# Date 2008-01-16 Time 06:23:10 PST -0800 (1200493390.40 s)
#phil __OFF__

Command line arguments: "../1122.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 18093
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1122

-------------------------------------------------------------------------------
  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: (71.655, 46.4607, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 46.4607, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1017 1.95119
Completeness in resolution range: 0.930815
Completeness with d_max=infinity: 0.928081

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1017
                             d_min =   1.9512

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: (71.655, 46.4607, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1017 1.95119
Completeness in resolution range: 0.930815
Completeness with d_max=infinity: 0.928081

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1022 -  4.1769 [2209/2238]  1991   218   9.9%
  bin  2:  4.1769 -  3.3270 [2118/2134]  1904   214  10.1%
  bin  3:  3.3270 -  2.9098 [2099/2118]  1884   215  10.2%
  bin  4:  2.9098 -  2.6453 [2075/2105]  1875   200   9.6%
  bin  5:  2.6453 -  2.4566 [2065/2084]  1860   205   9.9%
  bin  6:  2.4566 -  2.3123 [2048/2084]  1836   212  10.4%
  bin  7:  2.3123 -  2.1968 [2053/2086]  1844   209  10.2%
  bin  8:  2.1968 -  2.1015 [2030/2064]  1837   193   9.5%
  bin  9:  2.1015 -  2.0208 [1992/2065]  1787   205  10.3%
  bin 10:  2.0208 -  1.9512 [ 900/2067]   812    88   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1122/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:
        1.57 -     2.23: 22
        2.23 -     2.90: 1425
        2.90 -     3.57: 4516
        3.57 -     4.23: 9305
        4.23 -     4.90: 13303
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.567 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.698 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.722 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  1.770 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.794 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28566 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_1122/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1122/model_refine_001.geo

CPU time processing inputs: 9.19


============================ 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 = 71.655 46.4607 84.23025 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: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4577   r_free= 0.4608   ksol= 0.00   Bsol= 0.00   scale= 0.906    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.262886                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1022 -  4.6595 0.99   1431  161 0.3614 0.3686      6.5229      6.5417|
|  2:  4.6595 -  3.7165 0.99   1388  149 0.3913 0.3615        6.77      6.7719|
|  3:  3.7165 -  3.2521 0.99   1346  152 0.4377 0.4357      6.6414      6.6901|
|  4:  3.2521 -  2.9572 0.99   1352  154 0.4345 0.4502       6.489      6.4767|
|  5:  2.9572 -  2.7466 0.99   1331  147 0.4780 0.4652      6.3435      6.3112|
|  6:  2.7466 -  2.5855 0.99   1331  149 0.4960 0.5103       6.259      6.2742|
|  7:  2.5855 -  2.4566 0.99   1335  140 0.5031 0.4672      6.2277      6.1617|
|  8:  2.4566 -  2.3501 0.98   1308  154 0.5001 0.4945      6.1435      6.1551|
|  9:  2.3501 -  2.2599 0.98   1316  148 0.5017 0.4703      6.1222      6.0798|
| 10:  2.2599 -  2.1821 0.98   1299  147 0.5141 0.5552      6.0657      6.0956|
| 11:  2.1821 -  2.1141 1.00   1335  141 0.5042 0.5581      6.0374       6.046|
| 12:  2.1141 -  2.0538 0.97   1284  142 0.5087 0.5705       5.944      5.9847|
| 13:  2.0538 -  1.9999 0.86   1144  138 0.5251 0.5274      5.8732      5.8263|
| 14:  1.9999 -  1.9512 0.32    430   37 0.5344 0.4846      5.8153         5.8|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1022 -  4.6595  1431   161  0.72  32.15   0.83     0.77      62549.56|
|  2:  4.6595 -  3.7165  1388   149  0.72  33.25   0.92     0.84      95947.49|
|  3:  3.7165 -  3.2521  1346   152  0.61  42.91   0.92     0.81     106962.38|
|  4:  3.2521 -  2.9572  1352   154  0.52  50.10   0.94     0.73      99453.93|
|  5:  2.9572 -  2.7466  1331   147  0.43  57.48   0.89     0.61      80212.22|
|  6:  2.7466 -  2.5855  1331   149  0.41  58.90   0.90     0.58      68619.58|
|  7:  2.5855 -  2.4566  1335   140  0.41  59.35   0.92     0.56      61112.24|
|  8:  2.4566 -  2.3501  1308   154  0.41  59.40   0.91     0.60      55023.58|
|  9:  2.3501 -  2.2599  1316   148  0.37  61.95   0.95     0.55      52591.16|
| 10:  2.2599 -  2.1821  1299   147  0.31  66.83   0.93     0.46      51654.65|
| 11:  2.1821 -  2.1141  1335   141  0.24  71.95   0.98     0.37      52204.04|
| 12:  2.1141 -  2.0538  1284   142  0.23  72.92   0.95     0.37      46850.64|
| 13:  2.0538 -  1.9999  1144   138  0.25  71.74   0.94     0.41      40510.95|
| 14:  1.9999 -  1.9512   430    37  0.27  69.56   0.92     0.43      33604.42|
|alpha:            min =        0.37 max =            0.84 mean =         0.59|
|beta:             min =    33604.42 max =       106962.38 mean =     66915.47|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           90.00 mean =        56.69|
|phase err.(test): min =        0.00 max =           89.85 mean =        56.88|
|-----------------------------------------------------------------------------|

