# Date 2008-01-16 Time 06:11:29 PST -0800 (1200492689.51 s)
#phil __OFF__

Command line arguments: "../1043.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26590
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1043

-------------------------------------------------------------------------------
  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, 47.1647, 88.1178, 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: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.1647, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2391 2.01232
Completeness in resolution range: 0.964975
Completeness with d_max=infinity: 0.96199

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2391
                             d_min =   2.0123

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, 47.1647, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2391 2.01232
Completeness in resolution range: 0.964975
Completeness with d_max=infinity: 0.96199

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2395 -  4.3059 [2132/2156]  1918   214  10.0%
  bin  2:  4.3059 -  3.4305 [2037/2057]  1835   202   9.9%
  bin  3:  3.4305 -  3.0006 [2031/2050]  1824   207  10.2%
  bin  4:  3.0006 -  2.7280 [1997/2027]  1800   197   9.9%
  bin  5:  2.7280 -  2.5334 [2005/2024]  1804   201  10.0%
  bin  6:  2.5334 -  2.3847 [1956/1981]  1761   195  10.0%
  bin  7:  2.3847 -  2.2656 [1979/2007]  1779   200  10.1%
  bin  8:  2.2656 -  2.1673 [1969/2005]  1774   195   9.9%
  bin  9:  2.1673 -  2.0841 [1937/1979]  1745   192   9.9%
  bin 10:  2.0841 -  2.0123 [1546/2014]  1390   156  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1043/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: 11
        2.42 -     3.04: 2160
        3.04 -     3.66: 4563
        3.66 -     4.28: 8838
        4.28 -     4.90: 12170
  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 207 " - " O   HOH Z 341 "  1.955 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.119 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  2.181 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.181 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27737 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_1043/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1043/model_refine_001.geo

CPU time processing inputs: 9.16


============================ 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 47.16465 88.1178 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: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3874   r_free= 0.3788   ksol= 0.00   Bsol= 0.00   scale= 0.924    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.168947                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2395 -  4.8025 0.99   1387  153 0.3097 0.2932      6.4219      6.3176|
|  2:  4.8025 -  3.8319 0.99   1329  152 0.3059 0.3054      6.6103      6.6161|
|  3:  3.8319 -  3.3534 0.99   1305  140 0.3496 0.2990       6.524      6.4592|
|  4:  3.3534 -  3.0495 0.99   1293  149 0.3559 0.3742      6.3794      6.3459|
|  5:  3.0495 -  2.8324 0.99   1290  143 0.4062 0.3778      6.2549      6.2604|
|  6:  2.8324 -  2.6663 0.99   1300  137 0.4002 0.4222      6.1586      6.1048|
|  7:  2.6663 -  2.5334 0.99   1277  147 0.4278 0.4168      6.1313      6.1726|
|  8:  2.5334 -  2.4236 0.98   1271  141 0.4385 0.4176      6.1155      6.0723|
|  9:  2.4236 -  2.3306 0.98   1260  141 0.4305 0.4166      6.0297      6.0622|
| 10:  2.3306 -  2.2505 1.00   1282  142 0.4516 0.4186       6.046      6.0122|
| 11:  2.2505 -  2.1803 0.97   1251  138 0.4593 0.4664      5.9806      6.0382|
| 12:  2.1803 -  2.1182 0.98   1248  138 0.4571 0.4581       5.919      5.9687|
| 13:  2.1182 -  2.0625 0.99   1289  139 0.4575 0.4447      5.8268      5.7632|
| 14:  2.0625 -  2.0123 0.67    848   99 0.4340 0.4619      5.7767      5.7527|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2395 -  4.8025  1387   153  0.79  26.41   0.84     0.80      44342.60|
|  2:  4.8025 -  3.8319  1329   152  0.82  24.64   0.94     0.88      58406.15|
|  3:  3.8319 -  3.3534  1305   140  0.75  30.94   0.93     0.87      60938.19|
|  4:  3.3534 -  3.0495  1293   149  0.70  35.54   0.95     0.82      56889.89|
|  5:  3.0495 -  2.8324  1290   143  0.61  42.99   0.94     0.77      48476.11|
|  6:  2.8324 -  2.6663  1300   137  0.59  44.87   0.93     0.73      45693.36|
|  7:  2.6663 -  2.5334  1277   147  0.56  47.34   0.94     0.72      43017.75|
|  8:  2.5334 -  2.4236  1271   141  0.56  47.17   0.94     0.74      39935.92|
|  9:  2.4236 -  2.3306  1260   141  0.57  46.32   0.95     0.76      36071.30|
| 10:  2.3306 -  2.2505  1282   142  0.55  48.32   1.00     0.74      32996.94|
| 11:  2.2505 -  2.1803  1251   138  0.54  49.27   0.94     0.73      32576.65|
| 12:  2.1803 -  2.1182  1248   138  0.52  50.33   0.96     0.74      30896.74|
| 13:  2.1182 -  2.0625  1289   139  0.50  52.02   0.95     0.72      27162.05|
| 14:  2.0625 -  2.0123   848    99  0.52  50.37   0.97     0.67      22174.84|
|alpha:            min =        0.67 max =            0.88 mean =         0.77|
|beta:             min =    22174.84 max =        60938.19 mean =     42014.54|
|figures of merit: min =        0.00 max =            1.00 mean =         0.62|
|phase err.(work): min =        0.00 max =           89.87 mean =        42.22|
|phase err.(test): min =        0.00 max =           89.55 mean =        42.01|
|-----------------------------------------------------------------------------|

