# Date 2008-01-16 Time 05:55:38 PST -0800 (1200491738.29 s)
#phil __OFF__

Command line arguments: "../939.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 19994
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 939

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 47.6339, 85.9581, 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: 3.27, 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: (70.9525, 47.6339, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0819 1.99124
Completeness in resolution range: 0.955281
Completeness with d_max=infinity: 0.952309

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0819
                             d_min =   1.9912

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.6339, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0819 1.99124
Completeness in resolution range: 0.955281
Completeness with d_max=infinity: 0.952309

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0824 -  4.2608 [2151/2179]  1939   212   9.9%
  bin  2:  4.2608 -  3.3946 [2063/2082]  1854   209  10.1%
  bin  3:  3.3946 -  2.9692 [2046/2066]  1842   204  10.0%
  bin  4:  2.9692 -  2.6994 [2032/2057]  1834   198   9.7%
  bin  5:  2.6994 -  2.5069 [2014/2033]  1809   205  10.2%
  bin  6:  2.5069 -  2.3597 [1998/2043]  1797   201  10.1%
  bin  7:  2.3597 -  2.2419 [1973/2007]  1774   199  10.1%
  bin  8:  2.2419 -  2.1446 [1992/2027]  1792   200  10.0%
  bin  9:  2.1446 -  2.0622 [1993/2022]  1799   194   9.7%
  bin 10:  2.0622 -  1.9912 [1327/1990]  1190   137  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_939/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:
        1.70 -     2.34: 10
        2.34 -     2.98: 1768
        2.98 -     3.62: 4540
        3.62 -     4.26: 9032
        4.26 -     4.90: 12672
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.698 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.953 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  2.038 3.040 -x+1/2,-y+1,z-1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 28017 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_939/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_939/model_refine_001.geo

CPU time processing inputs: 9.17


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 47.63395 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3573   r_free= 0.3483   ksol= 0.00   Bsol= 0.00   scale= 0.947    |
|                                                                             |
| 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:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.125311                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7522 0.99   1393  154 0.2971 0.3111      6.3829      6.3397|
|  2:  4.7522 -  3.7917 0.99   1360  148 0.2812 0.2935      6.5472      6.5419|
|  3:  3.7917 -  3.3182 0.99   1306  153 0.3090 0.2871      6.4247      6.4056|
|  4:  3.3182 -  3.0175 0.99   1327  143 0.3338 0.3157      6.3265      6.2229|
|  5:  3.0175 -  2.8027 0.99   1303  145 0.3584 0.3453      6.1878      6.2206|
|  6:  2.8027 -  2.6384 0.98   1285  143 0.3842 0.3526      6.1235      6.0328|
|  7:  2.6384 -  2.5069 0.99   1304  142 0.3880 0.3538      6.1036      6.0052|
|  8:  2.5069 -  2.3982 0.98   1270  147 0.4110 0.4019      6.0509      6.0838|
|  9:  2.3982 -  2.3062 0.98   1298  141 0.4097 0.4086      6.0105      6.0575|
| 10:  2.3062 -  2.2269 0.98   1276  138 0.4154 0.4047      5.9958      5.9828|
| 11:  2.2269 -  2.1575 0.99   1267  146 0.4102 0.3756      5.9412      5.9472|
| 12:  2.1575 -  2.0960 0.98   1272  138 0.4116 0.4336      5.8895      5.9069|
| 13:  2.0960 -  2.0409 0.97   1263  141 0.4278 0.3856      5.8067      5.7386|
| 14:  2.0409 -  1.9912 0.55    706   80 0.3932 0.4305      5.7045      5.7402|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0824 -  4.7522  1393   154  0.77  27.64   0.86     0.79      47822.90|
|  2:  4.7522 -  3.7917  1360   148  0.82  24.07   0.96     0.88      53629.35|
|  3:  3.7917 -  3.3182  1306   153  0.77  28.90   0.96     0.91      53446.16|
|  4:  3.3182 -  3.0175  1327   143  0.74  31.62   0.96     0.89      46606.28|
|  5:  3.0175 -  2.8027  1303   145  0.68  37.03   0.96     0.85      40246.84|
|  6:  2.8027 -  2.6384  1285   143  0.67  38.59   0.97     0.84      35410.23|
|  7:  2.6384 -  2.5069  1304   142  0.66  39.29   0.97     0.83      33868.02|
|  8:  2.5069 -  2.3982  1270   147  0.61  43.34   0.98     0.82      33593.33|
|  9:  2.3982 -  2.3062  1298   141  0.60  44.18   0.97     0.80      32635.28|
| 10:  2.3062 -  2.2269  1276   138  0.59  44.64   0.99     0.81      30529.11|
| 11:  2.2269 -  2.1575  1267   146  0.61  43.65   1.00     0.83      27437.16|
| 12:  2.1575 -  2.0960  1272   138  0.61  43.18   1.00     0.87      24978.56|
| 13:  2.0960 -  2.0409  1263   141  0.59  45.20   0.97     0.83      21942.02|
| 14:  2.0409 -  1.9912   706    80  0.59  45.33   1.00     0.77      18986.59|
|alpha:            min =        0.77 max =            0.91 mean =         0.84|
|beta:             min =    18986.59 max =        53629.35 mean =     36581.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.67|
|phase err.(work): min =        0.00 max =           89.99 mean =        37.93|
|phase err.(test): min =        0.00 max =           89.43 mean =        37.94|
|-----------------------------------------------------------------------------|

