# Date 2008-01-16 Time 05:21:30 PST -0800 (1200489690.49 s)
#phil __OFF__

Command line arguments: "../700.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 15304
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 700

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 47.6339, 87.2539, 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: 3.33, per 1000 atoms: 1.18


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

F-obs:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA

R-free flags:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.6339, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0342 2.00061
Completeness in resolution range: 0.963314
Completeness with d_max=infinity: 0.960292

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0342
                             d_min =   2.0006

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.6339, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0342 2.00061
Completeness in resolution range: 0.963314
Completeness with d_max=infinity: 0.960292

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0346 -  4.2801 [2143/2170]  1928   215  10.0%
  bin  2:  4.2801 -  3.4103 [2040/2056]  1837   203  10.0%
  bin  3:  3.4103 -  2.9831 [2041/2060]  1838   203   9.9%
  bin  4:  2.9831 -  2.7121 [1994/2024]  1792   202  10.1%
  bin  5:  2.7121 -  2.5186 [1993/2012]  1792   201  10.1%
  bin  6:  2.5186 -  2.3707 [1977/2013]  1785   192   9.7%
  bin  7:  2.3707 -  2.2524 [1984/2017]  1783   201  10.1%
  bin  8:  2.2524 -  2.1547 [1955/1989]  1757   198  10.1%
  bin  9:  2.1547 -  2.0719 [1949/1977]  1756   193   9.9%
  bin 10:  2.0719 -  2.0006 [1513/2017]  1362   151  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_700/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:
        1.81 -     2.42: 16
        2.42 -     3.04: 2155
        3.04 -     3.66: 4625
        3.66 -     4.28: 8873
        4.28 -     4.90: 12299
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.032 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.047 3.040 -x+1,y+1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.277 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27963 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_700/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_700/model_refine_001.geo

CPU time processing inputs: 9.43


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 47.63395 87.2539 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: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3615   r_free= 0.3501   ksol= 0.00   Bsol= 0.00   scale= 0.942    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.135198                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0346 -  4.7735 0.99   1387  153 0.2952 0.3052      6.3778      6.3474|
|  2:  4.7735 -  3.8092 0.99   1328  150 0.2875 0.2838      6.5563      6.5718|
|  3:  3.8092 -  3.3336 0.99   1318  149 0.3168 0.3105       6.463      6.4267|
|  4:  3.3336 -  3.0316 0.99   1297  135 0.3492 0.3364      6.3488      6.2706|
|  5:  3.0316 -  2.8158 0.99   1287  146 0.3751 0.3090      6.2153      6.1329|
|  6:  2.8158 -  2.6507 0.99   1291  145 0.3820 0.3859      6.1343      6.0631|
|  7:  2.6507 -  2.5186 0.99   1279  146 0.3793 0.3702      6.0861      6.0117|
|  8:  2.5186 -  2.4095 0.98   1290  136 0.3990 0.3802      6.0619      6.0603|
|  9:  2.4095 -  2.3171 0.98   1261  144 0.4036 0.3835      6.0032      5.9642|
| 10:  2.3171 -  2.2374 0.98   1255  135 0.4273 0.3621      6.0316      5.9084|
| 11:  2.2374 -  2.1676 1.00   1281  150 0.4087 0.3831      5.9421      5.9547|
| 12:  2.1676 -  2.1058 0.97   1267  133 0.4203 0.4571      5.8881      5.9933|
| 13:  2.1058 -  2.0505 0.98   1255  139 0.4356 0.3932      5.8268      5.7729|
| 14:  2.0505 -  2.0006 0.66    834   98 0.4051 0.4914      5.7686      5.7478|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0346 -  4.7735  1387   153  0.77  27.87   0.86     0.79      48469.25|
|  2:  4.7735 -  3.8092  1328   150  0.82  24.61   0.95     0.88      56546.80|
|  3:  3.8092 -  3.3336  1318   149  0.78  28.54   0.96     0.90      54779.98|
|  4:  3.3336 -  3.0316  1297   135  0.74  31.72   0.95     0.88      46891.51|
|  5:  3.0316 -  2.8158  1287   146  0.68  36.84   0.97     0.84      38671.79|
|  6:  2.8158 -  2.6507  1291   145  0.66  38.85   0.95     0.82      35738.37|
|  7:  2.6507 -  2.5186  1279   146  0.65  39.77   0.98     0.81      32904.51|
|  8:  2.5186 -  2.4095  1290   136  0.65  40.11   0.97     0.83      31214.72|
|  9:  2.4095 -  2.3171  1261   144  0.65  40.01   0.97     0.85      27668.39|
| 10:  2.3171 -  2.2374  1255   135  0.65  40.37   0.99     0.86      25926.27|
| 11:  2.2374 -  2.1676  1281   150  0.63  41.67   0.99     0.86      25380.40|
| 12:  2.1676 -  2.1058  1267   133  0.58  45.88   0.98     0.82      27276.18|
| 13:  2.1058 -  2.0505  1255   139  0.52  50.89   0.96     0.72      26957.12|
| 14:  2.0505 -  2.0006   834    98  0.44  56.58   1.02     0.58      24591.61|
|alpha:            min =        0.58 max =            0.90 mean =         0.82|
|beta:             min =    24591.61 max =        56546.80 mean =     36440.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.67|
|phase err.(work): min =        0.00 max =           90.00 mean =        38.23|
|phase err.(test): min =        0.00 max =           89.22 mean =        38.43|
|-----------------------------------------------------------------------------|

