# Date 2008-01-16 Time 04:48:45 PST -0800 (1200487725.21 s)
#phil __OFF__

Command line arguments: "../469.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1470
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 469

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 47.8686, 87.2539, 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: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.8686, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9854 1.98075
Completeness in resolution range: 0.939926
Completeness with d_max=infinity: 0.937049

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9854
                             d_min =   1.9808

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.8686, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9854 1.98075
Completeness in resolution range: 0.939926
Completeness with d_max=infinity: 0.937049

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9858 -  4.2382 [2195/2223]  1972   223  10.2%
  bin  2:  4.2382 -  3.3767 [2092/2115]  1886   206   9.8%
  bin  3:  3.3767 -  2.9536 [2068/2093]  1860   208  10.1%
  bin  4:  2.9536 -  2.6852 [2066/2082]  1856   210  10.2%
  bin  5:  2.6852 -  2.4937 [2015/2052]  1814   201  10.0%
  bin  6:  2.4937 -  2.3472 [2051/2085]  1852   199   9.7%
  bin  7:  2.3472 -  2.2301 [2018/2055]  1816   202  10.0%
  bin  8:  2.2301 -  2.1333 [2000/2042]  1800   200  10.0%
  bin  9:  2.1333 -  2.0514 [2021/2060]  1825   196   9.7%
  bin 10:  2.0514 -  1.9808 [1063/2034]   949   114  10.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_469/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 27
        2.42 -     3.04: 2172
        3.04 -     3.66: 4650
        3.66 -     4.28: 8914
        4.28 -     4.90: 12312
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.826 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.892 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 296 "  1.960 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  2.013 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28070 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_469/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_469/model_refine_001.geo

CPU time processing inputs: 9.20


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 47.8686 87.2539 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: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4210   r_free= 0.4081   ksol= 0.00   Bsol= 0.00   scale= 0.914    |
|                                                                             |
| 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:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.228192                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9858 -  4.7271 0.99   1422  158 0.3329 0.3571      6.4761      6.4974|
|  2:  4.7271 -  3.7717 0.99   1370  152 0.3553 0.3494      6.7321      6.7131|
|  3:  3.7717 -  3.3007 0.99   1346  149 0.3894 0.3622      6.5941      6.5465|
|  4:  3.3007 -  3.0016 0.99   1321  144 0.4104 0.3790       6.443      6.3697|
|  5:  3.0016 -  2.7879 0.98   1326  147 0.4489 0.3932      6.3074      6.2955|
|  6:  2.7879 -  2.6245 0.99   1310  148 0.4490 0.4491      6.2332      6.0866|
|  7:  2.6245 -  2.4937 0.99   1293  150 0.4471 0.4076      6.1786       6.101|
|  8:  2.4937 -  2.3856 0.99   1337  140 0.4602 0.4471      6.1311      6.1159|
|  9:  2.3856 -  2.2941 0.99   1298  148 0.4625 0.4435      6.0746      6.1278|
| 10:  2.2941 -  2.2152 0.98   1301  140 0.4758 0.4179      6.0675        5.99|
| 11:  2.2152 -  2.1461 0.98   1289  147 0.4781 0.4701      6.0032      5.9974|
| 12:  2.1461 -  2.0849 1.00   1284  150 0.4742 0.5045      5.9213      5.9815|
| 13:  2.0849 -  2.0302 0.95   1276  129 0.4924 0.5281      5.8594      5.8458|
| 14:  2.0302 -  1.9808 0.35    457   57 0.4461 0.4454      5.8479      5.6799|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9858 -  4.7271  1422   158  0.72  32.33   0.84     0.75      62775.09|
|  2:  4.7271 -  3.7717  1370   152  0.76  29.79   0.93     0.84      79392.21|
|  3:  3.7717 -  3.3007  1346   149  0.70  35.31   0.92     0.86      79199.07|
|  4:  3.3007 -  3.0016  1321   144  0.65  39.94   0.93     0.81      67235.50|
|  5:  3.0016 -  2.7879  1326   147  0.58  45.29   0.91     0.76      54456.04|
|  6:  2.7879 -  2.6245  1310   148  0.57  46.54   0.92     0.74      47431.99|
|  7:  2.6245 -  2.4937  1293   150  0.56  47.35   0.95     0.73      43968.43|
|  8:  2.4937 -  2.3856  1337   140  0.55  48.32   0.93     0.73      40829.74|
|  9:  2.3856 -  2.2941  1298   148  0.53  49.44   0.94     0.74      38985.03|
| 10:  2.2941 -  2.2152  1301   140  0.53  49.90   0.95     0.73      35805.23|
| 11:  2.2152 -  2.1461  1289   147  0.49  53.09   0.95     0.72      36888.06|
| 12:  2.1461 -  2.0849  1284   150  0.43  57.96   0.95     0.65      37652.27|
| 13:  2.0849 -  2.0302  1276   129  0.36  63.45   0.93     0.55      35494.18|
| 14:  2.0302 -  1.9808   457    57  0.35  64.00   1.02     0.44      28205.08|
|alpha:            min =        0.44 max =            0.86 mean =         0.73|
