# Date 2008-01-16 Time 04:14:09 PST -0800 (1200485649.17 s)
#phil __OFF__

Command line arguments: "../229.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26663
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 229

-------------------------------------------------------------------------------
  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: (68.845, 47.8686, 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: 2.75, per 1000 atoms: 0.97


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 47.8686, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0027 1.96096
Completeness in resolution range: 0.912815
Completeness with d_max=infinity: 0.9101

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0027
                             d_min =   1.9610

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: (68.845, 47.8686, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0027 1.96096
Completeness in resolution range: 0.912815
Completeness with d_max=infinity: 0.9101

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0031 -  4.1968 [2246/2274]  2016   230  10.2%
  bin  2:  4.1968 -  3.3433 [2169/2192]  1951   218  10.1%
  bin  3:  3.3433 -  2.9242 [2137/2162]  1934   203   9.5%
  bin  4:  2.9242 -  2.6585 [2110/2127]  1892   218  10.3%
  bin  5:  2.6585 -  2.4688 [2092/2135]  1882   210  10.0%
  bin  6:  2.4688 -  2.3238 [2108/2136]  1901   207   9.8%
  bin  7:  2.3238 -  2.2078 [2067/2103]  1865   202   9.8%
  bin  8:  2.2078 -  2.1120 [2088/2130]  1878   210  10.1%
  bin  9:  2.1120 -  2.0309 [1986/2092]  1791   195   9.8%
  bin 10:  2.0309 -  1.9610 [ 586/2109]   520    66  11.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_229/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:
        1.22 -     1.96: 13
        1.96 -     2.69: 149
        2.69 -     3.43: 4474
        3.43 -     4.16: 9292
        4.16 -     4.90: 14221
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.225 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.368 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.404 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.591 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  57 " - " O   HOH Z 104 "  1.617 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28144 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_229/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_229/model_refine_001.geo

