# Date 2008-01-16 Time 06:16:27 PST -0800 (1200492987.96 s)
#phil __OFF__

Command line arguments: "../1074.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4858
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1074

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 47.8686, 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: 2.75, per 1000 atoms: 0.97


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.8686, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1984 2.02109
Completeness in resolution range: 0.973076
Completeness with d_max=infinity: 0.969993

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1984
                             d_min =   2.0211

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.8686, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1984 2.02109
Completeness in resolution range: 0.973076
Completeness with d_max=infinity: 0.969993

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1989 -  4.3240 [2112/2139]  1902   210   9.9%
  bin  2:  4.3240 -  3.4453 [2030/2046]  1826   204  10.0%
  bin  3:  3.4453 -  3.0136 [2005/2024]  1802   203  10.1%
  bin  4:  3.0136 -  2.7398 [1988/2018]  1794   194   9.8%
  bin  5:  2.7398 -  2.5444 [1961/1980]  1761   200  10.2%
  bin  6:  2.5444 -  2.3950 [1963/1988]  1769   194   9.9%
  bin  7:  2.3950 -  2.2755 [1966/1998]  1771   195   9.9%
  bin  8:  2.2755 -  2.1767 [1933/1965]  1737   196  10.1%
  bin  9:  2.1767 -  2.0932 [1940/1982]  1746   194  10.0%
  bin 10:  2.0932 -  2.0211 [1691/1991]  1522   169  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1074/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: 0.12 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:
        1.47 -     2.16: 5
        2.16 -     2.84: 1002
        2.84 -     3.53: 4291
        3.53 -     4.21: 9075
        4.21 -     4.90: 13337
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.470 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 343 " - " O   HOH Z 277 "  1.925 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.925 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.077 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27705 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_1074/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1074/model_refine_001.geo

CPU time processing inputs: 7.78


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 47.8686 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: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4352   r_free= 0.4191   ksol= 0.00   Bsol= 0.00   scale= 0.895    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.240140                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.8225 0.99   1374  153 0.3376 0.3473      6.4804      6.4374|
|  2:  4.8225 -  3.8482 0.99   1320  145 0.3666 0.3752      6.7616      6.7756|
|  3:  3.8482 -  3.3678 0.99   1300  145 0.3969 0.3601      6.6308      6.5472|
|  4:  3.3678 -  3.0626 0.99   1286  144 0.4297 0.4084      6.4951      6.4284|
|  5:  3.0626 -  2.8446 0.99   1271  140 0.4557 0.4181      6.3369       6.326|
|  6:  2.8446 -  2.6779 0.99   1278  143 0.4663 0.4489      6.2518      6.1891|
|  7:  2.6779 -  2.5444 0.99   1256  141 0.4707 0.4146      6.2013      6.1075|
|  8:  2.5444 -  2.4341 0.98   1268  140 0.4776 0.4203      6.1621      6.1406|
|  9:  2.4341 -  2.3408 0.98   1269  138 0.4793 0.4908      6.0915      6.1542|
| 10:  2.3408 -  2.2603 0.99   1235  137 0.4890 0.4564      6.0985      6.0548|
| 11:  2.2603 -  2.1898 0.99   1268  147 0.4881 0.4736      6.0279      6.0666|
| 12:  2.1898 -  2.1274 0.97   1248  129 0.4983 0.4773      5.9695      5.9907|
| 13:  2.1274 -  2.0715 0.99   1236  141 0.4957 0.5054      5.8787      5.8664|
| 14:  2.0715 -  2.0211 0.80   1021  116 0.4830 0.5005      5.8218      5.7666|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1989 -  4.8225  1374   153  0.74  31.09   0.83     0.77      59891.02|
|  2:  4.8225 -  3.8482  1320   145  0.76  29.99   0.91     0.83      80291.80|
|  3:  3.8482 -  3.3678  1300   145  0.69  36.42   0.91     0.82      85138.04|
|  4:  3.3678 -  3.0626  1286   144  0.62  42.29   0.90     0.76      76975.54|
|  5:  3.0626 -  2.8446  1271   140  0.54  48.71   0.90     0.70      62987.93|
|  6:  2.8446 -  2.6779  1278   143  0.53  49.56   0.89     0.69      53599.94|
|  7:  2.6779 -  2.5444  1256   141  0.52  50.60   0.92     0.68      48320.57|
|  8:  2.5444 -  2.4341  1268   140  0.50  51.87   0.91     0.67      46610.60|
|  9:  2.4341 -  2.3408  1269   138  0.48  53.84   0.91     0.65      44474.00|
| 10:  2.3408 -  2.2603  1235   137  0.47  54.60   0.93     0.64      41543.99|
| 11:  2.2603 -  2.1898  1268   147  0.45  56.37   0.93     0.63      39718.18|
| 12:  2.1898 -  2.1274  1248   129  0.42  58.62   0.92     0.60      38264.01|
| 13:  2.1274 -  2.0715  1236   141  0.38  61.33   0.91     0.55      34821.13|
| 14:  2.0715 -  2.0211  1021   116  0.37  62.18   0.92     0.50      28834.81|
|alpha:            min =        0.50 max =            0.83 mean =         0.68|
|beta:             min =    28834.81 max =        85138.04 mean =     53581.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.54|
|phase err.(work): min =        0.00 max =           90.00 mean =        48.68|
|phase err.(test): min =        0.00 max =           89.97 mean =        48.77|
|-----------------------------------------------------------------------------|

