# Date 2008-01-16 Time 06:36:53 PST -0800 (1200494213.33 s)
#phil __OFF__

Command line arguments: "../1218.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 11286
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1218

-------------------------------------------------------------------------------
  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: (72.0062, 45.7567, 87.6859, 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: 2.75, per 1000 atoms: 0.97


================================== 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: (72.0062, 45.7567, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3277 1.95482
Completeness in resolution range: 0.908286
Completeness with d_max=infinity: 0.905766

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.3277
                             d_min =   1.9548

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: (72.0062, 45.7567, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3277 1.95482
Completeness in resolution range: 0.908286
Completeness with d_max=infinity: 0.905766

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.3282 -  4.1856 [2263/2290]  2037   226  10.0%
  bin  2:  4.1856 -  3.3335 [2179/2199]  1966   213   9.8%
  bin  3:  3.3335 -  2.9154 [2140/2159]  1917   223  10.4%
  bin  4:  2.9154 -  2.6504 [2124/2154]  1911   213  10.0%
  bin  5:  2.6504 -  2.4612 [2130/2149]  1913   217  10.2%
  bin  6:  2.4612 -  2.3166 [2093/2118]  1886   207   9.9%
  bin  7:  2.3166 -  2.2010 [2109/2137]  1897   212  10.1%
  bin  8:  2.2010 -  2.1054 [2077/2113]  1875   202   9.7%
  bin  9:  2.1054 -  2.0245 [1956/2138]  1768   188   9.6%
  bin 10:  2.0245 -  1.9548 [ 518/2110]   460    58  11.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1218/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:
        1.66 -     2.30: 27
        2.30 -     2.95: 1681
        2.95 -     3.60: 4543
        3.60 -     4.25: 9131
        4.25 -     4.90: 12804
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.655 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28181 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_1218/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1218/model_refine_001.geo

CPU time processing inputs: 7.73


============================ 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 = 72.00625 45.75675 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4981   r_free= 0.5033   ksol= 0.00   Bsol= 0.00   scale= 0.859    |
|                                                                             |
| 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:   0.91 A                  |
| x-ray target function (ml) for work reflections: 6.306382                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3282 -  4.6698 0.99   1473  165 0.4144 0.4073      6.6416      6.6301|
|  2:  4.6698 -  3.7241 0.99   1417  154 0.4509 0.4457      6.8699      6.8729|
|  3:  3.7241 -  3.2585 0.99   1381  153 0.4732 0.4628      6.6926      6.6847|
|  4:  3.2585 -  2.9629 0.99   1379  158 0.5030 0.5448      6.5516      6.5492|
|  5:  2.9629 -  2.7518 0.99   1367  155 0.5242 0.5639       6.374      6.3894|
|  6:  2.7518 -  2.5904 0.99   1363  150 0.5340 0.5013      6.2965      6.2383|
|  7:  2.5904 -  2.4612 0.99   1364  157 0.5399 0.5278      6.2341      6.1714|
|  8:  2.4612 -  2.3545 0.98   1357  142 0.5457 0.5876      6.1687      6.2074|
|  9:  2.3545 -  2.2641 0.98   1333  155 0.5343 0.5701      6.1394      6.1839|
| 10:  2.2641 -  2.1862 1.00   1353  149 0.5385 0.5227      6.0647       6.017|
| 11:  2.1862 -  2.1181 0.98   1347  150 0.5253 0.5522      6.0098       6.059|
| 12:  2.1181 -  2.0577 0.98   1348  143 0.5253 0.5170      5.9215      5.8998|
| 13:  2.0577 -  2.0036 0.69    930  111 0.5367 0.4748      5.8855      5.7947|
| 14:  2.0036 -  1.9548 0.15    218   17 0.4981 0.4024      5.8566      5.9581|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3282 -  4.6698  1473   165  0.68  36.07   0.79     0.74      81608.10|
|  2:  4.6698 -  3.7241  1417   154  0.62  41.84   0.87     0.73     140757.17|
|  3:  3.7241 -  3.2585  1381   153  0.44  56.70   0.88     0.61     157122.18|
|  4:  3.2585 -  2.9629  1379   158  0.29  68.47   0.85     0.43     149919.91|
|  5:  2.9629 -  2.7518  1367   155  0.22  73.57   0.85     0.34     109050.30|
|  6:  2.7518 -  2.5904  1363   150  0.20  75.17   0.87     0.30      92003.31|
|  7:  2.5904 -  2.4612  1364   157  0.21  74.18   0.87     0.31      76387.12|
|  8:  2.4612 -  2.3545  1357   142  0.21  74.61   0.86     0.31      69283.31|
|  9:  2.3545 -  2.2641  1333   155  0.25  71.55   0.90     0.37      61150.96|
| 10:  2.2641 -  2.1862  1353   149  0.25  71.27   0.89     0.39      54049.80|
| 11:  2.1862 -  2.1181  1347   150  0.25  71.15   0.93     0.40      51244.34|
| 12:  2.1181 -  2.0577  1348   143  0.24  71.79   0.89     0.40      45824.18|
| 13:  2.0577 -  2.0036   930   111  0.28  68.85   0.94     0.48      39132.62|
| 14:  2.0036 -  1.9548   218    17  0.44  56.97   1.04     0.64      27670.46|
|alpha:            min =        0.30 max =            0.74 mean =         0.45|
|beta:             min =    27670.46 max =       157122.18 mean =     87574.30|
|figures of merit: min =        0.00 max =            1.00 mean =         0.32|
|phase err.(work): min =        0.00 max =           89.98 mean =        65.31|
|phase err.(test): min =        0.00 max =           89.90 mean =        65.72|
|-----------------------------------------------------------------------------|

