# Date 2008-01-16 Time 04:52:50 PST -0800 (1200487970.44 s)
#phil __OFF__

Command line arguments: "../498.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 6629
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 498

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 45.9914, 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: 2.78, 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: (69.8988, 45.9914, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8986 1.96249
Completeness in resolution range: 0.965308
Completeness with d_max=infinity: 0.962321

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8986
                             d_min =   1.9625

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 45.9914, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8986 1.96249
Completeness in resolution range: 0.965308
Completeness with d_max=infinity: 0.962321

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8990 -  4.1994 [2128/2152]  1915   213  10.0%
  bin  2:  4.1994 -  3.3456 [2041/2061]  1837   204  10.0%
  bin  3:  3.3456 -  2.9264 [2027/2046]  1824   203  10.0%
  bin  4:  2.9264 -  2.6605 [2006/2036]  1809   197   9.8%
  bin  5:  2.6605 -  2.4707 [2003/2022]  1803   200  10.0%
  bin  6:  2.4707 -  2.3256 [1967/1992]  1766   201  10.2%
  bin  7:  2.3256 -  2.2095 [1966/1994]  1766   200  10.2%
  bin  8:  2.2095 -  2.1136 [1973/2009]  1778   195   9.9%
  bin  9:  2.1136 -  2.0325 [1960/2002]  1767   193   9.8%
  bin 10:  2.0325 -  1.9625 [1518/1979]  1365   153  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_498/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:
        1.81 -     2.42: 42
        2.42 -     3.04: 2259
        3.04 -     3.66: 4793
        3.66 -     4.28: 9195
        4.28 -     4.90: 12489
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.867 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 302 " - " O   HOH Z  70 "  1.867 3.040 -x+1/2,-y+1,z-1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.907 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28773 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_498/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_498/model_refine_001.geo

