# Date 2008-01-16 Time 06:31:11 PST -0800 (1200493871.14 s)
#phil __OFF__

Command line arguments: "../1177.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 5512
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1177

-------------------------------------------------------------------------------
  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, 47.6339, 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: 3.24, per 1000 atoms: 1.15


================================== 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, 47.6339, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1017 1.95153
Completeness in resolution range: 0.908791
Completeness with d_max=infinity: 0.906143

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1017
                             d_min =   1.9515

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, 47.6339, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1017 1.95153
Completeness in resolution range: 0.908791
Completeness with d_max=infinity: 0.906143

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1022 -  4.1776 [2269/2298]  2045   224   9.9%
  bin  2:  4.1776 -  3.3275 [2156/2179]  1939   217  10.1%
  bin  3:  3.3275 -  2.9103 [2144/2169]  1925   219  10.2%
  bin  4:  2.9103 -  2.6458 [2134/2151]  1924   210   9.8%
  bin  5:  2.6458 -  2.4570 [2095/2138]  1891   204   9.7%
  bin  6:  2.4570 -  2.3127 [2105/2133]  1890   215  10.2%
  bin  7:  2.3127 -  2.1972 [2099/2135]  1884   215  10.2%
  bin  8:  2.1972 -  2.1018 [2066/2108]  1863   203   9.8%
  bin  9:  2.1018 -  2.0211 [1970/2131]  1773   197  10.0%
  bin 10:  2.0211 -  1.9515 [ 551/2113]   496    55  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1177/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:
        1.55 -     2.22: 26
        2.22 -     2.89: 1325
        2.89 -     3.56: 4458
        3.56 -     4.23: 9198
        4.23 -     4.90: 13271
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.546 3.040 -x+1/2,-y+1,z+1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.561 3.120 -x+1/2,-y+1,z-1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.609 3.040 -x+1/2,-y+1,z+1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.742 3.040 -x+1/2,-y+1,z-1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.754 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28273 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_1177/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1177/model_refine_001.geo

CPU time processing inputs: 9.07


============================ 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 47.63395 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= 0.4712   r_free= 0.4697   ksol= 0.00   Bsol= 0.00   scale= 0.888    |
|                                                                             |
| 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:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.278410                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1022 -  4.6603 0.99   1471  167 0.3630 0.3692      6.5407      6.5436|
|  2:  4.6603 -  3.7172 0.99   1408  156 0.3968 0.3817      6.7979      6.8135|
|  3:  3.7172 -  3.2526 0.99   1385  146 0.4427 0.4197      6.6535      6.6534|
|  4:  3.2526 -  2.9577 0.99   1378  160 0.4658 0.4567      6.4907      6.4868|
|  5:  2.9577 -  2.7470 0.99   1370  150 0.4917 0.4786      6.3431      6.3364|
|  6:  2.7470 -  2.5859 0.99   1359  155 0.5118 0.5211      6.2738       6.201|
|  7:  2.5859 -  2.4570 0.98   1353  140 0.5181 0.4946      6.2343      6.1868|
|  8:  2.4570 -  2.3505 0.98   1359  152 0.5198 0.5186      6.1372       6.192|
|  9:  2.3505 -  2.2603 0.99   1346  153 0.5397 0.5285      6.1501      6.1269|
| 10:  2.2603 -  2.1825 0.98   1335  157 0.5313 0.5663      6.0705      6.1137|
| 11:  2.1825 -  2.1145 0.97   1337  142 0.5282 0.6119      6.0293      5.9888|
| 12:  2.1145 -  2.0542 0.98   1322  145 0.5253 0.5478      5.9319      5.9707|
| 13:  2.0542 -  2.0002 0.71    971  115 0.5361 0.4827      5.8657      5.8313|
| 14:  2.0002 -  1.9515 0.17    236   21 0.5830 0.4184      5.7795      5.8212|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 -  4.6603  1471   167  0.72  32.39   0.83     0.75      63973.06|
|  2:  4.6603 -  3.7172  1408   156  0.71  34.18   0.91     0.80      98440.18|
|  3:  3.7172 -  3.2526  1385   146  0.59  44.27   0.90     0.76     110363.84|
|  4:  3.2526 -  2.9577  1378   160  0.48  53.40   0.90     0.68     103512.62|
|  5:  2.9577 -  2.7470  1370   150  0.41  59.20   0.87     0.59      83094.16|
|  6:  2.7470 -  2.5859  1359   155  0.39  60.83   0.89     0.56      70830.33|
|  7:  2.5859 -  2.4570  1353   140  0.37  61.97   0.89     0.51      62169.96|
|  8:  2.4570 -  2.3505  1359   152  0.32  65.96   0.88     0.48      62207.01|
|  9:  2.3505 -  2.2603  1346   153  0.26  71.00   0.92     0.38      58984.33|
| 10:  2.2603 -  2.1825  1335   157  0.20  75.36   0.91     0.30      59349.77|
| 11:  2.1825 -  2.1145  1337   142  0.10  82.46   0.93     0.15      55319.79|
| 12:  2.1145 -  2.0542  1322   145  0.07  84.49   0.90     0.13      52197.31|
| 13:  2.0542 -  2.0002   971   115  0.11  81.69   0.91     0.18      43217.88|
| 14:  2.0002 -  1.9515   236    21  0.23  72.97   0.85     0.39      34069.98|
|alpha:            min =        0.13 max =            0.80 mean =         0.49|
|beta:             min =    34069.98 max =       110363.84 mean =     71386.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.37|
|phase err.(work): min =        0.00 max =           90.00 mean =        61.41|
|phase err.(test): min =        0.00 max =           89.95 mean =        61.40|
|-----------------------------------------------------------------------------|

