# Date 2008-01-16 Time 04:02:07 PST -0800 (1200484927.51 s)
#phil __OFF__

Command line arguments: "../144.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 20786
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 144

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.845, 46.2261, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 46.2261, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6941 1.96043
Completeness in resolution range: 0.981511
Completeness with d_max=infinity: 0.978374

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.6941
                             d_min =   1.9604

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 46.2261, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6941 1.96043
Completeness in resolution range: 0.981511
Completeness with d_max=infinity: 0.978374

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.6945 -  4.1940 [2093/2118]  1884   209  10.0%
  bin  2:  4.1940 -  3.3417 [2025/2043]  1822   203  10.0%
  bin  3:  3.3417 -  2.9231 [1982/2001]  1784   198  10.0%
  bin  4:  2.9231 -  2.6576 [1956/1986]  1761   195  10.0%
  bin  5:  2.6576 -  2.4680 [1960/1979]  1764   196  10.0%
  bin  6:  2.4680 -  2.3231 [1949/1974]  1751   198  10.2%
  bin  7:  2.3231 -  2.2072 [1944/1972]  1755   189   9.7%
  bin  8:  2.2072 -  2.1114 [1941/1977]  1744   197  10.1%
  bin  9:  2.1114 -  2.0303 [1903/1945]  1712   191  10.0%
  bin 10:  2.0303 -  1.9604 [1836/1963]  1653   183  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_144/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:
        0.92 -     1.71: 6
        1.71 -     2.51: 94
        2.51 -     3.31: 3888
        3.31 -     4.10: 9695
        4.10 -     4.90: 15513
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  0.917 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.228 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.516 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.519 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.560 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 29191 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_144/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_144/model_refine_001.geo

CPU time processing inputs: 9.19


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 46.22605 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4706   r_free= 0.4729   ksol= 0.00   Bsol= 0.00   scale= 0.914    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.269244                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6945 -  4.6773 0.99   1370  153 0.3727 0.3709      6.5407       6.533|
|  2:  4.6773 -  3.7325 0.99   1304  145 0.4011 0.3852      6.7746      6.7638|
|  3:  3.7325 -  3.2666 0.99   1280  143 0.4390 0.4597      6.6815      6.7819|
|  4:  3.2666 -  2.9706 0.99   1280  139 0.4506 0.4579      6.5247      6.5188|
|  5:  2.9706 -  2.7592 0.99   1257  142 0.4903 0.4788      6.3713      6.3363|
|  6:  2.7592 -  2.5975 0.99   1275  140 0.5061 0.5173      6.2922       6.283|
|  7:  2.5975 -  2.4680 0.99   1249  139 0.5018 0.4857      6.2391      6.1711|
|  8:  2.4680 -  2.3611 0.98   1254  140 0.5110 0.5209      6.2002      6.2354|
|  9:  2.3611 -  2.2705 0.98   1241  140 0.5387 0.5163      6.1295      6.1163|
| 10:  2.2705 -  2.1924 0.99   1238  137 0.5256 0.5469      6.1176      6.1309|
| 11:  2.1924 -  2.1241 0.98   1251  137 0.5131 0.5525      6.0446      6.0843|
| 12:  2.1241 -  2.0635 0.97   1238  138 0.5291 0.5219      6.0003       6.035|
| 13:  2.0635 -  2.0093 1.00   1228  134 0.5196 0.5208      5.8994       5.886|
| 14:  2.0093 -  1.9604 0.91   1165  132 0.5230 0.4893      5.8489      5.7719|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.6945 -  4.6773  1370   153  0.69  35.10   0.84     0.74      72140.98|
|  2:  4.6773 -  3.7325  1304   145  0.69  35.96   0.92     0.81     110475.77|
|  3:  3.7325 -  3.2666  1280   143  0.58  45.00   0.95     0.78     120237.95|
|  4:  3.2666 -  2.9706  1280   139  0.49  52.65   0.94     0.69     109536.35|
|  5:  2.9706 -  2.7592  1257   142  0.41  58.66   0.90     0.59      85243.98|
|  6:  2.7592 -  2.5975  1275   140  0.38  61.28   0.89     0.54      74296.65|
|  7:  2.5975 -  2.4680  1249   139  0.36  62.81   0.91     0.51      67701.41|
|  8:  2.4680 -  2.3611  1254   140  0.34  64.16   0.94     0.51      62588.32|
|  9:  2.3611 -  2.2705  1241   140  0.34  64.39   0.90     0.51      55440.45|
| 10:  2.2705 -  2.1924  1238   137  0.35  63.97   0.97     0.52      50165.15|
| 11:  2.1924 -  2.1241  1251   137  0.30  67.22   0.96     0.47      49085.95|
| 12:  2.1241 -  2.0635  1238   138  0.28  68.98   0.99     0.45      46378.32|
| 13:  2.0635 -  2.0093  1228   134  0.29  68.40   0.96     0.46      39501.72|
| 14:  2.0093 -  1.9604  1165   132  0.40  59.84   0.96     0.57      27462.82|
|alpha:            min =        0.45 max =            0.81 mean =         0.58|
|beta:             min =    27462.82 max =       120237.95 mean =     69890.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.43|
|phase err.(work): min =        0.00 max =           89.98 mean =        57.46|
|phase err.(test): min =        0.00 max =           89.90 mean =        57.66|
|-----------------------------------------------------------------------------|

