# Date 2008-01-16 Time 04:38:09 PST -0800 (1200487089.43 s)
#phil __OFF__

Command line arguments: "../396.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 7232
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 396

-------------------------------------------------------------------------------
  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: (69.5475, 46.4607, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


================================== 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: (69.5475, 46.4607, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.782 1.95115
Completeness in resolution range: 0.958038
Completeness with d_max=infinity: 0.955095

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7820
                             d_min =   1.9511

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: (69.5475, 46.4607, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.782 1.95115
Completeness in resolution range: 0.958038
Completeness with d_max=infinity: 0.955095

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7824 -  4.1750 [2141/2169]  1929   212   9.9%
  bin  2:  4.1750 -  3.3262 [2059/2075]  1850   209  10.2%
  bin  3:  3.3262 -  2.9094 [2036/2055]  1833   203  10.0%
  bin  4:  2.9094 -  2.6451 [2022/2052]  1824   198   9.8%
  bin  5:  2.6451 -  2.4564 [2008/2027]  1807   201  10.0%
  bin  6:  2.4564 -  2.3122 [1987/2023]  1788   199  10.0%
  bin  7:  2.3122 -  2.1968 [1963/1996]  1764   199  10.1%
  bin  8:  2.1968 -  2.1014 [1997/2031]  1798   199  10.0%
  bin  9:  2.1014 -  2.0207 [1978/2006]  1780   198  10.0%
  bin 10:  2.0207 -  1.9511 [1398/2013]  1257   141  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_396/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: 0.14 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:
        1.43 -     2.12: 22
        2.12 -     2.82: 907
        2.82 -     3.51: 4578
        3.51 -     4.21: 9505
        4.21 -     4.90: 13970
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.429 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.454 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.597 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.722 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.748 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28977 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_396/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_396/model_refine_001.geo

CPU time processing inputs: 9.13


============================ 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 = 69.5475 46.4607 84.23025 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: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4300   r_free= 0.4325   ksol= 0.00   Bsol= 0.00   scale= 0.935    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.231468                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7824 -  4.6566 0.99   1387  154 0.3488 0.3513      6.5017      6.4803|
|  2:  4.6566 -  3.7154 0.99   1354  147 0.3588 0.3444      6.7091      6.6827|
|  3:  3.7154 -  3.2514 0.99   1307  150 0.3976 0.4238      6.6042      6.7382|
|  4:  3.2514 -  2.9568 0.99   1310  146 0.3967 0.4275      6.4569      6.4649|
|  5:  2.9568 -  2.7463 0.99   1304  142 0.4443 0.4300      6.3225      6.2805|
|  6:  2.7463 -  2.5853 0.99   1286  145 0.4638 0.4864      6.2275      6.2355|
|  7:  2.5853 -  2.4564 0.99   1295  139 0.4550 0.4166      6.1947      6.1568|
|  8:  2.4564 -  2.3499 0.98   1273  149 0.4716 0.4721      6.1489       6.146|
|  9:  2.3499 -  2.2598 0.98   1281  142 0.4826 0.4390      6.0974      6.0544|
| 10:  2.2598 -  2.1821 0.98   1275  134 0.4766 0.5071       6.063      6.0892|
| 11:  2.1821 -  2.1140 1.00   1265  147 0.4994 0.5277      6.0322      6.0733|
| 12:  2.1140 -  2.0538 0.97   1261  134 0.4858 0.4759      5.9483      5.9757|
| 13:  2.0538 -  1.9998 0.98   1268  145 0.4884 0.4806      5.8607      5.8255|
| 14:  1.9998 -  1.9511 0.59    764   85 0.5138 0.4534      5.8402      5.7086|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7824 -  4.6566  1387   154  0.72  32.30   0.85     0.76      61911.87|
|  2:  4.6566 -  3.7154  1354   147  0.74  31.88   0.94     0.85      90771.76|
|  3:  3.7154 -  3.2514  1307   150  0.64  40.05   0.96     0.85      98574.91|
|  4:  3.2514 -  2.9568  1310   146  0.57  45.99   0.98     0.78      88512.03|
|  5:  2.9568 -  2.7463  1304   142  0.51  50.82   0.93     0.73      69885.94|
|  6:  2.7463 -  2.5853  1286   145  0.49  52.43   0.92     0.69      59347.69|
|  7:  2.5853 -  2.4564  1295   139  0.51  51.23   0.95     0.70      52664.56|
|  8:  2.4564 -  2.3499  1273   149  0.48  53.40   0.95     0.70      47829.43|
|  9:  2.3499 -  2.2598  1281   142  0.49  53.22   0.97     0.69      42781.81|
| 10:  2.2598 -  2.1821  1275   134  0.46  55.04   0.99     0.67      41273.99|
| 11:  2.1821 -  2.1140  1265   147  0.43  57.96   0.99     0.64      39942.59|
| 12:  2.1140 -  2.0538  1261   134  0.43  57.89   1.00     0.67      38151.94|
| 13:  2.0538 -  1.9998  1268   145  0.42  58.20   0.98     0.66      31880.53|
| 14:  1.9998 -  1.9511   764    85  0.47  54.80   0.97     0.65      24122.69|
|alpha:            min =        0.64 max =            0.85 mean =         0.72|
|beta:             min =    24122.69 max =        98574.91 mean =     57573.67|
|figures of merit: min =        0.00 max =            1.00 mean =         0.53|
|phase err.(work): min =        0.00 max =           90.00 mean =        49.29|
|phase err.(test): min =        0.00 max =           89.96 mean =        49.44|
|-----------------------------------------------------------------------------|

