# Date 2008-01-16 Time 04:57:01 PST -0800 (1200488221.49 s)
#phil __OFF__

Command line arguments: "../531.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 18013
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 531

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 46.6953, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.30, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.6953, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8986 1.981
Completeness in resolution range: 0.977739
Completeness with d_max=infinity: 0.974626

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8986
                             d_min =   1.9810

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.6953, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8986 1.981
Completeness in resolution range: 0.977739
Completeness with d_max=infinity: 0.974626

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8990 -  4.2383 [2101/2125]  1892   209   9.9%
  bin  2:  4.2383 -  3.3769 [2029/2048]  1826   203  10.0%
  bin  3:  3.3769 -  2.9538 [1993/2012]  1790   203  10.2%
  bin  4:  2.9538 -  2.6855 [1969/1999]  1775   194   9.9%
  bin  5:  2.6855 -  2.4940 [1962/1981]  1766   196  10.0%
  bin  6:  2.4940 -  2.3475 [1951/1976]  1755   196  10.0%
  bin  7:  2.3475 -  2.2304 [1970/1998]  1773   197  10.0%
  bin  8:  2.2304 -  2.1336 [1929/1965]  1737   192  10.0%
  bin  9:  2.1336 -  2.0516 [1913/1955]  1724   189   9.9%
  bin 10:  2.0516 -  1.9810 [1772/1976]  1592   180  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_531/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:
        1.81 -     2.42: 19
        2.42 -     3.04: 2224
        3.04 -     3.66: 4737
        3.66 -     4.28: 9128
        4.28 -     4.90: 12446
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  52 " - " O   HOH Z 183 "  2.015 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  2.157 3.040 -x+1,y-1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 110 " - " O   HOH Z 355 "  2.264 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28549 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_531/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_531/model_refine_001.geo

CPU time processing inputs: 9.23


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 46.69535 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2701   r_free= 0.2735   ksol= 0.00   Bsol= 0.00   scale= 1.002    |
|                                                                             |
| 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:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.869021                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8990 -  4.7268 0.99   1372  153 0.2655 0.2610      6.2966      6.2562|
|  2:  4.7268 -  3.7719 0.99   1314  145 0.2137 0.2123      6.2512       6.243|
|  3:  3.7719 -  3.3010 0.99   1287  144 0.2245 0.2341      6.1352      6.2412|
|  4:  3.3010 -  3.0019 0.99   1278  143 0.2364 0.2491      6.0164      6.0484|
|  5:  3.0019 -  2.7882 0.99   1270  140 0.2591 0.2501      5.9012      5.8694|
|  6:  2.7882 -  2.6248 0.99   1278  140 0.2722 0.2898      5.8598      5.8492|
|  7:  2.6248 -  2.4940 0.99   1250  140 0.2850 0.2562        5.83      5.7362|
|  8:  2.4940 -  2.3858 0.98   1264  140 0.2891 0.3060      5.8087      5.8769|
|  9:  2.3858 -  2.2943 0.98   1258  138 0.2896 0.3044      5.7542      5.7259|
| 10:  2.2943 -  2.2154 0.99   1233  138 0.2925 0.3201      5.7267      5.7794|
| 11:  2.2154 -  2.1464 0.98   1250  142 0.3062 0.2997      5.6983       5.743|
| 12:  2.1464 -  2.0852 0.97   1240  134 0.3055 0.3015      5.6593      5.6716|
| 13:  2.0852 -  2.0304 1.00   1235  141 0.3073 0.3081      5.5659      5.5737|
| 14:  2.0304 -  1.9810 0.86   1101  121 0.3185 0.3168      5.5455       5.422|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8990 -  4.7268  1372   153  0.80  24.91   0.88     0.81      38951.52|
|  2:  4.7268 -  3.7719  1314   145  0.87  19.01   1.00     0.94      34731.50|
|  3:  3.7719 -  3.3010  1287   144  0.86  20.43   1.02     1.01      30035.52|
|  4:  3.3010 -  3.0019  1278   143  0.84  22.26   1.03     1.01      25325.48|
|  5:  3.0019 -  2.7882  1270   140  0.81  25.07   1.02     0.99      20659.94|
|  6:  2.7882 -  2.6248  1278   140  0.81  25.46   1.03     1.00      18029.32|
|  7:  2.6248 -  2.4940  1250   140  0.81  26.22   1.03     1.01      16317.61|
|  8:  2.4940 -  2.3858  1264   140  0.80  26.98   1.05     1.01      16204.19|
|  9:  2.3858 -  2.2943  1258   138  0.79  27.86   1.07     1.00      15357.06|
| 10:  2.2943 -  2.2154  1233   138  0.77  29.78   1.09     1.00      15141.58|
| 11:  2.2154 -  2.1464  1250   142  0.77  29.64   1.09     1.02      13982.63|
| 12:  2.1464 -  2.0852  1240   134  0.78  28.97   1.10     1.04      12851.01|
| 13:  2.0852 -  2.0304  1235   141  0.77  29.54   1.10     1.02      10814.07|
| 14:  2.0304 -  1.9810  1101   121  0.79  28.18   1.09     0.97       8409.37|
|alpha:            min =        0.81 max =            1.04 mean =         0.99|
|beta:             min =     8409.37 max =        38951.52 mean =     20095.03|
|figures of merit: min =        0.00 max =            1.00 mean =         0.81|
|phase err.(work): min =        0.00 max =           89.97 mean =        25.95|
|phase err.(test): min =        0.00 max =           89.70 mean =        26.13|
|-----------------------------------------------------------------------------|

