# Date 2008-01-16 Time 04:21:37 PST -0800 (1200486097.21 s)
#phil __OFF__

Command line arguments: "../286.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 32418
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 286

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 46.6953, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 46.6953, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.728 1.95121
Completeness in resolution range: 0.959305
Completeness with d_max=infinity: 0.956307

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7280
                             d_min =   1.9512

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 46.6953, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.728 1.95121
Completeness in resolution range: 0.959305
Completeness with d_max=infinity: 0.956307

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7284 -  4.1748 [2139/2167]  1927   212   9.9%
  bin  2:  4.1748 -  3.3262 [2057/2076]  1848   209  10.2%
  bin  3:  3.3262 -  2.9095 [2043/2063]  1841   202   9.9%
  bin  4:  2.9095 -  2.6451 [2017/2042]  1818   199   9.9%
  bin  5:  2.6451 -  2.4565 [2008/2028]  1805   203  10.1%
  bin  6:  2.4565 -  2.3122 [1965/2011]  1772   193   9.8%
  bin  7:  2.3122 -  2.1968 [1987/2019]  1786   201  10.1%
  bin  8:  2.1968 -  2.1015 [1985/2021]  1782   203  10.2%
  bin  9:  2.1015 -  2.0208 [1977/2007]  1787   190   9.6%
  bin 10:  2.0208 -  1.9512 [1411/1986]  1264   147  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_286/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.20 -     1.94: 19
        1.94 -     2.68: 156
        2.68 -     3.42: 4531
        3.42 -     4.16: 9613
        4.16 -     4.90: 14676
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.199 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.315 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.656 3.040 -x+1,y-1/2,-z+1/2
  " O   SER A  95 " - " O   HOH Z 404 "  1.689 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.693 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28990 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_286/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_286/model_refine_001.geo

CPU time processing inputs: 9.13


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 46.69535 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4192   r_free= 0.4196   ksol= 0.00   Bsol= 0.00   scale= 0.941    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.217366                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7284 -  4.6562 0.99   1387  154 0.3419 0.3455      6.4939      6.4877|
|  2:  4.6562 -  3.7153 0.99   1353  147 0.3501 0.3317      6.6831      6.6696|
|  3:  3.7153 -  3.2514 0.99   1313  153 0.3804 0.3919      6.5774      6.7117|
|  4:  3.2514 -  2.9568 0.99   1307  139 0.3896 0.4239      6.4292       6.472|
|  5:  2.9568 -  2.7463 0.99   1294  144 0.4304 0.4290      6.3104      6.2838|
|  6:  2.7463 -  2.5853 0.98   1295  146 0.4490 0.4602      6.2064      6.1819|
|  7:  2.5853 -  2.4565 0.99   1290  142 0.4457 0.3982      6.1891      6.1233|
|  8:  2.4565 -  2.3500 0.98   1275  145 0.4618 0.4486      6.1385      6.1289|
|  9:  2.3500 -  2.2598 0.98   1287  139 0.4795 0.4683      6.0853      6.0853|
| 10:  2.2598 -  2.1821 0.97   1260  141 0.4598 0.4884       6.054      6.0982|
| 11:  2.1821 -  2.1141 0.99   1261  143 0.4900 0.4787      6.0134      6.0281|
| 12:  2.1141 -  2.0538 0.98   1271  137 0.4715 0.4544       5.949      5.9579|
| 13:  2.0538 -  1.9999 0.97   1252  142 0.4800 0.5085       5.854        5.85|
| 14:  1.9999 -  1.9512 0.61    785   87 0.4919 0.4565      5.8312      5.7107|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7284 -  4.6562  1387   154  0.72  32.33   0.85     0.75      61655.24|
|  2:  4.6562 -  3.7153  1353   147  0.74  31.36   0.94     0.85      87301.98|
|  3:  3.7153 -  3.2514  1313   153  0.66  38.93   0.97     0.86      93276.36|
|  4:  3.2514 -  2.9568  1307   139  0.59  44.45   0.99     0.81      83153.49|
|  5:  2.9568 -  2.7463  1294   144  0.53  49.07   0.93     0.76      66271.04|
|  6:  2.7463 -  2.5853  1295   146  0.52  50.26   0.94     0.74      56350.64|
|  7:  2.5853 -  2.4565  1290   142  0.53  49.37   0.95     0.74      50633.06|
|  8:  2.4565 -  2.3500  1275   145  0.50  51.95   0.96     0.72      46601.65|
|  9:  2.3500 -  2.2598  1287   139  0.48  53.65   0.98     0.69      42915.75|
| 10:  2.2598 -  2.1821  1260   141  0.48  53.70   1.00     0.68      39992.44|
| 11:  2.1821 -  2.1141  1261   143  0.45  55.99   0.99     0.68      37816.87|
| 12:  2.1141 -  2.0538  1271   137  0.47  54.50   1.03     0.72      35226.59|
| 13:  2.0538 -  1.9999  1252   142  0.45  55.97   0.97     0.70      30586.97|
| 14:  1.9999 -  1.9512   785    87  0.48  54.00   0.98     0.66      23811.95|
|alpha:            min =        0.66 max =            0.86 mean =         0.74|
|beta:             min =    23811.95 max =        93276.36 mean =     55208.27|
|figures of merit: min =        0.00 max =            1.00 mean =         0.55|
|phase err.(work): min =        0.00 max =           89.99 mean =        47.88|
|phase err.(test): min =        0.00 max =           89.61 mean =        47.98|
|-----------------------------------------------------------------------------|

