# Date 2008-01-16 Time 04:30:06 PST -0800 (1200486606.35 s)
#phil __OFF__

Command line arguments: "../339.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 7784
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 339

-------------------------------------------------------------------------------
  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: (69.1963, 47.6339, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.35, per 1000 atoms: 1.19


================================== 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: (69.1963, 47.6339, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9376 1.97088
Completeness in resolution range: 0.926106
Completeness with d_max=infinity: 0.923313

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9376
                             d_min =   1.9709

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: (69.1963, 47.6339, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9376 1.97088
Completeness in resolution range: 0.926106
Completeness with d_max=infinity: 0.923313

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9380 -  4.2173 [2218/2246]  1995   223  10.1%
  bin  2:  4.2173 -  3.3599 [2130/2153]  1913   217  10.2%
  bin  3:  3.3599 -  2.9389 [2102/2127]  1898   204   9.7%
  bin  4:  2.9389 -  2.6718 [2089/2105]  1878   211  10.1%
  bin  5:  2.6718 -  2.4813 [2063/2101]  1851   212  10.3%
  bin  6:  2.4813 -  2.3355 [2057/2090]  1852   205  10.0%
  bin  7:  2.3355 -  2.2190 [2054/2091]  1858   196   9.5%
  bin  8:  2.2190 -  2.1227 [2051/2093]  1840   211  10.3%
  bin  9:  2.1227 -  2.0412 [2031/2070]  1836   195   9.6%
  bin 10:  2.0412 -  1.9709 [ 794/2076]   709    85  10.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_339/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:
        1.58 -     2.24: 19
        2.24 -     2.91: 1409
        2.91 -     3.57: 4421
        3.57 -     4.24: 9113
        4.24 -     4.90: 13106
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.578 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.593 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.647 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.723 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.732 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28063 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_339/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_339/model_refine_001.geo

CPU time processing inputs: 8.97


============================ 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 = 69.19625 47.63395 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4477   r_free= 0.4444   ksol= 0.00   Bsol= 0.00   scale= 0.900    |
|                                                                             |
| 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:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.250973                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9380 -  4.7038 0.99   1442  159 0.3418 0.3573      6.4984      6.4973|
|  2:  4.7038 -  3.7530 0.99   1395  155 0.3757 0.3959      6.7388      6.7908|
|  3:  3.7530 -  3.2843 0.99   1359  152 0.4234 0.3941      6.6277      6.5794|
|  4:  3.2843 -  2.9867 0.99   1352  144 0.4353 0.4312      6.4522      6.4545|
|  5:  2.9867 -  2.7741 0.98   1334  153 0.4737 0.4364      6.3261      6.3376|
|  6:  2.7741 -  2.6114 0.99   1340  149 0.4782 0.5199      6.2462        6.17|
|  7:  2.6114 -  2.4813 0.99   1313  155 0.4774 0.4413      6.1975      6.1144|
|  8:  2.4813 -  2.3737 0.99   1341  138 0.5049 0.4766      6.1561      6.1219|
|  9:  2.3737 -  2.2826 0.99   1330  147 0.5065 0.4713      6.1089      6.1548|
| 10:  2.2826 -  2.2041 0.98   1320  144 0.5089 0.5114      6.0776      6.0699|
| 11:  2.2041 -  2.1354 0.98   1283  156 0.5065 0.4947      6.0128      5.9948|
| 12:  2.1354 -  2.0745 1.00   1339  144 0.5158 0.5132      5.9296      5.9536|
| 13:  2.0745 -  2.0201 0.87   1189  125 0.5162 0.5719      5.8683       5.854|
| 14:  2.0201 -  1.9709 0.23    293   38 0.4752 0.4475      5.8795      5.7014|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9380 -  4.7038  1442   159  0.73  31.40   0.84     0.75      60328.87|
|  2:  4.7038 -  3.7530  1395   155  0.74  32.13   0.93     0.82      89436.43|
|  3:  3.7530 -  3.2843  1359   152  0.65  39.66   0.90     0.82      93697.20|
|  4:  3.2843 -  2.9867  1352   144  0.57  46.36   0.91     0.75      82746.31|
|  5:  2.9867 -  2.7741  1334   153  0.51  51.50   0.89     0.68      66227.81|
|  6:  2.7741 -  2.6114  1340   149  0.47  54.07   0.91     0.64      59251.84|
|  7:  2.6114 -  2.4813  1313   155  0.48  53.90   0.93     0.64      53413.37|
|  8:  2.4813 -  2.3737  1341   138  0.47  54.39   0.91     0.66      47572.77|
|  9:  2.3737 -  2.2826  1330   147  0.48  53.85   0.91     0.69      43897.75|
| 10:  2.2826 -  2.2041  1320   144  0.47  54.92   0.92     0.66      40111.75|
| 11:  2.2041 -  2.1354  1283   156  0.39  61.07   0.93     0.58      43513.08|
| 12:  2.1354 -  2.0745  1339   144  0.30  67.43   0.93     0.49      43393.83|
| 13:  2.0745 -  2.0201  1189   125  0.28  69.24   0.90     0.45      39701.41|
| 14:  2.0201 -  1.9709   293    38  0.39  60.79   1.01     0.50      28319.10|
|alpha:            min =        0.45 max =            0.82 mean =         0.66|
|beta:             min =    28319.10 max =        93697.20 mean =     58616.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.50|
|phase err.(work): min =        0.00 max =           89.99 mean =        51.30|
|phase err.(test): min =        0.00 max =           89.91 mean =        51.58|
|-----------------------------------------------------------------------------|

