# Date 2008-01-16 Time 06:01:01 PST -0800 (1200492061.16 s)
#phil __OFF__

Command line arguments: "../974.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21781
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 974

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 45.7567, 86.822, 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: 3.33, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 45.7567, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1778 1.95415
Completeness in resolution range: 0.924969
Completeness with d_max=infinity: 0.922356

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1778
                             d_min =   1.9542

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 45.7567, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1778 1.95415
Completeness in resolution range: 0.924969
Completeness with d_max=infinity: 0.922356

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1782 -  4.1835 [2222/2249]  2000   222  10.0%
  bin  2:  4.1835 -  3.3321 [2142/2162]  1930   212   9.9%
  bin  3:  3.3321 -  2.9143 [2107/2126]  1894   213  10.1%
  bin  4:  2.9143 -  2.6494 [2074/2104]  1862   212  10.2%
  bin  5:  2.6494 -  2.4603 [2092/2111]  1894   198   9.5%
  bin  6:  2.4603 -  2.3158 [2078/2103]  1861   217  10.4%
  bin  7:  2.3158 -  2.2002 [2044/2072]  1835   209  10.2%
  bin  8:  2.2002 -  2.1047 [2053/2089]  1851   202   9.8%
  bin  9:  2.1047 -  2.0238 [2035/2090]  1841   194   9.5%
  bin 10:  2.0238 -  1.9542 [ 742/2072]   662    80  10.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_974/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:
        1.58 -     2.24: 24
        2.24 -     2.91: 1444
        2.91 -     3.57: 4521
        3.57 -     4.24: 9229
        4.24 -     4.90: 13169
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.579 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28382 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_974/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_974/model_refine_001.geo