============================== 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 = 2.630687              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.205   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.444205              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.380   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       17 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      216 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2008 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1870 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2867 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4691 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4437 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5666 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6780 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.161 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.806 |       0.175 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.680)------------------------------------------|
|    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: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2701   r_free= 0.2735   ksol= 0.00   Bsol= 0.00   scale= 1.002    |
|                                                                             |
| 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:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.869021                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2528   r_free= 0.2526   ksol= 0.32   Bsol= 33.02   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-1.99,-0.32,-0.00,-0.00,-0.00); trace/3= -1.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.838700                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.298825              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.273   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.224503              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.323   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2528      final r-factor (work) = 0.1472          |
| start r-factor (free) = 0.2526      final r-factor (free) = 0.1670          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9083 = 2.30 * 0.50 * 5.8701 + 1.00 * 0.1611                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4098 = 2.30 * 0.50 * 5.5298 + 1.00 * 0.0538                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1472      final r-factor (work) = 0.1368          |
| start r-factor (free) = 0.1670      final r-factor (free) = 0.1703          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2476 = 0.22 * 1.00 * 5.5298 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2172 = 0.22 * 1.00 * 5.2704 + 1.00 * 0.0340                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.680)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    67.57   16.50    None  None   None       |
|    all(noH): 2823   0      0.00    67.57   16.50    None  None   None       |
|    Sol.    : 438    0      7.83    62.45   37.23    None  None   None       |
|    Mac.    : 2385   0      0.00    67.57   12.69    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.757:  227   |   5:    33.784 -  40.540:  106        |
|      1:     6.757 -  13.514: 1413   |   6:    40.540 -  47.297:   88        |
|      2:    13.514 -  20.270:  583   |   7:    47.297 -  54.054:   74        |
|      3:    20.270 -  27.027:  161   |   8:    54.054 -  60.811:   39        |
|      4:    27.027 -  33.784:  128   |   9:    60.811 -  67.567:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1368 r_free = 0.1703             target_work(ml) = 5.280         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1363 r_free = 0.1704             target_work(ml) = 5.278         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1363   r_free= 0.1704   ksol= 0.32   Bsol= 33.02   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-1.99,-0.32,-0.00,-0.00,-0.00); trace/3= -1.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.277964                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1362   r_free= 0.1694   ksol= 0.32   Bsol= 38.71   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.12,-2.65,-1.53,-0.00,-0.00,-0.00); trace/3= -2.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.276932                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.776363              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.409  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.207288              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.897   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1362      final r-factor (work) = 0.1163          |
| start r-factor (free) = 0.1694      final r-factor (free) = 0.1525          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7408 = 1.78 * 0.50 * 5.2777 + 1.00 * 0.0533                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6679 = 1.78 * 0.50 * 5.1968 + 1.00 * 0.0523                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1163      final r-factor (work) = 0.1122          |
| start r-factor (free) = 0.1525      final r-factor (free) = 0.1506          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1654 = 0.21 * 1.00 * 5.1968 + 1.00 * 0.0882                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0685 = 0.21 * 1.00 * 5.1208 + 1.00 * 0.0071                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.680)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.62    70.13   16.73    None  None   None       |
|    all(noH): 2823   0      1.62    70.13   16.73    None  None   None       |
|    Sol.    : 438    0      5.96    70.13   37.57    None  None   None       |
|    Mac.    : 2385   0      1.62    67.00   12.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.619 -   8.470:  558   |   5:    35.874 -  42.725:  116        |
|      1:     8.470 -  15.321: 1326   |   6:    42.725 -  49.576:   80        |
|      2:    15.321 -  22.172:  392   |   7:    49.576 -  56.427:   85        |
|      3:    22.172 -  29.023:  127   |   8:    56.427 -  63.278:   26        |
|      4:    29.023 -  35.874:  106   |   9:    63.278 -  70.129:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1122 r_free = 0.1506             target_work(ml) = 5.115         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1121 r_free = 0.1506             target_work(ml) = 5.115         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1506   ksol= 0.32   Bsol= 38.71   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.12,-2.65,-1.53,-0.00,-0.00,-0.00); trace/3= -2.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.114762                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1505   ksol= 0.32   Bsol= 39.12   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,-2.46,-1.50,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.114427                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.178317              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 145.552  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.600869              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.720  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1120      final r-factor (work) = 0.1109          |
| start r-factor (free) = 0.1505      final r-factor (free) = 0.1502          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.0694 = 1.18 * 0.50 * 5.1212 + 1.00 * 0.0523                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.0580 = 1.18 * 0.50 * 5.1115 + 1.00 * 0.0465                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1109      final r-factor (work) = 0.1096          |
| start r-factor (free) = 0.1502      final r-factor (free) = 0.1514          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0784 = 0.60 * 1.00 * 5.1115 + 1.00 * 0.0071                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0763 = 0.60 * 1.00 * 5.1059 + 1.00 * 0.0083                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.680)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.87    79.87   16.96    None  None   None       |
|    all(noH): 2823   0      0.87    79.87   16.96    None  None   None       |
|    Sol.    : 438    0      6.16    74.88   38.87    None  None   None       |
|    Mac.    : 2385   0      0.87    79.87   12.93    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:     0.872 -   8.771:  695   |   5:    40.369 -  48.268:  117        |
|      1:     8.771 -  16.671: 1286   |   6:    48.268 -  56.168:   85        |
|      2:    16.671 -  24.570:  340   |   7:    56.168 -  64.067:   43        |
|      3:    24.570 -  32.469:  126   |   8:    64.067 -  71.967:   19        |
|      4:    32.469 -  40.369:  107   |   9:    71.967 -  79.866:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1096 r_free = 0.1514             target_work(ml) = 5.111         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1095 r_free = 0.1515             target_work(ml) = 5.111         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1095   r_free= 0.1515   ksol= 0.32   Bsol= 39.12   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,-2.46,-1.50,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.111452                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1095   r_free= 0.1514   ksol= 0.32   Bsol= 41.80   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.65,-2.33,-1.42,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.111056                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.481871              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 157.602  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.137467              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.811  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1095      final r-factor (work) = 0.1049          |
| start r-factor (free) = 0.1514      final r-factor (free) = 0.1509          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3830 = 2.48 * 0.50 * 5.1062 + 1.00 * 0.0465                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3780 = 2.48 * 0.50 * 5.0906 + 1.00 * 0.0610                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1049      final r-factor (work) = 0.1060          |
| start r-factor (free) = 0.1509      final r-factor (free) = 0.1501          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7081 = 0.14 * 1.00 * 5.0906 + 1.00 * 0.0083                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7067 = 0.14 * 1.00 * 5.0921 + 1.00 * 0.0067                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.680)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.78    77.57   16.36    None  None   None       |
