# Date 2008-01-16 Time 06:37:13 PST -0800 (1200494233.19 s)
#phil __OFF__

Command line arguments: "../1220.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 8538
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1220

-------------------------------------------------------------------------------
  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, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


================================== 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, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3688 1.95497
Completeness in resolution range: 0.899444
Completeness with d_max=infinity: 0.896973

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.3688
                             d_min =   1.9550

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, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3688 1.95497
Completeness in resolution range: 0.899444
Completeness with d_max=infinity: 0.896973

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.3693 -  4.1862 [2286/2313]  2057   229  10.0%
  bin  2:  4.1862 -  3.3338 [2201/2221]  1987   214   9.7%
  bin  3:  3.3338 -  2.9157 [2168/2187]  1944   224  10.3%
  bin  4:  2.9157 -  2.6506 [2132/2162]  1913   219  10.3%
  bin  5:  2.6506 -  2.4614 [2149/2168]  1930   219  10.2%
  bin  6:  2.4614 -  2.3168 [2115/2140]  1911   204   9.6%
  bin  7:  2.3168 -  2.2011 [2133/2161]  1917   216  10.1%
  bin  8:  2.2011 -  2.1056 [2124/2160]  1916   208   9.8%
  bin  9:  2.1056 -  2.0247 [1839/2134]  1664   175   9.5%
  bin 10:  2.0247 -  1.9550 [ 442/2133]   391    51  11.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1220/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.68 -     2.32: 23
        2.32 -     2.97: 1787
        2.97 -     3.61: 4535
        3.61 -     4.26: 9079
        4.26 -     4.90: 12664
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 324 " - " O   HOH Z 374 "  1.854 3.040 -x,y-1/2,-z+1/2
  ... (remaining 28083 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_1220/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1220/model_refine_001.geo

CPU time processing inputs: 9.14


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


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


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


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

|--(resolution: 1.95 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5158   r_free= 0.5196   ksol= 0.00   Bsol= 0.00   scale= 0.841    |
|                                                                             |
| 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:   1.09 A                  |
| x-ray target function (ml) for work reflections: 6.318889                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3693 -  4.6705 0.99   1489  166 0.4368 0.4226      6.6822      6.6702|
|  2:  4.6705 -  3.7245 0.99   1416  157 0.4810 0.4843      6.9022      6.9281|
|  3:  3.7245 -  3.2588 0.99   1404  154 0.4974 0.4779      6.7099      6.6904|
|  4:  3.2588 -  2.9631 0.99   1400  159 0.5222 0.5609      6.5555      6.5505|
|  5:  2.9631 -  2.7521 0.99   1386  157 0.5423 0.5784      6.3807      6.3905|
|  6:  2.7521 -  2.5906 0.99   1372  146 0.5545 0.5151       6.307      6.2465|
|  7:  2.5906 -  2.4614 0.99   1364  166 0.5533 0.5414      6.2343      6.1868|
|  8:  2.4614 -  2.3547 0.98   1378  147 0.5528 0.5931      6.1618      6.1673|
|  9:  2.3547 -  2.2643 0.98   1353  148 0.5539 0.5848      6.1415       6.216|
| 10:  2.2643 -  2.1864 1.00   1365  149 0.5460 0.5193       6.065      6.0286|
| 11:  2.1864 -  2.1182 0.98   1335  153 0.5204 0.5467      6.0062      6.0505|
| 12:  2.1182 -  2.0578 0.98   1378  144 0.5387 0.5300      5.9185      5.8864|
| 13:  2.0578 -  2.0038 0.59    799   98 0.5376 0.4977      5.9015      5.7811|
| 14:  2.0038 -  1.9550 0.13    191   15 0.4922 0.3740      5.8188      6.0415|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3693 -  4.6705  1489   166  0.65  38.28   0.78     0.71      90167.55|
|  2:  4.6705 -  3.7245  1416   157  0.59  44.68   0.85     0.69     155942.56|
|  3:  3.7245 -  3.2588  1404   154  0.39  60.33   0.85     0.56     171905.08|
|  4:  3.2588 -  2.9631  1400   159  0.22  73.53   0.84     0.34     159339.07|
|  5:  2.9631 -  2.7521  1386   157  0.15  78.67   0.83     0.24     115430.82|
|  6:  2.7521 -  2.5906  1372   146  0.11  81.40   0.85     0.18      96450.39|
|  7:  2.5906 -  2.4614  1364   166  0.15  79.17   0.85     0.22      80906.99|
|  8:  2.4614 -  2.3547  1378   147  0.11  81.65   0.86     0.17      72831.80|
|  9:  2.3547 -  2.2643  1353   148  0.14  79.86   0.88     0.21      66668.37|
| 10:  2.2643 -  2.1864  1365   149  0.14  79.97   0.88     0.21      59613.16|
| 11:  2.1864 -  2.1182  1335   153  0.19  75.83   0.93     0.30      54570.93|
| 12:  2.1182 -  2.0578  1378   144  0.21  74.24   0.86     0.36      47172.32|
| 13:  2.0578 -  2.0038   799    98  0.26  70.41   0.94     0.44      39961.56|
| 14:  2.0038 -  1.9550   191    15  0.34  64.54   1.03     0.51      31024.49|
|alpha:            min =        0.17 max =            0.71 mean =         0.36|
|beta:             min =    31024.49 max =       171905.08 mean =     94714.97|
|figures of merit: min =        0.00 max =            1.00 mean =         0.26|
|phase err.(work): min =        0.00 max =           89.99 mean =        70.25|
|phase err.(test): min =        0.00 max =           89.92 mean =        70.57|
|-----------------------------------------------------------------------------|