============================== 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 = 4.763281              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.276   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.901392              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.873   (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 |  1.698 -  2.018:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.018 -  2.339:        7 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.339 -  2.659:       57 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.659 -  2.979:     1711 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.979 -  3.299:     1886 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.299 -  3.619:     2654 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.619 -  3.939:     4643 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.939 -  4.260:     4389 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.260 -  4.580:     5757 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.580 -  4.900:     6915 |
|-----------------------------------------------------------------------------|
|-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 |        0.164 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.698 |       0.179 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.147)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3573   r_free= 0.3483   ksol= 0.00   Bsol= 0.00   scale= 0.947    |
|                                                                             |
| 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:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.125311                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3450   r_free= 0.3359   ksol= 0.30   Bsol= 50.00   scale= 0.967   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.87,3.28,-1.70,0.00,-0.00,-0.00); trace/3= -0.10                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.105551                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.361243              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.304   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.483140              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.658   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3450      final r-factor (work) = 0.2244          |
| start r-factor (free) = 0.3359      final r-factor (free) = 0.2494          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.4876 = 4.36 * 0.50 * 6.1101 + 1.00 * 0.1638                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.8671 = 4.36 * 0.50 * 5.8628 + 1.00 * 0.0824                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2244      final r-factor (work) = 0.2039          |
| start r-factor (free) = 0.2494      final r-factor (free) = 0.2545          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8387 = 0.48 * 1.00 * 5.8628 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7470 = 0.48 * 1.00 * 5.6633 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.147)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.02   17.22    None  None   None       |
|    all(noH): 2823   0      0.00    81.02   17.22    None  None   None       |
|    Sol.    : 438    0      4.56    81.02   39.38    None  None   None       |
|    Mac.    : 2385   0      0.00    78.52   13.15    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.102:  682   |   5:    40.510 -  48.612:   97        |
|      1:     8.102 -  16.204: 1189   |   6:    48.612 -  56.714:   73        |
|      2:    16.204 -  24.306:  405   |   7:    56.714 -  64.816:   63        |
|      3:    24.306 -  32.408:  156   |   8:    64.816 -  72.918:   21        |
|      4:    32.408 -  40.510:  132   |   9:    72.918 -  81.021:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2039 r_free = 0.2545             target_work(ml) = 5.669         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2035 r_free = 0.2542             target_work(ml) = 5.668         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2035   r_free= 0.2542   ksol= 0.30   Bsol= 50.00   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.87,3.28,-1.70,0.00,-0.00,-0.00); trace/3= -0.10                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.668189                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2017   r_free= 0.2519   ksol= 0.32   Bsol= 66.16   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.20,0.10,-1.54,0.00,-0.00,-0.00); trace/3= -1.21                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.661969                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.094952              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.162   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.246813              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.550  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2017      final r-factor (work) = 0.1555          |
| start r-factor (free) = 0.2519      final r-factor (free) = 0.1931          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0157 = 2.09 * 0.50 * 5.6643 + 1.00 * 0.0824                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8684 = 2.09 * 0.50 * 5.5512 + 1.00 * 0.0536                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1555      final r-factor (work) = 0.1476          |
| start r-factor (free) = 0.1931      final r-factor (free) = 0.1843          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3809 = 0.25 * 1.00 * 5.5512 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3378 = 0.25 * 1.00 * 5.3839 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.147)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.91    81.01   16.96    None  None   None       |
|    all(noH): 2823   0      0.91    81.01   16.96    None  None   None       |
|    Sol.    : 438    0      4.87    81.01   39.50    None  None   None       |
|    Mac.    : 2385   0      0.91    80.29   12.82    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:     0.915 -   8.924:  854   |   5:    40.963 -  48.973:  103        |
|      1:     8.924 -  16.934: 1136   |   6:    48.973 -  56.983:   72        |
|      2:    16.934 -  24.944:  315   |   7:    56.983 -  64.993:   58        |
|      3:    24.944 -  32.954:  137   |   8:    64.993 -  73.002:   16        |
|      4:    32.954 -  40.963:  127   |   9:    73.002 -  81.012:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1476 r_free = 0.1843             target_work(ml) = 5.365         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1473 r_free = 0.1842             target_work(ml) = 5.364         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1473   r_free= 0.1842   ksol= 0.32   Bsol= 66.16   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.20,0.10,-1.54,0.00,-0.00,-0.00); trace/3= -1.21                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.363982                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1473   r_free= 0.1845   ksol= 0.33   Bsol= 65.49   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-0.85,-1.27,-0.00,-0.00,-0.00); trace/3= -1.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.363612                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.671519              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.743  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 10.283143             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 110.213  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1473      final r-factor (work) = 0.1268          |
| start r-factor (free) = 0.1845      final r-factor (free) = 0.1658          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5526 = 1.67 * 0.50 * 5.3831 + 1.00 * 0.0536                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4738 = 1.67 * 0.50 * 5.2901 + 1.00 * 0.0526                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1268      final r-factor (work) = 0.1219          |
| start r-factor (free) = 0.1658      final r-factor (free) = 0.1653          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 54.4077 = 10.28 * 1.00 * 5.2901 + 1.00 * 0.0090                             |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 53.6627 = 10.28 * 1.00 * 5.2173 + 1.00 * 0.0120                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.147)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.29  17.49    None  None   None       |
|    all(noH): 2823   0      0.00    106.29  17.49    None  None   None       |
|    Sol.    : 438    0      5.16    93.46   42.91    None  None   None       |
|    Mac.    : 2385   0      0.00    106.29  12.82    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.629: 1244   |   5:    53.146 -  63.775:   84        |
|      1:    10.629 -  21.258:  981   |   6:    63.775 -  74.404:   56        |
|      2:    21.258 -  31.888:  187   |   7:    74.404 -  85.034:   19        |
|      3:    31.888 -  42.517:  133   |   8:    85.034 -  95.663:    5        |
|      4:    42.517 -  53.146:  112   |   9:    95.663 - 106.292:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1219 r_free = 0.1653             target_work(ml) = 5.216         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1219 r_free = 0.1652             target_work(ml) = 5.215         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1219   r_free= 0.1652   ksol= 0.33   Bsol= 65.49   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-0.85,-1.27,-0.00,-0.00,-0.00); trace/3= -1.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.215454                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1218   r_free= 0.1652   ksol= 0.33   Bsol= 65.93   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-1.11,-1.04,-0.00,-0.00,-0.00); trace/3= -1.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.215020                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.202677              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.569  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.334007              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.546  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1218      final r-factor (work) = 0.1142          |
| start r-factor (free) = 0.1652      final r-factor (free) = 0.1623          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7983 = 2.20 * 0.50 * 5.2170 + 1.00 * 0.0526                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7745 = 2.20 * 0.50 * 5.1865 + 1.00 * 0.0624                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1142      final r-factor (work) = 0.1133          |