CPU time processing inputs: 8.18


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 45.9914 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 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4121   r_free= 0.4106   ksol= 0.00   Bsol= 0.00   scale= 0.937    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.220526                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8990 -  4.6839 0.99   1386  155 0.3402 0.3393      6.4944       6.491|
|  2:  4.6839 -  3.7371 0.99   1333  147 0.3473 0.3190      6.7095      6.6295|
|  3:  3.7371 -  3.2704 0.99   1307  143 0.3760 0.3614      6.6072      6.6747|
|  4:  3.2704 -  2.9740 0.99   1292  146 0.3867 0.4055      6.4542      6.4491|
|  5:  2.9740 -  2.7623 0.99   1289  145 0.4382 0.4146      6.3099      6.3033|
|  6:  2.7623 -  2.6003 0.99   1297  139 0.4320 0.4559      6.2296      6.1687|
|  7:  2.6003 -  2.4707 0.99   1284  142 0.4373 0.4619      6.1777      6.1661|
|  8:  2.4707 -  2.3636 0.98   1264  144 0.4578 0.4541      6.1439      6.1374|
|  9:  2.3636 -  2.2729 0.98   1266  140 0.4539 0.4628      6.0795      6.0973|
| 10:  2.2729 -  2.1947 1.00   1263  143 0.4498 0.4787      6.0514      6.0886|
| 11:  2.1947 -  2.1263 0.98   1268  139 0.4586 0.4538      5.9965      6.0389|
| 12:  2.1263 -  2.0657 0.98   1246  142 0.4468 0.4439      5.9353       5.953|
| 13:  2.0657 -  2.0114 0.99   1286  137 0.4639 0.4416      5.8454       5.784|
| 14:  2.0114 -  1.9625 0.67    849   97 0.4972 0.4447      5.8673      5.7501|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8990 -  4.6839  1386   155  0.73  31.24   0.84     0.78      61100.02|
|  2:  4.6839 -  3.7371  1333   147  0.76  29.77   0.94     0.87      81400.01|
|  3:  3.7371 -  3.2704  1307   143  0.69  36.58   0.96     0.87      86236.84|
|  4:  3.2704 -  2.9740  1292   146  0.62  42.41   0.97     0.81      80103.65|
|  5:  2.9740 -  2.7623  1289   145  0.53  49.29   0.93     0.74      64995.00|
|  6:  2.7623 -  2.6003  1297   139  0.52  50.09   0.94     0.71      57458.23|
|  7:  2.6003 -  2.4707  1284   142  0.50  52.17   0.96     0.69      52338.10|
|  8:  2.4707 -  2.3636  1264   144  0.48  53.51   0.97     0.69      48988.94|
|  9:  2.3636 -  2.2729  1266   140  0.49  53.05   0.95     0.69      44242.20|
| 10:  2.2729 -  2.1947  1263   143  0.49  52.72   0.99     0.70      39402.67|
| 11:  2.1947 -  2.1263  1268   139  0.49  53.31   1.01     0.73      37415.63|
| 12:  2.1263 -  2.0657  1246   142  0.50  52.09   1.03     0.75      32968.94|
| 13:  2.0657 -  2.0114  1286   137  0.50  52.43   0.99     0.77      27160.86|
| 14:  2.0114 -  1.9625   849    97  0.57  46.85   1.00     0.78      19550.40|
|alpha:            min =        0.69 max =            0.87 mean =         0.76|
|beta:             min =    19550.40 max =        86236.84 mean =     53468.41|
|figures of merit: min =        0.00 max =            1.00 mean =         0.56|
|phase err.(work): min =        0.00 max =           90.00 mean =        46.63|
|phase err.(test): min =        0.00 max =           89.95 mean =        46.92|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.060911             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.314   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.486778              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.942   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:       15 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       27 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      216 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2043 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1918 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2875 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4710 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4485 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5703 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6786 |
|-----------------------------------------------------------------------------|
|-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 |        0.173 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.806 |       0.373 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.484)------------------------------------------|
|    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 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4121   r_free= 0.4106   ksol= 0.00   Bsol= 0.00   scale= 0.937    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.220526                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3988   r_free= 0.3974   ksol= 0.34   Bsol= 29.77   scale= 0.955   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.17,3.22,-0.82,0.00,-0.00,-0.00); trace/3= -0.25                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.208101                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.349506              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.250   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.813252              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.877   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3988      final r-factor (work) = 0.2687          |
| start r-factor (free) = 0.3974      final r-factor (free) = 0.3020          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.1858 = 9.35 * 0.50 * 6.2062 + 1.00 * 0.1734                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.2321 = 9.35 * 0.50 * 6.0135 + 1.00 * 0.1205                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2687      final r-factor (work) = 0.2444          |
| start r-factor (free) = 0.3020      final r-factor (free) = 0.3155          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8965 = 0.81 * 1.00 * 6.0135 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7534 = 0.81 * 1.00 * 5.8275 + 1.00 * 0.0142                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.484)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.14   17.88    None  None   None       |
|    all(noH): 2823   0      0.00    99.14   17.88    None  None   None       |
|    Sol.    : 438    0      4.05    99.14   40.10    None  None   None       |
|    Mac.    : 2385   0      0.00    78.74   13.80    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:     0.000 -   9.915:  964   |   5:    49.572 -  59.487:  102        |
|      1:     9.915 -  19.829: 1035   |   6:    59.487 -  69.401:   33        |
|      2:    19.829 -  29.744:  362   |   7:    69.401 -  79.316:   19        |
|      3:    29.744 -  39.658:  171   |   8:    79.316 -  89.230:    0        |
|      4:    39.658 -  49.572:  136   |   9:    89.230 -  99.145:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2444 r_free = 0.3155             target_work(ml) = 5.845         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2440 r_free = 0.3151             target_work(ml) = 5.843         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2440   r_free= 0.3151   ksol= 0.34   Bsol= 29.77   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.17,3.22,-0.82,0.00,-0.00,-0.00); trace/3= -0.25                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.843477                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2416   r_free= 0.3107   ksol= 0.33   Bsol= 42.83   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-0.28,-0.93,-0.00,-0.00,-0.00); trace/3= -1.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.832849                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.350169              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.290   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.212226              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.403  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2416      final r-factor (work) = 0.1809          |
| start r-factor (free) = 0.3107      final r-factor (free) = 0.2323          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7900 = 4.35 * 0.50 * 5.8249 + 1.00 * 0.1205                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5063 = 4.35 * 0.50 * 5.7201 + 1.00 * 0.0646                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1809      final r-factor (work) = 0.1651          |
| start r-factor (free) = 0.2323      final r-factor (free) = 0.2129          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2281 = 0.21 * 1.00 * 5.7201 + 1.00 * 0.0142                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1790 = 0.21 * 1.00 * 5.5179 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.484)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.09    91.65   17.10    None  None   None       |
|    all(noH): 2823   0      1.09    91.65   17.10    None  None   None       |
|    Sol.    : 438    0      6.17    91.65   39.13    None  None   None       |
|    Mac.    : 2385   0      1.09    79.18   13.05    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.085 -  10.142: 1015   |   5:    46.369 -  55.425:   97        |
|      1:    10.142 -  19.199: 1081   |   6:    55.425 -  64.482:   48        |
|      2:    19.199 -  28.255:  268   |   7:    64.482 -  73.539:   14        |
|      3:    28.255 -  37.312:  150   |   8:    73.539 -  82.595:    2        |
|      4:    37.312 -  46.369:  147   |   9:    82.595 -  91.652:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1651 r_free = 0.2129             target_work(ml) = 5.481         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1649 r_free = 0.2129             target_work(ml) = 5.480         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1649   r_free= 0.2129   ksol= 0.33   Bsol= 42.83   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-0.28,-0.93,-0.00,-0.00,-0.00); trace/3= -1.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.479803                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1647   r_free= 0.2118   ksol= 0.33   Bsol= 42.83   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.22,-1.48,-0.94,-0.00,-0.00,-0.00); trace/3= -1.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.474570                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.339294              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.886  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.355125              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.498  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1647      final r-factor (work) = 0.1292          |
| start r-factor (free) = 0.2118      final r-factor (free) = 0.1758          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2745 = 3.34 * 0.50 * 5.5163 + 1.00 * 0.0642                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0168 = 3.34 * 0.50 * 5.3650 + 1.00 * 0.0592                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1292      final r-factor (work) = 0.1223          |
| start r-factor (free) = 0.1758      final r-factor (free) = 0.1702          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9131 = 0.36 * 1.00 * 5.3650 + 1.00 * 0.0079                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8664 = 0.36 * 1.00 * 5.2322 + 1.00 * 0.0083                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.484)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.51    90.92   17.02    None  None   None       |
|    all(noH): 2823   0      0.51    90.92   17.02    None  None   None       |
|    Sol.    : 438    0      6.36    90.92   40.26    None  None   None       |
|    Mac.    : 2385   0      0.51    82.56   12.75    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:     0.511 -   9.551:  942   |   5:    45.713 -  54.754:  120        |
|      1:     9.551 -  18.592: 1174   |   6:    54.754 -  63.795:   54        |
|      2:    18.592 -  27.632:  242   |   7:    63.795 -  72.835:   28        |
|      3:    27.632 -  36.673:  135   |   8:    72.835 -  81.876:    2        |
