# Date 2008-01-16 Time 06:05:50 PST -0800 (1200492350.25 s)
#phil __OFF__

Command line arguments: "../1006.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 24557
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1006

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 46.4607, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.4607, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1569 1.98276
Completeness in resolution range: 0.956354
Completeness with d_max=infinity: 0.953514

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1569
                             d_min =   1.9828

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.4607, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1569 1.98276
Completeness in resolution range: 0.956354
Completeness with d_max=infinity: 0.953514

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1573 -  4.2434 [2147/2173]  1934   213   9.9%
  bin  2:  4.2434 -  3.3804 [2067/2087]  1858   209  10.1%
  bin  3:  3.3804 -  2.9567 [2044/2063]  1842   202   9.9%
  bin  4:  2.9567 -  2.6880 [2025/2055]  1820   205  10.1%
  bin  5:  2.6880 -  2.4963 [2012/2031]  1817   195   9.7%
  bin  6:  2.4963 -  2.3496 [1993/2018]  1783   210  10.5%
  bin  7:  2.3496 -  2.2324 [2000/2028]  1803   197   9.8%
  bin  8:  2.2324 -  2.1355 [1972/2008]  1777   195   9.9%
  bin  9:  2.1355 -  2.0535 [1963/2005]  1764   199  10.1%
  bin 10:  2.0535 -  1.9828 [1366/2015]  1232   134   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1006/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: 0.13 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: 18
        2.42 -     3.04: 2184
        3.04 -     3.66: 4685
        3.66 -     4.28: 9036
        4.28 -     4.90: 12295
  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
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.230 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.257 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.304 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28213 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_1006/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1006/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 46.4607 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3330   r_free= 0.3301   ksol= 0.00   Bsol= 0.00   scale= 0.965    |
|                                                                             |
| 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:   0.39 A                  |
| x-ray target function (ml) for work reflections: 6.068299                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1573 -  4.7332 0.99   1395  157 0.2924 0.2809      6.3597      6.3047|
|  2:  4.7332 -  3.7760 0.99   1345  148 0.2652 0.2610      6.4754      6.4067|
|  3:  3.7760 -  3.3044 0.99   1326  144 0.2810 0.2573      6.3346      6.3965|
|  4:  3.3044 -  3.0048 0.99   1312  153 0.3091 0.3388      6.2556       6.278|
|  5:  3.0048 -  2.7909 0.99   1298  143 0.3468 0.3216      6.1356      6.1391|
|  6:  2.7909 -  2.6272 0.99   1304  140 0.3344 0.3456      6.0394      6.0213|
|  7:  2.6272 -  2.4963 0.99   1291  139 0.3575 0.3453      6.0462      6.0551|
|  8:  2.4963 -  2.3880 0.98   1259  147 0.3677 0.3598      5.9901      5.9596|
|  9:  2.3880 -  2.2964 0.98   1274  148 0.3613 0.3588      5.9343      5.9249|
| 10:  2.2964 -  2.2174 1.00   1296  140 0.3780 0.3783       5.934      5.9242|
| 11:  2.2174 -  2.1483 0.98   1291  136 0.3884 0.4213      5.9087      5.9404|
| 12:  2.1483 -  2.0870 0.98   1247  145 0.3944 0.3826      5.8476       5.866|
| 13:  2.0870 -  2.0322 0.99   1282  137 0.3934 0.4023      5.7443      5.6797|
| 14:  2.0322 -  1.9828 0.55    710   82 0.4131 0.4040      5.7385      5.7165|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1573 -  4.7332  1395   157  0.80  25.37   0.86     0.82      40981.40|
|  2:  4.7332 -  3.7760  1345   148  0.84  21.92   0.97     0.92      45518.95|
|  3:  3.7760 -  3.3044  1326   144  0.80  26.72   0.99     0.95      47350.75|
|  4:  3.3044 -  3.0048  1312   153  0.76  30.03   0.98     0.93      43476.85|
|  5:  3.0048 -  2.7909  1298   143  0.70  35.80   0.97     0.89      37924.71|
|  6:  2.7909 -  2.6272  1304   140  0.70  35.70   0.99     0.88      31978.18|
|  7:  2.6272 -  2.4963  1291   139  0.70  35.96   1.00     0.87      29419.96|
|  8:  2.4963 -  2.3880  1259   147  0.69  36.70   0.99     0.89      26685.36|
|  9:  2.3880 -  2.2964  1274   148  0.68  37.20   1.02     0.89      25464.90|
| 10:  2.2964 -  2.2174  1296   140  0.67  38.62   1.04     0.90      24234.56|
| 11:  2.2174 -  2.1483  1291   136  0.65  40.46   1.04     0.89      24363.94|
| 12:  2.1483 -  2.0870  1247   145  0.64  40.73   1.02     0.87      22478.87|
| 13:  2.0870 -  2.0322  1282   137  0.61  43.51   1.02     0.86      19723.17|
| 14:  2.0322 -  1.9828   710    82  0.65  40.24   1.02     0.86      15715.51|
|alpha:            min =        0.82 max =            0.95 mean =         0.89|
|beta:             min =    15715.51 max =        47350.75 mean =     31792.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.71|
|phase err.(work): min =        0.00 max =           89.98 mean =        34.61|
|phase err.(test): min =        0.00 max =           89.73 mean =        34.40|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.639866              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.909   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.807323              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.539   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       17 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      195 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1989 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1852 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2833 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4645 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4391 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5616 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6679 |
|-----------------------------------------------------------------------------|
|-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 |        0.162 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.806 |       0.160 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.972)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3330   r_free= 0.3301   ksol= 0.00   Bsol= 0.00   scale= 0.965    |
|                                                                             |
| 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:   0.39 A                  |
| x-ray target function (ml) for work reflections: 6.068299                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3206   r_free= 0.3192   ksol= 0.33   Bsol= 52.66   scale= 0.977   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.12,-0.24,-1.74,-0.00,-0.00,-0.00); trace/3= -0.62                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 6.049721                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.140688              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.215   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.402454              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.361   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3206      final r-factor (work) = 0.1784          |
| start r-factor (free) = 0.3192      final r-factor (free) = 0.2025          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.6970 = 4.14 * 0.50 * 6.0548 + 1.00 * 0.1616                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9977 = 4.14 * 0.50 * 5.7598 + 1.00 * 0.0731                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1784      final r-factor (work) = 0.1624          |
| start r-factor (free) = 0.2025      final r-factor (free) = 0.2084          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3242 = 0.40 * 1.00 * 5.7598 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1989 = 0.40 * 1.00 * 5.4405 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.972)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.51    76.54   17.27    None  None   None       |
|    all(noH): 2823   0      1.51    76.54   17.27    None  None   None       |
|    Sol.    : 438    0      5.04    76.54   40.01    None  None   None       |
|    Mac.    : 2385   0      1.51    70.54   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:     1.512 -   9.015:  745   |   5:    39.024 -  46.526:  101        |