============================== 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 = 6.588874              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.704   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.736895              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.406   (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 |  1.470 -  1.813:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.813 -  2.156:        3 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.156 -  2.499:       13 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.499 -  2.842:      989 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.842 -  3.185:     1934 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.185 -  3.528:     2357 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.528 -  3.871:     4565 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.871 -  4.214:     4510 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.214 -  4.557:     6031 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.557 -  4.900:     7306 |
|-----------------------------------------------------------------------------|
|-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 |        0.166 |
| 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  1.470 |       0.186 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.431)------------------------------------------|
|    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: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4352   r_free= 0.4191   ksol= 0.00   Bsol= 0.00   scale= 0.895    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.240140                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4269   r_free= 0.4112   ksol= 0.29   Bsol= 51.78   scale= 0.938   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.27,4.12,-0.19,0.00,-0.00,-0.00); trace/3= 0.89                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.230723                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.852266              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.539   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.871573              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.208   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4269      final r-factor (work) = 0.3144          |
| start r-factor (free) = 0.4112      final r-factor (free) = 0.3401          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.3968 = 5.85 * 0.50 * 6.2304 + 1.00 * 0.1657                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.8942 = 5.85 * 0.50 * 6.0746 + 1.00 * 0.1192                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3144      final r-factor (work) = 0.2863          |
| start r-factor (free) = 0.3401      final r-factor (free) = 0.3490          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3005 = 0.87 * 1.00 * 6.0746 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2055 = 0.87 * 1.00 * 5.9538 + 1.00 * 0.0163                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.431)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.77   17.96    None  None   None       |
|    all(noH): 2823   0      0.00    99.77   17.96    None  None   None       |
|    Sol.    : 438    0      0.00    99.77   38.60    None  None   None       |
|    Mac.    : 2385   0      0.00    81.85   14.17    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.977:  970   |   5:    49.885 -  59.862:   82        |
|      1:     9.977 -  19.954:  988   |   6:    59.862 -  69.839:   49        |
|      2:    19.954 -  29.931:  403   |   7:    69.839 -  79.816:   18        |
|      3:    29.931 -  39.908:  183   |   8:    79.816 -  89.793:    6        |
|      4:    39.908 -  49.885:  123   |   9:    89.793 -  99.770:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2863 r_free = 0.3490             target_work(ml) = 5.961         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2859 r_free = 0.3488             target_work(ml) = 5.960         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2859   r_free= 0.3488   ksol= 0.29   Bsol= 51.78   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.27,4.12,-0.19,0.00,-0.00,-0.00); trace/3= 0.89                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 5.960054                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2854   r_free= 0.3482   ksol= 0.32   Bsol= 73.91   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.18,2.01,-0.05,0.00,-0.00,-0.00); trace/3= 0.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 5.961392                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.653843              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.597   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.454974              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.232  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2854      final r-factor (work) = 0.2241          |
| start r-factor (free) = 0.3482      final r-factor (free) = 0.2683          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.9738 = 4.65 * 0.50 * 5.9540 + 1.00 * 0.1192                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.7363 = 4.65 * 0.50 * 5.8625 + 1.00 * 0.0946                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2241      final r-factor (work) = 0.2067          |
| start r-factor (free) = 0.2683      final r-factor (free) = 0.2504          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6836 = 0.45 * 1.00 * 5.8625 + 1.00 * 0.0163                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6037 = 0.45 * 1.00 * 5.6964 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.431)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.70  17.45    None  None   None       |
|    all(noH): 2823   0      0.00    100.70  17.45    None  None   None       |
|    Sol.    : 438    0      2.04    100.70  40.36    None  None   None       |
|    Mac.    : 2385   0      0.00    85.02   13.24    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.070: 1126   |   5:    50.351 -  60.421:   87        |
|      1:    10.070 -  20.141:  956   |   6:    60.421 -  70.492:   54        |
|      2:    20.141 -  30.211:  280   |   7:    70.492 -  80.562:   16        |
|      3:    30.211 -  40.281:  184   |   8:    80.562 -  90.632:    8        |
|      4:    40.281 -  50.351:  111   |   9:    90.632 - 100.702:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2067 r_free = 0.2504             target_work(ml) = 5.675         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2064 r_free = 0.2501             target_work(ml) = 5.674         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2064   r_free= 0.2501   ksol= 0.32   Bsol= 73.91   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.18,2.01,-0.05,0.00,-0.00,-0.00); trace/3= 0.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.673988                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2064   r_free= 0.2493   ksol= 0.32   Bsol= 78.30   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.14,0.61,-0.10,0.00,-0.00,-0.00); trace/3= -0.21                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.672646                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.810379              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.192   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.489484              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 155.497  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2064      final r-factor (work) = 0.1590          |
| start r-factor (free) = 0.2493      final r-factor (free) = 0.1984          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.9486 = 3.81 * 0.50 * 5.6966 + 1.00 * 0.0955                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6527 = 3.81 * 0.50 * 5.5537 + 1.00 * 0.0719                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1590      final r-factor (work) = 0.1465          |
| start r-factor (free) = 0.1984      final r-factor (free) = 0.1902          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7306 = 0.49 * 1.00 * 5.5537 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6522 = 0.49 * 1.00 * 5.3940 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.431)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.13   17.01    None  None   None       |
|    all(noH): 2823   0      0.00    99.13   17.01    None  None   None       |
|    Sol.    : 438    0      3.76    99.13   41.97    None  None   None       |
|    Mac.    : 2385   0      0.00    90.62   12.43    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.913: 1202   |   5:    49.564 -  59.476:   93        |
|      1:     9.913 -  19.826:  948   |   6:    59.476 -  69.389:   59        |
|      2:    19.826 -  29.738:  225   |   7:    69.389 -  79.302:   24        |
|      3:    29.738 -  39.651:  143   |   8:    79.302 -  89.215:   10        |
|      4:    39.651 -  49.564:  116   |   9:    89.215 -  99.127:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1465 r_free = 0.1902             target_work(ml) = 5.371         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1465 r_free = 0.1902             target_work(ml) = 5.370         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1465   r_free= 0.1902   ksol= 0.32   Bsol= 78.30   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.14,0.61,-0.10,0.00,-0.00,-0.00); trace/3= -0.21                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.370402                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1468   r_free= 0.1907   ksol= 0.33   Bsol= 80.00   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.31,-0.22,-0.12,-0.00,-0.00,-0.00); trace/3= -0.55                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.371472                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.083767              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 121.486  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.847754              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.336  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1468      final r-factor (work) = 0.1318          |
| start r-factor (free) = 0.1907      final r-factor (free) = 0.1762          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6936 = 2.08 * 0.50 * 5.3958 + 1.00 * 0.0719                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6077 = 2.08 * 0.50 * 5.3218 + 1.00 * 0.0630                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1318      final r-factor (work) = 0.1278          |
| start r-factor (free) = 0.1762      final r-factor (free) = 0.1743          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5233 = 0.85 * 1.00 * 5.3218 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4742 = 0.85 * 1.00 * 5.2626 + 1.00 * 0.0128                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.431)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.63  16.92    None  None   None       |
|    all(noH): 2823   0      0.00    101.63  16.92    None  None   None       |
|    Sol.    : 438    0      1.72    101.19  43.17    None  None   None       |
|    Mac.    : 2385   0      0.00    101.63  12.10    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.163: 1291   |   5:    50.816 -  60.979:   87        |
|      1:    10.163 -  20.326:  923   |   6:    60.979 -  71.142:   66        |
|      2:    20.326 -  30.490:  191   |   7:    71.142 -  81.305:   26        |
|      3:    30.490 -  40.653:  129   |   8:    81.305 -  91.468:    9        |
|      4:    40.653 -  50.816:   93   |   9:    91.468 - 101.632:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1278 r_free = 0.1743             target_work(ml) = 5.256         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1277 r_free = 0.1743             target_work(ml) = 5.256         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1277   r_free= 0.1743   ksol= 0.33   Bsol= 80.00   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.31,-0.22,-0.12,-0.00,-0.00,-0.00); trace/3= -0.55                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.255746                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1276   r_free= 0.1742   ksol= 0.32   Bsol= 75.17   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.02,-0.30,0.27,-0.00,0.00,0.00); trace/3= -0.35                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.255432                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.560877              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.490  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.373880              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.579  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1276      final r-factor (work) = 0.1170          |
| start r-factor (free) = 0.1742      final r-factor (free) = 0.1685          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4336 = 3.56 * 0.50 * 5.2631 + 1.00 * 0.0630                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3777 = 3.56 * 0.50 * 5.2194 + 1.00 * 0.0848                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1170      final r-factor (work) = 0.1163          |
| start r-factor (free) = 0.1685      final r-factor (free) = 0.1658          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9641 = 0.37 * 1.00 * 5.2194 + 1.00 * 0.0127                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9537 = 0.37 * 1.00 * 5.1947 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.431)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.81  16.48    None  None   None       |
|    all(noH): 2823   0      0.00    100.81  16.48    None  None   None       |
|    Sol.    : 438    0      2.22    100.19  42.05    None  None   None       |
|    Mac.    : 2385   0      0.00    100.81  11.78    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.081: 1339   |   5:    50.406 -  60.487:   88        |
|      1:    10.081 -  20.162:  896   |   6:    60.487 -  70.568:   58        |
|      2:    20.162 -  30.243:  182   |   7:    70.568 -  80.649:   23        |
|      3:    30.243 -  40.324:  124   |   8:    80.649 -  90.730:   10        |
|      4:    40.324 -  50.406:   95   |   9:    90.730 - 100.811:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1163 r_free = 0.1658             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1162 r_free = 0.1659             target_work(ml) = 5.187         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1162   r_free= 0.1659   ksol= 0.32   Bsol= 75.17   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.02,-0.30,0.27,-0.00,0.00,0.00); trace/3= -0.35                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.187438                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.8225 0.99   1374  153 0.1016 0.1351      5.4224       5.571|
|  2:  4.8225 -  3.8482 0.99   1320  145 0.0842 0.1093      5.4363      5.6259|
|  3:  3.8482 -  3.3678 0.99   1300  145 0.1029 0.1516        5.47      5.8621|
|  4:  3.3678 -  3.0626 0.99   1286  144 0.1244 0.1664      5.4894      5.6458|
|  5:  3.0626 -  2.8446 0.99   1271  140 0.1412 0.1863      5.3988      5.5977|
|  6:  2.8446 -  2.6779 0.99   1278  143 0.1326 0.1948      5.2876      5.5105|
|  7:  2.6779 -  2.5444 0.99   1256  141 0.1331 0.1821      5.2218      5.4505|
|  8:  2.5444 -  2.4341 0.98   1268  140 0.1257 0.1805      5.1382      5.4065|
|  9:  2.4341 -  2.3408 0.98   1269  138 0.1245 0.1796      5.0904      5.3229|
| 10:  2.3408 -  2.2603 0.99   1235  137 0.1205 0.2010      5.0418       5.312|
| 11:  2.2603 -  2.1898 0.99   1268  147 0.1233 0.1796      5.0023      5.2723|
| 12:  2.1898 -  2.1274 0.97   1248  129 0.1184 0.1876      4.9471      5.2906|
| 13:  2.1274 -  2.0715 0.99   1236  141 0.1187 0.1796      4.8392      5.1038|
| 14:  2.0715 -  2.0211 0.80   1021  116 0.1097 0.1812       4.682       4.987|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1989 -  4.8225  1374   153  0.94   9.83   0.96     0.93       8148.54|
|  2:  4.8225 -  3.8482  1320   145  0.95   8.35   1.00     0.98       9352.21|
|  3:  3.8482 -  3.3678  1300   145  0.94  11.15   1.01     1.01      10555.93|
|  4:  3.3678 -  3.0626  1286   144  0.91  14.23   1.00     0.98      11099.58|
|  5:  3.0626 -  2.8446  1271   140  0.89  17.12   1.00     0.97       9613.55|
|  6:  2.8446 -  2.6779  1278   143  0.89  17.09   0.98     0.95       8124.92|
|  7:  2.6779 -  2.5444  1256   141  0.89  16.94   0.99     0.96       7051.15|
|  8:  2.5444 -  2.4341  1268   140  0.90  16.24   0.98     0.96       6082.88|
|  9:  2.4341 -  2.3408  1269   138  0.90  16.61   0.99     0.94       5575.28|
| 10:  2.3408 -  2.2603  1235   137  0.89  16.72   0.99     0.94       5121.80|
| 11:  2.2603 -  2.1898  1268   147  0.89  17.42   0.98     0.93       4866.20|
| 12:  2.1898 -  2.1274  1248   129  0.90  16.59   0.99     0.98       4581.47|
| 13:  2.1274 -  2.0715  1236   141  0.90  16.34   0.98     0.97       3649.75|
| 14:  2.0715 -  2.0211  1021   116  0.91  14.78   0.95     0.92       2566.53|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2566.53 max =        11099.58 mean =      6984.09|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.89|
|phase err.(test): min =        0.00 max =           89.76 mean =        14.25|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1655   ksol= 0.32   Bsol= 72.55   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,-0.33,0.45,-0.00,0.00,0.00); trace/3= -0.24                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.186799                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1655   ksol= 0.32   Bsol= 72.55   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,-0.33,0.45,-0.00,0.00,0.00); trace/3= -0.24                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.186799                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.8225 0.99   1374  153 0.1016 0.1320      5.4139      5.5589|
|  2:  4.8225 -  3.8482 0.99   1320  145 0.0848 0.1088      5.4386      5.6245|
|  3:  3.8482 -  3.3678 0.99   1300  145 0.1033 0.1505      5.4712      5.8591|
|  4:  3.3678 -  3.0626 0.99   1286  144 0.1245 0.1661      5.4892      5.6466|
|  5:  3.0626 -  2.8446 0.99   1271  140 0.1411 0.1865      5.3985      5.5972|
|  6:  2.8446 -  2.6779 0.99   1278  143 0.1325 0.1943      5.2873      5.5086|
|  7:  2.6779 -  2.5444 0.99   1256  141 0.1331 0.1825      5.2216      5.4506|
|  8:  2.5444 -  2.4341 0.98   1268  140 0.1258 0.1808      5.1382      5.4068|
|  9:  2.4341 -  2.3408 0.98   1269  138 0.1242 0.1795      5.0899       5.323|
| 10:  2.3408 -  2.2603 0.99   1235  137 0.1204 0.2012      5.0415      5.3133|
| 11:  2.2603 -  2.1898 0.99   1268  147 0.1232 0.1796       5.002      5.2718|
| 12:  2.1898 -  2.1274 0.97   1248  129 0.1183 0.1878      4.9472      5.2909|
| 13:  2.1274 -  2.0715 0.99   1236  141 0.1188 0.1795      4.8387      5.1046|
| 14:  2.0715 -  2.0211 0.80   1021  116 0.1097 0.1809      4.6807       4.985|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1989 -  4.8225  1374   153  0.93   9.88   0.96     0.93       7997.77|
|  2:  4.8225 -  3.8482  1320   145  0.95   8.37   1.00     0.98       9290.59|
|  3:  3.8482 -  3.3678  1300   145  0.94  11.13   1.01     1.01      10545.92|
|  4:  3.3678 -  3.0626  1286   144  0.91  14.23   1.00     0.98      11078.96|
|  5:  3.0626 -  2.8446  1271   140  0.89  17.10   1.00     0.98       9588.47|
|  6:  2.8446 -  2.6779  1278   143  0.89  17.08   0.98     0.96       8123.47|
|  7:  2.6779 -  2.5444  1256   141  0.89  16.92   0.99     0.97       7043.45|
|  8:  2.5444 -  2.4341  1268   140  0.90  16.23   0.99     0.96       6082.46|
|  9:  2.4341 -  2.3408  1269   138  0.90  16.61   0.99     0.94       5578.30|
| 10:  2.3408 -  2.2603  1235   137  0.89  16.72   0.99     0.94       5120.63|
| 11:  2.2603 -  2.1898  1268   147  0.89  17.42   0.98     0.93       4870.50|
| 12:  2.1898 -  2.1274  1248   129  0.90  16.60   0.99     0.98       4586.08|
| 13:  2.1274 -  2.0715  1236   141  0.90  16.32   0.99     0.98       3643.69|
| 14:  2.0715 -  2.0211  1021   116  0.91  14.74   0.96     0.93       2553.53|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     2553.53 max =        11078.96 mean =      6962.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.89|
|phase err.(test): min =        0.00 max =           89.80 mean =        14.28|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.431)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.81  16.48    None  None   None       |
|    all(noH): 2823   0      0.00    100.81  16.48    None  None   None       |
|    Sol.    : 438    0      2.22    100.19  42.05    None  None   None       |
|    Mac.    : 2385   0      0.00    100.81  11.79    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.084: 1339   |   5:    50.409 -  60.490:   88        |
|      1:    10.084 -  20.165:  896   |   6:    60.490 -  70.571:   58        |
|      2:    20.165 -  30.246:  182   |   7:    70.571 -  80.652:   23        |
|      3:    30.246 -  40.327:  124   |   8:    80.652 -  90.733:   10        |
|      4:    40.327 -  50.409:   95   |   9:    90.733 - 100.814:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 315         
Filter by distance & map next to the model:
   mapped sites are within: 0.461 - 5.939
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 310 from: 315
   mapped sites are within: 0.701 - 5.939