|      4:    36.673 -  45.713:  124   |   9:    81.876 -  90.916:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1223 r_free = 0.1702             target_work(ml) = 5.213         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1222 r_free = 0.1701             target_work(ml) = 5.212         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1222   r_free= 0.1701   ksol= 0.33   Bsol= 42.83   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.22,-1.48,-0.94,-0.00,-0.00,-0.00); trace/3= -1.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.212347                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1223   r_free= 0.1697   ksol= 0.32   Bsol= 42.83   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,-2.26,-1.30,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.211689                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.174854              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 122.917  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.142968              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.432  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1223      final r-factor (work) = 0.1140          |
| start r-factor (free) = 0.1697      final r-factor (free) = 0.1608          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7532 = 2.17 * 0.50 * 5.2362 + 1.00 * 0.0592                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6901 = 2.17 * 0.50 * 5.1830 + 1.00 * 0.0540                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1140      final r-factor (work) = 0.1116          |
| start r-factor (free) = 0.1608      final r-factor (free) = 0.1595          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9323 = 1.14 * 1.00 * 5.1830 + 1.00 * 0.0083                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8915 = 1.14 * 1.00 * 5.1462 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.484)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.96   17.22    None  None   None       |
|    all(noH): 2823   0      0.00    93.96   17.22    None  None   None       |
|    Sol.    : 438    0      6.02    93.96   41.63    None  None   None       |
|    Mac.    : 2385   0      0.00    93.14   12.74    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.396:  930   |   5:    46.980 -  56.376:  107        |
|      1:     9.396 -  18.792: 1204   |   6:    56.376 -  65.772:   57        |
|      2:    18.792 -  28.188:  244   |   7:    65.772 -  75.169:   35        |
|      3:    28.188 -  37.584:  122   |   8:    75.169 -  84.565:   10        |
|      4:    37.584 -  46.980:  110   |   9:    84.565 -  93.961:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1116 r_free = 0.1595             target_work(ml) = 5.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1115 r_free = 0.1595             target_work(ml) = 5.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1115   r_free= 0.1595   ksol= 0.32   Bsol= 42.83   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,-2.26,-1.30,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.143257                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1115   r_free= 0.1594   ksol= 0.32   Bsol= 43.90   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-2.28,-1.21,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.142851                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.591221              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.986  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.470131              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.301  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1115      final r-factor (work) = 0.1075          |
| start r-factor (free) = 0.1594      final r-factor (free) = 0.1568          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7213 = 2.59 * 0.50 * 5.1461 + 1.00 * 0.0540                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7023 = 2.59 * 0.50 * 5.1261 + 1.00 * 0.0608                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1075      final r-factor (work) = 0.1071          |
| start r-factor (free) = 0.1568      final r-factor (free) = 0.1557          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4196 = 0.47 * 1.00 * 5.1261 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4129 = 0.47 * 1.00 * 5.1132 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.484)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.27    95.89   16.87    None  None   None       |
|    all(noH): 2823   0      0.27    95.89   16.87    None  None   None       |
|    Sol.    : 438    0      5.96    92.08   40.23    None  None   None       |
|    Mac.    : 2385   0      0.27    95.89   12.58    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:     0.270 -   9.831: 1065   |   5:    48.078 -  57.639:   90        |
|      1:     9.831 -  19.393: 1111   |   6:    57.639 -  67.201:   42        |
|      2:    19.393 -  28.955:  216   |   7:    67.201 -  76.763:   26        |
|      3:    28.955 -  38.516:  132   |   8:    76.763 -  86.324:    6        |
|      4:    38.516 -  48.078:  130   |   9:    86.324 -  95.886:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1071 r_free = 0.1557             target_work(ml) = 5.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1070 r_free = 0.1557             target_work(ml) = 5.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1070   r_free= 0.1557   ksol= 0.32   Bsol= 43.90   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-2.28,-1.21,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.110506                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8990 -  4.6839 0.99   1386  155 0.0938 0.1212      5.3339      5.5074|
|  2:  4.6839 -  3.7371 0.99   1333  147 0.0810 0.1146      5.4064      5.6185|
|  3:  3.7371 -  3.2704 0.99   1307  143 0.1037 0.1482      5.4602      5.8457|
|  4:  3.2704 -  2.9740 0.99   1292  146 0.1183 0.1574      5.4266      5.5715|
|  5:  2.9740 -  2.7623 0.99   1289  145 0.1272 0.1769      5.2982      5.5401|
|  6:  2.7623 -  2.6003 0.99   1297  139 0.1126 0.1733      5.1784      5.3976|
|  7:  2.6003 -  2.4707 0.99   1284  142 0.1229 0.1550      5.1366       5.354|
|  8:  2.4707 -  2.3636 0.98   1264  144 0.1107 0.1713      5.0196      5.3156|
|  9:  2.3636 -  2.2729 0.98   1266  140 0.1097 0.1648      4.9848      5.2335|
| 10:  2.2729 -  2.1947 1.00   1263  143 0.1054 0.1747      4.9171      5.2422|
| 11:  2.1947 -  2.1263 0.98   1268  139 0.1079 0.1776      4.9246      5.2746|
| 12:  2.1263 -  2.0657 0.98   1246  142 0.1076 0.1594      4.8569      5.1093|
| 13:  2.0657 -  2.0114 0.99   1286  137 0.1084 0.1835      4.7575      5.0766|
| 14:  2.0114 -  1.9625 0.67    849   97 0.0966 0.1557      4.6288      4.8592|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8990 -  4.6839  1386   155  0.94   8.60   0.98     0.96       6488.70|
|  2:  4.6839 -  3.7371  1333   147  0.95   7.64   1.03     1.02       8716.30|
|  3:  3.7371 -  3.2704  1307   143  0.94  11.06   1.04     1.03      10045.83|
|  4:  3.2704 -  2.9740  1292   146  0.92  13.50   1.02     1.00       9912.53|
|  5:  2.9740 -  2.7623  1289   145  0.90  15.49   1.00     0.98       7934.67|
|  6:  2.7623 -  2.6003  1297   139  0.91  15.36   0.99     0.97       6818.39|
|  7:  2.6003 -  2.4707  1284   142  0.91  15.39   0.99     0.96       5873.40|
|  8:  2.4707 -  2.3636  1264   144  0.91  14.42   1.00     0.98       4796.60|
|  9:  2.3636 -  2.2729  1266   140  0.92  14.39   1.01     0.98       4589.03|
| 10:  2.2729 -  2.1947  1263   143  0.91  14.83   1.01     0.97       4104.03|
| 11:  2.1947 -  2.1263  1268   139  0.90  16.06   1.00     0.96       4266.93|
| 12:  2.1263 -  2.0657  1246   142  0.91  14.89   1.02     1.01       3866.09|
| 13:  2.0657 -  2.0114  1286   137  0.91  15.58   1.01     0.99       3163.91|
| 14:  2.0114 -  1.9625   849    97  0.92  13.61   0.99     0.97       2438.82|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2438.82 max =        10045.83 mean =      6045.64|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.85 mean =        13.58|
|phase err.(test): min =        0.00 max =           89.29 mean =        13.10|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1070   r_free= 0.1557   ksol= 0.32   Bsol= 43.38   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-2.20,-1.04,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.110618                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1070   r_free= 0.1557   ksol= 0.32   Bsol= 43.38   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-2.20,-1.04,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.110618                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8990 -  4.6839 0.99   1386  155 0.0939 0.1215      5.3362      5.5099|
|  2:  4.6839 -  3.7371 0.99   1333  147 0.0810 0.1145      5.4065      5.6177|
|  3:  3.7371 -  3.2704 0.99   1307  143 0.1036 0.1482      5.4599      5.8454|
|  4:  3.2704 -  2.9740 0.99   1292  146 0.1183 0.1575      5.4264      5.5717|
|  5:  2.9740 -  2.7623 0.99   1289  145 0.1272 0.1769      5.2981      5.5399|
|  6:  2.7623 -  2.6003 0.99   1297  139 0.1125 0.1731      5.1783      5.3972|
|  7:  2.6003 -  2.4707 0.99   1284  142 0.1230 0.1552      5.1368      5.3546|
|  8:  2.4707 -  2.3636 0.98   1264  144 0.1107 0.1713      5.0197      5.3155|
|  9:  2.3636 -  2.2729 0.98   1266  140 0.1097 0.1647      4.9848      5.2331|
| 10:  2.2729 -  2.1947 1.00   1263  143 0.1053 0.1750      4.9173      5.2435|
| 11:  2.1947 -  2.1263 0.98   1268  139 0.1079 0.1775      4.9249      5.2748|
| 12:  2.1263 -  2.0657 0.98   1246  142 0.1075 0.1595      4.8567      5.1095|
| 13:  2.0657 -  2.0114 0.99   1286  137 0.1084 0.1834      4.7571      5.0758|
| 14:  2.0114 -  1.9625 0.67    849   97 0.0967 0.1553       4.628      4.8576|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8990 -  4.6839  1386   155  0.94   8.65   0.98     0.96       6527.21|
|  2:  4.6839 -  3.7371  1333   147  0.95   7.66   1.03     1.02       8735.08|
|  3:  3.7371 -  3.2704  1307   143  0.94  11.06   1.04     1.03      10040.58|
|  4:  3.2704 -  2.9740  1292   146  0.92  13.50   1.02     1.00       9908.26|
|  5:  2.9740 -  2.7623  1289   145  0.90  15.48   1.01     0.98       7929.17|
|  6:  2.7623 -  2.6003  1297   139  0.91  15.36   1.00     0.97       6816.39|
|  7:  2.6003 -  2.4707  1284   142  0.91  15.39   1.00     0.96       5874.11|
|  8:  2.4707 -  2.3636  1264   144  0.91  14.42   1.00     0.98       4796.07|
|  9:  2.3636 -  2.2729  1266   140  0.92  14.40   1.01     0.99       4589.95|
| 10:  2.2729 -  2.1947  1263   143  0.91  14.84   1.01     0.98       4108.41|
| 11:  2.1947 -  2.1263  1268   139  0.90  16.07   1.00     0.96       4271.38|
| 12:  2.1263 -  2.0657  1246   142  0.91  14.90   1.02     1.02       3867.26|
| 13:  2.0657 -  2.0114  1286   137  0.91  15.57   1.01     0.99       3159.62|
| 14:  2.0114 -  1.9625   849    97  0.92  13.59   1.00     0.98       2432.54|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2432.54 max =        10040.58 mean =      6049.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.58|
|phase err.(test): min =        0.00 max =           89.30 mean =        13.10|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.484)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.26    95.88   16.86    None  None   None       |
|    all(noH): 2823   0      0.26    95.88   16.86    None  None   None       |
|    Sol.    : 438    0      5.95    92.07   40.22    None  None   None       |
|    Mac.    : 2385   0      0.26    95.88   12.57    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:     0.262 -   9.824: 1065   |   5:    48.071 -  57.632:   90        |
|      1:     9.824 -  19.386: 1111   |   6:    57.632 -  67.194:   42        |
|      2:    19.386 -  28.947:  216   |   7:    67.194 -  76.755:   26        |
|      3:    28.947 -  38.509:  132   |   8:    76.755 -  86.317:    6        |
|      4:    38.509 -  48.071:  130   |   9:    86.317 -  95.879:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 303         
Filter by distance & map next to the model:
   mapped sites are within: 0.665 - 4.615
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 300 from: 303
   mapped sites are within: 0.738 - 4.615

