# Date 2008-01-16 Time 05:17:48 PST -0800 (1200489468.38 s)
#phil __OFF__

Command line arguments: "../671.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 20450
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 671

-------------------------------------------------------------------------------
  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: (70.25, 47.1647, 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: 3.34, per 1000 atoms: 1.18


================================== 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: (70.25, 47.1647, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8895 1.95137
Completeness in resolution range: 0.935616
Completeness with d_max=infinity: 0.93281

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8895
                             d_min =   1.9514

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: (70.25, 47.1647, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8895 1.95137
Completeness in resolution range: 0.935616
Completeness with d_max=infinity: 0.93281

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8899 -  4.1761 [2206/2235]  1987   219   9.9%
  bin  2:  4.1761 -  3.3268 [2098/2121]  1889   209  10.0%
  bin  3:  3.3268 -  2.9099 [2078/2103]  1865   213  10.3%
  bin  4:  2.9099 -  2.6454 [2077/2093]  1875   202   9.7%
  bin  5:  2.6454 -  2.4567 [2039/2078]  1832   207  10.2%
  bin  6:  2.4567 -  2.3124 [2060/2092]  1858   202   9.8%
  bin  7:  2.3124 -  2.1970 [2012/2049]  1809   203  10.1%
  bin  8:  2.1970 -  2.1017 [2019/2061]  1818   201  10.0%
  bin  9:  2.1017 -  2.0209 [2015/2053]  1811   204  10.1%
  bin 10:  2.0209 -  1.9514 [ 985/2052]   886    99  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_671/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.50 -     2.18: 20
        2.18 -     2.86: 1161
        2.86 -     3.54: 4473
        3.54 -     4.22: 9327
        4.22 -     4.90: 13637
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.495 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.560 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.789 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.810 3.120 -x,y-1/2,-z+1/2
  ... (remaining 28613 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_671/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_671/model_refine_001.geo

CPU time processing inputs: 9.01


============================ 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 = 70.25 47.16465 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 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3723   r_free= 0.3705   ksol= 0.00   Bsol= 0.00   scale= 0.953    |
|                                                                             |
| 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:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.160801                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8899 -  4.6581 0.99   1425  161 0.3092 0.3121      6.4312      6.4364|
|  2:  4.6581 -  3.7162 0.99   1370  145 0.3041 0.2839      6.5977      6.5385|
|  3:  3.7162 -  3.2520 0.99   1345  157 0.3265 0.3418      6.4815      6.6397|
|  4:  3.2520 -  2.9572 0.99   1347  147 0.3495 0.3461      6.3544      6.3552|
|  5:  2.9572 -  2.7467 0.98   1319  148 0.3762 0.3376       6.219      6.1935|
|  6:  2.7467 -  2.5856 0.99   1335  143 0.3950 0.3962      6.1446      6.0879|
|  7:  2.5856 -  2.4567 0.99   1307  149 0.3910 0.3321      6.1317      6.0546|
|  8:  2.4567 -  2.3502 0.99   1312  144 0.4060 0.4376      6.0509      6.1234|
|  9:  2.3502 -  2.2601 0.99   1314  153 0.4137 0.4138      6.0345      6.0385|
| 10:  2.2601 -  2.1823 0.98   1309  141 0.4238 0.4470      6.0159      6.0565|
| 11:  2.1823 -  2.1143 0.98   1293  139 0.4337 0.4846      5.9527      6.0321|
| 12:  2.1143 -  2.0540 1.00   1293  149 0.4202 0.4246      5.8785      5.9239|
| 13:  2.0540 -  2.0001 0.95   1262  142 0.4452 0.4499      5.8177      5.7951|
| 14:  2.0001 -  1.9514 0.30    399   41 0.5447 0.5188      5.8447      5.7557|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8899 -  4.6581  1425   161  0.76  29.01   0.86     0.77      51144.18|
|  2:  4.6581 -  3.7162  1370   145  0.79  27.39   0.96     0.88      66084.00|
|  3:  3.7162 -  3.2520  1345   157  0.73  32.51   0.97     0.91      68870.37|
|  4:  3.2520 -  2.9572  1347   147  0.67  37.73   0.99     0.89      60760.47|
|  5:  2.9572 -  2.7467  1319   148  0.63  41.31   0.95     0.85      48945.78|
|  6:  2.7467 -  2.5856  1335   143  0.62  42.20   0.97     0.83      41249.13|
|  7:  2.5856 -  2.4567  1307   149  0.63  41.64   0.99     0.82      38222.24|
|  8:  2.4567 -  2.3502  1312   144  0.58  45.64   0.96     0.80      37222.26|
|  9:  2.3502 -  2.2601  1314   153  0.56  47.68   1.00     0.77      35993.37|
| 10:  2.2601 -  2.1823  1309   141  0.52  50.64   1.04     0.73      36936.76|
| 11:  2.1823 -  2.1143  1293   139  0.49  53.05   1.01     0.71      35167.48|
| 12:  2.1143 -  2.0540  1293   149  0.47  54.73   1.02     0.72      34413.40|
| 13:  2.0540 -  2.0001  1262   142  0.45  56.03   1.00     0.69      29448.44|
| 14:  2.0001 -  1.9514   399    41  0.42  58.08   0.92     0.62      26242.09|
|alpha:            min =        0.62 max =            0.91 mean =         0.79|
|beta:             min =    26242.09 max =        68870.37 mean =     44784.90|
|figures of merit: min =        0.00 max =            1.00 mean =         0.61|
|phase err.(work): min =        0.00 max =           89.99 mean =        43.15|
|phase err.(test): min =        0.00 max =           89.73 mean =        42.96|
|-----------------------------------------------------------------------------|