============================== 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 = 18.161059             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.042   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.399112              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.928   (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 |  1.546 -  1.881:       11 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.881 -  2.217:       15 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.217 -  2.552:       40 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.552 -  2.888:     1285 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.888 -  3.223:     1885 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.223 -  3.558:     2573 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.558 -  3.894:     4640 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.894 -  4.229:     4558 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.229 -  4.565:     6052 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.565 -  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 |        0.191 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.546 |       0.596 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.975)------------------------------------------|
|    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= 0.4712   r_free= 0.4697   ksol= 0.00   Bsol= 0.00   scale= 0.888    |
|                                                                             |
| 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:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.278410                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4646   r_free= 0.4633   ksol= 0.30   Bsol= 50.00   scale= 0.933   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.05,1.32,1.43,0.00,0.00,0.00); trace/3= 0.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.97 A                  |
| x-ray target function (ml) for work reflections: 5.831477                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.745355             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.155   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.446391              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.518   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4646      final r-factor (work) = 0.3463          |
| start r-factor (free) = 0.4633      final r-factor (free) = 0.3885          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.2945 = 13.75 * 0.50 * 6.2717 + 1.00 * 0.1911                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.3790 = 13.75 * 0.50 * 5.7081 + 1.00 * 0.1488                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3463      final r-factor (work) = 0.3190          |
| start r-factor (free) = 0.3885      final r-factor (free) = 0.3897          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2627 = 1.45 * 1.00 * 5.7081 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7550 = 1.45 * 1.00 * 6.0331 + 1.00 * 0.0288                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.975)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.51  17.39    None  None   None       |
|    all(noH): 2823   0      0.00    109.51  17.39    None  None   None       |
|    Sol.    : 438    0      0.00    69.95   38.47    None  None   None       |
|    Mac.    : 2385   0      0.00    109.51  13.51    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.951: 1022   |   5:    54.754 -  65.705:   43        |
|      1:    10.951 -  21.902: 1038   |   6:    65.705 -  76.655:    1        |
|      2:    21.902 -  32.852:  388   |   7:    76.655 -  87.606:    0        |
|      3:    32.852 -  43.803:  203   |   8:    87.606 -  98.557:    0        |
|      4:    43.803 -  54.754:  127   |   9:    98.557 - 109.508:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3190 r_free = 0.3897             target_work(ml) = 6.035         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3189 r_free = 0.3899             target_work(ml) = 6.034         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3189   r_free= 0.3899   ksol= 0.30   Bsol= 50.00   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.05,1.32,1.43,0.00,0.00,0.00); trace/3= 0.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.033531                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3178   r_free= 0.3889   ksol= 0.34   Bsol= 66.49   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.51,0.45,0.46,0.00,0.00,0.00); trace/3= 0.14                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.033015                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.084789              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.001   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.947530              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 105.893  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3178      final r-factor (work) = 0.2371          |
| start r-factor (free) = 0.3889      final r-factor (free) = 0.2942          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.5385 = 8.08 * 0.50 * 6.0335 + 1.00 * 0.1488                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.0899 = 8.08 * 0.50 * 5.9376 + 1.00 * 0.0878                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2371      final r-factor (work) = 0.2150          |
| start r-factor (free) = 0.2942      final r-factor (free) = 0.2767          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6467 = 0.95 * 1.00 * 5.9376 + 1.00 * 0.0206                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4630 = 0.95 * 1.00 * 5.7500 + 1.00 * 0.0148                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.975)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.63   18.40    None  None   None       |
|    all(noH): 2823   0      0.00    98.63   18.40    None  None   None       |
|    Sol.    : 438    0      4.31    98.63   43.82    None  None   None       |
|    Mac.    : 2385   0      0.00    89.07   13.73    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.863: 1034   |   5:    49.316 -  59.179:   89        |
|      1:     9.863 -  19.726:  977   |   6:    59.179 -  69.042:   67        |
|      2:    19.726 -  29.590:  312   |   7:    69.042 -  78.905:   37        |
|      3:    29.590 -  39.453:  156   |   8:    78.905 -  88.769:   11        |
|      4:    39.453 -  49.316:  136   |   9:    88.769 -  98.632:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2150 r_free = 0.2767             target_work(ml) = 5.722         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2149 r_free = 0.2766             target_work(ml) = 5.722         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2149   r_free= 0.2766   ksol= 0.34   Bsol= 66.49   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.51,0.45,0.46,0.00,0.00,0.00); trace/3= 0.14                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.722292                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2145   r_free= 0.2763   ksol= 0.34   Bsol= 66.49   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.99,-0.43,-0.70,-0.00,-0.00,-0.00); trace/3= -0.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.720417                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.266511              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.062   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.353720              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.890  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2145      final r-factor (work) = 0.1597          |
| start r-factor (free) = 0.2763      final r-factor (free) = 0.2106          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.1063 = 6.27 * 0.50 * 5.7507 + 1.00 * 0.0878                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.6713 = 6.27 * 0.50 * 5.6165 + 1.00 * 0.0733                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1597      final r-factor (work) = 0.1506          |
| start r-factor (free) = 0.2106      final r-factor (free) = 0.2007          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6180 = 1.35 * 1.00 * 5.6165 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3782 = 1.35 * 1.00 * 5.4242 + 1.00 * 0.0354                               |
|-----------------------------------------------------------------------------|
| number of iterations = 3       |    number of function evaluations = 3      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.975)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.96   18.45    None  None   None       |
|    all(noH): 2823   0      0.00    98.96   18.45    None  None   None       |
|    Sol.    : 438    0      4.30    98.96   44.23    None  None   None       |
|    Mac.    : 2385   0      0.00    89.94   13.71    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 -   9.896: 1015   |   5:    49.480 -  59.376:   95        |
|      1:     9.896 -  19.792: 1040   |   6:    59.376 -  69.272:   67        |
|      2:    19.792 -  29.688:  273   |   7:    69.272 -  79.168:   36        |
|      3:    29.688 -  39.584:  156   |   8:    79.168 -  89.064:   12        |
|      4:    39.584 -  49.480:  125   |   9:    89.064 -  98.960:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1506 r_free = 0.2007             target_work(ml) = 5.402         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1505 r_free = 0.2007             target_work(ml) = 5.402         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1505   r_free= 0.2007   ksol= 0.34   Bsol= 66.49   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.99,-0.43,-0.70,-0.00,-0.00,-0.00); trace/3= -0.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.401952                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1505   r_free= 0.2008   ksol= 0.34   Bsol= 66.49   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.74,-1.29,-1.54,-0.00,-0.00,-0.00); trace/3= -1.52                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.404221                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.033741              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.214  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.174094              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.922   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1505      final r-factor (work) = 0.1381          |
| start r-factor (free) = 0.2008      final r-factor (free) = 0.1905          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3063 = 3.03 * 0.50 * 5.4276 + 1.00 * 0.0733                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2106 = 3.03 * 0.50 * 5.3711 + 1.00 * 0.0633                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1381      final r-factor (work) = 0.1271          |