|beta:             min =    28205.08 max =        79392.21 mean =     50510.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.57|
|phase err.(work): min =        0.00 max =           90.00 mean =        46.29|
|phase err.(test): min =        0.00 max =           89.95 mean =        46.48|
|-----------------------------------------------------------------------------|

============================== 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 = 6.194188              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.238   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.236813              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.905   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       20 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      180 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1992 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1844 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2806 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4601 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4313 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5593 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6719 |
|-----------------------------------------------------------------------------|
|-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 |        0.166 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.219 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.060)------------------------------------------|
|    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: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4210   r_free= 0.4081   ksol= 0.00   Bsol= 0.00   scale= 0.914    |
|                                                                             |
| 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:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.228192                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4104   r_free= 0.3958   ksol= 0.30   Bsol= 35.63   scale= 0.949   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,4.58,0.01,0.00,0.00,0.00); trace/3= 0.60                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.216413                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.565418              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.860   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.700358              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.695   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4104      final r-factor (work) = 0.2997          |
| start r-factor (free) = 0.3958      final r-factor (free) = 0.3224          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.4629 = 5.57 * 0.50 * 6.2158 + 1.00 * 0.1663                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.9136 = 5.57 * 0.50 * 6.0439 + 1.00 * 0.0953                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2997      final r-factor (work) = 0.2733          |
| start r-factor (free) = 0.3224      final r-factor (free) = 0.3363          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2388 = 0.70 * 1.00 * 6.0439 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1607 = 0.70 * 1.00 * 5.9210 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.060)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.33   17.73    None  None   None       |
|    all(noH): 2823   0      0.00    88.33   17.73    None  None   None       |
|    Sol.    : 438    0      1.12    88.33   37.14    None  None   None       |
|    Mac.    : 2385   0      0.00    73.09   14.16    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 -   8.833:  808   |   5:    44.164 -  52.996:  100        |
|      1:     8.833 -  17.665:  998   |   6:    52.996 -  61.829:   53        |
|      2:    17.665 -  26.498:  470   |   7:    61.829 -  70.662:   29        |
|      3:    26.498 -  35.331:  222   |   8:    70.662 -  79.494:   13        |
|      4:    35.331 -  44.164:  126   |   9:    79.494 -  88.327:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2733 r_free = 0.3363             target_work(ml) = 5.931         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2732 r_free = 0.3364             target_work(ml) = 5.930         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2732   r_free= 0.3364   ksol= 0.30   Bsol= 35.63   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,4.58,0.01,0.00,0.00,0.00); trace/3= 0.60                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.930022                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2721   r_free= 0.3341   ksol= 0.32   Bsol= 59.17   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,1.85,-0.23,0.00,-0.00,-0.00); trace/3= -0.24                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.928605                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.499755              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.066   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.358137              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.916  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2721      final r-factor (work) = 0.1999          |