peak=    6.018 closest distance to " O   HOH Z 210 " =    1.169
peak=    5.818 closest distance to " O   HOH Z 111 " =    2.180
peak=    5.567 closest distance to " CB  GLN A 223 " =    1.412
peak=    5.256 closest distance to " O   HOH Z 341 " =    0.973
peak=    5.255 closest distance to " CB  SER A  63 " =    1.257
peak=    4.964 closest distance to " CB  GLN A 183 " =    1.247
peak=    4.843 closest distance to " O   HOH Z 369 " =    2.157
peak=    4.835 closest distance to " CG  PRO A  54 " =    1.348
peak=    4.695 closest distance to " CB  ARG A 190 " =    1.731
peak=    4.639 closest distance to " O   PRO A 198 " =    1.552
peak=    4.539 closest distance to " O   HOH Z 134 " =    1.714
peak=    4.465 closest distance to " O   HOH Z 298 " =    2.106
peak=    4.406 closest distance to " O   HOH Z  15 " =    2.120
peak=    4.403 closest distance to " CD  LYS A 166 " =    1.383
peak=    4.387 closest distance to " CG  PRO A  90 " =    1.196
peak=    4.338 closest distance to " CB  VAL A 202 " =    1.526
peak=    4.338 closest distance to " O   HOH Z 425 " =    1.511
peak=    4.326 closest distance to " CG  PRO A 213 " =    1.214
peak=    4.324 closest distance to " O   HOH Z 433 " =    1.499
peak=    4.323 closest distance to " CB  GLU A 277 " =    3.817
peak=    4.300 closest distance to " O   HOH Z 232 " =    2.344
peak=    4.294 closest distance to " CB  ARG A 275 " =    0.921
peak=    4.291 closest distance to " O   HOH Z 403 " =    1.689
peak=    4.286 closest distance to " O   HOH Z 234 " =    3.836
peak=    4.270 closest distance to " O   HOH Z  40 " =    1.806
peak=    4.226 closest distance to " O   HOH Z  49 " =    0.923
peak=    4.217 closest distance to " O   HOH Z  43 " =    1.856
peak=    4.215 closest distance to " CZ  PHE A 218 " =    1.135
peak=    4.204 closest distance to " CA  TYR A  30 " =    0.980
peak=    4.181 closest distance to " CB  GLU A 152 " =    1.195
peak=    4.155 closest distance to " CG1 ILE A  33 " =    1.218
peak=    4.149 closest distance to " CB  TRP A 266 " =    1.015
peak=    4.147 closest distance to " CB  GLU A 128 " =    1.082
peak=    4.133 closest distance to " O   HOH Z  67 " =    2.138
peak=    4.096 closest distance to " CB  LEU A 228 " =    1.090
peak=    4.092 closest distance to " O   HOH Z  44 " =    2.139
peak=    4.067 closest distance to " O   HOH Z 214 " =    1.277
peak=    4.047 closest distance to " O   HOH Z 423 " =    1.852
peak=    4.022 closest distance to " O   HOH Z 412 " =    3.687
peak=    4.017 closest distance to " O   HOH Z 133 " =    2.506
peak=    4.016 closest distance to " CB  PRO A  54 " =    0.896
peak=    4.016 closest distance to " O   HOH Z 189 " =    2.700
peak=    4.015 closest distance to " O   HOH Z  63 " =    1.936
peak=    4.008 closest distance to " CD  ARG A 269 " =    0.916
peak=    4.005 closest distance to " CG  ARG A  66 " =    2.550
peak=    4.002 closest distance to " O   HOH Z  21 " =    1.815
peak=    3.990 closest distance to " CA  ALA A  51 " =    0.933
peak=    3.970 closest distance to " CD2 TRP A 179 " =    1.301
peak=    3.961 closest distance to " O   HOH Z 271 " =    2.843
peak=    3.955 closest distance to " CB  TYR A 169 " =    0.843
peak=    3.954 closest distance to " CB  ARG A  79 " =    1.381
peak=    3.948 closest distance to " O   HOH Z 368 " =    2.260
peak=    3.941 closest distance to " CB  ASP A 140 " =    0.854
peak=    3.940 closest distance to " CG2 THR A 221 " =    1.049
peak=    3.940 closest distance to " O   HOH Z 362 " =    3.430
peak=    3.934 closest distance to " O   HOH Z 128 " =    2.212
peak=    3.931 closest distance to " NH2 ARG A 156 " =    1.217
peak=    3.930 closest distance to " O   HOH Z 402 " =    1.569
peak=    3.919 closest distance to " OE1 GLN A  11 " =    2.036
peak=    3.899 closest distance to " O   SER A  87 " =    2.346
peak=    3.890 closest distance to " O   HOH Z 214 " =    2.342
peak=    3.886 closest distance to " O   ALA A 165 " =    1.365
peak=    3.883 closest distance to " C   ILE A 106 " =    1.895
peak=    3.878 closest distance to " NE2 GLN A  11 " =    1.105
peak=    3.850 closest distance to " CB  SER A 141 " =    1.034
peak=    3.841 closest distance to " CA  ASP A 191 " =    0.915
peak=    3.831 closest distance to " O   HOH Z 406 " =    1.609
peak=    3.828 closest distance to " CD1 LEU A 300 " =    1.145
peak=    3.827 closest distance to " O   HOH Z 265 " =    2.135
peak=    3.826 closest distance to " O   HOH Z  98 " =    1.841
peak=    3.823 closest distance to " O   HOH Z  19 " =    1.869
peak=    3.819 closest distance to " CA  ARG A 195 " =    1.153
peak=    3.814 closest distance to " O   HOH Z  97 " =    2.031
peak=    3.789 closest distance to " O   HOH Z 176 " =    1.751
peak=    3.788 closest distance to " CG  PRO A 243 " =    1.140
peak=    3.784 closest distance to " O   HOH Z  61 " =    1.626
peak=    3.783 closest distance to " ND2 ASN A 187 " =    1.490
peak=    3.781 closest distance to " CB  TRP A 179 " =    1.533
peak=    3.767 closest distance to " O   HOH Z 303 " =    2.272
peak=    3.766 closest distance to " O   HOH Z 418 " =    1.574
peak=    3.759 closest distance to " CB  ASN A  39 " =    0.872
peak=    3.758 closest distance to " O   HOH Z  80 " =    1.905
peak=    3.741 closest distance to " ND2 ASN A 249 " =    2.003
peak=    3.741 closest distance to " O   HOH Z  30 " =    1.320
peak=    3.736 closest distance to " O   HOH Z 285 " =    2.819
peak=    3.718 closest distance to " O   HOH Z 287 " =    2.086
peak=    3.718 closest distance to " CA  ALA A 295 " =    1.123
peak=    3.715 closest distance to " CD2 LEU A 297 " =    1.011
peak=    3.714 closest distance to " CG2BVAL A  41 " =    0.896
peak=    3.703 closest distance to " CB  GLN A  88 " =    1.199
peak=    3.685 closest distance to " O   HOH Z 196 " =    1.343
peak=    3.684 closest distance to " O   HOH Z 147 " =    1.756
peak=    3.680 closest distance to " CA  ALA A  21 " =    1.314
peak=    3.667 closest distance to " O   HOH Z 280 " =    3.003
peak=    3.665 closest distance to " OD1 ASN A  69 " =    2.478
peak=    3.663 closest distance to " O   HOH Z 374 " =    2.967
peak=    3.654 closest distance to " CA  GLU A  46 " =    0.828
peak=    3.651 closest distance to " O   HOH Z 193 " =    2.029
peak=    3.649 closest distance to " OD1 ASN A 217 " =    1.604
peak=    3.632 closest distance to " O   HOH Z 180 " =    2.181
peak=    3.620 closest distance to " CG  GLU A  37 " =    0.933
peak=    3.619 closest distance to " O   HOH Z 258 " =    2.124
peak=    3.615 closest distance to " O   ASN A  74 " =    1.660
peak=    3.613 closest distance to " CB  SER A  62 " =    0.845
peak=    3.613 closest distance to " OG BSER A 164 " =    2.348
peak=    3.610 closest distance to " O   HOH Z 435 " =    2.996
peak=    3.610 closest distance to " CB  GLN A  89 " =    1.212
peak=    3.609 closest distance to " O   HOH Z 279 " =    2.324
peak=    3.609 closest distance to " O   HOH Z 353 " =    2.797
peak=    3.605 closest distance to " CE1 TYR A 186 " =    1.255
peak=    3.601 closest distance to " CB  ASN A 148 " =    1.430
peak=    3.601 closest distance to " CG  PRO A 198 " =    1.216
peak=    3.597 closest distance to " CZ3 TRP A 266 " =    1.074
peak=    3.593 closest distance to " O   HOH Z 135 " =    1.998
peak=    3.582 closest distance to " O   HOH Z 126 " =    2.185
peak=    3.580 closest distance to " CB  GLU A  46 " =    1.040
peak=    3.574 closest distance to " O  BHOH Z 338 " =    2.230
peak=    3.572 closest distance to " CA  VAL A 125 " =    1.240
peak=    3.570 closest distance to " CB  ASN A 285 " =    0.857
peak=    3.564 closest distance to " O   HOH Z 386 " =    2.394
peak=    3.555 closest distance to " O   HOH Z 422 " =    2.522
peak=    3.553 closest distance to " CD  ARG A  66 " =    2.391
peak=    3.552 closest distance to " NZ  LYS A  48 " =    1.351
peak=    3.548 closest distance to " N   CYS A 260 " =    0.803
peak=    3.546 closest distance to " O   HOH Z 203 " =    1.814
peak=    3.546 closest distance to " CB  ALA A 291 " =    1.276
peak=    3.545 closest distance to " O   HOH Z 132 " =    2.755
peak=    3.533 closest distance to " O   HOH Z 281 " =    4.814
peak=    3.533 closest distance to " NE2 GLN A  77 " =    3.447
peak=    3.529 closest distance to " CA  ARG A  36 " =    1.186
peak=    3.523 closest distance to " O   HOH Z  59 " =    2.368
peak=    3.521 closest distance to " CB  ASN A 148 " =    2.026
peak=    3.519 closest distance to " CG AARG A 275 " =    1.159
peak=    3.516 closest distance to " O   HOH Z 346 " =    1.540
peak=    3.514 closest distance to " CB  ALA A   9 " =    1.596
peak=    3.512 closest distance to " CB  SER A   3 " =    1.518
peak=    3.511 closest distance to " O   ALA A 158 " =    1.222
peak=    3.496 closest distance to " CA  ASP A 162 " =    1.128
peak=    3.496 closest distance to " CA  SER A  87 " =    1.064
peak=    3.494 closest distance to " NH1AARG A 145 " =    1.254
peak=    3.489 closest distance to " O   HOH Z 189 " =    3.106
peak=    3.489 closest distance to " CB  ASN A 187 " =    1.069
peak=    3.485 closest distance to " O   HOH Z 128 " =    2.284
peak=    3.482 closest distance to " O   HOH Z 394 " =    1.655
peak=    3.477 closest distance to " O   HOH Z  88 " =    1.824
peak=    3.477 closest distance to " CG2 VAL A 197 " =    1.139
peak=    3.475 closest distance to " CB  VAL A 265 " =    1.307
peak=    3.471 closest distance to " CA  ALA A 160 " =    0.968
peak=    3.467 closest distance to " CB  ALA A 100 " =    1.357
peak=    3.465 closest distance to " O   HOH Z 291 " =    1.494
peak=    3.459 closest distance to " CG1 VAL A 153 " =    1.107
peak=    3.458 closest distance to " CZ  PHE A  38 " =    1.298
peak=    3.455 closest distance to " CA  GLY A  98 " =    1.154
peak=    3.454 closest distance to " OG  SER A 245 " =    1.743
peak=    3.453 closest distance to " O   HOH Z 141 " =    1.653
