# Date 2008-01-16 Time 06:21:05 PST -0800 (1200493265.89 s)
#phil __OFF__

Command line arguments: "../1107.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 13352
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1107

-------------------------------------------------------------------------------
  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: (71.655, 45.9914, 87.2539, 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: 3.34, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 45.9914, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2528 1.96416
Completeness in resolution range: 0.925406
Completeness with d_max=infinity: 0.922791

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2528
                             d_min =   1.9642

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: (71.655, 45.9914, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2528 1.96416
Completeness in resolution range: 0.925406
Completeness with d_max=infinity: 0.922791

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2532 -  4.2049 [2222/2249]  2000   222  10.0%
  bin  2:  4.2049 -  3.3492 [2140/2160]  1928   212   9.9%
  bin  3:  3.3492 -  2.9292 [2106/2125]  1893   213  10.1%
  bin  4:  2.9292 -  2.6629 [2077/2107]  1865   212  10.2%
  bin  5:  2.6629 -  2.4729 [2088/2107]  1890   198   9.5%
  bin  6:  2.4729 -  2.3277 [2079/2104]  1862   217  10.4%
  bin  7:  2.3277 -  2.2115 [2044/2072]  1835   209  10.2%
  bin  8:  2.2115 -  2.1155 [2052/2088]  1851   201   9.8%
  bin  9:  2.1155 -  2.0342 [2033/2087]  1838   195   9.6%
  bin 10:  2.0342 -  1.9642 [ 748/2069]   668    80  10.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1107/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 35
        2.42 -     3.04: 2196
        3.04 -     3.66: 4689
        3.66 -     4.28: 8995
        4.28 -     4.90: 12264
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.812 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  2.019 3.120 x,y-1,z
  ... (remaining 28174 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_1107/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1107/model_refine_001.geo

CPU time processing inputs: 9.82


============================ 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 = 71.655 45.9914 87.2539 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: 1.96 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4571   r_free= 0.4575   ksol= 0.00   Bsol= 0.00   scale= 0.893    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.269666                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2532 -  4.6909 0.99   1440  161 0.3691 0.3559      6.5516       6.515|
|  2:  4.6909 -  3.7414 0.99   1393  154 0.3913 0.3722      6.8027      6.7387|
|  3:  3.7414 -  3.2738 0.99   1353  149 0.4155 0.4055      6.6266      6.6537|
|  4:  3.2738 -  2.9769 0.99   1364  153 0.4533 0.4859      6.5065       6.522|
|  5:  2.9769 -  2.7649 0.99   1348  147 0.4824 0.4874      6.3487      6.3724|
|  6:  2.7649 -  2.6027 0.99   1340  152 0.4830 0.4697      6.2518      6.2013|
|  7:  2.6027 -  2.4729 0.99   1338  141 0.5001 0.4740      6.2212      6.1568|
|  8:  2.4729 -  2.3657 0.98   1321  154 0.5109 0.5484      6.1609      6.1847|
|  9:  2.3657 -  2.2749 0.98   1321  146 0.4995 0.5263       6.115      6.1605|
| 10:  2.2749 -  2.1967 1.00   1323  156 0.5151 0.4990      6.0616      6.0419|
| 11:  2.1967 -  2.1282 0.98   1309  138 0.5175 0.5444      6.0305       6.071|
| 12:  2.1282 -  2.0675 0.98   1319  149 0.5104 0.5261      5.9315      5.9421|
| 13:  2.0675 -  2.0132 0.87   1163  127 0.5091 0.4610      5.8707       5.785|
| 14:  2.0132 -  1.9642 0.22    298   32 0.5087 0.6370      5.8471       5.939|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2532 -  4.6909  1440   161  0.74  30.69   0.82     0.79      60419.70|
|  2:  4.6909 -  3.7414  1393   154  0.73  32.35   0.90     0.84      94250.31|
|  3:  3.7414 -  3.2738  1353   149  0.60  43.81   0.93     0.78     108343.99|
|  4:  3.2738 -  2.9769  1364   153  0.50  51.97   0.89     0.69     104272.58|
|  5:  2.9769 -  2.7649  1348   147  0.41  58.61   0.89     0.60      84547.12|
|  6:  2.7649 -  2.6027  1340   152  0.40  60.14   0.90     0.57      71596.90|
|  7:  2.6027 -  2.4729  1338   141  0.38  61.76   0.91     0.53      63882.29|
|  8:  2.4729 -  2.3657  1321   154  0.35  63.36   0.89     0.51      58490.83|
|  9:  2.3657 -  2.2749  1321   146  0.35  63.36   0.93     0.51      53524.83|
| 10:  2.2749 -  2.1967  1323   156  0.35  63.65   0.92     0.52      47983.74|
| 11:  2.1967 -  2.1282  1309   138  0.33  64.99   0.94     0.52      47655.32|
| 12:  2.1282 -  2.0675  1319   149  0.31  66.84   0.92     0.49      43382.24|
| 13:  2.0675 -  2.0132  1163   127  0.30  67.86   0.94     0.49      38645.70|
| 14:  2.0132 -  1.9642   298    32  0.37  62.17   0.97     0.52      29991.59|
|alpha:            min =        0.49 max =            0.84 mean =         0.61|
|beta:             min =    29991.59 max =       108343.99 mean =     67353.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           89.98 mean =        55.81|
|phase err.(test): min =        0.00 max =           89.94 mean =        56.06|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.074684             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.899   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.672598              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.670   (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:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       26 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      191 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2005 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1872 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2817 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4635 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4360 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5605 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6659 |
|-----------------------------------------------------------------------------|
|-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 |        0.172 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.806 |       0.308 |              |
|-----------------------------------------------------------------------------|