============================== 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 = 15.563461             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.935   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.534547              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.856   (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 |  1.567 -  1.900:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.900 -  2.234:       13 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.234 -  2.567:       46 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.567 -  2.900:     1379 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.900 -  3.234:     1912 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.234 -  3.567:     2604 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.567 -  3.900:     4740 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.900 -  4.233:     4565 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.233 -  4.567:     6084 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.567 -  4.900:     7219 |
|-----------------------------------------------------------------------------|
|-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 |        0.179 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.567 |       0.448 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.708)------------------------------------------|
|    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: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4577   r_free= 0.4608   ksol= 0.00   Bsol= 0.00   scale= 0.906    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.262886                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4494   r_free= 0.4527   ksol= 0.30   Bsol= 20.00   scale= 0.941   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.45,-1.42,2.05,-0.00,0.00,0.00); trace/3= 0.36                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.260366                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.856012             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.253   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.112715              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.538   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4494      final r-factor (work) = 0.2977          |
| start r-factor (free) = 0.4527      final r-factor (free) = 0.3353          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.2571 = 11.86 * 0.50 * 6.2546 + 1.00 * 0.1795                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.3216 = 11.86 * 0.50 * 6.1050 + 1.00 * 0.1313                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2977      final r-factor (work) = 0.2702          |
| start r-factor (free) = 0.3353      final r-factor (free) = 0.3429          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7992 = 1.11 * 1.00 * 6.1050 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5887 = 1.11 * 1.00 * 5.9060 + 1.00 * 0.0171                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.708)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.28   18.44    None  None   None       |
|    all(noH): 2823   0      0.00    76.28   18.44    None  None   None       |
|    Sol.    : 438    0      0.00    76.28   42.22    None  None   None       |
|    Mac.    : 2385   0      0.00    73.72   14.07    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.628:  643   |   5:    38.140 -  45.769:  117        |
|      1:     7.628 -  15.256:  971   |   6:    45.769 -  53.397:   97        |
|      2:    15.256 -  22.884:  474   |   7:    53.397 -  61.025:   70        |
|      3:    22.884 -  30.512:  221   |   8:    61.025 -  68.653:   49        |
|      4:    30.512 -  38.140:  165   |   9:    68.653 -  76.281:   16        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2702 r_free = 0.3429             target_work(ml) = 5.915         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2698 r_free = 0.3431             target_work(ml) = 5.914         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2698   r_free= 0.3431   ksol= 0.30   Bsol= 20.00   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.45,-1.42,2.05,-0.00,0.00,0.00); trace/3= 0.36                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.913828                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2681   r_free= 0.3425   ksol= 0.34   Bsol= 51.10   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.62,-1.79,0.19,-0.00,0.00,0.00); trace/3= -0.74                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.909336                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.481183              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.287   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.389692              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.153  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2681      final r-factor (work) = 0.2015          |
| start r-factor (free) = 0.3425      final r-factor (free) = 0.2638          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.3646 = 4.48 * 0.50 * 5.9062 + 1.00 * 0.1313                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.0880 = 4.48 * 0.50 * 5.8133 + 1.00 * 0.0628                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2015      final r-factor (work) = 0.1874          |
| start r-factor (free) = 0.2638      final r-factor (free) = 0.2476          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2824 = 0.39 * 1.00 * 5.8133 + 1.00 * 0.0170                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2169 = 0.39 * 1.00 * 5.6410 + 1.00 * 0.0186                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.708)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.03   17.82    None  None   None       |
|    all(noH): 2823   0      0.00    77.03   17.82    None  None   None       |
|    Sol.    : 438    0      3.79    77.03   41.84    None  None   None       |
|    Mac.    : 2385   0      0.00    75.53   13.40    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 -   7.703:  584   |   5:    38.514 -  46.216:  120        |
|      1:     7.703 -  15.405: 1201   |   6:    46.216 -  53.919:   84        |
|      2:    15.405 -  23.108:  405   |   7:    53.919 -  61.622:   75        |
|      3:    23.108 -  30.811:  167   |   8:    61.622 -  69.324:   39        |
|      4:    30.811 -  38.514:  135   |   9:    69.324 -  77.027:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1874 r_free = 0.2476             target_work(ml) = 5.610         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1872 r_free = 0.2476             target_work(ml) = 5.609         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1872   r_free= 0.2476   ksol= 0.34   Bsol= 51.10   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.62,-1.79,0.19,-0.00,0.00,0.00); trace/3= -0.74                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.609344                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1870   r_free= 0.2469   ksol= 0.33   Bsol= 48.00   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.27,-2.20,-0.87,-0.00,-0.00,-0.00); trace/3= -1.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.606107                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.745894              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.970  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.342677              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.406   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1870      final r-factor (work) = 0.1517          |
| start r-factor (free) = 0.2469      final r-factor (free) = 0.1985          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8080 = 2.75 * 0.50 * 5.6413 + 1.00 * 0.0628                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6363 = 2.75 * 0.50 * 5.5231 + 1.00 * 0.0533                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1517      final r-factor (work) = 0.1413          |
| start r-factor (free) = 0.1985      final r-factor (free) = 0.1884          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9080 = 0.34 * 1.00 * 5.5231 + 1.00 * 0.0154                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8510 = 0.34 * 1.00 * 5.3748 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.708)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.04    82.59   17.53    None  None   None       |
|    all(noH): 2823   0      1.04    82.59   17.53    None  None   None       |
|    Sol.    : 438    0      5.99    78.91   42.33    None  None   None       |
|    Mac.    : 2385   0      1.04    82.59   12.98    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:     1.043 -   9.198:  842   |   5:    41.817 -  49.972:  101        |
|      1:     9.198 -  17.353: 1183   |   6:    49.972 -  58.127:   86        |
|      2:    17.353 -  25.508:  280   |   7:    58.127 -  66.282:   55        |
|      3:    25.508 -  33.663:  130   |   8:    66.282 -  74.437:   22        |
|      4:    33.663 -  41.817:  111   |   9:    74.437 -  82.592:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1413 r_free = 0.1884             target_work(ml) = 5.343         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1412 r_free = 0.1882             target_work(ml) = 5.342         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1412   r_free= 0.1882   ksol= 0.33   Bsol= 48.00   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.27,-2.20,-0.87,-0.00,-0.00,-0.00); trace/3= -1.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.342052                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1415   r_free= 0.1884   ksol= 0.33   Bsol= 48.75   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.81,-2.52,-1.61,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.343373                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.304629              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.875  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.295602              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.520  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1415      final r-factor (work) = 0.1198          |
| start r-factor (free) = 0.1884      final r-factor (free) = 0.1666          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6277 = 4.30 * 0.50 * 5.3777 + 1.00 * 0.0533                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.4287 = 4.30 * 0.50 * 5.2752 + 1.00 * 0.0748                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1198      final r-factor (work) = 0.1160          |
