=    3.878 closest distance to " O   HOH Z 345 " =    2.788
peak=    3.862 closest distance to " O   HOH Z 147 " =    1.756
peak=    3.861 closest distance to " O   HOH Z 250 " =    1.463
peak=    3.853 closest distance to " O   HOH Z 421 " =    1.684
peak=    3.846 closest distance to " OD2 ASP A 286 " =    2.746
peak=    3.834 closest distance to " CB  PRO A  54 " =    0.867
peak=    3.833 closest distance to " O   HOH Z 423 " =    1.965
peak=    3.826 closest distance to " O   HOH Z  97 " =    2.514
peak=    3.822 closest distance to " CG  ARG A  66 " =    0.978
peak=    3.822 closest distance to " O   HOH Z  80 " =    1.648
peak=    3.821 closest distance to " O   HOH Z 303 " =    2.163
peak=    3.818 closest distance to " OD2 ASP A 298 " =    3.923
peak=    3.817 closest distance to " O   HOH Z 426 " =    1.462
peak=    3.816 closest distance to " CA  ALA A  84 " =    1.215
peak=    3.801 closest distance to " O   HOH Z 158 " =    2.970
peak=    3.801 closest distance to " CA  ASN A 176 " =    1.120
peak=    3.782 closest distance to " O   HOH Z  49 " =    2.083
peak=    3.779 closest distance to " O   HOH Z 261 " =    1.646
peak=    3.761 closest distance to " O   HOH Z 126 " =    1.852
peak=    3.744 closest distance to " CB  TRP A 179 " =    1.203
peak=    3.742 closest distance to " O   HOH Z 417 " =    3.084
peak=    3.733 closest distance to " CB  ARG A 139 " =    0.918
peak=    3.719 closest distance to " O   HOH Z 102 " =    1.304
peak=    3.711 closest distance to " O   HOH Z 189 " =    1.939
peak=    3.708 closest distance to " O   HOH Z 357 " =    1.842
peak=    3.703 closest distance to " O   HOH Z 344 " =    2.972
peak=    3.692 closest distance to " O   HOH Z  61 " =    1.539
peak=    3.685 closest distance to " O   HOH Z 416 " =    2.740
peak=    3.684 closest distance to " O   HOH Z 406 " =    1.538
peak=    3.669 closest distance to " O   HOH Z 365 " =    2.744
peak=    3.662 closest distance to " CB  GLU A 128 " =    1.199
peak=    3.650 closest distance to " O   HOH Z 134 " =    1.265
peak=    3.649 closest distance to " O   HOH Z  21 " =    1.826
peak=    3.646 closest distance to " CG  LYS A  76 " =    1.068
peak=    3.641 closest distance to " OG BSER A 164 " =    2.257
peak=    3.637 closest distance to " O   HOH Z 337 " =    3.578
peak=    3.636 closest distance to " NH2AARG A 145 " =    2.312
peak=    3.634 closest distance to " CA  LYS A 117 " =    1.241
peak=    3.632 closest distance to " C   ILE A 106 " =    1.905
peak=    3.630 closest distance to " CG  PRO A  90 " =    1.143
peak=    3.629 closest distance to " CA  ALA A 291 " =    0.820
peak=    3.628 closest distance to " CB  ASP A 140 " =    1.017
peak=    3.628 closest distance to " O   HOH Z 380 " =    1.960
peak=    3.626 closest distance to " O   HOH Z 411 " =    3.630
peak=    3.607 closest distance to " O   HOH Z 173 " =    2.032
peak=    3.606 closest distance to " CG1BVAL A  72 " =    1.622
peak=    3.605 closest distance to " N   ASN A  39 " =    1.282
peak=    3.603 closest distance to " O   HOH Z 291 " =    1.416
peak=    3.598 closest distance to " CG  PRO A 243 " =    1.120
peak=    3.594 closest distance to " CB  LEU A 228 " =    1.163
peak=    3.592 closest distance to " O   HOH Z  85 " =    1.318
peak=    3.580 closest distance to " O   HOH Z 425 " =    2.070
peak=    3.580 closest distance to " O   HOH Z 361 " =    3.579
peak=    3.570 closest distance to " CG AARG A 275 " =    1.089
peak=    3.565 closest distance to " CA  ALA A  51 " =    0.937
peak=    3.563 closest distance to " O   HOH Z 214 " =    2.210
peak=    3.561 closest distance to " CB  VAL A 202 " =    1.522
peak=    3.550 closest distance to " O   HOH Z 299 " =    4.225
peak=    3.549 closest distance to " CB  ASN A  39 " =    0.789
peak=    3.542 closest distance to " CG2 ILE A 120 " =    1.118
peak=    3.537 closest distance to " O   HOH Z 279 " =    2.084
peak=    3.537 closest distance to " CE  LYS A 119 " =    1.126
peak=    3.536 closest distance to " O   HOH Z  61 " =    1.503
peak=    3.532 closest distance to " O   HOH Z 380 " =    1.962
peak=    3.528 closest distance to " O   HOH Z 250 " =    1.620
peak=    3.524 closest distance to " NH1AARG A 145 " =    1.229
peak=    3.521 closest distance to " O   HOH Z   1 " =    2.175
peak=    3.513 closest distance to " O   HOH Z  19 " =    1.749
peak=    3.511 closest distance to " CA  ASN A 215 " =    1.153
peak=    3.510 closest distance to " O   HOH Z 298 " =    2.342
peak=    3.504 closest distance to " CB  TYR A 169 " =    0.973
peak=    3.499 closest distance to " O   HOH Z 359 " =    1.510
peak=    3.496 closest distance to " O   HOH Z 132 " =    2.520
peak=    3.495 closest distance to " CD2 LEU A 297 " =    0.915