============================== 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 = 11.136071             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.913   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.621037              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.810   (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 |  1.578 -  1.910:        8 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.910 -  2.242:       11 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.242 -  2.575:       33 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.575 -  2.907:     1376 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.907 -  3.239:     1893 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.239 -  3.571:     2528 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.571 -  3.903:     4666 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.903 -  4.236:     4447 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.236 -  4.568:     5962 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.568 -  4.900:     7144 |
|-----------------------------------------------------------------------------|
|-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 |        0.180 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.578 |       0.424 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.010)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4477   r_free= 0.4444   ksol= 0.00   Bsol= 0.00   scale= 0.900    |
|                                                                             |
| 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:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.250973                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4397   r_free= 0.4328   ksol= 0.31   Bsol= 40.65   scale= 0.948   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,1.78,3.22,0.00,0.00,0.00); trace/3= 1.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.243726                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.442013              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.534   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.908076              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.489   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4397      final r-factor (work) = 0.2804          |
| start r-factor (free) = 0.4328      final r-factor (free) = 0.3076          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.6487 = 9.44 * 0.50 * 6.2420 + 1.00 * 0.1804                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.6920 = 9.44 * 0.50 * 6.0520 + 1.00 * 0.1203                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2804      final r-factor (work) = 0.2527          |
| start r-factor (free) = 0.3076      final r-factor (free) = 0.3183          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5019 = 0.91 * 1.00 * 6.0520 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3156 = 0.91 * 1.00 * 5.8370 + 1.00 * 0.0152                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.010)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.28   18.25    None  None   None       |
|    all(noH): 2823   0      0.00    89.28   18.25    None  None   None       |
|    Sol.    : 438    0      2.39    89.28   41.08    None  None   None       |
|    Mac.    : 2385   0      0.00    78.79   14.06    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.928:  828   |   5:    44.641 -  53.569:  110        |
|      1:     8.928 -  17.856: 1029   |   6:    53.569 -  62.497:   64        |
|      2:    17.856 -  26.785:  395   |   7:    62.497 -  71.425:   37        |
|      3:    26.785 -  35.713:  204   |   8:    71.425 -  80.353:   19        |
|      4:    35.713 -  44.641:  131   |   9:    80.353 -  89.282:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2527 r_free = 0.3183             target_work(ml) = 5.850         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2525 r_free = 0.3184             target_work(ml) = 5.850         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2525   r_free= 0.3184   ksol= 0.31   Bsol= 40.65   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,1.78,3.22,0.00,0.00,0.00); trace/3= 1.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.849839                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2495   r_free= 0.3162   ksol= 0.33   Bsol= 68.99   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.47,-0.17,0.68,-0.00,0.00,0.00); trace/3= -0.65                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.845119                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.988442              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.171   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.336092              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.397  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2495      final r-factor (work) = 0.1872          |
| start r-factor (free) = 0.3162      final r-factor (free) = 0.2393          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7693 = 3.99 * 0.50 * 5.8414 + 1.00 * 0.1203                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.5154 = 3.99 * 0.50 * 5.7432 + 1.00 * 0.0622                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1872      final r-factor (work) = 0.1760          |
| start r-factor (free) = 0.2393      final r-factor (free) = 0.2228          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9454 = 0.34 * 1.00 * 5.7432 + 1.00 * 0.0151                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8796 = 0.34 * 1.00 * 5.5614 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.010)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.23   17.72    None  None   None       |
|    all(noH): 2823   0      0.00    87.23   17.72    None  None   None       |
|    Sol.    : 438    0      5.38    87.23   41.26    None  None   None       |
|    Mac.    : 2385   0      0.00    79.75   13.40    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.723:  797   |   5:    43.616 -  52.339:  111        |
|      1:     8.723 -  17.446: 1146   |   6:    52.339 -  61.062:   75        |
|      2:    17.446 -  26.170:  346   |   7:    61.062 -  69.786:   32        |
|      3:    26.170 -  34.893:  158   |   8:    69.786 -  78.509:   22        |
|      4:    34.893 -  43.616:  130   |   9:    78.509 -  87.232:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1760 r_free = 0.2228             target_work(ml) = 5.532         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1759 r_free = 0.2226             target_work(ml) = 5.531         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1759   r_free= 0.2226   ksol= 0.33   Bsol= 68.99   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.47,-0.17,0.68,-0.00,0.00,0.00); trace/3= -0.65                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.531037                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1760   r_free= 0.2220   ksol= 0.33   Bsol= 67.75   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.73,-0.90,0.08,-0.00,0.00,0.00); trace/3= -1.18                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.530220                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.760644              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.993  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 9.779943              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.126  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1760      final r-factor (work) = 0.1351          |
| start r-factor (free) = 0.2220      final r-factor (free) = 0.1803          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.3028 = 4.76 * 0.50 * 5.5625 + 1.00 * 0.0623                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.9851 = 4.76 * 0.50 * 5.4229 + 1.00 * 0.0767                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1351      final r-factor (work) = 0.1251          |
| start r-factor (free) = 0.1803      final r-factor (free) = 0.1759          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 53.0466 = 9.78 * 1.00 * 5.4229 + 1.00 * 0.0105                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 51.5383 = 9.78 * 1.00 * 5.2685 + 1.00 * 0.0131                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.010)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.15   17.96    None  None   None       |
|    all(noH): 2823   0      0.00    95.15   17.96    None  None   None       |
|    Sol.    : 438    0      5.25    91.02   44.57    None  None   None       |
|    Mac.    : 2385   0      0.00    95.15   13.07    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 -   9.515:  978   |   5:    47.576 -  57.091:   96        |
|      1:     9.515 -  19.030: 1144   |   6:    57.091 -  66.606:   73        |
|      2:    19.030 -  28.546:  228   |   7:    66.606 -  76.122:   51        |
|      3:    28.546 -  38.061:  128   |   8:    76.122 -  85.637:   16        |
|      4:    38.061 -  47.576:   99   |   9:    85.637 -  95.152:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1251 r_free = 0.1759             target_work(ml) = 5.253         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1250 r_free = 0.1759             target_work(ml) = 5.253         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1250   r_free= 0.1759   ksol= 0.33   Bsol= 67.75   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.73,-0.90,0.08,-0.00,0.00,0.00); trace/3= -1.18                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.252648                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1252   r_free= 0.1759   ksol= 0.33   Bsol= 67.75   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-1.29,-0.17,-0.00,-0.00,-0.00); trace/3= -1.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.253542                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.675007              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.430  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.372469              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 110.044  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1252      final r-factor (work) = 0.1168          |
| start r-factor (free) = 0.1759      final r-factor (free) = 0.1677          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7596 = 3.68 * 0.50 * 5.2696 + 1.00 * 0.0767                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6776 = 3.68 * 0.50 * 5.2251 + 1.00 * 0.0765                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1168      final r-factor (work) = 0.1152          |