|      1:     9.015 -  16.517: 1194   |   6:    46.526 -  54.028:   78        |
|      2:    16.517 -  24.019:  358   |   7:    54.028 -  61.531:   54        |
|      3:    24.019 -  31.521:  126   |   8:    61.531 -  69.033:   33        |
|      4:    31.521 -  39.024:  123   |   9:    69.033 -  76.535:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1624 r_free = 0.2084             target_work(ml) = 5.455         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1621 r_free = 0.2082             target_work(ml) = 5.454         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1621   r_free= 0.2082   ksol= 0.33   Bsol= 52.66   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.12,-0.24,-1.74,-0.00,-0.00,-0.00); trace/3= -0.62                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.454054                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1606   r_free= 0.2055   ksol= 0.34   Bsol= 60.32   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.83,-2.29,-1.85,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.448729                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.864838              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.962   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.163787              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.950  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1606      final r-factor (work) = 0.1297          |
| start r-factor (free) = 0.2055      final r-factor (free) = 0.1748          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1626 = 1.86 * 0.50 * 5.4584 + 1.00 * 0.0731                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0433 = 1.86 * 0.50 * 5.3557 + 1.00 * 0.0495                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1297      final r-factor (work) = 0.1260          |
| start r-factor (free) = 0.1748      final r-factor (free) = 0.1669          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8865 = 0.16 * 1.00 * 5.3557 + 1.00 * 0.0093                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8683 = 0.16 * 1.00 * 5.2569 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.972)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.70    75.58   16.91    None  None   None       |
|    all(noH): 2823   0      1.70    75.58   16.91    None  None   None       |
|    Sol.    : 438    0      5.89    75.58   38.42    None  None   None       |
|    Mac.    : 2385   0      1.70    72.45   12.96    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.698 -   9.086:  719   |   5:    38.641 -  46.029:  101        |
|      1:     9.086 -  16.475: 1254   |   6:    46.029 -  53.418:   80        |
|      2:    16.475 -  23.864:  340   |   7:    53.418 -  60.807:   57        |
|      3:    23.864 -  31.252:  131   |   8:    60.807 -  68.195:   20        |
|      4:    31.252 -  38.641:  112   |   9:    68.195 -  75.584:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1260 r_free = 0.1669             target_work(ml) = 5.232         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1259 r_free = 0.1670             target_work(ml) = 5.232         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1259   r_free= 0.1670   ksol= 0.34   Bsol= 60.32   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.83,-2.29,-1.85,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.231958                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1258   r_free= 0.1664   ksol= 0.34   Bsol= 60.32   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.65,-1.59,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.230607                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.611402              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.234  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.955859              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.526  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1258      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1664      final r-factor (free) = 0.1569          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9121 = 2.61 * 0.50 * 5.2559 + 1.00 * 0.0495                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8313 = 2.61 * 0.50 * 5.1852 + 1.00 * 0.0609                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1138      final r-factor (work) = 0.1113          |
| start r-factor (free) = 0.1569      final r-factor (free) = 0.1570          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9636 = 0.96 * 1.00 * 5.1852 + 1.00 * 0.0072                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9238 = 0.96 * 1.00 * 5.1414 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.972)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.46    86.74   17.38    None  None   None       |
|    all(noH): 2823   0      0.46    86.74   17.38    None  None   None       |
|    Sol.    : 438    0      3.82    86.74   40.82    None  None   None       |
|    Mac.    : 2385   0      0.46    85.25   13.08    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:     0.461 -   9.088:  775   |   5:    43.599 -  52.227:   94        |
|      1:     9.088 -  17.716: 1291   |   6:    52.227 -  60.855:   75        |
|      2:    17.716 -  26.344:  274   |   7:    60.855 -  69.482:   41        |
|      3:    26.344 -  34.972:  137   |   8:    69.482 -  78.110:   19        |
|      4:    34.972 -  43.599:  110   |   9:    78.110 -  86.738:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1113 r_free = 0.1570             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1113 r_free = 0.1571             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1571   ksol= 0.34   Bsol= 60.32   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.65,-1.59,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.141019                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1570   ksol= 0.33   Bsol= 60.32   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.61,-1.42,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.140702                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.649304              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.395  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.328592              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.935  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1113      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1570      final r-factor (free) = 0.1575          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3006 = 1.65 * 0.50 * 5.1412 + 1.00 * 0.0609                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2935 = 1.65 * 0.50 * 5.1444 + 1.00 * 0.0512                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1120      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1575      final r-factor (free) = 0.1573          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6997 = 0.33 * 1.00 * 5.1444 + 1.00 * 0.0093                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7003 = 0.33 * 1.00 * 5.1477 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.972)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.70    87.14   17.08    None  None   None       |
|    all(noH): 2823   0      0.70    87.14   17.08    None  None   None       |
|    Sol.    : 438    0      4.36    87.14   39.80    None  None   None       |
|    Mac.    : 2385   0      0.70    86.11   12.91    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.701 -   9.344:  885   |   5:    43.918 -  52.562:   81        |
|      1:     9.344 -  17.988: 1200   |   6:    52.562 -  61.205:   69        |
|      2:    17.988 -  26.631:  267   |   7:    61.205 -  69.849:   32        |
|      3:    26.631 -  35.275:  142   |   8:    69.849 -  78.492:   15        |
