# Date 2008-01-16 Time 06:09:53 PST -0800 (1200492593.35 s)
#phil __OFF__

Command line arguments: "../1027.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1549
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1027

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 46.93, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.93, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1358 1.99103
Completeness in resolution range: 0.963504
Completeness with d_max=infinity: 0.960575

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1358
                             d_min =   1.9910

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.93, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1358 1.99103
Completeness in resolution range: 0.963504
Completeness with d_max=infinity: 0.960575

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1362 -  4.2607 [2133/2159]  1922   211   9.9%
  bin  2:  4.2607 -  3.3943 [2046/2065]  1840   206  10.1%
  bin  3:  3.3943 -  2.9690 [2030/2049]  1825   205  10.1%
  bin  4:  2.9690 -  2.6992 [2009/2039]  1809   200  10.0%
  bin  5:  2.6992 -  2.5066 [1993/2012]  1799   194   9.7%
  bin  6:  2.5066 -  2.3594 [1979/2004]  1775   204  10.3%
  bin  7:  2.3594 -  2.2417 [1968/1996]  1770   198  10.1%
  bin  8:  2.2417 -  2.1444 [1972/2008]  1777   195   9.9%
  bin  9:  2.1444 -  2.0620 [1970/2012]  1771   199  10.1%
  bin 10:  2.0620 -  1.9910 [1489/1987]  1342   147   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1027/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: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 11
        2.42 -     3.04: 2191
        3.04 -     3.66: 4638
        3.66 -     4.28: 9013
        4.28 -     4.90: 12292
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.967 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.209 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.282 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28140 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_1027/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1027/model_refine_001.geo

CPU time processing inputs: 9.03


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 46.93 85.95805 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: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2696   r_free= 0.2718   ksol= 0.00   Bsol= 0.00   scale= 0.987    |
|                                                                             |
| 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:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.888770                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.7523 0.99   1386  155 0.2664 0.2563      6.2923      6.2358|
|  2:  4.7523 -  3.7915 0.99   1340  146 0.2063 0.2063      6.2498      6.2257|
|  3:  3.7915 -  3.3180 0.99   1305  144 0.2251 0.2077      6.1363      6.2014|
|  4:  3.3180 -  3.0173 0.99   1300  153 0.2353 0.2569      6.0404      6.0717|
|  5:  3.0173 -  2.8025 0.99   1297  139 0.2652 0.2795      5.9397      6.0467|
|  6:  2.8025 -  2.6381 0.99   1278  143 0.2741 0.2760      5.8727      5.8636|
|  7:  2.6381 -  2.5066 0.99   1289  136 0.2894 0.2775        5.88      5.8812|
|  8:  2.5066 -  2.3980 0.98   1263  151 0.2966 0.2734      5.8119      5.7729|
|  9:  2.3980 -  2.3060 0.98   1265  142 0.2848 0.2967      5.7504      5.7735|
| 10:  2.3060 -  2.2267 0.99   1274  135 0.2989 0.3432      5.7581      5.8339|
| 11:  2.2267 -  2.1572 0.98   1277  141 0.3117 0.3275      5.7354      5.8153|
| 12:  2.1572 -  2.0957 0.97   1236  144 0.3124 0.3144      5.6783      5.7293|
| 13:  2.0957 -  2.0407 1.00   1277  135 0.3237 0.3049       5.612      5.4825|
| 14:  2.0407 -  1.9910 0.65    843   95 0.2868 0.3357      5.4743      5.4961|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.7523  1386   155  0.81  23.81   0.87     0.82      36023.87|
|  2:  4.7523 -  3.7915  1340   146  0.88  18.33   0.99     0.92      33178.26|
|  3:  3.7915 -  3.3180  1305   144  0.85  21.40   1.01     0.97      30840.69|
|  4:  3.3180 -  3.0173  1300   153  0.83  23.64   1.01     0.96      27810.82|
|  5:  3.0173 -  2.8025  1297   139  0.78  28.35   1.00     0.94      24456.79|
|  6:  2.8025 -  2.6381  1278   143  0.78  28.37   1.03     0.94      20639.99|
|  7:  2.6381 -  2.5066  1289   136  0.79  27.36   1.02     0.96      18284.15|
|  8:  2.5066 -  2.3980  1263   151  0.78  28.49   1.03     0.98      16835.72|
|  9:  2.3980 -  2.3060  1265   142  0.78  29.14   1.05     0.98      16569.71|
| 10:  2.3060 -  2.2267  1274   135  0.75  31.28   1.07     0.97      16715.22|
| 11:  2.2267 -  2.1572  1277   141  0.74  32.08   1.09     0.97      16084.08|
| 12:  2.1572 -  2.0957  1236   144  0.76  30.81   1.06     1.00      14509.93|
| 13:  2.0957 -  2.0407  1277   135  0.75  31.71   1.05     1.00      11756.30|
| 14:  2.0407 -  1.9910   843    95  0.78  28.93   1.08     0.97       9010.41|
|alpha:            min =        0.82 max =            1.00 mean =         0.95|
|beta:             min =     9010.41 max =        36023.87 mean =     21387.26|
|figures of merit: min =        0.00 max =            1.00 mean =         0.79|
|phase err.(work): min =        0.00 max =           89.91 mean =        27.29|
|phase err.(test): min =        0.00 max =           89.72 mean =        27.12|
|-----------------------------------------------------------------------------|