CPU time processing inputs: 7.73


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 47.8686 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: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4841   r_free= 0.4836   ksol= 0.00   Bsol= 0.00   scale= 0.874    |
|                                                                             |
| 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:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.289356                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0031 -  4.6813 0.99   1461  161 0.3765 0.3947      6.5712      6.5939|
|  2:  4.6813 -  3.7346 0.99   1417  156 0.4257 0.4480      6.8296      6.8635|
|  3:  3.7346 -  3.2681 0.99   1369  156 0.4685 0.4574      6.6834      6.6622|
|  4:  3.2681 -  2.9718 0.99   1381  147 0.4799 0.4581      6.5071      6.4994|
|  5:  2.9718 -  2.7602 0.99   1355  153 0.5126 0.4927      6.3572      6.3735|
|  6:  2.7602 -  2.5983 0.99   1369  153 0.5143 0.5461      6.2762      6.1918|
|  7:  2.5983 -  2.4688 0.98   1323  153 0.5138 0.4596      6.2185      6.1488|
|  8:  2.4688 -  2.3618 0.98   1356  145 0.5451 0.5217      6.1758      6.1837|
|  9:  2.3618 -  2.2712 0.99   1345  146 0.5364 0.5279      6.1093      6.1859|
| 10:  2.2712 -  2.1930 0.98   1347  147 0.5329 0.5267      6.0952       6.094|
| 11:  2.1930 -  2.1247 0.97   1317  155 0.5396 0.5417      6.0009      6.0221|
| 12:  2.1247 -  2.0641 0.99   1335  150 0.5364 0.5446      5.9542       5.943|
| 13:  2.0641 -  2.0099 0.75   1024  108 0.5255 0.5836      5.8704      5.8237|
| 14:  2.0099 -  1.9610 0.17    231   29 0.4916 0.4452      5.9286      5.6891|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0031 -  4.6813  1461   161  0.69  35.57   0.82     0.70      74744.32|
|  2:  4.6813 -  3.7346  1417   156  0.68  37.17   0.90     0.77     114576.28|
|  3:  3.7346 -  3.2681  1369   156  0.56  46.97   0.88     0.74     121862.63|
|  4:  3.2681 -  2.9718  1381   147  0.47  54.60   0.89     0.64     105881.56|
|  5:  2.9718 -  2.7602  1355   153  0.39  60.23   0.86     0.57      83899.94|
|  6:  2.7602 -  2.5983  1369   153  0.37  62.12   0.88     0.53      71877.69|
|  7:  2.5983 -  2.4688  1323   153  0.36  62.63   0.88     0.51      65532.12|
|  8:  2.4688 -  2.3618  1356   145  0.34  64.68   0.88     0.50      58793.66|
|  9:  2.3618 -  2.2712  1345   146  0.33  65.47   0.89     0.50      56517.23|
| 10:  2.2712 -  2.1930  1347   147  0.32  65.77   0.89     0.47      50259.82|
| 11:  2.1930 -  2.1247  1317   155  0.25  71.43   0.89     0.40      51208.39|
| 12:  2.1247 -  2.0641  1335   150  0.19  75.97   0.91     0.31      49208.64|
| 13:  2.0641 -  2.0099  1024   108  0.15  78.70   0.91     0.26      44418.00|
| 14:  2.0099 -  1.9610   231    29  0.23  72.98   1.01     0.27      31669.08|
|alpha:            min =        0.26 max =            0.77 mean =         0.54|
|beta:             min =    31669.08 max =       121862.63 mean =     73327.67|
|figures of merit: min =        0.00 max =            1.00 mean =         0.40|
|phase err.(work): min =        0.00 max =           90.00 mean =        59.62|
|phase err.(test): min =        0.00 max =           89.92 mean =        59.77|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.138674             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.906   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.163352              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.711   (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 |  1.225 -  1.592:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.592 -  1.960:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.960 -  2.327:       15 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.327 -  2.695:      134 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.695 -  3.062:     2201 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.062 -  3.430:     2273 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.430 -  3.797:     4047 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.797 -  4.165:     5245 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.165 -  4.532:     6337 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.532 -  4.900:     7884 |
|-----------------------------------------------------------------------------|
|-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 |        0.199 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.225 |       0.708 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.962)------------------------------------------|
|    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: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4841   r_free= 0.4836   ksol= 0.00   Bsol= 0.00   scale= 0.874    |
|                                                                             |
| 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:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.289356                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4777   r_free= 0.4734   ksol= 0.30   Bsol= 31.25   scale= 0.924   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.67,2.82,2.37,0.00,0.00,0.00); trace/3= 1.17                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.285295                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.955825              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.376   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.581989              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.232   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4777      final r-factor (work) = 0.3822          |
| start r-factor (free) = 0.4734      final r-factor (free) = 0.4083          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.4801 = 9.96 * 0.50 * 6.2839 + 1.00 * 0.1995                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.9307 = 9.96 * 0.50 * 6.1882 + 1.00 * 0.1265                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3822      final r-factor (work) = 0.3419          |
| start r-factor (free) = 0.4083      final r-factor (free) = 0.4176          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.7956 = 1.58 * 1.00 * 6.1882 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.6616 = 1.58 * 1.00 * 6.0924 + 1.00 * 0.0235                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.962)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.91  20.40    None  None   None       |
|    all(noH): 2823   0      0.00    111.91  20.40    None  None   None       |
|    Sol.    : 438    0      0.00    111.91  39.79    None  None   None       |
|    Mac.    : 2385   0      0.00    99.46   16.84    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.191:  981   |   5:    55.956 -  67.147:   73        |
|      1:    11.191 -  22.383:  831   |   6:    67.147 -  78.339:   34        |
|      2:    22.383 -  33.574:  511   |   7:    78.339 -  89.530:   13        |
|      3:    33.574 -  44.765:  241   |   8:    89.530 - 100.721:    5        |
|      4:    44.765 -  55.956:  133   |   9:   100.721 - 111.912:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3419 r_free = 0.4176             target_work(ml) = 6.096         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3415 r_free = 0.4173             target_work(ml) = 6.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3415   r_free= 0.4173   ksol= 0.30   Bsol= 31.25   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.67,2.82,2.37,0.00,0.00,0.00); trace/3= 1.17                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.095765                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3409   r_free= 0.4159   ksol= 0.30   Bsol= 40.16   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.59,1.61,1.44,0.00,0.00,0.00); trace/3= 0.49                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.095429                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.872750             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.216   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.514605              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.924  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3409      final r-factor (work) = 0.2621          |
| start r-factor (free) = 0.4159      final r-factor (free) = 0.3150          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.2947 = 11.87 * 0.50 * 6.0926 + 1.00 * 0.1268                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.7521 = 11.87 * 0.50 * 6.0034 + 1.00 * 0.1133                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2621      final r-factor (work) = 0.2338          |
| start r-factor (free) = 0.3150      final r-factor (free) = 0.2967          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1133 = 0.51 * 1.00 * 6.0034 + 1.00 * 0.0239                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0026 = 0.51 * 1.00 * 5.8117 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.962)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.93  18.86    None  None   None       |
|    all(noH): 2823   0      0.00    100.93  18.86    None  None   None       |
|    Sol.    : 438    0      2.89    100.93  40.60    None  None   None       |
|    Mac.    : 2385   0      0.00    87.51   14.87    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.093:  927   |   5:    50.467 -  60.560:   83        |
|      1:    10.093 -  20.187: 1031   |   6:    60.560 -  70.653:   40        |
|      2:    20.187 -  30.280:  338   |   7:    70.653 -  80.746:   21        |
|      3:    30.280 -  40.373:  252   |   8:    80.746 -  90.840:    8        |
|      4:    40.373 -  50.467:  121   |   9:    90.840 - 100.933:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2338 r_free = 0.2967             target_work(ml) = 5.782         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2336 r_free = 0.2961             target_work(ml) = 5.781         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2336   r_free= 0.2961   ksol= 0.30   Bsol= 40.16   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.59,1.61,1.44,0.00,0.00,0.00); trace/3= 0.49                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.781303                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2318   r_free= 0.2949   ksol= 0.33   Bsol= 62.98   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.67,-0.40,-0.09,-0.00,-0.00,-0.00); trace/3= -1.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.779711                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.178501              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.090   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.316385              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.656  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2318      final r-factor (work) = 0.1786          |
| start r-factor (free) = 0.2949      final r-factor (free) = 0.2265          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.2629 = 4.18 * 0.50 * 5.8153 + 1.00 * 0.1133                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9378 = 4.18 * 0.50 * 5.6841 + 1.00 * 0.0622                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1786      final r-factor (work) = 0.1656          |
| start r-factor (free) = 0.2265      final r-factor (free) = 0.2145          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8102 = 0.32 * 1.00 * 5.6841 + 1.00 * 0.0119                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7531 = 0.32 * 1.00 * 5.5093 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.962)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.05   18.49    None  None   None       |
|    all(noH): 2823   0      0.00    97.05   18.49    None  None   None       |
|    Sol.    : 438    0      6.00    97.05   42.62    None  None   None       |
|    Mac.    : 2385   0      0.00    84.34   14.05    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 -   9.705:  856   |   5:    48.523 -  58.228:  111        |
|      1:     9.705 -  19.409: 1209   |   6:    58.228 -  67.932:   51        |
|      2:    19.409 -  29.114:  277   |   7:    67.932 -  77.637:   26        |
|      3:    29.114 -  38.819:  140   |   8:    77.637 -  87.342:   13        |