|-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: 1.96 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4571   r_free= 0.4575   ksol= 0.00   Bsol= 0.00   scale= 0.893    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.269666                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4491   r_free= 0.4528   ksol= 0.34   Bsol= 60.82   scale= 0.931   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.30,1.68,-0.47,0.00,-0.00,-0.00); trace/3= 0.50                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.264061                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.586095             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.927   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.296393              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.311   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4491      final r-factor (work) = 0.3116          |
| start r-factor (free) = 0.4528      final r-factor (free) = 0.3540          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.6913 = 13.59 * 0.50 * 6.2593 + 1.00 * 0.1719                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.7549 = 13.59 * 0.50 * 6.1248 + 1.00 * 0.1486                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3116      final r-factor (work) = 0.2826          |
| start r-factor (free) = 0.3540      final r-factor (free) = 0.3674          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9465 = 1.30 * 1.00 * 6.1248 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7333 = 1.30 * 1.00 * 5.9500 + 1.00 * 0.0198                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    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      0.00    103.35  18.98    None  None   None       |
|    all(noH): 2823   0      0.00    103.35  18.98    None  None   None       |
|    Sol.    : 438    0      1.11    103.35  42.11    None  None   None       |
|    Mac.    : 2385   0      0.00    72.08   14.73    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.335:  978   |   5:    51.675 -  62.010:   87        |
|      1:    10.335 -  20.670:  926   |   6:    62.010 -  72.345:   45        |
|      2:    20.670 -  31.005:  420   |   7:    72.345 -  82.680:   16        |
|      3:    31.005 -  41.340:  191   |   8:    82.680 -  93.014:    4        |
|      4:    41.340 -  51.675:  155   |   9:    93.014 - 103.349:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2826 r_free = 0.3674             target_work(ml) = 5.966         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2821 r_free = 0.3672             target_work(ml) = 5.966         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2821   r_free= 0.3672   ksol= 0.34   Bsol= 60.82   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.30,1.68,-0.47,0.00,-0.00,-0.00); trace/3= 0.50                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 5.965827                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2812   r_free= 0.3648   ksol= 0.35   Bsol= 78.27   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.75,-0.50,-0.27,-0.00,-0.00,-0.00); trace/3= -0.51                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 5.963866                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.998825              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.320   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.649133              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.642  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2812      final r-factor (work) = 0.2189          |
| start r-factor (free) = 0.3648      final r-factor (free) = 0.2846          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.9963 = 6.00 * 0.50 * 5.9504 + 1.00 * 0.1486                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.7001 = 6.00 * 0.50 * 5.8783 + 1.00 * 0.0687                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2189      final r-factor (work) = 0.2008          |
| start r-factor (free) = 0.2846      final r-factor (free) = 0.2661          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8354 = 0.65 * 1.00 * 5.8783 + 1.00 * 0.0196                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7176 = 0.65 * 1.00 * 5.7057 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| 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      0.00    106.76  18.67    None  None   None       |
|    all(noH): 2823   0      0.00    106.76  18.67    None  None   None       |
|    Sol.    : 438    0      3.44    106.76  44.65    None  None   None       |
|    Mac.    : 2385   0      0.00    88.61   13.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.677: 1117   |   5:    53.383 -  64.059:   90        |
|      1:    10.677 -  21.353:  970   |   6:    64.059 -  74.735:   50        |
|      2:    21.353 -  32.030:  284   |   7:    74.735 -  85.412:   21        |
|      3:    32.030 -  42.706:  152   |   8:    85.412 -  96.088:    5        |
|      4:    42.706 -  53.383:  133   |   9:    96.088 - 106.765:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2008 r_free = 0.2661             target_work(ml) = 5.673         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2006 r_free = 0.2661             target_work(ml) = 5.673         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2006   r_free= 0.2661   ksol= 0.35   Bsol= 78.27   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.75,-0.50,-0.27,-0.00,-0.00,-0.00); trace/3= -0.51                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.672901                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2008   r_free= 0.2655   ksol= 0.34   Bsol= 80.00   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.20,-1.39,-0.28,-0.00,-0.00,-0.00); trace/3= -0.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.671371                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.451106              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.722  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.272084              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.312  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2008      final r-factor (work) = 0.1578          |
| start r-factor (free) = 0.2655      final r-factor (free) = 0.2130          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9145 = 3.45 * 0.50 * 5.7059 + 1.00 * 0.0687                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6780 = 3.45 * 0.50 * 5.5750 + 1.00 * 0.0580                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1578      final r-factor (work) = 0.1475          |
| start r-factor (free) = 0.2130      final r-factor (free) = 0.1987          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5306 = 0.27 * 1.00 * 5.5750 + 1.00 * 0.0137                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4859 = 0.27 * 1.00 * 5.4251 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| 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      1.16    97.75   17.82    None  None   None       |
|    all(noH): 2823   0      1.16    97.75   17.82    None  None   None       |
|    Sol.    : 438    0      5.80    97.75   43.67    None  None   None       |
|    Mac.    : 2385   0      1.16    89.11   13.07    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:     1.161 -  10.820: 1196   |   5:    49.453 -  59.112:  102        |
|      1:    10.820 -  20.478:  954   |   6:    59.112 -  68.770:   66        |
|      2:    20.478 -  30.137:  234   |   7:    68.770 -  78.429:   26        |
|      3:    30.137 -  39.795:  126   |   8:    78.429 -  88.087:    7        |
|      4:    39.795 -  49.453:  109   |   9:    88.087 -  97.746:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1475 r_free = 0.1987             target_work(ml) = 5.386         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1474 r_free = 0.1986             target_work(ml) = 5.386         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1474   r_free= 0.1986   ksol= 0.34   Bsol= 80.00   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.20,-1.39,-0.28,-0.00,-0.00,-0.00); trace/3= -0.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.385679                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1475   r_free= 0.1978   ksol= 0.33   Bsol= 67.20   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.81,-2.41,-0.80,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.383987                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.129577              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.439  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.274404              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.426  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1475      final r-factor (work) = 0.1314          |
| start r-factor (free) = 0.1978      final r-factor (free) = 0.1792          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8381 = 2.13 * 0.50 * 5.4284 + 1.00 * 0.0580                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7351 = 2.13 * 0.50 * 5.3359 + 1.00 * 0.0535                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1314      final r-factor (work) = 0.1285          |
| start r-factor (free) = 0.1792      final r-factor (free) = 0.1760          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4739 = 0.27 * 1.00 * 5.3359 + 1.00 * 0.0097                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4552 = 0.27 * 1.00 * 5.2694 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-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      0.59    92.56   17.51    None  None   None       |
|    all(noH): 2823   0      0.59    92.56   17.51    None  None   None       |
|    Sol.    : 438    0      5.99    92.56   42.68    None  None   None       |
|    Mac.    : 2385   0      0.59    92.28   12.89    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:     0.587 -   9.784:  988   |   5:    46.572 -  55.769:   95        |
|      1:     9.784 -  18.981: 1132   |   6:    55.769 -  64.966:   66        |
|      2:    18.981 -  28.178:  248   |   7:    64.966 -  74.163:   37        |
|      3:    28.178 -  37.375:  132   |   8:    74.163 -  83.360:   17        |
|      4:    37.375 -  46.572:  104   |   9:    83.360 -  92.557:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1285 r_free = 0.1760             target_work(ml) = 5.260         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1284 r_free = 0.1759             target_work(ml) = 5.260         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1284   r_free= 0.1759   ksol= 0.33   Bsol= 67.20   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.81,-2.41,-0.80,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.259691                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1284   r_free= 0.1759   ksol= 0.32   Bsol= 60.02   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,-2.63,-0.93,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.259519                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.398876              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.924  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.206786              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 163.856  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1284      final r-factor (work) = 0.1192          |
| start r-factor (free) = 0.1759      final r-factor (free) = 0.1667          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3737 = 2.40 * 0.50 * 5.2693 + 1.00 * 0.0535                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3326 = 2.40 * 0.50 * 5.2277 + 1.00 * 0.0623                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1192      final r-factor (work) = 0.1184          |
| start r-factor (free) = 0.1667      final r-factor (free) = 0.1650          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0902 = 0.21 * 1.00 * 5.2277 + 1.00 * 0.0091                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0835 = 0.21 * 1.00 * 5.1998 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| 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      0.63    93.67   17.13    None  None   None       |
|    all(noH): 2823   0      0.63    93.67   17.13    None  None   None       |
|    Sol.    : 438    0      5.88    86.84   40.80    None  None   None       |
|    Mac.    : 2385   0      0.63    93.67   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:     0.631 -   9.935: 1028   |   5:    47.149 -  56.453:   97        |
|      1:     9.935 -  19.238: 1131   |   6:    56.453 -  65.756:   53        |
|      2:    19.238 -  28.542:  232   |   7:    65.756 -  75.060:   28        |
|      3:    28.542 -  37.846:  137   |   8:    75.060 -  84.364:   11        |
|      4:    37.846 -  47.149:  103   |   9:    84.364 -  93.667:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1184 r_free = 0.1650             target_work(ml) = 5.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1183 r_free = 0.1649             target_work(ml) = 5.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1183   r_free= 0.1649   ksol= 0.32   Bsol= 60.02   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,-2.63,-0.93,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.195702                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2532 -  4.6909 0.99   1440  161 0.0967 0.1354      5.3766      5.6318|
|  2:  4.6909 -  3.7414 0.99   1393  154 0.0878 0.1152      5.4709      5.6484|
|  3:  3.7414 -  3.2738 0.99   1353  149 0.1139 0.1618       5.522      5.8381|
|  4:  3.2738 -  2.9769 0.99   1364  153 0.1341 0.1757      5.5027      5.6297|
|  5:  2.9769 -  2.7649 0.99   1348  147 0.1417 0.1850      5.3707      5.6213|
|  6:  2.7649 -  2.6027 0.99   1340  152 0.1357 0.1987      5.2477      5.4946|
|  7:  2.6027 -  2.4729 0.99   1338  141 0.1355 0.1681      5.2109      5.3477|
|  8:  2.4729 -  2.3657 0.98   1321  154 0.1252 0.1776      5.1078      5.3634|
|  9:  2.3657 -  2.2749 0.98   1321  146 0.1272 0.1902      5.0854      5.3454|
| 10:  2.2749 -  2.1967 1.00   1323  156 0.1157 0.1707      4.9747      5.2072|
| 11:  2.1967 -  2.1282 0.98   1309  138 0.1175 0.1818      4.9637      5.3604|
| 12:  2.1282 -  2.0675 0.98   1319  149 0.1235 0.1887      4.9176      5.1439|
| 13:  2.0675 -  2.0132 0.87   1163  127 0.1180 0.1682      4.8093      5.0197|
| 14:  2.0132 -  1.9642 0.22    298   32 0.1003 0.1481       4.672      4.9193|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2532 -  4.6909  1440   161  0.94   9.00   0.97     0.94       7237.53|
|  2:  4.6909 -  3.7414  1393   154  0.95   8.41   1.01     1.00       9723.80|
|  3:  3.7414 -  3.2738  1353   149  0.93  12.34   1.02     1.02      11375.35|
|  4:  3.2738 -  2.9769  1364   153  0.90  15.32   1.01     0.98      11215.92|
|  5:  2.9769 -  2.7649  1348   147  0.90  16.22   1.00     0.99       8748.36|
|  6:  2.7649 -  2.6027  1340   152  0.89  16.97   0.98     0.96       7305.58|
|  7:  2.6027 -  2.4729  1338   141  0.90  15.97   1.00     0.98       6629.48|
|  8:  2.4729 -  2.3657  1321   154  0.90  16.47   0.98     0.95       5724.20|
|  9:  2.3657 -  2.2749  1321   146  0.89  16.82   1.00     0.95       5462.37|
| 10:  2.2749 -  2.1967  1323   156  0.90  16.22   1.00     0.97       4648.14|
| 11:  2.1967 -  2.1282  1309   138  0.90  16.76   0.99     0.94       4468.70|
| 12:  2.1282 -  2.0675  1319   149  0.89  16.98   1.00     1.01       4285.68|
| 13:  2.0675 -  2.0132  1163   127  0.89  17.37   0.99     0.98       3577.61|
| 14:  2.0132 -  1.9642   298    32  0.92  13.89   0.98     0.96       2701.12|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2701.12 max =        11375.35 mean =      6948.62|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        14.88|
|phase err.(test): min =        0.00 max =           89.81 mean =        14.38|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1184   r_free= 0.1640   ksol= 0.32   Bsol= 55.88   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.04,-2.73,-0.95,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.192862                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1184   r_free= 0.1640   ksol= 0.32   Bsol= 55.88   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.04,-2.73,-0.95,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.192862                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2532 -  4.6909 0.99   1440  161 0.0966 0.1304      5.3538      5.5803|
|  2:  4.6909 -  3.7414 0.99   1393  154 0.0875 0.1112       5.457      5.6323|
|  3:  3.7414 -  3.2738 0.99   1353  149 0.1142 0.1600      5.5174      5.8316|
|  4:  3.2738 -  2.9769 0.99   1364  153 0.1343 0.1766      5.5021      5.6338|
|  5:  2.9769 -  2.7649 0.99   1348  147 0.1416 0.1859      5.3722      5.6219|
|  6:  2.7649 -  2.6027 0.99   1340  152 0.1357 0.1993      5.2485      5.4955|
|  7:  2.6027 -  2.4729 0.99   1338  141 0.1357 0.1681      5.2123      5.3479|
|  8:  2.4729 -  2.3657 0.98   1321  154 0.1251 0.1776      5.1078      5.3633|
|  9:  2.3657 -  2.2749 0.98   1321  146 0.1274 0.1903      5.0857      5.3462|
| 10:  2.2749 -  2.1967 1.00   1323  156 0.1156 0.1712      4.9756      5.2108|
| 11:  2.1967 -  2.1282 0.98   1309  138 0.1173 0.1821      4.9649      5.3616|
| 12:  2.1282 -  2.0675 0.98   1319  149 0.1235 0.1886      4.9185      5.1432|
| 13:  2.0675 -  2.0132 0.87   1163  127 0.1179 0.1682      4.8091      5.0198|
| 14:  2.0132 -  1.9642 0.22    298   32 0.1004 0.1479      4.6718      4.9174|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2532 -  4.6909  1440   161  0.94   8.58   0.97     0.94       6608.78|
|  2:  4.6909 -  3.7414  1393   154  0.95   8.06   1.01     1.00       9105.91|
|  3:  3.7414 -  3.2738  1353   149  0.93  12.09   1.02     1.02      11043.48|
|  4:  3.2738 -  2.9769  1364   153  0.90  15.31   1.00     0.98      11195.92|
|  5:  2.9769 -  2.7649  1348   147  0.90  16.25   1.00     0.98       8786.04|
|  6:  2.7649 -  2.6027  1340   152  0.89  17.01   0.98     0.96       7327.69|
|  7:  2.6027 -  2.4729  1338   141  0.90  15.98   0.99     0.97       6647.85|
|  8:  2.4729 -  2.3657  1321   154  0.90  16.47   0.98     0.95       5725.75|
|  9:  2.3657 -  2.2749  1321   146  0.89  16.83   0.99     0.95       5468.90|
| 10:  2.2749 -  2.1967  1323   156  0.90  16.24   1.00     0.97       4665.48|
| 11:  2.1967 -  2.1282  1309   138  0.90  16.81   0.98     0.93       4492.01|
| 12:  2.1282 -  2.0675  1319   149  0.89  17.00   1.00     1.00       4298.52|
| 13:  2.0675 -  2.0132  1163   127  0.89  17.37   0.99     0.97       3578.74|
| 14:  2.0132 -  1.9642   298    32  0.92  13.88   0.98     0.96       2699.10|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2699.10 max =        11195.92 mean =      6832.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.81|
|phase err.(test): min =        0.00 max =           89.94 mean =        14.30|
|-----------------------------------------------------------------------------|