============================== 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 = 22.648119             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.079   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 5.475441              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.599   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.681 -  2.003:       11 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.003 -  2.325:       12 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.325 -  2.647:       81 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.647 -  2.969:     1706 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.969 -  3.290:     1896 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.290 -  3.612:     2639 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.612 -  3.934:     4698 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.934 -  4.256:     4381 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.256 -  4.578:     5765 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.578 -  4.900:     6899 |
|-----------------------------------------------------------------------------|
|-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 |        0.184 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.681 |       0.475 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.045)------------------------------------------|
|    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 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5158   r_free= 0.5196   ksol= 0.00   Bsol= 0.00   scale= 0.841    |
|                                                                             |
| 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:   1.09 A                  |
| x-ray target function (ml) for work reflections: 6.318889                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5097   r_free= 0.5175   ksol= 0.33   Bsol= 66.42   scale= 0.872   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.43,-0.87,2.09,-0.00,0.00,0.00); trace/3= 0.27                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.10 A                  |
| x-ray target function (ml) for work reflections: 6.319040                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 18.330729             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.836   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.212829              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.003   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5097      final r-factor (work) = 0.4605          |
| start r-factor (free) = 0.5175      final r-factor (free) = 0.5031          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 58.0541 = 18.33 * 0.50 * 6.3140 + 1.00 * 0.1838                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 57.6504 = 18.33 * 0.50 * 6.2753 + 1.00 * 0.1349                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4605      final r-factor (work) = 0.4333          |
| start r-factor (free) = 0.5031      final r-factor (free) = 0.5079          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.8922 = 2.21 * 1.00 * 6.2753 + 1.00 * 0.0060                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.8392 = 2.21 * 1.00 * 6.2451 + 1.00 * 0.0199                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.045)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.26   20.95    None  None   None       |
|    all(noH): 2823   0      0.00    90.26   20.95    None  None   None       |
|    Sol.    : 438    0      0.00    90.26   31.52    None  None   None       |
|    Mac.    : 2385   0      0.00    88.07   19.01    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.026:  525   |   5:    45.129 -  54.154:   87        |
|      1:     9.026 -  18.052:  877   |   6:    54.154 -  63.180:   44        |
|      2:    18.052 -  27.077:  667   |   7:    63.180 -  72.206:   25        |
|      3:    27.077 -  36.103:  371   |   8:    72.206 -  81.232:   11        |
|      4:    36.103 -  45.129:  210   |   9:    81.232 -  90.257:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4333 r_free = 0.5079             target_work(ml) = 6.247         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4329 r_free = 0.5085             target_work(ml) = 6.247         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4329   r_free= 0.5085   ksol= 0.33   Bsol= 66.42   scale= 0.975   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.43,-0.87,2.09,-0.00,0.00,0.00); trace/3= 0.27                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.92 A                  |
| x-ray target function (ml) for work reflections: 6.246802                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4341   r_free= 0.5089   ksol= 0.37   Bsol= 100.94   scale= 0.976  |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.43,-0.87,2.09,-0.00,0.00,0.00); trace/3= 0.27                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.92 A                  |
| x-ray target function (ml) for work reflections: 6.248309                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 18.015946             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.019  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.225645              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.295  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4341      final r-factor (work) = 0.4011          |
| start r-factor (free) = 0.5089      final r-factor (free) = 0.4851          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 56.4058 = 18.02 * 0.50 * 6.2468 + 1.00 * 0.1349                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 56.1809 = 18.02 * 0.50 * 6.2259 + 1.00 * 0.0983                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4011      final r-factor (work) = 0.3910          |
| start r-factor (free) = 0.4851      final r-factor (free) = 0.4829          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6504 = 1.23 * 1.00 * 6.2259 + 1.00 * 0.0197                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6055 = 1.23 * 1.00 * 6.1938 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.045)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.05   20.82    None  None   None       |
|    all(noH): 2823   0      0.00    88.05   20.82    None  None   None       |
|    Sol.    : 438    0      0.00    83.87   29.82    None  None   None       |
|    Mac.    : 2385   0      0.00    88.05   19.17    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 -   8.805:  487   |   5:    44.025 -  52.830:   99        |
|      1:     8.805 -  17.610:  888   |   6:    52.830 -  61.635:   52        |
|      2:    17.610 -  26.415:  663   |   7:    61.635 -  70.441:   31        |
|      3:    26.415 -  35.220:  408   |   8:    70.441 -  79.246:    5        |
|      4:    35.220 -  44.025:  185   |   9:    79.246 -  88.051:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3910 r_free = 0.4829             target_work(ml) = 6.191         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3909 r_free = 0.4831             target_work(ml) = 6.192         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3909   r_free= 0.4831   ksol= 0.37   Bsol= 100.94   scale= 1.004  |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.43,-0.87,2.09,-0.00,0.00,0.00); trace/3= 0.27                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.191950                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3914   r_free= 0.4828   ksol= 0.38   Bsol= 110.90   scale= 1.010  |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.12,-0.30,1.74,-0.00,0.00,0.00); trace/3= 0.52                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.192975                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.187232             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.650  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.924473              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 161.624  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3914      final r-factor (work) = 0.3447          |
| start r-factor (free) = 0.4828      final r-factor (free) = 0.4441          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 53.3369 = 17.19 * 0.50 * 6.1951 + 1.00 * 0.0983                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 53.0478 = 17.19 * 0.50 * 6.1598 + 1.00 * 0.1133                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3447      final r-factor (work) = 0.3231          |
| start r-factor (free) = 0.4441      final r-factor (free) = 0.4314          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.8685 = 1.92 * 1.00 * 6.1598 + 1.00 * 0.0143                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.7360 = 1.92 * 1.00 * 6.0860 + 1.00 * 0.0237                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.045)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.49  21.47    None  None   None       |
|    all(noH): 2823   0      0.00    102.49  21.47    None  None   None       |
|    Sol.    : 438    0      0.00    102.49  36.87    None  None   None       |
|    Mac.    : 2385   0      0.00    92.70   18.64    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 -  10.249:  813   |   5:    51.245 -  61.494:   86        |
|      1:    10.249 -  20.498:  801   |   6:    61.494 -  71.743:   55        |
|      2:    20.498 -  30.747:  555   |   7:    71.743 -  81.991:   26        |
|      3:    30.747 -  40.996:  311   |   8:    81.991 -  92.240:   10        |
|      4:    40.996 -  51.245:  162   |   9:    92.240 - 102.489:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3231 r_free = 0.4314             target_work(ml) = 6.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3229 r_free = 0.4306             target_work(ml) = 6.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3229   r_free= 0.4306   ksol= 0.38   Bsol= 110.90   scale= 1.025  |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.12,-0.30,1.74,-0.00,0.00,0.00); trace/3= 0.52                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.073675                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3233   r_free= 0.4300   ksol= 0.38   Bsol= 120.14   scale= 1.024  |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.34,-0.44,1.55,-0.00,0.00,0.00); trace/3= 0.48                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.073283                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.643662             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.276  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.727178              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.377  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3233      final r-factor (work) = 0.2812          |
| start r-factor (free) = 0.4300      final r-factor (free) = 0.3741          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.6361 = 13.64 * 0.50 * 6.0867 + 1.00 * 0.1137                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.2608 = 13.64 * 0.50 * 6.0340 + 1.00 * 0.0978                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2812      final r-factor (work) = 0.2635          |