| start r-factor (free) = 0.1623      final r-factor (free) = 0.1618          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9308 = 1.33 * 1.00 * 5.1865 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9044 = 1.33 * 1.00 * 5.1668 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.147)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.57  17.19    None  None   None       |
|    all(noH): 2823   0      0.00    109.57  17.19    None  None   None       |
|    Sol.    : 438    0      5.16    93.58   42.28    None  None   None       |
|    Mac.    : 2385   0      0.00    109.57  12.58    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.957: 1358   |   5:    54.786 -  65.743:   86        |
|      1:    10.957 -  21.914:  894   |   6:    65.743 -  76.700:   41        |
|      2:    21.914 -  32.871:  188   |   7:    76.700 -  87.657:   14        |
|      3:    32.871 -  43.829:  123   |   8:    87.657 -  98.614:    5        |
|      4:    43.829 -  54.786:  112   |   9:    98.614 - 109.571:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1133 r_free = 0.1618             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1133 r_free = 0.1618             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1618   ksol= 0.33   Bsol= 65.93   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-1.11,-1.04,-0.00,-0.00,-0.00); trace/3= -1.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.164805                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1135   r_free= 0.1615   ksol= 0.33   Bsol= 65.93   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.69,-1.09,-0.80,-0.00,-0.00,-0.00); trace/3= -1.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.166506                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.756082              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 158.041  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.152175              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.794  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1135      final r-factor (work) = 0.1104          |
| start r-factor (free) = 0.1615      final r-factor (free) = 0.1616          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1848 = 2.76 * 0.50 * 5.1685 + 1.00 * 0.0624                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1716 = 2.76 * 0.50 * 5.1549 + 1.00 * 0.0679                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1104      final r-factor (work) = 0.1101          |
| start r-factor (free) = 0.1616      final r-factor (free) = 0.1613          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.4159 = 4.15 * 1.00 * 5.1549 + 1.00 * 0.0117                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.4022 = 4.15 * 1.00 * 5.1516 + 1.00 * 0.0119                              |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.147)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.82  16.93    None  None   None       |
|    all(noH): 2823   0      0.00    113.82  16.93    None  None   None       |
|    Sol.    : 438    0      5.16    93.67   41.79    None  None   None       |
|    Mac.    : 2385   0      0.00    113.82  12.37    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.382: 1475   |   5:    56.911 -  68.293:   81        |
|      1:    11.382 -  22.765:  804   |   6:    68.293 -  79.676:   33        |
|      2:    22.765 -  34.147:  180   |   7:    79.676 -  91.058:    9        |
|      3:    34.147 -  45.529:  131   |   8:    91.058 - 102.440:    4        |
|      4:    45.529 -  56.911:  104   |   9:   102.440 - 113.822:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1101 r_free = 0.1613             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1101 r_free = 0.1613             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1101   r_free= 0.1613   ksol= 0.33   Bsol= 65.93   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.69,-1.09,-0.80,-0.00,-0.00,-0.00); trace/3= -1.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.153282                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7522 0.99   1393  154 0.0963 0.1281      5.3618      5.5193|
|  2:  4.7522 -  3.7917 0.99   1360  148 0.0812 0.1044      5.3914      5.5919|
|  3:  3.7917 -  3.3182 0.99   1306  153 0.1010 0.1470      5.4401      5.8434|
|  4:  3.3182 -  3.0175 0.99   1327  143 0.1209 0.1602      5.4573      5.6142|
|  5:  3.0175 -  2.8027 0.99   1303  145 0.1310 0.1815      5.3372      5.5503|
|  6:  2.8027 -  2.6384 0.98   1285  143 0.1238 0.1933      5.2383      5.4858|
|  7:  2.6384 -  2.5069 0.99   1304  142 0.1217 0.1735      5.1659      5.3984|
|  8:  2.5069 -  2.3982 0.98   1270  147 0.1145 0.1707      5.0808      5.3283|
|  9:  2.3982 -  2.3062 0.98   1298  141 0.1171 0.1896      5.0474      5.3702|
| 10:  2.3062 -  2.2269 0.98   1276  138 0.1125 0.1889      4.9914      5.2739|
| 11:  2.2269 -  2.1575 0.99   1267  146 0.1144 0.1816       4.956      5.2795|
| 12:  2.1575 -  2.0960 0.98   1272  138 0.1088 0.1671      4.8896      5.1474|
| 13:  2.0960 -  2.0409 0.97   1263  141 0.1144 0.1850      4.8194      5.1204|
| 14:  2.0409 -  1.9912 0.55    706   80 0.1079 0.1810      4.7078      4.9857|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0824 -  4.7522  1393   154  0.94   9.11   0.97     0.94       7022.89|
|  2:  4.7522 -  3.7917  1360   148  0.95   7.64   1.00     0.99       8439.55|
|  3:  3.7917 -  3.3182  1306   153  0.94  10.98   1.02     1.02       9926.48|
|  4:  3.3182 -  3.0175  1327   143  0.92  14.16   1.00     0.98      10661.65|
|  5:  3.0175 -  2.8027  1303   145  0.89  16.61   0.99     0.97       8842.99|
|  6:  2.8027 -  2.6384  1285   143  0.89  16.78   0.98     0.96       7734.23|
|  7:  2.6384 -  2.5069  1304   142  0.91  15.56   0.99     0.95       6384.12|
|  8:  2.5069 -  2.3982  1270   147  0.90  16.10   0.98     0.96       5787.74|
|  9:  2.3982 -  2.3062  1298   141  0.90  15.88   0.98     0.94       5213.23|
| 10:  2.3062 -  2.2269  1276   138  0.90  16.45   0.98     0.93       4828.96|
| 11:  2.2269 -  2.1575  1267   146  0.89  16.96   0.98     0.94       4633.51|
| 12:  2.1575 -  2.0960  1272   138  0.91  15.38   0.98     0.96       4154.42|
| 13:  2.0960 -  2.0409  1263   141  0.89  17.09   0.98     0.97       3708.42|
| 14:  2.0409 -  1.9912   706    80  0.90  16.15   0.96     0.91       2880.32|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     2880.32 max =        10661.65 mean =      6597.26|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.51|
|phase err.(test): min =        0.00 max =           89.32 mean =        13.96|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1100   r_free= 0.1612   ksol= 0.33   Bsol= 65.94   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.44,-0.93,-0.55,-0.00,-0.00,-0.00); trace/3= -0.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.153421                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1100   r_free= 0.1612   ksol= 0.33   Bsol= 65.94   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.44,-0.93,-0.55,-0.00,-0.00,-0.00); trace/3= -0.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.153421                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7522 0.99   1393  154 0.0964 0.1282      5.3629      5.5207|
|  2:  4.7522 -  3.7917 0.99   1360  148 0.0813 0.1044      5.3921      5.5919|
|  3:  3.7917 -  3.3182 0.99   1306  153 0.1010 0.1471      5.4403      5.8438|
|  4:  3.3182 -  3.0175 0.99   1327  143 0.1208 0.1602      5.4574      5.6144|
|  5:  3.0175 -  2.8027 0.99   1303  145 0.1310 0.1815       5.337        5.55|
|  6:  2.8027 -  2.6384 0.98   1285  143 0.1238 0.1931       5.238       5.485|
|  7:  2.6384 -  2.5069 0.99   1304  142 0.1217 0.1736      5.1659       5.399|
|  8:  2.5069 -  2.3982 0.98   1270  147 0.1145 0.1706      5.0808      5.3276|
|  9:  2.3982 -  2.3062 0.98   1298  141 0.1170 0.1895      5.0476      5.3703|
| 10:  2.3062 -  2.2269 0.98   1276  138 0.1125 0.1890      4.9917      5.2746|
| 11:  2.2269 -  2.1575 0.99   1267  146 0.1144 0.1815       4.956      5.2793|
| 12:  2.1575 -  2.0960 0.98   1272  138 0.1088 0.1673      4.8896      5.1485|
| 13:  2.0960 -  2.0409 0.97   1263  141 0.1144 0.1850      4.8192      5.1197|
| 14:  2.0409 -  1.9912 0.55    706   80 0.1079 0.1807      4.7076      4.9845|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0824 -  4.7522  1393   154  0.94   9.13   0.97     0.94       7041.01|
|  2:  4.7522 -  3.7917  1360   148  0.95   7.65   1.01     0.99       8451.81|
|  3:  3.7917 -  3.3182  1306   153  0.94  10.99   1.03     1.02       9933.87|
|  4:  3.3182 -  3.0175  1327   143  0.91  14.17   1.01     0.99      10662.84|
|  5:  3.0175 -  2.8027  1303   145  0.89  16.61   1.00     0.97       8836.18|
|  6:  2.8027 -  2.6384  1285   143  0.89  16.77   0.99     0.96       7727.67|
|  7:  2.6384 -  2.5069  1304   142  0.91  15.55   0.99     0.96       6381.22|
|  8:  2.5069 -  2.3982  1270   147  0.90  16.11   0.99     0.97       5788.28|
|  9:  2.3982 -  2.3062  1298   141  0.90  15.89   0.99     0.95       5215.50|
| 10:  2.3062 -  2.2269  1276   138  0.90  16.46   0.99     0.94       4831.09|
| 11:  2.2269 -  2.1575  1267   146  0.89  16.96   0.99     0.95       4634.75|
| 12:  2.1575 -  2.0960  1272   138  0.91  15.39   0.99     0.97       4155.61|
| 13:  2.0960 -  2.0409  1263   141  0.89  17.09   0.99     0.98       3706.47|
| 14:  2.0409 -  1.9912   706    80  0.90  16.14   0.97     0.93       2877.16|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2877.16 max =        10662.84 mean =      6599.35|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.51|
|phase err.(test): min =        0.00 max =           89.32 mean =        13.96|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.147)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.83  16.94    None  None   None       |
|    all(noH): 2823   0      0.00    113.83  16.94    None  None   None       |
|    Sol.    : 438    0      5.16    93.67   41.80    None  None   None       |
|    Mac.    : 2385   0      0.00    113.83  12.37    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  11.385: 1475   |   5:    56.914 -  68.296:   81        |
|      1:    11.385 -  22.767:  804   |   6:    68.296 -  79.679:   33        |
|      2:    22.767 -  34.150:  180   |   7:    79.679 -  91.061:    9        |
|      3:    34.150 -  45.532:  131   |   8:    91.061 - 102.443:    4        |
|      4:    45.532 -  56.914:  104   |   9:   102.443 - 113.825:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 294         
Filter by distance & map next to the model:
   mapped sites are within: 0.546 - 4.695
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 288 from: 294
   mapped sites are within: 0.708 - 4.695