============================== 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 = 3.012642              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.417   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.484684              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.442   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      186 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2005 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1822 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2816 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4651 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4362 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5576 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6716 |
|-----------------------------------------------------------------------------|
|-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 |        0.161 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.145 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    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: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2696   r_free= 0.2718   ksol= 0.00   Bsol= 0.00   scale= 0.987    |
|                                                                             |
| 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:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.888770                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2531   r_free= 0.2569   ksol= 0.33   Bsol= 47.85   scale= 0.981   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.26,-2.91,-1.46,-0.00,-0.00,-0.00); trace/3= -1.37                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.857580                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.730077              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.774   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.252675              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.106   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2531      final r-factor (work) = 0.1586          |
| start r-factor (free) = 0.2569      final r-factor (free) = 0.1771          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1855 = 2.73 * 0.50 * 5.8787 + 1.00 * 0.1609                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6902 = 2.73 * 0.50 * 5.5921 + 1.00 * 0.0568                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1586      final r-factor (work) = 0.1475          |
| start r-factor (free) = 0.1771      final r-factor (free) = 0.1797          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4194 = 0.25 * 1.00 * 5.5921 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3933 = 0.25 * 1.00 * 5.3466 + 1.00 * 0.0423                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 5      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.44   16.50    None  None   None       |
|    all(noH): 2823   0      0.00    72.44   16.50    None  None   None       |
|    Sol.    : 438    0      5.83    62.89   37.20    None  None   None       |
|    Mac.    : 2385   0      0.00    72.44   12.70    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.244:  333   |   5:    36.221 -  43.466:  116        |
|      1:     7.244 -  14.489: 1421   |   6:    43.466 -  50.710:   80        |
|      2:    14.489 -  21.733:  523   |   7:    50.710 -  57.954:   64        |
|      3:    21.733 -  28.977:  146   |   8:    57.954 -  65.198:   13        |
|      4:    28.977 -  36.221:  126   |   9:    65.198 -  72.443:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1475 r_free = 0.1797             target_work(ml) = 5.354         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1470 r_free = 0.1796             target_work(ml) = 5.351         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1470   r_free= 0.1796   ksol= 0.33   Bsol= 47.85   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.26,-2.91,-1.46,-0.00,-0.00,-0.00); trace/3= -1.37                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.351078                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1458   r_free= 0.1774   ksol= 0.33   Bsol= 55.58   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-3.01,-1.85,-0.00,-0.00,-0.00); trace/3= -2.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.345357                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.667755              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.397  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.284861              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.244   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1458      final r-factor (work) = 0.1198          |
| start r-factor (free) = 0.1774      final r-factor (free) = 0.1579          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1984 = 2.67 * 0.50 * 5.3540 + 1.00 * 0.0568                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0659 = 2.67 * 0.50 * 5.2503 + 1.00 * 0.0625                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1198      final r-factor (work) = 0.1143          |
| start r-factor (free) = 0.1579      final r-factor (free) = 0.1553          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5264 = 0.28 * 1.00 * 5.2503 + 1.00 * 0.0308                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4770 = 0.28 * 1.00 * 5.1575 + 1.00 * 0.0079                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.60    73.84   16.92    None  None   None       |
|    all(noH): 2823   0      1.60    73.84   16.92    None  None   None       |
|    Sol.    : 438    0      3.74    69.46   38.32    None  None   None       |
|    Mac.    : 2385   0      1.60    73.84   12.99    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:     1.598 -   8.823:  657   |   5:    37.722 -  44.946:  110        |
|      1:     8.823 -  16.048: 1282   |   6:    44.946 -  52.171:   90        |
|      2:    16.048 -  23.272:  358   |   7:    52.171 -  59.396:   67        |
|      3:    23.272 -  30.497:  131   |   8:    59.396 -  66.620:   22        |
|      4:    30.497 -  37.722:   99   |   9:    66.620 -  73.845:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1143 r_free = 0.1553             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1142 r_free = 0.1552             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1142   r_free= 0.1552   ksol= 0.33   Bsol= 55.58   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-3.01,-1.85,-0.00,-0.00,-0.00); trace/3= -2.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.148105                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1140   r_free= 0.1550   ksol= 0.33   Bsol= 55.58   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-2.64,-1.62,-0.00,-0.00,-0.00); trace/3= -2.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.147104                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.052081              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.630  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.230396              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.127  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1140      final r-factor (work) = 0.1083          |
| start r-factor (free) = 0.1550      final r-factor (free) = 0.1551          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9324 = 3.05 * 0.50 * 5.1570 + 1.00 * 0.0625                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8934 = 3.05 * 0.50 * 5.1247 + 1.00 * 0.0729                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1083      final r-factor (work) = 0.1078          |
| start r-factor (free) = 0.1551      final r-factor (free) = 0.1546          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1885 = 0.23 * 1.00 * 5.1247 + 1.00 * 0.0078                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1871 = 0.23 * 1.00 * 5.1193 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.58    74.77   16.77    None  None   None       |
|    all(noH): 2823   0      1.58    74.77   16.77    None  None   None       |
|    Sol.    : 438    0      3.30    70.24   37.96    None  None   None       |
|    Mac.    : 2385   0      1.58    74.77   12.88    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:     1.581 -   8.899:  704   |   5:    38.174 -  45.492:  107        |
|      1:     8.899 -  16.218: 1256   |   6:    45.492 -  52.811:   87        |
|      2:    16.218 -  23.537:  348   |   7:    52.811 -  60.129:   59        |
|      3:    23.537 -  30.855:  124   |   8:    60.129 -  67.448:   21        |
|      4:    30.855 -  38.174:  110   |   9:    67.448 -  74.767:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1078 r_free = 0.1546             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1077 r_free = 0.1547             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1077   r_free= 0.1547   ksol= 0.33   Bsol= 55.58   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-2.64,-1.62,-0.00,-0.00,-0.00); trace/3= -2.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.117420                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1079   r_free= 0.1543   ksol= 0.33   Bsol= 55.58   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.22,-2.50,-1.54,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.117443                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.123344              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 156.333  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.684903              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.184  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1079      final r-factor (work) = 0.1093          |
| start r-factor (free) = 0.1543      final r-factor (free) = 0.1555          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5079 = 2.12 * 0.50 * 5.1192 + 1.00 * 0.0729                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5004 = 2.12 * 0.50 * 5.1231 + 1.00 * 0.0613                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1093      final r-factor (work) = 0.1084          |