============================== 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 = 18.081334             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.876   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.946890              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.164   (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 |  1.655 -  1.980:       11 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.980 -  2.304:       16 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.304 -  2.629:       59 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.629 -  2.953:     1622 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.953 -  3.278:     1927 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.278 -  3.602:     2616 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.602 -  3.927:     4734 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.927 -  4.251:     4397 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.251 -  4.575:     5844 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.575 -  4.900:     6960 |
|-----------------------------------------------------------------------------|
|-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 |        0.185 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.655 |       0.492 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.970)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4981   r_free= 0.5033   ksol= 0.00   Bsol= 0.00   scale= 0.859    |
|                                                                             |
| 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:   0.91 A                  |
| x-ray target function (ml) for work reflections: 6.306382                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4918   r_free= 0.4996   ksol= 0.34   Bsol= 65.35   scale= 0.891   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.29,0.26,0.16,0.00,0.00,0.00); trace/3= 0.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.91 A                  |
| x-ray target function (ml) for work reflections: 6.305936                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.559199             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.708   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.081982              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.751   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4918      final r-factor (work) = 0.4317          |
| start r-factor (free) = 0.4996      final r-factor (free) = 0.4737          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 46.0480 = 14.56 * 0.50 * 6.3003 + 1.00 * 0.1845                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 45.6336 = 14.56 * 0.50 * 6.2514 + 1.00 * 0.1259                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4317      final r-factor (work) = 0.3967          |
| start r-factor (free) = 0.4737      final r-factor (free) = 0.4793          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.0213 = 2.08 * 1.00 * 6.2514 + 1.00 * 0.0060                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.9325 = 2.08 * 1.00 * 6.2002 + 1.00 * 0.0238                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.970)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.25   20.88    None  None   None       |
|    all(noH): 2823   0      0.00    95.25   20.88    None  None   None       |
|    Sol.    : 438    0      0.00    95.25   34.93    None  None   None       |
|    Mac.    : 2385   0      0.00    88.58   18.30    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 -   9.525:  699   |   5:    47.626 -  57.152:   97        |
|      1:     9.525 -  19.051:  844   |   6:    57.152 -  66.677:   46        |
|      2:    19.051 -  28.576:  589   |   7:    66.677 -  76.202:   34        |
|      3:    28.576 -  38.101:  321   |   8:    76.202 -  85.727:   11        |
|      4:    38.101 -  47.626:  179   |   9:    85.727 -  95.253:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3967 r_free = 0.4793             target_work(ml) = 6.201         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3963 r_free = 0.4792             target_work(ml) = 6.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3963   r_free= 0.4792   ksol= 0.34   Bsol= 65.35   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.29,0.26,0.16,0.00,0.00,0.00); trace/3= 0.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.200409                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3972   r_free= 0.4779   ksol= 0.38   Bsol= 103.79   scale= 0.993  |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.63,0.12,0.75,0.00,0.00,0.00); trace/3= 0.50                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.201926                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 20.091136             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.253  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.851255              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.755  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3972      final r-factor (work) = 0.3460          |
| start r-factor (free) = 0.4779      final r-factor (free) = 0.4352          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 62.4321 = 20.09 * 0.50 * 6.2024 + 1.00 * 0.1259                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 61.9804 = 20.09 * 0.50 * 6.1584 + 1.00 * 0.1161                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3460      final r-factor (work) = 0.3321          |
| start r-factor (free) = 0.4352      final r-factor (free) = 0.4281          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2661 = 0.85 * 1.00 * 6.1584 + 1.00 * 0.0237                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2030 = 0.85 * 1.00 * 6.0948 + 1.00 * 0.0148                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.970)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.66   20.11    None  None   None       |
|    all(noH): 2823   0      0.00    83.66   20.11    None  None   None       |
|    Sol.    : 438    0      0.00    83.66   34.79    None  None   None       |
|    Mac.    : 2385   0      0.00    80.04   17.41    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 -   8.366:  556   |   5:    41.829 -  50.195:  103        |
|      1:     8.366 -  16.732:  878   |   6:    50.195 -  58.561:   58        |
|      2:    16.732 -  25.098:  570   |   7:    58.561 -  66.927:   45        |
|      3:    25.098 -  33.463:  372   |   8:    66.927 -  75.293:   23        |
|      4:    33.463 -  41.829:  212   |   9:    75.293 -  83.659:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3321 r_free = 0.4281             target_work(ml) = 6.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3319 r_free = 0.4277             target_work(ml) = 6.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3319   r_free= 0.4277   ksol= 0.38   Bsol= 103.79   scale= 1.027  |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.63,0.12,0.75,0.00,0.00,0.00); trace/3= 0.50                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.086715                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3322   r_free= 0.4275   ksol= 0.37   Bsol= 94.02   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.11,-0.63,0.52,-0.00,0.00,0.00); trace/3= -0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.086704                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.515647              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.650  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.323166              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 159.437  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3322      final r-factor (work) = 0.2939          |
| start r-factor (free) = 0.4275      final r-factor (free) = 0.3763          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.0196 = 7.52 * 0.50 * 6.0949 + 1.00 * 0.1159                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.8027 = 7.52 * 0.50 * 6.0501 + 1.00 * 0.0675                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2939      final r-factor (work) = 0.2753          |
| start r-factor (free) = 0.3763      final r-factor (free) = 0.3703          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0200 = 1.32 * 1.00 * 6.0501 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9151 = 1.32 * 1.00 * 5.9672 + 1.00 * 0.0195                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.970)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.12   20.60    None  None   None       |
|    all(noH): 2823   0      0.00    90.12   20.60    None  None   None       |
|    Sol.    : 438    0      0.00    90.12   40.06    None  None   None       |
|    Mac.    : 2385   0      0.00    80.27   17.03    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 -   9.012:  719   |   5:    45.060 -  54.072:  114        |
|      1:     9.012 -  18.024:  837   |   6:    54.072 -  63.084:   83        |
|      2:    18.024 -  27.036:  514   |   7:    63.084 -  72.096:   32        |
|      3:    27.036 -  36.048:  298   |   8:    72.096 -  81.108:   22        |
|      4:    36.048 -  45.060:  200   |   9:    81.108 -  90.120:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2753 r_free = 0.3703             target_work(ml) = 5.960         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2750 r_free = 0.3703             target_work(ml) = 5.959         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2750   r_free= 0.3703   ksol= 0.37   Bsol= 94.02   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.11,-0.63,0.52,-0.00,0.00,0.00); trace/3= -0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 5.958937                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2755   r_free= 0.3700   ksol= 0.36   Bsol= 95.75   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.66,-1.17,0.21,-0.00,0.00,0.00); trace/3= -0.54                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 5.958755                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.772109              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.365  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.028480              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.633  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2755      final r-factor (work) = 0.2335          |
| start r-factor (free) = 0.3700      final r-factor (free) = 0.3134          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.2887 = 5.77 * 0.50 * 5.9670 + 1.00 * 0.0675                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.1009 = 5.77 * 0.50 * 5.8998 + 1.00 * 0.0737                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2335      final r-factor (work) = 0.2141          |
| start r-factor (free) = 0.3134      final r-factor (free) = 0.2892          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0871 = 1.03 * 1.00 * 5.8998 + 1.00 * 0.0193                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9596 = 1.03 * 1.00 * 5.7779 + 1.00 * 0.0172                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.970)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.71  20.40    None  None   None       |