peak=    3.494 closest distance to " CG  GLN A  58 " =    2.589
peak=    3.492 closest distance to " O   HOH Z  66 " =    2.063
peak=    3.481 closest distance to " O   HOH Z 374 " =    2.525
peak=    3.481 closest distance to " O   ALA A 165 " =    1.381
peak=    3.475 closest distance to " O   HOH Z 156 " =    3.348
peak=    3.475 closest distance to " CA  ARG A  36 " =    1.001
peak=    3.474 closest distance to " O   HOH Z 345 " =    1.626
peak=    3.473 closest distance to " O   HOH Z 334 " =    1.314
peak=    3.473 closest distance to " O  BHOH Z  74 " =    1.363
peak=    3.464 closest distance to " CB  ALA A 248 " =    1.400
peak=    3.460 closest distance to " O   HOH Z  66 " =    2.180
peak=    3.458 closest distance to " CA  ARG A 195 " =    1.238
peak=    3.458 closest distance to " CD  ARG A 159 " =    0.725
peak=    3.454 closest distance to " O   HOH Z  35 " =    2.405
peak=    3.452 closest distance to " O   HOH Z 183 " =    1.531
peak=    3.449 closest distance to " CG2BVAL A  41 " =    0.838
peak=    3.445 closest distance to " CA  ASP A 140 " =    1.112
peak=    3.440 closest distance to " NH2 ARG A 219 " =    1.907
peak=    3.440 closest distance to " CB  TRP A 266 " =    0.994
peak=    3.434 closest distance to " ND2 ASN A 110 " =    1.616
peak=    3.429 closest distance to " O   HOH Z 286 " =    2.176
peak=    3.426 closest distance to " O   HOH Z 148 " =    3.154
peak=    3.414 closest distance to " CA  ASP A 162 " =    1.137
peak=    3.413 closest distance to " O   HOH Z 305 " =    3.604
peak=    3.412 closest distance to " O   HOH Z 303 " =    1.715
peak=    3.409 closest distance to " OG  SER A  62 " =    2.822
peak=    3.404 closest distance to " CA  THR A 221 " =    0.965
peak=    3.399 closest distance to " O   HOH Z 193 " =    2.192
peak=    3.387 closest distance to " O   HOH Z 213 " =    1.703
peak=    3.385 closest distance to " ND1 HIS A  81 " =    1.547
peak=    3.373 closest distance to " CD  LYS A 166 " =    1.290
peak=    3.370 closest distance to " O   HOH Z 166 " =    3.873
peak=    3.369 closest distance to " O   HOH Z  88 " =    3.019
peak=    3.362 closest distance to " CG  GLN A  77 " =    2.060
peak=    3.359 closest distance to " O   HOH Z 171 " =    1.799
peak=    3.358 closest distance to " CZ  PHE A 218 " =    1.067
peak=    3.358 closest distance to " O   HOH Z  47 " =    1.504
peak=    3.358 closest distance to " O   HOH Z 427 " =    3.052
peak=    3.354 closest distance to " O   HOH Z 423 " =    3.351
peak=    3.349 closest distance to " O   HOH Z 257 " =    2.310
peak=    3.348 closest distance to " O   HOH Z 251 " =    1.599
peak=    3.341 closest distance to " O   HOH Z 255 " =    1.593
peak=    3.339 closest distance to " O   HOH Z 313 " =    1.691
peak=    3.338 closest distance to " CB  ALA A   9 " =    1.582
peak=    3.338 closest distance to " O   HOH Z 108 " =    2.561
peak=    3.334 closest distance to " O   HOH Z 336 " =    1.707
peak=    3.333 closest distance to " O   HOH Z 185 " =    1.758
peak=    3.333 closest distance to " O   HOH Z 422 " =    2.619
peak=    3.327 closest distance to " CD2 HIS A  81 " =    1.123
peak=    3.321 closest distance to " O   HOH Z 163 " =    1.434
peak=    3.319 closest distance to " CZ2 TRP A 179 " =    1.701
peak=    3.317 closest distance to " CB  THR A  31 " =    1.757
peak=    3.312 closest distance to " CB  ALA A 291 " =    1.321
peak=    3.306 closest distance to " O   HOH Z 273 " =    2.755
peak=    3.299 closest distance to " CD1 ILE A 106 " =    0.949
peak=    3.299 closest distance to " O   HOH Z  68 " =    1.703
peak=    3.297 closest distance to " CG  PRO A 198 " =    1.291
peak=    3.294 closest distance to " CB  ASN A 285 " =    0.973
peak=    3.290 closest distance to " O   HOH Z 419 " =    1.467
peak=    3.289 closest distance to " O   HOH Z  89 " =    2.136
peak=    3.287 closest distance to " CB  PRO A 163 " =    4.025
peak=    3.286 closest distance to " CB  SER A  62 " =    0.901
peak=    3.285 closest distance to " CG BARG A 102 " =    1.771
peak=    3.283 closest distance to " O   TRP A 274 " =    1.881
peak=    3.275 closest distance to " NH2 ARG A  79 " =    1.332
peak=    3.272 closest distance to " CD1 LEU A 228 " =    1.627
peak=    3.266 closest distance to " CD2 LEU A 255 " =    1.171
peak=    3.257 closest distance to " O   HOH Z 425 " =    1.283
peak=    3.257 closest distance to " CA  MET A 105 " =    1.071
peak=    3.253 closest distance to " O   HOH Z 214 " =    2.333
peak=    3.250 closest distance to " O   HOH Z 435 " =    1.817
peak=    3.247 closest distance to " O   HOH Z  10 " =    1.756
peak=    3.246 closest distance to " O   HOH Z 325 " =    2.338
peak=    3.242 closest distance to " N   ASP A 162 " =    1.149
