# Date 2008-01-16 Time 06:32:18 PST -0800 (1200493938.30 s)
#phil __OFF__

Command line arguments: "../1188.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 19105
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1188

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.655, 47.8686, 84.2302, 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: (71.655, 47.8686, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1017 1.95159
Completeness in resolution range: 0.90472
Completeness with d_max=infinity: 0.902095

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1017
                             d_min =   1.9516

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 47.8686, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1017 1.95159
Completeness in resolution range: 0.90472
Completeness with d_max=infinity: 0.902095

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1022 -  4.1777 [2277/2306]  2050   227  10.0%
  bin  2:  4.1777 -  3.3276 [2174/2197]  1957   217  10.0%
  bin  3:  3.3276 -  2.9104 [2147/2172]  1929   218  10.2%
  bin  4:  2.9104 -  2.6459 [2147/2173]  1938   209   9.7%
  bin  5:  2.6459 -  2.4571 [2109/2143]  1901   208   9.9%
  bin  6:  2.4571 -  2.3128 [2111/2139]  1894   217  10.3%
  bin  7:  2.3128 -  2.1973 [2099/2135]  1884   215  10.2%
  bin  8:  2.1973 -  2.1019 [2093/2135]  1886   207   9.9%
  bin  9:  2.1019 -  2.0212 [1924/2147]  1734   190   9.9%
  bin 10:  2.0212 -  1.9516 [ 508/2105]   457    51  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1188/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:
        1.39 -     2.09: 22
        2.09 -     2.79: 689
        2.79 -     3.49: 4467
        3.49 -     4.20: 9296
        4.20 -     4.90: 13776
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.386 3.120 -x+1/2,-y+1,z-1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.521 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.531 3.040 -x+1/2,-y+1,z+1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.555 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.585 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28245 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_1188/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1188/model_refine_001.geo

CPU time processing inputs: 9.21


============================ Non-default parameters ===========================

A complete record of all parameters was written to the .eff file above.
Below are only the non-defaults.

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.655 47.8686 84.23025 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 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4879   r_free= 0.4795   ksol= 0.00   Bsol= 0.00   scale= 0.873    |
|                                                                             |
| 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:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.295120                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1022 -  4.6604 0.99   1479  167 0.3815 0.3887      6.5815      6.5862|
|  2:  4.6604 -  3.7173 0.99   1420  158 0.4251 0.4068      6.8472      6.8428|
|  3:  3.7173 -  3.2527 0.99   1381  145 0.4679 0.4335      6.6856      6.6791|
|  4:  3.2527 -  2.9578 0.98   1388  166 0.4895 0.4768      6.5163      6.5057|
|  5:  2.9578 -  2.7471 0.99   1372  146 0.5119 0.4991      6.3653      6.3397|
|  6:  2.7471 -  2.5860 0.99   1372  159 0.5315 0.5202      6.2841      6.1964|
|  7:  2.5860 -  2.4571 0.98   1363  138 0.5282 0.4992      6.2392      6.2064|
|  8:  2.4571 -  2.3505 0.98   1355  152 0.5294 0.5157      6.1412      6.1954|
|  9:  2.3505 -  2.2604 0.99   1350  154 0.5538 0.5242      6.1539      6.1157|
| 10:  2.2604 -  2.1826 0.99   1348  160 0.5419 0.5776      6.0775      6.1146|
| 11:  2.1826 -  2.1145 0.97   1344  137 0.5322 0.5842      6.0147      5.9899|
| 12:  2.1145 -  2.0542 0.98   1334  146 0.5244 0.5464      5.9336      5.9651|
| 13:  2.0542 -  2.0003 0.67    900  113 0.5403 0.4860      5.8589      5.8532|
| 14:  2.0003 -  1.9516 0.16    224   18 0.5825 0.3608      5.7842      5.7297|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1022 -  4.6604  1479   167  0.69  34.78   0.82     0.73      73276.11|
|  2:  4.6604 -  3.7173  1420   158  0.68  37.14   0.89     0.77     111729.33|
|  3:  3.7173 -  3.2527  1381   145  0.55  47.88   0.89     0.72     124055.74|
|  4:  3.2527 -  2.9578  1388   166  0.44  56.91   0.88     0.63     114542.22|
|  5:  2.9578 -  2.7471  1372   146  0.37  62.24   0.86     0.54      90021.77|
|  6:  2.7471 -  2.5860  1372   159  0.35  63.59   0.87     0.52      74926.30|
|  7:  2.5860 -  2.4571  1363   138  0.34  64.29   0.88     0.48      65751.65|
|  8:  2.4571 -  2.3505  1355   152  0.29  68.04   0.87     0.45      64091.14|
|  9:  2.3505 -  2.2604  1350   154  0.24  72.25   0.91     0.36      60052.11|
| 10:  2.2604 -  2.1826  1348   160  0.19  76.09   0.90     0.29      58934.93|
| 11:  2.1826 -  2.1145  1344   137  0.10  82.71   0.91     0.15      55282.35|
| 12:  2.1145 -  2.0542  1334   146  0.07  84.64   0.90     0.12      52555.62|
| 13:  2.0542 -  2.0003   900   113  0.10  82.31   0.91     0.17      43383.72|
| 14:  2.0003 -  1.9516   224    18  0.21  74.01   0.85     0.37      34449.13|
|alpha:            min =        0.12 max =            0.77 mean =         0.47|
|beta:             min =    34449.13 max =       124055.74 mean =     76675.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.35|
|phase err.(work): min =        0.00 max =           90.00 mean =        63.33|
|phase err.(test): min =        0.00 max =           89.98 mean =        63.33|
|-----------------------------------------------------------------------------|