| start r-factor (free) = 0.3341      final r-factor (free) = 0.2422          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.3782 = 5.50 * 0.50 * 5.9213 + 1.00 * 0.0953                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.0541 = 5.50 * 0.50 * 5.8078 + 1.00 * 0.0833                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1999      final r-factor (work) = 0.1816          |
| start r-factor (free) = 0.2422      final r-factor (free) = 0.2245          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0938 = 0.36 * 1.00 * 5.8078 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0119 = 0.36 * 1.00 * 5.5894 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.060)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.96   17.37    None  None   None       |
|    all(noH): 2823   0      0.00    87.96   17.37    None  None   None       |
|    Sol.    : 438    0      4.88    87.96   39.28    None  None   None       |
|    Mac.    : 2385   0      0.00    73.87   13.35    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 -   8.796:  836   |   5:    43.979 -  52.775:  103        |
|      1:     8.796 -  17.592: 1137   |   6:    52.775 -  61.571:   65        |
|      2:    17.592 -  26.388:  323   |   7:    61.571 -  70.367:   29        |
|      3:    26.388 -  35.184:  170   |   8:    70.367 -  79.163:   15        |
|      4:    35.184 -  43.979:  141   |   9:    79.163 -  87.959:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1816 r_free = 0.2245             target_work(ml) = 5.561         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1813 r_free = 0.2246             target_work(ml) = 5.560         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1813   r_free= 0.2246   ksol= 0.32   Bsol= 59.17   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,1.85,-0.23,0.00,-0.00,-0.00); trace/3= -0.24                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.560370                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1807   r_free= 0.2232   ksol= 0.32   Bsol= 60.52   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-0.14,-0.43,-0.00,-0.00,-0.00); trace/3= -1.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.557944                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.475199              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.269   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.860034              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.529  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1807      final r-factor (work) = 0.1383          |
| start r-factor (free) = 0.2232      final r-factor (free) = 0.1807          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5924 = 4.48 * 0.50 * 5.5904 + 1.00 * 0.0833                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.2457 = 4.48 * 0.50 * 5.4404 + 1.00 * 0.0721                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1383      final r-factor (work) = 0.1282          |
| start r-factor (free) = 0.1807      final r-factor (free) = 0.1736          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6891 = 0.86 * 1.00 * 5.4404 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5531 = 0.86 * 1.00 * 5.2812 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.060)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.33   17.38    None  None   None       |
|    all(noH): 2823   0      0.00    88.33   17.38    None  None   None       |
|    Sol.    : 438    0      5.59    88.33   41.98    None  None   None       |
|    Mac.    : 2385   0      0.00    88.07   12.86    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 -   8.833:  870   |   5:    44.166 -  52.999:   92        |
|      1:     8.833 -  17.666: 1178   |   6:    52.999 -  61.832:   88        |
|      2:    17.666 -  26.499:  278   |   7:    61.832 -  70.665:   46        |
|      3:    26.499 -  35.333:  134   |   8:    70.665 -  79.498:   22        |
|      4:    35.333 -  44.166:  108   |   9:    79.498 -  88.331:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1282 r_free = 0.1736             target_work(ml) = 5.260         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1282 r_free = 0.1738             target_work(ml) = 5.260         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1282   r_free= 0.1738   ksol= 0.32   Bsol= 60.52   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-0.14,-0.43,-0.00,-0.00,-0.00); trace/3= -1.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.260486                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1286   r_free= 0.1741   ksol= 0.33   Bsol= 66.36   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-0.85,-0.49,-0.00,-0.00,-0.00); trace/3= -1.27                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.262291                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.958172              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 121.442  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.878581              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.882  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1286      final r-factor (work) = 0.1219          |