|      4:    35.275 -  43.918:  125   |   9:    78.492 -  87.136:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1120 r_free = 0.1573             target_work(ml) = 5.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1119 r_free = 0.1572             target_work(ml) = 5.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1572   ksol= 0.33   Bsol= 60.32   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.61,-1.42,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.147160                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1572   ksol= 0.33   Bsol= 60.32   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,-2.51,-1.24,-0.00,-0.00,-0.00); trace/3= -1.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.147204                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.901949              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 165.581  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.983545              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.369  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1119      final r-factor (work) = 0.1076          |
| start r-factor (free) = 0.1572      final r-factor (free) = 0.1567          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5209 = 2.90 * 0.50 * 5.1481 + 1.00 * 0.0512                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5100 = 2.90 * 0.50 * 5.1296 + 1.00 * 0.0671                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1076      final r-factor (work) = 0.1073          |
| start r-factor (free) = 0.1567      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0540 = 0.98 * 1.00 * 5.1296 + 1.00 * 0.0088                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0468 = 0.98 * 1.00 * 5.1215 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.972)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.22    89.85   17.02    None  None   None       |
|    all(noH): 2823   0      0.22    89.85   17.02    None  None   None       |
|    Sol.    : 438    0      5.64    89.85   40.12    None  None   None       |
|    Mac.    : 2385   0      0.22    88.78   12.78    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:     0.218 -   9.182:  904   |   5:    45.035 -  53.998:   87        |
|      1:     9.182 -  18.145: 1197   |   6:    53.998 -  62.962:   71        |
|      2:    18.145 -  27.108:  255   |   7:    62.962 -  71.925:   25        |
|      3:    27.108 -  36.072:  143   |   8:    71.925 -  80.888:   13        |
|      4:    36.072 -  45.035:  121   |   9:    80.888 -  89.852:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1073 r_free = 0.1572             target_work(ml) = 5.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1073 r_free = 0.1571             target_work(ml) = 5.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1073   r_free= 0.1571   ksol= 0.33   Bsol= 60.32   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,-2.51,-1.24,-0.00,-0.00,-0.00); trace/3= -1.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.123791                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1573 -  4.7332 0.99   1395  157 0.0964 0.1289      5.3683       5.544|
|  2:  4.7332 -  3.7760 0.99   1345  148 0.0829 0.1108      5.4197      5.6111|
|  3:  3.7760 -  3.3044 0.99   1326  144 0.1038 0.1506      5.4584      5.8506|
|  4:  3.3044 -  3.0048 0.99   1312  153 0.1152 0.1667      5.4337      5.5977|
|  5:  3.0048 -  2.7909 0.99   1298  143 0.1305 0.1731      5.3133      5.5521|
|  6:  2.7909 -  2.6272 0.99   1304  140 0.1153 0.1829      5.1874      5.4447|
|  7:  2.6272 -  2.4963 0.99   1291  139 0.1208 0.1556      5.1442      5.3187|
|  8:  2.4963 -  2.3880 0.98   1259  147 0.1099 0.1725      5.0124      5.3299|
|  9:  2.3880 -  2.2964 0.98   1274  148 0.1100 0.1763      4.9988      5.3187|
| 10:  2.2964 -  2.2174 1.00   1296  140 0.1063 0.1693      4.9217      5.1836|
| 11:  2.2174 -  2.1483 0.98   1291  136 0.1077 0.1788      4.9297      5.2585|
| 12:  2.1483 -  2.0870 0.98   1247  145 0.1052 0.1630      4.8548       5.134|
| 13:  2.0870 -  2.0322 0.99   1282  137 0.1093 0.1755      4.7674      5.0492|
| 14:  2.0322 -  1.9828 0.55    710   82 0.0999 0.1670      4.6443      4.9184|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1573 -  4.7332  1395   157  0.94   8.93   0.98     0.95       7035.40|
|  2:  4.7332 -  3.7760  1345   148  0.95   7.94   1.01     1.00       8984.66|
|  3:  3.7760 -  3.3044  1326   144  0.94  11.13   1.02     1.02      10091.67|
|  4:  3.3044 -  3.0048  1312   153  0.92  13.62   1.01     0.98      10268.17|
|  5:  3.0048 -  2.7909  1298   143  0.90  16.07   0.99     0.97       8334.03|
|  6:  2.7909 -  2.6272  1304   140  0.90  15.79   0.99     0.96       7010.41|
|  7:  2.6272 -  2.4963  1291   139  0.91  15.21   0.99     0.96       6112.10|
|  8:  2.4963 -  2.3880  1259   147  0.91  14.79   0.98     0.96       4828.08|
|  9:  2.3880 -  2.2964  1274   148  0.91  14.71   0.99     0.96       4731.52|
| 10:  2.2964 -  2.2174  1296   140  0.91  15.25   0.99     0.96       4173.06|
| 11:  2.2174 -  2.1483  1291   136  0.90  15.81   0.98     0.94       4317.36|
| 12:  2.1483 -  2.0870  1247   145  0.91  14.96   1.00     0.99       3922.18|
| 13:  2.0870 -  2.0322  1282   137  0.90  16.22   0.98     0.96       3287.72|
| 14:  2.0322 -  1.9828   710    82  0.92  14.61   0.96     0.93       2554.88|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2554.88 max =        10268.17 mean =      6273.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.85|
|phase err.(test): min =        0.00 max =           89.91 mean =        13.39|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1072   r_free= 0.1571   ksol= 0.33   Bsol= 60.32   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-2.30,-1.01,-0.00,-0.00,-0.00); trace/3= -1.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.123921                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1072   r_free= 0.1571   ksol= 0.33   Bsol= 60.32   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-2.30,-1.01,-0.00,-0.00,-0.00); trace/3= -1.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.123921                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1573 -  4.7332 0.99   1395  157 0.0964 0.1290      5.3692      5.5456|
|  2:  4.7332 -  3.7760 0.99   1345  148 0.0829 0.1107      5.4201      5.6109|
|  3:  3.7760 -  3.3044 0.99   1326  144 0.1038 0.1506      5.4583      5.8507|
|  4:  3.3044 -  3.0048 0.99   1312  153 0.1152 0.1667      5.4337      5.5977|
|  5:  3.0048 -  2.7909 0.99   1298  143 0.1305 0.1731      5.3132      5.5519|
|  6:  2.7909 -  2.6272 0.99   1304  140 0.1152 0.1829      5.1874      5.4446|
|  7:  2.6272 -  2.4963 0.99   1291  139 0.1208 0.1556      5.1443      5.3189|
|  8:  2.4963 -  2.3880 0.98   1259  147 0.1099 0.1725      5.0125      5.3298|
|  9:  2.3880 -  2.2964 0.98   1274  148 0.1100 0.1763      4.9989      5.3187|
| 10:  2.2964 -  2.2174 1.00   1296  140 0.1063 0.1694      4.9219      5.1838|
| 11:  2.2174 -  2.1483 0.98   1291  136 0.1077 0.1788      4.9299      5.2587|
| 12:  2.1483 -  2.0870 0.98   1247  145 0.1052 0.1630      4.8547      5.1341|
| 13:  2.0870 -  2.0322 0.99   1282  137 0.1094 0.1754      4.7674      5.0488|
| 14:  2.0322 -  1.9828 0.55    710   82 0.0999 0.1670      4.6443      4.9183|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1573 -  4.7332  1395   157  0.94   8.95   0.98     0.95       7051.39|
|  2:  4.7332 -  3.7760  1345   148  0.95   7.96   1.01     1.00       8994.92|
|  3:  3.7760 -  3.3044  1326   144  0.94  11.13   1.02     1.02      10091.12|
|  4:  3.3044 -  3.0048  1312   153  0.92  13.62   1.01     0.99      10268.04|
|  5:  3.0048 -  2.7909  1298   143  0.90  16.08   1.00     0.97       8332.92|
|  6:  2.7909 -  2.6272  1304   140  0.90  15.80   0.99     0.97       7010.39|
|  7:  2.6272 -  2.4963  1291   139  0.91  15.22   1.00     0.97       6112.77|
|  8:  2.4963 -  2.3880  1259   147  0.91  14.79   0.99     0.97       4828.02|
|  9:  2.3880 -  2.2964  1274   148  0.91  14.72   1.00     0.97       4731.46|
| 10:  2.2964 -  2.2174  1296   140  0.91  15.26   1.00     0.97       4174.62|
| 11:  2.2174 -  2.1483  1291   136  0.90  15.82   0.99     0.95       4318.72|
| 12:  2.1483 -  2.0870  1247   145  0.91  14.96   1.01     1.00       3922.67|
| 13:  2.0870 -  2.0322  1282   137  0.90  16.22   1.00     0.97       3286.95|
| 14:  2.0322 -  1.9828   710    82  0.92  14.61   0.98     0.94       2554.13|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2554.13 max =        10268.04 mean =      6276.10|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.86|
|phase err.(test): min =        0.00 max =           89.91 mean =        13.39|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.972)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.21    89.85   17.02    None  None   None       |
|    all(noH): 2823   0      0.21    89.85   17.02    None  None   None       |
