# Date 2008-01-16 Time 04:04:27 PST -0800 (1200485067.98 s)
#phil __OFF__

Command line arguments: "../168.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 23875
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 168

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.845, 46.6953, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.76, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 46.6953, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7343 1.9606
Completeness in resolution range: 0.962794
Completeness with d_max=infinity: 0.959775

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7343
                             d_min =   1.9606

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 46.6953, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7343 1.9606
Completeness in resolution range: 0.962794
Completeness with d_max=infinity: 0.959775

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7347 -  4.1946 [2144/2171]  1929   215  10.0%
  bin  2:  4.1946 -  3.3421 [2040/2056]  1836   204  10.0%
  bin  3:  3.3421 -  2.9234 [2041/2060]  1838   203   9.9%
  bin  4:  2.9234 -  2.6578 [1998/2028]  1797   201  10.1%
  bin  5:  2.6578 -  2.4683 [1994/2013]  1792   202  10.1%
  bin  6:  2.4683 -  2.3233 [1976/2012]  1785   191   9.7%
  bin  7:  2.3233 -  2.2074 [1987/2020]  1785   202  10.2%
  bin  8:  2.2074 -  2.1116 [1953/1988]  1756   197  10.1%
  bin  9:  2.1116 -  2.0305 [1950/1977]  1757   193   9.9%
  bin 10:  2.0305 -  1.9606 [1506/2021]  1355   151  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_168/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.12 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.34 -     2.05: 12
        2.05 -     2.76: 478
        2.76 -     3.47: 4631
        3.47 -     4.19: 9583
        4.19 -     4.90: 14162
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.337 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.400 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.500 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.882 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28861 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_168/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_168/model_refine_001.geo

CPU time processing inputs: 7.83


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 46.69535 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3602   r_free= 0.3625   ksol= 0.00   Bsol= 0.00   scale= 0.972    |
|                                                                             |
| 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:   0.42 A                  |
| x-ray target function (ml) for work reflections: 6.114556                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7347 -  4.6781 0.99   1388  153 0.3044 0.2965      6.3961      6.3892|
|  2:  4.6781 -  3.7330 0.99   1329  150 0.2876 0.2868      6.5107      6.5395|
|  3:  3.7330 -  3.2670 0.99   1318  149 0.3157 0.3258      6.4259      6.5171|
|  4:  3.2670 -  2.9710 0.99   1298  136 0.3296 0.3656       6.297       6.379|
|  5:  2.9710 -  2.7595 0.99   1291  145 0.3606 0.3567      6.1703      6.1448|
|  6:  2.7595 -  2.5977 0.99   1291  146 0.3845 0.3999      6.1238      6.0398|
|  7:  2.5977 -  2.4683 0.99   1277  146 0.3858 0.3668      6.0872      6.0128|
|  8:  2.4683 -  2.3613 0.98   1289  137 0.4013 0.3873      6.0429      6.0623|
|  9:  2.3613 -  2.2707 0.98   1265  145 0.4178 0.4381      6.0006      6.0315|
| 10:  2.2707 -  2.1926 0.98   1254  132 0.4081 0.4236      5.9835      5.9735|
| 11:  2.1926 -  2.1243 1.00   1277  150 0.4129 0.4048      5.9192      5.9706|
| 12:  2.1243 -  2.0637 0.97   1271  134 0.4202 0.3883      5.8908      5.8544|
| 13:  2.0637 -  2.0095 0.98   1254  139 0.4147 0.4311      5.7916      5.7462|
| 14:  2.0095 -  1.9606 0.65    828   97 0.4240 0.3855      5.7842      5.6253|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7347 -  4.6781  1388   153  0.76  28.94   0.86     0.77      50736.15|
|  2:  4.6781 -  3.7330  1329   150  0.81  25.46   0.98     0.90      60501.28|
|  3:  3.7330 -  3.2670  1318   149  0.75  30.61   1.00     0.94      60972.63|
|  4:  3.2670 -  2.9710  1298   136  0.72  34.05   1.00     0.92      53390.97|
|  5:  2.9710 -  2.7595  1291   145  0.67  38.06   0.98     0.89      42971.43|
|  6:  2.7595 -  2.5977  1291   146  0.67  38.19   0.97     0.90      36561.91|
|  7:  2.5977 -  2.4683  1277   146  0.67  38.01   0.99     0.90      33424.05|
|  8:  2.4683 -  2.3613  1289   137  0.64  40.50   1.01     0.88      32120.06|
|  9:  2.3613 -  2.2707  1265   145  0.62  42.99   1.01     0.85      31131.79|
| 10:  2.2707 -  2.1926  1254   132  0.62  42.39   1.05     0.86      28792.12|
| 11:  2.1926 -  2.1243  1277   150  0.62  42.72   1.03     0.88      25909.52|
| 12:  2.1243 -  2.0637  1271   134  0.64  41.10   1.04     0.92      22752.37|
| 13:  2.0637 -  2.0095  1254   139  0.63  42.29   1.05     0.89      19643.08|
| 14:  2.0095 -  1.9606   828    97  0.64  40.93   1.02     0.80      15718.70|
|alpha:            min =        0.77 max =            0.94 mean =         0.88|
|beta:             min =    15718.70 max =        60972.63 mean =     37571.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.68|
|phase err.(work): min =        0.00 max =           89.98 mean =        37.38|
|phase err.(test): min =        0.00 max =           89.49 mean =        37.37|
|-----------------------------------------------------------------------------|