|      4:    38.819 -  48.523:  137   |   9:    87.342 -  97.046:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1656 r_free = 0.2145             target_work(ml) = 5.480         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1655 r_free = 0.2141             target_work(ml) = 5.479         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1655   r_free= 0.2141   ksol= 0.33   Bsol= 62.98   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.67,-0.40,-0.09,-0.00,-0.00,-0.00); trace/3= -1.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.479246                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1652   r_free= 0.2133   ksol= 0.34   Bsol= 62.98   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.53,-1.54,-0.95,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.479904                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.077962              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.647  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.596054              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.765  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1652      final r-factor (work) = 0.1368          |
| start r-factor (free) = 0.2133      final r-factor (free) = 0.1831          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5506 = 3.08 * 0.50 * 5.5156 + 1.00 * 0.0622                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3806 = 3.08 * 0.50 * 5.4006 + 1.00 * 0.0693                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1368      final r-factor (work) = 0.1307          |
| start r-factor (free) = 0.1831      final r-factor (free) = 0.1795          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2290 = 0.60 * 1.00 * 5.4006 + 1.00 * 0.0100                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1674 = 0.60 * 1.00 * 5.2956 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.962)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.17    96.57   18.47    None  None   None       |
|    all(noH): 2823   0      1.17    96.57   18.47    None  None   None       |
|    Sol.    : 438    0      6.14    96.57   44.22    None  None   None       |
|    Mac.    : 2385   0      1.17    90.45   13.74    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:     1.171 -  10.711: 1077   |   5:    48.870 -  58.410:  102        |
|      1:    10.711 -  20.251: 1064   |   6:    58.410 -  67.950:   70        |
|      2:    20.251 -  29.791:  226   |   7:    67.950 -  77.489:   36        |
|      3:    29.791 -  39.330:  121   |   8:    77.489 -  87.029:   12        |
|      4:    39.330 -  48.870:  109   |   9:    87.029 -  96.569:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1307 r_free = 0.1795             target_work(ml) = 5.284         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1306 r_free = 0.1793             target_work(ml) = 5.283         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1306   r_free= 0.1793   ksol= 0.34   Bsol= 62.98   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.53,-1.54,-0.95,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.283169                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1309   r_free= 0.1800   ksol= 0.33   Bsol= 66.76   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.62,-1.97,-1.06,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.284133                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.429085              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.293  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.549020              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.356  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1309      final r-factor (work) = 0.1241          |
| start r-factor (free) = 0.1800      final r-factor (free) = 0.1718          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5021 = 2.43 * 0.50 * 5.2965 + 1.00 * 0.0693                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4548 = 2.43 * 0.50 * 5.2631 + 1.00 * 0.0625                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1241      final r-factor (work) = 0.1224          |
| start r-factor (free) = 0.1718      final r-factor (free) = 0.1715          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1635 = 1.55 * 1.00 * 5.2631 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1235 = 1.55 * 1.00 * 5.2366 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.962)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.78    102.78  18.53    None  None   None       |
|    all(noH): 2823   0      0.78    102.78  18.53    None  None   None       |
|    Sol.    : 438    0      5.68    102.78  45.14    None  None   None       |
|    Mac.    : 2385   0      0.78    100.81  13.65    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:     0.782 -  10.982: 1165   |   5:    51.781 -  61.981:   86        |
|      1:    10.982 -  21.181: 1024   |   6:    61.981 -  72.180:   59        |
|      2:    21.181 -  31.381:  210   |   7:    72.180 -  82.380:   35        |
|      3:    31.381 -  41.581:  118   |   8:    82.380 -  92.580:   17        |
|      4:    41.581 -  51.781:  103   |   9:    92.580 - 102.780:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1224 r_free = 0.1715             target_work(ml) = 5.236         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1223 r_free = 0.1715             target_work(ml) = 5.236         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1223   r_free= 0.1715   ksol= 0.33   Bsol= 66.76   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.62,-1.97,-1.06,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.235934                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0031 -  4.6813 0.99   1461  161 0.0982 0.1347       5.401      5.6149|
|  2:  4.6813 -  3.7346 0.99   1417  156 0.0851 0.1003      5.4376      5.5996|
|  3:  3.7346 -  3.2681 0.99   1369  156 0.1157 0.1630      5.5297      5.8756|
|  4:  3.2681 -  2.9718 0.99   1381  147 0.1388 0.1831      5.5249      5.7137|
|  5:  2.9718 -  2.7602 0.99   1355  153 0.1501 0.1889      5.4453      5.6207|
|  6:  2.7602 -  2.5983 0.99   1369  153 0.1398 0.2301      5.3203      5.5856|
|  7:  2.5983 -  2.4688 0.98   1323  153 0.1416 0.1825      5.2731      5.4473|
|  8:  2.4688 -  2.3618 0.98   1356  145 0.1338 0.1939      5.1988       5.403|
|  9:  2.3618 -  2.2712 0.99   1345  146 0.1279 0.1995      5.1061      5.4024|
| 10:  2.2712 -  2.1930 0.98   1347  147 0.1282 0.1932      5.0461      5.2573|
| 11:  2.1930 -  2.1247 0.97   1317  155 0.1256 0.1966      4.9776      5.3271|
| 12:  2.1247 -  2.0641 0.99   1335  150 0.1222 0.1563      4.9145      5.0993|
| 13:  2.0641 -  2.0099 0.75   1024  108 0.1162 0.2038      4.8183      5.1062|
| 14:  2.0099 -  1.9610 0.17    231   29 0.1126 0.1890      4.8086      4.9728|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0031 -  4.6813  1461   161  0.94   9.51   0.97     0.94       7638.77|
|  2:  4.6813 -  3.7346  1417   156  0.95   8.39   1.01     1.00       9410.57|
|  3:  3.7346 -  3.2681  1369   156  0.93  12.37   1.03     1.03      11491.93|
|  4:  3.2681 -  2.9718  1381   147  0.90  16.00   1.01     1.00      11988.95|
|  5:  2.9718 -  2.7602  1355   153  0.88  18.52   1.00     0.98      11087.40|
|  6:  2.7602 -  2.5983  1369   153  0.87  19.09   0.98     0.94       9062.79|
|  7:  2.5983 -  2.4688  1323   153  0.88  18.33   0.99     0.95       7995.50|
|  8:  2.4688 -  2.3618  1356   145  0.88  18.58   1.00     0.96       7162.69|
|  9:  2.3618 -  2.2712  1345   146  0.89  17.86   0.98     0.93       6003.08|
| 10:  2.2712 -  2.1930  1347   147  0.88  18.02   0.98     0.95       5433.59|
| 11:  2.1930 -  2.1247  1317   155  0.89  17.89   0.98     0.93       4827.34|
| 12:  2.1247 -  2.0641  1335   150  0.90  17.06   0.99     0.99       4272.22|
| 13:  2.0641 -  2.0099  1024   108  0.89  17.85   0.97     0.95       3712.77|
| 14:  2.0099 -  1.9610   231    29  0.91  15.37   0.95     0.90       3285.05|
|alpha:            min =        0.90 max =            1.03 mean =         0.96|
|beta:             min =     3285.05 max =        11988.95 mean =      7743.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.95 mean =        15.99|
|phase err.(test): min =        0.00 max =           89.78 mean =        15.50|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1223   r_free= 0.1714   ksol= 0.33   Bsol= 66.73   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.41,-1.87,-0.90,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.236014                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1223   r_free= 0.1714   ksol= 0.33   Bsol= 66.73   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.41,-1.87,-0.90,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.236014                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0031 -  4.6813 0.99   1461  161 0.0981 0.1347      5.4003      5.6165|
|  2:  4.6813 -  3.7346 0.99   1417  156 0.0852 0.1003      5.4384      5.6001|
|  3:  3.7346 -  3.2681 0.99   1369  156 0.1158 0.1631      5.5301      5.8759|
|  4:  3.2681 -  2.9718 0.99   1381  147 0.1388 0.1830      5.5249      5.7137|
|  5:  2.9718 -  2.7602 0.99   1355  153 0.1501 0.1887      5.4451      5.6199|
|  6:  2.7602 -  2.5983 0.99   1369  153 0.1398 0.2300      5.3199      5.5854|
|  7:  2.5983 -  2.4688 0.98   1323  153 0.1416 0.1826      5.2731      5.4474|
|  8:  2.4688 -  2.3618 0.98   1356  145 0.1338 0.1937       5.199      5.4031|
|  9:  2.3618 -  2.2712 0.99   1345  146 0.1279 0.1997      5.1063      5.4033|
| 10:  2.2712 -  2.1930 0.98   1347  147 0.1281 0.1933      5.0461      5.2572|
| 11:  2.1930 -  2.1247 0.97   1317  155 0.1256 0.1964      4.9777       5.327|
| 12:  2.1247 -  2.0641 0.99   1335  150 0.1222 0.1563      4.9146      5.0997|
| 13:  2.0641 -  2.0099 0.75   1024  108 0.1163 0.2038      4.8185      5.1047|
| 14:  2.0099 -  1.9610 0.17    231   29 0.1124 0.1889      4.8096      4.9749|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0031 -  4.6813  1461   161  0.94   9.51   0.97     0.94       7630.44|
|  2:  4.6813 -  3.7346  1417   156  0.95   8.40   1.01     1.00       9419.75|
|  3:  3.7346 -  3.2681  1369   156  0.93  12.38   1.03     1.03      11512.64|
|  4:  3.2681 -  2.9718  1381   147  0.90  16.01   1.02     1.00      11992.35|
|  5:  2.9718 -  2.7602  1355   153  0.88  18.51   1.00     0.99      11080.42|
|  6:  2.7602 -  2.5983  1369   153  0.87  19.08   0.98     0.95       9055.71|
|  7:  2.5983 -  2.4688  1323   153  0.88  18.34   0.99     0.96       7994.73|
|  8:  2.4688 -  2.3618  1356   145  0.88  18.59   1.00     0.96       7166.89|
|  9:  2.3618 -  2.2712  1345   146  0.89  17.87   0.99     0.94       6008.31|
| 10:  2.2712 -  2.1930  1347   147  0.88  18.03   0.99     0.96       5434.88|
| 11:  2.1930 -  2.1247  1317   155  0.89  17.89   0.99     0.94       4826.13|
| 12:  2.1247 -  2.0641  1335   150  0.90  17.06   1.00     1.00       4273.30|
| 13:  2.0641 -  2.0099  1024   108  0.89  17.86   0.98     0.96       3712.22|
| 14:  2.0099 -  1.9610   231    29  0.91  15.39   0.96     0.91       3285.71|
|alpha:            min =        0.91 max =            1.03 mean =         0.97|
|beta:             min =     3285.71 max =        11992.35 mean =      7745.20|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.95 mean =        16.00|
|phase err.(test): min =        0.00 max =           89.77 mean =        15.50|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.962)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.76    102.75  18.51    None  None   None       |
|    all(noH): 2823   0      0.76    102.75  18.51    None  None   None       |
|    Sol.    : 438    0      5.66    102.75  45.12    None  None   None       |
|    Mac.    : 2385   0      0.76    100.79  13.62    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:     0.755 -  10.955: 1165   |   5:    51.754 -  61.954:   86        |
|      1:    10.955 -  21.155: 1024   |   6:    61.954 -  72.154:   59        |
|      2:    21.155 -  31.355:  210   |   7:    72.154 -  82.354:   35        |
|      3:    31.355 -  41.555:  118   |   8:    82.354 -  92.554:   17        |
|      4:    41.555 -  51.754:  103   |   9:    92.554 - 102.753:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 303         
Filter by distance & map next to the model:
   mapped sites are within: 0.494 - 4.755
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 299 from: 303
   mapped sites are within: 0.733 - 4.755