| start r-factor (free) = 0.1555      final r-factor (free) = 0.1573          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.6395 = 1.68 * 1.00 * 5.1231 + 1.00 * 0.0076                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.6404 = 1.68 * 1.00 * 5.1225 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.12    84.50   17.08    None  None   None       |
|    all(noH): 2823   0      0.12    84.50   17.08    None  None   None       |
|    Sol.    : 438    0      4.40    75.22   39.76    None  None   None       |
|    Mac.    : 2385   0      0.12    84.50   12.91    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:     0.122 -   8.560:  690   |   5:    42.312 -  50.749:  103        |
|      1:     8.560 -  16.998: 1332   |   6:    50.749 -  59.187:   81        |
|      2:    16.998 -  25.436:  312   |   7:    59.187 -  67.625:   45        |
|      3:    25.436 -  33.874:  131   |   8:    67.625 -  76.063:   14        |
|      4:    33.874 -  42.312:  109   |   9:    76.063 -  84.501:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1084 r_free = 0.1573             target_work(ml) = 5.129         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1083 r_free = 0.1573             target_work(ml) = 5.129         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1573   ksol= 0.33   Bsol= 55.58   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.22,-2.50,-1.54,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.129399                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1573   ksol= 0.33   Bsol= 55.58   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-2.27,-1.34,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.129521                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.397979              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 162.451  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.736889              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.933  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1083      final r-factor (work) = 0.1053          |
| start r-factor (free) = 0.1573      final r-factor (free) = 0.1580          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7657 = 3.40 * 0.50 * 5.1233 + 1.00 * 0.0613                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7699 = 3.40 * 0.50 * 5.1174 + 1.00 * 0.0755                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1053      final r-factor (work) = 0.1053          |
| start r-factor (free) = 0.1580      final r-factor (free) = 0.1578          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7804 = 0.74 * 1.00 * 5.1174 + 1.00 * 0.0095                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7798 = 0.74 * 1.00 * 5.1166 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.64   16.89    None  None   None       |
|    all(noH): 2823   0      0.00    85.64   16.89    None  None   None       |
|    Sol.    : 438    0      5.89    75.72   39.53    None  None   None       |
|    Mac.    : 2385   0      0.00    85.64   12.73    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.564:  735   |   5:    42.818 -  51.382:  101        |
|      1:     8.564 -  17.127: 1298   |   6:    51.382 -  59.945:   79        |
|      2:    17.127 -  25.691:  308   |   7:    59.945 -  68.509:   39        |
|      3:    25.691 -  34.254:  131   |   8:    68.509 -  77.073:   14        |
|      4:    34.254 -  42.818:  112   |   9:    77.073 -  85.636:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1053 r_free = 0.1578             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1053 r_free = 0.1578             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1053   r_free= 0.1578   ksol= 0.33   Bsol= 55.58   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-2.27,-1.34,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.116469                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.7523 0.99   1386  155 0.0943 0.1299      5.3573      5.5241|
|  2:  4.7523 -  3.7915 0.99   1340  146 0.0813 0.1100      5.4075      5.6128|
|  3:  3.7915 -  3.3180 0.99   1305  144 0.0995 0.1525      5.4377      5.8755|
|  4:  3.3180 -  3.0173 0.99   1300  153 0.1143 0.1472       5.427      5.5458|
|  5:  3.0173 -  2.8025 0.99   1297  139 0.1261 0.1873       5.304      5.5884|
|  6:  2.8025 -  2.6381 0.99   1278  143 0.1143 0.1782       5.187      5.4409|
|  7:  2.6381 -  2.5066 0.99   1289  136 0.1182 0.1600      5.1395      5.3482|
|  8:  2.5066 -  2.3980 0.98   1263  151 0.1074 0.1689      5.0166      5.3181|
|  9:  2.3980 -  2.3060 0.98   1265  142 0.1091 0.1793       5.003      5.3379|
| 10:  2.3060 -  2.2267 0.99   1274  135 0.1034 0.1826      4.9326      5.2117|
| 11:  2.2267 -  2.1572 0.98   1277  141 0.1082 0.1777       4.936      5.2903|
| 12:  2.1572 -  2.0957 0.97   1236  144 0.1049 0.1598      4.8704      5.1028|
| 13:  2.0957 -  2.0407 1.00   1277  135 0.1079 0.1787       4.769      5.1083|
| 14:  2.0407 -  1.9910 0.65    843   95 0.0967 0.1694      4.6093      4.8869|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.7523  1386   155  0.94   9.08   0.97     0.94       7021.94|
|  2:  4.7523 -  3.7915  1340   146  0.95   7.85   1.01     1.00       8896.58|
|  3:  3.7915 -  3.3180  1305   144  0.94  11.00   1.02     1.01      10015.10|
|  4:  3.3180 -  3.0173  1300   153  0.92  13.57   1.00     0.99      10198.36|
|  5:  3.0173 -  2.8025  1297   139  0.90  15.92   0.99     0.97       8262.06|
|  6:  2.8025 -  2.6381  1278   143  0.90  15.79   0.98     0.96       7109.10|
|  7:  2.6381 -  2.5066  1289   136  0.91  15.21   0.99     0.96       6080.10|
|  8:  2.5066 -  2.3980  1263   151  0.91  14.82   0.98     0.96       5018.38|
|  9:  2.3980 -  2.3060  1265   142  0.91  14.93   0.99     0.96       4834.53|
| 10:  2.3060 -  2.2267  1274   135  0.91  15.24   0.98     0.94       4300.96|
| 11:  2.2267 -  2.1572  1277   141  0.90  16.70   0.99     0.95       4522.33|
| 12:  2.1572 -  2.0957  1236   144  0.92  14.79   0.99     0.97       4050.28|
| 13:  2.0957 -  2.0407  1277   135  0.90  16.22   0.99     0.98       3340.74|
| 14:  2.0407 -  1.9910   843    95  0.92  13.83   0.96     0.93       2342.41|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2342.41 max =        10198.36 mean =      6271.99|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.87|
|phase err.(test): min =        0.00 max =           89.88 mean =        13.41|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1052   r_free= 0.1578   ksol= 0.32   Bsol= 55.58   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.86,-2.04,-1.12,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.116429                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1052   r_free= 0.1578   ksol= 0.32   Bsol= 55.58   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.86,-2.04,-1.12,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.116429                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.7523 0.99   1386  155 0.0943 0.1300      5.3564      5.5243|
|  2:  4.7523 -  3.7915 0.99   1340  146 0.0814 0.1100      5.4079      5.6128|
|  3:  3.7915 -  3.3180 0.99   1305  144 0.0995 0.1525      5.4376      5.8753|
|  4:  3.3180 -  3.0173 0.99   1300  153 0.1143 0.1473      5.4268      5.5457|
|  5:  3.0173 -  2.8025 0.99   1297  139 0.1261 0.1872      5.3039      5.5881|
|  6:  2.8025 -  2.6381 0.99   1278  143 0.1143 0.1781       5.187      5.4407|
|  7:  2.6381 -  2.5066 0.99   1289  136 0.1182 0.1600      5.1394      5.3481|
|  8:  2.5066 -  2.3980 0.98   1263  151 0.1074 0.1689      5.0166       5.318|
|  9:  2.3980 -  2.3060 0.98   1265  142 0.1091 0.1793      5.0031      5.3378|
| 10:  2.3060 -  2.2267 0.99   1274  135 0.1034 0.1826      4.9328      5.2114|
| 11:  2.2267 -  2.1572 0.98   1277  141 0.1082 0.1778      4.9361      5.2906|
| 12:  2.1572 -  2.0957 0.97   1236  144 0.1049 0.1598      4.8706       5.103|
| 13:  2.0957 -  2.0407 1.00   1277  135 0.1079 0.1787       4.769       5.108|
| 14:  2.0407 -  1.9910 0.65    843   95 0.0967 0.1695      4.6094      4.8872|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.7523  1386   155  0.94   9.07   0.97     0.95       7006.34|
|  2:  4.7523 -  3.7915  1340   146  0.95   7.84   1.01     1.00       8892.56|
|  3:  3.7915 -  3.3180  1305   144  0.94  11.00   1.02     1.02      10012.17|
|  4:  3.3180 -  3.0173  1300   153  0.92  13.57   1.01     0.99      10194.64|
|  5:  3.0173 -  2.8025  1297   139  0.90  15.92   1.00     0.97       8259.09|
|  6:  2.8025 -  2.6381  1278   143  0.90  15.79   0.99     0.96       7107.73|
|  7:  2.6381 -  2.5066  1289   136  0.91  15.22   1.00     0.96       6077.90|
|  8:  2.5066 -  2.3980  1263   151  0.91  14.82   0.99     0.97       5017.27|
|  9:  2.3980 -  2.3060  1265   142  0.91  14.93   1.00     0.97       4833.07|
| 10:  2.3060 -  2.2267  1274   135  0.91  15.25   0.99     0.95       4302.29|
| 11:  2.2267 -  2.1572  1277   141  0.89  16.70   1.00     0.96       4522.66|
| 12:  2.1572 -  2.0957  1236   144  0.92  14.80   1.00     0.99       4051.33|
| 13:  2.0957 -  2.0407  1277   135  0.90  16.22   1.00     0.99       3340.59|
| 14:  2.0407 -  1.9910   843    95  0.92  13.84   0.97     0.94       2343.39|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2343.39 max =        10194.64 mean =      6269.54|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.83 mean =        13.87|
|phase err.(test): min =        0.00 max =           89.88 mean =        13.41|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.64   16.89    None  None   None       |
|    all(noH): 2823   0      0.00    85.64   16.89    None  None   None       |
|    Sol.    : 438    0      5.89    75.72   39.53    None  None   None       |
|    Mac.    : 2385   0      0.00    85.64   12.73    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   8.567:  735   |   5:    42.821 -  51.385:  101        |
|      1:     8.567 -  17.130: 1298   |   6:    51.385 -  59.948:   79        |
|      2:    17.130 -  25.694:  308   |   7:    59.948 -  68.512:   39        |
|      3:    25.694 -  34.257:  131   |   8:    68.512 -  77.075:   14        |
|      4:    34.257 -  42.821:  112   |   9:    77.075 -  85.639:    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)= 275         
Filter by distance & map next to the model:
   mapped sites are within: 0.429 - 4.636
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 269 from: 275
   mapped sites are within: 0.767 - 4.636

