# Date 2008-01-16 Time 04:11:47 PST -0800 (1200485507.73 s)
#phil __OFF__

Command line arguments: "../213.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 11011
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 213

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.845, 47.6339, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.32, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 47.6339, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8941 1.96072
Completeness in resolution range: 0.939881
Completeness with d_max=infinity: 0.937004

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8941
                             d_min =   1.9607

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 47.6339, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8941 1.96072
Completeness in resolution range: 0.939881
Completeness with d_max=infinity: 0.937004

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8945 -  4.1957 [2197/2225]  1973   224  10.2%
  bin  2:  4.1957 -  3.3426 [2093/2116]  1888   205   9.8%
  bin  3:  3.3426 -  2.9237 [2075/2100]  1863   212  10.2%
  bin  4:  2.9237 -  2.6581 [2051/2067]  1850   201   9.8%
  bin  5:  2.6581 -  2.4685 [2030/2074]  1821   209  10.3%
  bin  6:  2.4685 -  2.3235 [2044/2072]  1850   194   9.5%
  bin  7:  2.3235 -  2.2075 [2006/2042]  1804   202  10.1%
  bin  8:  2.2075 -  2.1117 [2021/2063]  1820   201   9.9%
  bin  9:  2.1117 -  2.0306 [2004/2050]  1800   204  10.2%
  bin 10:  2.0306 -  1.9607 [1068/2033]   961   107  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_213/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:
        1.24 -     1.97: 11
        1.97 -     2.70: 159
        2.70 -     3.43: 4566
        3.43 -     4.17: 9414
        4.17 -     4.90: 14348
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.236 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.488 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.626 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.746 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.775 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28493 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_213/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_213/model_refine_001.geo