peak=   11.661 closest distance to " O  BHOH Z  74 " =    1.574
peak=    7.139 closest distance to " O   HOH Z 255 " =    1.195
peak=    6.704 closest distance to " O   HOH Z 117 " =    1.484
peak=    5.759 closest distance to " O   HOH Z  54 " =    1.799
peak=    5.440 closest distance to " O   HOH Z 210 " =    1.240
peak=    5.202 closest distance to " O   HOH Z 248 " =    1.433
peak=    5.150 closest distance to " O   HOH Z  49 " =    1.492
peak=    5.052 closest distance to " CG  PRO A  54 " =    1.392
peak=    4.983 closest distance to " O   HOH Z 113 " =    1.928
peak=    4.821 closest distance to " CB  ARG A 275 " =    0.979
peak=    4.802 closest distance to " O   HOH Z  43 " =    1.864
peak=    4.786 closest distance to " O   HOH Z 403 " =    1.969
peak=    4.782 closest distance to " O   HOH Z 124 " =    1.228
peak=    4.769 closest distance to " CD2 TRP A 179 " =    1.366
peak=    4.695 closest distance to " CG  PRO A  90 " =    1.216
peak=    4.692 closest distance to " CB  GLN A 223 " =    1.389
peak=    4.636 closest distance to " CA  TYR A  30 " =    0.941
peak=    4.547 closest distance to " CA  ARG A  36 " =    1.076
peak=    4.530 closest distance to " O   HOH Z 186 " =    1.468
peak=    4.498 closest distance to " O   HOH Z 394 " =    1.600
peak=    4.478 closest distance to " O   HOH Z  65 " =    1.055
peak=    4.456 closest distance to " O   HOH Z  43 " =    2.552
peak=    4.446 closest distance to " O   HOH Z 369 " =    2.037
peak=    4.324 closest distance to " O   HOH Z 412 " =    3.664
peak=    4.313 closest distance to " O   HOH Z 298 " =    1.838
peak=    4.260 closest distance to " O   HOH Z 346 " =    1.643
peak=    4.234 closest distance to " CZ3 TRP A 266 " =    1.060
peak=    4.234 closest distance to " CB  PRO A  54 " =    1.061
peak=    4.209 closest distance to " CA  ALA A  51 " =    0.997
peak=    4.201 closest distance to " O   HOH Z 287 " =    1.554
peak=    4.195 closest distance to " CG  GLN A  58 " =    0.777
peak=    4.193 closest distance to " O   HOH Z 232 " =    2.360
peak=    4.177 closest distance to " O   HOH Z 130 " =    2.537
peak=    4.165 closest distance to " CZ  PHE A 218 " =    1.198
peak=    4.152 closest distance to " NZ  LYS A 117 " =    2.901
peak=    4.127 closest distance to " O   HOH Z 189 " =    2.916
peak=    4.097 closest distance to " CB  TRP A 179 " =    1.275
peak=    4.097 closest distance to " CB  GLN A 183 " =    1.235
peak=    4.085 closest distance to " CB  ARG A 190 " =    1.817
peak=    4.083 closest distance to " O   HOH Z 361 " =    3.350
peak=    4.079 closest distance to " CB  GLU A 152 " =    1.081
peak=    4.061 closest distance to " O   HOH Z 234 " =    3.564
peak=    4.051 closest distance to " O   PRO A 198 " =    1.491
peak=    4.049 closest distance to " CB  SER A  63 " =    1.068
peak=    4.021 closest distance to " O   HOH Z 423 " =    1.900
peak=    4.006 closest distance to " CB  GLU A 277 " =    3.763
peak=    4.005 closest distance to " O   HOH Z 402 " =    1.508
peak=    4.000 closest distance to " O  BHOH Z 338 " =    1.078
peak=    3.999 closest distance to " CG  PRO A 198 " =    1.295
peak=    3.983 closest distance to " O   HOH Z  80 " =    1.916
peak=    3.981 closest distance to " CG2BVAL A  41 " =    0.874
peak=    3.968 closest distance to " CB  PRO A 213 " =    1.278
peak=    3.963 closest distance to " O   HOH Z 403 " =    1.582
peak=    3.962 closest distance to " O   HOH Z 261 " =    2.459
peak=    3.948 closest distance to " O   HOH Z  76 " =    0.963
peak=    3.945 closest distance to " N   ASN A  39 " =    1.270
peak=    3.939 closest distance to " O   HOH Z  63 " =    1.882
peak=    3.926 closest distance to " CZ  PHE A  38 " =    1.148
peak=    3.926 closest distance to " O   HOH Z 433 " =    1.529
peak=    3.913 closest distance to " O   HOH Z  97 " =    1.388
peak=    3.913 closest distance to " O   HOH Z 365 " =    2.452
peak=    3.899 closest distance to " CA  ARG A 195 " =    1.210
peak=    3.896 closest distance to " CB  ASN A 285 " =    0.957
peak=    3.889 closest distance to " O   HOH Z 102 " =    1.414
peak=    3.889 closest distance to " O   HOH Z 134 " =    1.703
peak=    3.887 closest distance to " O   HOH Z 214 " =    1.378
peak=    3.886 closest distance to " CA  ALA A 160 " =    0.912
peak=    3.880 closest distance to " CB  SER A  26 " =    1.833
peak=    3.878 closest distance to " O   HOH Z 368 " =    2.075
peak=    3.848 closest distance to " O   HOH Z 345 " =    1.631
peak=    3.840 closest distance to " CB  SER A  62 " =    0.926
peak=    3.832 closest distance to " CE  LYS A  76 " =    0.881
peak=    3.831 closest distance to " O   HOH Z  40 " =    1.986
peak=    3.826 closest distance to " CB  SER A 141 " =    1.152
peak=    3.817 closest distance to " CA  ALA A 100 " =    1.008
peak=    3.813 closest distance to " NH2BARG A 145 " =    2.261
peak=    3.810 closest distance to " O   HOH Z 251 " =    1.607
peak=    3.809 closest distance to " CG  GLN A  11 " =    1.403
peak=    3.795 closest distance to " CD1 LEU A  96 " =    0.798
peak=    3.787 closest distance to " CB  GLU A 128 " =    1.051
peak=    3.778 closest distance to " O   THR A 220 " =    1.126
peak=    3.764 closest distance to " CD  LYS A 166 " =    1.543
peak=    3.754 closest distance to " O   HOH Z 142 " =    1.462
peak=    3.754 closest distance to " CD2 LEU A 297 " =    0.922
peak=    3.753 closest distance to " CG1 ILE A  20 " =    1.291
peak=    3.752 closest distance to " O   HOH Z 299 " =    4.178
peak=    3.748 closest distance to " O   HOH Z 425 " =    1.429
peak=    3.744 closest distance to " ND2 ASN A 187 " =    1.589
peak=    3.733 closest distance to " CB  TYR A 169 " =    0.805
peak=    3.730 closest distance to " ND2 ASN A 249 " =    0.943
peak=    3.726 closest distance to " OD1 ASN A 217 " =    1.624
peak=    3.724 closest distance to " O   ASN A  74 " =    1.916
peak=    3.721 closest distance to " CD  ARG A 159 " =    0.820
peak=    3.719 closest distance to " O   HOH Z 406 " =    1.581
peak=    3.718 closest distance to " CD  PRO A  54 " =    0.989
peak=    3.714 closest distance to " CG  PRO A 243 " =    1.086
peak=    3.707 closest distance to " O   HOH Z 116 " =    1.284
peak=    3.707 closest distance to " CB  ASN A 148 " =    1.429
peak=    3.706 closest distance to " NE2 GLN A  11 " =    1.133
peak=    3.694 closest distance to " O   HOH Z 126 " =    1.557
peak=    3.681 closest distance to " O   HOH Z 427 " =    2.921
peak=    3.667 closest distance to " CG AARG A 275 " =    1.224
peak=    3.664 closest distance to " O   HOH Z  78 " =    1.772
peak=    3.662 closest distance to " CG1 ILE A  33 " =    1.212
peak=    3.657 closest distance to " O   HOH Z  68 " =    1.817
peak=    3.655 closest distance to " CB  THR A  52 " =    0.810
peak=    3.654 closest distance to " O   HOH Z 279 " =    2.137
peak=    3.650 closest distance to " CD  ARG A 269 " =    0.974
peak=    3.644 closest distance to " CD  ARG A 195 " =    0.893
peak=    3.639 closest distance to " O   HOH Z 316 " =    2.953
peak=    3.637 closest distance to " CB  ALA A 248 " =    1.379
peak=    3.622 closest distance to " O   HOH Z 404 " =    1.474
peak=    3.610 closest distance to " CG2AVAL A 121 " =    2.146
peak=    3.605 closest distance to " O   HOH Z 414 " =    1.535
peak=    3.603 closest distance to " O   HOH Z 250 " =    1.444
peak=    3.598 closest distance to " N   CYS A 260 " =    0.884
peak=    3.590 closest distance to " CB  PRO A 243 " =    1.293
peak=    3.583 closest distance to " CG2 VAL A 197 " =    1.172
peak=    3.576 closest distance to " O   HOH Z 344 " =    2.029
peak=    3.572 closest distance to " O   HOH Z 417 " =    2.420
peak=    3.570 closest distance to " O   SER A  87 " =    2.267
peak=    3.570 closest distance to " O   HOH Z  35 " =    2.299
peak=    3.563 closest distance to " CB  ARG A  79 " =    1.655
peak=    3.563 closest distance to " CB  ASN A  39 " =    0.888
peak=    3.558 closest distance to " O   HOH Z 126 " =    1.896
peak=    3.553 closest distance to " CB  ALA A 114 " =    0.826
peak=    3.552 closest distance to " O   HOH Z  21 " =    1.828
peak=    3.544 closest distance to " O   HOH Z 313 " =    1.557
peak=    3.541 closest distance to " O   HOH Z 298 " =    4.290
peak=    3.538 closest distance to " O   HOH Z 272 " =    1.830
peak=    3.537 closest distance to " O   ALA A 165 " =    1.396
peak=    3.537 closest distance to " CA  ARG A 156 " =    1.023
peak=    3.533 closest distance to " O   HOH Z 128 " =    1.504
peak=    3.527 closest distance to " O   HOH Z 203 " =    0.922
peak=    3.523 closest distance to " CD1 ILE A 199 " =    1.389
peak=    3.518 closest distance to " O   HOH Z 389 " =    1.929
peak=    3.510 closest distance to " O   HOH Z 132 " =    2.325
peak=    3.506 closest distance to " O   HOH Z 393 " =    3.247
peak=    3.505 closest distance to " CB  VAL A 265 " =    1.168
peak=    3.501 closest distance to " O   HOH Z 361 " =    2.683
peak=    3.498 closest distance to " O   HOH Z  63 " =    2.116
peak=    3.497 closest distance to " O   THR A 182 " =    1.470
peak=    3.496 closest distance to " NH1AARG A 145 " =    1.457
peak=    3.491 closest distance to " O   HOH Z 285 " =    2.696
peak=    3.489 closest distance to " O   HOH Z 421 " =    2.203
peak=    3.488 closest distance to " O   HOH Z 132 " =    2.617
peak=    3.488 closest distance to " O   HOH Z 126 " =    1.547
peak=    3.484 closest distance to " CB  ASN A 142 " =    1.148
peak=    3.479 closest distance to " OH  TYR A 116 " =    1.120
peak=    3.475 closest distance to " O   HOH Z 185 " =    1.733