peak=    5.815 closest distance to " NH2 ARG A  56 " =    2.237
peak=    5.311 closest distance to " CG  PRO A  54 " =    1.195
peak=    5.151 closest distance to " CB  GLN A 223 " =    1.470
peak=    5.143 closest distance to " NE2 GLN A  11 " =    1.108
peak=    5.140 closest distance to " O   HOH Z 126 " =    1.860
peak=    5.139 closest distance to " CB  SER A  63 " =    1.215
peak=    4.820 closest distance to " O   HOH Z  15 " =    2.218
peak=    4.814 closest distance to " CB  GLN A 183 " =    1.227
peak=    4.726 closest distance to " O   HOH Z 232 " =    2.315
peak=    4.659 closest distance to " C   PRO A 198 " =    1.477
peak=    4.631 closest distance to " O   HOH Z  78 " =    1.673
peak=    4.626 closest distance to " O   HOH Z 298 " =    1.939
peak=    4.524 closest distance to " CB  ARG A 275 " =    0.904
peak=    4.488 closest distance to " CB  PRO A  54 " =    0.867
peak=    4.474 closest distance to " OD1 ASN A  69 " =    2.551
peak=    4.461 closest distance to " O   HOH Z 142 " =    1.655
peak=    4.461 closest distance to " CA  TYR A  30 " =    0.942
peak=    4.446 closest distance to " CB  ARG A  79 " =    1.385
peak=    4.434 closest distance to " CG  PRO A 213 " =    1.162
peak=    4.430 closest distance to " CB  LEU A 228 " =    1.085
peak=    4.390 closest distance to " O   HOH Z 261 " =    2.147
peak=    4.380 closest distance to " O   HOH Z 236 " =    2.063
peak=    4.373 closest distance to " CB  GLU A 152 " =    1.182
peak=    4.318 closest distance to " O   HOH Z 369 " =    2.133
peak=    4.274 closest distance to " CB  ASN A 148 " =    1.418
peak=    4.271 closest distance to " O   HOH Z 427 " =    2.975
peak=    4.199 closest distance to " ND2 ASN A 187 " =    1.445
peak=    4.174 closest distance to " O   HOH Z 193 " =    1.829
peak=    4.170 closest distance to " CB  TYR A 169 " =    0.767
peak=    4.167 closest distance to " O   HOH Z 303 " =    2.127
peak=    4.107 closest distance to " CB  GLU A 128 " =    1.081
peak=    4.098 closest distance to " CD  ARG A  66 " =    2.314
peak=    4.087 closest distance to " O   HOH Z 234 " =    3.764
peak=    4.031 closest distance to " O   MET A 105 " =    1.851
peak=    4.029 closest distance to " CB  ARG A 190 " =    1.626
peak=    4.027 closest distance to " O   HOH Z 250 " =    1.486
peak=    4.024 closest distance to " O   HOH Z 403 " =    1.679
peak=    4.017 closest distance to " O   HOH Z 158 " =    3.047
peak=    4.013 closest distance to " O   HOH Z 203 " =    1.809
peak=    3.977 closest distance to " CB  ASP A 140 " =    0.979
peak=    3.975 closest distance to " CD1 LEU A 300 " =    1.200
peak=    3.972 closest distance to " O   HOH Z 214 " =    2.013
peak=    3.951 closest distance to " O   HOH Z 197 " =    3.138
peak=    3.948 closest distance to " O   HOH Z 368 " =    2.065
peak=    3.944 closest distance to " O   HOH Z 193 " =    1.732
peak=    3.934 closest distance to " NZ  LYS A 117 " =    3.272
peak=    3.931 closest distance to " CB  SER A   3 " =    1.377
peak=    3.916 closest distance to " OD2 ASP A 286 " =    2.877
peak=    3.913 closest distance to " O   HOH Z 316 " =    3.145
peak=    3.910 closest distance to " NH2 ARG A 156 " =    1.202
peak=    3.900 closest distance to " O   HOH Z   1 " =    1.985
peak=    3.894 closest distance to " O   HOH Z 180 " =    2.185
peak=    3.893 closest distance to " CB  GLU A 277 " =    3.630
peak=    3.891 closest distance to " O   HOH Z 346 " =    1.654
peak=    3.883 closest distance to " O   HOH Z  61 " =    1.582
peak=    3.878 closest distance to " O   HOH Z 209 " =    2.319
peak=    3.874 closest distance to " CG1 ILE A  33 " =    1.215
peak=    3.855 closest distance to " CB  VAL A 265 " =    1.284
peak=    3.852 closest distance to " CG2 THR A 221 " =    1.102
peak=    3.831 closest distance to " CZ  PHE A 218 " =    1.069
peak=    3.813 closest distance to " CB  TRP A 266 " =    0.980
peak=    3.802 closest distance to " CB  SER A 212 " =    1.092
peak=    3.794 closest distance to " O   HOH Z  66 " =    2.165
peak=    3.791 closest distance to " CB  VAL A 202 " =    1.604
peak=    3.781 closest distance to " CA  ASN A 215 " =    1.202
peak=    3.778 closest distance to " CB  TRP A 179 " =    1.396
peak=    3.777 closest distance to " O   HOH Z 425 " =    2.038
peak=    3.771 closest distance to " O   HOH Z 189 " =    2.253
peak=    3.771 closest distance to " O   HOH Z 272 " =    1.869
peak=    3.767 closest distance to " CG2 VAL A 257 " =    0.901
peak=    3.749 closest distance to " O   HOH Z 133 " =    1.657
peak=    3.736 closest distance to " O   HOH Z 426 " =    1.602
peak=    3.736 closest distance to " O   HOH Z  53 " =    2.554
peak=    3.734 closest distance to " O   HOH Z 147 " =    1.784
peak=    3.733 closest distance to " O   HOH Z 368 " =    3.626
peak=    3.731 closest distance to " ND1 HIS A  86 " =    1.726
peak=    3.725 closest distance to " O   HOH Z  54 " =    2.374
peak=    3.721 closest distance to " NH1AARG A 145 " =    1.196
peak=    3.714 closest distance to " O   HOH Z 344 " =    3.157
peak=    3.713 closest distance to " CG  LEU A 167 " =    1.264
peak=    3.710 closest distance to " CA  THR A 264 " =    0.873
peak=    3.704 closest distance to " CG  PRO A 243 " =    1.152
peak=    3.697 closest distance to " O   HOH Z 305 " =    3.686
peak=    3.687 closest distance to " CE  LYS A  76 " =    0.851
peak=    3.682 closest distance to " ND2 ASN A 249 " =    1.919
peak=    3.679 closest distance to " O   HOH Z 213 " =    1.908
peak=    3.675 closest distance to " CA  THR A 221 " =    0.994
peak=    3.668 closest distance to " O   HOH Z 132 " =    2.544
peak=    3.665 closest distance to " O   SER A  87 " =    2.281
peak=    3.664 closest distance to " ND1 HIS A  81 " =    1.617
peak=    3.658 closest distance to " CA  ALA A  21 " =    1.226
peak=    3.656 closest distance to " O   HOH Z  61 " =    1.503
peak=    3.653 closest distance to " CD  ARG A 159 " =    0.773
peak=    3.649 closest distance to " ND2 ASN A 110 " =    1.733
peak=    3.645 closest distance to " CG  PRO A 198 " =    1.229
peak=    3.644 closest distance to " O   HOH Z  43 " =    1.829
peak=    3.638 closest distance to " O   HOH Z  20 " =    1.624
peak=    3.638 closest distance to " CD2 TRP A 179 " =    1.357
peak=    3.634 closest distance to " O   HOH Z  10 " =    1.853
peak=    3.627 closest distance to " CA  MET A  40 " =    1.140
peak=    3.623 closest distance to " O   HOH Z 133 " =    2.416
peak=    3.618 closest distance to " O   HOH Z 423 " =    1.828
peak=    3.607 closest distance to " O   HOH Z 128 " =    2.351
peak=    3.607 closest distance to " CD  ARG A  66 " =    2.307
peak=    3.600 closest distance to " CB  TYR A 169 " =    0.803
peak=    3.598 closest distance to " O   HOH Z  21 " =    1.731
peak=    3.592 closest distance to " O   HOH Z 126 " =    1.988
peak=    3.592 closest distance to " O   HOH Z 245 " =    1.307
peak=    3.590 closest distance to " CD  ARG A 269 " =    0.923
peak=    3.586 closest distance to " CD2 LEU A 297 " =    0.873
peak=    3.581 closest distance to " O   HOH Z 135 " =    1.666
peak=    3.573 closest distance to " O   HOH Z 280 " =    3.016
peak=    3.563 closest distance to " CG  PRO A  90 " =    1.048
peak=    3.563 closest distance to " CB  ARG A 139 " =    0.973
peak=    3.562 closest distance to " O  BHOH Z 338 " =    2.326
peak=    3.559 closest distance to " CG1BVAL A  72 " =    1.637
peak=    3.542 closest distance to " CA  ALA A 291 " =    0.901
peak=    3.541 closest distance to " CD BLYS A 290 " =    1.007
peak=    3.532 closest distance to " CB  GLN A  88 " =    1.279
peak=    3.531 closest distance to " O   HOH Z 128 " =    2.132
peak=    3.530 closest distance to " O   HOH Z 172 " =    3.392
peak=    3.527 closest distance to " O   HOH Z 411 " =    3.908
peak=    3.521 closest distance to " O   HOH Z  88 " =    3.541
peak=    3.518 closest distance to " CA  ARG A 195 " =    1.199
peak=    3.510 closest distance to " O   HOH Z 193 " =    2.085
peak=    3.506 closest distance to " CD  LYS A 119 " =    1.311
peak=    3.506 closest distance to " OG BSER A 164 " =    2.334
peak=    3.498 closest distance to " O   HOH Z 359 " =    1.417
peak=    3.495 closest distance to " CD2 LEU A 255 " =    1.532
peak=    3.494 closest distance to " O   HOH Z 291 " =    1.614
peak=    3.493 closest distance to " O   HOH Z 371 " =    3.167
peak=    3.492 closest distance to " CA  ALA A  51 " =    0.936
peak=    3.492 closest distance to " CB  ASN A 142 " =    1.026
peak=    3.490 closest distance to " O   HOH Z 108 " =    2.558
peak=    3.487 closest distance to " NH2AARG A 275 " =    3.514