peak=    3.450 closest distance to " O   HOH Z 403 " =    2.276
peak=    3.449 closest distance to " O   HOH Z 174 " =    2.222
peak=    3.449 closest distance to " O   HOH Z 163 " =    1.698
peak=    3.447 closest distance to " CA  GLU A 152 " =    0.948
peak=    3.445 closest distance to " O   THR A 251 " =    1.178
peak=    3.441 closest distance to " NZ  LYS A 117 " =    3.170
peak=    3.433 closest distance to " CA  MET A 105 " =    1.041
peak=    3.430 closest distance to " CA  ILE A 106 " =    0.819
peak=    3.428 closest distance to " O   HOH Z 316 " =    3.120
peak=    3.425 closest distance to " O   ASP A 124 " =    1.259
peak=    3.424 closest distance to " O   HOH Z 427 " =    3.098
peak=    3.424 closest distance to " O   HOH Z 365 " =    2.837
peak=    3.422 closest distance to " CG2 THR A  29 " =    1.353
peak=    3.413 closest distance to " O   HOH Z 294 " =    1.533
peak=    3.409 closest distance to " CZ3 TRP A  85 " =    0.915
peak=    3.407 closest distance to " CA  THR A 221 " =    0.903
peak=    3.403 closest distance to " CA  ASN A 217 " =    1.342
peak=    3.397 closest distance to " O   HOH Z 261 " =    1.939
peak=    3.397 closest distance to " CB  ALA A  43 " =    0.890
peak=    3.392 closest distance to " O   HOH Z 432 " =    1.800
peak=    3.385 closest distance to " O   HOH Z  78 " =    1.645
peak=    3.384 closest distance to " OD2 ASP A 298 " =    3.924
peak=    3.382 closest distance to " O   HOH Z 156 " =    2.641
peak=    3.381 closest distance to " O   HOH Z 199 " =    1.702
peak=    3.378 closest distance to " O   HOH Z 368 " =    4.589
peak=    3.378 closest distance to " CA  ALA A 158 " =    1.196
peak=    3.374 closest distance to " OG  SER A 276 " =    1.570
peak=    3.371 closest distance to " O   HOH Z 421 " =    1.673
peak=    3.368 closest distance to " CB  ASN A 142 " =    1.148
peak=    3.368 closest distance to " O   HOH Z  57 " =    1.261
peak=    3.364 closest distance to " O   HOH Z 383 " =    2.245
peak=    3.364 closest distance to " CA  ALA A  84 " =    1.326
peak=    3.361 closest distance to " N   ILE A  33 " =    1.041
peak=    3.359 closest distance to " CD ALYS A 290 " =    1.046
peak=    3.355 closest distance to " O   HOH Z  48 " =    1.780
peak=    3.354 closest distance to " CA  ASP A 124 " =    0.782
peak=    3.353 closest distance to " O   TYR A 116 " =    1.413
peak=    3.346 closest distance to " O   HOH Z 139 " =    4.833
peak=    3.346 closest distance to " CD  ARG A 159 " =    0.845
peak=    3.344 closest distance to " N   ASN A  39 " =    1.356
peak=    3.344 closest distance to " CB  ILE A 120 " =    1.336
peak=    3.343 closest distance to " O   HOH Z 126 " =    1.603
peak=    3.342 closest distance to " CD  ARG A 195 " =    0.916
peak=    3.339 closest distance to " O   HOH Z 248 " =    1.827
peak=    3.335 closest distance to " O   HOH Z  44 " =    1.758
peak=    3.334 closest distance to " O   HOH Z 371 " =    2.981
peak=    3.333 closest distance to " NH2BARG A 145 " =    2.091
peak=    3.331 closest distance to " CG  LEU A 167 " =    1.123
peak=    3.330 closest distance to " O   HOH Z 295 " =    1.533
peak=    3.329 closest distance to " CB  HIS A 108 " =    0.791
peak=    3.327 closest distance to " O   HOH Z 357 " =    2.142
peak=    3.326 closest distance to " CG  MET A 185 " =    1.161
peak=    3.325 closest distance to " CB  GLN A 103 " =    0.978
peak=    3.324 closest distance to " O   HOH Z 250 " =    1.479
peak=    3.323 closest distance to " CD1 LEU A  96 " =    0.730
peak=    3.321 closest distance to " OD2 ASP A 200 " =    1.261
peak=    3.316 closest distance to " CA  ALA A 100 " =    1.054
peak=    3.316 closest distance to " CA  ALA A 154 " =    0.967
peak=    3.313 closest distance to " CB  LEU A  83 " =    0.849
peak=    3.312 closest distance to " O   HOH Z 387 " =    2.861
peak=    3.311 closest distance to " CB  PHE A 283 " =    0.739
peak=    3.310 closest distance to " O   HOH Z   1 " =    2.857
peak=    3.310 closest distance to " O   HOH Z 125 " =    3.797
peak=    3.306 closest distance to " O  BHOH Z  74 " =    1.367
peak=    3.306 closest distance to " O   HOH Z 405 " =    4.332
peak=    3.303 closest distance to " CA  MET A  40 " =    1.170
peak=    3.301 closest distance to " CA  GLN A  88 " =    1.364
peak=    3.300 closest distance to " CE1 HIS A 115 " =    1.028
peak=    3.298 closest distance to " CB  MET A  40 " =    0.850
peak=    3.297 closest distance to " CA  LEU A 282 " =    1.005
peak=    3.296 closest distance to " O   HOH Z  49 " =    1.446
peak=    3.294 closest distance to " CD2 TYR A 186 " =    1.026
peak=    3.290 closest distance to " O   HOH Z 146 " =    1.451
peak=    3.287 closest distance to " O   HOH Z 359 " =    1.555
peak=    3.286 closest distance to " CB  TYR A 116 " =    1.115
peak=    3.285 closest distance to " CA  GLY A 267 " =    0.930
peak=    3.284 closest distance to " O   HOH Z 158 " =    2.961
peak=    3.281 closest distance to " O   HOH Z 325 " =    2.185
peak=    3.280 closest distance to " O   HOH Z 134 " =    2.447
peak=    3.279 closest distance to " O   HOH Z 102 " =    1.293
peak=    3.277 closest distance to " O   HOH Z  66 " =    2.189
peak=    3.274 closest distance to " CZ  PHE A 192 " =    0.999
peak=    3.268 closest distance to " O   HOH Z 380 " =    1.740
peak=    3.265 closest distance to " N   VAL A 126 " =    1.502
peak=    3.265 closest distance to " O   HOH Z  78 " =    2.005
peak=    3.264 closest distance to " CD  PRO A  54 " =    1.046
peak=    3.262 closest distance to " O   HOH Z 345 " =    1.637
peak=    3.261 closest distance to " O   HOH Z 298 " =    2.518
peak=    3.260 closest distance to " O   HOH Z 344 " =    3.166
peak=    3.259 closest distance to " CA  ALA A 233 " =    1.789
peak=    3.257 closest distance to " CB  MET A 105 " =    1.106
peak=    3.254 closest distance to " O   HOH Z 339 " =    2.291
peak=    3.248 closest distance to " O   HOH Z  47 " =    1.233
peak=    3.246 closest distance to " CA  LEU A  83 " =    1.449
peak=    3.246 closest distance to " O   HOH Z 261 " =    1.694
peak=    3.245 closest distance to " CB  ALA A  34 " =    0.911
peak=    3.245 closest distance to " N   ASN A 127 " =    1.262
peak=    3.243 closest distance to " ND1 HIS A  81 " =    1.665
peak=    3.243 closest distance to " CB  THR A  52 " =    0.884
peak=    3.243 closest distance to " CB  GLU A  37 " =    0.830
peak=    3.241 closest distance to " CA  GLY A 241 " =    0.739
peak=    3.240 closest distance to " C   TYR A 214 " =    1.505
peak=    3.239 closest distance to " OG BSER A 134 " =    2.888
peak=    3.238 closest distance to " O   HOH Z 417 " =    3.221
peak=    3.238 closest distance to " CG  GLN A  89 " =    1.422
peak=    3.234 closest distance to " CD1 TRP A 266 " =    1.153
peak=    3.230 closest distance to " CB  VAL A 257 " =    0.864
peak=    3.230 closest distance to " CA  GLY A 196 " =    0.982
peak=    3.229 closest distance to " CG2 ILE A 234 " =    1.050
peak=    3.226 closest distance to " O   HOH Z 327 " =    1.660
peak=    3.225 closest distance to " CB  ASP A 140 " =    0.701
peak=    3.221 closest distance to " O   HOH Z 368 " =    4.149
peak=    3.220 closest distance to " CZ3 TRP A  92 " =    1.480
peak=    3.220 closest distance to " CG  LYS A  76 " =    1.103
peak=    3.216 closest distance to " O   HOH Z 162 " =    1.568
peak=    3.215 closest distance to " CB  ALA A 242 " =    0.854
peak=    3.214 closest distance to " O   HOH Z 327 " =    1.749
peak=    3.214 closest distance to " O   HOH Z 109 " =    2.633
peak=    3.194 closest distance to " O   HOH Z 171 " =    3.876
peak=    3.189 closest distance to " O   HOH Z 251 " =    1.566
peak=    3.187 closest distance to " OG  SER A  28 " =    1.667
peak=    3.185 closest distance to " O   HOH Z 298 " =    4.225
peak=    3.185 closest distance to " O   HOH Z 437 " =    1.371
peak=    3.183 closest distance to " O   HOH Z 130 " =    2.191
peak=    3.181 closest distance to " ND2 ASN A 301 " =    1.636
peak=    3.173 closest distance to " OG  SER A  62 " =    3.084
peak=    3.173 closest distance to " O   HOH Z 357 " =    2.415
peak=    3.167 closest distance to " CA  MET A 188 " =    1.020
peak=    3.162 closest distance to " CG  ARG A 219 " =    1.208
peak=    3.161 closest distance to " NH2AARG A 275 " =    3.261
peak=    3.157 closest distance to " O   HOH Z 164 " =    3.545
peak=    3.154 closest distance to " O   THR A 220 " =    1.129
peak=    3.153 closest distance to " O   HOH Z 116 " =    1.733
peak=    3.151 closest distance to " O   HOH Z 409 " =    2.904
peak=    3.139 closest distance to " O   HOH Z 301 " =    1.414
peak=    3.127 closest distance to " O   HOH Z 394 " =    4.033
peak=    3.122 closest distance to " CB  PRO A  90 " =    1.257
peak=    3.111 closest distance to " O   ASP A 200 " =    1.709
peak=    3.107 closest distance to " CA  THR A 221 " =    1.533
peak=    3.104 closest distance to " O   HOH Z 245 " =    1.330
peak=    3.100 closest distance to " CB  PRO A 243 " =    1.387
peak=    3.098 closest distance to " O   HOH Z 148 " =    3.310
peak=    3.090 closest distance to " O   HOH Z 197 " =    2.099
peak=    3.087 closest distance to " N   TYR A  15 " =    0.754
peak=    3.077 closest distance to " CB  THR A 157 " =    1.161
peak=    3.074 closest distance to " CD1AILE A 234 " =    0.848
peak=    3.065 closest distance to " NH1 ARG A  14 " =    1.108
peak=    3.063 closest distance to " O   HOH Z 128 " =    1.739
peak=    3.063 closest distance to " O   HOH Z 381 " =    1.956
peak=    3.061 closest distance to " O   HOH Z 418 " =    5.939
peak=    3.056 closest distance to " O   HOH Z 301 " =    1.934
peak=    3.043 closest distance to " O   HOH Z 213 " =    1.650
peak=    3.022 closest distance to " NH2BARG A 145 " =    1.048
peak=    3.016 closest distance to " O   ASP A 124 " =    1.786
peak=    3.006 closest distance to " CB  ASN A 215 " =    1.156