|    all(noH): 2823   0      0.00    104.71  20.40    None  None   None       |
|    Sol.    : 438    0      1.88    104.71  47.30    None  None   None       |
|    Mac.    : 2385   0      0.00    94.10   15.46    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 -  10.471:  987   |   5:    52.356 -  62.827:  117        |
|      1:    10.471 -  20.942:  945   |   6:    62.827 -  73.298:   68        |
|      2:    20.942 -  31.414:  331   |   7:    73.298 -  83.770:   32        |
|      3:    31.414 -  41.885:  206   |   8:    83.770 -  94.241:   17        |
|      4:    41.885 -  52.356:  116   |   9:    94.241 - 104.712:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2141 r_free = 0.2892             target_work(ml) = 5.738         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2140 r_free = 0.2887             target_work(ml) = 5.737         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2140   r_free= 0.2887   ksol= 0.36   Bsol= 95.75   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.66,-1.17,0.21,-0.00,0.00,0.00); trace/3= -0.54                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.737330                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2141   r_free= 0.2888   ksol= 0.35   Bsol= 85.54   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.15,-1.93,-0.14,-0.00,-0.00,-0.00); trace/3= -1.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.736087                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.893711              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.204  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.413081              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.549  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2141      final r-factor (work) = 0.1762          |
| start r-factor (free) = 0.2888      final r-factor (free) = 0.2440          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.2120 = 4.89 * 0.50 * 5.7782 + 1.00 * 0.0737                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.9221 = 4.89 * 0.50 * 5.6623 + 1.00 * 0.0672                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1762      final r-factor (work) = 0.1614          |
| start r-factor (free) = 0.2440      final r-factor (free) = 0.2225          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3562 = 0.41 * 1.00 * 5.6623 + 1.00 * 0.0172                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2976 = 0.41 * 1.00 * 5.5331 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.970)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.85    95.30   19.07    None  None   None       |
|    all(noH): 2823   0      0.85    95.30   19.07    None  None   None       |
|    Sol.    : 438    0      2.69    95.30   47.26    None  None   None       |
|    Mac.    : 2385   0      0.85    93.57   13.89    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.845 -  10.290: 1018   |   5:    48.071 -  57.516:   90        |
|      1:    10.290 -  19.736: 1024   |   6:    57.516 -  66.961:   80        |
|      2:    19.736 -  29.181:  283   |   7:    66.961 -  76.406:   54        |
|      3:    29.181 -  38.626:  134   |   8:    76.406 -  85.851:   22        |
|      4:    38.626 -  48.071:  107   |   9:    85.851 -  95.297:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1614 r_free = 0.2225             target_work(ml) = 5.483         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1612 r_free = 0.2222             target_work(ml) = 5.482         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1612   r_free= 0.2222   ksol= 0.35   Bsol= 85.54   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.15,-1.93,-0.14,-0.00,-0.00,-0.00); trace/3= -1.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.481979                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3282 -  4.6698 0.99   1473  165 0.1069 0.1558      5.4932      5.7667|
|  2:  4.6698 -  3.7241 0.99   1417  154 0.1085 0.1433      5.6632      5.9294|
|  3:  3.7241 -  3.2585 0.99   1381  153 0.1469 0.2074      5.7462      6.0472|
|  4:  3.2585 -  2.9629 0.99   1379  158 0.1834 0.2407      5.7678      5.9519|
|  5:  2.9629 -  2.7518 0.99   1367  155 0.1846 0.2521      5.6469      5.8711|
|  6:  2.7518 -  2.5904 0.99   1363  150 0.1838 0.2735       5.548      5.7539|
|  7:  2.5904 -  2.4612 0.99   1364  157 0.1835 0.2412      5.4847      5.6787|
|  8:  2.4612 -  2.3545 0.98   1357  142 0.1902 0.2562       5.458      5.6544|
|  9:  2.3545 -  2.2641 0.98   1333  155 0.1772 0.2664      5.3977      5.6641|
| 10:  2.2641 -  2.1862 1.00   1353  149 0.1756 0.2431      5.3294      5.4964|
| 11:  2.1862 -  2.1181 0.98   1347  150 0.1744 0.2538      5.2861      5.6024|
| 12:  2.1181 -  2.0577 0.98   1348  143 0.1803 0.2582      5.2123      5.3942|
| 13:  2.0577 -  2.0036 0.69    930  111 0.1879 0.2477      5.1741      5.3087|
| 14:  2.0036 -  1.9548 0.15    218   17 0.1651 0.2399      5.0853      5.5332|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3282 -  4.6698  1473   165  0.92  11.66   0.97     0.95      10418.44|
|  2:  4.6698 -  3.7241  1417   154  0.93  11.30   1.04     1.02      14465.75|
|  3:  3.7241 -  3.2585  1381   153  0.89  17.22   1.06     1.06      18639.17|
|  4:  3.2585 -  2.9629  1379   158  0.84  22.47   1.04     0.99      20669.86|
|  5:  2.9629 -  2.7518  1367   155  0.83  23.60   1.04     1.02      17242.60|
|  6:  2.7518 -  2.5904  1363   150  0.81  25.20   1.01     0.94      14622.73|
|  7:  2.5904 -  2.4612  1364   157  0.83  23.97   1.04     1.00      12832.71|
|  8:  2.4612 -  2.3545  1357   142  0.81  25.23   1.02     0.97      12171.88|
|  9:  2.3545 -  2.2641  1333   155  0.81  25.48   1.03     0.95      11153.56|
| 10:  2.2641 -  2.1862  1353   149  0.81  25.59   1.04     0.98       9946.87|
| 11:  2.1862 -  2.1181  1347   150  0.82  24.99   1.04     0.95       9227.58|
| 12:  2.1181 -  2.0577  1348   143  0.81  25.61   1.03     1.00       8176.30|
| 13:  2.0577 -  2.0036   930   111  0.81  26.19   1.02     0.98       7297.39|
| 14:  2.0036 -  1.9548   218    17  0.84  22.70   1.01     0.97       6029.37|
|alpha:            min =        0.94 max =            1.06 mean =         0.99|
|beta:             min =     6029.37 max =        20669.86 mean =     12903.53|
|figures of merit: min =        0.00 max =            1.00 mean =         0.84|
|phase err.(work): min =        0.00 max =           89.98 mean =        21.98|
|phase err.(test): min =        0.00 max =           88.68 mean =        20.88|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1612   r_free= 0.2216   ksol= 0.33   Bsol= 69.53   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.72,-2.66,-0.72,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.479765                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.33 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1612   r_free= 0.2216   ksol= 0.33   Bsol= 69.53   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.72,-2.66,-0.72,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.479765                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3282 -  4.6698 0.99   1473  165 0.1076 0.1500      5.4747      5.7297|
|  2:  4.6698 -  3.7241 0.99   1417  154 0.1087 0.1429       5.655      5.9233|
|  3:  3.7241 -  3.2585 0.99   1381  153 0.1472 0.2071      5.7456      6.0441|
|  4:  3.2585 -  2.9629 0.99   1379  158 0.1836 0.2399       5.767      5.9495|
|  5:  2.9629 -  2.7518 0.99   1367  155 0.1847 0.2523      5.6471      5.8733|
|  6:  2.7518 -  2.5904 0.99   1363  150 0.1838 0.2736      5.5479      5.7531|
|  7:  2.5904 -  2.4612 0.99   1364  157 0.1837 0.2412      5.4854      5.6788|
|  8:  2.4612 -  2.3545 0.98   1357  142 0.1901 0.2570      5.4582      5.6568|
|  9:  2.3545 -  2.2641 0.98   1333  155 0.1772 0.2661      5.3976      5.6631|
| 10:  2.2641 -  2.1862 1.00   1353  149 0.1756 0.2429      5.3295      5.4976|
| 11:  2.1862 -  2.1181 0.98   1347  150 0.1743 0.2540      5.2854      5.6021|
| 12:  2.1181 -  2.0577 0.98   1348  143 0.1803 0.2587      5.2132      5.3959|
| 13:  2.0577 -  2.0036 0.69    930  111 0.1879 0.2468      5.1742      5.3075|
| 14:  2.0036 -  1.9548 0.15    218   17 0.1652 0.2398      5.0842      5.5309|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3282 -  4.6698  1473   165  0.92  11.04   0.96     0.94       9497.24|
|  2:  4.6698 -  3.7241  1417   154  0.93  10.98   1.03     1.01      13836.69|
|  3:  3.7241 -  3.2585  1381   153  0.89  17.15   1.05     1.05      18503.13|
|  4:  3.2585 -  2.9629  1379   158  0.84  22.35   1.02     0.97      20481.73|
|  5:  2.9629 -  2.7518  1367   155  0.83  23.54   1.02     1.00      17199.75|
|  6:  2.7518 -  2.5904  1363   150  0.81  25.19   0.99     0.92      14625.73|
|  7:  2.5904 -  2.4612  1364   157  0.83  23.96   1.01     0.98      12840.48|
|  8:  2.4612 -  2.3545  1357   142  0.81  25.22   0.99     0.94      12185.51|
|  9:  2.3545 -  2.2641  1333   155  0.81  25.46   1.00     0.92      11161.27|
| 10:  2.2641 -  2.1862  1353   149  0.81  25.58   1.00     0.95       9957.73|
| 11:  2.1862 -  2.1181  1347   150  0.82  24.98   1.00     0.92       9241.99|
| 12:  2.1181 -  2.0577  1348   143  0.81  25.61   0.99     0.97       8193.41|
| 13:  2.0577 -  2.0036   930   111  0.81  26.15   0.98     0.94       7295.91|
| 14:  2.0036 -  1.9548   218    17  0.84  22.57   0.96     0.93       5990.17|
|alpha:            min =        0.92 max =            1.05 mean =         0.96|
|beta:             min =     5990.17 max =        20481.73 mean =     12752.45|
|figures of merit: min =        0.00 max =            1.00 mean =         0.84|
|phase err.(work): min =        0.00 max =           89.98 mean =        21.88|
|phase err.(test): min =        0.00 max =           88.80 mean =        20.77|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.970)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.82    95.27   19.04    None  None   None       |
|    all(noH): 2823   0      0.82    95.27   19.04    None  None   None       |
|    Sol.    : 438    0      2.66    95.27   47.23    None  None   None       |
|    Mac.    : 2385   0      0.82    93.55   13.86    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:     0.817 -  10.262: 1018   |   5:    48.042 -  57.487:   90        |
|      1:    10.262 -  19.707: 1024   |   6:    57.487 -  66.932:   80        |
|      2:    19.707 -  29.152:  283   |   7:    66.932 -  76.378:   54        |
|      3:    29.152 -  38.597:  134   |   8:    76.378 -  85.823:   22        |
|      4:    38.597 -  48.042:  107   |   9:    85.823 -  95.268:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 348         
Filter by distance & map next to the model:
   mapped sites are within: 0.694 - 5.014
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 345 from: 348
   mapped sites are within: 0.750 - 5.014

