# Date 2008-01-16 Time 05:43:22 PST -0800 (1200491002.53 s)
#phil __OFF__

Command line arguments: "../857.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 13585
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 857

-------------------------------------------------------------------------------
  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: (70.9525, 45.7567, 88.5498, 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: 3.30, per 1000 atoms: 1.17


================================== 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: (70.9525, 45.7567, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2039 1.9542
Completeness in resolution range: 0.911668
Completeness with d_max=infinity: 0.909087

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2039
                             d_min =   1.9542

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 45.7567, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2039 1.9542
Completeness in resolution range: 0.911668
Completeness with d_max=infinity: 0.909087

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2044 -  4.1837 [2255/2281]  2029   226  10.0%
  bin  2:  4.1837 -  3.3322 [2179/2199]  1967   212   9.7%
  bin  3:  3.3322 -  2.9144 [2125/2144]  1908   217  10.2%
  bin  4:  2.9144 -  2.6494 [2118/2148]  1898   220  10.4%
  bin  5:  2.6494 -  2.4604 [2117/2136]  1906   211  10.0%
  bin  6:  2.4604 -  2.3159 [2085/2110]  1879   206   9.9%
  bin  7:  2.3159 -  2.2002 [2110/2138]  1902   208   9.9%
  bin  8:  2.2002 -  2.1047 [2077/2113]  1865   212  10.2%
  bin  9:  2.1047 -  2.0239 [1960/2102]  1774   186   9.5%
  bin 10:  2.0239 -  1.9542 [ 563/2116]   502    61  10.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_857/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:
        1.68 -     2.32: 32
        2.32 -     2.97: 1781
        2.97 -     3.61: 4556
        3.61 -     4.26: 9128
        4.26 -     4.90: 12728
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 324 " - " O   HOH Z 374 "  1.854 3.040 -x,y-1/2,-z+1/2
  ... (remaining 28220 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_857/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_857/model_refine_001.geo

CPU time processing inputs: 9.20


============================ 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 = 70.9525 45.75675 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4927   r_free= 0.4968   ksol= 0.00   Bsol= 0.00   scale= 0.865    |
|                                                                             |
| 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:   0.88 A                  |
| x-ray target function (ml) for work reflections: 6.305541                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2044 -  4.6673 0.99   1467  164 0.4136 0.3947      6.6522      6.6128|
|  2:  4.6673 -  3.7225 0.99   1403  155 0.4447 0.4507      6.8641      6.8625|
|  3:  3.7225 -  3.2572 0.99   1383  156 0.4647 0.4460      6.6936      6.6923|
|  4:  3.2572 -  2.9618 0.99   1381  152 0.4960 0.5198      6.5485       6.537|
|  5:  2.9618 -  2.7509 0.99   1363  154 0.5283 0.5477      6.3752      6.4125|
|  6:  2.7509 -  2.5895 0.99   1378  148 0.5249 0.5345      6.2914       6.215|
|  7:  2.5895 -  2.4604 0.99   1333  157 0.5257 0.5462      6.2377      6.1989|
|  8:  2.4604 -  2.3537 0.98   1348  145 0.5287 0.5398      6.1633      6.1338|
|  9:  2.3537 -  2.2634 0.98   1342  147 0.5299 0.5567      6.1351       6.225|
| 10:  2.2634 -  2.1855 1.00   1355  158 0.5347 0.5436      6.0624      6.0669|
| 11:  2.1855 -  2.1174 0.98   1315  143 0.5150 0.4944      6.0151      6.0413|
| 12:  2.1174 -  2.0570 0.98   1352  140 0.5256 0.5383      5.9291      5.9231|
| 13:  2.0570 -  2.0030 0.73    981  112 0.5301 0.5150      5.8958      5.7966|
| 14:  2.0030 -  1.9542 0.17    229   28 0.5253 0.4998      5.8402      5.8954|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2044 -  4.6673  1467   164  0.69  35.15   0.80     0.75      77865.09|
|  2:  4.6673 -  3.7225  1403   155  0.64  40.50   0.87     0.74     136787.93|
|  3:  3.7225 -  3.2572  1383   156  0.47  54.56   0.89     0.65     151528.93|
|  4:  3.2572 -  2.9618  1381   152  0.32  65.90   0.86     0.47     142829.70|
|  5:  2.9618 -  2.7509  1363   154  0.27  70.03   0.85     0.40     103156.62|
|  6:  2.7509 -  2.5895  1378   148  0.24  71.83   0.87     0.36      86323.35|
|  7:  2.5895 -  2.4604  1333   157  0.26  70.57   0.88     0.37      73543.59|
|  8:  2.4604 -  2.3537  1348   145  0.23  72.98   0.89     0.34      67978.11|
|  9:  2.3537 -  2.2634  1342   147  0.20  74.98   0.90     0.31      65002.41|
| 10:  2.2634 -  2.1855  1355   158  0.19  75.99   0.89     0.29      57611.45|
| 11:  2.1855 -  2.1174  1315   143  0.19  76.11   0.95     0.30      54634.50|
| 12:  2.1174 -  2.0570  1352   140  0.23  72.84   0.89     0.38      46794.41|
| 13:  2.0570 -  2.0030   981   112  0.26  70.44   0.93     0.44      40414.98|
| 14:  2.0030 -  1.9542   229    28  0.35  63.68   1.00     0.52      29952.30|
|alpha:            min =        0.29 max =            0.75 mean =         0.45|
|beta:             min =    29952.30 max =       151528.93 mean =     85597.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.33|
|phase err.(work): min =        0.00 max =           89.99 mean =        65.09|
|phase err.(test): min =        0.00 max =           89.74 mean =        65.48|
|-----------------------------------------------------------------------------|