============================== 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 = 14.514818             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.079   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.005397              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.777   (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 |  1.386 -  1.737:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.737 -  2.089:       13 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.089 -  2.440:       30 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.440 -  2.792:      659 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.792 -  3.143:     2108 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.143 -  3.494:     2359 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.494 -  3.846:     4531 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.846 -  4.197:     4765 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.197 -  4.549:     6233 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.549 -  4.900:     7543 |
|-----------------------------------------------------------------------------|
|-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 |        0.200 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.386 |       0.726 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.018)------------------------------------------|
|    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 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4879   r_free= 0.4795   ksol= 0.00   Bsol= 0.00   scale= 0.873    |
|                                                                             |
| 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:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.295120                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4816   r_free= 0.4743   ksol= 0.28   Bsol= 20.61   scale= 0.917   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.37,2.33,0.84,0.00,0.00,0.00); trace/3= 0.93                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.293419                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.946696             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.128   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.656370              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.398   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4816      final r-factor (work) = 0.4017          |
| start r-factor (free) = 0.4743      final r-factor (free) = 0.4378          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.6228 = 10.95 * 0.50 * 6.2891 + 1.00 * 0.2002                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.0975 = 10.95 * 0.50 * 6.2052 + 1.00 * 0.1344                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4017      final r-factor (work) = 0.3722          |
| start r-factor (free) = 0.4378      final r-factor (free) = 0.4368          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2844 = 1.66 * 1.00 * 6.2052 + 1.00 * 0.0063                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2401 = 1.66 * 1.00 * 6.1446 + 1.00 * 0.0624                              |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.018)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.33  17.26    None  None   None       |
|    all(noH): 2823   0      0.00    113.33  17.26    None  None   None       |
|    Sol.    : 438    0      0.00    71.81   36.38    None  None   None       |
|    Mac.    : 2385   0      0.00    113.33  13.75    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 -  11.333: 1108   |   5:    56.665 -  67.998:   20        |
|      1:    11.333 -  22.666:  935   |   6:    67.998 -  79.331:    1        |
|      2:    22.666 -  33.999:  451   |   7:    79.331 -  90.664:    1        |
|      3:    33.999 -  45.332:  194   |   8:    90.664 - 101.997:    0        |
|      4:    45.332 -  56.665:  112   |   9:   101.997 - 113.330:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3722 r_free = 0.4368             target_work(ml) = 6.145         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3718 r_free = 0.4374             target_work(ml) = 6.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3718   r_free= 0.4374   ksol= 0.28   Bsol= 20.61   scale= 0.971   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.37,2.33,0.84,0.00,0.00,0.00); trace/3= 0.93                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.144703                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3713   r_free= 0.4361   ksol= 0.35   Bsol= 80.00   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.68,2.69,1.66,0.00,0.00,0.00); trace/3= 1.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.145127                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.055198             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.260   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.608567              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.245   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3713      final r-factor (work) = 0.2932          |
| start r-factor (free) = 0.4361      final r-factor (free) = 0.3594          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.1814 = 12.06 * 0.50 * 6.1462 + 1.00 * 0.1345                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.6968 = 12.06 * 0.50 * 6.0688 + 1.00 * 0.1164                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2932      final r-factor (work) = 0.2703          |
| start r-factor (free) = 0.3594      final r-factor (free) = 0.3492          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.7963 = 1.61 * 1.00 * 6.0688 + 1.00 * 0.0342                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.5669 = 1.61 * 1.00 * 5.9347 + 1.00 * 0.0205                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.018)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.42  19.02    None  None   None       |
|    all(noH): 2823   0      0.00    100.42  19.02    None  None   None       |
|    Sol.    : 438    0      0.00    100.42  41.91    None  None   None       |
|    Mac.    : 2385   0      0.00    80.71   14.82    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.042: 1041   |   5:    50.209 -  60.251:  113        |
|      1:    10.042 -  20.084:  854   |   6:    60.251 -  70.293:   59        |
|      2:    20.084 -  30.125:  341   |   7:    70.293 -  80.334:   23        |
|      3:    30.125 -  40.167:  238   |   8:    80.334 -  90.376:   10        |
|      4:    40.167 -  50.209:  142   |   9:    90.376 - 100.418:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2703 r_free = 0.3492             target_work(ml) = 5.924         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2702 r_free = 0.3487             target_work(ml) = 5.924         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2702   r_free= 0.3487   ksol= 0.35   Bsol= 80.00   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.68,2.69,1.66,0.00,0.00,0.00); trace/3= 1.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.923856                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2696   r_free= 0.3480   ksol= 0.33   Bsol= 68.11   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.25,1.24,0.45,0.00,0.00,0.00); trace/3= 0.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.922176                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.887466              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.677  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.952232              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.739  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2696      final r-factor (work) = 0.2218          |
| start r-factor (free) = 0.3480      final r-factor (free) = 0.2855          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.6184 = 4.89 * 0.50 * 5.9344 + 1.00 * 0.1164                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.3758 = 4.89 * 0.50 * 5.8541 + 1.00 * 0.0700                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2218      final r-factor (work) = 0.2042          |
| start r-factor (free) = 0.2855      final r-factor (free) = 0.2697          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 29.0110 = 4.95 * 1.00 * 5.8541 + 1.00 * 0.0203                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 28.2813 = 4.95 * 1.00 * 5.7063 + 1.00 * 0.0225                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.018)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    130.53  19.87    None  None   None       |
|    all(noH): 2823   0      0.00    130.53  19.87    None  None   None       |
|    Sol.    : 438    0      3.91    126.40  50.04    None  None   None       |
|    Mac.    : 2385   0      0.00    130.53  14.33    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 -  13.053: 1476   |   5:    65.263 -  78.316:   68        |
|      1:    13.053 -  26.105:  720   |   6:    78.316 -  91.369:   48        |
|      2:    26.105 -  39.158:  209   |   7:    91.369 - 104.421:   27        |
|      3:    39.158 -  52.211:  153   |   8:   104.421 - 117.474:    6        |
|      4:    52.211 -  65.263:  111   |   9:   117.474 - 130.527:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2042 r_free = 0.2697             target_work(ml) = 5.679         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2042 r_free = 0.2697             target_work(ml) = 5.679         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2042   r_free= 0.2697   ksol= 0.33   Bsol= 68.11   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.25,1.24,0.45,0.00,0.00,0.00); trace/3= 0.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.678978                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2043   r_free= 0.2696   ksol= 0.33   Bsol= 74.64   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.43,0.51,-0.33,0.00,-0.00,-0.00); trace/3= -0.08                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.679273                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.451378              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.320   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.454809              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.212  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2043      final r-factor (work) = 0.1635          |
| start r-factor (free) = 0.2696      final r-factor (free) = 0.2235          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.4832 = 6.45 * 0.50 * 5.7083 + 1.00 * 0.0700                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.1327 = 6.45 * 0.50 * 5.5965 + 1.00 * 0.0800                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1635      final r-factor (work) = 0.1492          |