============================== 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 = 12.382192             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.151   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.660844              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.054   (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 |  0.917 -  1.315:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.315 -  1.714:        4 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.714 -  2.112:       21 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.112 -  2.510:       73 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.510 -  2.909:     1454 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  2.909 -  3.307:     2434 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.307 -  3.705:     3813 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.705 -  4.103:     5882 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.103 -  4.502:     6811 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.502 -  4.900:     8702 |
|-----------------------------------------------------------------------------|
|-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 |        0.221 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.106    4.900  0.917 |       1.113 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.234)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4706   r_free= 0.4729   ksol= 0.00   Bsol= 0.00   scale= 0.914    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.269244                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4617   r_free= 0.4611   ksol= 0.34   Bsol= 4.79   scale= 0.949    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.87,0.76,1.60,0.00,0.00,0.00); trace/3= 0.49                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.263576                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.217934              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.061   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.431361              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.822   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4617      final r-factor (work) = 0.3215          |
| start r-factor (free) = 0.4611      final r-factor (free) = 0.3477          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.0803 = 9.22 * 0.50 * 6.2616 + 1.00 * 0.2208                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.3886 = 9.22 * 0.50 * 6.1299 + 1.00 * 0.1359                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3215      final r-factor (work) = 0.2892          |
| start r-factor (free) = 0.3477      final r-factor (free) = 0.3583          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7800 = 1.43 * 1.00 * 6.1299 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.5288 = 1.43 * 1.00 * 5.9443 + 1.00 * 0.0203                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.234)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.76   19.34    None  None   None       |
|    all(noH): 2823   0      0.00    95.76   19.34    None  None   None       |
|    Sol.    : 438    0      2.18    95.76   42.33    None  None   None       |
|    Mac.    : 2385   0      0.00    91.92   15.12    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 -   9.576:  897   |   5:    47.881 -  57.457:  103        |
|      1:     9.576 -  19.152:  875   |   6:    57.457 -  67.033:   73        |
|      2:    19.152 -  28.729:  441   |   7:    67.033 -  76.609:   31        |
|      3:    28.729 -  38.305:  247   |   8:    76.609 -  86.185:    7        |
|      4:    38.305 -  47.881:  145   |   9:    86.185 -  95.762:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2892 r_free = 0.3583             target_work(ml) = 5.956         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2888 r_free = 0.3587             target_work(ml) = 5.956         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2888   r_free= 0.3587   ksol= 0.34   Bsol= 4.79   scale= 1.045    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.87,0.76,1.60,0.00,0.00,0.00); trace/3= 0.49                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.956328                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2843   r_free= 0.3575   ksol= 0.33   Bsol= 30.19   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.65,-0.65,-0.12,-0.00,-0.00,-0.00); trace/3= -0.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.946653                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.360230              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.394   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.232219              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.557  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2843      final r-factor (work) = 0.2171          |
| start r-factor (free) = 0.3575      final r-factor (free) = 0.2781          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.0843 = 4.36 * 0.50 * 5.9394 + 1.00 * 0.1357                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.8119 = 4.36 * 0.50 * 5.8429 + 1.00 * 0.0738                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2171      final r-factor (work) = 0.2004          |
| start r-factor (free) = 0.2781      final r-factor (free) = 0.2543          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3769 = 0.23 * 1.00 * 5.8429 + 1.00 * 0.0201                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3276 = 0.23 * 1.00 * 5.6809 + 1.00 * 0.0084                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.234)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.69   17.41    None  None   None       |
|    all(noH): 2823   0      0.00    85.69   17.41    None  None   None       |
|    Sol.    : 438    0      5.23    78.86   38.72    None  None   None       |
|    Mac.    : 2385   0      0.00    85.69   13.50    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.569:  710   |   5:    42.843 -  51.411:  110        |
|      1:     8.569 -  17.137: 1187   |   6:    51.411 -  59.980:   64        |
|      2:    17.137 -  25.706:  385   |   7:    59.980 -  68.548:   28        |
|      3:    25.706 -  34.274:  184   |   8:    68.548 -  77.117:    5        |
|      4:    34.274 -  42.843:  146   |   9:    77.117 -  85.685:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2004 r_free = 0.2543             target_work(ml) = 5.640         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2000 r_free = 0.2539             target_work(ml) = 5.639         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2000   r_free= 0.2539   ksol= 0.33   Bsol= 30.19   scale= 1.045   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.65,-0.65,-0.12,-0.00,-0.00,-0.00); trace/3= -0.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.638813                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1996   r_free= 0.2529   ksol= 0.33   Bsol= 30.19   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-1.52,-0.85,-0.00,-0.00,-0.00); trace/3= -1.52                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.636400                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.411495              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.618   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.238141              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.970  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1996      final r-factor (work) = 0.1518          |
| start r-factor (free) = 0.2529      final r-factor (free) = 0.1963          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9233 = 2.41 * 0.50 * 5.6807 + 1.00 * 0.0738                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7035 = 2.41 * 0.50 * 5.5139 + 1.00 * 0.0551                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1518      final r-factor (work) = 0.1412          |
| start r-factor (free) = 0.1963      final r-factor (free) = 0.1875          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3227 = 0.24 * 1.00 * 5.5139 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2907 = 0.24 * 1.00 * 5.3510 + 1.00 * 0.0165                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.234)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.96   17.35    None  None   None       |
|    all(noH): 2823   0      0.00    84.96   17.35    None  None   None       |
|    Sol.    : 438    0      5.90    78.81   40.74    None  None   None       |
|    Mac.    : 2385   0      0.00    84.96   13.05    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.496:  656   |   5:    42.478 -  50.974:  120        |
|      1:     8.496 -  16.991: 1339   |   6:    50.974 -  59.470:   83        |
|      2:    16.991 -  25.487:  321   |   7:    59.470 -  67.965:   43        |
|      3:    25.487 -  33.983:  136   |   8:    67.965 -  76.461:    9        |
|      4:    33.983 -  42.478:  110   |   9:    76.461 -  84.956:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1412 r_free = 0.1875             target_work(ml) = 5.326         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1410 r_free = 0.1873             target_work(ml) = 5.325         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1410   r_free= 0.1873   ksol= 0.33   Bsol= 30.19   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-1.52,-0.85,-0.00,-0.00,-0.00); trace/3= -1.52                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.324771                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1412   r_free= 0.1862   ksol= 0.32   Bsol= 30.80   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-2.23,-1.48,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.321875                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.210473              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.307  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.380528              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.066   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1412      final r-factor (work) = 0.1221          |
| start r-factor (free) = 0.1862      final r-factor (free) = 0.1658          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9748 = 2.21 * 0.50 * 5.3561 + 1.00 * 0.0551                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8656 = 2.21 * 0.50 * 5.2559 + 1.00 * 0.0567                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1221      final r-factor (work) = 0.1184          |