============================== 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 = 7.022851              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.318   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.826842              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.831   (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 |  1.806 -  2.115:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       13 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      178 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1977 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1835 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2790 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4573 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4300 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5596 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6703 |
|-----------------------------------------------------------------------------|
|-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 |        0.162 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.115    4.900  1.806 |       0.152 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.171)------------------------------------------|
|    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: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3615   r_free= 0.3501   ksol= 0.00   Bsol= 0.00   scale= 0.942    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.135198                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3481   r_free= 0.3372   ksol= 0.31   Bsol= 52.73   scale= 0.967   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.42,3.26,0.36,0.00,0.00,0.00); trace/3= 0.07                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.114731                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.465610              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.168   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.463459              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.670   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3481      final r-factor (work) = 0.2037          |
| start r-factor (free) = 0.3372      final r-factor (free) = 0.2234          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.9420 = 6.47 * 0.50 * 6.1185 + 1.00 * 0.1621                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.9627 = 6.47 * 0.50 * 5.8378 + 1.00 * 0.0902                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2037      final r-factor (work) = 0.1891          |
| start r-factor (free) = 0.2234      final r-factor (free) = 0.2255          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7121 = 0.46 * 1.00 * 5.8378 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6358 = 0.46 * 1.00 * 5.5765 + 1.00 * 0.0513                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 5      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.171)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.90   16.20    None  None   None       |
|    all(noH): 2823   0      0.00    77.90   16.20    None  None   None       |
|    Sol.    : 438    0      6.52    63.96   37.39    None  None   None       |
|    Mac.    : 2385   0      0.00    77.90   12.31    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 -   7.790:  538   |   5:    38.951 -  46.741:  118        |
|      1:     7.790 -  15.581: 1346   |   6:    46.741 -  54.532:   81        |
|      2:    15.581 -  23.371:  431   |   7:    54.532 -  62.322:   37        |
|      3:    23.371 -  31.161:  147   |   8:    62.322 -  70.112:    2        |
|      4:    31.161 -  38.951:  122   |   9:    70.112 -  77.902:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1891 r_free = 0.2255             target_work(ml) = 5.581         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1887 r_free = 0.2254             target_work(ml) = 5.580         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1887   r_free= 0.2254   ksol= 0.31   Bsol= 52.73   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.42,3.26,0.36,0.00,0.00,0.00); trace/3= 0.07                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.579533                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1857   r_free= 0.2211   ksol= 0.33   Bsol= 67.83   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.99,-0.28,-0.58,-0.00,-0.00,-0.00); trace/3= -1.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.568817                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.384228              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.101   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.438917              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.173   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1857      final r-factor (work) = 0.1366          |
| start r-factor (free) = 0.2211      final r-factor (free) = 0.1687          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5369 = 3.38 * 0.50 * 5.5828 + 1.00 * 0.0902                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2597 = 3.38 * 0.50 * 5.4337 + 1.00 * 0.0654                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1366      final r-factor (work) = 0.1264          |
| start r-factor (free) = 0.1687      final r-factor (free) = 0.1647          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3989 = 0.44 * 1.00 * 5.4337 + 1.00 * 0.0139                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3090 = 0.44 * 1.00 * 5.2388 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.171)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.38   16.84    None  None   None       |
|    all(noH): 2823   0      0.00    83.38   16.84    None  None   None       |
|    Sol.    : 438    0      4.84    74.55   40.19    None  None   None       |
|    Mac.    : 2385   0      0.00    83.38   12.55    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 -   8.338:  727   |   5:    41.689 -  50.027:  101        |
|      1:     8.338 -  16.676: 1303   |   6:    50.027 -  58.365:   88        |
|      2:    16.676 -  25.014:  293   |   7:    58.365 -  66.703:   46        |
|      3:    25.014 -  33.351:  126   |   8:    66.703 -  75.040:   22        |
|      4:    33.351 -  41.689:  114   |   9:    75.040 -  83.378:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1264 r_free = 0.1647             target_work(ml) = 5.227         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1263 r_free = 0.1648             target_work(ml) = 5.227         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1263   r_free= 0.1648   ksol= 0.33   Bsol= 67.83   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.99,-0.28,-0.58,-0.00,-0.00,-0.00); trace/3= -1.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.226927                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1262   r_free= 0.1649   ksol= 0.33   Bsol= 67.18   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-1.02,-0.54,-0.00,-0.00,-0.00); trace/3= -1.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.225806                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.009603              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 122.515  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.295319              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.536  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1262      final r-factor (work) = 0.1169          |
| start r-factor (free) = 0.1649      final r-factor (free) = 0.1598          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3281 = 2.01 * 0.50 * 5.2376 + 1.00 * 0.0654                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2803 = 2.01 * 0.50 * 5.1930 + 1.00 * 0.0624                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1169      final r-factor (work) = 0.1159          |
| start r-factor (free) = 0.1598      final r-factor (free) = 0.1585          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5432 = 0.30 * 1.00 * 5.1930 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5364 = 0.30 * 1.00 * 5.1719 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.171)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.51    85.37   16.48    None  None   None       |
|    all(noH): 2823   0      0.51    85.37   16.48    None  None   None       |
|    Sol.    : 438    0      1.13    76.39   39.18    None  None   None       |
|    Mac.    : 2385   0      0.51    85.37   12.31    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:     0.513 -   8.998:  927   |   5:    42.939 -  51.424:   97        |
|      1:     8.998 -  17.483: 1162   |   6:    51.424 -  59.910:   74        |
|      2:    17.483 -  25.969:  263   |   7:    59.910 -  68.395:   39        |
|      3:    25.969 -  34.454:  126   |   8:    68.395 -  76.880:   11        |
|      4:    34.454 -  42.939:  121   |   9:    76.880 -  85.365:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1159 r_free = 0.1585             target_work(ml) = 5.168         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1158 r_free = 0.1584             target_work(ml) = 5.168         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1584   ksol= 0.33   Bsol= 67.18   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-1.02,-0.54,-0.00,-0.00,-0.00); trace/3= -1.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.168291                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1156   r_free= 0.1583   ksol= 0.32   Bsol= 60.69   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-1.17,-0.40,-0.00,-0.00,-0.00); trace/3= -1.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.167886                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.796216              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 123.185  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.541095              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.143  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1156      final r-factor (work) = 0.1144          |
| start r-factor (free) = 0.1583      final r-factor (free) = 0.1583          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7073 = 1.80 * 0.50 * 5.1718 + 1.00 * 0.0624                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6958 = 1.80 * 0.50 * 5.1628 + 1.00 * 0.0590                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1144      final r-factor (work) = 0.1140          |
| start r-factor (free) = 0.1583      final r-factor (free) = 0.1589          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8025 = 0.54 * 1.00 * 5.1628 + 1.00 * 0.0089                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8001 = 0.54 * 1.00 * 5.1573 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.171)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.77   16.32    None  None   None       |