CPU time processing inputs: 9.31


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 47.63395 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4068   r_free= 0.4019   ksol= 0.00   Bsol= 0.00   scale= 0.935    |
|                                                                             |
| 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:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.205361                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8945 -  4.6798 0.99   1421  158 0.3297 0.3495      6.4658      6.5281|
|  2:  4.6798 -  3.7338 0.99   1365  154 0.3322 0.3267      6.6575      6.6406|
|  3:  3.7338 -  3.2675 0.99   1351  146 0.3600 0.3387       6.537      6.5672|
|  4:  3.2675 -  2.9713 0.99   1323  143 0.3854 0.3621      6.3965      6.3388|
|  5:  2.9713 -  2.7598 0.98   1331  151 0.4192 0.3955       6.271      6.2578|
|  6:  2.7598 -  2.5980 0.99   1312  147 0.4293 0.4306      6.2032      6.0722|
|  7:  2.5980 -  2.4685 0.98   1292  152 0.4471 0.3997      6.1752       6.086|
|  8:  2.4685 -  2.3615 0.99   1329  136 0.4466 0.4691       6.121      6.1269|
|  9:  2.3615 -  2.2709 0.99   1302  150 0.4768 0.4680      6.0834      6.1541|
| 10:  2.2709 -  2.1928 0.98   1303  141 0.4507 0.4658       6.052      6.0718|
| 11:  2.1928 -  2.1244 0.97   1284  146 0.4798 0.5070      5.9956       6.004|
| 12:  2.1244 -  2.0638 0.99   1296  149 0.4690 0.4571      5.9175      5.9441|
| 13:  2.0638 -  2.0096 0.93   1231  132 0.4803 0.4927      5.8499      5.8201|
| 14:  2.0096 -  1.9607 0.38    490   54 0.4722 0.4871      5.8323      5.6833|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8945 -  4.6798  1421   158  0.72  32.44   0.85     0.73      62329.33|
|  2:  4.6798 -  3.7338  1365   154  0.77  28.93   0.95     0.86      75553.19|
|  3:  3.7338 -  3.2675  1351   146  0.72  34.08   0.96     0.89      74417.98|
|  4:  3.2675 -  2.9713  1323   143  0.67  37.93   0.95     0.87      62475.02|
|  5:  2.9713 -  2.7598  1331   151  0.62  42.39   0.94     0.83      50964.58|
|  6:  2.7598 -  2.5980  1312   147  0.60  44.20   0.95     0.80      45219.62|
|  7:  2.5980 -  2.4685  1292   152  0.59  45.26   0.95     0.78      42678.11|
|  8:  2.4685 -  2.3615  1329   136  0.54  48.92   0.96     0.75      42237.21|
|  9:  2.3615 -  2.2709  1302   150  0.51  51.30   0.94     0.73      40957.67|
| 10:  2.2709 -  2.1928  1303   141  0.49  53.20   0.99     0.69      40039.03|
| 11:  2.1928 -  2.1244  1284   146  0.46  55.18   0.96     0.70      38374.42|
| 12:  2.1244 -  2.0638  1296   149  0.43  57.39   0.98     0.68      36620.18|
| 13:  2.0638 -  2.0096  1231   132  0.42  58.94   0.98     0.64      31788.91|
| 14:  2.0096 -  1.9607   490    54  0.42  58.28   0.98     0.55      25818.57|
|alpha:            min =        0.55 max =            0.89 mean =         0.76|
|beta:             min =    25818.57 max =        75553.19 mean =     49196.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.58|
|phase err.(work): min =        0.00 max =           89.99 mean =        45.50|
|phase err.(test): min =        0.00 max =           89.87 mean =        45.83|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.820902              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.940   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.230715              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.451   (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 |  1.236 -  1.602:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.602 -  1.969:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.969 -  2.335:       19 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.335 -  2.701:      140 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.701 -  3.068:     2251 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.068 -  3.434:     2315 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.434 -  3.801:     4143 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.801 -  4.167:     5271 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.167 -  4.534:     6397 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.534 -  4.900:     7951 |
|-----------------------------------------------------------------------------|
|-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 |        0.190 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.236 |       0.592 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.699)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4068   r_free= 0.4019   ksol= 0.00   Bsol= 0.00   scale= 0.935    |
|                                                                             |
| 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:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.205361                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3974   r_free= 0.3902   ksol= 0.30   Bsol= 24.43   scale= 0.964   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.29,2.55,-1.46,0.00,-0.00,-0.00); trace/3= 0.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.191802                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.163998              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.741   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.658213              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.119   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3974      final r-factor (work) = 0.2540          |
| start r-factor (free) = 0.3902      final r-factor (free) = 0.2766          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.2872 = 6.16 * 0.50 * 6.1965 + 1.00 * 0.1897                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.5286 = 6.16 * 0.50 * 5.9817 + 1.00 * 0.0930                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2540      final r-factor (work) = 0.2303          |
| start r-factor (free) = 0.2766      final r-factor (free) = 0.2840          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9434 = 0.66 * 1.00 * 5.9817 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8056 = 0.66 * 1.00 * 5.7578 + 1.00 * 0.0157                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.699)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.55   17.46    None  None   None       |
|    all(noH): 2823   0      0.00    69.55   17.46    None  None   None       |
|    Sol.    : 438    0      4.99    69.55   38.41    None  None   None       |
|    Mac.    : 2385   0      0.00    65.14   13.61    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.955:  538   |   5:    34.777 -  41.732:  134        |
|      1:     6.955 -  13.911:  992   |   6:    41.732 -  48.687:   95        |
|      2:    13.911 -  20.866:  525   |   7:    48.687 -  55.642:   83        |
|      3:    20.866 -  27.821:  253   |   8:    55.642 -  62.598:   41        |
|      4:    27.821 -  34.777:  153   |   9:    62.598 -  69.553:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2303 r_free = 0.2840             target_work(ml) = 5.768         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2299 r_free = 0.2842             target_work(ml) = 5.768         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2299   r_free= 0.2842   ksol= 0.30   Bsol= 24.43   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.29,2.55,-1.46,0.00,-0.00,-0.00); trace/3= 0.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.768158                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2266   r_free= 0.2807   ksol= 0.32   Bsol= 50.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,0.02,-1.47,0.00,-0.00,-0.00); trace/3= -1.24                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.758969                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.765510              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.727   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.248997              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 100.272  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2266      final r-factor (work) = 0.1616          |
| start r-factor (free) = 0.2807      final r-factor (free) = 0.2043          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.9381 = 3.77 * 0.50 * 5.7602 + 1.00 * 0.0930                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6580 = 3.77 * 0.50 * 5.6279 + 1.00 * 0.0620                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1616      final r-factor (work) = 0.1477          |
| start r-factor (free) = 0.2043      final r-factor (free) = 0.1880          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4196 = 0.25 * 1.00 * 5.6279 + 1.00 * 0.0183                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3544 = 0.25 * 1.00 * 5.4065 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.699)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.12    77.76   17.03    None  None   None       |
|    all(noH): 2823   0      1.12    77.76   17.03    None  None   None       |
|    Sol.    : 438    0      5.07    70.16   38.76    None  None   None       |
|    Mac.    : 2385   0      1.12    77.76   13.04    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:     1.124 -   8.788:  753   |   5:    39.443 -  47.107:  111        |
|      1:     8.788 -  16.452: 1211   |   6:    47.107 -  54.771:   90        |
|      2:    16.452 -  24.115:  335   |   7:    54.771 -  62.434:   53        |
|      3:    24.115 -  31.779:  125   |   8:    62.434 -  70.098:   19        |
|      4:    31.779 -  39.443:  120   |   9:    70.098 -  77.762:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1477 r_free = 0.1880             target_work(ml) = 5.369         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1474 r_free = 0.1878             target_work(ml) = 5.368         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1474   r_free= 0.1878   ksol= 0.32   Bsol= 50.00   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,0.02,-1.47,0.00,-0.00,-0.00); trace/3= -1.24                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.367803                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1473   r_free= 0.1876   ksol= 0.32   Bsol= 47.59   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-1.06,-1.35,-0.00,-0.00,-0.00); trace/3= -1.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.366240                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.390310              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.980  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.256072              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.952  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1473      final r-factor (work) = 0.1233          |
| start r-factor (free) = 0.1876      final r-factor (free) = 0.1662          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5253 = 2.39 * 0.50 * 5.4078 + 1.00 * 0.0621                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3767 = 2.39 * 0.50 * 5.2869 + 1.00 * 0.0581                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1233      final r-factor (work) = 0.1196          |
| start r-factor (free) = 0.1662      final r-factor (free) = 0.1632          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3620 = 0.26 * 1.00 * 5.2869 + 1.00 * 0.0082                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3411 = 0.26 * 1.00 * 5.2059 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.699)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.84    80.14   16.86    None  None   None       |
|    all(noH): 2823   0      1.84    80.14   16.86    None  None   None       |
|    Sol.    : 438    0      2.86    69.33   38.93    None  None   None       |
|    Mac.    : 2385   0      1.84    80.14   12.80    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:     1.839 -   9.668:  958   |   5:    40.987 -  48.817:  109        |
|      1:     9.668 -  17.498: 1108   |   6:    48.817 -  56.647:   95        |
|      2:    17.498 -  25.328:  263   |   7:    56.647 -  64.476:   37        |
|      3:    25.328 -  33.157:  117   |   8:    64.476 -  72.306:   14        |