| start r-factor (free) = 0.1677      final r-factor (free) = 0.1640          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9590 = 0.37 * 1.00 * 5.2251 + 1.00 * 0.0128                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9458 = 0.37 * 1.00 * 5.1958 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.010)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.37   17.20    None  None   None       |
|    all(noH): 2823   0      0.00    95.37   17.20    None  None   None       |
|    Sol.    : 438    0      0.00    91.52   41.92    None  None   None       |
|    Mac.    : 2385   0      0.64    95.37   12.66    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 -   9.537: 1019   |   5:    47.684 -  57.220:   91        |
|      1:     9.537 -  19.073: 1137   |   6:    57.220 -  66.757:   58        |
|      2:    19.073 -  28.610:  227   |   7:    66.757 -  76.294:   39        |
|      3:    28.610 -  38.147:  127   |   8:    76.294 -  85.830:   17        |
|      4:    38.147 -  47.684:  104   |   9:    85.830 -  95.367:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1152 r_free = 0.1640             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1151 r_free = 0.1640             target_work(ml) = 5.184         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1151   r_free= 0.1640   ksol= 0.33   Bsol= 67.75   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-1.29,-0.17,-0.00,-0.00,-0.00); trace/3= -1.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.184116                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1640   ksol= 0.32   Bsol= 60.64   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-1.29,-0.10,-0.00,-0.00,-0.00); trace/3= -1.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.184254                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.460497              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 147.418  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.384144              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.664  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1150      final r-factor (work) = 0.1144          |
| start r-factor (free) = 0.1640      final r-factor (free) = 0.1623          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4685 = 2.46 * 0.50 * 5.1957 + 1.00 * 0.0765                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4433 = 2.46 * 0.50 * 5.1836 + 1.00 * 0.0662                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1144      final r-factor (work) = 0.1140          |
| start r-factor (free) = 0.1623      final r-factor (free) = 0.1629          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1853 = 1.38 * 1.00 * 5.1836 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1736 = 1.38 * 1.00 * 5.1745 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.010)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.44   17.02    None  None   None       |
|    all(noH): 2823   0      0.00    98.44   17.02    None  None   None       |
|    Sol.    : 438    0      0.00    97.02   41.78    None  None   None       |
|    Mac.    : 2385   0      0.17    98.44   12.48    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 -   9.844: 1135   |   5:    49.220 -  59.065:   93        |
|      1:     9.844 -  19.688: 1043   |   6:    59.065 -  68.909:   51        |
|      2:    19.688 -  29.532:  211   |   7:    68.909 -  78.753:   31        |
|      3:    29.532 -  39.376:  135   |   8:    78.753 -  88.597:   11        |
|      4:    39.376 -  49.220:  108   |   9:    88.597 -  98.441:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1140 r_free = 0.1629             target_work(ml) = 5.178         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1138 r_free = 0.1628             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1628   ksol= 0.32   Bsol= 60.64   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-1.29,-0.10,-0.00,-0.00,-0.00); trace/3= -1.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.177499                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9380 -  4.7038 0.99   1442  159 0.0972 0.1298      5.3855      5.5606|
|  2:  4.7038 -  3.7530 0.99   1395  155 0.0821 0.1068        5.41      5.6173|
|  3:  3.7530 -  3.2843 0.99   1359  152 0.1057 0.1496      5.4624       5.823|
|  4:  3.2843 -  2.9867 0.99   1352  144 0.1286 0.1670      5.4701      5.6439|
|  5:  2.9867 -  2.7741 0.98   1334  153 0.1349 0.1720      5.3514      5.5445|
|  6:  2.7741 -  2.6114 0.99   1340  149 0.1288 0.2166      5.2529      5.5363|
|  7:  2.6114 -  2.4813 0.99   1313  155 0.1300 0.1704       5.203      5.3915|
|  8:  2.4813 -  2.3737 0.99   1341  138 0.1202 0.1780      5.1268      5.3153|
|  9:  2.3737 -  2.2826 0.99   1330  147 0.1179 0.1865      5.0399      5.3549|
| 10:  2.2826 -  2.2041 0.98   1320  144 0.1169 0.1798      4.9875      5.1983|
| 11:  2.2041 -  2.1354 0.98   1283  156 0.1178 0.1975      4.9341      5.3226|
| 12:  2.1354 -  2.0745 1.00   1339  144 0.1160 0.1602      4.8859      5.0959|
| 13:  2.0745 -  2.0201 0.87   1189  125 0.1131 0.1914      4.8046      5.0845|
| 14:  2.0201 -  1.9709 0.23    293   38 0.1011 0.1536      4.7488      4.9011|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9380 -  4.7038  1442   159  0.94   9.42   0.97     0.94       7559.27|
|  2:  4.7038 -  3.7530  1395   155  0.95   8.01   1.01     0.99       8937.83|
|  3:  3.7530 -  3.2843  1359   152  0.94  11.25   1.02     1.02      10204.98|
|  4:  3.2843 -  2.9867  1352   144  0.91  14.68   1.00     0.99      10799.87|
|  5:  2.9867 -  2.7741  1334   153  0.90  16.57   0.99     0.97       8994.46|
|  6:  2.7741 -  2.6114  1340   149  0.89  17.62   0.98     0.95       7874.16|
|  7:  2.6114 -  2.4813  1313   155  0.90  16.49   0.98     0.95       6814.61|
|  8:  2.4813 -  2.3737  1341   138  0.90  16.79   0.99     0.95       6255.18|
|  9:  2.3737 -  2.2826  1330   147  0.90  16.71   0.98     0.94       5198.92|
| 10:  2.2826 -  2.2041  1320   144  0.90  16.57   0.98     0.94       4776.55|
| 11:  2.2041 -  2.1354  1283   156  0.90  16.25   0.98     0.94       4341.86|
| 12:  2.1354 -  2.0745  1339   144  0.90  16.71   0.99     0.98       4138.62|
| 13:  2.0745 -  2.0201  1189   125  0.89  17.15   0.97     0.95       3581.37|
| 14:  2.0201 -  1.9709   293    38  0.91  15.18   0.96     0.91       3068.10|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     3068.10 max =        10799.87 mean =      6875.41|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.86|
|phase err.(test): min =        0.00 max =           89.52 mean =        14.33|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1626   ksol= 0.32   Bsol= 60.64   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-1.14,0.08,-0.00,0.00,0.00); trace/3= -1.13                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.177554                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1626   ksol= 0.32   Bsol= 60.64   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-1.14,0.08,-0.00,0.00,0.00); trace/3= -1.13                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.177554                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9380 -  4.7038 0.99   1442  159 0.0971 0.1299      5.3848      5.5618|
|  2:  4.7038 -  3.7530 0.99   1395  155 0.0822 0.1068       5.411      5.6178|
|  3:  3.7530 -  3.2843 0.99   1359  152 0.1057 0.1496      5.4628      5.8233|
|  4:  3.2843 -  2.9867 0.99   1352  144 0.1285 0.1670        5.47      5.6438|
|  5:  2.9867 -  2.7741 0.98   1334  153 0.1348 0.1719      5.3511      5.5439|
|  6:  2.7741 -  2.6114 0.99   1340  149 0.1287 0.2166      5.2526      5.5362|
|  7:  2.6114 -  2.4813 0.99   1313  155 0.1300 0.1705       5.203      5.3915|
|  8:  2.4813 -  2.3737 0.99   1341  138 0.1202 0.1780       5.127      5.3153|
|  9:  2.3737 -  2.2826 0.99   1330  147 0.1179 0.1865      5.0402      5.3553|
| 10:  2.2826 -  2.2041 0.98   1320  144 0.1169 0.1798      4.9876      5.1984|
| 11:  2.2041 -  2.1354 0.98   1283  156 0.1178 0.1974      4.9342      5.3228|
| 12:  2.1354 -  2.0745 1.00   1339  144 0.1161 0.1602      4.8858      5.0958|
| 13:  2.0745 -  2.0201 0.87   1189  125 0.1131 0.1913      4.8045      5.0834|
| 14:  2.0201 -  1.9709 0.23    293   38 0.1010 0.1536      4.7494      4.9016|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9380 -  4.7038  1442   159  0.94   9.42   0.97     0.94       7550.76|
|  2:  4.7038 -  3.7530  1395   155  0.95   8.02   1.01     0.99       8947.81|
|  3:  3.7530 -  3.2843  1359   152  0.94  11.27   1.02     1.02      10222.10|
|  4:  3.2843 -  2.9867  1352   144  0.91  14.69   1.01     1.00      10800.62|
|  5:  2.9867 -  2.7741  1334   153  0.90  16.57   1.00     0.98       8989.74|
|  6:  2.7741 -  2.6114  1340   149  0.89  17.62   0.98     0.95       7868.88|
|  7:  2.6114 -  2.4813  1313   155  0.90  16.49   0.99     0.96       6813.13|
|  8:  2.4813 -  2.3737  1341   138  0.90  16.80   1.00     0.96       6256.24|
|  9:  2.3737 -  2.2826  1330   147  0.90  16.72   0.99     0.94       5200.73|
| 10:  2.2826 -  2.2041  1320   144  0.90  16.57   0.99     0.95       4776.46|
| 11:  2.2041 -  2.1354  1283   156  0.90  16.25   0.99     0.95       4340.67|
| 12:  2.1354 -  2.0745  1339   144  0.90  16.71   1.00     0.99       4137.45|
| 13:  2.0745 -  2.0201  1189   125  0.89  17.15   0.98     0.96       3579.28|
| 14:  2.0201 -  1.9709   293    38  0.91  15.18   0.97     0.92       3066.71|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     3066.71 max =        10800.62 mean =      6875.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.86|
|phase err.(test): min =        0.00 max =           89.53 mean =        14.33|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.010)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.44   17.03    None  None   None       |
|    all(noH): 2823   0      0.00    98.44   17.03    None  None   None       |
|    Sol.    : 438    0      0.00    97.02   41.78    None  None   None       |
|    Mac.    : 2385   0      0.17    98.44   12.48    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.847: 1135   |   5:    49.223 -  59.068:   93        |
|      1:     9.847 -  19.691: 1043   |   6:    59.068 -  68.912:   51        |
|      2:    19.691 -  29.535:  211   |   7:    68.912 -  78.756:   31        |
|      3:    29.535 -  39.379:  135   |   8:    78.756 -  88.600:   11        |
|      4:    39.379 -  49.223:  108   |   9:    88.600 -  98.444:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 305         
Filter by distance & map next to the model:
   mapped sites are within: 0.658 - 4.423
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 301 from: 305
   mapped sites are within: 0.708 - 4.423