CPU time processing inputs: 9.17


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 45.75675 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4515   r_free= 0.4500   ksol= 0.00   Bsol= 0.00   scale= 0.898    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.270251                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.6670 0.99   1441  161 0.3824 0.3813      6.5783      6.5768|
|  2:  4.6670 -  3.7223 0.99   1395  154 0.3931 0.3728      6.8042      6.7488|
|  3:  3.7223 -  3.2571 0.99   1353  149 0.4181 0.4137      6.6489      6.6774|
|  4:  3.2571 -  2.9617 0.99   1363  154 0.4513 0.4714      6.5155      6.5226|
|  5:  2.9617 -  2.7508 0.99   1347  149 0.4770 0.4827      6.3447      6.3753|
|  6:  2.7508 -  2.5894 0.99   1342  150 0.4795 0.4825      6.2581      6.2062|
|  7:  2.5894 -  2.4603 0.99   1339  140 0.4857 0.4389      6.2157      6.1463|
|  8:  2.4603 -  2.3536 0.98   1321  155 0.4909 0.5202      6.1524      6.2025|
|  9:  2.3536 -  2.2633 0.98   1322  145 0.4794 0.5148       6.108      6.1331|
| 10:  2.2633 -  2.1855 1.00   1322  157 0.5006 0.5022      6.0569      6.0561|
| 11:  2.1855 -  2.1173 0.98   1311  140 0.4921 0.4894      6.0168      6.0396|
| 12:  2.1173 -  2.0569 0.98   1320  147 0.4921 0.4875      5.9183       5.939|
| 13:  2.0569 -  2.0029 0.87   1158  126 0.4941 0.4359      5.8624      5.7717|
| 14:  2.0029 -  1.9542 0.22    296   32 0.5027 0.5333      5.8481      5.8853|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1782 -  4.6670  1441   161  0.71  33.46   0.82     0.77      70113.10|
|  2:  4.6670 -  3.7223  1395   154  0.70  34.98   0.90     0.82     107034.69|
|  3:  3.7223 -  3.2571  1353   149  0.58  45.81   0.93     0.77     117405.25|
|  4:  3.2571 -  2.9617  1363   154  0.48  53.74   0.90     0.67     109886.37|
|  5:  2.9617 -  2.7508  1347   149  0.41  58.91   0.89     0.60      84880.90|
|  6:  2.7508 -  2.5894  1342   150  0.39  60.21   0.90     0.57      72506.07|
|  7:  2.5894 -  2.4603  1339   140  0.39  60.75   0.93     0.55      63093.46|
|  8:  2.4603 -  2.3536  1321   155  0.37  62.43   0.91     0.53      58012.36|
|  9:  2.3536 -  2.2633  1322   145  0.37  62.28   0.95     0.53      52769.22|
| 10:  2.2633 -  2.1855  1322   157  0.37  62.25   0.94     0.55      47182.40|
| 11:  2.1855 -  2.1173  1311   140  0.37  62.37   0.97     0.58      45386.94|
| 12:  2.1173 -  2.0569  1320   147  0.38  61.89   0.95     0.59      39698.86|
| 13:  2.0569 -  2.0029  1158   126  0.39  61.16   0.97     0.63      33764.65|
| 14:  2.0029 -  1.9542   296    32  0.49  52.94   1.03     0.70      24362.25|
|alpha:            min =        0.53 max =            0.82 mean =         0.63|
|beta:             min =    24362.25 max =       117405.25 mean =     69318.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.46|
|phase err.(work): min =        0.00 max =           90.00 mean =        55.07|
|phase err.(test): min =        0.00 max =           89.97 mean =        55.29|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.103721             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.702   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.588580              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.672   (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 |  1.579 -  1.911:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.911 -  2.243:       18 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.243 -  2.575:       43 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.575 -  2.907:     1401 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.907 -  3.239:     1933 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.239 -  3.572:     2588 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.572 -  3.904:     4712 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.904 -  4.236:     4517 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.236 -  4.568:     6003 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.568 -  4.900:     7166 |
|-----------------------------------------------------------------------------|
|-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 |        0.185 |
| 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  1.579 |       0.511 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4515   r_free= 0.4500   ksol= 0.00   Bsol= 0.00   scale= 0.898    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.270251                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4420   r_free= 0.4433   ksol= 0.35   Bsol= 50.00   scale= 0.925   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.96,2.54,-1.50,0.00,-0.00,-0.00); trace/3= 0.03                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.264318                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.704828             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.705   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.375858              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.361   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4420      final r-factor (work) = 0.3542          |
| start r-factor (free) = 0.4433      final r-factor (free) = 0.4010          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.9560 = 12.70 * 0.50 * 6.2608 + 1.00 * 0.1847                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.2837 = 12.70 * 0.50 * 6.1623 + 1.00 * 0.1383                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3542      final r-factor (work) = 0.3234          |
| start r-factor (free) = 0.4010      final r-factor (free) = 0.4072          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.4845 = 1.38 * 1.00 * 6.1623 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.3693 = 1.38 * 1.00 * 6.0684 + 1.00 * 0.0201                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.95   18.71    None  None   None       |
|    all(noH): 2823   0      0.00    95.95   18.71    None  None   None       |
|    Sol.    : 438    0      0.00    95.95   36.42    None  None   None       |
|    Mac.    : 2385   0      0.00    75.63   15.45    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 -   9.595:  838   |   5:    47.976 -  57.571:   78        |
|      1:     9.595 -  19.190:  903   |   6:    57.571 -  67.166:   50        |
|      2:    19.190 -  28.786:  522   |   7:    67.166 -  76.762:   16        |
|      3:    28.786 -  38.381:  265   |   8:    76.762 -  86.357:    3        |
|      4:    38.381 -  47.976:  147   |   9:    86.357 -  95.952:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3234 r_free = 0.4072             target_work(ml) = 6.074         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3229 r_free = 0.4069             target_work(ml) = 6.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3229   r_free= 0.4069   ksol= 0.35   Bsol= 50.00   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.96,2.54,-1.50,0.00,-0.00,-0.00); trace/3= 0.03                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.072831                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3232   r_free= 0.4045   ksol= 0.36   Bsol= 73.35   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.77,0.47,-0.37,0.00,-0.00,-0.00); trace/3= -0.22                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.072864                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.303885             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.391  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.503067              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.762  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3232      final r-factor (work) = 0.2572          |
| start r-factor (free) = 0.4045      final r-factor (free) = 0.3267          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.4447 = 11.30 * 0.50 * 6.0698 + 1.00 * 0.1383                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.9897 = 11.30 * 0.50 * 5.9933 + 1.00 * 0.1162                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2572      final r-factor (work) = 0.2358          |
| start r-factor (free) = 0.3267      final r-factor (free) = 0.3057          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0350 = 0.50 * 1.00 * 5.9933 + 1.00 * 0.0199                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9635 = 0.50 * 1.00 * 5.8474 + 1.00 * 0.0219                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.88   18.18    None  None   None       |
|    all(noH): 2823   0      0.00    93.88   18.18    None  None   None       |
|    Sol.    : 438    0      0.00    93.88   38.97    None  None   None       |
|    Mac.    : 2385   0      0.00    79.99   14.37    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 -   9.388:  873   |   5:    46.941 -  56.330:   93        |
|      1:     9.388 -  18.777:  978   |   6:    56.330 -  65.718:   46        |
|      2:    18.777 -  28.165:  433   |   7:    65.718 -  75.106:   18        |
|      3:    28.165 -  37.553:  221   |   8:    75.106 -  84.494:    2        |
|      4:    37.553 -  46.941:  158   |   9:    84.494 -  93.883:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2358 r_free = 0.3057             target_work(ml) = 5.817         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2355 r_free = 0.3050             target_work(ml) = 5.816         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2355   r_free= 0.3050   ksol= 0.36   Bsol= 73.35   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.77,0.47,-0.37,0.00,-0.00,-0.00); trace/3= -0.22                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.816304                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2350   r_free= 0.3036   ksol= 0.34   Bsol= 67.38   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.18,-1.07,-0.41,-0.00,-0.00,-0.00); trace/3= -0.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.811765                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.174722              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.574   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.433639              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.965   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2350      final r-factor (work) = 0.1852          |
| start r-factor (free) = 0.3036      final r-factor (free) = 0.2432          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.2425 = 5.17 * 0.50 * 5.8462 + 1.00 * 0.1162                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.8574 = 5.17 * 0.50 * 5.7169 + 1.00 * 0.0658                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1852      final r-factor (work) = 0.1666          |
| start r-factor (free) = 0.2432      final r-factor (free) = 0.2240          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4946 = 0.43 * 1.00 * 5.7169 + 1.00 * 0.0156                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4142 = 0.43 * 1.00 * 5.5423 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.55   18.30    None  None   None       |
|    all(noH): 2823   0      0.00    92.55   18.30    None  None   None       |
|    Sol.    : 438    0      5.35    92.55   44.22    None  None   None       |
|    Mac.    : 2385   0      0.00    89.92   13.54    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 -   9.255:  856   |   5:    46.275 -  55.530:   99        |
|      1:     9.255 -  18.510: 1144   |   6:    55.530 -  64.785:   78        |
|      2:    18.510 -  27.765:  312   |   7:    64.785 -  74.040:   50        |
|      3:    27.765 -  37.020:  142   |   8:    74.040 -  83.295:   10        |