============================== 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 = 4.506483              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.389   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.855823              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.348   (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 |  1.337 -  1.693:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.693 -  2.049:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.049 -  2.406:       33 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.406 -  2.762:      445 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.762 -  3.118:     2272 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.118 -  3.475:     2359 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.475 -  3.831:     4507 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.831 -  4.187:     5076 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.187 -  4.544:     6349 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.544 -  4.900:     7813 |
|-----------------------------------------------------------------------------|
|-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 |        0.190 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.337 |       0.632 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.463)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3602   r_free= 0.3625   ksol= 0.00   Bsol= 0.00   scale= 0.972    |
|                                                                             |
| 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:   0.42 A                  |
| x-ray target function (ml) for work reflections: 6.114556                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3477   r_free= 0.3482   ksol= 0.32   Bsol= 22.80   scale= 0.981   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.39,-2.07,-0.39,-0.00,-0.00,-0.00); trace/3= -0.69                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 6.095371                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.988109              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.289   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.435703              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.113   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3477      final r-factor (work) = 0.1999          |
| start r-factor (free) = 0.3482      final r-factor (free) = 0.2208          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.3646 = 3.99 * 0.50 * 6.1053 + 1.00 * 0.1904                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6898 = 3.99 * 0.50 * 5.8274 + 1.00 * 0.0697                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1999      final r-factor (work) = 0.1819          |
| start r-factor (free) = 0.2208      final r-factor (free) = 0.2283          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5451 = 0.44 * 1.00 * 5.8274 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4208 = 0.44 * 1.00 * 5.5341 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.463)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.85   17.53    None  None   None       |
|    all(noH): 2823   0      0.00    74.85   17.53    None  None   None       |
|    Sol.    : 438    0      7.28    73.62   39.66    None  None   None       |
|    Mac.    : 2385   0      0.00    74.85   13.46    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 -   7.485:  483   |   5:    37.424 -  44.909:  118        |
|      1:     7.485 -  14.970: 1266   |   6:    44.909 -  52.394:  100        |
|      2:    14.970 -  22.454:  456   |   7:    52.394 -  59.878:   62        |
|      3:    22.454 -  29.939:  172   |   8:    59.878 -  67.363:   35        |
|      4:    29.939 -  37.424:  120   |   9:    67.363 -  74.848:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1819 r_free = 0.2283             target_work(ml) = 5.550         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1816 r_free = 0.2280             target_work(ml) = 5.549         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1816   r_free= 0.2280   ksol= 0.32   Bsol= 22.80   scale= 1.043   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.39,-2.07,-0.39,-0.00,-0.00,-0.00); trace/3= -0.69                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.548881                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1776   r_free= 0.2250   ksol= 0.32   Bsol= 31.80   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-2.70,-1.61,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.538316                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.553721              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.212   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.155535              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.407  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1776      final r-factor (work) = 0.1308          |
| start r-factor (free) = 0.2250      final r-factor (free) = 0.1745          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1530 = 2.55 * 0.50 * 5.5474 + 1.00 * 0.0697                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9644 = 2.55 * 0.50 * 5.4121 + 1.00 * 0.0539                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1308      final r-factor (work) = 0.1247          |
| start r-factor (free) = 0.1745      final r-factor (free) = 0.1654          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8514 = 0.16 * 1.00 * 5.4121 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8222 = 0.16 * 1.00 * 5.2405 + 1.00 * 0.0071                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.463)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.43    78.39   17.10    None  None   None       |
|    all(noH): 2823   0      1.43    78.39   17.10    None  None   None       |
|    Sol.    : 438    0      5.69    71.56   38.41    None  None   None       |
|    Mac.    : 2385   0      1.43    78.39   13.18    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:     1.428 -   9.124:  724   |   5:    39.908 -  47.604:  131        |
|      1:     9.124 -  16.820: 1261   |   6:    47.604 -  55.300:   85        |
|      2:    16.820 -  24.516:  323   |   7:    55.300 -  62.996:   42        |
|      3:    24.516 -  32.212:  125   |   8:    62.996 -  70.692:   12        |
|      4:    32.212 -  39.908:  116   |   9:    70.692 -  78.388:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1247 r_free = 0.1654             target_work(ml) = 5.209         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1246 r_free = 0.1654             target_work(ml) = 5.208         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1246   r_free= 0.1654   ksol= 0.32   Bsol= 31.80   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-2.70,-1.61,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.207965                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1247   r_free= 0.1646   ksol= 0.32   Bsol= 35.65   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.98,-2.59,-1.67,-0.00,-0.00,-0.00); trace/3= -2.41                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.206320                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.938934              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.557  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.646438              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.949  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1247      final r-factor (work) = 0.1129          |
| start r-factor (free) = 0.1646      final r-factor (free) = 0.1541          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1342 = 1.94 * 0.50 * 5.2406 + 1.00 * 0.0536                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0598 = 1.94 * 0.50 * 5.1616 + 1.00 * 0.0558                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1129      final r-factor (work) = 0.1102          |
| start r-factor (free) = 0.1541      final r-factor (free) = 0.1541          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3437 = 0.65 * 1.00 * 5.1616 + 1.00 * 0.0070                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3190 = 0.65 * 1.00 * 5.1213 + 1.00 * 0.0083                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.463)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.53    88.02   17.29    None  None   None       |
|    all(noH): 2823   0      1.53    88.02   17.29    None  None   None       |
|    Sol.    : 438    0      3.02    78.33   39.90    None  None   None       |
|    Mac.    : 2385   0      1.53    88.02   13.14    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:     1.525 -  10.175: 1020   |   5:    44.774 -  53.423:  111        |
|      1:    10.175 -  18.825: 1108   |   6:    53.423 -  62.073:   71        |
|      2:    18.825 -  27.474:  240   |   7:    62.073 -  70.723:   23        |
|      3:    27.474 -  36.124:  118   |   8:    70.723 -  79.372:   11        |
|      4:    36.124 -  44.774:  118   |   9:    79.372 -  88.022:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1102 r_free = 0.1541             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1102 r_free = 0.1540             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1102   r_free= 0.1540   ksol= 0.32   Bsol= 35.65   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.98,-2.59,-1.67,-0.00,-0.00,-0.00); trace/3= -2.41                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.121551                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1101   r_free= 0.1539   ksol= 0.32   Bsol= 38.75   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.02,-2.47,-1.59,-0.00,-0.00,-0.00); trace/3= -2.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.121063                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.745576              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.727  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.474794              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.337  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1101      final r-factor (work) = 0.1081          |
| start r-factor (free) = 0.1539      final r-factor (free) = 0.1530          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5254 = 1.75 * 0.50 * 5.1210 + 1.00 * 0.0558                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5161 = 1.75 * 0.50 * 5.1138 + 1.00 * 0.0529                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1081      final r-factor (work) = 0.1077          |
