# Date 2008-01-16 Time 04:09:58 PST -0800 (1200485398.47 s)
#phil __OFF__

Command line arguments: "../207.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25768
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 207

-------------------------------------------------------------------------------
  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: (68.845, 47.3993, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.31, 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: (68.845, 47.3993, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8927 1.96092
Completeness in resolution range: 0.921835
Completeness with d_max=infinity: 0.919067

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8927
                             d_min =   1.9609

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: (68.845, 47.3993, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8927 1.96092
Completeness in resolution range: 0.921835
Completeness with d_max=infinity: 0.919067

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8931 -  4.1961 [2227/2255]  2002   225  10.1%
  bin  2:  4.1961 -  3.3430 [2148/2171]  1931   217  10.1%
  bin  3:  3.3430 -  2.9240 [2114/2139]  1911   203   9.6%
  bin  4:  2.9240 -  2.6584 [2096/2112]  1878   218  10.4%
  bin  5:  2.6584 -  2.4687 [2073/2112]  1864   209  10.1%
  bin  6:  2.4687 -  2.3238 [2069/2101]  1864   205   9.9%
  bin  7:  2.3238 -  2.2078 [2057/2094]  1857   200   9.7%
  bin  8:  2.2078 -  2.1119 [2084/2126]  1876   208  10.0%
  bin  9:  2.1119 -  2.0308 [2005/2065]  1810   195   9.7%
  bin 10:  2.0308 -  1.9609 [ 716/2075]   637    79  11.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_207/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.30 -     2.02: 14
        2.02 -     2.74: 242
        2.74 -     3.46: 4603
        3.46 -     4.18: 9349
        4.18 -     4.90: 14045
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.295 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.364 3.040 -x+1,y-1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.470 3.120 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.569 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.586 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28248 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_207/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_207/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 = 68.845 47.3993 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4343   r_free= 0.4338   ksol= 0.00   Bsol= 0.00   scale= 0.912    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.235114                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8931 -  4.6803 0.99   1448  160 0.3298 0.3468      6.4762      6.4903|
|  2:  4.6803 -  3.7341 0.99   1402  155 0.3563 0.3652      6.6905      6.7283|
|  3:  3.7341 -  3.2678 0.99   1364  154 0.4085 0.3863      6.6001      6.5839|
|  4:  3.2678 -  2.9716 0.99   1361  144 0.4263 0.4376      6.4382      6.4653|
|  5:  2.9716 -  2.7601 0.98   1339  152 0.4575 0.4324      6.3049      6.3202|
|  6:  2.7601 -  2.5982 0.99   1349  151 0.4617 0.5132      6.2312       6.164|
|  7:  2.5982 -  2.4687 0.99   1323  156 0.4633 0.4058      6.1759      6.0836|
|  8:  2.4687 -  2.3617 0.99   1353  140 0.4963 0.4833      6.1429      6.1232|
|  9:  2.3617 -  2.2711 0.99   1331  147 0.4986 0.4614      6.0976      6.1427|
| 10:  2.2711 -  2.1930 0.98   1324  146 0.4984 0.5086      6.0691      6.0505|
| 11:  2.1930 -  2.1246 0.98   1289  157 0.5016 0.5122      5.9963      5.9949|
| 12:  2.1246 -  2.0641 1.00   1350  140 0.5021 0.4916      5.9264       5.937|
| 13:  2.0641 -  2.0098 0.83   1123  119 0.4945 0.5333      5.8607      5.8531|
| 14:  2.0098 -  1.9609 0.21    274   38 0.4674 0.4605      5.8746      5.7013|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8931 -  4.6803  1448   160  0.74  30.74   0.84     0.75      57876.19|
|  2:  4.6803 -  3.7341  1402   155  0.75  30.80   0.94     0.84      84245.37|
|  3:  3.7341 -  3.2678  1364   154  0.66  38.69   0.92     0.83      89064.60|
|  4:  3.2678 -  2.9716  1361   144  0.58  45.75   0.92     0.76      80407.37|
|  5:  2.9716 -  2.7601  1339   152  0.51  51.09   0.91     0.69      65005.45|
|  6:  2.7601 -  2.5982  1349   151  0.49  52.67   0.92     0.66      57438.25|
|  7:  2.5982 -  2.4687  1323   156  0.51  51.54   0.92     0.67      50378.76|
|  8:  2.4687 -  2.3617  1353   140  0.49  52.51   0.94     0.70      44823.88|
|  9:  2.3617 -  2.2711  1331   147  0.51  51.55   0.92     0.73      41249.99|
| 10:  2.2711 -  2.1930  1324   146  0.49  53.20   0.93     0.68      38103.71|
| 11:  2.1930 -  2.1246  1289   157  0.42  58.53   0.94     0.64      41407.72|
| 12:  2.1246 -  2.0641  1350   140  0.35  63.89   0.96     0.56      40874.64|
| 13:  2.0641 -  2.0098  1123   119  0.33  65.40   0.93     0.54      37449.99|
| 14:  2.0098 -  1.9609   274    38  0.42  58.30   1.02     0.54      27723.20|
|alpha:            min =        0.54 max =            0.84 mean =         0.70|
|beta:             min =    27723.20 max =        89064.60 mean =     56053.34|
|figures of merit: min =        0.00 max =            1.00 mean =         0.53|
|phase err.(work): min =        0.00 max =           89.95 mean =        49.44|
|phase err.(test): min =        0.00 max =           89.95 mean =        49.71|
|-----------------------------------------------------------------------------|