peak=    3.239 closest distance to " CB  TYR A 116 " =    0.825
peak=    3.236 closest distance to " CA  SER A  32 " =    1.577
peak=    3.234 closest distance to " O   HOH Z 126 " =    1.572
peak=    3.232 closest distance to " O   HOH Z 438 " =    1.863
peak=    3.228 closest distance to " O   HOH Z 267 " =    1.943
peak=    3.221 closest distance to " O   HOH Z  40 " =    2.840
peak=    3.219 closest distance to " CD1 LEU A 300 " =    1.309
peak=    3.219 closest distance to " CD  GLN A 194 " =    1.498
peak=    3.212 closest distance to " CB  SER A 141 " =    1.062
peak=    3.211 closest distance to " CG  MET A 185 " =    1.117
peak=    3.211 closest distance to " O   HOH Z 189 " =    2.525
peak=    3.210 closest distance to " CA  MET A  40 " =    1.074
peak=    3.210 closest distance to " CA  SER A 146 " =    1.790
peak=    3.209 closest distance to " O   HOH Z 353 " =    2.714
peak=    3.208 closest distance to " O   HOH Z  85 " =    2.152
peak=    3.201 closest distance to " CD BLYS A 290 " =    1.250
peak=    3.196 closest distance to " CD  LYS A  76 " =    1.863
peak=    3.194 closest distance to " CD  GLN A 240 " =    1.414
peak=    3.193 closest distance to " CB  ASN A 215 " =    1.108
peak=    3.190 closest distance to " O   HOH Z  87 " =    2.184
peak=    3.188 closest distance to " O   SER A  26 " =    1.670
peak=    3.188 closest distance to " CA  VAL A 125 " =    1.178
peak=    3.186 closest distance to " CB  ASN A 110 " =    1.071
peak=    3.185 closest distance to " O   HOH Z 156 " =    2.524
peak=    3.184 closest distance to " O   HOH Z  68 " =    1.864
peak=    3.181 closest distance to " N   TYR A 116 " =    1.580
peak=    3.181 closest distance to " O   HOH Z 341 " =    1.764
peak=    3.181 closest distance to " CG2 VAL A 257 " =    0.800
peak=    3.181 closest distance to " CB  ILE A 120 " =    1.301
peak=    3.174 closest distance to " O   HOH Z 336 " =    1.727
peak=    3.172 closest distance to " CG2 THR A 294 " =    1.510
peak=    3.170 closest distance to " CD1 LEU A  96 " =    0.759
peak=    3.163 closest distance to " CD  ARG A  79 " =    2.126
peak=    3.157 closest distance to " CB  GLN A 205 " =    1.159
peak=    3.156 closest distance to " O   HOH Z 433 " =    1.865
peak=    3.153 closest distance to " CA  GLY A  80 " =    0.814
peak=    3.152 closest distance to " NH2 ARG A 156 " =    1.123
peak=    3.149 closest distance to " CG  MET A 113 " =    1.133
peak=    3.143 closest distance to " CB  MET A  47 " =    1.091
peak=    3.138 closest distance to " CB  THR A  52 " =    0.857
peak=    3.131 closest distance to " O   HOH Z 152 " =    1.897
peak=    3.119 closest distance to " OE2 GLU A  53 " =    2.107
peak=    3.118 closest distance to " N   ARG A 156 " =    1.368
peak=    3.117 closest distance to " CG2 VAL A 197 " =    1.111
peak=    3.116 closest distance to " O   HOH Z 156 " =    2.838
peak=    3.115 closest distance to " CB  SER A 212 " =    1.079
peak=    3.111 closest distance to " OE1 GLN A  11 " =    1.945
peak=    3.103 closest distance to " CB  GLN A 278 " =    0.867
peak=    3.100 closest distance to " CA  ASN A 217 " =    1.239
peak=    3.097 closest distance to " CG2 VAL A 202 " =    1.158
peak=    3.097 closest distance to " OG BSER A 134 " =    2.837
peak=    3.096 closest distance to " O   HOH Z  63 " =    2.281
peak=    3.091 closest distance to " O   HOH Z 263 " =    1.791
peak=    3.089 closest distance to " O   HOH Z  30 " =    2.123
peak=    3.085 closest distance to " O   HOH Z 286 " =    2.272
peak=    3.084 closest distance to " O   HOH Z  88 " =    2.635
peak=    3.083 closest distance to " O   HOH Z 109 " =    2.159
peak=    3.081 closest distance to " CZ2 TRP A 150 " =    1.223
peak=    3.080 closest distance to " O   HOH Z 123 " =    2.278
peak=    3.078 closest distance to " CG  MET A 185 " =    0.979
peak=    3.057 closest distance to " O   HOH Z  47 " =    1.401
peak=    3.044 closest distance to " CA  VAL A 126 " =    1.190

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 214         
Filter by distance & map next to the model:
   mapped sites are within: 0.729 - 5.874
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 213 from: 214
   mapped sites are within: 0.729 - 5.874

peak=   -4.929 closest distance to " O   HOH Z 266 " =    4.579
peak=   -4.554 closest distance to " C   HIS A 108 " =    1.112
peak=   -4.468 closest distance to " N   ALA A 248 " =    1.745
peak=   -4.312 closest distance to " O   HOH Z  13 " =    1.657
peak=   -4.298 closest distance to " SG  CYS A 254 " =    3.312
peak=   -4.270 closest distance to " O   VAL A  67 " =    2.785
peak=   -4.252 closest distance to " O   HOH Z 377 " =    2.193
peak=   -4.197 closest distance to " OG BSER A 134 " =    1.287
peak=   -4.190 closest distance to " CD  ARG A 156 " =    2.071