============================== 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 = 9.519297              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.071   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.572911              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.815   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.199 -  1.569:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.569 -  1.939:       17 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.939 -  2.310:       21 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.310 -  2.680:      135 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.680 -  3.050:     2224 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.050 -  3.420:     2307 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.420 -  3.790:     4159 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.790 -  4.160:     5454 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.160 -  4.530:     6579 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.530 -  4.900:     8097 |
|-----------------------------------------------------------------------------|
|-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 |        0.202 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.199 |       0.809 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.356)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4192   r_free= 0.4196   ksol= 0.00   Bsol= 0.00   scale= 0.941    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.217366                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4072   r_free= 0.4045   ksol= 0.33   Bsol= 20.00   scale= 0.963   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.44,-2.29,3.16,-0.00,0.00,0.00); trace/3= -0.19                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.206834                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.591044              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.072   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.756523              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.737   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4072      final r-factor (work) = 0.2581          |
| start r-factor (free) = 0.4045      final r-factor (free) = 0.2806          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.7560 = 7.59 * 0.50 * 6.2058 + 1.00 * 0.2016                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.9087 = 7.59 * 0.50 * 6.0064 + 1.00 * 0.1113                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2581      final r-factor (work) = 0.2345          |
| start r-factor (free) = 0.2806      final r-factor (free) = 0.2892          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5502 = 0.76 * 1.00 * 6.0064 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3785 = 0.76 * 1.00 * 5.7670 + 1.00 * 0.0157                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.356)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.36   18.53    None  None   None       |
|    all(noH): 2823   0      0.00    95.36   18.53    None  None   None       |
|    Sol.    : 438    0      4.78    90.18   42.12    None  None   None       |
|    Mac.    : 2385   0      0.00    95.36   14.20    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 -   9.536:  875   |   5:    47.679 -  57.215:   85        |
|      1:     9.536 -  19.072: 1067   |   6:    57.215 -  66.750:   62        |
|      2:    19.072 -  28.607:  350   |   7:    66.750 -  76.286:   28        |
|      3:    28.607 -  38.143:  192   |   8:    76.286 -  85.822:   10        |
|      4:    38.143 -  47.679:  148   |   9:    85.822 -  95.358:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2345 r_free = 0.2892             target_work(ml) = 5.779         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2343 r_free = 0.2889             target_work(ml) = 5.778         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2343   r_free= 0.2889   ksol= 0.33   Bsol= 20.00   scale= 1.046   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.44,-2.29,3.16,-0.00,0.00,0.00); trace/3= -0.19                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.777859                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2291   r_free= 0.2856   ksol= 0.32   Bsol= 33.47   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.54,-2.38,-0.18,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.765273                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.345271              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.925   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.233734              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.354   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2291      final r-factor (work) = 0.1748          |
| start r-factor (free) = 0.2856      final r-factor (free) = 0.2261          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8739 = 2.35 * 0.50 * 5.7669 + 1.00 * 0.1114                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6837 = 2.35 * 0.50 * 5.6546 + 1.00 * 0.0529                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1748      final r-factor (work) = 0.1649          |
| start r-factor (free) = 0.2261      final r-factor (free) = 0.2136          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3355 = 0.23 * 1.00 * 5.6546 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2960 = 0.23 * 1.00 * 5.5027 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.356)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.76   17.71    None  None   None       |
|    all(noH): 2823   0      0.00    94.76   17.71    None  None   None       |
|    Sol.    : 438    0      6.95    78.79   40.13    None  None   None       |
|    Mac.    : 2385   0      0.00    94.76   13.60    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 -   9.476:  840   |   5:    47.382 -  56.858:   98        |
|      1:     9.476 -  18.953: 1211   |   6:    56.858 -  66.334:   38        |
|      2:    18.953 -  28.429:  300   |   7:    66.334 -  75.811:   22        |
|      3:    28.429 -  37.905:  158   |   8:    75.811 -  85.287:    5        |
|      4:    37.905 -  47.382:  149   |   9:    85.287 -  94.763:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1649 r_free = 0.2136             target_work(ml) = 5.472         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1645 r_free = 0.2135             target_work(ml) = 5.471         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1645   r_free= 0.2135   ksol= 0.32   Bsol= 33.47   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.54,-2.38,-0.18,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.470786                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1641   r_free= 0.2122   ksol= 0.32   Bsol= 33.47   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.91,-2.48,-1.40,-0.00,-0.00,-0.00); trace/3= -2.27                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.466237                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.193257              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.891  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.276713              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.577  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1641      final r-factor (work) = 0.1255          |
| start r-factor (free) = 0.2122      final r-factor (free) = 0.1690          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.5891 = 4.19 * 0.50 * 5.5023 + 1.00 * 0.0529                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2826 = 4.19 * 0.50 * 5.3490 + 1.00 * 0.0678                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1255      final r-factor (work) = 0.1182          |
| start r-factor (free) = 0.1690      final r-factor (free) = 0.1616          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4893 = 0.28 * 1.00 * 5.3490 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4466 = 0.28 * 1.00 * 5.1997 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.356)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.94    94.77   17.50    None  None   None       |
|    all(noH): 2823   0      1.94    94.77   17.50    None  None   None       |
|    Sol.    : 438    0      5.88    81.90   40.52    None  None   None       |
|    Mac.    : 2385   0      1.94    94.77   13.27    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.936 -  11.219: 1251   |   5:    48.351 -  57.634:   99        |
|      1:    11.219 -  20.502:  939   |   6:    57.634 -  66.916:   47        |
|      2:    20.502 -  29.785:  200   |   7:    66.916 -  76.199:   18        |
|      3:    29.785 -  39.068:  136   |   8:    76.199 -  85.482:    6        |
|      4:    39.068 -  48.351:  124   |   9:    85.482 -  94.765:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1182 r_free = 0.1616             target_work(ml) = 5.173         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1181 r_free = 0.1615             target_work(ml) = 5.172         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1181   r_free= 0.1615   ksol= 0.32   Bsol= 33.47   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.91,-2.48,-1.40,-0.00,-0.00,-0.00); trace/3= -2.27                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.172246                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1184   r_free= 0.1619   ksol= 0.32   Bsol= 34.43   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.07,-2.59,-1.97,-0.00,-0.00,-0.00); trace/3= -2.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.173052                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.293566              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.355  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.149241              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.432  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1184      final r-factor (work) = 0.1161          |
| start r-factor (free) = 0.1619      final r-factor (free) = 0.1593          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4320 = 1.29 * 0.50 * 5.2015 + 1.00 * 0.0678                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.3912 = 1.29 * 0.50 * 5.1699 + 1.00 * 0.0473                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1161      final r-factor (work) = 0.1158          |