peak=    7.067 closest distance to " O   HOH Z 390 " =    1.479
peak=    6.761 closest distance to " O   HOH Z 381 " =    1.483
peak=    6.593 closest distance to " O   HOH Z 103 " =    1.143
peak=    6.327 closest distance to " O   ASN A 285 " =    1.069
peak=    5.665 closest distance to " O   HOH Z  41 " =    1.261
peak=    5.623 closest distance to " O   HOH Z 399 " =    0.989
peak=    5.622 closest distance to " O   HOH Z 268 " =    1.212
peak=    5.621 closest distance to " O   HOH Z 375 " =    1.542
peak=    5.588 closest distance to " O   HOH Z 159 " =    1.117
peak=    5.537 closest distance to " O   HOH Z 245 " =    1.638
peak=    5.357 closest distance to " CG  PRO A  90 " =    1.246
peak=    5.292 closest distance to " O   HOH Z  46 " =    1.686
peak=    5.270 closest distance to " CB  LYS A 290 " =    0.942
peak=    5.162 closest distance to " NH1AARG A 145 " =    1.201
peak=    5.147 closest distance to " O   HOH Z 385 " =    1.234
peak=    5.090 closest distance to " CB  ASN A  60 " =    0.970
peak=    4.996 closest distance to " O   HOH Z 120 " =    1.244
peak=    4.892 closest distance to " O   HOH Z 360 " =    1.300
peak=    4.807 closest distance to " CZ  PHE A  16 " =    1.024
peak=    4.775 closest distance to " O   HOH Z  63 " =    1.735
peak=    4.767 closest distance to " O   HOH Z 287 " =    2.040
peak=    4.728 closest distance to " O   HOH Z 403 " =    2.313
peak=    4.724 closest distance to " O   HOH Z 416 " =    1.455
peak=    4.722 closest distance to " O   HOH Z 295 " =    1.868
peak=    4.720 closest distance to " O  BHOH Z  74 " =    1.082
peak=    4.706 closest distance to " CE2 PHE A  16 " =    1.166
peak=    4.696 closest distance to " NH2 ARG A 269 " =    0.910
peak=    4.669 closest distance to " O   HOH Z  66 " =    1.289
peak=    4.626 closest distance to " O   HOH Z 421 " =    2.721
peak=    4.597 closest distance to " O   HOH Z 131 " =    1.433
peak=    4.586 closest distance to " O   HOH Z  13 " =    1.330
peak=    4.579 closest distance to " NZ ALYS A 290 " =    1.211
peak=    4.550 closest distance to " CB  TRP A 266 " =    0.997
peak=    4.538 closest distance to " CZ  PHE A 218 " =    1.256
peak=    4.536 closest distance to " O   HOH Z 417 " =    2.627
peak=    4.528 closest distance to " O   HOH Z 255 " =    1.175
peak=    4.528 closest distance to " O   HOH Z   7 " =    2.069
peak=    4.511 closest distance to " CB  ASN A  60 " =    0.971
peak=    4.508 closest distance to " O   HOH Z  79 " =    1.082
peak=    4.480 closest distance to " O   HOH Z 431 " =    1.540
peak=    4.468 closest distance to " OG  SER A 276 " =    1.019
peak=    4.455 closest distance to " NE2 GLN A  11 " =    1.443
peak=    4.422 closest distance to " CB  SER A 216 " =    1.188
peak=    4.403 closest distance to " O   HOH Z  29 " =    1.534
peak=    4.399 closest distance to " O   HOH Z 144 " =    1.933
peak=    4.391 closest distance to " O   PRO A 198 " =    1.371
peak=    4.387 closest distance to " O   HOH Z   9 " =    2.571
peak=    4.335 closest distance to " O   ASN A  60 " =    1.119
peak=    4.316 closest distance to " N   GLY A 287 " =    0.883
peak=    4.313 closest distance to " OD2 ASP A 270 " =    1.161
peak=    4.299 closest distance to " O   HOH Z 117 " =    1.187
peak=    4.286 closest distance to " OE1 GLN A  88 " =    1.046
peak=    4.274 closest distance to " O   HOH Z 359 " =    1.657
peak=    4.272 closest distance to " O   HOH Z 316 " =    3.176
peak=    4.235 closest distance to " N   SER A  63 " =    0.814
peak=    4.233 closest distance to " O   HOH Z 287 " =    1.986
peak=    4.223 closest distance to " CA  PRO A  54 " =    0.928
peak=    4.183 closest distance to " O   HOH Z 217 " =    2.968
peak=    4.177 closest distance to " CB  SER A  63 " =    1.653
peak=    4.165 closest distance to " CB  PRO A  90 " =    1.372
peak=    4.164 closest distance to " O   HOH Z 182 " =    1.292
peak=    4.153 closest distance to " CB  PRO A  54 " =    1.247
peak=    4.126 closest distance to " O   HOH Z 154 " =    2.400
peak=    4.115 closest distance to " CB  ASN A  39 " =    0.998
peak=    4.115 closest distance to " CE  MET A  93 " =    1.691
peak=    4.113 closest distance to " O   HOH Z 126 " =    1.665
peak=    4.078 closest distance to " O   HOH Z  32 " =    1.868
peak=    4.060 closest distance to " OG  SER A  32 " =    1.181
peak=    4.058 closest distance to " CG2 THR A 221 " =    1.255
peak=    4.033 closest distance to " O   HOH Z 126 " =    1.946
peak=    4.033 closest distance to " NZ  LYS A 119 " =    2.535
peak=    4.028 closest distance to " O   HOH Z 176 " =    1.625
peak=    4.026 closest distance to " NH2 ARG A  36 " =    1.304
peak=    4.021 closest distance to " CA  VAL A 153 " =    0.967
peak=    4.016 closest distance to " N   GLN A  73 " =    1.085
peak=    4.015 closest distance to " O   HOH Z 232 " =    2.095
peak=    4.015 closest distance to " O   HOH Z 352 " =    1.853
peak=    4.015 closest distance to " O   HOH Z 186 " =    1.449
peak=    4.009 closest distance to " O   HOH Z 222 " =    1.573
peak=    4.004 closest distance to " O   HOH Z 422 " =    1.177
peak=    3.998 closest distance to " O   HOH Z 130 " =    0.931
peak=    3.985 closest distance to " O   HOH Z 396 " =    1.083
peak=    3.985 closest distance to " N   ARG A  56 " =    0.886
peak=    3.978 closest distance to " N   ASN A 285 " =    0.878
peak=    3.953 closest distance to " O   HOH Z 139 " =    1.647
peak=    3.945 closest distance to " CA  TYR A  30 " =    1.195
peak=    3.937 closest distance to " O   HOH Z 147 " =    1.454
peak=    3.929 closest distance to " CA  ASN A 284 " =    0.924
peak=    3.911 closest distance to " OD2 ASP A  27 " =    0.955
peak=    3.908 closest distance to " O   HOH Z 139 " =    2.543
peak=    3.905 closest distance to " O   HOH Z  65 " =    1.850
peak=    3.902 closest distance to " O   PRO A  54 " =    0.912
peak=    3.902 closest distance to " CB  ASP A 124 " =    1.064
peak=    3.888 closest distance to " O   HOH Z  97 " =    1.748
peak=    3.879 closest distance to " O   HOH Z 170 " =    2.039
peak=    3.876 closest distance to " CB  PHE A  61 " =    1.384
peak=    3.873 closest distance to " O   HOH Z 181 " =    2.456
peak=    3.860 closest distance to " CB  PRO A  54 " =    1.429
peak=    3.846 closest distance to " CB  SER A 276 " =    1.438
peak=    3.837 closest distance to " CB  SER A  62 " =    1.438
peak=    3.832 closest distance to " O   GLY A 211 " =    1.163
peak=    3.827 closest distance to " OD1 ASN A 285 " =    1.191
peak=    3.811 closest distance to " NH2 ARG A 269 " =    1.256
peak=    3.811 closest distance to " CE3 TRP A 274 " =    1.587
peak=    3.810 closest distance to " OG BSER A  12 " =    0.975
peak=    3.798 closest distance to " N   TYR A  15 " =    1.171
peak=    3.796 closest distance to " O   HOH Z 415 " =    1.146
peak=    3.792 closest distance to " CA  TRP A  92 " =    1.468
peak=    3.781 closest distance to " O   HOH Z  11 " =    1.477
peak=    3.776 closest distance to " CD ALYS A 290 " =    1.189
peak=    3.772 closest distance to " O   HOH Z  67 " =    1.988
peak=    3.771 closest distance to " O   HOH Z 105 " =    1.396
peak=    3.770 closest distance to " O   HOH Z 410 " =    1.478
peak=    3.769 closest distance to " CG  PRO A 243 " =    1.227
peak=    3.765 closest distance to " O   HOH Z 170 " =    1.368
peak=    3.764 closest distance to " O   HOH Z  49 " =    2.415
peak=    3.760 closest distance to " N   SER A  26 " =    1.091
peak=    3.757 closest distance to " CG2 THR A 279 " =    1.282
peak=    3.734 closest distance to " ND2BASN A 224 " =    0.891
peak=    3.731 closest distance to " CB  ASN A 285 " =    1.118
peak=    3.712 closest distance to " O   HOH Z 287 " =    1.870
peak=    3.711 closest distance to " NE1 TRP A 266 " =    1.782
peak=    3.709 closest distance to " CG2BVAL A  41 " =    1.282
peak=    3.696 closest distance to " CB  GLN A 183 " =    1.135
peak=    3.695 closest distance to " CB  VAL A 202 " =    1.575
peak=    3.690 closest distance to " O   HOH Z 346 " =    1.210
peak=    3.688 closest distance to " CB  TRP A 179 " =    1.440
peak=    3.686 closest distance to " O   HOH Z 119 " =    1.521
peak=    3.682 closest distance to " ND2 ASN A 285 " =    1.130
peak=    3.659 closest distance to " O   THR A 294 " =    0.955
peak=    3.655 closest distance to " O   HOH Z 427 " =    1.503
peak=    3.639 closest distance to " O   PHE A  59 " =    1.035
peak=    3.639 closest distance to " N   GLY A 302 " =    1.009
peak=    3.638 closest distance to " O   HOH Z 233 " =    1.265
peak=    3.626 closest distance to " CB  ALA A  10 " =    1.221
peak=    3.623 closest distance to " O   HOH Z  77 " =    1.497
peak=    3.623 closest distance to " CG  PRO A 198 " =    1.343
peak=    3.620 closest distance to " N   PHE A  59 " =    0.866
peak=    3.618 closest distance to " O   HOH Z 317 " =    2.398
peak=    3.618 closest distance to " CB  LEU A  83 " =    0.841
peak=    3.617 closest distance to " NE2 HIS A 207 " =    1.061
peak=    3.617 closest distance to " O   HOH Z 244 " =    1.719
peak=    3.616 closest distance to " CG  ASN A 252 " =    1.421
peak=    3.614 closest distance to " O   HOH Z 393 " =    1.408
peak=    3.612 closest distance to " CA  ILE A 234 " =    1.181
peak=    3.610 closest distance to " CZ3 TRP A 123 " =    1.675
peak=    3.609 closest distance to " CD  ARG A 195 " =    3.478
peak=    3.609 closest distance to " O   HOH Z 135 " =    1.457
peak=    3.608 closest distance to " O   HOH Z 369 " =    1.444
peak=    3.603 closest distance to " O   HOH Z 330 " =    1.122
peak=    3.602 closest distance to " CG  GLN A  88 " =    0.917
peak=    3.593 closest distance to " CB  GLN A  89 " =    1.196
peak=    3.592 closest distance to " O   HOH Z  69 " =    1.398
peak=    3.591 closest distance to " CB  ARG A 275 " =    1.201
peak=    3.588 closest distance to " CB  ALA A  43 " =    1.065
peak=    3.568 closest distance to " O   HOH Z 286 " =    1.906
peak=    3.567 closest distance to " CB  ARG A  66 " =    0.825
peak=    3.564 closest distance to " CA  SER A  12 " =    1.510
peak=    3.563 closest distance to " CB  ALA A   8 " =    0.876
peak=    3.544 closest distance to " N   GLU A   2 " =    1.480
peak=    3.542 closest distance to " O   ARG A  14 " =    1.081
peak=    3.541 closest distance to " N   ALA A 165 " =    1.351
peak=    3.540 closest distance to " NE2 GLN A  89 " =    1.457
peak=    3.528 closest distance to " CB  GLU A 152 " =    1.202
peak=    3.524 closest distance to " CG  LEU A 167 " =    1.386
peak=    3.521 closest distance to " O   HOH Z  59 " =    1.819
peak=    3.519 closest distance to " CD  LYS A  76 " =    1.598
peak=    3.518 closest distance to " OD1 ASP A 200 " =    1.571
peak=    3.517 closest distance to " O   HOH Z 419 " =    2.246
peak=    3.515 closest distance to " CB  PHE A  16 " =    1.267
peak=    3.515 closest distance to " CD2 LEU A   5 " =    1.750
peak=    3.511 closest distance to " CA  GLY A 241 " =    3.874
peak=    3.503 closest distance to " N   PHE A 130 " =    1.325