| start r-factor (free) = 0.1905      final r-factor (free) = 0.1773          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3227 = 1.17 * 1.00 * 5.3711 + 1.00 * 0.0165                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2396 = 1.17 * 1.00 * 5.3043 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.975)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.94  18.08    None  None   None       |
|    all(noH): 2823   0      0.00    104.94  18.08    None  None   None       |
|    Sol.    : 438    0      5.61    101.65  44.86    None  None   None       |
|    Mac.    : 2385   0      0.00    104.94  13.16    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.494: 1160   |   5:    52.470 -  62.964:  103        |
|      1:    10.494 -  20.988: 1022   |   6:    62.964 -  73.458:   41        |
|      2:    20.988 -  31.482:  218   |   7:    73.458 -  83.952:   31        |
|      3:    31.482 -  41.976:  123   |   8:    83.952 -  94.446:   14        |
|      4:    41.976 -  52.470:  107   |   9:    94.446 - 104.940:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1271 r_free = 0.1773             target_work(ml) = 5.265         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1270 r_free = 0.1772             target_work(ml) = 5.265         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1270   r_free= 0.1772   ksol= 0.34   Bsol= 66.49   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.74,-1.29,-1.54,-0.00,-0.00,-0.00); trace/3= -1.52                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.265002                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1270   r_free= 0.1772   ksol= 0.33   Bsol= 66.49   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-1.60,-1.82,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.264610                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.754238              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 133.301  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.153706              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.581  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1270      final r-factor (work) = 0.1237          |
| start r-factor (free) = 0.1772      final r-factor (free) = 0.1728          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7160 = 1.75 * 0.50 * 5.3045 + 1.00 * 0.0633                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6629 = 1.75 * 0.50 * 5.2551 + 1.00 * 0.0536                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1237      final r-factor (work) = 0.1239          |
| start r-factor (free) = 0.1728      final r-factor (free) = 0.1689          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8196 = 0.15 * 1.00 * 5.2551 + 1.00 * 0.0118                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8148 = 0.15 * 1.00 * 5.2464 + 1.00 * 0.0083                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.975)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.32    98.92   17.17    None  None   None       |
|    all(noH): 2823   0      2.32    98.92   17.17    None  None   None       |
|    Sol.    : 438    0      4.97    85.60   40.89    None  None   None       |
|    Mac.    : 2385   0      2.32    98.92   12.82    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.323 -  11.982: 1490   |   5:    50.622 -  60.282:   79        |
|      1:    11.982 -  21.642:  766   |   6:    60.282 -  69.942:   37        |
|      2:    21.642 -  31.302:  181   |   7:    69.942 -  79.601:   24        |
|      3:    31.302 -  40.962:  128   |   8:    79.601 -  89.261:    7        |
|      4:    40.962 -  50.622:  106   |   9:    89.261 -  98.921:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1239 r_free = 0.1689             target_work(ml) = 5.236         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1238 r_free = 0.1685             target_work(ml) = 5.235         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1238   r_free= 0.1685   ksol= 0.33   Bsol= 66.49   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-1.60,-1.82,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.234920                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1022 -  4.6603 0.99   1471  167 0.0988 0.1279      5.3763      5.5653|
|  2:  4.6603 -  3.7172 0.99   1408  156 0.0899 0.1125      5.4642      5.7034|
|  3:  3.7172 -  3.2526 0.99   1385  146 0.1146 0.1846      5.5272      5.9648|
|  4:  3.2526 -  2.9577 0.99   1378  160 0.1437 0.1673      5.5571      5.6759|
|  5:  2.9577 -  2.7470 0.99   1370  150 0.1492 0.1962      5.4119      5.5915|
|  6:  2.7470 -  2.5859 0.99   1359  155 0.1400 0.1973      5.2963      5.4853|
|  7:  2.5859 -  2.4570 0.98   1353  140 0.1367 0.1815      5.2339      5.4358|
|  8:  2.4570 -  2.3505 0.98   1359  152 0.1360 0.1790       5.161      5.3416|
|  9:  2.3505 -  2.2603 0.99   1346  153 0.1300 0.2046      5.0997      5.3742|
| 10:  2.2603 -  2.1825 0.98   1335  157 0.1299 0.1798      5.0516      5.3033|
| 11:  2.1825 -  2.1145 0.97   1337  142 0.1264 0.1897       4.992       5.259|
| 12:  2.1145 -  2.0542 0.98   1322  145 0.1323 0.1989      4.9519      5.2038|
| 13:  2.0542 -  2.0002 0.71    971  115 0.1318 0.1784      4.8618      5.0639|
| 14:  2.0002 -  1.9515 0.17    236   21 0.1328 0.1674       4.745      4.9319|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 -  4.6603  1471   167  0.94   9.13   0.97     0.95       7075.24|
|  2:  4.6603 -  3.7172  1408   156  0.95   8.26   1.00     0.99       9413.48|
|  3:  3.7172 -  3.2526  1385   146  0.92  13.00   1.02     1.02      11854.00|
|  4:  3.2526 -  2.9577  1378   160  0.90  16.52   1.00     0.96      12515.38|
|  5:  2.9577 -  2.7470  1370   150  0.88  18.02   1.00     0.97       9818.23|
|  6:  2.7470 -  2.5859  1359   155  0.89  17.62   0.99     0.96       8221.48|
|  7:  2.5859 -  2.4570  1353   140  0.89  16.96   0.99     0.96       7040.75|
|  8:  2.4570 -  2.3505  1359   152  0.89  17.79   1.00     0.96       6546.00|
|  9:  2.3505 -  2.2603  1346   153  0.88  17.75   1.01     0.97       5745.67|
| 10:  2.2603 -  2.1825  1335   157  0.89  16.98   0.98     0.93       5078.48|
| 11:  2.1825 -  2.1145  1337   142  0.89  17.01   0.99     0.95       4693.78|
| 12:  2.1145 -  2.0542  1322   145  0.89  18.32   0.99     0.99       4665.41|
| 13:  2.0542 -  2.0002   971   115  0.88  18.03   0.99     0.98       3815.74|
| 14:  2.0002 -  1.9515   236    21  0.88  17.80   0.98     0.95       2908.57|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2908.57 max =        12515.38 mean =      7471.36|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.94 mean =        15.70|
|phase err.(test): min =        0.00 max =           90.00 mean =        14.98|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1240   r_free= 0.1687   ksol= 0.32   Bsol= 57.49   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-1.66,-1.83,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.237391                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1240   r_free= 0.1687   ksol= 0.32   Bsol= 57.49   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-1.66,-1.83,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.237391                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1022 -  4.6603 0.99   1471  167 0.0982 0.1272      5.3865      5.5852|
|  2:  4.6603 -  3.7172 0.99   1408  156 0.0902 0.1129       5.472      5.7072|
|  3:  3.7172 -  3.2526 0.99   1385  146 0.1148 0.1838      5.5319      5.9586|
|  4:  3.2526 -  2.9577 0.99   1378  160 0.1441 0.1670       5.558      5.6749|
|  5:  2.9577 -  2.7470 0.99   1370  150 0.1496 0.1970      5.4147      5.5938|
|  6:  2.7470 -  2.5859 0.99   1359  155 0.1401 0.1969      5.2976      5.4853|
|  7:  2.5859 -  2.4570 0.98   1353  140 0.1369 0.1820      5.2351      5.4369|
|  8:  2.4570 -  2.3505 0.98   1359  152 0.1360 0.1793      5.1614      5.3431|
|  9:  2.3505 -  2.2603 0.99   1346  153 0.1299 0.2044      5.0997      5.3749|
| 10:  2.2603 -  2.1825 0.98   1335  157 0.1300 0.1799       5.052      5.3041|
| 11:  2.1825 -  2.1145 0.97   1337  142 0.1265 0.1898      4.9922      5.2593|
| 12:  2.1145 -  2.0542 0.98   1322  145 0.1324 0.1993      4.9526      5.2054|
| 13:  2.0542 -  2.0002 0.71    971  115 0.1318 0.1783      4.8622      5.0633|
| 14:  2.0002 -  1.9515 0.17    236   21 0.1328 0.1673      4.7448      4.9319|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 -  4.6603  1471   167  0.94   9.32   0.97     0.95       7340.24|
|  2:  4.6603 -  3.7172  1408   156  0.95   8.46   1.00     0.99       9709.33|
|  3:  3.7172 -  3.2526  1385   146  0.92  13.09   1.02     1.02      12038.09|
|  4:  3.2526 -  2.9577  1378   160  0.90  16.48   1.00     0.96      12485.90|
|  5:  2.9577 -  2.7470  1370   150  0.88  18.04   0.99     0.97       9839.00|
|  6:  2.7470 -  2.5859  1359   155  0.89  17.67   0.98     0.96       8254.52|
|  7:  2.5859 -  2.4570  1353   140  0.89  16.99   0.98     0.96       7062.77|
|  8:  2.4570 -  2.3505  1359   152  0.89  17.81   0.99     0.96       6556.75|
|  9:  2.3505 -  2.2603  1346   153  0.88  17.78   1.00     0.97       5756.93|
| 10:  2.2603 -  2.1825  1335   157  0.89  17.00   0.98     0.93       5085.52|
| 11:  2.1825 -  2.1145  1337   142  0.89  17.02   0.99     0.95       4701.52|
| 12:  2.1145 -  2.0542  1322   145  0.88  18.34   0.99     0.98       4674.93|
| 13:  2.0542 -  2.0002   971   115  0.88  18.04   0.99     0.97       3819.90|
| 14:  2.0002 -  1.9515   236    21  0.88  17.79   0.98     0.94       2903.46|
|alpha:            min =        0.93 max =            1.02 mean =         0.96|
|beta:             min =     2903.46 max =        12485.90 mean =      7538.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           90.00 mean =        15.75|
|phase err.(test): min =        0.00 max =           89.96 mean =        15.07|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.975)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.24    98.84   17.09    None  None   None       |
|    all(noH): 2823   0      2.24    98.84   17.09    None  None   None       |
|    Sol.    : 438    0      4.89    85.52   40.80    None  None   None       |
|    Mac.    : 2385   0      2.24    98.84   12.73    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.238 -  11.898: 1490   |   5:    50.538 -  60.198:   79        |
|      1:    11.898 -  21.558:  766   |   6:    60.198 -  69.857:   37        |
|      2:    21.558 -  31.218:  181   |   7:    69.857 -  79.517:   24        |
|      3:    31.218 -  40.878:  128   |   8:    79.517 -  89.177:    7        |
|      4:    40.878 -  50.538:  106   |   9:    89.177 -  98.837:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 345         
Filter by distance & map next to the model:
   mapped sites are within: 0.538 - 5.937
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 339 from: 345
   mapped sites are within: 0.714 - 5.937