|    all(noH): 2823   0      1.78    77.57   16.36    None  None   None       |
|    Sol.    : 438    0      6.09    74.59   36.49    None  None   None       |
|    Mac.    : 2385   0      1.78    77.57   12.66    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.784 -   9.362:  853   |   5:    39.677 -  47.256:  102        |
|      1:     9.362 -  16.941: 1191   |   6:    47.256 -  54.834:   78        |
|      2:    16.941 -  24.520:  290   |   7:    54.834 -  62.413:   25        |
|      3:    24.520 -  32.098:  129   |   8:    62.413 -  69.992:    9        |
|      4:    32.098 -  39.677:  140   |   9:    69.992 -  77.570:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1060 r_free = 0.1501             target_work(ml) = 5.089         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1060 r_free = 0.1502             target_work(ml) = 5.089         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1060   r_free= 0.1502   ksol= 0.32   Bsol= 41.80   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.65,-2.33,-1.42,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.088882                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1062   r_free= 0.1495   ksol= 0.32   Bsol= 41.80   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.57,-2.27,-1.35,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.089805                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.566239              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 163.435  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.407407              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.043  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1062      final r-factor (work) = 0.1051          |
| start r-factor (free) = 0.1495      final r-factor (free) = 0.1513          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5956 = 2.57 * 0.50 * 5.0928 + 1.00 * 0.0610                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5866 = 2.57 * 0.50 * 5.0852 + 1.00 * 0.0617                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1051      final r-factor (work) = 0.1044          |
| start r-factor (free) = 0.1513      final r-factor (free) = 0.1523          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0785 = 0.41 * 1.00 * 5.0852 + 1.00 * 0.0067                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0794 = 0.41 * 1.00 * 5.0854 + 1.00 * 0.0075                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.680)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.12    78.75   16.36    None  None   None       |
|    all(noH): 2823   0      1.12    78.75   16.36    None  None   None       |
|    Sol.    : 438    0      6.23    74.66   37.08    None  None   None       |
|    Mac.    : 2385   0      1.12    78.75   12.55    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.120 -   8.883:  785   |   5:    39.936 -  47.699:  111        |
|      1:     8.883 -  16.646: 1233   |   6:    47.699 -  55.462:   85        |
|      2:    16.646 -  24.409:  307   |   7:    55.462 -  63.225:   27        |
|      3:    24.409 -  32.172:  132   |   8:    63.225 -  70.989:    9        |
|      4:    32.172 -  39.936:  128   |   9:    70.989 -  78.752:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1044 r_free = 0.1523             target_work(ml) = 5.091         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1044 r_free = 0.1523             target_work(ml) = 5.091         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1044   r_free= 0.1523   ksol= 0.32   Bsol= 41.80   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.57,-2.27,-1.35,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.090691                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8990 -  4.7268 0.99   1372  153 0.0986 0.1231      5.3696      5.4891|
|  2:  4.7268 -  3.7719 0.99   1314  145 0.0838 0.1121       5.421      5.6215|
|  3:  3.7719 -  3.3010 0.99   1287  144 0.1005 0.1511      5.4457      5.8493|
|  4:  3.3010 -  3.0019 0.99   1278  143 0.1140 0.1473      5.4131      5.5588|
|  5:  3.0019 -  2.7882 0.99   1270  140 0.1202 0.1677      5.2714      5.5097|
|  6:  2.7882 -  2.6248 0.99   1278  140 0.1112 0.1705      5.1575      5.3686|
|  7:  2.6248 -  2.4940 0.99   1250  140 0.1172 0.1616      5.1027       5.364|
|  8:  2.4940 -  2.3858 0.98   1264  140 0.1070 0.1705      5.0152      5.3333|
|  9:  2.3858 -  2.2943 0.98   1258  138 0.1068 0.1647      4.9739      5.2149|
| 10:  2.2943 -  2.2154 0.99   1233  138 0.1018 0.1787       4.917      5.2261|
| 11:  2.2154 -  2.1464 0.98   1250  142 0.1061 0.1618      4.8967      5.2052|
| 12:  2.1464 -  2.0852 0.97   1240  134 0.1034 0.1642      4.8319      5.1781|
| 13:  2.0852 -  2.0304 1.00   1235  141 0.0976 0.1548      4.7275      4.9986|
| 14:  2.0304 -  1.9810 0.86   1101  121 0.0948 0.1721       4.594      4.9183|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8990 -  4.7268  1372   153  0.94   8.81   0.98     0.96       6689.53|
|  2:  4.7268 -  3.7719  1314   145  0.95   7.76   1.02     1.01       8706.80|
|  3:  3.7719 -  3.3010  1287   144  0.94  10.61   1.03     1.02       9960.72|
|  4:  3.3010 -  3.0019  1278   143  0.92  13.00   1.01     0.99       9720.48|
|  5:  3.0019 -  2.7882  1270   140  0.91  14.75   0.99     0.96       7566.63|
|  6:  2.7882 -  2.6248  1278   140  0.91  14.87   0.99     0.96       6420.84|
|  7:  2.6248 -  2.4940  1250   140  0.91  14.90   0.98     0.96       5574.20|
|  8:  2.4940 -  2.3858  1264   140  0.92  13.58   0.99     0.98       4754.89|
|  9:  2.3858 -  2.2943  1258   138  0.92  14.29   1.01     0.98       4519.24|
| 10:  2.2943 -  2.2154  1233   138  0.91  14.63   1.00     0.96       4078.21|
| 11:  2.2154 -  2.1464  1250   142  0.90  15.57   1.00     0.97       4108.06|
| 12:  2.1464 -  2.0852  1240   134  0.92  14.16   1.00     0.99       3622.66|
| 13:  2.0852 -  2.0304  1235   141  0.92  14.23   1.01     1.01       3030.58|
| 14:  2.0304 -  1.9810  1101   121  0.92  13.42   0.98     0.95       2234.78|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2234.78 max =         9960.72 mean =      5853.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.13|
|phase err.(test): min =        0.00 max =           89.66 mean =        12.75|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1043   r_free= 0.1523   ksol= 0.32   Bsol= 41.76   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-2.09,-1.17,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.090834                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1043   r_free= 0.1523   ksol= 0.32   Bsol= 41.76   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-2.09,-1.17,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.090834                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8990 -  4.7268 0.99   1372  153 0.0986 0.1233      5.3711      5.4911|
|  2:  4.7268 -  3.7719 0.99   1314  145 0.0837 0.1120      5.4212       5.621|
|  3:  3.7719 -  3.3010 0.99   1287  144 0.1005 0.1511      5.4455      5.8494|
|  4:  3.3010 -  3.0019 0.99   1278  143 0.1140 0.1473      5.4131      5.5589|
|  5:  3.0019 -  2.7882 0.99   1270  140 0.1202 0.1677      5.2714      5.5096|
|  6:  2.7882 -  2.6248 0.99   1278  140 0.1112 0.1705      5.1575      5.3686|
|  7:  2.6248 -  2.4940 0.99   1250  140 0.1172 0.1616      5.1029      5.3642|
|  8:  2.4940 -  2.3858 0.98   1264  140 0.1070 0.1705      5.0153      5.3332|
|  9:  2.3858 -  2.2943 0.98   1258  138 0.1068 0.1646       4.974      5.2148|
| 10:  2.2943 -  2.2154 0.99   1233  138 0.1018 0.1787      4.9171      5.2262|
| 11:  2.2154 -  2.1464 0.98   1250  142 0.1061 0.1618      4.8967      5.2051|
| 12:  2.1464 -  2.0852 0.97   1240  134 0.1034 0.1642      4.8318       5.178|
| 13:  2.0852 -  2.0304 1.00   1235  141 0.0976 0.1548      4.7274      4.9985|
| 14:  2.0304 -  1.9810 0.86   1101  121 0.0948 0.1721       4.594      4.9184|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8990 -  4.7268  1372   153  0.94   8.84   0.98     0.96       6719.32|
|  2:  4.7268 -  3.7719  1314   145  0.95   7.77   1.02     1.01       8721.62|
|  3:  3.7719 -  3.3010  1287   144  0.94  10.61   1.03     1.02       9958.41|
|  4:  3.3010 -  3.0019  1278   143  0.92  13.00   1.01     1.00       9719.84|
|  5:  3.0019 -  2.7882  1270   140  0.91  14.75   1.00     0.97       7566.42|
|  6:  2.7882 -  2.6248  1278   140  0.91  14.87   0.99     0.96       6420.93|
|  7:  2.6248 -  2.4940  1250   140  0.91  14.91   0.99     0.96       5575.52|
|  8:  2.4940 -  2.3858  1264   140  0.92  13.58   1.00     0.98       4755.32|
|  9:  2.3858 -  2.2943  1258   138  0.92  14.29   1.01     0.98       4520.36|
| 10:  2.2943 -  2.2154  1233   138  0.91  14.63   1.01     0.97       4078.35|
| 11:  2.2154 -  2.1464  1250   142  0.90  15.57   1.00     0.97       4107.73|
| 12:  2.1464 -  2.0852  1240   134  0.92  14.15   1.01     0.99       3621.61|
| 13:  2.0852 -  2.0304  1235   141  0.92  14.23   1.02     1.01       3029.97|
| 14:  2.0304 -  1.9810  1101   121  0.92  13.42   0.99     0.96       2234.86|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2234.86 max =         9958.41 mean =      5856.85|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.13|
|phase err.(test): min =        0.00 max =           89.67 mean =        12.76|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.680)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.08    78.71   16.32    None  None   None       |
|    all(noH): 2823   0      1.08    78.71   16.32    None  None   None       |
|    Sol.    : 438    0      6.19    74.62   37.04    None  None   None       |
|    Mac.    : 2385   0      1.08    78.71   12.52    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.081 -   8.844:  785   |   5:    39.897 -  47.660:  111        |
|      1:     8.844 -  16.607: 1233   |   6:    47.660 -  55.423:   85        |
|      2:    16.607 -  24.370:  307   |   7:    55.423 -  63.186:   27        |
|      3:    24.370 -  32.133:  132   |   8:    63.186 -  70.950:    9        |
|      4:    32.133 -  39.897:  128   |   9:    70.950 -  78.713:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 281         
Filter by distance & map next to the model:
   mapped sites are within: 0.451 - 4.632
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 277 from: 281
   mapped sites are within: 0.702 - 4.632

