# Date 2008-01-16 Time 06:07:32 PST -0800 (1200492452.22 s)
#phil __OFF__

Command line arguments: "../1018.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25686
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1018

-------------------------------------------------------------------------------
  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, 46.6953, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.6953, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1778 1.99276
Completeness in resolution range: 0.961565
Completeness with d_max=infinity: 0.958647

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1778
                             d_min =   1.9928

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, 46.6953, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1778 1.99276
Completeness in resolution range: 0.961565
Completeness with d_max=infinity: 0.958647

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1782 -  4.2645 [2137/2162]  1924   213  10.0%
  bin  2:  4.2645 -  3.3973 [2050/2070]  1845   205  10.0%
  bin  3:  3.3973 -  2.9716 [2040/2059]  1835   205  10.0%
  bin  4:  2.9716 -  2.7015 [2005/2035]  1806   199   9.9%
  bin  5:  2.7015 -  2.5088 [2009/2028]  1812   197   9.8%
  bin  6:  2.5088 -  2.3615 [1984/2009]  1778   206  10.4%
  bin  7:  2.3615 -  2.2436 [1974/2002]  1776   198  10.0%
  bin  8:  2.2436 -  2.1462 [1971/2007]  1776   195   9.9%
  bin  9:  2.1462 -  2.0638 [1973/2015]  1780   193   9.8%
  bin 10:  2.0638 -  1.9928 [1446/1985]  1298   148  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1018/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:
        1.81 -     2.42: 10
        2.42 -     3.04: 2176
        3.04 -     3.66: 4639
        3.66 -     4.28: 8989
        4.28 -     4.90: 12274
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 341 " - " O   HOH Z 207 "  2.128 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.128 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.312 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28083 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_1018/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1018/model_refine_001.geo

CPU time processing inputs: 9.05


============================ 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 46.69535 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: 1.99 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2965   r_free= 0.2922   ksol= 0.00   Bsol= 0.00   scale= 0.976    |
|                                                                             |
| 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:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.963984                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.7566 0.99   1390  155 0.2756 0.2531      6.3129       6.238|
|  2:  4.7566 -  3.7949 0.99   1337  150 0.2344 0.2271      6.3514      6.2977|
|  3:  3.7949 -  3.3209 0.99   1316  141 0.2470 0.2405      6.2096      6.2854|
|  4:  3.3209 -  3.0199 0.99   1304  151 0.2652 0.2840       6.125      6.1324|
|  5:  3.0199 -  2.8049 0.99   1295  144 0.3097 0.2871      6.0362      6.0602|
|  6:  2.8049 -  2.6404 0.99   1298  138 0.2919 0.3029      5.9259      5.8861|
|  7:  2.6404 -  2.5088 0.99   1282  140 0.3226 0.3211      5.9467      6.0159|
|  8:  2.5088 -  2.4001 0.98   1271  148 0.3233 0.2972      5.8986      5.8422|
|  9:  2.4001 -  2.3080 0.98   1258  145 0.3212 0.3186      5.8357      5.7973|
| 10:  2.3080 -  2.2286 1.00   1294  138 0.3314 0.3385      5.8286      5.8258|
| 11:  2.2286 -  2.1591 0.97   1266  138 0.3512 0.3708      5.8112      5.8911|
| 12:  2.1591 -  2.0976 0.98   1248  141 0.3398 0.3309      5.7465      5.7729|
| 13:  2.0976 -  2.0425 0.99   1280  140 0.3556 0.3616      5.6565      5.6098|
| 14:  2.0425 -  1.9928 0.62    791   90 0.3444 0.3514      5.6098      5.5877|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 -  4.7566  1390   155  0.81  23.88   0.86     0.83      35969.49|
|  2:  4.7566 -  3.7949  1337   150  0.87  19.39   0.98     0.92      36293.28|
|  3:  3.7949 -  3.3209  1316   141  0.83  23.23   1.00     0.96      35870.01|
|  4:  3.3209 -  3.0199  1304   151  0.81  25.24   1.00     0.95      31941.93|
|  5:  3.0199 -  2.8049  1295   144  0.76  30.55   0.99     0.92      28096.32|
|  6:  2.8049 -  2.6404  1298   138  0.76  30.55   1.01     0.91      23351.73|
|  7:  2.6404 -  2.5088  1282   140  0.76  30.74   1.01     0.92      21554.04|
|  8:  2.5088 -  2.4001  1271   148  0.76  30.42   1.02     0.93      19367.62|
|  9:  2.4001 -  2.3080  1258   145  0.76  30.96   1.03     0.95      18676.37|
| 10:  2.3080 -  2.2286  1294   138  0.73  33.15   1.06     0.95      18165.59|
| 11:  2.2286 -  2.1591  1266   138  0.71  35.01   1.06     0.93      18551.37|
| 12:  2.1591 -  2.0976  1248   141  0.72  34.34   1.05     0.94      17130.17|
| 13:  2.0976 -  2.0425  1280   140  0.70  35.81   1.04     0.95      14324.28|
| 14:  2.0425 -  1.9928   791    90  0.76  30.74   1.05     0.96      10242.97|
|alpha:            min =        0.83 max =            0.96 mean =         0.93|
|beta:             min =    10242.97 max =        36293.28 mean =     24085.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.77|
|phase err.(work): min =        0.00 max =           90.00 mean =        29.44|
|phase err.(test): min =        0.00 max =           89.95 mean =        29.06|
|-----------------------------------------------------------------------------|