============================== 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 = 5.701990              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.725   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.219372              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.047   (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 |  1.495 -  1.836:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.836 -  2.176:       14 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.176 -  2.517:       36 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.517 -  2.857:     1125 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.857 -  3.198:     1979 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.198 -  3.538:     2494 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.538 -  3.879:     4685 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.879 -  4.219:     4642 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.219 -  4.559:     6168 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.559 -  4.900:     7469 |
|-----------------------------------------------------------------------------|
|-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 |        0.180 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.495 |       0.457 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.664)------------------------------------------|
|    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 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3723   r_free= 0.3705   ksol= 0.00   Bsol= 0.00   scale= 0.953    |
|                                                                             |
| 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:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.160801                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3568   r_free= 0.3526   ksol= 0.34   Bsol= 50.00   scale= 0.966   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.24,-1.93,3.55,-0.00,0.00,0.00); trace/3= -0.54                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.146126                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.599203              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.686   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.588419              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.026   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3568      final r-factor (work) = 0.2530          |
| start r-factor (free) = 0.3526      final r-factor (free) = 0.2836          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.3093 = 4.60 * 0.50 * 6.1443 + 1.00 * 0.1799                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.7694 = 4.60 * 0.50 * 5.9484 + 1.00 * 0.0905                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2530      final r-factor (work) = 0.2343          |
| start r-factor (free) = 0.2836      final r-factor (free) = 0.2917          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5064 = 0.59 * 1.00 * 5.9484 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4362 = 0.59 * 1.00 * 5.7842 + 1.00 * 0.0327                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.664)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.96   17.04    None  None   None       |
|    all(noH): 2823   0      0.00    74.96   17.04    None  None   None       |
|    Sol.    : 438    0      4.41    64.58   37.94    None  None   None       |
|    Mac.    : 2385   0      0.00    74.96   13.20    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.496:  541   |   5:    37.479 -  44.975:  128        |
|      1:     7.496 -  14.992: 1090   |   6:    44.975 -  52.471:   87        |
|      2:    14.992 -  22.488:  573   |   7:    52.471 -  59.967:   54        |
|      3:    22.488 -  29.983:  201   |   8:    59.967 -  67.463:    8        |
|      4:    29.983 -  37.479:  140   |   9:    67.463 -  74.958:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2343 r_free = 0.2917             target_work(ml) = 5.795         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2340 r_free = 0.2922             target_work(ml) = 5.794         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2340   r_free= 0.2922   ksol= 0.34   Bsol= 50.00   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.24,-1.93,3.55,-0.00,0.00,0.00); trace/3= -0.54                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.793844                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2313   r_free= 0.2879   ksol= 0.34   Bsol= 50.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.93,-2.14,0.15,-0.00,0.00,0.00); trace/3= -1.64                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.785959                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.501033              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.746   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.357623              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.623   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2313      final r-factor (work) = 0.1665          |
| start r-factor (free) = 0.2879      final r-factor (free) = 0.2174          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2129 = 3.50 * 0.50 * 5.7826 + 1.00 * 0.0905                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9613 = 3.50 * 0.50 * 5.6559 + 1.00 * 0.0606                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1665      final r-factor (work) = 0.1527          |
| start r-factor (free) = 0.2174      final r-factor (free) = 0.2020          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1073 = 0.36 * 1.00 * 5.6559 + 1.00 * 0.0846                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9571 = 0.36 * 1.00 * 5.4490 + 1.00 * 0.0084                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.664)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.52    68.68   17.29    None  None   None       |
|    all(noH): 2823   0      1.52    68.68   17.29    None  None   None       |
|    Sol.    : 438    0      5.83    68.68   39.67    None  None   None       |
|    Mac.    : 2385   0      1.52    66.85   13.19    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:     1.517 -   8.233:  582   |   5:    35.099 -  41.815:  101        |
|      1:     8.233 -  14.950: 1190   |   6:    41.815 -  48.532:  108        |
|      2:    14.950 -  21.666:  427   |   7:    48.532 -  55.248:   86        |
|      3:    21.666 -  28.382:  156   |   8:    55.248 -  61.965:   44        |
|      4:    28.382 -  35.099:  109   |   9:    61.965 -  68.681:   20        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1527 r_free = 0.2020             target_work(ml) = 5.415         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1524 r_free = 0.2019             target_work(ml) = 5.414         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1524   r_free= 0.2019   ksol= 0.34   Bsol= 50.00   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.93,-2.14,0.15,-0.00,0.00,0.00); trace/3= -1.64                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.413919                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1520   r_free= 0.1999   ksol= 0.32   Bsol= 39.18   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.69,-2.16,-1.33,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.407229                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.233560              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.761  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.939340              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.758  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1520      final r-factor (work) = 0.1277          |
| start r-factor (free) = 0.1999      final r-factor (free) = 0.1713          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1440 = 2.23 * 0.50 * 5.4474 + 1.00 * 0.0604                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0073 = 2.23 * 0.50 * 5.3324 + 1.00 * 0.0522                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1277      final r-factor (work) = 0.1216          |
| start r-factor (free) = 0.1713      final r-factor (free) = 0.1679          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0173 = 0.94 * 1.00 * 5.3324 + 1.00 * 0.0083                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9221 = 0.94 * 1.00 * 5.2300 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.664)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.05   17.52    None  None   None       |
|    all(noH): 2823   0      0.00    84.05   17.52    None  None   None       |
|    Sol.    : 438    0      2.49    77.76   41.36    None  None   None       |
|    Mac.    : 2385   0      0.00    84.05   13.14    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.405:  635   |   5:    42.024 -  50.429:  123        |
|      1:     8.405 -  16.810: 1351   |   6:    50.429 -  58.834:   94        |
|      2:    16.810 -  25.215:  320   |   7:    58.834 -  67.239:   41        |
|      3:    25.215 -  33.620:  127   |   8:    67.239 -  75.644:   23        |
|      4:    33.620 -  42.024:  103   |   9:    75.644 -  84.049:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1216 r_free = 0.1679             target_work(ml) = 5.216         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1215 r_free = 0.1678             target_work(ml) = 5.215         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1215   r_free= 0.1678   ksol= 0.32   Bsol= 39.18   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.69,-2.16,-1.33,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.215102                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1214   r_free= 0.1675   ksol= 0.32   Bsol= 39.93   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.61,-2.17,-1.81,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.213811                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.589150              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 126.469  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.043157              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.056  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1214      final r-factor (work) = 0.1117          |
| start r-factor (free) = 0.1675      final r-factor (free) = 0.1585          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8219 = 2.59 * 0.50 * 5.2293 + 1.00 * 0.0522                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7663 = 2.59 * 0.50 * 5.1799 + 1.00 * 0.0606                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1117      final r-factor (work) = 0.1098          |