| start r-factor (free) = 0.1658      final r-factor (free) = 0.1631          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0091 = 0.38 * 1.00 * 5.2559 + 1.00 * 0.0091                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9819 = 0.38 * 1.00 * 5.1860 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.234)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.78    88.62   17.32    None  None   None       |
|    all(noH): 2823   0      0.78    88.62   17.32    None  None   None       |
|    Sol.    : 438    0      6.92    83.77   41.35    None  None   None       |
|    Mac.    : 2385   0      0.78    88.62   12.91    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:     0.780 -   9.564:  922   |   5:    44.700 -  53.484:  109        |
|      1:     9.564 -  18.348: 1176   |   6:    53.484 -  62.268:   76        |
|      2:    18.348 -  27.132:  259   |   7:    62.268 -  71.052:   32        |
|      3:    27.132 -  35.916:  116   |   8:    71.052 -  79.836:   13        |
|      4:    35.916 -  44.700:  115   |   9:    79.836 -  88.620:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1184 r_free = 0.1631             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1182 r_free = 0.1630             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1182   r_free= 0.1630   ksol= 0.32   Bsol= 30.80   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-2.23,-1.48,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.175094                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1182   r_free= 0.1629   ksol= 0.32   Bsol= 32.56   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-2.23,-1.48,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.174704                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.553023              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.174  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.799130              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.100  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1182      final r-factor (work) = 0.1143          |
| start r-factor (free) = 0.1629      final r-factor (free) = 0.1604          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0834 = 1.55 * 0.50 * 5.1857 + 1.00 * 0.0567                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0585 = 1.55 * 0.50 * 5.1625 + 1.00 * 0.0498                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1143      final r-factor (work) = 0.1129          |
| start r-factor (free) = 0.1604      final r-factor (free) = 0.1606          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1340 = 0.80 * 1.00 * 5.1625 + 1.00 * 0.0085                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1213 = 0.80 * 1.00 * 5.1457 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.234)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.59    95.76   17.31    None  None   None       |
|    all(noH): 2823   0      0.59    95.76   17.31    None  None   None       |
|    Sol.    : 438    0      6.16    90.34   41.70    None  None   None       |
|    Mac.    : 2385   0      0.59    95.76   12.83    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:     0.592 -  10.108: 1096   |   5:    48.174 -  57.691:   93        |
|      1:    10.108 -  19.625: 1072   |   6:    57.691 -  67.207:   61        |
|      2:    19.625 -  29.141:  226   |   7:    67.207 -  76.724:   26        |
|      3:    29.141 -  38.658:  118   |   8:    76.724 -  86.240:   10        |
|      4:    38.658 -  48.174:  117   |   9:    86.240 -  95.756:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1129 r_free = 0.1606             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1129 r_free = 0.1606             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1129   r_free= 0.1606   ksol= 0.32   Bsol= 32.56   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-2.23,-1.48,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.146290                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6945 -  4.6773 0.99   1370  153 0.1033 0.1230      5.4082      5.5203|
|  2:  4.6773 -  3.7325 0.99   1304  145 0.0851 0.1185      5.4462      5.6432|
|  3:  3.7325 -  3.2666 0.99   1280  143 0.1080 0.1530      5.4969      5.8639|
|  4:  3.2666 -  2.9706 0.99   1280  139 0.1243 0.1666      5.4757      5.6419|
|  5:  2.9706 -  2.7592 0.99   1257  142 0.1262 0.1672      5.2982      5.4501|
|  6:  2.7592 -  2.5975 0.99   1275  140 0.1190 0.1635      5.1853       5.376|
|  7:  2.5975 -  2.4680 0.99   1249  139 0.1210 0.1652      5.1277      5.3631|
|  8:  2.4680 -  2.3611 0.98   1254  140 0.1173 0.1732      5.0837      5.3723|
|  9:  2.3611 -  2.2705 0.98   1241  140 0.1168 0.1834      5.0428      5.3029|
| 10:  2.2705 -  2.1924 0.99   1238  137 0.1128 0.1966      4.9888      5.2628|
| 11:  2.1924 -  2.1241 0.98   1251  137 0.1169 0.1741      4.9605      5.2565|
| 12:  2.1241 -  2.0635 0.97   1238  138 0.1160 0.1715      4.9026      5.2078|
| 13:  2.0635 -  2.0093 1.00   1228  134 0.1130 0.1772      4.8196      5.0711|
| 14:  2.0093 -  1.9604 0.91   1165  132 0.1103 0.1900      4.7165      5.0025|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.6945 -  4.6773  1370   153  0.94   9.05   0.99     0.97       6987.30|
|  2:  4.6773 -  3.7325  1304   145  0.95   7.90   1.04     1.03       9143.48|
|  3:  3.7325 -  3.2666  1280   143  0.93  11.31   1.05     1.03      10554.20|
|  4:  3.2666 -  2.9706  1280   139  0.92  13.34   1.02     1.02      10289.10|
|  5:  2.9706 -  2.7592  1257   142  0.91  14.58   1.01     0.97       7589.20|
|  6:  2.7592 -  2.5975  1275   140  0.91  14.73   1.00     0.98       6438.25|
|  7:  2.5975 -  2.4680  1249   139  0.91  15.06   0.99     0.97       5700.04|
|  8:  2.4680 -  2.3611  1254   140  0.91  14.47   1.01     0.99       5245.61|
|  9:  2.3611 -  2.2705  1241   140  0.91  15.38   1.02     1.00       5125.27|
| 10:  2.2705 -  2.1924  1238   137  0.90  15.69   1.01     0.97       4619.73|
| 11:  2.1924 -  2.1241  1251   137  0.90  16.42   1.01     0.97       4555.27|
| 12:  2.1241 -  2.0635  1238   138  0.91  15.63   1.03     1.00       4067.30|
| 13:  2.0635 -  2.0093  1228   134  0.91  15.65   1.02     1.01       3511.42|
| 14:  2.0093 -  1.9604  1165   132  0.91  15.38   1.00     0.97       2831.26|
|alpha:            min =        0.97 max =            1.03 mean =         0.99|
|beta:             min =     2831.26 max =        10554.20 mean =      6241.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.81 mean =        13.83|
|phase err.(test): min =        0.00 max =           89.55 mean =        13.63|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1131   r_free= 0.1605   ksol= 0.32   Bsol= 33.84   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.65,-2.17,-1.41,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.147037                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1131   r_free= 0.1605   ksol= 0.32   Bsol= 33.84   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.65,-2.17,-1.41,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.147037                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6945 -  4.6773 0.99   1370  153 0.1022 0.1239      5.4016      5.5307|
|  2:  4.6773 -  3.7325 0.99   1304  145 0.0872 0.1193      5.4621       5.659|
|  3:  3.7325 -  3.2666 0.99   1280  143 0.1092 0.1521      5.5066      5.8606|
|  4:  3.2666 -  2.9706 0.99   1280  139 0.1248 0.1668      5.4787      5.6404|
|  5:  2.9706 -  2.7592 0.99   1257  142 0.1268 0.1674      5.3023      5.4538|
|  6:  2.7592 -  2.5975 0.99   1275  140 0.1192 0.1612      5.1843      5.3715|
|  7:  2.5975 -  2.4680 0.99   1249  139 0.1215 0.1646      5.1274      5.3641|
|  8:  2.4680 -  2.3611 0.98   1254  140 0.1168 0.1717      5.0809      5.3688|
|  9:  2.3611 -  2.2705 0.98   1241  140 0.1165 0.1842      5.0405      5.3046|
| 10:  2.2705 -  2.1924 0.99   1238  137 0.1125 0.1969      4.9869      5.2628|
| 11:  2.1924 -  2.1241 0.98   1251  137 0.1167 0.1741      4.9589      5.2543|
| 12:  2.1241 -  2.0635 0.97   1238  138 0.1156 0.1713      4.9002      5.2081|
| 13:  2.0635 -  2.0093 1.00   1228  134 0.1126 0.1764      4.8179      5.0674|
| 14:  2.0093 -  1.9604 0.91   1165  132 0.1102 0.1898      4.7144       5.001|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.6945 -  4.6773  1370   153  0.94   9.03   0.99     0.96       7086.95|
|  2:  4.6773 -  3.7325  1304   145  0.95   8.12   1.04     1.03       9349.64|
|  3:  3.7325 -  3.2666  1280   143  0.93  11.47   1.05     1.04      10815.54|
|  4:  3.2666 -  2.9706  1280   139  0.92  13.37   1.03     1.02      10335.76|
|  5:  2.9706 -  2.7592  1257   142  0.91  14.61   1.01     0.98       7604.89|
|  6:  2.7592 -  2.5975  1275   140  0.91  14.75   1.00     0.98       6428.31|
|  7:  2.5975 -  2.4680  1249   139  0.91  15.05   1.00     0.97       5686.22|
|  8:  2.4680 -  2.3611  1254   140  0.91  14.44   1.01     0.99       5228.33|
|  9:  2.3611 -  2.2705  1241   140  0.91  15.38   1.03     1.01       5121.48|
| 10:  2.2705 -  2.1924  1238   137  0.90  15.67   1.01     0.97       4605.01|
| 11:  2.1924 -  2.1241  1251   137  0.90  16.42   1.01     0.98       4548.75|
| 12:  2.1241 -  2.0635  1238   138  0.91  15.58   1.03     1.01       4046.64|
| 13:  2.0635 -  2.0093  1228   134  0.91  15.62   1.02     1.02       3503.98|
| 14:  2.0093 -  1.9604  1165   132  0.91  15.35   1.01     0.98       2820.03|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2820.03 max =        10815.54 mean =      6280.99|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.85|
|phase err.(test): min =        0.00 max =           89.74 mean =        13.66|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.234)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.57    95.74   17.29    None  None   None       |
|    all(noH): 2823   0      0.57    95.74   17.29    None  None   None       |
|    Sol.    : 438    0      6.14    90.33   41.68    None  None   None       |
|    Mac.    : 2385   0      0.57    95.74   12.81    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:     0.573 -  10.089: 1096   |   5:    48.155 -  57.671:   93        |
|      1:    10.089 -  19.606: 1072   |   6:    57.671 -  67.188:   61        |
|      2:    19.606 -  29.122:  226   |   7:    67.188 -  76.704:   26        |
|      3:    29.122 -  38.639:  118   |   8:    76.704 -  86.221:   10        |
|      4:    38.639 -  48.155:  117   |   9:    86.221 -  95.737:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 299         
Filter by distance & map next to the model:
   mapped sites are within: 0.686 - 5.835
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 297 from: 299
   mapped sites are within: 0.721 - 5.835