peak=    3.485 closest distance to " N   ARG A 156 " =    1.338
peak=    3.483 closest distance to " OD1BASN A 224 " =    2.387
peak=    3.480 closest distance to " CA  ALA A 158 " =    1.157
peak=    3.477 closest distance to " CB  TYR A 116 " =    0.834
peak=    3.476 closest distance to " O   HOH Z 406 " =    1.587
peak=    3.471 closest distance to " CB  ALA A  34 " =    1.024
peak=    3.467 closest distance to " OG  SER A  22 " =    2.781
peak=    3.463 closest distance to " O   HOH Z 175 " =    2.115
peak=    3.451 closest distance to " CA  ALA A 233 " =    1.311
peak=    3.450 closest distance to " NH2BARG A 145 " =    2.133
peak=    3.441 closest distance to " O   HOH Z 273 " =    2.724
peak=    3.435 closest distance to " CD1 ILE A 106 " =    0.822
peak=    3.424 closest distance to " CB  GLN A  89 " =    1.282
peak=    3.421 closest distance to " CD  LYS A 166 " =    1.259
peak=    3.418 closest distance to " O   HOH Z 299 " =    4.413
peak=    3.416 closest distance to " CB  SER A 216 " =    0.845
peak=    3.415 closest distance to " CB  MET A  40 " =    0.829
peak=    3.414 closest distance to " OD1 ASN A 217 " =    1.761
peak=    3.408 closest distance to " CB  LEU A 143 " =    1.101
peak=    3.407 closest distance to " O   HOH Z 327 " =    1.749
peak=    3.402 closest distance to " CB  ALA A   1 " =    4.636
peak=    3.401 closest distance to " CB  ASN A  39 " =    0.895
peak=    3.395 closest distance to " CB  SER A 141 " =    0.987
peak=    3.393 closest distance to " O   HOH Z 345 " =    3.448
peak=    3.393 closest distance to " CD  ARG A 219 " =    1.071
peak=    3.381 closest distance to " O   HOH Z  64 " =    2.133
peak=    3.374 closest distance to " O   HOH Z 219 " =    1.952
peak=    3.372 closest distance to " O   HOH Z  59 " =    2.031
peak=    3.370 closest distance to " O   HOH Z  44 " =    1.629
peak=    3.368 closest distance to " O   HOH Z  54 " =    1.665
peak=    3.365 closest distance to " N   ASN A 127 " =    1.270
peak=    3.361 closest distance to " CB  MET A  47 " =    1.038
peak=    3.356 closest distance to " CG2 ILE A 120 " =    1.198
peak=    3.349 closest distance to " OG1 THR A 294 " =    2.462
peak=    3.345 closest distance to " CA  MET A 105 " =    0.991
peak=    3.343 closest distance to " CA  ALA A  84 " =    1.453
peak=    3.341 closest distance to " CA  ASP A 140 " =    1.179
peak=    3.336 closest distance to " O   HOH Z  93 " =    2.726
peak=    3.332 closest distance to " O   HOH Z 423 " =    2.942
peak=    3.329 closest distance to " O   HOH Z  97 " =    1.947
peak=    3.323 closest distance to " CZ2 TRP A 179 " =    1.663
peak=    3.319 closest distance to " NH2 ARG A 219 " =    1.829
peak=    3.318 closest distance to " O   HOH Z 166 " =    3.717
peak=    3.318 closest distance to " O   HOH Z 295 " =    1.497
peak=    3.317 closest distance to " CA  ALA A 154 " =    0.982
peak=    3.315 closest distance to " O   HOH Z  66 " =    2.079
peak=    3.312 closest distance to " CB  ALA A 248 " =    0.916
peak=    3.312 closest distance to " CB  ILE A 120 " =    1.250
peak=    3.311 closest distance to " CA  ARG A  36 " =    1.093
peak=    3.301 closest distance to " CB  GLU A  46 " =    0.990
peak=    3.301 closest distance to " O   ALA A 158 " =    1.286
peak=    3.297 closest distance to " O   HOH Z 391 " =    2.908
peak=    3.296 closest distance to " O   HOH Z 281 " =    4.100
peak=    3.293 closest distance to " O   HOH Z 329 " =    3.802
peak=    3.282 closest distance to " CB  THR A 157 " =    1.122
peak=    3.282 closest distance to " O   HOH Z 411 " =    1.806
peak=    3.281 closest distance to " CG  GLN A  11 " =    1.734
peak=    3.279 closest distance to " CB  ASN A 224 " =    1.026
peak=    3.278 closest distance to " O   HOH Z 407 " =    2.468
peak=    3.278 closest distance to " O   HOH Z 334 " =    1.434
peak=    3.274 closest distance to " O   HOH Z 261 " =    2.186
peak=    3.272 closest distance to " NE2 HIS A 207 " =    1.416
peak=    3.271 closest distance to " CG  LYS A  76 " =    0.964
peak=    3.267 closest distance to " CB  THR A  31 " =    1.792
peak=    3.262 closest distance to " O   HOH Z 409 " =    2.859
peak=    3.262 closest distance to " CE1 TYR A 186 " =    1.300
peak=    3.260 closest distance to " O   GLY A  57 " =    2.614
peak=    3.256 closest distance to " O   HOH Z 359 " =    3.914
peak=    3.255 closest distance to " CG BARG A 275 " =    1.425
peak=    3.255 closest distance to " O   HOH Z 353 " =    2.761
peak=    3.255 closest distance to " O   TRP A 274 " =    1.871
peak=    3.251 closest distance to " CB  HIS A 108 " =    0.825
peak=    3.250 closest distance to " CB  LEU A 255 " =    0.771
peak=    3.248 closest distance to " O   HOH Z 313 " =    1.930
peak=    3.247 closest distance to " CA  GLY A 267 " =    1.131
peak=    3.245 closest distance to " O   TYR A 116 " =    1.281
peak=    3.243 closest distance to " N   VAL A 126 " =    1.351
peak=    3.239 closest distance to " O   HOH Z 227 " =    1.682
peak=    3.237 closest distance to " O   HOH Z 185 " =    1.815
peak=    3.235 closest distance to " CG  MET A 185 " =    1.164
peak=    3.226 closest distance to " O   HOH Z 419 " =    1.939
peak=    3.224 closest distance to " OE1 GLN A  11 " =    2.155
peak=    3.221 closest distance to " O   HOH Z 148 " =    3.287
peak=    3.220 closest distance to " O   HOH Z 248 " =    1.697
peak=    3.211 closest distance to " CB  LYS A 117 " =    1.153
peak=    3.210 closest distance to " CB  ALA A   9 " =    1.572
peak=    3.209 closest distance to " O   HOH Z 271 " =    2.446
peak=    3.204 closest distance to " CA  ILE A  33 " =    1.540
peak=    3.203 closest distance to " CG2BVAL A  41 " =    0.789
peak=    3.203 closest distance to " O   HOH Z 403 " =    1.329
peak=    3.199 closest distance to " O   HOH Z  49 " =    2.950
peak=    3.197 closest distance to " CA  LYS A 117 " =    1.205
peak=    3.195 closest distance to " O   HOH Z 287 " =    2.186
peak=    3.190 closest distance to " O   HOH Z 383 " =    1.908
peak=    3.189 closest distance to " NH1BARG A 145 " =    1.017
peak=    3.188 closest distance to " CB  ARG A 138 " =    0.989
peak=    3.187 closest distance to " CA  SER A 146 " =    1.701
peak=    3.184 closest distance to " CB  TRP A 150 " =    1.303
peak=    3.168 closest distance to " OG  SER A  62 " =    3.003
peak=    3.167 closest distance to " CB  ALA A 291 " =    1.401
peak=    3.164 closest distance to " O   HOH Z 116 " =    1.770
peak=    3.163 closest distance to " O   HOH Z 263 " =    1.726
peak=    3.159 closest distance to " O   HOH Z  44 " =    3.181
peak=    3.158 closest distance to " O   HOH Z 285 " =    2.966
peak=    3.154 closest distance to " CD2 HIS A  81 " =    1.053
peak=    3.152 closest distance to " CA  TYR A 116 " =    1.353
peak=    3.145 closest distance to " O   HOH Z 171 " =    2.092
peak=    3.144 closest distance to " O   THR A 251 " =    1.300
peak=    3.139 closest distance to " NE  ARG A  79 " =    1.145
peak=    3.139 closest distance to " CB  SER A  62 " =    1.221
peak=    3.136 closest distance to " N   ASN A 252 " =    1.404
peak=    3.134 closest distance to " CG  MET A 185 " =    1.066
peak=    3.129 closest distance to " O   HOH Z 173 " =    1.749
peak=    3.127 closest distance to " O   HOH Z 109 " =    2.631
peak=    3.122 closest distance to " O   HOH Z 425 " =    1.204
peak=    3.109 closest distance to " O   HOH Z 213 " =    2.297
peak=    3.108 closest distance to " CG  GLN A  89 " =    1.424
peak=    3.105 closest distance to " O   HOH Z 298 " =    2.699
peak=    3.088 closest distance to " CA  ALA A 248 " =    1.228
peak=    3.088 closest distance to " CB  GLU A 236 " =    0.988
peak=    3.087 closest distance to " OD2 ASP A 200 " =    1.261
peak=    3.077 closest distance to " CB  GLU A 152 " =    1.429
peak=    3.075 closest distance to " O   HOH Z  49 " =    2.187
peak=    3.074 closest distance to " CB  VAL A 265 " =    1.954
peak=    3.073 closest distance to " O   HOH Z 302 " =    1.956
peak=    3.065 closest distance to " CB  ASN A 215 " =    1.114
peak=    3.044 closest distance to " O   HOH Z 152 " =    1.661
peak=    3.041 closest distance to " CB  LYS A 193 " =    0.935
peak=    3.033 closest distance to " N   SER A 135 " =    1.341
peak=    3.032 closest distance to " O   HOH Z 183 " =    1.345
peak=    3.031 closest distance to " CB  VAL A 126 " =    1.195
peak=    3.027 closest distance to " O   HOH Z 365 " =    2.912
peak=    3.026 closest distance to " O   HOH Z 188 " =    2.569
peak=    3.018 closest distance to " O   HOH Z 371 " =    3.396