peak=    6.104 closest distance to " O   HOH Z 111 " =    2.299
peak=    5.499 closest distance to " CB  GLN A 223 " =    1.427
peak=    5.363 closest distance to " CG  PRO A  54 " =    1.224
peak=    5.321 closest distance to " CB  SER A  63 " =    1.235
peak=    4.846 closest distance to " CB  GLN A 183 " =    1.320
peak=    4.776 closest distance to " CG  PRO A 213 " =    1.183
peak=    4.699 closest distance to " CB  ARG A 275 " =    0.947
peak=    4.615 closest distance to " CA  TYR A  30 " =    0.951
peak=    4.574 closest distance to " O   HOH Z 298 " =    1.952
peak=    4.509 closest distance to " C   PRO A 198 " =    1.495
peak=    4.487 closest distance to " CB  GLU A 128 " =    1.154
peak=    4.483 closest distance to " O   HOH Z 232 " =    2.338
peak=    4.473 closest distance to " CB  ARG A 190 " =    1.686
peak=    4.390 closest distance to " O   HOH Z 403 " =    1.724
peak=    4.388 closest distance to " CG  PRO A 198 " =    1.261
peak=    4.371 closest distance to " O   HOH Z 369 " =    2.272
peak=    4.357 closest distance to " OD1 ASN A  69 " =    2.549
peak=    4.317 closest distance to " O   HOH Z  15 " =    2.187
peak=    4.315 closest distance to " CB  PRO A  54 " =    0.856
peak=    4.293 closest distance to " CB  TYR A 169 " =    0.828
peak=    4.285 closest distance to " NE2 GLN A  11 " =    0.997
peak=    4.261 closest distance to " NZ  LYS A 117 " =    3.157
peak=    4.207 closest distance to " O   HOH Z 234 " =    3.832
peak=    4.179 closest distance to " NH2 ARG A 156 " =    1.190
peak=    4.175 closest distance to " CG1 ILE A  33 " =    1.234
peak=    4.160 closest distance to " CA  ALA A  21 " =    1.329
peak=    4.147 closest distance to " CB  LEU A 228 " =    1.097
peak=    4.128 closest distance to " O   HOH Z  40 " =    1.893
peak=    4.115 closest distance to " CD  ARG A 269 " =    0.977
peak=    4.111 closest distance to " CB  ASN A 148 " =    1.383
peak=    4.097 closest distance to " O   HOH Z 134 " =    1.391
peak=    4.089 closest distance to " O   HOH Z  78 " =    1.646
peak=    4.059 closest distance to " O   HOH Z 133 " =    2.406
peak=    4.059 closest distance to " O   HOH Z 427 " =    3.062
peak=    4.058 closest distance to " O   HOH Z 193 " =    1.839
peak=    4.057 closest distance to " O   HOH Z  68 " =    1.864
peak=    4.040 closest distance to " O   HOH Z 126 " =    2.003
peak=    4.031 closest distance to " CG  PRO A  90 " =    1.107
peak=    4.019 closest distance to " CZ  PHE A 218 " =    1.121
peak=    4.015 closest distance to " C   ILE A 106 " =    1.875
peak=    4.003 closest distance to " O   HOH Z  43 " =    1.929
peak=    3.991 closest distance to " O   HOH Z 261 " =    1.998
peak=    3.983 closest distance to " CB  GLU A 277 " =    3.679
peak=    3.969 closest distance to " O   HOH Z 203 " =    1.918
peak=    3.967 closest distance to " O   HOH Z 142 " =    1.469
peak=    3.953 closest distance to " CB  GLU A 152 " =    1.114
peak=    3.949 closest distance to " O   HOH Z 280 " =    3.011
peak=    3.939 closest distance to " CD2 LEU A 297 " =    0.911
peak=    3.928 closest distance to " O   HOH Z 316 " =    3.122
peak=    3.921 closest distance to " O   HOH Z 189 " =    2.382
peak=    3.917 closest distance to " CB  ARG A  79 " =    1.372
peak=    3.916 closest distance to " O   SER A  87 " =    2.282
peak=    3.916 closest distance to " O   HOH Z  20 " =    1.693
peak=    3.911 closest distance to " O   HOH Z 368 " =    2.132
peak=    3.910 closest distance to " CA  ARG A 195 " =    1.216
peak=    3.906 closest distance to " CB  TRP A 266 " =    0.985
peak=    3.899 closest distance to " CA  ALA A  51 " =    1.002
peak=    3.896 closest distance to " CG2 THR A 221 " =    1.132
peak=    3.892 closest distance to " O   HOH Z  97 " =    2.042
peak=    3.885 closest distance to " O   HOH Z 287 " =    2.049
peak=    3.883 closest distance to " O   HOH Z 209 " =    2.323
peak=    3.880 closest distance to " O   HOH Z 423 " =    1.924
peak=    3.874 closest distance to " O   HOH Z  63 " =    1.852
peak=    3.872 closest distance to " O   HOH Z  21 " =    1.789
peak=    3.869 closest distance to " O   HOH Z 406 " =    1.612
peak=    3.866 closest distance to " CA  THR A 221 " =    0.956
peak=    3.866 closest distance to " CD1 LEU A 300 " =    1.176
peak=    3.865 closest distance to " CB  VAL A 202 " =    1.582
peak=    3.858 closest distance to " CB  SER A   3 " =    1.366
peak=    3.854 closest distance to " O   HOH Z 426 " =    1.589
peak=    3.852 closest distance to " ND1 HIS A  81 " =    1.645
peak=    3.851 closest distance to " CB  TRP A 179 " =    1.411
peak=    3.849 closest distance to " O   HOH Z 214 " =    2.154
peak=    3.842 closest distance to " O   HOH Z 412 " =    3.702
peak=    3.836 closest distance to " O   HOH Z 265 " =    2.263
peak=    3.828 closest distance to " CG  PRO A 243 " =    1.174
peak=    3.822 closest distance to " O   HOH Z 158 " =    3.025
peak=    3.797 closest distance to " CB  ASP A 140 " =    0.944
peak=    3.796 closest distance to " O   HOH Z 303 " =    2.132
peak=    3.781 closest distance to " O   HOH Z 250 " =    1.449
peak=    3.759 closest distance to " NH2BARG A 145 " =    2.182
peak=    3.744 closest distance to " CD2 TRP A 179 " =    1.372
peak=    3.741 closest distance to " O   HOH Z 180 " =    2.249
peak=    3.735 closest distance to " NH1AARG A 145 " =    1.184
peak=    3.731 closest distance to " O   HOH Z 108 " =    2.860
peak=    3.729 closest distance to " O   HOH Z 147 " =    1.814
peak=    3.727 closest distance to " CA  ARG A  36 " =    1.169
peak=    3.725 closest distance to " CA  ASN A 215 " =    1.166
peak=    3.721 closest distance to " CG2BVAL A  41 " =    0.790
peak=    3.720 closest distance to " O   ALA A 165 " =    1.423
peak=    3.718 closest distance to " O   HOH Z 135 " =    1.878
peak=    3.717 closest distance to " O   HOH Z 295 " =    1.498
peak=    3.716 closest distance to " O   HOH Z 346 " =    1.597
peak=    3.714 closest distance to " CG  ARG A  66 " =    2.454
peak=    3.713 closest distance to " O   HOH Z  80 " =    1.638
peak=    3.703 closest distance to " CG  GLN A  58 " =    2.639
peak=    3.696 closest distance to " O   HOH Z  19 " =    2.033
peak=    3.693 closest distance to " OG BSER A 164 " =    2.349
peak=    3.692 closest distance to " ND2 ASN A 187 " =    1.459
peak=    3.687 closest distance to " O   HOH Z 361 " =    3.500
peak=    3.682 closest distance to " O   HOH Z 279 " =    2.280
peak=    3.679 closest distance to " O   HOH Z 128 " =    2.168
peak=    3.667 closest distance to " CA  ALA A 160 " =    0.856
peak=    3.664 closest distance to " CB  VAL A 265 " =    1.264
peak=    3.654 closest distance to " O   HOH Z 132 " =    2.704
peak=    3.646 closest distance to " O   THR A 251 " =    1.273
peak=    3.644 closest distance to " CA  MET A  40 " =    1.159
peak=    3.637 closest distance to " CD  ARG A 159 " =    0.820
peak=    3.634 closest distance to " O   HOH Z 163 " =    1.560
peak=    3.631 closest distance to " CD BLYS A 290 " =    1.007
peak=    3.624 closest distance to " O   HOH Z 402 " =    1.458
peak=    3.621 closest distance to " O   ASN A  74 " =    1.616
peak=    3.615 closest distance to " CA  ASN A 176 " =    1.837
peak=    3.604 closest distance to " O   HOH Z 299 " =    4.460
peak=    3.604 closest distance to " O   HOH Z 421 " =    1.579
peak=    3.602 closest distance to " O   HOH Z 272 " =    1.860
peak=    3.594 closest distance to " O   HOH Z 374 " =    2.761
peak=    3.590 closest distance to " O   HOH Z 425 " =    1.255
peak=    3.588 closest distance to " O   HOH Z  44 " =    1.803
peak=    3.582 closest distance to " O   HOH Z  61 " =    1.559
peak=    3.575 closest distance to " CE1 TYR A 186 " =    1.256
peak=    3.574 closest distance to " O   HOH Z 391 " =    2.966
peak=    3.573 closest distance to " OD2 ASP A 286 " =    2.899
peak=    3.570 closest distance to " O   ALA A 158 " =    1.225
peak=    3.564 closest distance to " CA  ALA A 295 " =    1.176
peak=    3.563 closest distance to " CB  ASN A  39 " =    0.825
peak=    3.556 closest distance to " NZ  LYS A 166 " =    3.064
peak=    3.550 closest distance to " OG1 THR A 294 " =    2.426
peak=    3.546 closest distance to " O   HOH Z 193 " =    2.249
peak=    3.546 closest distance to " CA  PRO A  54 " =    1.342
peak=    3.545 closest distance to " CD1 ILE A 106 " =    0.859
peak=    3.544 closest distance to " O   HOH Z  88 " =    3.520
peak=    3.542 closest distance to " O   HOH Z 371 " =    3.407
peak=    3.538 closest distance to " O   HOH Z 357 " =    2.048
peak=    3.537 closest distance to " CB  SER A  62 " =    0.708
peak=    3.521 closest distance to " CA  VAL A 125 " =    1.278
peak=    3.518 closest distance to " O   HOH Z  61 " =    1.532
peak=    3.515 closest distance to " O   HOH Z 437 " =    1.358
peak=    3.513 closest distance to " O   HOH Z 102 " =    1.286
peak=    3.512 closest distance to " CB  TYR A 169 " =    0.901
peak=    3.512 closest distance to " O   HOH Z  66 " =    2.064
peak=    3.507 closest distance to " O   HOH Z  59 " =    2.236
peak=    3.504 closest distance to " CG1 ILE A 151 " =    0.918
peak=    3.502 closest distance to " O   HOH Z 126 " =    1.530