| start r-factor (free) = 0.1530      final r-factor (free) = 0.1533          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4363 = 0.47 * 1.00 * 5.1138 + 1.00 * 0.0083                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4336 = 0.47 * 1.00 * 5.1078 + 1.00 * 0.0084                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.463)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.22    90.09   17.10    None  None   None       |
|    all(noH): 2823   0      1.22    90.09   17.10    None  None   None       |
|    Sol.    : 438    0      4.52    79.80   39.49    None  None   None       |
|    Mac.    : 2385   0      1.22    90.09   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:     1.220 -  10.107: 1044   |   5:    45.656 -  54.543:  104        |
|      1:    10.107 -  18.994: 1093   |   6:    54.543 -  63.430:   61        |
|      2:    18.994 -  27.881:  236   |   7:    63.430 -  72.317:   20        |
|      3:    27.881 -  36.769:  126   |   8:    72.317 -  81.205:    8        |
|      4:    36.769 -  45.656:  128   |   9:    81.205 -  90.092:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1077 r_free = 0.1533             target_work(ml) = 5.110         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1076 r_free = 0.1533             target_work(ml) = 5.110         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1076   r_free= 0.1533   ksol= 0.32   Bsol= 38.75   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.02,-2.47,-1.59,-0.00,-0.00,-0.00); trace/3= -2.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.110044                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1075   r_free= 0.1533   ksol= 0.32   Bsol= 39.72   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,-2.27,-1.40,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.110068                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.768761              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 153.009  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.057238              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.450  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1075      final r-factor (work) = 0.1065          |
| start r-factor (free) = 0.1533      final r-factor (free) = 0.1534          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5707 = 1.77 * 0.50 * 5.1084 + 1.00 * 0.0529                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5691 = 1.77 * 0.50 * 5.1060 + 1.00 * 0.0535                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1065      final r-factor (work) = 0.1064          |
| start r-factor (free) = 0.1534      final r-factor (free) = 0.1542          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4066 = 1.06 * 1.00 * 5.1060 + 1.00 * 0.0084                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4074 = 1.06 * 1.00 * 5.1063 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.463)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.93    91.79   16.97    None  None   None       |
|    all(noH): 2823   0      0.93    91.79   16.97    None  None   None       |
|    Sol.    : 438    0      6.12    81.35   39.52    None  None   None       |
|    Mac.    : 2385   0      0.93    91.79   12.83    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:     0.931 -  10.017: 1062   |   5:    46.361 -  55.446:  101        |
|      1:    10.017 -  19.103: 1093   |   6:    55.446 -  64.532:   55        |
|      2:    19.103 -  28.189:  219   |   7:    64.532 -  73.618:   18        |
|      3:    28.189 -  37.275:  133   |   8:    73.618 -  82.704:    9        |
|      4:    37.275 -  46.361:  130   |   9:    82.704 -  91.790:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1064 r_free = 0.1542             target_work(ml) = 5.109         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1064 r_free = 0.1541             target_work(ml) = 5.109         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1064   r_free= 0.1541   ksol= 0.32   Bsol= 39.72   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,-2.27,-1.40,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.109351                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7347 -  4.6781 0.99   1388  153 0.0989 0.1219       5.368      5.5032|
|  2:  4.6781 -  3.7330 0.99   1329  150 0.0820 0.1103      5.4097      5.6178|
|  3:  3.7330 -  3.2670 0.99   1318  149 0.1024 0.1518      5.4481      5.8383|
|  4:  3.2670 -  2.9710 0.99   1298  136 0.1116 0.1541      5.3976      5.5807|
|  5:  2.9710 -  2.7595 0.99   1291  145 0.1208 0.1592      5.2673      5.4579|
|  6:  2.7595 -  2.5977 0.99   1291  146 0.1147 0.1867      5.1593      5.4081|
|  7:  2.5977 -  2.4683 0.99   1277  146 0.1149 0.1582      5.1077       5.344|
|  8:  2.4683 -  2.3613 0.98   1289  137 0.1108 0.1618       5.044      5.2902|
|  9:  2.3613 -  2.2707 0.98   1265  145 0.1120 0.1778      4.9892      5.2665|
| 10:  2.2707 -  2.1926 0.98   1254  132 0.1068 0.1690      4.9426      5.1688|
| 11:  2.1926 -  2.1243 1.00   1277  150 0.1086 0.1755       4.912      5.2855|
| 12:  2.1243 -  2.0637 0.97   1271  134 0.1055 0.1624      4.8425      5.1525|
| 13:  2.0637 -  2.0095 0.98   1254  139 0.1058 0.1671      4.7605      5.0048|
| 14:  2.0095 -  1.9606 0.65    828   97 0.1013 0.1813      4.6609      4.9798|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7347 -  4.6781  1388   153  0.94   8.82   0.98     0.96       6695.69|
|  2:  4.6781 -  3.7330  1329   150  0.96   7.52   1.03     1.02       8574.95|
|  3:  3.7330 -  3.2670  1318   149  0.94  10.96   1.04     1.03       9995.06|
|  4:  3.2670 -  2.9710  1298   136  0.93  12.58   1.02     1.01       9433.75|
|  5:  2.9710 -  2.7595  1291   145  0.91  15.11   1.00     0.97       7605.47|
|  6:  2.7595 -  2.5977  1291   146  0.90  15.42   0.99     0.96       6437.08|
|  7:  2.5977 -  2.4683  1277   146  0.91  14.57   0.99     0.95       5578.29|
|  8:  2.4683 -  2.3613  1289   137  0.92  14.40   1.00     0.98       5089.82|
|  9:  2.3613 -  2.2707  1265   145  0.91  14.91   1.01     0.98       4677.80|
| 10:  2.2707 -  2.1926  1254   132  0.90  15.49   1.00     0.97       4390.15|
| 11:  2.1926 -  2.1243  1277   150  0.90  15.81   1.00     0.97       4238.40|
| 12:  2.1243 -  2.0637  1271   134  0.91  14.90   1.01     1.00       3772.73|
| 13:  2.0637 -  2.0095  1254   139  0.91  15.49   1.01     1.00       3220.35|
| 14:  2.0095 -  1.9606   828    97  0.92  14.19   0.98     0.94       2496.65|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2496.65 max =         9995.06 mean =      5993.03|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.91 mean =        13.51|
|phase err.(test): min =        0.00 max =           89.57 mean =        13.15|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1063   r_free= 0.1541   ksol= 0.32   Bsol= 40.51   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.72,-2.06,-1.19,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.109430                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1063   r_free= 0.1541   ksol= 0.32   Bsol= 40.51   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.72,-2.06,-1.19,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.109430                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7347 -  4.6781 0.99   1388  153 0.0990 0.1221      5.3695      5.5051|
|  2:  4.6781 -  3.7330 0.99   1329  150 0.0821 0.1103      5.4105      5.6177|
|  3:  3.7330 -  3.2670 0.99   1318  149 0.1025 0.1518      5.4481      5.8384|
|  4:  3.2670 -  2.9710 0.99   1298  136 0.1116 0.1540      5.3974      5.5804|
|  5:  2.9710 -  2.7595 0.99   1291  145 0.1208 0.1592      5.2671      5.4577|
|  6:  2.7595 -  2.5977 0.99   1291  146 0.1147 0.1866      5.1591      5.4076|
|  7:  2.5977 -  2.4683 0.99   1277  146 0.1149 0.1581      5.1075      5.3437|
|  8:  2.4683 -  2.3613 0.98   1289  137 0.1108 0.1618      5.0436      5.2897|
|  9:  2.3613 -  2.2707 0.98   1265  145 0.1120 0.1779      4.9892      5.2665|
| 10:  2.2707 -  2.1926 0.98   1254  132 0.1068 0.1690      4.9426      5.1686|
| 11:  2.1926 -  2.1243 1.00   1277  150 0.1086 0.1755       4.912      5.2856|
| 12:  2.1243 -  2.0637 0.97   1271  134 0.1054 0.1625      4.8425      5.1528|
| 13:  2.0637 -  2.0095 0.98   1254  139 0.1059 0.1671      4.7605      5.0046|
| 14:  2.0095 -  1.9606 0.65    828   97 0.1013 0.1813      4.6607      4.9798|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7347 -  4.6781  1388   153  0.94   8.84   0.99     0.96       6722.54|
|  2:  4.6781 -  3.7330  1329   150  0.96   7.52   1.03     1.02       8590.08|
|  3:  3.7330 -  3.2670  1318   149  0.94  10.96   1.04     1.04       9994.00|
|  4:  3.2670 -  2.9710  1298   136  0.93  12.58   1.02     1.01       9430.83|
|  5:  2.9710 -  2.7595  1291   145  0.91  15.10   1.01     0.98       7601.96|
|  6:  2.7595 -  2.5977  1291   146  0.90  15.42   0.99     0.96       6433.27|
|  7:  2.5977 -  2.4683  1277   146  0.91  14.56   0.99     0.96       5572.41|
|  8:  2.4683 -  2.3613  1289   137  0.92  14.40   1.01     0.99       5084.67|
|  9:  2.3613 -  2.2707  1265   145  0.91  14.91   1.01     0.98       4675.14|
| 10:  2.2707 -  2.1926  1254   132  0.90  15.49   1.01     0.98       4390.11|
| 11:  2.1926 -  2.1243  1277   150  0.90  15.81   1.01     0.98       4238.01|
| 12:  2.1243 -  2.0637  1271   134  0.91  14.90   1.02     1.01       3772.90|
| 13:  2.0637 -  2.0095  1254   139  0.91  15.50   1.02     1.01       3220.63|
| 14:  2.0095 -  1.9606   828    97  0.92  14.19   0.99     0.95       2496.85|
|alpha:            min =        0.95 max =            1.04 mean =         0.99|
|beta:             min =     2496.85 max =         9994.00 mean =      5994.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.51|
|phase err.(test): min =        0.00 max =           89.29 mean =        13.15|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.463)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.90    91.76   16.94    None  None   None       |
|    all(noH): 2823   0      0.90    91.76   16.94    None  None   None       |
|    Sol.    : 438    0      6.09    81.32   39.49    None  None   None       |
|    Mac.    : 2385   0      0.90    91.76   12.80    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:     0.899 -   9.985: 1062   |   5:    46.329 -  55.415:  101        |
|      1:     9.985 -  19.071: 1093   |   6:    55.415 -  64.500:   55        |
|      2:    19.071 -  28.157:  219   |   7:    64.500 -  73.586:   18        |
|      3:    28.157 -  37.243:  133   |   8:    73.586 -  82.672:    9        |
|      4:    37.243 -  46.329:  130   |   9:    82.672 -  91.758:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 273         
Filter by distance & map next to the model:
   mapped sites are within: 0.416 - 4.250
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 269 from: 273
   mapped sites are within: 0.746 - 4.250