============================== 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 = 9.038689              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.211   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.662493              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.620   (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 |  1.429 -  1.776:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.776 -  2.123:       17 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.123 -  2.470:       38 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.470 -  2.817:      869 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.817 -  3.164:     2114 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.164 -  3.512:     2464 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.512 -  3.859:     4688 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.859 -  4.206:     4817 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.206 -  4.553:     6364 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.553 -  4.900:     7606 |
|-----------------------------------------------------------------------------|
|-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 |        0.189 |
| 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  1.429 |       0.616 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.373)------------------------------------------|
|    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: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4300   r_free= 0.4325   ksol= 0.00   Bsol= 0.00   scale= 0.935    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.231468                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4186   r_free= 0.4167   ksol= 0.34   Bsol= 20.91   scale= 0.958   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.58,-0.66,2.91,-0.00,0.00,0.00); trace/3= -0.11                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.223495                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.050428              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.164   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.860893              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.557   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4186      final r-factor (work) = 0.2743          |
| start r-factor (free) = 0.4167      final r-factor (free) = 0.2996          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.1149 = 7.05 * 0.50 * 6.2198 + 1.00 * 0.1888                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.3735 = 7.05 * 0.50 * 6.0307 + 1.00 * 0.1138                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2743      final r-factor (work) = 0.2498          |
| start r-factor (free) = 0.2996      final r-factor (free) = 0.3077          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1979 = 0.86 * 1.00 * 6.0307 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0281 = 0.86 * 1.00 * 5.8237 + 1.00 * 0.0145                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.373)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.55   18.38    None  None   None       |
|    all(noH): 2823   0      0.00    85.55   18.38    None  None   None       |
|    Sol.    : 438    0      4.31    84.34   41.55    None  None   None       |
|    Mac.    : 2385   0      0.00    85.55   14.12    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.555:  744   |   5:    42.774 -  51.328:  108        |
|      1:     8.555 -  17.109: 1052   |   6:    51.328 -  59.883:   77        |
|      2:    17.109 -  25.664:  418   |   7:    59.883 -  68.438:   44        |
|      3:    25.664 -  34.219:  192   |   8:    68.438 -  76.992:   18        |
|      4:    34.219 -  42.774:  159   |   9:    76.992 -  85.547:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2498 r_free = 0.3077             target_work(ml) = 5.835         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2495 r_free = 0.3078             target_work(ml) = 5.834         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2495   r_free= 0.3078   ksol= 0.34   Bsol= 20.91   scale= 1.041   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.58,-0.66,2.91,-0.00,0.00,0.00); trace/3= -0.11                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.833946                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2456   r_free= 0.3054   ksol= 0.32   Bsol= 34.70   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,-1.74,-0.02,-0.00,-0.00,-0.00); trace/3= -1.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.825958                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.752482              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.603   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.208873              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.497  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2456      final r-factor (work) = 0.1774          |
| start r-factor (free) = 0.3054      final r-factor (free) = 0.2303          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0394 = 3.75 * 0.50 * 5.8231 + 1.00 * 0.1138                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7579 = 3.75 * 0.50 * 5.7020 + 1.00 * 0.0595                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1774      final r-factor (work) = 0.1629          |
| start r-factor (free) = 0.2303      final r-factor (free) = 0.2118          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2052 = 0.21 * 1.00 * 5.7020 + 1.00 * 0.0142                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1579 = 0.21 * 1.00 * 5.5078 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.373)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.04    80.26   17.30    None  None   None       |
|    all(noH): 2823   0      1.04    80.26   17.30    None  None   None       |
|    Sol.    : 438    0      6.75    77.69   39.16    None  None   None       |
|    Mac.    : 2385   0      1.04    80.26   13.29    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:     1.038 -   8.960:  736   |   5:    40.649 -  48.572:  105        |
|      1:     8.960 -  16.882: 1205   |   6:    48.572 -  56.494:   89        |
|      2:    16.882 -  24.805:  346   |   7:    56.494 -  64.416:   28        |
|      3:    24.805 -  32.727:  147   |   8:    64.416 -  72.338:   19        |
|      4:    32.727 -  40.649:  142   |   9:    72.338 -  80.261:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1629 r_free = 0.2118             target_work(ml) = 5.461         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1626 r_free = 0.2120             target_work(ml) = 5.461         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1626   r_free= 0.2120   ksol= 0.32   Bsol= 34.70   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,-1.74,-0.02,-0.00,-0.00,-0.00); trace/3= -1.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.460551                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1622   r_free= 0.2111   ksol= 0.32   Bsol= 34.70   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.73,-2.36,-1.29,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.455358                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.680507              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.361  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.193902              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.881  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1622      final r-factor (work) = 0.1260          |
| start r-factor (free) = 0.2111      final r-factor (free) = 0.1678          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1966 = 3.68 * 0.50 * 5.5085 + 1.00 * 0.0595                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9056 = 3.68 * 0.50 * 5.3483 + 1.00 * 0.0634                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1260      final r-factor (work) = 0.1188          |
| start r-factor (free) = 0.1678      final r-factor (free) = 0.1610          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0445 = 0.19 * 1.00 * 5.3483 + 1.00 * 0.0074                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0148 = 0.19 * 1.00 * 5.1971 + 1.00 * 0.0071                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.373)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.35    82.08   17.08    None  None   None       |
|    all(noH): 2823   0      2.35    82.08   17.08    None  None   None       |
|    Sol.    : 438    0      5.40    77.60   39.31    None  None   None       |
|    Mac.    : 2385   0      2.35    82.08   13.00    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:     2.350 -  10.323: 1041   |   5:    42.213 -  50.185:  101        |
|      1:    10.323 -  18.295: 1059   |   6:    50.185 -  58.158:   73        |
|      2:    18.295 -  26.268:  249   |   7:    58.158 -  66.131:   36        |
|      3:    26.268 -  34.240:  120   |   8:    66.131 -  74.103:   15        |
|      4:    34.240 -  42.213:  125   |   9:    74.103 -  82.076:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1188 r_free = 0.1610             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1186 r_free = 0.1608             target_work(ml) = 5.172         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1186   r_free= 0.1608   ksol= 0.32   Bsol= 34.70   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.73,-2.36,-1.29,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.172206                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1189   r_free= 0.1614   ksol= 0.32   Bsol= 34.70   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,-2.56,-1.86,-0.00,-0.00,-0.00); trace/3= -2.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.173860                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.054823              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 123.842  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.182908              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.010  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1189      final r-factor (work) = 0.1126          |
| start r-factor (free) = 0.1614      final r-factor (free) = 0.1556          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4045 = 2.05 * 0.50 * 5.1986 + 1.00 * 0.0634                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3478 = 2.05 * 0.50 * 5.1508 + 1.00 * 0.0558                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1126      final r-factor (work) = 0.1112          |