============================== 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 = 26.410322             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.771   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.487628              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.902   (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 |  1.681 -  2.003:       15 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.003 -  2.325:       17 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.325 -  2.647:       78 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.647 -  2.969:     1703 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.969 -  3.290:     1904 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.290 -  3.612:     2652 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.612 -  3.934:     4729 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.934 -  4.256:     4399 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.256 -  4.578:     5790 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.578 -  4.900:     6938 |
|-----------------------------------------------------------------------------|
|-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 |        0.187 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.681 |       0.528 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4927   r_free= 0.4968   ksol= 0.00   Bsol= 0.00   scale= 0.865    |
|                                                                             |
| 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:   0.88 A                  |
| x-ray target function (ml) for work reflections: 6.305541                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4838   r_free= 0.4921   ksol= 0.34   Bsol= 50.00   scale= 0.904   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,0.77,3.35,0.00,0.00,0.00); trace/3= 0.55                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.88 A                  |
| x-ray target function (ml) for work reflections: 6.303436                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 20.380159             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.573   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.859618              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.469   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4838      final r-factor (work) = 0.4073          |
| start r-factor (free) = 0.4921      final r-factor (free) = 0.4554          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 64.3598 = 20.38 * 0.50 * 6.2976 + 1.00 * 0.1868                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 63.6508 = 20.38 * 0.50 * 6.2300 + 1.00 * 0.1663                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4073      final r-factor (work) = 0.3757          |
| start r-factor (free) = 0.4554      final r-factor (free) = 0.4636          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.5915 = 1.86 * 1.00 * 6.2300 + 1.00 * 0.0061                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.4841 = 1.86 * 1.00 * 6.1638 + 1.00 * 0.0218                              |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.88   19.60    None  None   None       |
|    all(noH): 2823   0      0.00    89.88   19.60    None  None   None       |
|    Sol.    : 438    0      0.00    89.88   35.24    None  None   None       |
|    Mac.    : 2385   0      0.00    77.08   16.73    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 -   8.988:  696   |   5:    44.942 -  53.930:   93        |
|      1:     8.988 -  17.977:  844   |   6:    53.930 -  62.919:   64        |
|      2:    17.977 -  26.965:  593   |   7:    62.919 -  71.907:   19        |
|      3:    26.965 -  35.954:  330   |   8:    71.907 -  80.895:   12        |
|      4:    35.954 -  44.942:  168   |   9:    80.895 -  89.884:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3757 r_free = 0.4636             target_work(ml) = 6.169         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3755 r_free = 0.4652             target_work(ml) = 6.169         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3755   r_free= 0.4652   ksol= 0.34   Bsol= 50.00   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,0.77,3.35,0.00,0.00,0.00); trace/3= 0.55                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.169135                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3756   r_free= 0.4644   ksol= 0.37   Bsol= 80.55   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.70,-0.18,2.10,-0.00,0.00,0.00); trace/3= 0.41                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.172662                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.281546             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.092  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.806814              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.493  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3756      final r-factor (work) = 0.3207          |
| start r-factor (free) = 0.4644      final r-factor (free) = 0.4102          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 50.3628 = 16.28 * 0.50 * 6.1661 + 1.00 * 0.1656                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 50.0073 = 16.28 * 0.50 * 6.1297 + 1.00 * 0.1065                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3207      final r-factor (work) = 0.3063          |
| start r-factor (free) = 0.4102      final r-factor (free) = 0.3986          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9672 = 0.81 * 1.00 * 6.1297 + 1.00 * 0.0217                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8915 = 0.81 * 1.00 * 6.0453 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.56   18.98    None  None   None       |
|    all(noH): 2823   0      0.00    89.56   18.98    None  None   None       |
|    Sol.    : 438    0      0.00    89.56   35.32    None  None   None       |
|    Mac.    : 2385   0      0.00    71.28   15.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.956:  686   |   5:    44.779 -  53.735:   93        |
|      1:     8.956 -  17.912:  926   |   6:    53.735 -  62.691:   53        |
|      2:    17.912 -  26.867:  576   |   7:    62.691 -  71.646:   15        |
|      3:    26.867 -  35.823:  309   |   8:    71.646 -  80.602:   10        |
|      4:    35.823 -  44.779:  153   |   9:    80.602 -  89.558:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3063 r_free = 0.3986             target_work(ml) = 6.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3061 r_free = 0.3989             target_work(ml) = 6.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3061   r_free= 0.3989   ksol= 0.37   Bsol= 80.55   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.70,-0.18,2.10,-0.00,0.00,0.00); trace/3= 0.41                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.031506                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3066   r_free= 0.3981   ksol= 0.36   Bsol= 88.32   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.60,-0.47,1.41,-0.00,0.00,0.00); trace/3= 0.12                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.030243                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.437507              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.718  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 21.772008             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.150  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3066      final r-factor (work) = 0.2641          |
| start r-factor (free) = 0.3981      final r-factor (free) = 0.3481          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.5662 = 6.44 * 0.50 * 6.0457 + 1.00 * 0.1065                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.3284 = 6.44 * 0.50 * 5.9835 + 1.00 * 0.0689                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2641      final r-factor (work) = 0.2461          |
| start r-factor (free) = 0.3481      final r-factor (free) = 0.3477          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 130.2874 = 21.77 * 1.00 * 5.9835 + 1.00 * 0.0141                            |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 127.9842 = 21.77 * 1.00 * 5.8769 + 1.00 * 0.0329                            |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    131.78  22.34    None  None   None       |
|    all(noH): 2823   0      0.00    131.78  22.34    None  None   None       |
|    Sol.    : 438    0      0.00    131.78  50.81    None  None   None       |
|    Mac.    : 2385   0      0.00    110.41  17.12    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 -  13.178: 1270   |   5:    65.891 -  79.069:   89        |
|      1:    13.178 -  26.357:  748   |   6:    79.069 -  92.248:   47        |
|      2:    26.357 -  39.535:  344   |   7:    92.248 - 105.426:   29        |
|      3:    39.535 -  52.713:  161   |   8:   105.426 - 118.604:   15        |
|      4:    52.713 -  65.891:  117   |   9:   118.604 - 131.782:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2461 r_free = 0.3477             target_work(ml) = 5.872         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2461 r_free = 0.3475             target_work(ml) = 5.872         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2461   r_free= 0.3475   ksol= 0.36   Bsol= 88.32   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.60,-0.47,1.41,-0.00,0.00,0.00); trace/3= 0.12                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.872078                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2465   r_free= 0.3477   ksol= 0.36   Bsol= 105.17   scale= 1.030  |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.51,-0.61,1.44,-0.00,0.00,0.00); trace/3= 0.11                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.873046                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.037725              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.209  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.381376              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.316  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2465      final r-factor (work) = 0.2127          |
| start r-factor (free) = 0.3477      final r-factor (free) = 0.3030          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.8729 = 5.04 * 0.50 * 5.8773 + 1.00 * 0.0689                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.7253 = 5.04 * 0.50 * 5.8214 + 1.00 * 0.0620                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2127      final r-factor (work) = 0.2030          |
| start r-factor (free) = 0.3030      final r-factor (free) = 0.2721          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2530 = 0.38 * 1.00 * 5.8214 + 1.00 * 0.0328                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2101 = 0.38 * 1.00 * 5.7328 + 1.00 * 0.0238                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    120.93  20.16    None  None   None       |