| start r-factor (free) = 0.3741      final r-factor (free) = 0.3500          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4115 = 0.73 * 1.00 * 6.0340 + 1.00 * 0.0237                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3369 = 0.73 * 1.00 * 5.9437 + 1.00 * 0.0147                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.045)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.01  19.61    None  None   None       |
|    all(noH): 2823   0      0.00    105.01  19.61    None  None   None       |
|    Sol.    : 438    0      0.00    105.01  40.15    None  None   None       |
|    Mac.    : 2385   0      0.00    84.14   15.84    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 -  10.501:  949   |   5:    52.507 -  63.008:   67        |
|      1:    10.501 -  21.003:  905   |   6:    63.008 -  73.509:   43        |
|      2:    21.003 -  31.504:  452   |   7:    73.509 -  84.010:   21        |
|      3:    31.504 -  42.005:  245   |   8:    84.010 -  94.512:    6        |
|      4:    42.005 -  52.507:  133   |   9:    94.512 - 105.013:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2635 r_free = 0.3500             target_work(ml) = 5.916         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2634 r_free = 0.3496             target_work(ml) = 5.915         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2634   r_free= 0.3496   ksol= 0.38   Bsol= 120.14   scale= 1.032  |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.34,-0.44,1.55,-0.00,0.00,0.00); trace/3= 0.48                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.914642                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2632   r_free= 0.3491   ksol= 0.37   Bsol= 102.17   scale= 1.011  |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.66,-1.26,0.90,-0.00,0.00,0.00); trace/3= -0.34                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.912197                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.912701              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.654  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.376059              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 159.460  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2632      final r-factor (work) = 0.2298          |
| start r-factor (free) = 0.3491      final r-factor (free) = 0.3020          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.6963 = 4.91 * 0.50 * 5.9431 + 1.00 * 0.0978                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.4778 = 4.91 * 0.50 * 5.8688 + 1.00 * 0.0621                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2298      final r-factor (work) = 0.2168          |
| start r-factor (free) = 0.3020      final r-factor (free) = 0.2859          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2216 = 0.38 * 1.00 * 5.8688 + 1.00 * 0.0146                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1792 = 0.38 * 1.00 * 5.7645 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.045)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.80   18.75    None  None   None       |
|    all(noH): 2823   0      0.00    99.80   18.75    None  None   None       |
|    Sol.    : 438    0      2.34    99.80   43.02    None  None   None       |
|    Mac.    : 2385   0      0.00    87.40   14.30    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 -   9.980:  986   |   5:    49.902 -  59.882:   97        |
|      1:     9.980 -  19.961:  996   |   6:    59.882 -  69.862:   52        |
|      2:    19.961 -  29.941:  321   |   7:    69.862 -  79.842:   26        |
|      3:    29.941 -  39.921:  185   |   8:    79.842 -  89.823:    7        |
|      4:    39.921 -  49.902:  150   |   9:    89.823 -  99.803:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2168 r_free = 0.2859             target_work(ml) = 5.739         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2168 r_free = 0.2857             target_work(ml) = 5.739         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2168   r_free= 0.2857   ksol= 0.37   Bsol= 102.17   scale= 1.020  |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.66,-1.26,0.90,-0.00,0.00,0.00); trace/3= -0.34                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.738524                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3693 -  4.6705 0.99   1489  166 0.1285 0.1741      5.6642      5.8918|
|  2:  4.6705 -  3.7245 0.99   1416  157 0.1457 0.2194      5.9361      6.3379|
|  3:  3.7245 -  3.2588 0.99   1404  154 0.2004 0.2489      6.0323      6.2297|
|  4:  3.2588 -  2.9631 0.99   1400  159 0.2418 0.2957      5.9997      6.1597|
|  5:  2.9631 -  2.7521 0.99   1386  157 0.2577 0.3167      5.9074      5.9989|
|  6:  2.7521 -  2.5906 0.99   1372  146 0.2540 0.3743        5.81      6.0446|
|  7:  2.5906 -  2.4614 0.99   1364  166 0.2534 0.3131      5.7626      5.8877|
|  8:  2.4614 -  2.3547 0.98   1378  147 0.2594 0.3283      5.7216      5.8351|
|  9:  2.3547 -  2.2643 0.98   1353  148 0.2380 0.3252      5.6332      5.8476|
| 10:  2.2643 -  2.1864 1.00   1365  149 0.2431 0.3316       5.589      5.7726|
| 11:  2.1864 -  2.1182 0.98   1335  153 0.2403 0.3404      5.5405      5.7866|
| 12:  2.1182 -  2.0578 0.98   1378  144 0.2653 0.3366      5.4838      5.6071|
| 13:  2.0578 -  2.0038 0.59    799   98 0.2438 0.3282      5.4278       5.528|
| 14:  2.0038 -  1.9550 0.13    191   15 0.2184 0.2800       5.326      5.7371|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3693 -  4.6705  1489   166  0.91  13.67   0.96     0.93      13175.09|
|  2:  4.6705 -  3.7245  1416   157  0.90  15.42   1.04     1.03      23876.20|
|  3:  3.7245 -  3.2588  1404   154  0.82  24.46   1.05     1.04      35101.30|
|  4:  3.2588 -  2.9631  1400   159  0.77  29.13   1.04     0.95      33694.17|
|  5:  2.9631 -  2.7521  1386   157  0.73  32.42   1.02     0.98      30663.67|
|  6:  2.7521 -  2.5906  1372   146  0.71  34.39   1.00     0.87      26044.93|
|  7:  2.5906 -  2.4614  1364   166  0.71  34.33   1.03     0.92      24291.58|
|  8:  2.4614 -  2.3547  1378   147  0.73  33.19   1.01     0.92      21650.98|
|  9:  2.3547 -  2.2643  1353   148  0.72  33.68   1.04     0.87      17774.19|
| 10:  2.2643 -  2.1864  1365   149  0.72  34.22   1.05     0.95      17532.80|
| 11:  2.1864 -  2.1182  1335   153  0.72  34.24   1.04     0.90      16518.00|
| 12:  2.1182 -  2.0578  1378   144  0.69  36.44   1.02     0.92      14835.31|
| 13:  2.0578 -  2.0038   799    98  0.71  34.61   1.04     0.92      13021.16|
| 14:  2.0038 -  1.9550   191    15  0.75  31.10   1.00     0.88      10678.91|
|alpha:            min =        0.87 max =            1.04 mean =         0.94|
|beta:             min =    10678.91 max =        35101.30 mean =     22348.36|
|figures of merit: min =        0.00 max =            1.00 mean =         0.76|
|phase err.(work): min =        0.00 max =           89.97 mean =        29.71|
|phase err.(test): min =        0.00 max =           89.85 mean =        28.48|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2168   r_free= 0.2851   ksol= 0.34   Bsol= 81.61   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.41,-2.26,0.11,-0.00,0.00,0.00); trace/3= -1.19                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.737396                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2168   r_free= 0.2851   ksol= 0.34   Bsol= 81.61   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.41,-2.26,0.11,-0.00,0.00,0.00); trace/3= -1.19                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.737396                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3693 -  4.6705 0.99   1489  166 0.1295 0.1718      5.6558      5.8697|
|  2:  4.6705 -  3.7245 0.99   1416  157 0.1452 0.2173      5.9318      6.3326|
|  3:  3.7245 -  3.2588 0.99   1404  154 0.2010 0.2478      6.0319      6.2289|
|  4:  3.2588 -  2.9631 0.99   1400  159 0.2420 0.2950      5.9989      6.1587|
|  5:  2.9631 -  2.7521 0.99   1386  157 0.2580 0.3169      5.9086      6.0008|
|  6:  2.7521 -  2.5906 0.99   1372  146 0.2540 0.3744      5.8099      6.0448|
|  7:  2.5906 -  2.4614 0.99   1364  166 0.2535 0.3128      5.7627      5.8876|
|  8:  2.4614 -  2.3547 0.98   1378  147 0.2594 0.3287      5.7219      5.8364|
|  9:  2.3547 -  2.2643 0.98   1353  148 0.2380 0.3251      5.6324      5.8467|
| 10:  2.2643 -  2.1864 1.00   1365  149 0.2431 0.3318      5.5893       5.774|
| 11:  2.1864 -  2.1182 0.98   1335  153 0.2402 0.3411      5.5399      5.7868|
| 12:  2.1182 -  2.0578 0.98   1378  144 0.2654 0.3366      5.4843      5.6077|
| 13:  2.0578 -  2.0038 0.59    799   98 0.2438 0.3280      5.4278      5.5297|
| 14:  2.0038 -  1.9550 0.13    191   15 0.2186 0.2801      5.3237      5.7333|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3693 -  4.6705  1489   166  0.91  13.54   0.95     0.93      12838.41|
|  2:  4.6705 -  3.7245  1416   157  0.90  15.21   1.03     1.02      23315.11|
|  3:  3.7245 -  3.2588  1404   154  0.82  24.30   1.03     1.03      34754.77|
|  4:  3.2588 -  2.9631  1400   159  0.77  29.02   1.01     0.94      33478.38|
|  5:  2.9631 -  2.7521  1386   157  0.73  32.39   1.00     0.96      30690.75|
|  6:  2.7521 -  2.5906  1372   146  0.71  34.37   0.97     0.85      26073.28|
|  7:  2.5906 -  2.4614  1364   166  0.71  34.29   1.00     0.89      24313.35|
|  8:  2.4614 -  2.3547  1378   147  0.73  33.17   0.98     0.89      21670.38|
|  9:  2.3547 -  2.2643  1353   148  0.72  33.64   1.00     0.84      17766.04|
| 10:  2.2643 -  2.1864  1365   149  0.72  34.19   1.00     0.91      17556.73|
| 11:  2.1864 -  2.1182  1335   153  0.72  34.20   1.00     0.86      16528.61|
| 12:  2.1182 -  2.0578  1378   144  0.69  36.45   0.98     0.88      14875.04|
| 13:  2.0578 -  2.0038   799    98  0.71  34.56   0.98     0.88      13030.23|
| 14:  2.0038 -  1.9550   191    15  0.76  30.94   0.95     0.84      10645.10|
|alpha:            min =        0.84 max =            1.03 mean =         0.92|
|beta:             min =    10645.10 max =        34754.77 mean =     22242.85|
|figures of merit: min =        0.00 max =            1.00 mean =         0.76|
|phase err.(work): min =        0.00 max =           89.99 mean =        29.64|
|phase err.(test): min =        0.00 max =           89.88 mean =        28.41|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.045)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.81   18.76    None  None   None       |
|    all(noH): 2823   0      0.00    99.81   18.76    None  None   None       |
|    Sol.    : 438    0      2.34    99.81   43.02    None  None   None       |
|    Mac.    : 2385   0      0.00    87.40   14.30    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:     0.003 -   9.983:  986   |   5:    49.905 -  59.885:   97        |
|      1:     9.983 -  19.964:  996   |   6:    59.885 -  69.865:   52        |
|      2:    19.964 -  29.944:  321   |   7:    69.865 -  79.845:   26        |
|      3:    29.944 -  39.924:  185   |   8:    79.845 -  89.826:    7        |
|      4:    39.924 -  49.905:  150   |   9:    89.826 -  99.806:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 375         
Filter by distance & map next to the model:
   mapped sites are within: 0.447 - 5.692
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 366 from: 375
   mapped sites are within: 0.704 - 5.692