============================== 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 = 9.826250              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.310   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.484848              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.535   (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 |  1.295 -  1.656:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.656 -  2.016:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.016 -  2.376:       17 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.376 -  2.737:      225 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.737 -  3.097:     2322 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.097 -  3.458:     2281 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.458 -  3.818:     4215 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.818 -  4.179:     5134 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.179 -  4.539:     6318 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.539 -  4.900:     7727 |
|-----------------------------------------------------------------------------|
|-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 |        0.196 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.295 |       0.664 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.874)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4343   r_free= 0.4338   ksol= 0.00   Bsol= 0.00   scale= 0.912    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.235114                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4264   r_free= 0.4224   ksol= 0.31   Bsol= 40.57   scale= 0.955   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.79,-0.47,3.43,-0.00,0.00,0.00); trace/3= 0.72                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.226794                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.357134              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.962   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.850323              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.150   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4264      final r-factor (work) = 0.2711          |
| start r-factor (free) = 0.4224      final r-factor (free) = 0.2972          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.2136 = 8.36 * 0.50 * 6.2265 + 1.00 * 0.1959                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.3221 = 8.36 * 0.50 * 6.0326 + 1.00 * 0.1145                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2711      final r-factor (work) = 0.2443          |
| start r-factor (free) = 0.2972      final r-factor (free) = 0.3061          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1359 = 0.85 * 1.00 * 6.0326 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9513 = 0.85 * 1.00 * 5.8060 + 1.00 * 0.0143                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.874)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.91   18.13    None  None   None       |
|    all(noH): 2823   0      0.00    91.91   18.13    None  None   None       |
|    Sol.    : 438    0      4.08    91.91   41.05    None  None   None       |
|    Mac.    : 2385   0      0.00    78.00   13.93    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 -   9.191:  867   |   5:    45.955 -  55.145:   98        |
|      1:     9.191 -  18.382: 1035   |   6:    55.145 -  64.336:   67        |
|      2:    18.382 -  27.573:  389   |   7:    64.336 -  73.527:   35        |
|      3:    27.573 -  36.764:  185   |   8:    73.527 -  82.718:   11        |
|      4:    36.764 -  45.955:  133   |   9:    82.718 -  91.909:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2443 r_free = 0.3061             target_work(ml) = 5.816         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2441 r_free = 0.3066             target_work(ml) = 5.816         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2441   r_free= 0.3066   ksol= 0.31   Bsol= 40.57   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.79,-0.47,3.43,-0.00,0.00,0.00); trace/3= 0.72                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.816369                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2404   r_free= 0.3043   ksol= 0.34   Bsol= 64.57   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,-1.32,0.67,-0.00,0.00,0.00); trace/3= -0.98                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.810499                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.162883              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.170   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.299711              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.201  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2404      final r-factor (work) = 0.1687          |
| start r-factor (free) = 0.3043      final r-factor (free) = 0.2176          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.1163 = 5.16 * 0.50 * 5.8114 + 1.00 * 0.1145                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.7576 = 5.16 * 0.50 * 5.6901 + 1.00 * 0.0688                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1687      final r-factor (work) = 0.1543          |
| start r-factor (free) = 0.2176      final r-factor (free) = 0.2033          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7197 = 0.30 * 1.00 * 5.6901 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7000 = 0.30 * 1.00 * 5.4482 + 1.00 * 0.0672                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.874)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.68   17.86    None  None   None       |
|    all(noH): 2823   0      0.00    89.68   17.86    None  None   None       |
|    Sol.    : 438    0      6.31    89.68   41.18    None  None   None       |
|    Mac.    : 2385   0      0.00    78.23   13.57    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.968:  793   |   5:    44.838 -  53.805:  107        |
|      1:     8.968 -  17.935: 1188   |   6:    53.805 -  62.773:   71        |
|      2:    17.935 -  26.903:  319   |   7:    62.773 -  71.740:   31        |
|      3:    26.903 -  35.870:  158   |   8:    71.740 -  80.708:   15        |
|      4:    35.870 -  44.838:  138   |   9:    80.708 -  89.675:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1543 r_free = 0.2033             target_work(ml) = 5.415         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1541 r_free = 0.2032             target_work(ml) = 5.414         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1541   r_free= 0.2032   ksol= 0.34   Bsol= 64.57   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,-1.32,0.67,-0.00,0.00,0.00); trace/3= -0.98                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.413761                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1541   r_free= 0.2020   ksol= 0.33   Bsol= 61.02   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.97,-1.73,-0.19,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.412640                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.998195              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.025  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.893366              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.896   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1541      final r-factor (work) = 0.1285          |
| start r-factor (free) = 0.2020      final r-factor (free) = 0.1746          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.9652 = 4.00 * 0.50 * 5.4506 + 1.00 * 0.0689                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7487 = 4.00 * 0.50 * 5.3402 + 1.00 * 0.0733                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1285      final r-factor (work) = 0.1210          |
| start r-factor (free) = 0.1746      final r-factor (free) = 0.1685          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7872 = 0.89 * 1.00 * 5.3402 + 1.00 * 0.0165                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6902 = 0.89 * 1.00 * 5.2382 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.874)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.78    85.89   17.69    None  None   None       |
|    all(noH): 2823   0      0.78    85.89   17.69    None  None   None       |
|    Sol.    : 438    0      4.96    85.89   42.35    None  None   None       |
|    Mac.    : 2385   0      0.78    83.46   13.16    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:     0.781 -   9.292:  865   |   5:    43.334 -  51.844:  103        |
|      1:     9.292 -  17.802: 1179   |   6:    51.844 -  60.355:   94        |
|      2:    17.802 -  26.313:  275   |   7:    60.355 -  68.866:   39        |
|      3:    26.313 -  34.823:  122   |   8:    68.866 -  77.376:   24        |
|      4:    34.823 -  43.334:  114   |   9:    77.376 -  85.887:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1210 r_free = 0.1685             target_work(ml) = 5.219         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1209 r_free = 0.1685             target_work(ml) = 5.219         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1209   r_free= 0.1685   ksol= 0.33   Bsol= 61.02   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.97,-1.73,-0.19,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.218797                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1211   r_free= 0.1686   ksol= 0.33   Bsol= 61.02   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.05,-1.89,-0.48,-0.00,-0.00,-0.00); trace/3= -1.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.219473                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.836868              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.156  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.260216              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.617  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1211      final r-factor (work) = 0.1196          |
| start r-factor (free) = 0.1686      final r-factor (free) = 0.1650          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8847 = 1.84 * 0.50 * 5.2388 + 1.00 * 0.0733                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8452 = 1.84 * 0.50 * 5.2150 + 1.00 * 0.0555                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1196      final r-factor (work) = 0.1181          |