|    all(noH): 2823   0      0.00    120.93  20.16    None  None   None       |
|    Sol.    : 438    0      1.93    120.93  48.76    None  None   None       |
|    Mac.    : 2385   0      0.00    106.86  14.91    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.093: 1336   |   5:    60.464 -  72.557:   79        |
|      1:    12.093 -  24.186:  779   |   6:    72.557 -  84.649:   48        |
|      2:    24.186 -  36.278:  258   |   7:    84.649 -  96.742:   22        |
|      3:    36.278 -  48.371:  172   |   8:    96.742 - 108.835:   18        |
|      4:    48.371 -  60.464:  106   |   9:   108.835 - 120.928:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2030 r_free = 0.2721             target_work(ml) = 5.679         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2030 r_free = 0.2718             target_work(ml) = 5.678         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2030   r_free= 0.2718   ksol= 0.36   Bsol= 105.17   scale= 1.034  |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.51,-0.61,1.44,-0.00,0.00,0.00); trace/3= 0.11                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.677692                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2029   r_free= 0.2717   ksol= 0.34   Bsol= 84.59   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.04,-1.31,0.88,-0.00,0.00,0.00); trace/3= -0.49                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.676161                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.767068              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.957  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.311432              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.729   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2029      final r-factor (work) = 0.1680          |
| start r-factor (free) = 0.2717      final r-factor (free) = 0.2258          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.7244 = 4.77 * 0.50 * 5.7320 + 1.00 * 0.0620                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.4164 = 4.77 * 0.50 * 5.6001 + 1.00 * 0.0685                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1680      final r-factor (work) = 0.1514          |
| start r-factor (free) = 0.2258      final r-factor (free) = 0.2086          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.0531 = 2.31 * 1.00 * 5.6001 + 1.00 * 0.1090                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.6237 = 2.31 * 1.00 * 5.4542 + 1.00 * 0.0167                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    126.82  19.33    None  None   None       |
|    all(noH): 2823   0      0.00    126.82  19.33    None  None   None       |
|    Sol.    : 438    0      3.84    126.82  51.94    None  None   None       |
|    Mac.    : 2385   0      0.00    106.97  13.34    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 -  12.682: 1553   |   5:    63.408 -  76.090:   87        |
|      1:    12.682 -  25.363:  702   |   6:    76.090 -  88.772:   47        |
|      2:    25.363 -  38.045:  180   |   7:    88.772 - 101.453:   24        |
|      3:    38.045 -  50.727:  104   |   8:   101.453 - 114.135:   14        |
|      4:    50.727 -  63.408:  111   |   9:   114.135 - 126.816:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1514 r_free = 0.2086             target_work(ml) = 5.413         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1513 r_free = 0.2086             target_work(ml) = 5.413         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1513   r_free= 0.2086   ksol= 0.34   Bsol= 84.59   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.04,-1.31,0.88,-0.00,0.00,0.00); trace/3= -0.49                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.412794                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2044 -  4.6673 0.99   1467  164 0.0982 0.1440      5.4199      5.6942|
|  2:  4.6673 -  3.7225 0.99   1403  155 0.0983 0.1457      5.5888      5.9038|
|  3:  3.7225 -  3.2572 0.99   1383  156 0.1427 0.2048      5.7272      6.0264|
|  4:  3.2572 -  2.9618 0.99   1381  152 0.1777 0.2282      5.7462      5.9302|
|  5:  2.9618 -  2.7509 0.99   1363  154 0.1801 0.2280      5.5972       5.811|
|  6:  2.7509 -  2.5895 0.99   1378  148 0.1745 0.2591      5.4913      5.7123|
|  7:  2.5895 -  2.4604 0.99   1333  157 0.1699 0.2278      5.4172      5.6127|
|  8:  2.4604 -  2.3537 0.98   1348  145 0.1764 0.2516      5.4073      5.6261|
|  9:  2.3537 -  2.2634 0.98   1342  147 0.1760 0.2348      5.3393      5.5751|
| 10:  2.2634 -  2.1855 1.00   1355  158 0.1624 0.2241      5.2358      5.4433|
| 11:  2.1855 -  2.1174 0.98   1315  143 0.1580 0.2316       5.183      5.5065|
| 12:  2.1174 -  2.0570 0.98   1352  140 0.1583 0.2199      5.1028      5.3276|
| 13:  2.0570 -  2.0030 0.73    981  112 0.1558 0.2226      5.0491      5.2171|
| 14:  2.0030 -  1.9542 0.17    229   28 0.1588 0.2362      5.0007      5.3313|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2044 -  4.6673  1467   164  0.93  10.57   0.96     0.94       8704.55|
|  2:  4.6673 -  3.7225  1403   155  0.94  10.60   1.04     1.02      13024.13|
|  3:  3.7225 -  3.2572  1383   156  0.89  16.82   1.06     1.06      17807.19|
|  4:  3.2572 -  2.9618  1381   152  0.85  21.34   1.04     1.00      19553.02|
|  5:  2.9618 -  2.7509  1363   154  0.84  22.62   1.02     0.98      15347.37|
|  6:  2.7509 -  2.5895  1378   148  0.83  23.92   1.00     0.94      12864.72|
|  7:  2.5895 -  2.4604  1333   157  0.84  22.47   1.03     0.97      10917.57|
|  8:  2.4604 -  2.3537  1348   145  0.83  23.50   1.02     0.98      10920.86|
|  9:  2.3537 -  2.2634  1342   147  0.83  23.89   1.01     0.95       9509.06|
| 10:  2.2634 -  2.1855  1355   158  0.84  22.92   1.02     0.98       8237.17|
| 11:  2.1855 -  2.1174  1315   143  0.84  22.28   1.02     0.95       7288.21|
| 12:  2.1174 -  2.0570  1352   140  0.84  22.79   1.02     1.00       6513.72|
| 13:  2.0570 -  2.0030   981   112  0.84  22.96   1.01     0.97       5821.40|
| 14:  2.0030 -  1.9542   229    28  0.87  20.01   0.99     0.96       4864.50|
|alpha:            min =        0.94 max =            1.06 mean =         0.98|
|beta:             min =     4864.50 max =        19553.02 mean =     11329.03|
|figures of merit: min =        0.00 max =            1.00 mean =         0.86|
|phase err.(work): min =        0.00 max =           89.97 mean =        20.36|
|phase err.(test): min =        0.00 max =           89.85 mean =        19.07|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1516   r_free= 0.2079   ksol= 0.32   Bsol= 73.33   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.34,-1.89,0.47,-0.00,0.00,0.00); trace/3= -0.92                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.410097                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1516   r_free= 0.2079   ksol= 0.32   Bsol= 73.33   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.34,-1.89,0.47,-0.00,0.00,0.00); trace/3= -0.92                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.410097                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2044 -  4.6673 0.99   1467  164 0.0992 0.1381      5.4001      5.6523|
|  2:  4.6673 -  3.7225 0.99   1403  155 0.0986 0.1451       5.579      5.9001|
|  3:  3.7225 -  3.2572 0.99   1383  156 0.1428 0.2043      5.7256      6.0263|
|  4:  3.2572 -  2.9618 0.99   1381  152 0.1777 0.2286       5.746      5.9304|
|  5:  2.9618 -  2.7509 0.99   1363  154 0.1799 0.2278      5.5969      5.8116|
|  6:  2.7509 -  2.5895 0.99   1378  148 0.1744 0.2593      5.4911      5.7126|
|  7:  2.5895 -  2.4604 0.99   1333  157 0.1699 0.2277      5.4169      5.6118|
|  8:  2.4604 -  2.3537 0.98   1348  145 0.1764 0.2520      5.4073      5.6281|
|  9:  2.3537 -  2.2634 0.98   1342  147 0.1758 0.2343      5.3387      5.5733|
| 10:  2.2634 -  2.1855 1.00   1355  158 0.1622 0.2243      5.2358      5.4445|
| 11:  2.1855 -  2.1174 0.98   1315  143 0.1578 0.2323      5.1824      5.5081|
| 12:  2.1174 -  2.0570 0.98   1352  140 0.1582 0.2202      5.1034      5.3285|
| 13:  2.0570 -  2.0030 0.73    981  112 0.1560 0.2218      5.0491      5.2148|
| 14:  2.0030 -  1.9542 0.17    229   28 0.1591 0.2354      5.0004      5.3289|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2044 -  4.6673  1467   164  0.93   9.97   0.96     0.94       7922.06|
|  2:  4.6673 -  3.7225  1403   155  0.94  10.23   1.04     1.02      12366.12|
|  3:  3.7225 -  3.2572  1383   156  0.89  16.71   1.06     1.05      17616.22|
|  4:  3.2572 -  2.9618  1381   152  0.85  21.30   1.03     0.99      19482.83|
|  5:  2.9618 -  2.7509  1363   154  0.84  22.60   1.01     0.97      15356.40|
|  6:  2.7509 -  2.5895  1378   148  0.83  23.93   0.99     0.93      12881.03|
|  7:  2.5895 -  2.4604  1333   157  0.84  22.46   1.01     0.95      10918.95|
|  8:  2.4604 -  2.3537  1348   145  0.83  23.51   1.00     0.97      10931.67|
|  9:  2.3537 -  2.2634  1342   147  0.83  23.87   0.99     0.93       9505.98|
| 10:  2.2634 -  2.1855  1355   158  0.84  22.90   0.99     0.96       8234.21|
| 11:  2.1855 -  2.1174  1315   143  0.84  22.28   0.99     0.93       7302.02|
| 12:  2.1174 -  2.0570  1352   140  0.84  22.80   1.00     0.98       6523.95|
| 13:  2.0570 -  2.0030   981   112  0.84  22.94   0.98     0.95       5820.47|
| 14:  2.0030 -  1.9542   229    28  0.87  19.85   0.96     0.94       4830.38|
|alpha:            min =        0.93 max =            1.05 mean =         0.97|
|beta:             min =     4830.38 max =        19482.83 mean =     11194.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.86|
|phase err.(work): min =        0.00 max =           90.00 mean =        20.26|
|phase err.(test): min =        0.00 max =           89.64 mean =        18.98|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    126.82  19.33    None  None   None       |
|    all(noH): 2823   0      0.00    126.82  19.33    None  None   None       |
|    Sol.    : 438    0      3.84    126.82  51.94    None  None   None       |
|    Mac.    : 2385   0      0.00    106.97  13.34    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  12.685: 1553   |   5:    63.411 -  76.093:   87        |
|      1:    12.685 -  25.366:  702   |   6:    76.093 -  88.775:   47        |
|      2:    25.366 -  38.048:  180   |   7:    88.775 - 101.456:   24        |
|      3:    38.048 -  50.730:  104   |   8:   101.456 - 114.138:   14        |
|      4:    50.730 -  63.411:  111   |   9:   114.138 - 126.819:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 351         
Filter by distance & map next to the model:
   mapped sites are within: 0.557 - 4.282
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 346 from: 351
   mapped sites are within: 0.762 - 4.282