peak=    6.045 closest distance to " O   HOH Z 142 " =    1.840
peak=    5.719 closest distance to " CB  ARG A 275 " =    0.970
peak=    5.674 closest distance to " O   HOH Z 126 " =    1.920
peak=    5.528 closest distance to " NE2 GLN A  11 " =    1.094
peak=    5.169 closest distance to " CG  PRO A  54 " =    1.221
peak=    4.961 closest distance to " O   HOH Z 232 " =    2.414
peak=    4.922 closest distance to " CB  GLN A 223 " =    1.512
peak=    4.879 closest distance to " CG  PRO A 213 " =    1.289
peak=    4.801 closest distance to " CB  SER A  63 " =    1.146
peak=    4.782 closest distance to " NH2 ARG A  56 " =    2.046
peak=    4.779 closest distance to " O   HOH Z  78 " =    1.780
peak=    4.741 closest distance to " CB  GLN A 183 " =    1.254
peak=    4.729 closest distance to " CB  GLU A 152 " =    1.244
peak=    4.727 closest distance to " O   HOH Z 272 " =    1.854
peak=    4.705 closest distance to " O   HOH Z 427 " =    2.788
peak=    4.681 closest distance to " CG  PRO A  90 " =    1.144
peak=    4.609 closest distance to " C   PRO A 198 " =    1.489
peak=    4.571 closest distance to " O   HOH Z 193 " =    1.722
peak=    4.523 closest distance to " O   HOH Z 209 " =    2.222
peak=    4.471 closest distance to " O   HOH Z 402 " =    1.456
peak=    4.422 closest distance to " O   HOH Z 236 " =    1.371
peak=    4.419 closest distance to " ND2 ASN A 187 " =    1.372
peak=    4.401 closest distance to " CB  PRO A  54 " =    0.994
peak=    4.398 closest distance to " O   HOH Z 287 " =    1.909
peak=    4.374 closest distance to " O   HOH Z  97 " =    2.470
peak=    4.351 closest distance to " CB  ASN A 148 " =    1.423
peak=    4.322 closest distance to " O   HOH Z 369 " =    2.081
peak=    4.304 closest distance to " O   HOH Z 316 " =    2.996
peak=    4.292 closest distance to " O   HOH Z 234 " =    3.535
peak=    4.291 closest distance to " O   SER A  87 " =    2.314
peak=    4.273 closest distance to " CB  VAL A 265 " =    1.230
peak=    4.263 closest distance to " O   HOH Z  59 " =    1.845
peak=    4.256 closest distance to " O   HOH Z 298 " =    1.829
peak=    4.251 closest distance to " CD2 TRP A 179 " =    1.373
peak=    4.235 closest distance to " CA  TYR A  30 " =    0.925
peak=    4.225 closest distance to " O   HOH Z  78 " =    2.111
peak=    4.223 closest distance to " CB  ARG A  79 " =    1.315
peak=    4.216 closest distance to " NZ  LYS A 117 " =    3.020
peak=    4.212 closest distance to " O   HOH Z 346 " =    1.669
peak=    4.160 closest distance to " O   HOH Z  54 " =    1.729
peak=    4.153 closest distance to " CG  PRO A 243 " =    1.103
peak=    4.149 closest distance to " CG1 ILE A  33 " =    1.244
peak=    4.120 closest distance to " O   HOH Z  44 " =    1.841
peak=    4.119 closest distance to " O   HOH Z 403 " =    1.778
peak=    4.113 closest distance to " O   HOH Z   6 " =    2.115
peak=    4.099 closest distance to " CB  SER A   3 " =    1.264
peak=    4.088 closest distance to " O   HOH Z  15 " =    2.288
peak=    4.083 closest distance to " CG  PRO A 198 " =    1.253
peak=    4.066 closest distance to " O   HOH Z 368 " =    2.006
peak=    4.065 closest distance to " O   HOH Z 250 " =    1.434
peak=    4.062 closest distance to " O   HOH Z 327 " =    1.646
peak=    4.049 closest distance to " O   HOH Z 344 " =    3.027
peak=    4.042 closest distance to " O   HOH Z  97 " =    1.943
peak=    4.029 closest distance to " CB  GLU A 128 " =    1.065
peak=    4.026 closest distance to " O   HOH Z 303 " =    2.038
peak=    4.008 closest distance to " O   HOH Z  40 " =    1.625
peak=    4.003 closest distance to " O   HOH Z 128 " =    2.094
peak=    3.998 closest distance to " O   HOH Z 128 " =    1.982
peak=    3.990 closest distance to " O   HOH Z 203 " =    1.722
peak=    3.973 closest distance to " NH2BARG A 145 " =    2.029
peak=    3.931 closest distance to " O   HOH Z 371 " =    1.540
peak=    3.926 closest distance to " CB  SER A  26 " =    1.648
peak=    3.924 closest distance to " CB  TRP A 266 " =    1.050
peak=    3.918 closest distance to " OG BSER A 164 " =    2.229
peak=    3.905 closest distance to " O   HOH Z 407 " =    2.523
peak=    3.900 closest distance to " CB  TYR A 169 " =    0.804
peak=    3.898 closest distance to " CG  ARG A  66 " =    2.690
peak=    3.896 closest distance to " O   HOH Z 389 " =    1.756
peak=    3.883 closest distance to " N   ASN A  39 " =    1.195
peak=    3.861 closest distance to " CA  ASN A 215 " =    1.131
peak=    3.856 closest distance to " O   HOH Z 371 " =    3.239
peak=    3.853 closest distance to " CA  ALA A  21 " =    1.094
peak=    3.848 closest distance to " O   HOH Z 368 " =    3.606
peak=    3.835 closest distance to " O   HOH Z 173 " =    1.980
peak=    3.834 closest distance to " CG AARG A 275 " =    1.049
peak=    3.823 closest distance to " CG2 VAL A 257 " =    0.839
peak=    3.822 closest distance to " O   HOH Z 132 " =    2.286
peak=    3.789 closest distance to " O   HOH Z 144 " =    2.123
peak=    3.787 closest distance to " OD1 ASN A  69 " =    2.688
peak=    3.782 closest distance to " CB  ARG A 190 " =    1.706
peak=    3.777 closest distance to " O   HOH Z  61 " =    1.502
peak=    3.774 closest distance to " O   HOH Z 392 " =    2.847
peak=    3.769 closest distance to " CG2 ILE A 120 " =    1.125
peak=    3.765 closest distance to " O   HOH Z  43 " =    1.859
peak=    3.765 closest distance to " CB  VAL A 202 " =    1.569
peak=    3.755 closest distance to " CB  TRP A 179 " =    1.177
peak=    3.750 closest distance to " O   HOH Z 245 " =    1.352
peak=    3.741 closest distance to " O   HOH Z  61 " =    1.680
peak=    3.732 closest distance to " O   HOH Z 425 " =    2.082
peak=    3.717 closest distance to " O   HOH Z 423 " =    1.943
peak=    3.703 closest distance to " OD2 ASP A 286 " =    2.658
peak=    3.680 closest distance to " O   HOH Z  66 " =    2.130
peak=    3.674 closest distance to " CD2 LEU A 297 " =    0.974
peak=    3.657 closest distance to " CG1BVAL A  72 " =    1.490
peak=    3.649 closest distance to " O   HOH Z 411 " =    3.735
peak=    3.632 closest distance to " O   HOH Z 336 " =    1.686
peak=    3.631 closest distance to " O   HOH Z   9 " =    2.130
peak=    3.618 closest distance to " O   HOH Z 284 " =    2.942
peak=    3.604 closest distance to " O   HOH Z  88 " =    2.756
peak=    3.603 closest distance to " O   HOH Z 172 " =    3.495
peak=    3.596 closest distance to " O   ALA A   1 " =    1.688
peak=    3.594 closest distance to " O   HOH Z  89 " =    2.141
peak=    3.574 closest distance to " O   HOH Z  10 " =    1.787
peak=    3.571 closest distance to " CA  ARG A  36 " =    0.996
peak=    3.558 closest distance to " O   HOH Z 365 " =    2.872
peak=    3.550 closest distance to " O   HOH Z 158 " =    2.902
peak=    3.544 closest distance to " O   HOH Z 180 " =    2.303
peak=    3.542 closest distance to " O  BHOH Z 338 " =    2.316
peak=    3.539 closest distance to " O   HOH Z 193 " =    1.941
peak=    3.538 closest distance to " N   TYR A 116 " =    1.579
peak=    3.535 closest distance to " CB  GLU A 277 " =    3.476
peak=    3.535 closest distance to " O   HOH Z 124 " =    1.280
peak=    3.534 closest distance to " N   ARG A 156 " =    1.290
peak=    3.531 closest distance to " O   HOH Z 286 " =    2.162
peak=    3.530 closest distance to " O   HOH Z   1 " =    1.844
peak=    3.528 closest distance to " O   HOH Z 426 " =    1.542
peak=    3.526 closest distance to " O   HOH Z 305 " =    3.548
peak=    3.511 closest distance to " OG  SER A  62 " =    2.799
peak=    3.510 closest distance to " O   HOH Z 222 " =    2.421
peak=    3.498 closest distance to " O   HOH Z 189 " =    1.927
peak=    3.493 closest distance to " CH2 TRP A  92 " =    2.106
peak=    3.485 closest distance to " CZ  PHE A 218 " =    1.038
peak=    3.481 closest distance to " CE  LYS A  76 " =    0.918
peak=    3.478 closest distance to " NH1AARG A 145 " =    1.228
peak=    3.476 closest distance to " O   HOH Z 406 " =    1.566
peak=    3.473 closest distance to " CA  ALA A  84 " =    1.324
peak=    3.472 closest distance to " CA  ASP A 162 " =    1.098
peak=    3.472 closest distance to " CB  ASN A  39 " =    0.823
peak=    3.471 closest distance to " CB  LEU A 228 " =    1.121
peak=    3.464 closest distance to " O   HOH Z 291 " =    1.406
peak=    3.463 closest distance to " CB  GLN A  88 " =    1.169
peak=    3.456 closest distance to " O   HOH Z 207 " =    1.744
peak=    3.452 closest distance to " O   HOH Z 112 " =    2.441
peak=    3.452 closest distance to " O   HOH Z 337 " =    3.472
peak=    3.451 closest distance to " CB  ARG A 139 " =    0.972