peak=    6.989 closest distance to " O   HOH Z 142 " =    2.057
peak=    6.585 closest distance to " O   HOH Z 236 " =    1.711
peak=    6.449 closest distance to " O   HOH Z 112 " =    1.517
peak=    6.178 closest distance to " NE2 GLN A  11 " =    1.197
peak=    5.694 closest distance to " O   HOH Z  37 " =    1.418
peak=    5.661 closest distance to " CB  ARG A 275 " =    0.973
peak=    5.606 closest distance to " CG  PRO A  54 " =    1.287
peak=    5.525 closest distance to " O   HOH Z 126 " =    1.981
peak=    5.501 closest distance to " NH2 ARG A  56 " =    2.035
peak=    5.474 closest distance to " O   HOH Z 375 " =    1.181
peak=    5.453 closest distance to " CG  PRO A 213 " =    1.298
peak=    5.397 closest distance to " O   HOH Z 124 " =    1.605
peak=    5.359 closest distance to " O   HOH Z 193 " =    1.652
peak=    4.986 closest distance to " O   HOH Z 213 " =    1.935
peak=    4.954 closest distance to " O   HOH Z  52 " =    1.309
peak=    4.932 closest distance to " O   HOH Z  78 " =    1.656
peak=    4.869 closest distance to " O   HOH Z 278 " =    1.175
peak=    4.844 closest distance to " O   HOH Z 209 " =    2.220
peak=    4.772 closest distance to " O   HOH Z 427 " =    2.656
peak=    4.721 closest distance to " CG  PRO A  90 " =    1.138
peak=    4.658 closest distance to " O   HOH Z 272 " =    1.903
peak=    4.596 closest distance to " CG  PRO A 198 " =    1.258
peak=    4.584 closest distance to " CB  ASN A 148 " =    1.372
peak=    4.570 closest distance to " O   HOH Z  92 " =    1.331
peak=    4.560 closest distance to " O   HOH Z 380 " =    1.597
peak=    4.505 closest distance to " O   HOH Z 260 " =    1.237
peak=    4.476 closest distance to " O   HOH Z 369 " =    2.184
peak=    4.447 closest distance to " CG  GLN A  11 " =    2.126
peak=    4.391 closest distance to " NZ  LYS A 117 " =    3.114
peak=    4.362 closest distance to " CG2 VAL A 257 " =    0.917
peak=    4.360 closest distance to " CA  TYR A  30 " =    0.962
peak=    4.358 closest distance to " CB  GLN A 183 " =    1.173
peak=    4.350 closest distance to " O   HOH Z 232 " =    2.271
peak=    4.338 closest distance to " CB  GLN A 223 " =    1.566
peak=    4.316 closest distance to " CB  SER A   3 " =    1.271
peak=    4.295 closest distance to " O   HOH Z 419 " =    1.947
peak=    4.287 closest distance to " O   HOH Z 423 " =    1.439
peak=    4.284 closest distance to " O   HOH Z 108 " =    1.288
peak=    4.268 closest distance to " C   PRO A 198 " =    1.555
peak=    4.267 closest distance to " O   HOH Z  59 " =    1.519
peak=    4.258 closest distance to " O   HOH Z 250 " =    1.458
peak=    4.253 closest distance to " O   HOH Z 183 " =    2.274
peak=    4.245 closest distance to " O   HOH Z 287 " =    1.601
peak=    4.239 closest distance to " O   HOH Z 234 " =    3.456
peak=    4.224 closest distance to " O   HOH Z  66 " =    2.055
peak=    4.214 closest distance to " O   HOH Z 371 " =    1.822
peak=    4.149 closest distance to " O   SER A  87 " =    2.334
peak=    4.146 closest distance to " O   HOH Z 203 " =    1.755
peak=    4.142 closest distance to " O   HOH Z 132 " =    1.192
peak=    4.120 closest distance to " O   HOH Z 207 " =    1.766
peak=    4.111 closest distance to " CB  GLU A 128 " =    1.035
peak=    4.099 closest distance to " CG1 ILE A  33 " =    1.240
peak=    4.095 closest distance to " CB  SER A  63 " =    1.175
peak=    4.069 closest distance to " CB  TYR A 169 " =    0.774
peak=    4.066 closest distance to " O   HOH Z  24 " =    1.487
peak=    4.065 closest distance to " O   HOH Z  44 " =    1.840
peak=    4.038 closest distance to " O   HOH Z 106 " =    2.292
peak=    4.031 closest distance to " O   HOH Z  97 " =    1.952
peak=    4.027 closest distance to " O   HOH Z 394 " =    1.549
peak=    4.026 closest distance to " O   HOH Z 298 " =    1.792
peak=    4.019 closest distance to " OD1 ASN A  69 " =    2.607
peak=    4.006 closest distance to " O   HOH Z 316 " =    2.903
peak=    4.001 closest distance to " O   HOH Z 402 " =    1.424
peak=    3.993 closest distance to " OG BSER A 164 " =    2.277
peak=    3.984 closest distance to " O   HOH Z  11 " =    1.490
peak=    3.963 closest distance to " CG  PRO A 243 " =    1.161
peak=    3.943 closest distance to " CB  ARG A 102 " =    0.867
peak=    3.942 closest distance to " CB  PRO A  54 " =    1.006
peak=    3.929 closest distance to " O   HOH Z 130 " =    2.829
peak=    3.909 closest distance to " O   HOH Z 134 " =    1.247
peak=    3.897 closest distance to " O   HOH Z   9 " =    2.262
peak=    3.895 closest distance to " NH1BARG A 145 " =    1.352
peak=    3.893 closest distance to " O   HOH Z 192 " =    1.508
peak=    3.877 closest distance to " CG AARG A 275 " =    1.016
peak=    3.861 closest distance to " O   HOH Z 357 " =    1.827
peak=    3.845 closest distance to " O   HOH Z 189 " =    1.710
peak=    3.844 closest distance to " CB  GLU A 152 " =    1.253
peak=    3.831 closest distance to " O   HOH Z 303 " =    2.285
peak=    3.828 closest distance to " O   HOH Z 403 " =    1.772
peak=    3.816 closest distance to " CB  VAL A 265 " =    1.211
peak=    3.800 closest distance to " O   HOH Z  71 " =    1.545
peak=    3.794 closest distance to " ND2 ASN A 187 " =    1.438
peak=    3.792 closest distance to " O   HOH Z 289 " =    1.480
peak=    3.792 closest distance to " O   HOH Z 425 " =    1.309
peak=    3.790 closest distance to " O   HOH Z 128 " =    1.928
peak=    3.779 closest distance to " O   HOH Z  61 " =    1.550
peak=    3.763 closest distance to " CB  TRP A 179 " =    1.172
peak=    3.762 closest distance to " O   HOH Z 368 " =    3.636
peak=    3.754 closest distance to " O   HOH Z  10 " =    1.723
peak=    3.753 closest distance to " O   HOH Z 153 " =    3.622
peak=    3.750 closest distance to " O   HOH Z  50 " =    1.514
peak=    3.744 closest distance to " C   ALA A 299 " =    0.965
peak=    3.738 closest distance to " O   HOH Z 366 " =    2.586
peak=    3.728 closest distance to " O   HOH Z  93 " =    1.908
peak=    3.724 closest distance to " O   HOH Z 173 " =    1.993
peak=    3.718 closest distance to " O   HOH Z 286 " =    2.281
peak=    3.703 closest distance to " CB  ARG A 139 " =    0.975
peak=    3.699 closest distance to " CB  THR A  31 " =    1.713
peak=    3.693 closest distance to " OE1 GLU A   2 " =    2.231
peak=    3.693 closest distance to " O   HOH Z 343 " =    1.404
peak=    3.678 closest distance to " O   HOH Z 368 " =    1.943
peak=    3.678 closest distance to " CB  SER A  26 " =    1.546
peak=    3.676 closest distance to " O   HOH Z 108 " =    1.884
peak=    3.670 closest distance to " O   HOH Z 291 " =    1.842
peak=    3.669 closest distance to " O   HOH Z 389 " =    1.431
peak=    3.669 closest distance to " CE  LYS A 119 " =    1.158
peak=    3.667 closest distance to " OE2 GLU A  53 " =    1.952
peak=    3.662 closest distance to " O   HOH Z 132 " =    1.958
peak=    3.661 closest distance to " OD2 ASP A 286 " =    2.475
peak=    3.657 closest distance to " O   HOH Z 327 " =    1.889
peak=    3.647 closest distance to " CA  ASN A 127 " =    0.945
peak=    3.647 closest distance to " NH2BARG A 145 " =    2.060
peak=    3.644 closest distance to " O   HOH Z   1 " =    1.586
peak=    3.631 closest distance to " O   HOH Z 146 " =    1.666
peak=    3.619 closest distance to " O   HOH Z  61 " =    1.688
peak=    3.611 closest distance to " O   HOH Z 227 " =    1.807
peak=    3.606 closest distance to " O   HOH Z 153 " =    1.599
peak=    3.603 closest distance to " O   HOH Z 345 " =    3.221
peak=    3.598 closest distance to " O   HOH Z 244 " =    1.691
peak=    3.598 closest distance to " O  BHOH Z  74 " =    1.509
peak=    3.597 closest distance to " O   HOH Z 212 " =    1.549
peak=    3.591 closest distance to " CA  ALA A  21 " =    1.156
peak=    3.586 closest distance to " CA  THR A 264 " =    0.777
peak=    3.583 closest distance to " CA  ALA A 233 " =    0.970
peak=    3.570 closest distance to " O   HOH Z 403 " =    1.354
peak=    3.566 closest distance to " O   HOH Z 344 " =    3.062
peak=    3.552 closest distance to " CG  ARG A  66 " =    2.441
peak=    3.547 closest distance to " O   HOH Z 334 " =    1.558
peak=    3.544 closest distance to " N   ARG A 156 " =    1.303
peak=    3.533 closest distance to " CG2 ILE A 120 " =    1.202
peak=    3.527 closest distance to " CB  THR A 157 " =    0.972
peak=    3.527 closest distance to " O   HOH Z 166 " =    1.291
peak=    3.513 closest distance to " O   HOH Z 245 " =    1.247
peak=    3.506 closest distance to " O   HOH Z  78 " =    2.147
peak=    3.503 closest distance to " O   HOH Z  54 " =    1.625
peak=    3.500 closest distance to " CA  GLY A 241 " =    3.729
peak=    3.498 closest distance to " CG  MET A 185 " =    1.395
peak=    3.492 closest distance to " N   PHE A 130 " =    1.291
peak=    3.491 closest distance to " CA  ASN A 215 " =    1.123
peak=    3.483 closest distance to " CG  GLU A 277 " =    2.014
peak=    3.479 closest distance to " CD2 LEU A 297 " =    1.066
peak=    3.479 closest distance to " O   SER A  26 " =    1.505
peak=    3.477 closest distance to " CD BLYS A 290 " =    1.092
peak=    3.470 closest distance to " NH1 ARG A  14 " =    1.099
peak=    3.462 closest distance to " O   HOH Z 422 " =    2.604
peak=    3.461 closest distance to " OD1BASN A 224 " =    2.118
peak=    3.456 closest distance to " O   HOH Z 194 " =    1.641
peak=    3.455 closest distance to " NE2 GLN A  55 " =    1.363
peak=    3.453 closest distance to " CB  LEU A 228 " =    1.126