| start r-factor (free) = 0.1666      final r-factor (free) = 0.1624          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5685 = 0.30 * 1.00 * 5.2752 + 1.00 * 0.0091                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5431 = 0.30 * 1.00 * 5.1917 + 1.00 * 0.0084                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.708)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.65    88.35   17.20    None  None   None       |
|    all(noH): 2823   0      1.65    88.35   17.20    None  None   None       |
|    Sol.    : 438    0      6.49    83.06   40.90    None  None   None       |
|    Mac.    : 2385   0      1.65    88.35   12.84    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.650 -  10.321: 1120   |   5:    45.002 -  53.672:  101        |
|      1:    10.321 -  18.991: 1023   |   6:    53.672 -  62.342:   64        |
|      2:    18.991 -  27.661:  230   |   7:    62.342 -  71.013:   27        |
|      3:    27.661 -  36.331:  120   |   8:    71.013 -  79.683:   19        |
|      4:    36.331 -  45.002:  113   |   9:    79.683 -  88.353:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1160 r_free = 0.1624             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1159 r_free = 0.1620             target_work(ml) = 5.173         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1159   r_free= 0.1620   ksol= 0.33   Bsol= 48.75   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.81,-2.52,-1.61,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.173243                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1163   r_free= 0.1617   ksol= 0.32   Bsol= 46.74   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-2.57,-1.87,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.174745                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.504184              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.033  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.093741              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 155.872  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1163      final r-factor (work) = 0.1106          |
| start r-factor (free) = 0.1617      final r-factor (free) = 0.1581          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1721 = 3.50 * 0.50 * 5.1923 + 1.00 * 0.0748                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1078 = 3.50 * 0.50 * 5.1563 + 1.00 * 0.0734                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1106      final r-factor (work) = 0.1125          |
| start r-factor (free) = 0.1581      final r-factor (free) = 0.1566          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.4917 = 0.09 * 1.00 * 5.1563 + 1.00 * 0.0084                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.4890 = 0.09 * 1.00 * 5.1524 + 1.00 * 0.0060                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.708)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.87    81.76   16.30    None  None   None       |
|    all(noH): 2823   0      2.87    81.76   16.30    None  None   None       |
|    Sol.    : 438    0      6.43    81.76   36.40    None  None   None       |
|    Mac.    : 2385   0      2.87    80.77   12.61    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:     2.873 -  10.762: 1198   |   5:    42.318 -  50.207:  101        |
|      1:    10.762 -  18.651:  966   |   6:    50.207 -  58.096:   37        |
|      2:    18.651 -  26.540:  221   |   7:    58.096 -  65.984:   22        |
|      3:    26.540 -  34.429:  127   |   8:    65.984 -  73.873:    8        |
|      4:    34.429 -  42.318:  139   |   9:    73.873 -  81.762:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1125 r_free = 0.1566             target_work(ml) = 5.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1123 r_free = 0.1562             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1123   r_free= 0.1562   ksol= 0.32   Bsol= 46.74   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-2.57,-1.87,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.145537                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1022 -  4.6595 0.99   1431  161 0.0991 0.1357      5.3946      5.6174|
|  2:  4.6595 -  3.7165 0.99   1388  149 0.0885 0.1136      5.4719      5.6502|
|  3:  3.7165 -  3.2521 0.99   1346  152 0.1091 0.1603      5.4816      5.8556|
|  4:  3.2521 -  2.9572 0.99   1352  154 0.1260 0.1581      5.4624      5.5808|
|  5:  2.9572 -  2.7466 0.99   1331  147 0.1317 0.1673      5.3108      5.4914|
|  6:  2.7466 -  2.5855 0.99   1331  149 0.1219 0.1675      5.1876       5.397|
|  7:  2.5855 -  2.4566 0.99   1335  140 0.1251 0.1798      5.1498      5.4363|
|  8:  2.4566 -  2.3501 0.98   1308  154 0.1137 0.1583      5.0291       5.225|
|  9:  2.3501 -  2.2599 0.98   1316  148 0.1155 0.1796      4.9997      5.2763|
| 10:  2.2599 -  2.1821 0.98   1299  147 0.1122 0.1676      4.9353      5.2012|
| 11:  2.1821 -  2.1141 1.00   1335  141 0.1121 0.1782      4.9183      5.2712|
| 12:  2.1141 -  2.0538 0.97   1284  142 0.1100 0.1636      4.8585      5.0563|
| 13:  2.0538 -  1.9999 0.86   1144  138 0.1171 0.1646      4.7588      4.9972|
| 14:  1.9999 -  1.9512 0.32    430   37 0.1027 0.1351      4.5872      4.8228|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1022 -  4.6595  1431   161  0.94   9.20   0.98     0.96       7386.60|
|  2:  4.6595 -  3.7165  1388   149  0.95   8.36   1.02     1.01       9617.88|
|  3:  3.7165 -  3.2521  1346   152  0.93  11.93   1.02     1.02      10685.74|
|  4:  3.2521 -  2.9572  1352   154  0.91  14.37   1.00     0.97      10392.42|
|  5:  2.9572 -  2.7466  1331   147  0.90  15.34   0.99     0.96       7769.56|
|  6:  2.7466 -  2.5855  1331   149  0.90  15.52   0.98     0.97       6596.47|
|  7:  2.5855 -  2.4566  1335   140  0.91  15.13   0.99     0.97       5859.95|
|  8:  2.4566 -  2.3501  1308   154  0.91  14.88   0.99     0.96       4889.95|
|  9:  2.3501 -  2.2599  1316   148  0.91  15.36   1.01     0.97       4683.71|
| 10:  2.2599 -  2.1821  1299   147  0.91  14.93   1.00     0.98       4152.60|
| 11:  2.1821 -  2.1141  1335   141  0.90  16.00   1.00     0.96       4191.94|
| 12:  2.1141 -  2.0538  1284   142  0.91  15.77   1.01     1.02       3918.02|
| 13:  2.0538 -  1.9999  1144   138  0.91  15.09   1.00     0.99       2978.40|
| 14:  1.9999 -  1.9512   430    37  0.92  13.78   1.00     0.97       2069.35|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2069.35 max =        10685.74 mean =      6362.78|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.90 mean =        13.92|
|phase err.(test): min =        0.00 max =           88.95 mean =        13.45|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1123   r_free= 0.1561   ksol= 0.33   Bsol= 46.63   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.87,-2.47,-1.81,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.145654                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1123   r_free= 0.1561   ksol= 0.33   Bsol= 46.63   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.87,-2.47,-1.81,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.145654                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1022 -  4.6595 0.99   1431  161 0.0991 0.1354      5.3965      5.6165|
|  2:  4.6595 -  3.7165 0.99   1388  149 0.0883 0.1135      5.4709      5.6494|
|  3:  3.7165 -  3.2521 0.99   1346  152 0.1090 0.1602      5.4809      5.8551|
|  4:  3.2521 -  2.9572 0.99   1352  154 0.1260 0.1581      5.4623      5.5809|
|  5:  2.9572 -  2.7466 0.99   1331  147 0.1317 0.1673       5.311      5.4917|
|  6:  2.7466 -  2.5855 0.99   1331  149 0.1220 0.1676      5.1879      5.3975|
|  7:  2.5855 -  2.4566 0.99   1335  140 0.1251 0.1798      5.1501      5.4364|
|  8:  2.4566 -  2.3501 0.98   1308  154 0.1138 0.1584      5.0293      5.2252|
|  9:  2.3501 -  2.2599 0.98   1316  148 0.1155 0.1796      4.9998      5.2763|
| 10:  2.2599 -  2.1821 0.98   1299  147 0.1123 0.1676      4.9353       5.201|
| 11:  2.1821 -  2.1141 1.00   1335  141 0.1121 0.1781      4.9183      5.2712|
| 12:  2.1141 -  2.0538 0.97   1284  142 0.1101 0.1636      4.8585      5.0563|
| 13:  2.0538 -  1.9999 0.86   1144  138 0.1171 0.1647      4.7589      4.9972|
| 14:  1.9999 -  1.9512 0.32    430   37 0.1028 0.1355      4.5879      4.8246|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1022 -  4.6595  1431   161  0.94   9.20   0.98     0.96       7414.04|
|  2:  4.6595 -  3.7165  1388   149  0.95   8.36   1.01     1.01       9617.16|
|  3:  3.7165 -  3.2521  1346   152  0.93  11.91   1.02     1.02      10667.76|
|  4:  3.2521 -  2.9572  1352   154  0.91  14.37   1.00     0.97      10389.81|
|  5:  2.9572 -  2.7466  1331   147  0.90  15.34   0.99     0.96       7774.04|
|  6:  2.7466 -  2.5855  1331   149  0.90  15.52   0.98     0.97       6600.19|
|  7:  2.5855 -  2.4566  1335   140  0.91  15.14   0.99     0.97       5864.41|
|  8:  2.4566 -  2.3501  1308   154  0.91  14.89   0.99     0.96       4892.81|
|  9:  2.3501 -  2.2599  1316   148  0.91  15.36   1.01     0.97       4684.47|
| 10:  2.2599 -  2.1821  1299   147  0.91  14.93   1.00     0.98       4152.89|
| 11:  2.1821 -  2.1141  1335   141  0.90  16.00   1.00     0.96       4190.95|
| 12:  2.1141 -  2.0538  1284   142  0.91  15.77   1.01     1.02       3917.17|
| 13:  2.0538 -  1.9999  1144   138  0.91  15.10   1.00     0.99       2980.37|
| 14:  1.9999 -  1.9512   430    37  0.92  13.79   0.99     0.97       2072.96|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2072.96 max =        10667.76 mean =      6364.70|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.88 mean =        13.92|
|phase err.(test): min =        0.00 max =           88.95 mean =        13.46|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.708)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.77    81.66   16.20    None  None   None       |
|    all(noH): 2823   0      2.77    81.66   16.20    None  None   None       |
|    Sol.    : 438    0      6.32    81.66   36.29    None  None   None       |
|    Mac.    : 2385   0      2.77    80.66   12.50    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:     2.768 -  10.657: 1198   |   5:    42.213 -  50.102:  101        |
|      1:    10.657 -  18.546:  966   |   6:    50.102 -  57.991:   37        |
|      2:    18.546 -  26.435:  221   |   7:    57.991 -  65.880:   22        |
|      3:    26.435 -  34.324:  127   |   8:    65.880 -  73.769:    8        |
|      4:    34.324 -  42.213:  139   |   9:    73.769 -  81.657:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 315         
Filter by distance & map next to the model:
   mapped sites are within: 0.488 - 5.648
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 312 from: 315
   mapped sites are within: 0.707 - 5.648