peak=    5.739 closest distance to " O   HOH Z 126 " =    1.889
peak=    5.319 closest distance to " CB  ARG A 275 " =    0.910
peak=    5.289 closest distance to " O   HOH Z 144 " =    1.749
peak=    5.229 closest distance to " CB  GLN A 223 " =    1.445
peak=    5.209 closest distance to " CG  PRO A  54 " =    1.234
peak=    5.203 closest distance to " NE2 GLN A  11 " =    1.129
peak=    5.157 closest distance to " CB  SER A  63 " =    1.153
peak=    5.138 closest distance to " NH2 ARG A  56 " =    2.185
peak=    5.042 closest distance to " O   HOH Z 232 " =    2.407
peak=    4.799 closest distance to " CB  GLN A 183 " =    1.195
peak=    4.769 closest distance to " CG  PRO A 213 " =    1.236
peak=    4.674 closest distance to " CB  GLU A 152 " =    1.199
peak=    4.668 closest distance to " C   PRO A 198 " =    1.433
peak=    4.645 closest distance to " O   HOH Z  78 " =    1.672
peak=    4.622 closest distance to " CB  ARG A  79 " =    1.394
peak=    4.531 closest distance to " O   HOH Z 272 " =    1.859
peak=    4.502 closest distance to " O   HOH Z 209 " =    2.310
peak=    4.489 closest distance to " O   HOH Z 236 " =    1.872
peak=    4.482 closest distance to " O   HOH Z  15 " =    2.260
peak=    4.469 closest distance to " O   HOH Z 193 " =    1.817
peak=    4.395 closest distance to " O   HOH Z 427 " =    2.825
peak=    4.349 closest distance to " O   HOH Z 303 " =    2.027
peak=    4.344 closest distance to " CB  ASN A 148 " =    1.446
peak=    4.341 closest distance to " CA  TYR A  30 " =    0.937
peak=    4.330 closest distance to " O   HOH Z 234 " =    3.612
peak=    4.327 closest distance to " O   HOH Z 298 " =    1.857
peak=    4.312 closest distance to " O   HOH Z 203 " =    1.726
peak=    4.302 closest distance to " O   HOH Z  40 " =    1.632
peak=    4.277 closest distance to " CB  PRO A  54 " =    0.909
peak=    4.272 closest distance to " OD1 ASN A  69 " =    2.638
peak=    4.271 closest distance to " O   HOH Z 369 " =    2.064
peak=    4.215 closest distance to " O   HOH Z 144 " =    2.208
peak=    4.142 closest distance to " CB  SER A   3 " =    1.287
peak=    4.134 closest distance to " O   HOH Z 316 " =    3.066
peak=    4.133 closest distance to " ND2 ASN A 187 " =    1.482
peak=    4.109 closest distance to " O   HOH Z 403 " =    1.675
peak=    4.108 closest distance to " O   HOH Z 392 " =    3.055
peak=    4.104 closest distance to " O   HOH Z  61 " =    1.628
peak=    4.076 closest distance to " O   HOH Z  66 " =    2.218
peak=    4.075 closest distance to " O   HOH Z 250 " =    1.459
peak=    4.066 closest distance to " CB  VAL A 265 " =    1.245
peak=    4.066 closest distance to " O   HOH Z 158 " =    3.039
peak=    4.044 closest distance to " O   HOH Z  10 " =    1.851
peak=    4.043 closest distance to " O   HOH Z 346 " =    1.725
peak=    4.033 closest distance to " O   HOH Z 344 " =    3.175
peak=    4.032 closest distance to " CG2 VAL A 257 " =    0.860
peak=    4.021 closest distance to " CD2 TRP A 179 " =    1.366
peak=    4.003 closest distance to " O   HOH Z 189 " =    2.025
peak=    3.997 closest distance to " O   HOH Z  59 " =    1.894
peak=    3.993 closest distance to " O   HOH Z  44 " =    1.826
peak=    3.974 closest distance to " O   SER A  87 " =    2.297
peak=    3.971 closest distance to " O   HOH Z 368 " =    1.962
peak=    3.962 closest distance to " NZ  LYS A 117 " =    3.277
peak=    3.942 closest distance to " CG1 ILE A  33 " =    1.217
peak=    3.935 closest distance to " O   HOH Z  93 " =    2.496
peak=    3.935 closest distance to " O   HOH Z  43 " =    1.840
peak=    3.925 closest distance to " O   HOH Z  54 " =    1.682
peak=    3.914 closest distance to " CB  LEU A 228 " =    1.071
peak=    3.899 closest distance to " CG  ARG A  66 " =    2.418
peak=    3.893 closest distance to " CB  ARG A 190 " =    1.656
peak=    3.866 closest distance to " CE  LYS A  76 " =    0.810
peak=    3.864 closest distance to " CA  ASN A 215 " =    1.107
peak=    3.861 closest distance to " O   HOH Z 132 " =    2.492
peak=    3.839 closest distance to " O   HOH Z 402 " =    1.460
peak=    3.827 closest distance to " O   HOH Z 423 " =    1.888
peak=    3.824 closest distance to " O   HOH Z   1 " =    1.966
peak=    3.811 closest distance to " O   HOH Z 245 " =    1.302
peak=    3.810 closest distance to " CZ  PHE A 218 " =    1.019
peak=    3.805 closest distance to " CB  TRP A 266 " =    0.962
peak=    3.804 closest distance to " O   HOH Z 128 " =    2.033
peak=    3.800 closest distance to " CB  ARG A 139 " =    0.991
peak=    3.792 closest distance to " O   HOH Z 389 " =    1.837
peak=    3.782 closest distance to " CB  TYR A 169 " =    0.800
peak=    3.772 closest distance to " CB  GLU A 128 " =    0.991
peak=    3.770 closest distance to " O   HOH Z 327 " =    1.603
peak=    3.761 closest distance to " O   HOH Z 425 " =    2.035
peak=    3.760 closest distance to " CG1BVAL A  72 " =    1.498
peak=    3.759 closest distance to " OD2 ASP A 286 " =    2.800
peak=    3.716 closest distance to " CA  ALA A  21 " =    1.142
peak=    3.714 closest distance to " CD1 ILE A 106 " =    0.842
peak=    3.714 closest distance to " CB  GLU A 277 " =    3.471
peak=    3.712 closest distance to " O   HOH Z 248 " =    1.659
peak=    3.702 closest distance to " O   HOH Z 147 " =    1.778
peak=    3.693 closest distance to " CB  TRP A 179 " =    1.288
peak=    3.691 closest distance to " O   HOH Z  61 " =    1.509
peak=    3.685 closest distance to " O   HOH Z 128 " =    2.165
peak=    3.679 closest distance to " O   HOH Z  21 " =    1.724
peak=    3.663 closest distance to " O   HOH Z  97 " =    1.931
peak=    3.662 closest distance to " N   ARG A 156 " =    1.300
peak=    3.650 closest distance to " CD BLYS A 290 " =    1.251
peak=    3.646 closest distance to " CG  PRO A 243 " =    1.062
peak=    3.645 closest distance to " O   HOH Z 291 " =    1.586
peak=    3.641 closest distance to " O   HOH Z 417 " =    3.076
peak=    3.638 closest distance to " O   MET A 105 " =    1.818
peak=    3.634 closest distance to " O   HOH Z 305 " =    3.526
peak=    3.629 closest distance to " CG  PRO A  90 " =    1.041
peak=    3.624 closest distance to " O   HOH Z 214 " =    2.073
peak=    3.614 closest distance to " O   HOH Z 419 " =    1.990
peak=    3.611 closest distance to " OG BSER A 164 " =    2.260
peak=    3.609 closest distance to " O   HOH Z 219 " =    2.092
peak=    3.604 closest distance to " O   HOH Z 407 " =    2.536
peak=    3.601 closest distance to " O   HOH Z 371 " =    3.077
peak=    3.600 closest distance to " CG  GLN A  11 " =    1.822
peak=    3.580 closest distance to " O   HOH Z 173 " =    1.896
peak=    3.574 closest distance to " CB  ALA A 291 " =    1.349
peak=    3.574 closest distance to " CG  LYS A  76 " =    0.984
peak=    3.573 closest distance to " CB  SER A  26 " =    1.548
peak=    3.562 closest distance to " CB  ASP A 140 " =    0.917
peak=    3.553 closest distance to " ND2 ASN A 110 " =    1.809
peak=    3.551 closest distance to " CA  THR A 264 " =    0.895
peak=    3.547 closest distance to " CD  ARG A  66 " =    2.391
peak=    3.546 closest distance to " O   HOH Z  88 " =    2.941
peak=    3.542 closest distance to " CA  ALA A  84 " =    1.314
peak=    3.541 closest distance to " O   HOH Z   1 " =    1.637
peak=    3.533 closest distance to " O   HOH Z 368 " =    3.572
peak=    3.533 closest distance to " O   HOH Z  19 " =    2.460
peak=    3.526 closest distance to " O   HOH Z 337 " =    3.604
peak=    3.525 closest distance to " O   HOH Z 433 " =    1.777
peak=    3.523 closest distance to " CB  ILE A 120 " =    1.243
peak=    3.522 closest distance to " NH2BARG A 145 " =    2.009
peak=    3.522 closest distance to " CG2 ILE A 120 " =    1.102
peak=    3.520 closest distance to " NH1AARG A 145 " =    1.147
peak=    3.509 closest distance to " CG  PRO A 198 " =    1.283
peak=    3.508 closest distance to " CA  ASP A 162 " =    1.072
peak=    3.500 closest distance to " CB  ALA A  34 " =    1.129
peak=    3.494 closest distance to " CB  VAL A 202 " =    1.566
peak=    3.491 closest distance to " CB  ASN A  39 " =    0.874
peak=    3.486 closest distance to " O   HOH Z 148 " =    3.225
peak=    3.483 closest distance to " O   HOH Z 365 " =    2.893
peak=    3.477 closest distance to " CD  ARG A 159 " =    0.702
peak=    3.450 closest distance to " O   HOH Z 273 " =    2.572
peak=    3.439 closest distance to " O   HOH Z 426 " =    1.502
peak=    3.438 closest distance to " CB  SER A 212 " =    1.079
peak=    3.430 closest distance to " OE1 GLU A   2 " =    2.180
peak=    3.412 closest distance to " CG  GLN A  77 " =    2.053
peak=    3.404 closest distance to " O   HOH Z 193 " =    1.636
peak=    3.402 closest distance to " O   HOH Z  64 " =    2.291
peak=    3.398 closest distance to " O   HOH Z 280 " =    3.019
peak=    3.397 closest distance to " O   HOH Z 193 " =    1.925