peak=    3.447 closest distance to " CG AARG A 275 " =    1.183
peak=    3.443 closest distance to " O   HOH Z 289 " =    1.502
peak=    3.436 closest distance to " O   HOH Z  43 " =    2.014
peak=    3.433 closest distance to " CE AMET A  47 " =    1.202
peak=    3.431 closest distance to " O   HOH Z  59 " =    1.927
peak=    3.431 closest distance to " O   HOH Z 261 " =    1.658
peak=    3.428 closest distance to " O   HOH Z 425 " =    1.967
peak=    3.427 closest distance to " CB  GLU A 277 " =    3.508
peak=    3.425 closest distance to " CE1 TYR A 186 " =    1.343
peak=    3.425 closest distance to " O   HOH Z 313 " =    1.661
peak=    3.424 closest distance to " O   HOH Z 222 " =    2.295
peak=    3.423 closest distance to " N   GLN A 278 " =    0.942
peak=    3.423 closest distance to " O   HOH Z 140 " =    1.458
peak=    3.422 closest distance to " CB  ALA A  34 " =    1.116
peak=    3.422 closest distance to " O   HOH Z 290 " =    1.016
peak=    3.422 closest distance to " OG  SER A  62 " =    2.816
peak=    3.418 closest distance to " CB  ALA A 291 " =    1.401
peak=    3.410 closest distance to " O   HOH Z 179 " =    0.751
peak=    3.407 closest distance to " O   HOH Z 189 " =    1.707
peak=    3.403 closest distance to " O   HOH Z 365 " =    5.326
peak=    3.402 closest distance to " O   HOH Z 353 " =    2.418
peak=    3.402 closest distance to " O   HOH Z 183 " =    2.025
peak=    3.400 closest distance to " O   HOH Z  64 " =    2.051
peak=    3.397 closest distance to " O   HOH Z   1 " =    1.571
peak=    3.396 closest distance to " CA  PHE A 283 " =    1.282
peak=    3.396 closest distance to " O   HOH Z  43 " =    2.528
peak=    3.391 closest distance to " O   HOH Z 261 " =    2.188
peak=    3.391 closest distance to " O   HOH Z 365 " =    1.724
peak=    3.384 closest distance to " O   HOH Z 344 " =    1.175
peak=    3.383 closest distance to " O   HOH Z 393 " =    1.316
peak=    3.378 closest distance to " O   HOH Z 156 " =    3.083
peak=    3.368 closest distance to " O   HOH Z  89 " =    1.799
peak=    3.359 closest distance to " N   TYR A  15 " =    1.037
peak=    3.357 closest distance to " CB  VAL A 126 " =    1.255
peak=    3.349 closest distance to " O   HOH Z 135 " =    1.857
peak=    3.346 closest distance to " O   HOH Z 383 " =    1.785
peak=    3.344 closest distance to " O   HOH Z 118 " =    1.460
peak=    3.341 closest distance to " O   HOH Z  98 " =    1.732
peak=    3.332 closest distance to " CD  GLN A  58 " =    5.835
peak=    3.331 closest distance to " O   HOH Z 435 " =    1.792
peak=    3.329 closest distance to " O   HOH Z  15 " =    1.493
peak=    3.328 closest distance to " CB  VAL A 268 " =    0.838
peak=    3.325 closest distance to " O   HOH Z  80 " =    1.962
peak=    3.322 closest distance to " CB  ARG A  79 " =    1.476
peak=    3.316 closest distance to " O   HOH Z 303 " =    1.729
peak=    3.314 closest distance to " O   HOH Z 328 " =    1.792
peak=    3.309 closest distance to " O   HOH Z 423 " =    1.878
peak=    3.305 closest distance to " O   HOH Z 162 " =    2.028
peak=    3.305 closest distance to " N   ASN A  39 " =    1.060
peak=    3.304 closest distance to " CG  LEU A 167 " =    1.159
peak=    3.298 closest distance to " O   HOH Z 423 " =    2.218
peak=    3.297 closest distance to " NE  ARG A  14 " =    1.353
peak=    3.296 closest distance to " O   HOH Z 392 " =    1.334
peak=    3.295 closest distance to " O   HOH Z 214 " =    1.105
peak=    3.295 closest distance to " O   HOH Z 191 " =    1.530
peak=    3.290 closest distance to " CB  SER A 276 " =    1.204
peak=    3.288 closest distance to " CG2 THR A 221 " =    1.181
peak=    3.287 closest distance to " CB  THR A 279 " =    1.737
peak=    3.283 closest distance to " CB  HIS A 108 " =    0.902
peak=    3.282 closest distance to " O   HOH Z  73 " =    1.776
peak=    3.281 closest distance to " O   HOH Z 276 " =    1.243
peak=    3.278 closest distance to " CB  ALA A  21 " =    1.900
peak=    3.278 closest distance to " O   HOH Z 234 " =    1.909
peak=    3.276 closest distance to " N   HIS A  86 " =    1.702
peak=    3.275 closest distance to " O   HOH Z 227 " =    2.134
peak=    3.273 closest distance to " O   HOH Z 185 " =    1.450
peak=    3.270 closest distance to " O   HOH Z  88 " =    2.308
peak=    3.268 closest distance to " N   GLU A   2 " =    1.384
peak=    3.267 closest distance to " O   HOH Z 302 " =    1.346
peak=    3.266 closest distance to " CA  LEU A 282 " =    1.392
peak=    3.266 closest distance to " CE  LYS A  76 " =    0.894
peak=    3.262 closest distance to " O   HOH Z  85 " =    1.449
peak=    3.261 closest distance to " O   HOH Z 144 " =    2.054
peak=    3.261 closest distance to " CB  LEU A 255 " =    0.736
peak=    3.257 closest distance to " O   HOH Z 388 " =    1.949
peak=    3.255 closest distance to " N   TRP A 150 " =    1.569
peak=    3.254 closest distance to " CB  TYR A 169 " =    1.194
peak=    3.251 closest distance to " O   HOH Z 247 " =    1.215
peak=    3.249 closest distance to " NH1 ARG A 138 " =    1.210
peak=    3.247 closest distance to " CA  LEU A 101 " =    1.472
peak=    3.244 closest distance to " CB  VAL A 202 " =    1.525
peak=    3.241 closest distance to " CB  SER A  62 " =    1.328
peak=    3.240 closest distance to " O   HOH Z 281 " =    1.872
peak=    3.239 closest distance to " O   HOH Z  88 " =    2.705
peak=    3.236 closest distance to " CB  ARG A 269 " =    0.797
peak=    3.236 closest distance to " O   HOH Z 128 " =    1.988
peak=    3.235 closest distance to " O   HOH Z 163 " =    1.872
peak=    3.231 closest distance to " O   HOH Z 284 " =    1.504
peak=    3.230 closest distance to " N   ALA A 256 " =    1.688
peak=    3.229 closest distance to " CA  ILE A  33 " =    1.316
peak=    3.229 closest distance to " O   HOH Z 305 " =    3.412
peak=    3.225 closest distance to " CG  ASP A 149 " =    1.244
peak=    3.224 closest distance to " O   HOH Z 409 " =    2.264
peak=    3.222 closest distance to " CB  TRP A 266 " =    1.113
peak=    3.220 closest distance to " O   HOH Z  32 " =    1.551
peak=    3.218 closest distance to " O   HOH Z 125 " =    2.164
peak=    3.217 closest distance to " NE1 TRP A 274 " =    0.969
peak=    3.214 closest distance to " O   HOH Z  94 " =    1.863
peak=    3.211 closest distance to " C   ALA A   1 " =    1.631
peak=    3.210 closest distance to " O   HOH Z 134 " =    2.111
peak=    3.208 closest distance to " CD2 TRP A 179 " =    1.360
peak=    3.205 closest distance to " C   TYR A 214 " =    1.409
peak=    3.205 closest distance to " CB  ILE A 120 " =    1.363
peak=    3.187 closest distance to " N   ALA A   1 " =    3.128
peak=    3.186 closest distance to " O   HOH Z 359 " =    1.234
peak=    3.179 closest distance to " O   HOH Z  44 " =    3.049
peak=    3.176 closest distance to " O   HOH Z 128 " =    1.662
peak=    3.175 closest distance to " CE  MET A 185 " =    2.005
peak=    3.175 closest distance to " O   HOH Z 410 " =    1.725
peak=    3.174 closest distance to " CB  ALA A   1 " =    4.413
peak=    3.173 closest distance to " O   HOH Z 392 " =    2.867
peak=    3.171 closest distance to " CA  LEU A 300 " =    0.988
peak=    3.169 closest distance to " O   HOH Z 299 " =    2.383
peak=    3.168 closest distance to " CA  GLY A  80 " =    0.721
peak=    3.163 closest distance to " O   HOH Z 130 " =    3.725
peak=    3.162 closest distance to " CB  ARG A 190 " =    1.782
peak=    3.160 closest distance to " O   HOH Z  10 " =    2.466
peak=    3.157 closest distance to " CG  ARG A 269 " =    1.368
peak=    3.157 closest distance to " O   HOH Z 189 " =    2.540
peak=    3.156 closest distance to " CB  LEU A 300 " =    0.996
peak=    3.147 closest distance to " CA  ASN A 176 " =    1.306
peak=    3.145 closest distance to " NH2 ARG A 219 " =    1.949
peak=    3.143 closest distance to " N   SER A  97 " =    0.986
peak=    3.138 closest distance to " O   HOH Z 172 " =    3.148
peak=    3.137 closest distance to " O   HOH Z 151 " =    1.430
peak=    3.131 closest distance to " CD  PRO A 243 " =    1.645
peak=    3.128 closest distance to " CB  GLN A  88 " =    1.259
peak=    3.127 closest distance to " CG2 ILE A  20 " =    1.026
peak=    3.125 closest distance to " NE AARG A 275 " =    1.243
peak=    3.123 closest distance to " CA  LYS A 290 " =    1.428
peak=    3.110 closest distance to " CB  TYR A  30 " =    1.489
peak=    3.109 closest distance to " O   HOH Z 419 " =    2.217
peak=    3.098 closest distance to " CB  ASN A 215 " =    1.001
peak=    3.097 closest distance to " N   ASP A 162 " =    1.244
peak=    3.096 closest distance to " O   HOH Z 332 " =    1.496
peak=    3.093 closest distance to " O   HOH Z 261 " =    1.495
peak=    3.087 closest distance to " SD BMET A  47 " =    1.312
peak=    3.085 closest distance to " CB  THR A  52 " =    1.147
peak=    3.084 closest distance to " CA  ILE A  20 " =    0.808
peak=    3.078 closest distance to " CD  LYS A 119 " =    2.018
peak=    3.065 closest distance to " O   HOH Z 172 " =    5.383
peak=    3.056 closest distance to " CB  GLU A 152 " =    1.356
peak=    3.054 closest distance to " CE  LYS A 166 " =    1.832
peak=    3.054 closest distance to " O   HOH Z 365 " =    3.124
peak=    3.049 closest distance to " OG BSER A 258 " =    2.740
peak=    3.034 closest distance to " O   HOH Z 282 " =    1.302
peak=    3.026 closest distance to " CB  MET A 188 " =    1.588
peak=    3.023 closest distance to " CG1BVAL A  72 " =    1.180