|      4:    33.157 -  40.987:  117   |   9:    72.306 -  80.136:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1196 r_free = 0.1632             target_work(ml) = 5.195         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1195 r_free = 0.1633             target_work(ml) = 5.195         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1195   r_free= 0.1633   ksol= 0.32   Bsol= 47.59   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-1.06,-1.35,-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: 5.194848                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1198   r_free= 0.1629   ksol= 0.32   Bsol= 48.00   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.91,-1.43,-1.27,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.195273                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.717033              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.881  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.502965              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.816  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1198      final r-factor (work) = 0.1112          |
| start r-factor (free) = 0.1629      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1319 = 2.72 * 0.50 * 5.2070 + 1.00 * 0.0581                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0825 = 2.72 * 0.50 * 5.1638 + 1.00 * 0.0675                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1112      final r-factor (work) = 0.1096          |
| start r-factor (free) = 0.1572      final r-factor (free) = 0.1571          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6052 = 0.50 * 1.00 * 5.1638 + 1.00 * 0.0080                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5915 = 0.50 * 1.00 * 5.1353 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.699)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.17   16.76    None  None   None       |
|    all(noH): 2823   0      0.00    86.17   16.76    None  None   None       |
|    Sol.    : 438    0      0.00    75.07   39.15    None  None   None       |
|    Mac.    : 2385   0      1.13    86.17   12.65    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.617:  753   |   5:    43.086 -  51.703:  107        |
|      1:     8.617 -  17.234: 1301   |   6:    51.703 -  60.320:   89        |
|      2:    17.234 -  25.852:  289   |   7:    60.320 -  68.938:   24        |
|      3:    25.852 -  34.469:  128   |   8:    68.938 -  77.555:    8        |
|      4:    34.469 -  43.086:  120   |   9:    77.555 -  86.172:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1096 r_free = 0.1571             target_work(ml) = 5.136         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1095 r_free = 0.1572             target_work(ml) = 5.135         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1095   r_free= 0.1572   ksol= 0.32   Bsol= 48.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.91,-1.43,-1.27,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.135392                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1095   r_free= 0.1572   ksol= 0.32   Bsol= 48.48   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.77,-1.38,-1.07,-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: 5.135466                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.082330              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 150.534  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.374886              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.908  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1095      final r-factor (work) = 0.1096          |
| start r-factor (free) = 0.1572      final r-factor (free) = 0.1570          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4143 = 2.08 * 0.50 * 5.1355 + 1.00 * 0.0675                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4081 = 2.08 * 0.50 * 5.1376 + 1.00 * 0.0590                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1096      final r-factor (work) = 0.1092          |
| start r-factor (free) = 0.1570      final r-factor (free) = 0.1578          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0722 = 1.37 * 1.00 * 5.1376 + 1.00 * 0.0086                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0694 = 1.37 * 1.00 * 5.1348 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.699)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.49    93.76   16.80    None  None   None       |
|    all(noH): 2823   0      0.49    93.76   16.80    None  None   None       |
|    Sol.    : 438    0      1.20    83.48   39.80    None  None   None       |
|    Mac.    : 2385   0      0.49    93.76   12.57    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:     0.494 -   9.821: 1080   |   5:    47.128 -  56.454:  104        |
|      1:     9.821 -  19.148: 1086   |   6:    56.454 -  65.781:   64        |
|      2:    19.148 -  28.474:  214   |   7:    65.781 -  75.107:   16        |
|      3:    28.474 -  37.801:  129   |   8:    75.107 -  84.434:    7        |
|      4:    37.801 -  47.128:  120   |   9:    84.434 -  93.761:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1092 r_free = 0.1578             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1091 r_free = 0.1579             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1579   ksol= 0.32   Bsol= 48.48   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.77,-1.38,-1.07,-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: 5.138900                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8945 -  4.6798 0.99   1421  158 0.0947 0.1256      5.3474      5.5311|
|  2:  4.6798 -  3.7338 0.99   1365  154 0.0821 0.1083      5.4047      5.6142|
|  3:  3.7338 -  3.2675 0.99   1351  146 0.1041 0.1491      5.4512      5.8223|
|  4:  3.2675 -  2.9713 0.99   1323  143 0.1200 0.1539        5.44      5.6014|
|  5:  2.9713 -  2.7598 0.98   1331  151 0.1275 0.1685       5.303      5.4977|
|  6:  2.7598 -  2.5980 0.99   1312  147 0.1232 0.2146      5.2132      5.5029|
|  7:  2.5980 -  2.4685 0.98   1292  152 0.1195 0.1551      5.1429      5.3265|
|  8:  2.4685 -  2.3615 0.99   1329  136 0.1143 0.1663      5.0716       5.287|
|  9:  2.3615 -  2.2709 0.99   1302  150 0.1147 0.1893       5.016       5.366|
| 10:  2.2709 -  2.1928 0.98   1303  141 0.1079 0.1642      4.9454      5.1706|
| 11:  2.1928 -  2.1244 0.97   1284  146 0.1125 0.1854      4.9214      5.2251|
| 12:  2.1244 -  2.0638 0.99   1296  149 0.1092 0.1664      4.8445      5.1174|
| 13:  2.0638 -  2.0096 0.93   1231  132 0.1113 0.1848      4.7909      5.0903|
| 14:  2.0096 -  1.9607 0.38    490   54 0.1047 0.1816      4.7109      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: 14.8945 -  4.6798  1421   158  0.94   8.66   0.98     0.96       6655.57|
|  2:  4.6798 -  3.7338  1365   154  0.95   7.81   1.02     1.00       8598.28|
|  3:  3.7338 -  3.2675  1351   146  0.93  11.23   1.03     1.02      10082.41|
|  4:  3.2675 -  2.9713  1323   143  0.92  13.64   1.01     1.01      10219.55|
|  5:  2.9713 -  2.7598  1331   151  0.90  16.02   1.00     0.97       8230.01|
|  6:  2.7598 -  2.5980  1312   147  0.90  16.26   0.98     0.95       7048.01|
|  7:  2.5980 -  2.4685  1292   152  0.91  15.48   0.98     0.95       6080.25|
|  8:  2.4685 -  2.3615  1329   136  0.91  15.54   1.00     0.97       5522.72|
|  9:  2.3615 -  2.2709  1302   150  0.90  15.83   1.00     0.95       4959.80|
| 10:  2.2709 -  2.1928  1303   141  0.90  15.50   0.99     0.95       4419.32|
| 11:  2.1928 -  2.1244  1284   146  0.90  16.34   0.99     0.96       4362.63|
| 12:  2.1244 -  2.0638  1296   149  0.91  15.36   1.00     0.98       3777.17|
| 13:  2.0638 -  2.0096  1231   132  0.90  16.46   0.99     0.98       3458.94|
| 14:  2.0096 -  1.9607   490    54  0.90  15.92   0.97     0.92       2870.19|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2870.19 max =        10219.55 mean =      6359.03|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.14|
|phase err.(test): min =        0.00 max =           89.91 mean =        13.74|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1579   ksol= 0.32   Bsol= 48.46   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.54,-1.20,-0.84,-0.00,-0.00,-0.00); trace/3= -1.52                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.139019                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1579   ksol= 0.32   Bsol= 48.46   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.54,-1.20,-0.84,-0.00,-0.00,-0.00); trace/3= -1.52                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.139019                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8945 -  4.6798 0.99   1421  158 0.0947 0.1257      5.3481      5.5324|
|  2:  4.6798 -  3.7338 0.99   1365  154 0.0821 0.1082      5.4053      5.6141|
|  3:  3.7338 -  3.2675 0.99   1351  146 0.1042 0.1492      5.4513      5.8226|
|  4:  3.2675 -  2.9713 0.99   1323  143 0.1200 0.1540      5.4399      5.6014|
|  5:  2.9713 -  2.7598 0.98   1331  151 0.1275 0.1685      5.3028      5.4973|
|  6:  2.7598 -  2.5980 0.99   1312  147 0.1231 0.2145      5.2131      5.5025|
|  7:  2.5980 -  2.4685 0.98   1292  152 0.1195 0.1552      5.1429      5.3267|
|  8:  2.4685 -  2.3615 0.99   1329  136 0.1142 0.1663      5.0716      5.2868|
|  9:  2.3615 -  2.2709 0.99   1302  150 0.1147 0.1893      5.0162      5.3661|
| 10:  2.2709 -  2.1928 0.98   1303  141 0.1079 0.1642      4.9457      5.1712|
| 11:  2.1928 -  2.1244 0.97   1284  146 0.1125 0.1853      4.9216      5.2249|
| 12:  2.1244 -  2.0638 0.99   1296  149 0.1092 0.1665      4.8444      5.1178|
| 13:  2.0638 -  2.0096 0.93   1231  132 0.1113 0.1846      4.7909      5.0894|
| 14:  2.0096 -  1.9607 0.38    490   54 0.1046 0.1816       4.711      4.9185|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8945 -  4.6798  1421   158  0.94   8.67   0.98     0.96       6663.42|
|  2:  4.6798 -  3.7338  1365   154  0.95   7.82   1.02     1.01       8606.39|
|  3:  3.7338 -  3.2675  1351   146  0.93  11.24   1.03     1.02      10085.82|
|  4:  3.2675 -  2.9713  1323   143  0.92  13.64   1.02     1.01      10218.83|
|  5:  2.9713 -  2.7598  1331   151  0.90  16.01   1.00     0.98       8224.17|
|  6:  2.7598 -  2.5980  1312   147  0.90  16.26   0.98     0.95       7043.79|
|  7:  2.5980 -  2.4685  1292   152  0.91  15.48   0.99     0.96       6077.64|
|  8:  2.4685 -  2.3615  1329   136  0.91  15.54   1.00     0.98       5522.36|
|  9:  2.3615 -  2.2709  1302   150  0.90  15.84   1.01     0.96       4961.53|
| 10:  2.2709 -  2.1928  1303   141  0.90  15.50   1.00     0.96       4420.58|
| 11:  2.1928 -  2.1244  1284   146  0.90  16.35   1.00     0.97       4364.14|
| 12:  2.1244 -  2.0638  1296   149  0.91  15.36   1.01     0.99       3776.63|
| 13:  2.0638 -  2.0096  1231   132  0.90  16.46   1.00     0.99       3457.23|
| 14:  2.0096 -  1.9607   490    54  0.90  15.92   0.98     0.93       2868.37|
|alpha:            min =        0.93 max =            1.02 mean =         0.98|
|beta:             min =     2868.37 max =        10218.83 mean =      6359.65|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.14|
|phase err.(test): min =        0.00 max =           89.91 mean =        13.74|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.699)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.48    93.75   16.78    None  None   None       |
|    all(noH): 2823   0      0.48    93.75   16.78    None  None   None       |
|    Sol.    : 438    0      1.18    83.46   39.78    None  None   None       |
|    Mac.    : 2385   0      0.48    93.75   12.56    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:     0.479 -   9.805: 1080   |   5:    47.112 -  56.439:  104        |
|      1:     9.805 -  19.132: 1086   |   6:    56.439 -  65.765:   64        |
|      2:    19.132 -  28.459:  214   |   7:    65.765 -  75.092:   16        |
|      3:    28.459 -  37.785:  129   |   8:    75.092 -  84.418:    7        |
|      4:    37.785 -  47.112:  120   |   9:    84.418 -  93.745:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 290         
Filter by distance & map next to the model:
   mapped sites are within: 0.499 - 4.492
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 288 from: 290
   mapped sites are within: 0.708 - 4.492