| start r-factor (free) = 0.1556      final r-factor (free) = 0.1557          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9493 = 0.18 * 1.00 * 5.1508 + 1.00 * 0.0071                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9451 = 0.18 * 1.00 * 5.1281 + 1.00 * 0.0071                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.373)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.28    83.16   16.92    None  None   None       |
|    all(noH): 2823   0      2.28    83.16   16.92    None  None   None       |
|    Sol.    : 438    0      6.32    78.98   38.74    None  None   None       |
|    Mac.    : 2385   0      2.28    83.16   12.91    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.277 -  10.365: 1067   |   5:    42.719 -  50.807:   97        |
|      1:    10.365 -  18.454: 1059   |   6:    50.807 -  58.896:   76        |
|      2:    18.454 -  26.542:  235   |   7:    58.896 -  66.984:   25        |
|      3:    26.542 -  34.630:  125   |   8:    66.984 -  75.072:   13        |
|      4:    34.630 -  42.719:  122   |   9:    75.072 -  83.161:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1112 r_free = 0.1557             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1111 r_free = 0.1556             target_work(ml) = 5.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1111   r_free= 0.1556   ksol= 0.32   Bsol= 34.70   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,-2.56,-1.86,-0.00,-0.00,-0.00); trace/3= -2.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.126292                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1111   r_free= 0.1556   ksol= 0.32   Bsol= 34.79   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-2.49,-1.91,-0.00,-0.00,-0.00); trace/3= -2.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.126346                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.270197              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 156.277  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.759784              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.974  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1111      final r-factor (work) = 0.1114          |
| start r-factor (free) = 0.1556      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.3125 = 1.27 * 0.50 * 5.1279 + 1.00 * 0.0558                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.3058 = 1.27 * 0.50 * 5.1299 + 1.00 * 0.0478                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1114      final r-factor (work) = 0.1102          |
| start r-factor (free) = 0.1549      final r-factor (free) = 0.1570          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.0346 = 1.76 * 1.00 * 5.1299 + 1.00 * 0.0071                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.0249 = 1.76 * 1.00 * 5.1233 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.373)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.74   17.22    None  None   None       |
|    all(noH): 2823   0      0.00    91.74   17.22    None  None   None       |
|    Sol.    : 438    0      6.11    83.37   40.54    None  None   None       |
|    Mac.    : 2385   0      0.00    91.74   12.94    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 -   9.174:  831   |   5:    45.871 -  55.046:  117        |
|      1:     9.174 -  18.349: 1280   |   6:    55.046 -  64.220:   58        |
|      2:    18.349 -  27.523:  254   |   7:    64.220 -  73.394:   30        |
|      3:    27.523 -  36.697:  130   |   8:    73.394 -  82.568:    7        |
|      4:    36.697 -  45.871:  112   |   9:    82.568 -  91.742:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1102 r_free = 0.1570             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1102 r_free = 0.1569             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1102   r_free= 0.1569   ksol= 0.32   Bsol= 34.79   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-2.49,-1.91,-0.00,-0.00,-0.00); trace/3= -2.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.130430                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7824 -  4.6566 0.99   1387  154 0.0990 0.1217      5.3704      5.4984|
|  2:  4.6566 -  3.7154 0.99   1354  147 0.0857 0.1152      5.4347      5.6341|
|  3:  3.7154 -  3.2514 0.99   1307  150 0.1064 0.1516      5.4729      5.8444|
|  4:  3.2514 -  2.9568 0.99   1310  146 0.1215 0.1589      5.4551      5.5979|
|  5:  2.9568 -  2.7463 0.99   1304  142 0.1237 0.1632      5.2711       5.454|
|  6:  2.7463 -  2.5853 0.99   1286  145 0.1167 0.1679       5.158      5.3809|
|  7:  2.5853 -  2.4564 0.99   1295  139 0.1185 0.1561      5.1124      5.3354|
|  8:  2.4564 -  2.3499 0.98   1273  149 0.1136 0.1743      5.0478      5.3121|
|  9:  2.3499 -  2.2598 0.98   1281  142 0.1158 0.1897      5.0242       5.331|
| 10:  2.2598 -  2.1821 0.98   1275  134 0.1113 0.1741       4.952      5.1744|
| 11:  2.1821 -  2.1140 1.00   1265  147 0.1117 0.1729      4.9334      5.2768|
| 12:  2.1140 -  2.0538 0.97   1261  134 0.1055 0.1656      4.8453      5.1225|
| 13:  2.0538 -  1.9998 0.98   1268  145 0.1136 0.1807      4.7978      5.0758|
| 14:  1.9998 -  1.9511 0.59    764   85 0.1100 0.1718      4.7195      4.9313|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7824 -  4.6566  1387   154  0.95   8.38   0.99     0.96       6427.99|
|  2:  4.6566 -  3.7154  1354   147  0.96   7.57   1.03     1.02       8643.84|
|  3:  3.7154 -  3.2514  1307   150  0.93  11.41   1.04     1.03      10287.19|
|  4:  3.2514 -  2.9568  1310   146  0.92  13.32   1.02     1.01      10163.92|
|  5:  2.9568 -  2.7463  1304   142  0.91  14.64   1.00     0.97       7288.24|
|  6:  2.7463 -  2.5853  1286   145  0.91  15.02   0.99     0.97       6319.38|
|  7:  2.5853 -  2.4564  1295   139  0.92  14.29   0.99     0.96       5448.15|
|  8:  2.4564 -  2.3499  1273   149  0.91  15.00   1.00     0.97       5130.76|
|  9:  2.3499 -  2.2598  1281   142  0.91  14.90   1.01     0.99       4896.73|
| 10:  2.2598 -  2.1821  1275   134  0.90  15.48   1.00     0.96       4335.87|
| 11:  2.1821 -  2.1140  1265   147  0.90  16.41   1.01     0.98       4373.19|
| 12:  2.1140 -  2.0538  1261   134  0.92  14.40   1.01     0.98       3699.65|
| 13:  2.0538 -  1.9998  1268   145  0.90  16.37   1.01     1.01       3429.07|
| 14:  1.9998 -  1.9511   764    85  0.91  15.77   0.99     0.96       2851.60|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2851.60 max =        10287.19 mean =      6076.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.66|
|phase err.(test): min =        0.00 max =           88.65 mean =        13.37|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1101   r_free= 0.1569   ksol= 0.32   Bsol= 37.14   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-2.29,-1.75,-0.00,-0.00,-0.00); trace/3= -2.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.130166                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1101   r_free= 0.1569   ksol= 0.32   Bsol= 37.14   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-2.29,-1.75,-0.00,-0.00,-0.00); trace/3= -2.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.130166                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7824 -  4.6566 0.99   1387  154 0.0991 0.1220      5.3712      5.5002|
|  2:  4.6566 -  3.7154 0.99   1354  147 0.0859 0.1152      5.4363       5.635|
|  3:  3.7154 -  3.2514 0.99   1307  150 0.1065 0.1517      5.4738      5.8458|
|  4:  3.2514 -  2.9568 0.99   1310  146 0.1215 0.1587      5.4551      5.5974|
|  5:  2.9568 -  2.7463 0.99   1304  142 0.1236 0.1628      5.2705      5.4522|
|  6:  2.7463 -  2.5853 0.99   1286  145 0.1167 0.1678      5.1575       5.381|
|  7:  2.5853 -  2.4564 0.99   1295  139 0.1184 0.1560      5.1116      5.3347|
|  8:  2.4564 -  2.3499 0.98   1273  149 0.1135 0.1738       5.047      5.3102|
|  9:  2.3499 -  2.2598 0.98   1281  142 0.1158 0.1899      5.0234      5.3316|
| 10:  2.2598 -  2.1821 0.98   1275  134 0.1112 0.1738      4.9512      5.1724|
| 11:  2.1821 -  2.1140 1.00   1265  147 0.1116 0.1727      4.9326      5.2761|
| 12:  2.1140 -  2.0538 0.97   1261  134 0.1054 0.1655      4.8446      5.1223|
| 13:  2.0538 -  1.9998 0.98   1268  145 0.1135 0.1804      4.7969       5.074|
| 14:  1.9998 -  1.9511 0.59    764   85 0.1100 0.1718      4.7187      4.9315|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7824 -  4.6566  1387   154  0.95   8.40   0.99     0.97       6443.82|
|  2:  4.6566 -  3.7154  1354   147  0.96   7.58   1.03     1.02       8664.64|
|  3:  3.7154 -  3.2514  1307   150  0.93  11.42   1.04     1.04      10301.17|
|  4:  3.2514 -  2.9568  1310   146  0.92  13.33   1.02     1.01      10159.91|
|  5:  2.9568 -  2.7463  1304   142  0.91  14.64   1.00     0.98       7281.93|
|  6:  2.7463 -  2.5853  1286   145  0.91  15.01   1.00     0.97       6313.24|
|  7:  2.5853 -  2.4564  1295   139  0.92  14.28   1.00     0.97       5439.18|
|  8:  2.4564 -  2.3499  1273   149  0.91  14.98   1.00     0.98       5118.40|
|  9:  2.3499 -  2.2598  1281   142  0.91  14.88   1.02     1.00       4885.49|
| 10:  2.2598 -  2.1821  1275   134  0.90  15.46   1.01     0.97       4329.54|
| 11:  2.1821 -  2.1140  1265   147  0.90  16.40   1.02     0.99       4365.33|
| 12:  2.1140 -  2.0538  1261   134  0.92  14.38   1.02     0.99       3692.13|
| 13:  2.0538 -  1.9998  1268   145  0.90  16.34   1.02     1.02       3421.08|
| 14:  1.9998 -  1.9511   764    85  0.91  15.75   1.01     0.97       2846.05|
|alpha:            min =        0.97 max =            1.04 mean =         0.99|
|beta:             min =     2846.05 max =        10301.17 mean =      6074.03|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.65|
|phase err.(test): min =        0.00 max =           88.55 mean =        13.36|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.373)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.75   17.23    None  None   None       |
|    all(noH): 2823   0      0.00    91.75   17.23    None  None   None       |
|    Sol.    : 438    0      6.11    83.37   40.54    None  None   None       |
|    Mac.    : 2385   0      0.00    91.75   12.95    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.177:  831   |   5:    45.874 -  55.048:  117        |
|      1:     9.177 -  18.352: 1280   |   6:    55.048 -  64.223:   58        |
|      2:    18.352 -  27.526:  254   |   7:    64.223 -  73.397:   30        |
|      3:    27.526 -  36.700:  130   |   8:    73.397 -  82.571:    7        |
|      4:    36.700 -  45.874:  112   |   9:    82.571 -  91.745:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 300         
Filter by distance & map next to the model:
   mapped sites are within: 0.420 - 5.480
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 296 from: 300
   mapped sites are within: 0.710 - 5.480