peak=    6.184 closest distance to " NH2BARG A 102 " =    1.024
peak=    5.713 closest distance to " CB  SER A  63 " =    1.335
peak=    5.685 closest distance to " CB  GLN A 223 " =    1.510
peak=    5.533 closest distance to " O   HOH Z 111 " =    2.084
peak=    5.398 closest distance to " CG  PRO A  54 " =    1.266
peak=    5.348 closest distance to " O   HOH Z  11 " =    1.346
peak=    5.071 closest distance to " CG  PRO A  90 " =    1.208
peak=    4.977 closest distance to " CG  PRO A 280 " =    0.839
peak=    4.889 closest distance to " CG  PRO A 213 " =    1.221
peak=    4.870 closest distance to " CG  PRO A 198 " =    1.355
peak=    4.786 closest distance to " O   HOH Z 134 " =    1.653
peak=    4.758 closest distance to " O   HOH Z 132 " =    1.388
peak=    4.741 closest distance to " O   HOH Z 282 " =    1.651
peak=    4.733 closest distance to " CB  LEU A 228 " =    1.112
peak=    4.718 closest distance to " O   HOH Z 193 " =    2.144
peak=    4.698 closest distance to " O   HOH Z  80 " =    1.909
peak=    4.693 closest distance to " O   HOH Z  15 " =    2.012
peak=    4.686 closest distance to " CB  ARG A 275 " =    0.907
peak=    4.681 closest distance to " O   HOH Z 214 " =    1.336
peak=    4.567 closest distance to " O   HOH Z 126 " =    1.794
peak=    4.501 closest distance to " O   HOH Z 260 " =    1.391
peak=    4.486 closest distance to " O   HOH Z  40 " =    1.957
peak=    4.467 closest distance to " CB  GLU A 128 " =    1.108
peak=    4.453 closest distance to " CB  PRO A  54 " =    0.836
peak=    4.429 closest distance to " O   HOH Z  48 " =    1.618
peak=    4.418 closest distance to " O   ASP A 132 " =    3.874
peak=    4.371 closest distance to " O   HOH Z 207 " =    1.941
peak=    4.369 closest distance to " O   HOH Z 272 " =    2.005
peak=    4.364 closest distance to " O   HOH Z 183 " =    1.708
peak=    4.347 closest distance to " CB  PRO A 198 " =    0.988
peak=    4.326 closest distance to " O   HOH Z 368 " =    2.046
peak=    4.318 closest distance to " O   HOH Z 127 " =    1.234
peak=    4.316 closest distance to " O   HOH Z 232 " =    2.181
peak=    4.304 closest distance to " O   HOH Z 247 " =    1.454
peak=    4.303 closest distance to " O   HOH Z 389 " =    1.902
peak=    4.298 closest distance to " O   HOH Z  30 " =    1.904
peak=    4.279 closest distance to " CG  PRO A 243 " =    1.115
peak=    4.258 closest distance to " O   HOH Z 182 " =    1.317
peak=    4.198 closest distance to " CB  GLU A 152 " =    1.162
peak=    4.197 closest distance to " CA  ALA A  21 " =    1.292
peak=    4.195 closest distance to " OD1 ASN A 217 " =    1.712
peak=    4.191 closest distance to " O   HOH Z  67 " =    1.890
peak=    4.178 closest distance to " N   ASN A  39 " =    1.347
peak=    4.175 closest distance to " O   HOH Z 298 " =    1.746
peak=    4.172 closest distance to " O   HOH Z 236 " =    1.945
peak=    4.168 closest distance to " O   HOH Z 246 " =    1.803
peak=    4.158 closest distance to " CD  LYS A 119 " =    1.424
peak=    4.156 closest distance to " CB  SER A   3 " =    1.538
peak=    4.154 closest distance to " O   HOH Z 108 " =    1.726
peak=    4.148 closest distance to " CB  GLN A 183 " =    1.169
peak=    4.138 closest distance to " OD2 ASP A 286 " =    2.931
peak=    4.128 closest distance to " CA  ASP A 191 " =    0.819
peak=    4.121 closest distance to " CB  VAL A 202 " =    1.553
peak=    4.111 closest distance to " CA  TYR A  30 " =    1.035
peak=    4.111 closest distance to " O   HOH Z 371 " =    3.348
peak=    4.110 closest distance to " O   PRO A 198 " =    1.544
peak=    4.097 closest distance to " NH2 ARG A 156 " =    1.255
peak=    4.084 closest distance to " CG1 ILE A  33 " =    1.310
peak=    4.080 closest distance to " CB  TRP A 179 " =    1.392
peak=    4.062 closest distance to " O   HOH Z 163 " =    1.766
peak=    4.057 closest distance to " CG2 THR A 221 " =    0.925
peak=    4.046 closest distance to " O   HOH Z 411 " =    3.305
peak=    4.023 closest distance to " O   HOH Z 132 " =    1.966
peak=    4.003 closest distance to " O   HOH Z 186 " =    1.197
peak=    3.997 closest distance to " CA  GLN A 223 " =    0.935
peak=    3.996 closest distance to " O   HOH Z 403 " =    1.792
peak=    3.989 closest distance to " CB  TYR A 169 " =    0.776
peak=    3.983 closest distance to " O   HOH Z 124 " =    1.365
peak=    3.975 closest distance to " O   HOH Z 112 " =    1.457
peak=    3.972 closest distance to " O   HOH Z  54 " =    2.281
peak=    3.970 closest distance to " CD1 LEU A 300 " =    1.274
peak=    3.967 closest distance to " OD1 ASP A 238 " =    0.905
peak=    3.964 closest distance to " O   SER A  87 " =    2.114
peak=    3.960 closest distance to " OE1 GLN A  11 " =    1.910
peak=    3.956 closest distance to " O   HOH Z 132 " =    2.509
peak=    3.952 closest distance to " CB  TRP A 266 " =    0.960
peak=    3.949 closest distance to " O   HOH Z 394 " =    1.706
peak=    3.944 closest distance to " O   HOH Z 426 " =    1.426
peak=    3.931 closest distance to " CB  ASN A 148 " =    1.080
peak=    3.922 closest distance to " O   HOH Z  54 " =    1.752
peak=    3.919 closest distance to " O   HOH Z 344 " =    3.074
peak=    3.919 closest distance to " CA  GLU A 152 " =    0.891
peak=    3.904 closest distance to " CA  THR A 221 " =    0.919
peak=    3.901 closest distance to " O   HOH Z 189 " =    2.034
peak=    3.898 closest distance to " O   HOH Z 154 " =    1.321
peak=    3.896 closest distance to " O   HOH Z  88 " =    3.616
peak=    3.879 closest distance to " O   HOH Z  97 " =    1.987
peak=    3.872 closest distance to " O   HOH Z 211 " =    1.309
peak=    3.860 closest distance to " O   HOH Z  39 " =    1.417
peak=    3.846 closest distance to " O   HOH Z  78 " =    2.251
peak=    3.843 closest distance to " CB  SER A 141 " =    0.947
peak=    3.838 closest distance to " CB  GLU A 277 " =    3.718
peak=    3.835 closest distance to " O   HOH Z 142 " =    1.656
peak=    3.830 closest distance to " NZ  LYS A 117 " =    3.202
peak=    3.827 closest distance to " CA  GLY A 196 " =    1.015
peak=    3.827 closest distance to " CB  MET A  47 " =    1.013
peak=    3.824 closest distance to " CB  SER A 216 " =    0.776
peak=    3.817 closest distance to " NE AARG A 275 " =    1.453
peak=    3.814 closest distance to " OD1 ASN A  69 " =    2.486
peak=    3.809 closest distance to " O   HOH Z 387 " =    2.457
peak=    3.786 closest distance to " CD1 TRP A 266 " =    1.325
peak=    3.773 closest distance to " O   HOH Z  21 " =    1.847
peak=    3.750 closest distance to " CG AARG A 275 " =    1.058
peak=    3.748 closest distance to " CG2 VAL A  78 " =    1.049
peak=    3.742 closest distance to " O   HOH Z   4 " =    1.966
peak=    3.739 closest distance to " O   HOH Z  44 " =    2.469
peak=    3.738 closest distance to " CG  ARG A  66 " =    2.684
peak=    3.738 closest distance to " CG1 VAL A 153 " =    1.047
peak=    3.734 closest distance to " CA  ARG A  36 " =    1.193
peak=    3.734 closest distance to " O   HOH Z 135 " =    1.932
peak=    3.731 closest distance to " CB  ASN A 187 " =    1.051
peak=    3.729 closest distance to " O   HOH Z 316 " =    3.056
peak=    3.727 closest distance to " CA  ASP A 124 " =    0.757
peak=    3.721 closest distance to " O   HOH Z 374 " =    2.599
peak=    3.714 closest distance to " O   HOH Z 215 " =    1.486
peak=    3.713 closest distance to " CB  PRO A  54 " =    1.349
peak=    3.705 closest distance to " O   HOH Z 276 " =    1.385
peak=    3.701 closest distance to " CB  PHE A  16 " =    1.089
peak=    3.700 closest distance to " O   HOH Z 108 " =    1.932
peak=    3.692 closest distance to " O   HOH Z 102 " =    1.319
peak=    3.692 closest distance to " C   SER A  32 " =    1.059
peak=    3.689 closest distance to " O   HOH Z 313 " =    2.302
peak=    3.686 closest distance to " CB  GLN A  58 " =    0.826
peak=    3.674 closest distance to " CB  ARG A 190 " =    1.759
peak=    3.661 closest distance to " O   HOH Z 193 " =    2.319
peak=    3.653 closest distance to " CZ  PHE A 192 " =    0.952
peak=    3.651 closest distance to " O   HOH Z 243 " =    1.279
peak=    3.648 closest distance to " CG1BVAL A  72 " =    1.703
peak=    3.647 closest distance to " O   HOH Z 128 " =    2.281
peak=    3.639 closest distance to " O   HOH Z  59 " =    2.443
peak=    3.636 closest distance to " CG  LEU A 167 " =    1.094
peak=    3.632 closest distance to " CB  ARG A  79 " =    1.333
peak=    3.621 closest distance to " O   HOH Z 128 " =    2.416
peak=    3.616 closest distance to " O   HOH Z 313 " =    1.669
peak=    3.615 closest distance to " O   HOH Z 145 " =    2.260
peak=    3.609 closest distance to " CZ  PHE A 208 " =    1.119
peak=    3.606 closest distance to " O   HOH Z 116 " =    1.810
peak=    3.606 closest distance to " O   HOH Z 368 " =    2.553
peak=    3.604 closest distance to " ND2 ASN A 187 " =    1.546
peak=    3.604 closest distance to " O   HOH Z 423 " =    1.942
peak=    3.602 closest distance to " O   HOH Z 425 " =    1.540
peak=    3.597 closest distance to " CA  ILE A 263 " =    0.958
peak=    3.597 closest distance to " O   HOH Z 326 " =    1.509
peak=    3.596 closest distance to " CD  ARG A 159 " =    0.807
peak=    3.595 closest distance to " CD  ARG A 269 " =    0.860
peak=    3.593 closest distance to " CD  LYS A 166 " =    1.415
peak=    3.592 closest distance to " O   HOH Z 369 " =    1.997
peak=    3.586 closest distance to " CG2BVAL A  41 " =    0.990
peak=    3.584 closest distance to " CB  GLU A 152 " =    1.580
peak=    3.579 closest distance to " NH2BARG A 145 " =    2.058
peak=    3.566 closest distance to " O   HOH Z 281 " =    3.953
peak=    3.565 closest distance to " O   HOH Z 184 " =    0.875
peak=    3.565 closest distance to " O   HOH Z 180 " =    2.130
peak=    3.565 closest distance to " CZ  PHE A 218 " =    1.060
peak=    3.562 closest distance to " NE  ARG A 156 " =    1.002
peak=    3.542 closest distance to " O   HOH Z  63 " =    2.041
peak=    3.538 closest distance to " CG  ASP A 231 " =    1.068
peak=    3.530 closest distance to " CB  ARG A 139 " =    0.893
peak=    3.521 closest distance to " O   HOH Z 155 " =    1.606
peak=    3.520 closest distance to " O   HOH Z 217 " =    1.376
peak=    3.519 closest distance to " O   HOH Z 287 " =    1.780
peak=    3.516 closest distance to " O   HOH Z 345 " =    3.241
peak=    3.513 closest distance to " O   HOH Z 261 " =    2.051
peak=    3.509 closest distance to " O   HOH Z 104 " =    3.113
peak=    3.506 closest distance to " O   HOH Z 199 " =    1.060
peak=    3.501 closest distance to " O   HOH Z  19 " =    2.370
peak=    3.500 closest distance to " O   THR A 251 " =    1.319
peak=    3.498 closest distance to " O   HOH Z 234 " =    1.904
peak=    3.493 closest distance to " OE1 GLN A  58 " =    1.391
peak=    3.488 closest distance to " O   HOH Z 173 " =    1.961