peak=    3.449 closest distance to " O   HOH Z   3 " =    1.786
peak=    3.447 closest distance to " CB  ALA A 248 " =    1.423
peak=    3.447 closest distance to " CB  SER A  62 " =    1.376
peak=    3.439 closest distance to " O   HOH Z 250 " =    1.909
peak=    3.439 closest distance to " O   HOH Z 421 " =    1.651
peak=    3.439 closest distance to " O   HOH Z 417 " =    3.251
peak=    3.437 closest distance to " O   HOH Z 227 " =    1.525
peak=    3.433 closest distance to " CA  PHE A 283 " =    1.308
peak=    3.430 closest distance to " O   HOH Z 298 " =    2.555
peak=    3.423 closest distance to " O   HOH Z 132 " =    2.602
peak=    3.408 closest distance to " CA  ASN A 176 " =    1.147
peak=    3.407 closest distance to " CG2BVAL A  41 " =    0.826
peak=    3.406 closest distance to " O   HOH Z  71 " =    1.936
peak=    3.404 closest distance to " O   HOH Z  21 " =    1.783
peak=    3.402 closest distance to " O   HOH Z 263 " =    2.401
peak=    3.400 closest distance to " O   HOH Z 279 " =    2.132
peak=    3.386 closest distance to " O   HOH Z 433 " =    1.807
peak=    3.385 closest distance to " N   PHE A 130 " =    1.278
peak=    3.384 closest distance to " O   HOH Z 329 " =    3.761
peak=    3.380 closest distance to " CB  ASN A 110 " =    1.053
peak=    3.379 closest distance to " CB  ALA A  34 " =    1.078
peak=    3.378 closest distance to " O   HOH Z 380 " =    1.929
peak=    3.377 closest distance to " O   HOH Z  49 " =    2.046
peak=    3.374 closest distance to " N   ASN A 127 " =    1.066
peak=    3.373 closest distance to " CG  GLN A  77 " =    2.134
peak=    3.372 closest distance to " CB  ALA A 291 " =    1.295
peak=    3.371 closest distance to " O   HOH Z 106 " =    2.523
peak=    3.371 closest distance to " CA  ARG A 195 " =    1.301
peak=    3.368 closest distance to " CG  LEU A 167 " =    1.221
peak=    3.362 closest distance to " CB  SER A  62 " =    1.020
peak=    3.357 closest distance to " O   HOH Z 427 " =    3.024
peak=    3.354 closest distance to " O   HOH Z 273 " =    2.703
peak=    3.353 closest distance to " NH1BARG A 145 " =    1.306
peak=    3.352 closest distance to " CB  GLN A  89 " =    1.425
peak=    3.352 closest distance to " O   HOH Z 108 " =    2.132
peak=    3.351 closest distance to " CG1 ILE A 120 " =    1.202
peak=    3.342 closest distance to " O   HOH Z 185 " =    1.683
peak=    3.342 closest distance to " CB  ILE A 120 " =    1.315
peak=    3.340 closest distance to " CG2 ILE A  20 " =    1.434
peak=    3.339 closest distance to " CD1 ILE A 106 " =    0.897
peak=    3.335 closest distance to " CG  MET A 185 " =    1.171
peak=    3.323 closest distance to " CA  ALA A 233 " =    0.996
peak=    3.321 closest distance to " O  BHOH Z  74 " =    1.400
peak=    3.318 closest distance to " O   HOH Z 214 " =    2.274
peak=    3.317 closest distance to " O   HOH Z 234 " =    1.855
peak=    3.313 closest distance to " CA  THR A 221 " =    0.976
peak=    3.313 closest distance to " C   TYR A 214 " =    1.476
peak=    3.309 closest distance to " CB  ASN A 215 " =    1.116
peak=    3.307 closest distance to " CA  LYS A 117 " =    1.204
peak=    3.306 closest distance to " O   HOH Z 299 " =    4.250
peak=    3.306 closest distance to " CB  VAL A 126 " =    1.163
peak=    3.303 closest distance to " CA  MET A  40 " =    1.059
peak=    3.302 closest distance to " CG  MET A 113 " =    1.010
peak=    3.302 closest distance to " CB  ASP A 140 " =    0.989
peak=    3.301 closest distance to " CA  ALA A 291 " =    0.847
peak=    3.295 closest distance to " O   HOH Z 257 " =    2.128
peak=    3.295 closest distance to " O   HOH Z 132 " =    2.882
peak=    3.293 closest distance to " O   HOH Z 357 " =    1.791
peak=    3.292 closest distance to " O   MET A 105 " =    1.886
peak=    3.289 closest distance to " CD  ARG A 269 " =    0.975
peak=    3.289 closest distance to " O   HOH Z 345 " =    3.118
peak=    3.284 closest distance to " O   HOH Z 219 " =    2.155
peak=    3.283 closest distance to " CG  GLU A 277 " =    1.997
peak=    3.281 closest distance to " CA  MET A 105 " =    0.964
peak=    3.280 closest distance to " O   HOH Z 435 " =    1.842
peak=    3.279 closest distance to " O   HOH Z 147 " =    1.717
peak=    3.278 closest distance to " O   HOH Z   1 " =    1.500
peak=    3.265 closest distance to " CA  GLY A  80 " =    0.756
peak=    3.261 closest distance to " OH  TYR A 116 " =    1.041
peak=    3.259 closest distance to " O   HOH Z  19 " =    2.368
peak=    3.258 closest distance to " CG2 THR A 294 " =    1.588
peak=    3.255 closest distance to " O   HOH Z  85 " =    2.384
peak=    3.255 closest distance to " CG  LYS A  76 " =    0.934
peak=    3.254 closest distance to " CB  THR A 279 " =    1.649
peak=    3.252 closest distance to " NZ  LYS A 119 " =    1.452
peak=    3.251 closest distance to " CA  THR A 264 " =    0.823
peak=    3.248 closest distance to " O   HOH Z 126 " =    1.497
peak=    3.244 closest distance to " CA  SER A 146 " =    1.818
peak=    3.239 closest distance to " O   HOH Z 425 " =    1.230
peak=    3.234 closest distance to " O   HOH Z 409 " =    2.883
peak=    3.225 closest distance to " O   HOH Z 261 " =    1.572
peak=    3.214 closest distance to " O   HOH Z  88 " =    2.412
peak=    3.213 closest distance to " CB  THR A  31 " =    1.730
peak=    3.213 closest distance to " CA  ASN A 217 " =    1.221
peak=    3.212 closest distance to " O   HOH Z  94 " =    1.963
peak=    3.211 closest distance to " O   HOH Z 148 " =    3.258
peak=    3.209 closest distance to " CA  ASP A 140 " =    1.089
peak=    3.200 closest distance to " O   HOH Z 342 " =    0.852
peak=    3.199 closest distance to " CD BLYS A 290 " =    1.252
peak=    3.197 closest distance to " CB  ALA A  10 " =    1.360
peak=    3.197 closest distance to " O   HOH Z 419 " =    1.980
peak=    3.196 closest distance to " O   HOH Z 135 " =    1.641
peak=    3.193 closest distance to " CE AMET A  47 " =    1.242
peak=    3.193 closest distance to " OD1BASN A 224 " =    2.215
peak=    3.193 closest distance to " N   ASP A 162 " =    1.151
peak=    3.190 closest distance to " N   SER A 134 " =    1.475
peak=    3.185 closest distance to " O   HOH Z 291 " =    1.776
peak=    3.182 closest distance to " O   HOH Z 187 " =    2.221
peak=    3.182 closest distance to " O   HOH Z  19 " =    2.128
peak=    3.178 closest distance to " CB  GLU A  46 " =    0.999
peak=    3.173 closest distance to " OE1 GLU A 236 " =    1.273
peak=    3.172 closest distance to " O   HOH Z 302 " =    1.875
peak=    3.166 closest distance to " O   HOH Z 422 " =    2.669
peak=    3.166 closest distance to " O   HOH Z  85 " =    1.355
peak=    3.163 closest distance to " CG2 VAL A 197 " =    1.118
peak=    3.163 closest distance to " CA  ALA A 299 " =    0.944
peak=    3.160 closest distance to " O   HOH Z  44 " =    2.259
peak=    3.159 closest distance to " CB  GLN A 278 " =    0.831
peak=    3.157 closest distance to " O   HOH Z 353 " =    2.627
peak=    3.155 closest distance to " CE  LYS A 119 " =    1.161
peak=    3.154 closest distance to " O   HOH Z  40 " =    2.028
peak=    3.151 closest distance to " CB  TYR A 116 " =    0.789
peak=    3.148 closest distance to " O   HOH Z 325 " =    3.729
peak=    3.144 closest distance to " O   HOH Z 248 " =    1.633
peak=    3.125 closest distance to " CB  TRP A 179 " =    1.371
peak=    3.120 closest distance to " O   HOH Z 394 " =    1.547
peak=    3.120 closest distance to " N   HIS A  86 " =    1.781
peak=    3.113 closest distance to " CG1 ILE A 151 " =    1.017
peak=    3.113 closest distance to " CB  LEU A 255 " =    0.746
peak=    3.113 closest distance to " O   HOH Z 163 " =    1.708
peak=    3.110 closest distance to " O   HOH Z 188 " =    1.997
peak=    3.110 closest distance to " CD2 TYR A 186 " =    1.064
peak=    3.108 closest distance to " CD2 LEU A 255 " =    1.378
peak=    3.103 closest distance to " CZ2 TRP A 179 " =    1.679
peak=    3.093 closest distance to " O   HOH Z  47 " =    1.458
peak=    3.079 closest distance to " OG BSER A  99 " =    2.289
peak=    3.070 closest distance to " O   GLY A 147 " =    1.587
peak=    3.069 closest distance to " O   HOH Z  47 " =    1.697
peak=    3.049 closest distance to " NH1 ARG A 138 " =    1.274
peak=    3.041 closest distance to " O   HOH Z 218 " =    2.424
peak=    3.039 closest distance to " CB  LEU A 300 " =    0.982
peak=    3.038 closest distance to " CG  ARG A  66 " =    2.707
peak=    3.026 closest distance to " CA  LYS A 290 " =    1.417
peak=    3.024 closest distance to " O   HOH Z 153 " =    3.751