|-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      0.61    93.65   17.11    None  None   None       |
|    all(noH): 2823   0      0.61    93.65   17.11    None  None   None       |
|    Sol.    : 438    0      5.86    86.82   40.78    None  None   None       |
|    Mac.    : 2385   0      0.61    93.65   12.76    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:     0.611 -   9.914: 1028   |   5:    47.129 -  56.432:   97        |
|      1:     9.914 -  19.218: 1131   |   6:    56.432 -  65.736:   53        |
|      2:    19.218 -  28.521:  232   |   7:    65.736 -  75.039:   28        |
|      3:    28.521 -  37.825:  137   |   8:    75.039 -  84.343:   11        |
|      4:    37.825 -  47.129:  103   |   9:    84.343 -  93.647:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 338         
Filter by distance & map next to the model:
   mapped sites are within: 0.656 - 4.717
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 333 from: 338
   mapped sites are within: 0.701 - 4.717

peak=    6.471 closest distance to " NE2 GLN A  11 " =    1.308
peak=    5.689 closest distance to " O   HOH Z   7 " =    1.764
peak=    5.546 closest distance to " O   HOH Z 222 " =    1.354
peak=    5.295 closest distance to " CB  GLN A 223 " =    1.502
peak=    5.265 closest distance to " CG  PRO A  54 " =    1.419
peak=    5.194 closest distance to " O   HOH Z 144 " =    1.831
peak=    5.126 closest distance to " O   HOH Z 417 " =    2.023
peak=    5.059 closest distance to " O   HOH Z  63 " =    1.611
peak=    4.970 closest distance to " O   HOH Z 126 " =    2.064
peak=    4.967 closest distance to " CB  SER A  63 " =    1.349
peak=    4.908 closest distance to " O   HOH Z 423 " =    2.138
peak=    4.905 closest distance to " O   HOH Z 111 " =    1.798
peak=    4.861 closest distance to " O   HOH Z 232 " =    2.224
peak=    4.790 closest distance to " O   HOH Z 183 " =    1.622
peak=    4.779 closest distance to " O   HOH Z 369 " =    2.090
peak=    4.654 closest distance to " O   HOH Z 287 " =    2.207
peak=    4.529 closest distance to " CB  ASN A 148 " =    1.383
peak=    4.522 closest distance to " O   HOH Z 425 " =    1.537
peak=    4.478 closest distance to " O   HOH Z 298 " =    2.197
peak=    4.419 closest distance to " CB  PRO A  54 " =    1.005
peak=    4.404 closest distance to " CG  PRO A 213 " =    1.324
peak=    4.381 closest distance to " O   HOH Z 427 " =    2.343
peak=    4.377 closest distance to " O   HOH Z 133 " =    2.363
peak=    4.326 closest distance to " O   HOH Z  78 " =    1.674
peak=    4.325 closest distance to " O   HOH Z   9 " =    1.564
peak=    4.320 closest distance to " CD  ARG A 159 " =    0.807
peak=    4.285 closest distance to " O   HOH Z 316 " =    3.106
peak=    4.268 closest distance to " CB  ARG A 190 " =    1.595
peak=    4.267 closest distance to " CG  PRO A 198 " =    1.307
peak=    4.224 closest distance to " O   HOH Z 380 " =    1.775
peak=    4.209 closest distance to " ND2 ASN A 187 " =    1.527
peak=    4.199 closest distance to " CB  ARG A 275 " =    0.974
peak=    4.172 closest distance to " O   HOH Z 209 " =    2.259
peak=    4.169 closest distance to " O   HOH Z   2 " =    1.907
peak=    4.165 closest distance to " O   HOH Z 403 " =    1.463
peak=    4.128 closest distance to " CB  GLN A 183 " =    1.220
peak=    4.122 closest distance to " CB  ASN A 187 " =    1.034
peak=    4.120 closest distance to " CB  SER A   3 " =    1.550
peak=    4.114 closest distance to " O   HOH Z 437 " =    1.843
peak=    4.100 closest distance to " O   HOH Z 126 " =    1.526
peak=    4.081 closest distance to " CB  SER A 216 " =    0.957
peak=    4.075 closest distance to " O   HOH Z  61 " =    1.674
peak=    4.061 closest distance to " O   HOH Z 419 " =    2.053
peak=    4.053 closest distance to " O   HOH Z 193 " =    1.699
peak=    4.042 closest distance to " CG  PRO A  90 " =    1.306
peak=    4.022 closest distance to " CB  TRP A 266 " =    1.020
peak=    4.020 closest distance to " O   HOH Z 272 " =    1.829
peak=    4.012 closest distance to " CD  ARG A  66 " =    2.010
peak=    3.995 closest distance to " CG2 THR A 221 " =    1.006
peak=    3.974 closest distance to " CG  LEU A 167 " =    1.259
peak=    3.960 closest distance to " O   HOH Z   1 " =    1.855
peak=    3.936 closest distance to " O   HOH Z 362 " =    1.855
peak=    3.918 closest distance to " O   HOH Z  58 " =    1.930
peak=    3.907 closest distance to " O   HOH Z 214 " =    2.125
peak=    3.904 closest distance to " ND1 HIS A  86 " =    1.791
peak=    3.887 closest distance to " OE1 GLN A  11 " =    2.193
peak=    3.885 closest distance to " CB  ASP A 124 " =    0.835
peak=    3.884 closest distance to " O   HOH Z  78 " =    2.010
peak=    3.877 closest distance to " CZ  PHE A 218 " =    1.092
peak=    3.853 closest distance to " CB  LEU A 228 " =    1.082
peak=    3.849 closest distance to " O   HOH Z  88 " =    3.913
peak=    3.824 closest distance to " CB  GLU A 152 " =    1.194
peak=    3.818 closest distance to " CG  TRP A 179 " =    2.186
peak=    3.817 closest distance to " O   ASN A 209 " =    1.534
peak=    3.816 closest distance to " CB  ASN A 142 " =    0.910
peak=    3.816 closest distance to " O   HOH Z  40 " =    2.165
peak=    3.800 closest distance to " O   HOH Z 225 " =    1.542
peak=    3.799 closest distance to " O   HOH Z 195 " =    1.468
peak=    3.793 closest distance to " O   HOH Z 261 " =    1.906
peak=    3.784 closest distance to " CB  SER A 212 " =    1.283
peak=    3.777 closest distance to " NH1AARG A 145 " =    1.212
peak=    3.775 closest distance to " CA  TYR A  30 " =    1.089
peak=    3.770 closest distance to " CG  PRO A 280 " =    0.820
peak=    3.768 closest distance to " CB  GLU A 128 " =    1.023
peak=    3.753 closest distance to " O   HOH Z 180 " =    2.133
peak=    3.752 closest distance to " O   HOH Z  61 " =    1.610
peak=    3.752 closest distance to " O   HOH Z 128 " =    2.210
peak=    3.736 closest distance to " CE3 TRP A 274 " =    1.293
peak=    3.733 closest distance to " O   HOH Z 258 " =    2.147
peak=    3.732 closest distance to " CA  ARG A 195 " =    1.374
peak=    3.725 closest distance to " O   HOH Z 158 " =    2.602
peak=    3.725 closest distance to " CB  ASN A  39 " =    0.940
peak=    3.718 closest distance to " O   HOH Z 135 " =    1.823
peak=    3.717 closest distance to " O   HOH Z 122 " =    1.886
peak=    3.711 closest distance to " CA  ILE A 234 " =    1.030
peak=    3.709 closest distance to " O   HOH Z  49 " =    1.315
peak=    3.708 closest distance to " NE AARG A 275 " =    1.548
peak=    3.698 closest distance to " CB  THR A 157 " =    1.198
peak=    3.696 closest distance to " O   HOH Z 394 " =    1.736
peak=    3.691 closest distance to " O   PRO A 198 " =    1.561
peak=    3.690 closest distance to " CB  SER A 210 " =    0.819
peak=    3.690 closest distance to " O   HOH Z 217 " =    2.785
peak=    3.690 closest distance to " CB  VAL A 265 " =    1.399
peak=    3.690 closest distance to " CB  TRP A 150 " =    1.108
peak=    3.686 closest distance to " CD1 LEU A 300 " =    1.238
peak=    3.686 closest distance to " CB  ARG A  79 " =    1.311
peak=    3.684 closest distance to " O   HOH Z  21 " =    1.749
peak=    3.680 closest distance to " O   HOH Z  30 " =    1.745
peak=    3.670 closest distance to " CB  TYR A 169 " =    0.857
peak=    3.669 closest distance to " O   HOH Z 132 " =    2.574