============================== 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 = 4.141610              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.481   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.548702              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.654   (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 |  1.806 -  2.115:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      192 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1984 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1833 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2806 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4626 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4363 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5606 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6668 |
|-----------------------------------------------------------------------------|
|-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 |        0.161 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.139 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.094)------------------------------------------|
|    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: 1.99 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2965   r_free= 0.2922   ksol= 0.00   Bsol= 0.00   scale= 0.976    |
|                                                                             |
| 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:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.963984                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2825   r_free= 0.2809   ksol= 0.33   Bsol= 56.86   scale= 0.979   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.20,-2.33,-0.97,-0.00,-0.00,-0.00); trace/3= -1.03                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.938988                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.721587              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.749   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.297214              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.401   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2825      final r-factor (work) = 0.1591          |
| start r-factor (free) = 0.2809      final r-factor (free) = 0.1796          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2324 = 3.72 * 0.50 * 5.9500 + 1.00 * 0.1607                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5518 = 3.72 * 0.50 * 5.6363 + 1.00 * 0.0637                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1591      final r-factor (work) = 0.1442          |
| start r-factor (free) = 0.1796      final r-factor (free) = 0.1843          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6813 = 0.30 * 1.00 * 5.6363 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5922 = 0.30 * 1.00 * 5.3295 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.094)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.36    72.53   17.07    None  None   None       |
|    all(noH): 2823   0      1.36    72.53   17.07    None  None   None       |
|    Sol.    : 438    0      5.06    72.53   39.02    None  None   None       |
|    Mac.    : 2385   0      1.36    67.43   13.04    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:     1.357 -   8.474:  585   |   5:    36.944 -  44.062:  106        |
|      1:     8.474 -  15.592: 1303   |   6:    44.062 -  51.179:   85        |
|      2:    15.592 -  22.709:  385   |   7:    51.179 -  58.296:   72        |
|      3:    22.709 -  29.827:  142   |   8:    58.296 -  65.414:   34        |
|      4:    29.827 -  36.944:   99   |   9:    65.414 -  72.531:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1442 r_free = 0.1843             target_work(ml) = 5.341         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1439 r_free = 0.1840             target_work(ml) = 5.339         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1439   r_free= 0.1840   ksol= 0.33   Bsol= 56.86   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.20,-2.33,-0.97,-0.00,-0.00,-0.00); trace/3= -1.03                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.339176                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1428   r_free= 0.1824   ksol= 0.33   Bsol= 61.68   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,-2.94,-1.56,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.337794                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.237774              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.212  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.140748              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.690  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1428      final r-factor (work) = 0.1174          |
| start r-factor (free) = 0.1824      final r-factor (free) = 0.1615          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7162 = 3.24 * 0.50 * 5.3447 + 1.00 * 0.0638                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5678 = 3.24 * 0.50 * 5.2507 + 1.00 * 0.0674                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1174      final r-factor (work) = 0.1155          |
| start r-factor (free) = 0.1615      final r-factor (free) = 0.1569          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7473 = 0.14 * 1.00 * 5.2507 + 1.00 * 0.0082                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7351 = 0.14 * 1.00 * 5.1752 + 1.00 * 0.0067                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.094)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.89    74.45   16.75    None  None   None       |
|    all(noH): 2823   0      1.89    74.45   16.75    None  None   None       |
|    Sol.    : 438    0      6.40    74.45   37.23    None  None   None       |
|    Mac.    : 2385   0      1.89    69.73   12.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.885 -   9.142:  697   |   5:    38.168 -  45.424:  109        |
|      1:     9.142 -  16.398: 1269   |   6:    45.424 -  52.681:   83        |
|      2:    16.398 -  23.655:  345   |   7:    52.681 -  59.938:   48        |
|      3:    23.655 -  30.911:  128   |   8:    59.938 -  67.194:   13        |
|      4:    30.911 -  38.168:  125   |   9:    67.194 -  74.451:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1155 r_free = 0.1569             target_work(ml) = 5.160         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1153 r_free = 0.1569             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1153   r_free= 0.1569   ksol= 0.33   Bsol= 61.68   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,-2.94,-1.56,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.159293                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1152   r_free= 0.1568   ksol= 0.33   Bsol= 61.68   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-2.82,-1.45,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.158521                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.804393              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.081  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.150279              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 162.439  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1152      final r-factor (work) = 0.1142          |
| start r-factor (free) = 0.1568      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7357 = 1.80 * 0.50 * 5.1744 + 1.00 * 0.0674                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7093 = 1.80 * 0.50 * 5.1566 + 1.00 * 0.0570                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1142      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1572      final r-factor (free) = 0.1566          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7816 = 0.15 * 1.00 * 5.1566 + 1.00 * 0.0067                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7814 = 0.15 * 1.00 * 5.1550 + 1.00 * 0.0067                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.094)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.90    74.51   16.66    None  None   None       |
|    all(noH): 2823   0      1.90    74.51   16.66    None  None   None       |
|    Sol.    : 438    0      6.16    74.51   37.11    None  None   None       |
|    Mac.    : 2385   0      1.90    69.92   12.91    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.895 -   9.157:  734   |   5:    38.205 -  45.466:  109        |
|      1:     9.157 -  16.419: 1234   |   6:    45.466 -  52.728:   82        |
|      2:    16.419 -  23.681:  350   |   7:    52.728 -  59.990:   49        |
|      3:    23.681 -  30.943:  126   |   8:    59.990 -  67.252:   12        |
|      4:    30.943 -  38.205:  121   |   9:    67.252 -  74.514:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1138 r_free = 0.1566             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1137 r_free = 0.1566             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1566   ksol= 0.33   Bsol= 61.68   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-2.82,-1.45,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.153531                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1554   ksol= 0.33   Bsol= 61.68   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.47,-2.80,-1.43,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.151706                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.511431              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 160.941  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 5.097276              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.236  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1138      final r-factor (work) = 0.1103          |
| start r-factor (free) = 0.1554      final r-factor (free) = 0.1554          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5298 = 2.51 * 0.50 * 5.1547 + 1.00 * 0.0570                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5181 = 2.51 * 0.50 * 5.1360 + 1.00 * 0.0688                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1103      final r-factor (work) = 0.1086          |
| start r-factor (free) = 0.1554      final r-factor (free) = 0.1566          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 26.1861 = 5.10 * 1.00 * 5.1360 + 1.00 * 0.0067                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 26.1313 = 5.10 * 1.00 * 5.1246 + 1.00 * 0.0097                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.094)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.30    85.27   17.28    None  None   None       |