peak=    6.333 closest distance to " O   HOH Z 142 " =    1.926
peak=    6.064 closest distance to " NE2 GLN A  11 " =    1.166
peak=    5.815 closest distance to " O   HOH Z 126 " =    1.979
peak=    5.724 closest distance to " O   HOH Z 236 " =    1.544
peak=    5.658 closest distance to " CB  ARG A 275 " =    0.919
peak=    5.620 closest distance to " NH2 ARG A  56 " =    2.075
peak=    5.506 closest distance to " CG  PRO A  54 " =    1.192
peak=    5.369 closest distance to " CG  PRO A 213 " =    1.289
peak=    5.263 closest distance to " CG  PRO A  90 " =    1.171
peak=    5.191 closest distance to " O   HOH Z 278 " =    1.282
peak=    4.917 closest distance to " CG  PRO A 198 " =    1.240
peak=    4.833 closest distance to " CB  GLN A 223 " =    1.482
peak=    4.801 closest distance to " O   HOH Z 193 " =    1.715
peak=    4.771 closest distance to " CB  SER A  63 " =    1.249
peak=    4.767 closest distance to " O   HOH Z 232 " =    2.307
peak=    4.763 closest distance to " O   HOH Z 427 " =    2.717
peak=    4.752 closest distance to " O   HOH Z 272 " =    1.852
peak=    4.749 closest distance to " O   HOH Z 124 " =    1.407
peak=    4.734 closest distance to " O   HOH Z 108 " =    1.400
peak=    4.727 closest distance to " O   HOH Z  78 " =    1.784
peak=    4.600 closest distance to " CB  SER A   3 " =    1.304
peak=    4.597 closest distance to " O   HOH Z 260 " =    1.157
peak=    4.569 closest distance to " C   PRO A 198 " =    1.504
peak=    4.506 closest distance to " CB  GLN A 183 " =    1.220
peak=    4.468 closest distance to " O   HOH Z 207 " =    1.533
peak=    4.459 closest distance to " CB  ASN A 148 " =    1.457
peak=    4.358 closest distance to " O   HOH Z 209 " =    2.223
peak=    4.352 closest distance to " O   HOH Z   6 " =    2.010
peak=    4.347 closest distance to " O   HOH Z 202 " =    1.166
peak=    4.336 closest distance to " CG2 VAL A 257 " =    0.878
peak=    4.328 closest distance to " O   HOH Z 316 " =    2.911
peak=    4.320 closest distance to " O   HOH Z 203 " =    1.831
peak=    4.320 closest distance to " CB  PRO A  54 " =    1.005
peak=    4.318 closest distance to " NZ  LYS A 117 " =    3.065
peak=    4.317 closest distance to " O   HOH Z 213 " =    1.806
peak=    4.291 closest distance to " CA  TYR A  30 " =    0.955
peak=    4.289 closest distance to " O   HOH Z 234 " =    3.631
peak=    4.288 closest distance to " CG1 ILE A  33 " =    1.274
peak=    4.272 closest distance to " O   HOH Z 134 " =    1.269
peak=    4.256 closest distance to " CB  TYR A 169 " =    0.844
peak=    4.212 closest distance to " CB  GLU A 128 " =    1.082
peak=    4.193 closest distance to " O   HOH Z  59 " =    1.728
peak=    4.182 closest distance to " CB  LEU A 228 " =    1.105
peak=    4.175 closest distance to " OD2 ASP A 286 " =    2.619
peak=    4.145 closest distance to " NH1BARG A 145 " =    1.407
peak=    4.143 closest distance to " O   HOH Z 344 " =    2.971
peak=    4.125 closest distance to " CB  TRP A 179 " =    1.252
peak=    4.121 closest distance to " CB  GLU A 152 " =    1.256
peak=    4.078 closest distance to " O   HOH Z  78 " =    2.105
peak=    4.065 closest distance to " O   HOH Z  10 " =    1.823
peak=    4.061 closest distance to " O   HOH Z 298 " =    1.823
peak=    4.050 closest distance to " O   HOH Z  97 " =    2.003
peak=    4.040 closest distance to " CB  VAL A 265 " =    1.362
peak=    4.031 closest distance to " OD1 ASN A  69 " =    2.573
peak=    4.022 closest distance to " OG BSER A 164 " =    2.386
peak=    4.014 closest distance to " O   HOH Z 369 " =    2.221
peak=    4.006 closest distance to " O   HOH Z  73 " =    1.757
peak=    4.003 closest distance to " ND2 ASN A 187 " =    1.479
peak=    4.002 closest distance to " CA  ALA A  21 " =    1.053
peak=    3.993 closest distance to " O   HOH Z   3 " =    1.933
peak=    3.982 closest distance to " O   HOH Z   9 " =    2.375
peak=    3.946 closest distance to " O   HOH Z  61 " =    1.584
peak=    3.937 closest distance to " O   HOH Z 287 " =    1.610
peak=    3.925 closest distance to " O   HOH Z 407 " =    2.163
peak=    3.921 closest distance to " O   HOH Z 303 " =    2.099
peak=    3.905 closest distance to " CG  PRO A 243 " =    1.130
peak=    3.895 closest distance to " O   HOH Z  43 " =    1.970
peak=    3.842 closest distance to " O   HOH Z 183 " =    1.546
peak=    3.838 closest distance to " O   HOH Z 326 " =    1.415
peak=    3.821 closest distance to " CB  ARG A 139 " =    0.972
peak=    3.814 closest distance to " O   HOH Z 368 " =    3.604
peak=    3.813 closest distance to " CA  THR A 264 " =    0.803
peak=    3.811 closest distance to " CG  PRO A 280 " =    0.710
peak=    3.810 closest distance to " O   HOH Z 156 " =    2.984
peak=    3.806 closest distance to " O   HOH Z  44 " =    1.954
peak=    3.802 closest distance to " O   HOH Z 289 " =    1.649
peak=    3.795 closest distance to " O   HOH Z 368 " =    1.848
peak=    3.790 closest distance to " CG2 ILE A 120 " =    1.235
peak=    3.788 closest distance to " O   HOH Z 284 " =    2.744
peak=    3.779 closest distance to " CD BLYS A 290 " =    1.233
peak=    3.777 closest distance to " O   HOH Z 141 " =    1.692
peak=    3.770 closest distance to " O   HOH Z 291 " =    1.863
peak=    3.769 closest distance to " O   HOH Z 106 " =    2.232
peak=    3.760 closest distance to " O   SER A  87 " =    2.182
peak=    3.759 closest distance to " N   ASN A  39 " =    1.101
peak=    3.751 closest distance to " CB  ARG A  79 " =    1.351
peak=    3.749 closest distance to " O   HOH Z 108 " =    1.937
peak=    3.749 closest distance to " O   HOH Z   1 " =    1.707
peak=    3.743 closest distance to " O   HOH Z 419 " =    1.901
peak=    3.734 closest distance to " O   HOH Z 365 " =    3.113
peak=    3.733 closest distance to " CG  ARG A  66 " =    2.606
peak=    3.717 closest distance to " O   HOH Z 128 " =    1.985
peak=    3.716 closest distance to " O   HOH Z 132 " =    2.177
peak=    3.714 closest distance to " NH2BARG A 145 " =    1.984
peak=    3.713 closest distance to " O   HOH Z 173 " =    2.048
peak=    3.704 closest distance to " CA  THR A 221 " =    0.928
peak=    3.704 closest distance to " O   HOH Z 261 " =    1.726
peak=    3.702 closest distance to " O   HOH Z 263 " =    2.228
peak=    3.699 closest distance to " O   HOH Z  66 " =    2.067
peak=    3.692 closest distance to " O   HOH Z 278 " =    1.440
peak=    3.684 closest distance to " CA  VAL A 126 " =    1.173
peak=    3.684 closest distance to " CB  SER A  26 " =    1.573
peak=    3.664 closest distance to " O   HOH Z 389 " =    1.651
peak=    3.662 closest distance to " O   HOH Z 425 " =    1.993
peak=    3.647 closest distance to " CA  GLY A 241 " =    3.742
peak=    3.643 closest distance to " O   HOH Z  88 " =    2.909
peak=    3.639 closest distance to " CA  ASN A 215 " =    1.155
peak=    3.633 closest distance to " O   HOH Z 371 " =    1.493
peak=    3.631 closest distance to " O   HOH Z 247 " =    1.165
peak=    3.627 closest distance to " CG  GLU A 277 " =    2.069
peak=    3.624 closest distance to " O   HOH Z  93 " =    2.002
peak=    3.614 closest distance to " O   HOH Z  21 " =    1.697
peak=    3.613 closest distance to " O   HOH Z 327 " =    1.665
peak=    3.612 closest distance to " O   HOH Z  61 " =    1.673
peak=    3.604 closest distance to " O   HOH Z 313 " =    1.609
peak=    3.604 closest distance to " O   HOH Z 402 " =    1.339
peak=    3.603 closest distance to " O   HOH Z  48 " =    1.439
peak=    3.600 closest distance to " CB  ALA A   1 " =    4.522
peak=    3.592 closest distance to " O   HOH Z 353 " =    2.465
peak=    3.591 closest distance to " O   HOH Z 132 " =    1.015
peak=    3.582 closest distance to " O   HOH Z 172 " =    3.328
peak=    3.581 closest distance to " O   HOH Z 276 " =    1.272
peak=    3.576 closest distance to " O   HOH Z 250 " =    1.360
peak=    3.575 closest distance to " O   HOH Z 403 " =    1.313
peak=    3.571 closest distance to " CG2BVAL A  41 " =    0.834
peak=    3.561 closest distance to " O   HOH Z 163 " =    1.780
peak=    3.561 closest distance to " O   HOH Z   9 " =    2.055
peak=    3.554 closest distance to " O  BHOH Z  74 " =    1.548
peak=    3.553 closest distance to " CG2 VAL A  78 " =    0.866
peak=    3.546 closest distance to " O   HOH Z 227 " =    1.707
peak=    3.540 closest distance to " O   MET A 105 " =    1.829
peak=    3.535 closest distance to " O   HOH Z  50 " =    1.452
peak=    3.523 closest distance to " O   HOH Z 132 " =    2.431
peak=    3.522 closest distance to " O   HOH Z 227 " =    2.132
peak=    3.522 closest distance to " O   HOH Z 144 " =    2.140
peak=    3.515 closest distance to " CD2 TRP A 179 " =    1.413
peak=    3.502 closest distance to " O   HOH Z 366 " =    2.703
peak=    3.499 closest distance to " CB  ALA A 291 " =    1.438
peak=    3.497 closest distance to " CE AMET A  47 " =    1.386
peak=    3.495 closest distance to " O   HOH Z 153 " =    1.618
peak=    3.492 closest distance to " O   HOH Z 409 " =    2.700
peak=    3.486 closest distance to " O   HOH Z 128 " =    2.101
peak=    3.483 closest distance to " CB  PRO A 198 " =    1.012
peak=    3.479 closest distance to " O   HOH Z 380 " =    1.947
peak=    3.478 closest distance to " O   HOH Z 286 " =    2.378
peak=    3.476 closest distance to " O   HOH Z   1 " =    1.578
peak=    3.474 closest distance to " CD2 LEU A 297 " =    0.993
peak=    3.471 closest distance to " CB  ARG A 190 " =    1.771