| start r-factor (free) = 0.1650      final r-factor (free) = 0.1657          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5825 = 1.26 * 1.00 * 5.2150 + 1.00 * 0.0104                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5642 = 1.26 * 1.00 * 5.2002 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.874)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.42   17.53    None  None   None       |
|    all(noH): 2823   0      0.00    87.42   17.53    None  None   None       |
|    Sol.    : 438    0      1.87    86.38   42.12    None  None   None       |
|    Mac.    : 2385   0      0.00    87.42   13.01    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.742:  768   |   5:    43.712 -  52.454:   94        |
|      1:     8.742 -  17.485: 1271   |   6:    52.454 -  61.197:   83        |
|      2:    17.485 -  26.227:  287   |   7:    61.197 -  69.939:   44        |
|      3:    26.227 -  34.970:  134   |   8:    69.939 -  78.681:   27        |
|      4:    34.970 -  43.712:  106   |   9:    78.681 -  87.424:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1181 r_free = 0.1657             target_work(ml) = 5.204         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1180 r_free = 0.1658             target_work(ml) = 5.203         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1180   r_free= 0.1658   ksol= 0.33   Bsol= 61.02   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.05,-1.89,-0.48,-0.00,-0.00,-0.00); trace/3= -1.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.203415                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1180   r_free= 0.1657   ksol= 0.33   Bsol= 61.02   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.93,-1.78,-0.42,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.203524                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.299276              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 152.814  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 6.836747              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 111.061  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1180      final r-factor (work) = 0.1140          |
| start r-factor (free) = 0.1657      final r-factor (free) = 0.1629          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0340 = 2.30 * 0.50 * 5.2003 + 1.00 * 0.0555                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0283 = 2.30 * 0.50 * 5.1888 + 1.00 * 0.0631                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1140      final r-factor (work) = 0.1135          |
| start r-factor (free) = 0.1629      final r-factor (free) = 0.1624          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 35.4855 = 6.84 * 1.00 * 5.1888 + 1.00 * 0.0108                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 35.3955 = 6.84 * 1.00 * 5.1755 + 1.00 * 0.0118                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.874)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.72  17.53    None  None   None       |
|    all(noH): 2823   0      0.00    100.72  17.53    None  None   None       |
|    Sol.    : 438    0      0.00    100.72  42.65    None  None   None       |
|    Mac.    : 2385   0      0.00    99.31   12.92    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 -  10.072: 1108   |   5:    50.361 -  60.434:   87        |
|      1:    10.072 -  20.145: 1072   |   6:    60.434 -  70.506:   54        |
|      2:    20.145 -  30.217:  213   |   7:    70.506 -  80.578:   25        |
|      3:    30.217 -  40.289:  133   |   8:    80.578 -  90.650:   15        |
|      4:    40.289 -  50.361:  110   |   9:    90.650 - 100.723:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1135 r_free = 0.1624             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1134 r_free = 0.1624             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1624   ksol= 0.33   Bsol= 61.02   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.93,-1.78,-0.42,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.175008                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8931 -  4.6803 0.99   1448  160 0.0965 0.1279      5.3776      5.5591|
|  2:  4.6803 -  3.7341 0.99   1402  155 0.0812 0.1075      5.4043      5.6108|
|  3:  3.7341 -  3.2678 0.99   1364  154 0.1066 0.1503      5.4641      5.8192|
|  4:  3.2678 -  2.9716 0.99   1361  144 0.1262 0.1656      5.4504      5.6329|
|  5:  2.9716 -  2.7601 0.98   1339  152 0.1316 0.1636      5.3362      5.5243|
|  6:  2.7601 -  2.5982 0.99   1349  151 0.1271 0.2128      5.2447      5.5363|
|  7:  2.5982 -  2.4687 0.99   1323  156 0.1296 0.1740      5.2006      5.3967|
|  8:  2.4687 -  2.3617 0.99   1353  140 0.1207 0.1800      5.1232      5.3286|
|  9:  2.3617 -  2.2711 0.99   1331  147 0.1171 0.1820      5.0406      5.3382|
| 10:  2.2711 -  2.1930 0.98   1324  146 0.1175 0.1943      4.9819      5.2534|
| 11:  2.1930 -  2.1246 0.98   1289  157 0.1187 0.1848      4.9368      5.2611|
| 12:  2.1246 -  2.0641 1.00   1350  140 0.1175 0.1589      4.8972        5.09|
| 13:  2.0641 -  2.0098 0.83   1123  119 0.1133 0.1957      4.8015      5.0903|
| 14:  2.0098 -  1.9609 0.21    274   38 0.1006 0.1664      4.7305      4.9007|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8931 -  4.6803  1448   160  0.94   9.35   0.97     0.94       7412.65|
|  2:  4.6803 -  3.7341  1402   155  0.95   7.96   1.01     1.00       8895.34|
|  3:  3.7341 -  3.2678  1364   154  0.93  11.48   1.03     1.02      10259.98|
|  4:  3.2678 -  2.9716  1361   144  0.91  14.46   1.01     1.00      10401.93|
|  5:  2.9716 -  2.7601  1339   152  0.90  16.47   1.00     0.98       8897.44|
|  6:  2.7601 -  2.5982  1349   151  0.89  17.37   0.98     0.95       7746.18|
|  7:  2.5982 -  2.4687  1323   156  0.90  16.69   0.98     0.95       6903.71|
|  8:  2.4687 -  2.3617  1353   140  0.89  16.96   0.99     0.95       6218.75|
|  9:  2.3617 -  2.2711  1331   147  0.90  16.57   0.99     0.95       5323.02|
| 10:  2.2711 -  2.1930  1324   146  0.89  16.65   0.98     0.94       4745.54|
| 11:  2.1930 -  2.1246  1289   157  0.90  16.68   0.98     0.94       4421.56|
| 12:  2.1246 -  2.0641  1350   140  0.89  17.10   0.99     0.99       4252.33|
| 13:  2.0641 -  2.0098  1123   119  0.89  17.13   0.97     0.95       3557.95|
| 14:  2.0098 -  1.9609   274    38  0.92  14.02   0.96     0.92       2843.87|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2843.87 max =        10401.93 mean =      6854.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.88|
|phase err.(test): min =        0.00 max =           89.80 mean =        14.37|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1623   ksol= 0.32   Bsol= 56.92   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.69,-1.55,-0.20,-0.00,-0.00,-0.00); trace/3= -1.48                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.175164                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1623   ksol= 0.32   Bsol= 56.92   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.69,-1.55,-0.20,-0.00,-0.00,-0.00); trace/3= -1.48                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.175164                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8931 -  4.6803 0.99   1448  160 0.0963 0.1279      5.3761      5.5586|
|  2:  4.6803 -  3.7341 0.99   1402  155 0.0810 0.1074      5.4032      5.6092|
|  3:  3.7341 -  3.2678 0.99   1364  154 0.1066 0.1504      5.4635        5.82|
|  4:  3.2678 -  2.9716 0.99   1361  144 0.1263 0.1658      5.4513      5.6337|
|  5:  2.9716 -  2.7601 0.98   1339  152 0.1317 0.1638      5.3374      5.5252|
|  6:  2.7601 -  2.5982 0.99   1349  151 0.1272 0.2131      5.2457       5.538|
|  7:  2.5982 -  2.4687 0.99   1323  156 0.1296 0.1741      5.2016      5.3967|
|  8:  2.4687 -  2.3617 0.99   1353  140 0.1207 0.1802      5.1238      5.3293|
|  9:  2.3617 -  2.2711 0.99   1331  147 0.1171 0.1819       5.041      5.3383|
| 10:  2.2711 -  2.1930 0.98   1324  146 0.1175 0.1943      4.9823      5.2534|
| 11:  2.1930 -  2.1246 0.98   1289  157 0.1187 0.1848      4.9371      5.2612|
| 12:  2.1246 -  2.0641 1.00   1350  140 0.1176 0.1589       4.897      5.0899|
| 13:  2.0641 -  2.0098 0.83   1123  119 0.1133 0.1957      4.8016      5.0898|
| 14:  2.0098 -  1.9609 0.21    274   38 0.1006 0.1664      4.7315      4.9013|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8931 -  4.6803  1448   160  0.94   9.35   0.97     0.94       7391.16|
|  2:  4.6803 -  3.7341  1402   155  0.95   7.95   1.02     1.00       8878.00|
|  3:  3.7341 -  3.2678  1364   154  0.93  11.47   1.03     1.03      10248.18|
|  4:  3.2678 -  2.9716  1361   144  0.91  14.47   1.02     1.01      10420.57|
|  5:  2.9716 -  2.7601  1339   152  0.90  16.49   1.00     0.98       8919.46|
|  6:  2.7601 -  2.5982  1349   151  0.89  17.39   0.99     0.95       7764.22|
|  7:  2.5982 -  2.4687  1323   156  0.90  16.71   0.99     0.96       6917.89|
|  8:  2.4687 -  2.3617  1353   140  0.89  16.97   1.00     0.96       6224.60|
|  9:  2.3617 -  2.2711  1331   147  0.90  16.58   1.00     0.96       5327.59|
| 10:  2.2711 -  2.1930  1324   146  0.89  16.66   0.99     0.95       4745.66|
| 11:  2.1930 -  2.1246  1289   157  0.90  16.69   0.99     0.95       4421.95|
| 12:  2.1246 -  2.0641  1350   140  0.89  17.11   1.00     1.00       4252.44|
| 13:  2.0641 -  2.0098  1123   119  0.89  17.14   0.99     0.96       3559.36|
| 14:  2.0098 -  1.9609   274    38  0.92  14.04   0.98     0.93       2846.94|
|alpha:            min =        0.93 max =            1.03 mean =         0.97|
|beta:             min =     2846.94 max =        10420.57 mean =      6857.28|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.89|
|phase err.(test): min =        0.00 max =           89.82 mean =        14.38|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.874)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.73  17.53    None  None   None       |
|    all(noH): 2823   0      0.00    100.73  17.53    None  None   None       |
|    Sol.    : 438    0      0.00    100.73  42.66    None  None   None       |
|    Mac.    : 2385   0      0.00    99.31   12.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.075: 1108   |   5:    50.364 -  60.437:   87        |
|      1:    10.075 -  20.148: 1072   |   6:    60.437 -  70.509:   54        |
|      2:    20.148 -  30.220:  213   |   7:    70.509 -  80.581:   25        |
|      3:    30.220 -  40.292:  133   |   8:    80.581 -  90.653:   15        |
|      4:    40.292 -  50.364:  110   |   9:    90.653 - 100.726:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 291         
Filter by distance & map next to the model:
   mapped sites are within: 0.559 - 4.275
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 287 from: 291
   mapped sites are within: 0.711 - 4.275