|    all(noH): 2823   0      0.30    85.27   17.28    None  None   None       |
|    Sol.    : 438    0      6.55    82.51   40.39    None  None   None       |
|    Mac.    : 2385   0      0.30    85.27   13.04    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:     0.296 -   8.793:  728   |   5:    42.781 -  51.278:   93        |
|      1:     8.793 -  17.290: 1313   |   6:    51.278 -  59.775:   82        |
|      2:    17.290 -  25.787:  295   |   7:    59.775 -  68.272:   47        |
|      3:    25.787 -  34.284:  135   |   8:    68.272 -  76.769:   19        |
|      4:    34.284 -  42.781:  105   |   9:    76.769 -  85.266:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1086 r_free = 0.1566             target_work(ml) = 5.129         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1086 r_free = 0.1566             target_work(ml) = 5.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1086   r_free= 0.1566   ksol= 0.33   Bsol= 61.68   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.47,-2.80,-1.43,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.128956                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1084   r_free= 0.1566   ksol= 0.32   Bsol= 57.89   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-2.50,-1.15,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.128827                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.363080              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 161.097  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.245143              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.381  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1084      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1566      final r-factor (free) = 0.1588          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5624 = 1.36 * 0.50 * 5.1260 + 1.00 * 0.0688                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5580 = 1.36 * 0.50 * 5.1439 + 1.00 * 0.0522                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1120      final r-factor (work) = 0.1124          |
| start r-factor (free) = 0.1588      final r-factor (free) = 0.1575          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2706 = 0.25 * 1.00 * 5.1439 + 1.00 * 0.0097                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2723 = 0.25 * 1.00 * 5.1542 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.094)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.01    85.05   17.01    None  None   None       |
|    all(noH): 2823   0      1.01    85.05   17.01    None  None   None       |
|    Sol.    : 438    0      6.42    81.79   39.75    None  None   None       |
|    Mac.    : 2385   0      1.01    85.05   12.84    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.005 -   9.410:  923   |   5:    43.027 -  51.431:   88        |
|      1:     9.410 -  17.814: 1167   |   6:    51.431 -  59.836:   82        |
|      2:    17.814 -  26.218:  258   |   7:    59.836 -  68.240:   41        |
|      3:    26.218 -  34.623:  137   |   8:    68.240 -  76.645:   17        |
|      4:    34.623 -  43.027:  104   |   9:    76.645 -  85.049:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1124 r_free = 0.1575             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1124 r_free = 0.1576             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1124   r_free= 0.1576   ksol= 0.32   Bsol= 57.89   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-2.50,-1.15,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.150294                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.7566 0.99   1390  155 0.0988 0.1246      5.3836      5.5096|
|  2:  4.7566 -  3.7949 0.99   1337  150 0.0864 0.1110      5.4408       5.622|
|  3:  3.7949 -  3.3209 0.99   1316  141 0.1052 0.1483      5.4723      5.8648|
|  4:  3.3209 -  3.0199 0.99   1304  151 0.1201 0.1604      5.4603      5.5846|
|  5:  3.0199 -  2.8049 0.99   1295  144 0.1362 0.1774      5.3467      5.5801|
|  6:  2.8049 -  2.6404 0.99   1298  138 0.1216 0.1896      5.2155      5.4747|
|  7:  2.6404 -  2.5088 0.99   1282  140 0.1296 0.1578      5.1852       5.352|
|  8:  2.5088 -  2.4001 0.98   1271  148 0.1144 0.1722      5.0496      5.3354|
|  9:  2.4001 -  2.3080 0.98   1258  145 0.1164 0.1791      5.0287       5.305|
| 10:  2.3080 -  2.2286 1.00   1294  138 0.1142 0.1734       4.954      5.2334|
| 11:  2.2286 -  2.1591 0.97   1266  138 0.1153 0.1755      4.9554      5.2638|
| 12:  2.1591 -  2.0976 0.98   1248  141 0.1111 0.1665      4.8869      5.1544|
| 13:  2.0976 -  2.0425 0.99   1280  140 0.1156 0.1780      4.7996      5.0785|
| 14:  2.0425 -  1.9928 0.62    791   90 0.1101 0.1654      4.6888      4.9093|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 -  4.7566  1390   155  0.94   9.12   0.97     0.94       6995.16|
|  2:  4.7566 -  3.7949  1337   150  0.95   7.80   1.00     0.99       8893.46|
|  3:  3.7949 -  3.3209  1316   141  0.94  11.08   1.01     1.01      10208.30|
|  4:  3.3209 -  3.0199  1304   151  0.92  13.80   1.00     0.98      10488.44|
|  5:  3.0199 -  2.8049  1295   144  0.90  16.08   0.99     0.96       8612.53|
|  6:  2.8049 -  2.6404  1298   138  0.90  16.23   0.98     0.96       7207.01|
|  7:  2.6404 -  2.5088  1282   140  0.90  15.69   0.99     0.95       6328.57|
|  8:  2.5088 -  2.4001  1271   148  0.91  14.77   0.98     0.96       5056.25|
|  9:  2.4001 -  2.3080  1258   145  0.91  14.96   0.99     0.96       4851.02|
| 10:  2.3080 -  2.2286  1294   138  0.90  15.37   0.99     0.96       4268.45|
| 11:  2.2286 -  2.1591  1266   138  0.90  16.25   0.98     0.93       4358.83|
| 12:  2.1591 -  2.0976  1248   141  0.92  14.86   0.99     0.99       4014.74|
| 13:  2.0976 -  2.0425  1280   140  0.90  16.45   0.98     0.97       3402.83|
| 14:  2.0425 -  1.9928   791    90  0.92  14.51   0.96     0.92       2629.27|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2629.27 max =        10488.44 mean =      6373.37|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.92 mean =        14.00|
|phase err.(test): min =        0.00 max =           89.74 mean =        13.51|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1123   r_free= 0.1575   ksol= 0.32   Bsol= 57.86   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-2.32,-0.98,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.150391                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1123   r_free= 0.1575   ksol= 0.32   Bsol= 57.86   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-2.32,-0.98,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.150391                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.7566 0.99   1390  155 0.0988 0.1247      5.3842      5.5102|
|  2:  4.7566 -  3.7949 0.99   1337  150 0.0864 0.1109      5.4409      5.6217|
|  3:  3.7949 -  3.3209 0.99   1316  141 0.1052 0.1483      5.4721      5.8646|
|  4:  3.3209 -  3.0199 0.99   1304  151 0.1201 0.1604      5.4602      5.5845|
|  5:  3.0199 -  2.8049 0.99   1295  144 0.1362 0.1775      5.3468      5.5802|
|  6:  2.8049 -  2.6404 0.99   1298  138 0.1216 0.1896      5.2156      5.4746|
|  7:  2.6404 -  2.5088 0.99   1282  140 0.1296 0.1578      5.1851      5.3518|
|  8:  2.5088 -  2.4001 0.98   1271  148 0.1143 0.1723      5.0496      5.3356|
|  9:  2.4001 -  2.3080 0.98   1258  145 0.1164 0.1791      5.0289      5.3049|
| 10:  2.3080 -  2.2286 1.00   1294  138 0.1142 0.1734      4.9541      5.2331|
| 11:  2.2286 -  2.1591 0.97   1266  138 0.1153 0.1756      4.9556       5.264|
| 12:  2.1591 -  2.0976 0.98   1248  141 0.1111 0.1665       4.887      5.1545|
| 13:  2.0976 -  2.0425 0.99   1280  140 0.1156 0.1780      4.7997      5.0786|
| 14:  2.0425 -  1.9928 0.62    791   90 0.1101 0.1655      4.6889      4.9095|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 -  4.7566  1390   155  0.94   9.13   0.97     0.94       7003.59|
|  2:  4.7566 -  3.7949  1337   150  0.95   7.80   1.01     0.99       8896.64|
|  3:  3.7949 -  3.3209  1316   141  0.94  11.08   1.02     1.01      10203.06|
|  4:  3.3209 -  3.0199  1304   151  0.92  13.80   1.00     0.98      10488.36|
|  5:  3.0199 -  2.8049  1295   144  0.90  16.08   0.99     0.97       8612.60|
|  6:  2.8049 -  2.6404  1298   138  0.90  16.23   0.99     0.96       7207.60|
|  7:  2.6404 -  2.5088  1282   140  0.90  15.69   0.99     0.96       6327.11|
|  8:  2.5088 -  2.4001  1271   148  0.91  14.77   0.99     0.97       5057.08|
|  9:  2.4001 -  2.3080  1258   145  0.91  14.96   1.00     0.96       4850.53|
| 10:  2.3080 -  2.2286  1294   138  0.90  15.37   1.00     0.96       4269.51|
| 11:  2.2286 -  2.1591  1266   138  0.90  16.26   0.98     0.94       4358.78|
| 12:  2.1591 -  2.0976  1248   141  0.92  14.86   1.00     0.99       4015.70|
| 13:  2.0976 -  2.0425  1280   140  0.90  16.45   0.99     0.97       3403.48|
| 14:  2.0425 -  1.9928   791    90  0.92  14.52   0.96     0.93       2630.66|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2630.66 max =        10488.36 mean =      6374.10|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.92 mean =        14.00|
|phase err.(test): min =        0.00 max =           89.74 mean =        13.51|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.094)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.97    85.01   16.98    None  None   None       |
|    all(noH): 2823   0      0.97    85.01   16.98    None  None   None       |
|    Sol.    : 438    0      6.38    81.75   39.71    None  None   None       |
|    Mac.    : 2385   0      0.97    85.01   12.80    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:     0.970 -   9.375:  923   |   5:    42.992 -  51.397:   88        |
|      1:     9.375 -  17.779: 1167   |   6:    51.397 -  59.801:   82        |
|      2:    17.779 -  26.184:  258   |   7:    59.801 -  68.206:   41        |
|      3:    26.184 -  34.588:  137   |   8:    68.206 -  76.610:   17        |
|      4:    34.588 -  42.992:  104   |   9:    76.610 -  85.014:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 301         
Filter by distance & map next to the model:
   mapped sites are within: 0.581 - 4.663
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 294 from: 301
   mapped sites are within: 0.710 - 4.663