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 223         
Filter by distance & map next to the model:
   mapped sites are within: 0.831 - 5.864
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 223 from: 223
   mapped sites are within: 0.831 - 5.864

peak=   -4.666 closest distance to " O   HOH Z 266 " =    5.309
peak=   -4.515 closest distance to " O   HOH Z  10 " =    1.651
peak=   -4.481 closest distance to " CB  PRO A 243 " =    2.687
peak=   -4.375 closest distance to " CG1 VAL A 250 " =    2.704
peak=   -4.368 closest distance to " CD  ARG A 156 " =    2.096
peak=   -4.327 closest distance to " CG1 VAL A 112 " =    2.571
peak=   -4.294 closest distance to " CD  GLN A 223 " =    1.386
peak=   -4.202 closest distance to " O   PRO A 198 " =    1.329
peak=   -4.146 closest distance to " OXT GLY A 302 " =    3.051
peak=   -4.130 closest distance to " CD  GLN A  58 " =    0.993
peak=   -4.074 closest distance to " ND2 ASN A  45 " =    2.009
peak=   -4.057 closest distance to " O   HOH Z 166 " =    2.581
peak=   -4.012 closest distance to " CD  ARG A  14 " =    3.371
peak=   -4.004 closest distance to " C   ASN A 285 " =    2.477
peak=   -3.999 closest distance to " CD1 PHE A  59 " =    1.997
peak=   -3.983 closest distance to " CD1 PHE A 130 " =    2.414
peak=   -3.976 closest distance to " O   HOH Z 166 " =    1.708
peak=   -3.955 closest distance to " CD1 LEU A 101 " =    2.547
peak=   -3.939 closest distance to " CG  ARG A 269 " =    2.359
peak=   -3.929 closest distance to " O   VAL A  67 " =    2.704
peak=   -3.926 closest distance to " OG  SER A  97 " =    2.234
peak=   -3.908 closest distance to " O   HOH Z 283 " =    2.220
peak=   -3.885 closest distance to " O   HOH Z  13 " =    1.825
peak=   -3.878 closest distance to " O   HOH Z 185 " =    2.512
peak=   -3.873 closest distance to " CD  GLN A  88 " =    0.841
peak=   -3.842 closest distance to " O   HOH Z 348 " =    2.315
peak=   -3.836 closest distance to " CB  ALA A 161 " =    2.678
peak=   -3.811 closest distance to " O   HOH Z 377 " =    2.009
peak=   -3.800 closest distance to " CE2 TYR A  30 " =    2.656
peak=   -3.770 closest distance to " CZ3 TRP A 179 " =    1.187
peak=   -3.757 closest distance to " O   HOH Z  19 " =    2.185
peak=   -3.754 closest distance to " O   PRO A 163 " =    2.210
peak=   -3.742 closest distance to " O   HOH Z 290 " =    1.168
peak=   -3.738 closest distance to " O   ALA A  10 " =    1.746
peak=   -3.731 closest distance to " OD1 ASP A 191 " =    1.670
peak=   -3.714 closest distance to " CB  ASP A 132 " =    2.383
peak=   -3.713 closest distance to " O   ALA A  34 " =    2.497
peak=   -3.709 closest distance to " O   HOH Z   6 " =    1.471
peak=   -3.704 closest distance to " CB  ALA A  10 " =    2.141
peak=   -3.696 closest distance to " O   HOH Z 150 " =    1.101
peak=   -3.695 closest distance to " O   VAL A  67 " =    2.957
peak=   -3.692 closest distance to " CA  GLY A 241 " =    3.127
peak=   -3.681 closest distance to " O   HOH Z 394 " =    1.515
peak=   -3.681 closest distance to " CG2 ILE A  49 " =    2.713
peak=   -3.677 closest distance to " O   SER A 210 " =    1.875
peak=   -3.673 closest distance to " O   HOH Z 377 " =    1.190
peak=   -3.673 closest distance to " OD1 ASN A 148 " =    1.490
peak=   -3.673 closest distance to " CA  ASP A 298 " =    1.091
peak=   -3.665 closest distance to " N   ALA A  43 " =    2.769
peak=   -3.635 closest distance to " O   HOH Z  52 " =    1.550
peak=   -3.634 closest distance to " O   HOH Z  38 " =    1.232
peak=   -3.623 closest distance to " O   HOH Z 149 " =    2.068
peak=   -3.618 closest distance to " CG  MET A 105 " =    0.965
peak=   -3.610 closest distance to " CG2 ILE A 263 " =    2.382
peak=   -3.580 closest distance to " CD2 TYR A 293 " =    1.877
peak=   -3.567 closest distance to " O   HOH Z 234 " =    4.421
peak=   -3.559 closest distance to " ND2 ASN A  45 " =    1.084
peak=   -3.553 closest distance to " CG  ARG A  66 " =    2.486
peak=   -3.552 closest distance to " CG  PHE A 225 " =    1.320
peak=   -3.544 closest distance to " CB  ALA A 291 " =    2.412
peak=   -3.532 closest distance to " O   HOH Z 111 " =    1.902
peak=   -3.529 closest distance to " C   SER A 206 " =    1.443
peak=   -3.525 closest distance to " NE2 GLN A 223 " =    1.127
peak=   -3.522 closest distance to " O   HOH Z 407 " =    3.770
peak=   -3.521 closest distance to " O   HOH Z 106 " =    2.018
peak=   -3.520 closest distance to " NE2 GLN A 194 " =    1.923
peak=   -3.520 closest distance to " O   SER A 271 " =    2.127
peak=   -3.510 closest distance to " CA  GLY A 133 " =    2.362
peak=   -3.506 closest distance to " O   HOH Z 407 " =    1.044
peak=   -3.501 closest distance to " ND2 ASN A 187 " =    1.714
peak=   -3.501 closest distance to " O   HOH Z 200 " =    1.312
peak=   -3.494 closest distance to " O   HOH Z 111 " =    1.474
peak=   -3.491 closest distance to " O   HOH Z 114 " =    1.323
peak=   -3.478 closest distance to " N   SER A 276 " =    1.487
peak=   -3.478 closest distance to " CD  GLN A  58 " =    0.887
peak=   -3.461 closest distance to " CE2 PHE A  61 " =    2.576
peak=   -3.460 closest distance to " NE2 GLN A 103 " =    1.772
peak=   -3.457 closest distance to " ND2 ASN A  69 " =    1.597
peak=   -3.452 closest distance to " O   HOH Z 197 " =    2.096
peak=   -3.450 closest distance to " CE BMET A  47 " =    1.961
peak=   -3.443 closest distance to " O   SER A 276 " =    1.729
peak=   -3.440 closest distance to " C   HIS A 108 " =    1.148
peak=   -3.439 closest distance to " O   HOH Z  37 " =    1.901
peak=   -3.434 closest distance to " CB  PHE A  16 " =    2.584
peak=   -3.432 closest distance to " N   ALA A 226 " =    2.055
peak=   -3.430 closest distance to " O   HOH Z 252 " =    3.879
peak=   -3.430 closest distance to " CG2 VAL A 189 " =    2.226
peak=   -3.427 closest distance to " O   HOH Z  58 " =    1.177
peak=   -3.426 closest distance to " O   HOH Z 236 " =    1.495
peak=   -3.423 closest distance to " CB  PHE A 192 " =    1.814
peak=   -3.422 closest distance to " O   HOH Z 396 " =    1.930
peak=   -3.418 closest distance to " CG  ASP A 231 " =    0.831
peak=   -3.416 closest distance to " NH2 ARG A  66 " =    1.779
peak=   -3.404 closest distance to " O   HOH Z 211 " =    1.494
peak=   -3.403 closest distance to " O   VAL A 189 " =    2.603
peak=   -3.402 closest distance to " O   PHE A 218 " =    1.498
peak=   -3.402 closest distance to " O   HOH Z 275 " =    1.843
peak=   -3.400 closest distance to " O   HOH Z 128 " =    2.537
peak=   -3.392 closest distance to " O   HOH Z 102 " =    1.634
peak=   -3.383 closest distance to " O   HOH Z 351 " =    1.514
peak=   -3.381 closest distance to " C   LEU A 143 " =    1.200
peak=   -3.380 closest distance to " CD2 PHE A  61 " =    2.007
peak=   -3.378 closest distance to " C   ALA A 158 " =    1.474
peak=   -3.377 closest distance to " O   HOH Z 371 " =    1.591
peak=   -3.377 closest distance to " O   HOH Z 166 " =    1.935
peak=   -3.375 closest distance to " CG  GLU A  53 " =    1.550
peak=   -3.375 closest distance to " OH  TYR A 247 " =    2.234
peak=   -3.373 closest distance to " O   HOH Z 154 " =    1.532
peak=   -3.371 closest distance to " CG2 THR A 221 " =    2.331