peak=    5.592 closest distance to " O   HOH Z 210 " =    1.083
peak=    5.533 closest distance to " O   HOH Z 113 " =    2.041
peak=    5.300 closest distance to " CG  PRO A  54 " =    1.330
peak=    5.075 closest distance to " CB  GLN A 223 " =    1.430
peak=    4.815 closest distance to " O   HOH Z  49 " =    1.272
peak=    4.794 closest distance to " CB  ARG A 275 " =    0.953
peak=    4.791 closest distance to " O   HOH Z 403 " =    1.846
peak=    4.711 closest distance to " CB  ARG A 190 " =    1.732
peak=    4.701 closest distance to " CA  ARG A  36 " =    1.074
peak=    4.610 closest distance to " CA  TYR A  30 " =    0.897
peak=    4.548 closest distance to " CB  SER A  63 " =    1.087
peak=    4.539 closest distance to " CB  GLN A 183 " =    1.286
peak=    4.519 closest distance to " O   HOH Z 369 " =    2.383
peak=    4.481 closest distance to " CG  PRO A  90 " =    1.177
peak=    4.428 closest distance to " CG  PRO A 213 " =    1.222
peak=    4.421 closest distance to " CB  GLU A 152 " =    1.160
peak=    4.390 closest distance to " NE2 GLN A  11 " =    1.078
peak=    4.386 closest distance to " CZ  PHE A 218 " =    1.137
peak=    4.376 closest distance to " CG  PRO A 198 " =    1.201
peak=    4.376 closest distance to " CG  PRO A 280 " =    0.838
peak=    4.348 closest distance to " O   HOH Z 232 " =    2.270
peak=    4.326 closest distance to " O   HOH Z 234 " =    3.814
peak=    4.316 closest distance to " CD2 TRP A 179 " =    1.333
peak=    4.314 closest distance to " CB  ARG A  79 " =    1.465
peak=    4.301 closest distance to " CB  PRO A  54 " =    0.959
peak=    4.272 closest distance to " O   PRO A 198 " =    1.540
peak=    4.213 closest distance to " O   HOH Z 189 " =    2.792
peak=    4.207 closest distance to " O   HOH Z  63 " =    1.877
peak=    4.193 closest distance to " O   HOH Z  43 " =    2.120
peak=    4.169 closest distance to " CZ  PHE A  38 " =    1.248
peak=    4.138 closest distance to " O   SER A  87 " =    2.240
peak=    4.137 closest distance to " O   HOH Z 298 " =    1.790
peak=    4.135 closest distance to " CG  PRO A 243 " =    1.102
peak=    4.134 closest distance to " O   HOH Z 142 " =    1.534
peak=    4.105 closest distance to " CD  ARG A 269 " =    1.023
peak=    4.078 closest distance to " NZ  LYS A 117 " =    3.048
peak=    4.077 closest distance to " O   HOH Z  97 " =    2.019
peak=    4.066 closest distance to " CG  ARG A  66 " =    2.572
peak=    4.050 closest distance to " CZ3 TRP A 266 " =    1.094
peak=    4.026 closest distance to " CB  GLU A 277 " =    3.715
peak=    4.024 closest distance to " O   HOH Z 346 " =    1.652
peak=    3.952 closest distance to " O   HOH Z 126 " =    1.861
peak=    3.948 closest distance to " ND2 ASN A 187 " =    1.531
peak=    3.941 closest distance to " CA  ALA A  51 " =    1.000
peak=    3.923 closest distance to " CG  GLN A  58 " =    0.906
peak=    3.911 closest distance to " O   HOH Z 287 " =    1.803
peak=    3.894 closest distance to " O   HOH Z 423 " =    1.947
peak=    3.893 closest distance to " O   HOH Z 389 " =    1.878
peak=    3.878 closest distance to " NH1AARG A 145 " =    1.388
peak=    3.871 closest distance to " CB  THR A  31 " =    1.553
peak=    3.860 closest distance to " O   HOH Z 248 " =    1.373
peak=    3.859 closest distance to " O   HOH Z 412 " =    3.871
peak=    3.846 closest distance to " O   HOH Z 303 " =    2.229
peak=    3.827 closest distance to " O   HOH Z  65 " =    0.908
peak=    3.826 closest distance to " ND2 ASN A 249 " =    0.901
peak=    3.825 closest distance to " CA  ARG A 195 " =    1.246
peak=    3.815 closest distance to " O   HOH Z  44 " =    2.159
peak=    3.812 closest distance to " O   HOH Z 361 " =    3.409
peak=    3.812 closest distance to " O   HOH Z 427 " =    2.965
peak=    3.808 closest distance to " N   ASN A  39 " =    1.279
peak=    3.803 closest distance to " O   HOH Z 359 " =    1.725
peak=    3.795 closest distance to " O   HOH Z 280 " =    2.994
peak=    3.793 closest distance to " O   HOH Z  40 " =    1.926
peak=    3.789 closest distance to " O   HOH Z 227 " =    1.582
peak=    3.788 closest distance to " CD  ARG A 159 " =    0.812
peak=    3.772 closest distance to " O   HOH Z 368 " =    2.157
peak=    3.763 closest distance to " O   HOH Z 132 " =    2.551
peak=    3.761 closest distance to " CB  ASN A 148 " =    1.417
peak=    3.761 closest distance to " O   HOH Z 365 " =    2.665
peak=    3.757 closest distance to " CG2 ILE A 120 " =    1.257
peak=    3.743 closest distance to " CB  TRP A 179 " =    1.343
peak=    3.730 closest distance to " O   HOH Z 345 " =    1.666
peak=    3.730 closest distance to " O   HOH Z 406 " =    1.554
peak=    3.727 closest distance to " N   HIS A 108 " =    1.803
peak=    3.724 closest distance to " O   HOH Z  97 " =    2.208
peak=    3.721 closest distance to " O   HOH Z 209 " =    2.267
peak=    3.721 closest distance to " CA  ALA A 160 " =    0.895
peak=    3.713 closest distance to " CB  VAL A 202 " =    1.504
peak=    3.708 closest distance to " O   HOH Z  15 " =    2.258
peak=    3.708 closest distance to " O   HOH Z 158 " =    3.052
peak=    3.706 closest distance to " O  BHOH Z 338 " =    2.210
peak=    3.704 closest distance to " CB  TRP A 266 " =    1.062
peak=    3.703 closest distance to " CE  LYS A  76 " =    0.845
peak=    3.703 closest distance to " CD  LYS A 166 " =    1.374
peak=    3.702 closest distance to " CB  GLU A 128 " =    1.148
peak=    3.699 closest distance to " O   ALA A 165 " =    1.423
peak=    3.699 closest distance to " O   HOH Z 265 " =    2.002
peak=    3.699 closest distance to " O   HOH Z 291 " =    1.446
peak=    3.698 closest distance to " O   HOH Z 180 " =    2.203
peak=    3.697 closest distance to " CA  ASN A 176 " =    1.597
peak=    3.696 closest distance to " O   HOH Z 361 " =    2.441
peak=    3.689 closest distance to " O   HOH Z 250 " =    1.400
peak=    3.684 closest distance to " CA  ALA A 295 " =    1.019
peak=    3.684 closest distance to " N   CYS A 260 " =    0.910
peak=    3.677 closest distance to " O   HOH Z 371 " =    3.012
peak=    3.675 closest distance to " O   HOH Z  80 " =    1.874
peak=    3.671 closest distance to " CD  LYS A  76 " =    1.928
peak=    3.668 closest distance to " NE2 GLN A  77 " =    3.276
peak=    3.666 closest distance to " O   TYR A 116 " =    1.465
peak=    3.665 closest distance to " O   HOH Z 214 " =    2.717
peak=    3.664 closest distance to " OG BSER A 164 " =    2.278
peak=    3.661 closest distance to " NH2BARG A 145 " =    2.114
peak=    3.661 closest distance to " O   HOH Z 316 " =    3.075
peak=    3.647 closest distance to " CD  PRO A  54 " =    1.033
peak=    3.640 closest distance to " CD2 LEU A 297 " =    1.058
peak=    3.639 closest distance to " O   HOH Z  21 " =    1.850
peak=    3.639 closest distance to " CB  PHE A 204 " =    0.788
peak=    3.635 closest distance to " O   HOH Z  59 " =    2.277
peak=    3.634 closest distance to " O   HOH Z 146 " =    2.334
peak=    3.631 closest distance to " CG1 ILE A  33 " =    1.202
peak=    3.627 closest distance to " CB  ALA A 248 " =    1.319
peak=    3.627 closest distance to " O   HOH Z 325 " =    2.221
peak=    3.622 closest distance to " CD1 ILE A 199 " =    1.132
peak=    3.621 closest distance to " O   HOH Z 185 " =    1.850
peak=    3.609 closest distance to " CA  VAL A 125 " =    1.244
peak=    3.596 closest distance to " CB  VAL A 265 " =    1.187
peak=    3.592 closest distance to " CA  MET A 105 " =    1.065
peak=    3.591 closest distance to " O   HOH Z 214 " =    1.574
peak=    3.590 closest distance to " O   HOH Z  19 " =    1.397
peak=    3.589 closest distance to " O   HOH Z 353 " =    2.804
peak=    3.578 closest distance to " CB  SER A 141 " =    1.071
peak=    3.577 closest distance to " O   HOH Z 173 " =    2.047
peak=    3.576 closest distance to " O   HOH Z 417 " =    2.990
peak=    3.573 closest distance to " CG  LEU A 167 " =    1.157
peak=    3.563 closest distance to " CB  SER A  26 " =    1.901
peak=    3.561 closest distance to " O   THR A 220 " =    1.152
peak=    3.561 closest distance to " O   HOH Z 402 " =    1.398
peak=    3.560 closest distance to " O   HOH Z 422 " =    2.685
peak=    3.560 closest distance to " NH2AARG A 275 " =    3.498
peak=    3.559 closest distance to " CG2 VAL A 257 " =    0.788
peak=    3.558 closest distance to " CG  MET A 185 " =    1.168
peak=    3.558 closest distance to " O   HOH Z 134 " =    1.297
peak=    3.555 closest distance to " O   HOH Z 261 " =    2.255
peak=    3.546 closest distance to " CA  MET A 188 " =    1.012
peak=    3.545 closest distance to " O   HOH Z 327 " =    1.621
peak=    3.543 closest distance to " CB  PRO A  90 " =    1.105
peak=    3.541 closest distance to " CA  ASN A 215 " =    0.979
peak=    3.540 closest distance to " CB  THR A  52 " =    0.751
peak=    3.535 closest distance to " CA  SER A  87 " =    1.050
peak=    3.523 closest distance to " O   HOH Z  63 " =    2.239
peak=    3.517 closest distance to " CB  TYR A 169 " =    0.708
peak=    3.516 closest distance to " CB  GLU A  46 " =    1.004
peak=    3.515 closest distance to " CG  GLU A  37 " =    1.019
peak=    3.514 closest distance to " NZ  LYS A  48 " =    1.131
peak=    3.512 closest distance to " O   HOH Z 258 " =    2.060
peak=    3.509 closest distance to " O   HOH Z 285 " =    1.939
peak=    3.506 closest distance to " N   ARG A 156 " =    1.446
peak=    3.504 closest distance to " O   HOH Z  88 " =    2.705
peak=    3.504 closest distance to " O   HOH Z 421 " =    1.969
peak=    3.502 closest distance to " CG  GLN A  11 " =    1.554
peak=    3.499 closest distance to " O   HOH Z 285 " =    2.372