peak=    3.668 closest distance to " O   HOH Z 365 " =    2.660
peak=    3.665 closest distance to " CB  GLU A 236 " =    1.259
peak=    3.663 closest distance to " O   HOH Z 250 " =    1.405
peak=    3.658 closest distance to " CB  VAL A 202 " =    1.646
peak=    3.657 closest distance to " CG  ARG A 159 " =    0.795
peak=    3.655 closest distance to " O   HOH Z   1 " =    1.604
peak=    3.653 closest distance to " CG2 VAL A 257 " =    0.950
peak=    3.649 closest distance to " O   ASN A  74 " =    1.522
peak=    3.646 closest distance to " CE  LYS A  76 " =    0.838
peak=    3.643 closest distance to " O   HOH Z  10 " =    1.744
peak=    3.635 closest distance to " CA  ALA A  51 " =    0.994
peak=    3.634 closest distance to " CG  PRO A 243 " =    1.084
peak=    3.633 closest distance to " O   HOH Z   7 " =    3.508
peak=    3.628 closest distance to " O   HOH Z 414 " =    1.318
peak=    3.624 closest distance to " N   PHE A 130 " =    1.215
peak=    3.618 closest distance to " O   HOH Z  91 " =    2.418
peak=    3.612 closest distance to " O   HOH Z 427 " =    1.181
peak=    3.609 closest distance to " CB  ALA A   1 " =    4.717
peak=    3.608 closest distance to " CA  SER A  87 " =    1.023
peak=    3.602 closest distance to " O   HOH Z 434 " =    1.481
peak=    3.601 closest distance to " O   HOH Z 352 " =    1.659
peak=    3.595 closest distance to " CA  THR A 264 " =    0.845
peak=    3.595 closest distance to " CD1 ILE A  33 " =    1.693
peak=    3.591 closest distance to " O   HOH Z 116 " =    3.026
peak=    3.587 closest distance to " CA  ALA A 158 " =    1.117
peak=    3.584 closest distance to " O   HOH Z 145 " =    1.824
peak=    3.579 closest distance to " CA  TYR A 116 " =    1.302
peak=    3.575 closest distance to " O   HOH Z 176 " =    2.133
peak=    3.574 closest distance to " O   HOH Z  44 " =    2.618
peak=    3.566 closest distance to " O   HOH Z 115 " =    1.872
peak=    3.564 closest distance to " O   PRO A 198 " =    1.297
peak=    3.563 closest distance to " O   HOH Z 148 " =    3.384
peak=    3.562 closest distance to " O   HOH Z 327 " =    1.952
peak=    3.560 closest distance to " N   TYR A  15 " =    0.883
peak=    3.553 closest distance to " CA  ARG A 102 " =    1.140
peak=    3.551 closest distance to " O   HOH Z 422 " =    2.790
peak=    3.548 closest distance to " OD1BASN A 224 " =    2.285
peak=    3.544 closest distance to " O   HOH Z 218 " =    1.979
peak=    3.544 closest distance to " O   HOH Z   9 " =    1.807
peak=    3.542 closest distance to " CG  LYS A  76 " =    1.717
peak=    3.538 closest distance to " O   TYR A 116 " =    1.312
peak=    3.534 closest distance to " N   ASN A 127 " =    1.363
peak=    3.523 closest distance to " O   HOH Z  68 " =    1.952
peak=    3.523 closest distance to " N   SER A  97 " =    0.920
peak=    3.520 closest distance to " CA  LEU A 101 " =    1.472
peak=    3.519 closest distance to " CA  ALA A 160 " =    0.934
peak=    3.517 closest distance to " CA  MET A 105 " =    0.876
peak=    3.517 closest distance to " CG1 ILE A 151 " =    1.127
peak=    3.514 closest distance to " CA  PRO A  54 " =    1.361
peak=    3.512 closest distance to " O   HOH Z 144 " =    2.184
peak=    3.511 closest distance to " O   HOH Z 411 " =    3.465
peak=    3.509 closest distance to " CZ3 TRP A 266 " =    1.098
peak=    3.509 closest distance to " O   HOH Z 393 " =    1.256
peak=    3.508 closest distance to " CB  SER A 276 " =    1.211
peak=    3.506 closest distance to " O   HOH Z  98 " =    1.846
peak=    3.505 closest distance to " O   HOH Z 302 " =    1.706
peak=    3.505 closest distance to " O   HOH Z 368 " =    1.861
peak=    3.503 closest distance to " O   HOH Z 389 " =    1.933
peak=    3.492 closest distance to " OE1 GLN A 240 " =    1.644
peak=    3.489 closest distance to " CB  GLU A 277 " =    3.639
peak=    3.489 closest distance to " O   HOH Z 128 " =    1.867
peak=    3.487 closest distance to " O   HOH Z 139 " =    1.226
peak=    3.486 closest distance to " O   HOH Z  59 " =    1.724
peak=    3.481 closest distance to " O   HOH Z 234 " =    3.923
peak=    3.480 closest distance to " OH  TYR A 186 " =    1.070
peak=    3.476 closest distance to " NH1 ARG A  14 " =    0.982
peak=    3.470 closest distance to " CD2 TRP A 179 " =    1.223
peak=    3.469 closest distance to " CA  SER A  95 " =    1.016
peak=    3.468 closest distance to " OD1 ASN A  69 " =    2.585
peak=    3.463 closest distance to " O   HOH Z 154 " =    2.011
peak=    3.457 closest distance to " O   HOH Z 409 " =    2.189
peak=    3.450 closest distance to " O   HOH Z 188 " =    2.179
peak=    3.448 closest distance to " O   HOH Z 392 " =    1.287
peak=    3.448 closest distance to " CB  GLU A  46 " =    0.991
peak=    3.445 closest distance to " CB  LEU A 143 " =    1.162
peak=    3.445 closest distance to " CD BLYS A 290 " =    1.023
peak=    3.440 closest distance to " OG BSER A 134 " =    2.896
peak=    3.430 closest distance to " O   HOH Z  85 " =    2.028
peak=    3.427 closest distance to " O   HOH Z 385 " =    3.868
peak=    3.426 closest distance to " O   HOH Z 135 " =    1.564
peak=    3.426 closest distance to " O   HOH Z 368 " =    4.314
peak=    3.426 closest distance to " CB  PRO A 243 " =    1.220
peak=    3.425 closest distance to " CG BARG A 275 " =    1.478
peak=    3.422 closest distance to " CB  GLN A  88 " =    1.322
peak=    3.419 closest distance to " CZ3 TRP A 123 " =    1.404
peak=    3.407 closest distance to " O   HOH Z 405 " =    1.562
peak=    3.406 closest distance to " O   HOH Z 217 " =    1.666
peak=    3.405 closest distance to " O   HOH Z 438 " =    2.035
peak=    3.402 closest distance to " OG BSER A  99 " =    2.327
peak=    3.398 closest distance to " ND1 HIS A  81 " =    1.684
peak=    3.397 closest distance to " O   HOH Z 172 " =    2.439
peak=    3.396 closest distance to " OG  SER A  26 " =    1.689
peak=    3.395 closest distance to " CA  ASN A 127 " =    1.128
peak=    3.386 closest distance to " OG  SER A  62 " =    2.921
peak=    3.383 closest distance to " CG  GLN A 278 " =    1.320
peak=    3.376 closest distance to " O   HOH Z  51 " =    1.913
peak=    3.371 closest distance to " O   HOH Z 213 " =    1.865
peak=    3.371 closest distance to " O   HOH Z 146 " =    1.607
peak=    3.370 closest distance to " CA  VAL A 125 " =    1.171
peak=    3.369 closest distance to " CD2 LEU A 255 " =    1.753
peak=    3.369 closest distance to " O   HOH Z 410 " =    1.575
peak=    3.367 closest distance to " O   HOH Z 346 " =    1.757
peak=    3.363 closest distance to " CD2 PHE A  59 " =    1.678
peak=    3.361 closest distance to " O   HOH Z 313 " =    1.657
peak=    3.349 closest distance to " NE  ARG A  66 " =    3.442
peak=    3.347 closest distance to " CZ  PHE A 192 " =    0.901
peak=    3.346 closest distance to " CA  GLU A  46 " =    0.842
peak=    3.342 closest distance to " CG1 VAL A 153 " =    0.927
peak=    3.342 closest distance to " OG  SER A  62 " =    3.064
peak=    3.341 closest distance to " CD  PRO A 243 " =    1.833
peak=    3.341 closest distance to " O   HOH Z   3 " =    2.519
peak=    3.336 closest distance to " O   HOH Z  57 " =    1.154
peak=    3.333 closest distance to " CD  LYS A 166 " =    1.303
peak=    3.332 closest distance to " O   HOH Z 273 " =    2.789
peak=    3.332 closest distance to " N   SER A 271 " =    0.941
peak=    3.329 closest distance to " O   HOH Z 211 " =    1.172
peak=    3.327 closest distance to " CA  ILE A 106 " =    0.814