peak=    6.830 closest distance to " NE2 GLN A  11 " =    1.293
peak=    5.961 closest distance to " O   HOH Z 144 " =    1.717
peak=    5.817 closest distance to " O   HOH Z 126 " =    2.030
peak=    5.526 closest distance to " NH2 ARG A  56 " =    2.109
peak=    5.475 closest distance to " O   HOH Z 427 " =    2.354
peak=    5.374 closest distance to " CG  PRO A  54 " =    1.252
peak=    5.130 closest distance to " O   HOH Z 423 " =    1.717
peak=    5.093 closest distance to " O   HOH Z 236 " =    1.463
peak=    5.087 closest distance to " O   HOH Z 417 " =    1.519
peak=    5.005 closest distance to " O   HOH Z  63 " =    1.733
peak=    4.948 closest distance to " O   HOH Z 287 " =    1.865
peak=    4.853 closest distance to " O   HOH Z 232 " =    2.290
peak=    4.769 closest distance to " CB  SER A  63 " =    1.238
peak=    4.763 closest distance to " CG  PRO A 213 " =    1.240
peak=    4.738 closest distance to " O   HOH Z 193 " =    1.839
peak=    4.734 closest distance to " O   HOH Z  78 " =    1.711
peak=    4.703 closest distance to " O   HOH Z 298 " =    1.946
peak=    4.646 closest distance to " CB  ARG A 275 " =    0.902
peak=    4.525 closest distance to " O   HOH Z 380 " =    1.696
peak=    4.507 closest distance to " O   HOH Z 209 " =    2.212
peak=    4.481 closest distance to " CB  GLN A 183 " =    1.203
peak=    4.468 closest distance to " CG  TRP A 179 " =    2.273
peak=    4.463 closest distance to " CB  GLN A 223 " =    1.529
peak=    4.458 closest distance to " CG  ARG A  66 " =    2.472
peak=    4.458 closest distance to " CB  PRO A  54 " =    0.967
peak=    4.428 closest distance to " CB  ARG A  79 " =    1.356
peak=    4.425 closest distance to " CB  ASN A 148 " =    1.385
peak=    4.402 closest distance to " O   HOH Z 368 " =    3.706
peak=    4.388 closest distance to " CB  GLU A 152 " =    1.292
peak=    4.374 closest distance to " O   HOH Z   1 " =    1.756
peak=    4.371 closest distance to " ND2 ASN A 187 " =    1.438
peak=    4.360 closest distance to " OG BSER A 164 " =    2.277
peak=    4.315 closest distance to " O   HOH Z 419 " =    2.372
peak=    4.294 closest distance to " CB  GLU A 128 " =    1.017
peak=    4.283 closest distance to " O   HOH Z 369 " =    2.206
peak=    4.277 closest distance to " O   HOH Z   9 " =    2.033
peak=    4.257 closest distance to " C   PRO A 198 " =    1.459
peak=    4.256 closest distance to " O   HOH Z 272 " =    1.795
peak=    4.228 closest distance to " O   HOH Z 217 " =    2.897
peak=    4.220 closest distance to " O   HOH Z 112 " =    1.172
peak=    4.219 closest distance to " O   HOH Z 371 " =    1.895
peak=    4.212 closest distance to " CA  TYR A  30 " =    0.934
peak=    4.209 closest distance to " O   HOH Z  44 " =    1.727
peak=    4.182 closest distance to " CG2 VAL A 257 " =    0.842
peak=    4.175 closest distance to " O   HOH Z 425 " =    1.371
peak=    4.169 closest distance to " CB  ASN A 187 " =    1.367
peak=    4.160 closest distance to " CB  VAL A 265 " =    1.323
peak=    4.143 closest distance to " CB  SER A   3 " =    1.334
peak=    4.107 closest distance to " O   HOH Z 375 " =    0.991
peak=    4.086 closest distance to " O   HOH Z  61 " =    1.623
peak=    4.081 closest distance to " O   HOH Z  78 " =    2.106
peak=    4.025 closest distance to " O   SER A  87 " =    2.191
peak=    4.022 closest distance to " CG  PRO A  90 " =    1.157
peak=    4.022 closest distance to " O   HOH Z  61 " =    1.495
peak=    4.008 closest distance to " O   HOH Z 425 " =    1.936
peak=    4.004 closest distance to " O   HOH Z   7 " =    1.342
peak=    3.997 closest distance to " O   HOH Z   1 " =    1.654
peak=    3.983 closest distance to " O   HOH Z 261 " =    1.755
peak=    3.979 closest distance to " O   HOH Z 128 " =    2.023
peak=    3.969 closest distance to " O   HOH Z 234 " =    3.601
peak=    3.944 closest distance to " O   HOH Z 316 " =    3.001
peak=    3.930 closest distance to " O   HOH Z 132 " =    2.058
peak=    3.929 closest distance to " O   HOH Z 352 " =    1.797
peak=    3.923 closest distance to " O   HOH Z 327 " =    1.695
peak=    3.921 closest distance to " CB  ARG A 139 " =    1.011
peak=    3.904 closest distance to " O   HOH Z 158 " =    2.875
peak=    3.899 closest distance to " O   HOH Z 250 " =    1.495
peak=    3.886 closest distance to " OD1 ASN A  69 " =    2.620
peak=    3.867 closest distance to " CB  ARG A 190 " =    1.631
peak=    3.867 closest distance to " O   HOH Z 426 " =    1.915
peak=    3.865 closest distance to " CB  LEU A 228 " =    1.075
peak=    3.849 closest distance to " O   HOH Z 124 " =    1.357
peak=    3.844 closest distance to " O   HOH Z 214 " =    2.142
peak=    3.839 closest distance to " O   HOH Z 146 " =    1.794
peak=    3.833 closest distance to " O   HOH Z 344 " =    3.085
peak=    3.831 closest distance to " O   HOH Z   2 " =    1.520
peak=    3.827 closest distance to " O   HOH Z 365 " =    2.705
peak=    3.816 closest distance to " OD1BASN A 224 " =    2.188
peak=    3.802 closest distance to " O   HOH Z 368 " =    1.925
peak=    3.790 closest distance to " NE2 GLN A  73 " =    3.579
peak=    3.788 closest distance to " CG  PRO A 198 " =    1.228
peak=    3.782 closest distance to " O   HOH Z   9 " =    1.104
peak=    3.777 closest distance to " CB  GLU A 277 " =    3.504
peak=    3.766 closest distance to " O   HOH Z  40 " =    2.150
peak=    3.763 closest distance to " O   HOH Z 405 " =    1.352
peak=    3.759 closest distance to " O   HOH Z   3 " =    1.948
peak=    3.750 closest distance to " CA  ASN A 215 " =    1.117
peak=    3.747 closest distance to " CB  TRP A 179 " =    1.386
peak=    3.742 closest distance to " OG BSER A  99 " =    2.288
peak=    3.741 closest distance to " O   HOH Z 394 " =    1.610
peak=    3.736 closest distance to " O   HOH Z 144 " =    2.270
peak=    3.733 closest distance to " CA  ALA A 299 " =    0.901
peak=    3.730 closest distance to " CD BLYS A 290 " =    1.151
peak=    3.724 closest distance to " O   HOH Z 362 " =    2.132
peak=    3.723 closest distance to " CE  LYS A  76 " =    0.882
peak=    3.721 closest distance to " OD2 ASP A 286 " =    2.632
peak=    3.718 closest distance to " NH1AARG A 145 " =    1.173
peak=    3.714 closest distance to " CE1 TYR A 186 " =    1.309
peak=    3.712 closest distance to " O   HOH Z 371 " =    2.896
peak=    3.708 closest distance to " O   HOH Z 386 " =    2.996
peak=    3.706 closest distance to " O   HOH Z 222 " =    2.415
peak=    3.705 closest distance to " O   HOH Z 389 " =    1.804
peak=    3.701 closest distance to " CB  ILE A 120 " =    1.312
peak=    3.695 closest distance to " O   HOH Z 286 " =    2.237
peak=    3.686 closest distance to " N   HIS A  86 " =    1.841
peak=    3.684 closest distance to " CD  ARG A 159 " =    0.763
peak=    3.676 closest distance to " N   PHE A 130 " =    1.251
peak=    3.672 closest distance to " O   HOH Z  10 " =    1.730
peak=    3.671 closest distance to " O   HOH Z 171 " =    2.862
peak=    3.666 closest distance to " CB  SER A 216 " =    0.759
peak=    3.633 closest distance to " NH1BARG A 145 " =    1.276
peak=    3.632 closest distance to " OG  SER A  62 " =    2.966
peak=    3.620 closest distance to " O   HOH Z 119 " =    4.341
peak=    3.618 closest distance to " O   HOH Z  59 " =    2.012
peak=    3.615 closest distance to " O   HOH Z 257 " =    2.184
peak=    3.614 closest distance to " CD2 LEU A 297 " =    1.001
peak=    3.614 closest distance to " O   HOH Z 180 " =    2.163
peak=    3.612 closest distance to " CG1 ILE A  33 " =    1.223
peak=    3.599 closest distance to " CB  ASN A  39 " =    0.823
peak=    3.597 closest distance to " CG  PRO A 243 " =    1.131
peak=    3.596 closest distance to " CB  TYR A 169 " =    0.814
peak=    3.586 closest distance to " N   ASN A 127 " =    1.347
peak=    3.583 closest distance to " CH2 TRP A  92 " =    2.107
peak=    3.579 closest distance to " CD2 TRP A 179 " =    1.320
peak=    3.579 closest distance to " O   HOH Z  93 " =    2.102
peak=    3.576 closest distance to " CG2 THR A 221 " =    1.171
peak=    3.570 closest distance to " CB  ALA A  34 " =    1.161
peak=    3.570 closest distance to " O   HOH Z  97 " =    1.919
peak=    3.568 closest distance to " CD  PRO A 243 " =    1.558
peak=    3.567 closest distance to " O   HOH Z 289 " =    1.623
peak=    3.563 closest distance to " O   HOH Z 133 " =    2.618
peak=    3.560 closest distance to " O   HOH Z 213 " =    2.096
peak=    3.554 closest distance to " CB  SER A  26 " =    1.653
peak=    3.552 closest distance to " O   HOH Z 422 " =    2.621
peak=    3.549 closest distance to " CB  ALA A  21 " =    1.930
peak=    3.545 closest distance to " O   HOH Z 261 " =    2.357
peak=    3.541 closest distance to " CB  ALA A   1 " =    4.615
peak=    3.539 closest distance to " O   HOH Z 437 " =    1.874
peak=    3.539 closest distance to " O   HOH Z  66 " =    2.148
peak=    3.537 closest distance to " CA  ALA A  21 " =    1.132
peak=    3.531 closest distance to " NH2BARG A 145 " =    2.124
peak=    3.513 closest distance to " O   HOH Z 423 " =    1.884
peak=    3.507 closest distance to " O   HOH Z 359 " =    1.364
peak=    3.501 closest distance to " O   HOH Z 227 " =    1.902
peak=    3.493 closest distance to " O   HOH Z 128 " =    2.070
peak=    3.487 closest distance to " O   HOH Z 298 " =    2.486
peak=    3.482 closest distance to " N   SER A 134 " =    1.380
peak=    3.481 closest distance to " O   HOH Z  21 " =    1.682
peak=    3.478 closest distance to " O   HOH Z 357 " =    1.886
peak=    3.477 closest distance to " O   HOH Z 266 " =    3.190