| start r-factor (free) = 0.1593      final r-factor (free) = 0.1587          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7793 = 0.15 * 1.00 * 5.1699 + 1.00 * 0.0078                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7772 = 0.15 * 1.00 * 5.1617 + 1.00 * 0.0068                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.356)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.61    90.23   17.09    None  None   None       |
|    all(noH): 2823   0      2.61    90.23   17.09    None  None   None       |
|    Sol.    : 438    0      6.47    80.37   38.60    None  None   None       |
|    Mac.    : 2385   0      2.61    90.23   13.14    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.609 -  11.371: 1263   |   5:    46.419 -  55.182:   98        |
|      1:    11.371 -  20.133:  950   |   6:    55.182 -  63.944:   41        |
|      2:    20.133 -  28.895:  182   |   7:    63.944 -  72.706:   14        |
|      3:    28.895 -  37.657:  135   |   8:    72.706 -  81.468:    6        |
|      4:    37.657 -  46.419:  131   |   9:    81.468 -  90.230:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1158 r_free = 0.1587             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1158 r_free = 0.1587             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1587   ksol= 0.32   Bsol= 34.43   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.07,-2.59,-1.97,-0.00,-0.00,-0.00); trace/3= -2.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.158302                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1157   r_free= 0.1587   ksol= 0.32   Bsol= 34.43   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.07,-2.59,-1.97,-0.00,-0.00,-0.00); trace/3= -2.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.158495                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.240914              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.025  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.346904              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 163.622  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1157      final r-factor (work) = 0.1088          |
| start r-factor (free) = 0.1587      final r-factor (free) = 0.1547          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8306 = 2.24 * 0.50 * 5.1616 + 1.00 * 0.0473                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8077 = 2.24 * 0.50 * 5.1295 + 1.00 * 0.0603                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1079          |
| start r-factor (free) = 0.1547      final r-factor (free) = 0.1552          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7863 = 0.35 * 1.00 * 5.1295 + 1.00 * 0.0068                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7801 = 0.35 * 1.00 * 5.1097 + 1.00 * 0.0075                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.356)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.03    90.18   17.08    None  None   None       |
|    all(noH): 2823   0      2.03    90.18   17.08    None  None   None       |
|    Sol.    : 438    0      6.31    80.42   38.96    None  None   None       |
|    Mac.    : 2385   0      2.03    90.18   13.06    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.030 -  10.845: 1162   |   5:    46.104 -  54.919:  104        |
|      1:    10.845 -  19.660: 1014   |   6:    54.919 -  63.734:   47        |
|      2:    19.660 -  28.474:  208   |   7:    63.734 -  72.549:   15        |
|      3:    28.474 -  37.289:  131   |   8:    72.549 -  81.364:    6        |
|      4:    37.289 -  46.104:  133   |   9:    81.364 -  90.179:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1079 r_free = 0.1552             target_work(ml) = 5.113         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1078 r_free = 0.1552             target_work(ml) = 5.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1078   r_free= 0.1552   ksol= 0.32   Bsol= 34.43   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.07,-2.59,-1.97,-0.00,-0.00,-0.00); trace/3= -2.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.112568                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7284 -  4.6562 0.99   1387  154 0.0997 0.1257      5.3761       5.527|
|  2:  4.6562 -  3.7153 0.99   1353  147 0.0848 0.1102      5.4234      5.5959|
|  3:  3.7153 -  3.2514 0.99   1313  153 0.1036 0.1510      5.4537      5.8342|
|  4:  3.2514 -  2.9568 0.99   1307  139 0.1185 0.1612      5.4312      5.6214|
|  5:  2.9568 -  2.7463 0.99   1294  144 0.1193 0.1540      5.2526       5.421|
|  6:  2.7463 -  2.5853 0.98   1295  146 0.1155 0.1768      5.1506      5.3707|
|  7:  2.5853 -  2.4565 0.99   1290  142 0.1161 0.1567      5.0938      5.3252|
|  8:  2.4565 -  2.3500 0.98   1275  145 0.1105 0.1737       5.033      5.3093|
|  9:  2.3500 -  2.2598 0.98   1287  139 0.1140 0.1829      4.9998      5.3003|
| 10:  2.2598 -  2.1821 0.97   1260  141 0.1094 0.1665      4.9391      5.1561|
| 11:  2.1821 -  2.1141 0.99   1261  143 0.1084 0.1788      4.8988      5.2734|
| 12:  2.1141 -  2.0538 0.98   1271  137 0.1034 0.1633      4.8297      5.0987|
| 13:  2.0538 -  1.9999 0.97   1252  142 0.1108 0.1786      4.7721      5.0718|
| 14:  1.9999 -  1.9512 0.61    785   87 0.1068 0.1609      4.6844      4.8492|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7284 -  4.6562  1387   154  0.94   8.66   0.99     0.97       6714.02|
|  2:  4.6562 -  3.7153  1353   147  0.96   7.65   1.03     1.02       8639.50|
|  3:  3.7153 -  3.2514  1313   153  0.94  10.96   1.04     1.03       9917.04|
|  4:  3.2514 -  2.9568  1307   139  0.92  13.05   1.02     1.00       9811.53|
|  5:  2.9568 -  2.7463  1294   144  0.91  14.59   1.00     0.97       7168.98|
|  6:  2.7463 -  2.5853  1295   146  0.91  14.84   0.99     0.96       6240.15|
|  7:  2.5853 -  2.4565  1290   142  0.91  14.35   0.99     0.97       5358.01|
|  8:  2.4565 -  2.3500  1275   145  0.91  14.59   1.00     0.99       5058.37|
|  9:  2.3500 -  2.2598  1287   139  0.91  14.71   1.02     1.00       4688.42|
| 10:  2.2598 -  2.1821  1260   141  0.91  14.87   1.01     0.97       4216.43|
| 11:  2.1821 -  2.1141  1261   143  0.90  15.97   1.01     0.98       4111.06|
| 12:  2.1141 -  2.0538  1271   137  0.92  14.26   1.02     1.00       3614.51|
| 13:  2.0538 -  1.9999  1252   142  0.90  15.86   1.02     1.01       3249.33|
| 14:  1.9999 -  1.9512   785    87  0.91  14.96   1.00     0.97       2637.57|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2637.57 max =         9917.04 mean =      5946.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.42|
|phase err.(test): min =        0.00 max =           89.87 mean =        13.15|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1078   r_free= 0.1552   ksol= 0.32   Bsol= 34.35   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.91,-2.38,-1.89,-0.00,-0.00,-0.00); trace/3= -2.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.112535                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1078   r_free= 0.1552   ksol= 0.32   Bsol= 34.35   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.91,-2.38,-1.89,-0.00,-0.00,-0.00); trace/3= -2.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.112535                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7284 -  4.6562 0.99   1387  154 0.0997 0.1257      5.3765      5.5276|
|  2:  4.6562 -  3.7153 0.99   1353  147 0.0847 0.1101      5.4234      5.5958|
|  3:  3.7153 -  3.2514 0.99   1313  153 0.1036 0.1510      5.4535      5.8339|
|  4:  3.2514 -  2.9568 0.99   1307  139 0.1185 0.1612      5.4311      5.6217|
|  5:  2.9568 -  2.7463 0.99   1294  144 0.1192 0.1539      5.2527      5.4207|
|  6:  2.7463 -  2.5853 0.98   1295  146 0.1156 0.1771      5.1509      5.3721|
|  7:  2.5853 -  2.4565 0.99   1290  142 0.1161 0.1566      5.0942      5.3249|
|  8:  2.4565 -  2.3500 0.98   1275  145 0.1105 0.1735      5.0329      5.3095|
|  9:  2.3500 -  2.2598 0.98   1287  139 0.1140 0.1830      4.9998      5.3006|
| 10:  2.2598 -  2.1821 0.97   1260  141 0.1094 0.1663      4.9386      5.1547|
| 11:  2.1821 -  2.1141 0.99   1261  143 0.1084 0.1786      4.8986      5.2731|
| 12:  2.1141 -  2.0538 0.98   1271  137 0.1035 0.1634      4.8293      5.0983|
| 13:  2.0538 -  1.9999 0.97   1252  142 0.1107 0.1786      4.7717      5.0704|
| 14:  1.9999 -  1.9512 0.61    785   87 0.1067 0.1614      4.6847      4.8516|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7284 -  4.6562  1387   154  0.94   8.66   0.99     0.97       6721.62|
|  2:  4.6562 -  3.7153  1353   147  0.96   7.66   1.03     1.02       8641.73|
|  3:  3.7153 -  3.2514  1313   153  0.94  10.96   1.04     1.03       9913.30|
|  4:  3.2514 -  2.9568  1307   139  0.92  13.05   1.02     1.01       9809.86|
|  5:  2.9568 -  2.7463  1294   144  0.91  14.61   1.00     0.98       7175.97|
|  6:  2.7463 -  2.5853  1295   146  0.91  14.84   0.99     0.96       6245.31|
|  7:  2.5853 -  2.4565  1290   142  0.91  14.36   1.00     0.97       5363.26|
|  8:  2.4565 -  2.3500  1275   145  0.91  14.58   1.01     0.99       5055.35|
|  9:  2.3500 -  2.2598  1287   139  0.91  14.70   1.02     1.00       4686.86|
| 10:  2.2598 -  2.1821  1260   141  0.91  14.86   1.01     0.98       4210.78|
| 11:  2.1821 -  2.1141  1261   143  0.90  15.96   1.02     0.98       4108.23|
| 12:  2.1141 -  2.0538  1271   137  0.92  14.24   1.02     1.00       3608.70|
| 13:  2.0538 -  1.9999  1252   142  0.90  15.86   1.02     1.02       3248.16|
| 14:  1.9999 -  1.9512   785    87  0.91  14.97   1.01     0.98       2640.88|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2640.88 max =         9913.30 mean =      5946.39|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.42|
|phase err.(test): min =        0.00 max =           89.87 mean =        13.15|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.356)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.96    90.11   17.01    None  None   None       |
|    all(noH): 2823   0      1.96    90.11   17.01    None  None   None       |
|    Sol.    : 438    0      6.23    80.34   38.89    None  None   None       |
|    Mac.    : 2385   0      1.96    90.11   12.99    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.956 -  10.771: 1162   |   5:    46.031 -  54.846:  104        |
|      1:    10.771 -  19.586: 1014   |   6:    54.846 -  63.661:   47        |
|      2:    19.586 -  28.401:  208   |   7:    63.661 -  72.476:   15        |
|      3:    28.401 -  37.216:  131   |   8:    72.476 -  81.291:    6        |
|      4:    37.216 -  46.031:  133   |   9:    81.291 -  90.106:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 287         
Filter by distance & map next to the model:
   mapped sites are within: 0.395 - 5.565
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 283 from: 287
   mapped sites are within: 0.776 - 5.565