peak=    3.467 closest distance to " N   ARG A 156 " =    1.242
peak=    3.464 closest distance to " CA  MET A  40 " =    1.055
peak=    3.463 closest distance to " O   HOH Z 345 " =    3.274
peak=    3.456 closest distance to " OD1BASN A 224 " =    2.178
peak=    3.451 closest distance to " O   HOH Z 425 " =    1.277
peak=    3.445 closest distance to " O   HOH Z 357 " =    1.775
peak=    3.443 closest distance to " O   HOH Z 193 " =    2.007
peak=    3.442 closest distance to " CB  SER A  62 " =    1.354
peak=    3.437 closest distance to " O   HOH Z  63 " =    2.321
peak=    3.434 closest distance to " CB  ARG A 102 " =    0.874
peak=    3.433 closest distance to " O   HOH Z 125 " =    2.212
peak=    3.426 closest distance to " O   HOH Z 112 " =    2.369
peak=    3.421 closest distance to " CB  TRP A 266 " =    1.093
peak=    3.417 closest distance to " CE1 TYR A 186 " =    1.267
peak=    3.410 closest distance to " O   HOH Z 423 " =    2.630
peak=    3.410 closest distance to " CG  LEU A 167 " =    1.132
peak=    3.409 closest distance to " O   HOH Z 271 " =    1.911
peak=    3.408 closest distance to " NH1AARG A 145 " =    1.071
peak=    3.407 closest distance to " O   HOH Z 180 " =    2.213
peak=    3.406 closest distance to " N   PHE A 130 " =    1.352
peak=    3.406 closest distance to " O   HOH Z 261 " =    1.541
peak=    3.401 closest distance to " O   HOH Z 286 " =    2.195
peak=    3.401 closest distance to " O   HOH Z 192 " =    1.713
peak=    3.400 closest distance to " O   HOH Z 374 " =    2.425
peak=    3.400 closest distance to " O   HOH Z 392 " =    1.336
peak=    3.396 closest distance to " C   ALA A 299 " =    0.949
peak=    3.394 closest distance to " O   HOH Z 189 " =    1.666
peak=    3.394 closest distance to " CB  VAL A 202 " =    1.615
peak=    3.391 closest distance to " O   HOH Z 279 " =    2.124
peak=    3.389 closest distance to " O   HOH Z 269 " =    3.430
peak=    3.387 closest distance to " CA  GLY A  80 " =    0.875
peak=    3.385 closest distance to " CG2 THR A 221 " =    1.133
peak=    3.376 closest distance to " CG1BVAL A  72 " =    1.310
peak=    3.369 closest distance to " O   HOH Z 158 " =    2.892
peak=    3.360 closest distance to " O   HOH Z 368 " =    2.586
peak=    3.357 closest distance to " CA  VAL A  41 " =    0.934
peak=    3.353 closest distance to " O   HOH Z 334 " =    1.380
peak=    3.353 closest distance to " CG AARG A 275 " =    0.988
peak=    3.350 closest distance to " CB  SER A 216 " =    0.757
peak=    3.344 closest distance to " NZ  LYS A  76 " =    1.362
peak=    3.342 closest distance to " CA  ALA A 233 " =    1.039
peak=    3.336 closest distance to " CA  PHE A 283 " =    1.325
peak=    3.325 closest distance to " O   HOH Z 185 " =    1.644
peak=    3.325 closest distance to " OE2 GLU A  53 " =    2.055
peak=    3.324 closest distance to " O   HOH Z 346 " =    1.422
peak=    3.324 closest distance to " OG  SER A  62 " =    2.903
peak=    3.321 closest distance to " NH2 ARG A 219 " =    1.978
peak=    3.320 closest distance to " CG  GLN A  77 " =    2.186
peak=    3.320 closest distance to " CG  ARG A 269 " =    1.255
peak=    3.316 closest distance to " O   HOH Z 336 " =    1.714
peak=    3.312 closest distance to " CB  SER A 273 " =    0.859
peak=    3.309 closest distance to " O   HOH Z 151 " =    1.554
peak=    3.307 closest distance to " O   HOH Z 114 " =    3.597
peak=    3.307 closest distance to " O   HOH Z 291 " =    1.560
peak=    3.304 closest distance to " NH2AARG A 190 " =    1.576
peak=    3.303 closest distance to " O   HOH Z  15 " =    1.476
peak=    3.301 closest distance to " CB  THR A  31 " =    1.739
peak=    3.300 closest distance to " CE2 TRP A 179 " =    1.578
peak=    3.298 closest distance to " O   HOH Z  64 " =    2.024
peak=    3.292 closest distance to " CG  MET A 185 " =    1.244
peak=    3.291 closest distance to " O   HOH Z 248 " =    1.748
peak=    3.290 closest distance to " CB  ALA A  21 " =    1.804
peak=    3.290 closest distance to " CB  ALA A  34 " =    1.097
peak=    3.282 closest distance to " O   HOH Z  40 " =    2.131
peak=    3.279 closest distance to " CA  LYS A 290 " =    1.273
peak=    3.279 closest distance to " OG  SER A  22 " =    2.651
peak=    3.277 closest distance to " CD2 LEU A 255 " =    1.085
peak=    3.277 closest distance to " O   HOH Z 392 " =    3.039
peak=    3.275 closest distance to " N   GLN A 278 " =    0.982
peak=    3.274 closest distance to " CD  LYS A 166 " =    1.253
peak=    3.272 closest distance to " N   TYR A  15 " =    0.900
peak=    3.271 closest distance to " O   HOH Z 284 " =    1.537
peak=    3.270 closest distance to " C   TYR A 214 " =    1.409
peak=    3.263 closest distance to " CB  THR A 157 " =    1.013
peak=    3.261 closest distance to " O   HOH Z 189 " =    1.337
peak=    3.260 closest distance to " O   HOH Z 214 " =    2.121
peak=    3.260 closest distance to " NH1 ARG A  14 " =    1.073
peak=    3.259 closest distance to " CG  MET A 113 " =    1.044
peak=    3.258 closest distance to " O   HOH Z 234 " =    1.835
peak=    3.256 closest distance to " O   GLY A 229 " =    1.466
peak=    3.254 closest distance to " O   HOH Z  85 " =    1.568
peak=    3.253 closest distance to " CB  VAL A 268 " =    0.811
peak=    3.245 closest distance to " CE  LYS A 119 " =    1.154
peak=    3.243 closest distance to " CZ2 TRP A 150 " =    1.172
peak=    3.242 closest distance to " O   HOH Z  98 " =    1.596
peak=    3.236 closest distance to " O   HOH Z  59 " =    2.216
peak=    3.236 closest distance to " O   HOH Z 211 " =    2.373
peak=    3.233 closest distance to " O   HOH Z   2 " =    1.498
peak=    3.229 closest distance to " OG BSER A 258 " =    3.487
peak=    3.227 closest distance to " O   SER A  26 " =    1.584
peak=    3.223 closest distance to " O   HOH Z 426 " =    1.589
peak=    3.220 closest distance to " O   HOH Z 403 " =    1.603
peak=    3.202 closest distance to " OG ASER A 134 " =    1.485
peak=    3.200 closest distance to " O   HOH Z  43 " =    2.675
peak=    3.199 closest distance to " O   HOH Z  40 " =    1.640
peak=    3.198 closest distance to " O   ALA A   1 " =    1.625
peak=    3.198 closest distance to " CD2 HIS A  81 " =    1.130
peak=    3.194 closest distance to " O   HOH Z 245 " =    1.205
peak=    3.184 closest distance to " O   HOH Z 106 " =    1.798
peak=    3.183 closest distance to " CA  ILE A 234 " =    0.955
peak=    3.179 closest distance to " O   HOH Z  68 " =    1.514
peak=    3.179 closest distance to " CG2 VAL A  67 " =    1.007
peak=    3.177 closest distance to " CB  ASP A 171 " =    1.075
peak=    3.172 closest distance to " CB  GLU A 277 " =    3.482
peak=    3.171 closest distance to " CD  LYS A 119 " =    1.152
peak=    3.170 closest distance to " CB  GLU A 152 " =    1.385
peak=    3.166 closest distance to " CB  ALA A 248 " =    1.366
peak=    3.159 closest distance to " CA  ILE A 263 " =    1.097
peak=    3.159 closest distance to " O   HOH Z 380 " =    1.583
peak=    3.154 closest distance to " O   HOH Z  59 " =    1.837
peak=    3.151 closest distance to " CG2 ILE A  20 " =    1.540
peak=    3.150 closest distance to " CA  ASP A 140 " =    1.077
peak=    3.149 closest distance to " CB  ILE A 120 " =    1.349
peak=    3.144 closest distance to " CB  TYR A 169 " =    1.180
peak=    3.144 closest distance to " O   GLY A  57 " =    2.500
peak=    3.144 closest distance to " O   HOH Z 343 " =    1.251
peak=    3.143 closest distance to " CB  ARG A 269 " =    0.776
peak=    3.141 closest distance to " OD1 ASP A 231 " =    1.890
peak=    3.139 closest distance to " O   HOH Z 260 " =    2.150
peak=    3.134 closest distance to " CB  LEU A 255 " =    0.759
peak=    3.132 closest distance to " O   HOH Z 273 " =    2.901
peak=    3.129 closest distance to " O   HOH Z 435 " =    1.851
peak=    3.128 closest distance to " CG1 ILE A 151 " =    0.879
peak=    3.125 closest distance to " O   HOH Z 299 " =    4.296
peak=    3.124 closest distance to " CB  ASN A  39 " =    0.852
peak=    3.123 closest distance to " CB  ASN A 215 " =    1.053
peak=    3.121 closest distance to " CA  LEU A 300 " =    1.085
peak=    3.120 closest distance to " N   ASN A 127 " =    1.219
peak=    3.119 closest distance to " O   HOH Z 411 " =    1.770
peak=    3.117 closest distance to " OG  SER A  62 " =    3.436
peak=    3.112 closest distance to " O   HOH Z 172 " =    5.480
peak=    3.107 closest distance to " O   HOH Z 379 " =    1.819
peak=    3.107 closest distance to " CB  TYR A  30 " =    1.505
peak=    3.106 closest distance to " O   HOH Z 135 " =    1.614
peak=    3.104 closest distance to " O  BHOH Z 338 " =    2.301
peak=    3.102 closest distance to " CB  TYR A 116 " =    0.824
peak=    3.098 closest distance to " O   HOH Z 140 " =    1.945
peak=    3.089 closest distance to " CA  MET A 105 " =    0.929
peak=    3.088 closest distance to " O   HOH Z 438 " =    2.219
peak=    3.088 closest distance to " O   HOH Z  49 " =    2.007
peak=    3.082 closest distance to " O   HOH Z 282 " =    1.518
peak=    3.081 closest distance to " O   HOH Z 250 " =    1.947
peak=    3.064 closest distance to " CA  ARG A  36 " =    0.959
peak=    3.051 closest distance to " NE AARG A 275 " =    1.579
peak=    3.048 closest distance to " CB  GLN A 278 " =    0.829
peak=    3.047 closest distance to " O   HOH Z 423 " =    1.472
peak=    3.043 closest distance to " O   HOH Z 433 " =    1.829
peak=    3.030 closest distance to " CB  MET A  47 " =    1.153