|    all(noH): 2823   0      0.00    86.77   16.32    None  None   None       |
|    Sol.    : 438    0      2.05    77.68   39.10    None  None   None       |
|    Mac.    : 2385   0      0.00    86.77   12.13    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 -   8.677:  896   |   5:    43.386 -  52.063:   96        |
|      1:     8.677 -  17.354: 1195   |   6:    52.063 -  60.740:   77        |
|      2:    17.354 -  26.032:  264   |   7:    60.740 -  69.418:   33        |
|      3:    26.032 -  34.709:  129   |   8:    69.418 -  78.095:   11        |
|      4:    34.709 -  43.386:  119   |   9:    78.095 -  86.772:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1140 r_free = 0.1589             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1140 r_free = 0.1590             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1140   r_free= 0.1590   ksol= 0.32   Bsol= 60.69   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-1.17,-0.40,-0.00,-0.00,-0.00); trace/3= -1.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.161491                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1589   ksol= 0.32   Bsol= 61.23   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.93,-1.07,-0.21,-0.00,-0.00,-0.00); trace/3= -1.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.161476                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.825815              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 146.538  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.462783              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.681  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1139      final r-factor (work) = 0.1103          |
| start r-factor (free) = 0.1589      final r-factor (free) = 0.1588          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3467 = 2.83 * 0.50 * 5.1579 + 1.00 * 0.0590                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3447 = 2.83 * 0.50 * 5.1476 + 1.00 * 0.0716                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1103      final r-factor (work) = 0.1102          |
| start r-factor (free) = 0.1588      final r-factor (free) = 0.1585          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3917 = 0.46 * 1.00 * 5.1476 + 1.00 * 0.0095                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3894 = 0.46 * 1.00 * 5.1426 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.171)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.16   16.09    None  None   None       |
|    all(noH): 2823   0      0.00    87.16   16.09    None  None   None       |
|    Sol.    : 438    0      3.95    78.17   38.89    None  None   None       |
|    Mac.    : 2385   0      0.00    87.16   11.90    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 -   8.716:  971   |   5:    43.579 -  52.295:   95        |
|      1:     8.716 -  17.432: 1144   |   6:    52.295 -  61.011:   73        |
|      2:    17.432 -  26.148:  248   |   7:    61.011 -  69.727:   34        |
|      3:    26.148 -  34.864:  124   |   8:    69.727 -  78.443:   10        |
|      4:    34.864 -  43.579:  121   |   9:    78.443 -  87.159:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1102 r_free = 0.1585             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1102 r_free = 0.1586             target_work(ml) = 5.143         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1102   r_free= 0.1586   ksol= 0.32   Bsol= 61.23   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.93,-1.07,-0.21,-0.00,-0.00,-0.00); trace/3= -1.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.142555                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0346 -  4.7735 0.99   1387  153 0.0988 0.1327      5.3982      5.5348|
|  2:  4.7735 -  3.8092 0.99   1328  150 0.0836 0.1105      5.4284      5.6368|
|  3:  3.8092 -  3.3336 0.99   1318  149 0.1029 0.1487      5.4603       5.841|
|  4:  3.3336 -  3.0316 0.99   1297  135 0.1181 0.1528      5.4345      5.5945|
|  5:  3.0316 -  2.8158 0.99   1287  146 0.1333 0.1677      5.3384      5.5184|
|  6:  2.8158 -  2.6507 0.99   1291  145 0.1219 0.2023      5.2217      5.4999|
|  7:  2.6507 -  2.5186 0.99   1279  146 0.1220 0.1690       5.158      5.3615|
|  8:  2.5186 -  2.4095 0.98   1290  136 0.1143 0.1648       5.077      5.3366|
|  9:  2.4095 -  2.3171 0.98   1261  144 0.1145 0.1843      5.0179      5.3031|
| 10:  2.3171 -  2.2374 0.98   1255  135 0.1130 0.1735      4.9865      5.2075|
| 11:  2.2374 -  2.1676 1.00   1281  150 0.1138 0.1797      4.9357      5.2702|
| 12:  2.1676 -  2.1058 0.97   1267  133 0.1096 0.1632      4.8694      5.1663|
| 13:  2.1058 -  2.0505 0.98   1255  139 0.1093 0.1751      4.7764      5.0526|
| 14:  2.0505 -  2.0006 0.66    834   98 0.1021 0.1833       4.666      4.9952|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0346 -  4.7735  1387   153  0.94   9.64   0.97     0.94       7759.26|
|  2:  4.7735 -  3.8092  1328   150  0.95   7.97   1.00     0.98       9005.61|
|  3:  3.8092 -  3.3336  1318   149  0.94  11.05   1.01     1.01      10221.57|
|  4:  3.3336 -  3.0316  1297   135  0.92  13.24   0.99     0.98       9989.47|
|  5:  3.0316 -  2.8158  1287   146  0.90  16.05   0.99     0.96       8561.59|
|  6:  2.8158 -  2.6507  1291   145  0.90  16.47   0.97     0.94       7238.87|
|  7:  2.6507 -  2.5186  1279   146  0.91  15.26   0.98     0.95       6153.15|
|  8:  2.5186 -  2.4095  1290   136  0.91  15.23   0.98     0.95       5488.37|
|  9:  2.4095 -  2.3171  1261   144  0.91  15.57   0.98     0.94       4981.79|
| 10:  2.3171 -  2.2374  1255   135  0.90  16.13   0.98     0.94       4719.04|
| 11:  2.2374 -  2.1676  1281   150  0.90  15.99   0.97     0.94       4333.39|
| 12:  2.1676 -  2.1058  1267   133  0.91  15.25   0.99     0.98       3925.34|
| 13:  2.1058 -  2.0505  1255   139  0.91  15.64   0.98     0.96       3285.44|
| 14:  2.0505 -  2.0006   834    98  0.92  14.47   0.94     0.90       2524.06|
|alpha:            min =        0.90 max =            1.01 mean =         0.96|
|beta:             min =     2524.06 max =        10221.57 mean =      6433.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.08|
|phase err.(test): min =        0.00 max =           89.71 mean =        13.59|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1101   r_free= 0.1584   ksol= 0.32   Bsol= 61.24   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.64,-0.86,0.04,-0.00,0.00,0.00); trace/3= -0.82                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.142660                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1101   r_free= 0.1584   ksol= 0.32   Bsol= 61.24   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.64,-0.86,0.04,-0.00,0.00,0.00); trace/3= -0.82                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.142660                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0346 -  4.7735 0.99   1387  153 0.0988 0.1329      5.3991      5.5361|
|  2:  4.7735 -  3.8092 0.99   1328  150 0.0837 0.1105       5.429      5.6367|
|  3:  3.8092 -  3.3336 0.99   1318  149 0.1030 0.1488      5.4604      5.8416|
|  4:  3.3336 -  3.0316 0.99   1297  135 0.1180 0.1528      5.4345      5.5947|
|  5:  3.0316 -  2.8158 0.99   1287  146 0.1333 0.1677      5.3383      5.5181|
|  6:  2.8158 -  2.6507 0.99   1291  145 0.1218 0.2022      5.2215      5.4995|
|  7:  2.6507 -  2.5186 0.99   1279  146 0.1221 0.1691       5.158      5.3618|
|  8:  2.5186 -  2.4095 0.98   1290  136 0.1144 0.1647      5.0772      5.3365|
|  9:  2.4095 -  2.3171 0.98   1261  144 0.1145 0.1843      5.0181      5.3031|
| 10:  2.3171 -  2.2374 0.98   1255  135 0.1130 0.1736      4.9865      5.2078|
| 11:  2.2374 -  2.1676 1.00   1281  150 0.1138 0.1796      4.9356      5.2701|
| 12:  2.1676 -  2.1058 0.97   1267  133 0.1096 0.1630      4.8693      5.1661|
| 13:  2.1058 -  2.0505 0.98   1255  139 0.1093 0.1751      4.7762      5.0525|
| 14:  2.0505 -  2.0006 0.66    834   98 0.1021 0.1832      4.6661      4.9948|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0346 -  4.7735  1387   153  0.94   9.65   0.97     0.94       7776.42|
|  2:  4.7735 -  3.8092  1328   150  0.95   7.98   1.00     0.99       9015.78|
|  3:  3.8092 -  3.3336  1318   149  0.94  11.06   1.02     1.02      10226.74|
|  4:  3.3336 -  3.0316  1297   135  0.92  13.25   1.00     0.98       9990.21|
|  5:  3.0316 -  2.8158  1287   146  0.90  16.05   1.00     0.97       8558.01|
|  6:  2.8158 -  2.6507  1291   145  0.90  16.47   0.98     0.95       7234.98|
|  7:  2.6507 -  2.5186  1279   146  0.91  15.26   0.99     0.96       6151.88|
|  8:  2.5186 -  2.4095  1290   136  0.91  15.23   0.99     0.96       5488.81|
|  9:  2.4095 -  2.3171  1261   144  0.91  15.57   0.99     0.95       4983.35|
| 10:  2.3171 -  2.2374  1255   135  0.90  16.13   0.99     0.95       4718.71|
| 11:  2.2374 -  2.1676  1281   150  0.90  15.98   0.99     0.95       4332.33|
| 12:  2.1676 -  2.1058  1267   133  0.91  15.25   1.00     0.99       3924.45|
| 13:  2.1058 -  2.0505  1255   139  0.91  15.64   0.99     0.98       3283.87|
| 14:  2.0505 -  2.0006   834    98  0.92  14.47   0.96     0.91       2522.60|
|alpha:            min =        0.91 max =            1.02 mean =         0.97|
|beta:             min =     2522.60 max =        10226.74 mean =      6435.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.08|
|phase err.(test): min =        0.00 max =           89.71 mean =        13.59|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.171)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.16   16.09    None  None   None       |
|    all(noH): 2823   0      0.00    87.16   16.09    None  None   None       |
|    Sol.    : 438    0      3.95    78.17   38.89    None  None   None       |
|    Mac.    : 2385   0      0.00    87.16   11.90    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 -   8.719:  971   |   5:    43.582 -  52.298:   95        |
|      1:     8.719 -  17.435: 1144   |   6:    52.298 -  61.014:   73        |
|      2:    17.435 -  26.151:  248   |   7:    61.014 -  69.730:   34        |
|      3:    26.151 -  34.866:  124   |   8:    69.730 -  78.446:   10        |
|      4:    34.866 -  43.582:  121   |   9:    78.446 -  87.162:    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)= 305         
Filter by distance & map next to the model:
   mapped sites are within: 0.488 - 4.929
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 300 from: 305
   mapped sites are within: 0.719 - 4.929