peak=    3.473 closest distance to " O   HOH Z 193 " =    1.796
peak=    3.471 closest distance to " O   HOH Z 193 " =    1.513
peak=    3.469 closest distance to " O   HOH Z 180 " =    2.214
peak=    3.453 closest distance to " OG BSER A 164 " =    2.103
peak=    3.451 closest distance to " CA  THR A  82 " =    1.776
peak=    3.451 closest distance to " O   HOH Z 209 " =    2.245
peak=    3.451 closest distance to " O   HOH Z 298 " =    2.143
peak=    3.447 closest distance to " O   HOH Z 258 " =    2.026
peak=    3.445 closest distance to " O   HOH Z 380 " =    1.991
peak=    3.440 closest distance to " CB  ASP A 107 " =    1.328
peak=    3.439 closest distance to " O   HOH Z 417 " =    1.200
peak=    3.437 closest distance to " NE2 GLN A  77 " =    3.154
peak=    3.435 closest distance to " O   HOH Z 359 " =    1.703
peak=    3.432 closest distance to " CB  TRP A 266 " =    1.081
peak=    3.431 closest distance to " CA  GLU A 152 " =    0.864
peak=    3.430 closest distance to " O   HOH Z  20 " =    1.347
peak=    3.429 closest distance to " CB  PHE A  16 " =    1.107
peak=    3.423 closest distance to " O   HOH Z 284 " =    2.989
peak=    3.422 closest distance to " O   TYR A 116 " =    1.440
peak=    3.421 closest distance to " CB  PRO A 198 " =    1.102
peak=    3.420 closest distance to " CB  VAL A 202 " =    1.474
peak=    3.419 closest distance to " CB  PHE A 204 " =    0.836
peak=    3.415 closest distance to " O   HOH Z 246 " =    1.383
peak=    3.414 closest distance to " N   HIS A 108 " =    1.744
peak=    3.411 closest distance to " O   HOH Z  40 " =    2.475
peak=    3.405 closest distance to " CB  ARG A  79 " =    0.857
peak=    3.399 closest distance to " CD  LYS A 119 " =    1.681
peak=    3.395 closest distance to " CB  GLN A 194 " =    0.904
peak=    3.391 closest distance to " CB  THR A  31 " =    1.622
peak=    3.388 closest distance to " O   HOH Z 200 " =    2.861
peak=    3.386 closest distance to " O   HOH Z 371 " =    2.742
peak=    3.384 closest distance to " O   HOH Z 214 " =    3.266
peak=    3.381 closest distance to " O   HOH Z 144 " =    1.656
peak=    3.381 closest distance to " CG2 ILE A 120 " =    1.257
peak=    3.380 closest distance to " CB  SER A 273 " =    0.931
peak=    3.378 closest distance to " CA  THR A  42 " =    1.008
peak=    3.376 closest distance to " O   HOH Z  69 " =    1.133
peak=    3.374 closest distance to " CA  ASP A 162 " =    1.115
peak=    3.372 closest distance to " O   HOH Z 366 " =    2.382
peak=    3.369 closest distance to " OG BSER A 258 " =    3.113
peak=    3.364 closest distance to " O   HOH Z  59 " =    2.356
peak=    3.358 closest distance to " O   HOH Z  39 " =    1.213
peak=    3.358 closest distance to " CA  ALA A 158 " =    1.410
peak=    3.349 closest distance to " O   HOH Z 394 " =    3.727
peak=    3.349 closest distance to " O   HOH Z 227 " =    1.616
peak=    3.349 closest distance to " O   HOH Z 213 " =    1.842
peak=    3.348 closest distance to " CD  ARG A 139 " =    1.203
peak=    3.347 closest distance to " O   HOH Z 299 " =    4.374
peak=    3.347 closest distance to " O   MET A 113 " =    1.611
peak=    3.345 closest distance to " CG  ARG A 138 " =    1.361
peak=    3.344 closest distance to " CG2 ILE A  20 " =    1.354
peak=    3.341 closest distance to " O   HOH Z 357 " =    2.114
peak=    3.340 closest distance to " OG1 THR A 264 " =    0.844
peak=    3.334 closest distance to " CA  SER A  87 " =    1.124
peak=    3.329 closest distance to " CA  ALA A 295 " =    1.011
peak=    3.328 closest distance to " CG2BVAL A 121 " =    0.877
peak=    3.324 closest distance to " O   HOH Z 176 " =    1.461
peak=    3.323 closest distance to " O   HOH Z  15 " =    2.272
peak=    3.320 closest distance to " O   HOH Z 313 " =    1.955
peak=    3.312 closest distance to " O   HOH Z 139 " =    4.755
peak=    3.308 closest distance to " O   HOH Z 214 " =    2.078
peak=    3.300 closest distance to " OG BSER A 212 " =    2.725
peak=    3.297 closest distance to " O   HOH Z  88 " =    3.487
peak=    3.297 closest distance to " CA  TYR A 116 " =    1.423
peak=    3.295 closest distance to " CB  ASP A 140 " =    1.089
peak=    3.288 closest distance to " CB  PRO A  90 " =    1.094
peak=    3.287 closest distance to " O   ASP A 191 " =    1.588
peak=    3.270 closest distance to " O   HOH Z 325 " =    2.110
peak=    3.264 closest distance to " CB  MET A 105 " =    1.043
peak=    3.260 closest distance to " OE1 GLN A 223 " =    2.260
peak=    3.260 closest distance to " O   HOH Z 303 " =    2.326
peak=    3.252 closest distance to " CB  SER A   3 " =    1.264
peak=    3.252 closest distance to " CA  ALA A 154 " =    1.051
peak=    3.247 closest distance to " O   HOH Z 163 " =    1.450
peak=    3.240 closest distance to " CA  ALA A  84 " =    1.042
peak=    3.238 closest distance to " O   HOH Z   1 " =    2.782
peak=    3.237 closest distance to " OD2 ASP A 298 " =    3.557
peak=    3.231 closest distance to " CB  LEU A  83 " =    0.733
peak=    3.230 closest distance to " CB  LYS A 289 " =    1.102
peak=    3.225 closest distance to " O   HOH Z 166 " =    4.098
peak=    3.224 closest distance to " CA  THR A 246 " =    1.044
peak=    3.220 closest distance to " CB  TYR A 247 " =    0.962
peak=    3.219 closest distance to " O   HOH Z 142 " =    1.879
peak=    3.216 closest distance to " CB  ASP A 253 " =    1.007
peak=    3.213 closest distance to " O   GLY A  91 " =    1.235
peak=    3.212 closest distance to " O   HOH Z  85 " =    1.327
peak=    3.204 closest distance to " CZ  ARG A  14 " =    1.272
peak=    3.204 closest distance to " O   HOH Z  44 " =    2.447
peak=    3.201 closest distance to " CG2 THR A 221 " =    1.280
peak=    3.200 closest distance to " CE  MET A  40 " =    0.986
peak=    3.195 closest distance to " O   HOH Z 154 " =    3.103
peak=    3.194 closest distance to " O   HOH Z 285 " =    1.782
peak=    3.191 closest distance to " O   HOH Z 268 " =    1.800
peak=    3.185 closest distance to " CB  ARG A 269 " =    0.811
peak=    3.185 closest distance to " O   HOH Z 371 " =    1.674
peak=    3.184 closest distance to " N   SER A 164 " =    1.056
peak=    3.183 closest distance to " CA  LEU A  83 " =    1.332
peak=    3.183 closest distance to " CA  ALA A 248 " =    1.272
peak=    3.182 closest distance to " CG2 VAL A 202 " =    1.155
peak=    3.179 closest distance to " CA  SER A  32 " =    1.733
peak=    3.179 closest distance to " NZ  LYS A  48 " =    1.162
peak=    3.177 closest distance to " CG1BVAL A  72 " =    1.858
peak=    3.176 closest distance to " CB  ASP A 191 " =    1.202
peak=    3.176 closest distance to " CG  GLU A  37 " =    0.935
peak=    3.174 closest distance to " O   HOH Z  88 " =    3.231
peak=    3.173 closest distance to " CG2 VAL A 257 " =    0.766
peak=    3.172 closest distance to " CB  ASN A 215 " =    1.249
peak=    3.170 closest distance to " NE2 GLN A  58 " =    4.733
peak=    3.170 closest distance to " O   HOH Z 437 " =    1.253
peak=    3.168 closest distance to " CB  ALA A  10 " =    1.232
peak=    3.166 closest distance to " CB  ALA A 291 " =    1.119
peak=    3.166 closest distance to " CD  GLN A 194 " =    1.620
peak=    3.165 closest distance to " CB  ALA A   9 " =    1.626
peak=    3.165 closest distance to " CB  LEU A   5 " =    1.132
peak=    3.164 closest distance to " C   GLY A  80 " =    0.970
peak=    3.160 closest distance to " O   THR A 251 " =    1.255
peak=    3.155 closest distance to " CE  LYS A 119 " =    1.128
peak=    3.153 closest distance to " NH2 ARG A 156 " =    1.080
peak=    3.153 closest distance to " O   HOH Z  85 " =    2.215
peak=    3.151 closest distance to " O   HOH Z 353 " =    2.794
peak=    3.151 closest distance to " CG  LEU A 167 " =    1.119
peak=    3.150 closest distance to " O   HOH Z 422 " =    2.855
peak=    3.144 closest distance to " CA  ALA A 291 " =    0.757
peak=    3.143 closest distance to " CA  ALA A 299 " =    1.117
peak=    3.134 closest distance to " CB  GLU A 236 " =    1.233
peak=    3.129 closest distance to " O   HOH Z 426 " =    1.373
peak=    3.129 closest distance to " O   HOH Z 361 " =    3.782
peak=    3.126 closest distance to " O   HOH Z 146 " =    2.101
peak=    3.124 closest distance to " O   HOH Z 173 " =    2.122
peak=    3.123 closest distance to " O   HOH Z 375 " =    1.880
peak=    3.112 closest distance to " O   HOH Z 305 " =    3.756
peak=    3.112 closest distance to " C   PHE A 208 " =    1.056
peak=    3.103 closest distance to " N   VAL A 265 " =    1.380
peak=    3.092 closest distance to " CB  HIS A 108 " =    0.811
peak=    3.087 closest distance to " OG  SER A 245 " =    1.452
peak=    3.086 closest distance to " O   HOH Z 391 " =    3.054
peak=    3.081 closest distance to " N   ARG A 156 " =    1.490
peak=    3.080 closest distance to " CB  MET A  47 " =    1.046
peak=    3.076 closest distance to " NE  ARG A  24 " =    0.941
peak=    3.076 closest distance to " CA  THR A 221 " =    0.967
peak=    3.075 closest distance to " CB  ARG A 219 " =    1.202
peak=    3.075 closest distance to " CB  GLU A  46 " =    1.099
peak=    3.073 closest distance to " CA  THR A 221 " =    1.573
peak=    3.072 closest distance to " CB  GLN A  88 " =    1.152
peak=    3.065 closest distance to " OD1 ASN A 301 " =    1.534
peak=    3.064 closest distance to " CG  ASP A  65 " =    1.144
peak=    3.060 closest distance to " NH1BARG A 145 " =    1.071
peak=    3.052 closest distance to " O   HOH Z 150 " =    1.196
peak=    3.031 closest distance to " O   HOH Z 419 " =    1.652