peak=    3.495 closest distance to " O   HOH Z 383 " =    2.111
peak=    3.491 closest distance to " O   HOH Z 389 " =    1.980
peak=    3.490 closest distance to " O   HOH Z 245 " =    1.315
peak=    3.484 closest distance to " ND2 ASN A 110 " =    1.598
peak=    3.472 closest distance to " CB  SER A 141 " =    1.004
peak=    3.468 closest distance to " CE  LYS A  76 " =    0.843
peak=    3.460 closest distance to " CG2 VAL A 257 " =    0.873
peak=    3.457 closest distance to " CD  LYS A 166 " =    1.329
peak=    3.447 closest distance to " CA  ASP A 191 " =    0.822
peak=    3.437 closest distance to " CG1BVAL A  72 " =    1.717
peak=    3.435 closest distance to " O   HOH Z 247 " =    1.333
peak=    3.427 closest distance to " CB  GLN A  89 " =    1.304
peak=    3.422 closest distance to " CB  SER A 273 " =    0.838
peak=    3.417 closest distance to " CB  SER A 212 " =    1.030
peak=    3.413 closest distance to " CA  MET A 105 " =    1.059
peak=    3.411 closest distance to " N   ILE A  33 " =    1.083
peak=    3.411 closest distance to " OG  SER A  62 " =    2.953
peak=    3.407 closest distance to " N   ASN A  39 " =    1.371
peak=    3.405 closest distance to " O   HOH Z 197 " =    2.811
peak=    3.402 closest distance to " O   HOH Z 327 " =    1.852
peak=    3.401 closest distance to " NE2 HIS A 115 " =    0.997
peak=    3.391 closest distance to " O   HOH Z  49 " =    2.471
peak=    3.390 closest distance to " O   HOH Z 393 " =    3.366
peak=    3.390 closest distance to " CB  ASN A 187 " =    1.293
peak=    3.388 closest distance to " CD  GLU A 152 " =    0.839
peak=    3.384 closest distance to " O   HOH Z 425 " =    2.009
peak=    3.384 closest distance to " O   HOH Z 305 " =    3.745
peak=    3.377 closest distance to " CB  MET A  47 " =    0.970
peak=    3.377 closest distance to " CG2 VAL A  78 " =    0.933
peak=    3.377 closest distance to " CG2 VAL A 197 " =    1.174
peak=    3.374 closest distance to " O   HOH Z 174 " =    2.482
peak=    3.371 closest distance to " CB  TYR A 116 " =    0.911
peak=    3.368 closest distance to " CB  ILE A 120 " =    1.299
peak=    3.366 closest distance to " CB  ARG A 139 " =    0.862
peak=    3.362 closest distance to " O   HOH Z 387 " =    2.807
peak=    3.359 closest distance to " N   VAL A 126 " =    1.482
peak=    3.359 closest distance to " O   HOH Z 359 " =    1.408
peak=    3.356 closest distance to " O   HOH Z 365 " =    2.941
peak=    3.351 closest distance to " CA  ASP A 140 " =    1.148
peak=    3.349 closest distance to " O   HOH Z 185 " =    1.811
peak=    3.348 closest distance to " CB  ASN A 285 " =    0.909
peak=    3.343 closest distance to " CG2 ILE A  20 " =    1.340
peak=    3.339 closest distance to " CB  ALA A 100 " =    1.325
peak=    3.337 closest distance to " NE2 GLN A  77 " =    3.360
peak=    3.337 closest distance to " C   GLY A  80 " =    1.033
peak=    3.333 closest distance to " O   HOH Z 291 " =    1.526
peak=    3.332 closest distance to " O   HOH Z 359 " =    3.908
peak=    3.330 closest distance to " O   TRP A 274 " =    1.901
peak=    3.329 closest distance to " CA  ALA A  84 " =    1.407
peak=    3.328 closest distance to " CZ  PHE A 192 " =    0.955
peak=    3.327 closest distance to " OE1 GLN A  11 " =    1.934
peak=    3.327 closest distance to " O   HOH Z 345 " =    1.640
peak=    3.322 closest distance to " CA  ALA A 291 " =    0.860
peak=    3.311 closest distance to " O   HOH Z 193 " =    1.591
peak=    3.306 closest distance to " OE1 GLU A   2 " =    2.169
peak=    3.297 closest distance to " O   HOH Z   1 " =    2.254
peak=    3.294 closest distance to " O   HOH Z 329 " =    3.685
peak=    3.292 closest distance to " N   ARG A 156 " =    1.417
peak=    3.290 closest distance to " CB  GLU A  46 " =    1.002
peak=    3.289 closest distance to " CA  ASP A 162 " =    1.203
peak=    3.289 closest distance to " O   HOH Z 353 " =    2.791
peak=    3.286 closest distance to " O   HOH Z 344 " =    3.183
peak=    3.286 closest distance to " O   HOH Z 281 " =    4.695
peak=    3.286 closest distance to " O   HOH Z 141 " =    1.662
peak=    3.286 closest distance to " CD  LYS A 119 " =    1.381
peak=    3.284 closest distance to " CB  SER A 216 " =    0.876
peak=    3.281 closest distance to " CG  LEU A 167 " =    1.175
peak=    3.276 closest distance to " CB  HIS A 108 " =    0.804
peak=    3.275 closest distance to " O   HOH Z 128 " =    2.302
peak=    3.275 closest distance to " O   HOH Z   1 " =    2.470
peak=    3.272 closest distance to " CD  ARG A  66 " =    2.549
peak=    3.272 closest distance to " N   ASN A 127 " =    1.280
peak=    3.267 closest distance to " CA  THR A 264 " =    0.886
peak=    3.264 closest distance to " O   HOH Z 422 " =    2.646
peak=    3.263 closest distance to " O   HOH Z 183 " =    1.451
peak=    3.261 closest distance to " CA  ASN A 127 " =    1.136
peak=    3.255 closest distance to " CA  LYS A 117 " =    1.248
peak=    3.254 closest distance to " CB  MET A 113 " =    1.854
peak=    3.252 closest distance to " OG  SER A 245 " =    1.655
peak=    3.249 closest distance to " O   THR A 220 " =    1.284
peak=    3.248 closest distance to " CB  MET A  40 " =    0.882
peak=    3.248 closest distance to " CG  ARG A 219 " =    1.179
peak=    3.245 closest distance to " CG2 ILE A 120 " =    1.074
peak=    3.245 closest distance to " CB  GLN A  88 " =    1.276
peak=    3.245 closest distance to " CB  ALA A   9 " =    1.570
peak=    3.241 closest distance to " CA  GLU A 152 " =    0.851
peak=    3.240 closest distance to " CB  ALA A 291 " =    1.339
peak=    3.238 closest distance to " OD2 ASP A 298 " =    4.008
peak=    3.238 closest distance to " CD2 LEU A 255 " =    1.505
peak=    3.238 closest distance to " O   HOH Z 133 " =    1.596
peak=    3.233 closest distance to " O   HOH Z 403 " =    1.391
peak=    3.229 closest distance to " O   HOH Z  85 " =    2.149
peak=    3.227 closest distance to " C   TYR A 214 " =    1.541
peak=    3.226 closest distance to " CA  SER A  87 " =    1.070
peak=    3.225 closest distance to " O   HOH Z 345 " =    3.217
peak=    3.225 closest distance to " O   HOH Z 290 " =    0.957
peak=    3.221 closest distance to " CG BARG A 102 " =    1.923
peak=    3.215 closest distance to " O   HOH Z 416 " =    2.896
peak=    3.209 closest distance to " NH2AARG A 275 " =    3.740
peak=    3.206 closest distance to " N   ASN A 252 " =    1.309
peak=    3.199 closest distance to " O   HOH Z  63 " =    2.307
peak=    3.191 closest distance to " O   HOH Z  10 " =    1.808
peak=    3.188 closest distance to " CA  ALA A 248 " =    1.181
peak=    3.185 closest distance to " O   HOH Z 334 " =    1.562
peak=    3.182 closest distance to " O   HOH Z 189 " =    3.057
peak=    3.180 closest distance to " CA  ALA A 158 " =    1.088
peak=    3.178 closest distance to " ND1 HIS A  86 " =    1.809
peak=    3.173 closest distance to " O   THR A 251 " =    1.992
peak=    3.156 closest distance to " CZ2 TRP A 179 " =    1.700
peak=    3.155 closest distance to " CA  LEU A  83 " =    1.393
peak=    3.152 closest distance to " CG2 THR A  29 " =    1.418
peak=    3.151 closest distance to " OH  TYR A 116 " =    1.102
peak=    3.148 closest distance to " O   HOH Z 336 " =    1.755
peak=    3.134 closest distance to " O   HOH Z  97 " =    2.726
peak=    3.134 closest distance to " CG  GLU A  53 " =    1.870
peak=    3.132 closest distance to " CB  LEU A  83 " =    0.875
peak=    3.129 closest distance to " O   HOH Z 423 " =    3.281
peak=    3.128 closest distance to " O   HOH Z 116 " =    1.793
peak=    3.127 closest distance to " CA  MET A 188 " =    1.037
peak=    3.127 closest distance to " O   HOH Z  44 " =    3.388
peak=    3.127 closest distance to " O   HOH Z 286 " =    2.277
peak=    3.127 closest distance to " CG  MET A 185 " =    1.208
peak=    3.126 closest distance to " O  BHOH Z 338 " =    2.316
peak=    3.124 closest distance to " O   HOH Z  85 " =    1.364
peak=    3.117 closest distance to " CB  SER A  62 " =    1.257
peak=    3.111 closest distance to " N   CYS A 260 " =    0.833
peak=    3.111 closest distance to " O   HOH Z 273 " =    2.881
peak=    3.104 closest distance to " CA  SER A 146 " =    1.694
peak=    3.104 closest distance to " CG  MET A 185 " =    1.115
peak=    3.101 closest distance to " O   HOH Z 325 " =    2.236
peak=    3.101 closest distance to " O   HOH Z 251 " =    1.479
peak=    3.101 closest distance to " O   HOH Z 130 " =    2.225
peak=    3.096 closest distance to " O   GLY A  57 " =    2.560
peak=    3.093 closest distance to " CB  ARG A 259 " =    1.867
peak=    3.092 closest distance to " NE2 GLN A  58 " =    3.740
peak=    3.091 closest distance to " O   HOH Z  30 " =    1.034
peak=    3.087 closest distance to " CB  ASN A 215 " =    1.172
peak=    3.086 closest distance to " O   HOH Z 148 " =    3.231
peak=    3.080 closest distance to " O   HOH Z 163 " =    1.987
peak=    3.071 closest distance to " CD1AILE A 234 " =    0.873
peak=    3.066 closest distance to " CB  ARG A 138 " =    0.954
peak=    3.063 closest distance to " O   HOH Z 371 " =    3.452
peak=    3.056 closest distance to " CB  TRP A 150 " =    0.938
peak=    3.024 closest distance to " O   HOH Z 271 " =    2.356