| start r-factor (free) = 0.1741      final r-factor (free) = 0.1677          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2446 = 1.96 * 0.50 * 5.2830 + 1.00 * 0.0721                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1880 = 1.96 * 0.50 * 5.2401 + 1.00 * 0.0575                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1219      final r-factor (work) = 0.1199          |
| start r-factor (free) = 0.1677      final r-factor (free) = 0.1667          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6149 = 0.88 * 1.00 * 5.2401 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5922 = 0.88 * 1.00 * 5.2140 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.060)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.91   17.12    None  None   None       |
|    all(noH): 2823   0      0.00    92.91   17.12    None  None   None       |
|    Sol.    : 438    0      0.00    87.71   41.98    None  None   None       |
|    Mac.    : 2385   0      0.00    92.91   12.56    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 -   9.291: 1006   |   5:    46.453 -  55.744:   98        |
|      1:     9.291 -  18.581: 1132   |   6:    55.744 -  65.035:   78        |
|      2:    18.581 -  27.872:  226   |   7:    65.035 -  74.325:   42        |
|      3:    27.872 -  37.163:  123   |   8:    74.325 -  83.616:   11        |
|      4:    37.163 -  46.453:  102   |   9:    83.616 -  92.907:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1199 r_free = 0.1667             target_work(ml) = 5.210         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1199 r_free = 0.1667             target_work(ml) = 5.210         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1199   r_free= 0.1667   ksol= 0.33   Bsol= 66.36   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-0.85,-0.49,-0.00,-0.00,-0.00); trace/3= -1.27                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.209941                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1199   r_free= 0.1667   ksol= 0.33   Bsol= 66.00   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-0.94,-0.34,-0.00,-0.00,-0.00); trace/3= -1.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.209961                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.788661              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 122.518  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.216733              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.188  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1199      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1667      final r-factor (free) = 0.1624          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9343 = 3.79 * 0.50 * 5.2139 + 1.00 * 0.0575                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8958 = 3.79 * 0.50 * 5.1809 + 1.00 * 0.0815                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1121      final r-factor (work) = 0.1112          |
| start r-factor (free) = 0.1624      final r-factor (free) = 0.1616          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.4959 = 2.22 * 1.00 * 5.1809 + 1.00 * 0.0112                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.4430 = 2.22 * 1.00 * 5.1569 + 1.00 * 0.0117                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.060)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.33  16.95    None  None   None       |
|    all(noH): 2823   0      0.00    104.33  16.95    None  None   None       |
|    Sol.    : 438    0      0.00    96.32   41.94    None  None   None       |
|    Mac.    : 2385   0      0.00    104.33  12.37    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 -  10.433: 1289   |   5:    52.166 -  62.599:   90        |
|      1:    10.433 -  20.867:  935   |   6:    62.599 -  73.033:   53        |
|      2:    20.867 -  31.300:  197   |   7:    73.033 -  83.466:   16        |
|      3:    31.300 -  41.733:  124   |   8:    83.466 -  93.899:    5        |
|      4:    41.733 -  52.166:  109   |   9:    93.899 - 104.332:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1112 r_free = 0.1616             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1112 r_free = 0.1616             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1616   ksol= 0.33   Bsol= 66.00   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-0.94,-0.34,-0.00,-0.00,-0.00); trace/3= -1.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.155175                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9858 -  4.7271 0.99   1422  158 0.0948 0.1291      5.3632      5.5592|
|  2:  4.7271 -  3.7717 0.99   1370  152 0.0799 0.1052      5.3951      5.5995|
|  3:  3.7717 -  3.3007 0.99   1346  149 0.1026 0.1469      5.4433      5.8353|
|  4:  3.3007 -  3.0016 0.99   1321  144 0.1226 0.1672      5.4543      5.6268|