peak=   -4.187 closest distance to " OXT GLY A 302 " =    2.796
peak=   -4.158 closest distance to " CD  GLN A  58 " =    1.147
peak=   -4.147 closest distance to " CG  GLN A 223 " =    2.194
peak=   -4.140 closest distance to " CB  PRO A 243 " =    2.652
peak=   -4.122 closest distance to " O   PRO A 163 " =    2.067
peak=   -4.085 closest distance to " CD1 PHE A 130 " =    2.352
peak=   -4.065 closest distance to " O   VAL A  67 " =    2.724
peak=   -4.048 closest distance to " O   HOH Z 165 " =    1.966
peak=   -4.006 closest distance to " CD1 LEU A 101 " =    2.412
peak=   -3.980 closest distance to " O   HOH Z 198 " =    1.894
peak=   -3.966 closest distance to " CG  ASP A 132 " =    2.314
peak=   -3.954 closest distance to " CB  ALA A 291 " =    2.350
peak=   -3.920 closest distance to " O   HOH Z 114 " =    3.318
peak=   -3.904 closest distance to " OG  SER A  97 " =    2.134
peak=   -3.891 closest distance to " CG1 VAL A 112 " =    2.728
peak=   -3.856 closest distance to " O   HOH Z 290 " =    1.050
peak=   -3.852 closest distance to " CA  ASP A 298 " =    1.064
peak=   -3.800 closest distance to " CD1 PHE A  59 " =    1.977
peak=   -3.797 closest distance to " CD  ARG A 139 " =    1.585
peak=   -3.794 closest distance to " O   PHE A 218 " =    1.563
peak=   -3.793 closest distance to " O   HOH Z 353 " =    2.181
peak=   -3.773 closest distance to " O   SER A 210 " =    1.876
peak=   -3.772 closest distance to " N   GLN A  58 " =    1.649
peak=   -3.766 closest distance to " ND2 ASN A 187 " =    1.506
peak=   -3.756 closest distance to " CB  PHE A 192 " =    1.952
peak=   -3.746 closest distance to " O   HOH Z 234 " =    4.019
peak=   -3.741 closest distance to " CB  ALA A 161 " =    2.512
peak=   -3.741 closest distance to " OD2 ASP A 171 " =    2.372
peak=   -3.730 closest distance to " CD1 LEU A  25 " =    2.508
peak=   -3.721 closest distance to " O   GLY A  80 " =    2.409
peak=   -3.719 closest distance to " N   ALA A 248 " =    2.223
peak=   -3.689 closest distance to " O   VAL A 174 " =    2.072
peak=   -3.687 closest distance to " O   HOH Z 407 " =    2.742
peak=   -3.685 closest distance to " O   PRO A 198 " =    1.282
peak=   -3.678 closest distance to " CD2 TYR A  30 " =    2.761
peak=   -3.666 closest distance to " CZ  TYR A 169 " =    1.836
peak=   -3.657 closest distance to " O   MET A  40 " =    2.634
peak=   -3.642 closest distance to " O   HOH Z 372 " =    2.201
peak=   -3.635 closest distance to " OD1 ASN A  39 " =    2.170
peak=   -3.635 closest distance to " OG BSER A 134 " =    1.705
peak=   -3.628 closest distance to " O   HOH Z  88 " =    4.434
peak=   -3.605 closest distance to " CB  ASN A  39 " =    2.276
peak=   -3.601 closest distance to " O   HOH Z 422 " =    1.541
peak=   -3.599 closest distance to " CD1 LEU A 228 " =    2.059
peak=   -3.592 closest distance to " O   HOH Z 351 " =    1.504
peak=   -3.587 closest distance to " OD2 ASP A 191 " =    1.465
peak=   -3.583 closest distance to " CA  GLY A 203 " =    2.291
peak=   -3.567 closest distance to " O   HOH Z  11 " =    2.015
peak=   -3.561 closest distance to " O   HOH Z 126 " =    1.850
peak=   -3.561 closest distance to " O   HOH Z 185 " =    2.316
peak=   -3.555 closest distance to " CG  PHE A 283 " =    2.471
peak=   -3.551 closest distance to " O   HOH Z 166 " =    1.561
peak=   -3.550 closest distance to " CB  ALA A 248 " =    2.277
peak=   -3.547 closest distance to " O   HOH Z 362 " =    5.821
peak=   -3.541 closest distance to " CG2 THR A 178 " =    2.232
peak=   -3.531 closest distance to " CE1 TYR A 247 " =    2.634
peak=   -3.529 closest distance to " CZ3 TRP A 179 " =    1.313
peak=   -3.526 closest distance to " CD1 LEU A 255 " =    2.711
peak=   -3.525 closest distance to " CG  GLN A  58 " =    1.055
peak=   -3.522 closest distance to " O   LEU A 167 " =    1.578
peak=   -3.519 closest distance to " O   SER A 135 " =    1.545
peak=   -3.519 closest distance to " OG  SER A   3 " =    1.738
peak=   -3.510 closest distance to " CB  ASP A 286 " =    1.909
peak=   -3.507 closest distance to " O   HOH Z 102 " =    1.713
peak=   -3.506 closest distance to " O   HOH Z  10 " =    1.468
peak=   -3.506 closest distance to " O   PRO A 198 " =    1.282
peak=   -3.502 closest distance to " CE  MET A 105 " =    2.228
peak=   -3.497 closest distance to " ND2 ASN A  45 " =    1.049
peak=   -3.491 closest distance to " O   HOH Z 196 " =    1.984
peak=   -3.490 closest distance to " CB  PHE A 208 " =    2.246
peak=   -3.487 closest distance to " CG  GLU A  53 " =    1.436
peak=   -3.484 closest distance to " NH1 ARG A 195 " =    2.584
peak=   -3.475 closest distance to " CZ  ARG A  66 " =    1.154
peak=   -3.472 closest distance to " N   ASP A 286 " =    2.319