|    Sol.    : 438    0      5.64    89.85   40.12    None  None   None       |
|    Mac.    : 2385   0      0.21    88.78   12.77    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:     0.213 -   9.176:  904   |   5:    45.030 -  53.993:   87        |
|      1:     9.176 -  18.140: 1197   |   6:    53.993 -  62.956:   71        |
|      2:    18.140 -  27.103:  255   |   7:    62.956 -  71.920:   25        |
|      3:    27.103 -  36.066:  143   |   8:    71.920 -  80.883:   13        |
|      4:    36.066 -  45.030:  121   |   9:    80.883 -  89.847:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 291         
Filter by distance & map next to the model:
   mapped sites are within: 0.463 - 4.664
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 286 from: 291
   mapped sites are within: 0.732 - 4.664

peak=    5.972 closest distance to " NH2 ARG A  56 " =    2.190
peak=    5.853 closest distance to " NE2 GLN A  11 " =    1.211
peak=    5.397 closest distance to " CG  PRO A  54 " =    1.239
peak=    5.240 closest distance to " O   HOH Z 126 " =    1.955
peak=    5.161 closest distance to " CB  GLN A 223 " =    1.428
peak=    5.048 closest distance to " O   HOH Z 232 " =    2.312
peak=    5.024 closest distance to " O   HOH Z 144 " =    1.752
peak=    4.960 closest distance to " CB  GLN A 183 " =    1.239
peak=    4.761 closest distance to " O   HOH Z 298 " =    2.047
peak=    4.739 closest distance to " CB  SER A  63 " =    1.218
peak=    4.683 closest distance to " O   HOH Z 369 " =    2.145
peak=    4.605 closest distance to " C   PRO A 198 " =    1.549
peak=    4.594 closest distance to " CG  PRO A 213 " =    1.209
peak=    4.584 closest distance to " O   HOH Z  78 " =    1.786
peak=    4.539 closest distance to " CB  ARG A  79 " =    1.438
peak=    4.526 closest distance to " CB  PRO A  54 " =    0.925
peak=    4.516 closest distance to " CB  LEU A 228 " =    1.105
peak=    4.515 closest distance to " O   HOH Z 287 " =    2.222
peak=    4.512 closest distance to " O   HOH Z 427 " =    2.875
peak=    4.451 closest distance to " CB  ARG A 275 " =    0.925
peak=    4.418 closest distance to " O   HOH Z  15 " =    2.260
peak=    4.314 closest distance to " CB  ARG A 190 " =    1.609
peak=    4.313 closest distance to " CA  TYR A  30 " =    0.983
peak=    4.307 closest distance to " CB  ASN A 148 " =    1.375
peak=    4.215 closest distance to " CB  GLU A 152 " =    1.281
peak=    4.166 closest distance to " CG2 VAL A 257 " =    0.957
peak=    4.165 closest distance to " ND2 ASN A 187 " =    1.410
peak=    4.147 closest distance to " CB  TRP A 266 " =    1.012
peak=    4.137 closest distance to " O   HOH Z 234 " =    3.735
peak=    4.131 closest distance to " O   HOH Z 193 " =    1.797
peak=    4.130 closest distance to " O   HOH Z 303 " =    2.216
peak=    4.125 closest distance to " O   HOH Z 132 " =    2.467
peak=    4.122 closest distance to " ND1 HIS A  86 " =    1.746
peak=    4.122 closest distance to " CB  GLU A 128 " =    1.013
peak=    4.084 closest distance to " CD  ARG A 159 " =    0.767
peak=    4.079 closest distance to " OD1 ASN A  69 " =    2.678
peak=    4.077 closest distance to " CD  ARG A  66 " =    2.199
peak=    4.073 closest distance to " CB  ASN A 187 " =    1.256
peak=    4.071 closest distance to " O   HOH Z 158 " =    3.031
peak=    4.064 closest distance to " O   HOH Z  61 " =    1.624
peak=    4.027 closest distance to " CE  LYS A  76 " =    0.875
peak=    4.023 closest distance to " O   HOH Z 250 " =    1.473
peak=    4.011 closest distance to " O   HOH Z 316 " =    3.039
peak=    3.999 closest distance to " O   HOH Z 272 " =    1.836
peak=    3.993 closest distance to " NH1AARG A 145 " =    1.200
peak=    3.992 closest distance to " CZ  PHE A 218 " =    1.040
peak=    3.989 closest distance to " O   HOH Z   1 " =    2.003
peak=    3.968 closest distance to " O   HOH Z 368 " =    2.070
peak=    3.967 closest distance to " O   HOH Z 261 " =    1.973
peak=    3.966 closest distance to " CB  VAL A 265 " =    1.299
peak=    3.950 closest distance to " O   HOH Z  21 " =    1.731
peak=    3.940 closest distance to " O   HOH Z 423 " =    1.455
peak=    3.910 closest distance to " CG  LEU A 167 " =    1.274
peak=    3.906 closest distance to " O   HOH Z 214 " =    2.062
peak=    3.900 closest distance to " CA  ASN A 215 " =    1.228
peak=    3.893 closest distance to " CB  SER A 212 " =    1.077
peak=    3.886 closest distance to " O   HOH Z 180 " =    2.115
peak=    3.883 closest distance to " O   HOH Z  40 " =    2.011
peak=    3.874 closest distance to " CB  TYR A 169 " =    0.760
peak=    3.866 closest distance to " CG  PRO A 198 " =    1.184
peak=    3.852 closest distance to " O   HOH Z 346 " =    1.680
peak=    3.846 closest distance to " O   HOH Z  54 " =    2.398
peak=    3.829 closest distance to " CB  SER A   3 " =    1.343
peak=    3.828 closest distance to " O   HOH Z 419 " =    2.053
peak=    3.824 closest distance to " O   HOH Z 217 " =    3.187
peak=    3.811 closest distance to " O   HOH Z 213 " =    2.052
peak=    3.808 closest distance to " CD BLYS A 290 " =    1.006
peak=    3.806 closest distance to " O   HOH Z  61 " =    1.493
peak=    3.801 closest distance to " O   HOH Z 133 " =    2.430
peak=    3.788 closest distance to " CB  SER A 216 " =    0.872
peak=    3.784 closest distance to " O   HOH Z 193 " =    1.737
peak=    3.758 closest distance to " O   HOH Z 209 " =    2.286
peak=    3.744 closest distance to " CG  PRO A 243 " =    1.093
peak=    3.743 closest distance to " CA  MET A  40 " =    1.176
peak=    3.742 closest distance to " O   HOH Z  68 " =    2.172
peak=    3.738 closest distance to " CB  ASP A 140 " =    0.949
peak=    3.728 closest distance to " O   HOH Z  10 " =    1.834
peak=    3.722 closest distance to " O   HOH Z 344 " =    3.201
peak=    3.718 closest distance to " CG1 ILE A  33 " =    1.218
peak=    3.717 closest distance to " CB  ASP A 132 " =    4.018
peak=    3.711 closest distance to " CD2 LEU A 255 " =    1.655
peak=    3.710 closest distance to " O   HOH Z 189 " =    2.526
peak=    3.706 closest distance to " O   HOH Z   1 " =    1.769
peak=    3.697 closest distance to " CD2 TRP A 179 " =    1.364
peak=    3.694 closest distance to " O   MET A 105 " =    1.850
peak=    3.692 closest distance to " O   HOH Z 285 " =    2.700
peak=    3.689 closest distance to " O   HOH Z 425 " =    1.252
peak=    3.675 closest distance to " O   HOH Z 386 " =    3.088
peak=    3.666 closest distance to " O   HOH Z 371 " =    2.976
peak=    3.660 closest distance to " O   HOH Z 219 " =    2.056
peak=    3.657 closest distance to " O   HOH Z 203 " =    1.870
peak=    3.656 closest distance to " O   HOH Z 327 " =    1.777
peak=    3.651 closest distance to " O   HOH Z  58 " =    1.467
peak=    3.649 closest distance to " O   HOH Z   9 " =    1.979
peak=    3.640 closest distance to " O   HOH Z 411 " =    3.763
peak=    3.638 closest distance to " CB  GLU A 277 " =    3.615
peak=    3.635 closest distance to " O   HOH Z 280 " =    3.045
peak=    3.628 closest distance to " O   HOH Z 425 " =    2.106
peak=    3.627 closest distance to " O   HOH Z 368 " =    3.588
peak=    3.625 closest distance to " CA  THR A 264 " =    0.859
peak=    3.619 closest distance to " CB  LYS A 117 " =    1.204
peak=    3.617 closest distance to " O   HOH Z 193 " =    2.139
peak=    3.614 closest distance to " CG2 THR A 221 " =    1.043
peak=    3.614 closest distance to " O   HOH Z  40 " =    1.914
peak=    3.611 closest distance to " O   HOH Z 133 " =    1.664
peak=    3.611 closest distance to " CB  ASN A 142 " =    0.928
peak=    3.609 closest distance to " O   HOH Z 391 " =    2.890
peak=    3.590 closest distance to " N   ASN A 127 " =    1.304
peak=    3.588 closest distance to " CB  ASN A  39 " =    0.911
peak=    3.582 closest distance to " O   ASN A 209 " =    1.355
peak=    3.582 closest distance to " CA  ALA A 158 " =    1.164
peak=    3.574 closest distance to " CB  ALA A  34 " =    1.062
peak=    3.572 closest distance to " CA  ALA A 233 " =    1.201
peak=    3.571 closest distance to " O   HOH Z 409 " =    2.562
peak=    3.560 closest distance to " CD1 LEU A 300 " =    1.213
peak=    3.555 closest distance to " O   HOH Z 329 " =    3.817
peak=    3.554 closest distance to " CA  ARG A 195 " =    1.267
peak=    3.550 closest distance to " O   HOH Z 188 " =    2.046
peak=    3.546 closest distance to " O   HOH Z 108 " =    2.367