============================== 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 = 5.347234              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.192   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.135323              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.344   (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:        2 |
| 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:      175 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1985 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1804 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2759 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4562 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4276 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5538 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6632 |
|-----------------------------------------------------------------------------|
|-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 |        0.163 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.806 |       0.145 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.364)------------------------------------------|
|    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: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3874   r_free= 0.3788   ksol= 0.00   Bsol= 0.00   scale= 0.924    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.168947                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3764   r_free= 0.3703   ksol= 0.30   Bsol= 80.00   scale= 0.955   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.80,-2.42,3.92,-0.00,0.00,0.00); trace/3= 0.23                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.152742                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.758182              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.995   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.636234              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.962   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3764      final r-factor (work) = 0.2431          |
| start r-factor (free) = 0.3703      final r-factor (free) = 0.2652          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.8012 = 4.76 * 0.50 * 6.1529 + 1.00 * 0.1627                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.2098 = 4.76 * 0.50 * 5.9367 + 1.00 * 0.0859                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2431      final r-factor (work) = 0.2199          |
| start r-factor (free) = 0.2652      final r-factor (free) = 0.2722          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7833 = 0.64 * 1.00 * 5.9367 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6487 = 0.64 * 1.00 * 5.7146 + 1.00 * 0.0129                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.364)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.98   18.01    None  None   None       |
|    all(noH): 2823   0      0.00    90.98   18.01    None  None   None       |
|    Sol.    : 438    0      2.71    90.98   41.99    None  None   None       |
|    Mac.    : 2385   0      0.00    81.99   13.61    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.098:  829   |   5:    45.490 -  54.589:  101        |
|      1:     9.098 -  18.196: 1116   |   6:    54.589 -  63.687:   73        |
|      2:    18.196 -  27.294:  376   |   7:    63.687 -  72.785:   39        |
|      3:    27.294 -  36.392:  156   |   8:    72.785 -  81.883:   13        |
|      4:    36.392 -  45.490:  116   |   9:    81.883 -  90.981:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2199 r_free = 0.2722             target_work(ml) = 5.724         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2194 r_free = 0.2716             target_work(ml) = 5.723         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2194   r_free= 0.2716   ksol= 0.30   Bsol= 80.00   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.80,-2.42,3.92,-0.00,0.00,0.00); trace/3= 0.23                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.723490                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2173   r_free= 0.2708   ksol= 0.34   Bsol= 89.35   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.84,-2.40,0.66,-0.00,0.00,0.00); trace/3= -1.19                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.721217                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.278109              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.378   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.303433              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.936  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2173      final r-factor (work) = 0.1669          |
| start r-factor (free) = 0.2708      final r-factor (free) = 0.2153          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6019 = 2.28 * 0.50 * 5.7205 + 1.00 * 0.0859                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4490 = 2.28 * 0.50 * 5.6101 + 1.00 * 0.0589                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1669      final r-factor (work) = 0.1582          |
| start r-factor (free) = 0.2153      final r-factor (free) = 0.2009          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7152 = 0.30 * 1.00 * 5.6101 + 1.00 * 0.0129                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6676 = 0.30 * 1.00 * 5.4629 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.364)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.92    91.10   17.50    None  None   None       |
|    all(noH): 2823   0      0.92    91.10   17.50    None  None   None       |
|    Sol.    : 438    0      4.36    91.10   41.54    None  None   None       |
|    Mac.    : 2385   0      0.92    80.01   13.09    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:     0.917 -   9.935: 1009   |   5:    46.007 -  55.025:  110        |
|      1:     9.935 -  18.953: 1084   |   6:    55.025 -  64.043:   60        |
|      2:    18.953 -  27.971:  265   |   7:    64.043 -  73.061:   33        |
|      3:    27.971 -  36.989:  136   |   8:    73.061 -  82.079:   13        |
|      4:    36.989 -  46.007:  110   |   9:    82.079 -  91.097:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1582 r_free = 0.2009             target_work(ml) = 5.434         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1580 r_free = 0.2010             target_work(ml) = 5.434         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1580   r_free= 0.2010   ksol= 0.34   Bsol= 89.35   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.84,-2.40,0.66,-0.00,0.00,0.00); trace/3= -1.19                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.433735                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1581   r_free= 0.2006   ksol= 0.34   Bsol= 81.43   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,-2.13,-0.03,-0.00,-0.00,-0.00); trace/3= -1.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.433187                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.912952              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.081  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.400103              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.686  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1581      final r-factor (work) = 0.1331          |
| start r-factor (free) = 0.2006      final r-factor (free) = 0.1752          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2839 = 1.91 * 0.50 * 5.4628 + 1.00 * 0.0589                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1773 = 1.91 * 0.50 * 5.3529 + 1.00 * 0.0573                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1331      final r-factor (work) = 0.1283          |
| start r-factor (free) = 0.1752      final r-factor (free) = 0.1721          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1516 = 0.40 * 1.00 * 5.3529 + 1.00 * 0.0099                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1168 = 0.40 * 1.00 * 5.2652 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.364)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.72    91.71   17.28    None  None   None       |
|    all(noH): 2823   0      0.72    91.71   17.28    None  None   None       |
|    Sol.    : 438    0      5.28    91.71   41.73    None  None   None       |
|    Mac.    : 2385   0      0.72    80.82   12.79    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:     0.720 -   9.819: 1031   |   5:    46.216 -  55.315:  100        |
|      1:     9.819 -  18.918: 1104   |   6:    55.315 -  64.414:   69        |
|      2:    18.918 -  28.018:  229   |   7:    64.414 -  73.513:   32        |
|      3:    28.018 -  37.117:  128   |   8:    73.513 -  82.612:   14        |
|      4:    37.117 -  46.216:  112   |   9:    82.612 -  91.711:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1283 r_free = 0.1721             target_work(ml) = 5.255         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1283 r_free = 0.1721             target_work(ml) = 5.255         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1283   r_free= 0.1721   ksol= 0.34   Bsol= 81.43   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,-2.13,-0.03,-0.00,-0.00,-0.00); trace/3= -1.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.254518                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1283   r_free= 0.1723   ksol= 0.33   Bsol= 74.28   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-1.94,-0.14,-0.00,-0.00,-0.00); trace/3= -1.33                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.254840                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.524689              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 121.487  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.400302              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.739  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1283      final r-factor (work) = 0.1254          |
| start r-factor (free) = 0.1723      final r-factor (free) = 0.1699          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0714 = 1.52 * 0.50 * 5.2654 + 1.00 * 0.0573                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0555 = 1.52 * 0.50 * 5.2438 + 1.00 * 0.0579                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1254      final r-factor (work) = 0.1246          |
| start r-factor (free) = 0.1699      final r-factor (free) = 0.1712          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3532 = 1.40 * 1.00 * 5.2438 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3374 = 1.40 * 1.00 * 5.2313 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.364)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.80   17.37    None  None   None       |