peak=    3.327 closest distance to " CB  ALA A 104 " =    0.701
peak=    3.325 closest distance to " CA  GLU A 152 " =    1.220
peak=    3.323 closest distance to " O   HOH Z 184 " =    1.518
peak=    3.322 closest distance to " O   HOH Z 171 " =    2.866
peak=    3.317 closest distance to " N   GLU A   2 " =    1.419
peak=    3.316 closest distance to " CA  TYR A 186 " =    1.518
peak=    3.309 closest distance to " O   HOH Z 371 " =    2.736
peak=    3.304 closest distance to " O   HOH Z 170 " =    1.140
peak=    3.304 closest distance to " O   HOH Z 124 " =    1.988
peak=    3.300 closest distance to " O   HOH Z 153 " =    3.698
peak=    3.299 closest distance to " CB  ALA A 114 " =    0.879
peak=    3.298 closest distance to " O   HOH Z 310 " =    2.419
peak=    3.298 closest distance to " O   HOH Z 272 " =    2.260
peak=    3.296 closest distance to " O   HOH Z 285 " =    2.410
peak=    3.295 closest distance to " CB  ALA A  43 " =    0.861
peak=    3.290 closest distance to " CB  TYR A 116 " =    0.956
peak=    3.289 closest distance to " O   HOH Z 201 " =    1.502
peak=    3.287 closest distance to " O   THR A 220 " =    1.505
peak=    3.286 closest distance to " CG2 ILE A  20 " =    1.497
peak=    3.278 closest distance to " CG1 ILE A  33 " =    1.255
peak=    3.278 closest distance to " O   HOH Z 153 " =    1.683
peak=    3.278 closest distance to " OD2 ASP A 286 " =    2.833
peak=    3.276 closest distance to " CA  CYS A 201 " =    1.638
peak=    3.275 closest distance to " CB  LEU A  83 " =    0.811
peak=    3.272 closest distance to " CB  LEU A 255 " =    1.403
peak=    3.266 closest distance to " OG  SER A  22 " =    2.966
peak=    3.266 closest distance to " O   HOH Z 244 " =    1.676
peak=    3.265 closest distance to " CZ  PHE A  38 " =    1.336
peak=    3.261 closest distance to " CA  ARG A  36 " =    1.233
peak=    3.261 closest distance to " O   HOH Z 175 " =    3.706
peak=    3.260 closest distance to " CB  ALA A 114 " =    1.569
peak=    3.259 closest distance to " CB  LYS A 117 " =    1.227
peak=    3.259 closest distance to " CE3 TRP A  85 " =    0.905
peak=    3.259 closest distance to " N   VAL A 296 " =    1.768
peak=    3.259 closest distance to " O   HOH Z 181 " =    2.191
peak=    3.258 closest distance to " O   HOH Z 240 " =    2.026
peak=    3.256 closest distance to " CD  ARG A 269 " =    0.942
peak=    3.253 closest distance to " O   HOH Z 345 " =    3.448
peak=    3.252 closest distance to " CA  ALA A 233 " =    1.201
peak=    3.251 closest distance to " CA  GLY A 267 " =    1.161
peak=    3.251 closest distance to " CB  TYR A  30 " =    1.365
peak=    3.248 closest distance to " CA  GLY A 241 " =    0.780
peak=    3.246 closest distance to " CA  MET A  40 " =    1.160
peak=    3.244 closest distance to " O   GLY A 302 " =    1.640
peak=    3.243 closest distance to " O   HOH Z  44 " =    1.867
peak=    3.242 closest distance to " CB  PHE A 204 " =    0.775
peak=    3.235 closest distance to " OD1 ASN A 217 " =    1.429
peak=    3.227 closest distance to " O   HOH Z  88 " =    2.992
peak=    3.227 closest distance to " O   HOH Z 368 " =    3.730
peak=    3.223 closest distance to " CB  ILE A 120 " =    1.402
peak=    3.222 closest distance to " CG1 VAL A 189 " =    1.776
peak=    3.218 closest distance to " CA  ASP A 162 " =    1.084
peak=    3.218 closest distance to " N   ARG A 156 " =    1.295
peak=    3.217 closest distance to " O   HOH Z 158 " =    1.689
peak=    3.214 closest distance to " O   HOH Z 409 " =    3.329
peak=    3.213 closest distance to " O   HOH Z 373 " =    1.574
peak=    3.212 closest distance to " O   HOH Z  80 " =    1.599
peak=    3.211 closest distance to " CB  PRO A  90 " =    1.188
peak=    3.209 closest distance to " O   HOH Z 193 " =    2.137
peak=    3.208 closest distance to " O   HOH Z 106 " =    3.982
peak=    3.206 closest distance to " NE2 GLN A  58 " =    3.979
peak=    3.205 closest distance to " CB  ARG A 138 " =    0.952
peak=    3.205 closest distance to " CA  ALA A 154 " =    0.999
peak=    3.204 closest distance to " N   CYS A 260 " =    0.801
peak=    3.200 closest distance to " CA  ASN A 215 " =    1.171
peak=    3.198 closest distance to " O   MET A 105 " =    1.745
peak=    3.194 closest distance to " CG  GLU A 277 " =    1.931
peak=    3.193 closest distance to " OE2 GLU A  53 " =    2.028
peak=    3.192 closest distance to " O   HOH Z 189 " =    2.603
peak=    3.191 closest distance to " CB  ALA A  10 " =    0.847
peak=    3.191 closest distance to " O   HOH Z 109 " =    2.336
peak=    3.191 closest distance to " CB  TRP A 274 " =    1.303
peak=    3.189 closest distance to " O   HOH Z 369 " =    1.696
peak=    3.188 closest distance to " O   HOH Z 113 " =    1.994
peak=    3.186 closest distance to " NE2 HIS A 207 " =    1.140
peak=    3.182 closest distance to " CB  SER A  99 " =    0.980
peak=    3.181 closest distance to " O   HOH Z 286 " =    2.017
peak=    3.181 closest distance to " O   HOH Z 325 " =    3.944
peak=    3.180 closest distance to " CG  MET A 113 " =    1.383
peak=    3.179 closest distance to " O   HOH Z 432 " =    1.809
peak=    3.178 closest distance to " O   HOH Z 219 " =    4.469
peak=    3.177 closest distance to " CA  ARG A 156 " =    1.036
peak=    3.175 closest distance to " CA  ASP A 124 " =    0.773
peak=    3.171 closest distance to " O   HOH Z 392 " =    2.146
peak=    3.171 closest distance to " O   HOH Z 280 " =    3.043
peak=    3.162 closest distance to " CA  ALA A 291 " =    0.923
peak=    3.158 closest distance to " CA  ALA A 160 " =    1.248
peak=    3.154 closest distance to " OG BSER A 212 " =    2.546
peak=    3.153 closest distance to " CA  ILE A 263 " =    1.110
peak=    3.151 closest distance to " O   THR A 294 " =    1.089
peak=    3.149 closest distance to " CG  GLU A   2 " =    1.165
peak=    3.140 closest distance to " CA  ALA A 100 " =    1.117
peak=    3.140 closest distance to " O   HOH Z 128 " =    1.952
peak=    3.139 closest distance to " CB  ASP A 171 " =    0.708
peak=    3.134 closest distance to " CG  GLN A 278 " =    3.726
peak=    3.124 closest distance to " O   HOH Z 407 " =    1.508
peak=    3.115 closest distance to " O   HOH Z 281 " =    1.848
peak=    3.114 closest distance to " NZ  LYS A 119 " =    1.306
peak=    3.114 closest distance to " O   HOH Z 282 " =    1.491
peak=    3.113 closest distance to " CA  THR A 221 " =    0.956
peak=    3.108 closest distance to " O   HOH Z 132 " =    3.867
peak=    3.101 closest distance to " O   LEU A 300 " =    1.313
peak=    3.098 closest distance to " O   HOH Z 130 " =    2.071
peak=    3.098 closest distance to " O   GLY A 302 " =    2.195
peak=    3.096 closest distance to " O   HOH Z 344 " =    3.360
peak=    3.091 closest distance to " O   HOH Z  88 " =    3.644
peak=    3.090 closest distance to " O  BHOH Z 338 " =    2.181
peak=    3.090 closest distance to " NH1 ARG A  66 " =    1.643
peak=    3.088 closest distance to " CA  TYR A  30 " =    1.062
peak=    3.087 closest distance to " O   HOH Z  99 " =    1.811
peak=    3.076 closest distance to " O   HOH Z   9 " =    1.680
peak=    3.074 closest distance to " O   HOH Z 359 " =    4.104
peak=    3.068 closest distance to " O   HOH Z 172 " =    4.620
peak=    3.066 closest distance to " CG BARG A 102 " =    1.862
peak=    3.059 closest distance to " O   HOH Z 425 " =    1.974
peak=    3.057 closest distance to " O   HOH Z 219 " =    1.954