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 197         
Filter by distance & map next to the model:
   mapped sites are within: 0.782 - 5.025
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 197
   mapped sites are within: 0.782 - 5.025

peak=   -4.490 closest distance to " O   PRO A 198 " =    1.258
peak=   -4.358 closest distance to " O   HOH Z 198 " =    1.946
peak=   -4.335 closest distance to " N   GLN A  58 " =    1.656
peak=   -4.316 closest distance to " O   HOH Z 266 " =    4.377
peak=   -4.285 closest distance to " SG  CYS A 254 " =    3.214
peak=   -4.246 closest distance to " O   VAL A  67 " =    2.727
peak=   -4.224 closest distance to " C   HIS A 108 " =    1.086
peak=   -4.215 closest distance to " CB  PRO A 243 " =    2.554
peak=   -4.203 closest distance to " O   HOH Z  13 " =    1.283
peak=   -4.175 closest distance to " CB  TYR A  15 " =    2.142
peak=   -4.170 closest distance to " O   HOH Z  98 " =    1.911
peak=   -4.150 closest distance to " CD  ARG A 156 " =    1.938
peak=   -4.123 closest distance to " O   HOH Z 377 " =    1.981
peak=   -4.098 closest distance to " ND2 ASN A  45 " =    0.891
peak=   -4.087 closest distance to " OXT GLY A 302 " =    2.695
peak=   -4.054 closest distance to " CB  ASN A  39 " =    2.176
peak=   -4.041 closest distance to " CG  LYS A 193 " =    2.225
peak=   -4.035 closest distance to " O   ALA A 161 " =    1.596
peak=   -4.000 closest distance to " CZ  PHE A  59 " =    1.491
peak=   -3.995 closest distance to " O   HOH Z  43 " =    1.765
peak=   -3.976 closest distance to " O   VAL A  67 " =    2.782
peak=   -3.968 closest distance to " C   ALA A 158 " =    1.199
peak=   -3.946 closest distance to " O   SER A 135 " =    1.475
peak=   -3.943 closest distance to " O   HOH Z 102 " =    1.654
peak=   -3.929 closest distance to " O   HOH Z 407 " =    3.002
peak=   -3.892 closest distance to " O   HOH Z 388 " =    1.971
peak=   -3.863 closest distance to " CB  CYS A 201 " =    2.446
peak=   -3.829 closest distance to " O   PRO A 163 " =    1.920
peak=   -3.817 closest distance to " O   HOH Z 290 " =    1.087
peak=   -3.813 closest distance to " O   HOH Z 166 " =    1.288
peak=   -3.813 closest distance to " O   HOH Z  47 " =    1.571
peak=   -3.801 closest distance to " OG  SER A   3 " =    1.492
peak=   -3.794 closest distance to " CG  PHE A 283 " =    2.598
peak=   -3.793 closest distance to " O   VAL A 153 " =    2.308
peak=   -3.791 closest distance to " CG  GLN A 223 " =    2.095
peak=   -3.788 closest distance to " N   ALA A 248 " =    1.592
peak=   -3.768 closest distance to " O   HOH Z  52 " =    1.611
peak=   -3.763 closest distance to " CB  ALA A 291 " =    2.369
peak=   -3.762 closest distance to " O   HOH Z 385 " =    1.896
peak=   -3.744 closest distance to " CB  ALA A 161 " =    2.523
peak=   -3.720 closest distance to " CB  ALA A 248 " =    1.973
peak=   -3.719 closest distance to " CG1 VAL A 112 " =    2.949
peak=   -3.717 closest distance to " CE2 TYR A  30 " =    2.893
peak=   -3.716 closest distance to " O   HOH Z 395 " =    5.025
peak=   -3.710 closest distance to " N   ASP A 286 " =    2.348
peak=   -3.706 closest distance to " OG BSER A 134 " =    1.225
peak=   -3.680 closest distance to " O   HOH Z 231 " =    2.009
peak=   -3.667 closest distance to " CE3 TRP A 274 " =    2.291
peak=   -3.659 closest distance to " O   HOH Z  24 " =    1.334
peak=   -3.653 closest distance to " CZ  TYR A 169 " =    1.718
peak=   -3.650 closest distance to " O   HOH Z 351 " =    1.524
peak=   -3.647 closest distance to " OXT GLY A 302 " =    3.538
peak=   -3.642 closest distance to " CD  ARG A 139 " =    1.449
peak=   -3.635 closest distance to " CE  MET A 105 " =    2.065
peak=   -3.627 closest distance to " N   HIS A 115 " =    1.920
peak=   -3.626 closest distance to " O   HOH Z 435 " =    2.776
peak=   -3.605 closest distance to " NH2 ARG A  79 " =    1.910
peak=   -3.599 closest distance to " O   HOH Z  11 " =    1.819
peak=   -3.599 closest distance to " O   HOH Z  11 " =    1.935
peak=   -3.581 closest distance to " O   TRP A  70 " =    1.451
peak=   -3.578 closest distance to " CG  ASP A 231 " =    0.782
peak=   -3.577 closest distance to " O   HOH Z 185 " =    2.099
peak=   -3.567 closest distance to " O   SER A 146 " =    0.898
peak=   -3.566 closest distance to " CA  GLY A 133 " =    1.928
peak=   -3.562 closest distance to " OD1 ASP A 191 " =    1.704
peak=   -3.559 closest distance to " CD1 PHE A  59 " =    1.818
peak=   -3.555 closest distance to " O   HOH Z  63 " =    1.484
peak=   -3.548 closest distance to " ND2 ASN A  39 " =    1.410
peak=   -3.532 closest distance to " C   LEU A 143 " =    1.114
peak=   -3.518 closest distance to " N   SER A 276 " =    1.061
peak=   -3.518 closest distance to " CB  ALA A 291 " =    2.134
peak=   -3.518 closest distance to " ND2 ASN A 187 " =    1.538
peak=   -3.513 closest distance to " OG  SER A  97 " =    1.981
peak=   -3.512 closest distance to " O   MET A  40 " =    2.657
peak=   -3.511 closest distance to " O   HOH Z 263 " =    2.809
peak=   -3.506 closest distance to " OE1 GLN A  88 " =    1.070
peak=   -3.501 closest distance to " NH1AARG A 275 " =    1.751
peak=   -3.500 closest distance to " O   HOH Z  93 " =    1.719
peak=   -3.500 closest distance to " O   TRP A  92 " =    1.654
peak=   -3.484 closest distance to " OD2 ASP A 191 " =    1.431
peak=   -3.483 closest distance to " NH1 ARG A 195 " =    2.559
peak=   -3.473 closest distance to " O   HOH Z 126 " =    1.860
peak=   -3.463 closest distance to " O   HOH Z 385 " =    1.881
peak=   -3.460 closest distance to " O   HOH Z 298 " =    1.244
peak=   -3.457 closest distance to " CD1 LEU A 228 " =    2.093
peak=   -3.457 closest distance to " O   PRO A 198 " =    1.288
peak=   -3.443 closest distance to " O   ASN A  45 " =    1.850
peak=   -3.442 closest distance to " OG  SER A 206 " =    1.678
peak=   -3.435 closest distance to " CD1 LEU A 101 " =    2.301
peak=   -3.426 closest distance to " O   HOH Z 250 " =    1.420
peak=   -3.422 closest distance to " O   HOH Z 114 " =    2.721
peak=   -3.417 closest distance to " CZ3 TRP A 179 " =    1.333
peak=   -3.416 closest distance to " O   HOH Z  88 " =    2.387
peak=   -3.400 closest distance to " CD2 LEU A 300 " =    3.026
peak=   -3.399 closest distance to " CD2 LEU A 300 " =    2.856
peak=   -3.398 closest distance to " CD1 ILE A 239 " =    2.498