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 213         
Filter by distance & map next to the model:
   mapped sites are within: 0.778 - 5.665
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 212 from: 213
   mapped sites are within: 0.778 - 5.665

peak=   -4.634 closest distance to " O   HOH Z 266 " =    4.924
peak=   -4.547 closest distance to " CB  PRO A 243 " =    2.611
peak=   -4.493 closest distance to " CD  ARG A 156 " =    2.076
peak=   -4.483 closest distance to " O   HOH Z 377 " =    2.138
peak=   -4.345 closest distance to " O   VAL A  67 " =    2.809
peak=   -4.283 closest distance to " SG  CYS A 254 " =    3.508
peak=   -4.169 closest distance to " CG  GLN A 223 " =    2.030
peak=   -4.148 closest distance to " O   HOH Z 198 " =    2.176
peak=   -4.109 closest distance to " N   ALA A  43 " =    2.633
peak=   -4.109 closest distance to " O   ILE A 109 " =    2.618
peak=   -4.091 closest distance to " O   HOH Z 372 " =    2.449
peak=   -4.056 closest distance to " C   HIS A 108 " =    1.110
peak=   -4.044 closest distance to " O   HOH Z 231 " =    2.287
peak=   -4.013 closest distance to " O   HOH Z  10 " =    1.517
peak=   -3.989 closest distance to " O   HOH Z 126 " =    1.878
peak=   -3.988 closest distance to " OG BSER A 134 " =    1.246
peak=   -3.960 closest distance to " CZ3 TRP A 179 " =    1.109
peak=   -3.948 closest distance to " CG1 VAL A 112 " =    2.840
peak=   -3.936 closest distance to " O   HOH Z 118 " =    3.266
peak=   -3.927 closest distance to " CE2 TYR A  30 " =    2.746
peak=   -3.869 closest distance to " O   HOH Z 389 " =    1.881
peak=   -3.858 closest distance to " O   HOH Z  43 " =    1.572
peak=   -3.831 closest distance to " O   HOH Z 435 " =    2.764
peak=   -3.824 closest distance to " SG ACYS A 201 " =    1.849
peak=   -3.811 closest distance to " NH2AARG A 275 " =    5.409
peak=   -3.808 closest distance to " CD1 PHE A  59 " =    1.853
peak=   -3.799 closest distance to " CG1 VAL A 250 " =    2.619
peak=   -3.774 closest distance to " CB  ALA A 291 " =    2.232
peak=   -3.762 closest distance to " O   HOH Z 353 " =    2.177
peak=   -3.753 closest distance to " CD1 LEU A 228 " =    2.334
peak=   -3.751 closest distance to " CG2 ILE A 263 " =    2.302
peak=   -3.743 closest distance to " O   PRO A 163 " =    2.116
peak=   -3.720 closest distance to " O   HOH Z 313 " =    1.987
peak=   -3.715 closest distance to " OG  SER A  97 " =    2.180
peak=   -3.711 closest distance to " O   PRO A 198 " =    1.324
peak=   -3.709 closest distance to " O   HOH Z 290 " =    1.248
peak=   -3.696 closest distance to " CA  GLY A 203 " =    2.369
peak=   -3.693 closest distance to " ND2 ASN A  45 " =    1.756
peak=   -3.690 closest distance to " O   HOH Z 211 " =    1.635
peak=   -3.681 closest distance to " CD  GLN A  58 " =    1.063
peak=   -3.681 closest distance to " O   HOH Z 196 " =    2.067
peak=   -3.672 closest distance to " CB  ALA A 291 " =    2.358
peak=   -3.671 closest distance to " CZ  PHE A  59 " =    1.631
peak=   -3.659 closest distance to " O   HOH Z 198 " =    1.406
peak=   -3.652 closest distance to " O   HOH Z  52 " =    1.354
peak=   -3.651 closest distance to " O   HOH Z 407 " =    3.198
peak=   -3.649 closest distance to " CE2 PHE A 218 " =    2.438
peak=   -3.646 closest distance to " CA  ASP A 298 " =    1.064
peak=   -3.644 closest distance to " OXT GLY A 302 " =    2.898
peak=   -3.641 closest distance to " CA  VAL A  67 " =    2.674
peak=   -3.623 closest distance to " OD1 ASN A 148 " =    1.630
peak=   -3.622 closest distance to " NH2 ARG A 159 " =    2.421
peak=   -3.618 closest distance to " O   HOH Z  60 " =    2.587
peak=   -3.618 closest distance to " CE  MET A 105 " =    2.301
peak=   -3.616 closest distance to " O   VAL A 189 " =    2.565
peak=   -3.615 closest distance to " O   HOH Z 185 " =    2.262
peak=   -3.596 closest distance to " NE2 GLN A  88 " =    1.896
peak=   -3.591 closest distance to " C   ASN A 285 " =    2.529
peak=   -3.588 closest distance to " CG  PHE A 283 " =    2.794
peak=   -3.576 closest distance to " O   HOH Z  73 " =    2.192
peak=   -3.571 closest distance to " O   HOH Z 311 " =    3.681
peak=   -3.570 closest distance to " OD1 ASP A 171 " =    1.608
peak=   -3.554 closest distance to " CB  TYR A  15 " =    2.175
peak=   -3.549 closest distance to " CD  ARG A 139 " =    1.589
peak=   -3.542 closest distance to " CG  ASP A 231 " =    0.811
peak=   -3.540 closest distance to " O   HOH Z  38 " =    1.444
peak=   -3.540 closest distance to " CB  ALA A  43 " =    2.534
peak=   -3.537 closest distance to " NH1 ARG A 195 " =    2.593
peak=   -3.536 closest distance to " CD1 LEU A 101 " =    2.417
peak=   -3.533 closest distance to " CZ  TYR A 169 " =    1.746
peak=   -3.531 closest distance to " OG BSER A 134 " =    1.742
peak=   -3.528 closest distance to " O   HOH Z 292 " =    4.626
peak=   -3.521 closest distance to " C   LEU A 143 " =    1.193
peak=   -3.517 closest distance to " O   HOH Z 111 " =    2.048
peak=   -3.513 closest distance to " CD2 PHE A 192 " =    2.068
peak=   -3.509 closest distance to " O   HOH Z  11 " =    1.797
peak=   -3.504 closest distance to " CB  PRO A 163 " =    2.536
peak=   -3.502 closest distance to " NH2 ARG A  79 " =    1.934
peak=   -3.497 closest distance to " O   GLY A 211 " =    1.508
peak=   -3.494 closest distance to " CD  ARG A 195 " =    5.206
peak=   -3.487 closest distance to " O   HOH Z 253 " =    3.928
peak=   -3.481 closest distance to " CG  ARG A 269 " =    2.591
peak=   -3.463 closest distance to " O   HOH Z 351 " =    1.532
peak=   -3.461 closest distance to " NH2BARG A 275 " =    1.831
peak=   -3.454 closest distance to " CB  ASN A  39 " =    2.351
peak=   -3.453 closest distance to " ND2 ASN A 249 " =    2.336
peak=   -3.451 closest distance to " ND2 ASN A  60 " =    1.411
peak=   -3.437 closest distance to " C   ALA A 158 " =    1.330
peak=   -3.432 closest distance to " O   PHE A 218 " =    1.601
peak=   -3.427 closest distance to " CG1 VAL A 112 " =    2.609
peak=   -3.423 closest distance to " ND2 ASN A  45 " =    1.097
peak=   -3.415 closest distance to " OG  SER A  62 " =    1.677
peak=   -3.410 closest distance to " CG  TRP A 266 " =    1.766
peak=   -3.410 closest distance to " CD2 LEU A 300 " =    2.890
peak=   -3.410 closest distance to " CD2 TYR A 247 " =    2.429
peak=   -3.409 closest distance to " CD1 LEU A 297 " =    2.445
peak=   -3.409 closest distance to " O   HOH Z  13 " =    1.628
peak=   -3.405 closest distance to " N   SER A 212 " =    2.066
peak=   -3.400 closest distance to " CA  GLY A 241 " =    3.098
peak=   -3.398 closest distance to " O   HOH Z  51 " =    1.639
peak=   -3.391 closest distance to " CD2 PHE A 225 " =    1.187
peak=   -3.379 closest distance to " OD2 ASP A 171 " =    1.814
peak=   -3.378 closest distance to " C   ILE A 234 " =    1.313
peak=   -3.377 closest distance to " CG  PRO A 163 " =    2.463