|      4:    37.020 -  46.275:  128   |   9:    83.295 -  92.550:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1666 r_free = 0.2240             target_work(ml) = 5.502         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1665 r_free = 0.2236             target_work(ml) = 5.501         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1665   r_free= 0.2236   ksol= 0.34   Bsol= 67.38   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.18,-1.07,-0.41,-0.00,-0.00,-0.00); trace/3= -0.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.501347                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1664   r_free= 0.2231   ksol= 0.33   Bsol= 67.38   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-2.36,-1.00,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.499508                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.433231              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.793  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.176545              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.137  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1664      final r-factor (work) = 0.1359          |
| start r-factor (free) = 0.2231      final r-factor (free) = 0.1891          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.3602 = 4.43 * 0.50 * 5.5465 + 1.00 * 0.0658                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0819 = 4.43 * 0.50 * 5.4205 + 1.00 * 0.0667                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1359      final r-factor (work) = 0.1308          |
| start r-factor (free) = 0.1891      final r-factor (free) = 0.1778          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9677 = 0.18 * 1.00 * 5.4205 + 1.00 * 0.0107                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9449 = 0.18 * 1.00 * 5.3067 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.13    90.65   17.38    None  None   None       |
|    all(noH): 2823   0      1.13    90.65   17.38    None  None   None       |
|    Sol.    : 438    0      4.71    86.28   41.66    None  None   None       |
|    Mac.    : 2385   0      1.13    90.65   12.93    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:     1.128 -  10.080: 1025   |   5:    45.890 -  54.843:  111        |
|      1:    10.080 -  19.033: 1102   |   6:    54.843 -  63.795:   65        |
|      2:    19.033 -  27.985:  237   |   7:    63.795 -  72.748:   37        |
|      3:    27.985 -  36.938:  138   |   8:    72.748 -  81.700:    6        |
|      4:    36.938 -  45.890:   97   |   9:    81.700 -  90.653:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1308 r_free = 0.1778             target_work(ml) = 5.275         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1307 r_free = 0.1775             target_work(ml) = 5.275         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1307   r_free= 0.1775   ksol= 0.33   Bsol= 67.38   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-2.36,-1.00,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.274641                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1309   r_free= 0.1770   ksol= 0.32   Bsol= 53.47   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-2.72,-1.12,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.273283                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.555128              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 127.402  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.331975              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.666  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1309      final r-factor (work) = 0.1216          |
| start r-factor (free) = 0.1770      final r-factor (free) = 0.1661          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8457 = 2.56 * 0.50 * 5.3062 + 1.00 * 0.0667                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7599 = 2.56 * 0.50 * 5.2450 + 1.00 * 0.0590                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1216      final r-factor (work) = 0.1189          |
| start r-factor (free) = 0.1661      final r-factor (free) = 0.1655          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7492 = 0.33 * 1.00 * 5.2450 + 1.00 * 0.0079                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7355 = 0.33 * 1.00 * 5.2018 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.46    93.81   17.33    None  None   None       |
|    all(noH): 2823   0      0.46    93.81   17.33    None  None   None       |
|    Sol.    : 438    0      4.53    86.63   41.80    None  None   None       |
|    Mac.    : 2385   0      0.46    93.81   12.83    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.458 -   9.793: 1000   |   5:    47.132 -  56.467:   96        |
|      1:     9.793 -  19.128: 1144   |   6:    56.467 -  65.802:   63        |
|      2:    19.128 -  28.462:  242   |   7:    65.802 -  75.137:   33        |
|      3:    28.462 -  37.797:  127   |   8:    75.137 -  84.472:    8        |
|      4:    37.797 -  47.132:  105   |   9:    84.472 -  93.807:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1189 r_free = 0.1655             target_work(ml) = 5.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1188 r_free = 0.1654             target_work(ml) = 5.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1188   r_free= 0.1654   ksol= 0.32   Bsol= 53.47   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-2.72,-1.12,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.198912                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.6670 0.99   1441  161 0.0982 0.1315      5.3675      5.6018|
|  2:  4.6670 -  3.7223 0.99   1395  154 0.0883 0.1149      5.4633       5.658|
|  3:  3.7223 -  3.2571 0.99   1353  149 0.1156 0.1577      5.5277      5.8314|
|  4:  3.2571 -  2.9617 0.99   1363  154 0.1387 0.1774       5.523      5.6543|
|  5:  2.9617 -  2.7508 0.99   1347  149 0.1425 0.1873       5.384      5.6273|
|  6:  2.7508 -  2.5894 0.99   1342  150 0.1326 0.2003      5.2494      5.5098|
|  7:  2.5894 -  2.4603 0.99   1339  140 0.1331 0.1793      5.2178      5.3783|
|  8:  2.4603 -  2.3536 0.98   1321  155 0.1245 0.1728      5.1043      5.3649|
|  9:  2.3536 -  2.2633 0.98   1322  145 0.1271 0.1808      5.0778      5.3278|
| 10:  2.2633 -  2.1855 1.00   1322  157 0.1158 0.1770      4.9749      5.2362|
| 11:  2.1855 -  2.1173 0.98   1311  140 0.1173 0.1854      4.9762      5.3699|
| 12:  2.1173 -  2.0569 0.98   1320  147 0.1218 0.1883      4.9255      5.1536|
| 13:  2.0569 -  2.0029 0.87   1158  126 0.1167 0.1731      4.8112       5.028|
| 14:  2.0029 -  1.9542 0.22    296   32 0.0983 0.1376      4.6664      4.8879|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1782 -  4.6670  1441   161  0.94   8.79   0.97     0.95       6815.06|
|  2:  4.6670 -  3.7223  1395   154  0.95   8.18   1.01     1.00       9420.37|
|  3:  3.7223 -  3.2571  1353   149  0.93  12.33   1.03     1.03      11436.89|
|  4:  3.2571 -  2.9617  1363   154  0.90  15.60   1.01     0.99      11535.63|
|  5:  2.9617 -  2.7508  1347   149  0.90  16.60   1.00     0.98       9143.73|
|  6:  2.7508 -  2.5894  1342   150  0.89  17.36   0.98     0.96       7604.94|
|  7:  2.5894 -  2.4603  1339   140  0.90  16.43   1.00     0.97       6946.15|
|  8:  2.4603 -  2.3536  1321   155  0.90  16.54   0.99     0.96       5695.01|
|  9:  2.3536 -  2.2633  1322   145  0.90  16.67   1.00     0.96       5402.82|
| 10:  2.2633 -  2.1855  1322   157  0.90  16.15   1.00     0.97       4678.98|
| 11:  2.1855 -  2.1173  1311   140  0.89  17.26   0.99     0.94       4708.77|
| 12:  2.1173 -  2.0569  1320   147  0.89  17.35   1.00     1.00       4453.45|
| 13:  2.0569 -  2.0029  1158   126  0.89  17.57   1.00     0.98       3646.06|
| 14:  2.0029 -  1.9542   296    32  0.92  14.14   0.99     0.96       2762.24|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2762.24 max =        11535.63 mean =      7029.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        15.03|
|phase err.(test): min =        0.00 max =           89.67 mean =        14.54|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1188   r_free= 0.1653   ksol= 0.30   Bsol= 49.51   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,-2.81,-1.10,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.198888                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1188   r_free= 0.1653   ksol= 0.30   Bsol= 49.51   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,-2.81,-1.10,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.198888                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.6670 0.99   1441  161 0.0978 0.1313      5.3657      5.6035|
|  2:  4.6670 -  3.7223 0.99   1395  154 0.0883 0.1149      5.4629      5.6572|
|  3:  3.7223 -  3.2571 0.99   1353  149 0.1155 0.1575      5.5272        5.83|
|  4:  3.2571 -  2.9617 0.99   1363  154 0.1387 0.1774      5.5229      5.6543|
|  5:  2.9617 -  2.7508 0.99   1347  149 0.1426 0.1874      5.3841      5.6279|
|  6:  2.7508 -  2.5894 0.99   1342  150 0.1326 0.2002      5.2495      5.5099|
|  7:  2.5894 -  2.4603 0.99   1339  140 0.1332 0.1794      5.2185      5.3794|
|  8:  2.4603 -  2.3536 0.98   1321  155 0.1247 0.1730       5.105      5.3658|
|  9:  2.3536 -  2.2633 0.98   1322  145 0.1272 0.1807      5.0784       5.327|
| 10:  2.2633 -  2.1855 1.00   1322  157 0.1159 0.1772      4.9754      5.2376|
| 11:  2.1855 -  2.1173 0.98   1311  140 0.1172 0.1856      4.9765      5.3708|
| 12:  2.1173 -  2.0569 0.98   1320  147 0.1218 0.1882      4.9258      5.1536|
| 13:  2.0569 -  2.0029 0.87   1158  126 0.1166 0.1728      4.8108       5.027|
| 14:  2.0029 -  1.9542 0.22    296   32 0.0984 0.1376      4.6653      4.8867|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1782 -  4.6670  1441   161  0.94   8.75   0.97     0.95       6797.68|
|  2:  4.6670 -  3.7223  1395   154  0.95   8.16   1.01     1.00       9410.38|
|  3:  3.7223 -  3.2571  1353   149  0.93  12.32   1.03     1.03      11426.23|
|  4:  3.2571 -  2.9617  1363   154  0.90  15.58   1.01     0.98      11522.77|
|  5:  2.9617 -  2.7508  1347   149  0.90  16.59   1.00     0.98       9140.65|
|  6:  2.7508 -  2.5894  1342   150  0.89  17.36   0.98     0.96       7608.03|
|  7:  2.5894 -  2.4603  1339   140  0.90  16.44   1.00     0.97       6955.48|
|  8:  2.4603 -  2.3536  1321   155  0.90  16.56   0.99     0.96       5702.79|
|  9:  2.3536 -  2.2633  1322   145  0.90  16.68   1.00     0.96       5408.73|
| 10:  2.2633 -  2.1855  1322   157  0.90  16.17   1.00     0.97       4686.35|
| 11:  2.1855 -  2.1173  1311   140  0.89  17.27   0.99     0.94       4718.45|
| 12:  2.1173 -  2.0569  1320   147  0.89  17.36   1.00     1.00       4458.96|
| 13:  2.0569 -  2.0029  1158   126  0.89  17.57   1.00     0.97       3644.58|
| 14:  2.0029 -  1.9542   296    32  0.92  14.09   0.99     0.96       2753.86|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     2753.86 max =        11522.77 mean =      7028.38|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.03|
|phase err.(test): min =        0.00 max =           89.78 mean =        14.54|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.791)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.44    93.79   17.31    None  None   None       |
|    all(noH): 2823   0      0.44    93.79   17.31    None  None   None       |
|    Sol.    : 438    0      4.51    86.61   41.79    None  None   None       |
|    Mac.    : 2385   0      0.44    93.79   12.82    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.443 -   9.778: 1000   |   5:    47.118 -  56.453:   96        |
|      1:     9.778 -  19.113: 1144   |   6:    56.453 -  65.788:   63        |
|      2:    19.113 -  28.448:  242   |   7:    65.788 -  75.123:   33        |
|      3:    28.448 -  37.783:  127   |   8:    75.123 -  84.458:    8        |
|      4:    37.783 -  47.118:  105   |   9:    84.458 -  93.793:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 335         
Filter by distance & map next to the model:
   mapped sites are within: 0.681 - 4.545
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 331 from: 335
   mapped sites are within: 0.712 - 4.545