peak=    5.856 closest distance to " NH2 ARG A  56 " =    2.341
peak=    5.344 closest distance to " CB  GLN A 223 " =    1.404
peak=    5.171 closest distance to " CG  PRO A  54 " =    1.322
peak=    4.985 closest distance to " CB  SER A  63 " =    1.184
peak=    4.983 closest distance to " CB  GLN A 183 " =    1.282
peak=    4.904 closest distance to " CB  ARG A 190 " =    1.698
peak=    4.802 closest distance to " O   HOH Z 232 " =    2.361
peak=    4.746 closest distance to " CB  ARG A 275 " =    0.936
peak=    4.699 closest distance to " CG  PRO A 213 " =    1.180
peak=    4.668 closest distance to " C   PRO A 198 " =    1.491
peak=    4.657 closest distance to " CB  GLU A 152 " =    1.122
peak=    4.582 closest distance to " O   HOH Z 126 " =    1.869
peak=    4.559 closest distance to " O   HOH Z 298 " =    1.887
peak=    4.467 closest distance to " CB  ARG A  79 " =    1.253
peak=    4.406 closest distance to " O   HOH Z 403 " =    1.674
peak=    4.399 closest distance to " O   HOH Z 369 " =    2.221
peak=    4.383 closest distance to " CA  TYR A  30 " =    0.943
peak=    4.274 closest distance to " O   HOH Z 234 " =    3.799
peak=    4.245 closest distance to " CB  TYR A 169 " =    0.788
peak=    4.223 closest distance to " CZ  PHE A 218 " =    1.134
peak=    4.204 closest distance to " CA  ALA A  51 " =    0.937
peak=    4.175 closest distance to " CG  PRO A 198 " =    1.146
peak=    4.148 closest distance to " O   SER A  87 " =    2.209
peak=    4.144 closest distance to " CB  ASN A 148 " =    1.397
peak=    4.120 closest distance to " CB  PRO A  54 " =    0.890
peak=    4.116 closest distance to " NE2 GLN A  11 " =    1.047
peak=    4.113 closest distance to " O   HOH Z  15 " =    2.149
peak=    4.087 closest distance to " CB  GLU A 277 " =    3.704
peak=    4.085 closest distance to " CG  PRO A  90 " =    1.207
peak=    4.079 closest distance to " O   HOH Z  40 " =    1.867
peak=    4.069 closest distance to " O   HOH Z 280 " =    2.993
peak=    4.067 closest distance to " O   HOH Z 236 " =    2.068
peak=    4.054 closest distance to " O   HOH Z 158 " =    3.089
peak=    4.024 closest distance to " O   HOH Z 368 " =    2.119
peak=    4.015 closest distance to " CD  ARG A 269 " =    0.963
peak=    4.000 closest distance to " CD  LYS A 166 " =    1.333
peak=    3.998 closest distance to " O   HOH Z 142 " =    1.543
peak=    3.997 closest distance to " O   HOH Z  78 " =    1.624
peak=    3.983 closest distance to " O   HOH Z 189 " =    2.641
peak=    3.972 closest distance to " O   HOH Z 423 " =    1.999
peak=    3.952 closest distance to " CA  ARG A 195 " =    1.339
peak=    3.946 closest distance to " O   HOH Z 214 " =    2.264
peak=    3.944 closest distance to " O   HOH Z 346 " =    1.599
peak=    3.937 closest distance to " O   HOH Z  43 " =    1.934
peak=    3.936 closest distance to " CB  TRP A 266 " =    0.972
peak=    3.930 closest distance to " CG1 ILE A  33 " =    1.192
peak=    3.922 closest distance to " CD2 TRP A 179 " =    1.333
peak=    3.920 closest distance to " CB  GLU A 128 " =    1.060
peak=    3.920 closest distance to " O   HOH Z 427 " =    3.028
peak=    3.919 closest distance to " CB  VAL A 202 " =    1.527
peak=    3.914 closest distance to " OD1 ASN A  69 " =    2.496
peak=    3.909 closest distance to " NH2 ARG A 156 " =    1.204
peak=    3.905 closest distance to " O   HOH Z 402 " =    1.469
peak=    3.887 closest distance to " O   HOH Z 303 " =    2.217
peak=    3.883 closest distance to " O   HOH Z 209 " =    2.256
peak=    3.882 closest distance to " NZ  LYS A 117 " =    3.259
peak=    3.867 closest distance to " O   HOH Z 203 " =    1.755
peak=    3.863 closest distance to " CB  LEU A 228 " =    1.097
peak=    3.849 closest distance to " O   HOH Z 128 " =    2.046
peak=    3.838 closest distance to " O   HOH Z 193 " =    1.857
peak=    3.838 closest distance to " O   HOH Z  97 " =    1.994
peak=    3.832 closest distance to " CA  ARG A  36 " =    1.131
peak=    3.829 closest distance to " CD2 LEU A 297 " =    0.857
peak=    3.828 closest distance to " O   HOH Z 250 " =    1.438
peak=    3.818 closest distance to " CG2 ILE A 120 " =    1.075
peak=    3.816 closest distance to " CB  ASN A  39 " =    0.856
peak=    3.816 closest distance to " O   HOH Z 265 " =    2.162
peak=    3.807 closest distance to " CB  ASP A 140 " =    0.978
peak=    3.806 closest distance to " O   HOH Z 147 " =    1.864
peak=    3.799 closest distance to " O   HOH Z 412 " =    3.773
peak=    3.757 closest distance to " CE  LYS A  76 " =    0.857
peak=    3.744 closest distance to " O   HOH Z 197 " =    2.788
peak=    3.741 closest distance to " O   HOH Z 126 " =    1.957
peak=    3.741 closest distance to " C   ILE A 106 " =    1.931
peak=    3.741 closest distance to " O   HOH Z 316 " =    3.157
peak=    3.737 closest distance to " ND2 ASN A 187 " =    1.512
peak=    3.737 closest distance to " O   HOH Z  21 " =    1.857
peak=    3.732 closest distance to " CG  PRO A 243 " =    1.048
peak=    3.728 closest distance to " O   HOH Z 291 " =    1.515
peak=    3.721 closest distance to " NH1AARG A 145 " =    1.306
peak=    3.715 closest distance to " CD1 LEU A 300 " =    1.173
peak=    3.712 closest distance to " O   HOH Z 406 " =    1.574
peak=    3.698 closest distance to " CG  MET A 185 " =    1.148
peak=    3.697 closest distance to " O   HOH Z 126 " =    1.595
peak=    3.687 closest distance to " CB  VAL A 265 " =    1.242
peak=    3.680 closest distance to " CA  ALA A  21 " =    1.223
peak=    3.677 closest distance to " CG2AVAL A  72 " =    1.773
peak=    3.665 closest distance to " CB  TRP A 179 " =    1.348
peak=    3.664 closest distance to " O   HOH Z 279 " =    2.205
peak=    3.663 closest distance to " O   HOH Z 371 " =    3.169
peak=    3.662 closest distance to " O   HOH Z 180 " =    2.158
peak=    3.656 closest distance to " CA  ASN A 176 " =    1.252
peak=    3.653 closest distance to " O   ASN A  74 " =    1.558
peak=    3.643 closest distance to " CG  ARG A  66 " =    2.553
peak=    3.642 closest distance to " CB  GLU A  46 " =    0.965
peak=    3.638 closest distance to " OD2 ASP A 298 " =    3.960
peak=    3.630 closest distance to " CD1 LEU A  96 " =    0.719
peak=    3.620 closest distance to " O   HOH Z 362 " =    3.625
peak=    3.615 closest distance to " NH2BARG A 145 " =    2.179
peak=    3.612 closest distance to " O   HOH Z 426 " =    1.590
peak=    3.605 closest distance to " OG BSER A 164 " =    2.351
peak=    3.596 closest distance to " O   HOH Z 353 " =    2.754
peak=    3.596 closest distance to " O   HOH Z 383 " =    2.173
peak=    3.595 closest distance to " O   HOH Z 133 " =    2.587
peak=    3.594 closest distance to " O   HOH Z  61 " =    1.572
peak=    3.594 closest distance to " ND1 HIS A  81 " =    1.675
peak=    3.593 closest distance to " O   HOH Z  68 " =    1.872
peak=    3.573 closest distance to " O   HOH Z 271 " =    2.719
peak=    3.570 closest distance to " CA  THR A 221 " =    0.930
peak=    3.569 closest distance to " O   HOH Z 365 " =    2.868
peak=    3.566 closest distance to " O  BHOH Z 338 " =    2.252
peak=    3.560 closest distance to " O   HOH Z 185 " =    1.801
peak=    3.556 closest distance to " CD  ARG A 159 " =    0.812
peak=    3.552 closest distance to " O   HOH Z 285 " =    2.768
peak=    3.545 closest distance to " O   HOH Z  44 " =    1.807
peak=    3.544 closest distance to " O   HOH Z 421 " =    1.661
peak=    3.537 closest distance to " O   HOH Z  19 " =    1.803
peak=    3.535 closest distance to " O   HOH Z 389 " =    1.908
peak=    3.529 closest distance to " O   HOH Z 305 " =    3.705
peak=    3.528 closest distance to " O   HOH Z 299 " =    4.432
peak=    3.522 closest distance to " CA  ASN A 215 " =    1.078
peak=    3.521 closest distance to " O   ALA A 165 " =    1.484
peak=    3.520 closest distance to " O   HOH Z 294 " =    1.505
peak=    3.520 closest distance to " O   HOH Z  97 " =    2.354
peak=    3.513 closest distance to " O   HOH Z  80 " =    1.722
peak=    3.513 closest distance to " OG1 THR A 294 " =    2.419
peak=    3.513 closest distance to " CB  ALA A 291 " =    1.260
peak=    3.504 closest distance to " CG1 VAL A 153 " =    0.991
peak=    3.493 closest distance to " O   HOH Z 183 " =    1.547
peak=    3.482 closest distance to " OG  SER A  22 " =    2.706
peak=    3.481 closest distance to " O   HOH Z  59 " =    2.479
peak=    3.461 closest distance to " N   ASN A  39 " =    1.353
peak=    3.460 closest distance to " CG2 THR A 221 " =    1.112
peak=    3.459 closest distance to " CA  ALA A 160 " =    0.930
peak=    3.455 closest distance to " NE2 GLN A  77 " =    3.341
peak=    3.453 closest distance to " CA  MET A 105 " =    1.025
peak=    3.450 closest distance to " O   HOH Z 261 " =    1.756
peak=    3.449 closest distance to " CA  ALA A  84 " =    1.259
peak=    3.447 closest distance to " CB  ASN A 142 " =    1.118
peak=    3.446 closest distance to " O   HOH Z   1 " =    2.332
peak=    3.443 closest distance to " CB  GLN A 103 " =    0.820
peak=    3.442 closest distance to " CB  SER A   3 " =    1.292
peak=    3.439 closest distance to " CB  ILE A 120 " =    1.271
peak=    3.438 closest distance to " CA  ALA A 295 " =    1.060
peak=    3.434 closest distance to " CG2 ILE A  20 " =    1.323
peak=    3.431 closest distance to " CA  THR A 264 " =    0.874
peak=    3.427 closest distance to " CG2 VAL A 257 " =    0.830
peak=    3.426 closest distance to " O   HOH Z  66 " =    2.234
peak=    3.426 closest distance to " O   HOH Z 272 " =    1.847
peak=    3.425 closest distance to " O   HOH Z  54 " =    1.696