peak=    5.589 closest distance to " NH2 ARG A  56 " =    2.142
peak=    5.319 closest distance to " CB  GLN A 223 " =    1.501
peak=    5.236 closest distance to " NE2 GLN A  11 " =    1.186
peak=    5.137 closest distance to " CB  SER A  63 " =    1.287
peak=    5.006 closest distance to " O   HOH Z 232 " =    2.277
peak=    4.957 closest distance to " O   HOH Z 221 " =    1.834
peak=    4.875 closest distance to " CB  GLU A 152 " =    1.194
peak=    4.866 closest distance to " O   HOH Z 260 " =    1.411
peak=    4.813 closest distance to " O   HOH Z 126 " =    1.880
peak=    4.739 closest distance to " CB  ASN A 148 " =    1.448
peak=    4.727 closest distance to " ND2 ASN A 187 " =    1.670
peak=    4.708 closest distance to " O   HOH Z 108 " =    1.912
peak=    4.678 closest distance to " O   HOH Z 214 " =    1.335
peak=    4.662 closest distance to " CG  PRO A  54 " =    1.138
peak=    4.617 closest distance to " O   HOH Z 236 " =    1.994
peak=    4.533 closest distance to " CB  SER A   3 " =    1.533
peak=    4.483 closest distance to " O   HOH Z 368 " =    1.922
peak=    4.444 closest distance to " C   PRO A 198 " =    1.522
peak=    4.441 closest distance to " O   HOH Z  21 " =    1.733
peak=    4.429 closest distance to " O   HOH Z 126 " =    1.531
peak=    4.427 closest distance to " O   HOH Z 193 " =    1.948
peak=    4.409 closest distance to " O   HOH Z 134 " =    1.689
peak=    4.408 closest distance to " OD1 ASN A  69 " =    2.553
peak=    4.371 closest distance to " O   HOH Z 124 " =    1.449
peak=    4.335 closest distance to " CB  GLN A 183 " =    1.122
peak=    4.330 closest distance to " OD2 ASP A 286 " =    2.817
peak=    4.310 closest distance to " CB  ARG A 275 " =    0.923
peak=    4.301 closest distance to " O   HOH Z 278 " =    1.116
peak=    4.258 closest distance to " O   HOH Z 132 " =    1.204
peak=    4.257 closest distance to " O   HOH Z 193 " =    1.722
peak=    4.255 closest distance to " O   HOH Z 369 " =    1.899
peak=    4.215 closest distance to " O   HOH Z 423 " =    1.683
peak=    4.198 closest distance to " O   HOH Z  48 " =    1.612
peak=    4.197 closest distance to " CB  LEU A 228 " =    1.025
peak=    4.188 closest distance to " O   HOH Z 425 " =    1.410
peak=    4.163 closest distance to " O   HOH Z 144 " =    1.618
peak=    4.138 closest distance to " CB  PRO A  54 " =    0.801
peak=    4.121 closest distance to " O   HOH Z  15 " =    2.181
peak=    4.120 closest distance to " O   HOH Z 303 " =    2.293
peak=    4.120 closest distance to " O   HOH Z 298 " =    1.846
peak=    4.113 closest distance to " CA  ALA A  21 " =    1.164
peak=    4.100 closest distance to " O   HOH Z 261 " =    1.779
peak=    4.092 closest distance to " O   HOH Z  10 " =    1.893
peak=    4.088 closest distance to " O   HOH Z 126 " =    1.811
peak=    4.047 closest distance to " O   HOH Z 234 " =    3.776
peak=    4.043 closest distance to " O   HOH Z  78 " =    2.313
peak=    4.040 closest distance to " NH1AARG A 145 " =    1.080
peak=    4.039 closest distance to " CB  SER A 216 " =    0.786
peak=    4.038 closest distance to " CA  THR A 264 " =    0.898
peak=    3.990 closest distance to " O   HOH Z 132 " =    2.002
peak=    3.985 closest distance to " O   HOH Z 203 " =    1.857
peak=    3.976 closest distance to " O   HOH Z 313 " =    1.796
peak=    3.972 closest distance to " CA  GLY A 241 " =    3.678
peak=    3.969 closest distance to " CA  ASN A 215 " =    1.237
peak=    3.955 closest distance to " O   HOH Z 128 " =    2.007
peak=    3.955 closest distance to " CB  GLU A 128 " =    0.982
peak=    3.950 closest distance to " O   HOH Z  78 " =    1.817
peak=    3.950 closest distance to " O   HOH Z  68 " =    1.683
peak=    3.936 closest distance to " O   SER A  87 " =    2.250
peak=    3.898 closest distance to " O   HOH Z 281 " =    4.403
peak=    3.896 closest distance to " O   HOH Z  61 " =    1.604
peak=    3.895 closest distance to " CB  TYR A 169 " =    0.765
peak=    3.889 closest distance to " CB  ARG A 139 " =    1.005
peak=    3.882 closest distance to " O   HOH Z 135 " =    1.731
peak=    3.871 closest distance to " CB  ARG A  79 " =    1.321
peak=    3.867 closest distance to " O   HOH Z 295 " =    1.544
peak=    3.857 closest distance to " O   HOH Z  58 " =    1.938
peak=    3.855 closest distance to " O   HOH Z 189 " =    2.243
peak=    3.848 closest distance to " CD BLYS A 290 " =    1.195
peak=    3.819 closest distance to " O   HOH Z 427 " =    2.864
peak=    3.798 closest distance to " CB  VAL A 265 " =    1.266
peak=    3.794 closest distance to " O   HOH Z 371 " =    2.795
peak=    3.789 closest distance to " NH2 ARG A 156 " =    1.305
peak=    3.789 closest distance to " O   HOH Z 389 " =    1.974
peak=    3.785 closest distance to " CD  ARG A  66 " =    2.207
peak=    3.784 closest distance to " O   HOH Z  88 " =    3.464
peak=    3.776 closest distance to " CG  PRO A 198 " =    1.434
peak=    3.771 closest distance to " CA  SER A  87 " =    0.898
peak=    3.768 closest distance to " O   HOH Z   6 " =    2.070
peak=    3.765 closest distance to " O   HOH Z 217 " =    3.160
peak=    3.745 closest distance to " O   HOH Z  40 " =    2.134
peak=    3.731 closest distance to " O   HOH Z 147 " =    1.684
peak=    3.727 closest distance to " NE AARG A 275 " =    1.519
peak=    3.723 closest distance to " O   HOH Z   3 " =    1.885
peak=    3.717 closest distance to " O   HOH Z 344 " =    3.005
peak=    3.717 closest distance to " O   HOH Z 193 " =    2.074
peak=    3.708 closest distance to " O   HOH Z 437 " =    1.948
peak=    3.706 closest distance to " ND1 HIS A  86 " =    1.639
peak=    3.700 closest distance to " CA  TYR A  30 " =    0.994
peak=    3.699 closest distance to " O   HOH Z 419 " =    1.900
peak=    3.698 closest distance to " O   HOH Z  85 " =    2.149
peak=    3.696 closest distance to " CB  TRP A 266 " =    0.947
peak=    3.688 closest distance to " OD1BASN A 224 " =    2.221
peak=    3.672 closest distance to " O   HOH Z 334 " =    1.481
peak=    3.670 closest distance to " N   PHE A 130 " =    1.260
peak=    3.667 closest distance to " O   HOH Z  66 " =    2.180
peak=    3.666 closest distance to " CD  LYS A 166 " =    1.306
peak=    3.665 closest distance to " O   HOH Z  64 " =    2.339
peak=    3.665 closest distance to " CB  VAL A 202 " =    1.647
peak=    3.653 closest distance to " O   HOH Z 272 " =    1.948
peak=    3.648 closest distance to " CB  ASN A 187 " =    0.941
peak=    3.644 closest distance to " CA  THR A 221 " =    0.934
peak=    3.638 closest distance to " CG  PRO A 243 " =    1.073
peak=    3.638 closest distance to " NH2AARG A 190 " =    1.501