peak=    3.543 closest distance to " O   HOH Z 426 " =    1.840
peak=    3.518 closest distance to " CB  ALA A   1 " =    4.664
peak=    3.512 closest distance to " CA  LYS A 290 " =    1.340
peak=    3.512 closest distance to " NH2 ARG A 156 " =    1.248
peak=    3.508 closest distance to " CA  SER A  87 " =    1.042
peak=    3.501 closest distance to " O   HOH Z 437 " =    1.427
peak=    3.501 closest distance to " CB  VAL A 202 " =    1.642
peak=    3.500 closest distance to " CB  GLN A  88 " =    1.254
peak=    3.494 closest distance to " OD2 ASP A 286 " =    2.846
peak=    3.490 closest distance to " CA  THR A 221 " =    0.973
peak=    3.486 closest distance to " OD1BASN A 224 " =    2.326
peak=    3.484 closest distance to " CE1 TYR A 186 " =    1.353
peak=    3.481 closest distance to " CG  PRO A  90 " =    1.034
peak=    3.480 closest distance to " O   HOH Z  53 " =    2.526
peak=    3.478 closest distance to " O   THR A 220 " =    1.328
peak=    3.478 closest distance to " O   HOH Z 389 " =    1.925
peak=    3.470 closest distance to " CD  LYS A 166 " =    1.277
peak=    3.468 closest distance to " O   HOH Z 128 " =    2.223
peak=    3.466 closest distance to " O   HOH Z 147 " =    1.785
peak=    3.463 closest distance to " O   SER A  87 " =    2.185
peak=    3.462 closest distance to " O  BHOH Z 338 " =    2.359
peak=    3.460 closest distance to " O   HOH Z  64 " =    2.126
peak=    3.452 closest distance to " O   HOH Z 371 " =    1.846
peak=    3.452 closest distance to " CB  TYR A 169 " =    0.854
peak=    3.447 closest distance to " CB  ARG A 139 " =    0.958
peak=    3.445 closest distance to " ND2 ASN A 110 " =    1.790
peak=    3.442 closest distance to " N   ARG A 156 " =    1.318
peak=    3.440 closest distance to " O   HOH Z 211 " =    2.837
peak=    3.438 closest distance to " N   PHE A 130 " =    1.233
peak=    3.438 closest distance to " CG  MET A 113 " =    1.374
peak=    3.436 closest distance to " O   HOH Z 403 " =    1.638
peak=    3.434 closest distance to " CB  MET A  40 " =    0.801
peak=    3.433 closest distance to " CB  ASN A 110 " =    1.166
peak=    3.430 closest distance to " CB  TYR A 116 " =    0.786
peak=    3.429 closest distance to " CG1 VAL A 189 " =    1.962
peak=    3.429 closest distance to " O   HOH Z 175 " =    2.158
peak=    3.427 closest distance to " O   HOH Z 286 " =    2.342
peak=    3.425 closest distance to " O   HOH Z 422 " =    2.692
peak=    3.421 closest distance to " O   ALA A 165 " =    1.450
peak=    3.419 closest distance to " O   HOH Z  59 " =    1.813
peak=    3.417 closest distance to " O   HOH Z 148 " =    3.375
peak=    3.415 closest distance to " CB  GLU A 236 " =    1.173
peak=    3.412 closest distance to " CA  ILE A 234 " =    1.006
peak=    3.407 closest distance to " OG BSER A 164 " =    2.328
peak=    3.406 closest distance to " O   HOH Z 407 " =    2.288
peak=    3.398 closest distance to " O   HOH Z 245 " =    1.273
peak=    3.396 closest distance to " O   HOH Z 172 " =    3.245
peak=    3.394 closest distance to " CA  ALA A 291 " =    0.876
peak=    3.394 closest distance to " CG BARG A 275 " =    1.489
peak=    3.389 closest distance to " CB  TRP A 179 " =    1.503
peak=    3.386 closest distance to " O   TYR A 116 " =    1.318
peak=    3.385 closest distance to " NH2BARG A 145 " =    2.088
peak=    3.378 closest distance to " CG  ARG A 159 " =    0.844
peak=    3.377 closest distance to " O   HOH Z 135 " =    1.756
peak=    3.374 closest distance to " CZ  ARG A  14 " =    2.053
peak=    3.372 closest distance to " CG  GLN A  89 " =    1.438
peak=    3.357 closest distance to " O   HOH Z 273 " =    2.783
peak=    3.353 closest distance to " N   SER A 134 " =    1.359
peak=    3.350 closest distance to " CB  LEU A 143 " =    1.129
peak=    3.347 closest distance to " O   HOH Z 188 " =    2.490
peak=    3.337 closest distance to " O   HOH Z 305 " =    3.601
peak=    3.334 closest distance to " N   ALA A   1 " =    2.200
peak=    3.333 closest distance to " OG  SER A  22 " =    2.828
peak=    3.332 closest distance to " O   HOH Z 291 " =    1.541
peak=    3.331 closest distance to " CB  ARG A 138 " =    1.001
peak=    3.330 closest distance to " O   HOH Z 109 " =    2.594
peak=    3.317 closest distance to " O   HOH Z 353 " =    2.717
peak=    3.317 closest distance to " O   HOH Z 313 " =    1.898
peak=    3.313 closest distance to " CB  MET A  47 " =    1.068
peak=    3.312 closest distance to " CD2 LEU A 297 " =    0.875
peak=    3.306 closest distance to " CD  GLN A 240 " =    1.633
peak=    3.303 closest distance to " O   THR A 251 " =    1.157
peak=    3.303 closest distance to " NE2 HIS A 207 " =    1.401
peak=    3.302 closest distance to " CD  ARG A 269 " =    0.910
peak=    3.302 closest distance to " CA  TYR A 116 " =    1.331
peak=    3.300 closest distance to " O   HOH Z 163 " =    1.828
peak=    3.294 closest distance to " N   SER A 146 " =    1.734
peak=    3.293 closest distance to " CA  ALA A  21 " =    1.142
peak=    3.290 closest distance to " ND2 ASN A 249 " =    0.859
peak=    3.280 closest distance to " CA  LEU A 101 " =    1.551
peak=    3.279 closest distance to " CG1BVAL A  72 " =    1.573
peak=    3.273 closest distance to " NE2 GLN A  73 " =    3.799
peak=    3.270 closest distance to " O   HOH Z  44 " =    2.936
peak=    3.269 closest distance to " CG1 ILE A 151 " =    1.003
peak=    3.267 closest distance to " CD1 ILE A 106 " =    0.747
peak=    3.267 closest distance to " CB  GLN A  89 " =    1.381
peak=    3.262 closest distance to " CA  ALA A 154 " =    1.001
peak=    3.260 closest distance to " CG  GLN A  88 " =    1.067
peak=    3.259 closest distance to " O   HOH Z 365 " =    2.953
peak=    3.259 closest distance to " CB  SER A 276 " =    1.137
peak=    3.258 closest distance to " O   HOH Z 227 " =    1.715
peak=    3.255 closest distance to " O   HOH Z 345 " =    1.750
peak=    3.250 closest distance to " OG  SER A  62 " =    2.994
peak=    3.250 closest distance to " O   HOH Z 185 " =    1.856
peak=    3.248 closest distance to " O   HOH Z  63 " =    1.361
peak=    3.247 closest distance to " O   HOH Z 116 " =    3.080
peak=    3.244 closest distance to " O   HOH Z 145 " =    2.276
peak=    3.241 closest distance to " ND1 HIS A  81 " =    1.578
peak=    3.235 closest distance to " CA  GLU A  46 " =    0.796
peak=    3.231 closest distance to " CD  PRO A 243 " =    1.601
peak=    3.229 closest distance to " O   HOH Z 406 " =    1.591
peak=    3.227 closest distance to " OD1 ASN A 217 " =    1.628
peak=    3.226 closest distance to " O   HOH Z 302 " =    1.800
peak=    3.223 closest distance to " CB  LEU A 237 " =    0.732
peak=    3.220 closest distance to " CB  GLU A  46 " =    1.083
peak=    3.216 closest distance to " CA  ALA A  84 " =    1.496
peak=    3.212 closest distance to " O   HOH Z 271 " =    2.512
peak=    3.207 closest distance to " CB  ILE A 120 " =    1.344
peak=    3.205 closest distance to " CG  GLN A 278 " =    1.309
peak=    3.205 closest distance to " CA  ARG A  36 " =    1.088
peak=    3.205 closest distance to " O   HOH Z 417 " =    3.352
peak=    3.205 closest distance to " O   HOH Z 386 " =    2.973
peak=    3.204 closest distance to " O   HOH Z 298 " =    2.424
peak=    3.204 closest distance to " CB  ALA A 248 " =    0.923
peak=    3.203 closest distance to " O   HOH Z 423 " =    2.550
peak=    3.200 closest distance to " CB  ALA A   9 " =    1.618
peak=    3.196 closest distance to " O   HOH Z 411 " =    1.812
peak=    3.195 closest distance to " OG BSER A 134 " =    3.151
peak=    3.192 closest distance to " O   HOH Z 325 " =    3.946
peak=    3.190 closest distance to " O   HOH Z   2 " =    1.357
peak=    3.190 closest distance to " NH2AARG A 275 " =    3.675
peak=    3.184 closest distance to " CA  GLY A 267 " =    1.177
peak=    3.178 closest distance to " CD  ARG A 219 " =    1.171
peak=    3.176 closest distance to " CA  ALA A  51 " =    0.924
peak=    3.175 closest distance to " O   ALA A 158 " =    1.338
peak=    3.174 closest distance to " N   TYR A  15 " =    0.762
peak=    3.172 closest distance to " OD2 ASP A 286 " =    3.403
peak=    3.169 closest distance to " CG  LYS A  76 " =    0.972
peak=    3.167 closest distance to " CB  ALA A 291 " =    1.367
peak=    3.166 closest distance to " CA  ASN A 217 " =    1.217
peak=    3.162 closest distance to " CA  MET A 105 " =    0.997
peak=    3.160 closest distance to " CG BARG A 102 " =    1.845
peak=    3.158 closest distance to " CB  HIS A 108 " =    0.758