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 212         
Filter by distance & map next to the model:
   mapped sites are within: 0.429 - 5.654
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 212
   mapped sites are within: 0.756 - 5.654

peak=   -4.724 closest distance to " CD  ARG A  14 " =    3.367
peak=   -4.636 closest distance to " CB  PRO A 243 " =    2.531
peak=   -4.463 closest distance to " O   PRO A 198 " =    1.216
peak=   -4.375 closest distance to " O   HOH Z 290 " =    1.057
peak=   -4.282 closest distance to " CA  GLY A  98 " =    1.824
peak=   -4.272 closest distance to " O   HOH Z  65 " =    1.081
peak=   -4.252 closest distance to " O   HOH Z 377 " =    1.661
peak=   -4.206 closest distance to " O   HOH Z  39 " =    0.962
peak=   -4.085 closest distance to " CD  ARG A 156 " =    2.122
peak=   -4.083 closest distance to " CA  GLY A 241 " =    2.278
peak=   -4.052 closest distance to " CZ3 TRP A 179 " =    1.156
peak=   -4.050 closest distance to " CG  MET A 105 " =    0.936
peak=   -3.989 closest distance to " CB  ALA A 291 " =    2.221
peak=   -3.988 closest distance to " O   HOH Z 351 " =    1.549
peak=   -3.983 closest distance to " O   HOH Z 389 " =    2.114
peak=   -3.968 closest distance to " O   HOH Z 185 " =    2.117
peak=   -3.888 closest distance to " O   HOH Z  60 " =    1.672
peak=   -3.879 closest distance to " O   HOH Z 313 " =    1.575
peak=   -3.876 closest distance to " O   HOH Z 282 " =    4.417
peak=   -3.859 closest distance to " CA  GLY A 203 " =    2.299
peak=   -3.846 closest distance to " O   ALA A  10 " =    1.699
peak=   -3.836 closest distance to " CB  ALA A 158 " =    1.620
peak=   -3.828 closest distance to " O   SER A  22 " =    2.782
peak=   -3.826 closest distance to " O   SER A 135 " =    1.480
peak=   -3.822 closest distance to " O   HOH Z 211 " =    1.183
peak=   -3.818 closest distance to " O   HOH Z  52 " =    1.102
peak=   -3.812 closest distance to " CG1 VAL A  78 " =    2.457
peak=   -3.795 closest distance to " O   HOH Z 231 " =    1.870
peak=   -3.794 closest distance to " CB  ALA A  43 " =    2.448
peak=   -3.765 closest distance to " CB  ASP A  27 " =    2.457
peak=   -3.753 closest distance to " OD1 ASP A 191 " =    1.989
peak=   -3.740 closest distance to " O   PRO A 243 " =    2.304
peak=   -3.737 closest distance to " O   HOH Z 290 " =    0.819
peak=   -3.726 closest distance to " ND2 ASN A 249 " =    2.111
peak=   -3.719 closest distance to " O   ILE A  49 " =    1.645
peak=   -3.706 closest distance to " O   HOH Z 407 " =    3.298
peak=   -3.692 closest distance to " OG BSER A 134 " =    1.455
peak=   -3.685 closest distance to " O   HOH Z 111 " =    1.768
peak=   -3.680 closest distance to " O   HOH Z  38 " =    1.295
peak=   -3.670 closest distance to " CD1 LEU A 255 " =    3.038
peak=   -3.669 closest distance to " O   VAL A  67 " =    2.678
peak=   -3.662 closest distance to " O   HOH Z  73 " =    2.065
peak=   -3.658 closest distance to " O   HOH Z  51 " =    0.975
peak=   -3.644 closest distance to " N   ASP A 171 " =    2.454
peak=   -3.641 closest distance to " C   LEU A 143 " =    1.318
peak=   -3.638 closest distance to " O   HOH Z 166 " =    1.212
peak=   -3.630 closest distance to " N   ALA A  43 " =    2.501
peak=   -3.630 closest distance to " CB  ALA A   9 " =    2.457
peak=   -3.628 closest distance to " CG2 THR A  18 " =    2.812
peak=   -3.627 closest distance to " CD  GLN A  88 " =    0.855
peak=   -3.624 closest distance to " O   PRO A 163 " =    1.891
peak=   -3.621 closest distance to " N   THR A 157 " =    1.565
peak=   -3.616 closest distance to " O   HOH Z  22 " =    2.375
peak=   -3.608 closest distance to " O   HOH Z 118 " =    1.510
peak=   -3.599 closest distance to " CB  PHE A 283 " =    2.834
peak=   -3.596 closest distance to " NE2 GLN A  55 " =    0.846
peak=   -3.593 closest distance to " CE BMET A  47 " =    1.416
peak=   -3.589 closest distance to " O   HOH Z 131 " =    4.123
peak=   -3.586 closest distance to " CB  PRO A  54 " =    2.481
peak=   -3.580 closest distance to " ND2 ASN A 209 " =    1.969
peak=   -3.569 closest distance to " CD  LYS A 289 " =    2.334
peak=   -3.568 closest distance to " NH2 ARG A  79 " =    1.935
peak=   -3.566 closest distance to " O   HOH Z 298 " =    1.185
peak=   -3.552 closest distance to " O   HOH Z 281 " =    2.800
peak=   -3.543 closest distance to " CE2 TYR A  30 " =    2.612
peak=   -3.538 closest distance to " CB  TRP A  85 " =    2.462
peak=   -3.528 closest distance to " NH2AARG A 275 " =    5.654
peak=   -3.518 closest distance to " O   TYR A 247 " =    2.851
peak=   -3.514 closest distance to " OG  SER A  97 " =    2.225
peak=   -3.504 closest distance to " O   HOH Z  24 " =    1.158
peak=   -3.503 closest distance to " O   HOH Z 372 " =    2.492
peak=   -3.495 closest distance to " O   HOH Z  49 " =    1.337
peak=   -3.467 closest distance to " CB  PHE A 130 " =    1.270
peak=   -3.462 closest distance to " O   GLY A 211 " =    1.220
peak=   -3.455 closest distance to " CE1 TYR A 169 " =    2.641
peak=   -3.450 closest distance to " CD2 TYR A 293 " =    1.931
peak=   -3.448 closest distance to " OG  SER A 245 " =    1.263
peak=   -3.447 closest distance to " O   HOH Z  32 " =    2.017
peak=   -3.443 closest distance to " O   HOH Z 102 " =    1.543
peak=   -3.430 closest distance to " CZ2 TRP A 274 " =    0.958
peak=   -3.430 closest distance to " CG2 THR A 178 " =    2.248
peak=   -3.427 closest distance to " O   HOH Z 134 " =    1.529
peak=   -3.421 closest distance to " CG  ASN A  39 " =    1.682
peak=   -3.415 closest distance to " OG BSER A 134 " =    1.824
peak=   -3.412 closest distance to " CD  GLN A 223 " =    0.788
peak=   -3.412 closest distance to " O   HOH Z  76 " =    1.119
peak=   -3.411 closest distance to " O   HOH Z   1 " =    1.373
peak=   -3.411 closest distance to " O   HOH Z  11 " =    1.686
peak=   -3.408 closest distance to " CG2 VAL A 232 " =    2.027
peak=   -3.407 closest distance to " CG1 VAL A 112 " =    2.518
peak=   -3.403 closest distance to " CB  ALA A 114 " =    2.495
peak=   -3.397 closest distance to " O   HOH Z  60 " =    0.911
peak=   -3.395 closest distance to " O   ALA A   1 " =    1.182
peak=   -3.393 closest distance to " O   HOH Z 241 " =    1.185
peak=   -3.391 closest distance to " CG  LEU A 167 " =    0.904
peak=   -3.388 closest distance to " O   HOH Z  28 " =    1.584
peak=   -3.387 closest distance to " O   HOH Z  53 " =    1.745
peak=   -3.380 closest distance to " ND2 ASN A 285 " =    2.119
peak=   -3.363 closest distance to " CG  GLN A 240 " =    2.392
peak=   -3.358 closest distance to " O   HOH Z 166 " =    1.707
peak=   -3.356 closest distance to " CE2 PHE A 218 " =    2.407
peak=   -3.354 closest distance to " CB  PRO A 163 " =    2.456