|    all(noH): 2823   0      0.00    95.80   17.37    None  None   None       |
|    Sol.    : 438    0      5.05    95.80   42.82    None  None   None       |
|    Mac.    : 2385   0      0.00    86.46   12.69    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.581: 1030   |   5:    47.902 -  57.483:   98        |
|      1:     9.581 -  19.161: 1102   |   6:    57.483 -  67.063:   72        |
|      2:    19.161 -  28.741:  234   |   7:    67.063 -  76.644:   32        |
|      3:    28.741 -  38.322:  136   |   8:    76.644 -  86.224:   15        |
|      4:    38.322 -  47.902:   99   |   9:    86.224 -  95.805:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1246 r_free = 0.1712             target_work(ml) = 5.236         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1246 r_free = 0.1712             target_work(ml) = 5.236         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1246   r_free= 0.1712   ksol= 0.33   Bsol= 74.28   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-1.94,-0.14,-0.00,-0.00,-0.00); trace/3= -1.33                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.236260                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1245   r_free= 0.1711   ksol= 0.33   Bsol= 75.24   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.78,-1.74,-0.09,-0.00,-0.00,-0.00); trace/3= -1.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.236319                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.751614              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 148.385  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.163745              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 113.861  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1245      final r-factor (work) = 0.1164          |
| start r-factor (free) = 0.1711      final r-factor (free) = 0.1670          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2554 = 2.75 * 0.50 * 5.2315 + 1.00 * 0.0579                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2358 = 2.75 * 0.50 * 5.2058 + 1.00 * 0.0737                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1164      final r-factor (work) = 0.1154          |
| start r-factor (free) = 0.1670      final r-factor (free) = 0.1660          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.6873 = 4.16 * 1.00 * 5.2058 + 1.00 * 0.0119                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.6052 = 4.16 * 1.00 * 5.1859 + 1.00 * 0.0126                              |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.364)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.18  17.20    None  None   None       |
|    all(noH): 2823   0      0.00    102.18  17.20    None  None   None       |
|    Sol.    : 438    0      2.27    102.18  42.86    None  None   None       |
|    Mac.    : 2385   0      0.00    92.72   12.49    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.218: 1230   |   5:    51.088 -  61.305:   87        |
|      1:    10.218 -  20.435:  960   |   6:    61.305 -  71.523:   57        |
|      2:    20.435 -  30.653:  218   |   7:    71.523 -  81.740:   30        |
|      3:    30.653 -  40.870:  131   |   8:    81.740 -  91.958:    9        |
|      4:    40.870 -  51.088:   98   |   9:    91.958 - 102.176:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1154 r_free = 0.1660             target_work(ml) = 5.182         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1154 r_free = 0.1661             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1154   r_free= 0.1661   ksol= 0.33   Bsol= 75.24   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.78,-1.74,-0.09,-0.00,-0.00,-0.00); trace/3= -1.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.182539                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2395 -  4.8025 0.99   1387  153 0.0978 0.1343      5.3934      5.5419|
|  2:  4.8025 -  3.8319 0.99   1329  152 0.0814 0.1074      5.4148      5.6131|
|  3:  3.8319 -  3.3534 0.99   1305  140 0.1065 0.1508      5.4784      5.8505|
|  4:  3.3534 -  3.0495 0.99   1293  149 0.1223 0.1787      5.4786      5.6765|
|  5:  3.0495 -  2.8324 0.99   1290  143 0.1436 0.1798      5.3976      5.5797|
|  6:  2.8324 -  2.6663 0.99   1300  137 0.1275 0.2167      5.2744       5.575|
|  7:  2.6663 -  2.5334 0.99   1277  147 0.1356 0.1669      5.2265      5.3977|
|  8:  2.5334 -  2.4236 0.98   1271  141 0.1229 0.1801      5.1335      5.3918|
|  9:  2.4236 -  2.3306 0.98   1260  141 0.1223 0.1811      5.0798      5.3157|
| 10:  2.3306 -  2.2505 1.00   1282  142 0.1178 0.1811      5.0072      5.2564|
| 11:  2.2505 -  2.1803 0.97   1251  138 0.1202 0.1847      4.9867      5.2752|
| 12:  2.1803 -  2.1182 0.98   1248  138 0.1181 0.1888      4.9381      5.2853|
| 13:  2.1182 -  2.0625 0.99   1289  139 0.1170 0.1890      4.8317      5.0968|
| 14:  2.0625 -  2.0123 0.67    848   99 0.1063 0.1723      4.7059      4.9718|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2395 -  4.8025  1387   153  0.94   9.52   0.96     0.94       7699.92|
|  2:  4.8025 -  3.8319  1329   152  0.95   7.90   1.00     0.98       8975.25|
|  3:  3.8319 -  3.3534  1305   140  0.93  11.17   1.02     1.01      10300.72|
|  4:  3.3534 -  3.0495  1293   149  0.92  14.05   1.00     0.98      10916.80|
|  5:  3.0495 -  2.8324  1290   143  0.89  17.04   1.00     0.97       9609.53|
|  6:  2.8324 -  2.6663  1300   137  0.89  17.31   0.98     0.95       8226.88|
|  7:  2.6663 -  2.5334  1277   147  0.89  17.18   0.98     0.95       7142.82|
|  8:  2.5334 -  2.4236  1271   141  0.90  16.30   0.98     0.95       6051.79|
|  9:  2.4236 -  2.3306  1260   141  0.91  15.89   0.98     0.94       5458.30|
| 10:  2.3306 -  2.2505  1282   142  0.89  16.55   0.98     0.93       4839.81|
| 11:  2.2505 -  2.1803  1251   138  0.89  17.22   0.97     0.93       4790.73|
| 12:  2.1803 -  2.1182  1248   138  0.90  16.49   0.99     0.98       4519.55|
| 13:  2.1182 -  2.0625  1289   139  0.89  17.18   0.96     0.93       3688.38|
| 14:  2.0625 -  2.0123   848    99  0.92  14.52   0.94     0.91       2786.14|
|alpha:            min =        0.91 max =            1.01 mean =         0.95|
|beta:             min =     2786.14 max =        10916.80 mean =      6914.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.83|
|phase err.(test): min =        0.00 max =           88.63 mean =        14.24|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1152   r_free= 0.1660   ksol= 0.32   Bsol= 69.27   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.31,-1.32,0.28,-0.00,0.00,0.00); trace/3= -0.79                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.182715                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1152   r_free= 0.1660   ksol= 0.32   Bsol= 69.27   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.31,-1.32,0.28,-0.00,0.00,0.00); trace/3= -0.79                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.182715                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2395 -  4.8025 0.99   1387  153 0.0975 0.1340      5.3912       5.542|
|  2:  4.8025 -  3.8319 0.99   1329  152 0.0811 0.1071      5.4135      5.6103|
|  3:  3.8319 -  3.3534 0.99   1305  140 0.1064 0.1511      5.4777      5.8528|
|  4:  3.3534 -  3.0495 0.99   1293  149 0.1225 0.1790      5.4803      5.6777|
|  5:  3.0495 -  2.8324 0.99   1290  143 0.1437 0.1799       5.399      5.5806|
|  6:  2.8324 -  2.6663 0.99   1300  137 0.1276 0.2174      5.2756      5.5767|
|  7:  2.6663 -  2.5334 0.99   1277  147 0.1358 0.1671      5.2277      5.3995|
|  8:  2.5334 -  2.4236 0.98   1271  141 0.1230 0.1801      5.1342      5.3913|
|  9:  2.4236 -  2.3306 0.98   1260  141 0.1223 0.1813      5.0799       5.316|
| 10:  2.3306 -  2.2505 1.00   1282  142 0.1178 0.1811      5.0075      5.2563|
| 11:  2.2505 -  2.1803 0.97   1251  138 0.1202 0.1845      4.9868      5.2749|
| 12:  2.1803 -  2.1182 0.98   1248  138 0.1180 0.1886      4.9378      5.2847|
| 13:  2.1182 -  2.0625 0.99   1289  139 0.1169 0.1892      4.8319       5.097|
| 14:  2.0625 -  2.0123 0.67    848   99 0.1063 0.1724      4.7065      4.9725|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2395 -  4.8025  1387   153  0.94   9.52   0.97     0.94       7686.39|
|  2:  4.8025 -  3.8319  1329   152  0.95   7.89   1.00     0.99       8956.85|
|  3:  3.8319 -  3.3534  1305   140  0.93  11.16   1.03     1.02      10283.37|
|  4:  3.3534 -  3.0495  1293   149  0.92  14.07   1.01     0.99      10943.57|
|  5:  3.0495 -  2.8324  1290   143  0.89  17.06   1.01     0.98       9636.44|
|  6:  2.8324 -  2.6663  1300   137  0.89  17.34   0.99     0.96       8247.82|
|  7:  2.6663 -  2.5334  1277   147  0.89  17.20   1.00     0.96       7157.60|
|  8:  2.5334 -  2.4236  1271   141  0.90  16.31   1.00     0.97       6057.55|
|  9:  2.4236 -  2.3306  1260   141  0.91  15.89   1.00     0.95       5462.50|
| 10:  2.3306 -  2.2505  1282   142  0.89  16.55   1.00     0.95       4837.80|
| 11:  2.2505 -  2.1803  1251   138  0.89  17.22   0.99     0.95       4788.90|
| 12:  2.1803 -  2.1182  1248   138  0.90  16.49   1.01     1.00       4517.40|
| 13:  2.1182 -  2.0625  1289   139  0.89  17.19   0.98     0.95       3689.35|
| 14:  2.0625 -  2.0123   848    99  0.92  14.53   0.97     0.94       2788.87|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2788.87 max =        10943.57 mean =      6917.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.83|
|phase err.(test): min =        0.00 max =           88.77 mean =        14.25|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.364)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.18  17.20    None  None   None       |
|    all(noH): 2823   0      0.00    102.18  17.20    None  None   None       |
|    Sol.    : 438    0      2.27    102.18  42.87    None  None   None       |
|    Mac.    : 2385   0      0.00    92.72   12.49    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:     0.003 -  10.221: 1230   |   5:    51.091 -  61.308:   87        |
|      1:    10.221 -  20.438:  960   |   6:    61.308 -  71.526:   57        |
|      2:    20.438 -  30.656:  218   |   7:    71.526 -  81.743:   30        |
|      3:    30.656 -  40.873:  131   |   8:    81.743 -  91.961:    9        |
|      4:    40.873 -  51.091:   98   |   9:    91.961 - 102.179:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 300         
Filter by distance & map next to the model:
   mapped sites are within: 0.505 - 4.864
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 293 from: 300
   mapped sites are within: 0.720 - 4.864