peak=    3.152 closest distance to " CG2 VAL A 197 " =    1.103
peak=    3.147 closest distance to " O   HOH Z 391 " =    2.620
peak=    3.147 closest distance to " NH1 ARG A 138 " =    1.051
peak=    3.144 closest distance to " NE  ARG A  79 " =    1.165
peak=    3.143 closest distance to " NH2 ARG A 219 " =    1.778
peak=    3.141 closest distance to " O   HOH Z  20 " =    1.664
peak=    3.141 closest distance to " O   HOH Z 345 " =    3.545
peak=    3.140 closest distance to " CB  LEU A 255 " =    0.794
peak=    3.140 closest distance to " O   HOH Z 435 " =    1.938
peak=    3.140 closest distance to " N   GLU A 152 " =    1.387
peak=    3.135 closest distance to " O   HOH Z  88 " =    2.890
peak=    3.131 closest distance to " CA  VAL A 125 " =    1.122
peak=    3.128 closest distance to " O   HOH Z 359 " =    3.978
peak=    3.127 closest distance to " O   HOH Z 281 " =    3.955
peak=    3.127 closest distance to " O   ALA A 291 " =    1.491
peak=    3.123 closest distance to " O   HOH Z  93 " =    2.832
peak=    3.123 closest distance to " CB  THR A 157 " =    1.133
peak=    3.117 closest distance to " O   HOH Z  85 " =    2.222
peak=    3.116 closest distance to " O   HOH Z 319 " =    2.288
peak=    3.115 closest distance to " CB  ASN A 224 " =    0.984
peak=    3.115 closest distance to " N   SER A 135 " =    1.300
peak=    3.111 closest distance to " N   GLN A 278 " =    1.181
peak=    3.109 closest distance to " CB  SER A  26 " =    1.673
peak=    3.108 closest distance to " O   ALA A   1 " =    1.674
peak=    3.099 closest distance to " O   HOH Z 130 " =    3.826
peak=    3.098 closest distance to " O   HOH Z 299 " =    4.402
peak=    3.095 closest distance to " NH1BARG A 145 " =    1.129
peak=    3.079 closest distance to " O   HOH Z 116 " =    1.756
peak=    3.067 closest distance to " CA  ASP A 140 " =    1.183
peak=    3.056 closest distance to " CA  SER A  95 " =    1.042
peak=    3.054 closest distance to " OG  SER A 206 " =    1.207
peak=    3.047 closest distance to " O   HOH Z 218 " =    2.274
peak=    3.030 closest distance to " OG BSER A  99 " =    2.209
peak=    3.026 closest distance to " O   HOH Z 248 " =    1.801

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 192         
Filter by distance & map next to the model:
   mapped sites are within: 0.705 - 5.691
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 191 from: 192
   mapped sites are within: 0.705 - 5.691

peak=   -4.757 closest distance to " CB  PRO A 243 " =    2.592
peak=   -4.682 closest distance to " O   HOH Z 377 " =    2.089
peak=   -4.539 closest distance to " CD  ARG A 156 " =    2.045
peak=   -4.427 closest distance to " O   HOH Z 266 " =    5.063
peak=   -4.282 closest distance to " O   HOH Z 389 " =    1.994
peak=   -4.234 closest distance to " O   VAL A  67 " =    2.731
peak=   -4.205 closest distance to " CG  GLN A 223 " =    1.971
peak=   -4.152 closest distance to " SG  CYS A 254 " =    3.523
peak=   -4.131 closest distance to " OG BSER A 134 " =    1.255
peak=   -4.121 closest distance to " O   HOH Z 435 " =    2.821
peak=   -4.108 closest distance to " O   HOH Z 231 " =    2.118
peak=   -4.047 closest distance to " CG1 VAL A 112 " =    2.940
peak=   -4.033 closest distance to " O   PRO A 198 " =    1.282
peak=   -4.022 closest distance to " N   ALA A  43 " =    2.641
peak=   -4.018 closest distance to " O   HOH Z 351 " =    1.528
peak=   -3.984 closest distance to " O   HOH Z  38 " =    1.417
peak=   -3.931 closest distance to " O   HOH Z 290 " =    1.250
peak=   -3.927 closest distance to " CZ3 TRP A 179 " =    1.119
peak=   -3.902 closest distance to " O   HOH Z 185 " =    2.173
peak=   -3.882 closest distance to " CE2 TYR A  30 " =    2.772
peak=   -3.872 closest distance to " O   HOH Z 407 " =    3.271
peak=   -3.869 closest distance to " C   HIS A 108 " =    1.123
peak=   -3.838 closest distance to " ND2 ASN A  45 " =    1.866
peak=   -3.831 closest distance to " O   HOH Z  52 " =    1.377
peak=   -3.817 closest distance to " CB  ALA A  43 " =    2.539
peak=   -3.795 closest distance to " CA  GLY A 203 " =    2.228
peak=   -3.787 closest distance to " CD  ARG A 195 " =    5.228
peak=   -3.766 closest distance to " O   HOH Z  43 " =    1.595
peak=   -3.758 closest distance to " O   HOH Z 198 " =    2.012
peak=   -3.757 closest distance to " CD1 PHE A  59 " =    1.886
peak=   -3.738 closest distance to " O   HOH Z 313 " =    1.813
peak=   -3.723 closest distance to " O   HOH Z  60 " =    2.588
peak=   -3.719 closest distance to " CZ  PHE A  59 " =    1.562
peak=   -3.715 closest distance to " O   HOH Z  73 " =    2.138
peak=   -3.690 closest distance to " O   HOH Z 372 " =    2.454
peak=   -3.683 closest distance to " CE  MET A 105 " =    2.237
peak=   -3.681 closest distance to " CB  ALA A 291 " =    2.230
peak=   -3.669 closest distance to " CB  ALA A 291 " =    2.219
peak=   -3.662 closest distance to " CA  GLY A  98 " =    1.921
peak=   -3.636 closest distance to " CG  PHE A 283 " =    2.663
peak=   -3.632 closest distance to " CE2 PHE A 218 " =    2.399
peak=   -3.628 closest distance to " ND2 ASN A 249 " =    2.350
peak=   -3.628 closest distance to " CB  TRP A  85 " =    2.492
peak=   -3.622 closest distance to " O   VAL A  67 " =    2.763
peak=   -3.618 closest distance to " O   PRO A 163 " =    2.015
peak=   -3.617 closest distance to " C   LEU A 222 " =    0.705
peak=   -3.615 closest distance to " NH2BARG A 275 " =    1.767
peak=   -3.614 closest distance to " CD1 LEU A 101 " =    2.334
peak=   -3.607 closest distance to " O   VAL A 189 " =    2.469
peak=   -3.602 closest distance to " O   HOH Z 198 " =    1.513
peak=   -3.588 closest distance to " OD1 ASN A 187 " =    1.632
peak=   -3.586 closest distance to " O   ILE A 109 " =    2.547
peak=   -3.584 closest distance to " N   ASP A 286 " =    2.432
peak=   -3.569 closest distance to " OG  SER A  97 " =    2.166
peak=   -3.569 closest distance to " O   SER A 135 " =    1.421
peak=   -3.555 closest distance to " CB  ASN A  39 " =    2.244
peak=   -3.540 closest distance to " O   HOH Z  10 " =    1.490
peak=   -3.535 closest distance to " O   HOH Z 298 " =    1.199
peak=   -3.533 closest distance to " NH2AARG A 275 " =    5.515
peak=   -3.528 closest distance to " O   HOH Z 394 " =    1.423
peak=   -3.528 closest distance to " O   HOH Z 114 " =    3.273
peak=   -3.525 closest distance to " OXT GLY A 302 " =    2.990
peak=   -3.525 closest distance to " ND2 ASN A  45 " =    1.149
peak=   -3.507 closest distance to " O   PRO A 243 " =    2.453
peak=   -3.505 closest distance to " O   HOH Z 126 " =    1.867
peak=   -3.500 closest distance to " OD1 ASP A 171 " =    1.642
peak=   -3.491 closest distance to " CZ  TYR A 169 " =    1.573
peak=   -3.491 closest distance to " NE  ARG A  36 " =    1.968
peak=   -3.477 closest distance to " CD  GLN A  58 " =    1.032
peak=   -3.470 closest distance to " C   LEU A 143 " =    1.299
peak=   -3.470 closest distance to " O   TYR A 247 " =    2.858
peak=   -3.468 closest distance to " O   HOH Z 353 " =    2.080
peak=   -3.465 closest distance to " CB  CYS A 254 " =    2.229
peak=   -3.463 closest distance to " O   PRO A 198 " =    1.325
peak=   -3.459 closest distance to " O   HOH Z 111 " =    1.306
peak=   -3.457 closest distance to " OD1 ASN A 148 " =    1.571
peak=   -3.452 closest distance to " CA  ASP A  27 " =    2.489
peak=   -3.450 closest distance to " OD1 ASP A 191 " =    1.810
peak=   -3.441 closest distance to " CD  ARG A 139 " =    1.533
peak=   -3.438 closest distance to " CG1 VAL A 250 " =    2.617
peak=   -3.436 closest distance to " C   ALA A 158 " =    1.435
peak=   -3.430 closest distance to " CE2 PHE A  61 " =    2.611
peak=   -3.428 closest distance to " CG  PRO A 163 " =    2.432
peak=   -3.425 closest distance to " C   GLY A  17 " =    1.178
peak=   -3.423 closest distance to " O   VAL A 125 " =    2.374
peak=   -3.422 closest distance to " CB  ALA A 131 " =    2.063
peak=   -3.420 closest distance to " CB  PRO A  54 " =    2.450
peak=   -3.414 closest distance to " CB  PHE A 192 " =    1.937
peak=   -3.410 closest distance to " O   HOH Z  44 " =    2.265
peak=   -3.398 closest distance to " CD1 LEU A 297 " =    2.540
peak=   -3.388 closest distance to " OG BSER A 134 " =    1.676
peak=   -3.387 closest distance to " O   HOH Z  47 " =    1.605
peak=   -3.386 closest distance to " O   HOH Z 281 " =    2.648
peak=   -3.379 closest distance to " OD1 ASP A 191 " =    1.580