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 221         
Filter by distance & map next to the model:
   mapped sites are within: 0.896 - 5.687
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 220 from: 221
   mapped sites are within: 0.896 - 5.687

peak=   -4.869 closest distance to " O   HOH Z 266 " =    4.825
peak=   -4.554 closest distance to " CD  ARG A 156 " =    2.046
peak=   -4.257 closest distance to " O   HOH Z  10 " =    1.623
peak=   -4.149 closest distance to " O   VAL A  67 " =    2.685
peak=   -4.132 closest distance to " O   HOH Z 377 " =    2.029
peak=   -4.097 closest distance to " CG1 VAL A 250 " =    2.685
peak=   -4.082 closest distance to " CB  ALA A 161 " =    2.690
peak=   -4.076 closest distance to " CB  PRO A 243 " =    2.651
peak=   -4.072 closest distance to " SG  CYS A 254 " =    3.452
peak=   -4.055 closest distance to " OE1 GLN A 223 " =    1.984
peak=   -3.985 closest distance to " O   HOH Z 292 " =    4.607
peak=   -3.979 closest distance to " O   HOH Z 283 " =    2.301
peak=   -3.958 closest distance to " OG  SER A  97 " =    2.196
peak=   -3.950 closest distance to " O   PRO A 163 " =    2.159
peak=   -3.945 closest distance to " O   HOH Z 196 " =    2.102
peak=   -3.916 closest distance to " CD1 PHE A  59 " =    1.929
peak=   -3.910 closest distance to " ND2 ASN A  45 " =    1.523
peak=   -3.910 closest distance to " C   HIS A 108 " =    1.089
peak=   -3.910 closest distance to " N   ALA A  43 " =    2.663
peak=   -3.893 closest distance to " OXT GLY A 302 " =    2.945
peak=   -3.877 closest distance to " O   HOH Z 372 " =    2.493
peak=   -3.872 closest distance to " O   HOH Z 231 " =    2.352
peak=   -3.845 closest distance to " CA  ASP A 298 " =    1.044
peak=   -3.830 closest distance to " CG  GLU A  53 " =    1.415
peak=   -3.828 closest distance to " CE2 TYR A  30 " =    2.712
peak=   -3.818 closest distance to " CB  ASP A 132 " =    2.384
peak=   -3.815 closest distance to " O   HOH Z 353 " =    2.274
peak=   -3.811 closest distance to " CD1 LEU A 101 " =    2.517
peak=   -3.807 closest distance to " OG BSER A 134 " =    1.292
peak=   -3.799 closest distance to " CG2 ILE A 263 " =    2.356
peak=   -3.785 closest distance to " O   HOH Z  13 " =    1.661
peak=   -3.775 closest distance to " O   PRO A 198 " =    1.344
peak=   -3.768 closest distance to " NH2 ARG A  66 " =    1.791
peak=   -3.766 closest distance to " ND2 ASN A  45 " =    1.111
peak=   -3.749 closest distance to " O   HOH Z 198 " =    2.349
peak=   -3.701 closest distance to " C   ASN A 187 " =    1.927
peak=   -3.701 closest distance to " O   HOH Z  52 " =    1.535
peak=   -3.675 closest distance to " CD1 LEU A 228 " =    2.310
peak=   -3.673 closest distance to " CB  ASN A  39 " =    2.355
peak=   -3.663 closest distance to " OD1 ASN A 148 " =    1.576
peak=   -3.651 closest distance to " O   HOH Z 165 " =    1.912
peak=   -3.636 closest distance to " O   HOH Z 166 " =    1.802
peak=   -3.626 closest distance to " O   HOH Z  38 " =    1.430
peak=   -3.622 closest distance to " O   HOH Z 394 " =    1.551
peak=   -3.620 closest distance to " OG  SER A  62 " =    1.654
peak=   -3.613 closest distance to " OG BSER A 134 " =    1.921
peak=   -3.611 closest distance to " CD  ARG A 139 " =    1.588
peak=   -3.610 closest distance to " O   HOH Z  37 " =    1.858
peak=   -3.609 closest distance to " NE2 GLN A  88 " =    1.849
peak=   -3.605 closest distance to " CE2 PHE A  61 " =    2.571
peak=   -3.603 closest distance to " O   SER A 210 " =    1.884
peak=   -3.595 closest distance to " OD1 ASN A 187 " =    1.665
peak=   -3.594 closest distance to " ND2 ASN A 249 " =    2.412
peak=   -3.593 closest distance to " OD1 ASP A 191 " =    1.700
peak=   -3.585 closest distance to " O   VAL A  67 " =    2.858
peak=   -3.584 closest distance to " CZ3 TRP A 179 " =    1.217
peak=   -3.576 closest distance to " O   HOH Z 166 " =    1.603
peak=   -3.572 closest distance to " O   HOH Z 426 " =    1.696
peak=   -3.569 closest distance to " O   HOH Z 118 " =    3.393
peak=   -3.561 closest distance to " O   HOH Z 252 " =    3.921
peak=   -3.560 closest distance to " O   HOH Z 348 " =    2.228
peak=   -3.555 closest distance to " O   HOH Z 234 " =    4.282
peak=   -3.542 closest distance to " CZ  PHE A  59 " =    1.886
peak=   -3.536 closest distance to " O   HOH Z  43 " =    1.580
peak=   -3.531 closest distance to " O   HOH Z 393 " =    1.511
peak=   -3.524 closest distance to " CD2 LEU A 300 " =    2.865
peak=   -3.521 closest distance to " O   HOH Z 407 " =    3.415
peak=   -3.509 closest distance to " O   HOH Z 185 " =    2.445
peak=   -3.507 closest distance to " CG1 VAL A 112 " =    2.541
peak=   -3.504 closest distance to " CG  ARG A  66 " =    2.440
peak=   -3.496 closest distance to " O   ALA A   1 " =    1.937
peak=   -3.495 closest distance to " N   SER A 276 " =    1.480
peak=   -3.493 closest distance to " NH2AARG A 275 " =    5.347
peak=   -3.490 closest distance to " CD  GLN A  58 " =    1.127
peak=   -3.489 closest distance to " CA  GLY A 133 " =    2.306
peak=   -3.485 closest distance to " C   ASN A 285 " =    2.447
peak=   -3.484 closest distance to " O   HOH Z 377 " =    1.439
peak=   -3.481 closest distance to " CB  ALA A 291 " =    2.326
peak=   -3.480 closest distance to " O   PHE A 218 " =    1.574
peak=   -3.478 closest distance to " C   ALA A 158 " =    1.382
peak=   -3.471 closest distance to " CA  GLY A 203 " =    2.307
peak=   -3.471 closest distance to " CE3 TRP A 274 " =    2.498
peak=   -3.461 closest distance to " NH2 ARG A  79 " =    2.016
peak=   -3.448 closest distance to " CD2 TYR A 293 " =    1.967
peak=   -3.439 closest distance to " CD2 PHE A 225 " =    1.222
peak=   -3.436 closest distance to " CB  TYR A  15 " =    2.253
peak=   -3.436 closest distance to " C   SER A 206 " =    1.529
peak=   -3.428 closest distance to " CG2 VAL A 189 " =    2.202
peak=   -3.428 closest distance to " O   HOH Z 311 " =    3.749
peak=   -3.420 closest distance to " O   HOH Z 290 " =    1.152
peak=   -3.419 closest distance to " O   HOH Z   6 " =    2.228
peak=   -3.417 closest distance to " ND2BASN A 224 " =    1.745
peak=   -3.415 closest distance to " O   VAL A 125 " =    2.287
peak=   -3.410 closest distance to " CA  GLY A 241 " =    3.110
peak=   -3.407 closest distance to " CG  ARG A 269 " =    2.500
peak=   -3.406 closest distance to " O   HOH Z 252 " =    3.979
peak=   -3.405 closest distance to " N   GLN A  58 " =    1.559
peak=   -3.401 closest distance to " O   HOH Z  71 " =    1.597
peak=   -3.398 closest distance to " O   HOH Z 256 " =    2.410
peak=   -3.393 closest distance to " CB  ALA A 291 " =    2.261
peak=   -3.393 closest distance to " NH1 ARG A 195 " =    2.670
peak=   -3.388 closest distance to " NH2 ARG A  66 " =    5.687
peak=   -3.386 closest distance to " NE1 TRP A 266 " =    2.278
peak=   -3.378 closest distance to " CB  ALA A 248 " =    2.032
peak=   -3.378 closest distance to " NE2 GLN A 103 " =    1.741
peak=   -3.368 closest distance to " CD  PRO A 213 " =    2.210
peak=   -3.363 closest distance to " CD2 PHE A  59 " =    2.548
peak=   -3.362 closest distance to " CG1 VAL A 112 " =    2.855