peak=    3.468 closest distance to " O   HOH Z 411 " =    3.733
peak=    3.462 closest distance to " O   HOH Z 403 " =    1.309
peak=    3.458 closest distance to " CB  GLN A  88 " =    1.236
peak=    3.458 closest distance to " CB  TRP A 266 " =    1.064
peak=    3.457 closest distance to " O   HOH Z  44 " =    3.051
peak=    3.438 closest distance to " CB  SER A  62 " =    1.253
peak=    3.437 closest distance to " O   HOH Z 175 " =    2.093
peak=    3.428 closest distance to " CG  LEU A 167 " =    1.239
peak=    3.427 closest distance to " O   HOH Z  88 " =    2.663
peak=    3.424 closest distance to " CB  LYS A 117 " =    1.188
peak=    3.424 closest distance to " O   HOH Z 281 " =    1.769
peak=    3.423 closest distance to " CG1BVAL A  72 " =    1.337
peak=    3.421 closest distance to " O   HOH Z 291 " =    1.473
peak=    3.418 closest distance to " O   HOH Z  17 " =    1.740
peak=    3.416 closest distance to " O   HOH Z 189 " =    1.954
peak=    3.415 closest distance to " N   GLU A   2 " =    1.367
peak=    3.415 closest distance to " CG2 ILE A 120 " =    1.038
peak=    3.414 closest distance to " O   HOH Z 126 " =    1.421
peak=    3.407 closest distance to " O   HOH Z 189 " =    2.072
peak=    3.407 closest distance to " O   HOH Z 432 " =    1.951
peak=    3.404 closest distance to " CA  PHE A 283 " =    1.427
peak=    3.402 closest distance to " CA  MET A  40 " =    1.093
peak=    3.399 closest distance to " O   HOH Z 147 " =    1.696
peak=    3.396 closest distance to " CD  ARG A 138 " =    0.738
peak=    3.396 closest distance to " CB  LEU A 143 " =    1.091
peak=    3.392 closest distance to " O   HOH Z  71 " =    2.031
peak=    3.391 closest distance to " O   HOH Z  88 " =    2.703
peak=    3.391 closest distance to " CB  TYR A 169 " =    0.860
peak=    3.387 closest distance to " O   HOH Z 195 " =    1.289
peak=    3.387 closest distance to " O   HOH Z 272 " =    2.056
peak=    3.385 closest distance to " N   ALA A   1 " =    1.894
peak=    3.380 closest distance to " CB  ALA A 114 " =    1.430
peak=    3.378 closest distance to " O   HOH Z 271 " =    2.340
peak=    3.370 closest distance to " O   HOH Z 130 " =    2.364
peak=    3.369 closest distance to " O   HOH Z 151 " =    1.466
peak=    3.369 closest distance to " O   HOH Z  59 " =    1.490
peak=    3.362 closest distance to " O   HOH Z 173 " =    1.907
peak=    3.362 closest distance to " CB  THR A  31 " =    1.812
peak=    3.362 closest distance to " N   GLN A 278 " =    1.114
peak=    3.358 closest distance to " O   HOH Z 284 " =    2.933
peak=    3.357 closest distance to " CB  THR A 157 " =    1.083
peak=    3.350 closest distance to " O   HOH Z   6 " =    2.053
peak=    3.340 closest distance to " O   HOH Z 128 " =    1.972
peak=    3.340 closest distance to " NE2 GLN A  58 " =    3.669
peak=    3.338 closest distance to " O   HOH Z 374 " =    2.489
peak=    3.335 closest distance to " O   HOH Z 345 " =    3.329
peak=    3.332 closest distance to " O   HOH Z 219 " =    2.389
peak=    3.331 closest distance to " O   HOH Z 305 " =    3.517
peak=    3.331 closest distance to " CA  ALA A 233 " =    1.046
peak=    3.330 closest distance to " N   CYS A 260 " =    0.838
peak=    3.330 closest distance to " CG  GLN A  77 " =    2.374
peak=    3.327 closest distance to " O   HOH Z 336 " =    1.893
peak=    3.326 closest distance to " O   HOH Z 329 " =    3.597
peak=    3.324 closest distance to " O   HOH Z 139 " =    1.158
peak=    3.324 closest distance to " NZ  LYS A 117 " =    1.325
peak=    3.322 closest distance to " NE AARG A 275 " =    1.444
peak=    3.319 closest distance to " O   HOH Z 313 " =    1.656
peak=    3.317 closest distance to " CG AARG A 275 " =    1.070
peak=    3.315 closest distance to " O   HOH Z 409 " =    2.272
peak=    3.314 closest distance to " O   HOH Z 193 " =    2.008
peak=    3.314 closest distance to " CD1 ILE A 263 " =    1.392
peak=    3.313 closest distance to " O  BHOH Z 338 " =    2.423
peak=    3.308 closest distance to " O   HOH Z 211 " =    2.713
peak=    3.305 closest distance to " O   HOH Z 245 " =    1.322
peak=    3.304 closest distance to " O   HOH Z 108 " =    1.210
peak=    3.303 closest distance to " O   HOH Z 263 " =    2.433
peak=    3.297 closest distance to " O   HOH Z 403 " =    1.573
peak=    3.297 closest distance to " CG  GLU A 277 " =    2.014
peak=    3.294 closest distance to " O   HOH Z 108 " =    2.148
peak=    3.285 closest distance to " CG  GLN A  89 " =    1.424
peak=    3.285 closest distance to " O   HOH Z  32 " =    1.941
peak=    3.272 closest distance to " CG  MET A 113 " =    1.161
peak=    3.270 closest distance to " O   HOH Z 290 " =    0.995
peak=    3.268 closest distance to " CB  VAL A 202 " =    1.620
peak=    3.263 closest distance to " CA  ASP A 162 " =    1.044
peak=    3.262 closest distance to " CB  VAL A 265 " =    2.301
peak=    3.257 closest distance to " O   HOH Z 116 " =    2.858
peak=    3.252 closest distance to " CE AMET A  47 " =    1.277
peak=    3.249 closest distance to " CA  TYR A 116 " =    1.321
peak=    3.245 closest distance to " CB  TYR A  30 " =    1.077
peak=    3.244 closest distance to " O   HOH Z 207 " =    2.053
peak=    3.243 closest distance to " O   HOH Z 273 " =    2.867
peak=    3.242 closest distance to " CB  MET A 188 " =    1.676
peak=    3.242 closest distance to " CD1 LEU A 300 " =    1.237
peak=    3.240 closest distance to " O   HOH Z 139 " =    2.372
peak=    3.239 closest distance to " CB  LEU A 300 " =    0.932
peak=    3.238 closest distance to " CB  ASP A 140 " =    0.848
peak=    3.236 closest distance to " O   HOH Z 325 " =    3.598
peak=    3.234 closest distance to " CA  MET A 105 " =    0.874
peak=    3.229 closest distance to " CA  ASN A 127 " =    0.965
peak=    3.225 closest distance to " CB  LYS A 290 " =    1.388
peak=    3.225 closest distance to " N   ASP A 162 " =    1.222
peak=    3.216 closest distance to " CA  ALA A  84 " =    1.396
peak=    3.216 closest distance to " O   HOH Z 109 " =    2.589
peak=    3.214 closest distance to " O   HOH Z 217 " =    1.639
peak=    3.209 closest distance to " CD  ARG A  79 " =    2.312
peak=    3.206 closest distance to " O   HOH Z  47 " =    1.853
peak=    3.204 closest distance to " CB  TYR A 116 " =    0.895
peak=    3.202 closest distance to " NZ  LYS A  76 " =    1.573
peak=    3.199 closest distance to " CA  THR A 264 " =    0.855
peak=    3.198 closest distance to " CD2 LEU A 255 " =    1.419
peak=    3.196 closest distance to " O   HOH Z  30 " =    1.686
peak=    3.191 closest distance to " N   TRP A 177 " =    1.697
peak=    3.190 closest distance to " NE2 GLN A 278 " =    3.359
peak=    3.188 closest distance to " CG BARG A 102 " =    1.828
peak=    3.186 closest distance to " ND1 HIS A  81 " =    1.545
peak=    3.186 closest distance to " CB  ARG A 138 " =    0.929
peak=    3.183 closest distance to " CA  ILE A 234 " =    1.023
peak=    3.183 closest distance to " O   HOH Z 193 " =    1.538
peak=    3.178 closest distance to " CD  LYS A 166 " =    1.327
peak=    3.178 closest distance to " O   HOH Z 302 " =    1.500
peak=    3.177 closest distance to " CZ  PHE A 218 " =    1.019
peak=    3.176 closest distance to " O   HOH Z 119 " =    1.580
peak=    3.172 closest distance to " O   HOH Z   9 " =    1.841
peak=    3.169 closest distance to " O   ARG A 145 " =    1.724
peak=    3.166 closest distance to " O   HOH Z  66 " =    2.021
peak=    3.166 closest distance to " CA  ALA A 291 " =    0.898
peak=    3.164 closest distance to " O   HOH Z 172 " =    2.771
peak=    3.164 closest distance to " NH2AARG A 190 " =    1.779
peak=    3.160 closest distance to " CG1 ILE A 151 " =    1.054
peak=    3.158 closest distance to " OG  SER A  22 " =    2.779
peak=    3.157 closest distance to " O   HOH Z 155 " =    1.575
peak=    3.157 closest distance to " O  BHOH Z  74 " =    1.435
peak=    3.153 closest distance to " CA  ALA A 158 " =    1.131
peak=    3.149 closest distance to " O   HOH Z 407 " =    2.161
peak=    3.144 closest distance to " O   ASN A 209 " =    1.343
peak=    3.144 closest distance to " O   HOH Z 207 " =    1.596
peak=    3.135 closest distance to " N   ASN A  39 " =    1.245
peak=    3.131 closest distance to " O   HOH Z 153 " =    1.640
peak=    3.126 closest distance to " N   ARG A 156 " =    1.306
peak=    3.120 closest distance to " N   ALA A   1 " =    2.980
peak=    3.118 closest distance to " CG1BVAL A  72 " =    1.336
peak=    3.113 closest distance to " O   HOH Z 291 " =    1.921
peak=    3.109 closest distance to " N   GLY A 241 " =    1.496
peak=    3.103 closest distance to " CG  GLU A 277 " =    4.369
peak=    3.100 closest distance to " O   HOH Z 303 " =    1.674
peak=    3.099 closest distance to " O   HOH Z 346 " =    1.462
peak=    3.095 closest distance to " CG2BVAL A  41 " =    0.789
peak=    3.094 closest distance to " O   HOH Z 218 " =    1.949
peak=    3.094 closest distance to " OH  TYR A 116 " =    1.043
peak=    3.085 closest distance to " CB  ASN A 215 " =    1.055
peak=    3.077 closest distance to " O   HOH Z 166 " =    1.440
peak=    3.075 closest distance to " CG  GLN A 278 " =    1.259
peak=    3.071 closest distance to " CD1 LEU A 167 " =    1.135
peak=    3.068 closest distance to " CB  GLU A 152 " =    1.351
peak=    3.063 closest distance to " O   HOH Z  88 " =    2.234
peak=    3.051 closest distance to " O   HOH Z 263 " =    1.841
peak=    3.034 closest distance to " O   HOH Z 189 " =    2.275
peak=    3.025 closest distance to " CB  VAL A 126 " =    1.190
peak=    3.018 closest distance to " O   HOH Z  43 " =    2.266