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 207         
Filter by distance & map next to the model:
   mapped sites are within: 0.774 - 5.793
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 207
   mapped sites are within: 0.774 - 5.793

peak=   -4.824 closest distance to " O   HOH Z 266 " =    4.780
peak=   -4.565 closest distance to " C   HIS A 108 " =    1.064
peak=   -4.494 closest distance to " OG BSER A 134 " =    1.225
peak=   -4.261 closest distance to " O   HOH Z 290 " =    1.067
peak=   -4.259 closest distance to " CD  ARG A 156 " =    2.076
peak=   -4.259 closest distance to " SG  CYS A 254 " =    3.308
peak=   -4.221 closest distance to " CA  VAL A  67 " =    2.821
peak=   -4.207 closest distance to " O   HOH Z 377 " =    2.053
peak=   -4.150 closest distance to " CB  PRO A 243 " =    2.636
peak=   -4.144 closest distance to " CG1 VAL A 112 " =    2.745
peak=   -4.116 closest distance to " OXT GLY A 302 " =    2.750
peak=   -4.116 closest distance to " O   HOH Z 372 " =    2.322
peak=   -4.095 closest distance to " O   VAL A  67 " =    2.667
peak=   -4.042 closest distance to " O   ALA A 161 " =    1.593
peak=   -4.041 closest distance to " CG  GLN A 223 " =    1.925
peak=   -4.037 closest distance to " CZ  TYR A 169 " =    1.754
peak=   -3.999 closest distance to " O   HOH Z 185 " =    2.218
peak=   -3.990 closest distance to " O   HOH Z 198 " =    1.782
peak=   -3.990 closest distance to " CG  GLN A  58 " =    1.155
peak=   -3.989 closest distance to " O   PRO A 198 " =    1.242
peak=   -3.985 closest distance to " CB  ASN A  39 " =    2.266
peak=   -3.966 closest distance to " N   GLN A  58 " =    1.701
peak=   -3.965 closest distance to " OD2 ASP A 191 " =    1.404
peak=   -3.940 closest distance to " O   HOH Z 407 " =    2.726
peak=   -3.906 closest distance to " CG  PHE A 283 " =    2.657
peak=   -3.890 closest distance to " O   HOH Z 435 " =    2.739
peak=   -3.890 closest distance to " O   HOH Z 231 " =    2.339
peak=   -3.875 closest distance to " N   ALA A 248 " =    1.638
peak=   -3.870 closest distance to " ND2 ASN A  45 " =    0.995
peak=   -3.867 closest distance to " O   HOH Z 351 " =    1.432
peak=   -3.847 closest distance to " OD1 ASN A 187 " =    1.660
peak=   -3.844 closest distance to " O   HOH Z  13 " =    1.607
peak=   -3.843 closest distance to " CD  ARG A 139 " =    1.553
peak=   -3.841 closest distance to " ND2 ASN A  45 " =    1.200
peak=   -3.833 closest distance to " CE2 TYR A  30 " =    2.792
peak=   -3.819 closest distance to " O   HOH Z 389 " =    1.839
peak=   -3.812 closest distance to " CD1 LEU A 101 " =    2.326
peak=   -3.790 closest distance to " CB  ALA A 161 " =    2.509
peak=   -3.770 closest distance to " O   HOH Z  52 " =    1.360
peak=   -3.769 closest distance to " OG  SER A  97 " =    2.068
peak=   -3.765 closest distance to " O   HOH Z 353 " =    2.313
peak=   -3.761 closest distance to " O   HOH Z 313 " =    1.986
peak=   -3.760 closest distance to " O   ALA A  51 " =    1.201
peak=   -3.749 closest distance to " O   HOH Z 126 " =    1.884
peak=   -3.721 closest distance to " CZ  PHE A  59 " =    1.460
peak=   -3.718 closest distance to " OD2 ASP A 171 " =    2.269
peak=   -3.709 closest distance to " O   PHE A 218 " =    1.553
peak=   -3.708 closest distance to " O   HOH Z 429 " =    1.907
peak=   -3.704 closest distance to " CB  ALA A 291 " =    2.390
peak=   -3.701 closest distance to " O   SER A 135 " =    1.465
peak=   -3.699 closest distance to " O   HOH Z  63 " =    1.529
peak=   -3.698 closest distance to " CA  GLY A 203 " =    2.359
peak=   -3.692 closest distance to " O   HOH Z 114 " =    3.091
peak=   -3.678 closest distance to " O   HOH Z 102 " =    1.591
peak=   -3.664 closest distance to " CB  PHE A 192 " =    1.924
peak=   -3.663 closest distance to " CD1 PHE A  59 " =    1.916
peak=   -3.662 closest distance to " N   HIS A 115 " =    2.029
peak=   -3.655 closest distance to " O   VAL A 174 " =    2.076
peak=   -3.645 closest distance to " O   HOH Z   3 " =    1.973
peak=   -3.638 closest distance to " O   PRO A 163 " =    1.912
peak=   -3.637 closest distance to " OD1 ASP A 191 " =    1.484
peak=   -3.635 closest distance to " O   HOH Z 263 " =    2.903
peak=   -3.634 closest distance to " O   HOH Z  11 " =    2.040
peak=   -3.616 closest distance to " CE  MET A 105 " =    2.248
peak=   -3.598 closest distance to " CZ3 TRP A 179 " =    1.265
peak=   -3.586 closest distance to " NE  ARG A 156 " =    1.853
peak=   -3.586 closest distance to " CB  TYR A  15 " =    2.185
peak=   -3.582 closest distance to " O   HOH Z 166 " =    1.527
peak=   -3.578 closest distance to " O   HOH Z  43 " =    1.786
peak=   -3.571 closest distance to " O   ARG A 145 " =    1.631
peak=   -3.561 closest distance to " N   ASP A 286 " =    2.262
peak=   -3.551 closest distance to " ND2 ASN A 187 " =    1.563
peak=   -3.550 closest distance to " C   MET A 188 " =    1.438
peak=   -3.544 closest distance to " CB  ALA A 291 " =    2.242
peak=   -3.542 closest distance to " CA  GLY A  98 " =    1.856
peak=   -3.535 closest distance to " O   HOH Z 139 " =    5.155
peak=   -3.532 closest distance to " O   SER A 210 " =    1.964
peak=   -3.531 closest distance to " N   ALA A  43 " =    2.406
peak=   -3.528 closest distance to " CG2 ILE A 263 " =    2.206
peak=   -3.509 closest distance to " O   GLN A  89 " =    1.500
peak=   -3.508 closest distance to " OXT GLY A 302 " =    3.408
peak=   -3.505 closest distance to " O   SER A  95 " =    1.455
peak=   -3.490 closest distance to " NH1 ARG A 195 " =    2.592
peak=   -3.483 closest distance to " O   HOH Z  11 " =    1.782
peak=   -3.480 closest distance to " CB  PRO A 163 " =    2.515
peak=   -3.464 closest distance to " O   HOH Z 362 " =    5.793
peak=   -3.457 closest distance to " O   MET A  40 " =    2.647
peak=   -3.456 closest distance to " O   HOH Z 385 " =    2.042
peak=   -3.454 closest distance to " O   HOH Z 165 " =    2.079
peak=   -3.434 closest distance to " O   HOH Z 139 " =    3.049
peak=   -3.432 closest distance to " CD2 LEU A 237 " =    2.453
peak=   -3.426 closest distance to " CA  GLY A  57 " =    2.133
peak=   -3.426 closest distance to " CB  ASP A 132 " =    2.359
peak=   -3.425 closest distance to " C   ALA A 158 " =    1.369
peak=   -3.425 closest distance to " OD1 ASP A 191 " =    1.707
peak=   -3.423 closest distance to " CB  ASP A 286 " =    2.072
peak=   -3.418 closest distance to " CG1 VAL A  78 " =    3.016
peak=   -3.402 closest distance to " NE2 GLN A  88 " =    1.838
peak=   -3.400 closest distance to " O   HOH Z  24 " =    1.395
peak=   -3.394 closest distance to " CG  PRO A 243 " =    1.567
peak=   -3.385 closest distance to " O   HOH Z 166 " =    2.071
peak=   -3.384 closest distance to " CB  ASP A 132 " =    2.220