peak=    6.114 closest distance to " O   PRO A  54 " =    1.088
peak=    6.054 closest distance to " OE2 GLU A  53 " =    1.158
peak=    5.971 closest distance to " O   HOH Z 103 " =    1.683
peak=    5.693 closest distance to " N   ARG A  56 " =    1.069
peak=    5.558 closest distance to " N   SER A  26 " =    1.004
peak=    5.538 closest distance to " OD2 ASP A  27 " =    1.187
peak=    5.518 closest distance to " O   HOH Z 381 " =    1.757
peak=    5.495 closest distance to " OG  SER A 273 " =    1.099
peak=    5.486 closest distance to " O   HOH Z  79 " =    1.376
peak=    5.480 closest distance to " O   ASN A 285 " =    1.167
peak=    5.423 closest distance to " O   PHE A  59 " =    1.222
peak=    5.345 closest distance to " O   HOH Z 399 " =    1.157
peak=    5.304 closest distance to " OE2 GLU A  46 " =    1.262
peak=    5.236 closest distance to " C   ASN A  60 " =    1.139
peak=    5.196 closest distance to " N   PHE A  59 " =    1.310
peak=    5.143 closest distance to " N   ASN A  69 " =    1.040
peak=    5.012 closest distance to " N   SER A  62 " =    0.714
peak=    4.977 closest distance to " O   HOH Z 204 " =    1.258
peak=    4.971 closest distance to " O   HOH Z  70 " =    1.886
peak=    4.955 closest distance to " O   HOH Z 360 " =    1.417
peak=    4.928 closest distance to " OG  SER A  22 " =    1.184
peak=    4.920 closest distance to " CB  LYS A 290 " =    0.994
peak=    4.918 closest distance to " OD2 ASP A  50 " =    1.374
peak=    4.907 closest distance to " OE1 GLU A  53 " =    1.266
peak=    4.851 closest distance to " O  BHOH Z  74 " =    1.283
peak=    4.827 closest distance to " N   SER A  63 " =    0.972
peak=    4.767 closest distance to " O   HOH Z  29 " =    2.204
peak=    4.758 closest distance to " O   HOH Z 396 " =    1.298
peak=    4.740 closest distance to " CD  ARG A  56 " =    1.175
peak=    4.735 closest distance to " NE2 GLN A 103 " =    1.179
peak=    4.723 closest distance to " CD1 LEU A 281 " =    1.054
peak=    4.701 closest distance to " O   HOH Z 190 " =    1.499
peak=    4.693 closest distance to " CD1 LEU A   5 " =    1.117
peak=    4.684 closest distance to " CB  ARG A  66 " =    1.063
peak=    4.669 closest distance to " O   HOH Z 385 " =    1.571
peak=    4.656 closest distance to " CE1 PHE A 218 " =    1.409
peak=    4.647 closest distance to " CB  ASN A  60 " =    1.245
peak=    4.632 closest distance to " CB  ALA A 161 " =    1.055
peak=    4.625 closest distance to " O   HOH Z 117 " =    1.559
peak=    4.587 closest distance to " CB  PRO A  90 " =    1.313
peak=    4.580 closest distance to " CB  ASP A  27 " =    1.105
peak=    4.576 closest distance to " O   GLU A  53 " =    0.837
peak=    4.513 closest distance to " SG ACYS A 201 " =    1.218
peak=    4.501 closest distance to " O   VAL A 268 " =    1.118
peak=    4.467 closest distance to " CA  ARG A 275 " =    0.980
peak=    4.453 closest distance to " O   HOH Z 130 " =    1.317
peak=    4.450 closest distance to " OD1 ASP A 272 " =    0.955
peak=    4.444 closest distance to " N   ASP A  65 " =    0.799
peak=    4.429 closest distance to " CE1 PHE A  16 " =    1.268
peak=    4.427 closest distance to " NH2 ARG A  24 " =    0.950
peak=    4.388 closest distance to " CB  ALA A 233 " =    1.519
peak=    4.372 closest distance to " OD1 ASP A  65 " =    0.806
peak=    4.366 closest distance to " CB  GLN A  55 " =    0.919
peak=    4.356 closest distance to " OD1 ASN A 249 " =    1.120
peak=    4.356 closest distance to " O   HOH Z  84 " =    1.141
peak=    4.349 closest distance to " CE2 PHE A  61 " =    1.331
peak=    4.349 closest distance to " O   HOH Z 262 " =    1.695
peak=    4.328 closest distance to " O   HOH Z 390 " =    1.719
peak=    4.321 closest distance to " CB  ASP A  50 " =    1.138
peak=    4.320 closest distance to " O   HOH Z  41 " =    1.342
peak=    4.294 closest distance to " O   HOH Z 131 " =    1.977
peak=    4.276 closest distance to " O   ASN A  60 " =    0.972
peak=    4.261 closest distance to " N   GLY A 287 " =    0.938
peak=    4.260 closest distance to " CB  SER A 271 " =    1.287
peak=    4.253 closest distance to " O   ALA A 114 " =    0.980
peak=    4.205 closest distance to " N   TYR A  15 " =    1.241
peak=    4.166 closest distance to " O   HOH Z 124 " =    2.124
peak=    4.148 closest distance to " CB  ILE A 120 " =    1.110
peak=    4.114 closest distance to " CG2BVAL A  41 " =    1.192
peak=    4.102 closest distance to " CG2 VAL A 232 " =    1.245
peak=    4.076 closest distance to " O   HOH Z 102 " =    1.486
peak=    4.067 closest distance to " N   ARG A  66 " =    0.947
peak=    4.066 closest distance to " O   HOH Z 268 " =    1.264
peak=    4.064 closest distance to " CD2 TYR A  68 " =    1.101
peak=    4.058 closest distance to " CA  VAL A 202 " =    1.689
peak=    4.051 closest distance to " N   THR A  29 " =    0.775
peak=    4.036 closest distance to " O   ARG A 269 " =    1.085
peak=    4.007 closest distance to " NE2 HIS A 207 " =    1.146
peak=    4.007 closest distance to " CB  ARG A 259 " =    1.358
peak=    4.005 closest distance to " O   HOH Z  62 " =    1.746
peak=    4.003 closest distance to " N   SER A 134 " =    0.853
peak=    3.989 closest distance to " O   HOH Z  13 " =    1.411
peak=    3.983 closest distance to " CB  SER A 216 " =    0.986
peak=    3.970 closest distance to " O   HOH Z 311 " =    2.438
peak=    3.945 closest distance to " CB  TYR A  30 " =    1.188
peak=    3.937 closest distance to " O   HOH Z 359 " =    1.988
peak=    3.931 closest distance to " N   TRP A  70 " =    1.053
peak=    3.926 closest distance to " O   SER A 273 " =    1.022
peak=    3.925 closest distance to " NZ  LYS A 166 " =    1.364
peak=    3.918 closest distance to " NH1AARG A 145 " =    1.036
peak=    3.912 closest distance to " CD2 LEU A   5 " =    1.404
peak=    3.912 closest distance to " N   TYR A 169 " =    1.104
peak=    3.903 closest distance to " C   ASP A  65 " =    0.759
peak=    3.901 closest distance to " O   HOH Z 119 " =    1.225
peak=    3.895 closest distance to " C   ASN A 284 " =    1.060
peak=    3.891 closest distance to " CE2 PHE A  16 " =    1.263
peak=    3.883 closest distance to " OG  SER A 273 " =    1.137
peak=    3.880 closest distance to " CG1 ILE A  20 " =    1.282
peak=    3.880 closest distance to " CB  ASN A 148 " =    2.148
peak=    3.877 closest distance to " CB  ALA A 114 " =    0.878
peak=    3.870 closest distance to " O   GLY A 211 " =    1.514
peak=    3.855 closest distance to " N   ALA A 165 " =    1.100
peak=    3.842 closest distance to " CD1 LEU A  96 " =    0.942
peak=    3.839 closest distance to " CB  ARG A 275 " =    1.355
peak=    3.824 closest distance to " O   HOH Z 415 " =    1.143
peak=    3.819 closest distance to " CG  GLN A  55 " =    1.367
peak=    3.810 closest distance to " NH2 ARG A 269 " =    0.990
peak=    3.802 closest distance to " CB  PHE A  61 " =    1.242
peak=    3.797 closest distance to " O   HOH Z  68 " =    2.292
peak=    3.792 closest distance to " ND2 ASN A 285 " =    1.154
peak=    3.787 closest distance to " CA  TRP A  92 " =    1.400
peak=    3.779 closest distance to " O   HOH Z 222 " =    2.816
peak=    3.774 closest distance to " O   HOH Z 213 " =    2.421
peak=    3.757 closest distance to " CB  ASP A 270 " =    0.858
peak=    3.756 closest distance to " CD2 LEU A 261 " =    1.118
peak=    3.750 closest distance to " C   PRO A 198 " =    1.514
peak=    3.745 closest distance to " CB  LEU A  83 " =    0.923
peak=    3.744 closest distance to " N   ASP A  27 " =    0.938
peak=    3.741 closest distance to " O   HOH Z 286 " =    2.260
peak=    3.738 closest distance to " CB  TRP A  70 " =    0.750
peak=    3.725 closest distance to " CG AARG A 102 " =    1.201
peak=    3.725 closest distance to " O   HOH Z 203 " =    1.083