peak=    5.648 closest distance to " CB  ARG A 275 " =    0.959
peak=    5.538 closest distance to " NH2 ARG A  56 " =    2.293
peak=    5.422 closest distance to " CG  PRO A  54 " =    1.261
peak=    5.118 closest distance to " CB  GLN A 223 " =    1.399
peak=    4.899 closest distance to " CA  TYR A  30 " =    0.915
peak=    4.869 closest distance to " O   HOH Z 232 " =    2.328
peak=    4.827 closest distance to " CB  GLN A 183 " =    1.321
peak=    4.786 closest distance to " CG  PRO A 213 " =    1.259
peak=    4.773 closest distance to " O   HOH Z 142 " =    1.654
peak=    4.753 closest distance to " CB  SER A  63 " =    1.123
peak=    4.712 closest distance to " CG  PRO A  90 " =    1.152
peak=    4.592 closest distance to " C   PRO A 198 " =    1.477
peak=    4.559 closest distance to " O   HOH Z 234 " =    3.652
peak=    4.539 closest distance to " O   HOH Z 272 " =    1.857
peak=    4.533 closest distance to " O   HOH Z 298 " =    1.763
peak=    4.524 closest distance to " O   HOH Z  97 " =    1.899
peak=    4.486 closest distance to " O   SER A  87 " =    2.195
peak=    4.476 closest distance to " O   HOH Z 403 " =    1.789
peak=    4.420 closest distance to " O   HOH Z 209 " =    2.207
peak=    4.415 closest distance to " CG  PRO A 198 " =    1.223
peak=    4.402 closest distance to " NE2 GLN A  11 " =    1.020
peak=    4.381 closest distance to " O   HOH Z 193 " =    1.751
peak=    4.362 closest distance to " CB  ARG A 190 " =    1.713
peak=    4.351 closest distance to " NH2BARG A 145 " =    2.076
peak=    4.330 closest distance to " CB  ARG A  79 " =    1.350
peak=    4.321 closest distance to " NZ  LYS A 117 " =    3.052
peak=    4.319 closest distance to " O   HOH Z  59 " =    2.154
peak=    4.305 closest distance to " CB  GLU A 152 " =    1.178
peak=    4.303 closest distance to " O  BHOH Z  74 " =    1.209
peak=    4.298 closest distance to " O   HOH Z  15 " =    2.162
peak=    4.281 closest distance to " CG  PRO A 243 " =    1.125
peak=    4.241 closest distance to " O   HOH Z 287 " =    1.955
peak=    4.220 closest distance to " CB  PRO A  54 " =    0.981
peak=    4.195 closest distance to " O   HOH Z 126 " =    1.784
peak=    4.195 closest distance to " CG1 ILE A  33 " =    1.255
peak=    4.193 closest distance to " O   HOH Z  44 " =    2.073
peak=    4.189 closest distance to " O   HOH Z 402 " =    1.450
peak=    4.175 closest distance to " O   HOH Z 389 " =    1.907
peak=    4.171 closest distance to " O   HOH Z 203 " =    1.758
peak=    4.106 closest distance to " O   HOH Z 368 " =    2.052
peak=    4.103 closest distance to " O   HOH Z 327 " =    1.694
peak=    4.094 closest distance to " O   HOH Z  97 " =    2.392
peak=    4.086 closest distance to " O   HOH Z 369 " =    2.429
peak=    4.064 closest distance to " O   HOH Z 423 " =    1.970
peak=    4.059 closest distance to " CD2 TRP A 179 " =    1.410
peak=    4.051 closest distance to " O   HOH Z  43 " =    2.234
peak=    4.048 closest distance to " O   HOH Z 227 " =    1.708
peak=    4.028 closest distance to " CB  ASN A 148 " =    1.478
peak=    4.014 closest distance to " O   HOH Z 346 " =    1.630
peak=    4.006 closest distance to " CG  ARG A  66 " =    2.670
peak=    4.003 closest distance to " CB  SER A   3 " =    1.247
peak=    3.986 closest distance to " O   HOH Z 345 " =    2.737
peak=    3.983 closest distance to " O   HOH Z 128 " =    1.926
peak=    3.981 closest distance to " CB  GLU A 277 " =    3.530
peak=    3.979 closest distance to " CG  ARG A  66 " =    1.012
peak=    3.961 closest distance to " O   HOH Z  80 " =    1.694
peak=    3.961 closest distance to " CD  ARG A 269 " =    0.993
peak=    3.941 closest distance to " O   HOH Z 357 " =    1.953
peak=    3.941 closest distance to " O   HOH Z 284 " =    2.903
peak=    3.934 closest distance to " CB  TYR A 169 " =    0.867
peak=    3.934 closest distance to " O   HOH Z 250 " =    1.442
peak=    3.925 closest distance to " ND2 ASN A 187 " =    1.543
peak=    3.918 closest distance to " CB  TRP A 179 " =    1.187
peak=    3.910 closest distance to " O   HOH Z 134 " =    1.366
peak=    3.909 closest distance to " CG2 ILE A 120 " =    1.172
peak=    3.908 closest distance to " CA  ARG A  36 " =    0.987
peak=    3.908 closest distance to " CG2BVAL A  41 " =    0.830
peak=    3.907 closest distance to " O   HOH Z  54 " =    1.767
peak=    3.905 closest distance to " O   HOH Z 189 " =    2.163
peak=    3.889 closest distance to " O   HOH Z 261 " =    1.757
peak=    3.885 closest distance to " O   HOH Z 426 " =    1.483
peak=    3.885 closest distance to " CA  ALA A  21 " =    1.231
peak=    3.884 closest distance to " O   HOH Z 124 " =    1.302
peak=    3.871 closest distance to " O   HOH Z 245 " =    1.383
peak=    3.862 closest distance to " CB  GLU A 128 " =    1.168
peak=    3.862 closest distance to " O   HOH Z 316 " =    2.983
peak=    3.855 closest distance to " O   HOH Z 406 " =    1.542
peak=    3.851 closest distance to " OE1 GLU A   2 " =    2.259
peak=    3.851 closest distance to " O   HOH Z 265 " =    2.192
peak=    3.842 closest distance to " CA  ARG A 195 " =    1.297
peak=    3.828 closest distance to " CA  ALA A  51 " =    0.944
peak=    3.827 closest distance to " O   HOH Z  63 " =    1.969
peak=    3.825 closest distance to " CD2 LEU A 297 " =    0.930
peak=    3.815 closest distance to " CA  ALA A  84 " =    1.182
peak=    3.813 closest distance to " O   HOH Z  40 " =    1.900
peak=    3.812 closest distance to " O   HOH Z  85 " =    1.372
peak=    3.811 closest distance to " O   HOH Z 158 " =    2.934
peak=    3.811 closest distance to " N   ASN A  39 " =    1.234
peak=    3.791 closest distance to " CB  ALA A 248 " =    1.424
peak=    3.787 closest distance to " CA  ASN A 176 " =    1.173
peak=    3.784 closest distance to " O   HOH Z 147 " =    1.761
peak=    3.773 closest distance to " O   HOH Z 421 " =    1.861
peak=    3.768 closest distance to " O   HOH Z 427 " =    2.800
peak=    3.754 closest distance to " O   HOH Z 298 " =    2.279
peak=    3.750 closest distance to " O   HOH Z 102 " =    1.321
peak=    3.747 closest distance to " O   HOH Z 132 " =    2.424
peak=    3.744 closest distance to " O   HOH Z 392 " =    2.560
peak=    3.744 closest distance to " OD1 ASN A  69 " =    2.497
peak=    3.743 closest distance to " O   HOH Z 359 " =    1.496
peak=    3.742 closest distance to " O   HOH Z 128 " =    2.287
peak=    3.740 closest distance to " CG2 ILE A  20 " =    1.374
peak=    3.721 closest distance to " O   HOH Z 380 " =    2.007
peak=    3.705 closest distance to " O   HOH Z  78 " =    1.664
peak=    3.689 closest distance to " OD2 ASP A 286 " =    2.784
peak=    3.673 closest distance to " CB  VAL A 265 " =    1.212
peak=    3.672 closest distance to " NH2AARG A 145 " =    2.288
peak=    3.659 closest distance to " O   HOH Z 345 " =    1.718
peak=    3.654 closest distance to " O   HOH Z  21 " =    1.858
peak=    3.651 closest distance to " N   HIS A 108 " =    1.840
peak=    3.647 closest distance to " O   HOH Z 185 " =    1.777
peak=    3.647 closest distance to " O   HOH Z  61 " =    1.539
peak=    3.644 closest distance to " O   HOH Z 247 " =    1.352
peak=    3.627 closest distance to " O   HOH Z 371 " =    3.193
peak=    3.619 closest distance to " CA  ASN A 215 " =    1.107
peak=    3.614 closest distance to " CD1 LEU A  96 " =    0.772
peak=    3.613 closest distance to " CE  LYS A 119 " =    1.134
peak=    3.612 closest distance to " O   HOH Z 109 " =    1.356
peak=    3.611 closest distance to " CG1BVAL A  72 " =    1.675
peak=    3.610 closest distance to " OD2 ASP A 298 " =    3.890
peak=    3.603 closest distance to " O   HOH Z 361 " =    3.436
peak=    3.595 closest distance to " CB  SER A  26 " =    1.749
peak=    3.591 closest distance to " O   HOH Z 303 " =    2.159
peak=    3.585 closest distance to " CG  GLN A  58 " =    2.603
peak=    3.578 closest distance to " O   HOH Z 173 " =    2.102
peak=    3.568 closest distance to " CZ  PHE A 218 " =    1.082
peak=    3.564 closest distance to " O   HOH Z  35 " =    2.342
peak=    3.564 closest distance to " O   HOH Z 250 " =    1.673
peak=    3.561 closest distance to " CB  SER A  62 " =    0.937
peak=    3.560 closest distance to " CA  LYS A 117 " =    1.278
peak=    3.559 closest distance to " CE  LYS A  76 " =    0.763
peak=    3.559 closest distance to " O   HOH Z  49 " =    2.239
peak=    3.554 closest distance to " O   HOH Z 183 " =    1.509
peak=    3.549 closest distance to " CD  LYS A 166 " =    1.362
peak=    3.544 closest distance to " O   HOH Z 334 " =    1.398
peak=    3.539 closest distance to " O   HOH Z 279 " =    2.114
peak=    3.539 closest distance to " CB  ASN A  39 " =    0.810
peak=    3.539 closest distance to " O   HOH Z 344 " =    2.994
peak=    3.538 closest distance to " NZ  LYS A 119 " =    1.721
peak=    3.536 closest distance to " O   HOH Z 411 " =    3.712
peak=    3.534 closest distance to " CB  ARG A 139 " =    0.905
peak=    3.526 closest distance to " O   ASN A  74 " =    1.990
peak=    3.525 closest distance to " O   HOH Z 337 " =    3.577
peak=    3.525 closest distance to " CB  LEU A 228 " =    1.145
peak=    3.519 closest distance to " O   HOH Z 325 " =    2.060