peak=    5.355 closest distance to " O   HOH Z 113 " =    2.053
peak=    5.179 closest distance to " CG  PRO A  54 " =    1.328
peak=    5.000 closest distance to " CB  ARG A 275 " =    1.007
peak=    4.979 closest distance to " CB  GLN A 223 " =    1.447
peak=    4.757 closest distance to " NE2 GLN A  11 " =    1.071
peak=    4.729 closest distance to " CA  ARG A  36 " =    1.094
peak=    4.716 closest distance to " CB  ARG A 190 " =    1.696
peak=    4.599 closest distance to " CG  PRO A  90 " =    1.190
peak=    4.580 closest distance to " O   HOH Z 369 " =    2.457
peak=    4.555 closest distance to " O   HOH Z 142 " =    1.520
peak=    4.554 closest distance to " O   HOH Z 403 " =    1.896
peak=    4.541 closest distance to " CA  TYR A  30 " =    0.909
peak=    4.464 closest distance to " CB  SER A  63 " =    1.118
peak=    4.435 closest distance to " CB  PRO A  54 " =    1.007
peak=    4.429 closest distance to " CD2 TRP A 179 " =    1.323
peak=    4.381 closest distance to " CB  GLN A 183 " =    1.268
peak=    4.380 closest distance to " O   HOH Z 287 " =    1.735
peak=    4.368 closest distance to " CG  PRO A 213 " =    1.215
peak=    4.360 closest distance to " CG  PRO A 198 " =    1.179
peak=    4.358 closest distance to " CZ  PHE A 218 " =    1.151
peak=    4.339 closest distance to " O   HOH Z 126 " =    1.787
peak=    4.329 closest distance to " O   HOH Z 188 " =    2.704
peak=    4.323 closest distance to " CB  ARG A  79 " =    1.417
peak=    4.250 closest distance to " O   HOH Z 298 " =    1.802
peak=    4.248 closest distance to " O   HOH Z 232 " =    2.342
peak=    4.235 closest distance to " O   HOH Z 234 " =    3.691
peak=    4.228 closest distance to " CG  ARG A  66 " =    2.495
peak=    4.219 closest distance to " O   HOH Z  49 " =    1.101
peak=    4.207 closest distance to " NZ  LYS A 117 " =    3.084
peak=    4.194 closest distance to " CB  GLU A 152 " =    1.164
peak=    4.187 closest distance to " C   PRO A 198 " =    1.536
peak=    4.175 closest distance to " O   HOH Z 346 " =    1.672
peak=    4.135 closest distance to " O   HOH Z  97 " =    2.064
peak=    4.130 closest distance to " O   SER A  87 " =    2.209
peak=    4.085 closest distance to " CG  GLN A  58 " =    0.928
peak=    4.079 closest distance to " O   HOH Z  43 " =    2.168
peak=    4.075 closest distance to " O   HOH Z 427 " =    2.993
peak=    4.061 closest distance to " CZ3 TRP A 266 " =    1.080
peak=    4.037 closest distance to " CB  ASN A 148 " =    1.461
peak=    4.035 closest distance to " ND2 ASN A 249 " =    0.887
peak=    4.033 closest distance to " O   HOH Z  15 " =    2.208
peak=    4.018 closest distance to " CB  GLU A 277 " =    3.666
peak=    4.007 closest distance to " CA  ALA A  51 " =    0.969
peak=    3.993 closest distance to " O   HOH Z  63 " =    1.865
peak=    3.959 closest distance to " O   HOH Z 248 " =    1.333
peak=    3.950 closest distance to " NH1AARG A 145 " =    1.349
peak=    3.941 closest distance to " ND2 ASN A 187 " =    1.613
peak=    3.931 closest distance to " CB  ARG A  79 " =    0.944
peak=    3.928 closest distance to " O   HOH Z  59 " =    2.192
peak=    3.925 closest distance to " O   HOH Z 180 " =    2.190
peak=    3.923 closest distance to " O   HOH Z 209 " =    2.275
peak=    3.923 closest distance to " O  BHOH Z  74 " =    1.196
peak=    3.922 closest distance to " CB  TRP A 266 " =    1.102
peak=    3.922 closest distance to " CD  ARG A 269 " =    0.995
peak=    3.916 closest distance to " CB  THR A  31 " =    1.650
peak=    3.899 closest distance to " O   HOH Z 406 " =    1.575
peak=    3.853 closest distance to " CG  PRO A 243 " =    1.071
peak=    3.852 closest distance to " CD  LYS A  76 " =    1.913
peak=    3.847 closest distance to " CA  ARG A 195 " =    1.248
peak=    3.842 closest distance to " O   HOH Z 227 " =    1.558
peak=    3.840 closest distance to " O   HOH Z 250 " =    1.426
peak=    3.838 closest distance to " O   HOH Z 412 " =    3.930
peak=    3.832 closest distance to " O   HOH Z  78 " =    1.703
peak=    3.825 closest distance to " CE  LYS A  76 " =    0.887
peak=    3.816 closest distance to " O   HOH Z  40 " =    1.851
peak=    3.814 closest distance to " O   HOH Z  44 " =    2.200
peak=    3.808 closest distance to " O   HOH Z  97 " =    2.063
peak=    3.796 closest distance to " O   HOH Z 368 " =    2.142
peak=    3.789 closest distance to " O   HOH Z  85 " =    1.288
peak=    3.784 closest distance to " O   HOH Z 303 " =    2.137
peak=    3.782 closest distance to " O   HOH Z 188 " =    1.480
peak=    3.780 closest distance to " CB  VAL A 202 " =    1.527
peak=    3.766 closest distance to " O   HOH Z  19 " =    1.542
peak=    3.765 closest distance to " O   HOH Z 280 " =    2.960
peak=    3.764 closest distance to " CA  ALA A 160 " =    0.902
peak=    3.752 closest distance to " CB  SER A  26 " =    1.890
peak=    3.751 closest distance to " O   HOH Z 361 " =    3.508
peak=    3.739 closest distance to " O   HOH Z 359 " =    1.669
peak=    3.735 closest distance to " CB  VAL A 265 " =    1.230
peak=    3.734 closest distance to " CB  PHE A 204 " =    0.863
peak=    3.733 closest distance to " CG2 ILE A 120 " =    1.285
peak=    3.729 closest distance to " O   ASN A  74 " =    1.472
peak=    3.723 closest distance to " CZ  PHE A  38 " =    1.229
peak=    3.718 closest distance to " O   HOH Z 132 " =    1.019
peak=    3.718 closest distance to " CG  MET A 185 " =    1.162
peak=    3.717 closest distance to " O   HOH Z 361 " =    2.572
peak=    3.712 closest distance to " O  BHOH Z 338 " =    2.215
peak=    3.708 closest distance to " O   HOH Z 316 " =    3.087
peak=    3.707 closest distance to " O   HOH Z 365 " =    2.696
peak=    3.705 closest distance to " CD  ARG A 159 " =    0.798
peak=    3.697 closest distance to " O   HOH Z 402 " =    1.349
peak=    3.691 closest distance to " O   HOH Z 327 " =    1.581
peak=    3.685 closest distance to " O   HOH Z 132 " =    2.416
peak=    3.685 closest distance to " NH2BARG A 145 " =    2.124
peak=    3.683 closest distance to " O   HOH Z 193 " =    1.530
peak=    3.682 closest distance to " O   HOH Z 291 " =    1.443
peak=    3.673 closest distance to " N   ASN A  39 " =    1.310
peak=    3.661 closest distance to " OG BSER A 164 " =    2.254
peak=    3.652 closest distance to " O   HOH Z 423 " =    1.938
peak=    3.650 closest distance to " O   HOH Z 265 " =    1.984
peak=    3.646 closest distance to " CD2 LEU A 297 " =    0.926
peak=    3.638 closest distance to " O   HOH Z 158 " =    3.007
peak=    3.637 closest distance to " O   HOH Z  61 " =    1.676
peak=    3.632 closest distance to " O   HOH Z 126 " =    1.531
peak=    3.627 closest distance to " O   HOH Z 353 " =    2.741
peak=    3.626 closest distance to " O   TYR A 116 " =    1.491
peak=    3.625 closest distance to " CB  GLU A 128 " =    1.090
peak=    3.625 closest distance to " O   HOH Z 325 " =    2.286
peak=    3.625 closest distance to " CD  LYS A 166 " =    1.383
peak=    3.611 closest distance to " CE  LYS A 119 " =    1.110
peak=    3.604 closest distance to " O   HOH Z 258 " =    2.056
peak=    3.601 closest distance to " O   HOH Z 214 " =    2.699
peak=    3.596 closest distance to " CB  ALA A 248 " =    1.344
peak=    3.592 closest distance to " CG2 ILE A  20 " =    1.388
peak=    3.587 closest distance to " CB  ASN A  39 " =    0.830
peak=    3.586 closest distance to " O   THR A 220 " =    1.167
peak=    3.585 closest distance to " O   HOH Z 109 " =    1.457
peak=    3.583 closest distance to " O   THR A 182 " =    1.453
peak=    3.580 closest distance to " CA  VAL A 125 " =    1.182
peak=    3.576 closest distance to " CB  PRO A  90 " =    1.102
peak=    3.574 closest distance to " O   HOH Z 246 " =    1.359
peak=    3.572 closest distance to " O   HOH Z 203 " =    1.810
peak=    3.567 closest distance to " O   HOH Z  88 " =    2.612
peak=    3.566 closest distance to " CB  TRP A 179 " =    1.335
peak=    3.559 closest distance to " O   HOH Z 421 " =    1.832
peak=    3.554 closest distance to " O   HOH Z 345 " =    1.671
peak=    3.553 closest distance to " O   HOH Z 417 " =    1.121
peak=    3.551 closest distance to " O   HOH Z 128 " =    2.441
peak=    3.547 closest distance to " O   HOH Z 371 " =    3.323
peak=    3.546 closest distance to " CG1 ILE A  33 " =    1.179
peak=    3.541 closest distance to " CG  GLU A  37 " =    1.094
peak=    3.540 closest distance to " N   CYS A 260 " =    0.967
peak=    3.539 closest distance to " CG2 VAL A 257 " =    0.757
peak=    3.534 closest distance to " CB  SER A 141 " =    1.130
peak=    3.532 closest distance to " O   HOH Z 357 " =    2.035
peak=    3.532 closest distance to " O   HOH Z 389 " =    1.799
peak=    3.530 closest distance to " O   HOH Z   1 " =    2.149
peak=    3.528 closest distance to " O   HOH Z 313 " =    2.020
peak=    3.528 closest distance to " CD  PRO A  54 " =    0.986
peak=    3.528 closest distance to " O   HOH Z 279 " =    2.195
peak=    3.526 closest distance to " CB  ASN A 142 " =    1.138
peak=    3.525 closest distance to " CD1 LEU A  96 " =    0.727
peak=    3.521 closest distance to " O   HOH Z 173 " =    2.003
peak=    3.519 closest distance to " O   HOH Z 299 " =    4.275