peak=   -3.374 closest distance to " O   HOH Z 359 " =    3.233
peak=   -3.366 closest distance to " CE3 TRP A 123 " =    1.312
peak=   -3.365 closest distance to " CD2 PHE A 225 " =    1.108
peak=   -3.365 closest distance to " O   HOH Z  65 " =    1.346
peak=   -3.364 closest distance to " NH1 ARG A 195 " =    2.644
peak=   -3.362 closest distance to " CB  PRO A 163 " =    2.528
peak=   -3.359 closest distance to " N   THR A 157 " =    1.507
peak=   -3.359 closest distance to " CG  MET A 105 " =    0.970
peak=   -3.356 closest distance to " CD1 LEU A 228 " =    2.363
peak=   -3.346 closest distance to " O   HOH Z 426 " =    1.641
peak=   -3.342 closest distance to " CB  ALA A 248 " =    2.398
peak=   -3.337 closest distance to " CG1 VAL A 197 " =    2.230
peak=   -3.333 closest distance to " CB  TYR A  15 " =    2.190
peak=   -3.327 closest distance to " O   HOH Z 211 " =    1.561
peak=   -3.319 closest distance to " O   HOH Z 253 " =    4.016
peak=   -3.317 closest distance to " O   HOH Z 292 " =    1.722
peak=   -3.314 closest distance to " N   SER A 212 " =    2.008
peak=   -3.312 closest distance to " CE3 TRP A 274 " =    2.366
peak=   -3.311 closest distance to " CA  GLY A 241 " =    2.235
peak=   -3.310 closest distance to " CG  ARG A 269 " =    2.613
peak=   -3.309 closest distance to " O   HOH Z  90 " =    2.858
peak=   -3.306 closest distance to " O   ALA A  10 " =    1.669
peak=   -3.305 closest distance to " O   PHE A 218 " =    1.541
peak=   -3.301 closest distance to " OG  SER A  87 " =    1.327
peak=   -3.300 closest distance to " O   SER A  95 " =    1.468
peak=   -3.298 closest distance to " CG  TRP A 266 " =    1.787
peak=   -3.297 closest distance to " CB  ASP A 286 " =    2.207
peak=   -3.297 closest distance to " CG2 ILE A 263 " =    2.318
peak=   -3.294 closest distance to " CE BMET A  47 " =    1.582
peak=   -3.282 closest distance to " CG  ASP A 231 " =    0.755
peak=   -3.282 closest distance to " O   HOH Z 174 " =    2.646
peak=   -3.279 closest distance to " NH1AARG A 275 " =    1.835
peak=   -3.275 closest distance to " CD1 ILE A 199 " =    2.615
peak=   -3.269 closest distance to " O   HOH Z 111 " =    1.814
peak=   -3.268 closest distance to " O   HOH Z 417 " =    2.902
peak=   -3.266 closest distance to " SG ACYS A 201 " =    1.934
peak=   -3.265 closest distance to " CA  GLY A 241 " =    3.148
peak=   -3.262 closest distance to " SD  MET A 188 " =    2.285
peak=   -3.259 closest distance to " CA  SER A 135 " =    1.357
peak=   -3.256 closest distance to " O   HOH Z 191 " =    5.691
peak=   -3.255 closest distance to " O   HOH Z 102 " =    1.587
peak=   -3.247 closest distance to " O   HOH Z 350 " =    1.569
peak=   -3.246 closest distance to " O   HOH Z 295 " =    1.619
peak=   -3.239 closest distance to " O   TRP A  70 " =    1.464
peak=   -3.235 closest distance to " C   GLY A  13 " =    1.027
peak=   -3.225 closest distance to " CB  PHE A 208 " =    2.258
peak=   -3.225 closest distance to " O   HOH Z  11 " =    1.843
peak=   -3.225 closest distance to " N   ALA A 248 " =    1.572
peak=   -3.223 closest distance to " O   HOH Z 298 " =    2.444
peak=   -3.212 closest distance to " NE2 GLN A  88 " =    1.869
peak=   -3.212 closest distance to " CB  ALA A 100 " =    2.178
peak=   -3.211 closest distance to " O   ALA A  34 " =    2.556
peak=   -3.208 closest distance to " O   HOH Z 189 " =    1.897
peak=   -3.206 closest distance to " O   HOH Z  13 " =    1.640
peak=   -3.202 closest distance to " O   HOH Z   6 " =    1.586
peak=   -3.201 closest distance to " O   TYR A  30 " =    2.870
peak=   -3.195 closest distance to " CG1 VAL A 268 " =    2.430
peak=   -3.194 closest distance to " N   ALA A 226 " =    2.094
peak=   -3.192 closest distance to " N   ASP A 171 " =    2.348
peak=   -3.189 closest distance to " O   ALA A 180 " =    1.301
peak=   -3.186 closest distance to " CB  ASP A 132 " =    2.369
peak=   -3.185 closest distance to " OH  TYR A 247 " =    1.809
peak=   -3.184 closest distance to " ND2 ASN A  60 " =    1.511
peak=   -3.183 closest distance to " O   HOH Z 348 " =    1.795
peak=   -3.183 closest distance to " O   ALA A  51 " =    1.423
peak=   -3.179 closest distance to " CG2 VAL A 189 " =    1.945
peak=   -3.171 closest distance to " NH2 ARG A 219 " =    1.720
peak=   -3.157 closest distance to " O   HOH Z 184 " =    1.799
peak=   -3.154 closest distance to " CD2 TYR A 293 " =    1.935
peak=   -3.148 closest distance to " CE3 TRP A 150 " =    2.126
peak=   -3.147 closest distance to " O   HOH Z 241 " =    1.365
peak=   -3.146 closest distance to " OXT GLY A 302 " =    3.382
peak=   -3.141 closest distance to " O   HOH Z 417 " =    2.537
peak=   -3.140 closest distance to " CG  GLN A  88 " =    0.868
peak=   -3.140 closest distance to " O   GLY A  80 " =    2.425
peak=   -3.137 closest distance to " O   HOH Z 324 " =    2.191
peak=   -3.121 closest distance to " CD2 PHE A  61 " =    2.105
peak=   -3.115 closest distance to " O   ALA A 161 " =    1.650
peak=   -3.111 closest distance to " O   SER A  62 " =    2.246
peak=   -3.106 closest distance to " CG1 VAL A 125 " =    1.918
peak=   -3.105 closest distance to " O   HOH Z 114 " =    0.885
peak=   -3.104 closest distance to " CD1 ILE A 239 " =    2.343
peak=   -3.103 closest distance to " NH2 ARG A  79 " =    1.579
peak=   -3.103 closest distance to " O   HOH Z  90 " =    1.637
peak=   -3.102 closest distance to " O   HOH Z  51 " =    1.594
peak=   -3.102 closest distance to " CG2 THR A  18 " =    2.813
peak=   -3.095 closest distance to " O   HOH Z 256 " =    1.570
peak=   -3.094 closest distance to " N   SER A 276 " =    1.307
peak=   -3.092 closest distance to " OH  TYR A 214 " =    1.256
peak=   -3.075 closest distance to " O   HOH Z  63 " =    1.574
peak=   -3.064 closest distance to " O   HOH Z 337 " =    1.610
peak=   -3.062 closest distance to " CD1 TYR A 247 " =    2.675
peak=   -3.057 closest distance to " CG  GLU A   2 " =    2.017
peak=   -3.053 closest distance to " CG1 VAL A  67 " =    2.912
peak=   -3.047 closest distance to " O   HOH Z 357 " =    2.148
peak=   -3.032 closest distance to " O   HOH Z 139 " =    2.915
peak=   -3.006 closest distance to " O   HOH Z 263 " =    5.207

================= 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    :  0.3330 0.3301   6.068299e+00   6.059151e+00
   1_bss:  0.3206 0.3192   6.049721e+00   6.036325e+00
   1_xyz:  0.1784 0.2025   5.509786e+00   5.609747e+00
   1_adp:  0.1624 0.2084   5.455476e+00   5.643689e+00
   1_occ:  0.1621 0.2082   5.454054e+00   5.642980e+00
   2_bss:  0.1606 0.2055   5.448729e+00   5.635208e+00
   2_xyz:  0.1297 0.1748   5.268036e+00   5.488580e+00
   2_adp:  0.1260 0.1669   5.232366e+00   5.445162e+00
   2_occ:  0.1259 0.1670   5.231958e+00   5.445331e+00
   3_bss:  0.1258 0.1664   5.230607e+00   5.443251e+00
   3_xyz:  0.1138 0.1569   5.153064e+00   5.386522e+00
   3_adp:  0.1113 0.1570   5.140978e+00   5.383806e+00
   3_occ:  0.1113 0.1571   5.141019e+00   5.384006e+00
   4_bss:  0.1113 0.1570   5.140702e+00   5.383761e+00
   4_xyz:  0.1120 0.1575   5.148434e+00   5.390447e+00
   4_adp:  0.1120 0.1573   5.147264e+00   5.389376e+00
   4_occ:  0.1119 0.1572   5.147160e+00   5.389387e+00
   5_bss:  0.1119 0.1572   5.147204e+00   5.389389e+00
   5_xyz:  0.1076 0.1567   5.124015e+00   5.381787e+00
   5_adp:  0.1073 0.1572   5.123874e+00   5.383591e+00
   5_occ:  0.1073 0.1571   5.123791e+00   5.383507e+00
   5_bss:  0.1072 0.1571   5.123921e+00   5.383608e+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:  0.335  52.659   0.115  -0.243  -1.736  -0.000  -0.000  -0.000
   1_xyz:  0.335  52.659   0.115  -0.243  -1.736  -0.000  -0.000  -0.000
   1_adp:  0.335  52.659   0.115  -0.243  -1.736  -0.000  -0.000  -0.000
   1_occ:  0.335  52.659   0.115  -0.243  -1.736  -0.000  -0.000  -0.000
   2_bss:  0.335  60.324  -1.831  -2.292  -1.848  -0.000  -0.000  -0.000
   2_xyz:  0.335  60.324  -1.831  -2.292  -1.848  -0.000  -0.000  -0.000
   2_adp:  0.335  60.324  -1.831  -2.292  -1.848  -0.000  -0.000  -0.000
   2_occ:  0.335  60.324  -1.831  -2.292  -1.848  -0.000  -0.000  -0.000
   3_bss:  0.335  60.324  -2.277  -2.653  -1.590  -0.000  -0.000  -0.000
   3_xyz:  0.335  60.324  -2.277  -2.653  -1.590  -0.000  -0.000  -0.000
   3_adp:  0.335  60.324  -2.277  -2.653  -1.590  -0.000  -0.000  -0.000
   3_occ:  0.335  60.324  -2.277  -2.653  -1.590  -0.000  -0.000  -0.000
   4_bss:  0.329  60.324  -2.236  -2.609  -1.419  -0.000  -0.000  -0.000