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.763 - 5.795
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 209 from: 209
   mapped sites are within: 0.763 - 5.795

peak=   -4.629 closest distance to " C   HIS A 108 " =    1.168
peak=   -4.567 closest distance to " O   HOH Z 377 " =    2.004
peak=   -4.466 closest distance to " CD1 LEU A 255 " =    2.904
peak=   -4.393 closest distance to " CB  PRO A 243 " =    2.570
peak=   -4.374 closest distance to " O   HOH Z  65 " =    1.008
peak=   -4.325 closest distance to " O   HOH Z 266 " =    4.542
peak=   -4.258 closest distance to " CD  ARG A 156 " =    1.988
peak=   -4.209 closest distance to " CD  ARG A  14 " =    3.229
peak=   -4.043 closest distance to " CA  GLY A  98 " =    1.788
peak=   -4.028 closest distance to " O   HOH Z 231 " =    2.110
peak=   -4.016 closest distance to " O   ARG A 145 " =    1.473
peak=   -4.009 closest distance to " CG  GLN A 223 " =    1.808
peak=   -4.002 closest distance to " O   HOH Z 290 " =    1.117
peak=   -3.998 closest distance to " O   PRO A 243 " =    2.483
peak=   -3.966 closest distance to " CZ  PHE A  59 " =    1.471
peak=   -3.966 closest distance to " O   HOH Z 185 " =    2.016
peak=   -3.944 closest distance to " OG BSER A 134 " =    1.364
peak=   -3.931 closest distance to " O   HOH Z 351 " =    1.624
peak=   -3.931 closest distance to " O   HOH Z  13 " =    1.465
peak=   -3.925 closest distance to " O   HOH Z 407 " =    3.104
peak=   -3.912 closest distance to " N   GLN A  58 " =    1.678
peak=   -3.902 closest distance to " O   VAL A  67 " =    2.585
peak=   -3.900 closest distance to " O   SER A 135 " =    1.477
peak=   -3.899 closest distance to " CG  PHE A 283 " =    2.515
peak=   -3.899 closest distance to " CG1 VAL A 112 " =    2.913
peak=   -3.874 closest distance to " OD1 ASP A 191 " =    1.516
peak=   -3.861 closest distance to " O   PRO A 198 " =    1.346
peak=   -3.858 closest distance to " O   HOH Z 372 " =    2.550
peak=   -3.848 closest distance to " CB  ALA A 291 " =    2.129
peak=   -3.794 closest distance to " O   HOH Z 313 " =    1.903
peak=   -3.793 closest distance to " O   HOH Z  43 " =    1.756
peak=   -3.789 closest distance to " O   HOH Z 152 " =    4.869
peak=   -3.787 closest distance to " O   VAL A  67 " =    2.791
peak=   -3.786 closest distance to " OD1 ASP A 191 " =    1.896
peak=   -3.772 closest distance to " OD2 ASP A 191 " =    1.407
peak=   -3.761 closest distance to " O   PRO A 198 " =    1.226
peak=   -3.753 closest distance to " O   HOH Z 438 " =    1.083
peak=   -3.748 closest distance to " O   HOH Z 389 " =    1.849
peak=   -3.745 closest distance to " O   SER A  22 " =    2.502
peak=   -3.742 closest distance to " CE  MET A 105 " =    2.230
peak=   -3.706 closest distance to " O   HOH Z 198 " =    1.983
peak=   -3.700 closest distance to " O   HOH Z  60 " =    2.335
peak=   -3.692 closest distance to " CB  ILE A  33 " =    2.794
peak=   -3.677 closest distance to " OD1 ASN A 187 " =    1.553
peak=   -3.674 closest distance to " NH2 ARG A  79 " =    2.019
peak=   -3.669 closest distance to " CB  ASN A  39 " =    2.293
peak=   -3.659 closest distance to " C   ALA A 158 " =    1.380
peak=   -3.648 closest distance to " O   HOH Z  52 " =    1.329
peak=   -3.645 closest distance to " O   HOH Z 131 " =    4.055
peak=   -3.640 closest distance to " O   SER A  95 " =    1.365
peak=   -3.624 closest distance to " CZ3 TRP A 179 " =    1.248
peak=   -3.622 closest distance to " ND2 ASN A  45 " =    1.094
peak=   -3.620 closest distance to " CA  GLY A 133 " =    1.976
peak=   -3.615 closest distance to " O   HOH Z 166 " =    1.273
peak=   -3.605 closest distance to " O   HOH Z  90 " =    2.342
peak=   -3.594 closest distance to " ND2 ASN A  45 " =    1.874
peak=   -3.593 closest distance to " CB  TYR A  15 " =    2.164
peak=   -3.593 closest distance to " CB  ALA A 248 " =    1.969
peak=   -3.589 closest distance to " O   HOH Z 345 " =    1.992
peak=   -3.586 closest distance to " OD2 ASP A 171 " =    2.020
peak=   -3.570 closest distance to " CD2 PHE A 225 " =    1.151
peak=   -3.564 closest distance to " O   HOH Z  60 " =    2.067
peak=   -3.562 closest distance to " O   HOH Z 126 " =    1.863
peak=   -3.556 closest distance to " CB  CYS A 254 " =    2.251
peak=   -3.550 closest distance to " O   ALA A 161 " =    1.568
peak=   -3.547 closest distance to " O   PHE A 218 " =    1.534
peak=   -3.534 closest distance to " O   HOH Z 298 " =    1.234
peak=   -3.533 closest distance to " CB  ALA A   7 " =    1.964
peak=   -3.529 closest distance to " N   THR A 157 " =    1.467
peak=   -3.528 closest distance to " O   HOH Z 211 " =    1.538
peak=   -3.527 closest distance to " O   VAL A 189 " =    2.414
peak=   -3.522 closest distance to " NH1AARG A 275 " =    1.785
peak=   -3.520 closest distance to " NE2 GLN A 194 " =    2.715
peak=   -3.512 closest distance to " O   HOH Z 388 " =    2.078
peak=   -3.507 closest distance to " CD1 PHE A  59 " =    2.005
peak=   -3.507 closest distance to " CE3 TRP A 123 " =    1.348
peak=   -3.501 closest distance to " OG BSER A 134 " =    1.538
peak=   -3.492 closest distance to " CE2 TYR A  30 " =    2.672
peak=   -3.486 closest distance to " CG  GLN A  58 " =    1.262
peak=   -3.485 closest distance to " CD1 LEU A 101 " =    2.224
peak=   -3.480 closest distance to " OG  SER A  87 " =    1.276
peak=   -3.479 closest distance to " CZ  TYR A 169 " =    1.563
peak=   -3.470 closest distance to " O   HOH Z 348 " =    1.857
peak=   -3.466 closest distance to " CE3 TRP A 274 " =    2.317
peak=   -3.463 closest distance to " O   HOH Z  93 " =    2.147
peak=   -3.461 closest distance to " O   VAL A 174 " =    2.230
peak=   -3.460 closest distance to " O   HOH Z  11 " =    1.876
peak=   -3.455 closest distance to " NE  ARG A  36 " =    1.880
peak=   -3.455 closest distance to " CB  ASP A  27 " =    2.408
peak=   -3.454 closest distance to " CB  PRO A 163 " =    2.490
peak=   -3.447 closest distance to " CG  MET A 105 " =    0.977
peak=   -3.441 closest distance to " O   HOH Z 263 " =    2.873
peak=   -3.439 closest distance to " O   HOH Z 250 " =    1.400
peak=   -3.437 closest distance to " C   ALA A 114 " =    2.378
peak=   -3.430 closest distance to " O   ASP A 162 " =    2.206
peak=   -3.427 closest distance to " O   HOH Z  63 " =    2.390
peak=   -3.427 closest distance to " C   LYS A  76 " =    1.645
peak=   -3.426 closest distance to " OE1 GLU A 277 " =    2.217
peak=   -3.419 closest distance to " CE  MET A  93 " =    1.188
peak=   -3.418 closest distance to " CA  GLY A  57 " =    2.121
peak=   -3.413 closest distance to " ND2 ASN A 187 " =    1.438
peak=   -3.406 closest distance to " CA  GLY A 203 " =    2.245
peak=   -3.396 closest distance to " ND2 ASN A 252 " =    1.755
peak=   -3.395 closest distance to " CE1 PHE A  59 " =    2.012
peak=   -3.395 closest distance to " NH2AARG A 275 " =    5.168
peak=   -3.391 closest distance to " O   HOH Z 409 " =    5.795
peak=   -3.391 closest distance to " CE2 PHE A 218 " =    2.388
peak=   -3.384 closest distance to " N   ASP A 286 " =    2.309
peak=   -3.383 closest distance to " O   HOH Z 359 " =    3.331
peak=   -3.379 closest distance to " O   HOH Z 134 " =    2.998
peak=   -3.378 closest distance to " CG  ASP A 231 " =    0.763
peak=   -3.376 closest distance to " O   HOH Z 191 " =    5.592
peak=   -3.365 closest distance to " OE1 GLN A  88 " =    1.197
peak=   -3.356 closest distance to " CD2 LEU A 237 " =    2.742
peak=   -3.355 closest distance to " O   HOH Z  24 " =    1.183
peak=   -3.353 closest distance to " CE  LYS A  76 " =    2.862
peak=   -3.350 closest distance to " O   HOH Z 148 " =    1.871
peak=   -3.350 closest distance to " OD1 ASP A 171 " =    1.596
peak=   -3.348 closest distance to " O   HOH Z 140 " =    1.765
peak=   -3.343 closest distance to " O   PRO A 163 " =    1.924
peak=   -3.341 closest distance to " O   HOH Z 266 " =    4.361
peak=   -3.338 closest distance to " CB  ALA A 161 " =    2.485
peak=   -3.337 closest distance to " OG1 THR A 178 " =    1.150
peak=   -3.333 closest distance to " O   ALA A  51 " =    1.308
peak=   -3.323 closest distance to " O   MET A  40 " =    2.767
peak=   -3.323 closest distance to " CG1 VAL A 197 " =    2.075
peak=   -3.317 closest distance to " O   HOH Z 213 " =    1.267
peak=   -3.315 closest distance to " NE2 GLN A 278 " =    1.654
peak=   -3.311 closest distance to " O   HOH Z 393 " =    3.240
peak=   -3.305 closest distance to " CD2 TYR A 293 " =    1.901
peak=   -3.304 closest distance to " O   HOH Z 385 " =    2.173
peak=   -3.300 closest distance to " CD1 LEU A 228 " =    2.097
peak=   -3.295 closest distance to " CB  PHE A 192 " =    1.812
peak=   -3.294 closest distance to " O   HOH Z  15 " =    1.645
peak=   -3.291 closest distance to " OD1 ASN A 148 " =    1.604
peak=   -3.290 closest distance to " O   HOH Z 234 " =    3.852
peak=   -3.284 closest distance to " O   HOH Z 309 " =    2.404
peak=   -3.281 closest distance to " O   HOH Z  51 " =    1.068
peak=   -3.281 closest distance to " O   HOH Z 198 " =    1.613
peak=   -3.275 closest distance to " CG  GLU A 152 " =    1.278
peak=   -3.271 closest distance to " OE1 GLN A 223 " =    2.017
peak=   -3.269 closest distance to " O   HOH Z  38 " =    1.793
peak=   -3.267 closest distance to " CG  PRO A 243 " =    1.615
peak=   -3.265 closest distance to " N   ALA A 248 " =    1.525
peak=   -3.262 closest distance to " O   HOH Z 298 " =    2.378
peak=   -3.254 closest distance to " O   ALA A  34 " =    2.575
peak=   -3.251 closest distance to " N   ASN A 127 " =    1.476
peak=   -3.249 closest distance to " O   HOH Z 352 " =    1.786
peak=   -3.248 closest distance to " OG  SER A  87 " =    1.658
peak=   -3.248 closest distance to " CB  ALA A 131 " =    1.869
peak=   -3.247 closest distance to " O   VAL A 153 " =    2.288
peak=   -3.247 closest distance to " CA  ASP A 298 " =    1.038
peak=   -3.243 closest distance to " CZ2 TRP A 274 " =    1.043
peak=   -3.242 closest distance to " NH2 ARG A 219 " =    1.740
peak=   -3.242 closest distance to " CB  TRP A  85 " =    2.394
peak=   -3.242 closest distance to " O   HOH Z 102 " =    1.641
peak=   -3.240 closest distance to " CE1 TYR A 169 " =    2.546
peak=   -3.237 closest distance to " O   HOH Z 337 " =    1.570
peak=   -3.235 closest distance to " ND2 ASN A  39 " =    1.478
peak=   -3.235 closest distance to " N   ALA A  43 " =    2.428
peak=   -3.229 closest distance to " O   HOH Z 103 " =    1.729
peak=   -3.228 closest distance to " N   PHE A  59 " =    1.852
peak=   -3.226 closest distance to " C   LEU A 143 " =    1.098
peak=   -3.222 closest distance to " O   SER A 146 " =    1.017
peak=   -3.217 closest distance to " O   HOH Z   1 " =    1.458
peak=   -3.214 closest distance to " O   HOH Z 236 " =    1.871
peak=   -3.211 closest distance to " OG  SER A  97 " =    2.114
peak=   -3.210 closest distance to " CB  ALA A  43 " =    2.305
peak=   -3.210 closest distance to " CD  ARG A 139 " =    1.593
peak=   -3.200 closest distance to " CB  ALA A 291 " =    2.011
peak=   -3.199 closest distance to " CB  CYS A 201 " =    2.382
peak=   -3.192 closest distance to " ND2 ASN A 249 " =    2.412
peak=   -3.190 closest distance to " CB  ASP A 132 " =    2.267
peak=   -3.189 closest distance to " O   HOH Z 282 " =    1.198
peak=   -3.189 closest distance to " CB  ALA A 248 " =    2.263
peak=   -3.188 closest distance to " CB  PHE A 208 " =    2.202
peak=   -3.184 closest distance to " CG  GLU A   2 " =    2.071
peak=   -3.182 closest distance to " OG  SER A 245 " =    1.250
peak=   -3.173 closest distance to " O   GLY A  80 " =    2.390
peak=   -3.172 closest distance to " O   HOH Z  97 " =    1.578
peak=   -3.167 closest distance to " CB  ASP A 132 " =    2.342
peak=   -3.165 closest distance to " O   HOH Z 256 " =    1.467
peak=   -3.165 closest distance to " N   SER A 212 " =    1.916
peak=   -3.159 closest distance to " CG  LYS A 193 " =    2.106
peak=   -3.158 closest distance to " O   HOH Z 111 " =    2.188
peak=   -3.156 closest distance to " ND2 ASN A  69 " =    1.523
peak=   -3.153 closest distance to " O   SER A   3 " =    1.183
peak=   -3.150 closest distance to " N   VAL A  72 " =    1.512
peak=   -3.146 closest distance to " CG2 VAL A 189 " =    1.925
peak=   -3.145 closest distance to " CG2 THR A 178 " =    2.138
peak=   -3.144 closest distance to " O   ALA A 292 " =    1.976
peak=   -3.141 closest distance to " O   GLN A 240 " =    1.761
peak=   -3.141 closest distance to " CD  LYS A 289 " =    2.355
peak=   -3.129 closest distance to " N   THR A 235 " =    1.321
peak=   -3.128 closest distance to " N   ALA A 295 " =    1.402
peak=   -3.123 closest distance to " CG  PRO A 163 " =    2.648
peak=   -3.113 closest distance to " OG ASER A 216 " =    0.983
peak=   -3.102 closest distance to " NH1 ARG A  36 " =    2.021
peak=   -3.095 closest distance to " CG1BVAL A  41 " =    2.832
peak=   -3.086 closest distance to " OE1 GLN A 183 " =    1.384
peak=   -3.085 closest distance to " OG  SER A 206 " =    1.767
peak=   -3.083 closest distance to " ND2 ASN A 285 " =    2.049
peak=   -3.079 closest distance to " O   HOH Z 281 " =    2.830
peak=   -3.069 closest distance to " CE  LYS A 166 " =    1.221
peak=   -3.047 closest distance to " OE2 GLU A 152 " =    1.092
peak=   -3.044 closest distance to " O   HOH Z 134 " =    3.459
peak=   -3.033 closest distance to " NH2 ARG A  79 " =    2.377
peak=   -3.025 closest distance to " CD  LYS A 166 " =    2.446
peak=   -3.003 closest distance to " C   LEU A 222 " =    0.853