| start r-factor (free) = 0.1585      final r-factor (free) = 0.1587          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4127 = 1.04 * 1.00 * 5.1799 + 1.00 * 0.0093                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3740 = 1.04 * 1.00 * 5.1425 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.664)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.84   17.39    None  None   None       |
|    all(noH): 2823   0      0.00    96.84   17.39    None  None   None       |
|    Sol.    : 438    0      2.23    85.29   41.09    None  None   None       |
|    Mac.    : 2385   0      0.00    96.84   13.03    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 -   9.684:  950   |   5:    48.420 -  58.104:  105        |
|      1:     9.684 -  19.368: 1203   |   6:    58.104 -  67.788:   54        |
|      2:    19.368 -  29.052:  225   |   7:    67.788 -  77.472:   20        |
|      3:    29.052 -  38.736:  133   |   8:    77.472 -  87.156:   10        |
|      4:    38.736 -  48.420:  120   |   9:    87.156 -  96.840:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1098 r_free = 0.1587             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1098 r_free = 0.1586             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1098   r_free= 0.1586   ksol= 0.32   Bsol= 39.93   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.61,-2.17,-1.81,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.140548                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1101   r_free= 0.1586   ksol= 0.32   Bsol= 42.09   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,-2.05,-1.85,-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: 5.141188                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.431031              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 156.406  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.305465              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.952  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1101      final r-factor (work) = 0.1076          |
| start r-factor (free) = 0.1586      final r-factor (free) = 0.1585          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3116 = 2.43 * 0.50 * 5.1427 + 1.00 * 0.0606                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2981 = 2.43 * 0.50 * 5.1329 + 1.00 * 0.0590                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1076      final r-factor (work) = 0.1076          |
| start r-factor (free) = 0.1585      final r-factor (free) = 0.1574          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5774 = 0.31 * 1.00 * 5.1329 + 1.00 * 0.0095                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5761 = 0.31 * 1.00 * 5.1327 + 1.00 * 0.0083                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.664)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.81    97.07   16.89    None  None   None       |
|    all(noH): 2823   0      1.81    97.07   16.89    None  None   None       |
|    Sol.    : 438    0      4.20    81.54   39.14    None  None   None       |
|    Mac.    : 2385   0      1.81    97.07   12.81    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:     1.806 -  11.333: 1344   |   5:    49.438 -  58.965:   81        |
|      1:    11.333 -  20.859:  886   |   6:    58.965 -  68.491:   34        |
|      2:    20.859 -  30.386:  195   |   7:    68.491 -  78.018:   14        |
|      3:    30.386 -  39.912:  129   |   8:    78.018 -  87.544:    6        |
|      4:    39.912 -  49.438:  131   |   9:    87.544 -  97.071:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1076 r_free = 0.1574             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1075 r_free = 0.1574             target_work(ml) = 5.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1075   r_free= 0.1574   ksol= 0.32   Bsol= 42.09   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,-2.05,-1.85,-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: 5.129241                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8899 -  4.6581 0.99   1425  161 0.0947 0.1255      5.3448      5.5289|
|  2:  4.6581 -  3.7162 0.99   1370  145 0.0816 0.1079      5.3952      5.6221|
|  3:  3.7162 -  3.2520 0.99   1345  157 0.1011 0.1572      5.4352      5.8474|
|  4:  3.2520 -  2.9572 0.99   1347  147 0.1190 0.1514      5.4434      5.5875|
|  5:  2.9572 -  2.7467 0.98   1319  148 0.1237 0.1755      5.2863      5.4793|
|  6:  2.7467 -  2.5856 0.99   1335  143 0.1190 0.1879      5.1935      5.4408|
|  7:  2.5856 -  2.4567 0.99   1307  149 0.1169 0.1716      5.1243      5.3711|
|  8:  2.4567 -  2.3502 0.99   1312  144 0.1144 0.1696      5.0455      5.2655|
|  9:  2.3502 -  2.2601 0.99   1314  153 0.1132 0.1821      5.0037      5.3057|
| 10:  2.2601 -  2.1823 0.98   1309  141 0.1096 0.1722      4.9565      5.2181|
| 11:  2.1823 -  2.1143 0.98   1293  139 0.1113 0.1817      4.9173      5.2615|
| 12:  2.1143 -  2.0540 1.00   1293  149 0.1075 0.1681      4.8495      5.0876|
| 13:  2.0540 -  2.0001 0.95   1262  142 0.1116 0.1736      4.7646      4.9984|
| 14:  2.0001 -  1.9514 0.30    399   41 0.1024 0.1583       4.638      4.9115|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8899 -  4.6581  1425   161  0.94   8.52   0.98     0.96       6591.00|
|  2:  4.6581 -  3.7162  1370   145  0.95   7.83   1.02     1.01       8486.30|
|  3:  3.7162 -  3.2520  1345   157  0.94  11.06   1.03     1.02       9968.48|
|  4:  3.2520 -  2.9572  1347   147  0.92  13.98   1.01     0.99      10505.30|
|  5:  2.9572 -  2.7467  1319   148  0.90  15.91   0.99     0.97       8022.12|
|  6:  2.7467 -  2.5856  1335   143  0.90  15.87   0.99     0.96       6932.88|
|  7:  2.5856 -  2.4567  1307   149  0.91  14.85   0.99     0.96       5790.87|
|  8:  2.4567 -  2.3502  1312   144  0.91  15.55   1.00     0.97       5284.40|
|  9:  2.3502 -  2.2601  1314   153  0.91  15.60   1.00     0.97       4857.87|
| 10:  2.2601 -  2.1823  1309   141  0.91  15.33   1.00     0.97       4477.88|
| 11:  2.1823 -  2.1143  1293   139  0.90  16.31   1.00     0.97       4302.13|
| 12:  2.1143 -  2.0540  1293   149  0.91  15.22   1.00     0.99       3845.95|
| 13:  2.0540 -  2.0001  1262   142  0.90  16.31   1.00     0.99       3248.83|
| 14:  2.0001 -  1.9514   399    41  0.91  15.28   0.99     0.96       2528.04|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2528.04 max =        10505.30 mean =      6284.97|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.91 mean =        13.99|
|phase err.(test): min =        0.00 max =           89.65 mean =        13.57|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1075   r_free= 0.1574   ksol= 0.32   Bsol= 42.02   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-1.89,-1.73,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.129407                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1075   r_free= 0.1574   ksol= 0.32   Bsol= 42.02   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-1.89,-1.73,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.129407                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8899 -  4.6581 0.99   1425  161 0.0947 0.1255      5.3468      5.5304|
|  2:  4.6581 -  3.7162 0.99   1370  145 0.0816 0.1078      5.3951      5.6212|
|  3:  3.7162 -  3.2520 0.99   1345  157 0.1011 0.1572      5.4348      5.8473|
|  4:  3.2520 -  2.9572 0.99   1347  147 0.1190 0.1514      5.4434      5.5876|
|  5:  2.9572 -  2.7467 0.98   1319  148 0.1237 0.1755      5.2865      5.4793|
|  6:  2.7467 -  2.5856 0.99   1335  143 0.1190 0.1880      5.1938      5.4413|
|  7:  2.5856 -  2.4567 0.99   1307  149 0.1169 0.1716      5.1246      5.3714|
|  8:  2.4567 -  2.3502 0.99   1312  144 0.1144 0.1696      5.0457      5.2656|
|  9:  2.3502 -  2.2601 0.99   1314  153 0.1132 0.1820      5.0038      5.3055|
| 10:  2.2601 -  2.1823 0.98   1309  141 0.1096 0.1722      4.9565      5.2179|
| 11:  2.1823 -  2.1143 0.98   1293  139 0.1113 0.1816      4.9173      5.2616|
| 12:  2.1143 -  2.0540 1.00   1293  149 0.1075 0.1680      4.8492      5.0874|
| 13:  2.0540 -  2.0001 0.95   1262  142 0.1116 0.1735      4.7645       4.998|
| 14:  2.0001 -  1.9514 0.30    399   41 0.1024 0.1584      4.6381      4.9124|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8899 -  4.6581  1425   161  0.94   8.55   0.98     0.96       6628.82|
|  2:  4.6581 -  3.7162  1370   145  0.95   7.84   1.02     1.01       8499.74|
|  3:  3.7162 -  3.2520  1345   157  0.94  11.06   1.03     1.03       9959.28|
|  4:  3.2520 -  2.9572  1347   147  0.92  13.98   1.01     0.99      10503.60|
|  5:  2.9572 -  2.7467  1319   148  0.90  15.91   0.99     0.97       8025.19|
|  6:  2.7467 -  2.5856  1335   143  0.90  15.88   0.99     0.96       6936.86|
|  7:  2.5856 -  2.4567  1307   149  0.91  14.86   0.99     0.96       5794.47|
|  8:  2.4567 -  2.3502  1312   144  0.91  15.56   1.00     0.97       5285.06|
|  9:  2.3502 -  2.2601  1314   153  0.91  15.60   1.00     0.98       4857.51|
| 10:  2.2601 -  2.1823  1309   141  0.91  15.33   1.00     0.97       4476.73|
| 11:  2.1823 -  2.1143  1293   139  0.90  16.31   1.00     0.97       4301.48|
| 12:  2.1143 -  2.0540  1293   149  0.91  15.22   1.00     0.99       3843.65|
| 13:  2.0540 -  2.0001  1262   142  0.90  16.31   1.01     1.00       3248.56|
| 14:  2.0001 -  1.9514   399    41  0.91  15.28   1.00     0.97       2529.37|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2529.37 max =        10503.60 mean =      6288.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.99|
|phase err.(test): min =        0.00 max =           89.66 mean =        13.57|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.664)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.74    97.01   16.83    None  None   None       |
|    all(noH): 2823   0      1.74    97.01   16.83    None  None   None       |
|    Sol.    : 438    0      4.13    81.47   39.07    None  None   None       |
|    Mac.    : 2385   0      1.74    97.01   12.74    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.742 -  11.268: 1344   |   5:    49.374 -  58.900:   81        |
|      1:    11.268 -  20.794:  886   |   6:    58.900 -  68.427:   34        |
|      2:    20.794 -  30.321:  195   |   7:    68.427 -  77.953:   14        |
|      3:    30.321 -  39.847:  129   |   8:    77.953 -  87.479:    6        |
|      4:    39.847 -  49.374:  131   |   9:    87.479 -  97.006:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 320         
Filter by distance & map next to the model:
   mapped sites are within: 0.513 - 5.904
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 316 from: 320
   mapped sites are within: 0.719 - 5.904