| start r-factor (free) = 0.2235      final r-factor (free) = 0.2014          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5680 = 0.45 * 1.00 * 5.5965 + 1.00 * 0.0226                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4928 = 0.45 * 1.00 * 5.4517 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.018)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    124.75  18.10    None  None   None       |
|    all(noH): 2823   0      0.00    124.75  18.10    None  None   None       |
|    Sol.    : 438    0      3.92    115.40  46.96    None  None   None       |
|    Mac.    : 2385   0      0.00    124.75  12.80    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.476: 1572   |   5:    62.377 -  74.853:   67        |
|      1:    12.476 -  24.951:  728   |   6:    74.853 -  87.328:   34        |
|      2:    24.951 -  37.426:  153   |   7:    87.328 -  99.804:   21        |
|      3:    37.426 -  49.902:  131   |   8:    99.804 - 112.279:    8        |
|      4:    49.902 -  62.377:  107   |   9:   112.279 - 124.755:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1492 r_free = 0.2014             target_work(ml) = 5.396         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1490 r_free = 0.2012             target_work(ml) = 5.395         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1490   r_free= 0.2012   ksol= 0.33   Bsol= 74.64   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.43,0.51,-0.33,0.00,-0.00,-0.00); trace/3= -0.08                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.395333                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1491   r_free= 0.2007   ksol= 0.33   Bsol= 66.85   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.96,-0.32,-0.83,-0.00,-0.00,-0.00); trace/3= -0.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.398309                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.587516              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 120.488  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.140839              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.954  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1491      final r-factor (work) = 0.1358          |
| start r-factor (free) = 0.2007      final r-factor (free) = 0.1847          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1372 = 2.59 * 0.50 * 5.4548 + 1.00 * 0.0800                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9975 = 2.59 * 0.50 * 5.3624 + 1.00 * 0.0599                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1358      final r-factor (work) = 0.1347          |
| start r-factor (free) = 0.1847      final r-factor (free) = 0.1811          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7684 = 0.14 * 1.00 * 5.3624 + 1.00 * 0.0132                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8176 = 0.14 * 1.00 * 5.3147 + 1.00 * 0.0691                               |
|-----------------------------------------------------------------------------|
| number of iterations = 3       |    number of function evaluations = 3      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.018)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    123.94  18.12    None  None   None       |
|    all(noH): 2823   0      0.00    123.94  18.12    None  None   None       |
|    Sol.    : 438    0      5.19    114.53  46.39    None  None   None       |
|    Mac.    : 2385   0      0.00    123.94  12.93    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 -  12.394: 1586   |   5:    61.971 -  74.365:   64        |
|      1:    12.394 -  24.788:  715   |   6:    74.365 -  86.759:   33        |
|      2:    24.788 -  37.183:  157   |   7:    86.759 -  99.153:   21        |
|      3:    37.183 -  49.577:  131   |   8:    99.153 - 111.547:    7        |
|      4:    49.577 -  61.971:  106   |   9:   111.547 - 123.942:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1347 r_free = 0.1811             target_work(ml) = 5.304         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1345 r_free = 0.1809             target_work(ml) = 5.303         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1345   r_free= 0.1809   ksol= 0.33   Bsol= 66.85   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.96,-0.32,-0.83,-0.00,-0.00,-0.00); trace/3= -0.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.303250                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1022 -  4.6604 0.99   1479  167 0.0989 0.1285      5.3928      5.5921|
|  2:  4.6604 -  3.7173 0.99   1420  158 0.0920 0.1224      5.4857      5.7736|
|  3:  3.7173 -  3.2527 0.99   1381  145 0.1239 0.1880      5.5881      5.9886|
|  4:  3.2527 -  2.9578 0.98   1388  166 0.1585 0.1869      5.6268      5.7724|
|  5:  2.9578 -  2.7471 0.99   1372  146 0.1611 0.2010      5.4799      5.6072|
|  6:  2.7471 -  2.5860 0.99   1372  159 0.1523 0.2186      5.3777       5.556|
|  7:  2.5860 -  2.4571 0.98   1363  138 0.1511 0.1973      5.3067      5.5212|
|  8:  2.4571 -  2.3505 0.98   1355  152 0.1523 0.1999       5.247       5.441|
|  9:  2.3505 -  2.2604 0.99   1350  154 0.1473 0.2152      5.1841      5.4152|
| 10:  2.2604 -  2.1826 0.99   1348  160 0.1432 0.1965      5.1481      5.3901|
| 11:  2.1826 -  2.1145 0.97   1344  137 0.1402 0.1981      5.0633      5.2815|
| 12:  2.1145 -  2.0542 0.98   1334  146 0.1427 0.2246       5.021      5.2958|
| 13:  2.0542 -  2.0003 0.67    900  113 0.1466 0.1789      4.9369       5.086|
| 14:  2.0003 -  1.9516 0.16    224   18 0.1412 0.1910      4.8204      5.0718|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1022 -  4.6604  1479   167  0.94   9.38   0.97     0.95       7487.16|
|  2:  4.6604 -  3.7173  1420   158  0.95   8.98   1.02     1.00      10135.72|
|  3:  3.7173 -  3.2527  1381   145  0.91  13.98   1.04     1.03      13033.92|
|  4:  3.2527 -  2.9578  1388   166  0.88  18.03   1.02     1.00      14408.32|
|  5:  2.9578 -  2.7471  1372   146  0.87  19.41   1.02     1.00      11355.60|
|  6:  2.7471 -  2.5860  1372   159  0.87  19.38   1.01     0.99       9704.81|
|  7:  2.5860 -  2.4571  1363   138  0.88  18.20   1.01     0.98       7981.74|
|  8:  2.4571 -  2.3505  1355   152  0.87  19.70   1.02     0.99       7825.29|
|  9:  2.3505 -  2.2604  1350   154  0.87  19.42   1.02     0.97       6675.85|
| 10:  2.2604 -  2.1826  1348   160  0.87  19.14   1.01     0.96       6208.73|
| 11:  2.1826 -  2.1145  1344   137  0.88  18.97   1.02     0.98       5586.61|
| 12:  2.1145 -  2.0542  1334   146  0.87  20.07   1.01     1.00       5403.23|
| 13:  2.0542 -  2.0003   900   113  0.87  20.04   1.02     1.00       4485.20|
| 14:  2.0003 -  1.9516   224    18  0.87  19.18   1.01     0.98       3408.70|
|alpha:            min =        0.95 max =            1.03 mean =         0.99|
|beta:             min =     3408.70 max =        14408.32 mean =      8550.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.98 mean =        17.15|
|phase err.(test): min =        0.00 max =           87.94 mean =        16.40|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1343   r_free= 0.1806   ksol= 0.32   Bsol= 62.87   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.52,-1.05,-1.36,-0.00,-0.00,-0.00); trace/3= -1.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.302624                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1343   r_free= 0.1806   ksol= 0.32   Bsol= 62.87   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.52,-1.05,-1.36,-0.00,-0.00,-0.00); trace/3= -1.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.302624                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1022 -  4.6604 0.99   1479  167 0.0985 0.1275      5.3872      5.5864|
|  2:  4.6604 -  3.7173 0.99   1420  158 0.0918 0.1220       5.483        5.77|
|  3:  3.7173 -  3.2527 0.99   1381  145 0.1239 0.1879      5.5877      5.9891|
|  4:  3.2527 -  2.9578 0.98   1388  166 0.1586 0.1869      5.6271      5.7719|
|  5:  2.9578 -  2.7471 0.99   1372  146 0.1612 0.2008      5.4804      5.6078|
|  6:  2.7471 -  2.5860 0.99   1372  159 0.1523 0.2184      5.3778      5.5569|
|  7:  2.5860 -  2.4571 0.98   1363  138 0.1511 0.1973      5.3066      5.5204|
|  8:  2.4571 -  2.3505 0.98   1355  152 0.1523 0.2002      5.2467      5.4428|
|  9:  2.3505 -  2.2604 0.99   1350  154 0.1472 0.2154      5.1833      5.4154|
| 10:  2.2604 -  2.1826 0.99   1348  160 0.1433 0.1966      5.1476      5.3902|
| 11:  2.1826 -  2.1145 0.97   1344  137 0.1403 0.1982      5.0632      5.2809|
| 12:  2.1145 -  2.0542 0.98   1334  146 0.1428 0.2250      5.0225      5.2981|
| 13:  2.0542 -  2.0003 0.67    900  113 0.1466 0.1790      4.9377      5.0859|
| 14:  2.0003 -  1.9516 0.16    224   18 0.1413 0.1912      4.8204      5.0725|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1022 -  4.6604  1479   167  0.94   9.32   0.96     0.94       7416.23|
|  2:  4.6604 -  3.7173  1420   158  0.95   8.93   1.01     0.99      10062.06|
|  3:  3.7173 -  3.2527  1381   145  0.91  13.94   1.03     1.02      12992.39|
|  4:  3.2527 -  2.9578  1388   166  0.88  18.01   1.01     0.98      14404.50|
|  5:  2.9578 -  2.7471  1372   146  0.87  19.40   1.00     0.98      11356.17|
|  6:  2.7471 -  2.5860  1372   159  0.87  19.35   0.99     0.97       9700.31|
|  7:  2.5860 -  2.4571  1363   138  0.88  18.18   0.99     0.96       7977.23|
|  8:  2.4571 -  2.3505  1355   152  0.87  19.69   1.00     0.96       7822.44|
|  9:  2.3505 -  2.2604  1350   154  0.87  19.41   0.99     0.95       6682.11|
| 10:  2.2604 -  2.1826  1348   160  0.87  19.13   0.98     0.93       6217.61|
| 11:  2.1826 -  2.1145  1344   137  0.88  18.96   0.98     0.95       5590.30|
| 12:  2.1145 -  2.0542  1334   146  0.87  20.07   0.98     0.97       5414.54|
| 13:  2.0542 -  2.0003   900   113  0.87  20.04   0.98     0.97       4488.61|
| 14:  2.0003 -  1.9516   224    18  0.87  19.18   0.97     0.94       3404.77|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     3404.77 max =        14404.50 mean =      8536.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.92 mean =        17.12|
|phase err.(test): min =        0.00 max =           88.18 mean =        16.37|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.018)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    123.94  18.12    None  None   None       |
|    all(noH): 2823   0      0.00    123.94  18.12    None  None   None       |
|    Sol.    : 438    0      5.19    114.54  46.39    None  None   None       |
|    Mac.    : 2385   0      0.00    123.94  12.93    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 -  12.397: 1586   |   5:    61.974 -  74.368:   64        |
|      1:    12.397 -  24.791:  715   |   6:    74.368 -  86.762:   33        |
|      2:    24.791 -  37.186:  157   |   7:    86.762 -  99.156:   21        |
|      3:    37.186 -  49.580:  131   |   8:    99.156 - 111.550:    7        |
|      4:    49.580 -  61.974:  106   |   9:   111.550 - 123.945:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 380         
Filter by distance & map next to the model:
   mapped sites are within: 0.074 - 5.818
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 357 from: 380
   mapped sites are within: 0.711 - 5.818