peak=    3.486 closest distance to " O   HOH Z 196 " =    1.062
peak=    3.478 closest distance to " OD1 ASP A 231 " =    1.839
peak=    3.478 closest distance to " CA  MET A  40 " =    1.085
peak=    3.477 closest distance to " CB  LEU A 143 " =    1.037
peak=    3.474 closest distance to " O   HOH Z  47 " =    1.432
peak=    3.467 closest distance to " O   HOH Z  44 " =    1.849
peak=    3.458 closest distance to " O   HOH Z 118 " =    1.748
peak=    3.453 closest distance to " O   HOH Z 174 " =    2.232
peak=    3.452 closest distance to " CD2 LEU A 255 " =    1.364
peak=    3.451 closest distance to " NH1 ARG A  56 " =    1.281
peak=    3.445 closest distance to " O   HOH Z 434 " =    1.429
peak=    3.443 closest distance to " O   HOH Z 263 " =    2.136
peak=    3.439 closest distance to " O   GLY A  75 " =    3.393
peak=    3.435 closest distance to " NE2 GLN A  11 " =    1.128
peak=    3.427 closest distance to " O   ALA A 165 " =    1.248
peak=    3.426 closest distance to " CB  ALA A 291 " =    1.304
peak=    3.425 closest distance to " O   HOH Z 346 " =    1.550
peak=    3.424 closest distance to " CD BLYS A 290 " =    1.018
peak=    3.424 closest distance to " CG  GLN A  77 " =    0.741
peak=    3.419 closest distance to " O   HOH Z 427 " =    2.973
peak=    3.414 closest distance to " NH1BARG A 145 " =    1.056
peak=    3.414 closest distance to " O   HOH Z   6 " =    2.127
peak=    3.414 closest distance to " O   HOH Z 301 " =    2.048
peak=    3.413 closest distance to " NH2AARG A 190 " =    1.592
peak=    3.411 closest distance to " CA  ALA A  51 " =    0.831
peak=    3.411 closest distance to " CA  ALA A 160 " =    0.883
peak=    3.409 closest distance to " N   TYR A  15 " =    0.788
peak=    3.408 closest distance to " CB  GLN A 194 " =    0.838
peak=    3.406 closest distance to " O   HOH Z  22 " =    2.401
peak=    3.401 closest distance to " CB  TYR A 116 " =    1.266
peak=    3.396 closest distance to " O   HOH Z 352 " =    1.868
peak=    3.396 closest distance to " O   MET A 105 " =    1.778
peak=    3.383 closest distance to " O   HOH Z 193 " =    1.638
peak=    3.383 closest distance to " O   HOH Z 295 " =    1.460
peak=    3.383 closest distance to " O   HOH Z 437 " =    1.668
peak=    3.381 closest distance to " CB  ILE A 199 " =    1.010
peak=    3.379 closest distance to " O   HOH Z 227 " =    1.757
peak=    3.379 closest distance to " CB  ALA A 244 " =    0.966
peak=    3.377 closest distance to " O   HOH Z 284 " =    3.038
peak=    3.372 closest distance to " CA  TYR A 116 " =    1.505
peak=    3.372 closest distance to " CB  ASN A 285 " =    0.930
peak=    3.366 closest distance to " O   SER A  26 " =    1.730
peak=    3.365 closest distance to " O   HOH Z 223 " =    1.116
peak=    3.363 closest distance to " O   HOH Z 368 " =    3.458
peak=    3.359 closest distance to " CA  LEU A 282 " =    1.022
peak=    3.358 closest distance to " CA  ALA A 154 " =    1.351
peak=    3.358 closest distance to " CD  ARG A 219 " =    0.922
peak=    3.356 closest distance to " NE BARG A 102 " =    1.397
peak=    3.356 closest distance to " O   HOH Z 139 " =    3.251
peak=    3.340 closest distance to " O   HOH Z 345 " =    1.805
peak=    3.339 closest distance to " O   HOH Z 332 " =    1.547
peak=    3.336 closest distance to " CB  ASN A 148 " =    1.736
peak=    3.332 closest distance to " CD  PRO A 280 " =    1.019
peak=    3.329 closest distance to " O   HOH Z 214 " =    1.869
peak=    3.328 closest distance to " O   TRP A 274 " =    1.608
peak=    3.325 closest distance to " NZ  LYS A  76 " =    1.242
peak=    3.325 closest distance to " CG  HIS A  81 " =    1.525
peak=    3.319 closest distance to " O   HOH Z  14 " =    2.084
peak=    3.317 closest distance to " O   HOH Z 147 " =    1.693
peak=    3.316 closest distance to " O   HOH Z 392 " =    1.946
peak=    3.314 closest distance to " O   HOH Z 404 " =    1.426
peak=    3.311 closest distance to " O   HOH Z  87 " =    2.690
peak=    3.310 closest distance to " CG1 ILE A 120 " =    1.125
peak=    3.310 closest distance to " O   HOH Z  93 " =    2.437
peak=    3.307 closest distance to " CB  ASP A 124 " =    0.714
peak=    3.306 closest distance to " O   HOH Z 155 " =    2.894
peak=    3.305 closest distance to " O   HOH Z  20 " =    2.020
peak=    3.303 closest distance to " OE1 GLN A  58 " =    5.747
peak=    3.301 closest distance to " O   HOH Z 420 " =    5.937
peak=    3.301 closest distance to " CG2 VAL A 197 " =    1.239
peak=    3.299 closest distance to " NE2 HIS A 115 " =    0.913
peak=    3.297 closest distance to " O   HOH Z 438 " =    2.538
peak=    3.294 closest distance to " O   HOH Z 426 " =    3.220
peak=    3.293 closest distance to " CD2 LEU A 297 " =    0.855
peak=    3.292 closest distance to " O   HOH Z 156 " =    2.709
peak=    3.286 closest distance to " CD  ARG A 195 " =    3.590
peak=    3.282 closest distance to " O   HOH Z 130 " =    3.882
peak=    3.279 closest distance to " CD  PRO A  54 " =    1.181
peak=    3.278 closest distance to " CA  LYS A  48 " =    1.314
peak=    3.277 closest distance to " N   ASN A 127 " =    1.247
peak=    3.275 closest distance to " CD  ARG A 195 " =    0.951
peak=    3.274 closest distance to " O   GLY A  57 " =    2.568
peak=    3.274 closest distance to " O   HOH Z 432 " =    1.666
peak=    3.273 closest distance to " N   ASN A 252 " =    1.166
peak=    3.271 closest distance to " O   HOH Z 406 " =    1.613
peak=    3.267 closest distance to " CB  GLN A  73 " =    0.991
peak=    3.264 closest distance to " CZ AARG A 102 " =    1.886
peak=    3.264 closest distance to " O   HOH Z 207 " =    1.696
peak=    3.259 closest distance to " CG2 ILE A  33 " =    1.564
peak=    3.258 closest distance to " SD  MET A  93 " =    1.500
peak=    3.256 closest distance to " CB  ALA A 100 " =    1.388
peak=    3.253 closest distance to " CB  TYR A  30 " =    1.333
peak=    3.250 closest distance to " O   ALA A   1 " =    1.439
peak=    3.247 closest distance to " OH  TYR A  30 " =    1.322
peak=    3.245 closest distance to " CB  MET A  40 " =    0.776
peak=    3.242 closest distance to " CB  ARG A  56 " =    1.225
peak=    3.242 closest distance to " CB  ALA A 248 " =    1.032
peak=    3.238 closest distance to " O   HOH Z 343 " =    2.433
peak=    3.235 closest distance to " OG  SER A  97 " =    3.588
peak=    3.231 closest distance to " CE3 TRP A 274 " =    3.710
peak=    3.226 closest distance to " O   GLN A  55 " =    1.881
peak=    3.222 closest distance to " CB  LEU A  83 " =    0.863
peak=    3.221 closest distance to " C   LYS A 290 " =    1.248
peak=    3.221 closest distance to " OD1 ASN A 252 " =    1.213
peak=    3.220 closest distance to " CA  GLU A  46 " =    0.760
peak=    3.216 closest distance to " O   HOH Z 291 " =    1.580
peak=    3.216 closest distance to " CD1 LEU A 222 " =    0.940
peak=    3.214 closest distance to " CB  PRO A 163 " =    3.996
peak=    3.214 closest distance to " CB  VAL A 265 " =    1.234
peak=    3.212 closest distance to " CA  ALA A 158 " =    1.039
peak=    3.212 closest distance to " CE1 PHE A 155 " =    1.349
peak=    3.204 closest distance to " O   HOH Z 197 " =    2.055
peak=    3.202 closest distance to " O   HOH Z  43 " =    1.262
peak=    3.202 closest distance to " O   HOH Z 133 " =    1.695
peak=    3.201 closest distance to " O   SER A 164 " =    1.087
peak=    3.193 closest distance to " O   HOH Z 185 " =    1.821
peak=    3.192 closest distance to " O   HOH Z 420 " =    2.003
peak=    3.191 closest distance to " O   GLY A  23 " =    2.359
peak=    3.189 closest distance to " CB  TRP A 123 " =    1.060
peak=    3.184 closest distance to " O   HOH Z 383 " =    1.995
peak=    3.183 closest distance to " O   HOH Z 377 " =    1.423
peak=    3.182 closest distance to " O   HOH Z 244 " =    1.704
peak=    3.182 closest distance to " CB  ILE A 120 " =    1.236
peak=    3.179 closest distance to " CB  SER A  62 " =    0.845
peak=    3.178 closest distance to " O   HOH Z  50 " =    1.700
peak=    3.172 closest distance to " CA  ALA A 154 " =    1.018
peak=    3.168 closest distance to " O   HOH Z 248 " =    1.565
peak=    3.167 closest distance to " NZ  LYS A 193 " =    1.539
peak=    3.167 closest distance to " OE1 GLU A 152 " =    0.879
peak=    3.166 closest distance to " O   GLY A  91 " =    1.127
peak=    3.165 closest distance to " CA  GLY A 211 " =    1.039
peak=    3.163 closest distance to " CA  ASP A 162 " =    1.146
peak=    3.155 closest distance to " CG2 VAL A 257 " =    0.878
peak=    3.153 closest distance to " CB  ALA A 256 " =    1.206
peak=    3.150 closest distance to " CA  THR A 264 " =    0.856
peak=    3.146 closest distance to " CE1 PHE A 208 " =    1.148
peak=    3.142 closest distance to " CB  ASN A  39 " =    0.889
peak=    3.138 closest distance to " CA  ASP A 140 " =    1.226
peak=    3.138 closest distance to " CB  MET A 105 " =    1.187
peak=    3.136 closest distance to " O   HOH Z 172 " =    2.412
peak=    3.132 closest distance to " O   HOH Z 427 " =    3.065
peak=    3.130 closest distance to " CA  MET A 105 " =    1.127
peak=    3.128 closest distance to " NZ ALYS A 290 " =    1.133
peak=    3.127 closest distance to " CA  LYS A 117 " =    1.253
peak=    3.126 closest distance to " CD1 TYR A 169 " =    1.529
peak=    3.124 closest distance to " O   HOH Z 126 " =    1.487
peak=    3.120 closest distance to " NH1 ARG A  14 " =    1.188
peak=    3.117 closest distance to " O   HOH Z  49 " =    1.379
peak=    3.115 closest distance to " O   HOH Z 329 " =    3.651
peak=    3.097 closest distance to " O   HOH Z 118 " =    1.433
peak=    3.090 closest distance to " CG ALYS A 290 " =    1.191
peak=    3.089 closest distance to " CB  GLU A 277 " =    1.091
peak=    3.084 closest distance to " CB  GLU A 236 " =    0.988
peak=    3.081 closest distance to " CB  ASN A 127 " =    0.890
peak=    3.077 closest distance to " O   HOH Z 424 " =    2.692
peak=    3.077 closest distance to " O   HOH Z 166 " =    1.575
peak=    3.069 closest distance to " O   HOH Z 302 " =    1.846
peak=    3.069 closest distance to " O   HOH Z 279 " =    2.432
peak=    3.067 closest distance to " CG  GLN A  11 " =    1.151
peak=    3.066 closest distance to " CA  VAL A  41 " =    0.766
peak=    3.061 closest distance to " O   HOH Z 303 " =    2.227
peak=    3.057 closest distance to " O   HOH Z  50 " =    3.581
peak=    3.047 closest distance to " O   HOH Z 299 " =    2.326
peak=    3.046 closest distance to " CG  MET A 188 " =    1.158
peak=    3.042 closest distance to " NH1BARG A 145 " =    1.176
peak=    3.039 closest distance to " O   HOH Z 152 " =    1.363
peak=    3.037 closest distance to " O   HOH Z  85 " =    2.130
peak=    3.028 closest distance to " O   HOH Z 162 " =    2.047
peak=    2.994 closest distance to " O   HOH Z 280 " =    2.257