peak=    5.475 closest distance to " NH2 ARG A  56 " =    2.132
peak=    5.426 closest distance to " CG  PRO A  54 " =    1.215
peak=    5.414 closest distance to " CB  GLN A 223 " =    1.456
peak=    5.411 closest distance to " CB  SER A  63 " =    1.170
peak=    5.226 closest distance to " O   HOH Z 126 " =    1.853
peak=    5.219 closest distance to " CG  PRO A 213 " =    1.206
peak=    4.985 closest distance to " CB  ARG A 275 " =    0.920
peak=    4.867 closest distance to " O   HOH Z 232 " =    2.277
peak=    4.821 closest distance to " O   HOH Z 144 " =    1.692
peak=    4.819 closest distance to " NE2 GLN A  11 " =    1.069
peak=    4.791 closest distance to " CG  PRO A  90 " =    1.108
peak=    4.671 closest distance to " CB  GLN A 183 " =    1.261
peak=    4.663 closest distance to " O   HOH Z 193 " =    1.842
peak=    4.659 closest distance to " O   HOH Z 236 " =    1.934
peak=    4.630 closest distance to " CB  PRO A  54 " =    0.911
peak=    4.627 closest distance to " CB  GLU A 152 " =    1.182
peak=    4.595 closest distance to " O   HOH Z 234 " =    3.707
peak=    4.560 closest distance to " C   PRO A 198 " =    1.517
peak=    4.539 closest distance to " CB  SER A   3 " =    1.366
peak=    4.484 closest distance to " CA  TYR A  30 " =    0.951
peak=    4.477 closest distance to " CB  ASN A 148 " =    1.543
peak=    4.454 closest distance to " OD1 ASN A  69 " =    2.627
peak=    4.445 closest distance to " O   HOH Z 124 " =    1.380
peak=    4.421 closest distance to " O   HOH Z 272 " =    1.859
peak=    4.410 closest distance to " O   HOH Z 389 " =    1.893
peak=    4.406 closest distance to " O   HOH Z 427 " =    2.796
peak=    4.338 closest distance to " O   HOH Z 209 " =    2.251
peak=    4.333 closest distance to " OD2 ASP A 286 " =    2.800
peak=    4.322 closest distance to " O   SER A  87 " =    2.203
peak=    4.303 closest distance to " ND2 ASN A 187 " =    1.623
peak=    4.254 closest distance to " CB  GLU A 128 " =    1.132
peak=    4.251 closest distance to " O   HOH Z 316 " =    2.942
peak=    4.249 closest distance to " CB  TYR A 169 " =    0.775
peak=    4.239 closest distance to " O   HOH Z 298 " =    1.859
peak=    4.237 closest distance to " O   HOH Z  78 " =    1.650
peak=    4.200 closest distance to " O   HOH Z  93 " =    2.476
peak=    4.187 closest distance to " O   HOH Z  15 " =    2.124
peak=    4.186 closest distance to " O   HOH Z 344 " =    2.964
peak=    4.182 closest distance to " O   HOH Z 352 " =    1.840
peak=    4.182 closest distance to " O   HOH Z 368 " =    1.965
peak=    4.180 closest distance to " CB  ARG A  79 " =    1.646
peak=    4.168 closest distance to " O   HOH Z 134 " =    1.448
peak=    4.167 closest distance to " CG  PRO A 198 " =    1.276
peak=    4.163 closest distance to " CB  TRP A 179 " =    1.298
peak=    4.151 closest distance to " O   HOH Z  97 " =    1.869
peak=    4.150 closest distance to " O   HOH Z 108 " =    1.383
peak=    4.086 closest distance to " O   HOH Z   6 " =    2.200
peak=    4.082 closest distance to " O   HOH Z 144 " =    2.284
peak=    4.070 closest distance to " CB  LEU A 228 " =    1.106
peak=    4.045 closest distance to " CB  VAL A 202 " =    1.660
peak=    4.039 closest distance to " O   HOH Z  54 " =    1.684
peak=    4.031 closest distance to " CA  ALA A  21 " =    1.125
peak=    4.024 closest distance to " O   HOH Z 426 " =    1.512
peak=    4.013 closest distance to " O   HOH Z 128 " =    2.105
peak=    3.989 closest distance to " O   HOH Z 207 " =    1.835
peak=    3.963 closest distance to " O   HOH Z 369 " =    1.905
peak=    3.944 closest distance to " NH2BARG A 145 " =    2.093
peak=    3.934 closest distance to " CA  THR A 221 " =    0.948
peak=    3.931 closest distance to " CD BLYS A 290 " =    1.176
peak=    3.921 closest distance to " O   HOH Z 371 " =    3.370
peak=    3.916 closest distance to " O   HOH Z  21 " =    1.681
peak=    3.904 closest distance to " CG  PRO A 243 " =    1.161
peak=    3.904 closest distance to " O   HOH Z 132 " =    2.243
peak=    3.894 closest distance to " O   HOH Z  44 " =    1.843
peak=    3.890 closest distance to " O   HOH Z 303 " =    1.930
peak=    3.889 closest distance to " O   HOH Z  10 " =    1.875
peak=    3.887 closest distance to " O   HOH Z 346 " =    1.654
peak=    3.886 closest distance to " CG1 ILE A  33 " =    1.299
peak=    3.882 closest distance to " O   HOH Z 278 " =    0.993
peak=    3.881 closest distance to " O   HOH Z 193 " =    2.049
peak=    3.868 closest distance to " O   HOH Z 279 " =    2.174
peak=    3.865 closest distance to " CG  ARG A  66 " =    2.467
peak=    3.863 closest distance to " CB  GLU A 277 " =    3.512
peak=    3.846 closest distance to " O   HOH Z  88 " =    3.266
peak=    3.838 closest distance to " O   HOH Z 284 " =    2.905
peak=    3.836 closest distance to " O   HOH Z 326 " =    1.530
peak=    3.835 closest distance to " NZ  LYS A 117 " =    3.293
peak=    3.796 closest distance to " NH1AARG A 145 " =    1.051
peak=    3.792 closest distance to " O   HOH Z 183 " =    1.514
peak=    3.791 closest distance to " O   HOH Z 214 " =    2.062
peak=    3.789 closest distance to " O   HOH Z 133 " =    1.490
peak=    3.787 closest distance to " O   HOH Z  59 " =    2.151
peak=    3.786 closest distance to " O   HOH Z  43 " =    2.053
peak=    3.784 closest distance to " O   HOH Z  49 " =    2.157
peak=    3.782 closest distance to " O   HOH Z 128 " =    2.223
peak=    3.770 closest distance to " O   MET A 105 " =    1.763
peak=    3.764 closest distance to " O   HOH Z 197 " =    2.791
peak=    3.764 closest distance to " CB  ARG A 139 " =    0.897
peak=    3.761 closest distance to " O   HOH Z  40 " =    1.475
peak=    3.760 closest distance to " O   HOH Z 132 " =    2.591
peak=    3.758 closest distance to " CA  ASN A 215 " =    1.196
peak=    3.749 closest distance to " O   HOH Z 189 " =    1.786
peak=    3.746 closest distance to " OG BSER A 164 " =    2.502
peak=    3.744 closest distance to " O   HOH Z 423 " =    1.974
peak=    3.743 closest distance to " O   HOH Z 180 " =    2.219
peak=    3.741 closest distance to " O   HOH Z  61 " =    1.632
peak=    3.734 closest distance to " O   HOH Z 334 " =    1.489
peak=    3.731 closest distance to " O   HOH Z 313 " =    1.756
peak=    3.716 closest distance to " O   HOH Z 250 " =    1.375
peak=    3.712 closest distance to " CB  ARG A 190 " =    1.737
peak=    3.697 closest distance to " O   HOH Z  48 " =    1.371
peak=    3.694 closest distance to " O   HOH Z 173 " =    1.907
peak=    3.686 closest distance to " NH2 ARG A 156 " =    1.186
peak=    3.680 closest distance to " O   HOH Z 374 " =    2.521
peak=    3.680 closest distance to " O   HOH Z 411 " =    3.752
peak=    3.675 closest distance to " O   HOH Z 345 " =    3.216
peak=    3.669 closest distance to " O   HOH Z  68 " =    1.613
peak=    3.641 closest distance to " O   ALA A 165 " =    1.365
peak=    3.636 closest distance to " O   HOH Z 403 " =    1.700
peak=    3.634 closest distance to " O   HOH Z 406 " =    1.735
peak=    3.624 closest distance to " CD  LYS A 119 " =    1.246
peak=    3.622 closest distance to " O   HOH Z   3 " =    1.638
peak=    3.612 closest distance to " O   HOH Z 273 " =    2.754
peak=    3.589 closest distance to " CA  ASP A 140 " =    1.099
peak=    3.588 closest distance to " CB  VAL A 265 " =    1.207
peak=    3.585 closest distance to " CG1BVAL A  72 " =    1.571
peak=    3.584 closest distance to " O   HOH Z 427 " =    3.039
peak=    3.579 closest distance to " CG2BVAL A  41 " =    0.763
peak=    3.579 closest distance to " O   HOH Z 327 " =    1.749
peak=    3.578 closest distance to " O   HOH Z  61 " =    1.593
peak=    3.575 closest distance to " N   ASN A  39 " =    1.261
peak=    3.574 closest distance to " CA  ASN A 176 " =    1.169
peak=    3.570 closest distance to " O   HOH Z 213 " =    1.739
peak=    3.569 closest distance to " O   HOH Z 108 " =    1.985
peak=    3.566 closest distance to " O   HOH Z 295 " =    1.458
peak=    3.564 closest distance to " O   HOH Z 172 " =    3.855
peak=    3.563 closest distance to " O   HOH Z 158 " =    3.099
peak=    3.559 closest distance to " CB  SER A 141 " =    1.083
peak=    3.557 closest distance to " O   ALA A   1 " =    1.487
peak=    3.556 closest distance to " CA  ALA A 291 " =    0.952
peak=    3.555 closest distance to " CG  LEU A 167 " =    1.169
peak=    3.553 closest distance to " CA  MET A  40 " =    1.037
peak=    3.551 closest distance to " CG2 ILE A 120 " =    1.222
peak=    3.550 closest distance to " O   HOH Z 368 " =    3.713
peak=    3.547 closest distance to " CA  ALA A 248 " =    1.358
peak=    3.545 closest distance to " CD  ARG A 159 " =    0.774
peak=    3.544 closest distance to " NH2AARG A 190 " =    1.305
peak=    3.538 closest distance to " O   HOH Z 260 " =    1.148
peak=    3.537 closest distance to " O   HOH Z  63 " =    1.978
peak=    3.533 closest distance to " CA  ARG A  36 " =    1.082
peak=    3.529 closest distance to " N   ARG A 156 " =    1.351
peak=    3.527 closest distance to " CD  ARG A 269 " =    0.980
peak=    3.525 closest distance to " CD2 LEU A 255 " =    1.174
peak=    3.522 closest distance to " O   HOH Z 403 " =    1.383
peak=    3.518 closest distance to " CA  THR A 264 " =    0.875
peak=    3.508 closest distance to " CD1 LEU A 300 " =    1.228
peak=    3.494 closest distance to " O   HOH Z 281 " =    4.356
peak=    3.492 closest distance to " O   HOH Z 135 " =    1.706
peak=    3.492 closest distance to " CD2 LEU A 297 " =    0.986
peak=    3.492 closest distance to " CD  LYS A 166 " =    1.312
peak=    3.490 closest distance to " O   HOH Z 227 " =    1.633
peak=    3.487 closest distance to " O   HOH Z 407 " =    2.740
peak=    3.465 closest distance to " O   HOH Z  20 " =    2.258
peak=    3.464 closest distance to " O   HOH Z 402 " =    1.444
peak=    3.462 closest distance to " O   HOH Z 132 " =    0.867
peak=    3.456 closest distance to " CG2 THR A 221 " =    1.072
peak=    3.448 closest distance to " O   HOH Z  19 " =    2.348
peak=    3.446 closest distance to " O   TRP A 274 " =    1.860