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 194         
Filter by distance & map next to the model:
   mapped sites are within: 0.760 - 5.841
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 194
   mapped sites are within: 0.760 - 5.841

peak=   -4.678 closest distance to " O   PRO A 198 " =    1.263
peak=   -4.552 closest distance to " CD  ARG A 156 " =    2.013
peak=   -4.486 closest distance to " O   VAL A  67 " =    2.639
peak=   -4.407 closest distance to " SG  CYS A 254 " =    3.226
peak=   -4.351 closest distance to " OD2 ASP A 191 " =    1.407
peak=   -4.334 closest distance to " CA  VAL A  67 " =    2.895
peak=   -4.263 closest distance to " C   HIS A 108 " =    1.095
peak=   -4.226 closest distance to " ND2 ASN A  45 " =    0.996
peak=   -4.223 closest distance to " N   GLN A  58 " =    1.723
peak=   -4.208 closest distance to " O   HOH Z  52 " =    0.839
peak=   -4.194 closest distance to " O   HOH Z 290 " =    1.111
peak=   -4.193 closest distance to " O   HOH Z  98 " =    1.886
peak=   -4.141 closest distance to " O   SER A 135 " =    1.457
peak=   -4.133 closest distance to " O   ALA A 161 " =    1.606
peak=   -4.121 closest distance to " O   HOH Z  13 " =    1.341
peak=   -4.101 closest distance to " OXT GLY A 302 " =    2.716
peak=   -4.087 closest distance to " CB  TYR A  15 " =    2.154
peak=   -4.055 closest distance to " O   HOH Z  65 " =    0.969
peak=   -4.040 closest distance to " O   HOH Z 385 " =    1.865
peak=   -4.011 closest distance to " OG BSER A 134 " =    1.354
peak=   -3.973 closest distance to " O   HOH Z 198 " =    1.740
peak=   -3.968 closest distance to " O   HOH Z 351 " =    1.494
peak=   -3.945 closest distance to " CZ  PHE A  59 " =    1.414
peak=   -3.934 closest distance to " O   HOH Z  43 " =    1.901
peak=   -3.932 closest distance to " O   HOH Z 263 " =    2.963
peak=   -3.914 closest distance to " OG  SER A   3 " =    1.471
peak=   -3.900 closest distance to " CB  PRO A 243 " =    2.554
peak=   -3.870 closest distance to " CG  GLN A 223 " =    1.513
peak=   -3.847 closest distance to " O   SER A  95 " =    1.436
peak=   -3.840 closest distance to " CD1 LEU A 255 " =    2.791
peak=   -3.806 closest distance to " O   HOH Z 372 " =    2.410
peak=   -3.805 closest distance to " O   HOH Z 266 " =    4.543
peak=   -3.802 closest distance to " O   HOH Z 102 " =    1.626
peak=   -3.790 closest distance to " CB  ALA A 248 " =    2.069
peak=   -3.783 closest distance to " O   HOH Z 407 " =    2.650
peak=   -3.780 closest distance to " CA  GLY A 133 " =    1.937
peak=   -3.763 closest distance to " O   HOH Z  11 " =    1.830
peak=   -3.761 closest distance to " O   PRO A 198 " =    1.219
peak=   -3.739 closest distance to " CD2 LEU A 237 " =    2.258
peak=   -3.739 closest distance to " O   HOH Z 147 " =    1.551
peak=   -3.728 closest distance to " OD2 ASP A  50 " =    1.471
peak=   -3.714 closest distance to " CB  ALA A 291 " =    2.113
peak=   -3.712 closest distance to " CB  ASN A  39 " =    2.236
peak=   -3.674 closest distance to " O   HOH Z 250 " =    1.369
peak=   -3.673 closest distance to " O   TRP A  92 " =    1.562
peak=   -3.667 closest distance to " CA  TYR A  30 " =    2.898
peak=   -3.657 closest distance to " CG  PHE A 283 " =    2.561
peak=   -3.651 closest distance to " O   MET A  40 " =    2.593
peak=   -3.640 closest distance to " CB  ALA A   7 " =    1.985
peak=   -3.627 closest distance to " ND2 ASN A 209 " =    1.746
peak=   -3.621 closest distance to " N   ASP A 286 " =    2.208
peak=   -3.620 closest distance to " O   PRO A 163 " =    1.137
peak=   -3.611 closest distance to " O   HOH Z 126 " =    1.831
peak=   -3.595 closest distance to " O   GLN A 183 " =    1.375
peak=   -3.582 closest distance to " O   HOH Z 377 " =    2.019
peak=   -3.570 closest distance to " OE1 GLN A  88 " =    1.140
peak=   -3.560 closest distance to " CD1 ILE A 239 " =    2.474
peak=   -3.554 closest distance to " CG1 VAL A 230 " =    1.876
peak=   -3.552 closest distance to " OG  SER A  87 " =    1.459
peak=   -3.552 closest distance to " C   ALA A 158 " =    1.211
peak=   -3.550 closest distance to " CG1 VAL A 112 " =    2.880
peak=   -3.547 closest distance to " O   HOH Z 313 " =    1.734
peak=   -3.546 closest distance to " OG  SER A 245 " =    1.236
peak=   -3.536 closest distance to " CE3 TRP A 274 " =    2.288
peak=   -3.534 closest distance to " O   HOH Z  24 " =    1.249
peak=   -3.529 closest distance to " O   ILE A  49 " =    1.567
peak=   -3.525 closest distance to " O   ALA A  51 " =    1.204
peak=   -3.521 closest distance to " OE2 GLU A 152 " =    1.168
peak=   -3.516 closest distance to " O   SER A 146 " =    0.802
peak=   -3.513 closest distance to " O   HOH Z 427 " =    1.477
peak=   -3.510 closest distance to " CB  GLN A  55 " =    1.359
peak=   -3.508 closest distance to " CB  ALA A 244 " =    2.019
peak=   -3.506 closest distance to " CG  ASP A 231 " =    0.760
peak=   -3.504 closest distance to " CD1 LEU A 101 " =    2.274
peak=   -3.504 closest distance to " OD2 ASP A 171 " =    2.107
peak=   -3.500 closest distance to " CZ  TYR A 169 " =    1.733
peak=   -3.500 closest distance to " O   HOH Z 393 " =    3.151
peak=   -3.494 closest distance to " O   HOH Z  52 " =    2.103
peak=   -3.494 closest distance to " CE3 TRP A 123 " =    1.314
peak=   -3.493 closest distance to " O   PRO A 163 " =    1.653
peak=   -3.492 closest distance to " CD  GLN A  88 " =    0.923
peak=   -3.485 closest distance to " O   HOH Z 137 " =    1.354
peak=   -3.479 closest distance to " O   HOH Z 185 " =    2.057
peak=   -3.479 closest distance to " O   HOH Z 421 " =    2.925
peak=   -3.475 closest distance to " CB  ALA A 291 " =    2.296
peak=   -3.472 closest distance to " O   HOH Z 388 " =    1.958
peak=   -3.467 closest distance to " CE  MET A 105 " =    2.234
peak=   -3.466 closest distance to " O   HOH Z 435 " =    2.967
peak=   -3.465 closest distance to " O   HOH Z 362 " =    5.841
peak=   -3.455 closest distance to " CD2 TYR A 293 " =    1.920
peak=   -3.453 closest distance to " CA  ASN A 127 " =    1.351
peak=   -3.452 closest distance to " OD1 ASP A 191 " =    1.899
peak=   -3.452 closest distance to " CB  PHE A 192 " =    1.715
peak=   -3.448 closest distance to " NH2 ARG A 139 " =    1.632
peak=   -3.447 closest distance to " OG  SER A  97 " =    1.983