peak=    3.497 closest distance to " O   HOH Z 383 " =    2.025
peak=    3.495 closest distance to " O   HOH Z 299 " =    4.423
peak=    3.494 closest distance to " OG BSER A 134 " =    2.848
peak=    3.485 closest distance to " O   HOH Z  85 " =    1.380
peak=    3.484 closest distance to " O   HOH Z  78 " =    1.653
peak=    3.484 closest distance to " CA  ALA A  84 " =    1.240
peak=    3.484 closest distance to " O   HOH Z 392 " =    2.396
peak=    3.483 closest distance to " CB  SER A  62 " =    0.904
peak=    3.481 closest distance to " CA  ALA A 100 " =    1.018
peak=    3.478 closest distance to " O   HOH Z 126 " =    1.504
peak=    3.478 closest distance to " CB  ASN A 285 " =    0.976
peak=    3.475 closest distance to " O   HOH Z 203 " =    1.836
peak=    3.474 closest distance to " CB  ALA A 114 " =    0.815
peak=    3.471 closest distance to " N   TYR A 116 " =    1.556
peak=    3.462 closest distance to " CD1 LEU A  96 " =    0.804
peak=    3.459 closest distance to " CB  ASN A 142 " =    1.109
peak=    3.459 closest distance to " O   ASN A  74 " =    1.383
peak=    3.455 closest distance to " O   HOH Z 251 " =    1.530
peak=    3.446 closest distance to " OH  TYR A 116 " =    1.128
peak=    3.442 closest distance to " O   HOH Z 132 " =    0.877
peak=    3.439 closest distance to " O   HOH Z  61 " =    1.586
peak=    3.439 closest distance to " CG1BVAL A  72 " =    1.842
peak=    3.438 closest distance to " O   HOH Z 128 " =    1.970
peak=    3.437 closest distance to " O   HOH Z 272 " =    1.866
peak=    3.429 closest distance to " CA  TYR A 116 " =    1.316
peak=    3.423 closest distance to " O   HOH Z 271 " =    2.610
peak=    3.420 closest distance to " O   HOH Z 279 " =    2.167
peak=    3.419 closest distance to " OD2 ASP A 298 " =    3.854
peak=    3.417 closest distance to " CA  SER A  32 " =    1.619
peak=    3.415 closest distance to " O   HOH Z 313 " =    1.971
peak=    3.411 closest distance to " CG2 THR A 221 " =    1.255
peak=    3.411 closest distance to " CA  ALA A 248 " =    1.190
peak=    3.402 closest distance to " O   HOH Z 357 " =    2.070
peak=    3.399 closest distance to " O   HOH Z 380 " =    2.065
peak=    3.399 closest distance to " O   THR A 182 " =    1.461
peak=    3.397 closest distance to " O   HOH Z 148 " =    3.425
peak=    3.395 closest distance to " N   ASP A 162 " =    1.161
peak=    3.383 closest distance to " CE  LYS A 119 " =    1.097
peak=    3.383 closest distance to " CG1 ILE A  20 " =    1.259
peak=    3.381 closest distance to " CG1 VAL A 153 " =    1.047
peak=    3.378 closest distance to " OG  SER A 135 " =    1.343
peak=    3.376 closest distance to " O   HOH Z 120 " =    2.657
peak=    3.374 closest distance to " CB  LEU A 228 " =    1.127
peak=    3.370 closest distance to " O   HOH Z  35 " =    2.426
peak=    3.368 closest distance to " CB  LEU A  83 " =    0.789
peak=    3.367 closest distance to " NE  ARG A  24 " =    0.931
peak=    3.363 closest distance to " CG2 THR A 220 " =    0.738
peak=    3.361 closest distance to " CB  ASN A  39 " =    0.806
peak=    3.361 closest distance to " CB  ASN A 215 " =    1.214
peak=    3.355 closest distance to " CB  PRO A 243 " =    1.359
peak=    3.354 closest distance to " O   HOH Z 193 " =    1.488
peak=    3.354 closest distance to " CA  ASP A 162 " =    1.131
peak=    3.353 closest distance to " O   HOH Z 313 " =    1.426
peak=    3.344 closest distance to " OG  SER A  28 " =    1.466
peak=    3.342 closest distance to " CB  ASN A 110 " =    1.117
peak=    3.337 closest distance to " OE1 GLN A  73 " =    2.532
peak=    3.329 closest distance to " O   HOH Z 425 " =    1.289
peak=    3.315 closest distance to " CA  ASP A 140 " =    1.282
peak=    3.312 closest distance to " CA  ILE A 234 " =    0.985
peak=    3.306 closest distance to " O   HOH Z 411 " =    1.673
peak=    3.300 closest distance to " CG2 ILE A  20 " =    1.288
peak=    3.298 closest distance to " CA  GLU A 152 " =    0.848
peak=    3.296 closest distance to " OG  SER A  22 " =    2.700
peak=    3.295 closest distance to " O   HOH Z 102 " =    1.282
peak=    3.295 closest distance to " O   HOH Z 366 " =    2.444
peak=    3.292 closest distance to " O   HOH Z 183 " =    1.503
peak=    3.291 closest distance to " O   ASP A 124 " =    1.552
peak=    3.290 closest distance to " O   HOH Z 245 " =    1.324
peak=    3.288 closest distance to " O   HOH Z   1 " =    2.411
peak=    3.287 closest distance to " CA  ALA A 158 " =    1.435
peak=    3.286 closest distance to " OD1 ASN A  69 " =    2.496
peak=    3.285 closest distance to " CG2 VAL A 197 " =    1.107
peak=    3.274 closest distance to " O   HOH Z  48 " =    1.628
peak=    3.272 closest distance to " CA  THR A 264 " =    0.956
peak=    3.270 closest distance to " O   HOH Z 395 " =    3.066
peak=    3.267 closest distance to " O   ASP A 191 " =    1.581
peak=    3.259 closest distance to " O   HOH Z 227 " =    2.065
peak=    3.258 closest distance to " O   HOH Z 298 " =    2.343
peak=    3.257 closest distance to " CB  ALA A 291 " =    1.111
peak=    3.254 closest distance to " CB  ALA A   9 " =    1.653
peak=    3.252 closest distance to " N   VAL A 265 " =    1.383
peak=    3.252 closest distance to " CB  ASP A 298 " =    1.170
peak=    3.248 closest distance to " O   HOH Z 219 " =    1.808
peak=    3.247 closest distance to " O   HOH Z 147 " =    1.898
peak=    3.240 closest distance to " O   HOH Z 130 " =    2.260
peak=    3.238 closest distance to " O   HOH Z 250 " =    1.617
peak=    3.236 closest distance to " CA  ALA A 154 " =    1.034
peak=    3.233 closest distance to " CE1 TYR A 186 " =    1.274
peak=    3.233 closest distance to " O   THR A 251 " =    1.153
peak=    3.226 closest distance to " CA  ASN A 127 " =    1.169
peak=    3.224 closest distance to " O   HOH Z 294 " =    1.525
peak=    3.223 closest distance to " CA  ALA A 233 " =    1.491
peak=    3.222 closest distance to " O   HOH Z 286 " =    2.178
peak=    3.221 closest distance to " O   HOH Z  85 " =    2.068
peak=    3.220 closest distance to " O   HOH Z 336 " =    1.814
peak=    3.219 closest distance to " O   GLY A  91 " =    1.271
peak=    3.218 closest distance to " O   HOH Z 141 " =    1.675
peak=    3.217 closest distance to " O   HOH Z 199 " =    1.634
peak=    3.216 closest distance to " CB  LYS A 117 " =    1.170
peak=    3.216 closest distance to " CD1AILE A 234 " =    0.846
peak=    3.216 closest distance to " CA  THR A 221 " =    1.094
peak=    3.215 closest distance to " CG2BVAL A  41 " =    0.791
peak=    3.211 closest distance to " O   HOH Z 240 " =    2.663
peak=    3.208 closest distance to " OD2 ASP A 286 " =    3.176
peak=    3.208 closest distance to " O   HOH Z 358 " =    2.138
peak=    3.201 closest distance to " CB  ARG A 138 " =    0.921
peak=    3.196 closest distance to " O   HOH Z 368 " =    4.293
peak=    3.194 closest distance to " O   HOH Z 345 " =    3.834
peak=    3.190 closest distance to " NH2 ARG A 156 " =    1.156
peak=    3.187 closest distance to " CB  SER A   3 " =    1.332
peak=    3.182 closest distance to " O   HOH Z 426 " =    1.478
peak=    3.179 closest distance to " CB  ASP A 191 " =    1.232
peak=    3.175 closest distance to " CB  PHE A  16 " =    1.054
peak=    3.173 closest distance to " CE1 HIS A  81 " =    1.508
peak=    3.173 closest distance to " CB  ASP A 140 " =    1.153
peak=    3.172 closest distance to " CA  ALA A  21 " =    1.252
peak=    3.171 closest distance to " N   PHE A 130 " =    1.341
peak=    3.171 closest distance to " CB  ASN A 148 " =    2.031
peak=    3.171 closest distance to " CA  LEU A  83 " =    1.341
peak=    3.170 closest distance to " CB  TYR A 169 " =    0.840
peak=    3.169 closest distance to " CA  GLY A 241 " =    0.993
peak=    3.168 closest distance to " O   HOH Z 193 " =    1.725
peak=    3.161 closest distance to " CB  ALA A  43 " =    0.748
peak=    3.160 closest distance to " O   HOH Z  20 " =    1.138
peak=    3.154 closest distance to " CD  LYS A 119 " =    1.659
peak=    3.152 closest distance to " CA  GLU A  46 " =    0.952
peak=    3.150 closest distance to " CB  MET A  47 " =    0.959
peak=    3.141 closest distance to " O   HOH Z 391 " =    3.011
peak=    3.140 closest distance to " CD  ARG A  66 " =    2.501
peak=    3.139 closest distance to " O   HOH Z 345 " =    3.006
peak=    3.139 closest distance to " O   HOH Z 394 " =    1.669
peak=    3.129 closest distance to " CA  LYS A 117 " =    1.215
peak=    3.129 closest distance to " CD1 LEU A 300 " =    1.150
peak=    3.120 closest distance to " CE1 HIS A  81 " =    1.411
peak=    3.119 closest distance to " CB  GLN A  88 " =    1.131
peak=    3.118 closest distance to " N   TYR A 247 " =    1.195
peak=    3.115 closest distance to " CG  ARG A 138 " =    1.235
peak=    3.112 closest distance to " O   HOH Z 371 " =    1.448
peak=    3.103 closest distance to " O   HOH Z 109 " =    2.082
peak=    3.099 closest distance to " CG2 ILE A 234 " =    0.972
peak=    3.088 closest distance to " O   HOH Z 162 " =    1.467
peak=    3.087 closest distance to " N   TRP A 150 " =    1.052
peak=    3.083 closest distance to " OG  SER A  62 " =    2.819
peak=    3.081 closest distance to " CB  TYR A 116 " =    0.795
peak=    3.081 closest distance to " O   HOH Z 365 " =    2.919
peak=    3.065 closest distance to " O  BHOH Z  74 " =    1.432
peak=    3.055 closest distance to " O   HOH Z  83 " =    1.509
peak=    3.055 closest distance to " OG  SER A 245 " =    1.551
peak=    3.028 closest distance to " O   HOH Z 141 " =    1.693
peak=    3.001 closest distance to " O   HOH Z 130 " =    2.422