peak=    5.630 closest distance to " CB  GLN A 223 " =    1.461
peak=    5.016 closest distance to " O   HOH Z 111 " =    2.165
peak=    4.953 closest distance to " CG  PRO A  54 " =    1.372
peak=    4.892 closest distance to " CZ  PHE A 218 " =    1.102
peak=    4.842 closest distance to " O   HOH Z 369 " =    2.169
peak=    4.827 closest distance to " CB  GLN A 183 " =    1.279
peak=    4.804 closest distance to " CB  ARG A 190 " =    1.559
peak=    4.775 closest distance to " CB  SER A  63 " =    1.203
peak=    4.562 closest distance to " NE2 GLN A  11 " =    1.008
peak=    4.510 closest distance to " O   HOH Z 298 " =    2.036
peak=    4.490 closest distance to " O   HOH Z 232 " =    2.236
peak=    4.430 closest distance to " CG  PRO A 198 " =    1.240
peak=    4.419 closest distance to " CG  PRO A 213 " =    1.170
peak=    4.349 closest distance to " CB  GLU A 277 " =    3.778
peak=    4.304 closest distance to " CB  ARG A 275 " =    0.978
peak=    4.292 closest distance to " O   HOH Z  19 " =    2.516
peak=    4.286 closest distance to " NH1AARG A 145 " =    1.304
peak=    4.248 closest distance to " O   HOH Z   9 " =    2.239
peak=    4.247 closest distance to " O   HOH Z 368 " =    2.118
peak=    4.237 closest distance to " O   HOH Z 188 " =    2.834
peak=    4.230 closest distance to " CB  LEU A 228 " =    1.110
peak=    4.220 closest distance to " CZ3 TRP A 266 " =    1.150
peak=    4.200 closest distance to " CA  ALA A  51 " =    0.902
peak=    4.191 closest distance to " CB  ARG A  79 " =    1.517
peak=    4.188 closest distance to " CA  ARG A 195 " =    1.253
peak=    4.181 closest distance to " O   HOH Z 142 " =    1.745
peak=    4.167 closest distance to " CE  LYS A  76 " =    0.825
peak=    4.164 closest distance to " CB  TYR A 169 " =    0.757
peak=    4.152 closest distance to " CA  TYR A  30 " =    1.035
peak=    4.145 closest distance to " CB  ASP A 124 " =    0.787
peak=    4.099 closest distance to " CD1 LEU A 300 " =    1.187
peak=    4.096 closest distance to " O   HOH Z 427 " =    3.219
peak=    4.084 closest distance to " O   HOH Z  78 " =    1.614
peak=    4.077 closest distance to " C   PRO A 198 " =    1.520
peak=    4.065 closest distance to " CD  ARG A 269 " =    0.903
peak=    4.063 closest distance to " CD  ARG A 159 " =    0.788
peak=    4.043 closest distance to " CB  TRP A 266 " =    1.047
peak=    4.034 closest distance to " CB  PRO A  54 " =    0.908
peak=    4.026 closest distance to " O   HOH Z 316 " =    3.214
peak=    4.013 closest distance to " O   HOH Z 214 " =    2.278
peak=    4.008 closest distance to " O   HOH Z 133 " =    2.704
peak=    4.004 closest distance to " O   HOH Z 180 " =    2.113
peak=    4.000 closest distance to " CB  GLU A 128 " =    0.993
peak=    3.977 closest distance to " O   HOH Z 265 " =    2.197
peak=    3.966 closest distance to " O  BHOH Z 338 " =    2.302
peak=    3.960 closest distance to " O   HOH Z 126 " =    2.054
peak=    3.947 closest distance to " CA  ALA A 160 " =    1.013
peak=    3.941 closest distance to " CB  VAL A 202 " =    1.627
peak=    3.938 closest distance to " CB  ASN A 148 " =    1.485
peak=    3.927 closest distance to " ND2 ASN A 187 " =    1.382
peak=    3.923 closest distance to " O   HOH Z 287 " =    2.005
peak=    3.922 closest distance to " CA  MET A 105 " =    1.043
peak=    3.912 closest distance to " O   HOH Z 411 " =    3.897
peak=    3.903 closest distance to " CB  ASP A 140 " =    1.038
peak=    3.889 closest distance to " CD  LYS A 166 " =    1.296
peak=    3.873 closest distance to " CB  ASN A 142 " =    0.974
peak=    3.857 closest distance to " O   HOH Z 406 " =    1.676
peak=    3.838 closest distance to " CB  VAL A 265 " =    1.255
peak=    3.836 closest distance to " CA  VAL A 125 " =    1.251
peak=    3.833 closest distance to " CG2 THR A 221 " =    1.054
peak=    3.816 closest distance to " CB  ASN A  39 " =    0.945
peak=    3.796 closest distance to " O   SER A  87 " =    2.260
peak=    3.790 closest distance to " CD1 LEU A  96 " =    0.720
peak=    3.774 closest distance to " CB  SER A 212 " =    1.102
peak=    3.770 closest distance to " CD ALYS A 290 " =    0.954
peak=    3.769 closest distance to " O   HOH Z 158 " =    2.966
peak=    3.745 closest distance to " O   HOH Z 234 " =    3.794
peak=    3.745 closest distance to " O   HOH Z 261 " =    1.631
peak=    3.739 closest distance to " CA  ARG A  36 " =    1.187
peak=    3.730 closest distance to " O   HOH Z 285 " =    2.318
peak=    3.727 closest distance to " N   HIS A 108 " =    1.920
peak=    3.725 closest distance to " O   HOH Z 193 " =    1.824
peak=    3.707 closest distance to " O   HOH Z 290 " =    0.976
peak=    3.700 closest distance to " O   HOH Z 425 " =    1.341
peak=    3.696 closest distance to " O   HOH Z 303 " =    2.164
peak=    3.692 closest distance to " O   HOH Z 172 " =    3.752
peak=    3.688 closest distance to " CA  ALA A 154 " =    1.070
peak=    3.688 closest distance to " CA  ALA A 295 " =    1.094
peak=    3.685 closest distance to " O   HOH Z 346 " =    1.668
peak=    3.671 closest distance to " ND2 ASN A 249 " =    0.832
peak=    3.666 closest distance to " O   HOH Z 353 " =    2.644
peak=    3.662 closest distance to " CA  GLU A  46 " =    0.829
peak=    3.655 closest distance to " CB  GLU A  46 " =    0.988
peak=    3.655 closest distance to " CD  ARG A  66 " =    2.310
peak=    3.650 closest distance to " O   HOH Z 313 " =    1.828
peak=    3.644 closest distance to " CB  PRO A  90 " =    1.167
peak=    3.641 closest distance to " CG2 VAL A 257 " =    0.803
peak=    3.632 closest distance to " O   HOH Z   1 " =    2.188
peak=    3.631 closest distance to " CG  LEU A 167 " =    1.219
peak=    3.619 closest distance to " O   HOH Z 392 " =    2.811
peak=    3.612 closest distance to " CG  PRO A 243 " =    1.056
peak=    3.604 closest distance to " CB  GLN A  89 " =    1.267
peak=    3.600 closest distance to " CG  MET A 185 " =    1.280
peak=    3.599 closest distance to " CD2 TRP A 179 " =    1.290
peak=    3.583 closest distance to " O   HOH Z 403 " =    1.511
peak=    3.583 closest distance to " O   TYR A 116 " =    1.280
peak=    3.576 closest distance to " O   HOH Z 272 " =    1.863
peak=    3.574 closest distance to " O   HOH Z 271 " =    2.660
peak=    3.572 closest distance to " CA  ARG A 139 " =    1.086
peak=    3.562 closest distance to " O   ASN A  74 " =    1.547
peak=    3.560 closest distance to " O   HOH Z 359 " =    1.454
peak=    3.559 closest distance to " CG  GLU A  37 " =    0.941
peak=    3.556 closest distance to " O   HOH Z  59 " =    2.302
peak=    3.555 closest distance to " CA  MET A  40 " =    1.242
peak=    3.549 closest distance to " CB  TYR A 116 " =    0.854
peak=    3.546 closest distance to " CZ  PHE A  38 " =    1.210
peak=    3.544 closest distance to " O   HOH Z 391 " =    2.972
peak=    3.543 closest distance to " OG  SER A 245 " =    1.854
peak=    3.542 closest distance to " CA  ALA A 100 " =    1.018
peak=    3.540 closest distance to " OD1 ASN A  69 " =    2.627
peak=    3.531 closest distance to " O   HOH Z 361 " =    3.725
peak=    3.527 closest distance to " O   HOH Z  40 " =    1.974
peak=    3.522 closest distance to " NZ  LYS A 117 " =    3.166
peak=    3.517 closest distance to " O   ASP A 124 " =    1.181
peak=    3.515 closest distance to " O   HOH Z 166 " =    3.848
peak=    3.511 closest distance to " CA  ASN A 217 " =    1.270
peak=    3.504 closest distance to " O   HOH Z  10 " =    1.824
peak=    3.503 closest distance to " O   HOH Z 203 " =    1.746
peak=    3.501 closest distance to " CG1 VAL A 153 " =    0.953
peak=    3.500 closest distance to " O   HOH Z 250 " =    1.357
peak=    3.496 closest distance to " CB  ALA A  43 " =    0.875
peak=    3.494 closest distance to " CG2 ILE A 234 " =    0.978
peak=    3.489 closest distance to " N   ASN A  39 " =    1.367
peak=    3.488 closest distance to " CB  LYS A 117 " =    1.154
peak=    3.486 closest distance to " O   HOH Z  80 " =    1.696
peak=    3.484 closest distance to " O   THR A 220 " =    1.233
peak=    3.474 closest distance to " O   ALA A 158 " =    1.309
peak=    3.472 closest distance to " N   ASN A 127 " =    1.310
peak=    3.471 closest distance to " CA  ALA A 291 " =    0.839
peak=    3.465 closest distance to " O   ASN A  74 " =    2.151
peak=    3.465 closest distance to " CG AARG A 275 " =    1.175
peak=    3.455 closest distance to " CA  PRO A  54 " =    1.387
peak=    3.454 closest distance to " CB  ALA A 104 " =    0.771
peak=    3.453 closest distance to " O   HOH Z 199 " =    1.568
peak=    3.452 closest distance to " CG  ARG A 138 " =    1.235
peak=    3.447 closest distance to " OH  TYR A 116 " =    1.108
peak=    3.446 closest distance to " CB  LEU A  96 " =    1.321
peak=    3.445 closest distance to " O   HOH Z  88 " =    3.990
peak=    3.444 closest distance to " CD2 LEU A 297 " =    0.965
peak=    3.444 closest distance to " CB  GLU A 152 " =    1.193
peak=    3.443 closest distance to " O   HOH Z 422 " =    2.685
peak=    3.442 closest distance to " CB  MET A  47 " =    0.959
peak=    3.437 closest distance to " O   HOH Z 193 " =    1.997
peak=    3.436 closest distance to " CA  THR A 221 " =    1.013
peak=    3.436 closest distance to " O   THR A 182 " =    1.424
peak=    3.433 closest distance to " CB  MET A  40 " =    0.804
peak=    3.431 closest distance to " CA  ARG A 102 " =    1.162