peak=    5.699 closest distance to " NH2 ARG A  56 " =    2.209
peak=    5.678 closest distance to " CB  GLN A 223 " =    1.420
peak=    5.491 closest distance to " CG  PRO A  54 " =    1.341
peak=    5.033 closest distance to " CG  PRO A 213 " =    1.241
peak=    4.976 closest distance to " O   HOH Z 126 " =    1.964
peak=    4.971 closest distance to " O   HOH Z 232 " =    2.328
peak=    4.906 closest distance to " NE2 GLN A  11 " =    1.098
peak=    4.866 closest distance to " O   HOH Z 298 " =    1.980
peak=    4.863 closest distance to " CB  SER A  63 " =    1.255
peak=    4.823 closest distance to " CB  ARG A 275 " =    0.905
peak=    4.822 closest distance to " CB  PRO A  54 " =    0.995
peak=    4.694 closest distance to " CB  LEU A 228 " =    1.092
peak=    4.672 closest distance to " CG  PRO A 198 " =    1.241
peak=    4.648 closest distance to " CB  GLN A 183 " =    1.226
peak=    4.568 closest distance to " CB  ASN A 148 " =    1.416
peak=    4.537 closest distance to " O   HOH Z  78 " =    1.716
peak=    4.516 closest distance to " C   PRO A 198 " =    1.515
peak=    4.516 closest distance to " O   HOH Z 369 " =    2.146
peak=    4.505 closest distance to " O   HOH Z 144 " =    1.784
peak=    4.480 closest distance to " CA  TYR A  30 " =    0.965
peak=    4.469 closest distance to " O   HOH Z  15 " =    2.227
peak=    4.465 closest distance to " O   HOH Z 287 " =    2.207
peak=    4.454 closest distance to " CB  ARG A 190 " =    1.617
peak=    4.372 closest distance to " CZ  PHE A 218 " =    1.044
peak=    4.339 closest distance to " CB  ARG A  79 " =    1.358
peak=    4.336 closest distance to " CB  GLU A 128 " =    1.011
peak=    4.283 closest distance to " CG2 VAL A 257 " =    0.999
peak=    4.256 closest distance to " CB  ASN A 187 " =    1.240
peak=    4.242 closest distance to " CG  PRO A 243 " =    1.082
peak=    4.240 closest distance to " CD  ARG A 159 " =    0.765
peak=    4.218 closest distance to " O   HOH Z 189 " =    2.630
peak=    4.192 closest distance to " ND2 ASN A 187 " =    1.434
peak=    4.179 closest distance to " O   HOH Z 250 " =    1.537
peak=    4.156 closest distance to " CB  TRP A 266 " =    0.987
peak=    4.144 closest distance to " CD1 LEU A 300 " =    1.169
peak=    4.144 closest distance to " O   HOH Z 427 " =    2.991
peak=    4.127 closest distance to " O   HOH Z 234 " =    3.830
peak=    4.081 closest distance to " CB  ASP A 124 " =    0.788
peak=    4.077 closest distance to " OD1 ASN A  69 " =    2.580
peak=    4.059 closest distance to " O   HOH Z 272 " =    1.854
peak=    4.021 closest distance to " CB  SER A 216 " =    0.843
peak=    4.021 closest distance to " O   HOH Z 303 " =    2.175
peak=    4.006 closest distance to " CA  ASN A 215 " =    1.146
peak=    4.006 closest distance to " CB  ASN A  39 " =    0.889
peak=    4.000 closest distance to " O   HOH Z  78 " =    2.132
peak=    3.994 closest distance to " CB  VAL A 265 " =    1.246
peak=    3.991 closest distance to " O   HOH Z 261 " =    2.012
peak=    3.988 closest distance to " O   HOH Z 368 " =    2.061
peak=    3.987 closest distance to " O   HOH Z 316 " =    3.124
peak=    3.981 closest distance to " CB  ASP A 140 " =    0.932
peak=    3.970 closest distance to " CB  SER A 212 " =    1.178
peak=    3.963 closest distance to " CG  LEU A 167 " =    1.246
peak=    3.953 closest distance to " CA  THR A 264 " =    0.879
peak=    3.950 closest distance to " CE  LYS A  76 " =    0.858
peak=    3.949 closest distance to " O   HOH Z 209 " =    2.298
peak=    3.929 closest distance to " NH1AARG A 145 " =    1.238
peak=    3.927 closest distance to " CA  SER A  87 " =    0.995
peak=    3.916 closest distance to " NZ  LYS A 117 " =    3.188
peak=    3.904 closest distance to " O   HOH Z 158 " =    3.022
peak=    3.894 closest distance to " O   HOH Z  61 " =    1.595
peak=    3.892 closest distance to " CB  GLU A 152 " =    1.252
peak=    3.880 closest distance to " CB  ALA A 104 " =    0.710
peak=    3.873 closest distance to " ND1 HIS A  86 " =    1.707
peak=    3.869 closest distance to " CD  ARG A 269 " =    0.908
peak=    3.865 closest distance to " O   HOH Z   1 " =    2.009
peak=    3.840 closest distance to " CB  VAL A 202 " =    1.607
peak=    3.834 closest distance to " CG2 THR A 221 " =    0.996
peak=    3.829 closest distance to " O   HOH Z 180 " =    2.129
peak=    3.828 closest distance to " NH2 ARG A 156 " =    1.207
peak=    3.808 closest distance to " CB  ASN A 142 " =    0.992
peak=    3.790 closest distance to " CD  ARG A  66 " =    2.251
peak=    3.789 closest distance to " O   HOH Z 214 " =    2.059
peak=    3.765 closest distance to " O   HOH Z 346 " =    1.667
peak=    3.761 closest distance to " O   HOH Z 133 " =    2.378
peak=    3.759 closest distance to " O   TYR A 116 " =    1.285
peak=    3.739 closest distance to " O   HOH Z 193 " =    1.932
peak=    3.732 closest distance to " CB  GLU A  46 " =    0.956
peak=    3.724 closest distance to " CD  LYS A 166 " =    1.229
peak=    3.718 closest distance to " O   HOH Z 203 " =    1.842
peak=    3.713 closest distance to " CB  SER A   3 " =    1.347
peak=    3.708 closest distance to " CD BLYS A 290 " =    0.985
peak=    3.707 closest distance to " CB  LEU A 143 " =    1.140
peak=    3.704 closest distance to " CB  ALA A  34 " =    1.020
peak=    3.676 closest distance to " ND2 ASN A 249 " =    1.948
peak=    3.673 closest distance to " CG1 ILE A  33 " =    1.286
peak=    3.673 closest distance to " O   HOH Z  21 " =    1.766
peak=    3.661 closest distance to " O   HOH Z 193 " =    1.699
peak=    3.660 closest distance to " CA  TYR A  30 " =    1.068
peak=    3.654 closest distance to " CB  TYR A 116 " =    0.808
peak=    3.649 closest distance to " O   HOH Z 344 " =    3.150
peak=    3.648 closest distance to " O   HOH Z 368 " =    3.594
peak=    3.647 closest distance to " O   HOH Z 135 " =    1.656
peak=    3.640 closest distance to " ND2 ASN A 249 " =    0.872
peak=    3.638 closest distance to " N   ASN A 127 " =    1.251
peak=    3.635 closest distance to " O   HOH Z 353 " =    2.683
peak=    3.635 closest distance to " CD2 TRP A 179 " =    1.300
peak=    3.633 closest distance to " CB  MET A  40 " =    0.777
peak=    3.630 closest distance to " CA  THR A 221 " =    0.943
peak=    3.629 closest distance to " O   HOH Z   9 " =    2.017
peak=    3.627 closest distance to " CA  ARG A 195 " =    1.256
peak=    3.619 closest distance to " O   HOH Z 132 " =    2.571
peak=    3.613 closest distance to " CB  ILE A 120 " =    1.209
peak=    3.608 closest distance to " O   HOH Z  10 " =    1.853
peak=    3.605 closest distance to " CB  GLU A 277 " =    3.668
peak=    3.602 closest distance to " O   THR A 251 " =    1.150
peak=    3.595 closest distance to " O   HOH Z  68 " =    2.159
peak=    3.595 closest distance to " O   HOH Z 411 " =    3.804
peak=    3.583 closest distance to " CB  SER A 210 " =    0.756
peak=    3.583 closest distance to " O   HOH Z  88 " =    3.511
peak=    3.579 closest distance to " O   HOH Z 419 " =    1.965
peak=    3.576 closest distance to " CA  ALA A  51 " =    0.909
peak=    3.569 closest distance to " CB  MET A  47 " =    0.994
peak=    3.565 closest distance to " O   HOH Z 285 " =    2.722
peak=    3.562 closest distance to " CA  MET A  40 " =    1.161
peak=    3.554 closest distance to " O   HOH Z 313 " =    1.898
peak=    3.553 closest distance to " O   SER A  87 " =    2.255
peak=    3.547 closest distance to " N   PHE A 130 " =    1.189
peak=    3.539 closest distance to " O   HOH Z 386 " =    3.167
peak=    3.539 closest distance to " O   HOH Z  54 " =    2.453
peak=    3.530 closest distance to " N   ASN A  39 " =    1.272
peak=    3.529 closest distance to " CZ  PHE A 192 " =    0.922
peak=    3.525 closest distance to " O   MET A 105 " =    1.824
peak=    3.524 closest distance to " O   HOH Z 426 " =    1.821
peak=    3.509 closest distance to " CA  ALA A  21 " =    1.170
peak=    3.508 closest distance to " O   HOH Z 291 " =    1.574
peak=    3.506 closest distance to " CG1 VAL A 153 " =    0.945
peak=    3.505 closest distance to " O   HOH Z 172 " =    3.259
peak=    3.489 closest distance to " OD1BASN A 224 " =    2.384
peak=    3.487 closest distance to " CA  ARG A  36 " =    1.128
peak=    3.476 closest distance to " OD2 ASP A 286 " =    2.904
peak=    3.474 closest distance to " NE2 HIS A 207 " =    1.282
peak=    3.471 closest distance to " O   HOH Z 213 " =    1.958
peak=    3.470 closest distance to " CB  ALA A 291 " =    1.248
peak=    3.470 closest distance to " CA  ALA A 154 " =    0.983
peak=    3.467 closest distance to " O   HOH Z  43 " =    1.768
peak=    3.463 closest distance to " CD  ARG A 219 " =    1.106
peak=    3.463 closest distance to " CG2 ILE A 120 " =    1.131
peak=    3.461 closest distance to " CB  TRP A 179 " =    1.420
peak=    3.459 closest distance to " CA  ALA A 233 " =    1.336
peak=    3.455 closest distance to " N   ARG A 156 " =    1.387
peak=    3.455 closest distance to " CB  LEU A  83 " =    0.772
peak=    3.454 closest distance to " CB  GLN A  88 " =    1.260
peak=    3.451 closest distance to " CA  ALA A 158 " =    1.187
peak=    3.450 closest distance to " O   HOH Z 437 " =    1.274
peak=    3.450 closest distance to " CG2AVAL A  72 " =    1.673
peak=    3.441 closest distance to " O   HOH Z 371 " =    2.977
peak=    3.438 closest distance to " CB  ALA A   1 " =    4.663