peak=    3.397 closest distance to " O   HOH Z 371 " =    1.660
peak=    3.396 closest distance to " O   HOH Z 234 " =    1.754
peak=    3.393 closest distance to " CB  SER A 216 " =    0.735
peak=    3.391 closest distance to " O   HOH Z 213 " =    1.616
peak=    3.390 closest distance to " CA  ALA A 233 " =    1.191
peak=    3.390 closest distance to " O  BHOH Z 338 " =    2.312
peak=    3.389 closest distance to " CZ2 TRP A 179 " =    1.770
peak=    3.388 closest distance to " CD1 LEU A 300 " =    1.297
peak=    3.382 closest distance to " O   HOH Z 227 " =    2.126
peak=    3.378 closest distance to " O   HOH Z 128 " =    2.077
peak=    3.373 closest distance to " O   HOH Z 163 " =    1.658
peak=    3.369 closest distance to " CG2 THR A 221 " =    1.147
peak=    3.369 closest distance to " NH1BARG A 145 " =    1.281
peak=    3.366 closest distance to " CB  GLN A 278 " =    0.861
peak=    3.366 closest distance to " CB  GLN A  89 " =    1.339
peak=    3.365 closest distance to " CB  LYS A 290 " =    1.045
peak=    3.355 closest distance to " O   HOH Z 108 " =    2.456
peak=    3.354 closest distance to " O   HOH Z 345 " =    3.293
peak=    3.353 closest distance to " O   HOH Z 175 " =    2.101
peak=    3.353 closest distance to " CB  ASN A 224 " =    1.003
peak=    3.347 closest distance to " N   ASN A  39 " =    1.201
peak=    3.339 closest distance to " CG2 ILE A  20 " =    1.455
peak=    3.328 closest distance to " O   HOH Z 286 " =    2.280
peak=    3.327 closest distance to " NH2AARG A 190 " =    1.958
peak=    3.326 closest distance to " NE2 GLN A  73 " =    3.768
peak=    3.325 closest distance to " O   HOH Z 172 " =    3.341
peak=    3.325 closest distance to " CA  ALA A 291 " =    0.892
peak=    3.321 closest distance to " O   HOH Z 144 " =    1.873
peak=    3.321 closest distance to " CB  THR A 157 " =    1.111
peak=    3.317 closest distance to " CA  ASP A 140 " =    1.134
peak=    3.316 closest distance to " CG  GLN A  58 " =    2.670
peak=    3.312 closest distance to " ND1 HIS A  86 " =    1.709
peak=    3.312 closest distance to " CD2 LEU A 297 " =    0.865
peak=    3.305 closest distance to " O   TRP A 274 " =    1.894
peak=    3.304 closest distance to " O   HOH Z 258 " =    1.696
peak=    3.303 closest distance to " CA  ALA A  51 " =    0.872
peak=    3.303 closest distance to " CB  THR A  31 " =    1.691
peak=    3.301 closest distance to " OG  SER A  22 " =    2.645
peak=    3.298 closest distance to " CD  LYS A 166 " =    1.212
peak=    3.296 closest distance to " CB  ASN A 110 " =    1.116
peak=    3.292 closest distance to " OD1BASN A 224 " =    2.288
peak=    3.287 closest distance to " N   PHE A 130 " =    1.318
peak=    3.286 closest distance to " CB  SER A 141 " =    0.987
peak=    3.284 closest distance to " O   ALA A 165 " =    1.473
peak=    3.277 closest distance to " CG  MET A 185 " =    1.135
peak=    3.276 closest distance to " O   HOH Z 125 " =    2.330
peak=    3.275 closest distance to " O   HOH Z  49 " =    2.117
peak=    3.268 closest distance to " CE BLYS A 290 " =    1.212
peak=    3.268 closest distance to " O   HOH Z 406 " =    1.616
peak=    3.267 closest distance to " CB  ALA A 114 " =    1.206
peak=    3.266 closest distance to " CG2 THR A 294 " =    1.649
peak=    3.265 closest distance to " CA  ASN A 176 " =    1.173
peak=    3.259 closest distance to " CA  THR A 221 " =    0.965
peak=    3.259 closest distance to " OG1 THR A 294 " =    2.405
peak=    3.259 closest distance to " CB  SER A  62 " =    1.256
peak=    3.258 closest distance to " CD  LYS A 119 " =    1.317
peak=    3.257 closest distance to " O   HOH Z  85 " =    2.227
peak=    3.257 closest distance to " O   HOH Z 359 " =    1.435
peak=    3.254 closest distance to " CA  ARG A  36 " =    0.983
peak=    3.254 closest distance to " O   HOH Z 421 " =    1.695
peak=    3.253 closest distance to " O   HOH Z  71 " =    2.254
peak=    3.240 closest distance to " CB  LYS A 117 " =    1.177
peak=    3.238 closest distance to " CE1 TYR A 186 " =    1.357
peak=    3.238 closest distance to " CB  ALA A 248 " =    1.354
peak=    3.236 closest distance to " CD2 LEU A 255 " =    1.324
peak=    3.234 closest distance to " OE1 GLN A  11 " =    2.082
peak=    3.230 closest distance to " CB  VAL A 126 " =    1.020
peak=    3.229 closest distance to " O   ALA A   1 " =    1.690
peak=    3.227 closest distance to " CA  LYS A 117 " =    1.202
peak=    3.227 closest distance to " CG1 VAL A 153 " =    0.964
peak=    3.216 closest distance to " CB  ASN A 142 " =    1.027
peak=    3.213 closest distance to " O   HOH Z 180 " =    2.139
peak=    3.211 closest distance to " O   HOH Z 299 " =    4.334
peak=    3.209 closest distance to " CG  GLU A 277 " =    2.140
peak=    3.209 closest distance to " O   HOH Z 342 " =    0.819
peak=    3.206 closest distance to " O   HOH Z  50 " =    1.505
peak=    3.205 closest distance to " CG  LEU A 167 " =    1.212
peak=    3.192 closest distance to " CB  GLN A  88 " =    1.208
peak=    3.192 closest distance to " CA  ARG A 195 " =    1.267
peak=    3.190 closest distance to " O   HOH Z 411 " =    3.832
peak=    3.190 closest distance to " O   HOH Z 227 " =    1.530
peak=    3.189 closest distance to " CG  MET A 113 " =    1.135
peak=    3.173 closest distance to " ND1 HIS A  81 " =    1.588
peak=    3.172 closest distance to " O   HOH Z 435 " =    1.850
peak=    3.172 closest distance to " CB  TYR A 116 " =    0.785
peak=    3.171 closest distance to " CB  LEU A 255 " =    0.793
peak=    3.168 closest distance to " CG1 ILE A 120 " =    1.194
peak=    3.165 closest distance to " O   HOH Z 261 " =    2.139
peak=    3.159 closest distance to " O   HOH Z  66 " =    2.083
peak=    3.159 closest distance to " O   HOH Z 353 " =    2.617
peak=    3.158 closest distance to " OG  SER A 206 " =    1.345
peak=    3.156 closest distance to " O   HOH Z 265 " =    2.463
peak=    3.155 closest distance to " O   HOH Z 133 " =    2.603
peak=    3.155 closest distance to " CA  ASN A 217 " =    1.235
peak=    3.154 closest distance to " O   HOH Z 409 " =    2.859
peak=    3.153 closest distance to " O   HOH Z 329 " =    3.841
peak=    3.144 closest distance to " O   HOH Z 263 " =    1.669
peak=    3.141 closest distance to " O   HOH Z  44 " =    3.211
peak=    3.138 closest distance to " CA  LYS A 290 " =    1.405
peak=    3.138 closest distance to " CA  ILE A  33 " =    1.433
peak=    3.138 closest distance to " O   HOH Z 417 " =    2.034
peak=    3.136 closest distance to " CB  ALA A   9 " =    1.558
peak=    3.134 closest distance to " CB  ASN A 215 " =    1.114
peak=    3.132 closest distance to " CA  SER A 146 " =    1.674
peak=    3.131 closest distance to " O   HOH Z  88 " =    2.188
peak=    3.131 closest distance to " CD2 HIS A  81 " =    1.091
peak=    3.129 closest distance to " O   HOH Z  83 " =    1.701
peak=    3.127 closest distance to " N   SER A 135 " =    1.223
peak=    3.122 closest distance to " CB  HIS A 108 " =    0.789
peak=    3.122 closest distance to " CB  GLN A 205 " =    1.151
peak=    3.119 closest distance to " O   HOH Z 175 " =    2.173
peak=    3.117 closest distance to " CA  ALA A 158 " =    1.284
peak=    3.114 closest distance to " O   HOH Z 336 " =    1.857
peak=    3.113 closest distance to " O   HOH Z 271 " =    2.305
peak=    3.113 closest distance to " O   HOH Z 279 " =    2.099
peak=    3.112 closest distance to " CA  GLY A  80 " =    0.715
peak=    3.111 closest distance to " CE  MET A 188 " =    2.373
peak=    3.106 closest distance to " CA  MET A 105 " =    0.915
peak=    3.104 closest distance to " CB  ALA A   1 " =    4.632
peak=    3.100 closest distance to " O   HOH Z 357 " =    1.774
peak=    3.096 closest distance to " O   HOH Z 124 " =    1.349
peak=    3.094 closest distance to " NZ  LYS A  76 " =    1.304
peak=    3.086 closest distance to " O   HOH Z 423 " =    3.042
peak=    3.084 closest distance to " NH2AARG A 190 " =    1.086
peak=    3.078 closest distance to " O   THR A 220 " =    1.323
peak=    3.076 closest distance to " CA  SER A  87 " =    1.043
peak=    3.075 closest distance to " CD1AILE A 234 " =    0.939
peak=    3.075 closest distance to " O   HOH Z 371 " =    3.432
peak=    3.068 closest distance to " O   HOH Z 389 " =    1.732
peak=    3.067 closest distance to " CG  GLN A  89 " =    1.518
peak=    3.063 closest distance to " O   HOH Z 302 " =    1.903
peak=    3.057 closest distance to " O   HOH Z 374 " =    2.558
peak=    3.056 closest distance to " O   HOH Z 256 " =    1.528
peak=    3.055 closest distance to " OE2 GLU A  53 " =    2.125
peak=    3.049 closest distance to " O   SER A 164 " =    1.111
peak=    3.035 closest distance to " O   HOH Z 218 " =    2.453
peak=    3.028 closest distance to " O  BHOH Z  74 " =    1.387
peak=    3.023 closest distance to " OE1 GLN A  55 " =    1.320