peak=    7.747 closest distance to " O   HOH Z 103 " =    1.353
peak=    6.577 closest distance to " O  BHOH Z  74 " =    1.139
peak=    6.568 closest distance to " O   HOH Z 381 " =    1.358
peak=    6.103 closest distance to " O   HOH Z 245 " =    1.563
peak=    6.075 closest distance to " O   HOH Z 385 " =    1.797
peak=    6.074 closest distance to " O   HOH Z 130 " =    1.168
peak=    5.757 closest distance to " O   HOH Z 396 " =    1.205
peak=    5.703 closest distance to " O   HOH Z 390 " =    1.194
peak=    5.635 closest distance to " CG  PRO A  90 " =    1.314
peak=    5.166 closest distance to " O   HOH Z 131 " =    1.381
peak=    5.137 closest distance to " ND2 ASN A  39 " =    0.926
peak=    5.079 closest distance to " O   HOH Z 117 " =    0.965
peak=    5.007 closest distance to " O   GLN A  73 " =    1.036
peak=    4.972 closest distance to " O   HOH Z 359 " =    1.967
peak=    4.927 closest distance to " O   HOH Z  65 " =    1.927
peak=    4.902 closest distance to " C   VAL A  72 " =    1.027
peak=    4.884 closest distance to " O   HOH Z  46 " =    1.448
peak=    4.847 closest distance to " O   HOH Z 127 " =    1.181
peak=    4.788 closest distance to " O   HOH Z 431 " =    1.858
peak=    4.770 closest distance to " O   HOH Z  77 " =    1.390
peak=    4.751 closest distance to " O   HOH Z 417 " =    2.938
peak=    4.734 closest distance to " O   HOH Z  29 " =    1.630
peak=    4.726 closest distance to " O   HOH Z 287 " =    2.032
peak=    4.720 closest distance to " O   HOH Z 147 " =    1.362
peak=    4.707 closest distance to " O   HOH Z 422 " =    1.286
peak=    4.679 closest distance to " O   HOH Z 424 " =    2.054
peak=    4.658 closest distance to " O   HOH Z  11 " =    1.354
peak=    4.608 closest distance to " O   HOH Z  66 " =    1.276
peak=    4.605 closest distance to " O   HOH Z 403 " =    1.860
peak=    4.595 closest distance to " CB  SER A  63 " =    1.561
peak=    4.594 closest distance to " NE2 GLN A 103 " =    0.832
peak=    4.570 closest distance to " O   HOH Z  63 " =    1.612
peak=    4.570 closest distance to " NH2 ARG A 269 " =    1.067
peak=    4.561 closest distance to " O   HOH Z 351 " =    0.895
peak=    4.545 closest distance to " O   HOH Z 126 " =    1.945
peak=    4.541 closest distance to " CZ  PHE A 218 " =    1.233
peak=    4.538 closest distance to " CB  SER A 216 " =    1.139
peak=    4.481 closest distance to " O   HOH Z 419 " =    2.175
peak=    4.470 closest distance to " O   HOH Z 217 " =    3.071
peak=    4.454 closest distance to " O   HOH Z  92 " =    1.349
peak=    4.453 closest distance to " O   HOH Z  70 " =    1.239
peak=    4.447 closest distance to " O   HOH Z 120 " =    1.051
peak=    4.444 closest distance to " CG2 ILE A 120 " =    1.023
peak=    4.441 closest distance to " O   HOH Z 427 " =    2.226
peak=    4.415 closest distance to " N   GLN A  73 " =    0.990
peak=    4.407 closest distance to " CE3 TRP A 274 " =    1.437
peak=    4.403 closest distance to " NE2 GLN A  11 " =    1.162
peak=    4.390 closest distance to " O   HOH Z 105 " =    1.495
peak=    4.387 closest distance to " O   HOH Z 255 " =    0.963
peak=    4.370 closest distance to " O   HOH Z 139 " =    1.324
peak=    4.339 closest distance to " O   HOH Z 203 " =    2.280
peak=    4.338 closest distance to " O   HOH Z  49 " =    2.137
peak=    4.327 closest distance to " NH1AARG A 145 " =    1.221
peak=    4.295 closest distance to " NH2AARG A 145 " =    2.314
peak=    4.287 closest distance to " OE1 GLN A  73 " =    2.168
peak=    4.269 closest distance to " O   HOH Z  67 " =    1.563
peak=    4.265 closest distance to " O   HOH Z  97 " =    1.775
peak=    4.265 closest distance to " CB  PRO A  54 " =    1.248
peak=    4.250 closest distance to " NZ BLYS A 290 " =    1.185
peak=    4.248 closest distance to " O   ASN A 285 " =    0.909
peak=    4.231 closest distance to " CE  MET A  93 " =    1.595
peak=    4.227 closest distance to " OG ASER A 258 " =    2.980
peak=    4.226 closest distance to " O   HOH Z 181 " =    1.412
peak=    4.225 closest distance to " CB  PRO A  90 " =    1.223
peak=    4.224 closest distance to " O   HOH Z 415 " =    1.126
peak=    4.214 closest distance to " O   HOH Z 410 " =    1.594
peak=    4.214 closest distance to " O   PRO A 198 " =    1.282
peak=    4.213 closest distance to " O   HOH Z 400 " =    0.893
peak=    4.204 closest distance to " N   ALA A 165 " =    1.310
peak=    4.171 closest distance to " N   TYR A  15 " =    1.224
peak=    4.160 closest distance to " N   GLN A 278 " =    1.230
peak=    4.158 closest distance to " CZ3 TRP A 266 " =    1.191
peak=    4.075 closest distance to " O   HOH Z 418 " =    1.252
peak=    4.073 closest distance to " O   HOH Z 222 " =    1.952
peak=    4.070 closest distance to " O   HOH Z  53 " =    2.206
peak=    4.069 closest distance to " O   HOH Z  21 " =    1.383
peak=    4.063 closest distance to " O   HOH Z 278 " =    1.211
peak=    4.053 closest distance to " O   HOH Z  91 " =    2.495
peak=    4.050 closest distance to " O   HOH Z 131 " =    2.492
peak=    4.048 closest distance to " O   HOH Z 244 " =    1.524
peak=    4.048 closest distance to " O   HOH Z 155 " =    1.937
peak=    4.037 closest distance to " ND2 ASN A 249 " =    0.775
peak=    4.031 closest distance to " CA  VAL A 125 " =    1.122
peak=    4.017 closest distance to " O   HOH Z 360 " =    1.262
peak=    4.014 closest distance to " O   HOH Z 295 " =    1.474
peak=    3.985 closest distance to " C   HIS A 115 " =    0.928
peak=    3.984 closest distance to " O   HOH Z 414 " =    1.637
peak=    3.983 closest distance to " O   HOH Z 363 " =    1.233
peak=    3.972 closest distance to " OG BSER A  12 " =    1.050
peak=    3.966 closest distance to " O   HOH Z 296 " =    1.387
peak=    3.962 closest distance to " NH2 ARG A 195 " =    0.940
peak=    3.961 closest distance to " CG2 THR A 221 " =    1.291
peak=    3.951 closest distance to " O   HOH Z   9 " =    2.207
peak=    3.951 closest distance to " O   HOH Z 280 " =    1.662
peak=    3.949 closest distance to " O   HOH Z  43 " =    1.514
peak=    3.943 closest distance to " CG  PRO A  54 " =    1.449
peak=    3.940 closest distance to " CG  GLN A  89 " =    1.570
peak=    3.925 closest distance to " O   HOH Z  28 " =    1.217
peak=    3.916 closest distance to " O   HOH Z 427 " =    1.077
peak=    3.902 closest distance to " O   HOH Z  61 " =    1.756
peak=    3.896 closest distance to " N   PHE A  59 " =    0.804
peak=    3.890 closest distance to " CB  PHE A  61 " =    1.251
peak=    3.889 closest distance to " O   HOH Z  57 " =    2.477
peak=    3.883 closest distance to " O   HOH Z 182 " =    1.337
peak=    3.877 closest distance to " CB  ASN A 148 " =    1.287
peak=    3.868 closest distance to " O   HOH Z  51 " =    2.131
peak=    3.866 closest distance to " O   HOH Z  27 " =    1.178
peak=    3.863 closest distance to " O   HOH Z  39 " =    1.388
peak=    3.861 closest distance to " O   HOH Z 357 " =    2.008
peak=    3.855 closest distance to " CE  LYS A 119 " =    1.249
peak=    3.850 closest distance to " O   HOH Z  30 " =    1.827
peak=    3.841 closest distance to " O   HOH Z 350 " =    1.431
peak=    3.835 closest distance to " CD  GLN A  77 " =    1.364
peak=    3.832 closest distance to " N   SER A  63 " =    0.883
peak=    3.831 closest distance to " O   HOH Z 250 " =    2.231
peak=    3.830 closest distance to " O   HOH Z 100 " =    1.188
peak=    3.828 closest distance to " CB  SER A  99 " =    0.890
peak=    3.827 closest distance to " CA  ALA A   7 " =    1.123
peak=    3.814 closest distance to " O   HOH Z 248 " =    1.633
peak=    3.813 closest distance to " OD1 ASP A 191 " =    1.148
peak=    3.793 closest distance to " O   HOH Z 143 " =    1.544
peak=    3.784 closest distance to " CB  TRP A 179 " =    1.341
peak=    3.783 closest distance to " O   HOH Z 239 " =    1.689
peak=    3.781 closest distance to " CD  ARG A 195 " =    3.646
peak=    3.778 closest distance to " O   HOH Z 286 " =    1.844
peak=    3.777 closest distance to " O   HOH Z 205 " =    1.028
peak=    3.771 closest distance to " O   HOH Z 371 " =    1.703
peak=    3.746 closest distance to " CE2 PHE A  16 " =    0.798
peak=    3.743 closest distance to " CA  PRO A  54 " =    0.924
peak=    3.742 closest distance to " CA  TYR A  30 " =    1.201
peak=    3.737 closest distance to " CD2 PHE A  59 " =    1.986
peak=    3.735 closest distance to " N   GLY A 302 " =    0.982
peak=    3.731 closest distance to " O   HOH Z 207 " =    1.407
peak=    3.725 closest distance to " C   PRO A  54 " =    0.905
peak=    3.718 closest distance to " O   HOH Z 434 " =    1.722
peak=    3.717 closest distance to " CB  GLU A 175 " =    1.008
peak=    3.714 closest distance to " O   HOH Z 374 " =    1.149
peak=    3.714 closest distance to " O   SER A  62 " =    0.896
peak=    3.712 closest distance to " O   HOH Z 158 " =    1.419
peak=    3.711 closest distance to " CB  ARG A 275 " =    1.150
peak=    3.711 closest distance to " CB  ALA A 114 " =    1.159
peak=    3.701 closest distance to " O   HOH Z 126 " =    1.638
peak=    3.690 closest distance to " CG  LEU A 101 " =    1.095
peak=    3.686 closest distance to " CA  ARG A 195 " =    1.356
peak=    3.683 closest distance to " NH2 ARG A  56 " =    1.078
peak=    3.679 closest distance to " O   HOH Z 365 " =    2.431
peak=    3.674 closest distance to " O   HOH Z 411 " =    3.670
peak=    3.674 closest distance to " O   HOH Z 293 " =    1.427
peak=    3.664 closest distance to " O   GLY A 302 " =    1.996
peak=    3.654 closest distance to " CD2 LEU A   5 " =    1.395
peak=    3.648 closest distance to " NZ  LYS A 166 " =    0.964
peak=    3.643 closest distance to " CB  MET A  40 " =    1.011
peak=    3.638 closest distance to " O   HOH Z  76 " =    1.468
peak=    3.635 closest distance to " CG2 VAL A 257 " =    0.951
peak=    3.634 closest distance to " O   HOH Z 153 " =    3.565
peak=    3.631 closest distance to " O   HOH Z  57 " =    1.572
peak=    3.631 closest distance to " CB  GLN A 223 " =    1.638
peak=    3.627 closest distance to " CA  ALA A  51 " =    1.178
peak=    3.609 closest distance to " O   HOH Z  54 " =    1.511
peak=    3.601 closest distance to " O   HOH Z 213 " =    2.066
peak=    3.598 closest distance to " CB  SER A 276 " =    1.399
peak=    3.595 closest distance to " CE3 TRP A  85 " =    1.046
peak=    3.589 closest distance to " CB  ARG A  79 " =    1.141
peak=    3.585 closest distance to " CB  ASN A  60 " =    0.934
peak=    3.577 closest distance to " N   ARG A 156 " =    1.218
peak=    3.575 closest distance to " CB  ALA A  10 " =    1.041
peak=    3.573 closest distance to " CB  VAL A 202 " =    1.613
peak=    3.573 closest distance to " CG  PRO A 243 " =    1.158
peak=    3.571 closest distance to " O   HOH Z 158 " =    2.709
peak=    3.571 closest distance to " CB  ASP A 124 " =    0.983
peak=    3.569 closest distance to " CG2 THR A 279 " =    1.027
peak=    3.567 closest distance to " O   HOH Z 233 " =    1.253
peak=    3.565 closest distance to " CB  SER A 273 " =    1.191