peak=    3.722 closest distance to " O   HOH Z 395 " =    1.567
peak=    3.720 closest distance to " C   HIS A 115 " =    0.950
peak=    3.719 closest distance to " O   HOH Z 181 " =    1.879
peak=    3.716 closest distance to " O   HOH Z  32 " =    2.305
peak=    3.714 closest distance to " O   HOH Z 356 " =    1.822
peak=    3.710 closest distance to " O   HOH Z  21 " =    1.559
peak=    3.709 closest distance to " CB  PHE A  59 " =    1.090
peak=    3.708 closest distance to " O   HOH Z 144 " =    2.086
peak=    3.702 closest distance to " OE1 GLN A  55 " =    1.672
peak=    3.698 closest distance to " O   ASN A  69 " =    1.208
peak=    3.696 closest distance to " O   ALA A  10 " =    1.044
peak=    3.695 closest distance to " NH2 ARG A 195 " =    1.334
peak=    3.693 closest distance to " CA  SER A  12 " =    1.482
peak=    3.691 closest distance to " O   HOH Z 303 " =    1.771
peak=    3.690 closest distance to " OE1 GLN A 103 " =    1.283
peak=    3.685 closest distance to " CA  ALA A   1 " =    1.658
peak=    3.682 closest distance to " OD2 ASP A 149 " =    0.938
peak=    3.681 closest distance to " O   HOH Z 215 " =    2.350
peak=    3.678 closest distance to " CB  PRO A 243 " =    1.373
peak=    3.677 closest distance to " O   GLN A  58 " =    1.196
peak=    3.676 closest distance to " O   HOH Z 287 " =    2.127
peak=    3.669 closest distance to " N   ASN A 142 " =    1.092
peak=    3.669 closest distance to " ND2 ASN A  74 " =    1.267
peak=    3.663 closest distance to " N   GLN A  73 " =    1.231
peak=    3.658 closest distance to " OE1 GLN A  77 " =    1.434
peak=    3.654 closest distance to " O   TRP A  70 " =    1.032
peak=    3.652 closest distance to " O   HOH Z 304 " =    1.086
peak=    3.650 closest distance to " O   HOH Z 411 " =    3.844
peak=    3.643 closest distance to " O   ARG A  14 " =    1.179
peak=    3.641 closest distance to " O   HOH Z 167 " =    1.076
peak=    3.641 closest distance to " CG  ARG A 219 " =    1.631
peak=    3.638 closest distance to " NH1 ARG A  79 " =    1.106
peak=    3.633 closest distance to " CD2 TYR A 169 " =    1.271
peak=    3.629 closest distance to " O   HOH Z 397 " =    1.072
peak=    3.628 closest distance to " CB  HIS A 115 " =    0.958
peak=    3.623 closest distance to " O   HOH Z 321 " =    0.964
peak=    3.613 closest distance to " CB  LEU A   5 " =    1.567
peak=    3.612 closest distance to " CD  PRO A  54 " =    1.079
peak=    3.612 closest distance to " O   HOH Z 111 " =    1.555
peak=    3.602 closest distance to " OD1 ASN A  69 " =    1.286
peak=    3.601 closest distance to " OG1 THR A  52 " =    1.478
peak=    3.599 closest distance to " OD2 ASP A 132 " =    1.206
peak=    3.598 closest distance to " O   HOH Z 143 " =    1.826
peak=    3.595 closest distance to " O   HOH Z 218 " =    1.799
peak=    3.590 closest distance to " CG1 VAL A 296 " =    1.199
peak=    3.589 closest distance to " O   HOH Z 329 " =    4.398
peak=    3.588 closest distance to " CE3 TRP A 274 " =    1.448
peak=    3.584 closest distance to " CB  PRO A  54 " =    1.122
peak=    3.581 closest distance to " O   HOH Z 366 " =    2.634
peak=    3.579 closest distance to " O   HOH Z  35 " =    4.717
peak=    3.579 closest distance to " O   HOH Z 301 " =    2.138
peak=    3.578 closest distance to " NE1 TRP A 266 " =    1.159
peak=    3.578 closest distance to " O   HOH Z 333 " =    1.087
peak=    3.575 closest distance to " NH1 ARG A  36 " =    2.191
peak=    3.574 closest distance to " CA  TYR A  30 " =    1.357
peak=    3.568 closest distance to " O   TYR A  30 " =    1.441
peak=    3.547 closest distance to " O   HOH Z 139 " =    2.944
peak=    3.542 closest distance to " CB  ASN A 173 " =    1.094
peak=    3.533 closest distance to " O   HOH Z 362 " =    2.508
peak=    3.532 closest distance to " CG  TYR A  68 " =    1.129
peak=    3.518 closest distance to " NZ ALYS A 290 " =    1.436
peak=    3.516 closest distance to " O   THR A  52 " =    0.938
peak=    3.512 closest distance to " O   HOH Z  45 " =    1.005
peak=    3.511 closest distance to " CG  ASN A  60 " =    0.924
peak=    3.505 closest distance to " N   ASN A 148 " =    0.930
peak=    3.504 closest distance to " NH2 ARG A  56 " =    1.539
peak=    3.504 closest distance to " O   HOH Z  11 " =    1.696
peak=    3.499 closest distance to " OG  SER A 276 " =    1.155
peak=    3.498 closest distance to " O   HOH Z 153 " =    2.204
peak=    3.493 closest distance to " OE1 GLN A  88 " =    2.010
peak=    3.490 closest distance to " O   ASP A 238 " =    1.204
peak=    3.489 closest distance to " O   HOH Z  11 " =    2.152
peak=    3.489 closest distance to " OG  SER A  28 " =    1.161
peak=    3.487 closest distance to " O   HOH Z 182 " =    1.893
peak=    3.482 closest distance to " CA  LEU A 282 " =    0.951
peak=    3.478 closest distance to " OE1 GLN A 278 " =    1.403
peak=    3.474 closest distance to " CD  ARG A 195 " =    3.745
peak=    3.456 closest distance to " O   HOH Z 144 " =    2.012
peak=    3.456 closest distance to " O   HOH Z 421 " =    2.942
peak=    3.455 closest distance to " O   HOH Z 171 " =    3.222
peak=    3.455 closest distance to " CB  THR A 235 " =    1.290
peak=    3.452 closest distance to " C   GLN A  11 " =    1.665
peak=    3.451 closest distance to " NE2 GLN A 205 " =    1.231
peak=    3.443 closest distance to " CB  GLU A 152 " =    1.353
peak=    3.443 closest distance to " CG1 VAL A 112 " =    1.063
peak=    3.437 closest distance to " O   HOH Z  83 " =    1.592
peak=    3.436 closest distance to " O   HOH Z 155 " =    2.570
peak=    3.435 closest distance to " O   HOH Z  46 " =    2.002
peak=    3.434 closest distance to " O   THR A 294 " =    1.117
peak=    3.431 closest distance to " CG1 VAL A 126 " =    1.473
peak=    3.430 closest distance to " O   HOH Z  66 " =    1.905
peak=    3.429 closest distance to " CD2 LEU A  96 " =    1.174
peak=    3.428 closest distance to " O   HOH Z 139 " =    1.542
peak=    3.427 closest distance to " OG1 THR A  82 " =    1.049
peak=    3.423 closest distance to " O   HOH Z 423 " =    3.345
peak=    3.417 closest distance to " CA  SER A 164 " =    1.312
peak=    3.417 closest distance to " O   HOH Z 183 " =    1.948
peak=    3.416 closest distance to " O   HOH Z 411 " =    3.353
peak=    3.414 closest distance to " O   SER A 288 " =    1.278
peak=    3.413 closest distance to " N   ASN A  60 " =    1.268
peak=    3.413 closest distance to " CA  GLY A  13 " =    1.149
peak=    3.411 closest distance to " O   HOH Z 120 " =    1.755
peak=    3.409 closest distance to " CG  GLN A  88 " =    1.176
peak=    3.409 closest distance to " CE1 PHE A  59 " =    0.704
peak=    3.405 closest distance to " O   PRO A 163 " =    1.088
peak=    3.404 closest distance to " CG2 ILE A 106 " =    1.101
peak=    3.403 closest distance to " O   LEU A  83 " =    1.115
peak=    3.400 closest distance to " CG  LYS A  76 " =    1.608
peak=    3.400 closest distance to " CB  PHE A 225 " =    1.641
peak=    3.399 closest distance to " O   HOH Z 227 " =    2.054
peak=    3.397 closest distance to " O   HOH Z 179 " =    1.455
peak=    3.396 closest distance to " CB  ASN A 148 " =    1.146
peak=    3.396 closest distance to " O   HOH Z  77 " =    1.320
peak=    3.395 closest distance to " CD1 ILE A 109 " =    1.188
peak=    3.392 closest distance to " CG2 THR A 221 " =    1.272
peak=    3.392 closest distance to " O   HOH Z 375 " =    1.961
peak=    3.380 closest distance to " O   LEU A 101 " =    1.109
peak=    3.379 closest distance to " CE3 TRP A 274 " =    3.911
peak=    3.378 closest distance to " O   HOH Z  67 " =    1.894
peak=    3.376 closest distance to " CD1 LEU A 261 " =    1.166
peak=    3.372 closest distance to " CA  TRP A  92 " =    1.285
peak=    3.369 closest distance to " O   HOH Z 362 " =    2.276