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.693 - 5.628
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 203
   mapped sites are within: 0.786 - 5.628

peak=   -4.802 closest distance to " O   HOH Z 266 " =    4.711
peak=   -4.563 closest distance to " O   VAL A  67 " =    2.732
peak=   -4.559 closest distance to " CD  ARG A 156 " =    2.039
peak=   -4.502 closest distance to " CB  PRO A 243 " =    2.570
peak=   -4.361 closest distance to " C   HIS A 108 " =    1.118
peak=   -4.341 closest distance to " CG  GLN A 223 " =    1.946
peak=   -4.278 closest distance to " SG  CYS A 254 " =    3.444
peak=   -4.233 closest distance to " O   HOH Z 372 " =    2.347
peak=   -4.199 closest distance to " CG1 VAL A 112 " =    2.779
peak=   -4.157 closest distance to " O   HOH Z 290 " =    1.138
peak=   -4.131 closest distance to " CB  PRO A 280 " =    2.105
peak=   -4.118 closest distance to " OG BSER A 134 " =    1.232
peak=   -4.092 closest distance to " CA  VAL A  67 " =    2.686
peak=   -4.072 closest distance to " O   HOH Z 389 " =    1.827
peak=   -4.069 closest distance to " CB  ALA A 161 " =    2.554
peak=   -4.024 closest distance to " N   GLN A  58 " =    1.664
peak=   -4.014 closest distance to " CD  GLN A  58 " =    1.047
peak=   -4.004 closest distance to " CE2 TYR A  30 " =    2.749
peak=   -4.002 closest distance to " CZ3 TRP A 179 " =    1.196
peak=   -3.991 closest distance to " O   HOH Z 198 " =    1.994
peak=   -3.972 closest distance to " O   HOH Z 313 " =    1.927
peak=   -3.961 closest distance to " ND2 ASN A  45 " =    1.575
peak=   -3.949 closest distance to " O   HOH Z 126 " =    1.802
peak=   -3.934 closest distance to " O   HOH Z 231 " =    2.267
peak=   -3.910 closest distance to " O   PRO A 198 " =    1.285
peak=   -3.910 closest distance to " O   ARG A 145 " =    1.607
peak=   -3.908 closest distance to " CG  ASP A 231 " =    0.786
peak=   -3.895 closest distance to " CD  ARG A 139 " =    1.502
peak=   -3.852 closest distance to " O   HOH Z 114 " =    3.133
peak=   -3.840 closest distance to " O   HOH Z 435 " =    2.780
peak=   -3.818 closest distance to " OG  SER A  97 " =    2.158
peak=   -3.806 closest distance to " CZ  TYR A 169 " =    1.718
peak=   -3.787 closest distance to " O   HOH Z 353 " =    2.148
peak=   -3.771 closest distance to " O   HOH Z  10 " =    1.438
peak=   -3.765 closest distance to " CD1 PHE A  59 " =    1.833
peak=   -3.745 closest distance to " CE  MET A 105 " =    2.255
peak=   -3.740 closest distance to " OD1 ASN A 187 " =    1.578
peak=   -3.732 closest distance to " O   HOH Z 198 " =    1.355
peak=   -3.729 closest distance to " O   HOH Z 211 " =    1.666
peak=   -3.724 closest distance to " CD2 PHE A 192 " =    1.978
peak=   -3.720 closest distance to " OXT GLY A 302 " =    2.745
peak=   -3.713 closest distance to " O   HOH Z 185 " =    2.155
peak=   -3.712 closest distance to " O   HOH Z 407 " =    2.963
peak=   -3.694 closest distance to " CG  PHE A 283 " =    2.736
peak=   -3.693 closest distance to " CB  ASN A  39 " =    2.250
peak=   -3.691 closest distance to " O   HOH Z 351 " =    1.494
peak=   -3.675 closest distance to " CZ  PHE A  59 " =    1.489
peak=   -3.672 closest distance to " CD1 LEU A 228 " =    2.132
peak=   -3.650 closest distance to " CA  GLY A 203 " =    2.192
peak=   -3.643 closest distance to " CB  ALA A 291 " =    2.322
peak=   -3.640 closest distance to " ND2 ASN A  45 " =    1.045
peak=   -3.632 closest distance to " NH2AARG A 275 " =    5.199
peak=   -3.623 closest distance to " OD1 ASP A 171 " =    1.615
peak=   -3.611 closest distance to " N   SER A 212 " =    2.017
peak=   -3.608 closest distance to " O   HOH Z 196 " =    2.058
peak=   -3.596 closest distance to " CG1 VAL A 230 " =    1.964
peak=   -3.587 closest distance to " CB  PRO A 163 " =    2.457
peak=   -3.583 closest distance to " CG  ASP A 132 " =    2.260
peak=   -3.570 closest distance to " O   HOH Z  13 " =    1.537
peak=   -3.569 closest distance to " CB  ALA A 291 " =    2.230
peak=   -3.563 closest distance to " N   ALA A 248 " =    1.564
peak=   -3.563 closest distance to " CG2 ILE A 263 " =    2.269
peak=   -3.553 closest distance to " O   ALA A 161 " =    1.596
peak=   -3.551 closest distance to " O   PRO A 163 " =    2.018
peak=   -3.550 closest distance to " CE2 PHE A 218 " =    2.480
peak=   -3.545 closest distance to " CB  ALA A 248 " =    2.039
peak=   -3.543 closest distance to " CD2 LEU A 300 " =    2.925
peak=   -3.535 closest distance to " CB  ALA A 248 " =    2.338
peak=   -3.535 closest distance to " O   HOH Z  43 " =    1.772
peak=   -3.522 closest distance to " O   MET A  40 " =    2.751
peak=   -3.514 closest distance to " N   ALA A  43 " =    2.553
peak=   -3.507 closest distance to " OD2 ASP A 171 " =    2.308
peak=   -3.494 closest distance to " O   HOH Z 102 " =    1.575
peak=   -3.490 closest distance to " CG  GLU A 152 " =    0.800
peak=   -3.481 closest distance to " C   LEU A 143 " =    1.028
peak=   -3.480 closest distance to " CB  ASP A 132 " =    2.357
peak=   -3.477 closest distance to " O   HOH Z 385 " =    1.994
peak=   -3.476 closest distance to " C   ALA A 158 " =    1.284
peak=   -3.456 closest distance to " O   HOH Z 311 " =    3.521
peak=   -3.450 closest distance to " SG ACYS A 201 " =    1.968
peak=   -3.438 closest distance to " O   VAL A 189 " =    2.571
peak=   -3.428 closest distance to " N   THR A 235 " =    1.340
peak=   -3.425 closest distance to " O   SER A 135 " =    1.473
peak=   -3.423 closest distance to " O   HOH Z 244 " =    2.047
peak=   -3.413 closest distance to " NH1 ARG A 195 " =    2.532
peak=   -3.413 closest distance to " OD1 ASN A 148 " =    1.596
peak=   -3.408 closest distance to " O   HOH Z  52 " =    1.231
peak=   -3.403 closest distance to " CB  PHE A 208 " =    2.214
peak=   -3.398 closest distance to " O   HOH Z 165 " =    2.007
peak=   -3.395 closest distance to " CD2 LEU A 237 " =    2.715
peak=   -3.395 closest distance to " CB  ASP A 286 " =    2.171
peak=   -3.394 closest distance to " C   MET A 188 " =    1.421
peak=   -3.379 closest distance to " CG1 VAL A  78 " =    3.163
peak=   -3.378 closest distance to " O   HOH Z  63 " =    1.673
peak=   -3.375 closest distance to " O   HOH Z  11 " =    1.752
peak=   -3.366 closest distance to " O   VAL A 174 " =    2.049
peak=   -3.365 closest distance to " OD1 ASP A 191 " =    1.473
peak=   -3.361 closest distance to " CG2 THR A 178 " =    2.251
peak=   -3.361 closest distance to " ND2 ASN A 249 " =    2.060