peak=    3.549 closest distance to " NZ  LYS A 119 " =    2.208
peak=    3.545 closest distance to " CB  PHE A 130 " =    1.554
peak=    3.544 closest distance to " O   HOH Z 380 " =    2.067
peak=    3.542 closest distance to " CG  PRO A 198 " =    1.329
peak=    3.541 closest distance to " CG  ARG A 159 " =    1.114
peak=    3.538 closest distance to " CG1 VAL A 296 " =    1.221
peak=    3.535 closest distance to " O   HOH Z 132 " =    1.227
peak=    3.532 closest distance to " CB  ASN A 187 " =    0.928
peak=    3.532 closest distance to " O   HOH Z 392 " =    1.317
peak=    3.526 closest distance to " CB  ASN A  39 " =    0.797
peak=    3.522 closest distance to " O   HOH Z   7 " =    2.631
peak=    3.519 closest distance to " CG  PRO A 213 " =    1.318
peak=    3.514 closest distance to " CG2 ILE A 239 " =    1.028
peak=    3.512 closest distance to " O   HOH Z 111 " =    2.073
peak=    3.512 closest distance to " O   HOH Z 422 " =    1.924
peak=    3.504 closest distance to " CG2 THR A 182 " =    0.981
peak=    3.501 closest distance to " O   HOH Z 189 " =    3.101
peak=    3.500 closest distance to " OG  SER A 276 " =    1.123
peak=    3.499 closest distance to " O   HOH Z 220 " =    1.651
peak=    3.498 closest distance to " O   HOH Z 133 " =    0.933
peak=    3.489 closest distance to " CG  LYS A 119 " =    1.142
peak=    3.488 closest distance to " CD  ARG A 259 " =    1.491
peak=    3.482 closest distance to " O   HOH Z 153 " =    4.148
peak=    3.482 closest distance to " CB  ARG A 102 " =    0.877
peak=    3.475 closest distance to " N   PHE A 130 " =    1.323
peak=    3.474 closest distance to " CE2 PHE A  61 " =    0.823
peak=    3.473 closest distance to " O   HOH Z 298 " =    2.329
peak=    3.472 closest distance to " O   HOH Z 389 " =    1.882
peak=    3.470 closest distance to " O   HOH Z 371 " =    3.179
peak=    3.467 closest distance to " O   HOH Z 424 " =    3.247
peak=    3.467 closest distance to " O   HOH Z 361 " =    1.637
peak=    3.465 closest distance to " O   HOH Z 225 " =    1.866
peak=    3.461 closest distance to " O   HOH Z 119 " =    1.579
peak=    3.458 closest distance to " O   HOH Z 273 " =    1.499
peak=    3.451 closest distance to " O   HOH Z 176 " =    1.236
peak=    3.449 closest distance to " CZ  PHE A  16 " =    0.790
peak=    3.449 closest distance to " CD  GLU A  53 " =    1.177
peak=    3.447 closest distance to " O   HOH Z 399 " =    1.044
peak=    3.446 closest distance to " O   MET A 105 " =    1.652
peak=    3.442 closest distance to " O   HOH Z  33 " =    1.822
peak=    3.438 closest distance to " CG  LEU A 167 " =    1.370
peak=    3.434 closest distance to " O   ALA A 165 " =    1.583
peak=    3.433 closest distance to " O   HOH Z 296 " =    1.237
peak=    3.430 closest distance to " O   ASN A 142 " =    1.080
peak=    3.425 closest distance to " CG2BVAL A  41 " =    1.162
peak=    3.418 closest distance to " O   HOH Z 112 " =    1.386
peak=    3.412 closest distance to " O   HOH Z 416 " =    1.445
peak=    3.410 closest distance to " O   HOH Z  68 " =    1.890
peak=    3.407 closest distance to " O   HOH Z 375 " =    1.105
peak=    3.400 closest distance to " CB  VAL A 296 " =    1.538
peak=    3.398 closest distance to " CG2 THR A 235 " =    0.762
peak=    3.389 closest distance to " N   VAL A 296 " =    1.993
peak=    3.389 closest distance to " CB  THR A  52 " =    0.992
peak=    3.386 closest distance to " NE2 HIS A 207 " =    1.050
peak=    3.379 closest distance to " CB  VAL A 230 " =    0.897
peak=    3.377 closest distance to " N   SER A 210 " =    1.189
peak=    3.373 closest distance to " O   HOH Z 425 " =    1.399
peak=    3.372 closest distance to " O   HOH Z 368 " =    3.387
peak=    3.372 closest distance to " O   HOH Z 333 " =    0.984
peak=    3.368 closest distance to " O   HOH Z 146 " =    1.259
peak=    3.367 closest distance to " O   HOH Z 298 " =    4.109
peak=    3.364 closest distance to " O   HOH Z 341 " =    1.296
peak=    3.363 closest distance to " CA  LEU A 282 " =    1.053
peak=    3.357 closest distance to " O   HOH Z 358 " =    1.392
peak=    3.357 closest distance to " CB  LYS A 290 " =    0.951
peak=    3.353 closest distance to " CG  TRP A 179 " =    2.148
peak=    3.349 closest distance to " CB  ASN A 176 " =    1.129
peak=    3.349 closest distance to " CG1 VAL A 265 " =    0.919
peak=    3.342 closest distance to " O   HOH Z 393 " =    1.449
peak=    3.341 closest distance to " CG  GLN A  55 " =    0.779
peak=    3.334 closest distance to " CD2 TYR A  15 " =    1.198
peak=    3.334 closest distance to " CD1 LEU A 228 " =    1.828
peak=    3.330 closest distance to " N   ALA A   1 " =    1.566
peak=    3.327 closest distance to " CG2 THR A 264 " =    1.399
peak=    3.327 closest distance to " O   HOH Z 394 " =    1.631
peak=    3.323 closest distance to " CG AARG A 275 " =    1.396
peak=    3.323 closest distance to " CA  LEU A  83 " =    1.770
peak=    3.321 closest distance to " CD ALYS A 290 " =    1.114
peak=    3.319 closest distance to " CH2 TRP A 177 " =    0.854
peak=    3.317 closest distance to " CB  ASN A 110 " =    1.050
peak=    3.316 closest distance to " CB  THR A   4 " =    1.249
peak=    3.315 closest distance to " O   HOH Z  91 " =    2.553
peak=    3.314 closest distance to " CB  GLU A 152 " =    1.229
peak=    3.314 closest distance to " O   HOH Z 180 " =    2.288
peak=    3.314 closest distance to " N   LYS A 119 " =    1.484
peak=    3.312 closest distance to " CZ  PHE A  16 " =    1.057
peak=    3.310 closest distance to " O   HOH Z 219 " =    2.369
peak=    3.306 closest distance to " CA  ARG A  36 " =    1.322
peak=    3.297 closest distance to " O   HOH Z 368 " =    1.918
peak=    3.296 closest distance to " CD2 LEU A 300 " =    1.354
peak=    3.295 closest distance to " CB  ASP A  50 " =    1.215
peak=    3.295 closest distance to " CB  GLU A 277 " =    3.689
peak=    3.292 closest distance to " CB  VAL A 265 " =    1.432
peak=    3.288 closest distance to " CB  ILE A 120 " =    1.349
peak=    3.288 closest distance to " O   HOH Z  20 " =    1.613
peak=    3.279 closest distance to " CA  TYR A 116 " =    1.719
peak=    3.278 closest distance to " CZ3 TRP A 123 " =    1.665
peak=    3.274 closest distance to " O   HOH Z 349 " =    1.957
peak=    3.272 closest distance to " O   THR A 294 " =    1.116
peak=    3.265 closest distance to " ND2 ASN A  74 " =    1.057
peak=    3.259 closest distance to " CD  LYS A 166 " =    1.639
peak=    3.257 closest distance to " O   HOH Z 171 " =    1.850
peak=    3.255 closest distance to " O   HOH Z 212 " =    1.613
peak=    3.253 closest distance to " CA  SER A 164 " =    1.304
peak=    3.252 closest distance to " NE2 GLN A 240 " =    3.246
peak=    3.249 closest distance to " CD1 PHE A  61 " =    1.072
peak=    3.249 closest distance to " O   HOH Z 437 " =    2.000
peak=    3.247 closest distance to " O   HOH Z 219 " =    4.282
peak=    3.247 closest distance to " N   VAL A 125 " =    1.456
peak=    3.245 closest distance to " O   HOH Z 218 " =    1.863
peak=    3.244 closest distance to " NH1AARG A 275 " =    1.137
peak=    3.243 closest distance to " CB  SER A  62 " =    1.472
peak=    3.242 closest distance to " CB  TRP A 274 " =    0.956
peak=    3.241 closest distance to " OD1 ASN A 170 " =    1.340
peak=    3.239 closest distance to " OG  SER A 146 " =    1.184
peak=    3.237 closest distance to " O   HOH Z   6 " =    1.633
peak=    3.235 closest distance to " O   HOH Z 124 " =    1.251
peak=    3.233 closest distance to " O   HOH Z 406 " =    1.534
peak=    3.231 closest distance to " CB  SER A 141 " =    1.071
peak=    3.228 closest distance to " O   HOH Z 240 " =    1.769
peak=    3.225 closest distance to " OG BSER A  99 " =    3.125
peak=    3.225 closest distance to " CG2 VAL A 268 " =    0.879
peak=    3.225 closest distance to " ND1 HIS A  81 " =    1.850
peak=    3.223 closest distance to " CB  ARG A 138 " =    0.932
peak=    3.222 closest distance to " NE AARG A 145 " =    1.207
peak=    3.222 closest distance to " O   HOH Z 189 " =    3.212
peak=    3.218 closest distance to " CG2AVAL A 121 " =    1.701
peak=    3.214 closest distance to " O   HOH Z 313 " =    1.953
peak=    3.214 closest distance to " CA  LYS A 289 " =    0.838
peak=    3.211 closest distance to " CB  ARG A 219 " =    0.780
peak=    3.208 closest distance to " CA  PHE A 283 " =    1.211
peak=    3.201 closest distance to " CA  GLU A 152 " =    1.129
peak=    3.200 closest distance to " CB  SER A   3 " =    1.312
peak=    3.199 closest distance to " O   HOH Z 102 " =    1.205
peak=    3.193 closest distance to " CA  TRP A  92 " =    1.212
peak=    3.192 closest distance to " O   HOH Z 414 " =    1.914
peak=    3.191 closest distance to " O   HOH Z 362 " =    1.930
peak=    3.184 closest distance to " CG2 ILE A 234 " =    1.227
peak=    3.184 closest distance to " CA  PRO A 280 " =    1.359
peak=    3.181 closest distance to " CE2 PHE A 155 " =    0.872
peak=    3.180 closest distance to " O   HOH Z 313 " =    1.634
peak=    3.180 closest distance to " CD1 ILE A 199 " =    1.184
peak=    3.180 closest distance to " CD1BILE A 234 " =    1.138
peak=    3.170 closest distance to " O   HOH Z  47 " =    1.277
peak=    3.169 closest distance to " CA  SER A  12 " =    1.476
peak=    3.164 closest distance to " CG2 THR A 294 " =    1.261
peak=    3.164 closest distance to " O   HOH Z 302 " =    1.585
peak=    3.158 closest distance to " O   HOH Z 116 " =    1.244
peak=    3.151 closest distance to " O   HOH Z 197 " =    2.226
peak=    3.147 closest distance to " CB  THR A  31 " =    1.547
peak=    3.144 closest distance to " O   HOH Z 424 " =    1.344
peak=    3.143 closest distance to " CB  TRP A 266 " =    1.079
peak=    3.136 closest distance to " N   CYS A 260 " =    1.200
peak=    3.130 closest distance to " CB  SER A 210 " =    1.192
peak=    3.123 closest distance to " O   HOH Z  40 " =    2.279
peak=    3.118 closest distance to " CG  LYS A  76 " =    1.512
peak=    3.117 closest distance to " ND2 ASN A  60 " =    2.980
peak=    3.117 closest distance to " CB  ALA A 114 " =    0.972
peak=    3.115 closest distance to " O   HOH Z 426 " =    1.267
peak=    3.114 closest distance to " O   HOH Z  59 " =    1.849
peak=    3.113 closest distance to " O   HOH Z 353 " =    1.983
peak=    3.107 closest distance to " CB  PHE A 225 " =    1.522
peak=    3.107 closest distance to " CB  ASP A 200 " =    1.342
peak=    3.106 closest distance to " CD2 LEU A 261 " =    1.060
peak=    3.104 closest distance to " CB  ALA A 291 " =    1.326
peak=    3.103 closest distance to " CG1 VAL A 125 " =    2.109
peak=    3.102 closest distance to " O   HOH Z 303 " =    1.376
peak=    3.087 closest distance to " CA  ILE A 234 " =    1.280
peak=    3.085 closest distance to " C   ASN A 209 " =    1.808
peak=    3.084 closest distance to " N   GLU A   2 " =    1.376
peak=    3.080 closest distance to " NE1 TRP A 266 " =    1.851
peak=    3.054 closest distance to " O   ASN A  69 " =    1.264
peak=    3.046 closest distance to " O   HOH Z 369 " =    1.804