peak=    6.459 closest distance to " NE2 GLN A  11 " =    1.381
peak=    6.281 closest distance to " O   HOH Z 431 " =    1.798
peak=    6.016 closest distance to " O   HOH Z 385 " =    1.244
peak=    5.811 closest distance to " O   HOH Z  65 " =    1.408
peak=    5.774 closest distance to " O   HOH Z 424 " =    1.987
peak=    5.523 closest distance to " O   HOH Z 417 " =    2.459
peak=    5.373 closest distance to " O   HOH Z 126 " =    2.155
peak=    5.266 closest distance to " CB  GLN A 223 " =    1.496
peak=    5.160 closest distance to " O   HOH Z 222 " =    1.335
peak=    5.100 closest distance to " CG  PRO A  54 " =    1.377
peak=    5.027 closest distance to " O   HOH Z  63 " =    1.797
peak=    4.996 closest distance to " O   HOH Z 144 " =    1.776
peak=    4.824 closest distance to " O   HOH Z 423 " =    2.036
peak=    4.817 closest distance to " CG  PRO A 198 " =    1.260
peak=    4.793 closest distance to " O   HOH Z 287 " =    2.190
peak=    4.772 closest distance to " O   HOH Z 427 " =    2.255
peak=    4.769 closest distance to " O   HOH Z 232 " =    2.252
peak=    4.717 closest distance to " O   HOH Z 369 " =    2.074
peak=    4.688 closest distance to " CB  ARG A 275 " =    0.936
peak=    4.572 closest distance to " O   HOH Z 380 " =    1.965
peak=    4.548 closest distance to " CB  SER A  63 " =    1.360
peak=    4.525 closest distance to " O   HOH Z 298 " =    1.910
peak=    4.480 closest distance to " CB  PRO A  54 " =    1.058
peak=    4.480 closest distance to " O   HOH Z  78 " =    1.628
peak=    4.476 closest distance to " O   HOH Z 214 " =    1.445
peak=    4.461 closest distance to " CB  SER A 216 " =    0.998
peak=    4.430 closest distance to " O   HOH Z  57 " =    2.419
peak=    4.422 closest distance to " O   HOH Z 111 " =    1.760
peak=    4.392 closest distance to " O   HOH Z 316 " =    3.066
peak=    4.378 closest distance to " O   HOH Z 209 " =    2.215
peak=    4.361 closest distance to " O   HOH Z 414 " =    1.438
peak=    4.352 closest distance to " CA  TYR A  30 " =    1.060
peak=    4.346 closest distance to " O   HOH Z 425 " =    1.620
peak=    4.343 closest distance to " CB  ASN A 148 " =    1.305
peak=    4.320 closest distance to " CG  PRO A 213 " =    1.260
peak=    4.314 closest distance to " O   HOH Z 392 " =    1.437
peak=    4.312 closest distance to " CG  LEU A 167 " =    1.292
peak=    4.264 closest distance to " O   HOH Z 225 " =    1.616
peak=    4.262 closest distance to " O   SER A  87 " =    2.288
peak=    4.251 closest distance to " CB  SER A   3 " =    1.470
peak=    4.248 closest distance to " CG  PRO A 280 " =    0.964
peak=    4.186 closest distance to " O   HOH Z 424 " =    1.266
peak=    4.154 closest distance to " CG  PRO A  90 " =    1.260
peak=    4.138 closest distance to " ND2 ASN A 187 " =    1.521
peak=    4.135 closest distance to " CB  GLN A 183 " =    1.171
peak=    4.121 closest distance to " CD  ARG A 159 " =    0.801
peak=    4.120 closest distance to " CG2 VAL A 257 " =    0.937
peak=    4.091 closest distance to " O   HOH Z 389 " =    1.873
peak=    4.091 closest distance to " CB  GLU A 128 " =    1.034
peak=    4.089 closest distance to " CB  LEU A 228 " =    1.122
peak=    4.060 closest distance to " O   HOH Z 171 " =    2.632
peak=    4.057 closest distance to " CB  TRP A 266 " =    1.042
peak=    4.052 closest distance to " CB  ASN A 187 " =    1.060
peak=    4.051 closest distance to " O   HOH Z 411 " =    3.537
peak=    4.047 closest distance to " O   HOH Z   2 " =    1.848
peak=    4.010 closest distance to " O   HOH Z  17 " =    1.935
peak=    4.004 closest distance to " O   HOH Z   9 " =    1.431
peak=    3.982 closest distance to " O   HOH Z  30 " =    1.707
peak=    3.977 closest distance to " O   HOH Z 133 " =    2.365
peak=    3.974 closest distance to " O   HOH Z 158 " =    1.333
peak=    3.963 closest distance to " OG BSER A  99 " =    2.312
peak=    3.944 closest distance to " CB  ARG A 190 " =    1.792
peak=    3.941 closest distance to " O   HOH Z 261 " =    1.959
peak=    3.926 closest distance to " CB  GLU A 152 " =    1.242
peak=    3.920 closest distance to " O   HOH Z 361 " =    1.423
peak=    3.916 closest distance to " O   HOH Z 211 " =    1.278
peak=    3.913 closest distance to " O   HOH Z 193 " =    1.803
peak=    3.912 closest distance to " O   HOH Z 245 " =    1.099
peak=    3.910 closest distance to " O   HOH Z 427 " =    1.199
peak=    3.896 closest distance to " O   HOH Z  88 " =    3.071
peak=    3.868 closest distance to " O   HOH Z  59 " =    1.588
peak=    3.867 closest distance to " O   HOH Z 139 " =    1.320
peak=    3.863 closest distance to " CB  LYS A 117 " =    1.251
peak=    3.860 closest distance to " O   HOH Z  44 " =    2.749
peak=    3.856 closest distance to " ND1 HIS A  86 " =    1.890
peak=    3.849 closest distance to " O   HOH Z 115 " =    1.854
peak=    3.842 closest distance to " O   HOH Z 145 " =    1.972
peak=    3.835 closest distance to " O   HOH Z 135 " =    1.876
peak=    3.821 closest distance to " O   HOH Z  78 " =    2.027
peak=    3.821 closest distance to " O   HOH Z  61 " =    1.584
peak=    3.801 closest distance to " CB  THR A 157 " =    1.208
peak=    3.800 closest distance to " O   HOH Z 437 " =    2.109
peak=    3.799 closest distance to " O   HOH Z 236 " =    1.562
peak=    3.798 closest distance to " O   HOH Z 313 " =    1.840
peak=    3.791 closest distance to " N   ALA A   1 " =    1.990
peak=    3.788 closest distance to " CG  GLN A 278 " =    3.816
peak=    3.780 closest distance to " CG2 THR A 221 " =    1.108
peak=    3.760 closest distance to " CA  ILE A 234 " =    1.026
peak=    3.744 closest distance to " CD  ARG A  66 " =    2.081
peak=    3.741 closest distance to " O   HOH Z  61 " =    1.637
peak=    3.740 closest distance to " O   HOH Z 403 " =    1.441
peak=    3.733 closest distance to " OD1 ASN A  69 " =    2.504
peak=    3.729 closest distance to " O   HOH Z  29 " =    1.239
peak=    3.729 closest distance to " CA  ALA A 180 " =    1.336
peak=    3.727 closest distance to " NH1AARG A 145 " =    1.173
peak=    3.719 closest distance to " O   HOH Z 407 " =    1.759
peak=    3.717 closest distance to " CG  TRP A 179 " =    2.196
peak=    3.696 closest distance to " O   ASN A 209 " =    1.534
peak=    3.689 closest distance to " CG  GLN A  11 " =    2.108
peak=    3.684 closest distance to " O   HOH Z 116 " =    3.010
peak=    3.683 closest distance to " ND2 ASN A  60 " =    3.036
peak=    3.682 closest distance to " O   HOH Z 126 " =    1.412
peak=    3.679 closest distance to " NE AARG A 275 " =    1.554
peak=    3.677 closest distance to " N   TYR A  15 " =    0.892
peak=    3.672 closest distance to " OD2 ASP A 286 " =    2.844
peak=    3.668 closest distance to " O   PRO A 198 " =    1.209
peak=    3.668 closest distance to " O   HOH Z 390 " =    1.113
peak=    3.667 closest distance to " O   HOH Z 106 " =    3.964
peak=    3.666 closest distance to " O   HOH Z 311 " =    2.218
peak=    3.665 closest distance to " CA  ALA A 160 " =    1.005