peak=    3.367 closest distance to " CB  PHE A 283 " =    1.310
peak=    3.362 closest distance to " CG1 VAL A 125 " =    1.809
peak=    3.362 closest distance to " O   HOH Z 423 " =    1.932
peak=    3.361 closest distance to " O   HOH Z 217 " =    2.982
peak=    3.360 closest distance to " CB  PRO A  90 " =    1.366
peak=    3.359 closest distance to " O   HOH Z 431 " =    2.124
peak=    3.358 closest distance to " CA  GLY A 241 " =    1.243
peak=    3.358 closest distance to " O   HOH Z 101 " =    0.962
peak=    3.350 closest distance to " CB  LYS A 181 " =    1.625
peak=    3.340 closest distance to " CG  GLU A  53 " =    0.841
peak=    3.339 closest distance to " C   PHE A 208 " =    1.271
peak=    3.337 closest distance to " O   HOH Z 153 " =    3.614
peak=    3.327 closest distance to " NH2AARG A 275 " =    4.057
peak=    3.327 closest distance to " O   HOH Z 172 " =    2.358
peak=    3.324 closest distance to " O   HOH Z  82 " =    1.380
peak=    3.321 closest distance to " O   GLY A  23 " =    1.343
peak=    3.318 closest distance to " NH1 ARG A 139 " =    1.180
peak=    3.318 closest distance to " C   SER A  26 " =    0.920
peak=    3.315 closest distance to " N   TYR A 116 " =    1.082
peak=    3.315 closest distance to " O   HOH Z 181 " =    2.378
peak=    3.315 closest distance to " N   GLN A 278 " =    1.150
peak=    3.315 closest distance to " N   TRP A  85 " =    0.943
peak=    3.313 closest distance to " CB  MET A  40 " =    1.581
peak=    3.310 closest distance to " CG  GLN A  58 " =    2.752
peak=    3.310 closest distance to " O   HOH Z 416 " =    1.521
peak=    3.309 closest distance to " CD  LYS A 166 " =    1.522
peak=    3.308 closest distance to " N   ALA A  71 " =    0.894
peak=    3.300 closest distance to " O   HOH Z 110 " =    1.031
peak=    3.289 closest distance to " O   HOH Z  32 " =    2.187
peak=    3.287 closest distance to " O   MET A 105 " =    1.648
peak=    3.285 closest distance to " O   HOH Z 223 " =    1.916
peak=    3.284 closest distance to " O   ASP A  27 " =    0.952
peak=    3.281 closest distance to " CG2 ILE A 239 " =    1.213
peak=    3.276 closest distance to " C   SER A 164 " =    1.066
peak=    3.275 closest distance to " N   SER A 134 " =    0.795
peak=    3.275 closest distance to " O   HOH Z  57 " =    2.478
peak=    3.274 closest distance to " CA  ALA A  51 " =    1.521
peak=    3.273 closest distance to " O   HOH Z 383 " =    1.155
peak=    3.269 closest distance to " CD  ARG A 259 " =    1.298
peak=    3.262 closest distance to " CB  SER A  26 " =    1.456
peak=    3.260 closest distance to " CA  LEU A 222 " =    1.671
peak=    3.259 closest distance to " O   HOH Z 422 " =    1.515
peak=    3.258 closest distance to " CA  GLU A 152 " =    1.120
peak=    3.257 closest distance to " O   HOH Z 369 " =    1.895
peak=    3.256 closest distance to " ND2BASN A 224 " =    1.022
peak=    3.254 closest distance to " O   HOH Z 183 " =    1.351
peak=    3.254 closest distance to " O   HOH Z 104 " =    1.255
peak=    3.254 closest distance to " CB  ARG A 195 " =    1.068
peak=    3.252 closest distance to " O   HOH Z 232 " =    1.701
peak=    3.251 closest distance to " O   HOH Z 437 " =    1.956
peak=    3.249 closest distance to " CA  PRO A  54 " =    0.905
peak=    3.248 closest distance to " CG1BVAL A 121 " =    1.893
peak=    3.246 closest distance to " O   HOH Z 245 " =    2.018
peak=    3.245 closest distance to " O   HOH Z 131 " =    1.544
peak=    3.244 closest distance to " CA  TRP A 274 " =    1.356
peak=    3.244 closest distance to " CA  GLY A 133 " =    1.084
peak=    3.240 closest distance to " CD2 LEU A 281 " =    1.188
peak=    3.239 closest distance to " O   GLY A 302 " =    1.590
peak=    3.239 closest distance to " O   HOH Z  55 " =    2.138
peak=    3.230 closest distance to " CA  GLY A 133 " =    1.369
peak=    3.225 closest distance to " CB  THR A 178 " =    1.879
peak=    3.216 closest distance to " O   HOH Z 403 " =    2.027
peak=    3.216 closest distance to " O   HOH Z 241 " =    2.345
peak=    3.214 closest distance to " CA  SER A  87 " =    1.532
peak=    3.214 closest distance to " O   HOH Z 410 " =    1.482
peak=    3.213 closest distance to " CB  HIS A  86 " =    1.014
peak=    3.212 closest distance to " NH1 ARG A  36 " =    1.331
peak=    3.212 closest distance to " N   SER A  97 " =    0.983
peak=    3.211 closest distance to " O   HOH Z 200 " =    5.692
peak=    3.208 closest distance to " CA  GLY A 118 " =    0.973
peak=    3.207 closest distance to " CA  ALA A 184 " =    1.917
peak=    3.207 closest distance to " NH1 ARG A 195 " =    1.139
peak=    3.206 closest distance to " N   VAL A  67 " =    0.937
peak=    3.204 closest distance to " CB  SER A  99 " =    0.974
peak=    3.201 closest distance to " CB  THR A  29 " =    1.263
peak=    3.198 closest distance to " OG  SER A  22 " =    1.696
peak=    3.194 closest distance to " O   THR A  82 " =    0.855
peak=    3.194 closest distance to " N   SER A 164 " =    0.983
peak=    3.192 closest distance to " O   HOH Z 328 " =    2.213
peak=    3.192 closest distance to " CA  ALA A   9 " =    0.909
peak=    3.186 closest distance to " CA  ARG A  36 " =    1.210
peak=    3.186 closest distance to " CB  SER A  63 " =    1.534
peak=    3.183 closest distance to " O   HOH Z 222 " =    2.340
peak=    3.182 closest distance to " N   LEU A  25 " =    0.716
peak=    3.182 closest distance to " CB  HIS A 115 " =    1.243
peak=    3.177 closest distance to " O   HOH Z  49 " =    2.429
peak=    3.174 closest distance to " CB  PHE A  59 " =    1.934
peak=    3.172 closest distance to " CE1 PHE A 208 " =    0.932
peak=    3.169 closest distance to " O   ALA A 158 " =    1.348
peak=    3.168 closest distance to " CB  SER A  62 " =    1.618
peak=    3.168 closest distance to " CA  LYS A 289 " =    1.035
peak=    3.168 closest distance to " CA  ASP A 231 " =    1.996
peak=    3.166 closest distance to " O   HOH Z 342 " =    1.085
peak=    3.165 closest distance to " NH1 ARG A  24 " =    0.985
peak=    3.162 closest distance to " CD2 PHE A 192 " =    1.909
peak=    3.158 closest distance to " O   HOH Z 305 " =    1.764
peak=    3.151 closest distance to " CZ  PHE A 192 " =    1.060
peak=    3.151 closest distance to " CE2 TRP A  70 " =    1.232
peak=    3.143 closest distance to " O   HOH Z  31 " =    1.805
peak=    3.140 closest distance to " CG AARG A 102 " =    1.405
peak=    3.139 closest distance to " N   ALA A 295 " =    1.597
peak=    3.132 closest distance to " OG BSER A  12 " =    1.230
peak=    3.132 closest distance to " CB  TRP A 150 " =    1.277
peak=    3.131 closest distance to " NE2 GLN A  11 " =    2.086
peak=    3.128 closest distance to " O   HOH Z 217 " =    1.972
peak=    3.127 closest distance to " CB  ALA A 292 " =    1.417
peak=    3.125 closest distance to " OD1 ASN A  39 " =    1.232
peak=    3.124 closest distance to " O   PRO A  90 " =    1.458
peak=    3.122 closest distance to " O   HOH Z 193 " =    1.657
peak=    3.120 closest distance to " O   ALA A 161 " =    1.148
peak=    3.112 closest distance to " CE3 TRP A  85 " =    1.174
peak=    3.101 closest distance to " O   HOH Z 336 " =    1.463
peak=    3.100 closest distance to " O   HOH Z  88 " =    3.495
peak=    3.093 closest distance to " N   PHE A  61 " =    1.451
peak=    3.091 closest distance to " O   HOH Z 430 " =    2.877
peak=    3.086 closest distance to " CE1 PHE A  61 " =    1.628
peak=    3.083 closest distance to " CD1 ILE A 199 " =    2.311
peak=    3.079 closest distance to " N   PHE A 218 " =    0.967
peak=    3.067 closest distance to " OG ASER A 210 " =    1.140
peak=    3.051 closest distance to " CD1BILE A 234 " =    1.273
peak=    3.044 closest distance to " CG1 VAL A  78 " =    0.919
peak=    3.038 closest distance to " O   HOH Z 419 " =    2.189