peak=   -3.351 closest distance to " CA  GLY A 241 " =    3.063
peak=   -3.343 closest distance to " O   HOH Z 266 " =    5.102
peak=   -3.342 closest distance to " OG  SER A  87 " =    1.322
peak=   -3.341 closest distance to " O   HOH Z 298 " =    2.528
peak=   -3.339 closest distance to " CA  GLY A  57 " =    2.283
peak=   -3.339 closest distance to " CB  ASN A  39 " =    2.239
peak=   -3.333 closest distance to " CG  GLN A 223 " =    2.096
peak=   -3.328 closest distance to " CG1 VAL A 112 " =    2.733
peak=   -3.327 closest distance to " ND2 ASN A  60 " =    4.048
peak=   -3.325 closest distance to " O   HOH Z 108 " =    1.435
peak=   -3.324 closest distance to " OE1 GLN A  58 " =    3.200
peak=   -3.318 closest distance to " O   HOH Z  90 " =    2.917
peak=   -3.316 closest distance to " O   VAL A 189 " =    2.539
peak=   -3.314 closest distance to " O   HOH Z 384 " =    3.070
peak=   -3.314 closest distance to " CB  ASP A 132 " =    2.385
peak=   -3.313 closest distance to " OE1 GLN A  88 " =    1.202
peak=   -3.308 closest distance to " CD  GLN A  58 " =    0.821
peak=   -3.306 closest distance to " ND2 ASN A 187 " =    1.418
peak=   -3.305 closest distance to " O   HOH Z 174 " =    2.781
peak=   -3.304 closest distance to " NE  ARG A  36 " =    2.007
peak=   -3.303 closest distance to " O   VAL A 125 " =    2.249
peak=   -3.292 closest distance to " O   HOH Z 300 " =    2.142
peak=   -3.291 closest distance to " ND2 ASN A  45 " =    2.231
peak=   -3.287 closest distance to " O   PHE A 218 " =    1.376
peak=   -3.283 closest distance to " CG  ARG A 269 " =    2.700
peak=   -3.282 closest distance to " O   GLY A  80 " =    2.404
peak=   -3.280 closest distance to " OXT GLY A 302 " =    3.326
peak=   -3.280 closest distance to " O   ALA A 180 " =    1.194
peak=   -3.277 closest distance to " C   GLU A 236 " =    0.813
peak=   -3.276 closest distance to " CE  MET A 105 " =    2.530
peak=   -3.276 closest distance to " CD1 TRP A 179 " =    1.004
peak=   -3.273 closest distance to " O   HOH Z 286 " =    1.615
peak=   -3.272 closest distance to " CE  LYS A  76 " =    2.833
peak=   -3.272 closest distance to " CA  GLY A 133 " =    1.945
peak=   -3.270 closest distance to " ND2BASN A 224 " =    1.514
peak=   -3.269 closest distance to " CG2 THR A 157 " =    2.263
peak=   -3.264 closest distance to " O   GLN A 240 " =    1.915
peak=   -3.263 closest distance to " O   ASP A 162 " =    2.292
peak=   -3.262 closest distance to " C   HIS A 108 " =    1.186
peak=   -3.259 closest distance to " CG  LEU A  83 " =    2.006
peak=   -3.259 closest distance to " O   HOH Z 275 " =    1.740
peak=   -3.259 closest distance to " CD2 LEU A 143 " =    2.559
peak=   -3.254 closest distance to " N   SER A 141 " =    1.870
peak=   -3.252 closest distance to " O   HOH Z 191 " =    5.463
peak=   -3.250 closest distance to " CG  ARG A  66 " =    1.726
peak=   -3.248 closest distance to " O   HOH Z 317 " =    1.410
peak=   -3.241 closest distance to " CB  CYS A 254 " =    2.148
peak=   -3.235 closest distance to " O   HOH Z 109 " =    1.872
peak=   -3.234 closest distance to " O   SER A  62 " =    2.398
peak=   -3.225 closest distance to " CD2 PHE A 130 " =    3.008
peak=   -3.224 closest distance to " O   HOH Z 198 " =    2.019
peak=   -3.221 closest distance to " NZ  LYS A 166 " =    1.168
peak=   -3.219 closest distance to " O   HOH Z 357 " =    2.110
peak=   -3.217 closest distance to " CG  TRP A 266 " =    1.584
peak=   -3.214 closest distance to " C   GLY A  13 " =    0.929
peak=   -3.210 closest distance to " O   HOH Z 216 " =    1.767
peak=   -3.209 closest distance to " OG  SER A 206 " =    1.893
peak=   -3.206 closest distance to " OD2 ASP A 171 " =    1.621
peak=   -3.204 closest distance to " O   HOH Z 414 " =    1.836
peak=   -3.201 closest distance to " C   LEU A 222 " =    0.756
peak=   -3.200 closest distance to " O   HOH Z 250 " =    1.295
peak=   -3.195 closest distance to " O   HOH Z 318 " =    1.721
peak=   -3.195 closest distance to " O   PRO A 198 " =    1.352
peak=   -3.194 closest distance to " CG  PRO A 163 " =    2.399
peak=   -3.193 closest distance to " O   HOH Z 412 " =    4.445
peak=   -3.192 closest distance to " CB  ALA A 248 " =    2.000
peak=   -3.188 closest distance to " CD  PRO A 213 " =    2.038
peak=   -3.186 closest distance to " O   HOH Z  43 " =    1.536
peak=   -3.180 closest distance to " O   GLY A  17 " =    1.155
peak=   -3.175 closest distance to " CD1 ILE A 199 " =    2.732
peak=   -3.173 closest distance to " O   HOH Z 152 " =    4.842
peak=   -3.167 closest distance to " O   HOH Z 218 " =    3.714
peak=   -3.165 closest distance to " CB  ALA A 100 " =    2.314
peak=   -3.165 closest distance to " O   HOH Z 378 " =    1.079
peak=   -3.164 closest distance to " O   HOH Z 147 " =    1.323
peak=   -3.161 closest distance to " CE3 TRP A 123 " =    1.396
peak=   -3.159 closest distance to " CG2BVAL A  41 " =    1.203
peak=   -3.153 closest distance to " O   HOH Z 200 " =    3.645
peak=   -3.146 closest distance to " CG1 VAL A 250 " =    2.721
peak=   -3.145 closest distance to " O   HOH Z 359 " =    3.197
peak=   -3.145 closest distance to " NE2 GLN A  58 " =    3.007
peak=   -3.136 closest distance to " CG  LEU A 282 " =    2.426
peak=   -3.135 closest distance to " O   GLU A 152 " =    1.534
peak=   -3.134 closest distance to " O   ASP A  27 " =    1.763
peak=   -3.132 closest distance to " CB  ALA A 131 " =    1.995
peak=   -3.127 closest distance to " CD1 ILE A 239 " =    2.292
peak=   -3.125 closest distance to " CD  GLU A 277 " =    0.950
peak=   -3.117 closest distance to " O   HOH Z 253 " =    4.176
peak=   -3.113 closest distance to " CB  ALA A  10 " =    2.258
peak=   -3.113 closest distance to " CZ BARG A 275 " =    1.508
peak=   -3.111 closest distance to " O   SER A  87 " =    1.983
peak=   -3.102 closest distance to " CB  PHE A 208 " =    2.291
peak=   -3.095 closest distance to " O   HOH Z 285 " =    4.214
peak=   -3.095 closest distance to " OD1 ASP A 171 " =    1.635
peak=   -3.091 closest distance to " OD2 ASP A 171 " =    2.155
peak=   -3.091 closest distance to " O   HOH Z 426 " =    2.207
peak=   -3.089 closest distance to " O   HOH Z 163 " =    1.540
peak=   -3.084 closest distance to " CB  GLN A  55 " =    1.456
peak=   -3.080 closest distance to " N   ALA A 226 " =    2.120
peak=   -3.068 closest distance to " OE1 GLN A  89 " =    1.999
peak=   -3.066 closest distance to " CG1 VAL A 112 " =    3.224
peak=   -3.058 closest distance to " CZ  PHE A  16 " =    2.331
peak=   -3.055 closest distance to " O   HOH Z 114 " =    1.669
peak=   -3.037 closest distance to " O   HOH Z  60 " =    0.978
peak=   -3.024 closest distance to " NH2 ARG A 156 " =    1.051