peak=    6.482 closest distance to " O   HOH Z 126 " =    1.981
peak=    6.052 closest distance to " O   HOH Z 142 " =    1.854
peak=    5.884 closest distance to " NE2 GLN A  11 " =    1.148
peak=    5.785 closest distance to " NH2 ARG A  56 " =    2.082
peak=    5.570 closest distance to " O   HOH Z 236 " =    1.487
peak=    5.179 closest distance to " O   HOH Z 108 " =    1.420
peak=    5.178 closest distance to " CB  SER A  63 " =    1.174
peak=    5.117 closest distance to " CB  ARG A 275 " =    0.925
peak=    5.057 closest distance to " O   HOH Z 193 " =    1.708
peak=    5.044 closest distance to " O   HOH Z 278 " =    1.322
peak=    4.977 closest distance to " C   PRO A 198 " =    1.486
peak=    4.880 closest distance to " O   HOH Z 124 " =    1.417
peak=    4.857 closest distance to " CG  PRO A  54 " =    1.139
peak=    4.832 closest distance to " O   HOH Z 427 " =    2.629
peak=    4.781 closest distance to " O   HOH Z 232 " =    2.343
peak=    4.731 closest distance to " CB  ASN A 148 " =    1.738
peak=    4.714 closest distance to " O   HOH Z 213 " =    1.912
peak=    4.708 closest distance to " CG  PRO A 213 " =    1.230
peak=    4.550 closest distance to " O   HOH Z 368 " =    1.935
peak=    4.536 closest distance to " CB  GLN A 183 " =    1.234
peak=    4.532 closest distance to " CB  GLU A 152 " =    1.260
peak=    4.524 closest distance to " O   HOH Z 207 " =    1.831
peak=    4.487 closest distance to " O   HOH Z 209 " =    2.336
peak=    4.463 closest distance to " O   HOH Z   6 " =    2.234
peak=    4.463 closest distance to " CB  GLN A 223 " =    1.487
peak=    4.449 closest distance to " O   HOH Z  78 " =    1.788
peak=    4.445 closest distance to " O   HOH Z  54 " =    1.666
peak=    4.362 closest distance to " O   HOH Z 203 " =    1.676
peak=    4.351 closest distance to " O   HOH Z  59 " =    1.956
peak=    4.335 closest distance to " O   SER A  87 " =    2.346
peak=    4.333 closest distance to " CA  TYR A  30 " =    1.010
peak=    4.324 closest distance to " CB  SER A   3 " =    1.308
peak=    4.322 closest distance to " O   HOH Z 272 " =    1.860
peak=    4.236 closest distance to " O   HOH Z 344 " =    2.967
peak=    4.230 closest distance to " OD2 ASP A 286 " =    2.595
peak=    4.222 closest distance to " O   HOH Z  93 " =    2.166
peak=    4.220 closest distance to " CB  TYR A 169 " =    0.875
peak=    4.169 closest distance to " O   HOH Z 134 " =    1.388
peak=    4.162 closest distance to " CA  ALA A  21 " =    1.100
peak=    4.160 closest distance to " O   HOH Z 234 " =    3.566
peak=    4.157 closest distance to " O   HOH Z 132 " =    1.013
peak=    4.137 closest distance to " NH1BARG A 145 " =    1.424
peak=    4.121 closest distance to " O   HOH Z 316 " =    2.925
peak=    4.117 closest distance to " O   HOH Z 407 " =    2.320
peak=    4.112 closest distance to " O   HOH Z 346 " =    1.651
peak=    4.098 closest distance to " O   HOH Z  61 " =    1.572
peak=    4.098 closest distance to " CG  PRO A  90 " =    1.206
peak=    4.098 closest distance to " OD1 ASN A  69 " =    2.649
peak=    4.079 closest distance to " O   HOH Z  10 " =    1.810
peak=    4.066 closest distance to " CB  GLU A 128 " =    1.070
peak=    4.043 closest distance to " O   HOH Z  97 " =    1.968
peak=    4.037 closest distance to " O   HOH Z  43 " =    2.058
peak=    4.029 closest distance to " O   HOH Z 173 " =    1.984
peak=    4.018 closest distance to " O   HOH Z 403 " =    1.779
peak=    4.017 closest distance to " O   HOH Z   3 " =    1.831
peak=    4.003 closest distance to " CA  THR A 221 " =    0.929
peak=    3.998 closest distance to " O   HOH Z 128 " =    2.026
peak=    3.998 closest distance to " CG1 ILE A  33 " =    1.241
peak=    3.990 closest distance to " NZ  LYS A 117 " =    3.164
peak=    3.982 closest distance to " CB  TRP A 179 " =    1.246
peak=    3.959 closest distance to " O   HOH Z  44 " =    2.002
peak=    3.958 closest distance to " O   HOH Z 287 " =    1.764
peak=    3.955 closest distance to " O   HOH Z 402 " =    1.428
peak=    3.946 closest distance to " O   HOH Z 389 " =    1.732
peak=    3.937 closest distance to " O   HOH Z 260 " =    1.195
peak=    3.922 closest distance to " O   HOH Z 128 " =    1.989
peak=    3.918 closest distance to " OG BSER A 164 " =    2.371
peak=    3.913 closest distance to " O   HOH Z 303 " =    2.027
peak=    3.909 closest distance to " CG  GLN A  77 " =    1.968
peak=    3.894 closest distance to " CB  ARG A  79 " =    1.465
peak=    3.882 closest distance to " O   HOH Z 298 " =    1.883
peak=    3.879 closest distance to " CB  LEU A 228 " =    1.098
peak=    3.878 closest distance to " O   HOH Z 250 " =    1.337
peak=    3.869 closest distance to " O   HOH Z 326 " =    1.491
peak=    3.869 closest distance to " O   HOH Z 156 " =    3.129
peak=    3.852 closest distance to " CG  PRO A 198 " =    1.258
peak=    3.844 closest distance to " O   HOH Z  15 " =    2.186
peak=    3.835 closest distance to " CB  SER A  26 " =    1.550
peak=    3.827 closest distance to " O   HOH Z  66 " =    2.130
peak=    3.815 closest distance to " N   ASN A  39 " =    1.193
peak=    3.811 closest distance to " C   ALA A   1 " =    1.656
peak=    3.807 closest distance to " CB  VAL A 265 " =    1.316
peak=    3.806 closest distance to " O   HOH Z 327 " =    1.692
peak=    3.792 closest distance to " O   HOH Z 183 " =    1.789
peak=    3.787 closest distance to " O   HOH Z 392 " =    2.868
peak=    3.782 closest distance to " O   HOH Z  21 " =    1.715
peak=    3.773 closest distance to " O   HOH Z 108 " =    1.956
peak=    3.766 closest distance to " O   HOH Z 199 " =    0.845
peak=    3.759 closest distance to " O   HOH Z 144 " =    2.080
peak=    3.753 closest distance to " ND2 ASN A 187 " =    1.498
peak=    3.753 closest distance to " O   HOH Z 369 " =    2.017
peak=    3.750 closest distance to " CB  PRO A  54 " =    0.943
peak=    3.725 closest distance to " O   HOH Z 365 " =    2.689
peak=    3.706 closest distance to " O   HOH Z 411 " =    3.778
peak=    3.695 closest distance to " O   HOH Z 278 " =    1.504
peak=    3.690 closest distance to " CA  ASN A 215 " =    1.219
peak=    3.678 closest distance to " O   MET A 105 " =    1.802
peak=    3.677 closest distance to " O   HOH Z 279 " =    2.091
peak=    3.675 closest distance to " O   HOH Z  73 " =    1.715
peak=    3.672 closest distance to " CG2 ILE A 120 " =    1.157
peak=    3.662 closest distance to " O   HOH Z 112 " =    2.445
peak=    3.656 closest distance to " CD2 TRP A 179 " =    1.370
peak=    3.653 closest distance to " O   HOH Z  49 " =    2.014
peak=    3.646 closest distance to " CB  TRP A 266 " =    1.082
peak=    3.646 closest distance to " CB  ARG A 139 " =    1.082
peak=    3.622 closest distance to " O   HOH Z 357 " =    1.731
peak=    3.616 closest distance to " CE1 TYR A 186 " =    1.233
peak=    3.614 closest distance to " O   HOH Z 313 " =    1.660
peak=    3.613 closest distance to " O   HOH Z  48 " =    1.578
peak=    3.601 closest distance to " NH2BARG A 145 " =    2.073
peak=    3.593 closest distance to " O   HOH Z 345 " =    3.149
peak=    3.586 closest distance to " O   HOH Z 193 " =    2.106
peak=    3.581 closest distance to " O   HOH Z 426 " =    1.460
peak=    3.580 closest distance to " O   HOH Z 425 " =    1.910
peak=    3.578 closest distance to " CA  THR A 264 " =    0.832
peak=    3.570 closest distance to " O   HOH Z  61 " =    1.642
peak=    3.569 closest distance to " OE2 GLU A  53 " =    2.105
peak=    3.565 closest distance to " CE2 TRP A 179 " =    1.653
peak=    3.562 closest distance to " O   HOH Z 106 " =    2.090
peak=    3.561 closest distance to " N   ARG A 156 " =    1.265
peak=    3.560 closest distance to " O   HOH Z 284 " =    2.784
peak=    3.555 closest distance to " CG  MET A 185 " =    1.272
peak=    3.551 closest distance to " O   HOH Z 189 " =    1.649
peak=    3.545 closest distance to " O   HOH Z 281 " =    4.524
peak=    3.542 closest distance to " CG2 ILE A  20 " =    1.539
peak=    3.537 closest distance to " CG  PRO A 243 " =    1.220
peak=    3.536 closest distance to " O   HOH Z 427 " =    3.069
peak=    3.530 closest distance to " CE BLYS A 290 " =    1.103
peak=    3.529 closest distance to " CG AARG A 275 " =    1.017
peak=    3.529 closest distance to " O   HOH Z 380 " =    1.969
peak=    3.524 closest distance to " O   SER A  26 " =    1.596
peak=    3.521 closest distance to " O   HOH Z 291 " =    1.599
peak=    3.520 closest distance to " O   HOH Z 234 " =    1.837
peak=    3.511 closest distance to " O   HOH Z 423 " =    1.999
peak=    3.506 closest distance to " O   HOH Z 286 " =    2.270
peak=    3.502 closest distance to " CB  ARG A 190 " =    1.726
peak=    3.499 closest distance to " CA  ALA A 233 " =    1.060
peak=    3.494 closest distance to " O   HOH Z 172 " =    3.547
peak=    3.494 closest distance to " CB  SER A  62 " =    1.352
peak=    3.487 closest distance to " CG  ARG A  66 " =    2.826
peak=    3.485 closest distance to " O   HOH Z 227 " =    1.802
peak=    3.485 closest distance to " O   HOH Z 291 " =    1.789