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 210         
Filter by distance & map next to the model:
   mapped sites are within: 0.868 - 5.360
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 209 from: 210
   mapped sites are within: 0.868 - 5.360

peak=   -4.711 closest distance to " CD  ARG A  14 " =    3.479
peak=   -4.403 closest distance to " CD  GLN A  58 " =    0.998
peak=   -4.336 closest distance to " O   HOH Z 266 " =    5.360
peak=   -4.322 closest distance to " CG2 ILE A  49 " =    2.779
peak=   -4.280 closest distance to " CG1 VAL A 250 " =    2.688
peak=   -4.252 closest distance to " CB  PRO A 243 " =    2.740
peak=   -4.233 closest distance to " CD1 LEU A 101 " =    2.435
peak=   -4.217 closest distance to " C   HIS A 108 " =    1.097
peak=   -4.177 closest distance to " OXT GLY A 302 " =    3.014
peak=   -4.145 closest distance to " O   PRO A 198 " =    1.336
peak=   -4.127 closest distance to " CD2 TYR A 293 " =    1.873
peak=   -4.088 closest distance to " CD  ARG A 156 " =    2.131
peak=   -4.083 closest distance to " O   HOH Z 377 " =    2.098
peak=   -4.019 closest distance to " O   VAL A  67 " =    2.838
peak=   -3.933 closest distance to " CA  VAL A  67 " =    3.026
peak=   -3.928 closest distance to " CH2 TRP A 179 " =    1.265
peak=   -3.927 closest distance to " CB  ALA A 161 " =    2.573
peak=   -3.919 closest distance to " CG1 VAL A 112 " =    2.580
peak=   -3.911 closest distance to " CE2 PHE A  61 " =    2.673
peak=   -3.909 closest distance to " CA  ASP A 298 " =    1.058
peak=   -3.909 closest distance to " OG  SER A  97 " =    2.211
peak=   -3.907 closest distance to " O   HOH Z  10 " =    1.602
peak=   -3.899 closest distance to " O   HOH Z 166 " =    1.655
peak=   -3.897 closest distance to " O   HOH Z 348 " =    2.152
peak=   -3.895 closest distance to " CE2 TYR A  30 " =    2.688
peak=   -3.865 closest distance to " O   HOH Z 196 " =    2.023
peak=   -3.855 closest distance to " O   ALA A  34 " =    2.320
peak=   -3.849 closest distance to " O   HOH Z 198 " =    1.546
peak=   -3.816 closest distance to " CG  ARG A  66 " =    2.545
peak=   -3.790 closest distance to " CE3 TRP A 150 " =    2.245
peak=   -3.787 closest distance to " OG BSER A 134 " =    1.393
peak=   -3.783 closest distance to " CB  ALA A 184 " =    2.342
peak=   -3.783 closest distance to " CG  PRO A 243 " =    1.731
peak=   -3.782 closest distance to " O   HOH Z 394 " =    1.578
peak=   -3.768 closest distance to " CZ  TYR A 169 " =    1.848
peak=   -3.768 closest distance to " O   HOH Z  71 " =    2.426
peak=   -3.748 closest distance to " CD  GLN A 223 " =    1.286
peak=   -3.717 closest distance to " O   HOH Z  13 " =    1.827
peak=   -3.705 closest distance to " O   HOH Z 193 " =    1.282
peak=   -3.704 closest distance to " O   HOH Z 283 " =    2.315
peak=   -3.702 closest distance to " O   HOH Z 102 " =    1.517
peak=   -3.691 closest distance to " CD2 PHE A 192 " =    2.091
peak=   -3.688 closest distance to " CG  GLU A  53 " =    1.462
peak=   -3.684 closest distance to " CG1AVAL A  41 " =    2.623
peak=   -3.667 closest distance to " CA  GLY A 241 " =    2.431
peak=   -3.663 closest distance to " ND2 ASN A 249 " =    2.264
peak=   -3.662 closest distance to " CE  MET A 105 " =    2.739
peak=   -3.658 closest distance to " CD2 HIS A 207 " =    2.274
peak=   -3.638 closest distance to " O   HOH Z 372 " =    2.289
peak=   -3.636 closest distance to " O   HOH Z 210 " =    0.939
peak=   -3.622 closest distance to " N   THR A  52 " =    1.752
peak=   -3.619 closest distance to " O   HOH Z 150 " =    2.247
peak=   -3.604 closest distance to " NE2 GLN A  88 " =    1.834
peak=   -3.600 closest distance to " CA  GLY A 241 " =    3.217
peak=   -3.598 closest distance to " CD2 TYR A 247 " =    2.385
peak=   -3.589 closest distance to " CD1 PHE A  59 " =    2.045
peak=   -3.588 closest distance to " NE2 GLN A  11 " =    1.705
peak=   -3.569 closest distance to " O   SER A 210 " =    1.900
peak=   -3.568 closest distance to " OE1 GLN A 223 " =    2.031
peak=   -3.566 closest distance to " CG  ASP A 132 " =    2.358
peak=   -3.564 closest distance to " NE2 GLN A  88 " =    1.133
peak=   -3.564 closest distance to " O   HOH Z 165 " =    1.820
peak=   -3.563 closest distance to " NE2 GLN A 194 " =    1.987
peak=   -3.562 closest distance to " O   PRO A 163 " =    2.086
peak=   -3.550 closest distance to " O   PHE A 218 " =    1.556
peak=   -3.544 closest distance to " O   HOH Z 351 " =    1.603
peak=   -3.523 closest distance to " CD  ARG A  79 " =    1.213
peak=   -3.523 closest distance to " O   VAL A 174 " =    2.208
peak=   -3.522 closest distance to " OD1 ASN A 148 " =    1.441
peak=   -3.518 closest distance to " CB  TRP A  85 " =    2.534
peak=   -3.516 closest distance to " O   TRP A  92 " =    1.999
peak=   -3.514 closest distance to " ND2BASN A 224 " =    1.804
peak=   -3.513 closest distance to " O   HOH Z 357 " =    2.133
peak=   -3.507 closest distance to " CD  ARG A 195 " =    5.146
peak=   -3.505 closest distance to " O   HOH Z 264 " =    1.764
peak=   -3.503 closest distance to " O   HOH Z   6 " =    1.625
peak=   -3.496 closest distance to " N   SER A 276 " =    1.409
peak=   -3.488 closest distance to " O   HOH Z 421 " =    3.986
peak=   -3.481 closest distance to " CG1 VAL A 112 " =    2.686
peak=   -3.474 closest distance to " CG  GLU A 277 " =    1.268
peak=   -3.468 closest distance to " O   HOH Z 211 " =    1.519
peak=   -3.462 closest distance to " O   HOH Z 174 " =    2.396
peak=   -3.461 closest distance to " CB  ALA A 291 " =    2.414
peak=   -3.460 closest distance to " O   HOH Z 185 " =    2.434
peak=   -3.457 closest distance to " CE BMET A  47 " =    1.669
peak=   -3.450 closest distance to " CG  PHE A 283 " =    2.593
peak=   -3.445 closest distance to " N   ASP A 286 " =    2.228
peak=   -3.439 closest distance to " O   ALA A  10 " =    1.818
peak=   -3.439 closest distance to " O   HOH Z 113 " =    1.903
peak=   -3.432 closest distance to " CG2 VAL A 189 " =    2.212
peak=   -3.432 closest distance to " O   HOH Z 366 " =    1.594
peak=   -3.431 closest distance to " CB  ALA A  43 " =    2.558
peak=   -3.427 closest distance to " N   ALA A  43 " =    2.672
peak=   -3.427 closest distance to " CB  ALA A 248 " =    2.285
peak=   -3.424 closest distance to " O   HOH Z 252 " =    3.876
peak=   -3.423 closest distance to " CZ  PHE A  38 " =    2.354
peak=   -3.423 closest distance to " CG  LEU A  83 " =    2.090
peak=   -3.423 closest distance to " OD2 ASP A 191 " =    1.525
peak=   -3.419 closest distance to " O   HOH Z 106 " =    1.944
peak=   -3.416 closest distance to " CB  ALA A  10 " =    2.264
peak=   -3.412 closest distance to " O   HOH Z 252 " =    3.888
peak=   -3.409 closest distance to " CB  ALA A 129 " =    2.392