peak=    3.517 closest distance to " CD  ARG A 159 " =    0.771
peak=    3.516 closest distance to " CB  ASP A 140 " =    0.990
peak=    3.512 closest distance to " CB  SER A 141 " =    1.001
peak=    3.507 closest distance to " O   HOH Z 416 " =    2.890
peak=    3.507 closest distance to " O   HOH Z 214 " =    2.345
peak=    3.503 closest distance to " O   HOH Z 291 " =    1.395
peak=    3.496 closest distance to " CA  ALA A 160 " =    0.832
peak=    3.492 closest distance to " CB  VAL A 202 " =    1.475
peak=    3.492 closest distance to " O   HOH Z 163 " =    1.468
peak=    3.478 closest distance to " CA  THR A 221 " =    0.965
peak=    3.476 closest distance to " O   HOH Z 438 " =    1.993
peak=    3.474 closest distance to " O   HOH Z 108 " =    2.645
peak=    3.473 closest distance to " O   HOH Z 365 " =    2.694
peak=    3.473 closest distance to " CG AARG A 275 " =    1.206
peak=    3.468 closest distance to " O   HOH Z 126 " =    1.867
peak=    3.467 closest distance to " O   HOH Z 258 " =    2.267
peak=    3.467 closest distance to " NH1AARG A 145 " =    1.238
peak=    3.464 closest distance to " O   HOH Z  47 " =    1.504
peak=    3.463 closest distance to " CZ  PHE A  38 " =    1.342
peak=    3.461 closest distance to " CG2 VAL A 197 " =    1.128
peak=    3.454 closest distance to " CB  TRP A 266 " =    1.032
peak=    3.448 closest distance to " O   HOH Z 126 " =    1.531
peak=    3.447 closest distance to " O   HOH Z 171 " =    1.899
peak=    3.441 closest distance to " OG BSER A 164 " =    2.283
peak=    3.437 closest distance to " O   HOH Z 154 " =    1.325
peak=    3.437 closest distance to " CB  THR A  31 " =    1.693
peak=    3.435 closest distance to " CB  TYR A 169 " =    0.976
peak=    3.428 closest distance to " O   HOH Z 193 " =    2.173
peak=    3.418 closest distance to " CA  ASP A 162 " =    1.156
peak=    3.416 closest distance to " O   HOH Z 417 " =    3.060
peak=    3.406 closest distance to " O   ALA A 165 " =    1.402
peak=    3.395 closest distance to " O   HOH Z  66 " =    2.212
peak=    3.395 closest distance to " O   HOH Z 374 " =    2.564
peak=    3.387 closest distance to " CG2 VAL A 257 " =    0.809
peak=    3.386 closest distance to " CB  ASN A 285 " =    0.998
peak=    3.385 closest distance to " O   HOH Z 380 " =    1.848
peak=    3.370 closest distance to " O   HOH Z 336 " =    1.627
peak=    3.367 closest distance to " O   HOH Z  88 " =    3.264
peak=    3.367 closest distance to " O   HOH Z  68 " =    1.901
peak=    3.363 closest distance to " N   TYR A 116 " =    1.583
peak=    3.358 closest distance to " O   HOH Z 261 " =    1.980
peak=    3.357 closest distance to " CB  ALA A 291 " =    1.234
peak=    3.350 closest distance to " O   HOH Z 427 " =    3.091
peak=    3.350 closest distance to " CB  ILE A 120 " =    1.301
peak=    3.346 closest distance to " CB  PRO A 163 " =    3.972
peak=    3.344 closest distance to " O   HOH Z 305 " =    3.653
peak=    3.341 closest distance to " OG  SER A  62 " =    2.797
peak=    3.341 closest distance to " CB  MET A  47 " =    1.087
peak=    3.339 closest distance to " O   HOH Z 358 " =    2.114
peak=    3.337 closest distance to " O   HOH Z 422 " =    2.636
peak=    3.330 closest distance to " O   HOH Z 375 " =    2.194
peak=    3.322 closest distance to " O   HOH Z  63 " =    2.231
peak=    3.318 closest distance to " CA  ALA A 291 " =    0.822
peak=    3.317 closest distance to " O   HOH Z 299 " =    4.233
peak=    3.314 closest distance to " O   HOH Z 132 " =    2.570
peak=    3.304 closest distance to " O   HOH Z 313 " =    1.751
peak=    3.299 closest distance to " O   HOH Z 267 " =    1.964
peak=    3.299 closest distance to " CD  GLN A 194 " =    1.553
peak=    3.296 closest distance to " NE2 GLN A  77 " =    3.164
peak=    3.291 closest distance to " CA  ASP A 140 " =    1.100
peak=    3.282 closest distance to " O   HOH Z 419 " =    1.529
peak=    3.282 closest distance to " CA  LEU A  83 " =    1.327
peak=    3.281 closest distance to " CA  MET A  40 " =    1.064
peak=    3.274 closest distance to " O   HOH Z 403 " =    1.387
peak=    3.273 closest distance to " N   TRP A 150 " =    1.104
peak=    3.272 closest distance to " O   HOH Z 353 " =    2.850
peak=    3.272 closest distance to " O   TRP A 274 " =    1.932
peak=    3.269 closest distance to " O   HOH Z 425 " =    1.981
peak=    3.269 closest distance to " CD1 LEU A 300 " =    1.283
peak=    3.269 closest distance to " CB  GLN A 278 " =    0.864
peak=    3.260 closest distance to " CB  ALA A 131 " =    1.275
peak=    3.259 closest distance to " CB  TYR A 116 " =    0.832
peak=    3.256 closest distance to " CG  LYS A  76 " =    1.067
peak=    3.256 closest distance to " O   HOH Z  88 " =    2.667
peak=    3.255 closest distance to " CB  THR A  52 " =    0.708
peak=    3.253 closest distance to " CG  LEU A 167 " =    1.156
peak=    3.248 closest distance to " O   HOH Z 234 " =    1.846
peak=    3.242 closest distance to " O   SER A  26 " =    1.638
peak=    3.242 closest distance to " CA  VAL A 125 " =    1.183
peak=    3.239 closest distance to " O   HOH Z   1 " =    2.251
peak=    3.239 closest distance to " O   HOH Z 350 " =    1.944
peak=    3.237 closest distance to " CD1 ILE A 106 " =    0.880
peak=    3.235 closest distance to " O   HOH Z 227 " =    1.788
peak=    3.230 closest distance to " CG  MET A 185 " =    1.155
peak=    3.230 closest distance to " O   HOH Z 148 " =    3.194
peak=    3.227 closest distance to " CB  ARG A 269 " =    0.727
peak=    3.224 closest distance to " O   HOH Z  61 " =    1.484
peak=    3.221 closest distance to " CB  PRO A 198 " =    1.037
peak=    3.220 closest distance to " O   HOH Z 189 " =    2.459
peak=    3.213 closest distance to " CD  LYS A 119 " =    1.623
peak=    3.213 closest distance to " CA  GLU A 152 " =    0.872
peak=    3.212 closest distance to " CB  LYS A 289 " =    1.049
peak=    3.209 closest distance to " CD2 HIS A  81 " =    1.177
peak=    3.203 closest distance to " CG2AVAL A 121 " =    2.118
peak=    3.202 closest distance to " CA  SER A  32 " =    1.629
peak=    3.196 closest distance to " O   HOH Z 273 " =    2.871
peak=    3.195 closest distance to " O   HOH Z 152 " =    1.847
peak=    3.194 closest distance to " O   HOH Z 130 " =    2.360
peak=    3.193 closest distance to " CB  ALA A   9 " =    1.603
peak=    3.193 closest distance to " CA  SER A  87 " =    1.011
peak=    3.192 closest distance to " O   HOH Z 408 " =    1.607
peak=    3.181 closest distance to " CD  GLN A 240 " =    1.396
peak=    3.179 closest distance to " O   THR A 220 " =    1.174
peak=    3.178 closest distance to " NH2 ARG A 219 " =    1.899
peak=    3.176 closest distance to " O   HOH Z 393 " =    3.336
peak=    3.172 closest distance to " O   ILE A  33 " =    1.295
peak=    3.172 closest distance to " O   HOH Z  46 " =    1.370
peak=    3.166 closest distance to " NZ  LYS A 166 " =    3.033
peak=    3.166 closest distance to " CA  MET A 105 " =    1.114
peak=    3.165 closest distance to " N   ASP A 162 " =    1.179
peak=    3.164 closest distance to " CG2 VAL A 202 " =    1.189
peak=    3.161 closest distance to " CG  ARG A 219 " =    1.186
peak=    3.160 closest distance to " CG  GLN A  11 " =    1.513
peak=    3.159 closest distance to " CZ2 TRP A 179 " =    1.745
peak=    3.158 closest distance to " O   HOH Z 281 " =    4.492
peak=    3.155 closest distance to " O   HOH Z 423 " =    3.384
peak=    3.153 closest distance to " O   HOH Z  19 " =    1.701
peak=    3.153 closest distance to " ND1 HIS A  81 " =    1.594
peak=    3.150 closest distance to " CB  ASN A 215 " =    1.153
peak=    3.149 closest distance to " O   HOH Z  19 " =    1.530
peak=    3.148 closest distance to " OE1 GLN A  11 " =    1.895
peak=    3.145 closest distance to " O   GLY A  91 " =    1.371
peak=    3.135 closest distance to " CA  ASP A 191 " =    1.230
peak=    3.134 closest distance to " O   HOH Z  30 " =    2.084
peak=    3.126 closest distance to " OG1 THR A 221 " =    1.278
peak=    3.125 closest distance to " CA  SER A 146 " =    1.884
peak=    3.124 closest distance to " O   HOH Z 367 " =    3.590
peak=    3.123 closest distance to " CD1AILE A 234 " =    0.919
peak=    3.122 closest distance to " NH2 ARG A 156 " =    1.125
peak=    3.122 closest distance to " CB  GLN A 103 " =    0.825
peak=    3.120 closest distance to " CG2 VAL A  78 " =    0.839
peak=    3.118 closest distance to " CA  GLY A  80 " =    0.731
peak=    3.117 closest distance to " OD1 ASN A 148 " =    2.153
peak=    3.116 closest distance to " OG  SER A 245 " =    1.437
peak=    3.115 closest distance to " O   HOH Z  48 " =    1.614
peak=    3.111 closest distance to " C   SER A  32 " =    1.108
peak=    3.105 closest distance to " O   HOH Z 182 " =    1.987
peak=    3.079 closest distance to " CD  ARG A  66 " =    2.954
peak=    3.077 closest distance to " CD  GLU A 236 " =    1.049
peak=    3.075 closest distance to " CB  ALA A 295 " =    1.274
peak=    3.066 closest distance to " O   HOH Z 414 " =    1.591
peak=    3.065 closest distance to " CA  ALA A 299 " =    0.938
peak=    3.055 closest distance to " CD1 LEU A 228 " =    1.624
peak=    3.032 closest distance to " O   HOH Z 406 " =    2.807