peak=    3.501 closest distance to " O   HOH Z 158 " =    2.904
peak=    3.500 closest distance to " N   SER A 210 " =    1.052
peak=    3.497 closest distance to " O   HOH Z  88 " =    3.767
peak=    3.489 closest distance to " CB  SER A   3 " =    1.576
peak=    3.481 closest distance to " O   HOH Z   7 " =    2.736
peak=    3.479 closest distance to " O   HOH Z 172 " =    1.888
peak=    3.478 closest distance to " O   HOH Z  39 " =    1.365
peak=    3.476 closest distance to " O   HOH Z 155 " =    1.845
peak=    3.474 closest distance to " O   HOH Z  84 " =    0.997
peak=    3.467 closest distance to " CB  SER A 210 " =    1.104
peak=    3.466 closest distance to " O   HOH Z 313 " =    2.175
peak=    3.466 closest distance to " NZ  LYS A  48 " =    2.278
peak=    3.452 closest distance to " O   HOH Z 213 " =    2.107
peak=    3.448 closest distance to " O   HOH Z 427 " =    2.142
peak=    3.447 closest distance to " O   HOH Z  92 " =    1.368
peak=    3.447 closest distance to " O   PHE A 283 " =    1.268
peak=    3.446 closest distance to " O   HOH Z  61 " =    1.111
peak=    3.444 closest distance to " O   HOH Z 272 " =    1.865
peak=    3.439 closest distance to " N   SER A  87 " =    1.487
peak=    3.438 closest distance to " O   HOH Z 184 " =    1.973
peak=    3.434 closest distance to " CE2 TYR A 186 " =    0.969
peak=    3.433 closest distance to " CB  SER A 271 " =    1.279
peak=    3.433 closest distance to " O   HOH Z 380 " =    2.221
peak=    3.431 closest distance to " O   HOH Z 239 " =    1.593
peak=    3.431 closest distance to " OD1 ASN A  69 " =    3.006
peak=    3.428 closest distance to " CA  ARG A  36 " =    1.222
peak=    3.424 closest distance to " CD1AILE A 234 " =    1.228
peak=    3.423 closest distance to " CB  GLN A 223 " =    1.486
peak=    3.421 closest distance to " OD1 ASN A 249 " =    1.159
peak=    3.420 closest distance to " O   HOH Z  35 " =    4.376
peak=    3.420 closest distance to " CE3 TRP A  85 " =    1.026
peak=    3.417 closest distance to " CG2 ILE A 239 " =    1.191
peak=    3.415 closest distance to " CB  ALA A 233 " =    1.229
peak=    3.415 closest distance to " CA  ARG A 275 " =    0.946
peak=    3.411 closest distance to " CB  TRP A 150 " =    1.052
peak=    3.408 closest distance to " CG1 ILE A 120 " =    1.232
peak=    3.408 closest distance to " O   HOH Z 298 " =    2.453
peak=    3.408 closest distance to " O   HOH Z 258 " =    1.953
peak=    3.407 closest distance to " CD  ARG A 259 " =    1.316
peak=    3.406 closest distance to " CD2 LEU A 143 " =    1.452
peak=    3.406 closest distance to " O   HOH Z 423 " =    2.101
peak=    3.405 closest distance to " O   HOH Z  57 " =    2.339
peak=    3.402 closest distance to " N   ALA A  84 " =    1.924
peak=    3.401 closest distance to " CB  ALA A 114 " =    1.154
peak=    3.397 closest distance to " O   HOH Z 422 " =    2.276
peak=    3.396 closest distance to " O   HOH Z 386 " =    3.058
peak=    3.394 closest distance to " CA  SER A 271 " =    0.999
peak=    3.390 closest distance to " O   HOH Z 219 " =    2.719
peak=    3.388 closest distance to " CE1 PHE A 225 " =    1.126
peak=    3.386 closest distance to " C   ASN A 209 " =    1.838
peak=    3.386 closest distance to " CE1 PHE A  59 " =    0.871
peak=    3.381 closest distance to " O   HOH Z 239 " =    1.433
peak=    3.381 closest distance to " CA  ASN A 285 " =    1.106
peak=    3.381 closest distance to " O   HOH Z 112 " =    1.194
peak=    3.379 closest distance to " CA  ASN A 284 " =    1.094
peak=    3.378 closest distance to " O   SER A 273 " =    0.903
peak=    3.366 closest distance to " CB  MET A  47 " =    1.062
peak=    3.363 closest distance to " N   LYS A 290 " =    1.170
peak=    3.362 closest distance to " CA  SER A  87 " =    0.903
peak=    3.359 closest distance to " O   HOH Z 128 " =    1.800
peak=    3.344 closest distance to " O   HOH Z 189 " =    3.351
peak=    3.334 closest distance to " O   HOH Z 135 " =    1.748
peak=    3.332 closest distance to " O   HOH Z  69 " =    1.466
peak=    3.331 closest distance to " O   HOH Z 171 " =    3.556
peak=    3.330 closest distance to " CD1 PHE A 283 " =    1.228
peak=    3.330 closest distance to " N   CYS A 260 " =    1.075
peak=    3.328 closest distance to " O   HOH Z 293 " =    1.246
peak=    3.328 closest distance to " O   THR A  82 " =    2.581
peak=    3.327 closest distance to " O   HOH Z 127 " =    1.587
peak=    3.326 closest distance to " CG2 VAL A 232 " =    1.248
peak=    3.320 closest distance to " O   HOH Z  30 " =    1.692
peak=    3.316 closest distance to " O   HOH Z 333 " =    0.958
peak=    3.314 closest distance to " CE2 PHE A  61 " =    0.931
peak=    3.314 closest distance to " O   SER A 271 " =    1.176
peak=    3.313 closest distance to " O   HOH Z  52 " =    1.262
peak=    3.310 closest distance to " O   GLN A  55 " =    1.498
peak=    3.306 closest distance to " OD1 ASP A  65 " =    1.875
peak=    3.303 closest distance to " CB  LYS A  48 " =    1.130
peak=    3.303 closest distance to " O   HOH Z 175 " =    3.893
peak=    3.300 closest distance to " O   HOH Z 153 " =    3.668
peak=    3.300 closest distance to " O   ASN A  69 " =    1.248
peak=    3.299 closest distance to " CA  ARG A 195 " =    1.433
peak=    3.298 closest distance to " CA  GLU A 152 " =    1.150
peak=    3.291 closest distance to " NE2 GLN A  55 " =    1.345
peak=    3.290 closest distance to " CD2 LEU A 300 " =    1.390
peak=    3.289 closest distance to " O   HOH Z 171 " =    1.821
peak=    3.287 closest distance to " CB  ASP A 286 " =    1.298
peak=    3.286 closest distance to " O   HOH Z 143 " =    1.400
peak=    3.286 closest distance to " C   GLN A  73 " =    1.060
peak=    3.281 closest distance to " O   HOH Z 115 " =    2.119
peak=    3.272 closest distance to " N   VAL A 296 " =    2.017
peak=    3.269 closest distance to " CG2 THR A 251 " =    1.669
peak=    3.268 closest distance to " O   HOH Z 302 " =    1.478
peak=    3.265 closest distance to " O   HOH Z 287 " =    1.923
peak=    3.264 closest distance to " CB  ASP A  50 " =    1.381
peak=    3.262 closest distance to " CA  SER A 273 " =    1.037
peak=    3.258 closest distance to " O   HOH Z 266 " =    1.666
peak=    3.258 closest distance to " CG1 VAL A 296 " =    1.230
peak=    3.257 closest distance to " CA  GLU A  46 " =    0.765
peak=    3.256 closest distance to " CD2 TRP A 179 " =    2.221
peak=    3.254 closest distance to " O   GLY A 302 " =    1.615
peak=    3.252 closest distance to " O   HOH Z  91 " =    2.490
peak=    3.251 closest distance to " CG2 ILE A 106 " =    1.055
peak=    3.250 closest distance to " CA  TRP A 150 " =    0.837
peak=    3.246 closest distance to " O   HOH Z 248 " =    1.797
peak=    3.235 closest distance to " CB  THR A 235 " =    1.301
peak=    3.233 closest distance to " CB  THR A   4 " =    1.172
peak=    3.230 closest distance to " C   GLY A 111 " =    1.445
peak=    3.227 closest distance to " O   ASN A 142 " =    1.181
peak=    3.226 closest distance to " CG  GLN A  58 " =    2.509
peak=    3.225 closest distance to " O   HOH Z  22 " =    1.560
peak=    3.221 closest distance to " CG2 ILE A  20 " =    1.554
peak=    3.221 closest distance to " O   HOH Z 332 " =    1.403
peak=    3.221 closest distance to " CD  ARG A  56 " =    0.939
peak=    3.215 closest distance to " O   HOH Z 276 " =    1.462
peak=    3.212 closest distance to " O   THR A 182 " =    1.624
peak=    3.203 closest distance to " O   HOH Z 349 " =    1.096
peak=    3.197 closest distance to " CA  ILE A 263 " =    1.091
peak=    3.196 closest distance to " O   HOH Z 401 " =    1.113
peak=    3.190 closest distance to " C   HIS A 115 " =    1.093
peak=    3.190 closest distance to " O   HOH Z 284 " =    1.734
peak=    3.189 closest distance to " CG  GLN A 144 " =    0.940
peak=    3.189 closest distance to " OD1 ASN A  45 " =    1.553
peak=    3.185 closest distance to " CG2 THR A 246 " =    1.808
peak=    3.185 closest distance to " CB  ASN A 148 " =    1.167
peak=    3.180 closest distance to " O   HOH Z 362 " =    2.103
peak=    3.180 closest distance to " CA  ARG A  66 " =    1.325
peak=    3.178 closest distance to " O   HOH Z 212 " =    1.733
peak=    3.174 closest distance to " O   HOH Z  89 " =    1.861
peak=    3.174 closest distance to " CB  GLU A 128 " =    1.094
peak=    3.173 closest distance to " O   HOH Z 313 " =    1.859
peak=    3.172 closest distance to " CH2 TRP A 150 " =    1.203
peak=    3.169 closest distance to " CB  SER A  63 " =    1.165
peak=    3.168 closest distance to " CG  GLN A  55 " =    0.797
peak=    3.167 closest distance to " O   HOH Z 353 " =    2.622
peak=    3.167 closest distance to " CB  ARG A 190 " =    0.789
peak=    3.166 closest distance to " CG  GLU A   2 " =    0.972
peak=    3.158 closest distance to " O   HOH Z 412 " =    1.628
peak=    3.157 closest distance to " O   HOH Z  53 " =    1.784
peak=    3.155 closest distance to " N   ALA A 295 " =    1.674
peak=    3.153 closest distance to " O   HOH Z 102 " =    1.238
peak=    3.153 closest distance to " CB  ASP A 107 " =    1.130
peak=    3.147 closest distance to " CB  ALA A 248 " =    1.577
peak=    3.146 closest distance to " CA  LEU A 101 " =    1.124
peak=    3.132 closest distance to " CB  LYS A 181 " =    1.977
peak=    3.132 closest distance to " CD1 LEU A   5 " =    1.781
peak=    3.127 closest distance to " O   HOH Z 395 " =    1.365
peak=    3.123 closest distance to " O   HOH Z 437 " =    2.111
peak=    3.117 closest distance to " O   HOH Z 407 " =    2.038
peak=    3.117 closest distance to " O   HOH Z  80 " =    1.487
peak=    3.115 closest distance to " O   THR A 251 " =    1.189
peak=    3.113 closest distance to " NH2BARG A 190 " =    1.301
peak=    3.108 closest distance to " O   HOH Z 149 " =    2.109
peak=    3.104 closest distance to " O   HOH Z 193 " =    1.978
peak=    3.103 closest distance to " O   HOH Z 368 " =    2.173
peak=    3.102 closest distance to " O   HOH Z 363 " =    1.272
peak=    3.098 closest distance to " CA  ASP A 200 " =    1.069
peak=    3.097 closest distance to " CA  GLY A  57 " =    1.572
peak=    3.092 closest distance to " CE2 PHE A  61 " =    0.929
peak=    3.087 closest distance to " O   HOH Z 325 " =    2.192
peak=    3.084 closest distance to " O   HOH Z  51 " =    2.176
peak=    3.084 closest distance to " O   TRP A  70 " =    1.237
peak=    3.081 closest distance to " O   HOH Z 303 " =    1.278
peak=    3.079 closest distance to " N   GLN A 278 " =    0.961
peak=    3.076 closest distance to " CG  ARG A 159 " =    0.860
peak=    3.068 closest distance to " NH2 ARG A  24 " =    0.750
peak=    3.065 closest distance to " NE2 GLN A  73 " =    1.589
peak=    3.065 closest distance to " CG1 VAL A 125 " =    2.191
peak=    3.055 closest distance to " CB  ALA A 114 " =    0.821
peak=    3.051 closest distance to " O   HOH Z 336 " =    5.014
peak=    3.034 closest distance to " CA  ALA A 180 " =    1.277
peak=    3.028 closest distance to " CG  GLU A 277 " =    2.309