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 227         
Filter by distance & map next to the model:
   mapped sites are within: 0.229 - 5.220
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 216 from: 227
   mapped sites are within: 0.716 - 5.220

peak=   -5.471 closest distance to " N   PRO A  54 " =    1.054
peak=   -5.420 closest distance to " N   ARG A 275 " =    1.319
peak=   -5.230 closest distance to " C   ASN A  69 " =    1.057
peak=   -5.196 closest distance to " O   ASN A  60 " =    1.129
peak=   -5.048 closest distance to " C   ASP A  65 " =    1.073
peak=   -4.952 closest distance to " CB  TYR A  68 " =    1.137
peak=   -4.825 closest distance to " O   SER A  26 " =    1.119
peak=   -4.610 closest distance to " NE2 GLN A 103 " =    1.078
peak=   -4.560 closest distance to " C   ALA A 114 " =    0.970
peak=   -4.476 closest distance to " O   TRP A  70 " =    1.003
peak=   -4.396 closest distance to " CA  SER A  63 " =    1.155
peak=   -4.327 closest distance to " O   HOH Z  27 " =    0.745
peak=   -4.259 closest distance to " C   PHE A  61 " =    1.036
peak=   -4.209 closest distance to " O   ASN A 209 " =    2.055
peak=   -4.171 closest distance to " ND2 ASN A 285 " =    2.401
peak=   -4.168 closest distance to " O   HOH Z 163 " =    1.199
peak=   -4.159 closest distance to " N   SER A  26 " =    1.110
peak=   -4.045 closest distance to " CZ  ARG A 156 " =    1.140
peak=   -4.030 closest distance to " O   HOH Z 313 " =    0.837
peak=   -4.024 closest distance to " OG  SER A 273 " =    1.129
peak=   -4.003 closest distance to " CG  GLN A  55 " =    1.097
peak=   -3.987 closest distance to " CA  ARG A  56 " =    0.832
peak=   -3.983 closest distance to " O   THR A  52 " =    0.969
peak=   -3.959 closest distance to " CD1 PHE A  61 " =    1.154
peak=   -3.948 closest distance to " O   ASN A 285 " =    1.102
peak=   -3.945 closest distance to " O   HOH Z 222 " =    2.005
peak=   -3.927 closest distance to " O   HOH Z 293 " =    1.771
peak=   -3.916 closest distance to " N   PHE A 218 " =    1.047
peak=   -3.880 closest distance to " CD  ARG A 219 " =    2.645
peak=   -3.873 closest distance to " N   THR A  29 " =    1.071
peak=   -3.867 closest distance to " O   HOH Z 179 " =    1.372
peak=   -3.857 closest distance to " C   PHE A  59 " =    0.871
peak=   -3.846 closest distance to " N   PRO A  54 " =    0.859
peak=   -3.842 closest distance to " N   GLN A  55 " =    1.045
peak=   -3.835 closest distance to " O   HOH Z 244 " =    1.541
peak=   -3.833 closest distance to " OE2 GLU A 152 " =    1.761
peak=   -3.832 closest distance to " O   SER A   3 " =    1.070
peak=   -3.820 closest distance to " O   GLN A  55 " =    1.228
peak=   -3.808 closest distance to " O   HOH Z 139 " =    3.004
peak=   -3.807 closest distance to " C   GLY A  23 " =    1.771
peak=   -3.801 closest distance to " CB  PHE A  61 " =    1.130
peak=   -3.800 closest distance to " CA  ALA A 161 " =    1.068
peak=   -3.789 closest distance to " CB  ASP A  27 " =    1.006
peak=   -3.787 closest distance to " OG  SER A  22 " =    2.327
peak=   -3.782 closest distance to " CA  SER A 273 " =    1.115
peak=   -3.777 closest distance to " O   HOH Z  32 " =    0.923
peak=   -3.775 closest distance to " O   HOH Z 336 " =    5.218
peak=   -3.764 closest distance to " CB  TRP A  70 " =    1.224
peak=   -3.759 closest distance to " CD2 LEU A 237 " =    2.593
peak=   -3.756 closest distance to " O   GLY A 203 " =    2.168
peak=   -3.752 closest distance to " O   ALA A 161 " =    1.126
peak=   -3.750 closest distance to " CG  TRP A 274 " =    1.027
peak=   -3.747 closest distance to " CG1 VAL A 125 " =    2.318
peak=   -3.738 closest distance to " O   HOH Z 408 " =    1.909
peak=   -3.738 closest distance to " OG  SER A  28 " =    1.048
peak=   -3.736 closest distance to " O   HOH Z 374 " =    2.150
peak=   -3.733 closest distance to " O   GLN A 240 " =    3.116
peak=   -3.730 closest distance to " CA  SER A 288 " =    1.135
peak=   -3.706 closest distance to " NH2 ARG A  56 " =    1.029
peak=   -3.705 closest distance to " CB  ASP A 171 " =    2.755
peak=   -3.705 closest distance to " CA  GLY A  57 " =    2.177
peak=   -3.695 closest distance to " C   PRO A 163 " =    1.055
peak=   -3.694 closest distance to " O   GLU A  53 " =    1.116
peak=   -3.684 closest distance to " OE1 GLU A  44 " =    1.288
peak=   -3.671 closest distance to " O   HOH Z  24 " =    1.055
peak=   -3.655 closest distance to " CD  GLN A  55 " =    0.807
peak=   -3.644 closest distance to " CE2 PHE A 204 " =    2.485
peak=   -3.641 closest distance to " C   PRO A  54 " =    1.172
peak=   -3.638 closest distance to " CZ  ARG A  36 " =    2.130
peak=   -3.632 closest distance to " C   ALA A 180 " =    0.939
peak=   -3.628 closest distance to " CG2 THR A 220 " =    1.924
peak=   -3.625 closest distance to " CD2 LEU A 261 " =    0.984
peak=   -3.619 closest distance to " O   HOH Z  60 " =    1.009
peak=   -3.612 closest distance to " O   PRO A 198 " =    1.173
peak=   -3.604 closest distance to " O   GLY A  80 " =    2.475
peak=   -3.604 closest distance to " O   HOH Z 166 " =    3.649
peak=   -3.590 closest distance to " CB  ALA A 104 " =    2.149
peak=   -3.590 closest distance to " O   SER A 273 " =    0.749
peak=   -3.584 closest distance to " CZ2 TRP A  70 " =    0.949
peak=   -3.576 closest distance to " O   HOH Z 100 " =    2.146
peak=   -3.573 closest distance to " CG  GLN A  73 " =    1.097
peak=   -3.557 closest distance to " O   HOH Z 334 " =    1.395
peak=   -3.556 closest distance to " CG  ARG A  24 " =    2.822
peak=   -3.542 closest distance to " CG1BVAL A  41 " =    2.188
peak=   -3.522 closest distance to " OG  SER A  63 " =    0.849
peak=   -3.519 closest distance to " C   ASN A 284 " =    2.278
peak=   -3.515 closest distance to " O   CYS A 260 " =    1.159
peak=   -3.512 closest distance to " O   PRO A 243 " =    2.529
peak=   -3.509 closest distance to " O   THR A 178 " =    0.955
peak=   -3.508 closest distance to " O   HOH Z  84 " =    0.832
peak=   -3.501 closest distance to " O   HOH Z 181 " =    1.274
peak=   -3.500 closest distance to " OG ASER A 258 " =    1.367
peak=   -3.496 closest distance to " O   HOH Z 430 " =    0.897
peak=   -3.491 closest distance to " CZ  ARG A 259 " =    0.859
peak=   -3.488 closest distance to " O   HOH Z 386 " =    1.507
peak=   -3.482 closest distance to " O   HOH Z 111 " =    1.542
peak=   -3.479 closest distance to " C   ALA A  64 " =    0.999
peak=   -3.476 closest distance to " CA  SER A 210 " =    1.032
peak=   -3.476 closest distance to " CD1 TYR A 214 " =    1.562
peak=   -3.472 closest distance to " NE2 GLN A  88 " =    1.268
peak=   -3.472 closest distance to " OG1 THR A  82 " =    1.342
peak=   -3.465 closest distance to " O   ASN A 301 " =    1.180
peak=   -3.464 closest distance to " CB  GLN A 122 " =    2.059
peak=   -3.461 closest distance to " N   ASN A  69 " =    1.117
peak=   -3.460 closest distance to " O   HOH Z  54 " =    1.221
peak=   -3.458 closest distance to " O   HOH Z  33 " =    1.953
peak=   -3.458 closest distance to " O   HOH Z 109 " =    2.795
peak=   -3.454 closest distance to " O   PHE A 208 " =    1.542
peak=   -3.453 closest distance to " N   LYS A 290 " =    0.837
peak=   -3.451 closest distance to " OD2 ASP A  50 " =    1.678
peak=   -3.445 closest distance to " O   HOH Z 118 " =    1.522
peak=   -3.441 closest distance to " OG  SER A  97 " =    2.046
peak=   -3.440 closest distance to " O   HOH Z 231 " =    0.961
peak=   -3.437 closest distance to " O   HOH Z 241 " =    1.443
peak=   -3.437 closest distance to " O   HOH Z 127 " =    2.057
peak=   -3.430 closest distance to " CB  ASN A 285 " =    1.958
peak=   -3.428 closest distance to " O   GLU A  37 " =    1.983
peak=   -3.428 closest distance to " N   ARG A 138 " =    1.809
peak=   -3.425 closest distance to " O   HOH Z 257 " =    0.815
peak=   -3.414 closest distance to " CB  ALA A   9 " =    2.944
peak=   -3.411 closest distance to " CG  PRO A 163 " =    2.476
peak=   -3.408 closest distance to " O   HOH Z  35 " =    2.683
peak=   -3.406 closest distance to " NH2 ARG A  24 " =    2.191
peak=   -3.398 closest distance to " CA  GLY A  98 " =    1.688
peak=   -3.394 closest distance to " O   HOH Z  40 " =    2.110
peak=   -3.392 closest distance to " O   HOH Z 266 " =    2.346
peak=   -3.386 closest distance to " O   HOH Z  83 " =    0.892
peak=   -3.386 closest distance to " O   HOH Z 433 " =    1.423
peak=   -3.385 closest distance to " O   HOH Z 399 " =    1.413
peak=   -3.385 closest distance to " CA  ASP A  50 " =    1.070
peak=   -3.379 closest distance to " N   GLN A  11 " =    0.864
peak=   -3.371 closest distance to " N   GLY A 287 " =    1.018
peak=   -3.368 closest distance to " CA  GLY A 203 " =    2.209
peak=   -3.364 closest distance to " O   HOH Z  10 " =    0.803
peak=   -3.354 closest distance to " O   HOH Z 394 " =    1.463
peak=   -3.351 closest distance to " O   HOH Z 306 " =    1.770
peak=   -3.346 closest distance to " O   ASP A 298 " =    2.103
peak=   -3.343 closest distance to " O   HOH Z 389 " =    2.476
peak=   -3.336 closest distance to " C   ASP A  50 " =    1.325
peak=   -3.334 closest distance to " O   VAL A 268 " =    0.769
peak=   -3.330 closest distance to " OG  SER A 273 " =    1.233
peak=   -3.325 closest distance to " O   TYR A 172 " =    1.419
peak=   -3.323 closest distance to " O   HOH Z 206 " =    1.451
peak=   -3.323 closest distance to " O   HOH Z  77 " =    1.511
peak=   -3.322 closest distance to " N   SER A  62 " =    1.779
peak=   -3.321 closest distance to " CD2 TYR A 293 " =    1.907
peak=   -3.321 closest distance to " O   LEU A 261 " =    1.022
peak=   -3.307 closest distance to " O   THR A   4 " =    1.109
peak=   -3.300 closest distance to " C   LEU A 143 " =    1.077
peak=   -3.300 closest distance to " CG  ARG A  56 " =    1.452
peak=   -3.294 closest distance to " O   HOH Z 404 " =    1.005
peak=   -3.291 closest distance to " O   HOH Z  20 " =    2.126
peak=   -3.290 closest distance to " O   HOH Z  77 " =    1.548
peak=   -3.286 closest distance to " OG  SER A 135 " =    2.421
peak=   -3.279 closest distance to " O   HOH Z 407 " =    5.220
peak=   -3.277 closest distance to " CB  LEU A 261 " =    2.698
peak=   -3.268 closest distance to " CA  ILE A 120 " =    1.087
peak=   -3.263 closest distance to " C   ASP A 162 " =    1.167
peak=   -3.257 closest distance to " O   PHE A  59 " =    2.172
peak=   -3.253 closest distance to " O   HOH Z 368 " =    4.774
peak=   -3.252 closest distance to " O   HOH Z 412 " =    2.134
peak=   -3.239 closest distance to " CG  LEU A 167 " =    1.127
peak=   -3.232 closest distance to " CA  ARG A 156 " =    1.017
peak=   -3.231 closest distance to " CG BLYS A 290 " =    0.769
peak=   -3.227 closest distance to " O   ALA A 226 " =    1.507
peak=   -3.227 closest distance to " O   HOH Z 371 " =    2.253
peak=   -3.226 closest distance to " O   GLY A  57 " =    1.054
peak=   -3.224 closest distance to " O   HOH Z 367 " =    3.490
peak=   -3.223 closest distance to " O   PRO A  54 " =    1.521
peak=   -3.217 closest distance to " CB  MET A 113 " =    1.691
peak=   -3.213 closest distance to " O   HOH Z 223 " =    1.582
peak=   -3.210 closest distance to " O   SER A  99 " =    1.567
peak=   -3.209 closest distance to " N   ASP A 162 " =    1.487
peak=   -3.206 closest distance to " O   GLY A  57 " =    1.570
peak=   -3.205 closest distance to " CG1 VAL A  78 " =    2.542
peak=   -3.203 closest distance to " O   HOH Z  72 " =    1.052
peak=   -3.193 closest distance to " CD2 PHE A  61 " =    1.641
peak=   -3.191 closest distance to " O   HOH Z 426 " =    1.942
peak=   -3.185 closest distance to " O   HOH Z  97 " =    2.829
peak=   -3.185 closest distance to " O   HOH Z 414 " =    1.352
peak=   -3.181 closest distance to " O   TYR A  30 " =    1.873
peak=   -3.178 closest distance to " O   HOH Z 168 " =    2.172
peak=   -3.177 closest distance to " CB  PHE A  59 " =    1.578
peak=   -3.176 closest distance to " OE1 GLN A 122 " =    2.709
peak=   -3.175 closest distance to " CA  MET A  47 " =    1.596
peak=   -3.171 closest distance to " O   HOH Z 364 " =    2.706
peak=   -3.168 closest distance to " O   HOH Z 417 " =    4.537
peak=   -3.165 closest distance to " CB  HIS A  86 " =    1.043
peak=   -3.164 closest distance to " O   HOH Z 145 " =    2.940
peak=   -3.159 closest distance to " CA  HIS A  86 " =    2.107
peak=   -3.158 closest distance to " O   HOH Z  13 " =    1.358
peak=   -3.156 closest distance to " CA  GLY A  80 " =    1.248
peak=   -3.155 closest distance to " OG BSER A 134 " =    2.705
peak=   -3.146 closest distance to " O   HOH Z 390 " =    2.754
peak=   -3.141 closest distance to " C   VAL A 265 " =    0.938
peak=   -3.136 closest distance to " O   ASP A 171 " =    0.716
peak=   -3.136 closest distance to " O   HOH Z 348 " =    1.592
peak=   -3.134 closest distance to " NE  ARG A 138 " =    1.772
peak=   -3.130 closest distance to " CB  ASN A 301 " =    1.823
peak=   -3.128 closest distance to " O   LYS A  48 " =    0.968
peak=   -3.120 closest distance to " CG  PHE A  38 " =    1.399
peak=   -3.120 closest distance to " N   LEU A  25 " =    1.024
peak=   -3.118 closest distance to " O   HOH Z  40 " =    3.380
peak=   -3.106 closest distance to " OD1 ASP A 107 " =    1.182
peak=   -3.105 closest distance to " O   HOH Z  67 " =    0.887
peak=   -3.104 closest distance to " O   HOH Z 381 " =    1.132
peak=   -3.102 closest distance to " CA  LEU A  96 " =    1.112
peak=   -3.102 closest distance to " O   HOH Z 219 " =    3.713
peak=   -3.086 closest distance to " O   HOH Z  76 " =    1.167
peak=   -3.080 closest distance to " O   ALA A 161 " =    2.016
peak=   -3.071 closest distance to " CG  ASP A  65 " =    1.253
peak=   -3.061 closest distance to " O   HOH Z  87 " =    1.561
peak=   -3.060 closest distance to " OD2 ASP A 270 " =    1.457
peak=   -3.047 closest distance to " ND2 ASN A 170 " =    2.008
peak=   -3.045 closest distance to " N   ASN A  60 " =    1.237
peak=   -3.024 closest distance to " CB  ALA A 161 " =    0.770