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.624 - 5.480
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 206 from: 209
   mapped sites are within: 0.716 - 5.480

peak=   -4.599 closest distance to " O   HOH Z 290 " =    0.897
peak=   -4.223 closest distance to " OG ASER A 134 " =    1.343
peak=   -4.169 closest distance to " O   HOH Z  17 " =    1.123
peak=   -4.144 closest distance to " N   ALA A  43 " =    2.458
peak=   -4.142 closest distance to " O   HOH Z 266 " =    4.313
peak=   -4.109 closest distance to " O   HOH Z 221 " =    1.222
peak=   -4.100 closest distance to " O   HOH Z  19 " =    1.806
peak=   -4.015 closest distance to " O   HOH Z 231 " =    1.840
peak=   -4.005 closest distance to " NH2 ARG A  66 " =    1.663
peak=   -4.002 closest distance to " O   HOH Z 166 " =    1.857
peak=   -3.994 closest distance to " O   HOH Z  52 " =    1.799
peak=   -3.965 closest distance to " O   HOH Z 407 " =    3.729
peak=   -3.962 closest distance to " CD2 LEU A 300 " =    2.931
peak=   -3.946 closest distance to " CE  MET A  93 " =    1.152
peak=   -3.944 closest distance to " OG  SER A  97 " =    2.276
peak=   -3.942 closest distance to " O   GLY A 196 " =    1.185
peak=   -3.933 closest distance to " O   HOH Z 283 " =    1.810
peak=   -3.926 closest distance to " CG  GLN A  58 " =    1.136
peak=   -3.923 closest distance to " O   GLY A 118 " =    2.363
peak=   -3.923 closest distance to " O   HOH Z  11 " =    1.756
peak=   -3.912 closest distance to " CD2 PHE A  59 " =    2.418
peak=   -3.908 closest distance to " O   HOH Z  71 " =    1.195
peak=   -3.900 closest distance to " C   ALA A 158 " =    1.187
peak=   -3.894 closest distance to " OXT GLY A 302 " =    2.894
peak=   -3.881 closest distance to " O   HOH Z  13 " =    1.223
peak=   -3.866 closest distance to " CG  GLU A  53 " =    1.505
peak=   -3.865 closest distance to " O   HOH Z  98 " =    1.765
peak=   -3.865 closest distance to " CG  ASP A 231 " =    0.779
peak=   -3.859 closest distance to " CG1 VAL A 112 " =    2.619
peak=   -3.856 closest distance to " O   HOH Z  43 " =    1.556
peak=   -3.829 closest distance to " C   ASN A 285 " =    2.610
peak=   -3.818 closest distance to " CG  MET A 105 " =    0.940
peak=   -3.811 closest distance to " CH2 TRP A 179 " =    1.138
peak=   -3.764 closest distance to " O   HOH Z 377 " =    0.910
peak=   -3.755 closest distance to " O   HOH Z 241 " =    1.015
peak=   -3.724 closest distance to " O   HOH Z 185 " =    2.475
peak=   -3.719 closest distance to " CE  MET A 105 " =    2.019
peak=   -3.719 closest distance to " OE2 GLU A   2 " =    1.278
peak=   -3.711 closest distance to " CD2 LEU A 143 " =    2.562
peak=   -3.705 closest distance to " CE2 TYR A  30 " =    2.727
peak=   -3.703 closest distance to " O   HOH Z 221 " =    1.650
peak=   -3.699 closest distance to " CA  SER A 164 " =    2.093
peak=   -3.676 closest distance to " CD2 LEU A 237 " =    2.531
peak=   -3.669 closest distance to " O   ILE A 109 " =    2.684
peak=   -3.666 closest distance to " O   HOH Z  91 " =    2.171
peak=   -3.664 closest distance to " CB  LEU A 167 " =    2.152
peak=   -3.663 closest distance to " CD1 LEU A 101 " =    2.619
peak=   -3.656 closest distance to " CB  CYS A 254 " =    2.400
peak=   -3.648 closest distance to " O   HOH Z 377 " =    1.684
peak=   -3.645 closest distance to " OD2 ASP A 171 " =    1.811
peak=   -3.643 closest distance to " O   HOH Z 184 " =    1.223
peak=   -3.642 closest distance to " O   HOH Z 151 " =    1.378
peak=   -3.631 closest distance to " O   HOH Z 313 " =    1.021
peak=   -3.617 closest distance to " OG BSER A 134 " =    1.816
peak=   -3.604 closest distance to " N   ALA A 226 " =    2.023
peak=   -3.602 closest distance to " O   HOH Z 213 " =    1.327
peak=   -3.592 closest distance to " O   HOH Z 388 " =    1.910
peak=   -3.591 closest distance to " SG ACYS A 201 " =    2.423
peak=   -3.580 closest distance to " CG  ARG A 269 " =    2.290
peak=   -3.578 closest distance to " OG1 THR A  82 " =    1.933
peak=   -3.574 closest distance to " CD  ARG A 195 " =    5.110
peak=   -3.552 closest distance to " N   GLN A  58 " =    1.694
peak=   -3.551 closest distance to " OD1 ASN A 148 " =    1.711
peak=   -3.550 closest distance to " O   HOH Z 222 " =    1.232
peak=   -3.548 closest distance to " O   HOH Z 353 " =    2.312
peak=   -3.547 closest distance to " O   HOH Z  38 " =    1.213
peak=   -3.540 closest distance to " CB  PRO A 163 " =    2.757
peak=   -3.540 closest distance to " O   HOH Z 150 " =    1.181
peak=   -3.532 closest distance to " CD1 PHE A  59 " =    1.830
peak=   -3.530 closest distance to " NE2 GLN A  58 " =    0.835
peak=   -3.527 closest distance to " OD2 ASP A 171 " =    2.237
peak=   -3.519 closest distance to " C   ASN A 187 " =    1.872
peak=   -3.516 closest distance to " CB  ALA A  43 " =    2.501
peak=   -3.515 closest distance to " O   HOH Z  92 " =    1.281
peak=   -3.514 closest distance to " CD1 LEU A 228 " =    2.453
peak=   -3.510 closest distance to " ND2 ASN A  45 " =    0.906
peak=   -3.502 closest distance to " CB  TYR A  15 " =    2.257
peak=   -3.502 closest distance to " CD  ARG A 156 " =    1.966
peak=   -3.500 closest distance to " CA  SER A 276 " =    1.411
peak=   -3.491 closest distance to " OE1 GLN A  88 " =    1.019
peak=   -3.487 closest distance to " CG2 THR A   4 " =    1.905
peak=   -3.486 closest distance to " OD1 ASP A 191 " =    1.555
peak=   -3.476 closest distance to " CA  VAL A 197 " =    1.008
peak=   -3.462 closest distance to " O   HOH Z   5 " =    1.549
peak=   -3.461 closest distance to " O   HOH Z 423 " =    2.335
peak=   -3.457 closest distance to " O   PRO A 198 " =    1.273
peak=   -3.444 closest distance to " O   HOH Z  92 " =    1.375
peak=   -3.439 closest distance to " CZ  ARG A  66 " =    0.716
peak=   -3.438 closest distance to " OG  SER A  32 " =    0.994
peak=   -3.437 closest distance to " CD  ARG A 139 " =    1.593
peak=   -3.435 closest distance to " O   HOH Z  15 " =    1.692
peak=   -3.435 closest distance to " CB  PRO A 243 " =    2.637
peak=   -3.430 closest distance to " O   HOH Z 117 " =    4.512
peak=   -3.430 closest distance to " O   HOH Z 275 " =    1.614
peak=   -3.424 closest distance to " C   LEU A 143 " =    1.928
peak=   -3.423 closest distance to " CD  LYS A 289 " =    2.513
peak=   -3.420 closest distance to " CA  GLY A 241 " =    2.267
peak=   -3.416 closest distance to " OH  TYR A 169 " =    1.021
peak=   -3.416 closest distance to " O   HOH Z 385 " =    3.958
peak=   -3.415 closest distance to " CD2 LEU A 167 " =    1.787
peak=   -3.412 closest distance to " O   HOH Z  93 " =    1.599
peak=   -3.406 closest distance to " O   HOH Z 259 " =    1.065