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 214         
Filter by distance & map next to the model:
   mapped sites are within: 0.390 - 5.713
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 214
   mapped sites are within: 0.709 - 5.713

peak=   -5.194 closest distance to " O   ASN A 285 " =    1.145
peak=   -4.983 closest distance to " CB  ASN A 285 " =    2.002
peak=   -4.655 closest distance to " O   HOH Z 401 " =    0.811
peak=   -4.622 closest distance to " O   HOH Z  84 " =    1.059
peak=   -4.574 closest distance to " N   ARG A 275 " =    1.290
peak=   -4.564 closest distance to " OE1 GLU A  44 " =    1.449
peak=   -4.509 closest distance to " O   PRO A 198 " =    1.059
peak=   -4.468 closest distance to " CA  ARG A  56 " =    0.927
peak=   -4.393 closest distance to " OG  SER A  63 " =    1.150
peak=   -4.387 closest distance to " O   HOH Z  27 " =    0.726
peak=   -4.312 closest distance to " O   HOH Z 316 " =    1.914
peak=   -4.299 closest distance to " N   PRO A  54 " =    1.131
peak=   -4.278 closest distance to " OG  SER A  97 " =    1.841
peak=   -4.256 closest distance to " O   GLY A  80 " =    2.531
peak=   -4.249 closest distance to " O   HOH Z 313 " =    1.433
peak=   -4.152 closest distance to " CB  GLN A  55 " =    1.310
peak=   -4.128 closest distance to " OG1 THR A 157 " =    1.278
peak=   -4.120 closest distance to " CA  GLY A 241 " =    2.310
peak=   -4.082 closest distance to " CG BLYS A 290 " =    0.747
peak=   -4.053 closest distance to " O   HOH Z 404 " =    0.952
peak=   -4.052 closest distance to " CD  ARG A  14 " =    3.250
peak=   -4.028 closest distance to " O   HOH Z  32 " =    1.781
peak=   -4.019 closest distance to " CG  GLN A  88 " =    0.845
peak=   -4.016 closest distance to " O   VAL A 125 " =    2.288
peak=   -4.009 closest distance to " O   HOH Z  54 " =    1.085
peak=   -3.991 closest distance to " O   ALA A  10 " =    1.563
peak=   -3.986 closest distance to " ND2 ASN A 209 " =    1.845
peak=   -3.939 closest distance to " O   HOH Z  28 " =    0.818
peak=   -3.925 closest distance to " CG  TRP A 274 " =    1.147
peak=   -3.918 closest distance to " OE1 GLN A  88 " =    0.904
peak=   -3.901 closest distance to " O   HOH Z 163 " =    1.192
peak=   -3.876 closest distance to " OG  SER A  32 " =    0.738
peak=   -3.872 closest distance to " O   HOH Z 385 " =    1.223
peak=   -3.858 closest distance to " C   PHE A  61 " =    0.983
peak=   -3.790 closest distance to " O   HOH Z 111 " =    1.788
peak=   -3.787 closest distance to " N   ARG A  66 " =    1.163
peak=   -3.775 closest distance to " CD1 TYR A 214 " =    1.595
peak=   -3.773 closest distance to " CB  PHE A 130 " =    1.163
peak=   -3.768 closest distance to " O   MET A  47 " =    2.800
peak=   -3.762 closest distance to " OD2 ASP A 270 " =    1.057
peak=   -3.756 closest distance to " N   ALA A  43 " =    2.562
peak=   -3.738 closest distance to " CD1 TYR A 247 " =    2.671
peak=   -3.722 closest distance to " C   ILE A 239 " =    1.911
peak=   -3.718 closest distance to " CG1 VAL A 265 " =    2.466
peak=   -3.704 closest distance to " O   SER A 271 " =    1.349
peak=   -3.703 closest distance to " O   HOH Z  83 " =    1.141
peak=   -3.700 closest distance to " O   HOH Z 323 " =    1.694
peak=   -3.687 closest distance to " O   HOH Z 417 " =    1.477
peak=   -3.682 closest distance to " C   VAL A  72 " =    0.767
peak=   -3.669 closest distance to " O   HOH Z 255 " =    0.772
peak=   -3.640 closest distance to " CG2BVAL A  41 " =    1.354
peak=   -3.639 closest distance to " O   ALA A 226 " =    1.355
peak=   -3.632 closest distance to " O   LYS A 193 " =    1.583
peak=   -3.632 closest distance to " NH2AARG A 275 " =    5.713
peak=   -3.613 closest distance to " CG  GLN A  73 " =    1.243
peak=   -3.611 closest distance to " N   GLY A 287 " =    0.950
peak=   -3.599 closest distance to " C   LEU A 101 " =    1.354
peak=   -3.593 closest distance to " CD2 TYR A 116 " =    2.267
peak=   -3.592 closest distance to " O   HOH Z  85 " =    2.103
peak=   -3.590 closest distance to " CA  ASN A 284 " =    0.843
peak=   -3.583 closest distance to " CB  ALA A 291 " =    2.008
peak=   -3.566 closest distance to " CE2 TYR A  30 " =    2.453
peak=   -3.564 closest distance to " CD1 PHE A  61 " =    1.299
peak=   -3.562 closest distance to " O   HOH Z  37 " =    1.278
peak=   -3.558 closest distance to " O   SER A 273 " =    1.000
peak=   -3.551 closest distance to " CD2 HIS A 207 " =    1.462
peak=   -3.547 closest distance to " N   ASP A 171 " =    2.589
peak=   -3.544 closest distance to " O   HOH Z 368 " =    1.882
peak=   -3.542 closest distance to " O   HOH Z  51 " =    1.317
peak=   -3.536 closest distance to " O   TRP A  70 " =    1.338
peak=   -3.529 closest distance to " O   HOH Z 389 " =    2.666
peak=   -3.528 closest distance to " CA  GLY A 133 " =    1.987
peak=   -3.525 closest distance to " CG  TRP A 266 " =    1.504
peak=   -3.522 closest distance to " O   HOH Z 257 " =    1.144
peak=   -3.521 closest distance to " CD2 LEU A 167 " =    2.041
peak=   -3.517 closest distance to " O   HOH Z 102 " =    1.870
peak=   -3.516 closest distance to " CG2 ILE A 120 " =    0.852
peak=   -3.515 closest distance to " O   HOH Z 103 " =    0.709
peak=   -3.513 closest distance to " CA  GLY A 203 " =    2.376
peak=   -3.504 closest distance to " CD  LYS A 166 " =    2.609
peak=   -3.504 closest distance to " C   PHE A  59 " =    0.953
peak=   -3.500 closest distance to " CG  MET A 105 " =    0.897
peak=   -3.499 closest distance to " NE1 TRP A 179 " =    1.099
peak=   -3.498 closest distance to " CB  ALA A   9 " =    2.662
peak=   -3.495 closest distance to " NH1 ARG A  36 " =    0.978
peak=   -3.494 closest distance to " CZ  ARG A  24 " =    2.099
peak=   -3.492 closest distance to " CA  GLY A  98 " =    1.739
peak=   -3.490 closest distance to " O   HOH Z 133 " =    1.218
peak=   -3.487 closest distance to " O   GLN A 240 " =    3.157
peak=   -3.483 closest distance to " O   HOH Z 286 " =    1.767
peak=   -3.479 closest distance to " CG1 VAL A 125 " =    1.542
peak=   -3.476 closest distance to " CD  GLN A  55 " =    0.976
peak=   -3.475 closest distance to " O   PRO A 163 " =    1.964
peak=   -3.471 closest distance to " O   HOH Z 242 " =    1.690
peak=   -3.468 closest distance to " C   ARG A 275 " =    1.070
peak=   -3.467 closest distance to " O   HOH Z 118 " =    1.149
peak=   -3.464 closest distance to " O   HOH Z 390 " =    2.730
peak=   -3.464 closest distance to " O   HOH Z  69 " =    2.136
peak=   -3.462 closest distance to " CG2 ILE A 151 " =    2.441
peak=   -3.458 closest distance to " O   HOH Z 216 " =    1.747
peak=   -3.457 closest distance to " O   HOH Z 131 " =    1.071
peak=   -3.455 closest distance to " O   HOH Z 139 " =    2.550