================= 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    :  0.5158 0.5196   6.318889e+00   6.311626e+00
   1_bss:  0.5097 0.5175   6.319040e+00   6.310413e+00
   1_xyz:  0.4605 0.5031   6.265826e+00   6.293222e+00
   1_adp:  0.4333 0.5079   6.247206e+00   6.297720e+00
   1_occ:  0.4329 0.5085   6.246802e+00   6.297836e+00
   2_bss:  0.4341 0.5089   6.248309e+00   6.297755e+00
   2_xyz:  0.4011 0.4851   6.198224e+00   6.274462e+00
   2_adp:  0.3910 0.4829   6.191497e+00   6.271738e+00
   2_occ:  0.3909 0.4831   6.191950e+00   6.272193e+00
   3_bss:  0.3914 0.4828   6.192975e+00   6.272048e+00
   3_xyz:  0.3447 0.4441   6.105514e+00   6.223113e+00
   3_adp:  0.3231 0.4314   6.074533e+00   6.213694e+00
   3_occ:  0.3229 0.4306   6.073675e+00   6.213206e+00
   4_bss:  0.3233 0.4300   6.073283e+00   6.212393e+00
   4_xyz:  0.2812 0.3741   5.957610e+00   6.131717e+00
   4_adp:  0.2635 0.3500   5.915823e+00   6.091194e+00
   4_occ:  0.2634 0.3496   5.914642e+00   6.090491e+00
   5_bss:  0.2632 0.3491   5.912197e+00   6.089061e+00
   5_xyz:  0.2298 0.3020   5.784220e+00   5.976914e+00
   5_adp:  0.2168 0.2859   5.739370e+00   5.931166e+00
   5_occ:  0.2168 0.2857   5.738524e+00   5.930297e+00
   5_bss:  0.2168 0.2851   5.737396e+00   5.928274e+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:  0.327  66.421  -0.427  -0.870   2.092  -0.000   0.000   0.000
   1_xyz:  0.327  66.421  -0.427  -0.870   2.092  -0.000   0.000   0.000
   1_adp:  0.327  66.421  -0.427  -0.870   2.092  -0.000   0.000   0.000
   1_occ:  0.327  66.421  -0.427  -0.870   2.092  -0.000   0.000   0.000
   2_bss:  0.365 100.938  -0.427  -0.870   2.092  -0.000   0.000   0.000
   2_xyz:  0.365 100.938  -0.427  -0.870   2.092  -0.000   0.000   0.000
   2_adp:  0.365 100.938  -0.427  -0.870   2.092  -0.000   0.000   0.000
   2_occ:  0.365 100.938  -0.427  -0.870   2.092  -0.000   0.000   0.000
   3_bss:  0.381 110.900   0.117  -0.300   1.738  -0.000   0.000   0.000
   3_xyz:  0.381 110.900   0.117  -0.300   1.738  -0.000   0.000   0.000
   3_adp:  0.381 110.900   0.117  -0.300   1.738  -0.000   0.000   0.000
   3_occ:  0.381 110.900   0.117  -0.300   1.738  -0.000   0.000   0.000
   4_bss:  0.385 120.136   0.336  -0.442   1.547  -0.000   0.000   0.000
   4_xyz:  0.385 120.136   0.336  -0.442   1.547  -0.000   0.000   0.000
   4_adp:  0.385 120.136   0.336  -0.442   1.547  -0.000   0.000   0.000
   4_occ:  0.385 120.136   0.336  -0.442   1.547  -0.000   0.000   0.000
   5_bss:  0.369 102.174  -0.657  -1.262   0.895  -0.000   0.000   0.000
   5_xyz:  0.369 102.174  -0.657  -1.262   0.895  -0.000   0.000   0.000
   5_adp:  0.369 102.174  -0.657  -1.262   0.895  -0.000   0.000   0.000
   5_occ:  0.369 102.174  -0.657  -1.262   0.895  -0.000   0.000   0.000
   5_bss:  0.340  81.607  -1.415  -2.262   0.114  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  70.281 0.2590  0.3585    94731.648
   1_bss:  70.117 0.2607  0.3764    95182.280
   1_xyz:  66.018 0.3139  0.4475    87784.763
   1_adp:  66.249 0.3107  0.4650    88401.397
   1_occ:  66.139 0.3122  0.4672    88391.568
   2_bss:  66.122 0.3124  0.4672    88275.003
   2_xyz:  60.109 0.3902  0.5809    76052.696
   2_adp:  59.425 0.3990  0.5894    74829.438
   2_occ:  59.491 0.3982  0.5882    74998.907
   3_bss:  59.487 0.3982  0.5927    74957.450
   3_xyz:  51.645 0.4979  0.7386    59108.763
   3_adp:  49.462 0.5256  0.7514    56274.334
   3_occ:  49.408 0.5262  0.7522    56103.879
   4_bss:  49.330 0.5271  0.7522    55884.971
   4_xyz:  41.915 0.6176  0.8621    41089.587
   4_adp:  38.785 0.6558  0.8806    36284.493
   4_occ:  38.730 0.6563  0.8810    36158.422
   5_bss:  38.577 0.6579  0.8585    35841.076
   5_xyz:  31.843 0.7354  0.9323    25236.836
   5_adp:  29.621 0.7610  0.9408    22398.267
   5_occ:  29.586 0.7613  0.9408    22353.100
   5_bss:  29.518 0.7619  0.9154    22247.582
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.8379e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.8379e-01
   1_xyz:   1.552  0.011  0.100 16.080  0.006  4.104   1.3491e-01
   1_adp:   1.552  0.011  0.100 16.080  0.006  4.104   1.3491e-01
   1_occ:   1.552  0.011  0.100 16.080  0.006  4.104   1.3491e-01
   2_bss:   1.552  0.011  0.100 16.080  0.006  4.104   1.3491e-01
   2_xyz:   1.273  0.009  0.084 15.427  0.005  4.100   9.8266e-02
   2_adp:   1.273  0.009  0.084 15.427  0.005  4.100   9.8266e-02
   2_occ:   1.273  0.009  0.084 15.427  0.005  4.100   9.8266e-02
   3_bss:   1.273  0.009  0.084 15.427  0.005  4.100   9.8266e-02
   3_xyz:   1.324  0.010  0.096 16.144  0.006  4.115   1.1327e-01
   3_adp:   1.324  0.010  0.096 16.144  0.006  4.115   1.1327e-01
   3_occ:   1.324  0.010  0.096 16.144  0.006  4.115   1.1327e-01
   4_bss:   1.324  0.010  0.096 16.144  0.006  4.115   1.1327e-01
   4_xyz:   1.279  0.010  0.092 15.758  0.005  4.118   9.7845e-02
   4_adp:   1.279  0.010  0.092 15.758  0.005  4.118   9.7845e-02
   4_occ:   1.279  0.010  0.092 15.758  0.005  4.118   9.7845e-02
   5_bss:   1.279  0.010  0.092 15.758  0.005  4.118   9.7845e-02
   5_xyz:   0.994  0.007  0.069 14.585  0.003  4.108   6.2054e-02
   5_adp:   0.994  0.007  0.069 14.585  0.003  4.108   6.2054e-02
   5_occ:   0.994  0.007  0.069 14.585  0.003  4.108   6.2054e-02
   5_bss:   0.994  0.007  0.069 14.585  0.003  4.108   6.2054e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.681   2.4318e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.681   2.4318e-01
   1_xyz:   8.770  0.053  0.344 84.526  0.040  1.937   8.8200e-02
   1_adp:   8.770  0.053  0.344 84.526  0.040  1.937   8.8200e-02
   1_occ:   8.770  0.053  0.344 84.526  0.040  1.937   8.8200e-02
   2_bss:   8.770  0.053  0.344 84.526  0.040  1.937   8.8200e-02
   2_xyz:   7.836  0.059  0.270 82.380  0.039  1.978   5.8960e-02
   2_adp:   7.836  0.059  0.270 82.380  0.039  1.978   5.8960e-02
   2_occ:   7.836  0.059  0.270 82.380  0.039  1.978   5.8960e-02
   3_bss:   7.836  0.059  0.270 82.380  0.039  1.978   5.8960e-02
   3_xyz:   8.042  0.074  0.331 80.973  0.035  2.044   1.0490e-01
   3_adp:   8.042  0.074  0.331 80.973  0.035  2.044   1.0490e-01
   3_occ:   8.042  0.074  0.331 80.973  0.035  2.044   1.0490e-01
   4_bss:   8.042  0.074  0.331 80.973  0.035  2.044   1.0490e-01
   4_xyz:   7.744  0.075  0.265 85.289  0.041  2.240   7.3303e-02
   4_adp:   7.744  0.075  0.265 85.289  0.041  2.240   7.3303e-02
   4_occ:   7.744  0.075  0.265 85.289  0.041  2.240   7.3303e-02
   5_bss:   7.744  0.075  0.265 85.289  0.041  2.240   7.3303e-02
   5_xyz:   7.960  0.047  0.262 80.672  0.029  2.301   4.8464e-02
   5_adp:   7.960  0.047  0.262 80.672  0.029  2.301   4.8464e-02
   5_occ:   7.960  0.047  0.262 80.672  0.029  2.301   4.8464e-02
   5_bss:   7.960  0.047  0.262 80.672  0.029  2.301   4.8464e-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:  90.26   0.00  20.95  88.07   0.00  19.01  90.26   0.00  31.52
   1_occ:  90.26   0.00  20.95  88.07   0.00  19.01  90.26   0.00  31.52
   2_bss:  90.26   0.00  20.95  88.07   0.00  19.01  90.26   0.00  31.52
   2_xyz:  90.26   0.00  20.95  88.07   0.00  19.01  90.26   0.00  31.52
   2_adp:  88.05   0.00  20.82  88.05   0.00  19.17  83.87   0.00  29.82
   2_occ:  88.05   0.00  20.82  88.05   0.00  19.17  83.87   0.00  29.82
   3_bss:  88.05   0.00  20.82  88.05   0.00  19.17  83.87   0.00  29.82
   3_xyz:  88.05   0.00  20.82  88.05   0.00  19.17  83.87   0.00  29.82
   3_adp: 102.49   0.00  21.47  92.70   0.00  18.64 102.49   0.00  36.87
   3_occ: 102.49   0.00  21.47  92.70   0.00  18.64 102.49   0.00  36.87
   4_bss: 102.49   0.00  21.47  92.70   0.00  18.64 102.49   0.00  36.87
   4_xyz: 102.49   0.00  21.47  92.70   0.00  18.64 102.49   0.00  36.87
   4_adp: 105.01   0.00  19.61  84.14   0.00  15.84 105.01   0.00  40.15
   4_occ: 105.01   0.00  19.61  84.14   0.00  15.84 105.01   0.00  40.15
   5_bss: 105.01   0.00  19.61  84.14   0.00  15.84 105.01   0.00  40.15
   5_xyz: 105.01   0.00  19.61  84.14   0.00  15.84 105.01   0.00  40.15
   5_adp:  99.80   0.00  18.75  87.40   0.00  14.30  99.80   2.34  43.02
   5_occ:  99.80   0.00  18.75  87.40   0.00  14.30  99.80   2.34  43.02
   5_bss:  99.81   0.00  18.76  87.40   0.00  14.30  99.81   2.34  43.02
------------------------------------------------------------------------
 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:    1.714    0.016    0.297
   1_adp:    1.714    0.016    0.297
   1_occ:    1.714    0.016    0.297
   2_bss:    1.714    0.016    0.297
   2_xyz:    1.463    0.048    0.450
   2_adp:    1.463    0.048    0.450
   2_occ:    1.463    0.048    0.450
   3_bss:    1.463    0.048    0.450
   3_xyz:    1.638    0.030    0.664
   3_adp:    1.638    0.030    0.664
   3_occ:    1.638    0.030    0.664
   4_bss:    1.638    0.030    0.664
   4_xyz:    1.913    0.055    0.808
   4_adp:    1.913    0.055    0.808
   4_occ:    1.913    0.055    0.808
   5_bss:    1.913    0.055    0.808
   5_xyz:    2.081    0.079    0.906
   5_adp:    2.081    0.079    0.906
   5_occ:    2.081    0.079    0.906
   5_bss:    2.081    0.079    0.906
------------------------------------------------------------------------

CPU time actual refinement: 357.36


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1220/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_1220/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1220/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1220/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1220/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 357.21 
  Macro-tasks:
    bulk solvent and scale       = 60.88  
    individual site refinement   = 151.64 
    weights calculation          = 30.86  
    collect and process          = 6.13   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 249.62 
  Micro-tasks:
    mask                            = 3.11   
    f_calc                          = 107.66 
    alpha_beta                      = 8.29   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 117.22 
    fmodel                         = 9.33   
    r_factors                      = 0.32   
    phase_errors                   = 8.91   
    foms                           = 0.27   
    TOTAL for micro-tasks          = 256.26 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.076 micro seconds
Total CPU time: 6.18 minutes
from_scatterers_fft:    571 calls, 107.31 s
gradients_fft:          516 calls, 104.64 s

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

# Date 2008-01-16 Time 06:43:22 PST -0800 (1200494602.94 s)
Start R-work = 0.5158, R-free = 0.5196 (no bulk solvent and anisotropic scale)
Final R-work = 0.2317, R-free = 0.2990 (no bulk solvent and anisotropic scale)

Start R-work = 0.5097, R-free = 0.5175
Final R-work = 0.2168, R-free = 0.2851