peak=   -3.360 closest distance to " C   PRO A  90 " =    1.451
peak=   -3.358 closest distance to " N   ASP A 286 " =    2.342
peak=   -3.357 closest distance to " O   HOH Z 253 " =    3.738
peak=   -3.356 closest distance to " O   SER A  95 " =    1.503
peak=   -3.354 closest distance to " OG BSER A 134 " =    1.672
peak=   -3.354 closest distance to " O   HOH Z 298 " =    1.311
peak=   -3.349 closest distance to " O   HOH Z  37 " =    1.811
peak=   -3.339 closest distance to " CG  ARG A 269 " =    2.341
peak=   -3.338 closest distance to " CD2 LEU A 300 " =    2.920
peak=   -3.337 closest distance to " CA  GLY A  98 " =    1.891
peak=   -3.336 closest distance to " CD1 LEU A 101 " =    2.319
peak=   -3.333 closest distance to " O   HOH Z 385 " =    1.900
peak=   -3.330 closest distance to " NZ  LYS A 119 " =    3.391
peak=   -3.330 closest distance to " CA  GLY A 133 " =    1.974
peak=   -3.323 closest distance to " CG  GLU A   2 " =    1.904
peak=   -3.321 closest distance to " O   TRP A  70 " =    1.528
peak=   -3.317 closest distance to " NH2BARG A 275 " =    1.941
peak=   -3.310 closest distance to " OD2 ASP A  50 " =    1.421
peak=   -3.306 closest distance to " NH2 ARG A  79 " =    1.945
peak=   -3.301 closest distance to " N   PHE A  59 " =    2.115
peak=   -3.300 closest distance to " O   HOH Z 200 " =    4.776
peak=   -3.298 closest distance to " CZ3 TRP A 274 " =    1.110
peak=   -3.297 closest distance to " O   HOH Z 166 " =    1.436
peak=   -3.292 closest distance to " O   ALA A  51 " =    1.387
peak=   -3.289 closest distance to " OG  SER A  62 " =    1.493
peak=   -3.289 closest distance to " OH  TYR A 214 " =    1.245
peak=   -3.288 closest distance to " NH2 ARG A  79 " =    1.636
peak=   -3.284 closest distance to " CB  TYR A  15 " =    2.160
peak=   -3.282 closest distance to " N   GLY A  23 " =    2.346
peak=   -3.282 closest distance to " CD1 LEU A 297 " =    2.299
peak=   -3.273 closest distance to " ND2 ASN A 187 " =    1.487
peak=   -3.268 closest distance to " O   HOH Z 243 " =    2.047
peak=   -3.266 closest distance to " O   GLY A 196 " =    1.015
peak=   -3.265 closest distance to " O   HOH Z 322 " =    1.615
peak=   -3.261 closest distance to " O   PRO A 198 " =    1.249
peak=   -3.258 closest distance to " OD2 ASP A 191 " =    1.454
peak=   -3.256 closest distance to " O   HOH Z 421 " =    3.035
peak=   -3.254 closest distance to " CG  GLU A 277 " =    1.205
peak=   -3.252 closest distance to " O   HOH Z 250 " =    1.457
peak=   -3.251 closest distance to " OXT GLY A 302 " =    3.386
peak=   -3.249 closest distance to " O   HOH Z  11 " =    2.074
peak=   -3.246 closest distance to " CD2 TYR A 247 " =    2.571
peak=   -3.243 closest distance to " CG  MET A 105 " =    0.944
peak=   -3.241 closest distance to " CB  ALA A  43 " =    2.411
peak=   -3.240 closest distance to " O   HOH Z 139 " =    5.229
peak=   -3.237 closest distance to " O   HOH Z 427 " =    1.457
peak=   -3.228 closest distance to " OD1 ASN A 176 " =    1.279
peak=   -3.222 closest distance to " O   HOH Z 348 " =    1.814
peak=   -3.221 closest distance to " CG  ARG A  66 " =    2.410
peak=   -3.220 closest distance to " CA  TYR A  68 " =    2.913
peak=   -3.218 closest distance to " O   ASN A 249 " =    1.409
peak=   -3.216 closest distance to " NE2 GLN A 278 " =    1.743
peak=   -3.213 closest distance to " CA  GLY A 241 " =    3.021
peak=   -3.209 closest distance to " O   HOH Z  60 " =    2.416
peak=   -3.209 closest distance to " OG1 THR A 178 " =    1.279
peak=   -3.206 closest distance to " N   PHE A  59 " =    1.905
peak=   -3.204 closest distance to " O   PRO A  90 " =    1.826
peak=   -3.198 closest distance to " O   PHE A 218 " =    1.619
peak=   -3.195 closest distance to " O   HOH Z 210 " =    1.145
peak=   -3.193 closest distance to " OD1 ASP A 191 " =    1.797
peak=   -3.184 closest distance to " O   HOH Z 111 " =    2.395
peak=   -3.180 closest distance to " N   ALA A 226 " =    1.990
peak=   -3.179 closest distance to " O   SER A 146 " =    1.141
peak=   -3.175 closest distance to " OG  SER A 206 " =    1.683
peak=   -3.169 closest distance to " O   HOH Z 369 " =    2.128
peak=   -3.167 closest distance to " O   GLN A 240 " =    1.963
peak=   -3.163 closest distance to " O   HOH Z  91 " =    1.602
peak=   -3.163 closest distance to " O   LYS A 117 " =    1.640
peak=   -3.158 closest distance to " O   HOH Z 234 " =    3.934
peak=   -3.153 closest distance to " CE  LYS A  76 " =    2.973
peak=   -3.152 closest distance to " CG1 VAL A 268 " =    2.437
peak=   -3.149 closest distance to " CG  TRP A 266 " =    1.882
peak=   -3.147 closest distance to " CG2 VAL A 189 " =    2.008
peak=   -3.144 closest distance to " O   HOH Z 351 " =    1.333
peak=   -3.143 closest distance to " NE2 GLN A  88 " =    1.858
peak=   -3.143 closest distance to " O   GLY A  80 " =    2.510
peak=   -3.135 closest distance to " CE3 TRP A 150 " =    2.107
peak=   -3.130 closest distance to " O   HOH Z 134 " =    2.924
peak=   -3.129 closest distance to " CE  LYS A  76 " =    2.709
peak=   -3.128 closest distance to " O   HOH Z 263 " =    2.922
peak=   -3.127 closest distance to " CA  TYR A  30 " =    2.883
peak=   -3.125 closest distance to " O   ALA A   1 " =    1.790
peak=   -3.125 closest distance to " O   HOH Z   6 " =    1.458
peak=   -3.121 closest distance to " CZ  ARG A 259 " =    0.852
peak=   -3.116 closest distance to " CB  TRP A  85 " =    2.524
peak=   -3.115 closest distance to " O   HOH Z  51 " =    1.620
peak=   -3.115 closest distance to " O   ALA A  10 " =    1.681
peak=   -3.109 closest distance to " SD  MET A 188 " =    2.172
peak=   -3.105 closest distance to " CD  GLN A  88 " =    0.817
peak=   -3.086 closest distance to " OE2 GLU A 152 " =    1.148
peak=   -3.086 closest distance to " CD  GLN A  58 " =    1.037
peak=   -3.083 closest distance to " CG1 VAL A 197 " =    2.140
peak=   -3.081 closest distance to " O   HOH Z  73 " =    2.426
peak=   -3.073 closest distance to " O   HOH Z 283 " =    5.628
peak=   -3.064 closest distance to " O   LYS A 289 " =    2.956
peak=   -3.053 closest distance to " O   HOH Z 265 " =    1.971
peak=   -3.053 closest distance to " O   HOH Z 137 " =    1.495
peak=   -3.050 closest distance to " OD1AASN A 224 " =    1.796
peak=   -3.044 closest distance to " O   HOH Z  41 " =    2.501
peak=   -3.038 closest distance to " O   HOH Z 174 " =    4.312
peak=   -3.023 closest distance to " C   PHE A 218 " =    1.667
peak=   -3.017 closest distance to " OD2 ASP A  50 " =    2.303