peak=    3.481 closest distance to " OD1 ASP A 231 " =    1.924
peak=    3.477 closest distance to " O   HOH Z  85 " =    2.257
peak=    3.477 closest distance to " O   HOH Z 261 " =    1.831
peak=    3.474 closest distance to " O   HOH Z 374 " =    2.420
peak=    3.473 closest distance to " OG  SER A  62 " =    2.900
peak=    3.471 closest distance to " O   HOH Z 368 " =    3.636
peak=    3.470 closest distance to " NE2 GLN A  58 " =    4.289
peak=    3.468 closest distance to " O   HOH Z 219 " =    2.183
peak=    3.467 closest distance to " O   HOH Z 180 " =    2.191
peak=    3.464 closest distance to " CG  GLU A 277 " =    2.090
peak=    3.463 closest distance to " O   HOH Z   1 " =    1.793
peak=    3.460 closest distance to " O   HOH Z  52 " =    1.189
peak=    3.457 closest distance to " CB  GLU A 277 " =    3.428
peak=    3.445 closest distance to " O   HOH Z  88 " =    2.846
peak=    3.443 closest distance to " CA  ALA A 291 " =    0.928
peak=    3.442 closest distance to " O   HOH Z  28 " =    2.275
peak=    3.438 closest distance to " CD2 LEU A 297 " =    0.967
peak=    3.432 closest distance to " O   HOH Z 273 " =    2.880
peak=    3.428 closest distance to " O   HOH Z 261 " =    1.627
peak=    3.426 closest distance to " CA  MET A  40 " =    1.049
peak=    3.423 closest distance to " CB  ALA A 291 " =    1.343
peak=    3.404 closest distance to " O   HOH Z  89 " =    2.111
peak=    3.402 closest distance to " CG2 THR A 221 " =    1.136
peak=    3.401 closest distance to " CB  VAL A 202 " =    1.605
peak=    3.399 closest distance to " O   HOH Z  30 " =    2.286
peak=    3.389 closest distance to " O   HOH Z 132 " =    2.218
peak=    3.386 closest distance to " O   HOH Z 425 " =    1.299
peak=    3.385 closest distance to " O   HOH Z 258 " =    1.716
peak=    3.384 closest distance to " O   HOH Z 192 " =    1.802
peak=    3.378 closest distance to " O   HOH Z 263 " =    2.219
peak=    3.377 closest distance to " NH2 ARG A 219 " =    1.945
peak=    3.370 closest distance to " O   HOH Z  85 " =    1.698
peak=    3.364 closest distance to " CA  GLY A  80 " =    0.776
peak=    3.360 closest distance to " CD  PRO A 243 " =    1.544
peak=    3.360 closest distance to " O   HOH Z  50 " =    1.491
peak=    3.360 closest distance to " O  BHOH Z 338 " =    2.271
peak=    3.346 closest distance to " NH1AARG A 145 " =    1.064
peak=    3.344 closest distance to " N   ASP A 162 " =    1.241
peak=    3.334 closest distance to " O   HOH Z 163 " =    1.745
peak=    3.328 closest distance to " OD1BASN A 224 " =    2.184
peak=    3.327 closest distance to " O   HOH Z 417 " =    3.126
peak=    3.326 closest distance to " CD BLYS A 290 " =    1.269
peak=    3.325 closest distance to " CA  ASN A 176 " =    1.110
peak=    3.324 closest distance to " CG2 VAL A 257 " =    0.819
peak=    3.315 closest distance to " O   HOH Z 248 " =    1.825
peak=    3.313 closest distance to " O   HOH Z 126 " =    2.240
peak=    3.309 closest distance to " O   HOH Z 158 " =    2.876
peak=    3.307 closest distance to " O   HOH Z 211 " =    2.450
peak=    3.306 closest distance to " O   HOH Z 343 " =    1.379
peak=    3.304 closest distance to " CG1BVAL A  72 " =    1.423
peak=    3.301 closest distance to " O   HOH Z 214 " =    2.053
peak=    3.300 closest distance to " O   HOH Z 417 " =    2.006
peak=    3.299 closest distance to " O   HOH Z 433 " =    1.789
peak=    3.296 closest distance to " CB  SER A 141 " =    1.099
peak=    3.292 closest distance to " CB  ARG A 102 " =    0.834
peak=    3.280 closest distance to " O   HOH Z 185 " =    1.603
peak=    3.279 closest distance to " NH2AARG A 190 " =    1.483
peak=    3.268 closest distance to " O   HOH Z  59 " =    2.075
peak=    3.263 closest distance to " O   HOH Z 118 " =    1.144
peak=    3.259 closest distance to " N   PHE A 130 " =    1.369
peak=    3.257 closest distance to " O   HOH Z 251 " =    1.597
peak=    3.256 closest distance to " O   HOH Z  40 " =    1.445
peak=    3.256 closest distance to " O   HOH Z  15 " =    1.547
peak=    3.255 closest distance to " O   HOH Z   9 " =    2.048
peak=    3.254 closest distance to " O   HOH Z  63 " =    2.241
peak=    3.254 closest distance to " CG  ARG A  66 " =    0.965
peak=    3.254 closest distance to " CB  ASN A 110 " =    1.088
peak=    3.252 closest distance to " O   HOH Z 334 " =    1.344
peak=    3.249 closest distance to " O   HOH Z 106 " =    1.763
peak=    3.246 closest distance to " O   HOH Z  43 " =    2.699
peak=    3.245 closest distance to " O   HOH Z 245 " =    1.260
peak=    3.242 closest distance to " O   HOH Z 118 " =    1.061
peak=    3.242 closest distance to " CB  ASN A  39 " =    0.780
peak=    3.240 closest distance to " CA  VAL A  41 " =    0.903
peak=    3.240 closest distance to " O   HOH Z 380 " =    2.077
peak=    3.240 closest distance to " CG  LYS A 166 " =    1.630
peak=    3.239 closest distance to " CD2 LEU A 255 " =    1.129
peak=    3.238 closest distance to " CB  THR A  31 " =    1.738
peak=    3.238 closest distance to " O   HOH Z  64 " =    2.062
peak=    3.233 closest distance to " O   HOH Z 106 " =    2.096
peak=    3.233 closest distance to " CA  LEU A 282 " =    1.246
peak=    3.232 closest distance to " O   HOH Z 368 " =    2.573
peak=    3.231 closest distance to " CB  ALA A 248 " =    1.370
peak=    3.230 closest distance to " O   HOH Z 365 " =    2.488
peak=    3.225 closest distance to " O   HOH Z 276 " =    1.293
peak=    3.217 closest distance to " N   TYR A  15 " =    0.927
peak=    3.216 closest distance to " O   HOH Z 371 " =    2.128
peak=    3.212 closest distance to " CB  GLU A  46 " =    1.069
peak=    3.212 closest distance to " OG BSER A 258 " =    3.038
peak=    3.211 closest distance to " CG  MET A 113 " =    1.024
peak=    3.208 closest distance to " CE  LYS A 119 " =    1.143
peak=    3.207 closest distance to " O   HOH Z 125 " =    2.358
peak=    3.204 closest distance to " CZ2 TRP A 274 " =    1.603
peak=    3.202 closest distance to " CE AMET A  47 " =    1.332
peak=    3.202 closest distance to " CE BMET A  47 " =    1.327
peak=    3.201 closest distance to " OG  SER A  22 " =    2.582
peak=    3.200 closest distance to " O   HOH Z 337 " =    3.462
peak=    3.194 closest distance to " O   HOH Z 438 " =    1.730
peak=    3.193 closest distance to " NE2 GLN A 223 " =    1.820
peak=    3.193 closest distance to " O   HOH Z 175 " =    2.067
peak=    3.182 closest distance to " O   ALA A   1 " =    1.406
peak=    3.176 closest distance to " NE AARG A 275 " =    1.738
peak=    3.173 closest distance to " O   HOH Z  40 " =    1.955
peak=    3.171 closest distance to " CG2 THR A 294 " =    1.551
peak=    3.170 closest distance to " CG2BVAL A  41 " =    0.870
peak=    3.163 closest distance to " O   HOH Z  83 " =    1.725
peak=    3.156 closest distance to " CA  VAL A 126 " =    1.191
peak=    3.152 closest distance to " O   HOH Z 255 " =    1.639
peak=    3.151 closest distance to " CG  MET A  93 " =    0.935
peak=    3.150 closest distance to " N   TRP A 150 " =    1.574
peak=    3.148 closest distance to " O   HOH Z 148 " =    3.165
peak=    3.143 closest distance to " CA  ASP A 140 " =    1.081
peak=    3.139 closest distance to " O   HOH Z  68 " =    2.443
peak=    3.130 closest distance to " O   HOH Z 140 " =    2.113
peak=    3.120 closest distance to " CA  ARG A  36 " =    0.929
peak=    3.115 closest distance to " O   HOH Z 411 " =    1.694
peak=    3.109 closest distance to " CD  LYS A 166 " =    1.244
peak=    3.109 closest distance to " CH2 TRP A 150 " =    1.146
peak=    3.104 closest distance to " CG2 VAL A  67 " =    1.063
peak=    3.104 closest distance to " O   HOH Z  68 " =    1.537
peak=    3.103 closest distance to " CG  LYS A 119 " =    1.150
peak=    3.103 closest distance to " O   HOH Z 151 " =    1.537
peak=    3.097 closest distance to " CA  ASN A 217 " =    1.208
peak=    3.096 closest distance to " O   HOH Z  19 " =    2.340
peak=    3.094 closest distance to " O   HOH Z 172 " =    5.565
peak=    3.091 closest distance to " O   HOH Z 214 " =    1.003
peak=    3.089 closest distance to " O   HOH Z 271 " =    2.040
peak=    3.084 closest distance to " O   HOH Z 367 " =    3.624
peak=    3.078 closest distance to " O   HOH Z 280 " =    2.461
peak=    3.077 closest distance to " N   TYR A 116 " =    1.692
peak=    3.071 closest distance to " O   HOH Z 132 " =    2.297
peak=    3.070 closest distance to " O   HOH Z 329 " =    3.389
peak=    3.064 closest distance to " O   HOH Z 299 " =    2.150
peak=    3.057 closest distance to " OD1 ASP A 286 " =    1.702
peak=    3.054 closest distance to " CB  TYR A  30 " =    1.084
peak=    3.051 closest distance to " CB  ASN A 215 " =    1.064
peak=    3.048 closest distance to " O   HOH Z  88 " =    2.079
peak=    3.038 closest distance to " CB  GLN A 278 " =    0.813
peak=    3.031 closest distance to " CB  ILE A 120 " =    1.310
peak=    3.027 closest distance to " O   HOH Z 334 " =    1.491
peak=    3.006 closest distance to " O   HOH Z 189 " =    1.804