peak=    3.435 closest distance to " O   HOH Z  53 " =    2.565
peak=    3.417 closest distance to " CB  ASN A 110 " =    1.096
peak=    3.412 closest distance to " O   HOH Z 166 " =    3.869
peak=    3.411 closest distance to " O   HOH Z 391 " =    2.893
peak=    3.408 closest distance to " ND2 ASN A 110 " =    1.749
peak=    3.406 closest distance to " CD2 LEU A 255 " =    1.598
peak=    3.403 closest distance to " O   HOH Z 128 " =    2.155
peak=    3.401 closest distance to " CA  MET A 105 " =    0.995
peak=    3.401 closest distance to " O  BHOH Z 338 " =    2.340
peak=    3.400 closest distance to " O   HOH Z 402 " =    1.438
peak=    3.399 closest distance to " O   HOH Z 305 " =    3.632
peak=    3.385 closest distance to " O   THR A 220 " =    1.252
peak=    3.375 closest distance to " O   HOH Z 280 " =    3.049
peak=    3.374 closest distance to " CZ  PHE A 208 " =    1.092
peak=    3.374 closest distance to " O   HOH Z 403 " =    1.668
peak=    3.370 closest distance to " CZ  PHE A  38 " =    1.281
peak=    3.367 closest distance to " CG  ARG A 159 " =    0.903
peak=    3.364 closest distance to " OG  SER A  22 " =    2.830
peak=    3.358 closest distance to " CB  ALA A 114 " =    0.766
peak=    3.357 closest distance to " O   HOH Z 423 " =    1.484
peak=    3.355 closest distance to " CB  SER A 141 " =    0.983
peak=    3.353 closest distance to " CB  ALA A 248 " =    1.262
peak=    3.349 closest distance to " CB  THR A  82 " =    1.415
peak=    3.349 closest distance to " CB  ARG A 139 " =    0.918
peak=    3.348 closest distance to " CA  ILE A 234 " =    0.929
peak=    3.346 closest distance to " O   HOH Z 234 " =    1.768
peak=    3.345 closest distance to " O   HOH Z 409 " =    2.732
peak=    3.344 closest distance to " CB  ALA A 242 " =    0.839
peak=    3.343 closest distance to " CD1 LEU A  96 " =    0.799
peak=    3.342 closest distance to " O   HOH Z 128 " =    2.359
peak=    3.340 closest distance to " O   HOH Z 425 " =    1.228
peak=    3.338 closest distance to " CA  ASN A 217 " =    1.246
peak=    3.332 closest distance to " CB  HIS A 108 " =    0.789
peak=    3.327 closest distance to " O   HOH Z  40 " =    1.987
peak=    3.316 closest distance to " O   HOH Z 273 " =    2.784
peak=    3.310 closest distance to " O   HOH Z 133 " =    1.664
peak=    3.310 closest distance to " CD2 LEU A 297 " =    0.879
peak=    3.310 closest distance to " CA  ALA A 160 " =    0.956
peak=    3.308 closest distance to " O   HOH Z 147 " =    1.750
peak=    3.304 closest distance to " OE1 GLU A 236 " =    1.208
peak=    3.303 closest distance to " O   HOH Z 193 " =    2.021
peak=    3.303 closest distance to " CB  THR A 235 " =    1.156
peak=    3.301 closest distance to " CE1 TYR A 186 " =    1.392
peak=    3.300 closest distance to " O   HOH Z 219 " =    1.855
peak=    3.300 closest distance to " O   HOH Z 329 " =    3.859
peak=    3.297 closest distance to " O   HOH Z 245 " =    1.274
peak=    3.297 closest distance to " CB  TYR A 169 " =    1.234
peak=    3.295 closest distance to " CA  LEU A 282 " =    1.040
peak=    3.294 closest distance to " CA  ARG A 102 " =    1.133
peak=    3.289 closest distance to " O   HOH Z 406 " =    1.575
peak=    3.288 closest distance to " CB  THR A 157 " =    1.112
peak=    3.285 closest distance to " CB  LYS A 117 " =    1.213
peak=    3.281 closest distance to " O   HOH Z 108 " =    2.635
peak=    3.281 closest distance to " O   HOH Z 261 " =    2.299
peak=    3.278 closest distance to " O   HOH Z 227 " =    1.662
peak=    3.271 closest distance to " O   HOH Z 294 " =    1.544
peak=    3.270 closest distance to " O   GLN A 278 " =    1.475
peak=    3.268 closest distance to " O   HOH Z 425 " =    2.106
peak=    3.267 closest distance to " CB  SER A  62 " =    1.171
peak=    3.265 closest distance to " O   HOH Z 213 " =    2.477
peak=    3.257 closest distance to " CB  PRO A  90 " =    1.175
peak=    3.246 closest distance to " CB  ASP A 171 " =    0.757
peak=    3.241 closest distance to " O   HOH Z  44 " =    3.073
peak=    3.240 closest distance to " N   GLY A  98 " =    1.084
peak=    3.240 closest distance to " CB  GLN A 103 " =    0.871
peak=    3.239 closest distance to " O   HOH Z  93 " =    2.876
peak=    3.239 closest distance to " CB  PRO A 198 " =    0.908
peak=    3.237 closest distance to " O   HOH Z 365 " =    2.948
peak=    3.237 closest distance to " CA  GLY A 267 " =    1.151
peak=    3.236 closest distance to " O   HOH Z 175 " =    2.256
peak=    3.235 closest distance to " CA  ALA A 291 " =    0.844
peak=    3.231 closest distance to " O   HOH Z 152 " =    2.325
peak=    3.231 closest distance to " O   HOH Z 185 " =    1.814
peak=    3.227 closest distance to " CG  MET A 113 " =    1.352
peak=    3.226 closest distance to " N   SER A 146 " =    1.709
peak=    3.226 closest distance to " CG1 ILE A 120 " =    1.028
peak=    3.226 closest distance to " O   HOH Z  59 " =    1.863
peak=    3.225 closest distance to " NH2BARG A 145 " =    2.104
peak=    3.225 closest distance to " CD1 ILE A 106 " =    0.783
peak=    3.225 closest distance to " O   HOH Z  20 " =    1.615
peak=    3.219 closest distance to " CA  TYR A 116 " =    1.352
peak=    3.218 closest distance to " CZ3 TRP A 266 " =    1.084
peak=    3.215 closest distance to " O   HOH Z  61 " =    1.495
peak=    3.212 closest distance to " CB  ALA A 248 " =    1.021
peak=    3.210 closest distance to " CB  LYS A 193 " =    1.013
peak=    3.209 closest distance to " CA  LYS A 290 " =    1.237
peak=    3.208 closest distance to " CB  ALA A 137 " =    1.052
peak=    3.207 closest distance to " O   HOH Z 271 " =    2.386
peak=    3.205 closest distance to " CD1AILE A 234 " =    0.941
peak=    3.203 closest distance to " N   VAL A 296 " =    1.730
peak=    3.201 closest distance to " O   HOH Z   1 " =    1.709
peak=    3.199 closest distance to " O   HOH Z 302 " =    1.914
peak=    3.195 closest distance to " O   ASN A 209 " =    1.334
peak=    3.194 closest distance to " CB  ASN A 215 " =    1.114
peak=    3.194 closest distance to " CG1 ILE A 151 " =    1.056
peak=    3.192 closest distance to " OG BSER A 164 " =    2.409
peak=    3.192 closest distance to " O   HOH Z 411 " =    1.751
peak=    3.191 closest distance to " N   CYS A 260 " =    0.798
peak=    3.189 closest distance to " O   HOH Z 327 " =    1.890
peak=    3.177 closest distance to " CG2BVAL A  41 " =    0.876
peak=    3.174 closest distance to " O   HOH Z 109 " =    2.628
peak=    3.173 closest distance to " O   HOH Z  66 " =    2.110
peak=    3.173 closest distance to " O   HOH Z 345 " =    3.565
peak=    3.172 closest distance to " O   HOH Z 359 " =    4.081
peak=    3.171 closest distance to " O   HOH Z 290 " =    1.019
peak=    3.171 closest distance to " CG  GLN A  89 " =    1.484
peak=    3.169 closest distance to " OG  SER A 206 " =    1.193
peak=    3.168 closest distance to " O   HOH Z 325 " =    3.973
peak=    3.167 closest distance to " ND1 HIS A  81 " =    1.664
peak=    3.164 closest distance to " N   VAL A 126 " =    1.336
peak=    3.160 closest distance to " CD2 HIS A  81 " =    1.112
peak=    3.158 closest distance to " O   HOH Z 339 " =    2.274
peak=    3.153 closest distance to " CB  PHE A  16 " =    1.017
peak=    3.152 closest distance to " N   GLN A 278 " =    1.218
peak=    3.149 closest distance to " O   HOH Z 371 " =    1.778
peak=    3.143 closest distance to " OD1 ASP A 238 " =    0.976
peak=    3.140 closest distance to " NZ  LYS A  76 " =    1.576
peak=    3.139 closest distance to " CB  ALA A   9 " =    1.568
peak=    3.135 closest distance to " O   HOH Z 183 " =    1.370
peak=    3.126 closest distance to " N   ASN A 252 " =    1.466
peak=    3.126 closest distance to " CB  ALA A 161 " =    0.858
peak=    3.126 closest distance to " O   HOH Z 216 " =    2.906
peak=    3.125 closest distance to " O   HOH Z 379 " =    3.537
peak=    3.122 closest distance to " CD  PRO A 243 " =    1.496
peak=    3.118 closest distance to " CG  GLN A 278 " =    1.349
peak=    3.113 closest distance to " OG  SER A  62 " =    3.024
peak=    3.113 closest distance to " O   HOH Z 326 " =    2.436
peak=    3.112 closest distance to " CB  TRP A 150 " =    1.365
peak=    3.111 closest distance to " N   SER A 135 " =    1.302
peak=    3.107 closest distance to " CB  ARG A 138 " =    1.012
peak=    3.105 closest distance to " O   HOH Z  88 " =    2.096
peak=    3.104 closest distance to " CA  VAL A 125 " =    1.083
peak=    3.104 closest distance to " O   HOH Z 188 " =    2.071
peak=    3.102 closest distance to " CB  VAL A 268 " =    0.847
peak=    3.100 closest distance to " CD  LYS A 119 " =    1.186
peak=    3.098 closest distance to " CA  ILE A 106 " =    0.818
peak=    3.097 closest distance to " CA  GLU A  46 " =    0.781
peak=    3.089 closest distance to " O   ALA A 158 " =    1.312
peak=    3.089 closest distance to " NZ  LYS A  48 " =    1.345
peak=    3.083 closest distance to " O   HOH Z 373 " =    1.552
peak=    3.076 closest distance to " O   HOH Z 359 " =    1.373
peak=    3.074 closest distance to " CB  ALA A  43 " =    0.923
peak=    3.063 closest distance to " NH1BARG A 145 " =    1.005
peak=    3.049 closest distance to " CA  THR A 221 " =    1.428
peak=    3.049 closest distance to " O   HOH Z 130 " =    3.845
peak=    3.033 closest distance to " CA  GLY A 136 " =    0.989
peak=    3.024 closest distance to " CG2 ILE A  20 " =    1.302