   4_xyz:  0.329  60.324  -2.236  -2.609  -1.419  -0.000  -0.000  -0.000
   4_adp:  0.329  60.324  -2.236  -2.609  -1.419  -0.000  -0.000  -0.000
   4_occ:  0.329  60.324  -2.236  -2.609  -1.419  -0.000  -0.000  -0.000
   5_bss:  0.329  60.324  -2.144  -2.506  -1.238  -0.000  -0.000  -0.000
   5_xyz:  0.329  60.324  -2.144  -2.506  -1.238  -0.000  -0.000  -0.000
   5_adp:  0.329  60.324  -2.144  -2.506  -1.238  -0.000  -0.000  -0.000
   5_occ:  0.329  60.324  -2.144  -2.506  -1.238  -0.000  -0.000  -0.000
   5_bss:  0.329  60.318  -1.919  -2.296  -1.012  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  34.589 0.7094  0.8881    31792.433
   1_bss:  33.620 0.7187  0.8827    29209.867
   1_xyz:  18.747 0.8752  1.0100    10344.406
   1_adp:  19.687 0.8656  1.0061    10994.496
   1_occ:  19.672 0.8656  1.0057    10958.493
   2_bss:  19.415 0.8681  0.9604    10762.145
   2_xyz:  16.157 0.8968  0.9769     7759.937
   2_adp:  15.104 0.9062  0.9791     7162.859
   2_occ:  15.108 0.9061  0.9790     7160.221
   3_bss:  15.073 0.9064  0.9724     7125.754
   3_xyz:  13.944 0.9155  0.9771     6341.439
   3_adp:  13.873 0.9161  0.9728     6284.186
   3_occ:  13.878 0.9161  0.9727     6287.020
   4_bss:  13.872 0.9161  0.9756     6280.444
   4_xyz:  13.955 0.9157  0.9740     6363.779
   4_adp:  13.908 0.9162  0.9684     6357.102
   4_occ:  13.909 0.9162  0.9683     6355.154
   5_bss:  13.910 0.9162  0.9727     6355.387
   5_xyz:  13.771 0.9171  0.9741     6273.297
   5_adp:  13.807 0.9168  0.9675     6275.476
   5_occ:  13.806 0.9168  0.9675     6274.014
   5_bss:  13.811 0.9168  0.9750     6276.131
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6158e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6158e-01
   1_xyz:   1.087  0.009  0.075 15.012  0.005  4.114   7.3080e-02
   1_adp:   1.087  0.009  0.075 15.012  0.005  4.114   7.3080e-02
   1_occ:   1.087  0.009  0.075 15.012  0.005  4.114   7.3080e-02
   2_bss:   1.087  0.009  0.075 15.012  0.005  4.114   7.3080e-02
   2_xyz:   0.915  0.006  0.070 14.194  0.003  4.121   4.9546e-02
   2_adp:   0.915  0.006  0.070 14.194  0.003  4.121   4.9546e-02
   2_occ:   0.915  0.006  0.070 14.194  0.003  4.121   4.9546e-02
   3_bss:   0.915  0.006  0.070 14.194  0.003  4.121   4.9546e-02
   3_xyz:   1.001  0.008  0.078 14.478  0.004  4.112   6.0903e-02
   3_adp:   1.001  0.008  0.078 14.478  0.004  4.112   6.0903e-02
   3_occ:   1.001  0.008  0.078 14.478  0.004  4.112   6.0903e-02
   4_bss:   1.001  0.008  0.078 14.478  0.004  4.112   6.0903e-02
   4_xyz:   0.911  0.006  0.070 14.214  0.004  4.113   5.1166e-02
   4_adp:   0.911  0.006  0.070 14.214  0.004  4.113   5.1166e-02
   4_occ:   0.911  0.006  0.070 14.214  0.004  4.113   5.1166e-02
   5_bss:   0.911  0.006  0.070 14.214  0.004  4.113   5.1166e-02
   5_xyz:   1.054  0.009  0.080 14.605  0.004  4.114   6.7066e-02
   5_adp:   1.054  0.009  0.080 14.605  0.004  4.114   6.7066e-02
   5_occ:   1.054  0.009  0.080 14.605  0.004  4.114   6.7066e-02
   5_bss:   1.054  0.009  0.080 14.605  0.004  4.114   6.7066e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4140e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4140e-01
   1_xyz:   9.388  0.093  0.260 85.274  0.046  2.327   1.3527e-01
   1_adp:   9.388  0.093  0.260 85.274  0.046  2.327   1.3527e-01
   1_occ:   9.388  0.093  0.260 85.274  0.046  2.327   1.3527e-01
   2_bss:   9.388  0.093  0.260 85.274  0.046  2.327   1.3527e-01
   2_xyz:   8.323  0.050  0.214 81.266  0.034  2.384   4.4971e-02
   2_adp:   8.323  0.050  0.214 81.266  0.034  2.384   4.4971e-02
   2_occ:   8.323  0.050  0.214 81.266  0.034  2.384   4.4971e-02
   3_bss:   8.323  0.050  0.214 81.266  0.034  2.384   4.4971e-02
   3_xyz:   8.106  0.040  0.230 84.055  0.036  2.307   5.2196e-02
   3_adp:   8.106  0.040  0.230 84.055  0.036  2.307   5.2196e-02
   3_occ:   8.106  0.040  0.230 84.055  0.036  2.307   5.2196e-02
   4_bss:   8.106  0.040  0.230 84.055  0.036  2.307   5.2196e-02
   4_xyz:   7.578  0.043  0.211 83.893  0.034  2.381   3.4747e-02
   4_adp:   7.578  0.043  0.211 83.893  0.034  2.381   3.4747e-02
   4_occ:   7.578  0.043  0.211 83.893  0.034  2.381   3.4747e-02
   5_bss:   7.578  0.043  0.211 83.893  0.034  2.381   3.4747e-02
   5_xyz:   7.491  0.041  0.255 84.456  0.032  2.286   5.3052e-02
   5_adp:   7.491  0.041  0.255 84.456  0.032  2.286   5.3052e-02
   5_occ:   7.491  0.041  0.255 84.456  0.032  2.286   5.3052e-02
   5_bss:   7.491  0.041  0.255 84.456  0.032  2.286   5.3052e-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:  76.54   1.51  17.27  70.54   1.51  13.09  76.54   5.04  40.01
   1_occ:  76.54   1.51  17.27  70.54   1.51  13.09  76.54   5.04  40.01
   2_bss:  76.54   1.51  17.27  70.54   1.51  13.09  76.54   5.04  40.01
   2_xyz:  76.54   1.51  17.27  70.54   1.51  13.09  76.54   5.04  40.01
   2_adp:  75.58   1.70  16.91  72.45   1.70  12.96  75.58   5.89  38.42
   2_occ:  75.58   1.70  16.91  72.45   1.70  12.96  75.58   5.89  38.42
   3_bss:  75.58   1.70  16.91  72.45   1.70  12.96  75.58   5.89  38.42
   3_xyz:  75.58   1.70  16.91  72.45   1.70  12.96  75.58   5.89  38.42
   3_adp:  86.74   0.46  17.38  85.25   0.46  13.08  86.74   3.82  40.82
   3_occ:  86.74   0.46  17.38  85.25   0.46  13.08  86.74   3.82  40.82
   4_bss:  86.74   0.46  17.38  85.25   0.46  13.08  86.74   3.82  40.82
   4_xyz:  86.74   0.46  17.38  85.25   0.46  13.08  86.74   3.82  40.82
   4_adp:  87.14   0.70  17.08  86.11   0.70  12.91  87.14   4.36  39.80
   4_occ:  87.14   0.70  17.08  86.11   0.70  12.91  87.14   4.36  39.80
   5_bss:  87.14   0.70  17.08  86.11   0.70  12.91  87.14   4.36  39.80
   5_xyz:  87.14   0.70  17.08  86.11   0.70  12.91  87.14   4.36  39.80
   5_adp:  89.85   0.22  17.02  88.78   0.22  12.78  89.85   5.64  40.12
   5_occ:  89.85   0.22  17.02  88.78   0.22  12.78  89.85   5.64  40.12
   5_bss:  89.85   0.21  17.02  88.78   0.21  12.77  89.85   5.64  40.12
------------------------------------------------------------------------
 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:    1.067    0.025    0.319
   1_adp:    1.067    0.025    0.319
   1_occ:    1.067    0.025    0.319
   2_bss:    1.067    0.025    0.319
   2_xyz:    0.855    0.014    0.367
   2_adp:    0.855    0.014    0.367
   2_occ:    0.855    0.014    0.367
   3_bss:    0.855    0.014    0.367
   3_xyz:    0.900    0.027    0.404
   3_adp:    0.900    0.027    0.404
   3_occ:    0.900    0.027    0.404
   4_bss:    0.900    0.027    0.404
   4_xyz:    1.000    0.036    0.415
   4_adp:    1.000    0.036    0.415
   4_occ:    1.000    0.036    0.415
   5_bss:    1.000    0.036    0.415
   5_xyz:    1.034    0.038    0.423
   5_adp:    1.034    0.038    0.423
   5_occ:    1.034    0.038    0.423
   5_bss:    1.034    0.038    0.423
------------------------------------------------------------------------

CPU time actual refinement: 323.48


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1006/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_1006/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1006/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1006/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1006/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 323.33 
  Macro-tasks:
    bulk solvent and scale       = 34.04  
    individual site refinement   = 137.42 
    weights calculation          = 28.63  
    collect and process          = 6.52   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 206.70 
  Micro-tasks:
    mask                            = 1.20   
    f_calc                          = 104.14 
    alpha_beta                      = 8.12   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 114.26 
    fmodel                         = 6.46   
    r_factors                      = 0.22   
    phase_errors                   = 11.11  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 246.99 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.524 micro seconds
Total CPU time: 5.61 minutes
from_scatterers_fft:    667 calls, 103.74 s
gradients_fft:          612 calls, 100.11 s

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

# Date 2008-01-16 Time 06:11:26 PST -0800 (1200492686.44 s)
Start R-work = 0.3330, R-free = 0.3301 (no bulk solvent and anisotropic scale)
Final R-work = 0.1306, R-free = 0.1760 (no bulk solvent and anisotropic scale)

Start R-work = 0.3206, R-free = 0.3192
Final R-work = 0.1072, R-free = 0.1571