peak=    3.664 closest distance to " O   HOH Z 175 " =    2.043
peak=    3.663 closest distance to " O  BHOH Z  74 " =    1.432
peak=    3.662 closest distance to " O   HOH Z   9 " =    1.891
peak=    3.661 closest distance to " CG1 ILE A 151 " =    1.066
peak=    3.658 closest distance to " CB  ASP A 124 " =    0.830
peak=    3.656 closest distance to " O   HOH Z  88 " =    3.728
peak=    3.647 closest distance to " O   HOH Z 258 " =    2.169
peak=    3.643 closest distance to " CB  ALA A   1 " =    4.545
peak=    3.639 closest distance to " CB  ASN A  39 " =    0.952
peak=    3.638 closest distance to " O   HOH Z 122 " =    1.858
peak=    3.636 closest distance to " CB  TRP A 150 " =    1.062
peak=    3.632 closest distance to " CA  GLY A 267 " =    1.277
peak=    3.620 closest distance to " OE1 GLN A 240 " =    1.648
peak=    3.617 closest distance to " OG BSER A 258 " =    0.843
peak=    3.610 closest distance to " O   HOH Z 371 " =    2.877
peak=    3.608 closest distance to " O   HOH Z 155 " =    1.701
peak=    3.604 closest distance to " CB  SER A 276 " =    1.174
peak=    3.602 closest distance to " CB  ALA A 114 " =    1.052
peak=    3.592 closest distance to " CB  SER A 210 " =    0.779
peak=    3.590 closest distance to " N   GLN A 278 " =    1.121
peak=    3.589 closest distance to " CA  ARG A 195 " =    1.422
peak=    3.588 closest distance to " CB  TYR A 116 " =    1.015
peak=    3.584 closest distance to " O   HOH Z 422 " =    2.722
peak=    3.578 closest distance to " O   HOH Z 272 " =    2.033
peak=    3.576 closest distance to " O   HOH Z  11 " =    1.138
peak=    3.569 closest distance to " O   HOH Z 272 " =    1.756
peak=    3.564 closest distance to " O   HOH Z 119 " =    4.200
peak=    3.555 closest distance to " O   HOH Z 183 " =    1.462
peak=    3.541 closest distance to " O   HOH Z 327 " =    1.629
peak=    3.539 closest distance to " O   ALA A   1 " =    1.633
peak=    3.538 closest distance to " O   HOH Z  40 " =    2.218
peak=    3.536 closest distance to " N   ASN A 127 " =    1.417
peak=    3.531 closest distance to " O   HOH Z 276 " =    1.184
peak=    3.526 closest distance to " N   SER A  97 " =    0.880
peak=    3.525 closest distance to " CB  MET A  40 " =    0.759
peak=    3.524 closest distance to " CB  GLU A 236 " =    1.361
peak=    3.517 closest distance to " O   HOH Z  20 " =    1.838
peak=    3.515 closest distance to " O   HOH Z 362 " =    1.748
peak=    3.514 closest distance to " O   HOH Z  50 " =    1.741
peak=    3.513 closest distance to " CE3 TRP A  85 " =    0.915
peak=    3.511 closest distance to " CA  TYR A 116 " =    1.314
peak=    3.511 closest distance to " CB  VAL A 202 " =    1.635
peak=    3.509 closest distance to " CE3 TRP A 274 " =    1.231
peak=    3.507 closest distance to " CZ  PHE A 218 " =    1.143
peak=    3.504 closest distance to " O   HOH Z 104 " =    1.557
peak=    3.496 closest distance to " O   HOH Z 217 " =    2.812
peak=    3.494 closest distance to " O   HOH Z 385 " =    3.458
peak=    3.492 closest distance to " O   HOH Z 345 " =    1.987
peak=    3.487 closest distance to " CG2 ILE A 106 " =    1.077
peak=    3.487 closest distance to " O   HOH Z 193 " =    2.076
peak=    3.486 closest distance to " OG BSER A 134 " =    2.960
peak=    3.483 closest distance to " O   HOH Z 112 " =    1.070
peak=    3.478 closest distance to " O   HOH Z 352 " =    1.695
peak=    3.474 closest distance to " CA  MET A 105 " =    0.904
peak=    3.471 closest distance to " CZ  PHE A 192 " =    0.915
peak=    3.468 closest distance to " O   HOH Z 158 " =    2.371
peak=    3.465 closest distance to " O   HOH Z 371 " =    2.280
peak=    3.464 closest distance to " CE3 TRP A 150 " =    1.091
peak=    3.464 closest distance to " CA  THR A 264 " =    0.820
peak=    3.462 closest distance to " NZ  LYS A 117 " =    1.291
peak=    3.461 closest distance to " O   HOH Z 234 " =    3.943
peak=    3.460 closest distance to " O   HOH Z  49 " =    1.351
peak=    3.458 closest distance to " CD1 ILE A  33 " =    1.646
peak=    3.456 closest distance to " CA  SER A  87 " =    1.027
peak=    3.453 closest distance to " O   HOH Z   7 " =    3.143
peak=    3.452 closest distance to " O   THR A 220 " =    1.580
peak=    3.448 closest distance to " O   HOH Z  51 " =    1.695
peak=    3.439 closest distance to " O   HOH Z 368 " =    3.785
peak=    3.434 closest distance to " O   HOH Z 244 " =    1.586
peak=    3.432 closest distance to " O   HOH Z  67 " =    1.783
peak=    3.432 closest distance to " OG  SER A  62 " =    2.944
peak=    3.431 closest distance to " CG  LEU A 101 " =    1.101
peak=    3.431 closest distance to " O   HOH Z 405 " =    1.623
peak=    3.428 closest distance to " O   HOH Z  47 " =    1.834
peak=    3.427 closest distance to " CA  ALA A 291 " =    0.967
peak=    3.424 closest distance to " O   HOH Z 133 " =    1.576
peak=    3.424 closest distance to " CD1 LEU A 300 " =    1.218
peak=    3.420 closest distance to " O   HOH Z   1 " =    1.699
peak=    3.418 closest distance to " O   HOH Z 365 " =    2.542
peak=    3.413 closest distance to " O   HOH Z 334 " =    2.895
peak=    3.413 closest distance to " CB  GLU A 277 " =    3.589
peak=    3.410 closest distance to " NE2 GLN A  58 " =    4.094
peak=    3.410 closest distance to " O   HOH Z 359 " =    1.365
peak=    3.410 closest distance to " O   HOH Z 214 " =    1.614
peak=    3.408 closest distance to " O   HOH Z 222 " =    2.044
peak=    3.408 closest distance to " CD  LYS A 166 " =    1.419
peak=    3.403 closest distance to " CA  ALA A 299 " =    0.891
peak=    3.403 closest distance to " CG BARG A 275 " =    1.511
peak=    3.402 closest distance to " CA  TYR A  30 " =    1.065
peak=    3.402 closest distance to " O   HOH Z 289 " =    1.628
peak=    3.402 closest distance to " N   CYS A 260 " =    0.851
peak=    3.401 closest distance to " O   HOH Z  10 " =    1.763
peak=    3.398 closest distance to " CA  THR A 221 " =    0.981
peak=    3.393 closest distance to " O   HOH Z 195 " =    1.638
peak=    3.391 closest distance to " O   GLY A 302 " =    1.774
peak=    3.390 closest distance to " N   VAL A 296 " =    1.752
peak=    3.386 closest distance to " O   PRO A 198 " =    1.517
peak=    3.385 closest distance to " O   HOH Z 250 " =    1.456
peak=    3.378 closest distance to " CE  LYS A  76 " =    0.845
peak=    3.376 closest distance to " O   HOH Z  88 " =    2.763
peak=    3.375 closest distance to " CG1 ILE A  33 " =    1.323
peak=    3.372 closest distance to " NH2 ARG A 219 " =    1.801
peak=    3.366 closest distance to " N   PHE A 130 " =    1.186
peak=    3.365 closest distance to " O   HOH Z 148 " =    3.406
peak=    3.365 closest distance to " CB  ALA A  43 " =    0.786
peak=    3.361 closest distance to " CB  ILE A 120 " =    1.373
peak=    3.360 closest distance to " O   HOH Z 386 " =    2.502
peak=    3.356 closest distance to " CA  ALA A  51 " =    1.028
peak=    3.353 closest distance to " O   THR A  52 " =    2.013
peak=    3.351 closest distance to " O   HOH Z 166 " =    1.459
peak=    3.349 closest distance to " CD  ARG A  66 " =    2.364