peak=   -3.394 closest distance to " O   ALA A  51 " =    1.261
peak=   -3.394 closest distance to " CA  SER A 146 " =    2.244
peak=   -3.391 closest distance to " CA  TRP A 274 " =    1.550
peak=   -3.376 closest distance to " N   ALA A  43 " =    2.342
peak=   -3.374 closest distance to " ND2 ASN A  60 " =    1.372
peak=   -3.371 closest distance to " O   HOH Z 423 " =    2.162
peak=   -3.370 closest distance to " CG  MET A 105 " =    0.907
peak=   -3.366 closest distance to " O   HOH Z   3 " =    1.797
peak=   -3.364 closest distance to " CA  TYR A  30 " =    2.928
peak=   -3.360 closest distance to " OD2 ASP A  50 " =    1.444
peak=   -3.344 closest distance to " CG  PRO A 243 " =    1.481
peak=   -3.340 closest distance to " O   HOH Z  88 " =    1.989
peak=   -3.328 closest distance to " O   HOH Z 198 " =    1.501
peak=   -3.326 closest distance to " O   SER A  95 " =    1.340
peak=   -3.324 closest distance to " CB  PRO A 163 " =    2.705
peak=   -3.317 closest distance to " OD1 ASP A 200 " =    1.261
peak=   -3.315 closest distance to " O   PHE A 218 " =    1.443
peak=   -3.312 closest distance to " O   HOH Z 389 " =    1.795
peak=   -3.311 closest distance to " O   HOH Z 389 " =    4.502
peak=   -3.294 closest distance to " CD  GLN A  88 " =    0.881
peak=   -3.293 closest distance to " CB  ALA A 244 " =    2.010
peak=   -3.292 closest distance to " C   LEU A   5 " =    0.976
peak=   -3.291 closest distance to " O   GLN A 183 " =    1.341
peak=   -3.287 closest distance to " O   HOH Z 438 " =    1.118
peak=   -3.284 closest distance to " O   VAL A 197 " =    1.159
peak=   -3.284 closest distance to " CD2 TYR A 293 " =    2.035
peak=   -3.283 closest distance to " N   GLN A 122 " =    1.446
peak=   -3.282 closest distance to " ND2 ASN A 252 " =    1.597
peak=   -3.278 closest distance to " CB  ALA A 100 " =    2.554
peak=   -3.277 closest distance to " OD2 ASP A 270 " =    1.322
peak=   -3.276 closest distance to " CZ  PHE A 130 " =    0.863
peak=   -3.275 closest distance to " O   HOH Z 137 " =    1.343
peak=   -3.272 closest distance to " OH  TYR A 214 " =    1.287
peak=   -3.269 closest distance to " O   ARG A  66 " =    1.202
peak=   -3.263 closest distance to " O   SER A   3 " =    1.242
peak=   -3.258 closest distance to " N   GLN A  58 " =    1.221
peak=   -3.257 closest distance to " N   ARG A 139 " =    1.146
peak=   -3.252 closest distance to " O   ASN A 249 " =    1.405
peak=   -3.251 closest distance to " CG2 VAL A  78 " =    1.384
peak=   -3.247 closest distance to " OD1 ASP A 191 " =    1.381
peak=   -3.246 closest distance to " O   HOH Z 423 " =    1.163
peak=   -3.244 closest distance to " O   GLN A  89 " =    1.568
peak=   -3.239 closest distance to " CG1BVAL A  41 " =    2.976
peak=   -3.238 closest distance to " CD2 LEU A 237 " =    2.351
peak=   -3.236 closest distance to " CG2 VAL A 189 " =    2.053
peak=   -3.236 closest distance to " O   HOH Z  90 " =    2.427
peak=   -3.231 closest distance to " O   HOH Z 148 " =    3.252
peak=   -3.226 closest distance to " OD2 ASP A 171 " =    2.222
peak=   -3.222 closest distance to " N   SER A 212 " =    1.880
peak=   -3.221 closest distance to " CA  ASP A 298 " =    1.062
peak=   -3.221 closest distance to " O   VAL A 174 " =    1.977
peak=   -3.220 closest distance to " O   HOH Z 326 " =    1.637
peak=   -3.216 closest distance to " CB  ASP A 132 " =    2.256
peak=   -3.215 closest distance to " O   HOH Z 418 " =    1.534
peak=   -3.209 closest distance to " CG  GLU A 277 " =    1.137
peak=   -3.196 closest distance to " O   HOH Z  37 " =    1.635
peak=   -3.194 closest distance to " CA  TRP A  70 " =    2.341
peak=   -3.194 closest distance to " O   HOH Z 317 " =    2.447
peak=   -3.193 closest distance to " O   HOH Z  60 " =    1.757
peak=   -3.189 closest distance to " CE3 TRP A 123 " =    1.261
peak=   -3.186 closest distance to " CE2 PHE A 192 " =    1.978
peak=   -3.177 closest distance to " N   THR A 157 " =    1.413
peak=   -3.176 closest distance to " CG2 ILE A 263 " =    2.210
peak=   -3.176 closest distance to " OD1 ASN A 249 " =    1.047
peak=   -3.174 closest distance to " O   HOH Z 385 " =    1.633
peak=   -3.170 closest distance to " O   HOH Z 297 " =    2.725
peak=   -3.167 closest distance to " CG  GLU A 152 " =    1.273
peak=   -3.163 closest distance to " OD1 ASP A 171 " =    1.534
peak=   -3.157 closest distance to " NH2 ARG A  66 " =    4.305
peak=   -3.154 closest distance to " O   ALA A 292 " =    1.874
peak=   -3.151 closest distance to " O   HOH Z 337 " =    1.479
peak=   -3.150 closest distance to " CZ2 TRP A 274 " =    0.988
peak=   -3.148 closest distance to " O   SER A  22 " =    2.405
peak=   -3.143 closest distance to " CA  GLY A  57 " =    2.088
peak=   -3.136 closest distance to " ND2 ASN A  69 " =    1.393
peak=   -3.127 closest distance to " CD2 LEU A 237 " =    2.769
peak=   -3.127 closest distance to " O   HOH Z 236 " =    1.979
peak=   -3.125 closest distance to " OG1 THR A 246 " =    1.436
peak=   -3.120 closest distance to " OG ASER A 134 " =    0.904
peak=   -3.120 closest distance to " O   HOH Z 427 " =    1.497
peak=   -3.119 closest distance to " O   HOH Z 311 " =    3.388
peak=   -3.118 closest distance to " OG  SER A 245 " =    1.151
peak=   -3.117 closest distance to " O   ASN A 187 " =    1.448
peak=   -3.117 closest distance to " CD  GLU A 152 " =    2.330
peak=   -3.114 closest distance to " CB  ASP A 132 " =    2.123
peak=   -3.112 closest distance to " O   ILE A  49 " =    1.709
peak=   -3.105 closest distance to " O   HOH Z 197 " =    4.975
peak=   -3.099 closest distance to " CG  GLN A  58 " =    1.273
peak=   -3.091 closest distance to " O   HOH Z 359 " =    3.234
peak=   -3.079 closest distance to " CD  PRO A  90 " =    1.729
peak=   -3.074 closest distance to " O   HOH Z 210 " =    1.117
peak=   -3.064 closest distance to " CB  PHE A 208 " =    2.155
peak=   -3.062 closest distance to " SG ACYS A 201 " =    1.940
peak=   -3.049 closest distance to " O   HOH Z 111 " =    4.118
peak=   -3.046 closest distance to " OD1 ASN A 301 " =    1.966
peak=   -3.045 closest distance to " O   SER A 146 " =    0.933
peak=   -3.042 closest distance to " OE2 GLU A 152 " =    1.266
peak=   -3.032 closest distance to " CG  GLU A 152 " =    1.761
peak=   -3.023 closest distance to " O   HOH Z 298 " =    2.444
peak=   -2.952 closest distance to " OG1 THR A 246 " =    1.514