peak=    3.517 closest distance to " O   HOH Z 285 " =    2.340
peak=    3.509 closest distance to " O   HOH Z 272 " =    1.863
peak=    3.509 closest distance to " CG2AVAL A  72 " =    1.786
peak=    3.497 closest distance to " N   ARG A 156 " =    1.419
peak=    3.492 closest distance to " N   HIS A 108 " =    1.799
peak=    3.492 closest distance to " O   HOH Z  80 " =    1.793
peak=    3.490 closest distance to " O   HOH Z  88 " =    3.107
peak=    3.484 closest distance to " O   HOH Z  63 " =    2.318
peak=    3.478 closest distance to " O   HOH Z 185 " =    1.837
peak=    3.475 closest distance to " CG  LEU A 167 " =    1.202
peak=    3.468 closest distance to " O   HOH Z 380 " =    2.193
peak=    3.467 closest distance to " CB  ALA A 114 " =    0.861
peak=    3.466 closest distance to " OD1 ASN A  69 " =    2.420
peak=    3.465 closest distance to " O   HOH Z 422 " =    2.650
peak=    3.460 closest distance to " CB  LEU A  83 " =    0.757
peak=    3.460 closest distance to " O   HOH Z 425 " =    1.262
peak=    3.460 closest distance to " O   HOH Z 146 " =    2.357
peak=    3.454 closest distance to " CA  MET A 105 " =    1.075
peak=    3.449 closest distance to " CG2AVAL A 121 " =    2.255
peak=    3.442 closest distance to " O   HOH Z 251 " =    1.561
peak=    3.441 closest distance to " NE2 GLN A  77 " =    3.088
peak=    3.440 closest distance to " O   ALA A 165 " =    1.445
peak=    3.440 closest distance to " O   HOH Z 298 " =    2.262
peak=    3.434 closest distance to " CB  THR A  52 " =    0.718
peak=    3.426 closest distance to " CB  TYR A 169 " =    0.711
peak=    3.420 closest distance to " CB  SER A  62 " =    0.904
peak=    3.418 closest distance to " CB  ASN A 285 " =    0.980
peak=    3.416 closest distance to " CA  ASN A 176 " =    1.354
peak=    3.412 closest distance to " CD1 ILE A 199 " =    1.154
peak=    3.412 closest distance to " CB  GLU A  46 " =    1.039
peak=    3.409 closest distance to " CB  ASN A 215 " =    1.155
peak=    3.403 closest distance to " CA  SER A  87 " =    1.048
peak=    3.399 closest distance to " CA  SER A  32 " =    1.659
peak=    3.399 closest distance to " CA  ASN A 127 " =    1.236
peak=    3.395 closest distance to " O   HOH Z  21 " =    1.879
peak=    3.392 closest distance to " CB  ASN A 110 " =    1.101
peak=    3.391 closest distance to " CA  ALA A  84 " =    1.202
peak=    3.390 closest distance to " O   ASP A 124 " =    1.187
peak=    3.386 closest distance to " O   HOH Z 148 " =    3.460
peak=    3.385 closest distance to " CG  GLN A  11 " =    1.804
peak=    3.381 closest distance to " O   HOH Z 141 " =    1.686
peak=    3.380 closest distance to " CA  ALA A 158 " =    1.379
peak=    3.379 closest distance to " O   HOH Z 290 " =    0.916
peak=    3.378 closest distance to " N   ASP A 162 " =    1.142
peak=    3.374 closest distance to " O   HOH Z 345 " =    3.867
peak=    3.373 closest distance to " O   HOH Z 392 " =    2.564
peak=    3.371 closest distance to " CA  ASN A 215 " =    1.024
peak=    3.370 closest distance to " CG2 THR A 221 " =    1.208
peak=    3.367 closest distance to " O   HOH Z 417 " =    3.175
peak=    3.367 closest distance to " CA  TYR A 116 " =    1.370
peak=    3.364 closest distance to " CB  ASP A 124 " =    0.770
peak=    3.362 closest distance to " O   HOH Z 214 " =    1.798
peak=    3.362 closest distance to " O   HOH Z 261 " =    2.268
peak=    3.361 closest distance to " O   HOH Z  43 " =    1.090
peak=    3.358 closest distance to " O   HOH Z 366 " =    2.338
peak=    3.352 closest distance to " CG AARG A 275 " =    1.193
peak=    3.346 closest distance to " N   TYR A 116 " =    1.617
peak=    3.344 closest distance to " O   HOH Z 421 " =    2.727
peak=    3.332 closest distance to " CB  ASP A 298 " =    1.192
peak=    3.328 closest distance to " O   HOH Z 171 " =    2.034
peak=    3.327 closest distance to " CA  ALA A 154 " =    1.030
peak=    3.326 closest distance to " CB  LEU A 228 " =    1.161
peak=    3.324 closest distance to " CB  ASP A 140 " =    1.274
peak=    3.319 closest distance to " CB  PRO A 198 " =    1.287
peak=    3.317 closest distance to " CA  ALA A 295 " =    1.054
peak=    3.317 closest distance to " NZ  LYS A  48 " =    1.120
peak=    3.312 closest distance to " OG1 THR A 264 " =    0.747
peak=    3.304 closest distance to " O   HOH Z 394 " =    3.794
peak=    3.294 closest distance to " CB  LYS A 117 " =    1.173
peak=    3.294 closest distance to " O   ASP A 191 " =    1.587
peak=    3.290 closest distance to " CB  ALA A 291 " =    1.085
peak=    3.285 closest distance to " NH2AARG A 275 " =    3.567
peak=    3.281 closest distance to " O   HOH Z 130 " =    2.254
peak=    3.279 closest distance to " N   PHE A 130 " =    1.305
peak=    3.278 closest distance to " CD  LYS A 119 " =    1.693
peak=    3.277 closest distance to " CB  ALA A   9 " =    1.646
peak=    3.277 closest distance to " OD2 ASP A 298 " =    3.942
peak=    3.274 closest distance to " CB  SER A   3 " =    1.311
peak=    3.269 closest distance to " CD1AILE A 234 " =    0.836
peak=    3.265 closest distance to " CG2 THR A  29 " =    1.303
peak=    3.265 closest distance to " CA  THR A 221 " =    1.094
peak=    3.265 closest distance to " CA  ASN A 217 " =    1.208
peak=    3.261 closest distance to " NE  ARG A  24 " =    0.905
peak=    3.260 closest distance to " OG  SER A  22 " =    2.668
peak=    3.258 closest distance to " O   HOH Z 132 " =    2.533
peak=    3.253 closest distance to " CB  ALA A 227 " =    1.262
peak=    3.250 closest distance to " CA  ASP A 140 " =    1.603
peak=    3.250 closest distance to " O   HOH Z 411 " =    1.606
peak=    3.243 closest distance to " CA  ILE A 106 " =    0.866
peak=    3.242 closest distance to " CB  ASN A 148 " =    2.026
peak=    3.236 closest distance to " OG  SER A  62 " =    2.769
peak=    3.230 closest distance to " CE1 TYR A 186 " =    1.228
peak=    3.228 closest distance to " O   HOH Z 227 " =    2.136
peak=    3.228 closest distance to " N   VAL A 265 " =    1.310
peak=    3.227 closest distance to " OG BSER A  99 " =    2.438
peak=    3.227 closest distance to " OE1 GLU A   2 " =    2.179
peak=    3.227 closest distance to " O   HOH Z 128 " =    1.936
peak=    3.225 closest distance to " O   HOH Z 394 " =    1.832
peak=    3.219 closest distance to " O   HOH Z 383 " =    1.935
peak=    3.207 closest distance to " O   HOH Z 199 " =    1.659
peak=    3.200 closest distance to " O   HOH Z 305 " =    3.541
peak=    3.200 closest distance to " OG  SER A  28 " =    1.510
peak=    3.199 closest distance to " N   ALA A 158 " =    1.588
peak=    3.189 closest distance to " O   HOH Z  88 " =    3.296
peak=    3.188 closest distance to " O   HOH Z 299 " =    4.272
peak=    3.186 closest distance to " CB  ARG A 138 " =    0.793
peak=    3.179 closest distance to " O   HOH Z  10 " =    1.750
peak=    3.174 closest distance to " CE1 HIS A  81 " =    1.440
peak=    3.173 closest distance to " O   HOH Z 285 " =    1.870
peak=    3.172 closest distance to " CA  ALA A 291 " =    0.759
peak=    3.170 closest distance to " O   GLY A  91 " =    1.395
peak=    3.169 closest distance to " O   HOH Z 134 " =    1.004
peak=    3.167 closest distance to " CB  GLN A 205 " =    1.135
peak=    3.166 closest distance to " O   HOH Z 350 " =    2.010
peak=    3.166 closest distance to " CA  GLN A  94 " =    0.742
peak=    3.165 closest distance to " CA  ASP A 162 " =    1.061
peak=    3.164 closest distance to " CA  ILE A 234 " =    0.980
peak=    3.156 closest distance to " O   HOH Z 193 " =    1.857
peak=    3.153 closest distance to " CA  ALA A 100 " =    1.004
peak=    3.152 closest distance to " CB  HIS A 108 " =    0.846
peak=    3.143 closest distance to " O   HOH Z 334 " =    1.315
peak=    3.142 closest distance to " O   HOH Z 250 " =    1.500
peak=    3.141 closest distance to " CA  LEU A  83 " =    1.291
peak=    3.140 closest distance to " CB  ASP A 191 " =    1.219
peak=    3.137 closest distance to " CA  ALA A 248 " =    1.190
peak=    3.128 closest distance to " CB  GLN A  88 " =    1.166
peak=    3.117 closest distance to " CB  SER A  99 " =    1.341
peak=    3.116 closest distance to " CG2 VAL A 197 " =    1.092
peak=    3.112 closest distance to " O   HOH Z 141 " =    1.604
peak=    3.111 closest distance to " O   HOH Z 162 " =    1.943
peak=    3.109 closest distance to " O   HOH Z 187 " =    2.281
peak=    3.108 closest distance to " O   HOH Z 371 " =    1.453
peak=    3.104 closest distance to " O   HOH Z 391 " =    2.909
peak=    3.100 closest distance to " O   HOH Z  35 " =    2.437
peak=    3.092 closest distance to " CG  MET A 113 " =    1.233
peak=    3.087 closest distance to " CA  GLY A 241 " =    1.006
peak=    3.086 closest distance to " O   HOH Z 403 " =    1.443
peak=    3.074 closest distance to " O   THR A 251 " =    1.202
peak=    3.061 closest distance to " OD2 ASP A 286 " =    3.228
peak=    3.057 closest distance to " CA  SER A 146 " =    1.992
peak=    3.051 closest distance to " OG1 THR A 294 " =    4.013
peak=    3.045 closest distance to " O   HOH Z  28 " =    1.818
peak=    3.011 closest distance to " CA  THR A  82 " =    1.939