peak=    3.423 closest distance to " O   HOH Z 148 " =    3.309
peak=    3.416 closest distance to " O   HOH Z  78 " =    1.900
peak=    3.415 closest distance to " O   HOH Z 313 " =    1.951
peak=    3.412 closest distance to " O   HOH Z 359 " =    1.496
peak=    3.409 closest distance to " O   HOH Z 171 " =    1.840
peak=    3.404 closest distance to " O   HOH Z  62 " =    2.267
peak=    3.396 closest distance to " O   HOH Z 425 " =    1.986
peak=    3.395 closest distance to " CG  GLN A  58 " =    2.819
peak=    3.393 closest distance to " O   THR A 251 " =    1.139
peak=    3.392 closest distance to " CB  SER A  62 " =    0.832
peak=    3.388 closest distance to " CA  ASP A 191 " =    0.913
peak=    3.388 closest distance to " CB  ASN A 215 " =    1.159
peak=    3.387 closest distance to " N   CYS A 260 " =    0.824
peak=    3.386 closest distance to " CG  GLU A  37 " =    0.908
peak=    3.386 closest distance to " O   HOH Z 245 " =    1.331
peak=    3.385 closest distance to " OG BSER A 134 " =    2.900
peak=    3.381 closest distance to " CG  ARG A 219 " =    1.152
peak=    3.380 closest distance to " O   HOH Z 128 " =    2.321
peak=    3.379 closest distance to " CB  SER A 212 " =    1.112
peak=    3.378 closest distance to " O   HOH Z 380 " =    1.931
peak=    3.377 closest distance to " O   HOH Z 417 " =    3.220
peak=    3.369 closest distance to " O   HOH Z 403 " =    1.414
peak=    3.369 closest distance to " O   HOH Z 261 " =    1.915
peak=    3.366 closest distance to " O   ASP A 124 " =    1.290
peak=    3.364 closest distance to " CB  TYR A 116 " =    0.792
peak=    3.359 closest distance to " CZ  PHE A  38 " =    1.257
peak=    3.358 closest distance to " CB  SER A 141 " =    1.026
peak=    3.351 closest distance to " O   HOH Z 345 " =    1.672
peak=    3.351 closest distance to " O   HOH Z 422 " =    2.647
peak=    3.348 closest distance to " CB  THR A  31 " =    1.686
peak=    3.347 closest distance to " CG2 VAL A 197 " =    1.119
peak=    3.347 closest distance to " ND2 ASN A 110 " =    1.589
peak=    3.346 closest distance to " CB  GLN A  88 " =    1.180
peak=    3.343 closest distance to " CB  ALA A 248 " =    1.280
peak=    3.341 closest distance to " O   HOH Z 285 " =    1.575
peak=    3.340 closest distance to " O   ASN A  74 " =    2.089
peak=    3.339 closest distance to " OE1 GLU A   2 " =    2.096
peak=    3.337 closest distance to " O   HOH Z 173 " =    2.135
peak=    3.333 closest distance to " CB  ARG A 139 " =    0.978
peak=    3.329 closest distance to " N   ASN A 127 " =    1.288
peak=    3.329 closest distance to " CB  ALA A   1 " =    4.929
peak=    3.327 closest distance to " CA  TYR A 116 " =    1.411
peak=    3.327 closest distance to " O   HOH Z 250 " =    1.500
peak=    3.326 closest distance to " CA  VAL A 125 " =    1.216
peak=    3.325 closest distance to " O   HOH Z 391 " =    2.945
peak=    3.321 closest distance to " O   HOH Z 193 " =    2.179
peak=    3.320 closest distance to " O   HOH Z 374 " =    2.724
peak=    3.320 closest distance to " CA  GLU A 152 " =    0.892
peak=    3.319 closest distance to " CA  GLY A 241 " =    0.844
peak=    3.318 closest distance to " O   HOH Z 357 " =    2.095
peak=    3.316 closest distance to " CA  ALA A 248 " =    1.176
peak=    3.315 closest distance to " CA  SER A  87 " =    1.080
peak=    3.314 closest distance to " N   GLY A  98 " =    1.163
peak=    3.313 closest distance to " CA  LYS A 117 " =    1.264
peak=    3.306 closest distance to " OD2 ASP A 286 " =    2.925
peak=    3.304 closest distance to " CZ3 TRP A 266 " =    1.086
peak=    3.304 closest distance to " CB  TYR A 169 " =    0.877
peak=    3.303 closest distance to " CG BARG A 275 " =    1.385
peak=    3.300 closest distance to " CG AARG A 275 " =    1.094
peak=    3.299 closest distance to " CB  PHE A 204 " =    0.906
peak=    3.297 closest distance to " CZ2 TRP A 179 " =    1.746
peak=    3.296 closest distance to " CD1 ILE A 106 " =    0.875
peak=    3.294 closest distance to " O   THR A 220 " =    1.202
peak=    3.292 closest distance to " N   ARG A 156 " =    1.400
peak=    3.291 closest distance to " O   HOH Z 163 " =    1.569
peak=    3.284 closest distance to " CB  GLN A  89 " =    1.238
peak=    3.284 closest distance to " NH2AARG A 275 " =    3.585
peak=    3.277 closest distance to " O   HOH Z 325 " =    2.317
peak=    3.276 closest distance to " ND2 ASN A 249 " =    0.884
peak=    3.276 closest distance to " CA  ALA A 154 " =    0.957
peak=    3.272 closest distance to " O   TRP A 274 " =    1.880
peak=    3.270 closest distance to " CB  ASP A 298 " =    1.183
peak=    3.270 closest distance to " CA  ASP A 162 " =    1.054
peak=    3.269 closest distance to " CE1 TYR A 186 " =    1.285
peak=    3.264 closest distance to " O   HOH Z  20 " =    1.447
peak=    3.263 closest distance to " O   HOH Z 132 " =    2.693
peak=    3.257 closest distance to " CB  MET A  47 " =    0.963
peak=    3.255 closest distance to " CB  MET A  40 " =    0.903
peak=    3.253 closest distance to " CD BLYS A 290 " =    1.009
peak=    3.252 closest distance to " O   HOH Z 234 " =    1.837
peak=    3.252 closest distance to " NZ  LYS A  48 " =    1.308
peak=    3.251 closest distance to " O   HOH Z 411 " =    1.729
peak=    3.248 closest distance to " O   HOH Z 327 " =    1.574
peak=    3.248 closest distance to " O   HOH Z  88 " =    3.239
peak=    3.246 closest distance to " O   HOH Z 258 " =    2.102
peak=    3.245 closest distance to " O   ALA A 158 " =    1.149
peak=    3.243 closest distance to " O   HOH Z 427 " =    3.143
peak=    3.242 closest distance to " O   HOH Z 248 " =    1.717
peak=    3.235 closest distance to " CB  ALA A 227 " =    1.082
peak=    3.234 closest distance to " CA  ILE A 106 " =    0.812
peak=    3.231 closest distance to " CB  ALA A  34 " =    0.973
peak=    3.228 closest distance to " O   HOH Z 193 " =    1.651
peak=    3.226 closest distance to " O   HOH Z 298 " =    2.491
peak=    3.226 closest distance to " CG1 ILE A 151 " =    1.057
peak=    3.224 closest distance to " O   HOH Z  48 " =    1.707
peak=    3.222 closest distance to " O   HOH Z 361 " =    2.539
peak=    3.220 closest distance to " CA  ASN A 217 " =    1.230
peak=    3.220 closest distance to " CB  ALA A 242 " =    0.935
peak=    3.215 closest distance to " CG  GLN A  11 " =    1.531
peak=    3.204 closest distance to " CG  MET A 185 " =    1.032
peak=    3.201 closest distance to " O   HOH Z 130 " =    2.245
peak=    3.200 closest distance to " CB  GLN A 205 " =    1.091
peak=    3.197 closest distance to " CB  ALA A   9 " =    1.561
peak=    3.196 closest distance to " CA  ALA A 233 " =    1.547
peak=    3.192 closest distance to " O   HOH Z 134 " =    1.285
peak=    3.192 closest distance to " O   HOH Z 416 " =    2.858
peak=    3.185 closest distance to " O   ASP A 191 " =    1.553
peak=    3.184 closest distance to " CB  PRO A  90 " =    1.154
peak=    3.183 closest distance to " O   HOH Z 251 " =    1.535
peak=    3.180 closest distance to " CA  PRO A  54 " =    1.110
peak=    3.178 closest distance to " CG  LEU A 167 " =    1.181
peak=    3.176 closest distance to " CB  GLU A 236 " =    1.132
peak=    3.174 closest distance to " CZ3 TRP A  85 " =    0.887
peak=    3.174 closest distance to " O   HOH Z  10 " =    1.792
peak=    3.168 closest distance to " N   VAL A 126 " =    1.527
peak=    3.166 closest distance to " O   HOH Z 345 " =    3.076
peak=    3.164 closest distance to " C   SER A  32 " =    1.048
peak=    3.160 closest distance to " OD1 ASN A 301 " =    1.684
peak=    3.159 closest distance to " CB  ALA A 248 " =    0.939
peak=    3.153 closest distance to " CB  ALA A 114 " =    1.132
peak=    3.151 closest distance to " O   HOH Z 171 " =    4.024
peak=    3.150 closest distance to " CB  LEU A  83 " =    0.782
peak=    3.147 closest distance to " NE2 HIS A 207 " =    1.232
peak=    3.144 closest distance to " CG2 ILE A 234 " =    0.835
peak=    3.142 closest distance to " CB  TYR A 247 " =    0.954
peak=    3.141 closest distance to " OD1 ASP A 231 " =    1.912
peak=    3.134 closest distance to " O   HOH Z  85 " =    1.902
peak=    3.134 closest distance to " CG BARG A 102 " =    1.825
peak=    3.134 closest distance to " CG2BVAL A  72 " =    1.660
peak=    3.131 closest distance to " N   PHE A 130 " =    1.301
peak=    3.128 closest distance to " CA  ALA A 291 " =    0.783
peak=    3.128 closest distance to " O   GLN A  88 " =    1.879
peak=    3.123 closest distance to " C   TYR A 214 " =    1.470
peak=    3.121 closest distance to " O   GLU A   2 " =    1.761
peak=    3.119 closest distance to " OD1BASN A 224 " =    2.255
peak=    3.117 closest distance to " O   HOH Z 332 " =    1.525
peak=    3.117 closest distance to " CA  ASP A 140 " =    1.191
peak=    3.115 closest distance to " O   HOH Z 387 " =    2.966
peak=    3.113 closest distance to " CD1 ILE A 199 " =    1.067
peak=    3.111 closest distance to " O   HOH Z  88 " =    3.443
peak=    3.103 closest distance to " O   HOH Z 329 " =    4.025
peak=    3.100 closest distance to " CG1 ILE A 120 " =    1.054
peak=    3.085 closest distance to " CD  ARG A  66 " =    2.504
peak=    3.083 closest distance to " CB  ALA A 100 " =    1.186
peak=    3.073 closest distance to " OG  SER A 245 " =    1.595
peak=    3.069 closest distance to " O   ASP A 124 " =    1.772
peak=    3.058 closest distance to " OG  SER A  62 " =    2.830
peak=    3.057 closest distance to " OG1 THR A 279 " =    1.818
peak=    3.034 closest distance to " O   HOH Z 417 " =    2.513
peak=    3.030 closest distance to " NH1AARG A 145 " =    0.946