peak=   -3.404 closest distance to " CB  ASN A  39 " =    2.107
peak=   -3.402 closest distance to " CG  LYS A 193 " =    2.540
peak=   -3.396 closest distance to " OG  SER A 245 " =    0.898
peak=   -3.395 closest distance to " O   HOH Z 380 " =    4.829
peak=   -3.385 closest distance to " O   HOH Z 231 " =    1.354
peak=   -3.378 closest distance to " CG  TRP A 266 " =    1.631
peak=   -3.377 closest distance to " O   HOH Z 308 " =    1.627
peak=   -3.372 closest distance to " NH2 ARG A  66 " =    5.136
peak=   -3.371 closest distance to " O   HOH Z 265 " =    1.965
peak=   -3.371 closest distance to " O   HOH Z 414 " =    1.306
peak=   -3.365 closest distance to " ND2 ASN A  60 " =    1.517
peak=   -3.364 closest distance to " O   HOH Z 189 " =    1.816
peak=   -3.359 closest distance to " NH1 ARG A 195 " =    2.715
peak=   -3.354 closest distance to " O   HOH Z 396 " =    1.631
peak=   -3.351 closest distance to " O   HOH Z 177 " =    1.363
peak=   -3.351 closest distance to " CA  VAL A  67 " =    2.882
peak=   -3.349 closest distance to " O   VAL A 153 " =    2.147
peak=   -3.348 closest distance to " C   SER A 271 " =    1.220
peak=   -3.337 closest distance to " CZ  TYR A 169 " =    1.826
peak=   -3.331 closest distance to " CA  PRO A 198 " =    1.124
peak=   -3.330 closest distance to " C   HIS A 108 " =    1.112
peak=   -3.327 closest distance to " O   HOH Z 182 " =    0.847
peak=   -3.325 closest distance to " O   TRP A  92 " =    1.862
peak=   -3.323 closest distance to " CA  TYR A  68 " =    2.719
peak=   -3.316 closest distance to " CD  ARG A 159 " =    1.234
peak=   -3.310 closest distance to " O   HOH Z 418 " =    1.474
peak=   -3.308 closest distance to " NH2AARG A 275 " =    5.480
peak=   -3.308 closest distance to " C   GLN A 240 " =    2.261
peak=   -3.308 closest distance to " O   HOH Z 252 " =    4.266
peak=   -3.303 closest distance to " O   HOH Z  98 " =    1.434
peak=   -3.301 closest distance to " O   GLY A 211 " =    1.519
peak=   -3.300 closest distance to " CD1 TRP A 179 " =    0.992
peak=   -3.297 closest distance to " O   HOH Z  94 " =    2.169
peak=   -3.296 closest distance to " N   ARG A 275 " =    1.656
peak=   -3.291 closest distance to " O   HOH Z 409 " =    4.704
peak=   -3.289 closest distance to " O   HOH Z 100 " =    0.768
peak=   -3.289 closest distance to " CG2 THR A 221 " =    2.295
peak=   -3.286 closest distance to " CG  ASP A  50 " =    2.261
peak=   -3.285 closest distance to " O   HOH Z 136 " =    1.392
peak=   -3.282 closest distance to " CD2 TYR A 293 " =    2.063
peak=   -3.280 closest distance to " O   HOH Z 111 " =    1.231
peak=   -3.280 closest distance to " CE2 TRP A  85 " =    1.058
peak=   -3.277 closest distance to " CA  ASN A 127 " =    1.188
peak=   -3.276 closest distance to " CH2 TRP A 177 " =    2.073
peak=   -3.270 closest distance to " O   HOH Z 236 " =    1.490
peak=   -3.264 closest distance to " NZ  LYS A 117 " =    1.734
peak=   -3.262 closest distance to " O   HOH Z 390 " =    2.359
peak=   -3.262 closest distance to " O   VAL A 125 " =    2.030
peak=   -3.261 closest distance to " OG  SER A  63 " =    1.390
peak=   -3.258 closest distance to " CD  LYS A 119 " =    0.994
peak=   -3.257 closest distance to " CD  GLU A 236 " =    1.052
peak=   -3.254 closest distance to " O   HOH Z 148 " =    3.404
peak=   -3.253 closest distance to " O   HOH Z 234 " =    4.264
peak=   -3.243 closest distance to " CE3 TRP A 150 " =    1.809
peak=   -3.243 closest distance to " O   HOH Z 423 " =    1.069
peak=   -3.237 closest distance to " O   VAL A 174 " =    2.036
peak=   -3.233 closest distance to " O   HOH Z 435 " =    2.589
peak=   -3.230 closest distance to " O   HOH Z  37 " =    1.509
peak=   -3.229 closest distance to " OG  SER A  62 " =    1.487
peak=   -3.226 closest distance to " O   HOH Z 384 " =    2.207
peak=   -3.222 closest distance to " ND2 ASN A 249 " =    1.891
peak=   -3.209 closest distance to " CB  GLN A  55 " =    1.353
peak=   -3.206 closest distance to " OG  SER A  87 " =    1.459
peak=   -3.206 closest distance to " CD  PRO A 198 " =    1.198
peak=   -3.201 closest distance to " O   ALA A 256 " =    1.465
peak=   -3.199 closest distance to " CD1 TYR A 247 " =    2.387
peak=   -3.199 closest distance to " CG  LEU A  83 " =    2.028
peak=   -3.198 closest distance to " C   SER A 206 " =    1.630
peak=   -3.196 closest distance to " O   HOH Z 243 " =    1.674
peak=   -3.194 closest distance to " CD2 TRP A 274 " =    2.371
peak=   -3.194 closest distance to " CA  GLY A 133 " =    1.886
peak=   -3.193 closest distance to " CB  ALA A 248 " =    1.936
peak=   -3.189 closest distance to " O   HOH Z 292 " =    4.354
peak=   -3.186 closest distance to " OD1 ASN A 249 " =    1.045
peak=   -3.182 closest distance to " CA  GLY A 133 " =    2.343
peak=   -3.177 closest distance to " O   HOH Z 166 " =    1.666
peak=   -3.175 closest distance to " CB  ALA A 291 " =    2.465
peak=   -3.174 closest distance to " C   THR A 279 " =    1.224
peak=   -3.173 closest distance to " O   LEU A 167 " =    1.574
peak=   -3.172 closest distance to " OG  SER A 206 " =    1.805
peak=   -3.168 closest distance to " NH2 ARG A 159 " =    2.330
peak=   -3.167 closest distance to " O   HOH Z 389 " =    2.013
peak=   -3.160 closest distance to " CG  ARG A 219 " =    2.382
peak=   -3.157 closest distance to " OD2 ASP A 200 " =    1.336
peak=   -3.155 closest distance to " CA  ASP A 298 " =    1.099
peak=   -3.143 closest distance to " ND2 ASN A  45 " =    1.164
peak=   -3.143 closest distance to " O   HOH Z  97 " =    1.722
peak=   -3.133 closest distance to " O   LEU A 300 " =    2.440
peak=   -3.132 closest distance to " ND2 ASN A 215 " =    2.218
peak=   -3.131 closest distance to " CA  VAL A 232 " =    2.438
peak=   -3.128 closest distance to " O   HOH Z 312 " =    1.334
peak=   -3.121 closest distance to " CE1 TYR A 169 " =    2.409
peak=   -3.117 closest distance to " CB  SER A 258 " =    2.016
peak=   -3.116 closest distance to " N   MET A 105 " =    2.573
peak=   -3.099 closest distance to " CA  ASP A 107 " =    2.403
peak=   -3.099 closest distance to " O   HOH Z  25 " =    1.996
peak=   -3.094 closest distance to " CB  ALA A 227 " =    2.323
peak=   -3.093 closest distance to " NH1 ARG A 195 " =    2.247
peak=   -3.090 closest distance to " O   HOH Z 165 " =    2.105
peak=   -3.083 closest distance to " O   HOH Z 298 " =    2.829
peak=   -3.079 closest distance to " CB  ALA A 291 " =    2.173
peak=   -3.072 closest distance to " O   HOH Z  86 " =    2.387
peak=   -3.042 closest distance to " O   HOH Z   1 " =    3.694
peak=   -3.035 closest distance to " O   HOH Z 198 " =    1.861