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 212         
Filter by distance & map next to the model:
   mapped sites are within: 0.904 - 5.984
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 211 from: 212
   mapped sites are within: 0.904 - 5.984

peak=   -4.875 closest distance to " CD  ARG A  14 " =    3.376
peak=   -4.490 closest distance to " CG2 ILE A  49 " =    2.793
peak=   -4.466 closest distance to " CG  GLN A  58 " =    1.085
peak=   -4.412 closest distance to " O   HOH Z 210 " =    0.904
peak=   -4.372 closest distance to " O   HOH Z 266 " =    5.429
peak=   -4.339 closest distance to " C   HIS A 108 " =    1.122
peak=   -4.265 closest distance to " O   HOH Z 377 " =    2.076
peak=   -4.245 closest distance to " O   PRO A 198 " =    1.333
peak=   -4.178 closest distance to " CB  PRO A 243 " =    2.733
peak=   -4.126 closest distance to " CD2 TYR A 293 " =    1.861
peak=   -4.120 closest distance to " OXT GLY A 302 " =    3.000
peak=   -4.105 closest distance to " CD1 LEU A 101 " =    2.399
peak=   -4.104 closest distance to " O   HOH Z 348 " =    2.180
peak=   -4.047 closest distance to " OG BSER A 134 " =    1.334
peak=   -4.034 closest distance to " CA  VAL A  67 " =    3.027
peak=   -4.024 closest distance to " O   HOH Z 193 " =    1.118
peak=   -3.987 closest distance to " CG1 VAL A 250 " =    2.663
peak=   -3.983 closest distance to " CB  ALA A 184 " =    2.369
peak=   -3.933 closest distance to " CE2 TYR A  30 " =    2.737
peak=   -3.932 closest distance to " CD  ARG A 156 " =    2.125
peak=   -3.920 closest distance to " OG  SER A  97 " =    2.229
peak=   -3.913 closest distance to " CE2 PHE A  61 " =    2.676
peak=   -3.885 closest distance to " O   VAL A  67 " =    2.705
peak=   -3.871 closest distance to " O   HOH Z 394 " =    1.520
peak=   -3.861 closest distance to " CD2 HIS A 207 " =    2.301
peak=   -3.849 closest distance to " CE  MET A 105 " =    2.513
peak=   -3.834 closest distance to " O   ILE A  49 " =    1.728
peak=   -3.827 closest distance to " O   HOH Z 198 " =    1.539
peak=   -3.819 closest distance to " O   HOH Z 211 " =    1.324
peak=   -3.817 closest distance to " CD1 LEU A  25 " =    2.534
peak=   -3.810 closest distance to " CE3 TRP A 150 " =    2.218
peak=   -3.803 closest distance to " CH2 TRP A 179 " =    1.309
peak=   -3.786 closest distance to " CG1 VAL A 112 " =    2.785
peak=   -3.771 closest distance to " CA  ASP A 298 " =    1.057
peak=   -3.768 closest distance to " CD2 PHE A 192 " =    2.127
peak=   -3.748 closest distance to " O   HOH Z  13 " =    1.826
peak=   -3.734 closest distance to " O   PHE A 218 " =    1.494
peak=   -3.733 closest distance to " O   HOH Z 102 " =    1.601
peak=   -3.731 closest distance to " OE1 GLN A 223 " =    2.274
peak=   -3.728 closest distance to " CB  ASN A  39 " =    2.402
peak=   -3.722 closest distance to " O   VAL A 174 " =    2.234
peak=   -3.702 closest distance to " O   ALA A  34 " =    2.341
peak=   -3.699 closest distance to " O   HOH Z 196 " =    2.020
peak=   -3.699 closest distance to " O   HOH Z   6 " =    2.086
peak=   -3.697 closest distance to " OD2 ASP A 191 " =    1.511
peak=   -3.694 closest distance to " O   SER A 210 " =    1.899
peak=   -3.686 closest distance to " CD2 TYR A 247 " =    2.375
peak=   -3.675 closest distance to " O   PRO A 163 " =    2.032
peak=   -3.669 closest distance to " O   GLY A  80 " =    2.621
peak=   -3.665 closest distance to " CE BMET A  47 " =    1.404
peak=   -3.661 closest distance to " CA  GLY A 241 " =    2.402
peak=   -3.657 closest distance to " CB  ALA A 161 " =    2.578
peak=   -3.642 closest distance to " O   HOH Z 357 " =    2.194
peak=   -3.637 closest distance to " O   HOH Z 166 " =    1.802
peak=   -3.635 closest distance to " NE2 GLN A  11 " =    1.738
peak=   -3.635 closest distance to " ND2 ASN A 249 " =    2.354
peak=   -3.622 closest distance to " CG  PRO A 243 " =    1.710
peak=   -3.621 closest distance to " CG1AVAL A  41 " =    2.578
peak=   -3.597 closest distance to " O   HOH Z 421 " =    3.875
peak=   -3.584 closest distance to " CB  HIS A  86 " =    1.170
peak=   -3.578 closest distance to " O   HOH Z  71 " =    2.575
peak=   -3.576 closest distance to " CG  GLU A  53 " =    1.475
peak=   -3.574 closest distance to " CB  ALA A  43 " =    2.524
peak=   -3.573 closest distance to " NE2 GLN A  88 " =    1.822
peak=   -3.571 closest distance to " N   ALA A  43 " =    2.620
peak=   -3.570 closest distance to " N   ALA A 248 " =    1.676
peak=   -3.564 closest distance to " CG  PHE A 283 " =    2.625
peak=   -3.563 closest distance to " O   HOH Z 113 " =    1.732
peak=   -3.554 closest distance to " CG1 VAL A 112 " =    2.601
peak=   -3.539 closest distance to " CD  ARG A 195 " =    5.130
peak=   -3.539 closest distance to " CD  PRO A 243 " =    2.087
peak=   -3.532 closest distance to " O   HOH Z   6 " =    1.587
peak=   -3.530 closest distance to " CG  ASP A 132 " =    2.366
peak=   -3.528 closest distance to " O   HOH Z 374 " =    1.895
peak=   -3.526 closest distance to " OE2 GLU A 152 " =    1.441
peak=   -3.523 closest distance to " CZ  TYR A 169 " =    1.858
peak=   -3.522 closest distance to " O   HOH Z  38 " =    1.712
peak=   -3.513 closest distance to " CD  GLN A 223 " =    1.647
peak=   -3.510 closest distance to " O   HOH Z  63 " =    1.435
peak=   -3.505 closest distance to " O   HOH Z 165 " =    1.906
peak=   -3.501 closest distance to " ND2 ASN A  45 " =    1.289
peak=   -3.499 closest distance to " CB  TRP A  85 " =    2.589
peak=   -3.498 closest distance to " O   HOH Z  10 " =    1.523
peak=   -3.488 closest distance to " CB  ALA A 248 " =    2.274
peak=   -3.485 closest distance to " N   ASP A 286 " =    2.207
peak=   -3.477 closest distance to " OD1 ASN A 148 " =    1.437
peak=   -3.472 closest distance to " O   HOH Z 174 " =    2.410
peak=   -3.465 closest distance to " O   HOH Z 283 " =    2.363
peak=   -3.453 closest distance to " O   SER A 276 " =    1.655
peak=   -3.448 closest distance to " CG  ARG A 269 " =    2.272
peak=   -3.444 closest distance to " OE1 GLN A 183 " =    1.529
peak=   -3.433 closest distance to " O   ALA A  10 " =    1.772
peak=   -3.432 closest distance to " O   HOH Z 314 " =    1.642
peak=   -3.427 closest distance to " CD2 PHE A  61 " =    2.273
peak=   -3.424 closest distance to " CA  GLY A 241 " =    3.095
peak=   -3.412 closest distance to " O   ILE A 106 " =    1.765
peak=   -3.396 closest distance to " CZ3 TRP A 274 " =    2.356
peak=   -3.396 closest distance to " CD1 PHE A  59 " =    2.040
peak=   -3.393 closest distance to " OD1 ASP A 171 " =    1.533
peak=   -3.392 closest distance to " O   HOH Z 252 " =    3.795
peak=   -3.387 closest distance to " O   ASN A 252 " =    1.352
peak=   -3.386 closest distance to " O   HOH Z 281 " =    2.607
peak=   -3.385 closest distance to " O   HOH Z 265 " =    2.503