peak=    3.637 closest distance to " O   HOH Z 346 " =    1.632
peak=    3.634 closest distance to " CB  GLU A 152 " =    1.437
peak=    3.630 closest distance to " O   HOH Z 227 " =    2.083
peak=    3.627 closest distance to " CG  LEU A 167 " =    1.248
peak=    3.625 closest distance to " CG  PRO A  90 " =    1.085
peak=    3.619 closest distance to " O   ALA A   1 " =    1.619
peak=    3.599 closest distance to " O   HOH Z 175 " =    3.559
peak=    3.597 closest distance to " O   HOH Z 244 " =    1.772
peak=    3.596 closest distance to " O   HOH Z 182 " =    1.399
peak=    3.595 closest distance to " OD1 ASP A 231 " =    1.795
peak=    3.591 closest distance to " O   HOH Z 133 " =    1.719
peak=    3.578 closest distance to " O   MET A 105 " =    1.661
peak=    3.575 closest distance to " O   HOH Z  93 " =    2.532
peak=    3.573 closest distance to " CG1 ILE A  33 " =    1.246
peak=    3.570 closest distance to " O   HOH Z 403 " =    1.412
peak=    3.570 closest distance to " O   HOH Z  44 " =    1.738
peak=    3.566 closest distance to " O   HOH Z 334 " =    2.995
peak=    3.564 closest distance to " CA  ALA A  51 " =    1.006
peak=    3.558 closest distance to " O   ASN A 209 " =    1.309
peak=    3.558 closest distance to " O   HOH Z 410 " =    1.740
peak=    3.536 closest distance to " OD1 ASN A 217 " =    1.654
peak=    3.535 closest distance to " O   HOH Z 248 " =    1.831
peak=    3.534 closest distance to " CB  ILE A 234 " =    0.938
peak=    3.522 closest distance to " O   HOH Z 345 " =    1.798
peak=    3.522 closest distance to " CD2 LEU A 255 " =    1.397
peak=    3.521 closest distance to " O   HOH Z 188 " =    2.104
peak=    3.521 closest distance to " O   HOH Z  73 " =    1.637
peak=    3.517 closest distance to " O   HOH Z 213 " =    1.777
peak=    3.506 closest distance to " OG ASER A 258 " =    3.134
peak=    3.504 closest distance to " O   HOH Z  61 " =    1.690
peak=    3.503 closest distance to " O   HOH Z  20 " =    1.927
peak=    3.500 closest distance to " O   HOH Z 227 " =    1.765
peak=    3.498 closest distance to " O   HOH Z  59 " =    2.093
peak=    3.497 closest distance to " CG2 THR A 221 " =    1.057
peak=    3.493 closest distance to " N   ARG A 156 " =    1.312
peak=    3.492 closest distance to " O   HOH Z  20 " =    2.422
peak=    3.490 closest distance to " O   HOH Z 154 " =    2.020
peak=    3.490 closest distance to " CG2 VAL A 257 " =    0.969
peak=    3.486 closest distance to " CB  TRP A 179 " =    1.429
peak=    3.479 closest distance to " CE  LYS A  76 " =    0.844
peak=    3.478 closest distance to " CG BARG A 275 " =    1.445
peak=    3.477 closest distance to " CG  GLU A 277 " =    2.332
peak=    3.476 closest distance to " O   HOH Z 292 " =    1.817
peak=    3.471 closest distance to " O   HOH Z   1 " =    1.717
peak=    3.471 closest distance to " CG  GLN A  55 " =    1.915
peak=    3.469 closest distance to " CA  ALA A 154 " =    0.949
peak=    3.465 closest distance to " CB  ASN A  39 " =    0.811
peak=    3.459 closest distance to " O   HOH Z 409 " =    2.437
peak=    3.457 closest distance to " CA  MET A  40 " =    1.084
peak=    3.454 closest distance to " NH2 ARG A 219 " =    1.840
peak=    3.453 closest distance to " O   HOH Z 151 " =    2.400
peak=    3.450 closest distance to " O   HOH Z 258 " =    1.823
peak=    3.448 closest distance to " CA  TYR A 186 " =    1.488
peak=    3.443 closest distance to " O   HOH Z 280 " =    1.777
peak=    3.440 closest distance to " CD  ARG A 159 " =    0.707
peak=    3.433 closest distance to " N   ASN A  39 " =    1.339
peak=    3.430 closest distance to " O   HOH Z 388 " =    2.021
peak=    3.430 closest distance to " O   HOH Z 380 " =    1.966
peak=    3.428 closest distance to " CA  VAL A  41 " =    0.975
peak=    3.422 closest distance to " O   HOH Z 139 " =    3.019
peak=    3.421 closest distance to " O   HOH Z 209 " =    2.519
peak=    3.420 closest distance to " O   HOH Z 332 " =    1.525
peak=    3.419 closest distance to " O   HOH Z 194 " =    2.077
peak=    3.419 closest distance to " O   HOH Z 359 " =    3.907
peak=    3.416 closest distance to " O   HOH Z 250 " =    1.483
peak=    3.416 closest distance to " CB  LEU A 143 " =    1.095
peak=    3.415 closest distance to " O   HOH Z  98 " =    1.773
peak=    3.414 closest distance to " O   HOH Z 374 " =    2.900
peak=    3.413 closest distance to " CD1 ILE A 263 " =    1.393
peak=    3.410 closest distance to " O   HOH Z 255 " =    1.549
peak=    3.409 closest distance to " CZ  PHE A 192 " =    0.880
peak=    3.409 closest distance to " CB  THR A 157 " =    1.072
peak=    3.407 closest distance to " O   HOH Z  43 " =    1.891
peak=    3.406 closest distance to " CG1BVAL A  72 " =    1.600
peak=    3.403 closest distance to " O   HOH Z 273 " =    2.834
peak=    3.395 closest distance to " O   HOH Z 186 " =    1.298
peak=    3.386 closest distance to " O   HOH Z  49 " =    2.250
peak=    3.382 closest distance to " O   GLY A 147 " =    1.352
peak=    3.382 closest distance to " O   HOH Z 353 " =    2.557
peak=    3.379 closest distance to " CB  ALA A 248 " =    0.945
peak=    3.378 closest distance to " CA  PRO A  54 " =    1.306
peak=    3.374 closest distance to " CG2 THR A 220 " =    1.068
peak=    3.371 closest distance to " O   HOH Z 128 " =    2.078
peak=    3.366 closest distance to " CB  MET A  47 " =    1.067
peak=    3.359 closest distance to " O   HOH Z   2 " =    1.553
peak=    3.354 closest distance to " O   HOH Z 394 " =    1.739
peak=    3.353 closest distance to " OE1 GLN A  11 " =    2.130
peak=    3.352 closest distance to " O   HOH Z 327 " =    1.689
peak=    3.352 closest distance to " O   HOH Z 291 " =    1.767
peak=    3.348 closest distance to " NH2AARG A 275 " =    3.674
peak=    3.345 closest distance to " O   HOH Z 183 " =    1.489
peak=    3.343 closest distance to " O   HOH Z 379 " =    1.851
peak=    3.338 closest distance to " O   HOH Z 153 " =    1.798
peak=    3.333 closest distance to " CG  PRO A 280 " =    0.733
peak=    3.332 closest distance to " O   HOH Z  54 " =    1.498
peak=    3.329 closest distance to " CD1 LEU A 300 " =    1.273
peak=    3.325 closest distance to " O   HOH Z  63 " =    2.311
peak=    3.324 closest distance to " O   HOH Z 163 " =    1.933
peak=    3.324 closest distance to " CB  GLU A 236 " =    1.049
peak=    3.323 closest distance to " O   ALA A 165 " =    1.280
peak=    3.315 closest distance to " O   HOH Z 180 " =    2.075
peak=    3.313 closest distance to " NE  ARG A  66 " =    3.737
peak=    3.312 closest distance to " CB  ASP A 171 " =    0.731
peak=    3.312 closest distance to " O   HOH Z 343 " =    2.664