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 221         
Filter by distance & map next to the model:
   mapped sites are within: 0.500 - 5.426
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 219 from: 221
   mapped sites are within: 0.713 - 5.426

peak=   -4.529 closest distance to " OE1 GLU A  44 " =    1.825
peak=   -4.521 closest distance to " ND2 ASN A  39 " =    1.271
peak=   -4.441 closest distance to " O   HOH Z 415 " =    1.066
peak=   -4.358 closest distance to " C   PHE A  61 " =    0.923
peak=   -4.337 closest distance to " OG  SER A  63 " =    1.379
peak=   -4.317 closest distance to " O   PRO A 198 " =    1.084
peak=   -4.316 closest distance to " O   ASN A  69 " =    0.929
peak=   -4.304 closest distance to " O   HOH Z 216 " =    1.234
peak=   -4.299 closest distance to " CD2 HIS A 207 " =    1.397
peak=   -4.253 closest distance to " O   ALA A  10 " =    1.505
peak=   -4.234 closest distance to " CD  ARG A  14 " =    3.135
peak=   -4.215 closest distance to " CG  MET A 105 " =    0.944
peak=   -4.144 closest distance to " C   VAL A  72 " =    0.766
peak=   -4.131 closest distance to " NH2 ARG A 195 " =    2.473
peak=   -4.092 closest distance to " OG  SER A  97 " =    1.810
peak=   -4.090 closest distance to " CG  GLN A  88 " =    1.107
peak=   -4.072 closest distance to " NE  ARG A 195 " =    1.218
peak=   -4.054 closest distance to " CA  ASN A 110 " =    1.006
peak=   -4.006 closest distance to " O   GLY A 203 " =    2.363
peak=   -3.984 closest distance to " O   HOH Z 231 " =    0.787
peak=   -3.958 closest distance to " O   HOH Z 242 " =    1.476
peak=   -3.903 closest distance to " O   PHE A  59 " =    1.069
peak=   -3.901 closest distance to " N   ALA A  43 " =    2.602
peak=   -3.893 closest distance to " O   GLN A 240 " =    3.133
peak=   -3.892 closest distance to " O   HOH Z  70 " =    2.024
peak=   -3.882 closest distance to " ND2 ASN A 209 " =    1.718
peak=   -3.877 closest distance to " OG BSER A 134 " =    1.834
peak=   -3.865 closest distance to " O   SER A  62 " =    1.286
peak=   -3.850 closest distance to " CA  GLY A 133 " =    1.930
peak=   -3.805 closest distance to " CA  ILE A 120 " =    1.140
peak=   -3.794 closest distance to " O   HOH Z 389 " =    2.601
peak=   -3.794 closest distance to " O   HOH Z 313 " =    1.247
peak=   -3.776 closest distance to " O   VAL A 125 " =    2.382
peak=   -3.770 closest distance to " O   HOH Z 285 " =    1.606
peak=   -3.766 closest distance to " CB  ALA A   9 " =    2.538
peak=   -3.759 closest distance to " CB  GLN A  55 " =    1.190
peak=   -3.759 closest distance to " O   HOH Z  69 " =    1.514
peak=   -3.748 closest distance to " CG1 VAL A 265 " =    2.457
peak=   -3.710 closest distance to " NZ  LYS A 166 " =    1.694
peak=   -3.700 closest distance to " CB  ASN A 285 " =    2.030
peak=   -3.697 closest distance to " N   GLU A 277 " =    1.477
peak=   -3.694 closest distance to " O   HOH Z 426 " =    1.531
peak=   -3.682 closest distance to " CB  ALA A 291 " =    2.289
peak=   -3.677 closest distance to " OE2 GLU A 152 " =    1.196
peak=   -3.667 closest distance to " O   HOH Z 181 " =    1.167
peak=   -3.652 closest distance to " O   HOH Z 385 " =    1.221
peak=   -3.650 closest distance to " OE1 GLN A  88 " =    0.893
peak=   -3.642 closest distance to " N   PRO A  54 " =    1.044
peak=   -3.628 closest distance to " C   LEU A 101 " =    1.518
peak=   -3.627 closest distance to " O   ASP A 191 " =    1.890
peak=   -3.622 closest distance to " O   HOH Z 435 " =    3.135
peak=   -3.615 closest distance to " NE2 GLN A 194 " =    1.842
peak=   -3.607 closest distance to " CA  GLY A 241 " =    2.325
peak=   -3.603 closest distance to " O   HOH Z  32 " =    2.165
peak=   -3.602 closest distance to " O   ILE A 234 " =    1.275
peak=   -3.596 closest distance to " CB  SER A  62 " =    5.128
peak=   -3.590 closest distance to " O   HOH Z  37 " =    1.415
peak=   -3.588 closest distance to " CD1 TYR A 247 " =    2.461
peak=   -3.570 closest distance to " O   HOH Z  25 " =    2.103
peak=   -3.560 closest distance to " O   ASP A 253 " =    1.799
peak=   -3.560 closest distance to " CE2 TYR A  30 " =    2.410
peak=   -3.556 closest distance to " O   GLY A  80 " =    2.672
peak=   -3.554 closest distance to " O   TRP A  70 " =    1.425
peak=   -3.552 closest distance to " O   HOH Z 257 " =    1.006
peak=   -3.547 closest distance to " O   HOH Z  24 " =    0.876
peak=   -3.542 closest distance to " CD1 TYR A 214 " =    1.485
peak=   -3.530 closest distance to " N   ALA A  19 " =    2.137
peak=   -3.528 closest distance to " CD  GLU A 277 " =    2.354
peak=   -3.515 closest distance to " CD2 TYR A 293 " =    1.897
peak=   -3.512 closest distance to " O   HOH Z 381 " =    1.262
peak=   -3.509 closest distance to " CD  GLU A 277 " =    1.056
peak=   -3.505 closest distance to " C   ASP A  65 " =    1.105
peak=   -3.497 closest distance to " CE3 TRP A 274 " =    2.152
peak=   -3.497 closest distance to " NH2AARG A 275 " =    5.426
peak=   -3.492 closest distance to " CB  ASP A 132 " =    2.643
peak=   -3.490 closest distance to " NE2 GLN A  58 " =    3.476
peak=   -3.488 closest distance to " CE3 TRP A 179 " =    1.395
peak=   -3.473 closest distance to " O   HOH Z 358 " =    3.514
peak=   -3.471 closest distance to " O  BHOH Z  74 " =    1.083
peak=   -3.467 closest distance to " N   GLN A  11 " =    1.060
peak=   -3.465 closest distance to " O   HOH Z  54 " =    1.426
peak=   -3.459 closest distance to " O   HOH Z  60 " =    1.537
peak=   -3.455 closest distance to " CB  ASP A  27 " =    2.525
peak=   -3.453 closest distance to " CB  PHE A  61 " =    1.442
peak=   -3.447 closest distance to " O   HOH Z 357 " =    1.496
peak=   -3.446 closest distance to " NE1 TRP A 179 " =    1.185
peak=   -3.443 closest distance to " O   HOH Z 438 " =    1.352
peak=   -3.441 closest distance to " CB  PHE A 130 " =    1.135
peak=   -3.434 closest distance to " O   HOH Z 411 " =    5.181
peak=   -3.425 closest distance to " CG2 THR A 221 " =    2.221
peak=   -3.422 closest distance to " CB  ALA A  43 " =    2.436
peak=   -3.418 closest distance to " O   HOH Z 348 " =    2.195
peak=   -3.414 closest distance to " CZ  TYR A 169 " =    1.995
peak=   -3.413 closest distance to " O   HOH Z 286 " =    1.561
peak=   -3.411 closest distance to " O   HOH Z 385 " =    2.007
peak=   -3.408 closest distance to " O   HOH Z 163 " =    1.804
peak=   -3.396 closest distance to " O   HOH Z  69 " =    2.084
peak=   -3.395 closest distance to " CA  GLY A 133 " =    2.153
peak=   -3.394 closest distance to " O   SER A  22 " =    2.715
peak=   -3.394 closest distance to " O   HOH Z  37 " =    2.026
peak=   -3.389 closest distance to " CA  GLY A 203 " =    2.684
peak=   -3.375 closest distance to " O   PHE A 208 " =    1.591
peak=   -3.374 closest distance to " CG  ARG A 219 " =    2.355
peak=   -3.373 closest distance to " CG  GLN A  73 " =    1.536
peak=   -3.373 closest distance to " O   HOH Z 105 " =    2.119
peak=   -3.372 closest distance to " N   ARG A 159 " =    2.110
peak=   -3.370 closest distance to " O   HOH Z 241 " =    1.362