peak=    3.433 closest distance to " CB  MET A  47 " =    1.062
peak=    3.428 closest distance to " O   HOH Z 411 " =    1.777
peak=    3.428 closest distance to " CG AARG A 275 " =    0.950
peak=    3.428 closest distance to " O   HOH Z 291 " =    1.477
peak=    3.427 closest distance to " CA  ALA A  51 " =    0.858
peak=    3.427 closest distance to " CA  VAL A 126 " =    1.091
peak=    3.421 closest distance to " CB  TRP A 266 " =    0.919
peak=    3.420 closest distance to " O   HOH Z 267 " =    2.116
peak=    3.419 closest distance to " O   HOH Z 299 " =    4.330
peak=    3.413 closest distance to " CB  SER A  62 " =    1.271
peak=    3.411 closest distance to " CG  MET A 185 " =    1.218
peak=    3.408 closest distance to " CG  MET A 185 " =    1.073
peak=    3.405 closest distance to " O   HOH Z 263 " =    2.251
peak=    3.404 closest distance to " CE1 TYR A 186 " =    1.246
peak=    3.395 closest distance to " O   HOH Z 163 " =    1.874
peak=    3.394 closest distance to " CD1 ILE A 106 " =    0.977
peak=    3.392 closest distance to " O   HOH Z 248 " =    1.562
peak=    3.385 closest distance to " OD1 ASP A 231 " =    1.903
peak=    3.385 closest distance to " CA  ALA A 233 " =    1.331
peak=    3.385 closest distance to " OG  SER A  22 " =    2.686
peak=    3.383 closest distance to " NZ  LYS A  76 " =    1.179
peak=    3.382 closest distance to " CZ2 TRP A 179 " =    1.696
peak=    3.377 closest distance to " O   HOH Z 106 " =    2.277
peak=    3.374 closest distance to " O   HOH Z 353 " =    2.636
peak=    3.374 closest distance to " O   HOH Z 366 " =    3.026
peak=    3.369 closest distance to " CA  ASP A 191 " =    0.934
peak=    3.363 closest distance to " OE1 GLU A 277 " =    1.960
peak=    3.363 closest distance to " CB  PRO A 198 " =    0.969
peak=    3.362 closest distance to " O   HOH Z 227 " =    2.202
peak=    3.353 closest distance to " O   HOH Z 247 " =    1.225
peak=    3.349 closest distance to " O   HOH Z 147 " =    1.690
peak=    3.349 closest distance to " O   HOH Z 261 " =    1.515
peak=    3.345 closest distance to " NH2 ARG A 219 " =    1.898
peak=    3.343 closest distance to " O   HOH Z   1 " =    1.970
peak=    3.334 closest distance to " CG2 ILE A  20 " =    1.393
peak=    3.334 closest distance to " CG  GLN A  77 " =    1.873
peak=    3.332 closest distance to " O   HOH Z 291 " =    1.842
peak=    3.329 closest distance to " O   HOH Z 171 " =    2.394
peak=    3.328 closest distance to " CA  ILE A  33 " =    1.598
peak=    3.324 closest distance to " N   ASN A 127 " =    1.241
peak=    3.319 closest distance to " O   HOH Z 211 " =    2.391
peak=    3.316 closest distance to " O   HOH Z 368 " =    2.568
peak=    3.301 closest distance to " CG  GLU A 277 " =    2.177
peak=    3.301 closest distance to " O   HOH Z  71 " =    1.081
peak=    3.301 closest distance to " NH1BARG A 145 " =    1.187
peak=    3.299 closest distance to " ND1 HIS A  81 " =    1.542
peak=    3.294 closest distance to " CA  LYS A 117 " =    1.226
peak=    3.292 closest distance to " O   HOH Z 276 " =    1.287
peak=    3.289 closest distance to " CB  SER A 212 " =    1.073
peak=    3.288 closest distance to " CG1 VAL A 202 " =    1.998
peak=    3.286 closest distance to " CB  PHE A  16 " =    0.986
peak=    3.277 closest distance to " O   SER A 164 " =    1.254
peak=    3.275 closest distance to " O   HOH Z  14 " =    2.251
peak=    3.274 closest distance to " CB  SER A 216 " =    0.766
peak=    3.274 closest distance to " O   HOH Z  59 " =    2.203
peak=    3.268 closest distance to " CB  LEU A 255 " =    0.719
peak=    3.267 closest distance to " CD2 TRP A 179 " =    1.364
peak=    3.266 closest distance to " CZ  PHE A 218 " =    1.000
peak=    3.266 closest distance to " CG  MET A 113 " =    1.262
peak=    3.265 closest distance to " O   HOH Z 175 " =    2.159
peak=    3.262 closest distance to " O   HOH Z 227 " =    1.620
peak=    3.262 closest distance to " O   HOH Z  80 " =    1.638
peak=    3.261 closest distance to " O   HOH Z 189 " =    1.373
peak=    3.261 closest distance to " CB  ALA A   1 " =    1.164
peak=    3.260 closest distance to " O   HOH Z 337 " =    3.654
peak=    3.260 closest distance to " CG2 VAL A 257 " =    0.902
peak=    3.258 closest distance to " O   HOH Z 409 " =    3.197
peak=    3.258 closest distance to " O   HOH Z 287 " =    2.253
peak=    3.258 closest distance to " CA  ALA A  84 " =    1.321
peak=    3.255 closest distance to " O   HOH Z 392 " =    1.776
peak=    3.254 closest distance to " CB  ASP A 140 " =    0.829
peak=    3.252 closest distance to " O   HOH Z 214 " =    2.346
peak=    3.251 closest distance to " O   HOH Z 116 " =    1.830
peak=    3.249 closest distance to " CG  GLN A  58 " =    2.580
peak=    3.247 closest distance to " CB  SER A  26 " =    1.561
peak=    3.247 closest distance to " O   HOH Z 163 " =    1.652
peak=    3.246 closest distance to " O   HOH Z 437 " =    1.764
peak=    3.243 closest distance to " OG BSER A 258 " =    3.304
peak=    3.240 closest distance to " O   HOH Z  49 " =    2.442
peak=    3.238 closest distance to " O   HOH Z 263 " =    1.766
peak=    3.237 closest distance to " O   HOH Z 425 " =    1.914
peak=    3.235 closest distance to " OG  SER A  62 " =    3.027
peak=    3.232 closest distance to " O   HOH Z 438 " =    1.883
peak=    3.232 closest distance to " CB  GLU A 152 " =    1.524
peak=    3.229 closest distance to " O   HOH Z 125 " =    2.250
peak=    3.223 closest distance to " O   ALA A   1 " =    1.650
peak=    3.221 closest distance to " O   HOH Z 329 " =    3.488
peak=    3.220 closest distance to " ND2 ASN A 301 " =    1.272
peak=    3.219 closest distance to " O   HOH Z 106 " =    2.238
peak=    3.219 closest distance to " O   HOH Z 286 " =    2.153
peak=    3.218 closest distance to " O   HOH Z 265 " =    2.341
peak=    3.213 closest distance to " O   ALA A 158 " =    1.252
peak=    3.213 closest distance to " CB  GLU A  46 " =    1.025
peak=    3.213 closest distance to " CG2 VAL A  78 " =    0.914
peak=    3.209 closest distance to " O   HOH Z 345 " =    1.669
peak=    3.207 closest distance to " O   SER A  26 " =    1.703
peak=    3.204 closest distance to " O   HOH Z 357 " =    1.912
peak=    3.201 closest distance to " C   TYR A 214 " =    1.450
peak=    3.198 closest distance to " OE1 GLN A  11 " =    1.891
peak=    3.191 closest distance to " CB  ASN A  39 " =    0.856
peak=    3.191 closest distance to " CD  PRO A 243 " =    1.409
peak=    3.190 closest distance to " O   HOH Z 425 " =    1.266
peak=    3.190 closest distance to " O   HOH Z 266 " =    2.822
peak=    3.190 closest distance to " O   HOH Z 261 " =    1.924
peak=    3.188 closest distance to " O   HOH Z 245 " =    1.339
peak=    3.188 closest distance to " O   HOH Z 409 " =    3.565
peak=    3.188 closest distance to " CB  ALA A 291 " =    1.340
peak=    3.186 closest distance to " O   HOH Z 166 " =    3.644
peak=    3.183 closest distance to " O   HOH Z 151 " =    1.912
peak=    3.182 closest distance to " O   GLY A  91 " =    1.511
peak=    3.176 closest distance to " O   HOH Z 367 " =    3.505
peak=    3.175 closest distance to " CE BMET A  47 " =    1.537
peak=    3.171 closest distance to " O   HOH Z 271 " =    2.161
peak=    3.166 closest distance to " OD1 ASP A 286 " =    1.484
peak=    3.163 closest distance to " O   HOH Z 234 " =    1.757
peak=    3.162 closest distance to " OD1 ASP A 238 " =    0.891
peak=    3.160 closest distance to " CG1 ILE A 151 " =    0.937
peak=    3.159 closest distance to " O   HOH Z 250 " =    1.654
peak=    3.156 closest distance to " CB  LEU A 143 " =    1.071
peak=    3.150 closest distance to " O   HOH Z 380 " =    1.968
peak=    3.145 closest distance to " O   HOH Z  35 " =    2.601
peak=    3.145 closest distance to " O   HOH Z 192 " =    1.963
peak=    3.144 closest distance to " O   HOH Z 422 " =    2.694
peak=    3.143 closest distance to " N   SER A 135 " =    1.336
peak=    3.143 closest distance to " O   HOH Z 341 " =    1.765
peak=    3.140 closest distance to " CG  MET A  93 " =    0.931
peak=    3.140 closest distance to " CG  GLN A  89 " =    1.477
peak=    3.139 closest distance to " O   HOH Z 388 " =    1.871
peak=    3.136 closest distance to " CA  SER A  87 " =    0.922
peak=    3.130 closest distance to " O   HOH Z 126 " =    1.596
peak=    3.128 closest distance to " O   HOH Z  66 " =    2.101
peak=    3.125 closest distance to " C   ALA A 299 " =    0.919
peak=    3.124 closest distance to " CB  THR A 294 " =    1.677
peak=    3.120 closest distance to " OG BSER A  99 " =    2.136
peak=    3.118 closest distance to " CA  GLY A 211 " =    1.196
peak=    3.117 closest distance to " CA  ALA A 158 " =    1.124
peak=    3.117 closest distance to " O   HOH Z 368 " =    2.498
peak=    3.117 closest distance to " CA  ALA A  43 " =    1.241
peak=    3.115 closest distance to " CG  LYS A  76 " =    1.019
peak=    3.100 closest distance to " CB  ARG A 102 " =    0.737
peak=    3.098 closest distance to " O   THR A  31 " =    1.592
peak=    3.095 closest distance to " O   HOH Z  53 " =    1.531
peak=    3.091 closest distance to " O   HOH Z  73 " =    1.448
peak=    3.088 closest distance to " O   HOH Z 387 " =    2.783
peak=    3.088 closest distance to " OG  SER A 206 " =    1.310
peak=    3.075 closest distance to " CD2 HIS A  81 " =    1.169
peak=    3.073 closest distance to " O   HOH Z 106 " =    1.852
peak=    3.069 closest distance to " O   HOH Z  40 " =    2.962
peak=    3.068 closest distance to " O   HOH Z 215 " =    1.492
peak=    3.053 closest distance to " CG1 ILE A 120 " =    1.149
peak=    3.046 closest distance to " CD  GLN A  58 " =    5.904
peak=    3.046 closest distance to " O   HOH Z 148 " =    3.056
peak=    3.041 closest distance to " O   HOH Z   4 " =    1.883
peak=    3.041 closest distance to " CB  ASN A 215 " =    1.090
peak=    3.029 closest distance to " O   HOH Z  85 " =    2.052
peak=    3.029 closest distance to " O   HOH Z 438 " =    2.524
peak=    3.028 closest distance to " O  BHOH Z  74 " =    1.306
peak=    3.001 closest distance to " O   HOH Z 134 " =    3.340