peak=    3.430 closest distance to " N   ARG A 156 " =    1.391
peak=    3.426 closest distance to " CD2 LEU A 255 " =    1.703
peak=    3.424 closest distance to " CG1 ILE A  33 " =    1.179
peak=    3.422 closest distance to " O   HOH Z 251 " =    1.652
peak=    3.421 closest distance to " O   HOH Z 185 " =    1.920
peak=    3.420 closest distance to " CA  ASP A 124 " =    0.758
peak=    3.419 closest distance to " CB  LEU A  83 " =    0.808
peak=    3.416 closest distance to " O   HOH Z 325 " =    2.340
peak=    3.416 closest distance to " O   HOH Z  21 " =    1.820
peak=    3.414 closest distance to " CB  TRP A 179 " =    1.492
peak=    3.414 closest distance to " O   HOH Z 394 " =    3.882
peak=    3.413 closest distance to " O   HOH Z 248 " =    1.628
peak=    3.412 closest distance to " CB  ASN A 285 " =    0.946
peak=    3.412 closest distance to " CB  ALA A   9 " =    1.624
peak=    3.411 closest distance to " O   HOH Z 124 " =    1.848
peak=    3.410 closest distance to " OG  SER A  22 " =    2.832
peak=    3.402 closest distance to " CG BARG A 275 " =    1.414
peak=    3.397 closest distance to " CA  ALA A 158 " =    1.204
peak=    3.387 closest distance to " CB  SER A   3 " =    1.475
peak=    3.382 closest distance to " O   ALA A 165 " =    1.538
peak=    3.380 closest distance to " CA  TYR A 116 " =    1.369
peak=    3.377 closest distance to " CB  SER A 141 " =    1.100
peak=    3.377 closest distance to " CB  THR A  82 " =    1.409
peak=    3.376 closest distance to " OG BSER A 134 " =    2.847
peak=    3.374 closest distance to " O   HOH Z  61 " =    1.654
peak=    3.374 closest distance to " O   HOH Z 261 " =    1.782
peak=    3.373 closest distance to " O   HOH Z 193 " =    2.164
peak=    3.368 closest distance to " O   HOH Z 126 " =    1.884
peak=    3.367 closest distance to " O   ASP A 191 " =    1.476
peak=    3.364 closest distance to " NE  ARG A  79 " =    1.072
peak=    3.358 closest distance to " OE1 GLN A  11 " =    2.120
peak=    3.357 closest distance to " CA  ASN A 127 " =    1.172
peak=    3.357 closest distance to " O   HOH Z 126 " =    1.619
peak=    3.353 closest distance to " CG2 THR A  29 " =    1.385
peak=    3.350 closest distance to " O   HOH Z 167 " =    1.693
peak=    3.350 closest distance to " O   HOH Z  88 " =    1.856
peak=    3.346 closest distance to " CE1 HIS A 115 " =    0.944
peak=    3.345 closest distance to " CG2 ILE A 120 " =    1.043
peak=    3.342 closest distance to " O   HOH Z  43 " =    1.972
peak=    3.341 closest distance to " O   HOH Z 305 " =    3.594
peak=    3.336 closest distance to " O   HOH Z 417 " =    3.264
peak=    3.335 closest distance to " CG2AVAL A 121 " =    2.335
peak=    3.329 closest distance to " O   HOH Z 102 " =    1.300
peak=    3.328 closest distance to " NH2AARG A 275 " =    3.563
peak=    3.328 closest distance to " CA  THR A 264 " =    0.880
peak=    3.326 closest distance to " O   HOH Z 365 " =    2.944
peak=    3.325 closest distance to " OE2 GLU A  53 " =    1.652
peak=    3.322 closest distance to " O   HOH Z 106 " =    4.163
peak=    3.321 closest distance to " O   HOH Z 213 " =    2.094
peak=    3.321 closest distance to " CA  GLU A 152 " =    0.880
peak=    3.320 closest distance to " CD  ARG A  66 " =    2.282
peak=    3.320 closest distance to " NH2 ARG A 156 " =    1.246
peak=    3.319 closest distance to " CA  ALA A 233 " =    1.653
peak=    3.318 closest distance to " CB  ALA A 248 " =    1.326
peak=    3.315 closest distance to " O   HOH Z 409 " =    2.990
peak=    3.313 closest distance to " CB  ASN A 187 " =    1.141
peak=    3.310 closest distance to " NH2BARG A 145 " =    2.198
peak=    3.310 closest distance to " CB  ARG A 138 " =    0.976
peak=    3.310 closest distance to " CA  GLY A 211 " =    1.374
peak=    3.309 closest distance to " CB  ALA A   1 " =    4.864
peak=    3.309 closest distance to " CG1BVAL A  72 " =    1.874
peak=    3.307 closest distance to " CB  ASN A 110 " =    1.122
peak=    3.307 closest distance to " CB  ALA A 291 " =    1.245
peak=    3.304 closest distance to " CD  GLU A 152 " =    0.781
peak=    3.302 closest distance to " O   HOH Z 227 " =    1.767
peak=    3.298 closest distance to " NE2 HIS A 207 " =    1.146
peak=    3.293 closest distance to " O   HOH Z 371 " =    3.092
peak=    3.290 closest distance to " CE  LYS A  48 " =    1.046
peak=    3.288 closest distance to " O   HOH Z  90 " =    2.386
peak=    3.284 closest distance to " CB  SER A  62 " =    0.750
peak=    3.284 closest distance to " CB  GLN A  88 " =    1.220
peak=    3.283 closest distance to " O   HOH Z 148 " =    3.431
peak=    3.280 closest distance to " CA  GLY A 241 " =    0.818
peak=    3.276 closest distance to " CG2 VAL A 197 " =    1.151
peak=    3.275 closest distance to " CA  TYR A  30 " =    1.062
peak=    3.273 closest distance to " O   HOH Z 280 " =    2.981
peak=    3.271 closest distance to " CE1 PHE A 218 " =    1.234
peak=    3.267 closest distance to " CB  ALA A  34 " =    1.006
peak=    3.261 closest distance to " CB  TRP A 150 " =    1.310
peak=    3.255 closest distance to " NE2 GLN A  77 " =    3.533
peak=    3.250 closest distance to " CB  SER A 210 " =    0.880
peak=    3.249 closest distance to " O   HOH Z 294 " =    1.498
peak=    3.244 closest distance to " CB  ASN A 215 " =    1.157
peak=    3.242 closest distance to " CD  ARG A 195 " =    3.428
peak=    3.242 closest distance to " O   HOH Z 383 " =    2.173
peak=    3.242 closest distance to " O   HOH Z 163 " =    1.861
peak=    3.239 closest distance to " CG2 ILE A  20 " =    1.289
peak=    3.238 closest distance to " OD1 ASP A 171 " =    1.237
peak=    3.232 closest distance to " O   HOH Z 116 " =    1.790
peak=    3.229 closest distance to " CB  PRO A 243 " =    1.441
peak=    3.228 closest distance to " O   PHE A 192 " =    1.433
peak=    3.227 closest distance to " O   HOH Z 183 " =    1.345
peak=    3.220 closest distance to " O   HOH Z 147 " =    1.801
peak=    3.216 closest distance to " O   HOH Z  20 " =    1.658
peak=    3.216 closest distance to " OG  SER A  28 " =    1.552
peak=    3.215 closest distance to " CA  SER A  87 " =    1.026
peak=    3.208 closest distance to " CA  LEU A  83 " =    1.466
peak=    3.206 closest distance to " O   HOH Z 128 " =    2.590
peak=    3.202 closest distance to " ND1 HIS A  81 " =    1.734
peak=    3.202 closest distance to " O   HOH Z 171 " =    4.028
peak=    3.201 closest distance to " CG1 ILE A  20 " =    1.366
peak=    3.200 closest distance to " CB  ASP A 298 " =    1.166
peak=    3.199 closest distance to " O   HOH Z 423 " =    1.802
peak=    3.194 closest distance to " CA  ASN A 215 " =    1.151
peak=    3.187 closest distance to " CA  ARG A 156 " =    1.070
peak=    3.187 closest distance to " N   PHE A 130 " =    1.243
peak=    3.186 closest distance to " CA  LEU A 101 " =    1.494
peak=    3.179 closest distance to " O   THR A 251 " =    1.118
peak=    3.178 closest distance to " O   HOH Z 402 " =    1.377
peak=    3.177 closest distance to " CG1 ILE A 151 " =    1.060
peak=    3.176 closest distance to " CB  ALA A 248 " =    1.019
peak=    3.173 closest distance to " O   PRO A 213 " =    1.641
peak=    3.171 closest distance to " CA  ASP A 162 " =    1.044
peak=    3.168 closest distance to " OG BSER A 164 " =    2.362
peak=    3.168 closest distance to " CB  ALA A 227 " =    1.134
peak=    3.149 closest distance to " NZ  LYS A  48 " =    1.353
peak=    3.148 closest distance to " O   HOH Z 299 " =    4.536
peak=    3.146 closest distance to " CB  LEU A 300 " =    0.889
peak=    3.142 closest distance to " O   HOH Z  44 " =    2.263
peak=    3.139 closest distance to " CG  ARG A 159 " =    0.890
peak=    3.139 closest distance to " CA  ALA A  21 " =    1.210
peak=    3.139 closest distance to " N   TYR A 247 " =    1.107
peak=    3.139 closest distance to " O   HOH Z 248 " =    1.685
peak=    3.135 closest distance to " O   ASN A 284 " =    1.672
peak=    3.131 closest distance to " CB  SER A 216 " =    0.945
peak=    3.130 closest distance to " O   PHE A  61 " =    1.351
peak=    3.125 closest distance to " CA  ASP A 191 " =    0.888
peak=    3.123 closest distance to " ND2 ASN A 249 " =    1.934
peak=    3.119 closest distance to " O   HOH Z 174 " =    2.525
peak=    3.118 closest distance to " O   HOH Z 145 " =    1.116
peak=    3.117 closest distance to " CA  ALA A 129 " =    1.282
peak=    3.114 closest distance to " O   HOH Z 340 " =    2.148
peak=    3.105 closest distance to " OE1 GLN A 240 " =    1.623
peak=    3.102 closest distance to " NH1 ARG A 138 " =    1.008
peak=    3.102 closest distance to " O   HOH Z 282 " =    1.793
peak=    3.099 closest distance to " O   HOH Z  22 " =    2.608
peak=    3.094 closest distance to " OD2 ASP A  50 " =    3.083
peak=    3.080 closest distance to " O   HOH Z 128 " =    2.321
peak=    3.070 closest distance to " O   HOH Z 134 " =    2.904
peak=    3.065 closest distance to " O   GLU A   2 " =    1.571
peak=    3.055 closest distance to " O   HOH Z 425 " =    2.137
peak=    3.047 closest distance to " CD1 ILE A 199 " =    0.851
peak=    3.042 closest distance to " CB  ARG A 156 " =    1.122
peak=    3.041 closest distance to " OD2 ASP A 200 " =    1.204
peak=    3.032 closest distance to " O   ASP A 124 " =    1.793
peak=    3.026 closest distance to " O   HOH Z  88 " =    2.930