peak=    6.569 closest distance to " O   HOH Z 332 " =    0.960
peak=    5.817 closest distance to " NH2BARG A 102 " =    1.080
peak=    5.551 closest distance to " O   HOH Z 210 " =    1.428
peak=    5.395 closest distance to " O   HOH Z 111 " =    2.183
peak=    5.351 closest distance to " O   HOH Z  11 " =    1.369
peak=    5.062 closest distance to " O   HOH Z 124 " =    1.413
peak=    5.032 closest distance to " O   HOH Z 192 " =    1.516
peak=    5.018 closest distance to " CG  PRO A  54 " =    1.319
peak=    5.002 closest distance to " O   HOH Z  80 " =    2.179
peak=    4.998 closest distance to " CG  GLN A  77 " =    0.801
peak=    4.973 closest distance to " O   HOH Z 134 " =    1.948
peak=    4.921 closest distance to " O   HOH Z 127 " =    1.289
peak=    4.897 closest distance to " O   HOH Z 126 " =    2.001
peak=    4.867 closest distance to " O   HOH Z  49 " =    1.047
peak=    4.847 closest distance to " CB  GLN A 223 " =    1.565
peak=    4.779 closest distance to " CB  SER A  63 " =    1.382
peak=    4.761 closest distance to " CA  TYR A  30 " =    1.059
peak=    4.758 closest distance to " CG  PRO A 280 " =    0.989
peak=    4.725 closest distance to " CB  ARG A 275 " =    0.985
peak=    4.707 closest distance to " O   HOH Z  15 " =    2.067
peak=    4.650 closest distance to " CG  PRO A  90 " =    1.287
peak=    4.596 closest distance to " O   HOH Z 132 " =    1.641
peak=    4.553 closest distance to " O   HOH Z 207 " =    1.952
peak=    4.531 closest distance to " O   HOH Z 182 " =    1.185
peak=    4.530 closest distance to " CG  PRO A 213 " =    1.379
peak=    4.523 closest distance to " O   PRO A 198 " =    1.626
peak=    4.519 closest distance to " OG ASER A 164 " =    0.757
peak=    4.507 closest distance to " O   HOH Z 394 " =    1.528
peak=    4.469 closest distance to " O   HOH Z 411 " =    3.043
peak=    4.437 closest distance to " O   HOH Z 243 " =    1.107
peak=    4.434 closest distance to " O   HOH Z 234 " =    3.745
peak=    4.431 closest distance to " O   HOH Z 117 " =    1.047
peak=    4.415 closest distance to " CG  PRO A 198 " =    1.364
peak=    4.402 closest distance to " CB  LEU A 228 " =    1.162
peak=    4.385 closest distance to " CD BLYS A 290 " =    0.990
peak=    4.358 closest distance to " O   HOH Z 102 " =    1.123
peak=    4.349 closest distance to " O   HOH Z 221 " =    1.255
peak=    4.344 closest distance to " O   HOH Z 214 " =    1.551
peak=    4.316 closest distance to " O   HOH Z 211 " =    1.571
peak=    4.266 closest distance to " CA  GLN A 223 " =    0.897
peak=    4.260 closest distance to " O   HOH Z 260 " =    1.631
peak=    4.257 closest distance to " O   HOH Z 282 " =    1.605
peak=    4.241 closest distance to " CB  PRO A  54 " =    0.833
peak=    4.222 closest distance to " O   HOH Z 163 " =    1.828
peak=    4.197 closest distance to " O   HOH Z 363 " =    1.258
peak=    4.195 closest distance to " OD1 ASN A 217 " =    1.668
peak=    4.191 closest distance to " O   HOH Z 246 " =    1.485
peak=    4.186 closest distance to " O   HOH Z 433 " =    1.539
peak=    4.183 closest distance to " O   HOH Z 389 " =    1.869
peak=    4.168 closest distance to " O   HOH Z 120 " =    0.843
peak=    4.166 closest distance to " CG2 VAL A  78 " =    1.066
peak=    4.165 closest distance to " O   HOH Z 371 " =    3.115
peak=    4.147 closest distance to " CG2BVAL A  41 " =    1.107
peak=    4.135 closest distance to " CB  GLN A 183 " =    1.125
peak=    4.117 closest distance to " NE2 HIS A 115 " =    0.755
peak=    4.106 closest distance to " O   HOH Z 154 " =    1.459
peak=    4.092 closest distance to " O   HOH Z 232 " =    2.229
peak=    4.092 closest distance to " CB  PRO A 198 " =    1.054
peak=    4.088 closest distance to " CB  TRP A 179 " =    1.346
peak=    4.081 closest distance to " O   HOH Z 426 " =    1.212
peak=    4.060 closest distance to " O   HOH Z 261 " =    1.666
peak=    4.045 closest distance to " CG  PRO A 243 " =    1.102
peak=    4.043 closest distance to " CB  SER A  62 " =    0.753
peak=    4.025 closest distance to " O   HOH Z 369 " =    2.399
peak=    4.021 closest distance to " O   HOH Z 404 " =    1.495
peak=    4.018 closest distance to " CG1 VAL A 153 " =    1.132
peak=    3.987 closest distance to " CA  ALA A  21 " =    1.465
peak=    3.981 closest distance to " O   HOH Z 246 " =    1.919
peak=    3.973 closest distance to " O   HOH Z 133 " =    1.582
peak=    3.957 closest distance to " OE1 GLN A  11 " =    1.994
peak=    3.950 closest distance to " O   HOH Z  88 " =    3.730
peak=    3.950 closest distance to " CA  GLY A 196 " =    1.025
peak=    3.944 closest distance to " O   HOH Z  47 " =    1.693
peak=    3.932 closest distance to " O   HOH Z  63 " =    1.296
peak=    3.925 closest distance to " O   HOH Z 374 " =    2.559
peak=    3.924 closest distance to " O   HOH Z  43 " =    1.990
peak=    3.918 closest distance to " CB  ASN A 187 " =    1.113
peak=    3.914 closest distance to " CB  TYR A 169 " =    1.078
peak=    3.911 closest distance to " O   HOH Z 217 " =    1.472
peak=    3.910 closest distance to " O   HOH Z 186 " =    1.199
peak=    3.898 closest distance to " O   HOH Z 287 " =    1.925
peak=    3.896 closest distance to " O   HOH Z 104 " =    3.590
peak=    3.891 closest distance to " O   HOH Z 196 " =    1.566
peak=    3.882 closest distance to " O   HOH Z  39 " =    1.951
peak=    3.882 closest distance to " O   HOH Z 298 " =    1.830
peak=    3.878 closest distance to " C   SER A  32 " =    1.153
peak=    3.877 closest distance to " CB  VAL A 202 " =    1.521
peak=    3.865 closest distance to " O   HOH Z 200 " =    1.437
peak=    3.861 closest distance to " O   HOH Z 118 " =    2.017
peak=    3.853 closest distance to " O   HOH Z 112 " =    1.448
peak=    3.849 closest distance to " CB  GLU A 128 " =    1.018
peak=    3.846 closest distance to " CB  GLN A 194 " =    0.937
peak=    3.843 closest distance to " N   GLN A  55 " =    0.711
peak=    3.840 closest distance to " O   HOH Z 193 " =    1.857
peak=    3.839 closest distance to " O   HOH Z 437 " =    1.814
peak=    3.835 closest distance to " O   HOH Z 183 " =    1.640
peak=    3.834 closest distance to " N   ASN A  39 " =    1.201
peak=    3.828 closest distance to " O   HOH Z 184 " =    1.036
peak=    3.828 closest distance to " OE1 GLN A  58 " =    5.801
peak=    3.816 closest distance to " O   HOH Z 387 " =    2.457
peak=    3.813 closest distance to " O   HOH Z 142 " =    1.676
peak=    3.807 closest distance to " O   HOH Z  99 " =    2.555
peak=    3.807 closest distance to " O   HOH Z 189 " =    2.032
peak=    3.803 closest distance to " CD  LYS A 119 " =    1.203
peak=    3.800 closest distance to " CG1 ILE A  33 " =    1.248
peak=    3.798 closest distance to " O   HOH Z 350 " =    0.762
peak=    3.785 closest distance to " NZ  LYS A 117 " =    3.155
peak=    3.780 closest distance to " CA  GLU A 152 " =    0.893
peak=    3.776 closest distance to " O   HOH Z 108 " =    1.970
peak=    3.774 closest distance to " O   HOH Z 425 " =    1.644
peak=    3.765 closest distance to " OE1 GLN A  58 " =    1.242
peak=    3.761 closest distance to " O   HOH Z  47 " =    1.625
peak=    3.756 closest distance to " CD2 LEU A 255 " =    1.355
peak=    3.755 closest distance to " O   HOH Z 357 " =    2.006
peak=    3.751 closest distance to " CB  ASN A 217 " =    1.035
peak=    3.745 closest distance to " O   HOH Z 223 " =    1.161
peak=    3.744 closest distance to " O   HOH Z  44 " =    2.421
peak=    3.738 closest distance to " O   HOH Z  39 " =    1.777
peak=    3.733 closest distance to " O   HOH Z 215 " =    1.570
peak=    3.718 closest distance to " CG2 VAL A 197 " =    1.239
peak=    3.718 closest distance to " CB  TRP A 123 " =    1.321
peak=    3.711 closest distance to " CB  VAL A 265 " =    1.408
peak=    3.707 closest distance to " O   HOH Z 272 " =    1.962
peak=    3.704 closest distance to " O   HOH Z  68 " =    1.912
peak=    3.697 closest distance to " O   HOH Z 431 " =    1.208
peak=    3.694 closest distance to " O   HOH Z 406 " =    1.251
peak=    3.681 closest distance to " N   THR A  52 " =    1.069
peak=    3.676 closest distance to " O   HOH Z 326 " =    1.481
peak=    3.665 closest distance to " O   HOH Z 108 " =    1.786
peak=    3.661 closest distance to " CB  ALA A 100 " =    1.470
peak=    3.658 closest distance to " CD  ARG A 269 " =    0.902
peak=    3.658 closest distance to " NZ  LYS A 193 " =    1.558
peak=    3.650 closest distance to " CB  GLN A  58 " =    1.029
peak=    3.648 closest distance to " CB  GLU A 277 " =    0.885
peak=    3.647 closest distance to " CB  SER A  26 " =    0.911
peak=    3.645 closest distance to " OD2 ASP A 286 " =    2.970
peak=    3.642 closest distance to " O   THR A 251 " =    1.328
peak=    3.621 closest distance to " O   SER A  87 " =    2.212
peak=    3.617 closest distance to " CG2 THR A 221 " =    1.092
peak=    3.617 closest distance to " CA  ARG A 195 " =    1.178
peak=    3.614 closest distance to " CZ  PHE A 218 " =    1.177
peak=    3.609 closest distance to " CB  GLN A  73 " =    0.903
peak=    3.608 closest distance to " CA  GLU A 152 " =    1.454
peak=    3.606 closest distance to " CB  GLU A 152 " =    1.264
peak=    3.603 closest distance to " O   HOH Z 316 " =    2.978
peak=    3.602 closest distance to " O   HOH Z 132 " =    2.331
peak=    3.602 closest distance to " CD1 TRP A 274 " =    1.149
peak=    3.599 closest distance to " O   HOH Z  78 " =    2.127
peak=    3.596 closest distance to " O   HOH Z 150 " =    3.319
peak=    3.595 closest distance to " CB  PRO A  90 " =    1.182
peak=    3.587 closest distance to " CB  PHE A  16 " =    1.302
peak=    3.584 closest distance to " O   HOH Z  93 " =    2.657
peak=    3.583 closest distance to " CZ  PHE A 192 " =    0.945
peak=    3.582 closest distance to " CG  GLN A  11 " =    1.554
peak=    3.576 closest distance to " NE2 HIS A 115 " =    0.798
peak=    3.568 closest distance to " O   HOH Z 427 " =    3.433
peak=    3.567 closest distance to " CB  ASP A 140 " =    0.730
peak=    3.565 closest distance to " CG2 THR A  42 " =    0.956
peak=    3.564 closest distance to " O   HOH Z 227 " =    1.945
peak=    3.563 closest distance to " O   HOH Z 119 " =    2.223
peak=    3.562 closest distance to " O   HOH Z 132 " =    1.704
peak=    3.557 closest distance to " CD1 LEU A 300 " =    1.209
peak=    3.556 closest distance to " NH2BARG A 145 " =    1.925
peak=    3.554 closest distance to " O   HOH Z 203 " =    1.871
peak=    3.552 closest distance to " OD1 ASP A 238 " =    0.914
peak=    3.548 closest distance to " CA  SER A  87 " =    0.794
peak=    3.535 closest distance to " O   HOH Z 345 " =    3.235
peak=    3.532 closest distance to " NH2 ARG A 156 " =    1.231
peak=    3.527 closest distance to " O   HOH Z  22 " =    2.097
peak=    3.522 closest distance to " ND1 HIS A  81 " =    1.230
peak=    3.521 closest distance to " CB  TRP A 266 " =    1.024
peak=    3.513 closest distance to " O   HOH Z 327 " =    2.529
peak=    3.509 closest distance to " CD1 TRP A 266 " =    1.047
peak=    3.509 closest distance to " CB  ALA A  71 " =    1.384
peak=    3.503 closest distance to " NH1AARG A 145 " =    1.058
peak=    3.503 closest distance to " O   HOH Z  19 " =    2.059
peak=    3.495 closest distance to " CB  MET A  47 " =    1.037
peak=    3.493 closest distance to " O   HOH Z 395 " =    1.408
peak=    3.492 closest distance to " O   HOH Z  97 " =    1.856