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.779 - 5.251
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 206
   mapped sites are within: 0.779 - 5.251

peak=   -4.621 closest distance to " O   HOH Z 266 " =    4.182
peak=   -4.402 closest distance to " CB  ALA A 161 " =    2.576
peak=   -4.344 closest distance to " O   HOH Z 372 " =    2.365
peak=   -4.306 closest distance to " CB  PRO A 243 " =    2.574
peak=   -4.226 closest distance to " N   GLN A  58 " =    1.747
peak=   -4.225 closest distance to " O   HOH Z 377 " =    1.919
peak=   -4.201 closest distance to " CD  ARG A 156 " =    1.984
peak=   -4.126 closest distance to " C   HIS A 108 " =    1.079
peak=   -4.098 closest distance to " OXT GLY A 302 " =    2.777
peak=   -4.091 closest distance to " SG  CYS A 254 " =    3.313
peak=   -4.074 closest distance to " O   HOH Z 198 " =    2.209
peak=   -4.059 closest distance to " O   HOH Z 290 " =    1.053
peak=   -4.025 closest distance to " O   VAL A  67 " =    2.787
peak=   -4.008 closest distance to " O   HOH Z 126 " =    1.915
peak=   -3.968 closest distance to " O   PRO A 163 " =    2.033
peak=   -3.957 closest distance to " O   HOH Z  13 " =    1.454
peak=   -3.933 closest distance to " OE1 GLN A 223 " =    2.104
peak=   -3.903 closest distance to " O   SER A 210 " =    1.917
peak=   -3.890 closest distance to " O   HOH Z 388 " =    2.009
peak=   -3.887 closest distance to " CA  VAL A  67 " =    2.773
peak=   -3.860 closest distance to " OG  SER A  97 " =    2.131
peak=   -3.854 closest distance to " O   PRO A 198 " =    1.306
peak=   -3.847 closest distance to " ND2 ASN A  45 " =    0.928
peak=   -3.842 closest distance to " C   ALA A 158 " =    1.221
peak=   -3.836 closest distance to " CD  ARG A 139 " =    1.601
peak=   -3.832 closest distance to " O   HOH Z 118 " =    2.904
peak=   -3.828 closest distance to " O   HOH Z  10 " =    1.487
peak=   -3.822 closest distance to " O   HOH Z  11 " =    1.880
peak=   -3.804 closest distance to " CB  TYR A  15 " =    2.173
peak=   -3.802 closest distance to " O   HOH Z 231 " =    2.130
peak=   -3.799 closest distance to " CD1 LEU A 228 " =    2.238
peak=   -3.788 closest distance to " O   HOH Z 407 " =    3.100
peak=   -3.786 closest distance to " O   HOH Z 353 " =    2.247
peak=   -3.780 closest distance to " N   ALA A  43 " =    2.479
peak=   -3.766 closest distance to " O   HOH Z  52 " =    1.387
peak=   -3.766 closest distance to " CZ  TYR A 169 " =    1.760
peak=   -3.744 closest distance to " CZ3 TRP A 179 " =    1.326
peak=   -3.741 closest distance to " O   VAL A 153 " =    2.295
peak=   -3.734 closest distance to " NH2 ARG A  79 " =    1.869
peak=   -3.731 closest distance to " OG BSER A 134 " =    1.238
peak=   -3.730 closest distance to " O   HOH Z 102 " =    1.706
peak=   -3.726 closest distance to " CE2 TYR A  30 " =    2.832
peak=   -3.720 closest distance to " CD1 PHE A  59 " =    1.831
peak=   -3.711 closest distance to " CD2 LEU A 237 " =    2.628
peak=   -3.707 closest distance to " OG ASER A 134 " =    1.286
peak=   -3.698 closest distance to " O   HOH Z 292 " =    4.522
peak=   -3.688 closest distance to " CD2 LEU A 300 " =    2.896
peak=   -3.686 closest distance to " CZ  PHE A  59 " =    1.617
peak=   -3.653 closest distance to " CB  ASN A  39 " =    2.209
peak=   -3.638 closest distance to " O   HOH Z  43 " =    1.628
peak=   -3.638 closest distance to " N   ASP A 286 " =    2.425
peak=   -3.634 closest distance to " CG  ASP A  50 " =    2.561
peak=   -3.629 closest distance to " OE2 GLU A   2 " =    1.916
peak=   -3.613 closest distance to " CB  ALA A 291 " =    2.424
peak=   -3.599 closest distance to " O   HOH Z  93 " =    1.582
peak=   -3.591 closest distance to " N   ALA A 248 " =    1.642
peak=   -3.589 closest distance to " CD  LYS A 289 " =    2.550
peak=   -3.584 closest distance to " O   SER A 135 " =    1.594
peak=   -3.580 closest distance to " O   GLY A 196 " =    1.028
peak=   -3.573 closest distance to " O   HOH Z  19 " =    2.287
peak=   -3.565 closest distance to " O   HOH Z 166 " =    1.455
peak=   -3.560 closest distance to " NE2 GLN A  58 " =    1.151
peak=   -3.556 closest distance to " O   HOH Z  11 " =    1.846
peak=   -3.546 closest distance to " NH2 ARG A  66 " =    4.901
peak=   -3.543 closest distance to " O   HOH Z 234 " =    4.093
peak=   -3.541 closest distance to " OG BSER A 134 " =    1.757
peak=   -3.536 closest distance to " CG  ASP A 231 " =    0.779
peak=   -3.533 closest distance to " CD1 LEU A 101 " =    2.478
peak=   -3.519 closest distance to " C   LEU A 143 " =    1.196
peak=   -3.518 closest distance to " O   ASP A 231 " =    2.523
peak=   -3.511 closest distance to " ND2 ASN A 187 " =    1.482
peak=   -3.506 closest distance to " O   HOH Z 185 " =    2.262
peak=   -3.503 closest distance to " O   VAL A 174 " =    2.076
peak=   -3.491 closest distance to " CG  GLU A  53 " =    1.437
peak=   -3.489 closest distance to " CG  PHE A 283 " =    2.668
peak=   -3.489 closest distance to " CE  MET A 105 " =    2.025
peak=   -3.487 closest distance to " N   SER A 276 " =    1.325
peak=   -3.486 closest distance to " O   HOH Z 435 " =    2.650
peak=   -3.482 closest distance to " O   HOH Z 351 " =    1.473
peak=   -3.480 closest distance to " NH1 ARG A 195 " =    2.582
peak=   -3.480 closest distance to " O   HOH Z 166 " =    1.778
peak=   -3.469 closest distance to " CB  ASP A 132 " =    2.301
peak=   -3.462 closest distance to " OD1 ASN A 148 " =    1.695
peak=   -3.461 closest distance to " O   HOH Z 395 " =    5.124
peak=   -3.459 closest distance to " NH2AARG A 275 " =    5.251
peak=   -3.448 closest distance to " O   HOH Z  76 " =    1.935
peak=   -3.444 closest distance to " O   HOH Z 283 " =    1.763
peak=   -3.440 closest distance to " OG  SER A   3 " =    1.776
peak=   -3.435 closest distance to " CD2 LEU A 237 " =    2.406
peak=   -3.431 closest distance to " O   HOH Z 311 " =    3.390
peak=   -3.420 closest distance to " O   HOH Z 385 " =    2.062
peak=   -3.414 closest distance to " OG  SER A  62 " =    1.548
peak=   -3.413 closest distance to " CB  CYS A 201 " =    2.608
peak=   -3.410 closest distance to " O   HOH Z  97 " =    1.710
peak=   -3.408 closest distance to " O   HOH Z 222 " =    1.120
peak=   -3.403 closest distance to " O   HOH Z 148 " =    3.352
peak=   -3.400 closest distance to " O   HOH Z  38 " =    1.575
peak=   -3.397 closest distance to " CE2 PHE A 218 " =    2.509
peak=   -3.394 closest distance to " OXT GLY A 302 " =    3.148
peak=   -3.391 closest distance to " OE1 GLN A  88 " =    1.243
peak=   -3.388 closest distance to " O   ALA A 161 " =    1.688