peak=   -3.406 closest distance to " ND2 ASN A  45 " =    1.243
peak=   -3.405 closest distance to " CG2 ILE A 263 " =    2.270
peak=   -3.397 closest distance to " O   HOH Z 171 " =    2.380
peak=   -3.388 closest distance to " CG1 VAL A  78 " =    2.627
peak=   -3.387 closest distance to " OD1 ASP A 191 " =    1.493
peak=   -3.387 closest distance to " ND2 ASN A  45 " =    2.005
peak=   -3.382 closest distance to " NH2 ARG A  79 " =    2.197
peak=   -3.372 closest distance to " O   GLY A  80 " =    2.551
peak=   -3.367 closest distance to " O   SER A   3 " =    1.074
peak=   -3.367 closest distance to " O   HOH Z 154 " =    1.779
peak=   -3.365 closest distance to " OE1 GLN A 183 " =    1.509
peak=   -3.365 closest distance to " ND2 ASN A  69 " =    1.854
peak=   -3.364 closest distance to " N   ALA A 248 " =    1.765
peak=   -3.352 closest distance to " O   HOH Z  38 " =    1.674
peak=   -3.344 closest distance to " ND2 ASN A 187 " =    1.651
peak=   -3.343 closest distance to " O   HOH Z 174 " =    3.658
peak=   -3.342 closest distance to " OD1 ASP A 171 " =    1.518
peak=   -3.342 closest distance to " C   THR A 279 " =    1.144
peak=   -3.332 closest distance to " O   HOH Z 114 " =    3.349
peak=   -3.329 closest distance to " CD2 PHE A  61 " =    2.216
peak=   -3.323 closest distance to " O   VAL A 189 " =    2.707
peak=   -3.319 closest distance to " O   SER A 276 " =    1.699
peak=   -3.309 closest distance to " CB  ALA A 114 " =    2.555
peak=   -3.308 closest distance to " O   HOH Z 290 " =    1.086
peak=   -3.301 closest distance to " NH2 ARG A  79 " =    1.585
peak=   -3.297 closest distance to " O   ASN A 252 " =    1.448
peak=   -3.294 closest distance to " CD  PRO A 243 " =    2.095
peak=   -3.292 closest distance to " O   HOH Z 156 " =    3.499
peak=   -3.292 closest distance to " O   HOH Z 197 " =    2.069
peak=   -3.283 closest distance to " O   HOH Z  78 " =    1.838
peak=   -3.282 closest distance to " OD1 ASN A 301 " =    1.970
peak=   -3.280 closest distance to " O   HOH Z 407 " =    2.844
peak=   -3.279 closest distance to " N   ALA A 248 " =    2.253
peak=   -3.279 closest distance to " OH  TYR A 172 " =    1.892
peak=   -3.275 closest distance to " CD1 ILE A 106 " =    2.274
peak=   -3.275 closest distance to " CG  GLN A  58 " =    1.145
peak=   -3.274 closest distance to " O   HOH Z  60 " =    1.747
peak=   -3.273 closest distance to " O   HOH Z  43 " =    1.420
peak=   -3.272 closest distance to " O   HOH Z 216 " =    1.518
peak=   -3.272 closest distance to " O   HOH Z 166 " =    1.710
peak=   -3.270 closest distance to " OE2 GLU A 152 " =    1.398
peak=   -3.269 closest distance to " C   SER A 206 " =    1.521
peak=   -3.268 closest distance to " CG  HIS A  86 " =    1.131
peak=   -3.266 closest distance to " CZ3 TRP A 274 " =    2.371
peak=   -3.266 closest distance to " O   HOH Z 145 " =    3.013
peak=   -3.264 closest distance to " O   HOH Z   6 " =    1.973
peak=   -3.258 closest distance to " C   GLY A  17 " =    0.955
peak=   -3.257 closest distance to " CA  TYR A  68 " =    3.096
peak=   -3.255 closest distance to " O   HOH Z 393 " =    1.411
peak=   -3.252 closest distance to " NH2AARG A 275 " =    5.181
peak=   -3.252 closest distance to " OG BSER A 134 " =    1.895
peak=   -3.252 closest distance to " O   HOH Z 422 " =    1.421
peak=   -3.249 closest distance to " O   ALA A  34 " =    2.083
peak=   -3.248 closest distance to " CD  ARG A 139 " =    1.533
peak=   -3.247 closest distance to " NE2 GLN A 223 " =    1.165
peak=   -3.246 closest distance to " CG  MET A 105 " =    0.993
peak=   -3.245 closest distance to " O   HOH Z  19 " =    2.349
peak=   -3.241 closest distance to " OD1 ASN A 173 " =    1.407
peak=   -3.232 closest distance to " CZ  PHE A  38 " =    1.985
peak=   -3.230 closest distance to " OD2 ASP A 171 " =    2.490
peak=   -3.230 closest distance to " O   HOH Z 262 " =    2.616
peak=   -3.228 closest distance to " CG  ARG A 269 " =    2.301
peak=   -3.225 closest distance to " O   GLY A 196 " =    1.080
peak=   -3.224 closest distance to " O   HOH Z 256 " =    2.421
peak=   -3.224 closest distance to " OD1 ASN A 249 " =    2.514
peak=   -3.224 closest distance to " CA  GLY A 203 " =    2.329
peak=   -3.220 closest distance to " O   HOH Z 285 " =    1.503
peak=   -3.218 closest distance to " O   VAL A 189 " =    1.863
peak=   -3.216 closest distance to " CG  ASN A 252 " =    1.570
peak=   -3.216 closest distance to " O   HOH Z 148 " =    3.909
peak=   -3.212 closest distance to " O   GLU A 152 " =    1.394
peak=   -3.212 closest distance to " CD1 ILE A 109 " =    2.815
peak=   -3.206 closest distance to " O   HOH Z 128 " =    2.692
peak=   -3.205 closest distance to " CD  LYS A 289 " =    2.373
peak=   -3.202 closest distance to " CB  PRO A 213 " =    2.135
peak=   -3.195 closest distance to " CA  GLY A 241 " =    2.910
peak=   -3.191 closest distance to " CH2 TRP A 150 " =    1.166
peak=   -3.190 closest distance to " O   HOH Z  37 " =    1.844
peak=   -3.189 closest distance to " O   HOH Z 110 " =    1.333
peak=   -3.186 closest distance to " CB  ALA A 291 " =    2.184
peak=   -3.178 closest distance to " O   HOH Z 340 " =    1.845
peak=   -3.175 closest distance to " C   LEU A 143 " =    1.069
peak=   -3.172 closest distance to " CG1BVAL A  72 " =    2.407
peak=   -3.170 closest distance to " O   HOH Z 171 " =    1.728
peak=   -3.169 closest distance to " CG1BVAL A  41 " =    2.794
peak=   -3.157 closest distance to " CA  GLY A 133 " =    2.073
peak=   -3.146 closest distance to " N   ALA A 226 " =    1.964
peak=   -3.130 closest distance to " CA  ILE A 263 " =    1.167
peak=   -3.125 closest distance to " O   ALA A   1 " =    2.068
peak=   -3.113 closest distance to " CB  PHE A  16 " =    2.434
peak=   -3.112 closest distance to " O   HOH Z 278 " =    1.382
peak=   -3.111 closest distance to " O   HOH Z  51 " =    2.042
peak=   -3.097 closest distance to " O   HOH Z 166 " =    1.696
peak=   -3.095 closest distance to " CB  SER A 210 " =    1.133
peak=   -3.086 closest distance to " O   HOH Z 423 " =    2.410
peak=   -3.082 closest distance to " O   HOH Z 350 " =    1.950
peak=   -3.082 closest distance to " CD2 LEU A 282 " =    2.183
peak=   -3.081 closest distance to " O   ILE A 263 " =    2.156
peak=   -3.078 closest distance to " CD  GLN A  88 " =    0.868
peak=   -3.078 closest distance to " CB  ALA A   9 " =    2.372
peak=   -3.071 closest distance to " O   HOH Z 287 " =    2.024
peak=   -3.069 closest distance to " NE1 TRP A 266 " =    2.543
peak=   -3.054 closest distance to " O   HOH Z 236 " =    1.723
peak=   -3.041 closest distance to " O   HOH Z 396 " =    2.129
peak=   -3.030 closest distance to " CE1 TYR A 247 " =    2.729
peak=   -3.029 closest distance to " O   HOH Z 150 " =    2.028
peak=   -3.028 closest distance to " CA  GLY A  57 " =    2.157