peak=   -3.470 closest distance to " NE2 GLN A  88 " =    1.733
peak=   -3.470 closest distance to " CD2 LEU A 237 " =    2.413
peak=   -3.466 closest distance to " N   ALA A  43 " =    2.752
peak=   -3.465 closest distance to " NH2 ARG A  79 " =    2.020
peak=   -3.455 closest distance to " O   HOH Z  15 " =    1.586
peak=   -3.452 closest distance to " CG1 VAL A  78 " =    3.081
peak=   -3.449 closest distance to " O   ALA A  34 " =    2.191
peak=   -3.444 closest distance to " ND2 ASN A  39 " =    1.159
peak=   -3.442 closest distance to " O   HOH Z  52 " =    1.415
peak=   -3.441 closest distance to " OD1 ASN A 148 " =    1.552
peak=   -3.438 closest distance to " CG2 ILE A 263 " =    2.128
peak=   -3.437 closest distance to " NH2 ARG A  66 " =    5.172
peak=   -3.436 closest distance to " CD  ARG A 195 " =    5.126
peak=   -3.429 closest distance to " C   ILE A 234 " =    1.394
peak=   -3.428 closest distance to " CZ  PHE A  59 " =    1.621
peak=   -3.424 closest distance to " C   GLN A 205 " =    1.841
peak=   -3.423 closest distance to " O   HOH Z 394 " =    1.515
peak=   -3.418 closest distance to " O   HOH Z 166 " =    1.839
peak=   -3.398 closest distance to " O   HOH Z 389 " =    1.725
peak=   -3.396 closest distance to " CB  ALA A 248 " =    1.990
peak=   -3.375 closest distance to " O   GLY A  75 " =    1.704
peak=   -3.373 closest distance to " OD1 ASP A 171 " =    1.570
peak=   -3.367 closest distance to " O   HOH Z  11 " =    1.793
peak=   -3.362 closest distance to " CA  GLY A 133 " =    1.876
peak=   -3.361 closest distance to " O   ASN A  45 " =    1.794
peak=   -3.360 closest distance to " O   HOH Z 250 " =    1.404
peak=   -3.358 closest distance to " OE1 GLN A 183 " =    1.486
peak=   -3.358 closest distance to " C   PRO A  90 " =    1.503
peak=   -3.357 closest distance to " C   LEU A 143 " =    1.008
peak=   -3.356 closest distance to " O   HOH Z 243 " =    2.012
peak=   -3.352 closest distance to " O   TRP A  92 " =    1.805
peak=   -3.345 closest distance to " CG2 VAL A 189 " =    2.175
peak=   -3.342 closest distance to " N   SER A  12 " =    1.385
peak=   -3.342 closest distance to " O   HOH Z 377 " =    1.644
peak=   -3.341 closest distance to " OG  SER A  26 " =    1.282
peak=   -3.340 closest distance to " ND2 ASN A  45 " =    1.691
peak=   -3.333 closest distance to " O   HOH Z 283 " =    2.009
peak=   -3.329 closest distance to " ND2 ASN A 209 " =    1.497
peak=   -3.329 closest distance to " CD2 TYR A 247 " =    2.372
peak=   -3.328 closest distance to " OG ASER A 134 " =    1.271
peak=   -3.327 closest distance to " NE2 GLN A 194 " =    1.677
peak=   -3.322 closest distance to " CG  ASP A 231 " =    0.839
peak=   -3.322 closest distance to " O   ALA A 161 " =    1.653
peak=   -3.321 closest distance to " O   HOH Z 414 " =    1.463
peak=   -3.316 closest distance to " O   HOH Z  71 " =    1.808
peak=   -3.309 closest distance to " O   HOH Z 193 " =    1.694
peak=   -3.308 closest distance to " CG1AVAL A  41 " =    2.731
peak=   -3.308 closest distance to " O   HOH Z 311 " =    3.606
peak=   -3.308 closest distance to " NH2 ARG A  56 " =    2.192
peak=   -3.305 closest distance to " O   HOH Z  60 " =    2.353
peak=   -3.305 closest distance to " O   HOH Z 198 " =    1.489
peak=   -3.304 closest distance to " O   HOH Z 427 " =    1.393
peak=   -3.301 closest distance to " CD  GLN A 223 " =    1.386
peak=   -3.300 closest distance to " O   HOH Z   6 " =    1.720
peak=   -3.296 closest distance to " CB  PRO A 163 " =    2.555
peak=   -3.294 closest distance to " O   ALA A   8 " =    1.960
peak=   -3.294 closest distance to " NH2 ARG A  66 " =    5.026
peak=   -3.293 closest distance to " O   HOH Z  61 " =    1.630
peak=   -3.287 closest distance to " O   HOH Z 263 " =    2.876
peak=   -3.287 closest distance to " OD1 ASP A 191 " =    1.761
peak=   -3.283 closest distance to " O   SER A 146 " =    1.106
peak=   -3.281 closest distance to " O   HOH Z 265 " =    2.186
peak=   -3.273 closest distance to " CD2 LEU A 300 " =    2.840
peak=   -3.269 closest distance to " O   SER A   3 " =    1.049
peak=   -3.268 closest distance to " O   VAL A 189 " =    2.602
peak=   -3.265 closest distance to " CG  PRO A 163 " =    2.677
peak=   -3.263 closest distance to " OE1 GLN A 223 " =    1.888
peak=   -3.259 closest distance to " O   HOH Z 326 " =    1.670
peak=   -3.252 closest distance to " SG ACYS A 201 " =    1.917
peak=   -3.251 closest distance to " O   HOH Z  38 " =    1.589
peak=   -3.247 closest distance to " N   SER A 276 " =    1.371
peak=   -3.245 closest distance to " OG  SER A  62 " =    1.413
peak=   -3.245 closest distance to " O   HOH Z 281 " =    2.583
peak=   -3.235 closest distance to " O   HOH Z 367 " =    2.528