peak=   -3.358 closest distance to " ND2 ASN A  60 " =    1.461
peak=   -3.357 closest distance to " ND2 ASN A  60 " =    1.804
peak=   -3.348 closest distance to " SG ACYS A 201 " =    1.976
peak=   -3.347 closest distance to " N   ALA A 226 " =    2.125
peak=   -3.343 closest distance to " CE  MET A  93 " =    1.263
peak=   -3.338 closest distance to " CB  ALA A  43 " =    2.581
peak=   -3.331 closest distance to " CG  GLU A 277 " =    1.145
peak=   -3.328 closest distance to " O   HOH Z   6 " =    1.626
peak=   -3.325 closest distance to " OD2 ASP A 171 " =    1.786
peak=   -3.324 closest distance to " CB  PHE A  16 " =    2.631
peak=   -3.320 closest distance to " CG  ASP A 231 " =    0.896
peak=   -3.318 closest distance to " O   ALA A  10 " =    1.742
peak=   -3.318 closest distance to " C   LEU A 143 " =    1.162
peak=   -3.318 closest distance to " O   HOH Z 111 " =    1.419
peak=   -3.317 closest distance to " OG ASER A 134 " =    1.258
peak=   -3.307 closest distance to " OE2 GLU A   2 " =    1.752
peak=   -3.305 closest distance to " CD  LYS A 289 " =    2.426
peak=   -3.302 closest distance to " O   HOH Z 418 " =    1.415
peak=   -3.301 closest distance to " CD  ARG A 195 " =    5.094
peak=   -3.300 closest distance to " O   VAL A 189 " =    2.580
peak=   -3.300 closest distance to " CE  MET A 105 " =    2.065
peak=   -3.298 closest distance to " ND2 ASN A 187 " =    1.697
peak=   -3.297 closest distance to " O   HOH Z 128 " =    2.513
peak=   -3.296 closest distance to " O   HOH Z 211 " =    1.678
peak=   -3.295 closest distance to " CE3 TRP A  70 " =    1.785
peak=   -3.294 closest distance to " C   ALA A   8 " =    1.626
peak=   -3.293 closest distance to " CE3 TRP A 150 " =    2.064
peak=   -3.291 closest distance to " O   HOH Z 275 " =    1.526
peak=   -3.286 closest distance to " O   HOH Z 323 " =    1.457
peak=   -3.281 closest distance to " CZ  TYR A 169 " =    1.844
peak=   -3.276 closest distance to " O   HOH Z 117 " =    4.492
peak=   -3.271 closest distance to " O   HOH Z 389 " =    1.813
peak=   -3.266 closest distance to " NH2 ARG A  79 " =    1.575
peak=   -3.260 closest distance to " O   ASN A 301 " =    1.431
peak=   -3.259 closest distance to " O   HOH Z 145 " =    2.084
peak=   -3.259 closest distance to " CD2 LEU A 167 " =    1.819
peak=   -3.255 closest distance to " CG  TRP A 266 " =    1.753
peak=   -3.254 closest distance to " O   ASN A 187 " =    1.535
peak=   -3.246 closest distance to " O   ALA A  34 " =    2.424
peak=   -3.246 closest distance to " O   VAL A 174 " =    2.101
peak=   -3.245 closest distance to " O   HOH Z 298 " =    2.654
peak=   -3.243 closest distance to " O   HOH Z 351 " =    1.527
peak=   -3.242 closest distance to " CA  GLY A 241 " =    2.331
peak=   -3.242 closest distance to " O   HOH Z 350 " =    2.178
peak=   -3.241 closest distance to " OG BSER A 210 " =    2.109
peak=   -3.237 closest distance to " O   HOH Z  19 " =    2.055
peak=   -3.236 closest distance to " CB  ALA A  10 " =    2.131
peak=   -3.235 closest distance to " O   GLY A 118 " =    2.225
peak=   -3.235 closest distance to " CB  PHE A 192 " =    1.872
peak=   -3.233 closest distance to " O   HOH Z  11 " =    1.855
peak=   -3.230 closest distance to " CG1 VAL A 112 " =    2.925
peak=   -3.227 closest distance to " C   ILE A 234 " =    1.302
peak=   -3.226 closest distance to " O   HOH Z 177 " =    1.659
peak=   -3.220 closest distance to " O   HOH Z  97 " =    1.735
peak=   -3.217 closest distance to " CH2 TRP A 177 " =    2.099
peak=   -3.210 closest distance to " O   HOH Z 189 " =    1.739
peak=   -3.209 closest distance to " O   HOH Z 102 " =    1.577
peak=   -3.208 closest distance to " CB  ASP A 286 " =    2.257
peak=   -3.207 closest distance to " O   HOH Z 414 " =    1.634
peak=   -3.206 closest distance to " C   THR A 279 " =    1.148
peak=   -3.202 closest distance to " CG  ASN A 301 " =    1.991
peak=   -3.201 closest distance to " O   HOH Z 111 " =    1.995
peak=   -3.200 closest distance to " CB  PRO A 163 " =    2.582
peak=   -3.199 closest distance to " CG2 ILE A  49 " =    2.686
peak=   -3.199 closest distance to " CG2 THR A 221 " =    2.251
peak=   -3.198 closest distance to " O   TRP A  92 " =    1.853
peak=   -3.194 closest distance to " CB  ALA A   9 " =    2.617
peak=   -3.194 closest distance to " CB  TRP A  85 " =    2.403
peak=   -3.191 closest distance to " O   HOH Z 123 " =    2.320
peak=   -3.189 closest distance to " O   HOH Z 385 " =    1.840
peak=   -3.188 closest distance to " CG  PRO A 243 " =    1.773
peak=   -3.183 closest distance to " CD2 TYR A 247 " =    2.363
peak=   -3.181 closest distance to " CB  CYS A 254 " =    2.470
peak=   -3.181 closest distance to " CB  ALA A 131 " =    2.356
peak=   -3.179 closest distance to " CA  VAL A 197 " =    1.019
peak=   -3.177 closest distance to " O   GLY A 196 " =    1.089
peak=   -3.177 closest distance to " CE BMET A  47 " =    2.247
peak=   -3.177 closest distance to " CD2 LEU A 237 " =    2.695
peak=   -3.171 closest distance to " O   HOH Z 435 " =    2.581
peak=   -3.168 closest distance to " O   HOH Z 423 " =    2.300
peak=   -3.167 closest distance to " CD  GLU A 236 " =    1.075
peak=   -3.154 closest distance to " O   HOH Z 436 " =    1.544
peak=   -3.149 closest distance to " O   HOH Z 198 " =    1.539
peak=   -3.148 closest distance to " O   HOH Z 264 " =    1.789
peak=   -3.148 closest distance to " O   HOH Z  88 " =    2.111
peak=   -3.144 closest distance to " O   HOH Z 421 " =    3.475
peak=   -3.143 closest distance to " O   HOH Z 200 " =    1.635
peak=   -3.142 closest distance to " O   HOH Z  61 " =    1.611
peak=   -3.141 closest distance to " O   HOH Z 378 " =    1.383
peak=   -3.141 closest distance to " O   HOH Z 388 " =    1.969
peak=   -3.138 closest distance to " N   ALA A 248 " =    1.617
peak=   -3.133 closest distance to " O   HOH Z 396 " =    1.707
peak=   -3.128 closest distance to " CB  PHE A 283 " =    2.982
peak=   -3.128 closest distance to " N   MET A 105 " =    2.734
peak=   -3.124 closest distance to " CB  ALA A 248 " =    2.353
peak=   -3.117 closest distance to " O   HOH Z  60 " =    2.405
peak=   -3.116 closest distance to " CB  GLN A  11 " =    1.817
peak=   -3.115 closest distance to " CG  PRO A 163 " =    2.500
peak=   -3.115 closest distance to " CB  ALA A 131 " =    1.962
peak=   -3.111 closest distance to " OH  TYR A 247 " =    1.809
peak=   -3.111 closest distance to " O   HOH Z  90 " =    1.831
peak=   -3.107 closest distance to " C   ARG A  79 " =    2.625
peak=   -3.097 closest distance to " O   HOH Z 380 " =    4.743
peak=   -3.095 closest distance to " O   HOH Z 134 " =    2.697
peak=   -3.084 closest distance to " CA  GLY A  98 " =    2.107
peak=   -3.084 closest distance to " O   HOH Z 357 " =    2.097
peak=   -3.073 closest distance to " CD2 TYR A 293 " =    2.170
peak=   -3.070 closest distance to " CB  ALA A 291 " =    2.142
peak=   -3.050 closest distance to " O   HOH Z 357 " =    2.059
peak=   -3.050 closest distance to " CD  GLN A  88 " =    0.940
peak=   -3.050 closest distance to " OD2 ASP A  50 " =    2.188
peak=   -3.026 closest distance to " O   PRO A 198 " =    1.667