|  5:  3.0016 -  2.7879 0.98   1326  147 0.1350 0.1774       5.346      5.5369|
|  6:  2.7879 -  2.6245 0.99   1310  148 0.1269 0.2153       5.249      5.5232|
|  7:  2.6245 -  2.4937 0.99   1293  150 0.1264 0.1666      5.1763      5.3667|
|  8:  2.4937 -  2.3856 0.99   1337  140 0.1161 0.1696      5.0955      5.3124|
|  9:  2.3856 -  2.2941 0.99   1298  148 0.1175 0.1951      5.0386      5.3789|
| 10:  2.2941 -  2.2152 0.98   1301  140 0.1122 0.1683      4.9734      5.1666|
| 11:  2.2152 -  2.1461 0.98   1289  147 0.1150 0.1961      4.9308      5.2933|
| 12:  2.1461 -  2.0849 1.00   1284  150 0.1091 0.1632      4.8541      5.1111|
| 13:  2.0849 -  2.0302 0.95   1276  129 0.1149 0.1718      4.7936      5.0263|
| 14:  2.0302 -  1.9808 0.35    457   57 0.0994 0.1853      4.7043      4.9586|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9858 -  4.7271  1422   158  0.94   9.31   0.97     0.94       7364.89|
|  2:  4.7271 -  3.7717  1370   152  0.95   7.90   1.01     0.99       8806.89|
|  3:  3.7717 -  3.3007  1346   149  0.94  11.13   1.02     1.02      10007.50|
|  4:  3.3007 -  3.0016  1321   144  0.92  14.14   1.01     0.99      10612.31|
|  5:  3.0016 -  2.7879  1326   147  0.89  16.97   1.00     0.97       8971.80|
|  6:  2.7879 -  2.6245  1310   148  0.89  17.17   0.98     0.95       7738.46|
|  7:  2.6245 -  2.4937  1293   150  0.90  16.01   0.99     0.96       6499.58|
|  8:  2.4937 -  2.3856  1337   140  0.90  16.05   0.98     0.95       5837.64|
|  9:  2.3856 -  2.2941  1298   148  0.90  16.25   0.98     0.94       5117.98|
| 10:  2.2941 -  2.2152  1301   140  0.90  16.36   0.98     0.94       4709.73|
| 11:  2.2152 -  2.1461  1289   147  0.90  16.39   0.98     0.95       4390.89|
| 12:  2.1461 -  2.0849  1284   150  0.91  15.66   0.99     0.98       3876.58|
| 13:  2.0849 -  2.0302  1276   129  0.90  16.64   0.97     0.96       3424.50|
| 14:  2.0302 -  1.9808   457    57  0.90  15.60   0.94     0.90       2887.34|
|alpha:            min =        0.90 max =            1.02 mean =         0.96|
|beta:             min =     2887.34 max =        10612.31 mean =      6657.24|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.57|
|phase err.(test): min =        0.00 max =           87.93 mean =        14.05|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1110   r_free= 0.1615   ksol= 0.32   Bsol= 63.96   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-0.77,-0.07,-0.00,-0.00,-0.00); trace/3= -0.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.155344                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1110   r_free= 0.1615   ksol= 0.32   Bsol= 63.96   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-0.77,-0.07,-0.00,-0.00,-0.00); trace/3= -0.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.155344                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9858 -  4.7271 0.99   1422  158 0.0947 0.1292       5.363      5.5599|
|  2:  4.7271 -  3.7717 0.99   1370  152 0.0799 0.1051      5.3948      5.5986|
|  3:  3.7717 -  3.3007 0.99   1346  149 0.1026 0.1469      5.4432      5.8362|
|  4:  3.3007 -  3.0016 0.99   1321  144 0.1227 0.1674      5.4548      5.6273|
|  5:  3.0016 -  2.7879 0.98   1326  147 0.1351 0.1775      5.3465      5.5369|
|  6:  2.7879 -  2.6245 0.99   1310  148 0.1268 0.2153      5.2489      5.5231|
|  7:  2.6245 -  2.4937 0.99   1293  150 0.1264 0.1668      5.1766      5.3669|
|  8:  2.4937 -  2.3856 0.99   1337  140 0.1160 0.1697       5.096      5.3127|
|  9:  2.3856 -  2.2941 0.99   1298  148 0.1175 0.1951      5.0392      5.3795|
| 10:  2.2941 -  2.2152 0.98   1301  140 0.1122 0.1684      4.9739      5.1674|
| 11:  2.2152 -  2.1461 0.98   1289  147 0.1151 0.1961      4.9309      5.2931|
| 12:  2.1461 -  2.0849 1.00   1284  150 0.1091 0.1633      4.8541      5.1117|
| 13:  2.0849 -  2.0302 0.95   1276  129 0.1150 0.1717      4.7936      5.0249|
| 14:  2.0302 -  1.9808 0.35    457   57 0.0994 0.1855      4.7048      4.9592|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9858 -  4.7271  1422   158  0.94   9.31   0.97     0.94       7363.31|
|  2:  4.7271 -  3.7717  1370   152  0.95   7.91   1.01     1.00       8799.69|
|  3:  3.7717 -  3.3007  1346   149  0.94  11.13   1.03     1.02      10002.18|
|  4:  3.3007 -  3.0016  1321   144  0.92  14.15   1.01     1.00      10623.16|
|  5:  3.0016 -  2.7879  1326   147  0.89  16.97   1.00     0.98       8974.18|
|  6:  2.7879 -  2.6245  1310   148  0.89  17.17   0.98     0.95       7736.66|
|  7:  2.6245 -  2.4937  1293   150  0.90  16.02   0.99     0.96       6501.07|
|  8:  2.4937 -  2.3856  1337   140  0.90  16.06   0.99     0.96       5842.45|
|  9:  2.3856 -  2.2941  1298   148  0.90  16.26   1.00     0.95       5125.13|
| 10:  2.2941 -  2.2152  1301   140  0.90  16.36   0.99     0.95       4713.83|
| 11:  2.2152 -  2.1461  1289   147  0.90  16.40   0.99     0.96       4392.48|
| 12:  2.1461 -  2.0849  1284   150  0.91  15.66   1.00     0.99       3878.50|
| 13:  2.0849 -  2.0302  1276   129  0.90  16.64   0.99     0.97       3422.62|