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 201         
Filter by distance & map next to the model:
   mapped sites are within: 0.847 - 5.731
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 201
   mapped sites are within: 0.847 - 5.731

peak=   -4.813 closest distance to " O   HOH Z 266 " =    4.688
peak=   -4.618 closest distance to " C   HIS A 108 " =    1.077
peak=   -4.330 closest distance to " CD  GLN A  58 " =    1.160
peak=   -4.311 closest distance to " O   HOH Z  13 " =    1.679
peak=   -4.299 closest distance to " SG  CYS A 254 " =    3.372
peak=   -4.275 closest distance to " CD  ARG A 156 " =    2.077
peak=   -4.264 closest distance to " OXT GLY A 302 " =    2.848
peak=   -4.191 closest distance to " O   HOH Z 377 " =    2.052
peak=   -4.150 closest distance to " OG BSER A 134 " =    1.353
peak=   -4.116 closest distance to " CD1 LEU A 101 " =    2.437
peak=   -4.106 closest distance to " O   VAL A  67 " =    2.893
peak=   -4.075 closest distance to " O   HOH Z 165 " =    1.906
peak=   -4.054 closest distance to " OE1 GLN A 223 " =    2.151
peak=   -4.040 closest distance to " ND2 ASN A  45 " =    1.020
peak=   -4.003 closest distance to " O   HOH Z 198 " =    1.894
peak=   -3.998 closest distance to " O   VAL A  67 " =    2.677
peak=   -3.990 closest distance to " N   ALA A 248 " =    1.736
peak=   -3.980 closest distance to " CA  ASP A 298 " =    1.074
peak=   -3.977 closest distance to " O   HOH Z 353 " =    2.247
peak=   -3.970 closest distance to " CB  ALA A 291 " =    2.312
peak=   -3.947 closest distance to " CB  PRO A 243 " =    2.675
peak=   -3.945 closest distance to " CB  ALA A 161 " =    2.513
peak=   -3.914 closest distance to " O   PRO A 163 " =    2.105
peak=   -3.896 closest distance to " O   PHE A 218 " =    1.587
peak=   -3.872 closest distance to " CZ3 TRP A 179 " =    1.324
peak=   -3.840 closest distance to " CB  PHE A 192 " =    2.025
peak=   -3.825 closest distance to " CG1 VAL A 112 " =    2.732
peak=   -3.821 closest distance to " ND2 ASN A 187 " =    1.530
peak=   -3.806 closest distance to " OD2 ASP A 171 " =    2.417
peak=   -3.798 closest distance to " CZ  TYR A 169 " =    1.874
peak=   -3.765 closest distance to " O   HOH Z 372 " =    2.259
peak=   -3.764 closest distance to " CD  ARG A 139 " =    1.591
peak=   -3.764 closest distance to " CG  ASP A 132 " =    2.331
peak=   -3.735 closest distance to " O   HOH Z 351 " =    1.509
peak=   -3.723 closest distance to " O   PRO A 198 " =    1.285
peak=   -3.722 closest distance to " CD2 LEU A 237 " =    2.322
peak=   -3.714 closest distance to " CD1 PHE A 130 " =    2.353
peak=   -3.692 closest distance to " CE2 TYR A  30 " =    2.712
peak=   -3.688 closest distance to " N   GLN A  58 " =    1.690
peak=   -3.681 closest distance to " O   HOH Z 377 " =    1.642
peak=   -3.670 closest distance to " CD1 LEU A  25 " =    2.489
peak=   -3.669 closest distance to " O   HOH Z  11 " =    1.989
peak=   -3.658 closest distance to " O   HOH Z 234 " =    3.967
peak=   -3.650 closest distance to " OG  SER A  97 " =    2.176
peak=   -3.625 closest distance to " C   THR A 279 " =    1.176
peak=   -3.623 closest distance to " CB  ASN A  39 " =    2.304
peak=   -3.619 closest distance to " O   ALA A  34 " =    2.188
peak=   -3.616 closest distance to " O   HOH Z 114 " =    3.400
peak=   -3.611 closest distance to " O   VAL A 174 " =    2.104
peak=   -3.610 closest distance to " O   HOH Z 407 " =    2.756
peak=   -3.600 closest distance to " O   HOH Z 422 " =    1.455
peak=   -3.594 closest distance to " CZ  ARG A  66 " =    1.082
peak=   -3.591 closest distance to " NE2 GLN A  88 " =    1.700
peak=   -3.586 closest distance to " O   HOH Z 166 " =    1.761
peak=   -3.581 closest distance to " O   TRP A  92 " =    1.924
peak=   -3.578 closest distance to " CG1 VAL A  78 " =    3.150
peak=   -3.560 closest distance to " N   THR A 235 " =    1.352
peak=   -3.556 closest distance to " O   HOH Z 369 " =    2.286
peak=   -3.555 closest distance to " O   HOH Z 292 " =    4.512
peak=   -3.551 closest distance to " O   SER A 210 " =    1.891
peak=   -3.541 closest distance to " O   HOH Z 102 " =    1.669
peak=   -3.534 closest distance to " OD2 ASP A 191 " =    1.456
peak=   -3.532 closest distance to " O   HOH Z 394 " =    1.575
peak=   -3.532 closest distance to " CG1AVAL A  41 " =    2.660
peak=   -3.525 closest distance to " CB  PHE A 208 " =    2.290
peak=   -3.521 closest distance to " ND2 ASN A  39 " =    1.133
peak=   -3.521 closest distance to " CE1 TYR A 247 " =    2.647
peak=   -3.515 closest distance to " O   HOH Z  71 " =    1.816
peak=   -3.514 closest distance to " O   HOH Z  10 " =    1.550
peak=   -3.511 closest distance to " CA  TYR A  68 " =    2.949
peak=   -3.505 closest distance to " O   HOH Z 290 " =    1.079
peak=   -3.497 closest distance to " O   LEU A 167 " =    1.586
peak=   -3.495 closest distance to " O   GLY A  80 " =    2.421
peak=   -3.494 closest distance to " N   THR A  52 " =    1.746
peak=   -3.490 closest distance to " CG  GLU A  53 " =    1.389
peak=   -3.485 closest distance to " OD1 ASN A 148 " =    1.520
peak=   -3.479 closest distance to " O   SER A   3 " =    1.067
peak=   -3.479 closest distance to " CD1 PHE A  59 " =    1.970
peak=   -3.479 closest distance to " O   HOH Z 395 " =    5.131
peak=   -3.472 closest distance to " N   ALA A  43 " =    2.654
peak=   -3.461 closest distance to " OD1 ASN A  39 " =    2.192
peak=   -3.458 closest distance to " CG  ASP A 231 " =    0.847
peak=   -3.449 closest distance to " CB  ALA A 248 " =    2.251
peak=   -3.448 closest distance to " O   ALA A   1 " =    1.947
peak=   -3.445 closest distance to " CD1 LEU A 228 " =    2.091
peak=   -3.441 closest distance to " CD2 TYR A 247 " =    2.360
peak=   -3.441 closest distance to " NH2 ARG A  79 " =    2.168
peak=   -3.430 closest distance to " CB  ASP A 286 " =    1.901
peak=   -3.429 closest distance to " OE1 GLN A 223 " =    1.936
peak=   -3.429 closest distance to " O   HOH Z 109 " =    5.731
peak=   -3.428 closest distance to " O   HOH Z 196 " =    1.941
peak=   -3.422 closest distance to " O   HOH Z 414 " =    1.462
peak=   -3.421 closest distance to " O   HOH Z 301 " =    2.276
peak=   -3.411 closest distance to " O   HOH Z 126 " =    1.921
peak=   -3.411 closest distance to " O   GLN A  11 " =    1.371
peak=   -3.410 closest distance to " CB  ALA A 248 " =    1.994
peak=   -3.400 closest distance to " O   HOH Z 185 " =    2.423
peak=   -3.399 closest distance to " O   HOH Z  15 " =    1.526