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.811 - 5.299
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 200 from: 200
   mapped sites are within: 0.811 - 5.299

peak=   -4.897 closest distance to " CD  GLN A  58 " =    0.965
peak=   -4.850 closest distance to " O   HOH Z 266 " =    5.140
peak=   -4.473 closest distance to " CB  PRO A 243 " =    2.679
peak=   -4.369 closest distance to " CD  ARG A  14 " =    3.415
peak=   -4.283 closest distance to " O   HOH Z  10 " =    1.559
peak=   -4.281 closest distance to " C   HIS A 108 " =    1.138
peak=   -4.273 closest distance to " O   HOH Z 231 " =    2.342
peak=   -4.268 closest distance to " O   HOH Z 196 " =    2.036
peak=   -4.258 closest distance to " CB  ALA A 161 " =    2.619
peak=   -4.225 closest distance to " CG1 VAL A 112 " =    2.610
peak=   -4.200 closest distance to " CD  ARG A 156 " =    2.166
peak=   -4.199 closest distance to " CD1 LEU A 101 " =    2.450
peak=   -4.163 closest distance to " O   HOH Z 283 " =    2.357
peak=   -4.129 closest distance to " O   VAL A  67 " =    2.681
peak=   -4.107 closest distance to " OE1 GLN A 223 " =    2.036
peak=   -4.074 closest distance to " CZ3 TRP A 179 " =    1.196
peak=   -4.046 closest distance to " CG  ASP A 132 " =    2.333
peak=   -4.045 closest distance to " O   HOH Z 372 " =    2.418
peak=   -4.027 closest distance to " OXT GLY A 302 " =    2.843
peak=   -4.022 closest distance to " CE2 PHE A  61 " =    2.566
peak=   -3.960 closest distance to " O   HOH Z 290 " =    1.167
peak=   -3.953 closest distance to " CG1 VAL A 250 " =    2.707
peak=   -3.945 closest distance to " O   HOH Z 394 " =    1.532
peak=   -3.936 closest distance to " OG  SER A  97 " =    2.277
peak=   -3.922 closest distance to " CA  ASP A 298 " =    1.060
peak=   -3.897 closest distance to " O   PRO A 198 " =    1.318
peak=   -3.882 closest distance to " CD1 PHE A  59 " =    1.991
peak=   -3.838 closest distance to " CA  VAL A  67 " =    2.954
peak=   -3.806 closest distance to " CE2 TYR A  30 " =    2.707
peak=   -3.793 closest distance to " O   SER A 210 " =    1.906
peak=   -3.785 closest distance to " OD1 ASN A 148 " =    1.463
peak=   -3.779 closest distance to " O   HOH Z 377 " =    2.036
peak=   -3.771 closest distance to " O   PRO A 163 " =    2.081
peak=   -3.763 closest distance to " CD  GLN A 223 " =    1.286
peak=   -3.746 closest distance to " OG BSER A 134 " =    1.349
peak=   -3.731 closest distance to " CG2 ILE A 263 " =    2.371
peak=   -3.730 closest distance to " CB  ALA A 291 " =    2.303
peak=   -3.729 closest distance to " O   HOH Z 198 " =    2.149
peak=   -3.726 closest distance to " NE2 GLN A 194 " =    1.920
peak=   -3.721 closest distance to " O   HOH Z 166 " =    1.802
peak=   -3.716 closest distance to " N   ALA A  43 " =    2.687
peak=   -3.685 closest distance to " CD2 TYR A 293 " =    2.079
peak=   -3.681 closest distance to " ND2 ASN A  45 " =    1.814
peak=   -3.668 closest distance to " O   HOH Z 211 " =    1.549
peak=   -3.662 closest distance to " N   THR A  52 " =    1.645
peak=   -3.655 closest distance to " O   HOH Z  13 " =    1.716
peak=   -3.654 closest distance to " CB  PHE A 192 " =    2.057
peak=   -3.644 closest distance to " CG1 VAL A 112 " =    2.812
peak=   -3.643 closest distance to " CG  ARG A  66 " =    2.454
peak=   -3.631 closest distance to " CB  PHE A 208 " =    2.269
peak=   -3.615 closest distance to " O   HOH Z 292 " =    4.670
peak=   -3.603 closest distance to " CD  ARG A 139 " =    1.585
peak=   -3.596 closest distance to " CB  ALA A  43 " =    2.589
peak=   -3.591 closest distance to " O   HOH Z 234 " =    4.332
peak=   -3.590 closest distance to " CB  ALA A 291 " =    2.355
peak=   -3.587 closest distance to " C   SER A 206 " =    1.495
peak=   -3.564 closest distance to " O   HOH Z 311 " =    3.804
peak=   -3.563 closest distance to " ND2 ASN A 187 " =    1.540
peak=   -3.562 closest distance to " O   HOH Z 353 " =    2.233
peak=   -3.553 closest distance to " ND2 ASN A 249 " =    2.404
peak=   -3.552 closest distance to " NE2 GLN A  88 " =    1.833
peak=   -3.548 closest distance to " O   HOH Z  52 " =    1.469
peak=   -3.538 closest distance to " O   HOH Z 177 " =    1.776
peak=   -3.530 closest distance to " CA  GLY A 241 " =    2.360
peak=   -3.525 closest distance to " CD1 ILE A 151 " =    2.384
peak=   -3.520 closest distance to " O   HOH Z 165 " =    1.904
peak=   -3.509 closest distance to " ND2 ASN A  45 " =    1.128
peak=   -3.506 closest distance to " O   HOH Z  37 " =    1.821
peak=   -3.504 closest distance to " CB  ASN A  39 " =    2.386
peak=   -3.503 closest distance to " CB  TRP A  85 " =    2.495
peak=   -3.499 closest distance to " O   HOH Z  71 " =    1.917
peak=   -3.494 closest distance to " NE  ARG A 156 " =    1.943
peak=   -3.487 closest distance to " O   ALA A  10 " =    1.748
peak=   -3.487 closest distance to " CG2 ILE A  49 " =    2.703
peak=   -3.487 closest distance to " N   MET A 188 " =    1.974
peak=   -3.486 closest distance to " CD  ARG A 195 " =    5.131
peak=   -3.484 closest distance to " O   HOH Z 351 " =    1.496
peak=   -3.482 closest distance to " OD1 ASP A 171 " =    1.594
peak=   -3.480 closest distance to " CB  ALA A 248 " =    2.296
peak=   -3.478 closest distance to " NH2AARG A 275 " =    5.299
peak=   -3.474 closest distance to " CE3 TRP A 150 " =    2.227
peak=   -3.471 closest distance to " O   HOH Z 111 " =    1.620
peak=   -3.463 closest distance to " CE  MET A 105 " =    2.358
peak=   -3.460 closest distance to " O   HOH Z 377 " =    1.688
peak=   -3.454 closest distance to " CE BMET A  47 " =    1.866
peak=   -3.451 closest distance to " CG1 VAL A 112 " =    2.841
peak=   -3.443 closest distance to " CZ  PHE A 155 " =    1.227
peak=   -3.440 closest distance to " NH2 ARG A 159 " =    2.361
peak=   -3.438 closest distance to " CA  GLY A 133 " =    2.354
peak=   -3.434 closest distance to " O   HOH Z  15 " =    1.453
peak=   -3.431 closest distance to " O   HOH Z 264 " =    1.766
peak=   -3.431 closest distance to " O   HOH Z   6 " =    2.196
peak=   -3.426 closest distance to " CB  PHE A  16 " =    2.593
peak=   -3.424 closest distance to " O   HOH Z 393 " =    1.426
peak=   -3.422 closest distance to " NH2 ARG A  79 " =    1.607
peak=   -3.422 closest distance to " O   VAL A 189 " =    2.642
peak=   -3.422 closest distance to " NE2 GLN A 103 " =    1.800
peak=   -3.420 closest distance to " O   HOH Z 407 " =    3.226
peak=   -3.419 closest distance to " O   HOH Z 389 " =    1.843