peak=    3.310 closest distance to " O   HOH Z  44 " =    3.215
peak=    3.307 closest distance to " NH2BARG A 145 " =    2.040
peak=    3.305 closest distance to " CG  GLN A 144 " =    1.038
peak=    3.304 closest distance to " O   HOH Z 128 " =    1.509
peak=    3.304 closest distance to " O   HOH Z 116 " =    1.629
peak=    3.299 closest distance to " CB  ALA A  21 " =    1.737
peak=    3.297 closest distance to " CG  GLN A  88 " =    1.022
peak=    3.297 closest distance to " O   HOH Z 133 " =    2.283
peak=    3.294 closest distance to " O   HOH Z 156 " =    2.780
peak=    3.293 closest distance to " CD1 ILE A  33 " =    1.517
peak=    3.290 closest distance to " O   HOH Z 151 " =    1.899
peak=    3.288 closest distance to " CB  GLN A  88 " =    1.258
peak=    3.286 closest distance to " O   HOH Z 247 " =    1.355
peak=    3.285 closest distance to " O   HOH Z 158 " =    2.945
peak=    3.285 closest distance to " OE1 GLU A 277 " =    1.830
peak=    3.283 closest distance to " CG  GLN A  77 " =    1.787
peak=    3.282 closest distance to " CB  ALA A 291 " =    1.465
peak=    3.280 closest distance to " CA  ASP A 191 " =    0.743
peak=    3.277 closest distance to " O   HOH Z  97 " =    1.853
peak=    3.277 closest distance to " OG  SER A  22 " =    2.807
peak=    3.273 closest distance to " O   HOH Z 217 " =    1.450
peak=    3.272 closest distance to " NZ ALYS A 290 " =    1.067
peak=    3.271 closest distance to " O   HOH Z 112 " =    1.523
peak=    3.268 closest distance to " CG  MET A 185 " =    1.120
peak=    3.262 closest distance to " O   HOH Z 125 " =    2.266
peak=    3.259 closest distance to " CB  GLU A 277 " =    3.533
peak=    3.255 closest distance to " CB  ARG A 190 " =    1.502
peak=    3.255 closest distance to " O   HOH Z 352 " =    1.379
peak=    3.254 closest distance to " CZ AARG A 102 " =    1.962
peak=    3.250 closest distance to " O   HOH Z 106 " =    2.406
peak=    3.248 closest distance to " O   HOH Z 365 " =    5.545
peak=    3.248 closest distance to " CB  ILE A 120 " =    1.142
peak=    3.248 closest distance to " NH1 ARG A  56 " =    1.045
peak=    3.245 closest distance to " O   HOH Z 423 " =    2.501
peak=    3.241 closest distance to " CD BARG A 102 " =    1.203
peak=    3.241 closest distance to " O   GLN A 240 " =    2.319
peak=    3.240 closest distance to " CA  ILE A 234 " =    0.930
peak=    3.237 closest distance to " ND1 HIS A  81 " =    1.598
peak=    3.231 closest distance to " O   HOH Z 173 " =    2.011
peak=    3.230 closest distance to " O   HOH Z 175 " =    2.177
peak=    3.227 closest distance to " O   HOH Z 234 " =    1.740
peak=    3.223 closest distance to " CA  ALA A  43 " =    1.215
peak=    3.222 closest distance to " OG BSER A 164 " =    2.462
peak=    3.221 closest distance to " CB  ALA A  71 " =    1.383
peak=    3.219 closest distance to " O   HOH Z  64 " =    2.071
peak=    3.216 closest distance to " N   TYR A  15 " =    0.861
peak=    3.213 closest distance to " O   HOH Z 263 " =    1.661
peak=    3.210 closest distance to " CE BMET A  47 " =    1.261
peak=    3.209 closest distance to " NH2BARG A 190 " =    1.727
peak=    3.201 closest distance to " O   HOH Z 266 " =    1.484
peak=    3.200 closest distance to " O   TYR A 116 " =    1.353
peak=    3.200 closest distance to " CB  GLU A  46 " =    1.047
peak=    3.199 closest distance to " O   HOH Z 286 " =    2.141
peak=    3.196 closest distance to " O   HOH Z 392 " =    1.477
peak=    3.195 closest distance to " CB  ALA A  34 " =    1.051
peak=    3.194 closest distance to " O   HOH Z 207 " =    1.754
peak=    3.192 closest distance to " NE2 GLN A  73 " =    3.614
peak=    3.190 closest distance to " CD2 TRP A 179 " =    1.299
peak=    3.190 closest distance to " CB  ASN A 142 " =    0.861
peak=    3.188 closest distance to " CA  LEU A 282 " =    1.150
peak=    3.187 closest distance to " CD  LYS A 119 " =    1.429
peak=    3.185 closest distance to " CG  ARG A 159 " =    0.929
peak=    3.182 closest distance to " O   HOH Z 387 " =    2.771
peak=    3.179 closest distance to " CA  ALA A 233 " =    1.236
peak=    3.168 closest distance to " CA  ALA A 158 " =    1.104
peak=    3.168 closest distance to " CA  GLY A 267 " =    1.199
peak=    3.166 closest distance to " O   THR A 220 " =    1.436
peak=    3.164 closest distance to " O   HOH Z 329 " =    3.653
peak=    3.164 closest distance to " O   HOH Z 368 " =    3.715
peak=    3.163 closest distance to " O   HOH Z 115 " =    2.155
peak=    3.162 closest distance to " CB  MET A  40 " =    0.914
peak=    3.162 closest distance to " CD  ARG A  14 " =    1.302
peak=    3.155 closest distance to " O   HOH Z 287 " =    1.788
peak=    3.154 closest distance to " O   GLY A  57 " =    2.504
peak=    3.147 closest distance to " CG1 VAL A 153 " =    0.975
peak=    3.139 closest distance to " O   HOH Z 301 " =    1.846
peak=    3.138 closest distance to " CB  ALA A 291 " =    3.417
peak=    3.131 closest distance to " CA  LYS A 117 " =    1.193
peak=    3.125 closest distance to " O   HOH Z  59 " =    1.800
peak=    3.122 closest distance to " CD2 HIS A  81 " =    1.310
peak=    3.115 closest distance to " NE2 GLN A  58 " =    5.648
peak=    3.110 closest distance to " CB  ALA A 114 " =    1.244
peak=    3.106 closest distance to " O   HOH Z 271 " =    2.294
peak=    3.105 closest distance to " NZ  LYS A  76 " =    1.176
peak=    3.104 closest distance to " O   GLY A 302 " =    1.774
peak=    3.101 closest distance to " O   HOH Z 276 " =    1.256
peak=    3.101 closest distance to " O   HOH Z  50 " =    1.724
peak=    3.098 closest distance to " O   HOH Z 184 " =    1.989
peak=    3.098 closest distance to " NH1BARG A 145 " =    1.172
peak=    3.096 closest distance to " O   HOH Z 380 " =    1.671
peak=    3.089 closest distance to " CE2 TRP A 179 " =    1.738
peak=    3.083 closest distance to " CB  ARG A 138 " =    1.021
peak=    3.080 closest distance to " CB  TRP A 150 " =    1.475
peak=    3.078 closest distance to " OG  SER A  62 " =    3.037
peak=    3.074 closest distance to " O   HOH Z 128 " =    2.175
peak=    3.073 closest distance to " O   HOH Z 417 " =    3.655
peak=    3.065 closest distance to " CA  ALA A 299 " =    0.940
peak=    3.054 closest distance to " O   HOH Z   1 " =    1.746
peak=    3.051 closest distance to " CG  LYS A  76 " =    0.956
peak=    3.043 closest distance to " CH2 TRP A  92 " =    2.010
peak=    3.041 closest distance to " O   HOH Z  66 " =    2.059
peak=    3.038 closest distance to " NZ  LYS A 181 " =    0.721
peak=    3.028 closest distance to " O   HOH Z 427 " =    3.623
peak=    3.024 closest distance to " O   HOH Z 108 " =    1.597