peak=   -3.233 closest distance to " O   HOH Z  41 " =    2.239
peak=   -3.230 closest distance to " O   ALA A  10 " =    1.817
peak=   -3.228 closest distance to " O   HOH Z  63 " =    1.373
peak=   -3.228 closest distance to " O   HOH Z 191 " =    5.874
peak=   -3.224 closest distance to " O   HOH Z 369 " =    2.254
peak=   -3.224 closest distance to " O   HOH Z 174 " =    4.090
peak=   -3.223 closest distance to " N   ALA A 226 " =    1.946
peak=   -3.223 closest distance to " C   ALA A 158 " =    1.254
peak=   -3.218 closest distance to " O   SER A  95 " =    1.554
peak=   -3.216 closest distance to " O   ALA A   1 " =    1.799
peak=   -3.211 closest distance to " O   HOH Z 301 " =    2.256
peak=   -3.210 closest distance to " O   ALA A  51 " =    1.370
peak=   -3.210 closest distance to " O   HOH Z 361 " =    3.424
peak=   -3.209 closest distance to " O   GLU A 152 " =    1.500
peak=   -3.208 closest distance to " CG1 VAL A 125 " =    2.300
peak=   -3.205 closest distance to " CG  GLU A 152 " =    1.167
peak=   -3.203 closest distance to " CB  SER A 258 " =    2.003
peak=   -3.200 closest distance to " O   HOH Z  43 " =    1.759
peak=   -3.199 closest distance to " O   SER A  26 " =    1.185
peak=   -3.197 closest distance to " OD1 ASN A 301 " =    1.947
peak=   -3.196 closest distance to " O   ALA A 292 " =    1.954
peak=   -3.194 closest distance to " O   ILE A 120 " =    1.394
peak=   -3.187 closest distance to " CG  GLU A   2 " =    1.813
peak=   -3.186 closest distance to " O   HOH Z 219 " =    3.114
peak=   -3.185 closest distance to " O   GLY A  80 " =    2.530
peak=   -3.184 closest distance to " O   ILE A 234 " =    1.259
peak=   -3.181 closest distance to " OG  SER A  22 " =    4.776
peak=   -3.179 closest distance to " O   GLY A 196 " =    0.949
peak=   -3.176 closest distance to " CD  GLN A 223 " =    0.729
peak=   -3.174 closest distance to " CD1 LEU A  83 " =    2.320
peak=   -3.172 closest distance to " CG  GLU A 277 " =    1.193
peak=   -3.170 closest distance to " O   HOH Z 139 " =    3.113
peak=   -3.169 closest distance to " O   HOH Z  37 " =    1.731
peak=   -3.164 closest distance to " NE2 GLN A 103 " =    1.659
peak=   -3.157 closest distance to " OD2 ASP A  50 " =    2.301
peak=   -3.153 closest distance to " O   HOH Z 134 " =    2.769
peak=   -3.153 closest distance to " CZ3 TRP A 274 " =    2.395
peak=   -3.150 closest distance to " O   HOH Z 211 " =    1.627
peak=   -3.142 closest distance to " O   HOH Z 137 " =    1.444
peak=   -3.140 closest distance to " O   HOH Z 317 " =    1.569
peak=   -3.140 closest distance to " O   HOH Z 111 " =    3.732
peak=   -3.134 closest distance to " N   VAL A 189 " =    1.575
peak=   -3.130 closest distance to " CG  PHE A 225 " =    1.361
peak=   -3.128 closest distance to " O   HOH Z 351 " =    1.356
peak=   -3.115 closest distance to " O   HOH Z 252 " =    3.432
peak=   -3.114 closest distance to " O   HOH Z 417 " =    2.456
peak=   -3.111 closest distance to " CD2 TYR A 293 " =    1.891
peak=   -3.105 closest distance to " CE  MET A  93 " =    1.177
peak=   -3.102 closest distance to " CB  ALA A   9 " =    2.546
peak=   -3.085 closest distance to " CA  GLY A 241 " =    3.136
peak=   -3.084 closest distance to " O   HOH Z  60 " =    1.966
peak=   -3.062 closest distance to " CA  GLY A 133 " =    2.178
peak=   -3.036 closest distance to " O   ASP A 171 " =    1.886
peak=   -3.031 closest distance to " O   ASN A 301 " =    1.346
peak=   -3.020 closest distance to " CB  ASN A  39 " =    2.108
peak=   -3.001 closest distance to " N   LYS A 289 " =    1.349

================= 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    :  0.3895 0.3864   6.167265e+00   6.161976e+00
   1_bss:  0.3801 0.3758   6.154785e+00   6.142226e+00
   1_xyz:  0.2329 0.2522   5.739540e+00   5.814692e+00
   1_adp:  0.2123 0.2594   5.685037e+00   5.843910e+00
   1_occ:  0.2119 0.2595   5.684312e+00   5.844065e+00
   2_bss:  0.2082 0.2562   5.676546e+00   5.837005e+00
   2_xyz:  0.1518 0.1956   5.394049e+00   5.583949e+00
   2_adp:  0.1412 0.1830   5.327976e+00   5.520215e+00
   2_occ:  0.1410 0.1829   5.327347e+00   5.519876e+00
   3_bss:  0.1415 0.1824   5.327957e+00   5.517220e+00
   3_xyz:  0.1203 0.1623   5.196053e+00   5.412143e+00
   3_adp:  0.1176 0.1600   5.175051e+00   5.394047e+00
   3_occ:  0.1175 0.1599   5.174285e+00   5.393256e+00
   4_bss:  0.1175 0.1599   5.174176e+00   5.393101e+00
   4_xyz:  0.1105 0.1550   5.130782e+00   5.365731e+00
   4_adp:  0.1092 0.1554   5.127033e+00   5.368495e+00
   4_occ:  0.1092 0.1554   5.126824e+00   5.368496e+00
   5_bss:  0.1092 0.1544   5.125088e+00   5.364013e+00
   5_xyz:  0.1051 0.1544   5.106882e+00   5.361444e+00
   5_adp:  0.1047 0.1548   5.106551e+00   5.364984e+00