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 216         
Filter by distance & map next to the model:
   mapped sites are within: 0.742 - 5.914
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 216 from: 216
   mapped sites are within: 0.742 - 5.914

peak=   -4.586 closest distance to " CD  ARG A  14 " =    3.509
peak=   -4.559 closest distance to " CG1 VAL A 112 " =    2.612
peak=   -4.535 closest distance to " CB  PRO A 243 " =    2.643
peak=   -4.419 closest distance to " CD  GLN A  58 " =    0.886
peak=   -4.340 closest distance to " O   HOH Z  73 " =    2.308
peak=   -4.298 closest distance to " O   HOH Z 231 " =    2.312
peak=   -4.295 closest distance to " CD  ARG A 156 " =    2.070
peak=   -4.219 closest distance to " CG1 VAL A 250 " =    2.679
peak=   -4.197 closest distance to " N   ALA A  43 " =    2.691
peak=   -4.188 closest distance to " O   PRO A 198 " =    1.357
peak=   -4.168 closest distance to " O   HOH Z 377 " =    1.953
peak=   -4.151 closest distance to " CE2 PHE A  61 " =    2.657
peak=   -4.148 closest distance to " CG  GLN A 223 " =    2.175
peak=   -4.113 closest distance to " CG2 ILE A  49 " =    2.806
peak=   -4.108 closest distance to " O   HOH Z 411 " =    5.645
peak=   -4.086 closest distance to " C   HIS A 108 " =    1.109
peak=   -4.075 closest distance to " CD2 TYR A 293 " =    2.049
peak=   -4.055 closest distance to " O   HOH Z 211 " =    1.064
peak=   -4.026 closest distance to " O   VAL A  67 " =    2.755
peak=   -3.967 closest distance to " O   HOH Z 198 " =    2.130
peak=   -3.937 closest distance to " O   HOH Z 216 " =    1.071
peak=   -3.922 closest distance to " CG1 VAL A 112 " =    2.881
peak=   -3.921 closest distance to " CE2 TYR A  30 " =    2.725
peak=   -3.919 closest distance to " CZ3 TRP A 179 " =    1.172
peak=   -3.905 closest distance to " CG  GLN A  11 " =    1.699
peak=   -3.894 closest distance to " CA  GLY A 241 " =    3.282
peak=   -3.892 closest distance to " O   HOH Z 196 " =    2.161
peak=   -3.888 closest distance to " O   HOH Z 394 " =    1.602
peak=   -3.875 closest distance to " O   HOH Z 128 " =    2.784
peak=   -3.867 closest distance to " OD1 ASN A 148 " =    1.458
peak=   -3.860 closest distance to " CD1 PHE A  59 " =    2.026
peak=   -3.820 closest distance to " OG BSER A 134 " =    1.391
peak=   -3.806 closest distance to " O   HOH Z   6 " =    2.364
peak=   -3.786 closest distance to " CB  ALA A  43 " =    2.717
peak=   -3.782 closest distance to " O   HOH Z  10 " =    1.569
peak=   -3.780 closest distance to " CG  ARG A 269 " =    2.387
peak=   -3.774 closest distance to " O   HOH Z 185 " =    2.295
peak=   -3.761 closest distance to " ND2 ASN A  45 " =    2.177
peak=   -3.757 closest distance to " CA  GLY A 241 " =    2.330
peak=   -3.756 closest distance to " O   HOH Z  38 " =    1.269
peak=   -3.746 closest distance to " OE1 GLN A  88 " =    0.999
peak=   -3.745 closest distance to " CB  ALA A 291 " =    2.394
peak=   -3.740 closest distance to " CA  ASP A 298 " =    1.072
peak=   -3.734 closest distance to " CA  GLY A 203 " =    2.516
peak=   -3.724 closest distance to " OG  SER A  97 " =    2.308
peak=   -3.658 closest distance to " C   GLY A  17 " =    1.186
peak=   -3.623 closest distance to " O   HOH Z 166 " =    1.809
peak=   -3.620 closest distance to " CA  VAL A  67 " =    2.960
peak=   -3.617 closest distance to " O   HOH Z 368 " =    1.760
peak=   -3.616 closest distance to " O   HOH Z  51 " =    1.571
peak=   -3.604 closest distance to " C   ASN A 285 " =    2.538
peak=   -3.596 closest distance to " CE BMET A  47 " =    1.719
peak=   -3.593 closest distance to " CE3 TRP A 150 " =    2.175
peak=   -3.582 closest distance to " O   HOH Z 111 " =    1.731
peak=   -3.578 closest distance to " CB  ALA A 129 " =    2.454
peak=   -3.577 closest distance to " OD1 ASP A 171 " =    1.595
peak=   -3.572 closest distance to " C   ALA A 158 " =    1.457
peak=   -3.571 closest distance to " O   ILE A 109 " =    2.642
peak=   -3.569 closest distance to " O   HOH Z 407 " =    3.383
peak=   -3.559 closest distance to " O   PHE A 218 " =    1.483
peak=   -3.552 closest distance to " CB  ASN A  39 " =    2.298
peak=   -3.543 closest distance to " O   HOH Z 393 " =    1.253
peak=   -3.543 closest distance to " CG1 VAL A 125 " =    1.937
peak=   -3.542 closest distance to " CE  MET A 105 " =    2.478
peak=   -3.542 closest distance to " O   HOH Z 290 " =    1.268
peak=   -3.538 closest distance to " O   HOH Z 232 " =    1.832
peak=   -3.537 closest distance to " CB  PRO A  54 " =    2.553
peak=   -3.535 closest distance to " CG1AVAL A  41 " =    2.901
peak=   -3.526 closest distance to " O   HOH Z  69 " =    1.679
peak=   -3.525 closest distance to " CG2 VAL A 189 " =    2.195
peak=   -3.523 closest distance to " CD1 LEU A 101 " =    2.451
peak=   -3.521 closest distance to " O   HOH Z  52 " =    1.477
peak=   -3.518 closest distance to " ND2 ASN A  60 " =    1.516
peak=   -3.517 closest distance to " OD2 ASP A 171 " =    1.872
peak=   -3.506 closest distance to " CA  GLY A 241 " =    2.905
peak=   -3.501 closest distance to " CG  HIS A  86 " =    1.141
peak=   -3.494 closest distance to " O   TYR A 186 " =    1.791
peak=   -3.486 closest distance to " O   HOH Z 114 " =    1.128
peak=   -3.482 closest distance to " NH2AARG A 275 " =    5.545
peak=   -3.482 closest distance to " CG  MET A 105 " =    0.956
peak=   -3.480 closest distance to " O   HOH Z 357 " =    2.157
peak=   -3.476 closest distance to " C   LEU A 143 " =    1.182
peak=   -3.450 closest distance to " O   HOH Z   6 " =    1.424
peak=   -3.441 closest distance to " O   HOH Z 275 " =    1.631
peak=   -3.434 closest distance to " O   HOH Z  19 " =    2.435
peak=   -3.432 closest distance to " O   HOH Z 193 " =    1.549
peak=   -3.425 closest distance to " NH2 ARG A  79 " =    1.528
peak=   -3.422 closest distance to " O   HOH Z 106 " =    1.976
peak=   -3.420 closest distance to " N   THR A 264 " =    1.333
peak=   -3.417 closest distance to " CA  GLY A 133 " =    2.319
peak=   -3.416 closest distance to " OXT GLY A 302 " =    3.227
peak=   -3.404 closest distance to " O   ALA A  10 " =    1.698
peak=   -3.400 closest distance to " O   HOH Z  65 " =    1.180
peak=   -3.398 closest distance to " O   VAL A 189 " =    2.620
peak=   -3.396 closest distance to " O   HOH Z 133 " =    1.204
peak=   -3.396 closest distance to " CB  ASP A 286 " =    2.332
peak=   -3.393 closest distance to " SG BCYS A 201 " =    1.198
peak=   -3.392 closest distance to " ND2 ASN A 249 " =    2.433
peak=   -3.390 closest distance to " CB  PHE A 192 " =    2.043
peak=   -3.386 closest distance to " O   HOH Z  37 " =    1.894
peak=   -3.384 closest distance to " O   SER A 210 " =    1.927
peak=   -3.366 closest distance to " O   HOH Z 189 " =    2.200
peak=   -3.366 closest distance to " CG2 ILE A 263 " =    2.348
peak=   -3.361 closest distance to " O   HOH Z 191 " =    5.914
peak=   -3.360 closest distance to " O   PRO A 163 " =    2.144
peak=   -3.357 closest distance to " O   HOH Z 102 " =    1.607