================= 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    :  0.4300 0.4325   6.231468e+00   6.228483e+00
   1_bss:  0.4186 0.4167   6.223495e+00   6.204564e+00
   1_xyz:  0.2743 0.2996   5.888187e+00   5.969573e+00
   1_adp:  0.2498 0.3077   5.834558e+00   5.990362e+00
   1_occ:  0.2495 0.3078   5.833946e+00   5.989808e+00
   2_bss:  0.2456 0.3054   5.825958e+00   5.982824e+00
   2_xyz:  0.1774 0.2303   5.543479e+00   5.738663e+00
   2_adp:  0.1629 0.2118   5.461300e+00   5.655554e+00
   2_occ:  0.1626 0.2120   5.460551e+00   5.655386e+00
   3_bss:  0.1622 0.2111   5.455358e+00   5.649873e+00
   3_xyz:  0.1260 0.1678   5.224526e+00   5.443487e+00
   3_adp:  0.1188 0.1610   5.173569e+00   5.395681e+00
   3_occ:  0.1186 0.1608   5.172206e+00   5.394134e+00
   4_bss:  0.1189 0.1614   5.173860e+00   5.395460e+00
   4_xyz:  0.1126 0.1556   5.133068e+00   5.364327e+00
   4_adp:  0.1112 0.1557   5.126984e+00   5.362588e+00
   4_occ:  0.1111 0.1556   5.126292e+00   5.361944e+00
   5_bss:  0.1111 0.1556   5.126346e+00   5.362066e+00
   5_xyz:  0.1114 0.1549   5.129605e+00   5.360728e+00
   5_adp:  0.1102 0.1570   5.130490e+00   5.372240e+00
   5_occ:  0.1102 0.1569   5.130430e+00   5.372315e+00
   5_bss:  0.1101 0.1569   5.130166e+00   5.371986e+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:  0.338  20.914  -2.583  -0.663   2.906  -0.000   0.000   0.000
   1_xyz:  0.338  20.914  -2.583  -0.663   2.906  -0.000   0.000   0.000
   1_adp:  0.338  20.914  -2.583  -0.663   2.906  -0.000   0.000   0.000
   1_occ:  0.338  20.914  -2.583  -0.663   2.906  -0.000   0.000   0.000
   2_bss:  0.324  34.699  -2.505  -1.743  -0.017  -0.000  -0.000  -0.000
   2_xyz:  0.324  34.699  -2.505  -1.743  -0.017  -0.000  -0.000  -0.000
   2_adp:  0.324  34.699  -2.505  -1.743  -0.017  -0.000  -0.000  -0.000
   2_occ:  0.324  34.699  -2.505  -1.743  -0.017  -0.000  -0.000  -0.000
   3_bss:  0.319  34.699  -2.725  -2.361  -1.289  -0.000  -0.000  -0.000
   3_xyz:  0.319  34.699  -2.725  -2.361  -1.289  -0.000  -0.000  -0.000
   3_adp:  0.319  34.699  -2.725  -2.361  -1.289  -0.000  -0.000  -0.000
   3_occ:  0.319  34.699  -2.725  -2.361  -1.289  -0.000  -0.000  -0.000
   4_bss:  0.318  34.699  -2.896  -2.564  -1.856  -0.000  -0.000  -0.000
   4_xyz:  0.318  34.699  -2.896  -2.564  -1.856  -0.000  -0.000  -0.000
   4_adp:  0.318  34.699  -2.896  -2.564  -1.856  -0.000  -0.000  -0.000
   4_occ:  0.318  34.699  -2.896  -2.564  -1.856  -0.000  -0.000  -0.000
   5_bss:  0.320  34.792  -2.806  -2.489  -1.907  -0.000  -0.000  -0.000
   5_xyz:  0.320  34.792  -2.806  -2.489  -1.907  -0.000  -0.000  -0.000
   5_adp:  0.320  34.792  -2.806  -2.489  -1.907  -0.000  -0.000  -0.000
   5_occ:  0.320  34.792  -2.806  -2.489  -1.907  -0.000  -0.000  -0.000
   5_bss:  0.322  37.144  -2.594  -2.287  -1.753  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.302 0.5309  0.7208    57575.661
   1_bss:  47.536 0.5508  0.7455    52486.722
   1_xyz:  30.619 0.7520  0.9635    24053.245
   1_adp:  31.967 0.7358  0.9500    25388.724
   1_occ:  31.974 0.7357  0.9497    25373.260
   2_bss:  31.562 0.7399  0.9134    24747.229
   2_xyz:  22.795 0.8338  0.9931    13674.945
   2_adp:  20.110 0.8612  1.0081    11376.983
   2_occ:  20.115 0.8611  1.0077    11364.527
   3_bss:  19.903 0.8630  0.9823    11137.794
   3_xyz:  15.294 0.9035  1.0014     7031.731
   3_adp:  14.291 0.9122  1.0012     6480.684
   3_occ:  14.250 0.9126  1.0011     6447.152
   4_bss:  14.271 0.9125  0.9896     6504.582
   4_xyz:  13.558 0.9184  0.9922     6005.758
   4_adp:  13.453 0.9194  0.9896     5996.374
   4_occ:  13.437 0.9195  0.9896     5988.197
   5_bss:  13.441 0.9195  0.9909     5992.469
   5_xyz:  13.416 0.9197  0.9905     5973.146
   5_adp:  13.625 0.9181  0.9851     6073.972
   5_occ:  13.628 0.9181  0.9850     6076.726
   5_bss:  13.621 0.9182  0.9922     6074.647
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.8876e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.8876e-01
   1_xyz:   1.401  0.011  0.085 15.732  0.007  4.106   1.1383e-01
   1_adp:   1.401  0.011  0.085 15.732  0.007  4.106   1.1383e-01
   1_occ:   1.401  0.011  0.085 15.732  0.007  4.106   1.1383e-01
   2_bss:   1.401  0.011  0.085 15.732  0.007  4.106   1.1383e-01
   2_xyz:   1.043  0.007  0.070 14.312  0.004  4.108   5.9523e-02
   2_adp:   1.043  0.007  0.070 14.312  0.004  4.108   5.9523e-02
   2_occ:   1.043  0.007  0.070 14.312  0.004  4.108   5.9523e-02
   3_bss:   1.043  0.007  0.070 14.312  0.004  4.108   5.9523e-02
   3_xyz:   1.053  0.007  0.072 14.735  0.004  4.108   6.3417e-02
   3_adp:   1.053  0.007  0.072 14.735  0.004  4.108   6.3417e-02
   3_occ:   1.053  0.007  0.072 14.735  0.004  4.108   6.3417e-02
   4_bss:   1.053  0.007  0.072 14.735  0.004  4.108   6.3417e-02
   4_xyz:   0.972  0.006  0.069 14.639  0.004  4.107   5.5792e-02
   4_adp:   0.972  0.006  0.069 14.639  0.004  4.107   5.5792e-02
   4_occ:   0.972  0.006  0.069 14.639  0.004  4.107   5.5792e-02
   5_bss:   0.972  0.006  0.069 14.639  0.004  4.107   5.5792e-02
   5_xyz:   0.879  0.005  0.063 14.260  0.004  4.106   4.7780e-02
   5_adp:   0.879  0.005  0.063 14.260  0.004  4.106   4.7780e-02
   5_occ:   0.879  0.005  0.063 14.260  0.004  4.106   4.7780e-02
   5_bss:   0.879  0.005  0.063 14.260  0.004  4.106   4.7780e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.429   2.3775e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.429   2.3775e-01
   1_xyz:   9.118  0.059  0.364 87.486  0.068  2.136   1.5018e-01
   1_adp:   9.118  0.059  0.364 87.486  0.068  2.136   1.5018e-01
   1_occ:   9.118  0.059  0.364 87.486  0.068  2.136   1.5018e-01
   2_bss:   9.118  0.059  0.364 87.486  0.068  2.136   1.5018e-01
   2_xyz:   6.645  0.062  0.213 84.672  0.038  2.378   5.0707e-02
   2_adp:   6.645  0.062  0.213 84.672  0.038  2.378   5.0707e-02
   2_occ:   6.645  0.062  0.213 84.672  0.038  2.378   5.0707e-02
   3_bss:   6.645  0.062  0.213 84.672  0.038  2.378   5.0707e-02
   3_xyz:   6.347  0.044  0.272 83.544  0.034  2.282   5.7286e-02
   3_adp:   6.347  0.044  0.272 83.544  0.034  2.282   5.7286e-02
   3_occ:   6.347  0.044  0.272 83.544  0.034  2.282   5.7286e-02
   4_bss:   6.347  0.044  0.272 83.544  0.034  2.282   5.7286e-02
   4_xyz:   5.811  0.039  0.211 84.932  0.044  2.308   3.7433e-02
   4_adp:   5.811  0.039  0.211 84.932  0.044  2.308   3.7433e-02
   4_occ:   5.811  0.039  0.211 84.932  0.044  2.308   3.7433e-02
   5_bss:   5.811  0.039  0.211 84.932  0.044  2.308   3.7433e-02
   5_xyz:   5.990  0.034  0.206 83.958  0.037  2.362   2.8074e-02
   5_adp:   5.990  0.034  0.206 83.958  0.037  2.362   2.8074e-02
   5_occ:   5.990  0.034  0.206 83.958  0.037  2.362   2.8074e-02
   5_bss:   5.990  0.034  0.206 83.958  0.037  2.362   2.8074e-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:  85.55   0.00  18.38  85.55   0.00  14.12  84.34   4.31  41.55
   1_occ:  85.55   0.00  18.38  85.55   0.00  14.12  84.34   4.31  41.55
   2_bss:  85.55   0.00  18.38  85.55   0.00  14.12  84.34   4.31  41.55
   2_xyz:  85.55   0.00  18.38  85.55   0.00  14.12  84.34   4.31  41.55
   2_adp:  80.26   1.04  17.30  80.26   1.04  13.29  77.69   6.75  39.16
   2_occ:  80.26   1.04  17.30  80.26   1.04  13.29  77.69   6.75  39.16
   3_bss:  80.26   1.04  17.30  80.26   1.04  13.29  77.69   6.75  39.16
   3_xyz:  80.26   1.04  17.30  80.26   1.04  13.29  77.69   6.75  39.16
   3_adp:  82.08   2.35  17.08  82.08   2.35  13.00  77.60   5.40  39.31
   3_occ:  82.08   2.35  17.08  82.08   2.35  13.00  77.60   5.40  39.31
   4_bss:  82.08   2.35  17.08  82.08   2.35  13.00  77.60   5.40  39.31
   4_xyz:  82.08   2.35  17.08  82.08   2.35  13.00  77.60   5.40  39.31
   4_adp:  83.16   2.28  16.92  83.16   2.28  12.91  78.98   6.32  38.74
   4_occ:  83.16   2.28  16.92  83.16   2.28  12.91  78.98   6.32  38.74
   5_bss:  83.16   2.28  16.92  83.16   2.28  12.91  78.98   6.32  38.74
   5_xyz:  83.16   2.28  16.92  83.16   2.28  12.91  78.98   6.32  38.74
   5_adp:  91.74   0.00  17.22  91.74   0.00  12.94  83.37   6.11  40.54
   5_occ:  91.74   0.00  17.22  91.74   0.00  12.94  83.37   6.11  40.54
   5_bss:  91.75   0.00  17.23  91.75   0.00  12.95  83.37   6.11  40.54
------------------------------------------------------------------------
 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:    1.846    0.028    0.421
   1_adp:    1.846    0.028    0.421
   1_occ:    1.846    0.028    0.421
   2_bss:    1.846    0.028    0.421
   2_xyz:    1.601    0.052    0.519
   2_adp:    1.601    0.052    0.519
   2_occ:    1.601    0.052    0.519
   3_bss:    1.601    0.052    0.519
   3_xyz:    1.398    0.055    0.603
   3_adp:    1.398    0.055    0.603
   3_occ:    1.398    0.055    0.603
   4_bss:    1.398    0.055    0.603
   4_xyz:    1.431    0.040    0.616
   4_adp:    1.431    0.040    0.616
   4_occ:    1.431    0.040    0.616
   5_bss:    1.431    0.040    0.616
   5_xyz:    1.493    0.037    0.626
   5_adp:    1.493    0.037    0.626
   5_occ:    1.493    0.037    0.626
   5_bss:    1.493    0.037    0.626
------------------------------------------------------------------------

CPU time actual refinement: 321.94


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_396/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_396/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_396/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_396/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_396/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 321.80 
  Macro-tasks:
    bulk solvent and scale       = 40.22  
    individual site refinement   = 127.87 
    weights calculation          = 28.51  
    collect and process          = 6.19   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 202.91 
  Micro-tasks:
    mask                            = 1.81   
    f_calc                          = 101.68 
    alpha_beta                      = 8.19   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 109.14 
    fmodel                         = 7.51   
    r_factors                      = 0.25   
    phase_errors                   = 10.73  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 240.73 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.625 micro seconds
Total CPU time: 5.59 minutes
from_scatterers_fft:    631 calls, 101.42 s
gradients_fft:          576 calls,  96.41 s

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

# Date 2008-01-16 Time 04:43:44 PST -0800 (1200487424.85 s)
Start R-work = 0.4300, R-free = 0.4325 (no bulk solvent and anisotropic scale)
Final R-work = 0.1364, R-free = 0.1785 (no bulk solvent and anisotropic scale)

Start R-work = 0.4186, R-free = 0.4167
Final R-work = 0.1101, R-free = 0.1569