================= 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    :  0.4477 0.4444   6.250973e+00   6.236051e+00
   1_bss:  0.4397 0.4328   6.243726e+00   6.225869e+00
   1_xyz:  0.2804 0.3076   5.898439e+00   5.983425e+00
   1_adp:  0.2527 0.3183   5.849683e+00   6.008568e+00
   1_occ:  0.2525 0.3184   5.849839e+00   6.009605e+00
   2_bss:  0.2495 0.3162   5.845119e+00   6.005939e+00
   2_xyz:  0.1872 0.2393   5.587722e+00   5.779814e+00
   2_adp:  0.1760 0.2228   5.531850e+00   5.722772e+00
   2_occ:  0.1759 0.2226   5.531037e+00   5.722379e+00
   3_bss:  0.1760 0.2220   5.530220e+00   5.720631e+00
   3_xyz:  0.1351 0.1803   5.303876e+00   5.522173e+00
   3_adp:  0.1251 0.1759   5.252808e+00   5.489220e+00
   3_occ:  0.1250 0.1759   5.252648e+00   5.489104e+00
   4_bss:  0.1252 0.1759   5.253542e+00   5.488914e+00
   4_xyz:  0.1168 0.1677   5.200329e+00   5.445519e+00
   4_adp:  0.1152 0.1640   5.184589e+00   5.423521e+00
   4_occ:  0.1151 0.1640   5.184116e+00   5.423059e+00
   5_bss:  0.1150 0.1640   5.184254e+00   5.423345e+00
   5_xyz:  0.1144 0.1623   5.177912e+00   5.415890e+00
   5_adp:  0.1140 0.1629   5.177799e+00   5.419602e+00
   5_occ:  0.1138 0.1628   5.177499e+00   5.419462e+00
   5_bss:  0.1137 0.1626   5.177554e+00   5.419541e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.307  40.645  -2.000   1.785   3.218   0.000   0.000   0.000
   1_xyz:  0.307  40.645  -2.000   1.785   3.218   0.000   0.000   0.000
   1_adp:  0.307  40.645  -2.000   1.785   3.218   0.000   0.000   0.000
   1_occ:  0.307  40.645  -2.000   1.785   3.218   0.000   0.000   0.000
   2_bss:  0.331  68.988  -2.474  -0.166   0.684  -0.000   0.000   0.000
   2_xyz:  0.331  68.988  -2.474  -0.166   0.684  -0.000   0.000   0.000
   2_adp:  0.331  68.988  -2.474  -0.166   0.684  -0.000   0.000   0.000
   2_occ:  0.331  68.988  -2.474  -0.166   0.684  -0.000   0.000   0.000
   3_bss:  0.333  67.748  -2.726  -0.896   0.084  -0.000   0.000   0.000
   3_xyz:  0.333  67.748  -2.726  -0.896   0.084  -0.000   0.000   0.000
   3_adp:  0.333  67.748  -2.726  -0.896   0.084  -0.000   0.000   0.000
   3_occ:  0.333  67.748  -2.726  -0.896   0.084  -0.000   0.000   0.000
   4_bss:  0.333  67.748  -2.704  -1.287  -0.174  -0.000  -0.000  -0.000
   4_xyz:  0.333  67.748  -2.704  -1.287  -0.174  -0.000  -0.000  -0.000
   4_adp:  0.333  67.748  -2.704  -1.287  -0.174  -0.000  -0.000  -0.000
   4_occ:  0.333  67.748  -2.704  -1.287  -0.174  -0.000  -0.000  -0.000
   5_bss:  0.325  60.638  -2.533  -1.288  -0.095  -0.000  -0.000  -0.000
   5_xyz:  0.325  60.638  -2.533  -1.288  -0.095  -0.000  -0.000  -0.000
   5_adp:  0.325  60.638  -2.533  -1.288  -0.095  -0.000  -0.000  -0.000
   5_occ:  0.325  60.638  -2.533  -1.288  -0.095  -0.000  -0.000  -0.000
   5_bss:  0.320  60.641  -2.320  -1.137   0.079  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  51.328 0.5044  0.6633    58610.743
   1_bss:  50.121 0.5179  0.7077    55436.509
   1_xyz:  32.103 0.7350  0.9521    25573.318
   1_adp:  33.540 0.7178  0.9329    27418.425
   1_occ:  33.602 0.7171  0.9318    27513.847
   2_bss:  33.228 0.7214  0.8870    27060.616
   2_xyz:  24.113 0.8199  0.9676    14952.492
   2_adp:  22.057 0.8417  0.9725    13155.267
   2_occ:  22.040 0.8418  0.9726    13137.797
   3_bss:  21.950 0.8426  0.9555    13043.205
   3_xyz:  17.110 0.8880  0.9826     8428.632
   3_adp:  16.338 0.8951  0.9759     7950.000
   3_occ:  16.331 0.8952  0.9759     7948.873
   4_bss:  16.327 0.8952  0.9689     7951.185
   4_xyz:  15.396 0.9034  0.9717     7208.886
   4_adp:  14.972 0.9070  0.9653     6958.321
   4_occ:  14.966 0.9071  0.9653     6950.477
   5_bss:  14.975 0.9070  0.9681     6953.497
   5_xyz:  14.756 0.9089  0.9699     6837.024
   5_adp:  14.808 0.9086  0.9613     6880.954
   5_occ:  14.805 0.9086  0.9612     6874.554
   5_bss:  14.808 0.9086  0.9673     6875.024
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.8043e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.8043e-01
   1_xyz:   1.500  0.013  0.093 15.484  0.006  4.114   1.2031e-01
   1_adp:   1.500  0.013  0.093 15.484  0.006  4.114   1.2031e-01
   1_occ:   1.500  0.013  0.093 15.484  0.006  4.114   1.2031e-01
   2_bss:   1.500  0.013  0.093 15.484  0.006  4.114   1.2031e-01
   2_xyz:   1.044  0.007  0.074 14.556  0.004  4.128   6.2200e-02
   2_adp:   1.044  0.007  0.074 14.556  0.004  4.128   6.2200e-02
   2_occ:   1.044  0.007  0.074 14.556  0.004  4.128   6.2200e-02
   3_bss:   1.044  0.007  0.074 14.556  0.004  4.128   6.2200e-02
   3_xyz:   1.168  0.010  0.081 14.873  0.004  4.130   7.6733e-02
   3_adp:   1.168  0.010  0.081 14.873  0.004  4.130   7.6733e-02
   3_occ:   1.168  0.010  0.081 14.873  0.004  4.130   7.6733e-02
   4_bss:   1.168  0.010  0.081 14.873  0.004  4.130   7.6733e-02
   4_xyz:   1.153  0.010  0.086 14.655  0.004  4.114   7.6494e-02
   4_adp:   1.153  0.010  0.086 14.655  0.004  4.114   7.6494e-02
   4_occ:   1.153  0.010  0.086 14.655  0.004  4.114   7.6494e-02
   5_bss:   1.153  0.010  0.086 14.655  0.004  4.114   7.6494e-02
   5_xyz:   1.072  0.009  0.080 14.442  0.004  4.116   6.6183e-02
   5_adp:   1.072  0.009  0.080 14.442  0.004  4.116   6.6183e-02
   5_occ:   1.072  0.009  0.080 14.442  0.004  4.116   6.6183e-02
   5_bss:   1.072  0.009  0.080 14.442  0.004  4.116   6.6183e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.578   2.4331e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.578   2.4331e-01
   1_xyz:  10.102  0.088  0.313 84.891  0.027  2.008   1.1166e-01
   1_adp:  10.102  0.088  0.313 84.891  0.027  2.008   1.1166e-01
   1_occ:  10.102  0.088  0.313 84.891  0.027  2.008   1.1166e-01
   2_bss:  10.102  0.088  0.313 84.891  0.027  2.008   1.1166e-01
   2_xyz:   7.102  0.042  0.233 79.650  0.053  2.380   4.7984e-02
   2_adp:   7.102  0.042  0.233 79.650  0.053  2.380   4.7984e-02
   2_occ:   7.102  0.042  0.233 79.650  0.053  2.380   4.7984e-02
   3_bss:   7.102  0.042  0.233 79.650  0.053  2.380   4.7984e-02
   3_xyz:   8.735  0.058  0.246 83.356  0.043  2.135   5.5903e-02
   3_adp:   8.735  0.058  0.246 83.356  0.043  2.135   5.5903e-02
   3_occ:   8.735  0.058  0.246 83.356  0.043  2.135   5.5903e-02
   4_bss:   8.735  0.058  0.246 83.356  0.043  2.135   5.5903e-02
   4_xyz:   8.613  0.048  0.304 81.612  0.030  2.331   6.0640e-02
   4_adp:   8.613  0.048  0.304 81.612  0.030  2.331   6.0640e-02
   4_occ:   8.613  0.048  0.304 81.612  0.030  2.331   6.0640e-02
   5_bss:   8.613  0.048  0.304 81.612  0.030  2.331   6.0640e-02
   5_xyz:   8.086  0.043  0.265 81.640  0.035  2.345   4.3597e-02
   5_adp:   8.086  0.043  0.265 81.640  0.035  2.345   4.3597e-02
   5_occ:   8.086  0.043  0.265 81.640  0.035  2.345   4.3597e-02
   5_bss:   8.086  0.043  0.265 81.640  0.035  2.345   4.3597e-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:  89.28   0.00  18.25  78.79   0.00  14.06  89.28   2.39  41.08
   1_occ:  89.28   0.00  18.25  78.79   0.00  14.06  89.28   2.39  41.08
   2_bss:  89.28   0.00  18.25  78.79   0.00  14.06  89.28   2.39  41.08
   2_xyz:  89.28   0.00  18.25  78.79   0.00  14.06  89.28   2.39  41.08
   2_adp:  87.23   0.00  17.72  79.75   0.00  13.40  87.23   5.38  41.26
   2_occ:  87.23   0.00  17.72  79.75   0.00  13.40  87.23   5.38  41.26
   3_bss:  87.23   0.00  17.72  79.75   0.00  13.40  87.23   5.38  41.26
   3_xyz:  87.23   0.00  17.72  79.75   0.00  13.40  87.23   5.38  41.26
   3_adp:  95.15   0.00  17.96  95.15   0.00  13.07  91.02   5.25  44.57
   3_occ:  95.15   0.00  17.96  95.15   0.00  13.07  91.02   5.25  44.57
   4_bss:  95.15   0.00  17.96  95.15   0.00  13.07  91.02   5.25  44.57
   4_xyz:  95.15   0.00  17.96  95.15   0.00  13.07  91.02   5.25  44.57
   4_adp:  95.37   0.00  17.20  95.37   0.64  12.66  91.52   0.00  41.92
   4_occ:  95.37   0.00  17.20  95.37   0.64  12.66  91.52   0.00  41.92
   5_bss:  95.37   0.00  17.20  95.37   0.64  12.66  91.52   0.00  41.92
   5_xyz:  95.37   0.00  17.20  95.37   0.64  12.66  91.52   0.00  41.92
   5_adp:  98.44   0.00  17.02  98.44   0.17  12.48  97.02   0.00  41.78
   5_occ:  98.44   0.00  17.02  98.44   0.17  12.48  97.02   0.00  41.78
   5_bss:  98.44   0.00  17.03  98.44   0.17  12.48  97.02   0.00  41.78
------------------------------------------------------------------------
 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:    1.759    0.030    0.453
   1_adp:    1.759    0.030    0.453
   1_occ:    1.759    0.030    0.453
   2_bss:    1.759    0.030    0.453
   2_xyz:    1.550    0.060    0.538
   2_adp:    1.550    0.060    0.538
   2_occ:    1.550    0.060    0.538
   3_bss:    1.550    0.060    0.538
   3_xyz:    1.268    0.045    0.655
   3_adp:    1.268    0.045    0.655
   3_occ:    1.268    0.045    0.655
   4_bss:    1.268    0.045    0.655
   4_xyz:    1.252    0.064    0.676
   4_adp:    1.252    0.064    0.676
   4_occ:    1.252    0.064    0.676
   5_bss:    1.252    0.064    0.676
   5_xyz:    1.281    0.056    0.688
   5_adp:    1.281    0.056    0.688
   5_occ:    1.281    0.056    0.688
   5_bss:    1.281    0.056    0.688
------------------------------------------------------------------------

CPU time actual refinement: 337.68


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_339/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_339/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_339/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_339/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_339/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 337.54 
  Macro-tasks:
    bulk solvent and scale       = 39.50  
    individual site refinement   = 136.55 
    weights calculation          = 29.89  
    collect and process          = 6.66   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 212.69 
  Micro-tasks:
    mask                            = 1.67   
    f_calc                          = 110.85 
    alpha_beta                      = 8.38   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 113.68 
    fmodel                         = 6.84   
    r_factors                      = 0.14   
    phase_errors                   = 11.68  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 254.70 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.806 micro seconds
Total CPU time: 5.85 minutes
from_scatterers_fft:    649 calls, 110.45 s
gradients_fft:          594 calls, 102.42 s

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

# Date 2008-01-16 Time 04:35:57 PST -0800 (1200486957.36 s)
Start R-work = 0.4477, R-free = 0.4444 (no bulk solvent and anisotropic scale)
Final R-work = 0.1348, R-free = 0.1785 (no bulk solvent and anisotropic scale)

Start R-work = 0.4397, R-free = 0.4328
Final R-work = 0.1137, R-free = 0.1626