peak=   -3.370 closest distance to " O   HOH Z  15 " =    1.483
peak=   -3.368 closest distance to " NH2 ARG A 159 " =    2.435
peak=   -3.366 closest distance to " CE3 TRP A 150 " =    2.107
peak=   -3.357 closest distance to " O   HOH Z 292 " =    4.689
peak=   -3.354 closest distance to " O   HOH Z 123 " =    2.494
peak=   -3.351 closest distance to " O   HOH Z 264 " =    1.772
peak=   -3.343 closest distance to " OG BSER A 210 " =    1.409
peak=   -3.336 closest distance to " O   HOH Z 177 " =    1.909
peak=   -3.335 closest distance to " O   HOH Z  49 " =    1.326
peak=   -3.331 closest distance to " O   HOH Z 150 " =    2.044
peak=   -3.330 closest distance to " OD2 ASP A 171 " =    1.915
peak=   -3.329 closest distance to " CB  CYS A 254 " =    2.437
peak=   -3.328 closest distance to " CZ  TYR A 169 " =    1.907
peak=   -3.327 closest distance to " ND2BASN A 224 " =    1.846
peak=   -3.322 closest distance to " O   HOH Z 126 " =    1.938
peak=   -3.318 closest distance to " CE3 TRP A  70 " =    1.967
peak=   -3.317 closest distance to " OE1 GLN A  88 " =    1.146
peak=   -3.315 closest distance to " O   HOH Z 109 " =    3.501
peak=   -3.313 closest distance to " O   HOH Z 210 " =    0.896
peak=   -3.308 closest distance to " O   HOH Z 275 " =    1.597
peak=   -3.301 closest distance to " CD2 PHE A  59 " =    2.483
peak=   -3.297 closest distance to " O   HOH Z 372 " =    2.580
peak=   -3.292 closest distance to " ND2 ASN A  60 " =    1.562
peak=   -3.292 closest distance to " O   HOH Z 191 " =    5.864
peak=   -3.287 closest distance to " ND2 ASN A 249 " =    2.263
peak=   -3.286 closest distance to " O   ASN A 301 " =    1.331
peak=   -3.278 closest distance to " O   HOH Z  88 " =    2.404
peak=   -3.277 closest distance to " NH2 ARG A  79 " =    2.059
peak=   -3.271 closest distance to " CD1 ILE A 151 " =    2.433
peak=   -3.270 closest distance to " O   HOH Z  78 " =    1.869
peak=   -3.270 closest distance to " OH  TYR A 247 " =    1.844
peak=   -3.267 closest distance to " CD1 LEU A 228 " =    2.409
peak=   -3.266 closest distance to " O   HOH Z  40 " =    3.150
peak=   -3.263 closest distance to " O   HOH Z  11 " =    1.731
peak=   -3.262 closest distance to " O   HOH Z 120 " =    4.341
peak=   -3.262 closest distance to " C   GLY A  17 " =    1.264
peak=   -3.260 closest distance to " N   THR A  52 " =    1.673
peak=   -3.253 closest distance to " NH2 ARG A  79 " =    1.649
peak=   -3.251 closest distance to " CG2BVAL A  41 " =    1.688
peak=   -3.251 closest distance to " O   HOH Z 353 " =    2.298
peak=   -3.242 closest distance to " CB  ALA A 100 " =    1.935
peak=   -3.241 closest distance to " CB  ASP A 286 " =    2.230
peak=   -3.241 closest distance to " O   HOH Z  60 " =    2.291
peak=   -3.240 closest distance to " O   HOH Z 341 " =    1.170
peak=   -3.240 closest distance to " O   HOH Z  43 " =    1.484
peak=   -3.237 closest distance to " CG1 VAL A 197 " =    2.314
peak=   -3.236 closest distance to " CB  ALA A  43 " =    2.604
peak=   -3.233 closest distance to " SG  CYS A 168 " =    1.076
peak=   -3.233 closest distance to " O   ALA A   1 " =    1.953
peak=   -3.229 closest distance to " O   HOH Z 323 " =    1.380
peak=   -3.227 closest distance to " O   HOH Z 171 " =    2.171
peak=   -3.222 closest distance to " O   HOH Z 418 " =    1.315
peak=   -3.220 closest distance to " O   HOH Z 216 " =    1.943
peak=   -3.218 closest distance to " O   HOH Z 165 " =    1.930
peak=   -3.217 closest distance to " O   HOH Z 156 " =    3.633
peak=   -3.215 closest distance to " CD1 ILE A 263 " =    1.987
peak=   -3.212 closest distance to " O   HOH Z  90 " =    3.692
peak=   -3.210 closest distance to " CD  GLN A  88 " =    0.851
peak=   -3.206 closest distance to " CG  LEU A  83 " =    2.091
peak=   -3.204 closest distance to " OG  SER A  26 " =    1.330
peak=   -3.201 closest distance to " CD  ARG A 139 " =    1.616
peak=   -3.195 closest distance to " OD2 ASP A 171 " =    2.430
peak=   -3.193 closest distance to " CD  PRO A 213 " =    2.196
peak=   -3.193 closest distance to " ND1 HIS A 115 " =    2.039
peak=   -3.190 closest distance to " OE1 GLN A 223 " =    2.210
peak=   -3.186 closest distance to " CB  PRO A 163 " =    2.533
peak=   -3.185 closest distance to " O   HOH Z 298 " =    2.634
peak=   -3.182 closest distance to " CD1 TRP A 179 " =    1.060
peak=   -3.181 closest distance to " O   HOH Z 227 " =    1.446
peak=   -3.180 closest distance to " OG BSER A 134 " =    1.386
peak=   -3.179 closest distance to " CG2AVAL A  41 " =    2.862
peak=   -3.177 closest distance to " CG1 VAL A  78 " =    2.672
peak=   -3.173 closest distance to " O   HOH Z  65 " =    1.414
peak=   -3.171 closest distance to " CG  ARG A 219 " =    2.714
peak=   -3.169 closest distance to " O   ASP A  27 " =    2.153
peak=   -3.168 closest distance to " OE2 GLU A 152 " =    2.351
peak=   -3.165 closest distance to " CG  TRP A 266 " =    1.879
peak=   -3.160 closest distance to " CH2 TRP A 150 " =    1.211
peak=   -3.159 closest distance to " O   HOH Z 201 " =    2.073
peak=   -3.155 closest distance to " NE  ARG A  66 " =    4.337
peak=   -3.152 closest distance to " O   HOH Z 136 " =    2.182
peak=   -3.151 closest distance to " O   HOH Z 281 " =    2.370
peak=   -3.151 closest distance to " O   HOH Z  51 " =    1.670
peak=   -3.150 closest distance to " O   HOH Z 150 " =    1.972
peak=   -3.148 closest distance to " NE2 GLN A  58 " =    2.711
peak=   -3.147 closest distance to " CG  GLN A  11 " =    1.585
peak=   -3.145 closest distance to " OD1 ASN A 187 " =    1.593
peak=   -3.141 closest distance to " OD1 ASP A 171 " =    1.579
peak=   -3.140 closest distance to " O   GLY A  98 " =    2.228
peak=   -3.140 closest distance to " O   HOH Z 193 " =    2.317
peak=   -3.140 closest distance to " CG1 VAL A 112 " =    3.033
peak=   -3.139 closest distance to " O   HOH Z 117 " =    4.552
peak=   -3.138 closest distance to " NH2 ARG A  66 " =    4.099
peak=   -3.137 closest distance to " CZ3 TRP A 274 " =    2.437
peak=   -3.136 closest distance to " OD1 ASN A 173 " =    1.475
peak=   -3.130 closest distance to " CG  PRO A 243 " =    1.730
peak=   -3.128 closest distance to " CB  TRP A  85 " =    2.482
peak=   -3.127 closest distance to " O   HOH Z 311 " =    3.859
peak=   -3.127 closest distance to " CH2 TRP A 177 " =    2.104
peak=   -3.121 closest distance to " CB  PRO A 163 " =    2.589
peak=   -3.120 closest distance to " CG  PRO A 163 " =    2.222
peak=   -3.119 closest distance to " O   HOH Z 259 " =    2.038
peak=   -3.111 closest distance to " O   GLN A 240 " =    2.603
peak=   -3.104 closest distance to " O   HOH Z 198 " =    2.283
peak=   -3.104 closest distance to " C   ARG A  79 " =    2.655
peak=   -3.098 closest distance to " CB  ALA A 291 " =    2.262
peak=   -3.096 closest distance to " OE1 GLN A  88 " =    0.979
peak=   -3.089 closest distance to " O   HOH Z  17 " =    1.498
peak=   -3.082 closest distance to " O   HOH Z 189 " =    1.804
peak=   -3.070 closest distance to " O   HOH Z 210 " =    1.279
peak=   -3.060 closest distance to " O   SER A 164 " =    1.990
peak=   -3.053 closest distance to " OG BSER A 134 " =    1.979
peak=   -3.042 closest distance to " O   ASP A 171 " =    1.136
peak=   -3.038 closest distance to " O   GLY A 262 " =    2.343