peak=   -3.367 closest distance to " C   SER A  63 " =    1.251
peak=   -3.363 closest distance to " OD1 ASN A 249 " =    1.346
peak=   -3.360 closest distance to " O   ASN A 285 " =    1.080
peak=   -3.359 closest distance to " CG2BVAL A  41 " =    1.328
peak=   -3.356 closest distance to " NE2 GLN A 223 " =    1.509
peak=   -3.352 closest distance to " O   PHE A 218 " =    1.583
peak=   -3.351 closest distance to " N   PRO A 163 " =    1.508
peak=   -3.350 closest distance to " O   HOH Z 111 " =    1.899
peak=   -3.349 closest distance to " O   PRO A 163 " =    2.109
peak=   -3.348 closest distance to " O   HOH Z 131 " =    1.075
peak=   -3.345 closest distance to " CB  ALA A   7 " =    1.950
peak=   -3.335 closest distance to " NE2 GLN A 122 " =    1.080
peak=   -3.335 closest distance to " CG  GLN A  55 " =    1.210
peak=   -3.334 closest distance to " O   HOH Z 100 " =    1.245
peak=   -3.331 closest distance to " O   ALA A  84 " =    1.671
peak=   -3.322 closest distance to " O   HOH Z 210 " =    1.764
peak=   -3.320 closest distance to " C   ILE A 239 " =    1.987
peak=   -3.319 closest distance to " O   HOH Z 200 " =    3.536
peak=   -3.313 closest distance to " C   HIS A 108 " =    1.477
peak=   -3.310 closest distance to " O   HOH Z   5 " =    1.178
peak=   -3.303 closest distance to " CD2 TYR A 116 " =    2.311
peak=   -3.299 closest distance to " O   THR A 178 " =    1.088
peak=   -3.298 closest distance to " O   ARG A  24 " =    2.108
peak=   -3.296 closest distance to " O   HOH Z 100 " =    1.656
peak=   -3.292 closest distance to " CB  ASN A  74 " =    1.205
peak=   -3.291 closest distance to " OD1 ASP A 107 " =    1.090
peak=   -3.282 closest distance to " ND2 ASN A  45 " =    2.846
peak=   -3.281 closest distance to " O   HOH Z  39 " =    0.713
peak=   -3.278 closest distance to " CG2 THR A 178 " =    2.142
peak=   -3.277 closest distance to " OH  TYR A 247 " =    1.485
peak=   -3.275 closest distance to " CE BMET A  47 " =    1.417
peak=   -3.268 closest distance to " O   HOH Z  73 " =    2.275
peak=   -3.267 closest distance to " CG  ARG A 259 " =    2.432
peak=   -3.265 closest distance to " O   HOH Z 174 " =    2.634
peak=   -3.264 closest distance to " CD  ARG A 156 " =    1.979
peak=   -3.263 closest distance to " O   HOH Z 105 " =    1.647
peak=   -3.263 closest distance to " NE2 GLN A  55 " =    0.869
peak=   -3.258 closest distance to " N   GLN A 122 " =    1.369
peak=   -3.253 closest distance to " N   TYR A 172 " =    1.473
peak=   -3.249 closest distance to " O   HOH Z  97 " =    2.234
peak=   -3.246 closest distance to " ND1 HIS A 207 " =    1.875
peak=   -3.244 closest distance to " O   HOH Z 139 " =    2.989
peak=   -3.244 closest distance to " O   HOH Z 179 " =    1.723
peak=   -3.237 closest distance to " O   VAL A  72 " =    0.851
peak=   -3.233 closest distance to " O   HOH Z 292 " =    1.404
peak=   -3.230 closest distance to " CG  GLN A 122 " =    2.447
peak=   -3.225 closest distance to " CB  ALA A 248 " =    2.031
peak=   -3.221 closest distance to " CA  MET A 113 " =    1.199
peak=   -3.220 closest distance to " O   HOH Z 139 " =    3.151
peak=   -3.218 closest distance to " CG2 ILE A 120 " =    0.946
peak=   -3.218 closest distance to " O   HOH Z 368 " =    1.664
peak=   -3.214 closest distance to " CB  ALA A 161 " =    1.648
peak=   -3.213 closest distance to " NH1 ARG A  36 " =    0.965
peak=   -3.213 closest distance to " O   HOH Z 114 " =    1.504
peak=   -3.212 closest distance to " CZ  ARG A  36 " =    1.489
peak=   -3.209 closest distance to " CA  ARG A 156 " =    1.087
peak=   -3.208 closest distance to " O   ARG A 275 " =    0.990
peak=   -3.203 closest distance to " O   ALA A 114 " =    1.108
peak=   -3.198 closest distance to " OD2 ASP A 272 " =    1.668
peak=   -3.196 closest distance to " O   HOH Z 277 " =    1.658
peak=   -3.196 closest distance to " O   HOH Z 275 " =    1.874
peak=   -3.194 closest distance to " O   HOH Z  99 " =    1.920
peak=   -3.193 closest distance to " O   HOH Z 394 " =    1.724
peak=   -3.192 closest distance to " CB  PRO A  54 " =    2.354
peak=   -3.189 closest distance to " O   HOH Z  68 " =    1.411
peak=   -3.188 closest distance to " CA  GLY A  57 " =    1.997
peak=   -3.188 closest distance to " NE1 TRP A 177 " =    1.997
peak=   -3.188 closest distance to " ND2 ASN A 285 " =    2.179
peak=   -3.181 closest distance to " CZ  PHE A  38 " =    2.369
peak=   -3.178 closest distance to " CZ  ARG A  66 " =    2.124
peak=   -3.177 closest distance to " O   HOH Z 358 " =    1.463
peak=   -3.175 closest distance to " CZ2 TRP A 123 " =    2.315
peak=   -3.172 closest distance to " O   HOH Z 396 " =    0.937
peak=   -3.167 closest distance to " CG  TRP A  85 " =    1.029
peak=   -3.165 closest distance to " CB  ALA A 227 " =    2.414
peak=   -3.164 closest distance to " O   SER A  62 " =    1.131
peak=   -3.163 closest distance to " O   HOH Z 198 " =    1.411
peak=   -3.159 closest distance to " SG BCYS A 201 " =    2.554
peak=   -3.158 closest distance to " CB  ALA A 129 " =    2.806
peak=   -3.157 closest distance to " O   HOH Z 128 " =    2.712
peak=   -3.153 closest distance to " O   HOH Z 353 " =    4.386
peak=   -3.152 closest distance to " OD2 ASP A 140 " =    1.227
peak=   -3.150 closest distance to " O   HOH Z 333 " =    1.029
peak=   -3.139 closest distance to " O   HOH Z 390 " =    2.378
peak=   -3.135 closest distance to " O   ASP A 286 " =    0.819
peak=   -3.134 closest distance to " O   HOH Z 155 " =    0.997
peak=   -3.133 closest distance to " CD2 PHE A 225 " =    2.608
peak=   -3.132 closest distance to " C   GLU A   2 " =    2.001
peak=   -3.131 closest distance to " O   HOH Z 174 " =    1.538
peak=   -3.130 closest distance to " SD  MET A  40 " =    1.959
peak=   -3.130 closest distance to " SG  CYS A 254 " =    2.831
peak=   -3.127 closest distance to " O   HOH Z 118 " =    1.735
peak=   -3.125 closest distance to " O   HOH Z 130 " =    0.892
peak=   -3.124 closest distance to " CD2 PHE A  61 " =    2.038
peak=   -3.117 closest distance to " O   LYS A 119 " =    1.623
peak=   -3.116 closest distance to " O   LYS A 193 " =    1.481
peak=   -3.110 closest distance to " CB  TRP A  85 " =    1.985
peak=   -3.100 closest distance to " CG  ASP A 140 " =    1.084
peak=   -3.091 closest distance to " ND2BASN A 224 " =    1.676
peak=   -3.090 closest distance to " CG  TRP A 266 " =    1.613
peak=   -3.089 closest distance to " CD  LYS A 166 " =    2.643
peak=   -3.085 closest distance to " O   HOH Z 140 " =    1.076
peak=   -3.085 closest distance to " CB  GLN A 144 " =    1.188
peak=   -3.081 closest distance to " O   HOH Z 323 " =    2.024
peak=   -3.075 closest distance to " N   ASN A 127 " =    1.297
peak=   -3.072 closest distance to " OG  SER A  87 " =    1.949
peak=   -3.063 closest distance to " O   HOH Z 134 " =    3.991
peak=   -3.062 closest distance to " O   HOH Z  12 " =    1.202
peak=   -3.058 closest distance to " CB  TYR A  68 " =    1.004
peak=   -3.054 closest distance to " O   HOH Z 378 " =    1.796
peak=   -3.022 closest distance to " CA  THR A  29 " =    1.306
peak=   -2.921 closest distance to " O   VAL A 125 " =    2.179