peak=    3.482 closest distance to " CB  GLN A  88 " =    1.267
peak=    3.480 closest distance to " O   HOH Z 259 " =    1.634
peak=    3.479 closest distance to " CA  VAL A  41 " =    0.902
peak=    3.475 closest distance to " O   HOH Z 278 " =    0.732
peak=    3.473 closest distance to " ND2 ASN A  45 " =    1.290
peak=    3.472 closest distance to " O   HOH Z 336 " =    2.575
peak=    3.468 closest distance to " O   HOH Z 418 " =    1.418
peak=    3.462 closest distance to " O   HOH Z 361 " =    2.914
peak=    3.461 closest distance to " CG AARG A 275 " =    0.957
peak=    3.458 closest distance to " N   TYR A  15 " =    0.772
peak=    3.454 closest distance to " CE  LYS A 119 " =    1.109
peak=    3.449 closest distance to " CD1 LEU A  96 " =    0.800
peak=    3.448 closest distance to " CA  ILE A  33 " =    1.554
peak=    3.447 closest distance to " CA  THR A 221 " =    0.963
peak=    3.445 closest distance to " CB  ALA A 242 " =    0.885
peak=    3.444 closest distance to " O   HOH Z 174 " =    2.003
peak=    3.438 closest distance to " O   HOH Z  30 " =    2.029
peak=    3.438 closest distance to " NH2AARG A 145 " =    0.948
peak=    3.438 closest distance to " CD  GLU A 152 " =    0.856
peak=    3.434 closest distance to " O   HOH Z 374 " =    1.114
peak=    3.428 closest distance to " CB  SER A 276 " =    0.717
peak=    3.428 closest distance to " O   HOH Z 172 " =    2.143
peak=    3.425 closest distance to " CD  ARG A 159 " =    0.802
peak=    3.421 closest distance to " CB  SER A 141 " =    0.927
peak=    3.414 closest distance to " O   HOH Z 214 " =    1.780
peak=    3.406 closest distance to " CA  LEU A 282 " =    1.211
peak=    3.403 closest distance to " CA  ALA A 100 " =    1.135
peak=    3.401 closest distance to " O   HOH Z 336 " =    1.629
peak=    3.400 closest distance to " O   MET A 105 " =    1.856
peak=    3.399 closest distance to " O   HOH Z 420 " =    5.818
peak=    3.395 closest distance to " O   SER A  26 " =    1.602
peak=    3.395 closest distance to " O   HOH Z  63 " =    2.148
peak=    3.394 closest distance to " NE BARG A 102 " =    1.380
peak=    3.392 closest distance to " O   HOH Z 368 " =    3.352
peak=    3.391 closest distance to " O   SER A 164 " =    1.212
peak=    3.387 closest distance to " O   HOH Z  44 " =    1.835
peak=    3.383 closest distance to " CB  ALA A 291 " =    1.378
peak=    3.382 closest distance to " CA  ALA A 295 " =    1.053
peak=    3.377 closest distance to " O   HOH Z 352 " =    1.234
peak=    3.376 closest distance to " CA  ASP A 191 " =    0.840
peak=    3.375 closest distance to " CB  LYS A  76 " =    0.833
peak=    3.367 closest distance to " N   ALA A 100 " =    0.933
peak=    3.365 closest distance to " NE AARG A 275 " =    1.594
peak=    3.364 closest distance to " CE3 TRP A  85 " =    0.935
peak=    3.363 closest distance to " NH2AARG A 145 " =    2.113
peak=    3.362 closest distance to " CA  ASP A 124 " =    0.779
peak=    3.362 closest distance to " CB  GLU A 175 " =    1.368
peak=    3.362 closest distance to " CD2 LEU A 297 " =    1.098
peak=    3.360 closest distance to " CE2 TYR A 186 " =    0.938
peak=    3.358 closest distance to " CB  ASN A 285 " =    0.850
peak=    3.358 closest distance to " O   HOH Z 344 " =    3.161
peak=    3.357 closest distance to " CD  ARG A  66 " =    2.648
peak=    3.348 closest distance to " O   HOH Z 150 " =    1.623
peak=    3.345 closest distance to " O   HOH Z  54 " =    1.746
peak=    3.341 closest distance to " O   HOH Z 358 " =    1.540
peak=    3.339 closest distance to " O   HOH Z 244 " =    1.653
peak=    3.335 closest distance to " OG  SER A  62 " =    3.295
peak=    3.335 closest distance to " N   PHE A 130 " =    1.355
peak=    3.332 closest distance to " CA  ARG A  36 " =    1.175
peak=    3.330 closest distance to " CB  MET A  40 " =    0.775
peak=    3.326 closest distance to " O   HOH Z 128 " =    2.166
peak=    3.322 closest distance to " CB  ALA A 244 " =    1.078
peak=    3.319 closest distance to " CB  SER A 216 " =    0.827
peak=    3.318 closest distance to " CD  GLU A 236 " =    1.157
peak=    3.316 closest distance to " O   VAL A  72 " =    3.433
peak=    3.315 closest distance to " O   HOH Z 109 " =    2.266
peak=    3.314 closest distance to " NH1 ARG A  56 " =    1.423
peak=    3.314 closest distance to " O   HOH Z 377 " =    1.546
peak=    3.309 closest distance to " C   VAL A 265 " =    1.179
peak=    3.303 closest distance to " CA  ARG A  66 " =    1.113
peak=    3.302 closest distance to " CB  GLN A 278 " =    1.140
peak=    3.290 closest distance to " O   HOH Z 155 " =    2.880
peak=    3.284 closest distance to " N   GLY A 111 " =    1.247
peak=    3.284 closest distance to " O   HOH Z 145 " =    1.958
peak=    3.282 closest distance to " O   SER A 164 " =    1.535
peak=    3.279 closest distance to " OG BSER A 164 " =    2.344
peak=    3.279 closest distance to " O   GLY A  91 " =    1.247
peak=    3.275 closest distance to " CB  ARG A 190 " =    1.802
peak=    3.274 closest distance to " O   HOH Z 155 " =    1.646
peak=    3.268 closest distance to " CG  LEU A 167 " =    1.018
peak=    3.268 closest distance to " CB  ALA A 256 " =    1.210
peak=    3.268 closest distance to " CB  SER A   3 " =    1.581
peak=    3.263 closest distance to " CA  VAL A 197 " =    1.142
peak=    3.261 closest distance to " O   VAL A  72 " =    1.197
peak=    3.259 closest distance to " O   HOH Z  14 " =    2.271
peak=    3.259 closest distance to " O   HOH Z 403 " =    1.825
peak=    3.258 closest distance to " O   HOH Z 240 " =    2.038
peak=    3.256 closest distance to " O   HOH Z 324 " =    1.604
peak=    3.254 closest distance to " O   HOH Z 410 " =    1.528
peak=    3.254 closest distance to " CB  ALA A 137 " =    1.156
peak=    3.252 closest distance to " CD  PRO A  54 " =    1.007
peak=    3.250 closest distance to " O   HOH Z 313 " =    2.341
peak=    3.249 closest distance to " O   HOH Z   4 " =    0.995
peak=    3.246 closest distance to " CG ALYS A 290 " =    1.167
peak=    3.245 closest distance to " O   HOH Z 432 " =    1.756
peak=    3.245 closest distance to " O   HOH Z  21 " =    1.922
peak=    3.243 closest distance to " O   HOH Z   6 " =    1.083
peak=    3.242 closest distance to " OG BSER A 258 " =    3.180
peak=    3.242 closest distance to " CA  GLN A  88 " =    1.377
peak=    3.241 closest distance to " O   HOH Z 270 " =    1.507
peak=    3.241 closest distance to " CB  ILE A 120 " =    1.300
peak=    3.241 closest distance to " O   GLY A 211 " =    1.149
peak=    3.241 closest distance to " CA  ARG A 156 " =    1.050
peak=    3.237 closest distance to " O   HOH Z 136 " =    1.126
peak=    3.237 closest distance to " CA  LEU A  83 " =    1.615
peak=    3.235 closest distance to " N   VAL A 296 " =    1.621
peak=    3.235 closest distance to " CD  LYS A 166 " =    1.481
peak=    3.233 closest distance to " O   HOH Z 355 " =    1.730
peak=    3.227 closest distance to " N   ASN A 252 " =    1.134
peak=    3.227 closest distance to " NE  ARG A 156 " =    1.102
peak=    3.222 closest distance to " O   HOH Z   1 " =    2.810
peak=    3.218 closest distance to " CB  ASN A 148 " =    2.036
peak=    3.215 closest distance to " O   HOH Z 368 " =    1.912
peak=    3.214 closest distance to " O   HOH Z 301 " =    1.449
peak=    3.212 closest distance to " O   HOH Z  54 " =    2.292
peak=    3.208 closest distance to " CA  GLY A  80 " =    1.091
peak=    3.207 closest distance to " CD  ARG A 219 " =    0.924
peak=    3.206 closest distance to " CG1 VAL A 174 " =    1.267
peak=    3.205 closest distance to " NE2 GLN A 278 " =    2.449
peak=    3.201 closest distance to " O   HOH Z 156 " =    2.573
peak=    3.198 closest distance to " O   HOH Z  20 " =    4.039
peak=    3.197 closest distance to " O   HOH Z 281 " =    3.932
peak=    3.195 closest distance to " CE3 TRP A 274 " =    3.644
peak=    3.194 closest distance to " CA  ALA A 158 " =    1.071
peak=    3.193 closest distance to " CB  GLN A 103 " =    0.837
peak=    3.192 closest distance to " CB  GLU A 277 " =    3.762
peak=    3.191 closest distance to " CG1 VAL A 250 " =    2.027
peak=    3.190 closest distance to " CB  LEU A 167 " =    1.176
peak=    3.185 closest distance to " CA  ASP A 149 " =    1.512
peak=    3.184 closest distance to " O   HOH Z 327 " =    1.613
peak=    3.183 closest distance to " O   HOH Z 379 " =    3.351
peak=    3.181 closest distance to " CA  ASP A 162 " =    1.184
peak=    3.180 closest distance to " CB  ALA A 114 " =    1.011
peak=    3.178 closest distance to " O   HOH Z 185 " =    1.867
peak=    3.177 closest distance to " CG2 THR A 220 " =    0.712
peak=    3.177 closest distance to " O   HOH Z 135 " =    2.019
peak=    3.177 closest distance to " O   HOH Z 174 " =    1.332
peak=    3.176 closest distance to " O   HOH Z 419 " =    2.958
peak=    3.172 closest distance to " CB  TYR A 116 " =    1.401
peak=    3.170 closest distance to " O   HOH Z  87 " =    2.415
peak=    3.170 closest distance to " O   HOH Z 409 " =    2.896
peak=    3.168 closest distance to " OG  SER A  97 " =    3.422
peak=    3.165 closest distance to " O   HOH Z 194 " =    1.771
peak=    3.165 closest distance to " O   HOH Z  94 " =    1.799
peak=    3.162 closest distance to " CA  LYS A  48 " =    1.378
peak=    3.158 closest distance to " CB  ARG A  56 " =    1.051
peak=    3.158 closest distance to " O   HOH Z  20 " =    2.104
peak=    3.153 closest distance to " CD  PRO A 280 " =    0.866
peak=    3.150 closest distance to " CG  ASP A 231 " =    0.957
peak=    3.148 closest distance to " CA  VAL A 112 " =    1.194
peak=    3.145 closest distance to " NZ  LYS A 119 " =    1.431
peak=    3.140 closest distance to " NH1BARG A 145 " =    1.715
peak=    3.138 closest distance to " O   HOH Z 424 " =    2.846
peak=    3.136 closest distance to " NH2BARG A 145 " =    1.658
peak=    3.136 closest distance to " CD2 PHE A  59 " =    1.861
peak=    3.133 closest distance to " CB  ASN A 215 " =    1.146
peak=    3.131 closest distance to " CA  ALA A 248 " =    1.284
peak=    3.129 closest distance to " CA  ALA A 160 " =    0.977
peak=    3.128 closest distance to " O   HOH Z 422 " =    0.841
peak=    3.127 closest distance to " NZ  LYS A 181 " =    0.869
peak=    3.127 closest distance to " O   HOH Z 197 " =    2.089
peak=    3.122 closest distance to " O   HOH Z 162 " =    1.786
peak=    3.110 closest distance to " O   HOH Z 426 " =    3.161
peak=    3.109 closest distance to " O   HOH Z 139 " =    4.483
peak=    3.097 closest distance to " CB  PRO A  90 " =    1.139
peak=    3.096 closest distance to " O   HOH Z 117 " =    1.880
peak=    3.079 closest distance to " CG2 ILE A 106 " =    0.984
peak=    3.069 closest distance to " CA  ALA A  43 " =    1.204
peak=    3.067 closest distance to " O   HOH Z 152 " =    1.450
peak=    3.066 closest distance to " CA  THR A 182 " =    1.001
peak=    3.057 closest distance to " O   HOH Z 261 " =    1.773
peak=    3.051 closest distance to " O   HOH Z 173 " =    1.908
peak=    3.041 closest distance to " CB  LEU A 261 " =    1.287
peak=    3.017 closest distance to " O   HOH Z 361 " =    2.954
peak=    3.007 closest distance to " SD  MET A 185 " =    1.649
peak=    3.006 closest distance to " ND2 ASN A  45 " =    3.905
peak=    3.005 closest distance to " O   HOH Z 234 " =    2.113
peak=    3.004 closest distance to " O   HOH Z  50 " =    3.487