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 196         
Filter by distance & map next to the model:
   mapped sites are within: 0.184 - 5.990
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 181 from: 196
   mapped sites are within: 0.725 - 5.990

peak=   -5.434 closest distance to " O   HOH Z 290 " =    0.885
peak=   -4.662 closest distance to " CB  PRO A 243 " =    2.507
peak=   -4.571 closest distance to " O   HOH Z 198 " =    2.511
peak=   -4.288 closest distance to " O   HOH Z 377 " =    1.835
peak=   -4.267 closest distance to " O   HOH Z  98 " =    1.771
peak=   -4.251 closest distance to " CD  ARG A  14 " =    3.198
peak=   -4.235 closest distance to " CG  LYS A 193 " =    2.396
peak=   -4.194 closest distance to " O   VAL A 153 " =    2.430
peak=   -4.072 closest distance to " N   GLN A  58 " =    1.691
peak=   -4.047 closest distance to " C   ASN A 285 " =    2.450
peak=   -3.983 closest distance to " CG  GLN A 223 " =    1.695
peak=   -3.933 closest distance to " O   PRO A 198 " =    1.295
peak=   -3.911 closest distance to " C   ALA A 158 " =    1.348
peak=   -3.904 closest distance to " SG  CYS A 254 " =    3.101
peak=   -3.895 closest distance to " O   VAL A  67 " =    2.647
peak=   -3.893 closest distance to " N   ALA A  43 " =    2.317
peak=   -3.873 closest distance to " CD1 LEU A 228 " =    2.421
peak=   -3.864 closest distance to " O   HOH Z 266 " =    4.208
peak=   -3.861 closest distance to " N   HIS A 115 " =    2.083
peak=   -3.857 closest distance to " CB  CYS A 201 " =    2.632
peak=   -3.842 closest distance to " CG  ASP A 231 " =    0.738
peak=   -3.841 closest distance to " O   HOH Z 388 " =    1.904
peak=   -3.823 closest distance to " CD  GLN A 223 " =    1.116
peak=   -3.818 closest distance to " CH2 TRP A 179 " =    1.214
peak=   -3.810 closest distance to " O   GLY A 196 " =    1.162
peak=   -3.783 closest distance to " O   HOH Z 231 " =    0.908
peak=   -3.782 closest distance to " O   HOH Z  13 " =    1.114
peak=   -3.780 closest distance to " O   HOH Z  52 " =    1.188
peak=   -3.761 closest distance to " CB  CYS A 254 " =    2.345
peak=   -3.749 closest distance to " CG1 VAL A 250 " =    2.727
peak=   -3.748 closest distance to " CE2 TYR A  30 " =    2.949
peak=   -3.729 closest distance to " O   HOH Z  68 " =    2.515
peak=   -3.715 closest distance to " CD  ARG A 156 " =    1.920
peak=   -3.703 closest distance to " CG  MET A 105 " =    0.972
peak=   -3.701 closest distance to " O   HOH Z 395 " =    5.162
peak=   -3.692 closest distance to " O   HOH Z  51 " =    1.081
peak=   -3.688 closest distance to " CG  GLU A 152 " =    0.808
peak=   -3.688 closest distance to " O   ILE A 109 " =    2.629
peak=   -3.679 closest distance to " CD  GLN A  88 " =    0.787
peak=   -3.662 closest distance to " OG ASER A 216 " =    1.078
peak=   -3.650 closest distance to " ND2 ASN A  45 " =    0.983
peak=   -3.640 closest distance to " CE  LYS A  76 " =    2.801
peak=   -3.637 closest distance to " O   HOH Z 407 " =    3.224
peak=   -3.633 closest distance to " O   HOH Z 423 " =    0.996
peak=   -3.608 closest distance to " O   HOH Z  98 " =    2.297
peak=   -3.601 closest distance to " O   HOH Z 148 " =    1.907
peak=   -3.598 closest distance to " O   TRP A  70 " =    1.519
peak=   -3.569 closest distance to " O   GLY A 211 " =    1.405
peak=   -3.563 closest distance to " CD2 LEU A 300 " =    2.982
peak=   -3.556 closest distance to " OG BSER A 134 " =    1.289
peak=   -3.532 closest distance to " O   HOH Z  88 " =    2.166
peak=   -3.532 closest distance to " O   HOH Z 389 " =    1.900
peak=   -3.526 closest distance to " O   HOH Z 186 " =    0.725
peak=   -3.523 closest distance to " CB  ASP A 132 " =    2.269
peak=   -3.520 closest distance to " CB  TRP A  85 " =    2.568
peak=   -3.514 closest distance to " O   HOH Z  11 " =    1.881
peak=   -3.513 closest distance to " CE  MET A  93 " =    1.082
peak=   -3.508 closest distance to " O   HOH Z 111 " =    2.188
peak=   -3.507 closest distance to " CB  PHE A 283 " =    2.859
peak=   -3.505 closest distance to " CD1 PHE A  59 " =    1.845
peak=   -3.503 closest distance to " O   HOH Z  71 " =    0.989
peak=   -3.502 closest distance to " O   PRO A 198 " =    1.200
peak=   -3.494 closest distance to " CA  GLY A 241 " =    2.256
peak=   -3.494 closest distance to " O   HOH Z 185 " =    2.052
peak=   -3.490 closest distance to " OXT GLY A 302 " =    2.807
peak=   -3.488 closest distance to " O   HOH Z  97 " =    1.456
peak=   -3.480 closest distance to " O   HOH Z 426 " =    2.321
peak=   -3.471 closest distance to " CZ  PHE A  59 " =    1.557
peak=   -3.465 closest distance to " O   HOH Z  15 " =    1.835
peak=   -3.463 closest distance to " CD2 LEU A 237 " =    2.694
peak=   -3.462 closest distance to " CG  PRO A 163 " =    2.422
peak=   -3.462 closest distance to " NH2 ARG A  79 " =    1.725
peak=   -3.460 closest distance to " OG  SER A  97 " =    2.184
peak=   -3.446 closest distance to " C   HIS A 108 " =    1.195
peak=   -3.444 closest distance to " CB  ALA A 291 " =    2.236
peak=   -3.442 closest distance to " O   HOH Z 281 " =    2.958
peak=   -3.440 closest distance to " N   GLY A  23 " =    2.113
peak=   -3.439 closest distance to " CB  ALA A  43 " =    2.339
peak=   -3.436 closest distance to " O   HOH Z 409 " =    5.990
peak=   -3.429 closest distance to " O   HOH Z 102 " =    1.630
peak=   -3.425 closest distance to " N   GLN A 122 " =    1.544
peak=   -3.424 closest distance to " O   HOH Z  93 " =    2.301
peak=   -3.422 closest distance to " N   ASP A 171 " =    2.521
peak=   -3.419 closest distance to " OD1 ASP A 171 " =    1.521
peak=   -3.419 closest distance to " N   MET A 188 " =    1.726
peak=   -3.417 closest distance to " OD1 ASP A 191 " =    1.851
peak=   -3.414 closest distance to " O   HOH Z 313 " =    2.078
peak=   -3.413 closest distance to " CG  LEU A  83 " =    1.881
peak=   -3.412 closest distance to " O   HOH Z 313 " =    0.766
peak=   -3.412 closest distance to " O   ALA A 161 " =    1.473
peak=   -3.410 closest distance to " O   HOH Z 436 " =    1.120
peak=   -3.409 closest distance to " CZ BARG A 275 " =    1.886
peak=   -3.405 closest distance to " N   THR A 157 " =    1.690
peak=   -3.399 closest distance to " CG1 VAL A 112 " =    2.828
peak=   -3.398 closest distance to " CB  ASN A  39 " =    2.134
peak=   -3.397 closest distance to " O   HOH Z 205 " =    0.931
peak=   -3.394 closest distance to " O   HOH Z 435 " =    2.699
peak=   -3.392 closest distance to " O   HOH Z 426 " =    1.585
peak=   -3.392 closest distance to " CD  ARG A 139 " =    1.580
peak=   -3.389 closest distance to " O   VAL A  67 " =    2.556
peak=   -3.387 closest distance to " O   SER A 135 " =    1.491
peak=   -3.378 closest distance to " O   HOH Z 103 " =    1.767
peak=   -3.373 closest distance to " O   HOH Z 198 " =    1.165
peak=   -3.365 closest distance to " O   HOH Z 438 " =    1.249
peak=   -3.355 closest distance to " CZ  TYR A 169 " =    1.687
peak=   -3.349 closest distance to " O   VAL A 189 " =    2.526
peak=   -3.348 closest distance to " O   HOH Z 353 " =    2.123
peak=   -3.344 closest distance to " O   HOH Z 351 " =    1.354
peak=   -3.344 closest distance to " CE1 TYR A 169 " =    2.462
peak=   -3.342 closest distance to " CB  ASP A  27 " =    2.405
peak=   -3.332 closest distance to " O   HOH Z  43 " =    1.670
peak=   -3.331 closest distance to " O   HOH Z  24 " =    1.449
peak=   -3.330 closest distance to " CB  PRO A 163 " =    2.651
peak=   -3.330 closest distance to " CG1 VAL A 197 " =    2.205
peak=   -3.326 closest distance to " O   HOH Z  10 " =    1.459
peak=   -3.326 closest distance to " OG ASER A 134 " =    1.305
peak=   -3.326 closest distance to " OG BSER A 134 " =    1.619
peak=   -3.312 closest distance to " NH2AARG A 275 " =    5.481
peak=   -3.310 closest distance to " C   LEU A 143 " =    1.414
peak=   -3.309 closest distance to " O   HOH Z 137 " =    1.433
peak=   -3.309 closest distance to " OD1 ASN A  39 " =    2.194
peak=   -3.305 closest distance to " CZ  ARG A 259 " =    0.886
peak=   -3.301 closest distance to " OD1 ASN A 148 " =    1.645
peak=   -3.292 closest distance to " O   HOH Z 359 " =    3.122
peak=   -3.290 closest distance to " CB  LEU A 167 " =    1.999
peak=   -3.288 closest distance to " SG ACYS A 201 " =    1.979
peak=   -3.286 closest distance to " CE  MET A 105 " =    2.186
peak=   -3.283 closest distance to " C   LEU A 222 " =    0.739
peak=   -3.278 closest distance to " O   HOH Z 275 " =    1.547
peak=   -3.266 closest distance to " CB  ALA A 248 " =    1.893
peak=   -3.263 closest distance to " O   HOH Z 323 " =    1.238
peak=   -3.255 closest distance to " O   HOH Z  53 " =    1.630
peak=   -3.250 closest distance to " CE3 TRP A 274 " =    2.602
peak=   -3.249 closest distance to " O   HOH Z 166 " =    1.280
peak=   -3.248 closest distance to " ND2 ASN A 249 " =    2.135
peak=   -3.248 closest distance to " O   PRO A 163 " =    1.875
peak=   -3.247 closest distance to " O   HOH Z 310 " =    3.318
peak=   -3.246 closest distance to " OG  SER A 245 " =    0.902
peak=   -3.243 closest distance to " O   HOH Z  51 " =    1.035
peak=   -3.241 closest distance to " O   HOH Z 298 " =    1.272
peak=   -3.240 closest distance to " O   HOH Z 388 " =    1.887
peak=   -3.238 closest distance to " O   HOH Z  93 " =    1.320
peak=   -3.235 closest distance to " O   HOH Z 150 " =    1.200
peak=   -3.234 closest distance to " O   HOH Z 319 " =    2.669
peak=   -3.223 closest distance to " O   HOH Z 283 " =    2.142
peak=   -3.221 closest distance to " CA  TRP A 274 " =    1.572
peak=   -3.220 closest distance to " O   SER A  62 " =    2.092
peak=   -3.210 closest distance to " CB  ILE A 239 " =    1.979
peak=   -3.207 closest distance to " O   HOH Z  65 " =    1.126
peak=   -3.206 closest distance to " O   ASP A 231 " =    2.504
peak=   -3.204 closest distance to " CE3 TRP A 274 " =    0.978
peak=   -3.200 closest distance to " OXT GLY A 302 " =    3.308
peak=   -3.191 closest distance to " O   ARG A 145 " =    1.573
peak=   -3.185 closest distance to " O   HOH Z  11 " =    1.971
peak=   -3.181 closest distance to " CA  GLY A 203 " =    2.017
peak=   -3.166 closest distance to " CG  GLN A 278 " =    2.233
peak=   -3.163 closest distance to " CG  ARG A 138 " =    2.753
peak=   -3.153 closest distance to " CD1 ILE A 199 " =    2.523
peak=   -3.146 closest distance to " ND2 ASN A 187 " =    0.843
peak=   -3.138 closest distance to " O   HOH Z 222 " =    1.155
peak=   -3.138 closest distance to " O   HOH Z 211 " =    1.552
peak=   -3.135 closest distance to " CD1 LEU A 101 " =    2.487
peak=   -3.135 closest distance to " CD2 TYR A 293 " =    2.024
peak=   -3.134 closest distance to " OD1 ASN A 301 " =    1.871
peak=   -3.111 closest distance to " O   HOH Z  60 " =    1.692
peak=   -3.109 closest distance to " OG  SER A   3 " =    1.525
peak=   -3.106 closest distance to " O   HOH Z   3 " =    1.023
peak=   -3.096 closest distance to " N   ALA A 226 " =    2.127
peak=   -3.093 closest distance to " N   ALA A   9 " =    1.405
peak=   -3.089 closest distance to " CD  GLN A  55 " =    1.076
peak=   -3.086 closest distance to " O   HOH Z  97 " =    2.344
peak=   -3.085 closest distance to " O   HOH Z 385 " =    1.987
peak=   -3.085 closest distance to " N   PHE A  59 " =    2.118
peak=   -3.084 closest distance to " CB  PHE A 192 " =    1.738
peak=   -3.082 closest distance to " CG  TRP A 266 " =    1.538
peak=   -3.078 closest distance to " O   HOH Z 119 " =    4.165
peak=   -3.044 closest distance to " O   HOH Z 396 " =    1.782
peak=   -3.043 closest distance to " ND2 ASN A  60 " =    1.895
peak=   -3.037 closest distance to " O   HOH Z 109 " =    1.589
peak=   -3.012 closest distance to " O   HOH Z 193 " =    1.511
peak=   -3.011 closest distance to " CA  GLY A 133 " =    2.002