peak=    3.348 closest distance to " CA  VAL A 125 " =    1.080
peak=    3.347 closest distance to " CG  GLU A   2 " =    1.166
peak=    3.345 closest distance to " O   HOH Z 153 " =    3.663
peak=    3.338 closest distance to " CB  ARG A  79 " =    1.179
peak=    3.334 closest distance to " O   HOH Z 239 " =    1.534
peak=    3.334 closest distance to " CZ  PHE A  38 " =    1.276
peak=    3.332 closest distance to " O   HOH Z 217 " =    1.683
peak=    3.332 closest distance to " CB  SER A 212 " =    1.484
peak=    3.331 closest distance to " CB  GLU A  46 " =    1.094
peak=    3.331 closest distance to " OE2 GLU A  53 " =    2.043
peak=    3.330 closest distance to " O   HOH Z 128 " =    2.233
peak=    3.329 closest distance to " CD1 ILE A 263 " =    1.248
peak=    3.327 closest distance to " O   HOH Z 180 " =    2.185
peak=    3.324 closest distance to " CA  ASN A 215 " =    1.120
peak=    3.323 closest distance to " CD  PRO A 243 " =    1.794
peak=    3.323 closest distance to " O   HOH Z 218 " =    2.196
peak=    3.323 closest distance to " CA  ASN A 127 " =    1.050
peak=    3.323 closest distance to " CG2 VAL A 232 " =    0.968
peak=    3.314 closest distance to " N   GLU A   2 " =    1.316
peak=    3.312 closest distance to " O   HOH Z 409 " =    2.201
peak=    3.311 closest distance to " CG1 ILE A 263 " =    1.296
peak=    3.309 closest distance to " O   HOH Z 394 " =    1.728
peak=    3.307 closest distance to " CB  ASN A 142 " =    0.900
peak=    3.305 closest distance to " CA  ALA A 233 " =    0.938
peak=    3.304 closest distance to " ND1 HIS A  81 " =    1.713
peak=    3.303 closest distance to " CE AMET A  47 " =    1.275
peak=    3.301 closest distance to " O   HOH Z 344 " =    3.365
peak=    3.301 closest distance to " O   HOH Z 273 " =    2.826
peak=    3.301 closest distance to " O   HOH Z 431 " =    1.342
peak=    3.297 closest distance to " CB  VAL A 265 " =    1.348
peak=    3.284 closest distance to " CA  ARG A 102 " =    1.119
peak=    3.284 closest distance to " O   HOH Z  68 " =    1.934
peak=    3.280 closest distance to " CG  GLN A  88 " =    1.110
peak=    3.279 closest distance to " O   HOH Z 152 " =    2.199
peak=    3.278 closest distance to " O   HOH Z 393 " =    1.335
peak=    3.277 closest distance to " CA  ILE A 106 " =    0.764
peak=    3.276 closest distance to " CB  MET A 105 " =    1.174
peak=    3.266 closest distance to " CZ3 TRP A 266 " =    1.125
peak=    3.264 closest distance to " O   HOH Z 302 " =    1.561
peak=    3.264 closest distance to " O   HOH Z 132 " =    2.632
peak=    3.263 closest distance to " CB  GLN A  88 " =    1.290
peak=    3.260 closest distance to " O   TYR A 116 " =    1.326
peak=    3.259 closest distance to " CB  ALA A 291 " =    1.333
peak=    3.256 closest distance to " O   HOH Z 227 " =    1.844
peak=    3.249 closest distance to " O   HOH Z  92 " =    1.261
peak=    3.242 closest distance to " O   HOH Z 130 " =    2.022
peak=    3.242 closest distance to " C   GLU A 277 " =    1.383
peak=    3.242 closest distance to " N   SER A 271 " =    1.054
peak=    3.237 closest distance to " CG  PRO A 243 " =    1.029
peak=    3.237 closest distance to " NZ  LYS A 119 " =    1.254
peak=    3.228 closest distance to " CA  LEU A 282 " =    1.232
peak=    3.219 closest distance to " CA  GLU A 152 " =    1.149
peak=    3.216 closest distance to " CG  ARG A 159 " =    0.781
peak=    3.214 closest distance to " CB  ALA A 114 " =    1.562
peak=    3.212 closest distance to " CD BLYS A 290 " =    1.028
peak=    3.208 closest distance to " O   HOH Z  44 " =    1.764
peak=    3.205 closest distance to " O   HOH Z 213 " =    2.203
peak=    3.202 closest distance to " CB  LEU A 143 " =    1.116
peak=    3.201 closest distance to " O   HOH Z 113 " =    1.873
peak=    3.193 closest distance to " CA  ALA A 100 " =    1.063
peak=    3.188 closest distance to " CD  LYS A  76 " =    1.747
peak=    3.180 closest distance to " O   HOH Z 119 " =    1.589
peak=    3.175 closest distance to " O   HOH Z 128 " =    1.946
peak=    3.173 closest distance to " CH2 TRP A 150 " =    0.979
peak=    3.172 closest distance to " OG  SER A  26 " =    1.545
peak=    3.171 closest distance to " O   HOH Z 282 " =    1.600
peak=    3.170 closest distance to " OG  SER A  22 " =    2.893
peak=    3.169 closest distance to " CD2 LEU A 255 " =    1.662
peak=    3.168 closest distance to " O   HOH Z 218 " =    1.535
peak=    3.165 closest distance to " O   HOH Z 172 " =    2.168
peak=    3.161 closest distance to " CG  GLN A 278 " =    1.198
peak=    3.158 closest distance to " CB  ASP A 171 " =    0.856
peak=    3.158 closest distance to " CB  ALA A 248 " =    0.957
peak=    3.158 closest distance to " CB  ALA A  10 " =    0.817
peak=    3.157 closest distance to " CB  ARG A 138 " =    0.878
peak=    3.155 closest distance to " O   HOH Z 184 " =    1.634
peak=    3.154 closest distance to " CA  TYR A 186 " =    1.523
peak=    3.150 closest distance to " NE  ARG A  66 " =    3.522
peak=    3.143 closest distance to " CD  ARG A 138 " =    0.712
peak=    3.142 closest distance to " O   HOH Z 108 " =    2.338
peak=    3.142 closest distance to " O   HOH Z 368 " =    1.774
peak=    3.142 closest distance to " O   HOH Z 146 " =    1.674
peak=    3.141 closest distance to " O   HOH Z 286 " =    2.215
peak=    3.140 closest distance to " CB  LEU A 300 " =    0.911
peak=    3.137 closest distance to " O   HOH Z 288 " =    1.908
peak=    3.133 closest distance to " N   ARG A 156 " =    1.276
peak=    3.129 closest distance to " CB  SER A  99 " =    0.936
peak=    3.124 closest distance to " CB  TYR A  30 " =    1.287
peak=    3.123 closest distance to " CG1 VAL A 153 " =    0.853
peak=    3.120 closest distance to " CB  TRP A 274 " =    1.224
peak=    3.120 closest distance to " CB  PRO A 243 " =    1.120
peak=    3.117 closest distance to " CB  LEU A  83 " =    0.854
peak=    3.113 closest distance to " CB  ARG A 139 " =    1.005
peak=    3.112 closest distance to " O   HOH Z  57 " =    1.015
peak=    3.110 closest distance to " OD1 ASN A 217 " =    1.495
peak=    3.097 closest distance to " CB  ALA A  34 " =    1.096
peak=    3.096 closest distance to " CB  ALA A 161 " =    0.974
peak=    3.092 closest distance to " NH1BARG A 145 " =    1.302
peak=    3.092 closest distance to " CA  ARG A  36 " =    1.329
peak=    3.085 closest distance to " CA  ILE A  33 " =    1.376
peak=    3.084 closest distance to " O   MET A 105 " =    1.747
peak=    3.080 closest distance to " O   HOH Z 409 " =    3.274
peak=    3.074 closest distance to " O   HOH Z 188 " =    2.166
peak=    3.074 closest distance to " O   ASN A  74 " =    1.516
peak=    3.071 closest distance to " O   GLY A 302 " =    2.324
peak=    3.069 closest distance to " CA  ARG A 156 " =    1.016
peak=    3.064 closest distance to " O   HOH Z   1 " =    1.374
peak=    3.055 closest distance to " O   HOH Z 425 " =    1.890
peak=    3.038 closest distance to " O   HOH Z 284 " =    1.248
peak=    2.936 closest distance to " O   HOH Z 154 " =    2.131