peak=   -3.356 closest distance to " CG2 THR A 178 " =    2.421
peak=   -3.348 closest distance to " NE2 GLN A 194 " =    1.918
peak=   -3.345 closest distance to " O   HOH Z 275 " =    1.893
peak=   -3.339 closest distance to " NE2 GLN A  88 " =    2.122
peak=   -3.338 closest distance to " O   HOH Z 421 " =    3.274
peak=   -3.337 closest distance to " O   GLY A 203 " =    2.496
peak=   -3.336 closest distance to " O   GLN A 240 " =    2.786
peak=   -3.333 closest distance to " CG  LEU A  83 " =    2.102
peak=   -3.328 closest distance to " ND2 ASN A  45 " =    1.187
peak=   -3.326 closest distance to " CB  ALA A  10 " =    2.214
peak=   -3.321 closest distance to " ND2 ASN A  69 " =    1.816
peak=   -3.321 closest distance to " CG  GLU A 277 " =    1.315
peak=   -3.319 closest distance to " OD1 ASP A 191 " =    1.760
peak=   -3.315 closest distance to " O   ALA A  34 " =    2.541
peak=   -3.312 closest distance to " O   HOH Z 372 " =    2.493
peak=   -3.308 closest distance to " NH2 ARG A 159 " =    2.362
peak=   -3.308 closest distance to " O   HOH Z 298 " =    2.564
peak=   -3.307 closest distance to " O   HOH Z 174 " =    3.022
peak=   -3.301 closest distance to " CD2 PHE A 225 " =    1.197
peak=   -3.295 closest distance to " O   HOH Z 259 " =    4.122
peak=   -3.292 closest distance to " NE2 GLN A 240 " =    1.711
peak=   -3.287 closest distance to " OH  TYR A 247 " =    1.804
peak=   -3.287 closest distance to " O   HOH Z  43 " =    1.576
peak=   -3.285 closest distance to " CG  ARG A  66 " =    2.319
peak=   -3.285 closest distance to " O   HOH Z 281 " =    2.472
peak=   -3.283 closest distance to " O   HOH Z 198 " =    1.446
peak=   -3.282 closest distance to " CB  ASP A 132 " =    2.331
peak=   -3.280 closest distance to " CD2 LEU A 237 " =    2.866
peak=   -3.278 closest distance to " O   HOH Z 156 " =    3.528
peak=   -3.277 closest distance to " O   HOH Z 114 " =    3.617
peak=   -3.277 closest distance to " CE3 TRP A  70 " =    1.890
peak=   -3.270 closest distance to " CG  PRO A 163 " =    2.110
peak=   -3.268 closest distance to " O   HOH Z 353 " =    2.227
peak=   -3.262 closest distance to " O   HOH Z 348 " =    2.221
peak=   -3.257 closest distance to " O   HOH Z  60 " =    1.490
peak=   -3.255 closest distance to " O   HOH Z 176 " =    0.742
peak=   -3.252 closest distance to " O   HOH Z 359 " =    2.978
peak=   -3.251 closest distance to " CD1 LEU A  83 " =    2.801
peak=   -3.251 closest distance to " O   HOH Z  78 " =    2.102
peak=   -3.250 closest distance to " CG2AVAL A  72 " =    3.011
peak=   -3.250 closest distance to " OH  TYR A 247 " =    2.214
peak=   -3.249 closest distance to " CZ  PHE A  38 " =    2.767
peak=   -3.248 closest distance to " O   HOH Z 389 " =    2.122
peak=   -3.245 closest distance to " O   HOH Z 183 " =    1.472
peak=   -3.245 closest distance to " O   GLY A 211 " =    1.403
peak=   -3.243 closest distance to " CG  GLN A  88 " =    0.946
peak=   -3.240 closest distance to " O   GLY A  80 " =    2.662
peak=   -3.236 closest distance to " O   SER A 135 " =    1.444
peak=   -3.235 closest distance to " O   HOH Z 113 " =    2.489
peak=   -3.234 closest distance to " O   VAL A 189 " =    1.726
peak=   -3.234 closest distance to " CB  ALA A   9 " =    2.541
peak=   -3.233 closest distance to " CD1 LEU A 228 " =    2.394
peak=   -3.232 closest distance to " O   HOH Z   1 " =    1.702
peak=   -3.230 closest distance to " O   HOH Z  64 " =    1.495
peak=   -3.229 closest distance to " CG  GLU A  53 " =    1.514
peak=   -3.223 closest distance to " O   HOH Z 313 " =    1.868
peak=   -3.222 closest distance to " O   HOH Z 396 " =    1.838
peak=   -3.222 closest distance to " CG1BVAL A  72 " =    2.447
peak=   -3.216 closest distance to " O   HOH Z 236 " =    1.407
peak=   -3.214 closest distance to " O   HOH Z 145 " =    0.931
peak=   -3.212 closest distance to " O   HOH Z  32 " =    1.948
peak=   -3.212 closest distance to " N   ALA A 248 " =    1.691
peak=   -3.202 closest distance to " O   HOH Z 351 " =    1.617
peak=   -3.199 closest distance to " CB  PHE A  16 " =    2.495
peak=   -3.195 closest distance to " CB  ALA A 100 " =    2.093
peak=   -3.193 closest distance to " O   HOH Z 365 " =    1.448
peak=   -3.193 closest distance to " NE2 GLN A 103 " =    1.835
peak=   -3.183 closest distance to " OG BSER A 210 " =    1.588
peak=   -3.181 closest distance to " O   HOH Z   9 " =    1.911
peak=   -3.180 closest distance to " O   HOH Z 264 " =    1.769
peak=   -3.179 closest distance to " O   GLY A  98 " =    2.207
peak=   -3.174 closest distance to " OD1 ASN A 187 " =    1.544
peak=   -3.173 closest distance to " CG  TRP A 266 " =    1.848
peak=   -3.173 closest distance to " O   HOH Z 409 " =    4.646
peak=   -3.171 closest distance to " CD1 LEU A   5 " =    2.619
peak=   -3.168 closest distance to " CG2BVAL A  41 " =    2.305
peak=   -3.168 closest distance to " O   ALA A 180 " =    1.466
peak=   -3.163 closest distance to " O   HOH Z 411 " =    1.191
peak=   -3.156 closest distance to " CG1BVAL A  41 " =    2.713
peak=   -3.154 closest distance to " O   HOH Z 350 " =    1.915
peak=   -3.148 closest distance to " N   SER A 276 " =    1.365
peak=   -3.147 closest distance to " O   HOH Z 323 " =    1.455
peak=   -3.144 closest distance to " CB  TRP A  85 " =    2.483
peak=   -3.136 closest distance to " O   HOH Z 435 " =    2.801
peak=   -3.133 closest distance to " O   HOH Z 219 " =    4.515
peak=   -3.130 closest distance to " CZ  PHE A  38 " =    2.053
peak=   -3.129 closest distance to " ND2 ASN A  60 " =    4.113
peak=   -3.129 closest distance to " O   ASP A  27 " =    2.066
peak=   -3.128 closest distance to " NE1 TRP A 266 " =    2.200
peak=   -3.117 closest distance to " OD1 ASN A 173 " =    1.295
peak=   -3.113 closest distance to " C   ASN A 176 " =    1.407
peak=   -3.112 closest distance to " N   LYS A 166 " =    2.045
peak=   -3.106 closest distance to " O   SER A 276 " =    1.722
peak=   -3.100 closest distance to " O   HOH Z  70 " =    2.168
peak=   -3.094 closest distance to " O   HOH Z 357 " =    2.137
peak=   -3.093 closest distance to " O   HOH Z 171 " =    2.100
peak=   -3.092 closest distance to " NZ  LYS A 166 " =    1.311
peak=   -3.086 closest distance to " CD2 PHE A  59 " =    2.458
peak=   -3.078 closest distance to " O   HOH Z 251 " =    1.841
peak=   -3.078 closest distance to " O   HOH Z 364 " =    2.930
peak=   -3.076 closest distance to " C   SER A 206 " =    1.327
peak=   -3.062 closest distance to " NH2 ARG A  66 " =    2.257
peak=   -3.060 closest distance to " O   HOH Z 318 " =    2.034
peak=   -3.059 closest distance to " CG  GLN A  58 " =    1.191
peak=   -3.058 closest distance to " CD  GLU A 236 " =    1.150
peak=   -3.055 closest distance to " CG  PHE A 283 " =    2.669
peak=   -3.050 closest distance to " O   HOH Z 150 " =    2.079
peak=   -3.048 closest distance to " CD1 TRP A  70 " =    1.127
peak=   -3.043 closest distance to " O   HOH Z 418 " =    1.545
peak=   -3.003 closest distance to " ND2 ASN A 249 " =    2.232