peak=   -3.381 closest distance to " O   HOH Z 191 " =    5.945
peak=   -3.380 closest distance to " O   HOH Z 407 " =    2.634
peak=   -3.377 closest distance to " N   ALA A 248 " =    2.124
peak=   -3.375 closest distance to " ND2BASN A 224 " =    1.750
peak=   -3.373 closest distance to " O   HOH Z 252 " =    4.028
peak=   -3.372 closest distance to " CB  ALA A 291 " =    2.445
peak=   -3.370 closest distance to " CG  GLU A 277 " =    1.353
peak=   -3.368 closest distance to " CB  ALA A  10 " =    2.323
peak=   -3.366 closest distance to " O   HOH Z  43 " =    1.331
peak=   -3.360 closest distance to " O   TRP A  92 " =    1.927
peak=   -3.358 closest distance to " CG1 VAL A  78 " =    2.800
peak=   -3.357 closest distance to " NE2 GLN A  88 " =    1.192
peak=   -3.357 closest distance to " CG1 VAL A  67 " =    3.086
peak=   -3.357 closest distance to " O   HOH Z 114 " =    3.296
peak=   -3.356 closest distance to " O   HOH Z 366 " =    1.618
peak=   -3.351 closest distance to " O   HOH Z 216 " =    1.508
peak=   -3.349 closest distance to " CG  TRP A 266 " =    1.958
peak=   -3.343 closest distance to " CG1BVAL A  41 " =    2.864
peak=   -3.341 closest distance to " O   HOH Z 185 " =    2.360
peak=   -3.334 closest distance to " O   VAL A 189 " =    1.894
peak=   -3.332 closest distance to " O   ALA A 292 " =    2.212
peak=   -3.332 closest distance to " O   HOH Z 148 " =    3.868
peak=   -3.332 closest distance to " O   GLU A 152 " =    1.389
peak=   -3.328 closest distance to " CA  GLY A 133 " =    2.055
peak=   -3.326 closest distance to " CG2 ILE A 263 " =    2.196
peak=   -3.325 closest distance to " CG  GLN A  58 " =    1.162
peak=   -3.323 closest distance to " O   HOH Z 116 " =    1.707
peak=   -3.323 closest distance to " N   SER A 276 " =    1.357
peak=   -3.318 closest distance to " C   THR A 279 " =    1.170
peak=   -3.317 closest distance to " OH  TYR A 172 " =    1.908
peak=   -3.316 closest distance to " OD1 ASP A 191 " =    1.548
peak=   -3.300 closest distance to " ND2 ASN A  45 " =    1.863
peak=   -3.297 closest distance to " OG BSER A 134 " =    1.913
peak=   -3.296 closest distance to " ND2 ASN A  69 " =    1.870
peak=   -3.294 closest distance to " O   HOH Z 171 " =    2.309
peak=   -3.293 closest distance to " CZ  PHE A  38 " =    2.312
peak=   -3.292 closest distance to " CA  GLY A 133 " =    2.381
peak=   -3.283 closest distance to " CG2 VAL A 189 " =    2.244
peak=   -3.281 closest distance to " O   HOH Z 154 " =    1.868
peak=   -3.280 closest distance to " O   HOH Z 418 " =    1.496
peak=   -3.280 closest distance to " O   HOH Z 285 " =    1.479
peak=   -3.270 closest distance to " O   ALA A 248 " =    1.751
peak=   -3.265 closest distance to " O   HOH Z  88 " =    4.521
peak=   -3.261 closest distance to " O   ILE A 263 " =    2.233
peak=   -3.253 closest distance to " CD  GLN A 223 " =    1.442
peak=   -3.251 closest distance to " NH2 ARG A  66 " =    1.102
peak=   -3.250 closest distance to " OD1 ASN A  39 " =    2.225
peak=   -3.250 closest distance to " CA  TYR A  68 " =    3.059
peak=   -3.249 closest distance to " CD1 ILE A 106 " =    2.270
peak=   -3.248 closest distance to " O   HOH Z 264 " =    1.730
peak=   -3.246 closest distance to " O   HOH Z 174 " =    3.647
peak=   -3.244 closest distance to " NH2 ARG A  66 " =    5.984
peak=   -3.240 closest distance to " O   HOH Z 437 " =    2.188
peak=   -3.235 closest distance to " CZ  ARG A 259 " =    0.967
peak=   -3.234 closest distance to " CD1 ILE A 151 " =    2.382
peak=   -3.229 closest distance to " O   HOH Z 426 " =    1.612
peak=   -3.229 closest distance to " O   ASN A  45 " =    1.934
peak=   -3.220 closest distance to " O   ALA A 227 " =    1.364
peak=   -3.217 closest distance to " CG1BVAL A  72 " =    2.269
peak=   -3.215 closest distance to " O   HOH Z 372 " =    2.242
peak=   -3.213 closest distance to " O   HOH Z  37 " =    1.824
peak=   -3.213 closest distance to " O   HOH Z  68 " =    1.483
peak=   -3.211 closest distance to " O   HOH Z 116 " =    1.627
peak=   -3.210 closest distance to " CD  ARG A  79 " =    1.223
peak=   -3.209 closest distance to " CG  ASN A 148 " =    2.327
peak=   -3.208 closest distance to " OE1 GLN A 223 " =    2.157
peak=   -3.206 closest distance to " CG  LEU A  83 " =    2.152
peak=   -3.203 closest distance to " O   HOH Z 156 " =    3.518
peak=   -3.200 closest distance to " O   HOH Z 110 " =    1.371
peak=   -3.199 closest distance to " O   HOH Z  19 " =    2.250
peak=   -3.196 closest distance to " CZ  PHE A  38 " =    2.007
peak=   -3.195 closest distance to " O   HOH Z 111 " =    1.921
peak=   -3.181 closest distance to " O   HOH Z 145 " =    3.102
peak=   -3.179 closest distance to " CG  ASP A 286 " =    1.588
peak=   -3.178 closest distance to " O   GLY A 196 " =    1.035
peak=   -3.176 closest distance to " OD1 ASN A 301 " =    1.885
peak=   -3.174 closest distance to " N   GLN A  58 " =    1.289
peak=   -3.172 closest distance to " O   HOH Z 208 " =    2.164
peak=   -3.169 closest distance to " O   HOH Z 177 " =    1.699
peak=   -3.163 closest distance to " OG BSER A  99 " =    1.017
peak=   -3.160 closest distance to " O   ALA A 180 " =    1.308
peak=   -3.160 closest distance to " O   HOH Z 166 " =    1.881
peak=   -3.156 closest distance to " CA  GLY A  57 " =    2.170
peak=   -3.156 closest distance to " CE1 PHE A 192 " =    1.974
peak=   -3.155 closest distance to " O   HOH Z 166 " =    1.622
peak=   -3.153 closest distance to " OD2 ASP A 171 " =    2.452
peak=   -3.140 closest distance to " CB  ALA A   9 " =    2.419
peak=   -3.140 closest distance to " O   SER A   3 " =    1.013
peak=   -3.140 closest distance to " O   HOH Z 351 " =    1.578
peak=   -3.140 closest distance to " O   TRP A  70 " =    1.579
peak=   -3.126 closest distance to " O   GLY A  80 " =    2.521
peak=   -3.124 closest distance to " O   HOH Z 287 " =    2.101
peak=   -3.122 closest distance to " O   HOH Z 278 " =    1.310
peak=   -3.120 closest distance to " CH2 TRP A 150 " =    1.132
peak=   -3.114 closest distance to " CD  ARG A 139 " =    1.521
peak=   -3.113 closest distance to " O   HOH Z 197 " =    2.094
peak=   -3.109 closest distance to " O   HOH Z 422 " =    1.496
peak=   -3.109 closest distance to " O   HOH Z 363 " =    1.264
peak=   -3.103 closest distance to " O   HOH Z 232 " =    2.183
peak=   -3.103 closest distance to " O   HOH Z 340 " =    1.830
peak=   -3.101 closest distance to " O   HOH Z 250 " =    1.754
peak=   -3.098 closest distance to " C   GLY A  17 " =    0.969
peak=   -3.084 closest distance to " N   ALA A 226 " =    1.939
peak=   -3.080 closest distance to " CG2BVAL A  41 " =    1.243
peak=   -3.078 closest distance to " CG  GLN A 103 " =    2.490
peak=   -3.053 closest distance to " OD1 ASN A 173 " =    1.411
peak=   -3.052 closest distance to " C   LEU A 143 " =    1.070
peak=   -3.002 closest distance to " CA  GLY A 133 " =    1.826