peak=   -3.382 closest distance to " O   HOH Z 298 " =    1.330
peak=   -3.381 closest distance to " O   HOH Z 253 " =    3.649
peak=   -3.379 closest distance to " O   ASP A 162 " =    2.175
peak=   -3.375 closest distance to " CA  ASP A 298 " =    1.071
peak=   -3.375 closest distance to " CD1 ILE A 239 " =    2.520
peak=   -3.372 closest distance to " O   HOH Z  44 " =    2.236
peak=   -3.369 closest distance to " CA  GLY A 133 " =    1.875
peak=   -3.369 closest distance to " N   GLN A 122 " =    1.356
peak=   -3.363 closest distance to " O   HOH Z 211 " =    1.745
peak=   -3.360 closest distance to " NH2AARG A 275 " =    4.985
peak=   -3.357 closest distance to " O   PRO A 198 " =    1.244
peak=   -3.354 closest distance to " O   HOH Z  88 " =    4.299
peak=   -3.353 closest distance to " OD1 ASN A 148 " =    1.519
peak=   -3.352 closest distance to " OE2 GLU A 152 " =    1.288
peak=   -3.351 closest distance to " O   SER A 146 " =    1.059
peak=   -3.345 closest distance to " O   HOH Z 309 " =    2.476
peak=   -3.345 closest distance to " CG  ASP A 231 " =    0.774
peak=   -3.340 closest distance to " CZ  PHE A 130 " =    0.921
peak=   -3.332 closest distance to " C   LEU A 143 " =    1.047
peak=   -3.324 closest distance to " CB  PHE A 208 " =    2.203
peak=   -3.320 closest distance to " O   HOH Z 198 " =    1.552
peak=   -3.317 closest distance to " CB  GLN A  11 " =    1.755
peak=   -3.316 closest distance to " OG BSER A 134 " =    1.648
peak=   -3.313 closest distance to " CZ3 TRP A 274 " =    2.252
peak=   -3.312 closest distance to " CB  TRP A  85 " =    2.538
peak=   -3.312 closest distance to " O   HOH Z 421 " =    3.166
peak=   -3.311 closest distance to " CD1 LEU A 228 " =    2.036
peak=   -3.308 closest distance to " O   HOH Z 427 " =    1.409
peak=   -3.304 closest distance to " OH  TYR A 172 " =    1.738
peak=   -3.302 closest distance to " O   HOH Z 326 " =    1.628
peak=   -3.300 closest distance to " C   GLN A 205 " =    1.775
peak=   -3.297 closest distance to " CB  ALA A   9 " =    2.952
peak=   -3.294 closest distance to " NH2 ARG A  66 " =    4.885
peak=   -3.291 closest distance to " O   ALA A 292 " =    1.951
peak=   -3.289 closest distance to " O   LEU A 167 " =    1.511
peak=   -3.285 closest distance to " CB  SER A 210 " =    1.290
peak=   -3.284 closest distance to " OE1 GLN A  88 " =    1.115
peak=   -3.283 closest distance to " CG  GLU A 152 " =    1.012
peak=   -3.282 closest distance to " O   HOH Z  37 " =    1.767
peak=   -3.271 closest distance to " OD2 ASP A  50 " =    1.516
peak=   -3.268 closest distance to " O   HOH Z 197 " =    5.057
peak=   -3.264 closest distance to " CG1 VAL A 230 " =    1.884
peak=   -3.260 closest distance to " O   HOH Z 191 " =    5.691
peak=   -3.258 closest distance to " CB  ALA A 248 " =    2.238
peak=   -3.251 closest distance to " CD2 TYR A 293 " =    1.924
peak=   -3.251 closest distance to " OG ASER A 134 " =    1.197
peak=   -3.244 closest distance to " N   PRO A 163 " =    1.619
peak=   -3.242 closest distance to " ND2 ASN A  39 " =    1.292
peak=   -3.235 closest distance to " O   HOH Z 394 " =    1.461
peak=   -3.233 closest distance to " CZ2 TRP A 274 " =    1.048
peak=   -3.232 closest distance to " O   HOH Z 369 " =    2.072
peak=   -3.229 closest distance to " NH2 ARG A  79 " =    1.968
peak=   -3.220 closest distance to " O   HOH Z  93 " =    1.736
peak=   -3.220 closest distance to " O   ASN A 187 " =    1.470
peak=   -3.219 closest distance to " CG  ARG A  66 " =    2.433
peak=   -3.216 closest distance to " OE1 GLN A 183 " =    1.378
peak=   -3.212 closest distance to " SG ACYS A 201 " =    1.746
peak=   -3.211 closest distance to " O   HOH Z  60 " =    1.992
peak=   -3.203 closest distance to " O   HOH Z 123 " =    2.356
peak=   -3.198 closest distance to " CB  ALA A  43 " =    2.371
peak=   -3.195 closest distance to " OG1 THR A 178 " =    1.250
peak=   -3.191 closest distance to " C   ASP A 231 " =    2.532
peak=   -3.184 closest distance to " CE1 HIS A  81 " =    1.764
peak=   -3.181 closest distance to " O   SER A  22 " =    2.354
peak=   -3.180 closest distance to " O   TRP A  92 " =    1.676
peak=   -3.180 closest distance to " O   HOH Z 234 " =    3.897
peak=   -3.180 closest distance to " O   HOH Z 422 " =    1.516
peak=   -3.179 closest distance to " O   GLY A  75 " =    1.689
peak=   -3.169 closest distance to " CB  ASN A  39 " =    2.068
peak=   -3.168 closest distance to " O   HOH Z  10 " =    1.377
peak=   -3.167 closest distance to " O   HOH Z 250 " =    1.363
peak=   -3.163 closest distance to " O   HOH Z 265 " =    1.902
peak=   -3.161 closest distance to " NH1BARG A 145 " =    3.544
peak=   -3.156 closest distance to " ND2 ASN A  69 " =    1.530
peak=   -3.155 closest distance to " CZ  ARG A 259 " =    0.891
peak=   -3.153 closest distance to " O   HOH Z 193 " =    1.932
peak=   -3.152 closest distance to " CA  TRP A 274 " =    1.478
peak=   -3.141 closest distance to " OD1 ASP A 171 " =    1.561
peak=   -3.141 closest distance to " N   PHE A  59 " =    1.768
peak=   -3.139 closest distance to " O   HOH Z 134 " =    3.009
peak=   -3.135 closest distance to " O   ALA A  34 " =    2.289
peak=   -3.127 closest distance to " O   GLU A 152 " =    1.434
peak=   -3.109 closest distance to " CB  ASP A 132 " =    2.225
peak=   -3.109 closest distance to " OH  TYR A 169 " =    0.933
peak=   -3.102 closest distance to " O   HOH Z 119 " =    2.228
peak=   -3.101 closest distance to " O   ASN A  45 " =    1.871
peak=   -3.099 closest distance to " OE1 GLN A 194 " =    1.580
peak=   -3.097 closest distance to " O   VAL A 189 " =    2.555
peak=   -3.095 closest distance to " OE1 GLN A 223 " =    1.674
peak=   -3.084 closest distance to " OG1 THR A 246 " =    1.391
peak=   -3.084 closest distance to " OD1 ASN A 301 " =    2.000
peak=   -3.079 closest distance to " O   HOH Z 210 " =    1.165
peak=   -3.077 closest distance to " O   PRO A 163 " =    1.294
peak=   -3.076 closest distance to " O   HOH Z 168 " =    1.609
peak=   -3.075 closest distance to " O   HOH Z 281 " =    2.667
peak=   -3.075 closest distance to " O   HOH Z 111 " =    2.521
peak=   -3.071 closest distance to " O   HOH Z 361 " =    3.427
peak=   -3.070 closest distance to " CE  MET A  93 " =    1.188
peak=   -3.068 closest distance to " CG1 VAL A 265 " =    2.508
peak=   -3.065 closest distance to " CG1 VAL A 197 " =    2.154
peak=   -3.043 closest distance to " NH2BARG A 275 " =    2.078
peak=   -3.033 closest distance to " O   HOH Z 357 " =    2.083
peak=   -3.029 closest distance to " O   HOH Z 200 " =    3.092
peak=   -3.029 closest distance to " O   HOH Z  60 " =    1.979
peak=   -3.012 closest distance to " CA  GLY A  57 " =    2.089