================= 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    :  0.4571 0.4575   6.269666e+00   6.261220e+00
   1_bss:  0.4491 0.4528   6.264061e+00   6.254448e+00
   1_xyz:  0.3116 0.3540   6.011969e+00   6.082058e+00
   1_adp:  0.2826 0.3674   5.966311e+00   6.109681e+00
   1_occ:  0.2821 0.3672   5.965827e+00   6.110097e+00
   2_bss:  0.2812 0.3648   5.963866e+00   6.107002e+00
   2_xyz:  0.2189 0.2846   5.740017e+00   5.922116e+00
   2_adp:  0.2008 0.2661   5.673303e+00   5.867620e+00
   2_occ:  0.2006 0.2661   5.672901e+00   5.867551e+00
   3_bss:  0.2008 0.2655   5.671371e+00   5.865793e+00
   3_xyz:  0.1578 0.2130   5.450125e+00   5.673504e+00
   3_adp:  0.1475 0.1987   5.385995e+00   5.602602e+00
   3_occ:  0.1474 0.1986   5.385679e+00   5.602183e+00
   4_bss:  0.1475 0.1978   5.383987e+00   5.599569e+00
   4_xyz:  0.1314 0.1792   5.278420e+00   5.503655e+00
   4_adp:  0.1285 0.1760   5.259961e+00   5.485664e+00
   4_occ:  0.1284 0.1759   5.259691e+00   5.485310e+00
   5_bss:  0.1284 0.1759   5.259519e+00   5.485102e+00
   5_xyz:  0.1192 0.1667   5.201375e+00   5.439580e+00
   5_adp:  0.1184 0.1650   5.195851e+00   5.433204e+00
   5_occ:  0.1183 0.1649   5.195702e+00   5.432957e+00
   5_bss:  0.1184 0.1640   5.192862e+00   5.427752e+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:  0.344  60.824   0.297   1.678  -0.471   0.000  -0.000  -0.000
   1_xyz:  0.344  60.824   0.297   1.678  -0.471   0.000  -0.000  -0.000
   1_adp:  0.344  60.824   0.297   1.678  -0.471   0.000  -0.000  -0.000
   1_occ:  0.344  60.824   0.297   1.678  -0.471   0.000  -0.000  -0.000
   2_bss:  0.352  78.270  -0.753  -0.504  -0.272  -0.000  -0.000  -0.000
   2_xyz:  0.352  78.270  -0.753  -0.504  -0.272  -0.000  -0.000  -0.000
   2_adp:  0.352  78.270  -0.753  -0.504  -0.272  -0.000  -0.000  -0.000
   2_occ:  0.352  78.270  -0.753  -0.504  -0.272  -0.000  -0.000  -0.000
   3_bss:  0.345  80.000  -1.201  -1.388  -0.278  -0.000  -0.000  -0.000
   3_xyz:  0.345  80.000  -1.201  -1.388  -0.278  -0.000  -0.000  -0.000
   3_adp:  0.345  80.000  -1.201  -1.388  -0.278  -0.000  -0.000  -0.000
   3_occ:  0.345  80.000  -1.201  -1.388  -0.278  -0.000  -0.000  -0.000
   4_bss:  0.327  67.201  -1.805  -2.405  -0.795  -0.000  -0.000  -0.000
   4_xyz:  0.327  67.201  -1.805  -2.405  -0.795  -0.000  -0.000  -0.000
   4_adp:  0.327  67.201  -1.805  -2.405  -0.795  -0.000  -0.000  -0.000
   4_occ:  0.327  67.201  -1.805  -2.405  -0.795  -0.000  -0.000  -0.000
   5_bss:  0.318  60.017  -1.980  -2.626  -0.933  -0.000  -0.000  -0.000
   5_xyz:  0.318  60.017  -1.980  -2.626  -0.933  -0.000  -0.000  -0.000
   5_adp:  0.318  60.017  -1.980  -2.626  -0.933  -0.000  -0.000  -0.000
   5_occ:  0.318  60.017  -1.980  -2.626  -0.933  -0.000  -0.000  -0.000
   5_bss:  0.315  55.880  -2.037  -2.732  -0.954  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.835 0.4466  0.6062    67349.491
   1_bss:  55.419 0.4507  0.6292    65941.514
   1_xyz:  37.503 0.6728  0.8861    34568.308
   1_adp:  39.800 0.6443  0.8559    37584.286
   1_occ:  39.854 0.6435  0.8539    37586.157
   2_bss:  39.528 0.6473  0.8297    37066.521
   2_xyz:  29.656 0.7598  0.9436    21568.253
   2_adp:  27.057 0.7889  0.9552    18688.984
   2_occ:  27.059 0.7889  0.9548    18684.431
   3_bss:  26.969 0.7897  0.9402    18555.451
   3_xyz:  20.900 0.8518  0.9847    11617.435
   3_adp:  18.947 0.8716  0.9920    10125.416
   3_occ:  18.945 0.8716  0.9916    10110.158
   4_bss:  18.865 0.8721  0.9675    10015.548
   4_xyz:  16.492 0.8937  0.9775     8025.827
   4_adp:  16.009 0.8983  0.9769     7782.371
   4_occ:  16.003 0.8984  0.9768     7777.441
   5_bss:  16.001 0.8984  0.9707     7772.456
   5_xyz:  15.031 0.9065  0.9753     7038.929
   5_adp:  14.831 0.9084  0.9742     6951.422
   5_occ:  14.830 0.9084  0.9742     6948.246
   5_bss:  14.762 0.9088  0.9717     6831.655
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.7187e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.7187e-01
   1_xyz:   1.620  0.013  0.111 16.484  0.007  4.110   1.4857e-01
   1_adp:   1.620  0.013  0.111 16.484  0.007  4.110   1.4857e-01
   1_occ:   1.620  0.013  0.111 16.484  0.007  4.110   1.4857e-01
   2_bss:   1.620  0.013  0.111 16.484  0.007  4.110   1.4857e-01
   2_xyz:   1.103  0.007  0.080 14.629  0.004  4.110   6.8703e-02
   2_adp:   1.103  0.007  0.080 14.629  0.004  4.110   6.8703e-02
   2_occ:   1.103  0.007  0.080 14.629  0.004  4.110   6.8703e-02
   3_bss:   1.103  0.007  0.080 14.629  0.004  4.110   6.8703e-02
   3_xyz:   0.974  0.007  0.068 14.402  0.003  4.121   5.8006e-02
   3_adp:   0.974  0.007  0.068 14.402  0.003  4.121   5.8006e-02
   3_occ:   0.974  0.007  0.068 14.402  0.003  4.121   5.8006e-02
   4_bss:   0.974  0.007  0.068 14.402  0.003  4.121   5.8006e-02
   4_xyz:   0.950  0.006  0.071 14.192  0.003  4.113   5.3500e-02
   4_adp:   0.950  0.006  0.071 14.192  0.003  4.113   5.3500e-02
   4_occ:   0.950  0.006  0.071 14.192  0.003  4.113   5.3500e-02
   5_bss:   0.950  0.006  0.071 14.192  0.003  4.113   5.3500e-02
   5_xyz:   1.033  0.008  0.076 14.439  0.004  4.118   6.2311e-02
   5_adp:   1.033  0.008  0.076 14.439  0.004  4.118   6.2311e-02
   5_occ:   1.033  0.008  0.076 14.439  0.004  4.118   6.2311e-02
   5_bss:   1.033  0.008  0.076 14.439  0.004  4.118   6.2311e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4196e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4196e-01
   1_xyz:   9.225  0.084  0.354 84.952  0.052  2.044   1.0978e-01
   1_adp:   9.225  0.084  0.354 84.952  0.052  2.044   1.0978e-01
   1_occ:   9.225  0.084  0.354 84.952  0.052  2.044   1.0978e-01
   2_bss:   9.225  0.084  0.354 84.952  0.052  2.044   1.0978e-01
   2_xyz:   8.139  0.040  0.241 82.591  0.036  2.287   7.6662e-02
   2_adp:   8.139  0.040  0.241 82.591  0.036  2.287   7.6662e-02
   2_occ:   8.139  0.040  0.241 82.591  0.036  2.287   7.6662e-02
   3_bss:   8.139  0.040  0.241 82.591  0.036  2.287   7.6662e-02
   3_xyz:   8.827  0.055  0.240 83.466  0.015  2.311   6.9104e-02
   3_adp:   8.827  0.055  0.240 83.466  0.015  2.311   6.9104e-02
   3_occ:   8.827  0.055  0.240 83.466  0.015  2.311   6.9104e-02
   4_bss:   8.827  0.055  0.240 83.466  0.015  2.311   6.9104e-02
   4_xyz:   8.311  0.051  0.240 81.286  0.027  2.351   3.6066e-02
   4_adp:   8.311  0.051  0.240 81.286  0.027  2.351   3.6066e-02
   4_occ:   8.311  0.051  0.240 81.286  0.027  2.351   3.6066e-02
   5_bss:   8.311  0.051  0.240 81.286  0.027  2.351   3.6066e-02
   5_xyz:   8.433  0.043  0.240 83.729  0.028  2.295   4.3712e-02
   5_adp:   8.433  0.043  0.240 83.729  0.028  2.295   4.3712e-02
   5_occ:   8.433  0.043  0.240 83.729  0.028  2.295   4.3712e-02
   5_bss:   8.433  0.043  0.240 83.729  0.028  2.295   4.3712e-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: 103.35   0.00  18.98  72.08   0.00  14.73 103.35   1.11  42.11
   1_occ: 103.35   0.00  18.98  72.08   0.00  14.73 103.35   1.11  42.11
   2_bss: 103.35   0.00  18.98  72.08   0.00  14.73 103.35   1.11  42.11
   2_xyz: 103.35   0.00  18.98  72.08   0.00  14.73 103.35   1.11  42.11
   2_adp: 106.76   0.00  18.67  88.61   0.00  13.90 106.76   3.44  44.65
   2_occ: 106.76   0.00  18.67  88.61   0.00  13.90 106.76   3.44  44.65
   3_bss: 106.76   0.00  18.67  88.61   0.00  13.90 106.76   3.44  44.65
   3_xyz: 106.76   0.00  18.67  88.61   0.00  13.90 106.76   3.44  44.65
   3_adp:  97.75   1.16  17.82  89.11   1.16  13.07  97.75   5.80  43.67
   3_occ:  97.75   1.16  17.82  89.11   1.16  13.07  97.75   5.80  43.67
   4_bss:  97.75   1.16  17.82  89.11   1.16  13.07  97.75   5.80  43.67
   4_xyz:  97.75   1.16  17.82  89.11   1.16  13.07  97.75   5.80  43.67
   4_adp:  92.56   0.59  17.51  92.28   0.59  12.89  92.56   5.99  42.68
   4_occ:  92.56   0.59  17.51  92.28   0.59  12.89  92.56   5.99  42.68
   5_bss:  92.56   0.59  17.51  92.28   0.59  12.89  92.56   5.99  42.68
   5_xyz:  92.56   0.59  17.51  92.28   0.59  12.89  92.56   5.99  42.68
   5_adp:  93.67   0.63  17.13  93.67   0.63  12.78  86.84   5.88  40.80
   5_occ:  93.67   0.63  17.13  93.67   0.63  12.78  86.84   5.88  40.80
   5_bss:  93.65   0.61  17.11  93.65   0.61  12.76  86.82   5.86  40.78
------------------------------------------------------------------------
 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:    1.582    0.032    0.472
   1_adp:    1.582    0.032    0.472
   1_occ:    1.582    0.032    0.472
   2_bss:    1.582    0.032    0.472
   2_xyz:    1.293    0.057    0.568
   2_adp:    1.293    0.057    0.568
   2_occ:    1.293    0.057    0.568
   3_bss:    1.293    0.057    0.568
   3_xyz:    1.364    0.063    0.684
   3_adp:    1.364    0.063    0.684
   3_occ:    1.364    0.063    0.684
   4_bss:    1.364    0.063    0.684
   4_xyz:    1.446    0.042    0.715
   4_adp:    1.446    0.042    0.715
   4_occ:    1.446    0.042    0.715
   5_bss:    1.446    0.042    0.715
   5_xyz:    1.632    0.043    0.742
   5_adp:    1.632    0.043    0.742
   5_occ:    1.632    0.043    0.742
   5_bss:    1.632    0.043    0.742
------------------------------------------------------------------------

CPU time actual refinement: 359.38


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1107/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_1107/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1107/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1107/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1107/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 359.23 
  Macro-tasks:
    bulk solvent and scale       = 48.76  
    individual site refinement   = 146.21 
    weights calculation          = 30.02  
    collect and process          = 6.67   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 231.77 
  Micro-tasks:
    mask                            = 2.57   
    f_calc                          = 115.17 
    alpha_beta                      = 8.51   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 122.78 
    fmodel                         = 7.96   
    r_factors                      = 0.27   
    phase_errors                   = 10.48  
    foms                           = 0.20   
    TOTAL for micro-tasks          = 269.12 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.079 micro seconds
Total CPU time: 6.22 minutes
from_scatterers_fft:    637 calls, 114.83 s
gradients_fft:          582 calls, 109.42 s

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

# Date 2008-01-16 Time 06:27:18 PST -0800 (1200493638.90 s)
Start R-work = 0.4571, R-free = 0.4575 (no bulk solvent and anisotropic scale)
Final R-work = 0.1416, R-free = 0.1847 (no bulk solvent and anisotropic scale)

Start R-work = 0.4491, R-free = 0.4528
Final R-work = 0.1184, R-free = 0.1640