   5_occ:  0.1047 0.1548   5.106517e+00   5.365134e+00
   5_bss:  0.1046 0.1548   5.106709e+00   5.365306e+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:  0.308  25.809   0.000   0.000   0.000   0.000   0.000   0.000
   1_xyz:  0.308  25.809   0.000   0.000   0.000   0.000   0.000   0.000
   1_adp:  0.308  25.809   0.000   0.000   0.000   0.000   0.000   0.000
   1_occ:  0.308  25.809   0.000   0.000   0.000   0.000   0.000   0.000
   2_bss:  0.315  36.859  -2.444  -1.443  -1.414  -0.000  -0.000  -0.000
   2_xyz:  0.315  36.859  -2.444  -1.443  -1.414  -0.000  -0.000  -0.000
   2_adp:  0.315  36.859  -2.444  -1.443  -1.414  -0.000  -0.000  -0.000
   2_occ:  0.315  36.859  -2.444  -1.443  -1.414  -0.000  -0.000  -0.000
   3_bss:  0.316  36.859  -2.935  -1.691  -1.538  -0.000  -0.000  -0.000
   3_xyz:  0.316  36.859  -2.935  -1.691  -1.538  -0.000  -0.000  -0.000
   3_adp:  0.316  36.859  -2.935  -1.691  -1.538  -0.000  -0.000  -0.000
   3_occ:  0.316  36.859  -2.935  -1.691  -1.538  -0.000  -0.000  -0.000
   4_bss:  0.324  40.152  -2.935  -1.691  -1.538  -0.000  -0.000  -0.000
   4_xyz:  0.324  40.152  -2.935  -1.691  -1.538  -0.000  -0.000  -0.000
   4_adp:  0.324  40.152  -2.935  -1.691  -1.538  -0.000  -0.000  -0.000
   4_occ:  0.324  40.152  -2.935  -1.691  -1.538  -0.000  -0.000  -0.000
   5_bss:  0.320  42.564  -2.935  -1.691  -1.538  -0.000  -0.000  -0.000
   5_xyz:  0.320  42.564  -2.935  -1.691  -1.538  -0.000  -0.000  -0.000
   5_adp:  0.320  42.564  -2.935  -1.691  -1.538  -0.000  -0.000  -0.000
   5_occ:  0.320  42.564  -2.935  -1.691  -1.538  -0.000  -0.000  -0.000
   5_bss:  0.322  42.701  -2.739  -1.564  -1.232  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  42.161 0.6189  0.8098    43606.762
   1_bss:  41.015 0.6309  0.8296    40240.115
   1_xyz:  24.708 0.8157  1.0061    16309.197
   1_adp:  25.854 0.8026  0.9960    17315.263
   1_occ:  25.867 0.8025  0.9957    17340.180
   2_bss:  25.534 0.8057  0.9371    16852.329
   2_xyz:  18.561 0.8746  0.9856     9426.569
   2_adp:  16.934 0.8902  0.9896     8304.975
   2_occ:  16.936 0.8901  0.9895     8296.222
   3_bss:  16.888 0.8904  0.9792     8224.517
   3_xyz:  14.753 0.9085  0.9877     6673.455
   3_adp:  14.328 0.9123  0.9858     6510.689
   3_occ:  14.313 0.9124  0.9857     6494.320
   4_bss:  14.310 0.9124  0.9859     6500.336
   4_xyz:  13.702 0.9173  0.9877     6114.752
   4_adp:  13.719 0.9173  0.9830     6147.521
   4_occ:  13.718 0.9173  0.9830     6143.330
   5_bss:  13.648 0.9178  0.9831     6067.485
   5_xyz:  13.563 0.9185  0.9833     6032.751
   5_adp:  13.619 0.9180  0.9773     6057.770
   5_occ:  13.619 0.9180  0.9773     6058.208
   5_bss:  13.622 0.9180  0.9836     6061.120
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.9149e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.9149e-01
   1_xyz:   1.201  0.009  0.074 15.251  0.004  4.108   7.9987e-02
   1_adp:   1.201  0.009  0.074 15.251  0.004  4.108   7.9987e-02
   1_occ:   1.201  0.009  0.074 15.251  0.004  4.108   7.9987e-02
   2_bss:   1.201  0.009  0.074 15.251  0.004  4.108   7.9987e-02
   2_xyz:   0.964  0.006  0.065 14.320  0.004  4.119   5.6634e-02
   2_adp:   0.964  0.006  0.065 14.320  0.004  4.119   5.6634e-02
   2_occ:   0.964  0.006  0.065 14.320  0.004  4.119   5.6634e-02
   3_bss:   0.964  0.006  0.065 14.320  0.004  4.119   5.6634e-02
   3_xyz:   0.956  0.006  0.067 14.528  0.004  4.109   5.3666e-02
   3_adp:   0.956  0.006  0.067 14.528  0.004  4.109   5.3666e-02
   3_occ:   0.956  0.006  0.067 14.528  0.004  4.109   5.3666e-02
   4_bss:   0.956  0.006  0.067 14.528  0.004  4.109   5.3666e-02
   4_xyz:   1.017  0.007  0.074 14.651  0.004  4.110   6.0122e-02
   4_adp:   1.017  0.007  0.074 14.651  0.004  4.110   6.0122e-02
   4_occ:   1.017  0.007  0.074 14.651  0.004  4.110   6.0122e-02
   5_bss:   1.017  0.007  0.074 14.651  0.004  4.110   6.0122e-02
   5_xyz:   1.113  0.009  0.081 14.904  0.005  4.109   7.0776e-02
   5_adp:   1.113  0.009  0.081 14.904  0.005  4.109   7.0776e-02
   5_occ:   1.113  0.009  0.081 14.904  0.005  4.109   7.0776e-02
   5_bss:   1.113  0.009  0.081 14.904  0.005  4.109   7.0776e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.287   2.4060e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.287   2.4060e-01
   1_xyz:   8.247  0.049  0.277 86.192  0.038  2.040   6.4475e-02
   1_adp:   8.247  0.049  0.277 86.192  0.038  2.040   6.4475e-02
   1_occ:   8.247  0.049  0.277 86.192  0.038  2.040   6.4475e-02
   2_bss:   8.247  0.049  0.277 86.192  0.038  2.040   6.4475e-02
   2_xyz:   7.521  0.034  0.189 80.375  0.033  2.280   1.2690e-01
   2_adp:   7.521  0.034  0.189 80.375  0.033  2.280   1.2690e-01
   2_occ:   7.521  0.034  0.189 80.375  0.033  2.280   1.2690e-01