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.763 - 5.623
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 200
   mapped sites are within: 0.763 - 5.623

peak=   -4.480 closest distance to " CG1 VAL A 112 " =    2.655
peak=   -4.478 closest distance to " CD  ARG A 156 " =    2.032
peak=   -4.465 closest distance to " CB  PRO A 243 " =    2.633
peak=   -4.287 closest distance to " O   HOH Z 266 " =    5.251
peak=   -4.270 closest distance to " O   HOH Z 231 " =    2.184
peak=   -4.263 closest distance to " CD  ARG A  14 " =    3.418
peak=   -4.244 closest distance to " CG  GLN A 223 " =    1.966
peak=   -4.222 closest distance to " O   PRO A 198 " =    1.227
peak=   -4.200 closest distance to " O   HOH Z 377 " =    2.001
peak=   -4.146 closest distance to " O   VAL A  67 " =    2.637
peak=   -4.117 closest distance to " CZ3 TRP A 179 " =    1.135
peak=   -4.075 closest distance to " OG BSER A 134 " =    1.239
peak=   -4.031 closest distance to " CD  GLN A  58 " =    0.991
peak=   -4.026 closest distance to " CE2 TYR A  30 " =    2.788
peak=   -3.952 closest distance to " O   HOH Z 198 " =    2.120
peak=   -3.945 closest distance to " O   HOH Z  38 " =    1.327
peak=   -3.934 closest distance to " CG  MET A 105 " =    0.952
peak=   -3.926 closest distance to " N   ALA A  43 " =    2.582
peak=   -3.922 closest distance to " O   HOH Z 389 " =    1.959
peak=   -3.911 closest distance to " O   HOH Z 372 " =    2.416
peak=   -3.886 closest distance to " O   HOH Z 351 " =    1.446
peak=   -3.865 closest distance to " CB  ALA A 291 " =    2.271
peak=   -3.846 closest distance to " O   HOH Z 435 " =    2.831
peak=   -3.830 closest distance to " O   HOH Z 290 " =    1.244
peak=   -3.818 closest distance to " NH2AARG A 275 " =    5.489
peak=   -3.788 closest distance to " O   HOH Z  10 " =    1.491
peak=   -3.780 closest distance to " CG1 VAL A 112 " =    2.965
peak=   -3.779 closest distance to " O   ILE A 109 " =    2.612
peak=   -3.772 closest distance to " C   HIS A 108 " =    1.111
peak=   -3.731 closest distance to " O   HOH Z 185 " =    2.289
peak=   -3.727 closest distance to " N   ASP A 171 " =    2.426
peak=   -3.720 closest distance to " O   HOH Z  73 " =    2.126
peak=   -3.720 closest distance to " CG2 ILE A 263 " =    2.370
peak=   -3.701 closest distance to " O   HOH Z 114 " =    3.266
peak=   -3.695 closest distance to " O   HOH Z 313 " =    1.926
peak=   -3.692 closest distance to " CE  MET A 105 " =    2.356
peak=   -3.691 closest distance to " CB  ALA A  43 " =    2.622
peak=   -3.686 closest distance to " O   HOH Z 394 " =    1.445
peak=   -3.667 closest distance to " O   HOH Z  43 " =    1.655
peak=   -3.666 closest distance to " ND2 ASN A  45 " =    1.801
peak=   -3.658 closest distance to " O   HOH Z 407 " =    3.291
peak=   -3.651 closest distance to " CB  ASN A  39 " =    2.279
peak=   -3.649 closest distance to " O   HOH Z 126 " =    1.892
peak=   -3.647 closest distance to " CA  GLY A 203 " =    2.417
peak=   -3.639 closest distance to " N   THR A 157 " =    1.546
peak=   -3.637 closest distance to " CD2 TYR A 293 " =    2.016
peak=   -3.634 closest distance to " O   HOH Z  52 " =    1.298
peak=   -3.628 closest distance to " ND2 ASN A  45 " =    1.089
peak=   -3.621 closest distance to " CD  ARG A 139 " =    1.564
peak=   -3.619 closest distance to " CD1 PHE A  59 " =    1.874
peak=   -3.615 closest distance to " OG  SER A  97 " =    2.220
peak=   -3.607 closest distance to " OD1 ASN A 148 " =    1.489
peak=   -3.605 closest distance to " O   VAL A 189 " =    2.567
peak=   -3.605 closest distance to " C   ASN A 285 " =    2.493
peak=   -3.587 closest distance to " O   HOH Z  11 " =    1.777
peak=   -3.575 closest distance to " O   GLY A  17 " =    1.294
peak=   -3.570 closest distance to " O   GLY A 211 " =    1.366
peak=   -3.563 closest distance to " O   TYR A 247 " =    2.870
peak=   -3.561 closest distance to " O   HOH Z 353 " =    2.125
peak=   -3.553 closest distance to " CA  GLY A 241 " =    3.151
peak=   -3.549 closest distance to " CG1 VAL A 250 " =    2.663
peak=   -3.538 closest distance to " ND2 ASN A 249 " =    2.158
peak=   -3.535 closest distance to " CG  ASP A 231 " =    0.763
peak=   -3.534 closest distance to " CD2 PHE A 192 " =    2.026
peak=   -3.533 closest distance to " C   LEU A 222 " =    0.767
peak=   -3.518 closest distance to " O   HOH Z  51 " =    1.674
peak=   -3.513 closest distance to " CA  GLY A 241 " =    2.300
peak=   -3.511 closest distance to " O   HOH Z 426 " =    1.614
peak=   -3.493 closest distance to " CB  ALA A 291 " =    2.209
peak=   -3.489 closest distance to " CG  ARG A 269 " =    2.564
peak=   -3.483 closest distance to " C   ALA A 158 " =    1.504
peak=   -3.480 closest distance to " CG2 THR A 178 " =    2.278
peak=   -3.462 closest distance to " O   HOH Z 198 " =    1.479
peak=   -3.460 closest distance to " OXT GLY A 302 " =    2.961
peak=   -3.457 closest distance to " CD1 LEU A 101 " =    2.354
peak=   -3.450 closest distance to " O   HOH Z 196 " =    2.164
peak=   -3.449 closest distance to " OE1 GLN A  88 " =    1.125
peak=   -3.442 closest distance to " CB  PRO A 163 " =    2.545
peak=   -3.441 closest distance to " O   HOH Z 253 " =    4.054
peak=   -3.437 closest distance to " OD2 ASP A 171 " =    1.850
peak=   -3.428 closest distance to " CD1 LEU A 228 " =    2.372
peak=   -3.427 closest distance to " CB  ALA A 248 " =    2.045
peak=   -3.426 closest distance to " O   PRO A 163 " =    2.044
peak=   -3.421 closest distance to " CZ  TYR A 169 " =    1.695
peak=   -3.421 closest distance to " CA  GLY A  98 " =    1.923
peak=   -3.413 closest distance to " O   HOH Z 102 " =    1.609
peak=   -3.412 closest distance to " CZ BARG A 275 " =    1.829
peak=   -3.411 closest distance to " O   HOH Z  60 " =    2.487
peak=   -3.411 closest distance to " NH2 ARG A 159 " =    2.370
peak=   -3.399 closest distance to " O   PHE A 218 " =    1.518
peak=   -3.394 closest distance to " O   HOH Z 211 " =    1.625
peak=   -3.390 closest distance to " O   ALA A 180 " =    1.410
peak=   -3.387 closest distance to " CB  TYR A  15 " =    2.202
peak=   -3.386 closest distance to " CG  TRP A 266 " =    1.828
peak=   -3.384 closest distance to " O   HOH Z 298 " =    2.462
peak=   -3.383 closest distance to " CB  ALA A 131 " =    2.108
peak=   -3.382 closest distance to " CD  ARG A 195 " =    5.163
peak=   -3.380 closest distance to " CB  TRP A  85 " =    2.440