peak=   -3.387 closest distance to " O   HOH Z 427 " =    1.347
peak=   -3.385 closest distance to " CD1 ILE A 239 " =    2.552
peak=   -3.383 closest distance to " O   HOH Z  24 " =    1.492
peak=   -3.379 closest distance to " O   TRP A  92 " =    1.725
peak=   -3.374 closest distance to " CD1 ILE A 239 " =    1.990
peak=   -3.372 closest distance to " O   HOH Z  15 " =    1.598
peak=   -3.371 closest distance to " OD1 ASP A 191 " =    1.629
peak=   -3.370 closest distance to " OE1 GLN A  77 " =    1.792
peak=   -3.362 closest distance to " CD  GLN A  88 " =    1.860
peak=   -3.361 closest distance to " CB  ALA A  51 " =    1.814
peak=   -3.352 closest distance to " N   THR A 157 " =    1.577
peak=   -3.348 closest distance to " CE3 TRP A 150 " =    1.936
peak=   -3.345 closest distance to " O   HOH Z 417 " =    2.485
peak=   -3.341 closest distance to " N   ALA A 226 " =    2.016
peak=   -3.329 closest distance to " CG  LEU A  83 " =    1.918
peak=   -3.320 closest distance to " OG  SER A  87 " =    1.312
peak=   -3.320 closest distance to " O   HOH Z 436 " =    1.441
peak=   -3.309 closest distance to " CA  TYR A  68 " =    2.886
peak=   -3.308 closest distance to " O   PRO A 198 " =    1.245
peak=   -3.306 closest distance to " CG1 VAL A 112 " =    2.782
peak=   -3.304 closest distance to " CE3 TRP A 274 " =    2.476
peak=   -3.299 closest distance to " O   HOH Z  63 " =    1.322
peak=   -3.295 closest distance to " N   GLN A 122 " =    1.524
peak=   -3.291 closest distance to " CE  MET A  93 " =    1.180
peak=   -3.290 closest distance to " O   HOH Z 423 " =    2.243
peak=   -3.290 closest distance to " N   HIS A 115 " =    2.012
peak=   -3.286 closest distance to " O   HOH Z 281 " =    2.737
peak=   -3.283 closest distance to " CB  PHE A 192 " =    1.901
peak=   -3.272 closest distance to " O   HOH Z 198 " =    1.490
peak=   -3.269 closest distance to " O   HOH Z  98 " =    1.940
peak=   -3.263 closest distance to " CG2 ILE A 263 " =    2.227
peak=   -3.261 closest distance to " O   HOH Z 407 " =    3.546
peak=   -3.257 closest distance to " O   ALA A  34 " =    2.635
peak=   -3.257 closest distance to " N   VAL A 189 " =    1.663
peak=   -3.256 closest distance to " O   LYS A 117 " =    1.607
peak=   -3.248 closest distance to " CE2 TYR A 186 " =    2.156
peak=   -3.248 closest distance to " O   ALA A 160 " =    1.495
peak=   -3.243 closest distance to " CG  PRO A 163 " =    2.513
peak=   -3.242 closest distance to " CB  ALA A 248 " =    1.951
peak=   -3.242 closest distance to " CB  CYS A 254 " =    2.410
peak=   -3.242 closest distance to " O   ALA A 292 " =    1.930
peak=   -3.241 closest distance to " N   GLN A  58 " =    1.330
peak=   -3.238 closest distance to " O   MET A  40 " =    2.822
peak=   -3.238 closest distance to " CB  ALA A 100 " =    2.581
peak=   -3.236 closest distance to " O   HOH Z 210 " =    0.983
peak=   -3.231 closest distance to " SG ACYS A 201 " =    1.995
peak=   -3.229 closest distance to " O   HOH Z 263 " =    2.950
peak=   -3.226 closest distance to " CA  TRP A  70 " =    2.533
peak=   -3.224 closest distance to " NH2 ARG A  66 " =    2.014
peak=   -3.224 closest distance to " ND2 ASN A 209 " =    1.770
peak=   -3.222 closest distance to " OD2 ASP A 171 " =    2.283
peak=   -3.221 closest distance to " CA  GLY A 133 " =    1.906
peak=   -3.220 closest distance to " O   HOH Z  60 " =    1.989
peak=   -3.217 closest distance to " CG  ARG A  66 " =    2.468
peak=   -3.216 closest distance to " O   HOH Z 211 " =    1.756
peak=   -3.211 closest distance to " O   HOH Z 396 " =    1.593
peak=   -3.210 closest distance to " CG2 VAL A 189 " =    2.115
peak=   -3.208 closest distance to " O   PHE A 218 " =    1.560
peak=   -3.208 closest distance to " OG BSER A 210 " =    2.049
peak=   -3.201 closest distance to " OG1 THR A 178 " =    1.219
peak=   -3.196 closest distance to " O   HOH Z 348 " =    2.219
peak=   -3.195 closest distance to " CA  TRP A 274 " =    1.580
peak=   -3.190 closest distance to " O   HOH Z  47 " =    1.436
peak=   -3.185 closest distance to " CG  GLU A 277 " =    1.154
peak=   -3.185 closest distance to " ND2 ASN A 249 " =    2.178
peak=   -3.182 closest distance to " O   HOH Z  71 " =    1.345
peak=   -3.182 closest distance to " O   HOH Z 165 " =    1.954
peak=   -3.176 closest distance to " O   HOH Z 298 " =    1.213
peak=   -3.173 closest distance to " OD1 ASP A 171 " =    1.617
peak=   -3.171 closest distance to " O   HOH Z 361 " =    3.413
peak=   -3.169 closest distance to " ND2 ASN A  39 " =    1.405
peak=   -3.167 closest distance to " CE  LYS A  76 " =    2.801
peak=   -3.166 closest distance to " CA  ASP A 298 " =    1.064
peak=   -3.166 closest distance to " CB  ASP A 132 " =    2.352
peak=   -3.164 closest distance to " N   ALA A 248 " =    2.629
peak=   -3.163 closest distance to " OD1 ASN A 249 " =    1.281
peak=   -3.152 closest distance to " CG  GLN A 278 " =    2.211
peak=   -3.149 closest distance to " CG  ASN A 301 " =    2.050
peak=   -3.147 closest distance to " O   HOH Z 377 " =    1.379
peak=   -3.147 closest distance to " OD1 ASP A 200 " =    1.316
peak=   -3.146 closest distance to " CG  GLU A 152 " =    0.865
peak=   -3.133 closest distance to " O   ALA A   1 " =    1.836
peak=   -3.127 closest distance to " CG  TRP A 266 " =    1.681
peak=   -3.126 closest distance to " O   ALA A  51 " =    1.398
peak=   -3.121 closest distance to " OD2 ASP A 171 " =    1.648
peak=   -3.121 closest distance to " O   HOH Z  88 " =    2.427
peak=   -3.120 closest distance to " CG  GLU A 152 " =    2.017
peak=   -3.114 closest distance to " CD  GLN A  88 " =    0.958
peak=   -3.112 closest distance to " O   HOH Z 153 " =    2.397
peak=   -3.112 closest distance to " O   HOH Z 244 " =    1.862
peak=   -3.108 closest distance to " CG  ARG A 269 " =    2.311
peak=   -3.104 closest distance to " O   HOH Z 323 " =    1.338
peak=   -3.097 closest distance to " O   HOH Z 371 " =    1.853
peak=   -3.090 closest distance to " CD2 TYR A 293 " =    2.105
peak=   -3.083 closest distance to " CG  ARG A 259 " =    2.877
peak=   -3.077 closest distance to " O   HOH Z 295 " =    1.417
peak=   -3.073 closest distance to " CB  SER A 245 " =    2.470
peak=   -3.070 closest distance to " O   HOH Z 378 " =    1.768
peak=   -3.070 closest distance to " NH2 ARG A  79 " =    1.738
peak=   -3.055 closest distance to " CD1 TYR A 247 " =    2.417
peak=   -3.050 closest distance to " O   HOH Z 310 " =    3.493
peak=   -3.045 closest distance to " O   HOH Z 421 " =    3.003
peak=   -3.031 closest distance to " CB  ALA A 291 " =    2.166
peak=   -3.031 closest distance to " CB  PRO A  54 " =    2.224