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 220         
Filter by distance & map next to the model:
   mapped sites are within: 0.555 - 5.386
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 219 from: 220
   mapped sites are within: 0.702 - 5.386

peak=   -4.234 closest distance to " NH2 ARG A  66 " =    1.400
peak=   -4.222 closest distance to " CE  MET A  93 " =    1.164
peak=   -4.178 closest distance to " N   ALA A  43 " =    2.501
peak=   -4.163 closest distance to " O   HOH Z 184 " =    1.339
peak=   -4.149 closest distance to " O   HOH Z 109 " =    3.543
peak=   -4.145 closest distance to " O   HOH Z 266 " =    4.368
peak=   -4.101 closest distance to " O   HOH Z 221 " =    1.157
peak=   -4.092 closest distance to " O   HOH Z 166 " =    1.848
peak=   -4.090 closest distance to " C   ASN A 285 " =    2.581
peak=   -4.081 closest distance to " O   HOH Z  52 " =    2.047
peak=   -3.994 closest distance to " O   HOH Z  13 " =    1.366
peak=   -3.971 closest distance to " O   HOH Z 290 " =    1.032
peak=   -3.943 closest distance to " O   HOH Z  71 " =    1.153
peak=   -3.934 closest distance to " CD1 PHE A  59 " =    1.794
peak=   -3.915 closest distance to " OG ASER A 134 " =    1.173
peak=   -3.914 closest distance to " CG  GLN A  58 " =    1.121
peak=   -3.901 closest distance to " OG1 THR A  82 " =    1.891
peak=   -3.864 closest distance to " CD2 PHE A  59 " =    2.410
peak=   -3.862 closest distance to " OG  SER A  97 " =    2.268
peak=   -3.856 closest distance to " O   HOH Z 151 " =    1.478
peak=   -3.843 closest distance to " O   HOH Z 231 " =    1.886
peak=   -3.836 closest distance to " O   HOH Z  17 " =    1.071
peak=   -3.835 closest distance to " CA  VAL A 197 " =    0.892
peak=   -3.833 closest distance to " N   GLN A  58 " =    1.504
peak=   -3.827 closest distance to " O   HOH Z 221 " =    1.743
peak=   -3.808 closest distance to " O   GLY A 118 " =    2.120
peak=   -3.779 closest distance to " CB  LEU A 167 " =    2.142
peak=   -3.773 closest distance to " O   HOH Z 118 " =    5.331
peak=   -3.770 closest distance to " CB  ALA A 161 " =    2.710
peak=   -3.768 closest distance to " N   ARG A 275 " =    1.057
peak=   -3.758 closest distance to " CB  GLN A  55 " =    1.511
peak=   -3.747 closest distance to " O   HOH Z 210 " =    1.124
peak=   -3.738 closest distance to " CG2 ILE A  49 " =    2.611
peak=   -3.710 closest distance to " N   ARG A 275 " =    1.301
peak=   -3.707 closest distance to " C   ASN A 187 " =    1.882
peak=   -3.706 closest distance to " O   HOH Z 185 " =    2.426
peak=   -3.701 closest distance to " OD2 ASP A 171 " =    2.425
peak=   -3.696 closest distance to " OD2 ASP A  65 " =    1.821
peak=   -3.686 closest distance to " O   HOH Z 426 " =    1.998
peak=   -3.680 closest distance to " O   MET A 113 " =    1.060
peak=   -3.673 closest distance to " CG  ASP A 231 " =    0.901
peak=   -3.667 closest distance to " O   HOH Z  19 " =    1.733
peak=   -3.666 closest distance to " CB  ALA A 227 " =    2.329
peak=   -3.649 closest distance to " CE  MET A 105 " =    1.945
peak=   -3.642 closest distance to " CA  VAL A  67 " =    2.881
peak=   -3.640 closest distance to " NH2AARG A 275 " =    5.386
peak=   -3.637 closest distance to " CG  GLU A  53 " =    1.400
peak=   -3.625 closest distance to " CA  SER A 276 " =    1.364
peak=   -3.623 closest distance to " OG  SER A  63 " =    1.419
peak=   -3.620 closest distance to " CZ  ARG A  66 " =    0.791
peak=   -3.617 closest distance to " O   HOH Z  92 " =    1.136
peak=   -3.615 closest distance to " CD  GLN A  88 " =    0.863
peak=   -3.614 closest distance to " O   HOH Z  86 " =    2.638
peak=   -3.606 closest distance to " O   HOH Z 274 " =    2.773
peak=   -3.600 closest distance to " OG ASER A 216 " =    1.135
peak=   -3.587 closest distance to " OH  TYR A 169 " =    1.031
peak=   -3.586 closest distance to " C   LEU A 101 " =    0.897
peak=   -3.581 closest distance to " CB  ASP A  50 " =    2.573
peak=   -3.577 closest distance to " CD1 TYR A 247 " =    2.392
peak=   -3.575 closest distance to " O   HOH Z 388 " =    1.828
peak=   -3.573 closest distance to " CG  MET A 105 " =    0.949
peak=   -3.567 closest distance to " O   HOH Z 418 " =    1.602
peak=   -3.563 closest distance to " N   ALA A 226 " =    2.134
peak=   -3.559 closest distance to " OG  SER A  32 " =    0.994
peak=   -3.557 closest distance to " C   HIS A 108 " =    1.011
peak=   -3.555 closest distance to " O   HOH Z 396 " =    1.441
peak=   -3.554 closest distance to " O   HOH Z 377 " =    1.609
peak=   -3.554 closest distance to " CA  GLY A  23 " =    2.273
peak=   -3.551 closest distance to " O   HOH Z 380 " =    4.475
peak=   -3.539 closest distance to " CD2 HIS A 115 " =    1.178
peak=   -3.535 closest distance to " CD2 LEU A 237 " =    2.386
peak=   -3.533 closest distance to " O   HOH Z 139 " =    4.633
peak=   -3.533 closest distance to " CD  ARG A  14 " =    3.241
peak=   -3.528 closest distance to " O   HOH Z 292 " =    1.659
peak=   -3.527 closest distance to " CG2 THR A 221 " =    2.184
peak=   -3.524 closest distance to " O   HOH Z  11 " =    1.514
peak=   -3.521 closest distance to " O   HOH Z 325 " =    1.841
peak=   -3.514 closest distance to " O   HOH Z  38 " =    1.125
peak=   -3.495 closest distance to " O   HOH Z 222 " =    1.365
peak=   -3.492 closest distance to " CD  PRO A 198 " =    1.139
peak=   -3.488 closest distance to " O   HOH Z 134 " =    1.981
peak=   -3.487 closest distance to " O   HOH Z 243 " =    1.838
peak=   -3.487 closest distance to " O   GLY A 196 " =    1.195
peak=   -3.477 closest distance to " OD2 ASP A 171 " =    1.732
peak=   -3.474 closest distance to " O   HOH Z 407 " =    0.776
peak=   -3.473 closest distance to " CD2 TRP A 274 " =    2.328
peak=   -3.468 closest distance to " O   HOH Z 166 " =    1.947
peak=   -3.467 closest distance to " CA  SER A 164 " =    2.001
peak=   -3.465 closest distance to " CA  VAL A 232 " =    2.438
peak=   -3.462 closest distance to " CA  GLY A 133 " =    1.818
peak=   -3.459 closest distance to " O   HOH Z 423 " =    2.139
peak=   -3.456 closest distance to " O   PRO A 198 " =    1.309
peak=   -3.441 closest distance to " O   HOH Z  10 " =    1.332
peak=   -3.439 closest distance to " O   ASN A 170 " =    0.959
peak=   -3.428 closest distance to " O   HOH Z 369 " =    2.281
peak=   -3.426 closest distance to " O   HOH Z  94 " =    2.124
peak=   -3.425 closest distance to " O   ALA A 256 " =    1.492
peak=   -3.420 closest distance to " O   HOH Z 213 " =    1.468
peak=   -3.419 closest distance to " O   HOH Z 236 " =    1.826
peak=   -3.405 closest distance to " C   SER A 271 " =    1.187
peak=   -3.400 closest distance to " O   VAL A  67 " =    2.861
peak=   -3.399 closest distance to " O   HOH Z 385 " =    4.114
peak=   -3.397 closest distance to " O   HOH Z  91 " =    2.271
peak=   -3.394 closest distance to " O   HOH Z 103 " =    1.938
peak=   -3.393 closest distance to " O   HOH Z 177 " =    1.437
peak=   -3.383 closest distance to " CA  GLY A 133 " =    2.327
peak=   -3.378 closest distance to " OE1 GLN A  88 " =    1.104