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 181         
Filter by distance & map next to the model:
   mapped sites are within: 0.601 - 5.564
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 178 from: 181
   mapped sites are within: 0.740 - 5.564

peak=   -4.693 closest distance to " CB  PRO A 243 " =    2.501
peak=   -4.690 closest distance to " CD  ARG A  14 " =    3.357
peak=   -4.602 closest distance to " O   HOH Z 385 " =    1.306
peak=   -4.552 closest distance to " CA  GLY A  98 " =    1.757
peak=   -4.454 closest distance to " O   PRO A 198 " =    1.242
peak=   -4.372 closest distance to " O   HOH Z 231 " =    0.740
peak=   -4.230 closest distance to " N   THR A 157 " =    1.525
peak=   -4.096 closest distance to " CZ3 TRP A 179 " =    1.241
peak=   -4.073 closest distance to " O   HOH Z  60 " =    2.045
peak=   -4.034 closest distance to " CA  GLY A 203 " =    2.258
peak=   -4.020 closest distance to " CB  ALA A 291 " =    2.196
peak=   -3.984 closest distance to " O   HOH Z 185 " =    2.039
peak=   -3.966 closest distance to " O   HOH Z  52 " =    1.080
peak=   -3.906 closest distance to " OG BSER A 134 " =    1.562
peak=   -3.906 closest distance to " O   HOH Z  39 " =    1.110
peak=   -3.893 closest distance to " O   HOH Z 407 " =    3.189
peak=   -3.867 closest distance to " CA  GLY A 241 " =    2.195
peak=   -3.865 closest distance to " O   HOH Z 111 " =    1.719
peak=   -3.853 closest distance to " O   HOH Z 377 " =    1.688
peak=   -3.830 closest distance to " CG2 THR A  18 " =    2.888
peak=   -3.830 closest distance to " CB  ASP A 132 " =    2.431
peak=   -3.829 closest distance to " O   SER A  22 " =    2.778
peak=   -3.826 closest distance to " CB  ALA A 248 " =    2.085
peak=   -3.810 closest distance to " O   HOH Z 231 " =    1.685
peak=   -3.803 closest distance to " N   ALA A  43 " =    2.574
peak=   -3.778 closest distance to " ND2 ASN A 285 " =    2.075
peak=   -3.778 closest distance to " ND2 ASN A 249 " =    2.082
peak=   -3.762 closest distance to " CD  ARG A 156 " =    2.063
peak=   -3.762 closest distance to " O   HOH Z 351 " =    1.555
peak=   -3.758 closest distance to " O   HOH Z  28 " =    1.533
peak=   -3.757 closest distance to " CB  ASP A  27 " =    2.457
peak=   -3.753 closest distance to " CD  GLN A  58 " =    1.233
peak=   -3.732 closest distance to " CB  ALA A 158 " =    1.691
peak=   -3.727 closest distance to " O   HOH Z 313 " =    1.454
peak=   -3.710 closest distance to " CG  MET A 105 " =    0.934
peak=   -3.698 closest distance to " O   HOH Z 211 " =    1.529
peak=   -3.696 closest distance to " O   ALA A   1 " =    1.187
peak=   -3.691 closest distance to " O   SER A 135 " =    1.428
peak=   -3.685 closest distance to " CB  PHE A 283 " =    2.807
peak=   -3.681 closest distance to " CD  GLN A  58 " =    0.864
peak=   -3.680 closest distance to " OG  SER A  97 " =    2.223
peak=   -3.659 closest distance to " NH1AARG A 275 " =    1.933
peak=   -3.657 closest distance to " O   HOH Z 166 " =    1.320
peak=   -3.635 closest distance to " CB  ALA A 100 " =    2.089
peak=   -3.634 closest distance to " OD2 ASP A  27 " =    1.737
peak=   -3.630 closest distance to " O   HOH Z   1 " =    1.394
peak=   -3.626 closest distance to " NH2 ARG A 219 " =    1.805
peak=   -3.624 closest distance to " O   HOH Z 290 " =    1.179
peak=   -3.622 closest distance to " O   ASP A 191 " =    2.009
peak=   -3.621 closest distance to " CZ2 TRP A 274 " =    0.924
peak=   -3.616 closest distance to " CB  ALA A 114 " =    2.504
peak=   -3.616 closest distance to " O   HOH Z  65 " =    1.162
peak=   -3.598 closest distance to " O   HOH Z  73 " =    2.219
peak=   -3.594 closest distance to " CD2 TYR A 293 " =    1.892
peak=   -3.581 closest distance to " O   HOH Z 298 " =    2.597
peak=   -3.558 closest distance to " C   ALA A 114 " =    2.320
peak=   -3.555 closest distance to " CG  ASP A 231 " =    0.811
peak=   -3.546 closest distance to " CD  ARG A 139 " =    1.599
peak=   -3.541 closest distance to " CG1 VAL A  78 " =    2.447
peak=   -3.541 closest distance to " O   HOH Z 131 " =    4.087
peak=   -3.534 closest distance to " NH2 ARG A  79 " =    1.984
peak=   -3.530 closest distance to " CE2 TYR A  30 " =    2.606
peak=   -3.521 closest distance to " O   HOH Z 389 " =    2.074
peak=   -3.518 closest distance to " O   HOH Z 281 " =    2.871
peak=   -3.515 closest distance to " CG  GLN A  88 " =    0.843
peak=   -3.514 closest distance to " O   ALA A  10 " =    1.686
peak=   -3.513 closest distance to " O   ASP A 162 " =    2.246
peak=   -3.509 closest distance to " NH2AARG A 275 " =    5.564
peak=   -3.503 closest distance to " O   HOH Z 122 " =    2.322
peak=   -3.496 closest distance to " O   PRO A 243 " =    2.393
peak=   -3.484 closest distance to " OE1 GLU A 277 " =    2.366
peak=   -3.478 closest distance to " O   LEU A 261 " =    1.149
peak=   -3.475 closest distance to " CG2 ILE A  49 " =    2.766
peak=   -3.464 closest distance to " O   HOH Z 384 " =    3.335
peak=   -3.463 closest distance to " OG  SER A   3 " =    1.649
peak=   -3.460 closest distance to " O   HOH Z 108 " =    1.917
peak=   -3.454 closest distance to " OG ASER A 216 " =    1.142
peak=   -3.443 closest distance to " O   HOH Z 298 " =    1.178
peak=   -3.436 closest distance to " O   VAL A  67 " =    2.555
peak=   -3.429 closest distance to " O   HOH Z  60 " =    2.423
peak=   -3.426 closest distance to " O   HOH Z 166 " =    1.670
peak=   -3.421 closest distance to " NE2 GLN A 278 " =    2.034
peak=   -3.418 closest distance to " CB  ALA A  10 " =    2.263
peak=   -3.412 closest distance to " O   HOH Z  51 " =    0.869
peak=   -3.408 closest distance to " CB  ASN A  39 " =    2.266
peak=   -3.407 closest distance to " OG  SER A  26 " =    1.130
peak=   -3.402 closest distance to " O   HOH Z 352 " =    2.105
peak=   -3.399 closest distance to " O   LYS A 181 " =    2.965
peak=   -3.397 closest distance to " N   ASP A 171 " =    2.400
peak=   -3.397 closest distance to " O   PRO A 163 " =    1.910
peak=   -3.395 closest distance to " CA  GLY A 133 " =    2.112
peak=   -3.385 closest distance to " O   HOH Z 286 " =    1.759
peak=   -3.381 closest distance to " CB  PHE A 130 " =    1.223
peak=   -3.377 closest distance to " O   ILE A  49 " =    1.595
peak=   -3.377 closest distance to " OD2 ASP A 191 " =    1.558
peak=   -3.372 closest distance to " CD2 LEU A 237 " =    2.865
peak=   -3.372 closest distance to " CG1 VAL A 197 " =    2.246
peak=   -3.365 closest distance to " N   GLN A 122 " =    1.471
peak=   -3.362 closest distance to " O   HOH Z  90 " =    2.751
peak=   -3.352 closest distance to " OG  SER A  87 " =    1.258
peak=   -3.350 closest distance to " CB  ALA A 248 " =    2.446
peak=   -3.349 closest distance to " O   GLY A  80 " =    2.415
peak=   -3.346 closest distance to " CB  ALA A  43 " =    2.365
peak=   -3.343 closest distance to " CD2 PHE A  61 " =    2.425
peak=   -3.340 closest distance to " CG  ASN A  39 " =    1.743
peak=   -3.327 closest distance to " CB  GLN A  55 " =    1.250
peak=   -3.326 closest distance to " NE2 GLN A  55 " =    0.796
peak=   -3.323 closest distance to " O   HOH Z 241 " =    1.357
peak=   -3.322 closest distance to " CG2 VAL A 232 " =    1.973
peak=   -3.308 closest distance to " CB  ALA A 227 " =    2.359
peak=   -3.305 closest distance to " OG ASER A 134 " =    1.249
peak=   -3.302 closest distance to " CD  LYS A 166 " =    2.361
peak=   -3.302 closest distance to " CZ3 TRP A 123 " =    1.560
peak=   -3.300 closest distance to " O   HOH Z 171 " =    2.972
peak=   -3.298 closest distance to " O   HOH Z  49 " =    1.258
peak=   -3.297 closest distance to " CG  PRO A 163 " =    2.554
peak=   -3.291 closest distance to " CB  TRP A  85 " =    2.440
peak=   -3.290 closest distance to " CE1 PHE A  59 " =    1.433
peak=   -3.290 closest distance to " CB  CYS A 201 " =    2.112
peak=   -3.289 closest distance to " CG  GLN A 278 " =    2.239
peak=   -3.288 closest distance to " ND2BASN A 224 " =    1.422
peak=   -3.287 closest distance to " N   GLN A  58 " =    1.690
peak=   -3.284 closest distance to " CG1BVAL A  41 " =    2.957
peak=   -3.269 closest distance to " OG  SER A 141 " =    1.845
peak=   -3.266 closest distance to " O   HOH Z 196 " =    1.816
peak=   -3.260 closest distance to " CG  ARG A 269 " =    2.531
peak=   -3.257 closest distance to " NE  ARG A  36 " =    1.895
peak=   -3.255 closest distance to " ND2 ASN A 187 " =    1.402
peak=   -3.250 closest distance to " O   ASN A 301 " =    1.368
peak=   -3.250 closest distance to " NH1 ARG A 195 " =    2.299
peak=   -3.249 closest distance to " OD1 ASN A 148 " =    1.618
peak=   -3.247 closest distance to " OG  SER A 206 " =    1.959
peak=   -3.245 closest distance to " O   HOH Z 426 " =    1.635
peak=   -3.233 closest distance to " O   HOH Z 387 " =    0.988
peak=   -3.232 closest distance to " OG BSER A 134 " =    1.798
peak=   -3.231 closest distance to " CD  GLN A 223 " =    1.230
peak=   -3.231 closest distance to " O   HOH Z 140 " =    1.373
peak=   -3.220 closest distance to " OG  SER A 245 " =    1.275
peak=   -3.220 closest distance to " OD2 ASP A 171 " =    1.922
peak=   -3.212 closest distance to " O   HOH Z 201 " =    1.932
peak=   -3.207 closest distance to " CG2 THR A  52 " =    3.183
peak=   -3.200 closest distance to " O   HOH Z 147 " =    1.329
peak=   -3.199 closest distance to " O   HOH Z 389 " =    1.236
peak=   -3.199 closest distance to " O   HOH Z 317 " =    1.443
peak=   -3.193 closest distance to " CD  LYS A 289 " =    2.390
peak=   -3.184 closest distance to " O   HOH Z  76 " =    1.103
peak=   -3.173 closest distance to " O   SER A  62 " =    2.406
peak=   -3.172 closest distance to " OD1 ASP A 171 " =    1.557
peak=   -3.166 closest distance to " N   ALA A   1 " =    1.546
peak=   -3.165 closest distance to " CB  PHE A 192 " =    1.581
peak=   -3.161 closest distance to " O   HOH Z 359 " =    1.529
peak=   -3.158 closest distance to " O   HOH Z 253 " =    4.179
peak=   -3.154 closest distance to " CZ  PHE A  16 " =    2.210
peak=   -3.151 closest distance to " CE BMET A  47 " =    1.351
peak=   -3.143 closest distance to " O   HOH Z  71 " =    2.335
peak=   -3.142 closest distance to " O   GLU A 152 " =    1.486
peak=   -3.137 closest distance to " CA  ASP A 298 " =    1.085
peak=   -3.134 closest distance to " O   HOH Z 200 " =    3.606
peak=   -3.129 closest distance to " O   ALA A 180 " =    1.290
peak=   -3.117 closest distance to " O   HOH Z 275 " =    1.692
peak=   -3.114 closest distance to " C   MET A 188 " =    1.767
peak=   -3.110 closest distance to " C   LYS A  76 " =    1.169
peak=   -3.104 closest distance to " O   HOH Z 292 " =    1.510
peak=   -3.100 closest distance to " CD2 LEU A  25 " =    2.209
peak=   -3.099 closest distance to " O   HOH Z 414 " =    1.478
peak=   -3.099 closest distance to " ND2 ASN A  45 " =    1.166
peak=   -3.096 closest distance to " CG  GLN A 223 " =    2.325
peak=   -3.094 closest distance to " O   ARG A 145 " =    1.352
peak=   -3.076 closest distance to " OD2 ASP A 132 " =    2.153
peak=   -3.076 closest distance to " O   HOH Z 340 " =    1.711
peak=   -3.069 closest distance to " OD1 ASN A 301 " =    1.743
peak=   -3.056 closest distance to " OE1 GLN A  58 " =    3.087
peak=   -3.054 closest distance to " O   HOH Z   2 " =    1.066
peak=   -3.044 closest distance to " CZ  TYR A 169 " =    1.837
peak=   -3.037 closest distance to " CB  TYR A  15 " =    2.053
peak=   -3.035 closest distance to " NH2BARG A 275 " =    1.580
peak=   -3.033 closest distance to " CA  GLY A  57 " =    2.113
peak=   -3.005 closest distance to " N   VAL A  72 " =    1.343