peak=   -3.397 closest distance to " O   HOH Z 389 " =    1.734
peak=   -3.396 closest distance to " O   HOH Z 435 " =    2.646
peak=   -3.394 closest distance to " O   HOH Z 171 " =    2.171
peak=   -3.392 closest distance to " NH2 ARG A  66 " =    5.398
peak=   -3.391 closest distance to " NH1 ARG A 195 " =    2.608
peak=   -3.389 closest distance to " CE  MET A 105 " =    2.182
peak=   -3.387 closest distance to " ND2 ASN A  69 " =    1.619
peak=   -3.375 closest distance to " CA  GLY A 203 " =    2.263
peak=   -3.372 closest distance to " OE1 GLN A 183 " =    1.432
peak=   -3.372 closest distance to " CD  LYS A 289 " =    2.428
peak=   -3.368 closest distance to " OG  SER A   3 " =    1.601
peak=   -3.368 closest distance to " OD1 ASP A 191 " =    1.483
peak=   -3.366 closest distance to " O   ALA A 160 " =    1.459
peak=   -3.364 closest distance to " CG2 ILE A 263 " =    2.207
peak=   -3.359 closest distance to " CA  GLY A 133 " =    1.948
peak=   -3.357 closest distance to " O   HOH Z 166 " =    1.776
peak=   -3.351 closest distance to " O   HOH Z  52 " =    1.558
peak=   -3.347 closest distance to " C   LEU A 143 " =    1.003
peak=   -3.337 closest distance to " N   ALA A 248 " =    2.248
peak=   -3.328 closest distance to " CG1 VAL A 125 " =    2.284
peak=   -3.327 closest distance to " O   HOH Z 174 " =    3.773
peak=   -3.325 closest distance to " OD1 ASP A 171 " =    1.489
peak=   -3.325 closest distance to " O   VAL A 189 " =    2.614
peak=   -3.322 closest distance to " CG  PHE A 283 " =    2.527
peak=   -3.318 closest distance to " O   HOH Z   6 " =    1.769
peak=   -3.318 closest distance to " O   PRO A 198 " =    1.282
peak=   -3.317 closest distance to " O   GLU A 152 " =    1.492
peak=   -3.314 closest distance to " CE  LYS A 166 " =    2.915
peak=   -3.313 closest distance to " O   MET A  40 " =    2.622
peak=   -3.310 closest distance to " O   HOH Z 423 " =    2.258
peak=   -3.302 closest distance to " O  BHOH Z 338 " =    1.315
peak=   -3.298 closest distance to " CG2 THR A 178 " =    2.196
peak=   -3.297 closest distance to " O   VAL A 189 " =    1.823
peak=   -3.281 closest distance to " CB  SER A 258 " =    2.082
peak=   -3.280 closest distance to " O   HOH Z 427 " =    1.425
peak=   -3.278 closest distance to " NE2 GLN A  88 " =    1.065
peak=   -3.275 closest distance to " CD  GLN A 223 " =    1.400
peak=   -3.273 closest distance to " N   ALA A 226 " =    1.887
peak=   -3.273 closest distance to " O   HOH Z  11 " =    1.864
peak=   -3.271 closest distance to " NE2 GLN A 194 " =    1.787
peak=   -3.266 closest distance to " OG BSER A 134 " =    1.754
peak=   -3.262 closest distance to " O   HOH Z 281 " =    2.551
peak=   -3.258 closest distance to " O   HOH Z  16 " =    2.506
peak=   -3.257 closest distance to " OG BSER A 210 " =    2.177
peak=   -3.256 closest distance to " CD2 TYR A 293 " =    1.944
peak=   -3.253 closest distance to " O   HOH Z 280 " =    2.372
peak=   -3.248 closest distance to " N   VAL A 189 " =    1.626
peak=   -3.246 closest distance to " OG  SER A  26 " =    1.243
peak=   -3.244 closest distance to " O   HOH Z 251 " =    1.557
peak=   -3.244 closest distance to " O   SER A  95 " =    1.569
peak=   -3.241 closest distance to " CE3 TRP A 150 " =    2.149
peak=   -3.241 closest distance to " O   HOH Z 139 " =    3.231
peak=   -3.239 closest distance to " O   HOH Z 111 " =    2.205
peak=   -3.239 closest distance to " O   HOH Z 252 " =    3.332
peak=   -3.238 closest distance to " CD2 LEU A 300 " =    2.713
peak=   -3.237 closest distance to " O   GLY A  75 " =    1.708
peak=   -3.229 closest distance to " CG2 VAL A 189 " =    2.167
peak=   -3.227 closest distance to " O   SER A 135 " =    1.591
peak=   -3.223 closest distance to " CA  GLY A 241 " =    2.354
peak=   -3.223 closest distance to " O   ASN A  45 " =    1.816
peak=   -3.220 closest distance to " OE2 GLU A   2 " =    1.766
peak=   -3.214 closest distance to " O   HOH Z 361 " =    3.407
peak=   -3.208 closest distance to " O   ILE A 234 " =    1.240
peak=   -3.205 closest distance to " O   GLY A 196 " =    0.999
peak=   -3.204 closest distance to " N   SER A 276 " =    1.362
peak=   -3.196 closest distance to " O   HOH Z 311 " =    3.639
peak=   -3.194 closest distance to " CG  PRO A 243 " =    1.700
peak=   -3.193 closest distance to " NE2 GLN A 103 " =    1.682
peak=   -3.192 closest distance to " O   ALA A 161 " =    1.557
peak=   -3.191 closest distance to " C   SER A 206 " =    1.597
peak=   -3.187 closest distance to " O   HOH Z 213 " =    1.497
peak=   -3.180 closest distance to " O   HOH Z  19 " =    2.118
peak=   -3.177 closest distance to " O   ILE A 106 " =    1.657
peak=   -3.168 closest distance to " O   HOH Z 326 " =    1.744
peak=   -3.162 closest distance to " O   HOH Z  38 " =    1.655
peak=   -3.158 closest distance to " O   HOH Z 233 " =    2.405
peak=   -3.156 closest distance to " O   HOH Z 193 " =    1.630
peak=   -3.150 closest distance to " CG  PRO A 163 " =    2.614
peak=   -3.150 closest distance to " C   GLN A 205 " =    1.810
peak=   -3.149 closest distance to " O   ALA A  10 " =    1.836
peak=   -3.141 closest distance to " C   ALA A 158 " =    1.289
peak=   -3.138 closest distance to " O   HOH Z 283 " =    2.058
peak=   -3.138 closest distance to " CE2 PHE A  38 " =    1.974
peak=   -3.135 closest distance to " O   GLY A  80 " =    2.583
peak=   -3.134 closest distance to " O   HOH Z  41 " =    2.230
peak=   -3.109 closest distance to " O   HOH Z 111 " =    3.712
peak=   -3.108 closest distance to " CG  ASP A  50 " =    2.323
peak=   -3.103 closest distance to " CB  GLN A  11 " =    1.824
peak=   -3.102 closest distance to " O   ALA A  51 " =    1.413
peak=   -3.098 closest distance to " O   HOH Z  61 " =    1.636
peak=   -3.090 closest distance to " O   HOH Z 265 " =    2.320
peak=   -3.089 closest distance to " O   HOH Z   9 " =    1.989
peak=   -3.080 closest distance to " O   HOH Z 263 " =    2.879
peak=   -3.077 closest distance to " OH  TYR A 169 " =    0.994
peak=   -3.076 closest distance to " OG ASER A 134 " =    1.274
peak=   -3.074 closest distance to " O   HOH Z 397 " =    1.145
peak=   -3.067 closest distance to " O   HOH Z 219 " =    3.439
peak=   -3.064 closest distance to " CB  PHE A  16 " =    2.554
peak=   -3.046 closest distance to " CZ3 TRP A 274 " =    2.444
peak=   -3.039 closest distance to " OE2 GLU A   2 " =    1.578
peak=   -3.028 closest distance to " CD2 LEU A 300 " =    2.812