================= 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    :  0.3573 0.3483   6.125311e+00   6.104003e+00
   1_bss:  0.3450 0.3359   6.105551e+00   6.078042e+00
   1_xyz:  0.2244 0.2494   5.726802e+00   5.815135e+00
   1_adp:  0.2039 0.2545   5.669278e+00   5.832979e+00
   1_occ:  0.2035 0.2542   5.668189e+00   5.832016e+00
   2_bss:  0.2017 0.2519   5.661969e+00   5.825386e+00
   2_xyz:  0.1555 0.1931   5.409687e+00   5.590984e+00
   2_adp:  0.1476 0.1843   5.364795e+00   5.548644e+00
   2_occ:  0.1473 0.1842   5.363982e+00   5.547950e+00
   3_bss:  0.1473 0.1845   5.363612e+00   5.546471e+00
   3_xyz:  0.1268 0.1658   5.237718e+00   5.450797e+00
   3_adp:  0.1219 0.1653   5.215667e+00   5.442831e+00
   3_occ:  0.1219 0.1652   5.215454e+00   5.442643e+00
   4_bss:  0.1218 0.1652   5.215020e+00   5.442305e+00
   4_xyz:  0.1142 0.1623   5.171398e+00   5.416175e+00
   4_adp:  0.1133 0.1618   5.164730e+00   5.410655e+00
   4_occ:  0.1133 0.1618   5.164805e+00   5.411030e+00
   5_bss:  0.1135 0.1615   5.166506e+00   5.410940e+00
   5_xyz:  0.1104 0.1616   5.153859e+00   5.409970e+00
   5_adp:  0.1101 0.1613   5.153321e+00   5.411070e+00
   5_occ:  0.1101 0.1613   5.153282e+00   5.411182e+00
   5_bss:  0.1100 0.1612   5.153421e+00   5.411275e+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:  0.300  50.000  -1.867   3.280  -1.699   0.000  -0.000  -0.000
   1_xyz:  0.300  50.000  -1.867   3.280  -1.699   0.000  -0.000  -0.000
   1_adp:  0.300  50.000  -1.867   3.280  -1.699   0.000  -0.000  -0.000
   1_occ:  0.300  50.000  -1.867   3.280  -1.699   0.000  -0.000  -0.000
   2_bss:  0.324  66.158  -2.195   0.095  -1.539   0.000  -0.000  -0.000
   2_xyz:  0.324  66.158  -2.195   0.095  -1.539   0.000  -0.000  -0.000
   2_adp:  0.324  66.158  -2.195   0.095  -1.539   0.000  -0.000  -0.000
   2_occ:  0.324  66.158  -2.195   0.095  -1.539   0.000  -0.000  -0.000
   3_bss:  0.327  65.488  -2.156  -0.849  -1.274  -0.000  -0.000  -0.000
   3_xyz:  0.327  65.488  -2.156  -0.849  -1.274  -0.000  -0.000  -0.000
   3_adp:  0.327  65.488  -2.156  -0.849  -1.274  -0.000  -0.000  -0.000
   3_occ:  0.327  65.488  -2.156  -0.849  -1.274  -0.000  -0.000  -0.000
   4_bss:  0.326  65.934  -1.944  -1.107  -1.036  -0.000  -0.000  -0.000
   4_xyz:  0.326  65.934  -1.944  -1.107  -1.036  -0.000  -0.000  -0.000
   4_adp:  0.326  65.934  -1.944  -1.107  -1.036  -0.000  -0.000  -0.000
   4_occ:  0.326  65.934  -1.944  -1.107  -1.036  -0.000  -0.000  -0.000
   5_bss:  0.326  65.934  -1.688  -1.092  -0.804  -0.000  -0.000  -0.000
   5_xyz:  0.326  65.934  -1.688  -1.092  -0.804  -0.000  -0.000  -0.000
   5_adp:  0.326  65.934  -1.688  -1.092  -0.804  -0.000  -0.000  -0.000
   5_occ:  0.326  65.934  -1.688  -1.092  -0.804  -0.000  -0.000  -0.000
   5_bss:  0.326  65.937  -1.443  -0.930  -0.553  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  37.930 0.6699  0.8399    36582.331
   1_bss:  36.898 0.6802  0.8496    33445.296
   1_xyz:  25.199 0.8105  0.9661    16485.967
   1_adp:  25.826 0.8031  0.9497    17100.673
   1_occ:  25.806 0.8033  0.9496    17063.334
   2_bss:  25.453 0.8070  0.9201    16718.987
   2_xyz:  18.610 0.8744  0.9677     9538.686
   2_adp:  17.400 0.8861  0.9678     8720.564
   2_occ:  17.391 0.8862  0.9678     8713.695
   3_bss:  17.364 0.8865  0.9613     8705.726
   3_xyz:  15.292 0.9042  0.9715     7087.215
   3_adp:  15.105 0.9061  0.9651     7001.305
   3_occ:  15.100 0.9061  0.9650     6999.876
   4_bss:  15.088 0.9062  0.9676     6998.289
   4_xyz:  14.606 0.9100  0.9698     6647.456
   4_adp:  14.476 0.9112  0.9628     6602.062
   4_occ:  14.479 0.9112  0.9627     6607.862
   5_bss:  14.500 0.9110  0.9683     6622.782
   5_xyz:  14.449 0.9114  0.9691     6589.665
   5_adp:  14.455 0.9114  0.9611     6595.340
   5_occ:  14.455 0.9114  0.9610     6597.265
   5_bss:  14.459 0.9114  0.9686     6599.352
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6381e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6381e-01
   1_xyz:   1.256  0.009  0.076 15.238  0.004  4.116   8.2442e-02
   1_adp:   1.256  0.009  0.076 15.238  0.004  4.116   8.2442e-02
   1_occ:   1.256  0.009  0.076 15.238  0.004  4.116   8.2442e-02
   2_bss:   1.256  0.009  0.076 15.238  0.004  4.116   8.2442e-02
   2_xyz:   0.972  0.006  0.068 14.167  0.004  4.128   5.3597e-02
   2_adp:   0.972  0.006  0.068 14.167  0.004  4.128   5.3597e-02
   2_occ:   0.972  0.006  0.068 14.167  0.004  4.128   5.3597e-02
   3_bss:   0.972  0.006  0.068 14.167  0.004  4.128   5.3597e-02
   3_xyz:   0.939  0.007  0.070 14.380  0.003  4.134   5.2600e-02
   3_adp:   0.939  0.007  0.070 14.380  0.003  4.134   5.2600e-02
   3_occ:   0.939  0.007  0.070 14.380  0.003  4.134   5.2600e-02
   4_bss:   0.939  0.007  0.070 14.380  0.003  4.134   5.2600e-02
   4_xyz:   1.025  0.008  0.077 14.569  0.004  4.114   6.2437e-02
   4_adp:   1.025  0.008  0.077 14.569  0.004  4.114   6.2437e-02
   4_occ:   1.025  0.008  0.077 14.569  0.004  4.114   6.2437e-02
   5_bss:   1.025  0.008  0.077 14.569  0.004  4.114   6.2437e-02
   5_xyz:   1.064  0.009  0.080 14.694  0.004  4.117   6.7892e-02
   5_adp:   1.064  0.009  0.080 14.694  0.004  4.117   6.7892e-02
   5_occ:   1.064  0.009  0.080 14.694  0.004  4.117   6.7892e-02
   5_bss:   1.064  0.009  0.080 14.694  0.004  4.117   6.7892e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.698   2.4288e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.698   2.4288e-01
   1_xyz:   9.254  0.056  0.371 89.136  0.022  2.197   1.1420e-01
   1_adp:   9.254  0.056  0.371 89.136  0.022  2.197   1.1420e-01
   1_occ:   9.254  0.056  0.371 89.136  0.022  2.197   1.1420e-01
   2_bss:   9.254  0.056  0.371 89.136  0.022  2.197   1.1420e-01
   2_xyz:   7.264  0.044  0.223 83.546  0.043  2.339   6.7138e-02
   2_adp:   7.264  0.044  0.223 83.546  0.043  2.339   6.7138e-02
   2_occ:   7.264  0.044  0.223 83.546  0.043  2.339   6.7138e-02
   3_bss:   7.264  0.044  0.223 83.546  0.043  2.339   6.7138e-02
   3_xyz:   6.851  0.040  0.223 80.874  0.036  2.380   3.5997e-02
   3_adp:   6.851  0.040  0.223 80.874  0.036  2.380   3.5997e-02
   3_occ:   6.851  0.040  0.223 80.874  0.036  2.380   3.5997e-02
   4_bss:   6.851  0.040  0.223 80.874  0.036  2.380   3.5997e-02
   4_xyz:   7.584  0.043  0.243 82.743  0.040  2.343   4.3789e-02
   4_adp:   7.584  0.043  0.243 82.743  0.040  2.343   4.3789e-02
   4_occ:   7.584  0.043  0.243 82.743  0.040  2.343   4.3789e-02
   5_bss:   7.584  0.043  0.243 82.743  0.040  2.343   4.3789e-02
   5_xyz:   7.872  0.046  0.252 81.431  0.038  2.318   4.9701e-02
   5_adp:   7.872  0.046  0.252 81.431  0.038  2.318   4.9701e-02
   5_occ:   7.872  0.046  0.252 81.431  0.038  2.318   4.9701e-02
   5_bss:   7.872  0.046  0.252 81.431  0.038  2.318   4.9701e-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:  81.02   0.00  17.22  78.52   0.00  13.15  81.02   4.56  39.38
   1_occ:  81.02   0.00  17.22  78.52   0.00  13.15  81.02   4.56  39.38
   2_bss:  81.02   0.00  17.22  78.52   0.00  13.15  81.02   4.56  39.38
   2_xyz:  81.02   0.00  17.22  78.52   0.00  13.15  81.02   4.56  39.38
   2_adp:  81.01   0.91  16.96  80.29   0.91  12.82  81.01   4.87  39.50
   2_occ:  81.01   0.91  16.96  80.29   0.91  12.82  81.01   4.87  39.50
   3_bss:  81.01   0.91  16.96  80.29   0.91  12.82  81.01   4.87  39.50
   3_xyz:  81.01   0.91  16.96  80.29   0.91  12.82  81.01   4.87  39.50
   3_adp: 106.29   0.00  17.49 106.29   0.00  12.82  93.46   5.16  42.91
   3_occ: 106.29   0.00  17.49 106.29   0.00  12.82  93.46   5.16  42.91
   4_bss: 106.29   0.00  17.49 106.29   0.00  12.82  93.46   5.16  42.91
   4_xyz: 106.29   0.00  17.49 106.29   0.00  12.82  93.46   5.16  42.91
   4_adp: 109.57   0.00  17.19 109.57   0.00  12.58  93.58   5.16  42.28
   4_occ: 109.57   0.00  17.19 109.57   0.00  12.58  93.58   5.16  42.28
   5_bss: 109.57   0.00  17.19 109.57   0.00  12.58  93.58   5.16  42.28
   5_xyz: 109.57   0.00  17.19 109.57   0.00  12.58  93.58   5.16  42.28
   5_adp: 113.82   0.00  16.93 113.82   0.00  12.37  93.67   5.16  41.79
   5_occ: 113.82   0.00  16.93 113.82   0.00  12.37  93.67   5.16  41.79
   5_bss: 113.83   0.00  16.94 113.83   0.00  12.37  93.67   5.16  41.80
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.564    0.014    0.338
   1_adp:    1.564    0.014    0.338
   1_occ:    1.564    0.014    0.338
   2_bss:    1.564    0.014    0.338
   2_xyz:    0.945    0.024    0.408
   2_adp:    0.945    0.024    0.408
   2_occ:    0.945    0.024    0.408
   3_bss:    0.945    0.024    0.408
   3_xyz:    0.964    0.023    0.476
   3_adp:    0.964    0.023    0.476
   3_occ:    0.964    0.023    0.476
   4_bss:    0.964    0.023    0.476
   4_xyz:    1.013    0.023    0.500
   4_adp:    1.013    0.023    0.500
   4_occ:    1.013    0.023    0.500
   5_bss:    1.013    0.023    0.500
   5_xyz:    1.047    0.032    0.515
   5_adp:    1.047    0.032    0.515
   5_occ:    1.047    0.032    0.515
   5_bss:    1.047    0.032    0.515
------------------------------------------------------------------------

CPU time actual refinement: 341.79


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_939/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_939/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_939/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_939/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_939/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 341.63 
  Macro-tasks:
    bulk solvent and scale       = 39.58  
    individual site refinement   = 145.15 
    weights calculation          = 29.09  
    collect and process          = 6.59   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 220.53 
  Micro-tasks:
    mask                            = 1.78   
    f_calc                          = 109.27 
    alpha_beta                      = 7.94   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 120.11 
    fmodel                         = 6.69   
    r_factors                      = 0.18   
    phase_errors                   = 11.32  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 258.75 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.723 micro seconds
Total CPU time: 5.92 minutes
from_scatterers_fft:    679 calls, 108.87 s
gradients_fft:          624 calls, 105.43 s

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

# Date 2008-01-16 Time 06:01:32 PST -0800 (1200492092.69 s)
Start R-work = 0.3573, R-free = 0.3483 (no bulk solvent and anisotropic scale)
Final R-work = 0.1284, R-free = 0.1767 (no bulk solvent and anisotropic scale)

Start R-work = 0.3450, R-free = 0.3359
Final R-work = 0.1100, R-free = 0.1612