| 14:  2.0302 -  1.9808   457    57  0.90  15.60   0.96     0.92       2883.95|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2883.95 max =        10623.16 mean =      6658.34|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.57|
|phase err.(test): min =        0.00 max =           87.91 mean =        14.06|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.060)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.34  16.96    None  None   None       |
|    all(noH): 2823   0      0.00    104.34  16.96    None  None   None       |
|    Sol.    : 438    0      0.00    96.33   41.94    None  None   None       |
|    Mac.    : 2385   0      0.00    104.34  12.37    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.436: 1289   |   5:    52.169 -  62.602:   90        |
|      1:    10.436 -  20.869:  935   |   6:    62.602 -  73.036:   53        |
|      2:    20.869 -  31.303:  197   |   7:    73.036 -  83.469:   16        |
|      3:    31.303 -  41.736:  124   |   8:    83.469 -  93.902:    5        |
|      4:    41.736 -  52.169:  109   |   9:    93.902 - 104.335:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 301         
Filter by distance & map next to the model:
   mapped sites are within: 0.603 - 5.550
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 297 from: 301
   mapped sites are within: 0.735 - 5.550

peak=    5.873 closest distance to " O   HOH Z 113 " =    2.219
peak=    5.405 closest distance to " O   HOH Z 210 " =    1.064
peak=    5.119 closest distance to " CG  PRO A  54 " =    1.270
peak=    5.092 closest distance to " O   HOH Z 403 " =    1.766
peak=    5.022 closest distance to " CB  GLN A 223 " =    1.421
peak=    4.960 closest distance to " CB  GLN A 183 " =    1.279
peak=    4.891 closest distance to " CB  SER A  63 " =    1.120
peak=    4.886 closest distance to " CB  ARG A 190 " =    1.762
peak=    4.727 closest distance to " O   HOH Z  43 " =    2.166
peak=    4.597 closest distance to " CA  TYR A  30 " =    0.899
peak=    4.576 closest distance to " C   PRO A 198 " =    1.512
peak=    4.567 closest distance to " CB  ARG A 275 " =    0.927
peak=    4.486 closest distance to " O   HOH Z 369 " =    2.436
peak=    4.432 closest distance to " CD2 TRP A 179 " =    1.355
peak=    4.427 closest distance to " O   HOH Z 234 " =    3.742
peak=    4.417 closest distance to " O   HOH Z 232 " =    2.282
peak=    4.389 closest distance to " CG  PRO A 213 " =    1.195
peak=    4.363 closest distance to " O   HOH Z 209 " =    2.389
peak=    4.291 closest distance to " CA  ALA A  51 " =    0.972
peak=    4.273 closest distance to " O   SER A  87 " =    2.232
peak=    4.252 closest distance to " NE2 GLN A  11 " =    1.054
peak=    4.238 closest distance to " O   HOH Z  44 " =    2.043
peak=    4.224 closest distance to " O   HOH Z 402 " =    1.529
peak=    4.206 closest distance to " CB  ARG A  79 " =    1.484
peak=    4.193 closest distance to " O   HOH Z 298 " =    1.843
peak=    4.174 closest distance to " O   HOH Z 142 " =    1.521
peak=    4.173 closest distance to " O   HOH Z  63 " =    1.955
peak=    4.171 closest distance to " CB  GLU A 152 " =    1.106
peak=    4.170 closest distance to " O   HOH Z 368 " =    2.168
peak=    4.150 closest distance to " CD  ARG A 269 " =    0.909
peak=    4.141 closest distance to " O   HOH Z  15 " =    2.175
peak=    4.129 closest distance to " CG  PRO A  90 " =    1.152
peak=    4.122 closest distance to " O   HOH Z 423 " =    1.914
peak=    4.118 closest distance to " CA  ARG A  36 " =    1.075
peak=    4.108 closest distance to " O   HOH Z  97 " =    2.013
peak=    4.095 closest distance to " O   HOH Z 345 " =    1.713
peak=    4.079 closest distance to " O   HOH Z  49 " =    1.082
peak=    4.060 closest distance to " O   HOH Z 203 " =    1.775
peak=    4.051 closest distance to " CG  ARG A  66 " =    2.663
peak=    4.051 closest distance to " CB  GLU A 277 " =    3.705
peak=    4.016 closest distance to " O   HOH Z 134 " =    1.453
peak=    4.012 closest distance to " CB  PRO A  54 " =    0.917
peak=    3.984 closest distance to " O   HOH Z 189 " =    2.628
peak=    3.980 closest distance to " CD  LYS A  76 " =    1.995
peak=    3.965 closest distance to " NZ  LYS A 117 " =    2.910
peak=    3.962 closest distance to " O   HOH Z 132 " =    2.641
peak=    3.952 closest distance to " CG1 ILE A  33 " =    1.140
peak=    3.948 closest distance to " O   HOH Z 261 " =    2.096
peak=    3.936 closest distance to " O   HOH Z 389 " =    1.977
peak=    3.924 closest distance to " O   HOH Z  80 " =    1.800
peak=    3.919 closest distance to " O   HOH Z 346 " =    1.557
peak=    3.918 closest distance to " O   HOH Z 284 " =    2.946
peak=    3.908 closest distance to " CZ  PHE A 218 " =    1.125
peak=    3.894 closest distance to " CA  ARG A 195 " =    1.259
peak=    3.893 closest distance to " CB  GLU A 128 " =    1.193
peak=    3.887 closest distance to " O   HOH Z  61 " =    1.536
peak=    3.875 closest distance to " O   HOH Z 406 " =    1.566
peak=    3.874 closest distance to " CB  TRP A 266 " =    1.002
peak=    3.861 closest distance to " O   HOH Z 279 " =    2.152
peak=    3.859 closest distance to " O   HOH Z 412 " =    3.739