================= 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    :  0.4577 0.4608   6.262886e+00   6.261601e+00
   1_bss:  0.4494 0.4527   6.260366e+00   6.250710e+00
   1_xyz:  0.2977 0.3353   5.964021e+00   6.055844e+00
   1_adp:  0.2702 0.3429   5.914941e+00   6.073567e+00
   1_occ:  0.2698 0.3431   5.913828e+00   6.072523e+00
   2_bss:  0.2681 0.3425   5.909336e+00   6.068734e+00
   2_xyz:  0.2015 0.2638   5.669153e+00   5.866205e+00
   2_adp:  0.1874 0.2476   5.610028e+00   5.810599e+00
   2_occ:  0.1872 0.2476   5.609344e+00   5.809863e+00
   3_bss:  0.1870 0.2469   5.606107e+00   5.807266e+00
   3_xyz:  0.1517 0.1985   5.404754e+00   5.621485e+00
   3_adp:  0.1413 0.1884   5.342720e+00   5.560621e+00
   3_occ:  0.1412 0.1882   5.342052e+00   5.559760e+00
   4_bss:  0.1415 0.1884   5.343373e+00   5.560670e+00
   4_xyz:  0.1198 0.1666   5.203964e+00   5.445782e+00
   4_adp:  0.1160 0.1624   5.174648e+00   5.417278e+00
   4_occ:  0.1159 0.1620   5.173243e+00   5.415791e+00
   5_bss:  0.1163 0.1617   5.174745e+00   5.416281e+00
   5_xyz:  0.1106 0.1581   5.142216e+00   5.391338e+00
   5_adp:  0.1125 0.1566   5.146896e+00   5.385227e+00
   5_occ:  0.1123 0.1562   5.145537e+00   5.384206e+00
   5_bss:  0.1123 0.1561   5.145654e+00   5.384147e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  20.000   0.452  -1.425   2.047  -0.000   0.000   0.000
   1_xyz:  0.300  20.000   0.452  -1.425   2.047  -0.000   0.000   0.000
   1_adp:  0.300  20.000   0.452  -1.425   2.047  -0.000   0.000   0.000
   1_occ:  0.300  20.000   0.452  -1.425   2.047  -0.000   0.000   0.000
   2_bss:  0.340  51.099  -0.617  -1.792   0.190  -0.000   0.000   0.000
   2_xyz:  0.340  51.099  -0.617  -1.792   0.190  -0.000   0.000   0.000
   2_adp:  0.340  51.099  -0.617  -1.792   0.190  -0.000   0.000   0.000
   2_occ:  0.340  51.099  -0.617  -1.792   0.190  -0.000   0.000   0.000
   3_bss:  0.327  47.997  -1.268  -2.200  -0.867  -0.000  -0.000  -0.000
   3_xyz:  0.327  47.997  -1.268  -2.200  -0.867  -0.000  -0.000  -0.000
   3_adp:  0.327  47.997  -1.268  -2.200  -0.867  -0.000  -0.000  -0.000
   3_occ:  0.327  47.997  -1.268  -2.200  -0.867  -0.000  -0.000  -0.000
   4_bss:  0.326  48.755  -1.807  -2.523  -1.612  -0.000  -0.000  -0.000
   4_xyz:  0.326  48.755  -1.807  -2.523  -1.612  -0.000  -0.000  -0.000
   4_adp:  0.326  48.755  -1.807  -2.523  -1.612  -0.000  -0.000  -0.000
   4_occ:  0.326  48.755  -1.807  -2.523  -1.612  -0.000  -0.000  -0.000
   5_bss:  0.322  46.737  -1.938  -2.574  -1.866  -0.000  -0.000  -0.000
   5_xyz:  0.322  46.737  -1.938  -2.574  -1.866  -0.000  -0.000  -0.000
   5_adp:  0.322  46.737  -1.938  -2.574  -1.866  -0.000  -0.000  -0.000
   5_occ:  0.322  46.737  -1.938  -2.574  -1.866  -0.000  -0.000  -0.000
   5_bss:  0.327  46.632  -1.865  -2.468  -1.808  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.711 0.4349  0.5901    66921.725
   1_bss:  55.356 0.4505  0.6223    63484.456
   1_xyz:  35.709 0.6937  0.9128    31579.962
   1_adp:  37.026 0.6771  0.8914    32942.386
   1_occ:  37.027 0.6769  0.8904    32829.024
   2_bss:  36.700 0.6805  0.8629    32370.139
   2_xyz:  27.174 0.7877  0.9660    18772.137
   2_adp:  24.965 0.8120  0.9805    16497.248
   2_occ:  24.938 0.8123  0.9804    16470.614
   3_bss:  24.798 0.8136  0.9561    16286.289
   3_xyz:  19.444 0.8666  0.9889    10440.804
   3_adp:  17.850 0.8820  0.9917     9257.655
   3_occ:  17.824 0.8822  0.9917     9237.384
   4_bss:  17.846 0.8821  0.9729     9293.455
   4_xyz:  15.392 0.9027  0.9853     7139.941
   4_adp:  14.705 0.9088  0.9852     6778.998
   4_occ:  14.665 0.9092  0.9853     6750.801
   5_bss:  14.683 0.9090  0.9799     6770.539
   5_xyz:  14.140 0.9137  0.9806     6416.167
   5_adp:  13.901 0.9160  0.9801     6388.389
   5_occ:  13.872 0.9162  0.9801     6363.766
   5_bss:  13.874 0.9162  0.9792     6365.690
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.7950e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.7950e-01
   1_xyz:   1.485  0.012  0.098 16.271  0.007  4.113   1.3128e-01
   1_adp:   1.485  0.012  0.098 16.271  0.007  4.113   1.3128e-01
   1_occ:   1.485  0.012  0.098 16.271  0.007  4.113   1.3128e-01
   2_bss:   1.485  0.012  0.098 16.271  0.007  4.113   1.3128e-01
   2_xyz:   1.072  0.007  0.072 14.485  0.004  4.127   6.2814e-02
   2_adp:   1.072  0.007  0.072 14.485  0.004  4.127   6.2814e-02
   2_occ:   1.072  0.007  0.072 14.485  0.004  4.127   6.2814e-02
   3_bss:   1.072  0.007  0.072 14.485  0.004  4.127   6.2814e-02
   3_xyz:   0.945  0.006  0.066 14.305  0.004  4.115   5.3298e-02
   3_adp:   0.945  0.006  0.066 14.305  0.004  4.115   5.3298e-02
   3_occ:   0.945  0.006  0.066 14.305  0.004  4.115   5.3298e-02
   4_bss:   0.945  0.006  0.066 14.305  0.004  4.115   5.3298e-02
   4_xyz:   1.150  0.009  0.081 14.974  0.005  4.122   7.4763e-02
   4_adp:   1.150  0.009  0.081 14.974  0.005  4.122   7.4763e-02
   4_occ:   1.150  0.009  0.081 14.974  0.005  4.122   7.4763e-02
   5_bss:   1.150  0.009  0.081 14.974  0.005  4.122   7.4763e-02
   5_xyz:   1.127  0.009  0.079 15.054  0.005  4.108   7.3432e-02
   5_adp:   1.127  0.009  0.079 15.054  0.005  4.108   7.3432e-02
   5_occ:   1.127  0.009  0.079 15.054  0.005  4.108   7.3432e-02
   5_bss:   1.127  0.009  0.079 15.054  0.005  4.108   7.3432e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.567   2.3994e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.567   2.3994e-01
   1_xyz:  10.031  0.092  0.411 88.630  0.044  2.120   1.1603e-01
   1_adp:  10.031  0.092  0.411 88.630  0.044  2.120   1.1603e-01
   1_occ:  10.031  0.092  0.411 88.630  0.044  2.120   1.1603e-01
   2_bss:  10.031  0.092  0.411 88.630  0.044  2.120   1.1603e-01
   2_xyz:   6.914  0.037  0.210 81.425  0.032  2.365   5.0648e-02
   2_adp:   6.914  0.037  0.210 81.425  0.032  2.365   5.0648e-02
   2_occ:   6.914  0.037  0.210 81.425  0.032  2.365   5.0648e-02
   3_bss:   6.914  0.037  0.210 81.425  0.032  2.365   5.0648e-02
   3_xyz:   8.352  0.029  0.281 80.414  0.037  2.343   5.3658e-02
   3_adp:   8.352  0.029  0.281 80.414  0.037  2.343   5.3658e-02
   3_occ:   8.352  0.029  0.281 80.414  0.037  2.343   5.3658e-02
   4_bss:   8.352  0.029  0.281 80.414  0.037  2.343   5.3658e-02
   4_xyz:   7.749  0.040  0.266 83.556  0.039  2.293   7.7438e-02
   4_adp:   7.749  0.040  0.266 83.556  0.039  2.293   7.7438e-02
   4_occ:   7.749  0.040  0.266 83.556  0.039  2.293   7.7438e-02
   5_bss:   7.749  0.040  0.266 83.556  0.039  2.293   7.7438e-02
   5_xyz:   7.681  0.045  0.251 84.143  0.035  2.286   6.1898e-02
   5_adp:   7.681  0.045  0.251 84.143  0.035  2.286   6.1898e-02
   5_occ:   7.681  0.045  0.251 84.143  0.035  2.286   6.1898e-02
   5_bss:   7.681  0.045  0.251 84.143  0.035  2.286   6.1898e-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:  76.28   0.00  18.44  73.72   0.00  14.07  76.28   0.00  42.22
   1_occ:  76.28   0.00  18.44  73.72   0.00  14.07  76.28   0.00  42.22
   2_bss:  76.28   0.00  18.44  73.72   0.00  14.07  76.28   0.00  42.22
   2_xyz:  76.28   0.00  18.44  73.72   0.00  14.07  76.28   0.00  42.22
   2_adp:  77.03   0.00  17.82  75.53   0.00  13.40  77.03   3.79  41.84
   2_occ:  77.03   0.00  17.82  75.53   0.00  13.40  77.03   3.79  41.84
   3_bss:  77.03   0.00  17.82  75.53   0.00  13.40  77.03   3.79  41.84
   3_xyz:  77.03   0.00  17.82  75.53   0.00  13.40  77.03   3.79  41.84
   3_adp:  82.59   1.04  17.53  82.59   1.04  12.98  78.91   5.99  42.33
   3_occ:  82.59   1.04  17.53  82.59   1.04  12.98  78.91   5.99  42.33
   4_bss:  82.59   1.04  17.53  82.59   1.04  12.98  78.91   5.99  42.33
   4_xyz:  82.59   1.04  17.53  82.59   1.04  12.98  78.91   5.99  42.33
   4_adp:  88.35   1.65  17.20  88.35   1.65  12.84  83.06   6.49  40.90
   4_occ:  88.35   1.65  17.20  88.35   1.65  12.84  83.06   6.49  40.90
   5_bss:  88.35   1.65  17.20  88.35   1.65  12.84  83.06   6.49  40.90
   5_xyz:  88.35   1.65  17.20  88.35   1.65  12.84  83.06   6.49  40.90
   5_adp:  81.76   2.87  16.30  80.77   2.87  12.61  81.76   6.43  36.40
   5_occ:  81.76   2.87  16.30  80.77   2.87  12.61  81.76   6.43  36.40
   5_bss:  81.66   2.77  16.20  80.66   2.77  12.50  81.66   6.32  36.29
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.850    0.022    0.455
   1_adp:    1.850    0.022    0.455
   1_occ:    1.850    0.022    0.455
   2_bss:    1.850    0.022    0.455
   2_xyz:    1.426    0.031    0.555
   2_adp:    1.426    0.031    0.555
   2_occ:    1.426    0.031    0.555
   3_bss:    1.426    0.031    0.555
   3_xyz:    1.250    0.028    0.645
   3_adp:    1.250    0.028    0.645
   3_occ:    1.250    0.028    0.645
   4_bss:    1.250    0.028    0.645
   4_xyz:    1.269    0.070    0.694
   4_adp:    1.269    0.070    0.694
   4_occ:    1.269    0.070    0.694
   5_bss:    1.269    0.070    0.694
   5_xyz:    1.318    0.061    0.707
   5_adp:    1.318    0.061    0.707
   5_occ:    1.318    0.061    0.707
   5_bss:    1.318    0.061    0.707
------------------------------------------------------------------------

CPU time actual refinement: 361.30


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1122/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_1122/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1122/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1122/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1122/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 361.15 
  Macro-tasks:
    bulk solvent and scale       = 43.62  
    individual site refinement   = 152.30 
    weights calculation          = 30.37  
    collect and process          = 6.55   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 232.95 
  Micro-tasks:
    mask                            = 2.45   
    f_calc                          = 117.35 
    alpha_beta                      = 8.32   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 127.13 
    fmodel                         = 7.46   
    r_factors                      = 0.27   
    phase_errors                   = 10.66  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 275.05 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.023 micro seconds
Total CPU time: 6.25 minutes
from_scatterers_fft:    666 calls, 116.97 s
gradients_fft:          611 calls, 112.94 s

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

# Date 2008-01-16 Time 06:29:25 PST -0800 (1200493765.13 s)
Start R-work = 0.4577, R-free = 0.4608 (no bulk solvent and anisotropic scale)
Final R-work = 0.1378, R-free = 0.1789 (no bulk solvent and anisotropic scale)

Start R-work = 0.4494, R-free = 0.4527
Final R-work = 0.1123, R-free = 0.1561