================= 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    :  0.4352 0.4191   6.240140e+00   6.214098e+00
   1_bss:  0.4269 0.4112   6.230723e+00   6.201396e+00
   1_xyz:  0.3144 0.3401   6.012388e+00   6.068006e+00
   1_adp:  0.2863 0.3490   5.960587e+00   6.084563e+00
   1_occ:  0.2859 0.3488   5.960054e+00   6.084558e+00
   2_bss:  0.2854 0.3482   5.961392e+00   6.085312e+00
   2_xyz:  0.2241 0.2683   5.732298e+00   5.882723e+00
   2_adp:  0.2067 0.2504   5.674527e+00   5.831751e+00
   2_occ:  0.2064 0.2501   5.673988e+00   5.831857e+00
   3_bss:  0.2064 0.2493   5.672646e+00   5.829189e+00
   3_xyz:  0.1590 0.1984   5.435001e+00   5.624384e+00
   3_adp:  0.1465 0.1902   5.370929e+00   5.576186e+00
   3_occ:  0.1465 0.1902   5.370402e+00   5.575525e+00
   4_bss:  0.1468 0.1907   5.371472e+00   5.575413e+00
   4_xyz:  0.1318 0.1762   5.278617e+00   5.497140e+00
   4_adp:  0.1278 0.1743   5.255901e+00   5.483399e+00
   4_occ:  0.1277 0.1743   5.255746e+00   5.483525e+00
   5_bss:  0.1276 0.1742   5.255432e+00   5.483219e+00
   5_xyz:  0.1170 0.1685   5.197801e+00   5.446856e+00
   5_adp:  0.1163 0.1658   5.187521e+00   5.434192e+00
   5_occ:  0.1162 0.1659   5.187438e+00   5.434499e+00
   5_bss:  0.1164 0.1655   5.186799e+00   5.433171e+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:  0.289  51.778  -1.274   4.124  -0.190   0.000  -0.000  -0.000
   1_xyz:  0.289  51.778  -1.274   4.124  -0.190   0.000  -0.000  -0.000
   1_adp:  0.289  51.778  -1.274   4.124  -0.190   0.000  -0.000  -0.000
   1_occ:  0.289  51.778  -1.274   4.124  -0.190   0.000  -0.000  -0.000
   2_bss:  0.319  73.907  -1.177   2.014  -0.052   0.000  -0.000  -0.000
   2_xyz:  0.319  73.907  -1.177   2.014  -0.052   0.000  -0.000  -0.000
   2_adp:  0.319  73.907  -1.177   2.014  -0.052   0.000  -0.000  -0.000
   2_occ:  0.319  73.907  -1.177   2.014  -0.052   0.000  -0.000  -0.000
   3_bss:  0.324  78.297  -1.140   0.611  -0.097   0.000  -0.000  -0.000
   3_xyz:  0.324  78.297  -1.140   0.611  -0.097   0.000  -0.000  -0.000
   3_adp:  0.324  78.297  -1.140   0.611  -0.097   0.000  -0.000  -0.000
   3_occ:  0.324  78.297  -1.140   0.611  -0.097   0.000  -0.000  -0.000
   4_bss:  0.330  80.000  -1.315  -0.220  -0.122  -0.000  -0.000  -0.000
   4_xyz:  0.330  80.000  -1.315  -0.220  -0.122  -0.000  -0.000  -0.000
   4_adp:  0.330  80.000  -1.315  -0.220  -0.122  -0.000  -0.000  -0.000
   4_occ:  0.330  80.000  -1.315  -0.220  -0.122  -0.000  -0.000  -0.000
   5_bss:  0.324  75.173  -1.016  -0.295   0.270  -0.000   0.000   0.000
   5_xyz:  0.324  75.173  -1.016  -0.295   0.270  -0.000   0.000   0.000
   5_adp:  0.324  75.173  -1.016  -0.295   0.270  -0.000   0.000   0.000
   5_occ:  0.324  75.173  -1.016  -0.295   0.270  -0.000   0.000   0.000
   5_bss:  0.323  72.553  -0.831  -0.328   0.451  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  48.693 0.5379  0.6820    53578.617
   1_bss:  47.984 0.5453  0.7154    51186.509
   1_xyz:  36.944 0.6793  0.8672    32725.939
   1_adp:  37.952 0.6669  0.8404    34336.374
   1_occ:  37.987 0.6664  0.8395    34349.098
   2_bss:  37.879 0.6679  0.8259    34386.299
   2_xyz:  27.989 0.7788  0.9362    19116.989
   2_adp:  25.541 0.8061  0.9396    16734.792
   2_occ:  25.539 0.8061  0.9393    16729.409
   3_bss:  25.404 0.8074  0.9259    16564.689
   3_xyz:  19.476 0.8662  0.9675    10237.627
   3_adp:  18.124 0.8795  0.9621     9375.644
   3_occ:  18.104 0.8797  0.9622     9366.021
   4_bss:  18.087 0.8799  0.9513     9363.452
   4_xyz:  16.262 0.8961  0.9608     7880.349
   4_adp:  15.856 0.8999  0.9539     7666.065
   4_occ:  15.854 0.8999  0.9538     7667.819
   5_bss:  15.847 0.9000  0.9611     7662.320
   5_xyz:  15.137 0.9059  0.9655     7145.370
   5_adp:  14.830 0.9085  0.9590     6979.281
   5_occ:  14.830 0.9085  0.9590     6983.748
   5_bss:  14.831 0.9084  0.9628     6962.241
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.115   1.6575e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.115   1.6575e-01
   1_xyz:   1.471  0.012  0.087 15.231  0.006  4.118   1.1918e-01
   1_adp:   1.471  0.012  0.087 15.231  0.006  4.118   1.1918e-01
   1_occ:   1.471  0.012  0.087 15.231  0.006  4.118   1.1918e-01
   2_bss:   1.471  0.012  0.087 15.231  0.006  4.118   1.1918e-01
   2_xyz:   1.297  0.010  0.081 14.596  0.005  4.140   9.4632e-02
   2_adp:   1.297  0.010  0.081 14.596  0.005  4.140   9.4632e-02
   2_occ:   1.297  0.010  0.081 14.596  0.005  4.140   9.4632e-02
   3_bss:   1.297  0.010  0.081 14.596  0.005  4.140   9.4632e-02
   3_xyz:   1.102  0.009  0.075 14.967  0.004  4.135   7.1868e-02
   3_adp:   1.102  0.009  0.075 14.967  0.004  4.135   7.1868e-02
   3_occ:   1.102  0.009  0.075 14.967  0.004  4.135   7.1868e-02
   4_bss:   1.102  0.009  0.075 14.967  0.004  4.135   7.1868e-02
   4_xyz:   1.046  0.008  0.076 14.461  0.004  4.117   6.2985e-02
   4_adp:   1.046  0.008  0.076 14.461  0.004  4.117   6.2985e-02
   4_occ:   1.046  0.008  0.076 14.461  0.004  4.117   6.2985e-02
   5_bss:   1.046  0.008  0.076 14.461  0.004  4.117   6.2985e-02
   5_xyz:   1.179  0.012  0.087 14.818  0.004  4.125   8.4838e-02
   5_adp:   1.179  0.012  0.087 14.818  0.004  4.125   8.4838e-02
   5_occ:   1.179  0.012  0.087 14.818  0.004  4.125   8.4838e-02
   5_bss:   1.179  0.012  0.087 14.818  0.004  4.125   8.4838e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.470   2.4513e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.470   2.4513e-01
   1_xyz:   9.140  0.083  0.362 85.153  0.050  2.063   2.1801e-01
   1_adp:   9.140  0.083  0.362 85.153  0.050  2.063   2.1801e-01
   1_occ:   9.140  0.083  0.362 85.153  0.050  2.063   2.1801e-01
   2_bss:   9.140  0.083  0.362 85.153  0.050  2.063   2.1801e-01
   2_xyz:   8.214  0.063  0.252 84.628  0.044  2.380   2.3492e-01
   2_adp:   8.214  0.063  0.252 84.628  0.044  2.380   2.3492e-01
   2_occ:   8.214  0.063  0.252 84.628  0.044  2.380   2.3492e-01
   3_bss:   8.214  0.063  0.252 84.628  0.044  2.380   2.3492e-01
   3_xyz:   7.777  0.064  0.223 84.609  0.042  2.258   5.0432e-02
   3_adp:   7.777  0.064  0.223 84.609  0.042  2.258   5.0432e-02
   3_occ:   7.777  0.064  0.223 84.609  0.042  2.258   5.0432e-02
   4_bss:   7.777  0.064  0.223 84.609  0.042  2.258   5.0432e-02
   4_xyz:   8.010  0.043  0.233 81.502  0.046  2.340   4.1350e-02
   4_adp:   8.010  0.043  0.233 81.502  0.046  2.340   4.1350e-02
   4_occ:   8.010  0.043  0.233 81.502  0.046  2.340   4.1350e-02
   5_bss:   8.010  0.043  0.233 81.502  0.046  2.340   4.1350e-02
   5_xyz:   8.641  0.053  0.306 82.561  0.042  2.293   6.1087e-02
   5_adp:   8.641  0.053  0.306 82.561  0.042  2.293   6.1087e-02
   5_occ:   8.641  0.053  0.306 82.561  0.042  2.293   6.1087e-02
   5_bss:   8.641  0.053  0.306 82.561  0.042  2.293   6.1087e-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:  99.77   0.00  17.96  81.85   0.00  14.17  99.77   0.00  38.60
   1_occ:  99.77   0.00  17.96  81.85   0.00  14.17  99.77   0.00  38.60
   2_bss:  99.77   0.00  17.96  81.85   0.00  14.17  99.77   0.00  38.60
   2_xyz:  99.77   0.00  17.96  81.85   0.00  14.17  99.77   0.00  38.60
   2_adp: 100.70   0.00  17.45  85.02   0.00  13.24 100.70   2.04  40.36
   2_occ: 100.70   0.00  17.45  85.02   0.00  13.24 100.70   2.04  40.36
   3_bss: 100.70   0.00  17.45  85.02   0.00  13.24 100.70   2.04  40.36
   3_xyz: 100.70   0.00  17.45  85.02   0.00  13.24 100.70   2.04  40.36
   3_adp:  99.13   0.00  17.01  90.62   0.00  12.43  99.13   3.76  41.97
   3_occ:  99.13   0.00  17.01  90.62   0.00  12.43  99.13   3.76  41.97
   4_bss:  99.13   0.00  17.01  90.62   0.00  12.43  99.13   3.76  41.97
   4_xyz:  99.13   0.00  17.01  90.62   0.00  12.43  99.13   3.76  41.97
   4_adp: 101.63   0.00  16.92 101.63   0.00  12.10 101.19   1.72  43.17
   4_occ: 101.63   0.00  16.92 101.63   0.00  12.10 101.19   1.72  43.17
   5_bss: 101.63   0.00  16.92 101.63   0.00  12.10 101.19   1.72  43.17
   5_xyz: 101.63   0.00  16.92 101.63   0.00  12.10 101.19   1.72  43.17
   5_adp: 100.81   0.00  16.48 100.81   0.00  11.78 100.19   2.22  42.05
   5_occ: 100.81   0.00  16.48 100.81   0.00  11.78 100.19   2.22  42.05
   5_bss: 100.81   0.00  16.48 100.81   0.00  11.79 100.19   2.22  42.05
------------------------------------------------------------------------
 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:    1.742    0.026    0.355
   1_adp:    1.742    0.026    0.355
   1_occ:    1.742    0.026    0.355
   2_bss:    1.742    0.026    0.355
   2_xyz:    1.556    0.027    0.499
   2_adp:    1.556    0.027    0.499
   2_occ:    1.556    0.027    0.499
   3_bss:    1.556    0.027    0.499
   3_xyz:    1.347    0.028    0.636
   3_adp:    1.347    0.028    0.636
   3_occ:    1.347    0.028    0.636
   4_bss:    1.347    0.028    0.636
   4_xyz:    1.337    0.044    0.675
   4_adp:    1.337    0.044    0.675
   4_occ:    1.337    0.044    0.675
   5_bss:    1.337    0.044    0.675
   5_xyz:    1.317    0.088    0.703
   5_adp:    1.317    0.088    0.703
   5_occ:    1.317    0.088    0.703
   5_bss:    1.317    0.088    0.703
------------------------------------------------------------------------