peak=    3.857 closest distance to " CB  TRP A 179 " =    1.322
peak=    3.853 closest distance to " O   HOH Z 214 " =    2.791
peak=    3.848 closest distance to " NH2BARG A 145 " =    2.129
peak=    3.847 closest distance to " NZ  LYS A  48 " =    1.223
peak=    3.844 closest distance to " N   HIS A 108 " =    1.865
peak=    3.838 closest distance to " CB  VAL A 202 " =    1.543
peak=    3.828 closest distance to " O   HOH Z 258 " =    2.111
peak=    3.814 closest distance to " CG  PRO A 243 " =    1.114
peak=    3.795 closest distance to " O   HOH Z 128 " =    2.013
peak=    3.788 closest distance to " CD  LYS A 166 " =    1.376
peak=    3.788 closest distance to " O   HOH Z  40 " =    1.899
peak=    3.788 closest distance to " CA  ASN A 176 " =    1.590
peak=    3.787 closest distance to " O   HOH Z 327 " =    1.629
peak=    3.776 closest distance to " CB  TYR A 169 " =    0.879
peak=    3.774 closest distance to " CA  ALA A 295 " =    1.086
peak=    3.771 closest distance to " O   HOH Z  20 " =    1.421
peak=    3.769 closest distance to " O   HOH Z  59 " =    2.369
peak=    3.768 closest distance to " O   HOH Z 336 " =    1.892
peak=    3.764 closest distance to " OG BSER A 164 " =    2.262
peak=    3.762 closest distance to " O   HOH Z 158 " =    3.007
peak=    3.761 closest distance to " O   HOH Z 147 " =    1.850
peak=    3.760 closest distance to " O   HOH Z 126 " =    1.545
peak=    3.758 closest distance to " NE2 GLN A  77 " =    3.258
peak=    3.757 closest distance to " O   HOH Z 285 " =    2.852
peak=    3.740 closest distance to " CA  ALA A  21 " =    1.381
peak=    3.736 closest distance to " O   HOH Z 193 " =    1.672
peak=    3.730 closest distance to " O   HOH Z 316 " =    3.023
peak=    3.728 closest distance to " O   HOH Z 427 " =    2.967
peak=    3.727 closest distance to " CB  SER A  26 " =    1.783
peak=    3.724 closest distance to " O   HOH Z 291 " =    1.471
peak=    3.721 closest distance to " CA  ALA A 160 " =    0.896
peak=    3.721 closest distance to " N   ASN A  39 " =    1.350
peak=    3.711 closest distance to " CD  PRO A  54 " =    1.018
peak=    3.710 closest distance to " O   HOH Z 433 " =    1.494
peak=    3.696 closest distance to " CB  ASP A 140 " =    1.053
peak=    3.691 closest distance to " O   ALA A 165 " =    1.399
peak=    3.691 closest distance to " O   HOH Z 417 " =    2.968
peak=    3.687 closest distance to " O   HOH Z 422 " =    2.640
peak=    3.677 closest distance to " O   HOH Z 193 " =    2.171
peak=    3.673 closest distance to " O   HOH Z  35 " =    2.277
peak=    3.671 closest distance to " O   HOH Z 180 " =    2.325
peak=    3.670 closest distance to " O   HOH Z 365 " =    2.694
peak=    3.670 closest distance to " CB  SER A 141 " =    1.017
peak=    3.668 closest distance to " O   HOH Z 418 " =    1.412
peak=    3.658 closest distance to " O   HOH Z 227 " =    1.562
peak=    3.652 closest distance to " O   HOH Z  68 " =    1.880
peak=    3.651 closest distance to " O   HOH Z 250 " =    1.356
peak=    3.649 closest distance to " N   CYS A 260 " =    0.839
peak=    3.644 closest distance to " O   HOH Z 214 " =    1.373
peak=    3.637 closest distance to " O  BHOH Z 338 " =    2.212
peak=    3.631 closest distance to " O   HOH Z 421 " =    1.927
peak=    3.630 closest distance to " NH1AARG A 145 " =    1.350
peak=    3.620 closest distance to " O   HOH Z 245 " =    1.335
peak=    3.618 closest distance to " OH  TYR A 116 " =    1.161
peak=    3.608 closest distance to " CB  ASN A  39 " =    0.818
peak=    3.604 closest distance to " O   HOH Z 299 " =    4.271
peak=    3.601 closest distance to " O   HOH Z 383 " =    2.277
peak=    3.599 closest distance to " CA  VAL A 125 " =    1.260
peak=    3.595 closest distance to " CE  LYS A  76 " =    0.784
peak=    3.594 closest distance to " O   HOH Z 102 " =    1.263
peak=    3.594 closest distance to " O   HOH Z 271 " =    2.662
peak=    3.575 closest distance to " O   HOH Z 361 " =    3.465
peak=    3.572 closest distance to " CB  ASN A 148 " =    1.466
peak=    3.571 closest distance to " O   ASP A 124 " =    1.625
peak=    3.553 closest distance to " O   ALA A 158 " =    1.150
peak=    3.550 closest distance to " O   HOH Z 248 " =    1.575
peak=    3.550 closest distance to " ND2 ASN A 187 " =    1.465
peak=    3.547 closest distance to " O   HOH Z  21 " =    1.821
peak=    3.543 closest distance to " O   HOH Z 380 " =    1.858
peak=    3.541 closest distance to " O   HOH Z 287 " =    1.848
peak=    3.539 closest distance to " O   HOH Z 393 " =    3.280
peak=    3.535 closest distance to " O   HOH Z 265 " =    2.017
peak=    3.530 closest distance to " CD  ARG A 159 " =    0.828
peak=    3.529 closest distance to " O   HOH Z 374 " =    2.712
peak=    3.524 closest distance to " CG1BVAL A  72 " =    1.862
peak=    3.520 closest distance to " O   HOH Z 371 " =    3.141
peak=    3.515 closest distance to " CB  ASN A 285 " =    0.970
peak=    3.511 closest distance to " CZ  PHE A  38 " =    1.279
peak=    3.510 closest distance to " O   HOH Z 358 " =    2.044