================= 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    :  0.4343 0.4338   6.235114e+00   6.225556e+00
   1_bss:  0.4264 0.4224   6.226794e+00   6.214145e+00
   1_xyz:  0.2711 0.2972   5.867851e+00   5.961584e+00
   1_adp:  0.2443 0.3061   5.816211e+00   5.984487e+00
   1_occ:  0.2441 0.3066   5.816369e+00   5.985845e+00
   2_bss:  0.2404 0.3043   5.810499e+00   5.981312e+00
   2_xyz:  0.1687 0.2176   5.488222e+00   5.686742e+00
   2_adp:  0.1543 0.2033   5.414789e+00   5.622271e+00
   2_occ:  0.1541 0.2032   5.413761e+00   5.621484e+00
   3_bss:  0.1541 0.2020   5.412640e+00   5.619171e+00
   3_xyz:  0.1285 0.1746   5.265120e+00   5.487039e+00
   3_adp:  0.1210 0.1685   5.219232e+00   5.449655e+00
   3_occ:  0.1209 0.1685   5.218797e+00   5.449167e+00
   4_bss:  0.1211 0.1686   5.219473e+00   5.449104e+00
   4_xyz:  0.1196 0.1650   5.205855e+00   5.432781e+00
   4_adp:  0.1181 0.1657   5.203612e+00   5.436402e+00
   4_occ:  0.1180 0.1658   5.203415e+00   5.436222e+00
   5_bss:  0.1180 0.1657   5.203524e+00   5.436290e+00
   5_xyz:  0.1140 0.1629   5.178565e+00   5.419413e+00
   5_adp:  0.1135 0.1624   5.175240e+00   5.417312e+00
   5_occ:  0.1134 0.1624   5.175008e+00   5.417176e+00
   5_bss:  0.1133 0.1623   5.175164e+00   5.417377e+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:  0.315  40.572  -0.789  -0.468   3.432  -0.000   0.000   0.000
   1_xyz:  0.315  40.572  -0.789  -0.468   3.432  -0.000   0.000   0.000
   1_adp:  0.315  40.572  -0.789  -0.468   3.432  -0.000   0.000   0.000
   1_occ:  0.315  40.572  -0.789  -0.468   3.432  -0.000   0.000   0.000
   2_bss:  0.336  64.567  -2.273  -1.324   0.669  -0.000   0.000   0.000
   2_xyz:  0.336  64.567  -2.273  -1.324   0.669  -0.000   0.000   0.000
   2_adp:  0.336  64.567  -2.273  -1.324   0.669  -0.000   0.000   0.000
   2_occ:  0.336  64.567  -2.273  -1.324   0.669  -0.000   0.000   0.000
   3_bss:  0.330  61.021  -2.966  -1.734  -0.195  -0.000  -0.000  -0.000
   3_xyz:  0.330  61.021  -2.966  -1.734  -0.195  -0.000  -0.000  -0.000
   3_adp:  0.330  61.021  -2.966  -1.734  -0.195  -0.000  -0.000  -0.000
   3_occ:  0.330  61.021  -2.966  -1.734  -0.195  -0.000  -0.000  -0.000
   4_bss:  0.328  61.021  -3.055  -1.889  -0.478  -0.000  -0.000  -0.000
   4_xyz:  0.328  61.021  -3.055  -1.889  -0.478  -0.000  -0.000  -0.000
   4_adp:  0.328  61.021  -3.055  -1.889  -0.478  -0.000  -0.000  -0.000
   4_occ:  0.328  61.021  -3.055  -1.889  -0.478  -0.000  -0.000  -0.000
   5_bss:  0.328  61.021  -2.935  -1.784  -0.422  -0.000  -0.000  -0.000
   5_xyz:  0.328  61.021  -2.935  -1.784  -0.422  -0.000  -0.000  -0.000
   5_adp:  0.328  61.021  -2.935  -1.784  -0.422  -0.000  -0.000  -0.000
   5_occ:  0.328  61.021  -2.935  -1.784  -0.422  -0.000  -0.000  -0.000
   5_bss:  0.321  56.915  -2.690  -1.554  -0.199  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.464 0.5281  0.6971    56045.845
   1_bss:  48.356 0.5404  0.7375    53114.422
   1_xyz:  30.833 0.7493  0.9648    23972.408
   1_adp:  32.025 0.7350  0.9492    25330.485
   1_occ:  32.087 0.7343  0.9483    25426.265
   2_bss:  31.771 0.7377  0.8981    25022.637
   2_xyz:  21.360 0.8474  0.9859    12009.444
   2_adp:  19.449 0.8669  0.9943    10609.403
   2_occ:  19.428 0.8671  0.9945    10587.477
   3_bss:  19.349 0.8677  0.9716    10504.694
   3_xyz:  16.413 0.8943  0.9835     7923.701
   3_adp:  15.599 0.9014  0.9784     7361.969
   3_occ:  15.587 0.9015  0.9784     7353.368
   4_bss:  15.587 0.9016  0.9724     7371.975
   4_xyz:  15.135 0.9057  0.9736     7052.739
   4_adp:  15.203 0.9053  0.9668     7116.968
   4_occ:  15.200 0.9053  0.9668     7113.396
   5_bss:  15.202 0.9053  0.9699     7115.174
   5_xyz:  14.873 0.9079  0.9724     6885.702
   5_adp:  14.830 0.9083  0.9653     6857.786
   5_occ:  14.828 0.9083  0.9652     6853.789
   5_bss:  14.837 0.9082  0.9730     6856.266
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.9593e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.9593e-01
   1_xyz:   1.456  0.012  0.090 15.344  0.006  4.113   1.1448e-01
   1_adp:   1.456  0.012  0.090 15.344  0.006  4.113   1.1448e-01
   1_occ:   1.456  0.012  0.090 15.344  0.006  4.113   1.1448e-01
   2_bss:   1.456  0.012  0.090 15.344  0.006  4.113   1.1448e-01
   2_xyz:   1.126  0.008  0.079 14.684  0.005  4.128   6.8818e-02
   2_adp:   1.126  0.008  0.079 14.684  0.005  4.128   6.8818e-02
   2_occ:   1.126  0.008  0.079 14.684  0.005  4.128   6.8818e-02
   3_bss:   1.126  0.008  0.079 14.684  0.005  4.128   6.8818e-02
   3_xyz:   1.151  0.009  0.082 14.824  0.004  4.126   7.3259e-02
   3_adp:   1.151  0.009  0.082 14.824  0.004  4.126   7.3259e-02
   3_occ:   1.151  0.009  0.082 14.824  0.004  4.126   7.3259e-02
   4_bss:   1.151  0.009  0.082 14.824  0.004  4.126   7.3259e-02
   4_xyz:   0.978  0.007  0.074 14.461  0.004  4.128   5.5537e-02
   4_adp:   0.978  0.007  0.074 14.461  0.004  4.128   5.5537e-02
   4_occ:   0.978  0.007  0.074 14.461  0.004  4.128   5.5537e-02
   5_bss:   0.978  0.007  0.074 14.461  0.004  4.128   5.5537e-02
   5_xyz:   1.037  0.008  0.078 14.565  0.004  4.112   6.3060e-02
   5_adp:   1.037  0.008  0.078 14.565  0.004  4.112   6.3060e-02
   5_occ:   1.037  0.008  0.078 14.565  0.004  4.112   6.3060e-02
   5_bss:   1.037  0.008  0.078 14.565  0.004  4.112   6.3060e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.295   2.4330e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.295   2.4330e-01
   1_xyz:   9.271  0.085  0.321 83.151  0.032  2.131   9.6071e-02
   1_adp:   9.271  0.085  0.321 83.151  0.032  2.131   9.6071e-02
   1_occ:   9.271  0.085  0.321 83.151  0.032  2.131   9.6071e-02
   2_bss:   9.271  0.085  0.321 83.151  0.032  2.131   9.6071e-02
   2_xyz:   7.452  0.057  0.279 79.947  0.042  2.301   5.3054e-02
   2_adp:   7.452  0.057  0.279 79.947  0.042  2.301   5.3054e-02
   2_occ:   7.452  0.057  0.279 79.947  0.042  2.301   5.3054e-02
   3_bss:   7.452  0.057  0.279 79.947  0.042  2.301   5.3054e-02
   3_xyz:   7.960  0.054  0.277 83.891  0.039  2.130   6.1108e-02
   3_adp:   7.960  0.054  0.277 83.891  0.039  2.130   6.1108e-02
   3_occ:   7.960  0.054  0.277 83.891  0.039  2.130   6.1108e-02
   4_bss:   7.960  0.054  0.277 83.891  0.039  2.130   6.1108e-02
   4_xyz:   7.021  0.046  0.245 80.901  0.035  2.416   3.5201e-02
   4_adp:   7.021  0.046  0.245 80.901  0.035  2.416   3.5201e-02
   4_occ:   7.021  0.046  0.245 80.901  0.035  2.416   3.5201e-02
   5_bss:   7.021  0.046  0.245 80.901  0.035  2.416   3.5201e-02
   5_xyz:   7.554  0.051  0.269 81.709  0.033  2.324   5.4215e-02
   5_adp:   7.554  0.051  0.269 81.709  0.033  2.324   5.4215e-02
   5_occ:   7.554  0.051  0.269 81.709  0.033  2.324   5.4215e-02
   5_bss:   7.554  0.051  0.269 81.709  0.033  2.324   5.4215e-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:  91.91   0.00  18.13  78.00   0.00  13.93  91.91   4.08  41.05
   1_occ:  91.91   0.00  18.13  78.00   0.00  13.93  91.91   4.08  41.05
   2_bss:  91.91   0.00  18.13  78.00   0.00  13.93  91.91   4.08  41.05
   2_xyz:  91.91   0.00  18.13  78.00   0.00  13.93  91.91   4.08  41.05
   2_adp:  89.68   0.00  17.86  78.23   0.00  13.57  89.68   6.31  41.18
   2_occ:  89.68   0.00  17.86  78.23   0.00  13.57  89.68   6.31  41.18
   3_bss:  89.68   0.00  17.86  78.23   0.00  13.57  89.68   6.31  41.18
   3_xyz:  89.68   0.00  17.86  78.23   0.00  13.57  89.68   6.31  41.18
   3_adp:  85.89   0.78  17.69  83.46   0.78  13.16  85.89   4.96  42.35
   3_occ:  85.89   0.78  17.69  83.46   0.78  13.16  85.89   4.96  42.35
   4_bss:  85.89   0.78  17.69  83.46   0.78  13.16  85.89   4.96  42.35
   4_xyz:  85.89   0.78  17.69  83.46   0.78  13.16  85.89   4.96  42.35
   4_adp:  87.42   0.00  17.53  87.42   0.00  13.01  86.38   1.87  42.12
   4_occ:  87.42   0.00  17.53  87.42   0.00  13.01  86.38   1.87  42.12
   5_bss:  87.42   0.00  17.53  87.42   0.00  13.01  86.38   1.87  42.12
   5_xyz:  87.42   0.00  17.53  87.42   0.00  13.01  86.38   1.87  42.12
   5_adp: 100.72   0.00  17.53  99.31   0.00  12.92 100.72   0.00  42.65
   5_occ: 100.72   0.00  17.53  99.31   0.00  12.92 100.72   0.00  42.65
   5_bss: 100.73   0.00  17.53  99.31   0.00  12.92 100.73   0.00  42.66
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.969    0.024    0.434
   1_adp:    1.969    0.024    0.434
   1_occ:    1.969    0.024    0.434
   2_bss:    1.969    0.024    0.434
   2_xyz:    1.889    0.055    0.548
   2_adp:    1.889    0.055    0.548
   2_occ:    1.889    0.055    0.548
   3_bss:    1.889    0.055    0.548
   3_xyz:    1.816    0.072    0.609
   3_adp:    1.816    0.072    0.609
   3_occ:    1.816    0.072    0.609
   4_bss:    1.816    0.072    0.609
   4_xyz:    1.721    0.060    0.624
   4_adp:    1.721    0.060    0.624
   4_occ:    1.721    0.060    0.624
   5_bss:    1.721    0.060    0.624
   5_xyz:    1.615    0.061    0.635
   5_adp:    1.615    0.061    0.635
   5_occ:    1.615    0.061    0.635
   5_bss:    1.615    0.061    0.635
------------------------------------------------------------------------

CPU time actual refinement: 335.10


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_207/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_207/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_207/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_207/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_207/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.94 
  Macro-tasks:
    bulk solvent and scale       = 37.98  
    individual site refinement   = 138.42 
    weights calculation          = 30.94  
    collect and process          = 6.68   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 214.14 
  Micro-tasks:
    mask                            = 1.80   
    f_calc                          = 107.69 
    alpha_beta                      = 8.35   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 115.76 
    fmodel                         = 6.65   
    r_factors                      = 0.21   
    phase_errors                   = 10.93  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 252.78 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.797 micro seconds
Total CPU time: 5.81 minutes
from_scatterers_fft:    628 calls, 107.30 s
gradients_fft:          573 calls, 102.45 s

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

# Date 2008-01-16 Time 04:15:46 PST -0800 (1200485746.04 s)
Start R-work = 0.4343, R-free = 0.4338 (no bulk solvent and anisotropic scale)
Final R-work = 0.1360, R-free = 0.1796 (no bulk solvent and anisotropic scale)

Start R-work = 0.4264, R-free = 0.4224
Final R-work = 0.1133, R-free = 0.1623