peak=   -3.429 closest distance to " CG1 VAL A  78 " =    2.600
peak=   -3.425 closest distance to " O   HOH Z 211 " =    1.662
peak=   -3.421 closest distance to " O   HOH Z   3 " =    2.093
peak=   -3.421 closest distance to " CD1 PHE A  59 " =    1.958
peak=   -3.417 closest distance to " C   ASP A 231 " =    2.408
peak=   -3.417 closest distance to " O   HOH Z  88 " =    2.198
peak=   -3.416 closest distance to " OE1 GLU A 277 " =    2.095
peak=   -3.415 closest distance to " O   HOH Z 111 " =    4.437
peak=   -3.395 closest distance to " C   LEU A 143 " =    1.140
peak=   -3.389 closest distance to " O   HOH Z 197 " =    5.097
peak=   -3.386 closest distance to " ND2 ASN A  39 " =    1.329
peak=   -3.385 closest distance to " OG  SER A  97 " =    1.466
peak=   -3.378 closest distance to " CD  GLU A 236 " =    1.030
peak=   -3.375 closest distance to " OG  SER A  87 " =    1.881
peak=   -3.374 closest distance to " O   VAL A 153 " =    2.297
peak=   -3.373 closest distance to " OD1 ASP A 191 " =    1.286
peak=   -3.364 closest distance to " O   HOH Z  47 " =    1.564
peak=   -3.363 closest distance to " OD1 ASP A 200 " =    1.280
peak=   -3.361 closest distance to " O   HOH Z 231 " =    2.086
peak=   -3.355 closest distance to " N   GLN A 122 " =    1.431
peak=   -3.353 closest distance to " O   HOH Z 166 " =    1.382
peak=   -3.352 closest distance to " O   HOH Z 298 " =    1.300
peak=   -3.347 closest distance to " C   ALA A 114 " =    2.072
peak=   -3.340 closest distance to " O   HOH Z 423 " =    2.218
peak=   -3.338 closest distance to " O   HOH Z  97 " =    1.371
peak=   -3.330 closest distance to " CG1BVAL A  41 " =    2.944
peak=   -3.327 closest distance to " O   HOH Z 191 " =    5.510
peak=   -3.326 closest distance to " CG2 VAL A  78 " =    1.460
peak=   -3.324 closest distance to " O   HOH Z  93 " =    1.600
peak=   -3.319 closest distance to " N   SER A 276 " =    1.154
peak=   -3.311 closest distance to " CB  SER A 210 " =    1.337
peak=   -3.307 closest distance to " O   PRO A 163 " =    0.983
peak=   -3.304 closest distance to " ND2 ASN A  69 " =    1.425
peak=   -3.300 closest distance to " CB  ALA A 100 " =    2.535
peak=   -3.300 closest distance to " O   GLN A  89 " =    1.521
peak=   -3.294 closest distance to " CE2 PHE A 218 " =    2.436
peak=   -3.293 closest distance to " O   LEU A 297 " =    0.985
peak=   -3.288 closest distance to " O   HOH Z 438 " =    0.952
peak=   -3.286 closest distance to " NH2 ARG A  66 " =    4.381
peak=   -3.284 closest distance to " NH2 ARG A  79 " =    1.968
peak=   -3.283 closest distance to " O   PHE A 218 " =    1.478
peak=   -3.275 closest distance to " OD2 ASP A 140 " =    1.471
peak=   -3.274 closest distance to " CZ3 TRP A 123 " =    1.803
peak=   -3.272 closest distance to " O   HOH Z 326 " =    1.495
peak=   -3.268 closest distance to " O   HOH Z 218 " =    3.342
peak=   -3.261 closest distance to " C   GLN A 205 " =    1.865
peak=   -3.252 closest distance to " N   THR A 157 " =    1.539
peak=   -3.251 closest distance to " O   HOH Z 256 " =    1.397
peak=   -3.250 closest distance to " O   HOH Z  60 " =    1.697
peak=   -3.247 closest distance to " C   LEU A   5 " =    0.943
peak=   -3.244 closest distance to " O   TRP A  70 " =    1.442
peak=   -3.244 closest distance to " O   HOH Z 131 " =    4.029
peak=   -3.242 closest distance to " CG2 THR A 178 " =    2.117
peak=   -3.234 closest distance to " ND2 ASN A 187 " =    1.636
peak=   -3.229 closest distance to " O   HOH Z   9 " =    2.013
peak=   -3.228 closest distance to " O   HOH Z 114 " =    2.665
peak=   -3.224 closest distance to " O   HOH Z 395 " =    5.030
peak=   -3.221 closest distance to " CZ  PHE A 130 " =    0.903
peak=   -3.220 closest distance to " ND2 ASN A 142 " =    1.913
peak=   -3.215 closest distance to " O   HOH Z 377 " =    0.956
peak=   -3.213 closest distance to " O   HOH Z 417 " =    2.229
peak=   -3.205 closest distance to " CG2BVAL A  72 " =    1.734
peak=   -3.204 closest distance to " O   ASP A 162 " =    2.121
peak=   -3.197 closest distance to " CG  MET A 105 " =    0.854
peak=   -3.193 closest distance to " OG1 THR A 246 " =    1.237
peak=   -3.192 closest distance to " O   HOH Z 234 " =    3.737
peak=   -3.191 closest distance to " O   ARG A  66 " =    1.223
peak=   -3.187 closest distance to " O   HOH Z 374 " =    2.752
peak=   -3.181 closest distance to " CD1 LEU A 228 " =    2.007
peak=   -3.177 closest distance to " CE1 TYR A 169 " =    2.425
peak=   -3.176 closest distance to " O   HOH Z 174 " =    4.535
peak=   -3.155 closest distance to " CA  TRP A  70 " =    2.328
peak=   -3.154 closest distance to " O   HOH Z  63 " =    1.921
peak=   -3.151 closest distance to " CB  PHE A 208 " =    2.190
peak=   -3.151 closest distance to " CG2 THR A  52 " =    3.009
peak=   -3.150 closest distance to " N   ALA A  43 " =    2.258
peak=   -3.143 closest distance to " O   VAL A 197 " =    1.407
peak=   -3.143 closest distance to " CG  GLU A 152 " =    1.180
peak=   -3.134 closest distance to " O   VAL A 125 " =    1.968
peak=   -3.129 closest distance to " CA  GLY A 133 " =    2.110
peak=   -3.121 closest distance to " CB  ASP A 132 " =    2.279
peak=   -3.116 closest distance to " O   HOH Z 165 " =    2.286
peak=   -3.107 closest distance to " O   ASP A 270 " =    1.753
peak=   -3.106 closest distance to " O   HOH Z 388 " =    1.940
peak=   -3.103 closest distance to " O   ILE A 120 " =    1.735
peak=   -3.100 closest distance to " OE1 GLN A 194 " =    1.477
peak=   -3.087 closest distance to " CB  SER A 245 " =    1.653
peak=   -3.082 closest distance to " CE  LYS A  76 " =    2.829
peak=   -3.082 closest distance to " SG ACYS A 201 " =    1.570
peak=   -3.076 closest distance to " CG  ARG A 139 " =    1.397
peak=   -3.070 closest distance to " OE1 GLN A 205 " =    1.148
peak=   -3.070 closest distance to " CB  ALA A  51 " =    1.802
peak=   -3.062 closest distance to " O   LYS A 289 " =    2.509
peak=   -3.061 closest distance to " O   GLY A  80 " =    2.150
peak=   -3.059 closest distance to " O   ASN A 127 " =    1.727
peak=   -3.045 closest distance to " O   ASN A 224 " =    1.013
peak=   -3.036 closest distance to " C   ALA A 299 " =    1.237
peak=   -3.023 closest distance to " O   HOH Z 281 " =    3.000