================= 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    :  0.3602 0.3625   6.114556e+00   6.108121e+00
   1_bss:  0.3477 0.3482   6.095371e+00   6.080344e+00
   1_xyz:  0.1999 0.2208   5.603732e+00   5.693694e+00
   1_adp:  0.1819 0.2283   5.549644e+00   5.728963e+00
   1_occ:  0.1816 0.2280   5.548881e+00   5.728471e+00
   2_bss:  0.1776 0.2250   5.538316e+00   5.720779e+00
   2_xyz:  0.1308 0.1745   5.263134e+00   5.475178e+00
   2_adp:  0.1247 0.1654   5.209019e+00   5.416037e+00
   2_occ:  0.1246 0.1654   5.207965e+00   5.415277e+00
   3_bss:  0.1247 0.1646   5.206320e+00   5.409490e+00
   3_xyz:  0.1129 0.1541   5.134047e+00   5.358447e+00
   3_adp:  0.1102 0.1541   5.121708e+00   5.357561e+00
   3_occ:  0.1102 0.1540   5.121551e+00   5.357511e+00
   4_bss:  0.1101 0.1539   5.121063e+00   5.356879e+00
   4_xyz:  0.1081 0.1530   5.110176e+00   5.351706e+00
   4_adp:  0.1077 0.1533   5.110062e+00   5.354841e+00
   4_occ:  0.1076 0.1533   5.110044e+00   5.354940e+00
   5_bss:  0.1075 0.1533   5.110068e+00   5.354871e+00
   5_xyz:  0.1065 0.1534   5.108123e+00   5.359473e+00
   5_adp:  0.1064 0.1542   5.109433e+00   5.363754e+00
   5_occ:  0.1064 0.1541   5.109351e+00   5.363661e+00
   5_bss:  0.1063 0.1541   5.109430e+00   5.363674e+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:  0.322  22.802   0.390  -2.066  -0.386  -0.000  -0.000  -0.000
   1_xyz:  0.322  22.802   0.390  -2.066  -0.386  -0.000  -0.000  -0.000
   1_adp:  0.322  22.802   0.390  -2.066  -0.386  -0.000  -0.000  -0.000
   1_occ:  0.322  22.802   0.390  -2.066  -0.386  -0.000  -0.000  -0.000
   2_bss:  0.316  31.802  -2.370  -2.703  -1.612  -0.000  -0.000  -0.000
   2_xyz:  0.316  31.802  -2.370  -2.703  -1.612  -0.000  -0.000  -0.000
   2_adp:  0.316  31.802  -2.370  -2.703  -1.612  -0.000  -0.000  -0.000
   2_occ:  0.316  31.802  -2.370  -2.703  -1.612  -0.000  -0.000  -0.000
   3_bss:  0.319  35.646  -2.976  -2.587  -1.669  -0.000  -0.000  -0.000
   3_xyz:  0.319  35.646  -2.976  -2.587  -1.669  -0.000  -0.000  -0.000
   3_adp:  0.319  35.646  -2.976  -2.587  -1.669  -0.000  -0.000  -0.000
   3_occ:  0.319  35.646  -2.976  -2.587  -1.669  -0.000  -0.000  -0.000
   4_bss:  0.321  38.753  -3.020  -2.467  -1.594  -0.000  -0.000  -0.000
   4_xyz:  0.321  38.753  -3.020  -2.467  -1.594  -0.000  -0.000  -0.000
   4_adp:  0.321  38.753  -3.020  -2.467  -1.594  -0.000  -0.000  -0.000
   4_occ:  0.321  38.753  -3.020  -2.467  -1.594  -0.000  -0.000  -0.000
   5_bss:  0.322  39.718  -2.904  -2.271  -1.399  -0.000  -0.000  -0.000
   5_xyz:  0.322  39.718  -2.904  -2.271  -1.399  -0.000  -0.000  -0.000
   5_adp:  0.322  39.718  -2.904  -2.271  -1.399  -0.000  -0.000  -0.000
   5_occ:  0.322  39.718  -2.904  -2.271  -1.399  -0.000  -0.000  -0.000
   5_bss:  0.323  40.507  -2.722  -2.060  -1.188  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  37.378 0.6773  0.8801    37568.618
   1_bss:  36.086 0.6907  0.8792    33902.868
   1_xyz:  20.747 0.8559  1.0211    12232.916
   1_adp:  21.855 0.8442  1.0176    13142.050
   1_occ:  21.856 0.8442  1.0176    13135.228
   2_bss:  21.583 0.8466  0.9643    12820.686
   2_xyz:  15.981 0.8979  0.9916     7512.038
   2_adp:  14.636 0.9097  0.9954     6749.188
   2_occ:  14.622 0.9097  0.9953     6732.428
   3_bss:  14.518 0.9105  0.9885     6624.000
   3_xyz:  13.504 0.9186  0.9915     5932.490
   3_adp:  13.454 0.9193  0.9871     5934.721
   3_occ:  13.451 0.9193  0.9870     5931.538
   4_bss:  13.439 0.9194  0.9889     5923.496
   4_xyz:  13.305 0.9205  0.9885     5863.794
   4_adp:  13.335 0.9204  0.9831     5897.473
   4_occ:  13.335 0.9204  0.9830     5899.076
   5_bss:  13.336 0.9204  0.9891     5898.891
   5_xyz:  13.402 0.9199  0.9886     5947.674
   5_adp:  13.474 0.9194  0.9823     5993.390
   5_occ:  13.473 0.9194  0.9822     5992.310
   5_bss:  13.474 0.9194  0.9883     5993.752
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.9042e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.9042e-01
   1_xyz:   1.077  0.008  0.072 14.886  0.005  4.107   6.9728e-02
   1_adp:   1.077  0.008  0.072 14.886  0.005  4.107   6.9728e-02
   1_occ:   1.077  0.008  0.072 14.886  0.005  4.107   6.9728e-02
   2_bss:   1.077  0.008  0.072 14.886  0.005  4.107   6.9728e-02
   2_xyz:   0.959  0.005  0.067 14.486  0.004  4.109   5.3928e-02
   2_adp:   0.959  0.005  0.067 14.486  0.004  4.109   5.3928e-02
   2_occ:   0.959  0.005  0.067 14.486  0.004  4.109   5.3928e-02
   3_bss:   0.959  0.005  0.067 14.486  0.004  4.109   5.3928e-02
   3_xyz:   0.965  0.006  0.070 14.663  0.004  4.108   5.5825e-02
   3_adp:   0.965  0.006  0.070 14.663  0.004  4.108   5.5825e-02
   3_occ:   0.965  0.006  0.070 14.663  0.004  4.108   5.5825e-02
   4_bss:   0.965  0.006  0.070 14.663  0.004  4.108   5.5825e-02
   4_xyz:   0.936  0.005  0.069 14.550  0.004  4.108   5.2854e-02
   4_adp:   0.936  0.005  0.069 14.550  0.004  4.108   5.2854e-02
   4_occ:   0.936  0.005  0.069 14.550  0.004  4.108   5.2854e-02
   5_bss:   0.936  0.005  0.069 14.550  0.004  4.108   5.2854e-02
   5_xyz:   0.947  0.005  0.070 14.532  0.004  4.108   5.3521e-02
   5_adp:   0.947  0.005  0.070 14.532  0.004  4.108   5.3521e-02
   5_occ:   0.947  0.005  0.070 14.532  0.004  4.108   5.3521e-02
   5_bss:   0.947  0.005  0.070 14.532  0.004  4.108   5.3521e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.337   2.3888e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.337   2.3888e-01
   1_xyz:   7.755  0.051  0.257 87.471  0.048  2.145   5.9548e-02
   1_adp:   7.755  0.051  0.257 87.471  0.048  2.145   5.9548e-02
   1_occ:   7.755  0.051  0.257 87.471  0.048  2.145   5.9548e-02
   2_bss:   7.755  0.051  0.257 87.471  0.048  2.145   5.9548e-02
   2_xyz:   6.935  0.038  0.193 82.299  0.040  2.341   7.1405e-02
   2_adp:   6.935  0.038  0.193 82.299  0.040  2.341   7.1405e-02
   2_occ:   6.935  0.038  0.193 82.299  0.040  2.341   7.1405e-02
   3_bss:   6.935  0.038  0.193 82.299  0.040  2.341   7.1405e-02
   3_xyz:   6.522  0.040  0.217 83.057  0.042  2.326   6.5685e-02
   3_adp:   6.522  0.040  0.217 83.057  0.042  2.326   6.5685e-02
   3_occ:   6.522  0.040  0.217 83.057  0.042  2.326   6.5685e-02
   4_bss:   6.522  0.040  0.217 83.057  0.042  2.326   6.5685e-02
   4_xyz:   6.397  0.040  0.215 82.481  0.040  2.308   3.6289e-02
   4_adp:   6.397  0.040  0.215 82.481  0.040  2.308   3.6289e-02
   4_occ:   6.397  0.040  0.215 82.481  0.040  2.308   3.6289e-02
   5_bss:   6.397  0.040  0.215 82.481  0.040  2.308   3.6289e-02
   5_xyz:   6.567  0.040  0.236 82.669  0.038  2.336   3.4709e-02
   5_adp:   6.567  0.040  0.236 82.669  0.038  2.336   3.4709e-02
   5_occ:   6.567  0.040  0.236 82.669  0.038  2.336   3.4709e-02
   5_bss:   6.567  0.040  0.236 82.669  0.038  2.336   3.4709e-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:  74.85   0.00  17.53  74.85   0.00  13.46  73.62   7.28  39.66
   1_occ:  74.85   0.00  17.53  74.85   0.00  13.46  73.62   7.28  39.66
   2_bss:  74.85   0.00  17.53  74.85   0.00  13.46  73.62   7.28  39.66
   2_xyz:  74.85   0.00  17.53  74.85   0.00  13.46  73.62   7.28  39.66
   2_adp:  78.39   1.43  17.10  78.39   1.43  13.18  71.56   5.69  38.41
   2_occ:  78.39   1.43  17.10  78.39   1.43  13.18  71.56   5.69  38.41
   3_bss:  78.39   1.43  17.10  78.39   1.43  13.18  71.56   5.69  38.41
   3_xyz:  78.39   1.43  17.10  78.39   1.43  13.18  71.56   5.69  38.41
   3_adp:  88.02   1.53  17.29  88.02   1.53  13.14  78.33   3.02  39.90
   3_occ:  88.02   1.53  17.29  88.02   1.53  13.14  78.33   3.02  39.90
   4_bss:  88.02   1.53  17.29  88.02   1.53  13.14  78.33   3.02  39.90
   4_xyz:  88.02   1.53  17.29  88.02   1.53  13.14  78.33   3.02  39.90
   4_adp:  90.09   1.22  17.10  90.09   1.22  12.99  79.80   4.52  39.49
   4_occ:  90.09   1.22  17.10  90.09   1.22  12.99  79.80   4.52  39.49
   5_bss:  90.09   1.22  17.10  90.09   1.22  12.99  79.80   4.52  39.49
   5_xyz:  90.09   1.22  17.10  90.09   1.22  12.99  79.80   4.52  39.49
   5_adp:  91.79   0.93  16.97  91.79   0.93  12.83  81.35   6.12  39.52
   5_occ:  91.79   0.93  16.97  91.79   0.93  12.83  81.35   6.12  39.52
   5_bss:  91.76   0.90  16.94  91.76   0.90  12.80  81.32   6.09  39.49
------------------------------------------------------------------------
 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:    1.689    0.012    0.327
   1_adp:    1.689    0.012    0.327
   1_occ:    1.689    0.012    0.327
   2_bss:    1.689    0.012    0.327
   2_xyz:    1.416    0.024    0.399
   2_adp:    1.416    0.024    0.399
   2_occ:    1.416    0.024    0.399
   3_bss:    1.416    0.024    0.399
   3_xyz:    1.210    0.026    0.433
   3_adp:    1.210    0.026    0.433
   3_occ:    1.210    0.026    0.433
   4_bss:    1.210    0.026    0.433
   4_xyz:    1.248    0.038    0.445
   4_adp:    1.248    0.038    0.445
   4_occ:    1.248    0.038    0.445
   5_bss:    1.248    0.038    0.445
   5_xyz:    1.250    0.062    0.451
   5_adp:    1.250    0.062    0.451
   5_occ:    1.250    0.062    0.451
   5_bss:    1.250    0.062    0.451
------------------------------------------------------------------------

CPU time actual refinement: 289.59


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_168/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_168/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_168/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_168/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_168/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 289.46 
  Macro-tasks:
    bulk solvent and scale       = 36.05  
    individual site refinement   = 121.49 
    weights calculation          = 24.87  
    collect and process          = 5.48   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 187.97 
  Micro-tasks:
    mask                            = 1.00   
    f_calc                          = 92.23  
    alpha_beta                      = 6.80   
    target                          = 1.00   
    gradients_wrt_atomic_parameters = 101.09 
    fmodel                         = 6.04   
    r_factors                      = 0.20   
    phase_errors                   = 9.05   
    foms                           = 0.24   
    TOTAL for micro-tasks          = 217.65 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.006 micro seconds
Total CPU time: 5.02 minutes
from_scatterers_fft:    681 calls, 91.88 s
gradients_fft:          626 calls, 88.50 s

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

# Date 2008-01-16 Time 04:09:28 PST -0800 (1200485368.35 s)
Start R-work = 0.3602, R-free = 0.3625 (no bulk solvent and anisotropic scale)
Final R-work = 0.1320, R-free = 0.1748 (no bulk solvent and anisotropic scale)

Start R-work = 0.3477, R-free = 0.3482
Final R-work = 0.1063, R-free = 0.1541