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.617 - 5.787
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 198 from: 200
   mapped sites are within: 0.785 - 5.787

peak=   -4.741 closest distance to " O   HOH Z  52 " =    0.818
peak=   -4.608 closest distance to " O   HOH Z 266 " =    4.364
peak=   -4.396 closest distance to " C   HIS A 108 " =    1.116
peak=   -4.328 closest distance to " N   GLN A  58 " =    1.631
peak=   -4.324 closest distance to " CD  ARG A 156 " =    1.969
peak=   -4.281 closest distance to " O   VAL A  67 " =    2.722
peak=   -4.264 closest distance to " OXT GLY A 302 " =    2.643
peak=   -4.239 closest distance to " SG  CYS A 254 " =    3.249
peak=   -4.180 closest distance to " O   HOH Z 407 " =    2.918
peak=   -4.164 closest distance to " O   HOH Z 290 " =    1.005
peak=   -4.072 closest distance to " O   HOH Z 377 " =    2.149
peak=   -4.053 closest distance to " O   VAL A 153 " =    2.317
peak=   -4.040 closest distance to " O   HOH Z  13 " =    1.376
peak=   -4.017 closest distance to " N   ALA A 248 " =    1.580
peak=   -4.014 closest distance to " O   HOH Z  52 " =    1.826
peak=   -4.008 closest distance to " O   PRO A 198 " =    1.309
peak=   -4.003 closest distance to " O   HOH Z 102 " =    1.754
peak=   -3.982 closest distance to " O   HOH Z 198 " =    1.949
peak=   -3.970 closest distance to " CG  LYS A 193 " =    2.168
peak=   -3.949 closest distance to " O   VAL A  67 " =    2.755
peak=   -3.946 closest distance to " C   ALA A 158 " =    1.143
peak=   -3.940 closest distance to " CB  PRO A 243 " =    2.548
peak=   -3.933 closest distance to " O   ALA A 161 " =    1.592
peak=   -3.917 closest distance to " O   SER A 146 " =    0.922
peak=   -3.912 closest distance to " CB  ASN A  39 " =    2.164
peak=   -3.863 closest distance to " N   HIS A 115 " =    1.905
peak=   -3.856 closest distance to " O   HOH Z 435 " =    2.715
peak=   -3.844 closest distance to " CB  ALA A 291 " =    2.448
peak=   -3.803 closest distance to " CZ  TYR A 169 " =    1.715
peak=   -3.798 closest distance to " OD1 ASN A  39 " =    2.199
peak=   -3.793 closest distance to " O   HOH Z  47 " =    1.544
peak=   -3.793 closest distance to " OG BSER A 134 " =    1.275
peak=   -3.776 closest distance to " OXT GLY A 302 " =    3.462
peak=   -3.768 closest distance to " O   HOH Z  98 " =    1.945
peak=   -3.745 closest distance to " O   HOH Z 114 " =    2.835
peak=   -3.722 closest distance to " NH2 ARG A  79 " =    1.908
peak=   -3.720 closest distance to " N   ASP A 286 " =    2.232
peak=   -3.703 closest distance to " O   HOH Z 353 " =    2.223
peak=   -3.703 closest distance to " O   HOH Z 388 " =    1.981
peak=   -3.699 closest distance to " O   HOH Z  11 " =    1.986
peak=   -3.697 closest distance to " OG  SER A  97 " =    1.987
peak=   -3.696 closest distance to " CB  PRO A 163 " =    2.704
peak=   -3.695 closest distance to " O   HOH Z 385 " =    1.979
peak=   -3.692 closest distance to " CG  ASP A 231 " =    0.785
peak=   -3.681 closest distance to " O   PRO A 163 " =    1.882
peak=   -3.681 closest distance to " O   HOH Z 385 " =    1.915
peak=   -3.675 closest distance to " O   HOH Z   3 " =    1.520
peak=   -3.665 closest distance to " O   HOH Z 250 " =    1.449
peak=   -3.659 closest distance to " O   HOH Z 166 " =    1.388
peak=   -3.655 closest distance to " OG  SER A   3 " =    1.503
peak=   -3.652 closest distance to " O   HOH Z 198 " =    1.430
peak=   -3.644 closest distance to " N   GLN A 122 " =    1.439
peak=   -3.642 closest distance to " CB  ALA A 161 " =    2.505
peak=   -3.640 closest distance to " CD  ARG A 139 " =    1.495
peak=   -3.625 closest distance to " O   HOH Z 126 " =    1.824
peak=   -3.621 closest distance to " CD1 LEU A 101 " =    2.344
peak=   -3.619 closest distance to " CG  GLU A 152 " =    2.444
peak=   -3.609 closest distance to " CG  ARG A 219 " =    2.304
peak=   -3.605 closest distance to " CD1 PHE A  59 " =    1.935
peak=   -3.603 closest distance to " O   HOH Z 231 " =    2.113
peak=   -3.597 closest distance to " CG  PHE A 283 " =    2.611
peak=   -3.594 closest distance to " O   SER A 135 " =    1.546
peak=   -3.588 closest distance to " O   HOH Z  24 " =    1.373
peak=   -3.586 closest distance to " N   SER A 276 " =    1.135
peak=   -3.577 closest distance to " O   PRO A 198 " =    1.286
peak=   -3.574 closest distance to " CZ  PHE A  59 " =    1.473
peak=   -3.572 closest distance to " O   HOH Z 263 " =    2.924
peak=   -3.567 closest distance to " CD1 LEU A 228 " =    2.067
peak=   -3.560 closest distance to " O   VAL A 174 " =    1.967
peak=   -3.557 closest distance to " O   ALA A  51 " =    1.231
peak=   -3.553 closest distance to " O   HOH Z  43 " =    1.685
peak=   -3.551 closest distance to " CD2 LEU A 300 " =    2.906
peak=   -3.540 closest distance to " O   HOH Z  11 " =    1.750
peak=   -3.538 closest distance to " O   HOH Z 362 " =    5.787
peak=   -3.532 closest distance to " OD2 ASP A  50 " =    1.319
peak=   -3.527 closest distance to " ND2 ASN A 209 " =    1.779
peak=   -3.522 closest distance to " CB  ASP A 132 " =    2.294
peak=   -3.518 closest distance to " O   HOH Z 185 " =    2.114
peak=   -3.517 closest distance to " ND2 ASN A  39 " =    1.290
peak=   -3.503 closest distance to " C   LEU A 143 " =    1.035
peak=   -3.502 closest distance to " O   HOH Z 351 " =    1.559
peak=   -3.499 closest distance to " ND2 ASN A  45 " =    0.950
peak=   -3.494 closest distance to " CE2 TYR A  30 " =    2.882
peak=   -3.489 closest distance to " O   TRP A  70 " =    1.527
peak=   -3.486 closest distance to " CA  TYR A  30 " =    2.889
peak=   -3.456 closest distance to " CZ3 TRP A 179 " =    1.389
peak=   -3.451 closest distance to " CB  ALA A 244 " =    2.029
peak=   -3.451 closest distance to " O   PHE A 218 " =    1.414
peak=   -3.449 closest distance to " CD  GLN A  58 " =    1.072
peak=   -3.447 closest distance to " CG1 VAL A 112 " =    2.775
peak=   -3.442 closest distance to " CG  ARG A 219 " =    2.524
peak=   -3.441 closest distance to " CA  GLY A 133 " =    1.889
peak=   -3.433 closest distance to " O   ASN A  45 " =    1.852
peak=   -3.417 closest distance to " C   TRP A 274 " =    1.569
peak=   -3.411 closest distance to " CB  ALA A 248 " =    1.966
peak=   -3.408 closest distance to " NH1 ARG A  56 " =    2.537
peak=   -3.406 closest distance to " O   HOH Z  93 " =    1.523
peak=   -3.404 closest distance to " C   GLN A 205 " =    1.906