================= 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    :  0.4706 0.4729   6.269244e+00   6.268273e+00
   1_bss:  0.4617 0.4611   6.263576e+00   6.249999e+00
   1_xyz:  0.3215 0.3477   6.012729e+00   6.069589e+00
   1_adp:  0.2892 0.3583   5.956203e+00   6.090310e+00
   1_occ:  0.2888 0.3587   5.956328e+00   6.091137e+00
   2_bss:  0.2843 0.3575   5.946653e+00   6.085438e+00
   2_xyz:  0.2171 0.2781   5.712574e+00   5.896810e+00
   2_adp:  0.2004 0.2543   5.640093e+00   5.819763e+00
   2_occ:  0.2000 0.2539   5.638813e+00   5.819065e+00
   3_bss:  0.1996 0.2529   5.636400e+00   5.816006e+00
   3_xyz:  0.1518 0.1963   5.387244e+00   5.589025e+00
   3_adp:  0.1412 0.1875   5.326197e+00   5.540334e+00
   3_occ:  0.1410 0.1873   5.324771e+00   5.538720e+00
   4_bss:  0.1412 0.1862   5.321875e+00   5.533435e+00
   4_xyz:  0.1221 0.1658   5.200106e+00   5.427518e+00
   4_adp:  0.1184 0.1631   5.175512e+00   5.408326e+00
   4_occ:  0.1182 0.1630   5.175094e+00   5.407766e+00
   5_bss:  0.1182 0.1629   5.174704e+00   5.407394e+00
   5_xyz:  0.1143 0.1604   5.152017e+00   5.386865e+00
   5_adp:  0.1129 0.1606   5.146449e+00   5.386660e+00
   5_occ:  0.1129 0.1606   5.146290e+00   5.386350e+00
   5_bss:  0.1131 0.1605   5.147037e+00   5.387388e+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:  0.343   4.791  -0.871   0.756   1.596   0.000   0.000   0.000
   1_xyz:  0.343   4.791  -0.871   0.756   1.596   0.000   0.000   0.000
   1_adp:  0.343   4.791  -0.871   0.756   1.596   0.000   0.000   0.000
   1_occ:  0.343   4.791  -0.871   0.756   1.596   0.000   0.000   0.000
   2_bss:  0.329  30.193  -1.645  -0.646  -0.115  -0.000  -0.000  -0.000
   2_xyz:  0.329  30.193  -1.645  -0.646  -0.115  -0.000  -0.000  -0.000
   2_adp:  0.329  30.193  -1.645  -0.646  -0.115  -0.000  -0.000  -0.000
   2_occ:  0.329  30.193  -1.645  -0.646  -0.115  -0.000  -0.000  -0.000
   3_bss:  0.327  30.193  -2.185  -1.522  -0.847  -0.000  -0.000  -0.000
   3_xyz:  0.327  30.193  -2.185  -1.522  -0.847  -0.000  -0.000  -0.000
   3_adp:  0.327  30.193  -2.185  -1.522  -0.847  -0.000  -0.000  -0.000
   3_occ:  0.327  30.193  -2.185  -1.522  -0.847  -0.000  -0.000  -0.000
   4_bss:  0.316  30.801  -2.787  -2.228  -1.481  -0.000  -0.000  -0.000
   4_xyz:  0.316  30.801  -2.787  -2.228  -1.481  -0.000  -0.000  -0.000
   4_adp:  0.316  30.801  -2.787  -2.228  -1.481  -0.000  -0.000  -0.000
   4_occ:  0.316  30.801  -2.787  -2.228  -1.481  -0.000  -0.000  -0.000
   5_bss:  0.317  32.556  -2.787  -2.228  -1.481  -0.000  -0.000  -0.000
   5_xyz:  0.317  32.556  -2.787  -2.228  -1.481  -0.000  -0.000  -0.000
   5_adp:  0.317  32.556  -2.787  -2.228  -1.481  -0.000  -0.000  -0.000
   5_occ:  0.317  32.556  -2.787  -2.228  -1.481  -0.000  -0.000  -0.000
   5_bss:  0.315  33.842  -2.652  -2.166  -1.409  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.482 0.4263  0.5845    69885.823
   1_bss:  56.122 0.4416  0.6122    65157.083
   1_xyz:  35.581 0.6962  0.9258    32250.469
   1_adp:  37.128 0.6773  0.9023    34145.445
   1_occ:  37.215 0.6762  0.9006    34259.111
   2_bss:  36.862 0.6800  0.8715    33600.250
   2_xyz:  27.697 0.7826  0.9777    19567.352
   2_adp:  24.281 0.8198  1.0031    16178.748
   2_occ:  24.249 0.8202  1.0028    16134.771
   3_bss:  24.124 0.8212  0.9767    15918.886
   3_xyz:  18.299 0.8780  1.0114     9625.476
   3_adp:  17.019 0.8902  1.0126     8774.388
   3_occ:  16.979 0.8905  1.0124     8723.141
   4_bss:  16.812 0.8917  0.9886     8524.273
   4_xyz:  14.723 0.9089  0.9985     6737.701
   4_adp:  14.265 0.9130  0.9980     6517.638
   4_occ:  14.257 0.9130  0.9980     6511.291
   5_bss:  14.247 0.9131  0.9982     6507.714
   5_xyz:  13.849 0.9164  0.9974     6253.631
   5_adp:  13.816 0.9168  0.9922     6245.042
   5_occ:  13.811 0.9168  0.9921     6241.514
   5_bss:  13.834 0.9166  0.9949     6280.596
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.106   2.2080e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.106   2.2080e-01
   1_xyz:   1.523  0.012  0.096 15.608  0.007  4.101   1.3593e-01
   1_adp:   1.523  0.012  0.096 15.608  0.007  4.101   1.3593e-01
   1_occ:   1.523  0.012  0.096 15.608  0.007  4.101   1.3593e-01
   2_bss:   1.523  0.012  0.096 15.608  0.007  4.101   1.3593e-01
   2_xyz:   1.139  0.008  0.076 14.154  0.005  4.105   7.3758e-02
   2_adp:   1.139  0.008  0.076 14.154  0.005  4.105   7.3758e-02
   2_occ:   1.139  0.008  0.076 14.154  0.005  4.105   7.3758e-02
   3_bss:   1.139  0.008  0.076 14.154  0.005  4.105   7.3758e-02
   3_xyz:   0.958  0.006  0.063 14.367  0.004  4.106   5.5103e-02
   3_adp:   0.958  0.006  0.063 14.367  0.004  4.106   5.5103e-02
   3_occ:   0.958  0.006  0.063 14.367  0.004  4.106   5.5103e-02
   4_bss:   0.958  0.006  0.063 14.367  0.004  4.106   5.5103e-02
   4_xyz:   0.996  0.006  0.069 14.554  0.004  4.105   5.6652e-02
   4_adp:   0.996  0.006  0.069 14.554  0.004  4.105   5.6652e-02
   4_occ:   0.996  0.006  0.069 14.554  0.004  4.105   5.6652e-02
   5_bss:   0.996  0.006  0.069 14.554  0.004  4.105   5.6652e-02
   5_xyz:   0.897  0.005  0.062 14.303  0.004  4.105   4.9765e-02
   5_adp:   0.897  0.005  0.062 14.303  0.004  4.105   4.9765e-02
   5_occ:   0.897  0.005  0.062 14.303  0.004  4.105   4.9765e-02
   5_bss:   0.897  0.005  0.062 14.303  0.004  4.105   4.9765e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  0.917   2.3917e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  0.917   2.3917e-01
   1_xyz:   9.528  0.059  0.396 88.292  0.080  1.601   1.2142e-01
   1_adp:   9.528  0.059  0.396 88.292  0.080  1.601   1.2142e-01
   1_occ:   9.528  0.059  0.396 88.292  0.080  1.601   1.2142e-01
   2_bss:   9.528  0.059  0.396 88.292  0.080  1.601   1.2142e-01
   2_xyz:   7.685  0.059  0.253 79.051  0.044  2.271   1.6254e-01
   2_adp:   7.685  0.059  0.253 79.051  0.044  2.271   1.6254e-01
   2_occ:   7.685  0.059  0.253 79.051  0.044  2.271   1.6254e-01
   3_bss:   7.685  0.059  0.253 79.051  0.044  2.271   1.6254e-01
   3_xyz:   7.924  0.040  0.233 80.809  0.037  2.301   4.6918e-02
   3_adp:   7.924  0.040  0.233 80.809  0.037  2.301   4.6918e-02
   3_occ:   7.924  0.040  0.233 80.809  0.037  2.301   4.6918e-02
   4_bss:   7.924  0.040  0.233 80.809  0.037  2.301   4.6918e-02
   4_xyz:   6.677  0.037  0.209 85.056  0.047  2.334   3.9400e-02
   4_adp:   6.677  0.037  0.209 85.056  0.047  2.334   3.9400e-02
   4_occ:   6.677  0.037  0.209 85.056  0.047  2.334   3.9400e-02
   5_bss:   6.677  0.037  0.209 85.056  0.047  2.334   3.9400e-02
   5_xyz:   7.118  0.037  0.200 84.289  0.040  2.332   3.5840e-02
   5_adp:   7.118  0.037  0.200 84.289  0.040  2.332   3.5840e-02
   5_occ:   7.118  0.037  0.200 84.289  0.040  2.332   3.5840e-02
   5_bss:   7.118  0.037  0.200 84.289  0.040  2.332   3.5840e-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:  95.76   0.00  19.34  91.92   0.00  15.12  95.76   2.18  42.33
   1_occ:  95.76   0.00  19.34  91.92   0.00  15.12  95.76   2.18  42.33
   2_bss:  95.76   0.00  19.34  91.92   0.00  15.12  95.76   2.18  42.33
   2_xyz:  95.76   0.00  19.34  91.92   0.00  15.12  95.76   2.18  42.33
   2_adp:  85.69   0.00  17.41  85.69   0.00  13.50  78.86   5.23  38.72
   2_occ:  85.69   0.00  17.41  85.69   0.00  13.50  78.86   5.23  38.72
   3_bss:  85.69   0.00  17.41  85.69   0.00  13.50  78.86   5.23  38.72
   3_xyz:  85.69   0.00  17.41  85.69   0.00  13.50  78.86   5.23  38.72
   3_adp:  84.96   0.00  17.35  84.96   0.00  13.05  78.81   5.90  40.74
   3_occ:  84.96   0.00  17.35  84.96   0.00  13.05  78.81   5.90  40.74
   4_bss:  84.96   0.00  17.35  84.96   0.00  13.05  78.81   5.90  40.74
   4_xyz:  84.96   0.00  17.35  84.96   0.00  13.05  78.81   5.90  40.74
   4_adp:  88.62   0.78  17.32  88.62   0.78  12.91  83.77   6.92  41.35
   4_occ:  88.62   0.78  17.32  88.62   0.78  12.91  83.77   6.92  41.35
   5_bss:  88.62   0.78  17.32  88.62   0.78  12.91  83.77   6.92  41.35
   5_xyz:  88.62   0.78  17.32  88.62   0.78  12.91  83.77   6.92  41.35
   5_adp:  95.76   0.59  17.31  95.76   0.59  12.83  90.34   6.16  41.70
   5_occ:  95.76   0.59  17.31  95.76   0.59  12.83  90.34   6.16  41.70
   5_bss:  95.74   0.57  17.29  95.74   0.57  12.81  90.33   6.14  41.68
------------------------------------------------------------------------
 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:    3.463    0.024    0.437
   1_adp:    3.463    0.024    0.437
   1_occ:    3.463    0.024    0.437
   2_bss:    3.463    0.024    0.437
   2_xyz:    2.916    0.054    0.552
   2_adp:    2.916    0.054    0.552
   2_occ:    2.916    0.054    0.552
   3_bss:    2.916    0.054    0.552
   3_xyz:    2.869    0.046    0.664
   3_adp:    2.869    0.046    0.664
   3_occ:    2.869    0.046    0.664
   4_bss:    2.869    0.046    0.664
   4_xyz:    2.683    0.038    0.704
   4_adp:    2.683    0.038    0.704
   4_occ:    2.683    0.038    0.704
   5_bss:    2.683    0.038    0.704
   5_xyz:    2.550    0.018    0.721
   5_adp:    2.550    0.018    0.721
   5_occ:    2.550    0.018    0.721
   5_bss:    2.550    0.018    0.721
------------------------------------------------------------------------

CPU time actual refinement: 348.67


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_144/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_144/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_144/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_144/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_144/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 348.52 
  Macro-tasks:
    bulk solvent and scale       = 44.53  
    individual site refinement   = 146.80 
    weights calculation          = 30.16  
    collect and process          = 6.65   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 228.25 
  Micro-tasks:
    mask                            = 2.43   
    f_calc                          = 109.32 
    alpha_beta                      = 8.26   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 119.01 
    fmodel                         = 7.25   
    r_factors                      = 0.23   
    phase_errors                   = 10.78  
    foms                           = 0.34   
    TOTAL for micro-tasks          = 258.78 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.883 micro seconds
Total CPU time: 6.04 minutes
from_scatterers_fft:    650 calls, 109.04 s
gradients_fft:          595 calls, 105.10 s

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

# Date 2008-01-16 Time 04:08:10 PST -0800 (1200485290.53 s)
Start R-work = 0.4706, R-free = 0.4729 (no bulk solvent and anisotropic scale)
Final R-work = 0.1383, R-free = 0.1800 (no bulk solvent and anisotropic scale)

Start R-work = 0.4617, R-free = 0.4611
Final R-work = 0.1131, R-free = 0.1605