peak=   -3.448 closest distance to " N   GLU A 277 " =    1.462
peak=   -3.443 closest distance to " O   HOH Z  70 " =    2.082
peak=   -3.439 closest distance to " CZ  PHE A  16 " =    0.851
peak=   -3.438 closest distance to " ND2 ASN A 285 " =    1.914
peak=   -3.437 closest distance to " CG2 ILE A 120 " =    1.208
peak=   -3.434 closest distance to " CD  GLN A 223 " =    1.118
peak=   -3.431 closest distance to " O   HOH Z 417 " =    2.619
peak=   -3.429 closest distance to " CD2 TYR A 293 " =    1.905
peak=   -3.426 closest distance to " CA  ILE A 120 " =    1.081
peak=   -3.422 closest distance to " CB  TYR A  68 " =    0.946
peak=   -3.419 closest distance to " ND2 ASN A 285 " =    1.517
peak=   -3.408 closest distance to " CG  PRO A 163 " =    2.403
peak=   -3.397 closest distance to " O   SER A  62 " =    1.109
peak=   -3.397 closest distance to " O   HOH Z 381 " =    1.135
peak=   -3.387 closest distance to " OE1 GLN A  55 " =    2.194
peak=   -3.383 closest distance to " CG2 VAL A 125 " =    1.707
peak=   -3.379 closest distance to " O   THR A 178 " =    1.104
peak=   -3.369 closest distance to " O   HOH Z 218 " =    3.606
peak=   -3.368 closest distance to " O   HOH Z 403 " =    1.460
peak=   -3.362 closest distance to " O   HOH Z 386 " =    1.625
peak=   -3.360 closest distance to " CG1 VAL A  78 " =    2.408
peak=   -3.357 closest distance to " N   ARG A 156 " =    1.181
peak=   -3.357 closest distance to " O   LEU A 300 " =    2.481
peak=   -3.355 closest distance to " O   HOH Z 179 " =    1.831
peak=   -3.343 closest distance to " OE1 GLN A 278 " =    1.121
peak=   -3.342 closest distance to " O   GLY A  23 " =    0.875
peak=   -3.342 closest distance to " O   HOH Z  35 " =    2.709
peak=   -3.338 closest distance to " N   ARG A 138 " =    1.819
peak=   -3.334 closest distance to " CG  GLN A  89 " =    2.029
peak=   -3.332 closest distance to " O   HOH Z 426 " =    2.150
peak=   -3.331 closest distance to " O   ASN A 209 " =    2.163
peak=   -3.327 closest distance to " OD2 ASP A 140 " =    1.151
peak=   -3.326 closest distance to " O   HOH Z  24 " =    1.078
peak=   -3.325 closest distance to " NZ  LYS A 166 " =    1.387
peak=   -3.321 closest distance to " OH  TYR A 247 " =    1.318
peak=   -3.321 closest distance to " CZ  ARG A  36 " =    1.845
peak=   -3.315 closest distance to " O   HOH Z 300 " =    2.225
peak=   -3.313 closest distance to " O   HOH Z  60 " =    1.329
peak=   -3.311 closest distance to " O   HOH Z 315 " =    1.502
peak=   -3.307 closest distance to " O   HOH Z  49 " =    1.139
peak=   -3.302 closest distance to " C   HIS A 108 " =    1.362
peak=   -3.291 closest distance to " N   PHE A 218 " =    0.956
peak=   -3.290 closest distance to " N   GLN A 223 " =    1.908
peak=   -3.289 closest distance to " O   HOH Z 268 " =    0.906
peak=   -3.282 closest distance to " O   HOH Z 135 " =    0.905
peak=   -3.281 closest distance to " CB  ALA A  43 " =    2.587
peak=   -3.279 closest distance to " ND2 ASN A  60 " =    3.950
peak=   -3.279 closest distance to " CD  ARG A  66 " =    1.452
peak=   -3.278 closest distance to " CB  ASP A  50 " =    2.298
peak=   -3.277 closest distance to " O   HOH Z 107 " =    1.396
peak=   -3.275 closest distance to " O   ASN A 301 " =    1.142
peak=   -3.275 closest distance to " O   HOH Z 407 " =    3.267
peak=   -3.274 closest distance to " NH1 ARG A 195 " =    2.422
peak=   -3.266 closest distance to " C   SER A 135 " =    1.285
peak=   -3.259 closest distance to " CB  ASP A 132 " =    2.306
peak=   -3.257 closest distance to " CA  ASN A 110 " =    1.018
peak=   -3.244 closest distance to " CD2 LEU A 261 " =    2.273
peak=   -3.235 closest distance to " OG  SER A   3 " =    1.455
peak=   -3.232 closest distance to " C   ASP A  50 " =    1.614
peak=   -3.231 closest distance to " OH  TYR A 247 " =    1.961
peak=   -3.230 closest distance to " O   HOH Z 358 " =    3.448
peak=   -3.228 closest distance to " OD1 ASP A 107 " =    1.210
peak=   -3.226 closest distance to " NH1AARG A 102 " =    1.583
peak=   -3.225 closest distance to " O   HOH Z 387 " =    0.812
peak=   -3.222 closest distance to " O   HOH Z 383 " =    1.613
peak=   -3.212 closest distance to " OD1 ASN A 249 " =    1.264
peak=   -3.212 closest distance to " CG  LEU A  83 " =    2.343
peak=   -3.210 closest distance to " CB  ALA A 161 " =    1.627
peak=   -3.205 closest distance to " CD  ARG A 219 " =    2.522
peak=   -3.204 closest distance to " CA  SER A  63 " =    1.002
peak=   -3.200 closest distance to " CD2 TYR A 169 " =    2.354
peak=   -3.198 closest distance to " N   LYS A 290 " =    1.103
peak=   -3.197 closest distance to " O   HOH Z 109 " =    2.294
peak=   -3.196 closest distance to " O   LYS A 119 " =    0.987
peak=   -3.188 closest distance to " CD1 PHE A  59 " =    2.365
peak=   -3.183 closest distance to " NH1 ARG A 195 " =    0.833
peak=   -3.182 closest distance to " O   ASP A 286 " =    0.927
peak=   -3.179 closest distance to " CB  ASN A  74 " =    1.088
peak=   -3.178 closest distance to " CB  GLN A 144 " =    1.136
peak=   -3.176 closest distance to " O   HOH Z 278 " =    1.051
peak=   -3.173 closest distance to " O   HOH Z 438 " =    1.573
peak=   -3.173 closest distance to " CA  ASN A 285 " =    1.084
peak=   -3.173 closest distance to " O   HOH Z 411 " =    4.874
peak=   -3.165 closest distance to " O   HOH Z 407 " =    5.618
peak=   -3.163 closest distance to " O   HOH Z 189 " =    1.313
peak=   -3.158 closest distance to " O   HOH Z 345 " =    1.232
peak=   -3.158 closest distance to " C   ASP A 124 " =    2.022
peak=   -3.152 closest distance to " CA  SER A  63 " =    1.079
peak=   -3.145 closest distance to " CZ3 TRP A 179 " =    1.343
peak=   -3.144 closest distance to " O   HOH Z 416 " =    1.607
peak=   -3.140 closest distance to " CD  LYS A 289 " =    2.241
peak=   -3.136 closest distance to " CG2 THR A  29 " =    2.578
peak=   -3.133 closest distance to " N   GLN A  55 " =    1.192
peak=   -3.126 closest distance to " O   HOH Z   4 " =    0.988
peak=   -3.122 closest distance to " CB  ALA A 104 " =    2.428
peak=   -3.121 closest distance to " CA  GLY A 133 " =    2.208
peak=   -3.120 closest distance to " O   HOH Z 280 " =    1.108
peak=   -3.118 closest distance to " O   HOH Z 131 " =    3.823
peak=   -3.117 closest distance to " CD  GLU A 277 " =    0.802
peak=   -3.103 closest distance to " O   HOH Z 413 " =    0.972
peak=   -3.084 closest distance to " OD1 ASN A 142 " =    1.855
peak=   -3.081 closest distance to " O   HOH Z  80 " =    4.569
peak=   -3.080 closest distance to " O   HOH Z 368 " =    1.815
peak=   -3.058 closest distance to " O   HOH Z 336 " =    5.234
peak=   -3.046 closest distance to " O   HOH Z 210 " =    2.034
peak=   -3.001 closest distance to " OE1 GLN A  88 " =    1.361