================= 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    :  0.4121 0.4106   6.220526e+00   6.210676e+00
   1_bss:  0.3988 0.3974   6.208101e+00   6.189308e+00
   1_xyz:  0.2687 0.3020   5.890872e+00   5.973867e+00
   1_adp:  0.2444 0.3155   5.844546e+00   6.009455e+00
   1_occ:  0.2440 0.3151   5.843477e+00   6.008672e+00
   2_bss:  0.2416 0.3107   5.832849e+00   5.997801e+00
   2_xyz:  0.1809 0.2323   5.558421e+00   5.750898e+00
   2_adp:  0.1651 0.2129   5.480649e+00   5.679061e+00
   2_occ:  0.1649 0.2129   5.479803e+00   5.678293e+00
   3_bss:  0.1647 0.2118   5.474570e+00   5.671998e+00
   3_xyz:  0.1292 0.1758   5.258106e+00   5.486069e+00
   3_adp:  0.1223 0.1702   5.212625e+00   5.449473e+00
   3_occ:  0.1222 0.1701   5.212347e+00   5.449138e+00
   4_bss:  0.1223 0.1697   5.211689e+00   5.446831e+00
   4_xyz:  0.1140 0.1608   5.156233e+00   5.398591e+00
   4_adp:  0.1116 0.1595   5.143414e+00   5.391656e+00
   4_occ:  0.1115 0.1595   5.143257e+00   5.391487e+00
   5_bss:  0.1115 0.1594   5.142851e+00   5.391080e+00
   5_xyz:  0.1075 0.1568   5.114928e+00   5.373144e+00
   5_adp:  0.1071 0.1557   5.110613e+00   5.368184e+00
   5_occ:  0.1070 0.1557   5.110506e+00   5.368101e+00
   5_bss:  0.1070 0.1557   5.110618e+00   5.368171e+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:  0.342  29.771  -3.171   3.222  -0.816   0.000  -0.000  -0.000
   1_xyz:  0.342  29.771  -3.171   3.222  -0.816   0.000  -0.000  -0.000
   1_adp:  0.342  29.771  -3.171   3.222  -0.816   0.000  -0.000  -0.000
   1_occ:  0.342  29.771  -3.171   3.222  -0.816   0.000  -0.000  -0.000
   2_bss:  0.331  42.827  -2.285  -0.285  -0.933  -0.000  -0.000  -0.000
   2_xyz:  0.331  42.827  -2.285  -0.285  -0.933  -0.000  -0.000  -0.000
   2_adp:  0.331  42.827  -2.285  -0.285  -0.933  -0.000  -0.000  -0.000
   2_occ:  0.331  42.827  -2.285  -0.285  -0.933  -0.000  -0.000  -0.000
   3_bss:  0.327  42.827  -2.217  -1.481  -0.937  -0.000  -0.000  -0.000
   3_xyz:  0.327  42.827  -2.217  -1.481  -0.937  -0.000  -0.000  -0.000
   3_adp:  0.327  42.827  -2.217  -1.481  -0.937  -0.000  -0.000  -0.000
   3_occ:  0.327  42.827  -2.217  -1.481  -0.937  -0.000  -0.000  -0.000
   4_bss:  0.320  42.827  -2.504  -2.258  -1.303  -0.000  -0.000  -0.000
   4_xyz:  0.320  42.827  -2.504  -2.258  -1.303  -0.000  -0.000  -0.000
   4_adp:  0.320  42.827  -2.504  -2.258  -1.303  -0.000  -0.000  -0.000
   4_occ:  0.320  42.827  -2.504  -2.258  -1.303  -0.000  -0.000  -0.000
   5_bss:  0.319  43.904  -2.371  -2.280  -1.210  -0.000  -0.000  -0.000
   5_xyz:  0.319  43.904  -2.371  -2.280  -1.210  -0.000  -0.000  -0.000
   5_adp:  0.319  43.904  -2.371  -2.280  -1.210  -0.000  -0.000  -0.000
   5_occ:  0.319  43.904  -2.371  -2.280  -1.210  -0.000  -0.000  -0.000
   5_bss:  0.321  43.376  -2.206  -2.203  -1.043  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.663 0.5640  0.7561    53465.567
   1_bss:  45.477 0.5767  0.7639    49367.641
   1_xyz:  30.897 0.7494  0.9437    24765.697
   1_adp:  32.829 0.7264  0.9182    27101.755
   1_occ:  32.794 0.7268  0.9179    27049.188
   2_bss:  32.001 0.7355  0.9020    25949.715
   2_xyz:  22.826 0.8332  0.9869    13662.145
   2_adp:  20.382 0.8586  0.9996    11662.066
   2_occ:  20.363 0.8587  0.9994    11629.687
   3_bss:  20.166 0.8604  0.9874    11395.080
   3_xyz:  16.167 0.8963  1.0056     7714.917
   3_adp:  15.294 0.9041  1.0032     7275.418
   3_occ:  15.290 0.9041  1.0030     7264.117
   4_bss:  15.247 0.9044  0.9860     7228.740
   4_xyz:  14.204 0.9131  0.9901     6469.464
   4_adp:  14.022 0.9148  0.9856     6375.753
   4_occ:  14.019 0.9148  0.9856     6370.819
   5_bss:  14.010 0.9149  0.9882     6365.604
   5_xyz:  13.655 0.9177  0.9889     6121.697
   5_adp:  13.531 0.9187  0.9839     6047.283
   5_occ:  13.529 0.9187  0.9838     6045.229
   5_bss:  13.533 0.9187  0.9886     6048.608
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.7343e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.7343e-01
   1_xyz:   1.500  0.012  0.100 15.473  0.006  4.103   1.2047e-01
   1_adp:   1.500  0.012  0.100 15.473  0.006  4.103   1.2047e-01
   1_occ:   1.500  0.012  0.100 15.473  0.006  4.103   1.2047e-01
   2_bss:   1.500  0.012  0.100 15.473  0.006  4.103   1.2047e-01
   2_xyz:   1.077  0.007  0.074 14.325  0.005  4.113   6.4609e-02
   2_adp:   1.077  0.007  0.074 14.325  0.005  4.113   6.4609e-02
   2_occ:   1.077  0.007  0.074 14.325  0.005  4.113   6.4609e-02
   3_bss:   1.077  0.007  0.074 14.325  0.005  4.113   6.4609e-02
   3_xyz:   1.005  0.006  0.071 14.584  0.004  4.109   5.9234e-02
   3_adp:   1.005  0.006  0.071 14.584  0.004  4.109   5.9234e-02
   3_occ:   1.005  0.006  0.071 14.584  0.004  4.109   5.9234e-02
   4_bss:   1.005  0.006  0.071 14.584  0.004  4.109   5.9234e-02
   4_xyz:   0.948  0.005  0.069 14.484  0.004  4.111   5.3980e-02
   4_adp:   0.948  0.005  0.069 14.484  0.004  4.111   5.3980e-02
   4_occ:   0.948  0.005  0.069 14.484  0.004  4.111   5.3980e-02
   5_bss:   0.948  0.005  0.069 14.484  0.004  4.111   5.3980e-02
   5_xyz:   1.017  0.007  0.073 14.667  0.004  4.107   6.0825e-02
   5_adp:   1.017  0.007  0.073 14.667  0.004  4.107   6.0825e-02
   5_occ:   1.017  0.007  0.073 14.667  0.004  4.107   6.0825e-02
   5_bss:   1.017  0.007  0.073 14.667  0.004  4.107   6.0825e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3803e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3803e-01
   1_xyz:   8.731  0.078  0.462 83.476  0.041  2.071   1.1961e-01
   1_adp:   8.731  0.078  0.462 83.476  0.041  2.071   1.1961e-01
   1_occ:   8.731  0.078  0.462 83.476  0.041  2.071   1.1961e-01
   2_bss:   8.731  0.078  0.462 83.476  0.041  2.071   1.1961e-01
   2_xyz:   7.271  0.036  0.206 81.566  0.031  2.332   7.0688e-02
   2_adp:   7.271  0.036  0.206 81.566  0.031  2.332   7.0688e-02
   2_occ:   7.271  0.036  0.206 81.566  0.031  2.332   7.0688e-02
   3_bss:   7.271  0.036  0.206 81.566  0.031  2.332   7.0688e-02
   3_xyz:   6.781  0.040  0.206 82.794  0.031  2.303   5.3829e-02
   3_adp:   6.781  0.040  0.206 82.794  0.031  2.303   5.3829e-02
   3_occ:   6.781  0.040  0.206 82.794  0.031  2.303   5.3829e-02
   4_bss:   6.781  0.040  0.206 82.794  0.031  2.303   5.3829e-02
   4_xyz:   6.608  0.036  0.214 84.325  0.039  2.327   4.0527e-02
   4_adp:   6.608  0.036  0.214 84.325  0.039  2.327   4.0527e-02
   4_occ:   6.608  0.036  0.214 84.325  0.039  2.327   4.0527e-02
   5_bss:   6.608  0.036  0.214 84.325  0.039  2.327   4.0527e-02
   5_xyz:   6.354  0.032  0.224 84.578  0.037  2.272   4.7494e-02
   5_adp:   6.354  0.032  0.224 84.578  0.037  2.272   4.7494e-02
   5_occ:   6.354  0.032  0.224 84.578  0.037  2.272   4.7494e-02
   5_bss:   6.354  0.032  0.224 84.578  0.037  2.272   4.7494e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  99.14   0.00  17.88  78.74   0.00  13.80  99.14   4.05  40.10
   1_occ:  99.14   0.00  17.88  78.74   0.00  13.80  99.14   4.05  40.10
   2_bss:  99.14   0.00  17.88  78.74   0.00  13.80  99.14   4.05  40.10
   2_xyz:  99.14   0.00  17.88  78.74   0.00  13.80  99.14   4.05  40.10
   2_adp:  91.65   1.09  17.10  79.18   1.09  13.05  91.65   6.17  39.13
   2_occ:  91.65   1.09  17.10  79.18   1.09  13.05  91.65   6.17  39.13
   3_bss:  91.65   1.09  17.10  79.18   1.09  13.05  91.65   6.17  39.13
   3_xyz:  91.65   1.09  17.10  79.18   1.09  13.05  91.65   6.17  39.13
   3_adp:  90.92   0.51  17.02  82.56   0.51  12.75  90.92   6.36  40.26
   3_occ:  90.92   0.51  17.02  82.56   0.51  12.75  90.92   6.36  40.26
   4_bss:  90.92   0.51  17.02  82.56   0.51  12.75  90.92   6.36  40.26
   4_xyz:  90.92   0.51  17.02  82.56   0.51  12.75  90.92   6.36  40.26
   4_adp:  93.96   0.00  17.22  93.14   0.00  12.74  93.96   6.02  41.63
   4_occ:  93.96   0.00  17.22  93.14   0.00  12.74  93.96   6.02  41.63
   5_bss:  93.96   0.00  17.22  93.14   0.00  12.74  93.96   6.02  41.63
   5_xyz:  93.96   0.00  17.22  93.14   0.00  12.74  93.96   6.02  41.63
   5_adp:  95.89   0.27  16.87  95.89   0.27  12.58  92.08   5.96  40.23
   5_occ:  95.89   0.27  16.87  95.89   0.27  12.58  92.08   5.96  40.23
   5_bss:  95.88   0.26  16.86  95.88   0.26  12.57  92.07   5.95  40.22
------------------------------------------------------------------------
 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:    1.564    0.031    0.436
   1_adp:    1.564    0.031    0.436
   1_occ:    1.564    0.031    0.436
   2_bss:    1.564    0.031    0.436
   2_xyz:    1.250    0.023    0.528
   2_adp:    1.250    0.023    0.528
   2_occ:    1.250    0.023    0.528
   3_bss:    1.250    0.023    0.528
   3_xyz:    1.197    0.048    0.615
   3_adp:    1.197    0.048    0.615
   3_occ:    1.197    0.048    0.615
   4_bss:    1.197    0.048    0.615
   4_xyz:    1.234    0.079    0.642
   4_adp:    1.234    0.079    0.642
   4_occ:    1.234    0.079    0.642
   5_bss:    1.234    0.079    0.642
   5_xyz:    1.389    0.114    0.656
   5_adp:    1.389    0.114    0.656
   5_occ:    1.389    0.114    0.656
   5_bss:    1.389    0.114    0.656
------------------------------------------------------------------------