peak=   -3.376 closest distance to " O   PRO A 198 " =    1.327
peak=   -3.373 closest distance to " CG  MET A 105 " =    0.980
peak=   -3.373 closest distance to " O   HOH Z 426 " =    1.664
peak=   -3.373 closest distance to " CB  ALA A   7 " =    2.193
peak=   -3.370 closest distance to " O   SER A 135 " =    1.486
peak=   -3.366 closest distance to " CG1 VAL A 197 " =    2.182
peak=   -3.363 closest distance to " OD1 ASP A 191 " =    1.828
peak=   -3.356 closest distance to " O   HOH Z   6 " =    1.546
peak=   -3.348 closest distance to " CB  ASP A 132 " =    2.326
peak=   -3.348 closest distance to " O   HOH Z 348 " =    2.246
peak=   -3.345 closest distance to " CG2 VAL A 189 " =    2.105
peak=   -3.345 closest distance to " O   MET A  40 " =    2.813
peak=   -3.345 closest distance to " CG  ARG A  66 " =    2.345
peak=   -3.339 closest distance to " O   HOH Z  70 " =    2.193
peak=   -3.336 closest distance to " CB  ALA A 248 " =    2.398
peak=   -3.323 closest distance to " OD1 ASN A 187 " =    1.598
peak=   -3.317 closest distance to " O   HOH Z 394 " =    1.441
peak=   -3.317 closest distance to " O   HOH Z 298 " =    2.561
peak=   -3.311 closest distance to " CE3 TRP A 150 " =    2.132
peak=   -3.306 closest distance to " CB  ALA A 131 " =    2.073
peak=   -3.305 closest distance to " O   HOH Z 174 " =    2.946
peak=   -3.303 closest distance to " N   ALA A 248 " =    1.581
peak=   -3.298 closest distance to " O   HOH Z 102 " =    1.599
peak=   -3.297 closest distance to " CZ  PHE A  38 " =    2.482
peak=   -3.296 closest distance to " CD2 TYR A 293 " =    2.027
peak=   -3.292 closest distance to " N   ASP A 171 " =    2.417
peak=   -3.292 closest distance to " CG  GLU A   2 " =    1.907
peak=   -3.292 closest distance to " N   THR A 157 " =    1.547
peak=   -3.286 closest distance to " OH  TYR A 214 " =    1.273
peak=   -3.285 closest distance to " OE1 GLN A 223 " =    2.109
peak=   -3.280 closest distance to " OE1 GLN A  88 " =    1.221
peak=   -3.279 closest distance to " CA  GLY A 241 " =    2.293
peak=   -3.269 closest distance to " CB  TRP A  85 " =    2.475
peak=   -3.268 closest distance to " NH2 ARG A  79 " =    1.559
peak=   -3.264 closest distance to " O   HOH Z 359 " =    3.161
peak=   -3.262 closest distance to " CE  MET A 105 " =    2.268
peak=   -3.262 closest distance to " OH  TYR A 247 " =    2.055
peak=   -3.258 closest distance to " CD2 PHE A  61 " =    2.552
peak=   -3.256 closest distance to " OG  SER A  87 " =    1.457
peak=   -3.255 closest distance to " O   HOH Z 166 " =    1.560
peak=   -3.255 closest distance to " O   ALA A  10 " =    1.666
peak=   -3.254 closest distance to " O   HOH Z 166 " =    1.879
peak=   -3.254 closest distance to " NE  ARG A  36 " =    1.882
peak=   -3.249 closest distance to " O   LEU A 101 " =    2.727
peak=   -3.246 closest distance to " CB  CYS A 201 " =    2.614
peak=   -3.245 closest distance to " O   HOH Z 234 " =    4.224
peak=   -3.241 closest distance to " CD2 LEU A 237 " =    2.696
peak=   -3.240 closest distance to " O   HOH Z 191 " =    5.665
peak=   -3.237 closest distance to " N   ALA A 226 " =    2.143
peak=   -3.234 closest distance to " O   HOH Z 281 " =    2.698
peak=   -3.232 closest distance to " O   HOH Z  93 " =    2.211
peak=   -3.231 closest distance to " O   HOH Z 385 " =    1.941
peak=   -3.231 closest distance to " O   HOH Z 350 " =    1.482
peak=   -3.225 closest distance to " O   ARG A 145 " =    1.599
peak=   -3.221 closest distance to " CB  ALA A 248 " =    1.994
peak=   -3.220 closest distance to " CG1 VAL A 125 " =    2.395
peak=   -3.217 closest distance to " O   HOH Z 385 " =    2.107
peak=   -3.217 closest distance to " CB  ASP A 286 " =    2.128
peak=   -3.216 closest distance to " SD  MET A 188 " =    2.299
peak=   -3.207 closest distance to " OG BSER A 210 " =    2.105
peak=   -3.202 closest distance to " O   GLY A  80 " =    2.516
peak=   -3.202 closest distance to " O   HOH Z 184 " =    1.814
peak=   -3.202 closest distance to " CG  GLU A 277 " =    1.177
peak=   -3.199 closest distance to " O   HOH Z 317 " =    1.611
peak=   -3.198 closest distance to " CB  CYS A 254 " =    2.331
peak=   -3.197 closest distance to " O   HOH Z 322 " =    1.578
peak=   -3.197 closest distance to " CA  GLY A 241 " =    2.810
peak=   -3.196 closest distance to " O   LYS A 117 " =    1.749
peak=   -3.195 closest distance to " CA  ASP A  27 " =    2.535
peak=   -3.187 closest distance to " O   TRP A  70 " =    1.526
peak=   -3.187 closest distance to " O   HOH Z 357 " =    2.068
peak=   -3.185 closest distance to " CG  ASN A 301 " =    1.954
peak=   -3.185 closest distance to " O   HOH Z 103 " =    1.889
peak=   -3.181 closest distance to " O   HOH Z 177 " =    1.692
peak=   -3.180 closest distance to " CE3 TRP A 274 " =    2.467
peak=   -3.176 closest distance to " C   LEU A 222 " =    0.778
peak=   -3.173 closest distance to " O   HOH Z 275 " =    1.555
peak=   -3.167 closest distance to " CE BMET A  47 " =    2.151
peak=   -3.160 closest distance to " O   GLN A 240 " =    2.458
peak=   -3.158 closest distance to " O   HOH Z 393 " =    1.424
peak=   -3.155 closest distance to " O   HOH Z  88 " =    2.223
peak=   -3.153 closest distance to " O   HOH Z 414 " =    1.675
peak=   -3.150 closest distance to " N   SER A 276 " =    1.296
peak=   -3.149 closest distance to " O   VAL A 174 " =    2.073
peak=   -3.148 closest distance to " CD  GLU A 236 " =    1.059
peak=   -3.147 closest distance to " O   HOH Z 111 " =    1.331
peak=   -3.147 closest distance to " CG  GLU A 152 " =    1.302
peak=   -3.143 closest distance to " O   HOH Z  51 " =    1.364
peak=   -3.142 closest distance to " CD1 ILE A 199 " =    2.554
peak=   -3.140 closest distance to " O   HOH Z 377 " =    1.503
peak=   -3.137 closest distance to " CB  ASP A 132 " =    2.349
peak=   -3.136 closest distance to " CE3 TRP A  70 " =    1.826
peak=   -3.135 closest distance to " O   HOH Z  44 " =    2.192
peak=   -3.125 closest distance to " CG2 THR A 221 " =    2.231
peak=   -3.117 closest distance to " CA  GLY A 133 " =    2.067
peak=   -3.117 closest distance to " CD1 ILE A 151 " =    2.375
peak=   -3.117 closest distance to " O   HOH Z 193 " =    1.568
peak=   -3.116 closest distance to " O   HOH Z  76 " =    1.942
peak=   -3.111 closest distance to " CZ2 TRP A 179 " =    2.318
peak=   -3.105 closest distance to " O   HOH Z 114 " =    1.679
peak=   -3.104 closest distance to " O   HOH Z 323 " =    1.424
peak=   -3.103 closest distance to " NH2 ARG A  66 " =    2.108
peak=   -3.090 closest distance to " O   GLY A  80 " =    2.609
peak=   -3.089 closest distance to " O   HOH Z 139 " =    2.896
peak=   -3.082 closest distance to " NH1 ARG A  36 " =    2.031
peak=   -3.068 closest distance to " CD2 PHE A  59 " =    2.498
peak=   -3.063 closest distance to " OG  SER A  97 " =    2.118
peak=   -3.025 closest distance to " O   PRO A 198 " =    1.679