================= 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    :  0.3723 0.3705   6.160801e+00   6.171496e+00
   1_bss:  0.3568 0.3526   6.146126e+00   6.141159e+00
   1_xyz:  0.2530 0.2836   5.837814e+00   5.925399e+00
   1_adp:  0.2343 0.2917   5.794789e+00   5.946652e+00
   1_occ:  0.2340 0.2922   5.793844e+00   5.946045e+00
   2_bss:  0.2313 0.2879   5.785959e+00   5.938148e+00
   2_xyz:  0.1665 0.2174   5.490160e+00   5.685622e+00
   2_adp:  0.1527 0.2020   5.414875e+00   5.621945e+00
   2_occ:  0.1524 0.2019   5.413919e+00   5.621232e+00
   3_bss:  0.1520 0.1999   5.407229e+00   5.613895e+00
   3_xyz:  0.1277 0.1713   5.250295e+00   5.470239e+00
   3_adp:  0.1216 0.1679   5.215884e+00   5.442776e+00
   3_occ:  0.1215 0.1678   5.215102e+00   5.442225e+00
   4_bss:  0.1214 0.1675   5.213811e+00   5.441394e+00
   4_xyz:  0.1117 0.1585   5.149469e+00   5.388542e+00
   4_adp:  0.1098 0.1587   5.140885e+00   5.383795e+00
   4_occ:  0.1098 0.1586   5.140548e+00   5.383681e+00
   5_bss:  0.1101 0.1586   5.141188e+00   5.384103e+00
   5_xyz:  0.1076 0.1585   5.132402e+00   5.384683e+00
   5_adp:  0.1076 0.1574   5.129626e+00   5.380491e+00
   5_occ:  0.1075 0.1574   5.129241e+00   5.380450e+00
   5_bss:  0.1075 0.1574   5.129407e+00   5.380530e+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:  0.345  50.000  -3.245  -1.925   3.553  -0.000   0.000   0.000
   1_xyz:  0.345  50.000  -3.245  -1.925   3.553  -0.000   0.000   0.000
   1_adp:  0.345  50.000  -3.245  -1.925   3.553  -0.000   0.000   0.000
   1_occ:  0.345  50.000  -3.245  -1.925   3.553  -0.000   0.000   0.000
   2_bss:  0.336  50.000  -2.925  -2.138   0.151  -0.000   0.000   0.000
   2_xyz:  0.336  50.000  -2.925  -2.138   0.151  -0.000   0.000   0.000
   2_adp:  0.336  50.000  -2.925  -2.138   0.151  -0.000   0.000   0.000
   2_occ:  0.336  50.000  -2.925  -2.138   0.151  -0.000   0.000   0.000
   3_bss:  0.320  39.181  -2.694  -2.162  -1.334  -0.000  -0.000  -0.000
   3_xyz:  0.320  39.181  -2.694  -2.162  -1.334  -0.000  -0.000  -0.000
   3_adp:  0.320  39.181  -2.694  -2.162  -1.334  -0.000  -0.000  -0.000
   3_occ:  0.320  39.181  -2.694  -2.162  -1.334  -0.000  -0.000  -0.000
   4_bss:  0.315  39.929  -2.614  -2.169  -1.809  -0.000  -0.000  -0.000
   4_xyz:  0.315  39.929  -2.614  -2.169  -1.809  -0.000  -0.000  -0.000
   4_adp:  0.315  39.929  -2.614  -2.169  -1.809  -0.000  -0.000  -0.000
   4_occ:  0.315  39.929  -2.614  -2.169  -1.809  -0.000  -0.000  -0.000
   5_bss:  0.315  42.091  -2.479  -2.048  -1.849  -0.000  -0.000  -0.000
   5_xyz:  0.315  42.091  -2.479  -2.048  -1.849  -0.000  -0.000  -0.000
   5_adp:  0.315  42.091  -2.479  -2.048  -1.849  -0.000  -0.000  -0.000
   5_occ:  0.315  42.091  -2.479  -2.048  -1.849  -0.000  -0.000  -0.000
   5_bss:  0.318  42.020  -2.328  -1.885  -1.726  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  43.131 0.6065  0.7948    44785.588
   1_bss:  41.196 0.6277  0.8084    39978.069
   1_xyz:  29.018 0.7691  0.9515    21507.907
   1_adp:  30.403 0.7528  0.9367    22891.353
   1_occ:  30.396 0.7528  0.9364    22852.666
   2_bss:  29.827 0.7592  0.9089    22296.843
   2_xyz:  21.230 0.8492  0.9801    12018.495
   2_adp:  19.307 0.8685  0.9898    10531.416
   2_occ:  19.283 0.8688  0.9897    10515.400
   3_bss:  19.038 0.8710  0.9751    10280.360
   3_xyz:  15.920 0.8987  0.9882     7558.703
   3_adp:  15.276 0.9045  0.9865     7180.691
   3_occ:  15.254 0.9047  0.9865     7172.384
   4_bss:  15.230 0.9049  0.9818     7164.899
   4_xyz:  14.256 0.9126  0.9845     6393.494
   4_adp:  14.130 0.9139  0.9801     6343.455
   4_occ:  14.123 0.9139  0.9800     6341.092
   5_bss:  14.126 0.9139  0.9821     6344.460
   5_xyz:  14.072 0.9144  0.9816     6345.277
   5_adp:  13.952 0.9155  0.9780     6287.377
   5_occ:  13.945 0.9156  0.9779     6285.063
   5_bss:  13.949 0.9156  0.9807     6288.858
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.7989e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.7989e-01
   1_xyz:   1.256  0.010  0.076 15.595  0.005  4.109   9.0451e-02
   1_adp:   1.256  0.010  0.076 15.595  0.005  4.109   9.0451e-02
   1_occ:   1.256  0.010  0.076 15.595  0.005  4.109   9.0451e-02
   2_bss:   1.256  0.010  0.076 15.595  0.005  4.109   9.0451e-02
   2_xyz:   1.061  0.006  0.069 14.068  0.004  4.119   6.0574e-02
   2_adp:   1.061  0.006  0.069 14.068  0.004  4.119   6.0574e-02
   2_occ:   1.061  0.006  0.069 14.068  0.004  4.119   6.0574e-02
   3_bss:   1.061  0.006  0.069 14.068  0.004  4.119   6.0574e-02
   3_xyz:   0.938  0.006  0.066 14.263  0.004  4.114   5.2179e-02
   3_adp:   0.938  0.006  0.066 14.263  0.004  4.114   5.2179e-02
   3_occ:   0.938  0.006  0.066 14.263  0.004  4.114   5.2179e-02
   4_bss:   0.938  0.006  0.066 14.263  0.004  4.114   5.2179e-02
   4_xyz:   1.037  0.007  0.073 14.616  0.004  4.116   6.0578e-02
   4_adp:   1.037  0.007  0.073 14.616  0.004  4.116   6.0578e-02
   4_occ:   1.037  0.007  0.073 14.616  0.004  4.116   6.0578e-02
   5_bss:   1.037  0.007  0.073 14.616  0.004  4.116   6.0578e-02
   5_xyz:   1.013  0.007  0.072 14.490  0.004  4.116   5.9024e-02
   5_adp:   1.013  0.007  0.072 14.490  0.004  4.116   5.9024e-02
   5_occ:   1.013  0.007  0.072 14.490  0.004  4.116   5.9024e-02
   5_bss:   1.013  0.007  0.072 14.490  0.004  4.116   5.9024e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.495   2.3972e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.495   2.3972e-01
   1_xyz:   8.182  0.057  0.274 87.313  0.025  2.014   9.0989e-02
   1_adp:   8.182  0.057  0.274 87.313  0.025  2.014   9.0989e-02
   1_occ:   8.182  0.057  0.274 87.313  0.025  2.014   9.0989e-02
   2_bss:   8.182  0.057  0.274 87.313  0.025  2.014   9.0989e-02
   2_xyz:   7.183  0.039  0.237 79.743  0.034  2.335   7.1075e-02
   2_adp:   7.183  0.039  0.237 79.743  0.034  2.335   7.1075e-02
   2_occ:   7.183  0.039  0.237 79.743  0.034  2.335   7.1075e-02
   3_bss:   7.183  0.039  0.237 79.743  0.034  2.335   7.1075e-02
   3_xyz:   6.867  0.038  0.273 83.045  0.031  2.369   4.5359e-02
   3_adp:   6.867  0.038  0.273 83.045  0.031  2.369   4.5359e-02
   3_occ:   6.867  0.038  0.273 83.045  0.031  2.369   4.5359e-02
   4_bss:   6.867  0.038  0.273 83.045  0.031  2.369   4.5359e-02
   4_xyz:   6.699  0.037  0.225 82.571  0.035  2.303   4.3511e-02
   4_adp:   6.699  0.037  0.225 82.571  0.035  2.303   4.3511e-02
   4_occ:   6.699  0.037  0.225 82.571  0.035  2.303   4.3511e-02
   5_bss:   6.699  0.037  0.225 82.571  0.035  2.303   4.3511e-02
   5_xyz:   6.739  0.035  0.226 82.226  0.034  2.310   4.3178e-02
   5_adp:   6.739  0.035  0.226 82.226  0.034  2.310   4.3178e-02
   5_occ:   6.739  0.035  0.226 82.226  0.034  2.310   4.3178e-02
   5_bss:   6.739  0.035  0.226 82.226  0.034  2.310   4.3178e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  74.96   0.00  17.04  74.96   0.00  13.20  64.58   4.41  37.94
   1_occ:  74.96   0.00  17.04  74.96   0.00  13.20  64.58   4.41  37.94
   2_bss:  74.96   0.00  17.04  74.96   0.00  13.20  64.58   4.41  37.94
   2_xyz:  74.96   0.00  17.04  74.96   0.00  13.20  64.58   4.41  37.94
   2_adp:  68.68   1.52  17.29  66.85   1.52  13.19  68.68   5.83  39.67
   2_occ:  68.68   1.52  17.29  66.85   1.52  13.19  68.68   5.83  39.67
   3_bss:  68.68   1.52  17.29  66.85   1.52  13.19  68.68   5.83  39.67
   3_xyz:  68.68   1.52  17.29  66.85   1.52  13.19  68.68   5.83  39.67
   3_adp:  84.05   0.00  17.52  84.05   0.00  13.14  77.76   2.49  41.36
   3_occ:  84.05   0.00  17.52  84.05   0.00  13.14  77.76   2.49  41.36
   4_bss:  84.05   0.00  17.52  84.05   0.00  13.14  77.76   2.49  41.36
   4_xyz:  84.05   0.00  17.52  84.05   0.00  13.14  77.76   2.49  41.36
   4_adp:  96.84   0.00  17.39  96.84   0.00  13.03  85.29   2.23  41.09
   4_occ:  96.84   0.00  17.39  96.84   0.00  13.03  85.29   2.23  41.09
   5_bss:  96.84   0.00  17.39  96.84   0.00  13.03  85.29   2.23  41.09
   5_xyz:  96.84   0.00  17.39  96.84   0.00  13.03  85.29   2.23  41.09
   5_adp:  97.07   1.81  16.89  97.07   1.81  12.81  81.54   4.20  39.14
   5_occ:  97.07   1.81  16.89  97.07   1.81  12.81  81.54   4.20  39.14
   5_bss:  97.01   1.74  16.83  97.01   1.74  12.74  81.47   4.13  39.07
------------------------------------------------------------------------
 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:    1.896    0.021    0.309
   1_adp:    1.896    0.021    0.309
   1_occ:    1.896    0.021    0.309
   2_bss:    1.896    0.021    0.309
   2_xyz:    1.423    0.013    0.426
   2_adp:    1.423    0.013    0.426
   2_occ:    1.423    0.013    0.426
   3_bss:    1.423    0.013    0.426
   3_xyz:    1.509    0.024    0.484
   3_adp:    1.509    0.024    0.484
   3_occ:    1.509    0.024    0.484
   4_bss:    1.509    0.024    0.484
   4_xyz:    1.632    0.059    0.512
   4_adp:    1.632    0.059    0.512
   4_occ:    1.632    0.059    0.512
   5_bss:    1.632    0.059    0.512
   5_xyz:    1.726    0.059    0.525
   5_adp:    1.726    0.059    0.525
   5_occ:    1.726    0.059    0.525
   5_bss:    1.726    0.059    0.525
------------------------------------------------------------------------

CPU time actual refinement: 361.32


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_671/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_671/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_671/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_671/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_671/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 361.18 
  Macro-tasks:
    bulk solvent and scale       = 40.81  
    individual site refinement   = 148.63 
    weights calculation          = 31.17  
    collect and process          = 6.71   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 227.41 
  Micro-tasks:
    mask                            = 1.79   
    f_calc                          = 122.57 
    alpha_beta                      = 8.35   
    target                          = 1.23   
    gradients_wrt_atomic_parameters = 123.86 
    fmodel                         = 6.88   
    r_factors                      = 0.17   
    phase_errors                   = 11.90  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 276.98 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 5.130 micro seconds
Total CPU time: 6.24 minutes
from_scatterers_fft:    646 calls, 122.16 s
gradients_fft:          591 calls, 112.64 s

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

# Date 2008-01-16 Time 05:24:03 PST -0800 (1200489843.29 s)
Start R-work = 0.3723, R-free = 0.3705 (no bulk solvent and anisotropic scale)
Final R-work = 0.1324, R-free = 0.1778 (no bulk solvent and anisotropic scale)

Start R-work = 0.3568, R-free = 0.3526
Final R-work = 0.1075, R-free = 0.1574