peak=   -3.412 closest distance to " CB  ASP A 286 " =    1.880
peak=   -3.410 closest distance to " CB  ALA A 248 " =    2.200
peak=   -3.409 closest distance to " O   HOH Z  60 " =    1.925
peak=   -3.405 closest distance to " CG  GLU A 277 " =    1.108
peak=   -3.404 closest distance to " O   ALA A  34 " =    2.375
peak=   -3.404 closest distance to " CG  ARG A 269 " =    2.296
peak=   -3.401 closest distance to " O   HOH Z 185 " =    2.453
peak=   -3.399 closest distance to " O   HOH Z 114 " =    3.241
peak=   -3.391 closest distance to " OG BSER A 134 " =    1.895
peak=   -3.389 closest distance to " CD  PRO A 213 " =    2.174
peak=   -3.389 closest distance to " O   HOH Z 123 " =    2.424
peak=   -3.364 closest distance to " O   HOH Z 171 " =    2.112
peak=   -3.360 closest distance to " CE3 TRP A 274 " =    2.521
peak=   -3.359 closest distance to " CD  LYS A 289 " =    2.462
peak=   -3.352 closest distance to " CG2 VAL A 189 " =    2.221
peak=   -3.346 closest distance to " CZ  TYR A 169 " =    1.829
peak=   -3.343 closest distance to " CB  ASP A 171 " =    2.501
peak=   -3.338 closest distance to " O   PHE A 218 " =    1.550
peak=   -3.336 closest distance to " CD2 LEU A 300 " =    2.875
peak=   -3.336 closest distance to " O   HOH Z 252 " =    4.067
peak=   -3.334 closest distance to " O   HOH Z   6 " =    1.545
peak=   -3.333 closest distance to " N   ALA A 248 " =    1.766
peak=   -3.325 closest distance to " CA  GLY A 203 " =    2.392
peak=   -3.324 closest distance to " OG BSER A 210 " =    2.123
peak=   -3.321 closest distance to " CG  ASP A 231 " =    0.811
peak=   -3.320 closest distance to " O   HOH Z 193 " =    1.844
peak=   -3.317 closest distance to " SG ACYS A 201 " =    2.113
peak=   -3.311 closest distance to " CA  GLY A 241 " =    3.230
peak=   -3.311 closest distance to " O   HOH Z 216 " =    2.065
peak=   -3.310 closest distance to " CD1 LEU A 228 " =    2.245
peak=   -3.302 closest distance to " O   SER A  62 " =    2.147
peak=   -3.302 closest distance to " O   HOH Z 149 " =    2.175
peak=   -3.297 closest distance to " O   HOH Z 166 " =    1.665
peak=   -3.294 closest distance to " O   HOH Z 128 " =    2.604
peak=   -3.291 closest distance to " CG  LEU A  83 " =    1.983
peak=   -3.289 closest distance to " O   GLY A 196 " =    1.106
peak=   -3.288 closest distance to " ND2BASN A 224 " =    1.778
peak=   -3.285 closest distance to " N   ALA A 226 " =    2.086
peak=   -3.277 closest distance to " CB  PRO A 163 " =    2.505
peak=   -3.276 closest distance to " CB  ALA A  10 " =    2.232
peak=   -3.274 closest distance to " O   HOH Z  38 " =    1.528
peak=   -3.273 closest distance to " NH2 ARG A  79 " =    2.114
peak=   -3.272 closest distance to " N   SER A 276 " =    1.472
peak=   -3.272 closest distance to " CG1 VAL A  67 " =    3.070
peak=   -3.262 closest distance to " C   ALA A 158 " =    1.372
peak=   -3.251 closest distance to " C   LEU A 143 " =    1.072
peak=   -3.249 closest distance to " CG  GLU A  53 " =    1.533
peak=   -3.234 closest distance to " CD  ARG A  79 " =    1.159
peak=   -3.233 closest distance to " N   GLN A  58 " =    1.687
peak=   -3.233 closest distance to " O   HOH Z  43 " =    1.562
peak=   -3.232 closest distance to " O   ALA A   1 " =    1.921
peak=   -3.231 closest distance to " CG  PHE A 283 " =    2.494
peak=   -3.231 closest distance to " CG  PRO A 243 " =    1.831
peak=   -3.230 closest distance to " O   HOH Z 421 " =    3.533
peak=   -3.216 closest distance to " NE2 GLN A  88 " =    1.021
peak=   -3.214 closest distance to " O   TYR A 186 " =    1.820
peak=   -3.209 closest distance to " CG  HIS A  86 " =    1.138
peak=   -3.206 closest distance to " ND2 ASN A  60 " =    1.392
peak=   -3.205 closest distance to " CG1 VAL A 125 " =    2.015
peak=   -3.201 closest distance to " OD2 ASP A 191 " =    1.536
peak=   -3.201 closest distance to " CG  TRP A 266 " =    1.925
peak=   -3.200 closest distance to " CG  GLN A  11 " =    1.765
peak=   -3.199 closest distance to " O   HOH Z 366 " =    1.897
peak=   -3.198 closest distance to " CG1 VAL A  78 " =    2.830
peak=   -3.197 closest distance to " OE1 GLN A 223 " =    2.119
peak=   -3.189 closest distance to " O   HOH Z 414 " =    1.546
peak=   -3.189 closest distance to " O   HOH Z 256 " =    2.426
peak=   -3.184 closest distance to " O   HOH Z 357 " =    2.029
peak=   -3.183 closest distance to " O   HOH Z 134 " =    2.719
peak=   -3.182 closest distance to " CG  PRO A 163 " =    2.548
peak=   -3.179 closest distance to " OD2 ASP A 171 " =    1.848
peak=   -3.168 closest distance to " CG1 VAL A 125 " =    2.325
peak=   -3.167 closest distance to " OE2 GLU A   2 " =    1.763
peak=   -3.163 closest distance to " CB  TYR A  15 " =    2.235
peak=   -3.157 closest distance to " CD1 LEU A   5 " =    2.507
peak=   -3.155 closest distance to " CD  GLN A 223 " =    0.873
peak=   -3.147 closest distance to " O   HOH Z  19 " =    0.919
peak=   -3.144 closest distance to " OD1 ASP A 191 " =    1.576
peak=   -3.142 closest distance to " CD2 LEU A 237 " =    2.809
peak=   -3.142 closest distance to " N   THR A 264 " =    1.416
peak=   -3.139 closest distance to " CD2 TYR A 247 " =    2.373
peak=   -3.137 closest distance to " OE1 GLN A 183 " =    1.515
peak=   -3.134 closest distance to " N   SER A   3 " =    2.112
peak=   -3.125 closest distance to " O   HOH Z  77 " =    2.071
peak=   -3.124 closest distance to " CG1AVAL A  41 " =    2.782
peak=   -3.121 closest distance to " O   ASN A 301 " =    1.377
peak=   -3.116 closest distance to " CG  ARG A 219 " =    2.706
peak=   -3.115 closest distance to " C   MET A 188 " =    1.617
peak=   -3.112 closest distance to " O   PRO A 198 " =    1.343
peak=   -3.109 closest distance to " O   HOH Z 106 " =    1.935
peak=   -3.107 closest distance to " C   GLY A 262 " =    2.021
peak=   -3.105 closest distance to " CA  GLY A  98 " =    2.240
peak=   -3.080 closest distance to " O   HOH Z 351 " =    1.478
peak=   -3.073 closest distance to " CD2 TYR A 293 " =    2.155
peak=   -3.068 closest distance to " OE1 GLN A  88 " =    1.152
peak=   -3.064 closest distance to " O   HOH Z 262 " =    2.898
peak=   -3.062 closest distance to " NH1BARG A 275 " =    2.295
peak=   -3.061 closest distance to " CE3 TRP A  70 " =    1.864
peak=   -3.058 closest distance to " O   HOH Z 377 " =    1.921
peak=   -3.032 closest distance to " CG2BVAL A  41 " =    1.879
peak=   -3.007 closest distance to " O   HOH Z 193 " =    2.004