CPU time actual refinement: 279.72


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1074/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_1074/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1074/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1074/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1074/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 279.59 
  Macro-tasks:
    bulk solvent and scale       = 46.15  
    individual site refinement   = 106.67 
    weights calculation          = 24.28  
    collect and process          = 5.41   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 182.59 
  Micro-tasks:
    mask                            = 1.94   
    f_calc                          = 83.85  
    alpha_beta                      = 6.96   
    target                          = 0.97   
    gradients_wrt_atomic_parameters = 90.57  
    fmodel                         = 7.15   
    r_factors                      = 0.27   
    phase_errors                   = 8.92   
    foms                           = 0.24   
    TOTAL for micro-tasks          = 200.87 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 3.996 micro seconds
Total CPU time: 4.85 minutes
from_scatterers_fft:    625 calls, 83.53 s
gradients_fft:          570 calls, 79.62 s

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

# Date 2008-01-16 Time 06:21:18 PST -0800 (1200493278.29 s)
Start R-work = 0.4352, R-free = 0.4191 (no bulk solvent and anisotropic scale)
Final R-work = 0.1326, R-free = 0.1797 (no bulk solvent and anisotropic scale)

Start R-work = 0.4269, R-free = 0.4112
Final R-work = 0.1164, R-free = 0.1655