================= 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    :  0.4712 0.4697   6.278410e+00   6.273712e+00
   1_bss:  0.4646 0.4633   5.831477e+00   5.824559e+00
   1_xyz:  0.3463 0.3885   6.076188e+00   6.158271e+00
   1_adp:  0.3190 0.3897   6.034748e+00   6.162878e+00
   1_occ:  0.3189 0.3899   6.033531e+00   6.162153e+00
   2_bss:  0.3178 0.3889   6.033015e+00   6.159742e+00
   2_xyz:  0.2371 0.2942   5.792784e+00   5.972072e+00
   2_adp:  0.2150 0.2767   5.722429e+00   5.923978e+00
   2_occ:  0.2149 0.2766   5.722292e+00   5.923733e+00
   3_bss:  0.2145 0.2763   5.720417e+00   5.921509e+00
   3_xyz:  0.1597 0.2106   5.448460e+00   5.678428e+00
   3_adp:  0.1506 0.2007   5.402494e+00   5.637351e+00
   3_occ:  0.1505 0.2007   5.401952e+00   5.637303e+00
   4_bss:  0.1505 0.2008   5.404221e+00   5.637677e+00
   4_xyz:  0.1381 0.1905   5.336620e+00   5.575282e+00
   4_adp:  0.1271 0.1773   5.265153e+00   5.505474e+00
   4_occ:  0.1270 0.1772   5.265002e+00   5.505472e+00
   5_bss:  0.1270 0.1772   5.264610e+00   5.505437e+00
   5_xyz:  0.1237 0.1728   5.241632e+00   5.481204e+00
   5_adp:  0.1239 0.1689   5.235581e+00   5.463549e+00
   5_occ:  0.1238 0.1685   5.234920e+00   5.463065e+00
   5_bss:  0.1240 0.1687   5.237391e+00   5.465113e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  50.000   0.046   1.315   1.428   0.000   0.000   0.000
   1_xyz:  0.300  50.000   0.046   1.315   1.428   0.000   0.000   0.000
   1_adp:  0.300  50.000   0.046   1.315   1.428   0.000   0.000   0.000
   1_occ:  0.300  50.000   0.046   1.315   1.428   0.000   0.000   0.000
   2_bss:  0.335  66.494  -0.509   0.451   0.463   0.000   0.000   0.000
   2_xyz:  0.335  66.494  -0.509   0.451   0.463   0.000   0.000   0.000
   2_adp:  0.335  66.494  -0.509   0.451   0.463   0.000   0.000   0.000
   2_occ:  0.335  66.494  -0.509   0.451   0.463   0.000   0.000   0.000
   3_bss:  0.335  66.494  -0.994  -0.427  -0.702  -0.000  -0.000  -0.000
   3_xyz:  0.335  66.494  -0.994  -0.427  -0.702  -0.000  -0.000  -0.000
   3_adp:  0.335  66.494  -0.994  -0.427  -0.702  -0.000  -0.000  -0.000
   3_occ:  0.335  66.494  -0.994  -0.427  -0.702  -0.000  -0.000  -0.000
   4_bss:  0.339  66.494  -1.739  -1.288  -1.541  -0.000  -0.000  -0.000
   4_xyz:  0.339  66.494  -1.739  -1.288  -1.541  -0.000  -0.000  -0.000
   4_adp:  0.339  66.494  -1.739  -1.288  -1.541  -0.000  -0.000  -0.000
   4_occ:  0.339  66.494  -1.739  -1.288  -1.541  -0.000  -0.000  -0.000
   5_bss:  0.334  66.493  -1.878  -1.605  -1.819  -0.000  -0.000  -0.000
   5_xyz:  0.334  66.493  -1.878  -1.605  -1.819  -0.000  -0.000  -0.000
   5_adp:  0.334  66.493  -1.878  -1.605  -1.819  -0.000  -0.000  -0.000
   5_occ:  0.334  66.493  -1.878  -1.605  -1.819  -0.000  -0.000  -0.000
   5_bss:  0.323  57.485  -1.902  -1.657  -1.826  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.406 0.3730  0.4938    71383.019
   1_bss:  60.641 0.3808  0.5217    68423.487
   1_xyz:  43.557 0.5982  0.8235    42730.531
   1_adp:  44.220 0.5894  0.8074    43503.833
   1_occ:  44.168 0.5900  0.8067    43380.046
   2_bss:  44.018 0.5918  0.7890    43130.462
   2_xyz:  31.764 0.7360  0.9415    24267.300
   2_adp:  29.262 0.7646  0.9563    21352.298
   2_occ:  29.267 0.7645  0.9561    21353.529
   3_bss:  29.139 0.7658  0.9289    21207.440
   3_xyz:  21.017 0.8501  0.9881    11604.576
   3_adp:  19.783 0.8628  1.0002    10686.198
   3_occ:  19.780 0.8629  1.0001    10676.748
   4_bss:  19.763 0.8631  0.9719    10686.582
   4_xyz:  18.229 0.8777  0.9789     9312.967
   4_adp:  16.688 0.8919  0.9789     8119.985
   4_occ:  16.684 0.8919  0.9787     8115.328
   5_bss:  16.674 0.8920  0.9706     8114.002
   5_xyz:  16.116 0.8970  0.9707     7677.270
   5_adp:  15.642 0.9015  0.9688     7478.380
   5_occ:  15.630 0.9016  0.9688     7471.051
   5_bss:  15.685 0.9012  0.9647     7538.435
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.9114e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.9114e-01
   1_xyz:   1.621  0.013  0.101 16.238  0.006  4.118   1.4880e-01
   1_adp:   1.621  0.013  0.101 16.238  0.006  4.118   1.4880e-01
   1_occ:   1.621  0.013  0.101 16.238  0.006  4.118   1.4880e-01
   2_bss:   1.621  0.013  0.101 16.238  0.006  4.118   1.4880e-01
   2_xyz:   1.303  0.009  0.089 14.652  0.005  4.113   8.7819e-02
   2_adp:   1.303  0.009  0.089 14.652  0.005  4.113   8.7819e-02
   2_occ:   1.303  0.009  0.089 14.652  0.005  4.113   8.7819e-02
   3_bss:   1.303  0.009  0.089 14.652  0.005  4.113   8.7819e-02
   3_xyz:   1.125  0.009  0.074 14.656  0.004  4.127   7.3305e-02
   3_adp:   1.125  0.009  0.074 14.656  0.004  4.127   7.3305e-02
   3_occ:   1.125  0.009  0.074 14.656  0.004  4.127   7.3305e-02
   4_bss:   1.125  0.009  0.074 14.656  0.004  4.127   7.3305e-02
   4_xyz:   1.061  0.008  0.072 14.375  0.004  4.113   6.3255e-02
   4_adp:   1.061  0.008  0.072 14.375  0.004  4.113   6.3255e-02
   4_occ:   1.061  0.008  0.072 14.375  0.004  4.113   6.3255e-02
   5_bss:   1.061  0.008  0.072 14.375  0.004  4.113   6.3255e-02
   5_xyz:   0.953  0.006  0.069 14.280  0.003  4.113   5.3557e-02
   5_adp:   0.953  0.006  0.069 14.280  0.003  4.113   5.3557e-02
   5_occ:   0.953  0.006  0.069 14.280  0.003  4.113   5.3557e-02
   5_bss:   0.953  0.006  0.069 14.280  0.003  4.113   5.3557e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.546   2.4269e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.546   2.4269e-01
   1_xyz:   9.349  0.117  0.341 89.623  0.034  1.958   1.2428e-01
   1_adp:   9.349  0.117  0.341 89.623  0.034  1.958   1.2428e-01
   1_occ:   9.349  0.117  0.341 89.623  0.034  1.958   1.2428e-01
   2_bss:   9.349  0.117  0.341 89.623  0.034  1.958   1.2428e-01
   2_xyz:   8.483  0.040  0.300 77.969  0.047  2.180   9.5872e-02
   2_adp:   8.483  0.040  0.300 77.969  0.047  2.180   9.5872e-02
   2_occ:   8.483  0.040  0.300 77.969  0.047  2.180   9.5872e-02
   3_bss:   8.483  0.040  0.300 77.969  0.047  2.180   9.5872e-02
   3_xyz:   7.871  0.060  0.279 86.403  0.045  2.244   5.8417e-02
   3_adp:   7.871  0.060  0.279 86.403  0.045  2.244   5.8417e-02
   3_occ:   7.871  0.060  0.279 86.403  0.045  2.244   5.8417e-02
   4_bss:   7.871  0.060  0.279 86.403  0.045  2.244   5.8417e-02
   4_xyz:   8.072  0.044  0.239 82.239  0.038  2.411   4.7083e-02
   4_adp:   8.072  0.044  0.239 82.239  0.038  2.411   4.7083e-02
   4_occ:   8.072  0.044  0.239 82.239  0.038  2.411   4.7083e-02
   5_bss:   8.072  0.044  0.239 82.239  0.038  2.411   4.7083e-02
   5_xyz:   7.829  0.048  0.224 82.700  0.034  2.327   3.5882e-02
   5_adp:   7.829  0.048  0.224 82.700  0.034  2.327   3.5882e-02
   5_occ:   7.829  0.048  0.224 82.700  0.034  2.327   3.5882e-02
   5_bss:   7.829  0.048  0.224 82.700  0.034  2.327   3.5882e-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: 109.51   0.00  17.39 109.51   0.00  13.51  69.95   0.00  38.47
   1_occ: 109.51   0.00  17.39 109.51   0.00  13.51  69.95   0.00  38.47
   2_bss: 109.51   0.00  17.39 109.51   0.00  13.51  69.95   0.00  38.47
   2_xyz: 109.51   0.00  17.39 109.51   0.00  13.51  69.95   0.00  38.47
   2_adp:  98.63   0.00  18.40  89.07   0.00  13.73  98.63   4.31  43.82
   2_occ:  98.63   0.00  18.40  89.07   0.00  13.73  98.63   4.31  43.82
   3_bss:  98.63   0.00  18.40  89.07   0.00  13.73  98.63   4.31  43.82
   3_xyz:  98.63   0.00  18.40  89.07   0.00  13.73  98.63   4.31  43.82
   3_adp:  98.96   0.00  18.45  89.94   0.00  13.71  98.96   4.30  44.23
   3_occ:  98.96   0.00  18.45  89.94   0.00  13.71  98.96   4.30  44.23
   4_bss:  98.96   0.00  18.45  89.94   0.00  13.71  98.96   4.30  44.23
   4_xyz:  98.96   0.00  18.45  89.94   0.00  13.71  98.96   4.30  44.23
   4_adp: 104.94   0.00  18.08 104.94   0.00  13.16 101.65   5.61  44.86
   4_occ: 104.94   0.00  18.08 104.94   0.00  13.16 101.65   5.61  44.86
   5_bss: 104.94   0.00  18.08 104.94   0.00  13.16 101.65   5.61  44.86
   5_xyz: 104.94   0.00  18.08 104.94   0.00  13.16 101.65   5.61  44.86
   5_adp:  98.92   2.32  17.17  98.92   2.32  12.82  85.60   4.97  40.89
   5_occ:  98.92   2.32  17.17  98.92   2.32  12.82  85.60   4.97  40.89
   5_bss:  98.84   2.24  17.09  98.84   2.24  12.73  85.52   4.89  40.80
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.996    0.017    0.421
   1_adp:    1.996    0.017    0.421
   1_occ:    1.996    0.017    0.421
   2_bss:    1.996    0.017    0.421
   2_xyz:    1.625    0.045    0.599
   2_adp:    1.625    0.045    0.599
   2_occ:    1.625    0.045    0.599
   3_bss:    1.625    0.045    0.599
   3_xyz:    1.498    0.074    0.732
   3_adp:    1.498    0.074    0.732
   3_occ:    1.498    0.074    0.732
   4_bss:    1.498    0.074    0.732
   4_xyz:    1.476    0.055    0.762
   4_adp:    1.476    0.055    0.762
   4_occ:    1.476    0.055    0.762
   5_bss:    1.476    0.055    0.762
   5_xyz:    1.501    0.058    0.781
   5_adp:    1.501    0.058    0.781
   5_occ:    1.501    0.058    0.781
   5_bss:    1.501    0.058    0.781
------------------------------------------------------------------------

CPU time actual refinement: 342.17


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1177/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_1177/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1177/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1177/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1177/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 342.02 
  Macro-tasks:
    bulk solvent and scale       = 38.59  
    individual site refinement   = 141.20 
    weights calculation          = 29.75  
    collect and process          = 6.47   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 216.13 
  Micro-tasks:
    mask                            = 2.51   
    f_calc                          = 112.91 
    alpha_beta                      = 8.23   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 119.56 
    fmodel                         = 6.23   
    r_factors                      = 0.21   
    phase_errors                   = 10.53  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 261.62 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.943 micro seconds
Total CPU time: 5.93 minutes
from_scatterers_fft:    613 calls, 112.60 s
gradients_fft:          558 calls, 107.11 s

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

# Date 2008-01-16 Time 06:37:06 PST -0800 (1200494226.71 s)
Start R-work = 0.4712, R-free = 0.4697 (no bulk solvent and anisotropic scale)
Final R-work = 0.1453, R-free = 0.1891 (no bulk solvent and anisotropic scale)

Start R-work = 0.4646, R-free = 0.4633
Final R-work = 0.1240, R-free = 0.1687