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 193         
Filter by distance & map next to the model:
   mapped sites are within: 0.826 - 5.982
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 192 from: 193
   mapped sites are within: 0.826 - 5.982

peak=   -4.647 closest distance to " CG2 ILE A  49 " =    2.850
peak=   -4.493 closest distance to " CD  ARG A  14 " =    3.414
peak=   -4.328 closest distance to " O   VAL A  67 " =    2.931
peak=   -4.313 closest distance to " O   HOH Z 422 " =    1.134
peak=   -4.303 closest distance to " CG  GLN A  58 " =    1.034
peak=   -4.278 closest distance to " O   HOH Z 377 " =    2.094
peak=   -4.237 closest distance to " CG2 ILE A  20 " =    3.052
peak=   -4.189 closest distance to " CD  GLN A 223 " =    1.494
peak=   -4.173 closest distance to " O   PRO A 198 " =    1.346
peak=   -4.129 closest distance to " CD2 LEU A 237 " =    2.481
peak=   -4.119 closest distance to " CD2 TYR A 293 " =    1.846
peak=   -4.107 closest distance to " CB  ALA A  43 " =    2.522
peak=   -4.061 closest distance to " O   HOH Z 411 " =    5.617
peak=   -4.048 closest distance to " O   HOH Z 166 " =    1.572
peak=   -3.970 closest distance to " C   HIS A 108 " =    1.044
peak=   -3.955 closest distance to " CD  ARG A 156 " =    2.064
peak=   -3.944 closest distance to " O   ALA A  34 " =    2.452
peak=   -3.933 closest distance to " O   HOH Z 150 " =    1.876
peak=   -3.925 closest distance to " CD2 TYR A  30 " =    2.790
peak=   -3.916 closest distance to " OXT GLY A 302 " =    2.977
peak=   -3.910 closest distance to " CD1 LEU A 101 " =    2.400
peak=   -3.908 closest distance to " O   HOH Z 214 " =    2.632
peak=   -3.908 closest distance to " CG  GLN A  11 " =    1.499
peak=   -3.906 closest distance to " CD  GLN A  58 " =    1.057
peak=   -3.877 closest distance to " CE3 TRP A 150 " =    2.206
peak=   -3.863 closest distance to " CG  GLN A  58 " =    1.273
peak=   -3.842 closest distance to " C   THR A 279 " =    1.205
peak=   -3.805 closest distance to " O   GLY A 241 " =    2.363
peak=   -3.801 closest distance to " O   HOH Z 191 " =    5.982
peak=   -3.794 closest distance to " ND2BASN A 224 " =    1.800
peak=   -3.791 closest distance to " O   HOH Z 366 " =    1.510
peak=   -3.787 closest distance to " CD2 PHE A  61 " =    2.095
peak=   -3.780 closest distance to " O   HOH Z 374 " =    2.000
peak=   -3.756 closest distance to " NE2 GLN A 223 " =    1.234
peak=   -3.753 closest distance to " O   HOH Z 165 " =    1.820
peak=   -3.741 closest distance to " OG BSER A 134 " =    1.417
peak=   -3.733 closest distance to " CA  ASP A 298 " =    1.075
peak=   -3.733 closest distance to " O   HOH Z 102 " =    1.600
peak=   -3.722 closest distance to " O   HOH Z  13 " =    1.866
peak=   -3.686 closest distance to " CG  PRO A 243 " =    1.677
peak=   -3.655 closest distance to " OG  SER A  97 " =    2.109
peak=   -3.653 closest distance to " ND2 ASN A  45 " =    2.040
peak=   -3.651 closest distance to " O   TRP A  92 " =    2.058
peak=   -3.645 closest distance to " O   HOH Z 198 " =    1.460
peak=   -3.633 closest distance to " N   ALA A  43 " =    2.766
peak=   -3.622 closest distance to " OD1 ASP A 171 " =    1.505
peak=   -3.618 closest distance to " CD1 LEU A  25 " =    2.477
peak=   -3.612 closest distance to " CD1 ILE A 109 " =    2.820
peak=   -3.611 closest distance to " CD1 PHE A  59 " =    2.054
peak=   -3.610 closest distance to " CE1 TYR A 247 " =    2.726
peak=   -3.606 closest distance to " O   SER A 210 " =    1.882
peak=   -3.601 closest distance to " CZ  PHE A  38 " =    2.214
peak=   -3.599 closest distance to " CH2 TRP A 150 " =    1.127
peak=   -3.593 closest distance to " O   HOH Z 423 " =    2.415
peak=   -3.590 closest distance to " O   HOH Z 193 " =    1.227
peak=   -3.587 closest distance to " CD1 ILE A 106 " =    2.181
peak=   -3.584 closest distance to " O   HOH Z  10 " =    1.719
peak=   -3.574 closest distance to " CE BMET A  47 " =    1.468
peak=   -3.564 closest distance to " CG2 VAL A 189 " =    2.238
peak=   -3.551 closest distance to " O   HOH Z 196 " =    1.697
peak=   -3.538 closest distance to " CD2 HIS A 207 " =    2.088
peak=   -3.536 closest distance to " O   HOH Z 149 " =    1.819
peak=   -3.531 closest distance to " O   HOH Z 171 " =    2.462
peak=   -3.530 closest distance to " CZ  TYR A 169 " =    1.982
peak=   -3.528 closest distance to " O   HOH Z 166 " =    1.668
peak=   -3.527 closest distance to " O   VAL A 174 " =    2.163
peak=   -3.523 closest distance to " CA  GLY A 203 " =    2.420
peak=   -3.518 closest distance to " CB  HIS A  86 " =    1.226
peak=   -3.515 closest distance to " C   ASN A 285 " =    2.176
peak=   -3.509 closest distance to " CB  PRO A 243 " =    2.714
peak=   -3.494 closest distance to " O   HOH Z 348 " =    2.210
peak=   -3.494 closest distance to " O   HOH Z 210 " =    1.885
peak=   -3.486 closest distance to " CA  GLY A 133 " =    2.040
peak=   -3.467 closest distance to " O   HOH Z 418 " =    1.268
peak=   -3.467 closest distance to " O   HOH Z 156 " =    3.498
peak=   -3.462 closest distance to " O   HOH Z 278 " =    1.097
peak=   -3.461 closest distance to " O   VAL A 257 " =    1.384
peak=   -3.460 closest distance to " CB  ALA A 248 " =    2.226
peak=   -3.453 closest distance to " O   GLN A  11 " =    1.223
peak=   -3.453 closest distance to " O   HOH Z 252 " =    3.594
peak=   -3.450 closest distance to " CB  ALA A   9 " =    2.443
peak=   -3.448 closest distance to " O   PRO A 163 " =    2.130
peak=   -3.442 closest distance to " CH2 TRP A 179 " =    1.310
peak=   -3.425 closest distance to " O   ILE A 263 " =    2.297
peak=   -3.420 closest distance to " O   SER A 271 " =    1.868
peak=   -3.414 closest distance to " CG  GLU A  53 " =    1.506
peak=   -3.414 closest distance to " ND2 ASN A 249 " =    2.186
peak=   -3.413 closest distance to " CB  GLU A 277 " =    1.410
peak=   -3.407 closest distance to " CB  ALA A 184 " =    2.288
peak=   -3.396 closest distance to " CD1 ILE A 151 " =    2.478
peak=   -3.395 closest distance to " O   HOH Z 128 " =    2.568
peak=   -3.395 closest distance to " O   SER A 146 " =    1.136
peak=   -3.394 closest distance to " O   ILE A 109 " =    2.604
peak=   -3.386 closest distance to " OD1 ASN A 148 " =    1.329