================= 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    :  0.3874 0.3788   6.168947e+00   6.152780e+00
   1_bss:  0.3764 0.3703   6.152742e+00   6.134845e+00
   1_xyz:  0.2431 0.2652   5.782149e+00   5.853910e+00
   1_adp:  0.2199 0.2722   5.724044e+00   5.879504e+00
   1_occ:  0.2194 0.2716   5.723490e+00   5.880190e+00
   2_bss:  0.2173 0.2708   5.721217e+00   5.879052e+00
   2_xyz:  0.1669 0.2153   5.485597e+00   5.679946e+00
   2_adp:  0.1582 0.2009   5.434267e+00   5.623158e+00
   2_occ:  0.1580 0.2010   5.433735e+00   5.623237e+00
   3_bss:  0.1581 0.2006   5.433187e+00   5.621251e+00
   3_xyz:  0.1331 0.1752   5.282698e+00   5.490421e+00
   3_adp:  0.1283 0.1721   5.254728e+00   5.468835e+00
   3_occ:  0.1283 0.1721   5.254518e+00   5.468636e+00
   4_bss:  0.1283 0.1723   5.254840e+00   5.468684e+00
   4_xyz:  0.1254 0.1699   5.236237e+00   5.455422e+00
   4_adp:  0.1246 0.1712   5.236357e+00   5.461477e+00
   4_occ:  0.1246 0.1712   5.236260e+00   5.461422e+00
   5_bss:  0.1245 0.1711   5.236319e+00   5.461517e+00
   5_xyz:  0.1164 0.1670   5.190491e+00   5.435792e+00
   5_adp:  0.1154 0.1660   5.182412e+00   5.428629e+00
   5_occ:  0.1154 0.1661   5.182539e+00   5.428928e+00
   5_bss:  0.1152 0.1660   5.182715e+00   5.429257e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  80.000  -0.801  -2.419   3.916  -0.000   0.000   0.000
   1_xyz:  0.300  80.000  -0.801  -2.419   3.916  -0.000   0.000   0.000
   1_adp:  0.300  80.000  -0.801  -2.419   3.916  -0.000   0.000   0.000
   1_occ:  0.300  80.000  -0.801  -2.419   3.916  -0.000   0.000   0.000
   2_bss:  0.341  89.345  -1.845  -2.401   0.662  -0.000   0.000   0.000
   2_xyz:  0.341  89.345  -1.845  -2.401   0.662  -0.000   0.000   0.000
   2_adp:  0.341  89.345  -1.845  -2.401   0.662  -0.000   0.000   0.000
   2_occ:  0.341  89.345  -1.845  -2.401   0.662  -0.000   0.000   0.000
   3_bss:  0.337  81.433  -2.022  -2.125  -0.028  -0.000  -0.000  -0.000
   3_xyz:  0.337  81.433  -2.022  -2.125  -0.028  -0.000  -0.000  -0.000
   3_adp:  0.337  81.433  -2.022  -2.125  -0.028  -0.000  -0.000  -0.000
   3_occ:  0.337  81.433  -2.022  -2.125  -0.028  -0.000  -0.000  -0.000
   4_bss:  0.330  74.281  -1.920  -1.941  -0.143  -0.000  -0.000  -0.000
   4_xyz:  0.330  74.281  -1.920  -1.941  -0.143  -0.000  -0.000  -0.000
   4_adp:  0.330  74.281  -1.920  -1.941  -0.143  -0.000  -0.000  -0.000
   4_occ:  0.330  74.281  -1.920  -1.941  -0.143  -0.000  -0.000  -0.000
   5_bss:  0.329  75.239  -1.785  -1.735  -0.085  -0.000  -0.000  -0.000
   5_xyz:  0.329  75.239  -1.785  -1.735  -0.085  -0.000  -0.000  -0.000
   5_adp:  0.329  75.239  -1.785  -1.735  -0.085  -0.000  -0.000  -0.000
   5_occ:  0.329  75.239  -1.785  -1.735  -0.085  -0.000  -0.000  -0.000
   5_bss:  0.323  69.271  -1.314  -1.323   0.280  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  42.203 0.6178  0.7663    42015.153
   1_bss:  41.261 0.6281  0.7927    39904.760
   1_xyz:  26.206 0.8003  0.9679    18158.675
   1_adp:  27.305 0.7877  0.9589    19399.002
   1_occ:  27.334 0.7874  0.9578    19414.395
   2_bss:  27.134 0.7898  0.9146    19344.178
   2_xyz:  20.862 0.8531  0.9574    11827.356
   2_adp:  19.069 0.8712  0.9560    10398.113
   2_occ:  19.069 0.8712  0.9558    10396.952
   3_bss:  19.012 0.8716  0.9491    10329.323
   3_xyz:  16.236 0.8961  0.9667     7832.207
   3_adp:  15.674 0.9013  0.9608     7524.251
   3_occ:  15.669 0.9013  0.9608     7520.990
   4_bss:  15.677 0.9013  0.9629     7530.121
   4_xyz:  15.355 0.9041  0.9638     7321.326
   4_adp:  15.475 0.9032  0.9540     7405.833
   4_occ:  15.471 0.9032  0.9539     7403.843
   5_bss:  15.473 0.9032  0.9583     7405.682
   5_xyz:  14.923 0.9078  0.9628     7014.641
   5_adp:  14.763 0.9092  0.9548     6912.947
   5_occ:  14.769 0.9091  0.9547     6914.525
   5_bss:  14.776 0.9091  0.9688     6917.831
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6274e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6274e-01
   1_xyz:   1.260  0.010  0.079 15.317  0.006  4.116   8.5931e-02
   1_adp:   1.260  0.010  0.079 15.317  0.006  4.116   8.5931e-02
   1_occ:   1.260  0.010  0.079 15.317  0.006  4.116   8.5931e-02
   2_bss:   1.260  0.010  0.079 15.317  0.006  4.116   8.5931e-02
   2_xyz:   1.035  0.007  0.073 14.575  0.004  4.131   5.8866e-02
   2_adp:   1.035  0.007  0.073 14.575  0.004  4.131   5.8866e-02
   2_occ:   1.035  0.007  0.073 14.575  0.004  4.131   5.8866e-02
   3_bss:   1.035  0.007  0.073 14.575  0.004  4.131   5.8866e-02
   3_xyz:   0.988  0.008  0.074 14.695  0.003  4.142   5.7326e-02
   3_adp:   0.988  0.008  0.074 14.695  0.003  4.142   5.7326e-02
   3_occ:   0.988  0.008  0.074 14.695  0.003  4.142   5.7326e-02
   4_bss:   0.988  0.008  0.074 14.695  0.003  4.142   5.7326e-02
   4_xyz:   0.976  0.008  0.075 14.659  0.003  4.115   5.7913e-02
   4_adp:   0.976  0.008  0.075 14.659  0.003  4.115   5.7913e-02
   4_occ:   0.976  0.008  0.075 14.659  0.003  4.115   5.7913e-02
   5_bss:   0.976  0.008  0.075 14.659  0.003  4.115   5.7913e-02
   5_xyz:   1.095  0.011  0.082 14.840  0.004  4.122   7.3729e-02
   5_adp:   1.095  0.011  0.082 14.840  0.004  4.122   7.3729e-02
   5_occ:   1.095  0.011  0.082 14.840  0.004  4.122   7.3729e-02
   5_bss:   1.095  0.011  0.082 14.840  0.004  4.122   7.3729e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4470e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4470e-01
   1_xyz:   8.665  0.070  0.279 84.852  0.047  2.219   8.7914e-02
   1_adp:   8.665  0.070  0.279 84.852  0.047  2.219   8.7914e-02
   1_occ:   8.665  0.070  0.279 84.852  0.047  2.219   8.7914e-02
   2_bss:   8.665  0.070  0.279 84.852  0.047  2.219   8.7914e-02
   2_xyz:   6.874  0.035  0.237 82.984  0.045  2.375   5.3872e-02
   2_adp:   6.874  0.035  0.237 82.984  0.045  2.375   5.3872e-02
   2_occ:   6.874  0.035  0.237 82.984  0.045  2.375   5.3872e-02
   3_bss:   6.874  0.035  0.237 82.984  0.045  2.375   5.3872e-02
   3_xyz:   7.554  0.041  0.229 84.165  0.031  2.411   4.5353e-02
   3_adp:   7.554  0.041  0.229 84.165  0.031  2.411   4.5353e-02
   3_occ:   7.554  0.041  0.229 84.165  0.031  2.411   4.5353e-02
   4_bss:   7.554  0.041  0.229 84.165  0.031  2.411   4.5353e-02
   4_xyz:   7.404  0.038  0.227 83.413  0.039  2.415   3.4808e-02
   4_adp:   7.404  0.038  0.227 83.413  0.039  2.415   3.4808e-02
   4_occ:   7.404  0.038  0.227 83.413  0.039  2.415   3.4808e-02
   5_bss:   7.404  0.038  0.227 83.413  0.039  2.415   3.4808e-02
   5_xyz:   7.502  0.056  0.263 83.494  0.038  2.353   5.1325e-02
   5_adp:   7.502  0.056  0.263 83.494  0.038  2.353   5.1325e-02
   5_occ:   7.502  0.056  0.263 83.494  0.038  2.353   5.1325e-02
   5_bss:   7.502  0.056  0.263 83.494  0.038  2.353   5.1325e-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:  90.98   0.00  18.01  81.99   0.00  13.61  90.98   2.71  41.99
   1_occ:  90.98   0.00  18.01  81.99   0.00  13.61  90.98   2.71  41.99
   2_bss:  90.98   0.00  18.01  81.99   0.00  13.61  90.98   2.71  41.99
   2_xyz:  90.98   0.00  18.01  81.99   0.00  13.61  90.98   2.71  41.99
   2_adp:  91.10   0.92  17.50  80.01   0.92  13.09  91.10   4.36  41.54
   2_occ:  91.10   0.92  17.50  80.01   0.92  13.09  91.10   4.36  41.54
   3_bss:  91.10   0.92  17.50  80.01   0.92  13.09  91.10   4.36  41.54
   3_xyz:  91.10   0.92  17.50  80.01   0.92  13.09  91.10   4.36  41.54
   3_adp:  91.71   0.72  17.28  80.82   0.72  12.79  91.71   5.28  41.73
   3_occ:  91.71   0.72  17.28  80.82   0.72  12.79  91.71   5.28  41.73
   4_bss:  91.71   0.72  17.28  80.82   0.72  12.79  91.71   5.28  41.73
   4_xyz:  91.71   0.72  17.28  80.82   0.72  12.79  91.71   5.28  41.73
   4_adp:  95.80   0.00  17.37  86.46   0.00  12.69  95.80   5.05  42.82
   4_occ:  95.80   0.00  17.37  86.46   0.00  12.69  95.80   5.05  42.82
   5_bss:  95.80   0.00  17.37  86.46   0.00  12.69  95.80   5.05  42.82
   5_xyz:  95.80   0.00  17.37  86.46   0.00  12.69  95.80   5.05  42.82
   5_adp: 102.18   0.00  17.20  92.72   0.00  12.49 102.18   2.27  42.86
   5_occ: 102.18   0.00  17.20  92.72   0.00  12.49 102.18   2.27  42.86
   5_bss: 102.18   0.00  17.20  92.72   0.00  12.49 102.18   2.27  42.87
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.472    0.024    0.327
   1_adp:    1.472    0.024    0.327
   1_occ:    1.472    0.024    0.327
   2_bss:    1.472    0.024    0.327
   2_xyz:    1.233    0.010    0.397
   2_adp:    1.233    0.010    0.397
   2_occ:    1.233    0.010    0.397
   3_bss:    1.233    0.010    0.397
   3_xyz:    1.185    0.026    0.480
   3_adp:    1.185    0.026    0.480
   3_occ:    1.185    0.026    0.480
   4_bss:    1.185    0.026    0.480
   4_xyz:    1.179    0.034    0.483
   4_adp:    1.179    0.034    0.483
   4_occ:    1.179    0.034    0.483
   5_bss:    1.179    0.034    0.483
   5_xyz:    1.299    0.054    0.507
   5_adp:    1.299    0.054    0.507
   5_occ:    1.299    0.054    0.507
   5_bss:    1.299    0.054    0.507
------------------------------------------------------------------------

CPU time actual refinement: 342.62


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1043/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_1043/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1043/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1043/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1043/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 342.48 
  Macro-tasks:
    bulk solvent and scale       = 62.76  
    individual site refinement   = 127.53 
    weights calculation          = 29.40  
    collect and process          = 6.73   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 226.52 
  Micro-tasks:
    mask                            = 1.75   
    f_calc                          = 99.64  
    alpha_beta                      = 8.54   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 107.89 
    fmodel                         = 9.54   
    r_factors                      = 0.39   
    phase_errors                   = 11.15  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 240.32 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.852 micro seconds
Total CPU time: 5.93 minutes
from_scatterers_fft:    629 calls, 99.34 s
gradients_fft:          574 calls, 95.07 s

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

# Date 2008-01-16 Time 06:17:25 PST -0800 (1200493045.14 s)
Start R-work = 0.3874, R-free = 0.3788 (no bulk solvent and anisotropic scale)
Final R-work = 0.1340, R-free = 0.1813 (no bulk solvent and anisotropic scale)

Start R-work = 0.3764, R-free = 0.3703
Final R-work = 0.1152, R-free = 0.1660