================= 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    :  0.4981 0.5033   6.306382e+00   6.298324e+00
   1_bss:  0.4918 0.4996   6.305936e+00   6.296394e+00
   1_xyz:  0.4317 0.4737   6.231631e+00   6.268801e+00
   1_adp:  0.3967 0.4793   6.200902e+00   6.272722e+00
   1_occ:  0.3963 0.4792   6.200409e+00   6.272838e+00
   2_bss:  0.3972 0.4779   6.201926e+00   6.273046e+00
   2_xyz:  0.3460 0.4352   6.103363e+00   6.217477e+00
   2_adp:  0.3321 0.4281   6.087472e+00   6.208633e+00
   2_occ:  0.3319 0.4277   6.086715e+00   6.208285e+00
   3_bss:  0.3322 0.4275   6.086704e+00   6.207458e+00
   3_xyz:  0.2939 0.3763   5.988966e+00   6.133469e+00
   3_adp:  0.2753 0.3703   5.960024e+00   6.125032e+00
   3_occ:  0.2750 0.3703   5.958937e+00   6.124211e+00
   4_bss:  0.2755 0.3700   5.958755e+00   6.123431e+00
   4_xyz:  0.2335 0.3134   5.806387e+00   6.000822e+00
   4_adp:  0.2141 0.2892   5.738192e+00   5.939652e+00
   4_occ:  0.2140 0.2887   5.737330e+00   5.938920e+00
   5_bss:  0.2141 0.2888   5.736087e+00   5.937563e+00
   5_xyz:  0.1762 0.2440   5.560379e+00   5.794786e+00
   5_adp:  0.1614 0.2225   5.482783e+00   5.712813e+00
   5_occ:  0.1612 0.2222   5.481979e+00   5.711987e+00
   5_bss:  0.1612 0.2216   5.479765e+00   5.708287e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.340  65.347   0.293   0.256   0.157   0.000   0.000   0.000
   1_xyz:  0.340  65.347   0.293   0.256   0.157   0.000   0.000   0.000
   1_adp:  0.340  65.347   0.293   0.256   0.157   0.000   0.000   0.000
   1_occ:  0.340  65.347   0.293   0.256   0.157   0.000   0.000   0.000
   2_bss:  0.376 103.789   0.629   0.117   0.754   0.000   0.000   0.000
   2_xyz:  0.376 103.789   0.629   0.117   0.754   0.000   0.000   0.000
   2_adp:  0.376 103.789   0.629   0.117   0.754   0.000   0.000   0.000
   2_occ:  0.376 103.789   0.629   0.117   0.754   0.000   0.000   0.000
   3_bss:  0.367  94.016   0.111  -0.626   0.515  -0.000   0.000   0.000
   3_xyz:  0.367  94.016   0.111  -0.626   0.515  -0.000   0.000   0.000
   3_adp:  0.367  94.016   0.111  -0.626   0.515  -0.000   0.000   0.000
   3_occ:  0.367  94.016   0.111  -0.626   0.515  -0.000   0.000   0.000
   4_bss:  0.364  95.753  -0.663  -1.173   0.214  -0.000   0.000   0.000
   4_xyz:  0.364  95.753  -0.663  -1.173   0.214  -0.000   0.000   0.000
   4_adp:  0.364  95.753  -0.663  -1.173   0.214  -0.000   0.000   0.000
   4_occ:  0.364  95.753  -0.663  -1.173   0.214  -0.000   0.000   0.000
   5_bss:  0.346  85.538  -1.153  -1.926  -0.140  -0.000  -0.000  -0.000
   5_xyz:  0.346  85.538  -1.153  -1.926  -0.140  -0.000  -0.000  -0.000
   5_adp:  0.346  85.538  -1.153  -1.926  -0.140  -0.000  -0.000  -0.000
   5_occ:  0.346  85.538  -1.153  -1.926  -0.140  -0.000  -0.000  -0.000
   5_bss:  0.326  69.532  -1.723  -2.660  -0.719  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  65.353 0.3240  0.4518    87596.284
   1_bss:  65.195 0.3252  0.4661    87280.515
   1_xyz:  58.197 0.4156  0.5850    72705.746
   1_adp:  58.454 0.4120  0.5968    74326.567
   1_occ:  58.380 0.4130  0.5980    74365.361
   2_bss:  58.308 0.4139  0.6038    74200.286
   2_xyz:  50.573 0.5113  0.7412    56645.810
   2_adp:  49.133 0.5296  0.7576    54418.641
   2_occ:  49.088 0.5301  0.7578    54287.981
   3_bss:  48.978 0.5313  0.7476    54076.051
   3_xyz:  41.809 0.6193  0.8576    41000.739
   3_adp:  40.747 0.6322  0.8590    39530.019
   3_occ:  40.713 0.6324  0.8586    39385.275
   4_bss:  40.641 0.6332  0.8438    39248.597
   4_xyz:  33.464 0.7168  0.9315    27045.110
   4_adp:  30.223 0.7540  0.9474    22827.652
   4_occ:  30.182 0.7544  0.9476    22763.289
   5_bss:  30.095 0.7553  0.9306    22625.861
   5_xyz:  24.644 0.8134  0.9744    15461.318
   5_adp:  21.898 0.8426  0.9855    12933.543
   5_occ:  21.873 0.8428  0.9853    12907.219
   5_bss:  21.766 0.8436  0.9635    12756.149
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.8451e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.8451e-01
   1_xyz:   1.500  0.011  0.099 15.992  0.006  4.105   1.2594e-01
   1_adp:   1.500  0.011  0.099 15.992  0.006  4.105   1.2594e-01
   1_occ:   1.500  0.011  0.099 15.992  0.006  4.105   1.2594e-01
   2_bss:   1.500  0.011  0.099 15.992  0.006  4.105   1.2594e-01
   2_xyz:   1.415  0.010  0.101 16.128  0.005  4.102   1.1610e-01
   2_adp:   1.415  0.010  0.101 16.128  0.005  4.102   1.1610e-01
   2_occ:   1.415  0.010  0.101 16.128  0.005  4.102   1.1610e-01
   3_bss:   1.415  0.010  0.101 16.128  0.005  4.102   1.1610e-01
   3_xyz:   1.010  0.007  0.072 15.001  0.004  4.115   6.7529e-02
   3_adp:   1.010  0.007  0.072 15.001  0.004  4.115   6.7529e-02
   3_occ:   1.010  0.007  0.072 15.001  0.004  4.115   6.7529e-02
   4_bss:   1.010  0.007  0.072 15.001  0.004  4.115   6.7529e-02
   4_xyz:   1.119  0.008  0.083 14.642  0.004  4.106   7.3654e-02
   4_adp:   1.119  0.008  0.083 14.642  0.004  4.106   7.3654e-02
   4_occ:   1.119  0.008  0.083 14.642  0.004  4.106   7.3654e-02
   5_bss:   1.119  0.008  0.083 14.642  0.004  4.106   7.3654e-02
   5_xyz:   1.066  0.008  0.076 14.347  0.003  4.118   6.7226e-02
   5_adp:   1.066  0.008  0.076 14.347  0.003  4.118   6.7226e-02
   5_occ:   1.066  0.008  0.076 14.347  0.003  4.118   6.7226e-02
   5_bss:   1.066  0.008  0.076 14.347  0.003  4.118   6.7226e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.655   2.4257e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.655   2.4257e-01
   1_xyz:   8.443  0.057  0.335 85.938  0.033  1.979   8.2930e-02
   1_adp:   8.443  0.057  0.335 85.938  0.033  1.979   8.2930e-02
   1_occ:   8.443  0.057  0.335 85.938  0.033  1.979   8.2930e-02
   2_bss:   8.443  0.057  0.335 85.938  0.033  1.979   8.2930e-02
   2_xyz:   9.180  0.053  0.365 82.500  0.064  1.879   1.0651e-01
   2_adp:   9.180  0.053  0.365 82.500  0.064  1.879   1.0651e-01
   2_occ:   9.180  0.053  0.365 82.500  0.064  1.879   1.0651e-01
   3_bss:   9.180  0.053  0.365 82.500  0.064  1.879   1.0651e-01
   3_xyz:   7.863  0.044  0.312 79.090  0.031  2.157   5.3136e-02
   3_adp:   7.863  0.044  0.312 79.090  0.031  2.157   5.3136e-02
   3_occ:   7.863  0.044  0.312 79.090  0.031  2.157   5.3136e-02
   4_bss:   7.863  0.044  0.312 79.090  0.031  2.157   5.3136e-02
   4_xyz:   7.441  0.045  0.249 78.260  0.040  2.234   6.6963e-02
   4_adp:   7.441  0.045  0.249 78.260  0.040  2.234   6.6963e-02
   4_occ:   7.441  0.045  0.249 78.260  0.040  2.234   6.6963e-02
   5_bss:   7.441  0.045  0.249 78.260  0.040  2.234   6.6963e-02
   5_xyz:   7.707  0.047  0.254 77.074  0.015  2.249   5.6811e-02
   5_adp:   7.707  0.047  0.254 77.074  0.015  2.249   5.6811e-02
   5_occ:   7.707  0.047  0.254 77.074  0.015  2.249   5.6811e-02
   5_bss:   7.707  0.047  0.254 77.074  0.015  2.249   5.6811e-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:  95.25   0.00  20.88  88.58   0.00  18.30  95.25   0.00  34.93
   1_occ:  95.25   0.00  20.88  88.58   0.00  18.30  95.25   0.00  34.93
   2_bss:  95.25   0.00  20.88  88.58   0.00  18.30  95.25   0.00  34.93
   2_xyz:  95.25   0.00  20.88  88.58   0.00  18.30  95.25   0.00  34.93
   2_adp:  83.66   0.00  20.11  80.04   0.00  17.41  83.66   0.00  34.79
   2_occ:  83.66   0.00  20.11  80.04   0.00  17.41  83.66   0.00  34.79
   3_bss:  83.66   0.00  20.11  80.04   0.00  17.41  83.66   0.00  34.79
   3_xyz:  83.66   0.00  20.11  80.04   0.00  17.41  83.66   0.00  34.79
   3_adp:  90.12   0.00  20.60  80.27   0.00  17.03  90.12   0.00  40.06
   3_occ:  90.12   0.00  20.60  80.27   0.00  17.03  90.12   0.00  40.06
   4_bss:  90.12   0.00  20.60  80.27   0.00  17.03  90.12   0.00  40.06
   4_xyz:  90.12   0.00  20.60  80.27   0.00  17.03  90.12   0.00  40.06
   4_adp: 104.71   0.00  20.40  94.10   0.00  15.46 104.71   1.88  47.30
   4_occ: 104.71   0.00  20.40  94.10   0.00  15.46 104.71   1.88  47.30
   5_bss: 104.71   0.00  20.40  94.10   0.00  15.46 104.71   1.88  47.30
   5_xyz: 104.71   0.00  20.40  94.10   0.00  15.46 104.71   1.88  47.30
   5_adp:  95.30   0.85  19.07  93.57   0.85  13.89  95.30   2.69  47.26
   5_occ:  95.30   0.85  19.07  93.57   0.85  13.89  95.30   2.69  47.26
   5_bss:  95.27   0.82  19.04  93.55   0.82  13.86  95.27   2.66  47.23
------------------------------------------------------------------------
 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:    1.729    0.014    0.303
   1_adp:    1.729    0.014    0.303
   1_occ:    1.729    0.014    0.303
   2_bss:    1.729    0.014    0.303
   2_xyz:    1.500    0.046    0.521
   2_adp:    1.500    0.046    0.521
   2_occ:    1.500    0.046    0.521
   3_bss:    1.500    0.046    0.521
   3_xyz:    1.723    0.030    0.652
   3_adp:    1.723    0.030    0.652
   3_occ:    1.723    0.030    0.652
   4_bss:    1.723    0.030    0.652
   4_xyz:    1.920    0.060    0.787
   4_adp:    1.920    0.060    0.787
   4_occ:    1.920    0.060    0.787
   5_bss:    1.920    0.060    0.787
   5_xyz:    2.024    0.060    0.888
   5_adp:    2.024    0.060    0.888
   5_occ:    2.024    0.060    0.888
   5_bss:    2.024    0.060    0.888
------------------------------------------------------------------------

CPU time actual refinement: 307.75


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1218/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_1218/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1218/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1218/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1218/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 307.62 
  Macro-tasks:
    bulk solvent and scale       = 51.03  
    individual site refinement   = 121.26 
    weights calculation          = 24.95  
    collect and process          = 5.10   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 202.43 
  Micro-tasks:
    mask                            = 2.52   
    f_calc                          = 96.00  
    alpha_beta                      = 6.89   
    target                          = 0.94   
    gradients_wrt_atomic_parameters = 102.29 
    fmodel                         = 7.46   
    r_factors                      = 0.29   
    phase_errors                   = 7.86   
    foms                           = 0.20   
    TOTAL for micro-tasks          = 224.45 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.380 micro seconds
Total CPU time: 5.32 minutes
from_scatterers_fft:    620 calls, 95.72 s
gradients_fft:          565 calls, 91.59 s

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

# Date 2008-01-16 Time 06:42:10 PST -0800 (1200494531.00 s)
Start R-work = 0.4981, R-free = 0.5033 (no bulk solvent and anisotropic scale)
Final R-work = 0.1795, R-free = 0.2373 (no bulk solvent and anisotropic scale)

Start R-work = 0.4918, R-free = 0.4996
Final R-work = 0.1612, R-free = 0.2216