CPU time actual refinement: 271.11


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_498/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_498/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_498/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_498/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_498/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 270.97 
  Macro-tasks:
    bulk solvent and scale       = 33.09  
    individual site refinement   = 107.90 
    weights calculation          = 25.51  
    collect and process          = 5.64   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 172.23 
  Micro-tasks:
    mask                            = 1.49   
    f_calc                          = 85.43  
    alpha_beta                      = 7.11   
    target                          = 1.02   
    gradients_wrt_atomic_parameters = 91.52  
    fmodel                         = 5.57   
    r_factors                      = 0.18   
    phase_errors                   = 8.91   
    foms                           = 0.18   
    TOTAL for micro-tasks          = 201.41 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 3.932 micro seconds
Total CPU time: 4.71 minutes
from_scatterers_fft:    616 calls, 85.11 s
gradients_fft:          561 calls, 80.74 s

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

# Date 2008-01-16 Time 04:57:32 PST -0800 (1200488252.32 s)
Start R-work = 0.4121, R-free = 0.4106 (no bulk solvent and anisotropic scale)
Final R-work = 0.1311, R-free = 0.1741 (no bulk solvent and anisotropic scale)

Start R-work = 0.3988, R-free = 0.3974
Final R-work = 0.1070, R-free = 0.1557