peak=   -3.377 closest distance to " O   ASN A 285 " =    2.565
peak=   -3.373 closest distance to " CG  LEU A 101 " =    2.541
peak=   -3.373 closest distance to " O   HOH Z 150 " =    1.880
peak=   -3.370 closest distance to " CA  ASP A 286 " =    2.127
peak=   -3.361 closest distance to " O   HOH Z 414 " =    1.541
peak=   -3.360 closest distance to " O   GLN A  11 " =    1.314
peak=   -3.349 closest distance to " OD1 ASN A 148 " =    1.686
peak=   -3.349 closest distance to " O   HOH Z  97 " =    1.771
peak=   -3.332 closest distance to " O   HOH Z 308 " =    1.467
peak=   -3.332 closest distance to " CG  ARG A 219 " =    2.246
peak=   -3.331 closest distance to " O   HOH Z 367 " =    4.882
peak=   -3.329 closest distance to " CD1 LEU A  25 " =    2.504
peak=   -3.322 closest distance to " O   HOH Z 350 " =    1.440
peak=   -3.320 closest distance to " O   GLY A 211 " =    1.490
peak=   -3.316 closest distance to " O   HOH Z 259 " =    1.017
peak=   -3.315 closest distance to " CD  ARG A 139 " =    1.650
peak=   -3.314 closest distance to " O   HOH Z 198 " =    1.728
peak=   -3.312 closest distance to " O   HOH Z 430 " =    1.249
peak=   -3.311 closest distance to " CG2BVAL A  41 " =    2.091
peak=   -3.311 closest distance to " O   HOH Z  93 " =    1.674
peak=   -3.306 closest distance to " O   HOH Z 283 " =    1.818
peak=   -3.302 closest distance to " O   ALA A  34 " =    1.937
peak=   -3.302 closest distance to " OXT GLY A 302 " =    3.196
peak=   -3.300 closest distance to " O   HOH Z  37 " =    1.554
peak=   -3.300 closest distance to " O   HOH Z 280 " =    1.426
peak=   -3.296 closest distance to " O   HOH Z 215 " =    3.160
peak=   -3.292 closest distance to " CA  GLY A 241 " =    2.222
peak=   -3.289 closest distance to " CB  TYR A  15 " =    2.298
peak=   -3.288 closest distance to " CG  GLU A   2 " =    1.520
peak=   -3.287 closest distance to " O   VAL A 174 " =    1.991
peak=   -3.285 closest distance to " CD2 TYR A  68 " =    2.352
peak=   -3.279 closest distance to " CA  GLU A 277 " =    1.165
peak=   -3.279 closest distance to " O   ARG A 275 " =    2.229
peak=   -3.276 closest distance to " O   HOH Z  58 " =    1.164
peak=   -3.274 closest distance to " CA  ASN A 127 " =    1.087
peak=   -3.271 closest distance to " O   ARG A  66 " =    1.234
peak=   -3.270 closest distance to " CB  ALA A 291 " =    2.295
peak=   -3.267 closest distance to " NE1 TRP A 266 " =    2.272
peak=   -3.262 closest distance to " O   HOH Z 198 " =    2.177
peak=   -3.259 closest distance to " O   HOH Z 407 " =    1.746
peak=   -3.259 closest distance to " CB  ALA A  43 " =    2.495
peak=   -3.258 closest distance to " O   LEU A 300 " =    2.536
peak=   -3.246 closest distance to " ND2 ASN A  60 " =    1.494
peak=   -3.245 closest distance to " CD  GLN A  77 " =    1.275
peak=   -3.245 closest distance to " O   HOH Z 231 " =    1.515
peak=   -3.242 closest distance to " O   HOH Z 329 " =    2.891
peak=   -3.242 closest distance to " C   GLU A  46 " =    0.918
peak=   -3.240 closest distance to " N   LEU A 261 " =    1.327
peak=   -3.240 closest distance to " O  BHOH Z 338 " =    1.583
peak=   -3.237 closest distance to " N   THR A 235 " =    1.337
peak=   -3.237 closest distance to " O   HOH Z 100 " =    1.137
peak=   -3.230 closest distance to " O   TYR A  15 " =    1.307
peak=   -3.227 closest distance to " O   HOH Z 210 " =    0.708
peak=   -3.219 closest distance to " CD  GLU A 236 " =    0.964
peak=   -3.218 closest distance to " N   GLY A  17 " =    1.486
peak=   -3.210 closest distance to " O   HOH Z  33 " =    1.056
peak=   -3.209 closest distance to " O   HOH Z 409 " =    3.130
peak=   -3.209 closest distance to " CB  ALA A   9 " =    2.820
peak=   -3.207 closest distance to " O   HOH Z 243 " =    2.263
peak=   -3.205 closest distance to " O   LEU A 143 " =    1.344
peak=   -3.203 closest distance to " N   SER A 134 " =    1.248
peak=   -3.198 closest distance to " C   VAL A 265 " =    0.912
peak=   -3.197 closest distance to " OD1 ASP A 298 " =    1.976
peak=   -3.197 closest distance to " CE  MET A 105 " =    2.192
peak=   -3.196 closest distance to " O   HOH Z 368 " =    2.268
peak=   -3.196 closest distance to " O   HOH Z 384 " =    2.186
peak=   -3.195 closest distance to " O   ARG A  79 " =    0.702
peak=   -3.194 closest distance to " NH2 ARG A 156 " =    1.239
peak=   -3.192 closest distance to " O   ALA A  19 " =    2.055
peak=   -3.192 closest distance to " CA  ARG A  24 " =    1.405
peak=   -3.192 closest distance to " ND2 ASN A  60 " =    1.562
peak=   -3.190 closest distance to " C   THR A 279 " =    1.313
peak=   -3.186 closest distance to " CD  GLN A  88 " =    0.982
peak=   -3.185 closest distance to " O   HOH Z 378 " =    1.395
peak=   -3.181 closest distance to " O   HOH Z  90 " =    1.820
peak=   -3.178 closest distance to " NH2BARG A 145 " =    1.888
peak=   -3.174 closest distance to " O   HOH Z 402 " =    1.094
peak=   -3.173 closest distance to " CG2 THR A   4 " =    1.809
peak=   -3.172 closest distance to " SG ACYS A 201 " =    1.488
peak=   -3.169 closest distance to " NE2 GLN A  58 " =    0.808
peak=   -3.168 closest distance to " CH2 TRP A 177 " =    2.000
peak=   -3.167 closest distance to " O   HOH Z  43 " =    2.152
peak=   -3.167 closest distance to " NZ  LYS A 119 " =    1.466
peak=   -3.160 closest distance to " O   HOH Z 158 " =    1.451
peak=   -3.159 closest distance to " O   HOH Z  98 " =    1.503
peak=   -3.158 closest distance to " CD1 LEU A 101 " =    2.532
peak=   -3.155 closest distance to " CA  ASP A 298 " =    1.039
peak=   -3.153 closest distance to " O   HOH Z 117 " =    1.179
peak=   -3.152 closest distance to " CD1 TRP A 179 " =    0.945
peak=   -3.149 closest distance to " O   HOH Z 148 " =    3.020
peak=   -3.147 closest distance to " O   HOH Z 434 " =    1.413
peak=   -3.139 closest distance to " O   HOH Z 427 " =    1.347
peak=   -3.135 closest distance to " O   HOH Z  41 " =    1.891
peak=   -3.133 closest distance to " N   THR A 157 " =    1.728
peak=   -3.121 closest distance to " CG  LEU A  25 " =    0.856
peak=   -3.118 closest distance to " CD2 TYR A 293 " =    2.039
peak=   -3.113 closest distance to " CA  ARG A 139 " =    1.008
peak=   -3.113 closest distance to " O   HOH Z 423 " =    1.171
peak=   -3.098 closest distance to " CD  ARG A 156 " =    1.846
peak=   -3.095 closest distance to " O   VAL A 197 " =    1.166
peak=   -3.089 closest distance to " O   HOH Z 381 " =    1.576
peak=   -3.088 closest distance to " CG1 VAL A  78 " =    2.419
peak=   -3.084 closest distance to " CG  LYS A 193 " =    2.667
peak=   -3.080 closest distance to " CD1 LEU A 228 " =    2.534
peak=   -3.079 closest distance to " O   HOH Z 389 " =    1.859
peak=   -3.066 closest distance to " O   HOH Z 136 " =    1.558
peak=   -3.062 closest distance to " NE2 GLN A 223 " =    1.018
peak=   -3.062 closest distance to " N   ALA A  84 " =    2.433
peak=   -3.053 closest distance to " CG  GLN A  58 " =    1.497
peak=   -3.037 closest distance to " CB  ALA A 248 " =    2.027
peak=   -3.027 closest distance to " N   GLY A 241 " =    2.299
peak=   -3.020 closest distance to " CE3 TRP A 150 " =    1.078