================= 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    :  0.4927 0.4968   6.305541e+00   6.297519e+00
   1_bss:  0.4838 0.4921   6.303436e+00   6.294162e+00
   1_xyz:  0.4073 0.4554   6.196000e+00   6.253668e+00
   1_adp:  0.3757 0.4636   6.169173e+00   6.262107e+00
   1_occ:  0.3755 0.4652   6.169135e+00   6.262340e+00
   2_bss:  0.3756 0.4644   6.172662e+00   6.263068e+00
   2_xyz:  0.3207 0.4102   6.056761e+00   6.189943e+00
   2_adp:  0.3063 0.3986   6.031786e+00   6.171084e+00
   2_occ:  0.3061 0.3989   6.031506e+00   6.171121e+00
   3_bss:  0.3066 0.3981   6.030243e+00   6.169745e+00
   3_xyz:  0.2641 0.3481   5.906232e+00   6.078127e+00
   3_adp:  0.2461 0.3477   5.872374e+00   6.071033e+00
   3_occ:  0.2461 0.3475   5.872078e+00   6.070986e+00
   4_bss:  0.2465 0.3477   5.873046e+00   6.071346e+00
   4_xyz:  0.2127 0.3030   5.742193e+00   5.968088e+00
   4_adp:  0.2030 0.2721   5.678596e+00   5.887724e+00
   4_occ:  0.2030 0.2718   5.677692e+00   5.886885e+00
   5_bss:  0.2029 0.2717   5.676161e+00   5.885356e+00
   5_xyz:  0.1680 0.2258   5.498321e+00   5.731024e+00
   5_adp:  0.1514 0.2086   5.413244e+00   5.653273e+00
   5_occ:  0.1513 0.2086   5.412794e+00   5.652985e+00
   5_bss:  0.1516 0.2079   5.410097e+00   5.649326e+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:  0.340  50.001  -2.462   0.766   3.349   0.000   0.000   0.000
   1_xyz:  0.340  50.001  -2.462   0.766   3.349   0.000   0.000   0.000
   1_adp:  0.340  50.001  -2.462   0.766   3.349   0.000   0.000   0.000
   1_occ:  0.340  50.001  -2.462   0.766   3.349   0.000   0.000   0.000
   2_bss:  0.368  80.548  -0.697  -0.183   2.096  -0.000   0.000   0.000
   2_xyz:  0.368  80.548  -0.697  -0.183   2.096  -0.000   0.000   0.000
   2_adp:  0.368  80.548  -0.697  -0.183   2.096  -0.000   0.000   0.000
   2_occ:  0.368  80.548  -0.697  -0.183   2.096  -0.000   0.000   0.000
   3_bss:  0.362  88.324  -0.597  -0.465   1.414  -0.000   0.000   0.000
   3_xyz:  0.362  88.324  -0.597  -0.465   1.414  -0.000   0.000   0.000
   3_adp:  0.362  88.324  -0.597  -0.465   1.414  -0.000   0.000   0.000
   3_occ:  0.362  88.324  -0.597  -0.465   1.414  -0.000   0.000   0.000
   4_bss:  0.362 105.169  -0.509  -0.612   1.441  -0.000   0.000   0.000
   4_xyz:  0.362 105.169  -0.509  -0.612   1.441  -0.000   0.000   0.000
   4_adp:  0.362 105.169  -0.509  -0.612   1.441  -0.000   0.000   0.000
   4_occ:  0.362 105.169  -0.509  -0.612   1.441  -0.000   0.000   0.000
   5_bss:  0.340  84.587  -1.041  -1.315   0.876  -0.000   0.000   0.000
   5_xyz:  0.340  84.587  -1.041  -1.315   0.876  -0.000   0.000   0.000
   5_adp:  0.340  84.587  -1.041  -1.315   0.876  -0.000   0.000   0.000
   5_occ:  0.340  84.587  -1.041  -1.315   0.876  -0.000   0.000   0.000
   5_bss:  0.324  73.330  -1.342  -1.894   0.469  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  65.131 0.3265  0.4512    85602.337
   1_bss:  64.072 0.3396  0.4869    84540.920
   1_xyz:  55.041 0.4558  0.6411    66391.286
   1_adp:  56.388 0.4381  0.6291    68894.600
   1_occ:  56.489 0.4367  0.6260    69039.400
   2_bss:  56.669 0.4343  0.6206    69306.221
   2_xyz:  47.315 0.5519  0.7795    50419.635
   2_adp:  45.102 0.5797  0.8033    47325.071
   2_occ:  45.105 0.5796  0.8033    47326.135
   3_bss:  44.981 0.5809  0.7960    46930.247
   3_xyz:  37.435 0.6716  0.8982    34013.086
   3_adp:  36.848 0.6782  0.8798    33129.044
   3_occ:  36.839 0.6783  0.8796    33102.825
   4_bss:  36.849 0.6782  0.8789    33131.575
   4_xyz:  31.754 0.7357  0.9359    24532.074
   4_adp:  27.669 0.7823  0.9647    19820.869
   4_occ:  27.653 0.7824  0.9644    19764.683
   5_bss:  27.570 0.7831  0.9453    19635.756
   5_xyz:  22.302 0.8379  0.9810    13332.296
   5_adp:  20.246 0.8586  0.9808    11345.751
   5_occ:  20.227 0.8588  0.9807    11329.510
   5_bss:  20.129 0.8595  0.9665    11195.273
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.8677e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.8677e-01
   1_xyz:   1.682  0.012  0.117 16.706  0.007  4.105   1.6632e-01
   1_adp:   1.682  0.012  0.117 16.706  0.007  4.105   1.6632e-01
   1_occ:   1.682  0.012  0.117 16.706  0.007  4.105   1.6632e-01
   2_bss:   1.682  0.012  0.117 16.706  0.007  4.105   1.6632e-01
   2_xyz:   1.343  0.010  0.096 15.798  0.006  4.109   1.0649e-01
   2_adp:   1.343  0.010  0.096 15.798  0.006  4.109   1.0649e-01
   2_occ:   1.343  0.010  0.096 15.798  0.006  4.109   1.0649e-01
   3_bss:   1.343  0.010  0.096 15.798  0.006  4.109   1.0649e-01
   3_xyz:   1.055  0.008  0.073 14.913  0.004  4.120   6.8874e-02
   3_adp:   1.055  0.008  0.073 14.913  0.004  4.120   6.8874e-02
   3_occ:   1.055  0.008  0.073 14.913  0.004  4.120   6.8874e-02
   4_bss:   1.055  0.008  0.073 14.913  0.004  4.120   6.8874e-02
   4_xyz:   1.020  0.007  0.075 14.576  0.004  4.120   6.2024e-02
   4_adp:   1.020  0.007  0.075 14.576  0.004  4.120   6.2024e-02
   4_occ:   1.020  0.007  0.075 14.576  0.004  4.120   6.2024e-02
   5_bss:   1.020  0.007  0.075 14.576  0.004  4.120   6.2024e-02
   5_xyz:   1.075  0.008  0.077 14.693  0.004  4.110   6.8466e-02
   5_adp:   1.075  0.008  0.077 14.693  0.004  4.110   6.8466e-02
   5_occ:   1.075  0.008  0.077 14.693  0.004  4.110   6.8466e-02
   5_bss:   1.075  0.008  0.077 14.693  0.004  4.110   6.8466e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.681   2.4235e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.681   2.4235e-01
   1_xyz:  11.401  0.068  0.419 82.231  0.050  1.990   1.0661e-01
   1_adp:  11.401  0.068  0.419 82.231  0.050  1.990   1.0661e-01
   1_occ:  11.401  0.068  0.419 82.231  0.050  1.990   1.0661e-01
   2_bss:  11.401  0.068  0.419 82.231  0.050  1.990   1.0661e-01
   2_xyz:   9.079  0.086  0.342 77.719  0.053  2.036   8.5109e-02
   2_adp:   9.079  0.086  0.342 77.719  0.053  2.036   8.5109e-02
   2_occ:   9.079  0.086  0.342 77.719  0.053  2.036   8.5109e-02
   3_bss:   9.079  0.086  0.342 77.719  0.053  2.036   8.5109e-02
   3_xyz:   6.826  0.045  0.248 86.559  0.030  2.297   7.2842e-02
   3_adp:   6.826  0.045  0.248 86.559  0.030  2.297   7.2842e-02
   3_occ:   6.826  0.045  0.248 86.559  0.030  2.297   7.2842e-02
   4_bss:   6.826  0.045  0.248 86.559  0.030  2.297   7.2842e-02
   4_xyz:   8.149  0.060  0.237 86.914  0.037  2.324   4.7265e-02
   4_adp:   8.149  0.060  0.237 86.914  0.037  2.324   4.7265e-02
   4_occ:   8.149  0.060  0.237 86.914  0.037  2.324   4.7265e-02
   5_bss:   8.149  0.060  0.237 86.914  0.037  2.324   4.7265e-02
   5_xyz:   7.566  0.044  0.264 88.841  0.035  2.298   5.2803e-02
   5_adp:   7.566  0.044  0.264 88.841  0.035  2.298   5.2803e-02
   5_occ:   7.566  0.044  0.264 88.841  0.035  2.298   5.2803e-02
   5_bss:   7.566  0.044  0.264 88.841  0.035  2.298   5.2803e-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:  89.88   0.00  19.60  77.08   0.00  16.73  89.88   0.00  35.24
   1_occ:  89.88   0.00  19.60  77.08   0.00  16.73  89.88   0.00  35.24
   2_bss:  89.88   0.00  19.60  77.08   0.00  16.73  89.88   0.00  35.24
   2_xyz:  89.88   0.00  19.60  77.08   0.00  16.73  89.88   0.00  35.24
   2_adp:  89.56   0.00  18.98  71.28   0.00  15.98  89.56   0.00  35.32
   2_occ:  89.56   0.00  18.98  71.28   0.00  15.98  89.56   0.00  35.32
   3_bss:  89.56   0.00  18.98  71.28   0.00  15.98  89.56   0.00  35.32
   3_xyz:  89.56   0.00  18.98  71.28   0.00  15.98  89.56   0.00  35.32
   3_adp: 131.78   0.00  22.34 110.41   0.00  17.12 131.78   0.00  50.81
   3_occ: 131.78   0.00  22.34 110.41   0.00  17.12 131.78   0.00  50.81
   4_bss: 131.78   0.00  22.34 110.41   0.00  17.12 131.78   0.00  50.81
   4_xyz: 131.78   0.00  22.34 110.41   0.00  17.12 131.78   0.00  50.81
   4_adp: 120.93   0.00  20.16 106.86   0.00  14.91 120.93   1.93  48.76
   4_occ: 120.93   0.00  20.16 106.86   0.00  14.91 120.93   1.93  48.76
   5_bss: 120.93   0.00  20.16 106.86   0.00  14.91 120.93   1.93  48.76
   5_xyz: 120.93   0.00  20.16 106.86   0.00  14.91 120.93   1.93  48.76
   5_adp: 126.82   0.00  19.33 106.97   0.00  13.34 126.82   3.84  51.94
   5_occ: 126.82   0.00  19.33 106.97   0.00  13.34 126.82   3.84  51.94
   5_bss: 126.82   0.00  19.33 106.97   0.00  13.34 126.82   3.84  51.94
------------------------------------------------------------------------
 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:    1.773    0.037    0.407
   1_adp:    1.773    0.037    0.407
   1_occ:    1.773    0.037    0.407
   2_bss:    1.773    0.037    0.407
   2_xyz:    1.554    0.066    0.588
   2_adp:    1.554    0.066    0.588
   2_occ:    1.554    0.066    0.588
   3_bss:    1.554    0.066    0.588
   3_xyz:    1.580    0.023    0.702
   3_adp:    1.580    0.023    0.702
   3_occ:    1.580    0.023    0.702
   4_bss:    1.580    0.023    0.702
   4_xyz:    1.668    0.039    0.805
   4_adp:    1.668    0.039    0.805
   4_occ:    1.668    0.039    0.805
   5_bss:    1.668    0.039    0.805
   5_xyz:    1.714    0.079    0.899
   5_adp:    1.714    0.079    0.899
   5_occ:    1.714    0.079    0.899
   5_bss:    1.714    0.079    0.899
------------------------------------------------------------------------

CPU time actual refinement: 384.45


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_857/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_857/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_857/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_857/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_857/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 384.29 
  Macro-tasks:
    bulk solvent and scale       = 60.94  
    individual site refinement   = 164.46 
    weights calculation          = 30.86  
    collect and process          = 6.26   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 262.64 
  Micro-tasks:
    mask                            = 3.10   
    f_calc                          = 120.11 
    alpha_beta                      = 8.42   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 130.01 
    fmodel                         = 9.26   
    r_factors                      = 0.41   
    phase_errors                   = 9.81   
    foms                           = 0.26   
    TOTAL for micro-tasks          = 282.51 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.392 micro seconds
Total CPU time: 6.63 minutes
from_scatterers_fft:    617 calls, 119.82 s
gradients_fft:          562 calls, 116.95 s

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

# Date 2008-01-16 Time 05:50:00 PST -0800 (1200491400.28 s)
Start R-work = 0.4927, R-free = 0.4968 (no bulk solvent and anisotropic scale)
Final R-work = 0.1677, R-free = 0.2229 (no bulk solvent and anisotropic scale)

Start R-work = 0.4838, R-free = 0.4921
Final R-work = 0.1516, R-free = 0.2079