peak=   -3.376 closest distance to " CB  CYS A 254 " =    2.314
peak=   -3.365 closest distance to " O   HOH Z 359 " =    3.241
peak=   -3.364 closest distance to " N   SER A 212 " =    1.776
peak=   -3.361 closest distance to " CA  ASP A 298 " =    1.086
peak=   -3.360 closest distance to " CG  PHE A 283 " =    2.728
peak=   -3.359 closest distance to " N   SER A 276 " =    1.266
peak=   -3.359 closest distance to " CA  ASP A  27 " =    2.470
peak=   -3.352 closest distance to " OD1 ASN A 187 " =    1.570
peak=   -3.343 closest distance to " NH2 ARG A  79 " =    1.542
peak=   -3.342 closest distance to " CD  GLU A 236 " =    1.083
peak=   -3.341 closest distance to " CD2 TYR A 247 " =    2.435
peak=   -3.341 closest distance to " CB  ALA A 248 " =    2.514
peak=   -3.338 closest distance to " OD1 ASP A 191 " =    1.674
peak=   -3.331 closest distance to " CB  PRO A  54 " =    2.513
peak=   -3.330 closest distance to " OG BSER A 134 " =    1.791
peak=   -3.330 closest distance to " CA  TRP A 274 " =    1.423
peak=   -3.329 closest distance to " CG2 ILE A  49 " =    2.751
peak=   -3.328 closest distance to " CG  GLU A 277 " =    1.215
peak=   -3.326 closest distance to " CE BMET A  47 " =    1.695
peak=   -3.324 closest distance to " OD1 ASP A 171 " =    1.616
peak=   -3.324 closest distance to " CA  VAL A  67 " =    2.962
peak=   -3.322 closest distance to " O   HOH Z 114 " =    1.568
peak=   -3.315 closest distance to " O   HOH Z 111 " =    1.914
peak=   -3.309 closest distance to " C   PHE A  59 " =    1.304
peak=   -3.309 closest distance to " O   HOH Z 281 " =    2.684
peak=   -3.307 closest distance to " O   ALA A  34 " =    2.633
peak=   -3.303 closest distance to " CZ  PHE A  59 " =    1.577
peak=   -3.285 closest distance to " CB  ASP A 132 " =    2.279
peak=   -3.285 closest distance to " CB  ASP A 286 " =    2.090
peak=   -3.281 closest distance to " O   HOH Z 298 " =    1.209
peak=   -3.280 closest distance to " CG1 VAL A 125 " =    1.884
peak=   -3.279 closest distance to " NH1 ARG A 195 " =    2.610
peak=   -3.278 closest distance to " NE2 GLN A 194 " =    1.782
peak=   -3.270 closest distance to " CE2 PHE A  61 " =    2.632
peak=   -3.270 closest distance to " O   TRP A  70 " =    1.434
peak=   -3.268 closest distance to " ND2 ASN A  60 " =    1.429
peak=   -3.267 closest distance to " O   HOH Z 166 " =    1.925
peak=   -3.262 closest distance to " C   GLY A  13 " =    0.947
peak=   -3.261 closest distance to " CB  ALA A   9 " =    2.533
peak=   -3.260 closest distance to " O   LEU A 101 " =    2.686
peak=   -3.259 closest distance to " CB  PHE A 208 " =    2.257
peak=   -3.259 closest distance to " NH2 ARG A  79 " =    2.010
peak=   -3.256 closest distance to " CB  CYS A 201 " =    2.623
peak=   -3.255 closest distance to " CE2 PHE A 218 " =    2.466
peak=   -3.254 closest distance to " O   HOH Z 311 " =    3.701
peak=   -3.251 closest distance to " C   LEU A 143 " =    1.255
peak=   -3.248 closest distance to " CD1 LEU A 297 " =    2.489
peak=   -3.241 closest distance to " O   HOH Z 275 " =    1.548
peak=   -3.239 closest distance to " O   SER A  62 " =    2.192
peak=   -3.231 closest distance to " CE3 TRP A 150 " =    2.136
peak=   -3.231 closest distance to " O   HOH Z  13 " =    1.545
peak=   -3.222 closest distance to " CD2 PHE A  61 " =    2.007
peak=   -3.220 closest distance to " O   SER A 135 " =    1.395
peak=   -3.215 closest distance to " O   HOH Z 295 " =    1.595
peak=   -3.212 closest distance to " OH  TYR A 247 " =    2.138
peak=   -3.212 closest distance to " O   HOH Z 377 " =    0.924
peak=   -3.209 closest distance to " O   HOH Z 393 " =    1.467
peak=   -3.199 closest distance to " O   HOH Z 177 " =    1.692
peak=   -3.198 closest distance to " CG1 VAL A 197 " =    2.259
peak=   -3.194 closest distance to " O   HOH Z  63 " =    1.551
peak=   -3.192 closest distance to " CE  LYS A  76 " =    2.661
peak=   -3.189 closest distance to " N   ALA A 248 " =    1.637
peak=   -3.185 closest distance to " O   HOH Z 191 " =    5.623
peak=   -3.184 closest distance to " CB  ALA A 129 " =    2.430
peak=   -3.183 closest distance to " O   HOH Z 292 " =    1.713
peak=   -3.180 closest distance to " CG  GLN A  88 " =    0.867
peak=   -3.180 closest distance to " O   ALA A  10 " =    1.637
peak=   -3.175 closest distance to " ND2 ASN A 187 " =    1.627
peak=   -3.175 closest distance to " O   HOH Z 123 " =    2.522
peak=   -3.169 closest distance to " CD2 LEU A 222 " =    2.173
peak=   -3.168 closest distance to " SD  MET A 188 " =    2.347
peak=   -3.159 closest distance to " O   HOH Z  90 " =    1.608
peak=   -3.155 closest distance to " O   HOH Z 176 " =    0.891
peak=   -3.154 closest distance to " OG  SER A  87 " =    1.442
peak=   -3.154 closest distance to " O   HOH Z 423 " =    1.256
peak=   -3.153 closest distance to " O   VAL A 189 " =    1.567
peak=   -3.152 closest distance to " CG  PRO A 163 " =    2.497
peak=   -3.151 closest distance to " O   HOH Z 103 " =    1.900
peak=   -3.144 closest distance to " O   HOH Z 184 " =    1.756
peak=   -3.143 closest distance to " NE2 GLN A  88 " =    1.906
peak=   -3.142 closest distance to " CA  SER A 135 " =    1.317
peak=   -3.137 closest distance to " C   MET A 188 " =    1.378
peak=   -3.135 closest distance to " OG  SER A 206 " =    1.862
peak=   -3.126 closest distance to " CG2 ILE A  20 " =    2.834
peak=   -3.125 closest distance to " O   HOH Z  51 " =    1.296
peak=   -3.125 closest distance to " O   HOH Z 207 " =    2.133
peak=   -3.121 closest distance to " O   HOH Z 357 " =    2.033
peak=   -3.103 closest distance to " O   HOH Z 174 " =    2.697
peak=   -3.103 closest distance to " O   HOH Z 317 " =    1.592
peak=   -3.102 closest distance to " O   HOH Z 282 " =    5.061
peak=   -3.101 closest distance to " CB  ASP A 132 " =    2.361
peak=   -3.099 closest distance to " O   HOH Z 350 " =    1.870
peak=   -3.088 closest distance to " O   HOH Z 128 " =    2.593
peak=   -3.087 closest distance to " CG2 VAL A 189 " =    2.023
peak=   -3.078 closest distance to " O   HOH Z 244 " =    2.047
peak=   -3.070 closest distance to " O   GLN A 240 " =    2.433
peak=   -3.048 closest distance to " O   HOH Z 283 " =    5.540
peak=   -3.043 closest distance to " O   SER A  22 " =    2.379
peak=   -3.042 closest distance to " OD1AASN A 224 " =    1.759
peak=   -3.041 closest distance to " N   LYS A 166 " =    2.006
peak=   -3.006 closest distance to " C   GLN A  58 " =    1.974