================= 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    :  0.4879 0.4795   6.295120e+00   6.286222e+00
   1_bss:  0.4816 0.4743   6.293419e+00   6.277880e+00
   1_xyz:  0.4017 0.4378   6.179045e+00   6.233973e+00
   1_adp:  0.3722 0.4368   6.145366e+00   6.232928e+00
   1_occ:  0.3718 0.4374   6.144703e+00   6.233082e+00
   2_bss:  0.3713 0.4361   6.145127e+00   6.231925e+00
   2_xyz:  0.2932 0.3594   5.970298e+00   6.112490e+00
   2_adp:  0.2703 0.3492   5.924458e+00   6.099377e+00
   2_occ:  0.2702 0.3487   5.923856e+00   6.098633e+00
   3_bss:  0.2696 0.3480   5.922176e+00   6.096905e+00
   3_xyz:  0.2218 0.2855   5.739310e+00   5.943403e+00
   3_adp:  0.2042 0.2697   5.679120e+00   5.897043e+00
   3_occ:  0.2042 0.2697   5.678978e+00   5.896543e+00
   4_bss:  0.2043 0.2696   5.679273e+00   5.896367e+00
   4_xyz:  0.1635 0.2235   5.481611e+00   5.726140e+00
   4_adp:  0.1492 0.2014   5.395682e+00   5.627638e+00
   4_occ:  0.1490 0.2012   5.395333e+00   5.627285e+00
   5_bss:  0.1491 0.2007   5.398309e+00   5.627871e+00
   5_xyz:  0.1358 0.1847   5.313382e+00   5.542105e+00
   5_adp:  0.1347 0.1811   5.303954e+00   5.525032e+00
   5_occ:  0.1345 0.1809   5.303250e+00   5.524662e+00
   5_bss:  0.1343 0.1806   5.302624e+00   5.524239e+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:  0.278  20.613  -0.368   2.333   0.840   0.000   0.000   0.000
   1_xyz:  0.278  20.613  -0.368   2.333   0.840   0.000   0.000   0.000
   1_adp:  0.278  20.613  -0.368   2.333   0.840   0.000   0.000   0.000
   1_occ:  0.278  20.613  -0.368   2.333   0.840   0.000   0.000   0.000
   2_bss:  0.348  80.000   0.679   2.695   1.658   0.000   0.000   0.000
   2_xyz:  0.348  80.000   0.679   2.695   1.658   0.000   0.000   0.000
   2_adp:  0.348  80.000   0.679   2.695   1.658   0.000   0.000   0.000
   2_occ:  0.348  80.000   0.679   2.695   1.658   0.000   0.000   0.000
   3_bss:  0.334  68.113   0.248   1.240   0.454   0.000   0.000   0.000
   3_xyz:  0.334  68.113   0.248   1.240   0.454   0.000   0.000   0.000
   3_adp:  0.334  68.113   0.248   1.240   0.454   0.000   0.000   0.000
   3_occ:  0.334  68.113   0.248   1.240   0.454   0.000   0.000   0.000
   4_bss:  0.331  74.644  -0.430   0.508  -0.331   0.000  -0.000  -0.000
   4_xyz:  0.331  74.644  -0.430   0.508  -0.331   0.000  -0.000  -0.000
   4_adp:  0.331  74.644  -0.430   0.508  -0.331   0.000  -0.000  -0.000
   4_occ:  0.331  74.644  -0.430   0.508  -0.331   0.000  -0.000  -0.000
   5_bss:  0.331  66.847  -0.958  -0.323  -0.831  -0.000  -0.000  -0.000
   5_xyz:  0.331  66.847  -0.958  -0.323  -0.831  -0.000  -0.000  -0.000
   5_adp:  0.331  66.847  -0.958  -0.323  -0.831  -0.000  -0.000  -0.000
   5_occ:  0.331  66.847  -0.958  -0.323  -0.831  -0.000  -0.000  -0.000
   5_bss:  0.323  62.870  -1.519  -1.049  -1.362  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  63.332 0.3487  0.4668    76675.937
   1_bss:  62.330 0.3601  0.4997    73731.247
   1_xyz:  52.848 0.4820  0.6720    58142.251
   1_adp:  53.039 0.4792  0.6546    58070.382
   1_occ:  53.060 0.4790  0.6532    58128.050
   2_bss:  52.918 0.4807  0.6736    57801.249
   2_xyz:  40.214 0.6383  0.8842    37239.770
   2_adp:  38.849 0.6546  0.9022    35412.596
   2_occ:  38.823 0.6549  0.9019    35354.110
   3_bss:  38.655 0.6567  0.8722    35094.196
   3_xyz:  30.245 0.7532  0.9562    22320.725
   3_adp:  27.966 0.7787  0.9568    19742.290
   3_occ:  27.963 0.7787  0.9568    19731.928
   4_bss:  27.920 0.7792  0.9335    19716.299
   4_xyz:  22.462 0.8353  0.9777    13030.758
   4_adp:  19.595 0.8647  0.9880    10632.471
   4_occ:  19.597 0.8647  0.9879    10633.504
   5_bss:  19.614 0.8647  0.9672    10678.379
   5_xyz:  17.520 0.8844  0.9752     8801.454
   5_adp:  17.082 0.8888  0.9867     8554.545
   5_occ:  17.072 0.8889  0.9867     8551.213
   5_bss:  17.049 0.8890  0.9666     8537.334
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   2.0015e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   2.0015e-01
   1_xyz:   1.543  0.012  0.096 15.955  0.006  4.109   1.3440e-01
   1_adp:   1.543  0.012  0.096 15.955  0.006  4.109   1.3440e-01
   1_occ:   1.543  0.012  0.096 15.955  0.006  4.109   1.3440e-01
   2_bss:   1.543  0.012  0.096 15.955  0.006  4.109   1.3440e-01
   2_xyz:   1.503  0.011  0.094 15.293  0.007  4.120   1.1640e-01
   2_adp:   1.503  0.011  0.094 15.293  0.007  4.120   1.1640e-01
   2_occ:   1.503  0.011  0.094 15.293  0.007  4.120   1.1640e-01
   3_bss:   1.503  0.011  0.094 15.293  0.007  4.120   1.1640e-01
   3_xyz:   1.049  0.009  0.069 14.329  0.004  4.113   7.0012e-02
   3_adp:   1.049  0.009  0.069 14.329  0.004  4.113   7.0012e-02
   3_occ:   1.049  0.009  0.069 14.329  0.004  4.113   7.0012e-02
   4_bss:   1.049  0.009  0.069 14.329  0.004  4.113   7.0012e-02
   4_xyz:   1.226  0.009  0.082 14.450  0.005  4.126   8.0028e-02
   4_adp:   1.226  0.009  0.082 14.450  0.005  4.126   8.0028e-02
   4_occ:   1.226  0.009  0.082 14.450  0.005  4.126   8.0028e-02
   5_bss:   1.226  0.009  0.082 14.450  0.005  4.126   8.0028e-02
   5_xyz:   1.028  0.007  0.071 14.339  0.004  4.132   5.9864e-02
   5_adp:   1.028  0.007  0.071 14.339  0.004  4.132   5.9864e-02
   5_occ:   1.028  0.007  0.071 14.339  0.004  4.132   5.9864e-02
   5_bss:   1.028  0.007  0.071 14.339  0.004  4.132   5.9864e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.386   2.4371e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.386   2.4371e-01
   1_xyz:   9.043  0.083  0.334 86.878  0.031  1.841   1.0935e-01
   1_adp:   9.043  0.083  0.334 86.878  0.031  1.841   1.0935e-01
   1_occ:   9.043  0.083  0.334 86.878  0.031  1.841   1.0935e-01
   2_bss:   9.043  0.083  0.334 86.878  0.031  1.841   1.0935e-01
   2_xyz:   8.993  0.060  0.262 77.701  0.037  2.141   8.2556e-02
   2_adp:   8.993  0.060  0.262 77.701  0.037  2.141   8.2556e-02
   2_occ:   8.993  0.060  0.262 77.701  0.037  2.141   8.2556e-02
   3_bss:   8.993  0.060  0.262 77.701  0.037  2.141   8.2556e-02
   3_xyz:   7.766  0.066  0.210 73.873  0.024  2.358   1.3495e-01
   3_adp:   7.766  0.066  0.210 73.873  0.024  2.358   1.3495e-01
   3_occ:   7.766  0.066  0.210 73.873  0.024  2.358   1.3495e-01
   4_bss:   7.766  0.066  0.210 73.873  0.024  2.358   1.3495e-01
   4_xyz:   7.750  0.072  0.322 80.741  0.036  2.235   5.6696e-02
   4_adp:   7.750  0.072  0.322 80.741  0.036  2.235   5.6696e-02
   4_occ:   7.750  0.072  0.322 80.741  0.036  2.235   5.6696e-02
   5_bss:   7.750  0.072  0.322 80.741  0.036  2.235   5.6696e-02
   5_xyz:   8.242  0.047  0.256 79.843  0.035  2.319   4.0092e-02
   5_adp:   8.242  0.047  0.256 79.843  0.035  2.319   4.0092e-02
   5_occ:   8.242  0.047  0.256 79.843  0.035  2.319   4.0092e-02
   5_bss:   8.242  0.047  0.256 79.843  0.035  2.319   4.0092e-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: 113.33   0.00  17.26 113.33   0.00  13.75  71.81   0.00  36.38
   1_occ: 113.33   0.00  17.26 113.33   0.00  13.75  71.81   0.00  36.38
   2_bss: 113.33   0.00  17.26 113.33   0.00  13.75  71.81   0.00  36.38
   2_xyz: 113.33   0.00  17.26 113.33   0.00  13.75  71.81   0.00  36.38
   2_adp: 100.42   0.00  19.02  80.71   0.00  14.82 100.42   0.00  41.91
   2_occ: 100.42   0.00  19.02  80.71   0.00  14.82 100.42   0.00  41.91
   3_bss: 100.42   0.00  19.02  80.71   0.00  14.82 100.42   0.00  41.91
   3_xyz: 100.42   0.00  19.02  80.71   0.00  14.82 100.42   0.00  41.91
   3_adp: 130.53   0.00  19.87 130.53   0.00  14.33 126.40   3.91  50.04
   3_occ: 130.53   0.00  19.87 130.53   0.00  14.33 126.40   3.91  50.04
   4_bss: 130.53   0.00  19.87 130.53   0.00  14.33 126.40   3.91  50.04
   4_xyz: 130.53   0.00  19.87 130.53   0.00  14.33 126.40   3.91  50.04
   4_adp: 124.75   0.00  18.10 124.75   0.00  12.80 115.40   3.92  46.96
   4_occ: 124.75   0.00  18.10 124.75   0.00  12.80 115.40   3.92  46.96
   5_bss: 124.75   0.00  18.10 124.75   0.00  12.80 115.40   3.92  46.96
   5_xyz: 124.75   0.00  18.10 124.75   0.00  12.80 115.40   3.92  46.96
   5_adp: 123.94   0.00  18.12 123.94   0.00  12.93 114.53   5.19  46.39
   5_occ: 123.94   0.00  18.12 123.94   0.00  12.93 114.53   5.19  46.39
   5_bss: 123.94   0.00  18.12 123.94   0.00  12.93 114.54   5.19  46.39
------------------------------------------------------------------------
 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:    2.534    0.016    0.334
   1_adp:    2.534    0.016    0.334
   1_occ:    2.534    0.016    0.334
   2_bss:    2.534    0.016    0.334
   2_xyz:    2.303    0.034    0.594
   2_adp:    2.303    0.034    0.594
   2_occ:    2.303    0.034    0.594
   3_bss:    2.303    0.034    0.594
   3_xyz:    2.254    0.056    0.718
   3_adp:    2.254    0.056    0.718
   3_occ:    2.254    0.056    0.718
   4_bss:    2.254    0.056    0.718
   4_xyz:    2.192    0.044    0.826
   4_adp:    2.192    0.044    0.826
   4_occ:    2.192    0.044    0.826
   5_bss:    2.192    0.044    0.826
   5_xyz:    2.076    0.102    0.864
   5_adp:    2.076    0.102    0.864
   5_occ:    2.076    0.102    0.864
   5_bss:    2.076    0.102    0.864
------------------------------------------------------------------------

CPU time actual refinement: 371.19


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1188/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_1188/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1188/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1188/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1188/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 371.05 
  Macro-tasks:
    bulk solvent and scale       = 49.57  
    individual site refinement   = 152.10 
    weights calculation          = 30.71  
    collect and process          = 6.37   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 238.86 
  Micro-tasks:
    mask                            = 2.54   
    f_calc                          = 120.80 
    alpha_beta                      = 8.29   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 127.82 
    fmodel                         = 7.98   
    r_factors                      = 0.29   
    phase_errors                   = 9.84   
    foms                           = 0.21   
    TOTAL for micro-tasks          = 278.91 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.312 micro seconds
Total CPU time: 6.41 minutes
from_scatterers_fft:    628 calls, 120.51 s
gradients_fft:          573 calls, 115.46 s

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

# Date 2008-01-16 Time 06:38:42 PST -0800 (1200494322.77 s)
Start R-work = 0.4879, R-free = 0.4795 (no bulk solvent and anisotropic scale)
Final R-work = 0.1521, R-free = 0.1992 (no bulk solvent and anisotropic scale)

Start R-work = 0.4816, R-free = 0.4743
Final R-work = 0.1343, R-free = 0.1806