   3_bss:   7.521  0.034  0.189 80.375  0.033  2.280   1.2690e-01
   3_xyz:   7.069  0.041  0.234 82.779  0.038  2.311   3.6986e-02
   3_adp:   7.069  0.041  0.234 82.779  0.038  2.311   3.6986e-02
   3_occ:   7.069  0.041  0.234 82.779  0.038  2.311   3.6986e-02
   4_bss:   7.069  0.041  0.234 82.779  0.038  2.311   3.6986e-02
   4_xyz:   7.295  0.042  0.232 81.968  0.041  2.306   4.6805e-02
   4_adp:   7.295  0.042  0.232 81.968  0.041  2.306   4.6805e-02
   4_occ:   7.295  0.042  0.232 81.968  0.041  2.306   4.6805e-02
   5_bss:   7.295  0.042  0.232 81.968  0.041  2.306   4.6805e-02
   5_xyz:   7.744  0.051  0.261 82.303  0.042  2.276   6.2816e-02
   5_adp:   7.744  0.051  0.261 82.303  0.042  2.276   6.2816e-02
   5_occ:   7.744  0.051  0.261 82.303  0.042  2.276   6.2816e-02
   5_bss:   7.744  0.051  0.261 82.303  0.042  2.276   6.2816e-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:  66.44   0.00  17.27  58.20   0.00  13.38  66.44   7.28  38.48
   1_occ:  66.44   0.00  17.27  58.20   0.00  13.38  66.44   7.28  38.48
   2_bss:  66.44   0.00  17.27  58.20   0.00  13.38  66.44   7.28  38.48
   2_xyz:  66.44   0.00  17.27  58.20   0.00  13.38  66.44   7.28  38.48
   2_adp:  78.12   0.92  17.17  78.12   0.92  13.21  69.69   5.57  38.74
   2_occ:  78.12   0.92  17.17  78.12   0.92  13.21  69.69   5.57  38.74
   3_bss:  78.12   0.92  17.17  78.12   0.92  13.21  69.69   5.57  38.74
   3_xyz:  78.12   0.92  17.17  78.12   0.92  13.21  69.69   5.57  38.74
   3_adp:  81.04   1.91  16.94  81.04   1.91  13.00  72.69   2.37  38.38
   3_occ:  81.04   1.91  16.94  81.04   1.91  13.00  72.69   2.37  38.38
   4_bss:  81.04   1.91  16.94  81.04   1.91  13.00  72.69   2.37  38.38
   4_xyz:  81.04   1.91  16.94  81.04   1.91  13.00  72.69   2.37  38.38
   4_adp:  85.11   1.56  16.91  85.11   1.56  12.89  75.81   3.46  38.84
   4_occ:  85.11   1.56  16.91  85.11   1.56  12.89  75.81   3.46  38.84
   5_bss:  85.11   1.56  16.91  85.11   1.56  12.89  75.81   3.46  38.84
   5_xyz:  85.11   1.56  16.91  85.11   1.56  12.89  75.81   3.46  38.84
   5_adp:  87.32   0.98  16.85  87.32   0.98  12.76  79.45   5.31  39.13
   5_occ:  87.32   0.98  16.85  87.32   0.98  12.76  79.45   5.31  39.13
   5_bss:  87.28   0.95  16.82  87.28   0.95  12.73  79.41   5.27  39.10
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    2.185    0.024    0.350
   1_adp:    2.185    0.024    0.350
   1_occ:    2.185    0.024    0.350
   2_bss:    2.185    0.024    0.350
   2_xyz:    1.863    0.018    0.437
   2_adp:    1.863    0.018    0.437
   2_occ:    1.863    0.018    0.437
   3_bss:    1.863    0.018    0.437
   3_xyz:    1.574    0.023    0.500
   3_adp:    1.574    0.023    0.500
   3_occ:    1.574    0.023    0.500
   4_bss:    1.574    0.023    0.500
   4_xyz:    1.294    0.050    0.520
   4_adp:    1.294    0.050    0.520
   4_occ:    1.294    0.050    0.520
   5_bss:    1.294    0.050    0.520
   5_xyz:    1.259    0.056    0.532
   5_adp:    1.259    0.056    0.532
   5_occ:    1.259    0.056    0.532
   5_bss:    1.259    0.056    0.532
------------------------------------------------------------------------

CPU time actual refinement: 335.49


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_201/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_201/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_201/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_201/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_201/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 335.35 
  Macro-tasks:
    bulk solvent and scale       = 37.34  
    individual site refinement   = 139.55 
    weights calculation          = 29.49  
    collect and process          = 6.67   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 213.16 
  Micro-tasks:
    mask                            = 1.83   
    f_calc                          = 108.30 
    alpha_beta                      = 8.17   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 117.03 
    fmodel                         = 6.24   
    r_factors                      = 0.17   
    phase_errors                   = 10.98  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 254.16 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.752 micro seconds
Total CPU time: 5.82 minutes
from_scatterers_fft:    650 calls, 108.01 s
gradients_fft:          595 calls, 103.55 s

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

# Date 2008-01-16 Time 04:15:01 PST -0800 (1200485701.74 s)
Start R-work = 0.3895, R-free = 0.3864 (no bulk solvent and anisotropic scale)
Final R-work = 0.1301, R-free = 0.1752 (no bulk solvent and anisotropic scale)

Start R-work = 0.3801, R-free = 0.3758
Final R-work = 0.1046, R-free = 0.1548