================= 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    :  0.2965 0.2922   5.963984e+00   5.959867e+00
   1_bss:  0.2825 0.2809   5.938988e+00   5.932873e+00
   1_xyz:  0.1591 0.1796   5.398934e+00   5.500901e+00
   1_adp:  0.1442 0.1843   5.340793e+00   5.527122e+00
   1_occ:  0.1439 0.1840   5.339176e+00   5.526777e+00
   2_bss:  0.1428 0.1824   5.337794e+00   5.525111e+00
   2_xyz:  0.1174 0.1615   5.181877e+00   5.412844e+00
   2_adp:  0.1155 0.1569   5.159748e+00   5.387883e+00
   2_occ:  0.1153 0.1569   5.159293e+00   5.387898e+00
   3_bss:  0.1152 0.1568   5.158521e+00   5.386883e+00
   3_xyz:  0.1142 0.1572   5.157468e+00   5.389435e+00
   3_adp:  0.1138 0.1566   5.153594e+00   5.387008e+00
   3_occ:  0.1137 0.1566   5.153531e+00   5.387204e+00
   4_bss:  0.1138 0.1554   5.151706e+00   5.382034e+00
   4_xyz:  0.1103 0.1554   5.133900e+00   5.378678e+00
   4_adp:  0.1086 0.1566   5.128726e+00   5.382143e+00
   4_occ:  0.1086 0.1566   5.128956e+00   5.382666e+00
   5_bss:  0.1084 0.1566   5.128827e+00   5.382633e+00
   5_xyz:  0.1120 0.1588   5.153517e+00   5.398961e+00
   5_adp:  0.1124 0.1575   5.150073e+00   5.391490e+00
   5_occ:  0.1124 0.1576   5.150294e+00   5.391987e+00
   5_bss:  0.1123 0.1575   5.150391e+00   5.392014e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.328  56.856   0.201  -2.327  -0.973  -0.000  -0.000  -0.000
   1_xyz:  0.328  56.856   0.201  -2.327  -0.973  -0.000  -0.000  -0.000
   1_adp:  0.328  56.856   0.201  -2.327  -0.973  -0.000  -0.000  -0.000
   1_occ:  0.328  56.856   0.201  -2.327  -0.973  -0.000  -0.000  -0.000
   2_bss:  0.334  61.681  -1.888  -2.936  -1.562  -0.000  -0.000  -0.000
   2_xyz:  0.334  61.681  -1.888  -2.936  -1.562  -0.000  -0.000  -0.000
   2_adp:  0.334  61.681  -1.888  -2.936  -1.562  -0.000  -0.000  -0.000
   2_occ:  0.334  61.681  -1.888  -2.936  -1.562  -0.000  -0.000  -0.000
   3_bss:  0.334  61.681  -2.292  -2.822  -1.446  -0.000  -0.000  -0.000
   3_xyz:  0.334  61.681  -2.292  -2.822  -1.446  -0.000  -0.000  -0.000
   3_adp:  0.334  61.681  -2.292  -2.822  -1.446  -0.000  -0.000  -0.000
   3_occ:  0.334  61.681  -2.292  -2.822  -1.446  -0.000  -0.000  -0.000
   4_bss:  0.334  61.681  -2.470  -2.800  -1.428  -0.000  -0.000  -0.000
   4_xyz:  0.334  61.681  -2.470  -2.800  -1.428  -0.000  -0.000  -0.000
   4_adp:  0.334  61.681  -2.470  -2.800  -1.428  -0.000  -0.000  -0.000
   4_occ:  0.334  61.681  -2.470  -2.800  -1.428  -0.000  -0.000  -0.000
   5_bss:  0.323  57.891  -2.187  -2.501  -1.154  -0.000  -0.000  -0.000
   5_xyz:  0.323  57.891  -2.187  -2.501  -1.154  -0.000  -0.000  -0.000
   5_adp:  0.323  57.891  -2.187  -2.501  -1.154  -0.000  -0.000  -0.000
   5_occ:  0.323  57.891  -2.187  -2.501  -1.154  -0.000  -0.000  -0.000
   5_bss:  0.323  57.856  -2.061  -2.324  -0.978  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  29.402 0.7683  0.9291    24084.731
   1_bss:  28.354 0.7780  0.9115    21644.757
   1_xyz:  16.320 0.8965  1.0040     8124.446
   1_adp:  16.977 0.8902  1.0046     8485.841
   1_occ:  16.953 0.8903  1.0042     8459.786
   2_bss:  16.887 0.8910  0.9659     8450.669
   2_xyz:  14.560 0.9103  0.9760     6693.047
   2_adp:  13.962 0.9154  0.9761     6383.621
   2_occ:  13.963 0.9154  0.9759     6376.768
   3_bss:  13.944 0.9155  0.9738     6361.299
   3_xyz:  13.884 0.9164  0.9725     6407.530
   3_adp:  13.806 0.9171  0.9690     6375.697
   3_occ:  13.812 0.9170  0.9688     6375.567
   4_bss:  13.744 0.9174  0.9670     6261.205
   4_xyz:  13.705 0.9176  0.9677     6240.572
   4_adp:  13.818 0.9166  0.9613     6239.475
   4_occ:  13.827 0.9166  0.9612     6244.939
   5_bss:  13.827 0.9165  0.9708     6239.445
   5_xyz:  14.087 0.9147  0.9691     6450.020
   5_adp:  13.942 0.9159  0.9640     6368.061
   5_occ:  13.951 0.9158  0.9639     6373.276
   5_bss:  13.953 0.9158  0.9682     6374.005
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6070e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6070e-01
   1_xyz:   1.038  0.008  0.072 15.165  0.005  4.121   6.3747e-02
   1_adp:   1.038  0.008  0.072 15.165  0.005  4.121   6.3747e-02
   1_occ:   1.038  0.008  0.072 15.165  0.005  4.121   6.3747e-02
   2_bss:   1.038  0.008  0.072 15.165  0.005  4.121   6.3747e-02
   2_xyz:   1.054  0.009  0.080 14.950  0.004  4.125   6.7427e-02
   2_adp:   1.054  0.009  0.080 14.950  0.004  4.125   6.7427e-02
   2_occ:   1.054  0.009  0.080 14.950  0.004  4.125   6.7427e-02
   3_bss:   1.054  0.009  0.080 14.950  0.004  4.125   6.7427e-02
   3_xyz:   0.954  0.007  0.074 14.774  0.003  4.126   5.7006e-02
   3_adp:   0.954  0.007  0.074 14.774  0.003  4.126   5.7006e-02
   3_occ:   0.954  0.007  0.074 14.774  0.003  4.126   5.7006e-02
   4_bss:   0.954  0.007  0.074 14.774  0.003  4.126   5.7006e-02
   4_xyz:   1.059  0.009  0.081 14.933  0.004  4.130   6.8833e-02
   4_adp:   1.059  0.009  0.081 14.933  0.004  4.130   6.8833e-02
   4_occ:   1.059  0.009  0.081 14.933  0.004  4.130   6.8833e-02
   5_bss:   1.059  0.009  0.081 14.933  0.004  4.130   6.8833e-02
   5_xyz:   0.913  0.006  0.071 14.667  0.003  4.128   5.2201e-02
   5_adp:   0.913  0.006  0.071 14.667  0.003  4.128   5.2201e-02
   5_occ:   0.913  0.006  0.071 14.667  0.003  4.128   5.2201e-02
   5_bss:   0.913  0.006  0.071 14.667  0.003  4.128   5.2201e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4228e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4228e-01
   1_xyz:   9.317  0.043  0.237 83.581  0.038  2.353   6.3428e-02
   1_adp:   9.317  0.043  0.237 83.581  0.038  2.353   6.3428e-02
   1_occ:   9.317  0.043  0.237 83.581  0.038  2.353   6.3428e-02
   2_bss:   9.317  0.043  0.237 83.581  0.038  2.353   6.3428e-02
   2_xyz:   7.838  0.041  0.250 82.587  0.035  2.316   5.2198e-02
   2_adp:   7.838  0.041  0.250 82.587  0.035  2.316   5.2198e-02
   2_occ:   7.838  0.041  0.250 82.587  0.035  2.316   5.2198e-02
   3_bss:   7.838  0.041  0.250 82.587  0.035  2.316   5.2198e-02
   3_xyz:   7.853  0.040  0.222 84.053  0.034  2.348   3.6723e-02
   3_adp:   7.853  0.040  0.222 84.053  0.034  2.348   3.6723e-02
   3_occ:   7.853  0.040  0.222 84.053  0.034  2.348   3.6723e-02
   4_bss:   7.853  0.040  0.222 84.053  0.034  2.348   3.6723e-02
   4_xyz:   7.469  0.045  0.253 84.277  0.037  2.276   4.9263e-02
   4_adp:   7.469  0.045  0.253 84.277  0.037  2.276   4.9263e-02
   4_occ:   7.469  0.045  0.253 84.277  0.037  2.276   4.9263e-02
   5_bss:   7.469  0.045  0.253 84.277  0.037  2.276   4.9263e-02
   5_xyz:   7.665  0.039  0.218 83.519  0.035  2.402   3.2891e-02
   5_adp:   7.665  0.039  0.218 83.519  0.035  2.402   3.2891e-02
   5_occ:   7.665  0.039  0.218 83.519  0.035  2.402   3.2891e-02
   5_bss:   7.665  0.039  0.218 83.519  0.035  2.402   3.2891e-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:  72.53   1.36  17.07  67.43   1.36  13.04  72.53   5.06  39.02
   1_occ:  72.53   1.36  17.07  67.43   1.36  13.04  72.53   5.06  39.02
   2_bss:  72.53   1.36  17.07  67.43   1.36  13.04  72.53   5.06  39.02
   2_xyz:  72.53   1.36  17.07  67.43   1.36  13.04  72.53   5.06  39.02
   2_adp:  74.45   1.89  16.75  69.73   1.89  12.98  74.45   6.40  37.23
   2_occ:  74.45   1.89  16.75  69.73   1.89  12.98  74.45   6.40  37.23
   3_bss:  74.45   1.89  16.75  69.73   1.89  12.98  74.45   6.40  37.23
   3_xyz:  74.45   1.89  16.75  69.73   1.89  12.98  74.45   6.40  37.23
   3_adp:  74.51   1.90  16.66  69.92   1.90  12.91  74.51   6.16  37.11
   3_occ:  74.51   1.90  16.66  69.92   1.90  12.91  74.51   6.16  37.11
   4_bss:  74.51   1.90  16.66  69.92   1.90  12.91  74.51   6.16  37.11
   4_xyz:  74.51   1.90  16.66  69.92   1.90  12.91  74.51   6.16  37.11
   4_adp:  85.27   0.30  17.28  85.27   0.30  13.04  82.51   6.55  40.39
   4_occ:  85.27   0.30  17.28  85.27   0.30  13.04  82.51   6.55  40.39
   5_bss:  85.27   0.30  17.28  85.27   0.30  13.04  82.51   6.55  40.39
   5_xyz:  85.27   0.30  17.28  85.27   0.30  13.04  82.51   6.55  40.39
   5_adp:  85.05   1.01  17.01  85.05   1.01  12.84  81.79   6.42  39.75
   5_occ:  85.05   1.01  17.01  85.05   1.01  12.84  81.79   6.42  39.75
   5_bss:  85.01   0.97  16.98  85.01   0.97  12.80  81.75   6.38  39.71
------------------------------------------------------------------------
 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:    0.732    0.014    0.277
   1_adp:    0.732    0.014    0.277
   1_occ:    0.732    0.014    0.277
   2_bss:    0.732    0.014    0.277
   2_xyz:    0.751    0.027    0.318
   2_adp:    0.751    0.027    0.318
   2_occ:    0.751    0.027    0.318
   3_bss:    0.751    0.027    0.318
   3_xyz:    0.927    0.034    0.331
   3_adp:    0.927    0.034    0.331
   3_occ:    0.927    0.034    0.331
   4_bss:    0.927    0.034    0.331
   4_xyz:    1.009    0.026    0.341
   4_adp:    1.009    0.026    0.341
   4_occ:    1.009    0.026    0.341
   5_bss:    1.009    0.026    0.341
   5_xyz:    1.072    0.018    0.343
   5_adp:    1.072    0.018    0.343
   5_occ:    1.072    0.018    0.343
   5_bss:    1.072    0.018    0.343
------------------------------------------------------------------------

CPU time actual refinement: 307.32


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1018/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_1018/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1018/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1018/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1018/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 307.17 
  Macro-tasks:
    bulk solvent and scale       = 36.65  
    individual site refinement   = 120.45 
    weights calculation          = 28.67  
    collect and process          = 6.47   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 192.35 
  Micro-tasks:
    mask                            = 1.15   
    f_calc                          = 96.75  
    alpha_beta                      = 8.17   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 104.87 
    fmodel                         = 6.32   
    r_factors                      = 0.20   
    phase_errors                   = 11.35  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 230.23 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.432 micro seconds
Total CPU time: 5.34 minutes
from_scatterers_fft:    633 calls, 96.33 s
gradients_fft:          578 calls, 92.13 s

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

# Date 2008-01-16 Time 06:12:51 PST -0800 (1200492771.28 s)
Start R-work = 0.2965, R-free = 0.2922 (no bulk solvent and anisotropic scale)
Final R-work = 0.1353, R-free = 0.1771 (no bulk solvent and anisotropic scale)

Start R-work = 0.2825, R-free = 0.2809
Final R-work = 0.1123, R-free = 0.1575