================= 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    :  0.4068 0.4019   6.205361e+00   6.192893e+00
   1_bss:  0.3974 0.3902   6.191802e+00   6.175659e+00
   1_xyz:  0.2540 0.2766   5.823021e+00   5.896895e+00
   1_adp:  0.2303 0.2840   5.768331e+00   5.921325e+00
   1_occ:  0.2299 0.2842   5.768158e+00   5.922099e+00
   2_bss:  0.2266 0.2807   5.758969e+00   5.913884e+00
   2_xyz:  0.1616 0.2043   5.450537e+00   5.636708e+00
   2_adp:  0.1477 0.1880   5.368608e+00   5.559762e+00
   2_occ:  0.1474 0.1878   5.367803e+00   5.559234e+00
   3_bss:  0.1473 0.1876   5.366240e+00   5.555673e+00
   3_xyz:  0.1233 0.1662   5.220766e+00   5.437259e+00
   3_adp:  0.1196 0.1632   5.195151e+00   5.416691e+00
   3_occ:  0.1195 0.1633   5.194848e+00   5.416570e+00
   4_bss:  0.1198 0.1629   5.195273e+00   5.414421e+00
   4_xyz:  0.1112 0.1572   5.142607e+00   5.381066e+00
   4_adp:  0.1096 0.1571   5.135654e+00   5.380740e+00
   4_occ:  0.1095 0.1572   5.135392e+00   5.380914e+00
   5_bss:  0.1095 0.1572   5.135466e+00   5.380983e+00
   5_xyz:  0.1096 0.1570   5.137958e+00   5.382028e+00
   5_adp:  0.1092 0.1578   5.138951e+00   5.387365e+00
   5_occ:  0.1091 0.1579   5.138900e+00   5.387504e+00
   5_bss:  0.1091 0.1579   5.139019e+00   5.387585e+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:  0.297  24.433  -0.294   2.545  -1.461   0.000  -0.000  -0.000
   1_xyz:  0.297  24.433  -0.294   2.545  -1.461   0.000  -0.000  -0.000
   1_adp:  0.297  24.433  -0.294   2.545  -1.461   0.000  -0.000  -0.000
   1_occ:  0.297  24.433  -0.294   2.545  -1.461   0.000  -0.000  -0.000
   2_bss:  0.323  50.001  -2.260   0.020  -1.470   0.000  -0.000  -0.000
   2_xyz:  0.323  50.001  -2.260   0.020  -1.470   0.000  -0.000  -0.000
   2_adp:  0.323  50.001  -2.260   0.020  -1.470   0.000  -0.000  -0.000
   2_occ:  0.323  50.001  -2.260   0.020  -1.470   0.000  -0.000  -0.000
   3_bss:  0.322  47.592  -2.808  -1.065  -1.349  -0.000  -0.000  -0.000
   3_xyz:  0.322  47.592  -2.808  -1.065  -1.349  -0.000  -0.000  -0.000
   3_adp:  0.322  47.592  -2.808  -1.065  -1.349  -0.000  -0.000  -0.000
   3_occ:  0.322  47.592  -2.808  -1.065  -1.349  -0.000  -0.000  -0.000
   4_bss:  0.323  47.997  -2.912  -1.433  -1.269  -0.000  -0.000  -0.000
   4_xyz:  0.323  47.997  -2.912  -1.433  -1.269  -0.000  -0.000  -0.000
   4_adp:  0.323  47.997  -2.912  -1.433  -1.269  -0.000  -0.000  -0.000
   4_occ:  0.323  47.997  -2.912  -1.433  -1.269  -0.000  -0.000  -0.000
   5_bss:  0.324  48.478  -2.768  -1.377  -1.067  -0.000  -0.000  -0.000
   5_xyz:  0.324  48.478  -2.768  -1.377  -1.067  -0.000  -0.000  -0.000
   5_adp:  0.324  48.478  -2.768  -1.377  -1.067  -0.000  -0.000  -0.000
   5_occ:  0.324  48.478  -2.768  -1.377  -1.067  -0.000  -0.000  -0.000
   5_bss:  0.323  48.462  -2.542  -1.196  -0.835  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  45.532 0.5774  0.7600    49192.766
   1_bss:  44.392 0.5897  0.7854    45710.103
   1_xyz:  28.297 0.7772  0.9743    20338.747
   1_adp:  29.416 0.7640  0.9583    21495.537
   1_occ:  29.470 0.7634  0.9575    21566.462
   2_bss:  29.000 0.7683  0.9154    20890.642
   2_xyz:  20.038 0.8604  0.9852    10646.176
   2_adp:  17.984 0.8805  0.9907     9092.536
   2_occ:  17.973 0.8806  0.9907     9077.311
   3_bss:  17.871 0.8814  0.9733     8957.048
   3_xyz:  15.355 0.9033  0.9840     7044.530
   3_adp:  14.853 0.9079  0.9804     6836.028
   3_occ:  14.853 0.9079  0.9803     6829.577
   4_bss:  14.817 0.9081  0.9761     6787.844
   4_xyz:  14.058 0.9144  0.9794     6302.851
   4_adp:  14.015 0.9148  0.9743     6300.547
   4_occ:  14.016 0.9148  0.9742     6296.717
   5_bss:  14.017 0.9148  0.9790     6297.612
   5_xyz:  14.000 0.9151  0.9785     6302.721
   5_adp:  14.097 0.9143  0.9717     6358.327
   5_occ:  14.098 0.9143  0.9716     6358.229
   5_bss:  14.101 0.9143  0.9786     6358.844
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.8969e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.8969e-01
   1_xyz:   1.304  0.010  0.082 15.302  0.005  4.107   9.2972e-02
   1_adp:   1.304  0.010  0.082 15.302  0.005  4.107   9.2972e-02
   1_occ:   1.304  0.010  0.082 15.302  0.005  4.107   9.2972e-02
   2_bss:   1.304  0.010  0.082 15.302  0.005  4.107   9.2972e-02
   2_xyz:   1.064  0.007  0.071 14.555  0.004  4.124   6.2006e-02
   2_adp:   1.064  0.007  0.071 14.555  0.004  4.124   6.2006e-02
   2_occ:   1.064  0.007  0.071 14.555  0.004  4.124   6.2006e-02
   3_bss:   1.064  0.007  0.071 14.555  0.004  4.124   6.2006e-02
   3_xyz:   1.004  0.006  0.070 14.594  0.004  4.120   5.8108e-02
   3_adp:   1.004  0.006  0.070 14.594  0.004  4.120   5.8108e-02
   3_occ:   1.004  0.006  0.070 14.594  0.004  4.120   5.8108e-02
   4_bss:   1.004  0.006  0.070 14.594  0.004  4.120   5.8108e-02
   4_xyz:   1.079  0.008  0.079 14.826  0.005  4.110   6.7465e-02
   4_adp:   1.079  0.008  0.079 14.826  0.005  4.110   6.7465e-02
   4_occ:   1.079  0.008  0.079 14.826  0.005  4.110   6.7465e-02
   5_bss:   1.079  0.008  0.079 14.826  0.005  4.110   6.7465e-02
   5_xyz:   1.004  0.007  0.075 14.567  0.004  4.110   5.9005e-02
   5_adp:   1.004  0.007  0.075 14.567  0.004  4.110   5.9005e-02
   5_occ:   1.004  0.007  0.075 14.567  0.004  4.110   5.9005e-02
   5_bss:   1.004  0.007  0.075 14.567  0.004  4.110   5.9005e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.236   2.4130e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.236   2.4130e-01
   1_xyz:   8.155  0.059  0.331 87.182  0.029  1.999   8.1805e-02
   1_adp:   8.155  0.059  0.331 87.182  0.029  1.999   8.1805e-02
   1_occ:   8.155  0.059  0.331 87.182  0.029  1.999   8.1805e-02
   2_bss:   8.155  0.059  0.331 87.182  0.029  1.999   8.1805e-02
   2_xyz:   7.932  0.041  0.223 80.702  0.046  2.257   5.5603e-02
   2_adp:   7.932  0.041  0.223 80.702  0.046  2.257   5.5603e-02
   2_occ:   7.932  0.041  0.223 80.702  0.046  2.257   5.5603e-02
   3_bss:   7.932  0.041  0.223 80.702  0.046  2.257   5.5603e-02
   3_xyz:   7.215  0.045  0.220 81.377  0.037  2.287   4.3941e-02
   3_adp:   7.215  0.045  0.220 81.377  0.037  2.287   4.3941e-02
   3_occ:   7.215  0.045  0.220 81.377  0.037  2.287   4.3941e-02
   4_bss:   7.215  0.045  0.220 81.377  0.037  2.287   4.3941e-02
   4_xyz:   7.809  0.045  0.246 82.646  0.041  2.308   5.4042e-02
   4_adp:   7.809  0.045  0.246 82.646  0.041  2.308   5.4042e-02
   4_occ:   7.809  0.045  0.246 82.646  0.041  2.308   5.4042e-02
   5_bss:   7.809  0.045  0.246 82.646  0.041  2.308   5.4042e-02
   5_xyz:   7.377  0.047  0.249 82.387  0.038  2.350   4.2116e-02
   5_adp:   7.377  0.047  0.249 82.387  0.038  2.350   4.2116e-02
   5_occ:   7.377  0.047  0.249 82.387  0.038  2.350   4.2116e-02
   5_bss:   7.377  0.047  0.249 82.387  0.038  2.350   4.2116e-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:  69.55   0.00  17.46  65.14   0.00  13.61  69.55   4.99  38.41
   1_occ:  69.55   0.00  17.46  65.14   0.00  13.61  69.55   4.99  38.41
   2_bss:  69.55   0.00  17.46  65.14   0.00  13.61  69.55   4.99  38.41
   2_xyz:  69.55   0.00  17.46  65.14   0.00  13.61  69.55   4.99  38.41
   2_adp:  77.76   1.12  17.03  77.76   1.12  13.04  70.16   5.07  38.76
   2_occ:  77.76   1.12  17.03  77.76   1.12  13.04  70.16   5.07  38.76
   3_bss:  77.76   1.12  17.03  77.76   1.12  13.04  70.16   5.07  38.76
   3_xyz:  77.76   1.12  17.03  77.76   1.12  13.04  70.16   5.07  38.76
   3_adp:  80.14   1.84  16.86  80.14   1.84  12.80  69.33   2.86  38.93
   3_occ:  80.14   1.84  16.86  80.14   1.84  12.80  69.33   2.86  38.93
   4_bss:  80.14   1.84  16.86  80.14   1.84  12.80  69.33   2.86  38.93
   4_xyz:  80.14   1.84  16.86  80.14   1.84  12.80  69.33   2.86  38.93
   4_adp:  86.17   0.00  16.76  86.17   1.13  12.65  75.07   0.00  39.15
   4_occ:  86.17   0.00  16.76  86.17   1.13  12.65  75.07   0.00  39.15
   5_bss:  86.17   0.00  16.76  86.17   1.13  12.65  75.07   0.00  39.15
   5_xyz:  86.17   0.00  16.76  86.17   1.13  12.65  75.07   0.00  39.15
   5_adp:  93.76   0.49  16.80  93.76   0.49  12.57  83.48   1.20  39.80
   5_occ:  93.76   0.49  16.80  93.76   0.49  12.57  83.48   1.20  39.80
   5_bss:  93.75   0.48  16.78  93.75   0.48  12.56  83.46   1.18  39.78
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    2.129    0.035    0.399
   1_adp:    2.129    0.035    0.399
   1_occ:    2.129    0.035    0.399
   2_bss:    2.129    0.035    0.399
   2_xyz:    1.886    0.051    0.506
   2_adp:    1.886    0.051    0.506
   2_occ:    1.886    0.051    0.506
   3_bss:    1.886    0.051    0.506
   3_xyz:    1.655    0.054    0.574
   3_adp:    1.655    0.054    0.574
   3_occ:    1.655    0.054    0.574
   4_bss:    1.655    0.054    0.574
   4_xyz:    1.390    0.066    0.599
   4_adp:    1.390    0.066    0.599
   4_occ:    1.390    0.066    0.599
   5_bss:    1.390    0.066    0.599
   5_xyz:    1.367    0.044    0.606
   5_adp:    1.367    0.044    0.606
   5_occ:    1.367    0.044    0.606
   5_bss:    1.367    0.044    0.606
------------------------------------------------------------------------

CPU time actual refinement: 346.82


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_213/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_213/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_213/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_213/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_213/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 346.68 
  Macro-tasks:
    bulk solvent and scale       = 44.80  
    individual site refinement   = 139.38 
    weights calculation          = 30.78  
    collect and process          = 6.63   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 221.72 
  Micro-tasks:
    mask                            = 1.87   
    f_calc                          = 109.44 
    alpha_beta                      = 8.36   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 118.13 
    fmodel                         = 7.25   
    r_factors                      = 0.21   
    phase_errors                   = 10.54  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 257.25 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.896 micro seconds
Total CPU time: 6.00 minutes
from_scatterers_fft:    658 calls, 109.09 s
gradients_fft:          603 calls, 104.70 s

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

# Date 2008-01-16 Time 04:17:47 PST -0800 (1200485867.69 s)
Start R-work = 0.4068, R-free = 0.4019 (no bulk solvent and anisotropic scale)
Final R-work = 0.1320, R-free = 0.1764 (no bulk solvent and anisotropic scale)

Start R-work = 0.3974, R-free = 0.3902
Final R-work = 0.1091, R-free = 0.1579