peak=   -3.379 closest distance to " CB  TRP A  85 " =    2.539
peak=   -3.378 closest distance to " O   SER A   3 " =    0.994
peak=   -3.374 closest distance to " O   GLY A  80 " =    2.621
peak=   -3.373 closest distance to " O   PHE A 218 " =    1.481
peak=   -3.373 closest distance to " CB  PRO A 213 " =    2.062
peak=   -3.371 closest distance to " O   HOH Z 244 " =    1.354
peak=   -3.371 closest distance to " OH  TYR A 172 " =    1.812
peak=   -3.370 closest distance to " OG BSER A 134 " =    4.092
peak=   -3.365 closest distance to " O   HOH Z 145 " =    2.881
peak=   -3.364 closest distance to " O   HOH Z 111 " =    3.812
peak=   -3.363 closest distance to " CG  ASP A 132 " =    2.284
peak=   -3.362 closest distance to " O   HOH Z 109 " =    2.417
peak=   -3.360 closest distance to " O   HOH Z 287 " =    1.894
peak=   -3.359 closest distance to " O   HOH Z 150 " =    1.116
peak=   -3.357 closest distance to " CD  LYS A 289 " =    2.312
peak=   -3.356 closest distance to " O   HOH Z  56 " =    1.132
peak=   -3.349 closest distance to " O   HOH Z  41 " =    2.052
peak=   -3.347 closest distance to " CD2 TYR A 247 " =    2.378
peak=   -3.339 closest distance to " CG1 VAL A 112 " =    2.683
peak=   -3.335 closest distance to " O   HOH Z   6 " =    1.766
peak=   -3.330 closest distance to " O   HOH Z  63 " =    1.171
peak=   -3.329 closest distance to " CG  GLN A 103 " =    2.494
peak=   -3.320 closest distance to " NE2 GLN A  88 " =    1.087
peak=   -3.317 closest distance to " NH2 ARG A  66 " =    1.083
peak=   -3.313 closest distance to " OE2 GLU A 152 " =    1.516
peak=   -3.311 closest distance to " CB  SER A  62 " =    5.641
peak=   -3.307 closest distance to " O   HOH Z  54 " =    2.004
peak=   -3.304 closest distance to " CB  PRO A 213 " =    1.684
peak=   -3.301 closest distance to " CG1 VAL A 112 " =    2.532
peak=   -3.299 closest distance to " CG2BVAL A  41 " =    1.176
peak=   -3.298 closest distance to " NE  ARG A  66 " =    4.573
peak=   -3.298 closest distance to " O   HOH Z 196 " =    2.076
peak=   -3.292 closest distance to " O   HOH Z 205 " =    0.826
peak=   -3.290 closest distance to " O   HOH Z 351 " =    1.687
peak=   -3.286 closest distance to " O   ALA A  10 " =    1.902
peak=   -3.283 closest distance to " O   HOH Z 197 " =    5.534
peak=   -3.274 closest distance to " N   THR A  52 " =    1.697
peak=   -3.274 closest distance to " O   HOH Z 154 " =    1.655
peak=   -3.272 closest distance to " O   HOH Z 313 " =    2.270
peak=   -3.266 closest distance to " O   HOH Z 433 " =    1.044
peak=   -3.265 closest distance to " O   LEU A 300 " =    2.358
peak=   -3.263 closest distance to " OE1 GLN A 223 " =    2.284
peak=   -3.259 closest distance to " O   HOH Z 285 " =    1.247
peak=   -3.258 closest distance to " CA  GLY A 241 " =    3.210
peak=   -3.258 closest distance to " CB  ALA A  10 " =    2.212
peak=   -3.251 closest distance to " CA  VAL A 197 " =    0.990
peak=   -3.241 closest distance to " O   HOH Z   1 " =    4.306
peak=   -3.241 closest distance to " O   ALA A 256 " =    1.740
peak=   -3.240 closest distance to " O   HOH Z 210 " =    0.853
peak=   -3.238 closest distance to " O   HOH Z 135 " =    1.668
peak=   -3.238 closest distance to " CG1AVAL A  41 " =    2.517
peak=   -3.237 closest distance to " CB  ALA A 291 " =    2.477
peak=   -3.232 closest distance to " O   HOH Z 174 " =    2.396
peak=   -3.225 closest distance to " O   HOH Z 113 " =    2.090
peak=   -3.225 closest distance to " O   HOH Z 326 " =    5.088
peak=   -3.221 closest distance to " CG  PHE A 283 " =    2.638
peak=   -3.214 closest distance to " O   HOH Z 215 " =    2.195
peak=   -3.211 closest distance to " O   HOH Z 407 " =    1.494
peak=   -3.208 closest distance to " O   GLU A 128 " =    1.239
peak=   -3.208 closest distance to " NE2 GLN A  88 " =    1.864
peak=   -3.207 closest distance to " CE1 PHE A  59 " =    2.292
peak=   -3.206 closest distance to " O   HOH Z 166 " =    1.625
peak=   -3.192 closest distance to " OD2 ASP A 191 " =    1.676
peak=   -3.191 closest distance to " O   GLU A 152 " =    1.399
peak=   -3.188 closest distance to " CG  LEU A  83 " =    2.220
peak=   -3.187 closest distance to " OD2 ASP A 270 " =    1.127
peak=   -3.179 closest distance to " O   HOH Z 283 " =    2.232
peak=   -3.179 closest distance to " CG1 VAL A  78 " =    2.580
peak=   -3.178 closest distance to " O   HOH Z 106 " =    1.970
peak=   -3.177 closest distance to " CD2 PHE A 192 " =    2.177
peak=   -3.169 closest distance to " O   HOH Z 345 " =    2.791
peak=   -3.169 closest distance to " CG  ARG A  79 " =    1.250
peak=   -3.166 closest distance to " OD1 ASN A 301 " =    2.002
peak=   -3.166 closest distance to " SG ACYS A 201 " =    1.120
peak=   -3.162 closest distance to " CD1 TYR A 247 " =    2.677
peak=   -3.153 closest distance to " OD2 ASP A 298 " =    1.045
peak=   -3.151 closest distance to " OD1 ASP A 191 " =    1.487
peak=   -3.150 closest distance to " OD2 ASP A 171 " =    1.770
peak=   -3.150 closest distance to " O   HOH Z 211 " =    1.400
peak=   -3.137 closest distance to " O   HOH Z 198 " =    1.078
peak=   -3.134 closest distance to " O   HOH Z  71 " =    2.611
peak=   -3.132 closest distance to " O   HOH Z 126 " =    2.017
peak=   -3.126 closest distance to " CG2 THR A  18 " =    2.897
peak=   -3.124 closest distance to " O   HOH Z 377 " =    1.890
peak=   -3.122 closest distance to " O   HOH Z 108 " =    2.033
peak=   -3.117 closest distance to " CD  PRO A 243 " =    1.979
peak=   -3.112 closest distance to " O   HOH Z 174 " =    3.625
peak=   -3.112 closest distance to " CA  ASN A 127 " =    1.059
peak=   -3.111 closest distance to " O   HOH Z 116 " =    1.911
peak=   -3.108 closest distance to " CD2 LEU A 237 " =    2.694
peak=   -3.105 closest distance to " O   LEU A 282 " =    2.310
peak=   -3.103 closest distance to " O   HOH Z 426 " =    1.615
peak=   -3.102 closest distance to " O   HOH Z 265 " =    2.357
peak=   -3.101 closest distance to " NH2 ARG A  79 " =    1.500
peak=   -3.098 closest distance to " NE  ARG A 156 " =    1.703
peak=   -3.097 closest distance to " CD2 HIS A 115 " =    0.967
peak=   -3.070 closest distance to " O   HOH Z 203 " =    0.988
peak=   -3.069 closest distance to " N   ALA A 226 " =    1.866