================= 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    :  0.2696 0.2718   5.888770e+00   5.902316e+00
   1_bss:  0.2531 0.2569   5.857580e+00   5.868452e+00
   1_xyz:  0.1586 0.1771   5.403930e+00   5.507734e+00
   1_adp:  0.1475 0.1797   5.353832e+00   5.527173e+00
   1_occ:  0.1470 0.1796   5.351078e+00   5.525315e+00
   2_bss:  0.1458 0.1774   5.345357e+00   5.518162e+00
   2_xyz:  0.1198 0.1579   5.181644e+00   5.397116e+00
   2_adp:  0.1143 0.1553   5.148310e+00   5.379835e+00
   2_occ:  0.1142 0.1552   5.148105e+00   5.380053e+00
   3_bss:  0.1140 0.1550   5.147104e+00   5.378938e+00
   3_xyz:  0.1083 0.1551   5.121627e+00   5.374282e+00
   3_adp:  0.1078 0.1546   5.117227e+00   5.370271e+00
   3_occ:  0.1077 0.1547   5.117420e+00   5.370871e+00
   4_bss:  0.1079 0.1543   5.117443e+00   5.369402e+00
   4_xyz:  0.1093 0.1555   5.127818e+00   5.377540e+00
   4_adp:  0.1084 0.1573   5.129221e+00   5.385402e+00
   4_occ:  0.1083 0.1573   5.129399e+00   5.385882e+00
   5_bss:  0.1083 0.1573   5.129521e+00   5.385922e+00
   5_xyz:  0.1053 0.1580   5.117880e+00   5.387598e+00
   5_adp:  0.1053 0.1578   5.116323e+00   5.385951e+00
   5_occ:  0.1053 0.1578   5.116469e+00   5.386260e+00
   5_bss:  0.1052 0.1578   5.116429e+00   5.386210e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.327  47.846   0.263  -2.911  -1.458  -0.000  -0.000  -0.000
   1_xyz:  0.327  47.846   0.263  -2.911  -1.458  -0.000  -0.000  -0.000
   1_adp:  0.327  47.846   0.263  -2.911  -1.458  -0.000  -0.000  -0.000
   1_occ:  0.327  47.846   0.263  -2.911  -1.458  -0.000  -0.000  -0.000
   2_bss:  0.332  55.578  -1.880  -3.015  -1.852  -0.000  -0.000  -0.000
   2_xyz:  0.332  55.578  -1.880  -3.015  -1.852  -0.000  -0.000  -0.000
   2_adp:  0.332  55.578  -1.880  -3.015  -1.852  -0.000  -0.000  -0.000
   2_occ:  0.332  55.578  -1.880  -3.015  -1.852  -0.000  -0.000  -0.000
   3_bss:  0.327  55.578  -2.155  -2.639  -1.625  -0.000  -0.000  -0.000
   3_xyz:  0.327  55.578  -2.155  -2.639  -1.625  -0.000  -0.000  -0.000
   3_adp:  0.327  55.578  -2.155  -2.639  -1.625  -0.000  -0.000  -0.000
   3_occ:  0.327  55.578  -2.155  -2.639  -1.625  -0.000  -0.000  -0.000
   4_bss:  0.327  55.578  -2.225  -2.503  -1.545  -0.000  -0.000  -0.000
   4_xyz:  0.327  55.578  -2.225  -2.503  -1.545  -0.000  -0.000  -0.000
   4_adp:  0.327  55.578  -2.225  -2.503  -1.545  -0.000  -0.000  -0.000
   4_occ:  0.327  55.578  -2.225  -2.503  -1.545  -0.000  -0.000  -0.000
   5_bss:  0.327  55.578  -2.062  -2.272  -1.342  -0.000  -0.000  -0.000
   5_xyz:  0.327  55.578  -2.062  -2.272  -1.342  -0.000  -0.000  -0.000
   5_adp:  0.327  55.578  -2.062  -2.272  -1.342  -0.000  -0.000  -0.000
   5_occ:  0.327  55.578  -2.062  -2.272  -1.342  -0.000  -0.000  -0.000
   5_bss:  0.324  55.581  -1.863  -2.040  -1.123  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  27.275 0.7914  0.9549    21388.069
   1_bss:  26.070 0.8025  0.9266    18692.761
   1_xyz:  16.232 0.8978  0.9953     8225.507
   1_adp:  16.728 0.8930  0.9930     8484.536
   1_occ:  16.691 0.8932  0.9930     8424.494
   2_bss:  16.512 0.8948  0.9633     8283.003
   2_xyz:  14.079 0.9145  0.9736     6503.978
   2_adp:  13.729 0.9173  0.9729     6219.952
   2_occ:  13.731 0.9173  0.9727     6220.323
   3_bss:  13.716 0.9174  0.9764     6207.415
   3_xyz:  13.571 0.9187  0.9760     6161.356
   3_adp:  13.472 0.9195  0.9723     6118.496
   3_occ:  13.483 0.9194  0.9722     6122.664
   4_bss:  13.481 0.9193  0.9733     6090.897
   4_xyz:  13.616 0.9183  0.9723     6172.524
   4_adp:  13.802 0.9169  0.9660     6247.876
   4_occ:  13.811 0.9168  0.9659     6254.907
   5_bss:  13.814 0.9168  0.9727     6255.893
   5_xyz:  13.849 0.9165  0.9725     6292.996
   5_adp:  13.817 0.9167  0.9665     6269.396
   5_occ:  13.824 0.9166  0.9664     6272.720
   5_bss:  13.824 0.9166  0.9740     6270.263
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6088e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6088e-01
   1_xyz:   0.991  0.007  0.067 14.816  0.004  4.113   5.6772e-02
   1_adp:   0.991  0.007  0.067 14.816  0.004  4.113   5.6772e-02
   1_occ:   0.991  0.007  0.067 14.816  0.004  4.113   5.6772e-02
   2_bss:   0.991  0.007  0.067 14.816  0.004  4.113   5.6772e-02
   2_xyz:   1.023  0.008  0.077 14.638  0.004  4.123   6.2537e-02
   2_adp:   1.023  0.008  0.077 14.638  0.004  4.123   6.2537e-02
   2_occ:   1.023  0.008  0.077 14.638  0.004  4.123   6.2537e-02
   3_bss:   1.023  0.008  0.077 14.638  0.004  4.123   6.2537e-02
   3_xyz:   1.088  0.010  0.084 14.928  0.005  4.127   7.2943e-02
   3_adp:   1.088  0.010  0.084 14.928  0.005  4.127   7.2943e-02
   3_occ:   1.088  0.010  0.084 14.928  0.005  4.127   7.2943e-02
   4_bss:   1.088  0.010  0.084 14.928  0.005  4.127   7.2943e-02
   4_xyz:   1.003  0.008  0.077 14.602  0.004  4.127   6.1285e-02
   4_adp:   1.003  0.008  0.077 14.602  0.004  4.127   6.1285e-02
   4_occ:   1.003  0.008  0.077 14.602  0.004  4.127   6.1285e-02
   5_bss:   1.003  0.008  0.077 14.602  0.004  4.127   6.1285e-02
   5_xyz:   1.115  0.010  0.085 14.910  0.005  4.129   7.5464e-02
   5_adp:   1.115  0.010  0.085 14.910  0.005  4.129   7.5464e-02
   5_occ:   1.115  0.010  0.085 14.910  0.005  4.129   7.5464e-02
   5_bss:   1.115  0.010  0.085 14.910  0.005  4.129   7.5464e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4192e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4192e-01
   1_xyz:   8.731  0.043  0.252 83.872  0.034  2.335   5.6975e-02
   1_adp:   8.731  0.043  0.252 83.872  0.034  2.335   5.6975e-02
   1_occ:   8.731  0.043  0.252 83.872  0.034  2.335   5.6975e-02
   2_bss:   8.731  0.043  0.252 83.872  0.034  2.335   5.6975e-02
   2_xyz:   7.142  0.046  0.235 83.658  0.037  2.342   4.8169e-02
   2_adp:   7.142  0.046  0.235 83.658  0.037  2.342   4.8169e-02
   2_occ:   7.142  0.046  0.235 83.658  0.037  2.342   4.8169e-02
   3_bss:   7.142  0.046  0.235 83.658  0.037  2.342   4.8169e-02
   3_xyz:   7.348  0.048  0.271 83.013  0.040  2.281   6.1898e-02
   3_adp:   7.348  0.048  0.271 83.013  0.040  2.281   6.1898e-02
   3_occ:   7.348  0.048  0.271 83.013  0.040  2.281   6.1898e-02
   4_bss:   7.348  0.048  0.271 83.013  0.040  2.281   6.1898e-02
   4_xyz:   7.283  0.043  0.234 83.453  0.037  2.343   4.4828e-02
   4_adp:   7.283  0.043  0.234 83.453  0.037  2.343   4.4828e-02
   4_occ:   7.283  0.043  0.234 83.453  0.037  2.343   4.4828e-02
   5_bss:   7.283  0.043  0.234 83.453  0.037  2.343   4.4828e-02
   5_xyz:   7.080  0.049  0.270 83.013  0.040  2.279   6.1300e-02
   5_adp:   7.080  0.049  0.270 83.013  0.040  2.279   6.1300e-02
   5_occ:   7.080  0.049  0.270 83.013  0.040  2.279   6.1300e-02
   5_bss:   7.080  0.049  0.270 83.013  0.040  2.279   6.1300e-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:  72.44   0.00  16.50  72.44   0.00  12.70  62.89   5.83  37.20
   1_occ:  72.44   0.00  16.50  72.44   0.00  12.70  62.89   5.83  37.20
   2_bss:  72.44   0.00  16.50  72.44   0.00  12.70  62.89   5.83  37.20
   2_xyz:  72.44   0.00  16.50  72.44   0.00  12.70  62.89   5.83  37.20
   2_adp:  73.84   1.60  16.92  73.84   1.60  12.99  69.46   3.74  38.32
   2_occ:  73.84   1.60  16.92  73.84   1.60  12.99  69.46   3.74  38.32
   3_bss:  73.84   1.60  16.92  73.84   1.60  12.99  69.46   3.74  38.32
   3_xyz:  73.84   1.60  16.92  73.84   1.60  12.99  69.46   3.74  38.32
   3_adp:  74.77   1.58  16.77  74.77   1.58  12.88  70.24   3.30  37.96
   3_occ:  74.77   1.58  16.77  74.77   1.58  12.88  70.24   3.30  37.96
   4_bss:  74.77   1.58  16.77  74.77   1.58  12.88  70.24   3.30  37.96
   4_xyz:  74.77   1.58  16.77  74.77   1.58  12.88  70.24   3.30  37.96
   4_adp:  84.50   0.12  17.08  84.50   0.12  12.91  75.22   4.40  39.76
   4_occ:  84.50   0.12  17.08  84.50   0.12  12.91  75.22   4.40  39.76
   5_bss:  84.50   0.12  17.08  84.50   0.12  12.91  75.22   4.40  39.76
   5_xyz:  84.50   0.12  17.08  84.50   0.12  12.91  75.22   4.40  39.76
   5_adp:  85.64   0.00  16.89  85.64   0.00  12.73  75.72   5.89  39.53
   5_occ:  85.64   0.00  16.89  85.64   0.00  12.73  75.72   5.89  39.53
   5_bss:  85.64   0.00  16.89  85.64   0.00  12.73  75.72   5.89  39.53
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.030    0.005    0.230
   1_adp:    1.030    0.005    0.230
   1_occ:    1.030    0.005    0.230
   2_bss:    1.030    0.005    0.230
   2_xyz:    0.693    0.013    0.273
   2_adp:    0.693    0.013    0.273
   2_occ:    0.693    0.013    0.273
   3_bss:    0.693    0.013    0.273
   3_xyz:    0.746    0.019    0.295
   3_adp:    0.746    0.019    0.295
   3_occ:    0.746    0.019    0.295
   4_bss:    0.746    0.019    0.295
   4_xyz:    0.878    0.018    0.300
   4_adp:    0.878    0.018    0.300
   4_occ:    0.878    0.018    0.300
   5_bss:    0.878    0.018    0.300
   5_xyz:    0.958    0.031    0.307
   5_adp:    0.958    0.031    0.307
   5_occ:    0.958    0.031    0.307
   5_bss:    0.958    0.031    0.307
------------------------------------------------------------------------

CPU time actual refinement: 328.17


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1027/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_1027/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1027/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1027/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1027/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 328.03 
  Macro-tasks:
    bulk solvent and scale       = 39.47  
    individual site refinement   = 130.42 
    weights calculation          = 28.35  
    collect and process          = 6.66   
    model show statistics        = 0.07   
    TOTAL for macro-tasks        = 204.97 
  Micro-tasks:
    mask                            = 1.12   
    f_calc                          = 106.12 
    alpha_beta                      = 8.24   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 110.37 
    fmodel                         = 6.79   
    r_factors                      = 0.14   
    phase_errors                   = 12.01  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 246.22 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.647 micro seconds
Total CPU time: 5.69 minutes
from_scatterers_fft:    668 calls, 105.58 s
gradients_fft:          613 calls,  98.79 s

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

# Date 2008-01-16 Time 06:15:36 PST -0800 (1200492936.07 s)
Start R-work = 0.2696, R-free = 0.2718 (no bulk solvent and anisotropic scale)
Final R-work = 0.1286, R-free = 0.1762 (no bulk solvent and anisotropic scale)

Start R-work = 0.2531, R-free = 0.2569
Final R-work = 0.1052, R-free = 0.1578