================= 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    :  0.2701 0.2735   5.869021e+00   5.869176e+00
   1_bss:  0.2528 0.2526   5.838700e+00   5.819046e+00
   1_xyz:  0.1472 0.1670   5.328088e+00   5.433334e+00
   1_adp:  0.1368 0.1703   5.280469e+00   5.459605e+00
   1_occ:  0.1363 0.1704   5.277964e+00   5.458151e+00
   2_bss:  0.1362 0.1694   5.276932e+00   5.454550e+00
   2_xyz:  0.1163 0.1525   5.140049e+00   5.350844e+00
   2_adp:  0.1122 0.1506   5.115158e+00   5.336340e+00
   2_occ:  0.1121 0.1506   5.114762e+00   5.336345e+00
   3_bss:  0.1120 0.1505   5.114427e+00   5.336102e+00
   3_xyz:  0.1109 0.1502   5.112483e+00   5.338772e+00
   3_adp:  0.1096 0.1514   5.111293e+00   5.346198e+00
   3_occ:  0.1095 0.1515   5.111452e+00   5.346683e+00
   4_bss:  0.1095 0.1514   5.111056e+00   5.346236e+00
   4_xyz:  0.1049 0.1509   5.086768e+00   5.342060e+00
   4_adp:  0.1060 0.1501   5.088634e+00   5.336338e+00
   4_occ:  0.1060 0.1502   5.088882e+00   5.336879e+00
   5_bss:  0.1062 0.1495   5.089805e+00   5.336473e+00
   5_xyz:  0.1051 0.1513   5.089818e+00   5.346443e+00
   5_adp:  0.1044 0.1523   5.090643e+00   5.352885e+00
   5_occ:  0.1044 0.1523   5.090691e+00   5.352983e+00
   5_bss:  0.1043 0.1523   5.090834e+00   5.353113e+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:  0.322  33.024  -2.918  -1.986  -0.317  -0.000  -0.000  -0.000
   1_xyz:  0.322  33.024  -2.918  -1.986  -0.317  -0.000  -0.000  -0.000
   1_adp:  0.322  33.024  -2.918  -1.986  -0.317  -0.000  -0.000  -0.000
   1_occ:  0.322  33.024  -2.918  -1.986  -0.317  -0.000  -0.000  -0.000
   2_bss:  0.322  38.710  -3.124  -2.649  -1.532  -0.000  -0.000  -0.000
   2_xyz:  0.322  38.710  -3.124  -2.649  -1.532  -0.000  -0.000  -0.000
   2_adp:  0.322  38.710  -3.124  -2.649  -1.532  -0.000  -0.000  -0.000
   2_occ:  0.322  38.710  -3.124  -2.649  -1.532  -0.000  -0.000  -0.000
   3_bss:  0.320  39.118  -2.836  -2.461  -1.496  -0.000  -0.000  -0.000
   3_xyz:  0.320  39.118  -2.836  -2.461  -1.496  -0.000  -0.000  -0.000
   3_adp:  0.320  39.118  -2.836  -2.461  -1.496  -0.000  -0.000  -0.000
   3_occ:  0.320  39.118  -2.836  -2.461  -1.496  -0.000  -0.000  -0.000
   4_bss:  0.321  41.799  -2.650  -2.332  -1.421  -0.000  -0.000  -0.000
   4_xyz:  0.321  41.799  -2.650  -2.332  -1.421  -0.000  -0.000  -0.000
   4_adp:  0.321  41.799  -2.650  -2.332  -1.421  -0.000  -0.000  -0.000
   4_occ:  0.321  41.799  -2.650  -2.332  -1.421  -0.000  -0.000  -0.000
   5_bss:  0.321  41.799  -2.573  -2.270  -1.345  -0.000  -0.000  -0.000
   5_xyz:  0.321  41.799  -2.573  -2.270  -1.345  -0.000  -0.000  -0.000
   5_adp:  0.321  41.799  -2.573  -2.270  -1.345  -0.000  -0.000  -0.000
   5_occ:  0.321  41.799  -2.573  -2.270  -1.345  -0.000  -0.000  -0.000
   5_bss:  0.322  41.760  -2.376  -2.091  -1.167  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  25.963 0.8056  0.9874    20095.257
   1_bss:  24.300 0.8208  0.9437    16391.321
   1_xyz:  14.624 0.9110  1.0001     6999.958
   1_adp:  15.219 0.9058  0.9987     7310.268
   1_occ:  15.181 0.9060  0.9986     7265.396
   2_bss:  15.091 0.9068  0.9749     7192.330
   2_xyz:  13.145 0.9217  0.9812     5819.484
   2_adp:  12.916 0.9234  0.9789     5666.452
   2_occ:  12.914 0.9234  0.9789     5661.638
   3_bss:  12.910 0.9234  0.9851     5660.299
   3_xyz:  12.883 0.9239  0.9848     5689.957
   3_adp:  13.021 0.9229  0.9794     5757.442
   3_occ:  13.028 0.9229  0.9792     5761.970
   4_bss:  13.019 0.9230  0.9842     5757.807
   4_xyz:  12.940 0.9234  0.9844     5710.019
   4_adp:  12.821 0.9243  0.9807     5664.362
   4_occ:  12.833 0.9242  0.9805     5668.400
   5_bss:  12.823 0.9243  0.9830     5655.078
   5_xyz:  12.961 0.9233  0.9828     5795.290
   5_adp:  13.087 0.9224  0.9771     5851.450
   5_occ:  13.090 0.9224  0.9770     5853.594
   5_bss:  13.094 0.9224  0.9823     5856.874
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6109e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6109e-01
   1_xyz:   0.938  0.006  0.066 14.699  0.004  4.105   5.3820e-02
   1_adp:   0.938  0.006  0.066 14.699  0.004  4.105   5.3820e-02
   1_occ:   0.938  0.006  0.066 14.699  0.004  4.105   5.3820e-02
   2_bss:   0.938  0.006  0.066 14.699  0.004  4.105   5.3820e-02
   2_xyz:   0.932  0.005  0.071 14.584  0.004  4.115   5.2270e-02
   2_adp:   0.932  0.005  0.071 14.584  0.004  4.115   5.2270e-02
   2_occ:   0.932  0.005  0.071 14.584  0.004  4.115   5.2270e-02
   3_bss:   0.932  0.005  0.071 14.584  0.004  4.115   5.2270e-02
   3_xyz:   0.854  0.005  0.066 14.404  0.003  4.115   4.6540e-02
   3_adp:   0.854  0.005  0.066 14.404  0.003  4.115   4.6540e-02
   3_occ:   0.854  0.005  0.066 14.404  0.003  4.115   4.6540e-02
   4_bss:   0.854  0.005  0.066 14.404  0.003  4.115   4.6540e-02
   4_xyz:   1.013  0.007  0.077 14.796  0.004  4.116   6.0988e-02
   4_adp:   1.013  0.007  0.077 14.796  0.004  4.116   6.0988e-02
   4_occ:   1.013  0.007  0.077 14.796  0.004  4.116   6.0988e-02
   5_bss:   1.013  0.007  0.077 14.796  0.004  4.116   6.0988e-02
   5_xyz:   1.008  0.007  0.077 14.765  0.004  4.116   6.1667e-02
   5_adp:   1.008  0.007  0.077 14.765  0.004  4.116   6.1667e-02
   5_occ:   1.008  0.007  0.077 14.765  0.004  4.116   6.1667e-02
   5_bss:   1.008  0.007  0.077 14.765  0.004  4.116   6.1667e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3919e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3919e-01
   1_xyz:   7.181  0.039  0.295 86.003  0.041  2.301   6.6371e-02
   1_adp:   7.181  0.039  0.295 86.003  0.041  2.301   6.6371e-02
   1_occ:   7.181  0.039  0.295 86.003  0.041  2.301   6.6371e-02
   2_bss:   7.181  0.039  0.295 86.003  0.041  2.301   6.6371e-02
   2_xyz:   6.700  0.034  0.232 83.318  0.040  2.347   3.5786e-02
   2_adp:   6.700  0.034  0.232 83.318  0.040  2.347   3.5786e-02
   2_occ:   6.700  0.034  0.232 83.318  0.040  2.347   3.5786e-02
   3_bss:   6.700  0.034  0.232 83.318  0.040  2.347   3.5786e-02
   3_xyz:   6.323  0.035  0.215 83.317  0.036  2.390   2.7673e-02
   3_adp:   6.323  0.035  0.215 83.317  0.036  2.390   2.7673e-02
   3_occ:   6.323  0.035  0.215 83.317  0.036  2.390   2.7673e-02
   4_bss:   6.323  0.035  0.215 83.317  0.036  2.390   2.7673e-02
   4_xyz:   6.530  0.040  0.250 82.847  0.039  2.283   4.6712e-02
   4_adp:   6.530  0.040  0.250 82.847  0.039  2.283   4.6712e-02
   4_occ:   6.530  0.040  0.250 82.847  0.039  2.283   4.6712e-02
   5_bss:   6.530  0.040  0.250 82.847  0.039  2.283   4.6712e-02
   5_xyz:   6.500  0.043  0.251 83.286  0.039  2.271   4.8636e-02
   5_adp:   6.500  0.043  0.251 83.286  0.039  2.271   4.8636e-02
   5_occ:   6.500  0.043  0.251 83.286  0.039  2.271   4.8636e-02
   5_bss:   6.500  0.043  0.251 83.286  0.039  2.271   4.8636e-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:  67.57   0.00  16.50  67.57   0.00  12.69  62.45   7.83  37.23
   1_occ:  67.57   0.00  16.50  67.57   0.00  12.69  62.45   7.83  37.23
   2_bss:  67.57   0.00  16.50  67.57   0.00  12.69  62.45   7.83  37.23
   2_xyz:  67.57   0.00  16.50  67.57   0.00  12.69  62.45   7.83  37.23
   2_adp:  70.13   1.62  16.73  67.00   1.62  12.90  70.13   5.96  37.57
   2_occ:  70.13   1.62  16.73  67.00   1.62  12.90  70.13   5.96  37.57
   3_bss:  70.13   1.62  16.73  67.00   1.62  12.90  70.13   5.96  37.57
   3_xyz:  70.13   1.62  16.73  67.00   1.62  12.90  70.13   5.96  37.57
   3_adp:  79.87   0.87  16.96  79.87   0.87  12.93  74.88   6.16  38.87
   3_occ:  79.87   0.87  16.96  79.87   0.87  12.93  74.88   6.16  38.87
   4_bss:  79.87   0.87  16.96  79.87   0.87  12.93  74.88   6.16  38.87
   4_xyz:  79.87   0.87  16.96  79.87   0.87  12.93  74.88   6.16  38.87
   4_adp:  77.57   1.78  16.36  77.57   1.78  12.66  74.59   6.09  36.49
   4_occ:  77.57   1.78  16.36  77.57   1.78  12.66  74.59   6.09  36.49
   5_bss:  77.57   1.78  16.36  77.57   1.78  12.66  74.59   6.09  36.49
   5_xyz:  77.57   1.78  16.36  77.57   1.78  12.66  74.59   6.09  36.49
   5_adp:  78.75   1.12  16.36  78.75   1.12  12.55  74.66   6.23  37.08
   5_occ:  78.75   1.12  16.36  78.75   1.12  12.55  74.66   6.23  37.08
   5_bss:  78.71   1.08  16.32  78.71   1.08  12.52  74.62   6.19  37.04
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    0.986    0.011    0.234
   1_adp:    0.986    0.011    0.234
   1_occ:    0.986    0.011    0.234
   2_bss:    0.986    0.011    0.234
   2_xyz:    0.825    0.019    0.265
   2_adp:    0.825    0.019    0.265
   2_occ:    0.825    0.019    0.265
   3_bss:    0.825    0.019    0.265
   3_xyz:    0.945    0.025    0.279
   3_adp:    0.945    0.025    0.279
   3_occ:    0.945    0.025    0.279
   4_bss:    0.945    0.025    0.279
   4_xyz:    0.871    0.035    0.288
   4_adp:    0.871    0.035    0.288
   4_occ:    0.871    0.035    0.288
   5_bss:    0.871    0.035    0.288
   5_xyz:    1.044    0.045    0.296
   5_adp:    1.044    0.045    0.296
   5_occ:    1.044    0.045    0.296
   5_bss:    1.044    0.045    0.296
------------------------------------------------------------------------

CPU time actual refinement: 316.28


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_531/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_531/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_531/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_531/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_531/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 316.13 
  Macro-tasks:
    bulk solvent and scale       = 35.81  
    individual site refinement   = 129.62 
    weights calculation          = 29.27  
    collect and process          = 6.63   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 201.45 
  Micro-tasks:
    mask                            = 1.19   
    f_calc                          = 100.40 
    alpha_beta                      = 8.28   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 109.31 
    fmodel                         = 6.45   
    r_factors                      = 0.20   
    phase_errors                   = 11.29  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 238.57 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.496 micro seconds
Total CPU time: 5.50 minutes
from_scatterers_fft:    642 calls, 100.08 s
gradients_fft:          587 calls,  95.91 s

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

# Date 2008-01-16 Time 05:02:31 PST -0800 (1200488551.30 s)
Start R-work = 0.2701, R-free = 0.2735 (no bulk solvent and anisotropic scale)
Final R-work = 0.1301, R-free = 0.1733 (no bulk solvent and anisotropic scale)

Start R-work = 0.2528, R-free = 0.2526
Final R-work = 0.1043, R-free = 0.1523