================= 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    :  0.4841 0.4836   6.289356e+00   6.281127e+00
   1_bss:  0.4777 0.4734   6.285295e+00   6.276622e+00
   1_xyz:  0.3822 0.4083   6.145365e+00   6.191387e+00
   1_adp:  0.3419 0.4176   6.096203e+00   6.203815e+00
   1_occ:  0.3415 0.4173   6.095765e+00   6.204398e+00
   2_bss:  0.3409 0.4159   6.095429e+00   6.203766e+00
   2_xyz:  0.2621 0.3150   5.857387e+00   6.011989e+00
   2_adp:  0.2338 0.2967   5.782025e+00   5.960191e+00
   2_occ:  0.2336 0.2961   5.781303e+00   5.959379e+00
   3_bss:  0.2318 0.2949   5.779711e+00   5.955573e+00
   3_xyz:  0.1786 0.2265   5.544976e+00   5.740617e+00
   3_adp:  0.1656 0.2145   5.479911e+00   5.680544e+00
   3_occ:  0.1655 0.2141   5.479246e+00   5.679388e+00
   4_bss:  0.1652 0.2133   5.479904e+00   5.678505e+00
   4_xyz:  0.1368 0.1831   5.316830e+00   5.535858e+00
   4_adp:  0.1307 0.1795   5.283722e+00   5.510043e+00
   4_occ:  0.1306 0.1793   5.283169e+00   5.509267e+00
   5_bss:  0.1309 0.1800   5.284133e+00   5.509468e+00
   5_xyz:  0.1241 0.1718   5.243527e+00   5.472419e+00
   5_adp:  0.1224 0.1715   5.236204e+00   5.469052e+00
   5_occ:  0.1223 0.1715   5.235934e+00   5.468767e+00
   5_bss:  0.1223 0.1714   5.236014e+00   5.468941e+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:  0.303  31.247  -1.666   2.818   2.369   0.000   0.000   0.000
   1_xyz:  0.303  31.247  -1.666   2.818   2.369   0.000   0.000   0.000
   1_adp:  0.303  31.247  -1.666   2.818   2.369   0.000   0.000   0.000
   1_occ:  0.303  31.247  -1.666   2.818   2.369   0.000   0.000   0.000
   2_bss:  0.303  40.156  -1.586   1.606   1.436   0.000   0.000   0.000
   2_xyz:  0.303  40.156  -1.586   1.606   1.436   0.000   0.000   0.000
   2_adp:  0.303  40.156  -1.586   1.606   1.436   0.000   0.000   0.000
   2_occ:  0.303  40.156  -1.586   1.606   1.436   0.000   0.000   0.000
   3_bss:  0.329  62.976  -2.670  -0.404  -0.093  -0.000  -0.000  -0.000
   3_xyz:  0.329  62.976  -2.670  -0.404  -0.093  -0.000  -0.000  -0.000
   3_adp:  0.329  62.976  -2.670  -0.404  -0.093  -0.000  -0.000  -0.000
   3_occ:  0.329  62.976  -2.670  -0.404  -0.093  -0.000  -0.000  -0.000
   4_bss:  0.335  62.976  -3.529  -1.537  -0.947  -0.000  -0.000  -0.000
   4_xyz:  0.335  62.976  -3.529  -1.537  -0.947  -0.000  -0.000  -0.000
   4_adp:  0.335  62.976  -3.529  -1.537  -0.947  -0.000  -0.000  -0.000
   4_occ:  0.335  62.976  -3.529  -1.537  -0.947  -0.000  -0.000  -0.000
   5_bss:  0.333  66.756  -3.618  -1.967  -1.060  -0.000  -0.000  -0.000
   5_xyz:  0.333  66.756  -3.618  -1.967  -1.060  -0.000  -0.000  -0.000
   5_adp:  0.333  66.756  -3.618  -1.967  -1.060  -0.000  -0.000  -0.000
   5_occ:  0.333  66.756  -3.618  -1.967  -1.060  -0.000  -0.000  -0.000
   5_bss:  0.329  66.730  -3.411  -1.873  -0.898  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.638 0.3980  0.5358    73322.222
   1_bss:  58.624 0.4098  0.5778    70916.882
   1_xyz:  46.376 0.5653  0.7807    49422.038
   1_adp:  47.308 0.5532  0.7806    51606.107
   1_occ:  47.305 0.5532  0.7797    51591.512
   2_bss:  47.104 0.5556  0.7672    51212.637
   2_xyz:  34.016 0.7112  0.9478    27560.887
   2_adp:  31.059 0.7454  0.9657    23813.826
   2_occ:  31.034 0.7457  0.9657    23754.820
   3_bss:  30.817 0.7482  0.9188    23548.900
   3_xyz:  22.668 0.8346  0.9877    13450.821
   3_adp:  20.881 0.8532  0.9965    12064.101
   3_occ:  20.857 0.8534  0.9968    12035.784
   4_bss:  20.794 0.8540  0.9648    11982.046
   4_xyz:  17.398 0.8857  0.9779     8702.185
   4_adp:  16.820 0.8910  0.9730     8376.483
   4_occ:  16.804 0.8912  0.9731     8366.516
   5_bss:  16.811 0.8911  0.9663     8383.651
   5_xyz:  16.010 0.8982  0.9700     7762.612
   5_adp:  15.950 0.8989  0.9645     7750.025
   5_occ:  15.944 0.8989  0.9645     7743.049
   5_bss:  15.948 0.8989  0.9688     7744.614
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.9949e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.9949e-01
   1_xyz:   1.552  0.011  0.093 15.378  0.006  4.104   1.2650e-01
   1_adp:   1.552  0.011  0.093 15.378  0.006  4.104   1.2650e-01
   1_occ:   1.552  0.011  0.093 15.378  0.006  4.104   1.2650e-01
   2_bss:   1.552  0.011  0.093 15.378  0.006  4.104   1.2650e-01
   2_xyz:   1.467  0.011  0.100 15.450  0.005  4.131   1.1335e-01
   2_adp:   1.467  0.011  0.100 15.450  0.005  4.131   1.1335e-01
   2_occ:   1.467  0.011  0.100 15.450  0.005  4.131   1.1335e-01
   3_bss:   1.467  0.011  0.100 15.450  0.005  4.131   1.1335e-01
   3_xyz:   1.022  0.008  0.069 14.655  0.004  4.116   6.2237e-02
   3_adp:   1.022  0.008  0.069 14.655  0.004  4.116   6.2237e-02
   3_occ:   1.022  0.008  0.069 14.655  0.004  4.116   6.2237e-02
   4_bss:   1.022  0.008  0.069 14.655  0.004  4.116   6.2237e-02
   4_xyz:   1.110  0.009  0.081 14.642  0.004  4.111   6.9270e-02
   4_adp:   1.110  0.009  0.081 14.642  0.004  4.111   6.9270e-02
   4_occ:   1.110  0.009  0.081 14.642  0.004  4.111   6.9270e-02
   5_bss:   1.110  0.009  0.081 14.642  0.004  4.111   6.9270e-02
   5_xyz:   1.040  0.008  0.077 14.518  0.004  4.117   6.2543e-02
   5_adp:   1.040  0.008  0.077 14.518  0.004  4.117   6.2543e-02
   5_occ:   1.040  0.008  0.077 14.518  0.004  4.117   6.2543e-02
   5_bss:   1.040  0.008  0.077 14.518  0.004  4.117   6.2543e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.225   2.4429e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.225   2.4429e-01
   1_xyz:   9.861  0.070  0.382 81.987  0.034  1.928   1.0427e-01
   1_adp:   9.861  0.070  0.382 81.987  0.034  1.928   1.0427e-01
   1_occ:   9.861  0.070  0.382 81.987  0.034  1.928   1.0427e-01
   2_bss:   9.861  0.070  0.382 81.987  0.034  1.928   1.0427e-01
   2_xyz:  11.293  0.057  0.302 79.821  0.031  2.004   1.2519e-01
   2_adp:  11.293  0.057  0.302 79.821  0.031  2.004   1.2519e-01
   2_occ:  11.293  0.057  0.302 79.821  0.031  2.004   1.2519e-01
   3_bss:  11.293  0.057  0.302 79.821  0.031  2.004   1.2519e-01
   3_xyz:   6.955  0.058  0.265 80.684  0.043  2.250   5.7205e-02
   3_adp:   6.955  0.058  0.265 80.684  0.043  2.250   5.7205e-02
   3_occ:   6.955  0.058  0.265 80.684  0.043  2.250   5.7205e-02
   4_bss:   6.955  0.058  0.265 80.684  0.043  2.250   5.7205e-02
   4_xyz:   8.090  0.050  0.246 82.074  0.038  2.247   4.7708e-02
   4_adp:   8.090  0.050  0.246 82.074  0.038  2.247   4.7708e-02
   4_occ:   8.090  0.050  0.246 82.074  0.038  2.247   4.7708e-02
   5_bss:   8.090  0.050  0.246 82.074  0.038  2.247   4.7708e-02
   5_xyz:   7.794  0.050  0.259 81.374  0.035  2.222   4.0134e-02
   5_adp:   7.794  0.050  0.259 81.374  0.035  2.222   4.0134e-02
   5_occ:   7.794  0.050  0.259 81.374  0.035  2.222   4.0134e-02
   5_bss:   7.794  0.050  0.259 81.374  0.035  2.222   4.0134e-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: 111.91   0.00  20.40  99.46   0.00  16.84 111.91   0.00  39.79
   1_occ: 111.91   0.00  20.40  99.46   0.00  16.84 111.91   0.00  39.79
   2_bss: 111.91   0.00  20.40  99.46   0.00  16.84 111.91   0.00  39.79
   2_xyz: 111.91   0.00  20.40  99.46   0.00  16.84 111.91   0.00  39.79
   2_adp: 100.93   0.00  18.86  87.51   0.00  14.87 100.93   2.89  40.60
   2_occ: 100.93   0.00  18.86  87.51   0.00  14.87 100.93   2.89  40.60
   3_bss: 100.93   0.00  18.86  87.51   0.00  14.87 100.93   2.89  40.60
   3_xyz: 100.93   0.00  18.86  87.51   0.00  14.87 100.93   2.89  40.60
   3_adp:  97.05   0.00  18.49  84.34   0.00  14.05  97.05   6.00  42.62
   3_occ:  97.05   0.00  18.49  84.34   0.00  14.05  97.05   6.00  42.62
   4_bss:  97.05   0.00  18.49  84.34   0.00  14.05  97.05   6.00  42.62
   4_xyz:  97.05   0.00  18.49  84.34   0.00  14.05  97.05   6.00  42.62
   4_adp:  96.57   1.17  18.47  90.45   1.17  13.74  96.57   6.14  44.22
   4_occ:  96.57   1.17  18.47  90.45   1.17  13.74  96.57   6.14  44.22
   5_bss:  96.57   1.17  18.47  90.45   1.17  13.74  96.57   6.14  44.22
   5_xyz:  96.57   1.17  18.47  90.45   1.17  13.74  96.57   6.14  44.22
   5_adp: 102.78   0.78  18.53 100.81   0.78  13.65 102.78   5.68  45.14
   5_occ: 102.78   0.78  18.53 100.81   0.78  13.65 102.78   5.68  45.14
   5_bss: 102.75   0.76  18.51 100.79   0.76  13.62 102.75   5.66  45.12
------------------------------------------------------------------------
 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:    2.396    0.026    0.341
   1_adp:    2.396    0.026    0.341
   1_occ:    2.396    0.026    0.341
   2_bss:    2.396    0.026    0.341
   2_xyz:    2.262    0.047    0.635
   2_adp:    2.262    0.047    0.635
   2_occ:    2.262    0.047    0.635
   3_bss:    2.262    0.047    0.635
   3_xyz:    2.220    0.040    0.730
   3_adp:    2.220    0.040    0.730
   3_occ:    2.220    0.040    0.730
   4_bss:    2.220    0.040    0.730
   4_xyz:    2.123    0.073    0.801
   4_adp:    2.123    0.073    0.801
   4_occ:    2.123    0.073    0.801
   5_bss:    2.123    0.073    0.801
   5_xyz:    2.029    0.060    0.823
   5_adp:    2.029    0.060    0.823
   5_occ:    2.029    0.060    0.823
   5_bss:    2.029    0.060    0.823
------------------------------------------------------------------------

CPU time actual refinement: 288.96


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_229/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_229/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_229/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_229/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_229/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 288.84 
  Macro-tasks:
    bulk solvent and scale       = 33.50  
    individual site refinement   = 116.41 
    weights calculation          = 25.55  
    collect and process          = 5.44   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 181.01 
  Micro-tasks:
    mask                            = 2.03   
    f_calc                          = 93.70  
    alpha_beta                      = 6.90   
    target                          = 1.00   
    gradients_wrt_atomic_parameters = 99.61  
    fmodel                         = 5.51   
    r_factors                      = 0.16   
    phase_errors                   = 8.65   
    foms                           = 0.25   
    TOTAL for micro-tasks          = 217.81 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.141 micro seconds
Total CPU time: 5.00 minutes
from_scatterers_fft:    645 calls, 93.41 s
gradients_fft:          590 calls, 88.59 s

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

# Date 2008-01-16 Time 04:19:09 PST -0800 (1200485949.00 s)
Start R-work = 0.4841, R-free = 0.4836 (no bulk solvent and anisotropic scale)
Final R-work = 0.1472, R-free = 0.1905 (no bulk solvent and anisotropic scale)

Start R-work = 0.4777, R-free = 0.4734
Final R-work = 0.1223, R-free = 0.1714