================= 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    :  0.3615 0.3501   6.135198e+00   6.100051e+00
   1_bss:  0.3481 0.3372   6.114731e+00   6.074713e+00
   1_xyz:  0.2037 0.2234   5.625681e+00   5.716553e+00
   1_adp:  0.1891 0.2255   5.580576e+00   5.727706e+00
   1_occ:  0.1887 0.2254   5.579533e+00   5.727567e+00
   2_bss:  0.1857 0.2211   5.568817e+00   5.715851e+00
   2_xyz:  0.1366 0.1687   5.280557e+00   5.459778e+00
   2_adp:  0.1264 0.1647   5.227097e+00   5.433762e+00
   2_occ:  0.1263 0.1648   5.226927e+00   5.433856e+00
   3_bss:  0.1262 0.1649   5.225806e+00   5.432762e+00
   3_xyz:  0.1169 0.1598   5.177123e+00   5.404218e+00
   3_adp:  0.1159 0.1585   5.168409e+00   5.396849e+00
   3_occ:  0.1158 0.1584   5.168291e+00   5.397139e+00
   4_bss:  0.1156 0.1583   5.167886e+00   5.397016e+00
   4_xyz:  0.1144 0.1583   5.160858e+00   5.394547e+00
   4_adp:  0.1140 0.1589   5.161184e+00   5.398855e+00
   4_occ:  0.1140 0.1590   5.161491e+00   5.399461e+00
   5_bss:  0.1139 0.1589   5.161476e+00   5.399484e+00
   5_xyz:  0.1103 0.1588   5.144198e+00   5.394876e+00
   5_adp:  0.1102 0.1585   5.142297e+00   5.392863e+00
   5_occ:  0.1102 0.1586   5.142555e+00   5.393451e+00
   5_bss:  0.1101 0.1584   5.142660e+00   5.393537e+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:  0.307  52.731  -3.425   3.260   0.362   0.000   0.000   0.000
   1_xyz:  0.307  52.731  -3.425   3.260   0.362   0.000   0.000   0.000
   1_adp:  0.307  52.731  -3.425   3.260   0.362   0.000   0.000   0.000
   1_occ:  0.307  52.731  -3.425   3.260   0.362   0.000   0.000   0.000
   2_bss:  0.329  67.828  -2.990  -0.275  -0.577  -0.000  -0.000  -0.000
   2_xyz:  0.329  67.828  -2.990  -0.275  -0.577  -0.000  -0.000  -0.000
   2_adp:  0.329  67.828  -2.990  -0.275  -0.577  -0.000  -0.000  -0.000
   2_occ:  0.329  67.828  -2.990  -0.275  -0.577  -0.000  -0.000  -0.000
   3_bss:  0.330  67.177  -2.506  -1.024  -0.544  -0.000  -0.000  -0.000
   3_xyz:  0.330  67.177  -2.506  -1.024  -0.544  -0.000  -0.000  -0.000
   3_adp:  0.330  67.177  -2.506  -1.024  -0.544  -0.000  -0.000  -0.000
   3_occ:  0.330  67.177  -2.506  -1.024  -0.544  -0.000  -0.000  -0.000
   4_bss:  0.324  60.687  -2.192  -1.167  -0.400  -0.000  -0.000  -0.000
   4_xyz:  0.324  60.687  -2.192  -1.167  -0.400  -0.000  -0.000  -0.000
   4_adp:  0.324  60.687  -2.192  -1.167  -0.400  -0.000  -0.000  -0.000
   4_occ:  0.324  60.687  -2.192  -1.167  -0.400  -0.000  -0.000  -0.000
   5_bss:  0.322  61.234  -1.926  -1.069  -0.207  -0.000  -0.000  -0.000
   5_xyz:  0.322  61.234  -1.926  -1.069  -0.207  -0.000  -0.000  -0.000
   5_adp:  0.322  61.234  -1.926  -1.069  -0.207  -0.000  -0.000  -0.000
   5_occ:  0.322  61.234  -1.926  -1.069  -0.207  -0.000  -0.000  -0.000
   5_bss:  0.322  61.237  -1.643  -0.856   0.040  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  38.248 0.6657  0.8232    36437.950
   1_bss:  37.203 0.6762  0.8395    33302.450
   1_xyz:  22.259 0.8400  0.9898    13057.063
   1_adp:  22.640 0.8357  0.9729    13338.765
   1_occ:  22.647 0.8356  0.9724    13330.139
   2_bss:  22.144 0.8408  0.9360    12944.444
   2_xyz:  15.722 0.9002  0.9712     7290.247
   2_adp:  15.080 0.9059  0.9659     6912.102
   2_occ:  15.088 0.9059  0.9657     6915.561
   3_bss:  15.066 0.9061  0.9642     6933.220
   3_xyz:  14.354 0.9123  0.9671     6543.102
   3_adp:  14.176 0.9139  0.9604     6485.196
   3_occ:  14.180 0.9138  0.9603     6488.133
   4_bss:  14.175 0.9139  0.9643     6486.109
   4_xyz:  14.096 0.9145  0.9650     6440.320
   4_adp:  14.159 0.9141  0.9567     6484.979
   4_occ:  14.171 0.9140  0.9565     6491.790
   5_bss:  14.171 0.9140  0.9630     6493.301
   5_xyz:  14.066 0.9148  0.9640     6451.992
   5_adp:  14.018 0.9152  0.9566     6425.244
   5_occ:  14.026 0.9152  0.9566     6432.472
   5_bss:  14.028 0.9152  0.9652     6434.189
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.115   1.6214e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.115   1.6214e-01
   1_xyz:   1.318  0.011  0.080 15.184  0.005  4.117   9.0176e-02
   1_adp:   1.318  0.011  0.080 15.184  0.005  4.117   9.0176e-02
   1_occ:   1.318  0.011  0.080 15.184  0.005  4.117   9.0176e-02
   2_bss:   1.318  0.011  0.080 15.184  0.005  4.117   9.0176e-02
   2_xyz:   1.069  0.008  0.076 14.680  0.005  4.132   6.5357e-02
   2_adp:   1.069  0.008  0.076 14.680  0.005  4.132   6.5357e-02
   2_occ:   1.069  0.008  0.076 14.680  0.005  4.132   6.5357e-02
   3_bss:   1.069  0.008  0.076 14.680  0.005  4.132   6.5357e-02
   3_xyz:   1.013  0.008  0.077 14.586  0.004  4.116   6.2391e-02
   3_adp:   1.013  0.008  0.077 14.586  0.004  4.116   6.2391e-02
   3_occ:   1.013  0.008  0.077 14.586  0.004  4.116   6.2391e-02
   4_bss:   1.013  0.008  0.077 14.586  0.004  4.116   6.2391e-02
   4_xyz:   0.988  0.008  0.076 14.426  0.004  4.118   5.8990e-02
   4_adp:   0.988  0.008  0.076 14.426  0.004  4.118   5.8990e-02
   4_occ:   0.988  0.008  0.076 14.426  0.004  4.118   5.8990e-02
   5_bss:   0.988  0.008  0.076 14.426  0.004  4.118   5.8990e-02
   5_xyz:   1.088  0.010  0.083 14.655  0.004  4.120   7.1616e-02
   5_adp:   1.088  0.010  0.083 14.655  0.004  4.120   7.1616e-02
   5_occ:   1.088  0.010  0.083 14.655  0.004  4.120   7.1616e-02
   5_bss:   1.088  0.010  0.083 14.655  0.004  4.120   7.1616e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4312e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4312e-01
   1_xyz:   8.745  0.061  0.287 86.316  0.027  2.198   9.7724e-02
   1_adp:   8.745  0.061  0.287 86.316  0.027  2.198   9.7724e-02
   1_occ:   8.745  0.061  0.287 86.316  0.027  2.198   9.7724e-02
   2_bss:   8.745  0.061  0.287 86.316  0.027  2.198   9.7724e-02
   2_xyz:   7.538  0.054  0.244 82.060  0.047  2.321   5.2457e-02
   2_adp:   7.538  0.054  0.244 82.060  0.047  2.321   5.2457e-02
   2_occ:   7.538  0.054  0.244 82.060  0.047  2.321   5.2457e-02
   3_bss:   7.538  0.054  0.244 82.060  0.047  2.321   5.2457e-02
   3_xyz:   7.685  0.044  0.245 82.822  0.040  2.388   6.4219e-02
   3_adp:   7.685  0.044  0.245 82.822  0.040  2.388   6.4219e-02
   3_occ:   7.685  0.044  0.245 82.822  0.040  2.388   6.4219e-02
   4_bss:   7.685  0.044  0.245 82.822  0.040  2.388   6.4219e-02
   4_xyz:   7.434  0.045  0.243 81.524  0.036  2.369   4.2404e-02
   4_adp:   7.434  0.045  0.243 81.524  0.036  2.369   4.2404e-02
   4_occ:   7.434  0.045  0.243 81.524  0.036  2.369   4.2404e-02
   5_bss:   7.434  0.045  0.243 81.524  0.036  2.369   4.2404e-02
   5_xyz:   8.167  0.051  0.284 82.392  0.037  2.324   5.2364e-02
   5_adp:   8.167  0.051  0.284 82.392  0.037  2.324   5.2364e-02
   5_occ:   8.167  0.051  0.284 82.392  0.037  2.324   5.2364e-02
   5_bss:   8.167  0.051  0.284 82.392  0.037  2.324   5.2364e-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:  77.90   0.00  16.20  77.90   0.00  12.31  63.96   6.52  37.39
   1_occ:  77.90   0.00  16.20  77.90   0.00  12.31  63.96   6.52  37.39
   2_bss:  77.90   0.00  16.20  77.90   0.00  12.31  63.96   6.52  37.39
   2_xyz:  77.90   0.00  16.20  77.90   0.00  12.31  63.96   6.52  37.39
   2_adp:  83.38   0.00  16.84  83.38   0.00  12.55  74.55   4.84  40.19
   2_occ:  83.38   0.00  16.84  83.38   0.00  12.55  74.55   4.84  40.19
   3_bss:  83.38   0.00  16.84  83.38   0.00  12.55  74.55   4.84  40.19
   3_xyz:  83.38   0.00  16.84  83.38   0.00  12.55  74.55   4.84  40.19
   3_adp:  85.37   0.51  16.48  85.37   0.51  12.31  76.39   1.13  39.18
   3_occ:  85.37   0.51  16.48  85.37   0.51  12.31  76.39   1.13  39.18
   4_bss:  85.37   0.51  16.48  85.37   0.51  12.31  76.39   1.13  39.18
   4_xyz:  85.37   0.51  16.48  85.37   0.51  12.31  76.39   1.13  39.18
   4_adp:  86.77   0.00  16.32  86.77   0.00  12.13  77.68   2.05  39.10
   4_occ:  86.77   0.00  16.32  86.77   0.00  12.13  77.68   2.05  39.10
   5_bss:  86.77   0.00  16.32  86.77   0.00  12.13  77.68   2.05  39.10
   5_xyz:  86.77   0.00  16.32  86.77   0.00  12.13  77.68   2.05  39.10
   5_adp:  87.16   0.00  16.09  87.16   0.00  11.90  78.17   3.95  38.89
   5_occ:  87.16   0.00  16.09  87.16   0.00  11.90  78.17   3.95  38.89
   5_bss:  87.16   0.00  16.09  87.16   0.00  11.90  78.17   3.95  38.89
------------------------------------------------------------------------
 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:    1.113    0.013    0.410
   1_adp:    1.113    0.013    0.410
   1_occ:    1.113    0.013    0.410
   2_bss:    1.113    0.013    0.410
   2_xyz:    0.959    0.031    0.463
   2_adp:    0.959    0.031    0.463
   2_occ:    0.959    0.031    0.463
   3_bss:    0.959    0.031    0.463
   3_xyz:    1.023    0.066    0.497
   3_adp:    1.023    0.066    0.497
   3_occ:    1.023    0.066    0.497
   4_bss:    1.023    0.066    0.497
   4_xyz:    1.074    0.031    0.508
   4_adp:    1.074    0.031    0.508
   4_occ:    1.074    0.031    0.508
   5_bss:    1.074    0.031    0.508
   5_xyz:    1.110    0.075    0.515
   5_adp:    1.110    0.075    0.515
   5_occ:    1.110    0.075    0.515
   5_bss:    1.110    0.075    0.515
------------------------------------------------------------------------

CPU time actual refinement: 330.52


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_700/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_700/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_700/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_700/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_700/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 330.36 
  Macro-tasks:
    bulk solvent and scale       = 38.48  
    individual site refinement   = 139.79 
    weights calculation          = 29.09  
    collect and process          = 6.63   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 214.09 
  Micro-tasks:
    mask                            = 1.24   
    f_calc                          = 104.91 
    alpha_beta                      = 8.51   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 114.81 
    fmodel                         = 6.54   
    r_factors                      = 0.16   
    phase_errors                   = 10.83  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 248.40 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.626 micro seconds
Total CPU time: 5.73 minutes
from_scatterers_fft:    657 calls, 104.63 s
gradients_fft:          602 calls, 100.64 s

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

# Date 2008-01-16 Time 05:27:14 PST -0800 (1200490034.70 s)
Start R-work = 0.3615, R-free = 0.3501 (no bulk solvent and anisotropic scale)
Final R-work = 0.1292, R-free = 0.1729 (no bulk solvent and anisotropic scale)

Start R-work = 0.3481, R-free = 0.3372
Final R-work = 0.1101, R-free = 0.1584