================= 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    :  0.4515 0.4500   6.270251e+00   6.265733e+00
   1_bss:  0.4420 0.4433   6.264318e+00   6.257618e+00
   1_xyz:  0.3542 0.4010   6.115718e+00   6.183806e+00
   1_adp:  0.3234 0.4072   6.073623e+00   6.193180e+00
   1_occ:  0.3229 0.4069   6.072831e+00   6.193457e+00
   2_bss:  0.3232 0.4045   6.072864e+00   6.193013e+00
   2_xyz:  0.2572 0.3267   5.881507e+00   6.035359e+00
   2_adp:  0.2358 0.3057   5.817130e+00   5.988266e+00
   2_occ:  0.2355 0.3050   5.816304e+00   5.987276e+00
   3_bss:  0.2350 0.3036   5.811765e+00   5.982814e+00
   3_xyz:  0.1852 0.2432   5.586771e+00   5.792522e+00
   3_adp:  0.1666 0.2240   5.502195e+00   5.720246e+00
   3_occ:  0.1665 0.2236   5.501347e+00   5.719296e+00
   4_bss:  0.1664 0.2231   5.499508e+00   5.716661e+00
   4_xyz:  0.1359 0.1891   5.319361e+00   5.559420e+00
   4_adp:  0.1308 0.1778   5.275248e+00   5.507756e+00
   4_occ:  0.1307 0.1775   5.274641e+00   5.507051e+00
   5_bss:  0.1309 0.1770   5.273283e+00   5.504339e+00
   5_xyz:  0.1216 0.1661   5.211660e+00   5.446240e+00
   5_adp:  0.1189 0.1655   5.199327e+00   5.440162e+00
   5_occ:  0.1188 0.1654   5.198912e+00   5.439640e+00
   5_bss:  0.1188 0.1653   5.198888e+00   5.439852e+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:  0.351  50.001  -0.960   2.543  -1.495   0.000  -0.000  -0.000
   1_xyz:  0.351  50.001  -0.960   2.543  -1.495   0.000  -0.000  -0.000
   1_adp:  0.351  50.001  -0.960   2.543  -1.495   0.000  -0.000  -0.000
   1_occ:  0.351  50.001  -0.960   2.543  -1.495   0.000  -0.000  -0.000
   2_bss:  0.357  73.347  -0.768   0.466  -0.367   0.000  -0.000  -0.000
   2_xyz:  0.357  73.347  -0.768   0.466  -0.367   0.000  -0.000  -0.000
   2_adp:  0.357  73.347  -0.768   0.466  -0.367   0.000  -0.000  -0.000
   2_occ:  0.357  73.347  -0.768   0.466  -0.367   0.000  -0.000  -0.000
   3_bss:  0.344  67.376  -1.182  -1.072  -0.412  -0.000  -0.000  -0.000
   3_xyz:  0.344  67.376  -1.182  -1.072  -0.412  -0.000  -0.000  -0.000
   3_adp:  0.344  67.376  -1.182  -1.072  -0.412  -0.000  -0.000  -0.000
   3_occ:  0.344  67.376  -1.182  -1.072  -0.412  -0.000  -0.000  -0.000
   4_bss:  0.332  67.376  -1.961  -2.364  -1.003  -0.000  -0.000  -0.000
   4_xyz:  0.332  67.376  -1.961  -2.364  -1.003  -0.000  -0.000  -0.000
   4_adp:  0.332  67.376  -1.961  -2.364  -1.003  -0.000  -0.000  -0.000
   4_occ:  0.332  67.376  -1.961  -2.364  -1.003  -0.000  -0.000  -0.000
   5_bss:  0.318  53.473  -2.150  -2.723  -1.123  -0.000  -0.000  -0.000
   5_xyz:  0.318  53.473  -2.150  -2.723  -1.123  -0.000  -0.000  -0.000
   5_adp:  0.318  53.473  -2.150  -2.723  -1.123  -0.000  -0.000  -0.000
   5_occ:  0.318  53.473  -2.150  -2.723  -1.123  -0.000  -0.000  -0.000
   5_bss:  0.304  49.509  -2.142  -2.812  -1.102  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.088 0.4572  0.6302    69319.267
   1_bss:  54.656 0.4615  0.6415    67491.532
   1_xyz:  45.482 0.5759  0.7759    48366.794
   1_adp:  46.216 0.5665  0.7694    49790.388
   1_occ:  46.252 0.5660  0.7680    49796.689
   2_bss:  45.867 0.5706  0.7685    49121.187
   2_xyz:  35.325 0.6963  0.9135    30164.905
   2_adp:  32.345 0.7312  0.9355    26311.847
   2_occ:  32.308 0.7316  0.9356    26235.346
   3_bss:  32.080 0.7338  0.9161    25779.338
   3_xyz:  24.499 0.8156  0.9839    15576.362
   3_adp:  22.231 0.8392  0.9910    13236.146
   3_occ:  22.205 0.8395  0.9906    13188.496
   4_bss:  22.095 0.8404  0.9606    13060.963
   4_xyz:  18.044 0.8792  0.9794     9125.855
   4_adp:  16.598 0.8929  0.9808     8224.858
   4_occ:  16.587 0.8930  0.9806     8203.213
   5_bss:  16.554 0.8931  0.9728     8136.651
   5_xyz:  15.183 0.9052  0.9783     7134.336
   5_adp:  14.988 0.9071  0.9754     7038.843
   5_occ:  14.982 0.9071  0.9754     7029.034
   5_bss:  14.980 0.9071  0.9741     7028.191
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.8472e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.8472e-01
   1_xyz:   1.576  0.012  0.109 16.393  0.006  4.109   1.3834e-01
   1_adp:   1.576  0.012  0.109 16.393  0.006  4.109   1.3834e-01
   1_occ:   1.576  0.012  0.109 16.393  0.006  4.109   1.3834e-01
   2_bss:   1.576  0.012  0.109 16.393  0.006  4.109   1.3834e-01
   2_xyz:   1.387  0.011  0.098 15.580  0.005  4.112   1.1615e-01
   2_adp:   1.387  0.011  0.098 15.580  0.005  4.112   1.1615e-01
   2_occ:   1.387  0.011  0.098 15.580  0.005  4.112   1.1615e-01
   3_bss:   1.387  0.011  0.098 15.580  0.005  4.112   1.1615e-01
   3_xyz:   1.053  0.007  0.073 14.418  0.004  4.107   6.5768e-02
   3_adp:   1.053  0.007  0.073 14.418  0.004  4.107   6.5768e-02
   3_occ:   1.053  0.007  0.073 14.418  0.004  4.107   6.5768e-02
   4_bss:   1.053  0.007  0.073 14.418  0.004  4.107   6.5768e-02
   4_xyz:   1.060  0.008  0.076 14.476  0.004  4.109   6.6666e-02
   4_adp:   1.060  0.008  0.076 14.476  0.004  4.109   6.6666e-02
   4_occ:   1.060  0.008  0.076 14.476  0.004  4.109   6.6666e-02
   5_bss:   1.060  0.008  0.076 14.476  0.004  4.109   6.6666e-02
   5_xyz:   0.989  0.007  0.074 14.374  0.004  4.113   5.9008e-02
   5_adp:   0.989  0.007  0.074 14.374  0.004  4.113   5.9008e-02
   5_occ:   0.989  0.007  0.074 14.374  0.004  4.113   5.9008e-02
   5_bss:   0.989  0.007  0.074 14.374  0.004  4.113   5.9008e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.579   2.4126e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.579   2.4126e-01
   1_xyz:   8.698  0.089  0.383 88.895  0.038  2.014   1.0570e-01
   1_adp:   8.698  0.089  0.383 88.895  0.038  2.014   1.0570e-01
   1_occ:   8.698  0.089  0.383 88.895  0.038  2.014   1.0570e-01
   2_bss:   8.698  0.089  0.383 88.895  0.038  2.014   1.0570e-01
   2_xyz:   8.548  0.079  0.323 85.714  0.049  1.955   1.9443e-01
   2_adp:   8.548  0.079  0.323 85.714  0.049  1.955   1.9443e-01
   2_occ:   8.548  0.079  0.323 85.714  0.049  1.955   1.9443e-01
   3_bss:   8.548  0.079  0.323 85.714  0.049  1.955   1.9443e-01
   3_xyz:   8.925  0.047  0.265 86.646  0.013  2.242   5.4947e-02
   3_adp:   8.925  0.047  0.265 86.646  0.013  2.242   5.4947e-02
   3_occ:   8.925  0.047  0.265 86.646  0.013  2.242   5.4947e-02
   4_bss:   8.925  0.047  0.265 86.646  0.013  2.242   5.4947e-02
   4_xyz:   8.205  0.042  0.217 83.093  0.033  2.277   5.9399e-02
   4_adp:   8.205  0.042  0.217 83.093  0.033  2.277   5.9399e-02
   4_occ:   8.205  0.042  0.217 83.093  0.033  2.277   5.9399e-02
   5_bss:   8.205  0.042  0.217 83.093  0.033  2.277   5.9399e-02
   5_xyz:   8.185  0.048  0.225 82.974  0.030  2.326   4.3856e-02
   5_adp:   8.185  0.048  0.225 82.974  0.030  2.326   4.3856e-02
   5_occ:   8.185  0.048  0.225 82.974  0.030  2.326   4.3856e-02
   5_bss:   8.185  0.048  0.225 82.974  0.030  2.326   4.3856e-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:  95.95   0.00  18.71  75.63   0.00  15.45  95.95   0.00  36.42
   1_occ:  95.95   0.00  18.71  75.63   0.00  15.45  95.95   0.00  36.42
   2_bss:  95.95   0.00  18.71  75.63   0.00  15.45  95.95   0.00  36.42
   2_xyz:  95.95   0.00  18.71  75.63   0.00  15.45  95.95   0.00  36.42
   2_adp:  93.88   0.00  18.18  79.99   0.00  14.37  93.88   0.00  38.97
   2_occ:  93.88   0.00  18.18  79.99   0.00  14.37  93.88   0.00  38.97
   3_bss:  93.88   0.00  18.18  79.99   0.00  14.37  93.88   0.00  38.97
   3_xyz:  93.88   0.00  18.18  79.99   0.00  14.37  93.88   0.00  38.97
   3_adp:  92.55   0.00  18.30  89.92   0.00  13.54  92.55   5.35  44.22
   3_occ:  92.55   0.00  18.30  89.92   0.00  13.54  92.55   5.35  44.22
   4_bss:  92.55   0.00  18.30  89.92   0.00  13.54  92.55   5.35  44.22
   4_xyz:  92.55   0.00  18.30  89.92   0.00  13.54  92.55   5.35  44.22
   4_adp:  90.65   1.13  17.38  90.65   1.13  12.93  86.28   4.71  41.66
   4_occ:  90.65   1.13  17.38  90.65   1.13  12.93  86.28   4.71  41.66
   5_bss:  90.65   1.13  17.38  90.65   1.13  12.93  86.28   4.71  41.66
   5_xyz:  90.65   1.13  17.38  90.65   1.13  12.93  86.28   4.71  41.66
   5_adp:  93.81   0.46  17.33  93.81   0.46  12.83  86.63   4.53  41.80
   5_occ:  93.81   0.46  17.33  93.81   0.46  12.83  86.63   4.53  41.80
   5_bss:  93.79   0.44  17.31  93.79   0.44  12.82  86.61   4.51  41.79
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.753    0.033    0.387
   1_adp:    1.753    0.033    0.387
   1_occ:    1.753    0.033    0.387
   2_bss:    1.753    0.033    0.387
   2_xyz:    1.702    0.061    0.612
   2_adp:    1.702    0.061    0.612
   2_occ:    1.702    0.061    0.612
   3_bss:    1.702    0.061    0.612
   3_xyz:    1.675    0.009    0.724
   3_adp:    1.675    0.009    0.724
   3_occ:    1.675    0.009    0.724
   4_bss:    1.675    0.009    0.724
   4_xyz:    1.795    0.060    0.788
   4_adp:    1.795    0.060    0.788
   4_occ:    1.795    0.060    0.788
   5_bss:    1.795    0.060    0.788
   5_xyz:    1.965    0.088    0.807
   5_adp:    1.965    0.088    0.807
   5_occ:    1.965    0.088    0.807
   5_bss:    1.965    0.088    0.807
------------------------------------------------------------------------

CPU time actual refinement: 338.02


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_974/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_974/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_974/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_974/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_974/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 337.86 
  Macro-tasks:
    bulk solvent and scale       = 36.81  
    individual site refinement   = 140.30 
    weights calculation          = 28.61  
    collect and process          = 5.96   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 211.79 
  Micro-tasks:
    mask                            = 2.46   
    f_calc                          = 111.72 
    alpha_beta                      = 8.21   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 119.22 
    fmodel                         = 6.49   
    r_factors                      = 0.19   
    phase_errors                   = 10.46  
    foms                           = 0.20   
    TOTAL for micro-tasks          = 260.11 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.844 micro seconds
Total CPU time: 5.86 minutes
from_scatterers_fft:    634 calls, 111.40 s
gradients_fft:          579 calls, 106.48 s

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

# Date 2008-01-16 Time 06:06:51 PST -0800 (1200492411.91 s)
Start R-work = 0.4515, R-free = 0.4500 (no bulk solvent and anisotropic scale)
Final R-work = 0.1423, R-free = 0.1844 (no bulk solvent and anisotropic scale)

Start R-work = 0.4420, R-free = 0.4433
Final R-work = 0.1188, R-free = 0.1653