peak=   -3.396 closest distance to " O   HOH Z 395 " =    5.099
peak=   -3.391 closest distance to " CG  GLU A 152 " =    0.988
peak=   -3.388 closest distance to " O   TRP A  92 " =    1.651
peak=   -3.388 closest distance to " CB  CYS A 201 " =    2.448
peak=   -3.381 closest distance to " O   HOH Z  56 " =    1.160
peak=   -3.380 closest distance to " ND2 ASN A 187 " =    1.504
peak=   -3.371 closest distance to " O   HOH Z 423 " =    2.185
peak=   -3.361 closest distance to " OD1 ASP A 191 " =    1.410
peak=   -3.338 closest distance to " CE  LYS A  76 " =    2.974
peak=   -3.336 closest distance to " CB  ALA A  43 " =    2.143
peak=   -3.325 closest distance to " OD2 ASP A 191 " =    1.467
peak=   -3.324 closest distance to " CA  ASP A 298 " =    1.065
peak=   -3.323 closest distance to " OG  SER A  62 " =    1.519
peak=   -3.323 closest distance to " O   SER A 146 " =    0.923
peak=   -3.321 closest distance to " O   SER A 210 " =    1.896
peak=   -3.318 closest distance to " CG  GLN A  58 " =    1.421
peak=   -3.317 closest distance to " CE3 TRP A 274 " =    2.365
peak=   -3.316 closest distance to " NH1 ARG A 195 " =    2.530
peak=   -3.315 closest distance to " OH  TYR A 214 " =    1.302
peak=   -3.314 closest distance to " OD1 ASP A 200 " =    1.179
peak=   -3.314 closest distance to " CD2 LEU A 237 " =    2.569
peak=   -3.313 closest distance to " CG1 VAL A 112 " =    2.909
peak=   -3.313 closest distance to " O   HOH Z 326 " =    1.657
peak=   -3.313 closest distance to " CZ3 TRP A 274 " =    1.081
peak=   -3.306 closest distance to " CE  MET A 105 " =    1.958
peak=   -3.304 closest distance to " CG1 VAL A 230 " =    1.947
peak=   -3.298 closest distance to " OG BSER A 134 " =    1.638
peak=   -3.292 closest distance to " CG  MET A 105 " =    0.920
peak=   -3.291 closest distance to " O   THR A 182 " =    1.123
peak=   -3.287 closest distance to " OD1 ASP A 191 " =    1.772
peak=   -3.287 closest distance to " O   HOH Z 174 " =    4.285
peak=   -3.284 closest distance to " CG2 VAL A 189 " =    2.084
peak=   -3.284 closest distance to " C   PRO A  90 " =    1.480
peak=   -3.284 closest distance to " CD1 ILE A 239 " =    2.500
peak=   -3.283 closest distance to " OG  SER A 206 " =    1.574
peak=   -3.278 closest distance to " O   HOH Z 298 " =    1.279
peak=   -3.275 closest distance to " CD  GLN A  88 " =    0.837
peak=   -3.271 closest distance to " OG ASER A 134 " =    1.064
peak=   -3.265 closest distance to " O   HOH Z  88 " =    1.718
peak=   -3.259 closest distance to " CD  LYS A 289 " =    2.509
peak=   -3.254 closest distance to " O   HOH Z 309 " =    2.502
peak=   -3.235 closest distance to " O   HOH Z 311 " =    3.356
peak=   -3.233 closest distance to " O   HOH Z 436 " =    1.184
peak=   -3.231 closest distance to " CG1 VAL A  78 " =    3.070
peak=   -3.215 closest distance to " OD1 ASP A 171 " =    1.655
peak=   -3.214 closest distance to " O   ASP A 162 " =    2.125
peak=   -3.214 closest distance to " O   HOH Z 310 " =    3.435
peak=   -3.214 closest distance to " O   HOH Z 139 " =    2.916
peak=   -3.212 closest distance to " O   HOH Z 429 " =    1.983
peak=   -3.207 closest distance to " CA  TRP A  70 " =    2.462
peak=   -3.206 closest distance to " OD2 ASP A 270 " =    1.311
peak=   -3.203 closest distance to " O   HOH Z  90 " =    2.528
peak=   -3.202 closest distance to " O   HOH Z 197 " =    4.929
peak=   -3.200 closest distance to " CG2 THR A 178 " =    2.172
peak=   -3.194 closest distance to " CD2 TYR A 293 " =    2.044
peak=   -3.194 closest distance to " O   HOH Z 211 " =    1.592
peak=   -3.192 closest distance to " CE3 TRP A 123 " =    1.228
peak=   -3.190 closest distance to " NH2 ARG A  66 " =    4.336
peak=   -3.186 closest distance to " O   HOH Z 427 " =    1.442
peak=   -3.183 closest distance to " OD1 ASN A 301 " =    2.001
peak=   -3.181 closest distance to " ND2 ASN A  60 " =    1.479
peak=   -3.177 closest distance to " O   HOH Z  63 " =    1.493
peak=   -3.169 closest distance to " O   ARG A  56 " =    1.583
peak=   -3.164 closest distance to " O   HOH Z 313 " =    1.980
peak=   -3.156 closest distance to " O   HOH Z  60 " =    1.728
peak=   -3.155 closest distance to " O   HOH Z 417 " =    2.328
peak=   -3.155 closest distance to " O   HOH Z  41 " =    2.244
peak=   -3.151 closest distance to " O   HOH Z 281 " =    2.838
peak=   -3.141 closest distance to " O   HOH Z 105 " =    3.394
peak=   -3.140 closest distance to " OD2 ASP A 171 " =    2.325
peak=   -3.138 closest distance to " N   ALA A  43 " =    2.288
peak=   -3.138 closest distance to " O   HOH Z 234 " =    3.872
peak=   -3.137 closest distance to " O   HOH Z 298 " =    2.484
peak=   -3.137 closest distance to " CB  ASP A 132 " =    2.102
peak=   -3.136 closest distance to " O   SER A 273 " =    1.467
peak=   -3.136 closest distance to " CG  GLU A 277 " =    1.227
peak=   -3.134 closest distance to " O   HOH Z 120 " =    2.170
peak=   -3.133 closest distance to " O   HOH Z 210 " =    1.188
peak=   -3.129 closest distance to " O   HOH Z 137 " =    1.370
peak=   -3.119 closest distance to " N   ALA A 226 " =    1.911
peak=   -3.119 closest distance to " CD2 LEU A 300 " =    2.736
peak=   -3.117 closest distance to " CG  PRO A 163 " =    2.521
peak=   -3.116 closest distance to " O   HOH Z 148 " =    1.765
peak=   -3.106 closest distance to " O   HOH Z 137 " =    1.524
peak=   -3.096 closest distance to " O   HOH Z 166 " =    1.750
peak=   -3.095 closest distance to " SG ACYS A 201 " =    1.875
peak=   -3.095 closest distance to " CE  LYS A  76 " =    2.798
peak=   -3.095 closest distance to " O   LYS A 117 " =    1.478
peak=   -3.090 closest distance to " O   HOH Z 378 " =    1.678
peak=   -3.085 closest distance to " CA  GLY A  23 " =    2.470
peak=   -3.081 closest distance to " O   ALA A 292 " =    1.930
peak=   -3.080 closest distance to " CD  PRO A  90 " =    1.852
peak=   -3.079 closest distance to " CG2BVAL A  72 " =    1.976
peak=   -3.079 closest distance to " CE  MET A 105 " =    1.968
peak=   -3.078 closest distance to " OG1 THR A 178 " =    1.167
peak=   -3.064 closest distance to " O   PRO A 163 " =    1.332
peak=   -3.044 closest distance to " N   ALA A 248 " =    2.499
peak=   -3.038 closest distance to " O   HOH Z  68 " =    1.828
peak=   -3.035 closest distance to " OD1 ASN A 249 " =    1.067
peak=   -3.031 closest distance to " CB  PHE A 208 " =    2.192

================= 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    :  0.4192 0.4196   6.217366e+00   6.219067e+00
   1_bss:  0.4072 0.4045   6.206834e+00   6.193558e+00
   1_xyz:  0.2581 0.2806   5.835014e+00   5.916514e+00
   1_adp:  0.2345 0.2892   5.778568e+00   5.937909e+00
   1_occ:  0.2343 0.2889   5.777859e+00   5.937349e+00
   2_bss:  0.2291 0.2856   5.765273e+00   5.927562e+00
   2_xyz:  0.1748 0.2261   5.528646e+00   5.717706e+00
   2_adp:  0.1649 0.2136   5.471619e+00   5.661173e+00
   2_occ:  0.1645 0.2135   5.470786e+00   5.660930e+00
   3_bss:  0.1641 0.2122   5.466237e+00   5.655724e+00
   3_xyz:  0.1255 0.1690   5.226628e+00   5.449349e+00
   3_adp:  0.1182 0.1616   5.173302e+00   5.398755e+00
   3_occ:  0.1181 0.1615   5.172246e+00   5.397708e+00
   4_bss:  0.1184 0.1619   5.173052e+00   5.397676e+00
   4_xyz:  0.1161 0.1593   5.162365e+00   5.383708e+00
   4_adp:  0.1158 0.1587   5.158792e+00   5.379743e+00
   4_occ:  0.1158 0.1587   5.158302e+00   5.379427e+00
   5_bss:  0.1157 0.1587   5.158495e+00   5.379629e+00
   5_xyz:  0.1088 0.1547   5.114479e+00   5.353946e+00
   5_adp:  0.1079 0.1552   5.112746e+00   5.358388e+00
   5_occ:  0.1078 0.1552   5.112568e+00   5.358342e+00
   5_bss:  0.1078 0.1552   5.112535e+00   5.358332e+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:  0.328  20.000  -1.444  -2.292   3.165  -0.000   0.000   0.000
   1_xyz:  0.328  20.000  -1.444  -2.292   3.165  -0.000   0.000   0.000
   1_adp:  0.328  20.000  -1.444  -2.292   3.165  -0.000   0.000   0.000
   1_occ:  0.328  20.000  -1.444  -2.292   3.165  -0.000   0.000   0.000
   2_bss:  0.320  33.473  -2.535  -2.384  -0.179  -0.000  -0.000  -0.000
   2_xyz:  0.320  33.473  -2.535  -2.384  -0.179  -0.000  -0.000  -0.000
   2_adp:  0.320  33.473  -2.535  -2.384  -0.179  -0.000  -0.000  -0.000
   2_occ:  0.320  33.473  -2.535  -2.384  -0.179  -0.000  -0.000  -0.000
   3_bss:  0.320  33.473  -2.913  -2.480  -1.402  -0.000  -0.000  -0.000
   3_xyz:  0.320  33.473  -2.913  -2.480  -1.402  -0.000  -0.000  -0.000
   3_adp:  0.320  33.473  -2.913  -2.480  -1.402  -0.000  -0.000  -0.000
   3_occ:  0.320  33.473  -2.913  -2.480  -1.402  -0.000  -0.000  -0.000
   4_bss:  0.317  34.425  -3.073  -2.586  -1.968  -0.000  -0.000  -0.000
   4_xyz:  0.317  34.425  -3.073  -2.586  -1.968  -0.000  -0.000  -0.000
   4_adp:  0.317  34.425  -3.073  -2.586  -1.968  -0.000  -0.000  -0.000
   4_occ:  0.317  34.425  -3.073  -2.586  -1.968  -0.000  -0.000  -0.000
   5_bss:  0.321  34.425  -3.073  -2.586  -1.968  -0.000  -0.000  -0.000
   5_xyz:  0.321  34.425  -3.073  -2.586  -1.968  -0.000  -0.000  -0.000
   5_adp:  0.321  34.425  -3.073  -2.586  -1.968  -0.000  -0.000  -0.000
   5_occ:  0.321  34.425  -3.073  -2.586  -1.968  -0.000  -0.000  -0.000
   5_bss:  0.321  34.352  -2.912  -2.376  -1.889  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  47.887 0.5487  0.7425    55207.010
   1_bss:  46.228 0.5673  0.7635    50312.868
   1_xyz:  28.290 0.7776  0.9860    20851.143
   1_adp:  29.582 0.7625  0.9783    22112.915
   1_occ:  29.569 0.7627  0.9785    22089.071
   2_bss:  28.939 0.7691  0.9348    21278.808
   2_xyz:  21.976 0.8419  0.9912    12897.655
   2_adp:  20.144 0.8608  1.0016    11384.486
   2_occ:  20.134 0.8609  1.0011    11364.606
   3_bss:  19.929 0.8627  0.9806    11152.402
   3_xyz:  15.480 0.9021  1.0017     7154.756
   3_adp:  14.413 0.9113  1.0023     6546.131
   3_occ:  14.383 0.9115  1.0023     6522.424
   4_bss:  14.361 0.9118  0.9926     6537.117
   4_xyz:  13.936 0.9156  0.9933     6267.407
   4_adp:  13.789 0.9170  0.9926     6245.638
   4_occ:  13.779 0.9171  0.9925     6239.524
   5_bss:  13.783 0.9171  0.9925     6245.602
   5_xyz:  13.328 0.9203  0.9936     5911.873
   5_adp:  13.393 0.9199  0.9899     5945.495
   5_occ:  13.390 0.9199  0.9898     5945.767
   5_bss:  13.391 0.9199  0.9926     5946.114
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   2.0162e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   2.0162e-01
   1_xyz:   1.395  0.012  0.087 15.732  0.007  4.106   1.1128e-01
   1_adp:   1.395  0.012  0.087 15.732  0.007  4.106   1.1128e-01
   1_occ:   1.395  0.012  0.087 15.732  0.007  4.106   1.1128e-01
   2_bss:   1.395  0.012  0.087 15.732  0.007  4.106   1.1128e-01
   2_xyz:   0.970  0.005  0.066 14.123  0.004  4.112   5.2868e-02
   2_adp:   0.970  0.005  0.066 14.123  0.004  4.112   5.2868e-02
   2_occ:   0.970  0.005  0.066 14.123  0.004  4.112   5.2868e-02
   3_bss:   0.970  0.005  0.066 14.123  0.004  4.112   5.2868e-02
   3_xyz:   1.100  0.008  0.074 14.756  0.004  4.112   6.7774e-02
   3_adp:   1.100  0.008  0.074 14.756  0.004  4.112   6.7774e-02
   3_occ:   1.100  0.008  0.074 14.756  0.004  4.112   6.7774e-02
   4_bss:   1.100  0.008  0.074 14.756  0.004  4.112   6.7774e-02
   4_xyz:   0.876  0.005  0.062 14.266  0.003  4.106   4.7334e-02
   4_adp:   0.876  0.005  0.062 14.266  0.003  4.106   4.7334e-02
   4_occ:   0.876  0.005  0.062 14.266  0.003  4.106   4.7334e-02
   5_bss:   0.876  0.005  0.062 14.266  0.003  4.106   4.7334e-02
   5_xyz:   1.031  0.006  0.071 14.690  0.004  4.105   6.0302e-02
   5_adp:   1.031  0.006  0.071 14.690  0.004  4.105   6.0302e-02
   5_occ:   1.031  0.006  0.071 14.690  0.004  4.105   6.0302e-02
   5_bss:   1.031  0.006  0.071 14.690  0.004  4.105   6.0302e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.199   2.3876e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.199   2.3876e-01
   1_xyz:   9.562  0.078  0.274 89.492  0.060  2.081   1.0704e-01
   1_adp:   9.562  0.078  0.274 89.492  0.060  2.081   1.0704e-01
   1_occ:   9.562  0.078  0.274 89.492  0.060  2.081   1.0704e-01
   2_bss:   9.562  0.078  0.274 89.492  0.060  2.081   1.0704e-01
   2_xyz:   6.776  0.033  0.204 82.888  0.034  2.392   3.6955e-02
   2_adp:   6.776  0.033  0.204 82.888  0.034  2.392   3.6955e-02
   2_occ:   6.776  0.033  0.204 82.888  0.034  2.392   3.6955e-02
   3_bss:   6.776  0.033  0.204 82.888  0.034  2.392   3.6955e-02
   3_xyz:   6.689  0.057  0.282 83.552  0.032  2.309   5.6513e-02
   3_adp:   6.689  0.057  0.282 83.552  0.032  2.309   5.6513e-02
   3_occ:   6.689  0.057  0.282 83.552  0.032  2.309   5.6513e-02
   4_bss:   6.689  0.057  0.282 83.552  0.032  2.309   5.6513e-02
   4_xyz:   6.090  0.037  0.188 83.530  0.038  2.393   4.5325e-02
   4_adp:   6.090  0.037  0.188 83.530  0.038  2.393   4.5325e-02
   4_occ:   6.090  0.037  0.188 83.530  0.038  2.393   4.5325e-02
   5_bss:   6.090  0.037  0.188 83.530  0.038  2.393   4.5325e-02
   5_xyz:   6.383  0.042  0.230 83.866  0.039  2.273   4.0972e-02
   5_adp:   6.383  0.042  0.230 83.866  0.039  2.273   4.0972e-02
   5_occ:   6.383  0.042  0.230 83.866  0.039  2.273   4.0972e-02
   5_bss:   6.383  0.042  0.230 83.866  0.039  2.273   4.0972e-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:  95.36   0.00  18.53  95.36   0.00  14.20  90.18   4.78  42.12
   1_occ:  95.36   0.00  18.53  95.36   0.00  14.20  90.18   4.78  42.12
   2_bss:  95.36   0.00  18.53  95.36   0.00  14.20  90.18   4.78  42.12
   2_xyz:  95.36   0.00  18.53  95.36   0.00  14.20  90.18   4.78  42.12
   2_adp:  94.76   0.00  17.71  94.76   0.00  13.60  78.79   6.95  40.13
   2_occ:  94.76   0.00  17.71  94.76   0.00  13.60  78.79   6.95  40.13
   3_bss:  94.76   0.00  17.71  94.76   0.00  13.60  78.79   6.95  40.13
   3_xyz:  94.76   0.00  17.71  94.76   0.00  13.60  78.79   6.95  40.13
   3_adp:  94.77   1.94  17.50  94.77   1.94  13.27  81.90   5.88  40.52
   3_occ:  94.77   1.94  17.50  94.77   1.94  13.27  81.90   5.88  40.52
   4_bss:  94.77   1.94  17.50  94.77   1.94  13.27  81.90   5.88  40.52
   4_xyz:  94.77   1.94  17.50  94.77   1.94  13.27  81.90   5.88  40.52
   4_adp:  90.23   2.61  17.09  90.23   2.61  13.14  80.37   6.47  38.60
   4_occ:  90.23   2.61  17.09  90.23   2.61  13.14  80.37   6.47  38.60
   5_bss:  90.23   2.61  17.09  90.23   2.61  13.14  80.37   6.47  38.60
   5_xyz:  90.23   2.61  17.09  90.23   2.61  13.14  80.37   6.47  38.60
   5_adp:  90.18   2.03  17.08  90.18   2.03  13.06  80.42   6.31  38.96
   5_occ:  90.18   2.03  17.08  90.18   2.03  13.06  80.42   6.31  38.96
   5_bss:  90.11   1.96  17.01  90.11   1.96  12.99  80.34   6.23  38.89
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    2.412    0.023    0.416
   1_adp:    2.412    0.023    0.416
   1_occ:    2.412    0.023    0.416
   2_bss:    2.412    0.023    0.416
   2_xyz:    2.293    0.022    0.478
   2_adp:    2.293    0.022    0.478
   2_occ:    2.293    0.022    0.478
   3_bss:    2.293    0.022    0.478
   3_xyz:    1.999    0.025    0.564
   3_adp:    1.999    0.025    0.564
   3_occ:    1.999    0.025    0.564
   4_bss:    1.999    0.025    0.564
   4_xyz:    1.756    0.044    0.575
   4_adp:    1.756    0.044    0.575
   4_occ:    1.756    0.044    0.575
   5_bss:    1.756    0.044    0.575
   5_xyz:    1.493    0.039    0.592
   5_adp:    1.493    0.039    0.592
   5_occ:    1.493    0.039    0.592
   5_bss:    1.493    0.039    0.592
------------------------------------------------------------------------

CPU time actual refinement: 333.06


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_286/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_286/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_286/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_286/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_286/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 332.91 
  Macro-tasks:
    bulk solvent and scale       = 43.43  
    individual site refinement   = 136.81 
    weights calculation          = 29.50  
    collect and process          = 6.58   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 216.45 
  Micro-tasks:
    mask                            = 1.77   
    f_calc                          = 104.07 
    alpha_beta                      = 8.33   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 113.22 
    fmodel                         = 7.12   
    r_factors                      = 0.26   
    phase_errors                   = 10.92  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 247.09 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.685 micro seconds
Total CPU time: 5.77 minutes
from_scatterers_fft:    647 calls, 103.73 s
gradients_fft:          592 calls,  99.80 s

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

# Date 2008-01-16 Time 04:27:22 PST -0800 (1200486442.92 s)
Start R-work = 0.4192, R-free = 0.4196 (no bulk solvent and anisotropic scale)
Final R-work = 0.1362, R-free = 0.1779 (no bulk solvent and anisotropic scale)

Start R-work = 0.4072, R-free = 0.4045
Final R-work = 0.1078, R-free = 0.1552