peak=    3.505 closest distance to " CA  ALA A 291 " =    0.779
peak=    3.504 closest distance to " NH2AARG A 275 " =    3.520
peak=    3.498 closest distance to " O   HOH Z 403 " =    1.498
peak=    3.497 closest distance to " O   HOH Z 156 " =    2.645
peak=    3.497 closest distance to " CB  LEU A 228 " =    1.141
peak=    3.496 closest distance to " O   HOH Z 126 " =    2.024
peak=    3.493 closest distance to " O   HOH Z 303 " =    2.271
peak=    3.492 closest distance to " O   HOH Z 130 " =    2.291
peak=    3.489 closest distance to " CB  ALA A 291 " =    1.288
peak=    3.488 closest distance to " OD1 ASN A  69 " =    2.475
peak=    3.480 closest distance to " CG2BVAL A  41 " =    0.873
peak=    3.478 closest distance to " O   HOH Z 132 " =    2.761
peak=    3.478 closest distance to " NH2 ARG A 156 " =    1.222
peak=    3.476 closest distance to " O   HOH Z 183 " =    1.608
peak=    3.476 closest distance to " CA  TYR A 116 " =    1.309
peak=    3.468 closest distance to " OE1 GLU A   2 " =    2.015
peak=    3.467 closest distance to " O   TYR A 116 " =    1.440
peak=    3.464 closest distance to " O   HOH Z 359 " =    1.494
peak=    3.463 closest distance to " CB  THR A  52 " =    0.844
peak=    3.463 closest distance to " O   HOH Z  78 " =    1.661
peak=    3.462 closest distance to " CG2 ILE A 120 " =    1.106
peak=    3.462 closest distance to " CB  ALA A 248 " =    1.260
peak=    3.461 closest distance to " O   HOH Z  97 " =    2.303
peak=    3.458 closest distance to " O   HOH Z 109 " =    2.297
peak=    3.451 closest distance to " O   HOH Z 250 " =    1.681
peak=    3.444 closest distance to " CB  SER A   3 " =    1.317
peak=    3.444 closest distance to " CB  LEU A  83 " =    0.893
peak=    3.442 closest distance to " O   HOH Z 345 " =    2.810
peak=    3.438 closest distance to " CG  MET A 185 " =    1.135
peak=    3.435 closest distance to " CD2 LEU A 297 " =    0.750
peak=    3.434 closest distance to " CG2 ILE A  20 " =    1.393
peak=    3.430 closest distance to " CA  MET A 188 " =    0.998
peak=    3.422 closest distance to " O   HOH Z 128 " =    2.304
peak=    3.416 closest distance to " CG  GLN A  58 " =    2.723
peak=    3.416 closest distance to " CB  SER A  62 " =    0.823
peak=    3.414 closest distance to " O   HOH Z 154 " =    1.385
peak=    3.413 closest distance to " OG BSER A 134 " =    2.968
peak=    3.413 closest distance to " CB  GLN A  88 " =    1.167
peak=    3.412 closest distance to " CD1 LEU A 300 " =    1.117
peak=    3.395 closest distance to " O   HOH Z  54 " =    1.661
peak=    3.394 closest distance to " O   HOH Z 435 " =    2.948
peak=    3.394 closest distance to " O   HOH Z 357 " =    2.161
peak=    3.392 closest distance to " O   HOH Z 361 " =    2.570
peak=    3.389 closest distance to " CG  PRO A 198 " =    1.201
peak=    3.387 closest distance to " O   HOH Z 298 " =    4.268
peak=    3.381 closest distance to " O   HOH Z 173 " =    2.165
peak=    3.380 closest distance to " CA  LYS A 117 " =    1.232
peak=    3.378 closest distance to " CD1 LEU A  96 " =    0.735
peak=    3.374 closest distance to " O   HOH Z 185 " =    1.762
peak=    3.372 closest distance to " O   HOH Z 325 " =    2.124
peak=    3.370 closest distance to " CA  ASP A 191 " =    0.972
peak=    3.366 closest distance to " CA  ALA A 248 " =    1.202
peak=    3.366 closest distance to " CG  ARG A 219 " =    1.194
peak=    3.356 closest distance to " CB  ALA A 100 " =    1.238
peak=    3.352 closest distance to " OG  SER A 135 " =    1.315
peak=    3.350 closest distance to " CE  LYS A 119 " =    1.126
peak=    3.349 closest distance to " CA  ALA A  84 " =    1.192
peak=    3.341 closest distance to " O   HOH Z 313 " =    1.640
peak=    3.339 closest distance to " CA  GLU A 152 " =    0.859
peak=    3.339 closest distance to " ND1 HIS A  81 " =    1.575
peak=    3.338 closest distance to " CA  ASP A 162 " =    1.160
peak=    3.337 closest distance to " CA  SER A  32 " =    1.602
peak=    3.333 closest distance to " O   HOH Z 392 " =    2.565
peak=    3.332 closest distance to " O   HOH Z  63 " =    2.245
peak=    3.332 closest distance to " CB  ASN A 142 " =    1.206
peak=    3.329 closest distance to " O   HOH Z 281 " =    4.875
peak=    3.328 closest distance to " O   HOH Z 427 " =    3.129
peak=    3.327 closest distance to " CG2 VAL A 197 " =    1.168
peak=    3.324 closest distance to " CG2 THR A 221 " =    1.094
peak=    3.323 closest distance to " OD2 ASP A 298 " =    3.885
peak=    3.323 closest distance to " OG1 THR A 294 " =    2.347
peak=    3.320 closest distance to " OG  SER A  22 " =    2.746
peak=    3.318 closest distance to " O   HOH Z 425 " =    1.304
peak=    3.317 closest distance to " CG2 THR A  29 " =    1.343
peak=    3.314 closest distance to " CZ3 TRP A 266 " =    1.061
peak=    3.313 closest distance to " CB  MET A  47 " =    1.040
peak=    3.312 closest distance to " OG  SER A  62 " =    2.876
peak=    3.311 closest distance to " O   HOH Z 163 " =    1.500
peak=    3.309 closest distance to " O   HOH Z 353 " =    2.857
peak=    3.307 closest distance to " CB  PHE A 204 " =    0.839
peak=    3.303 closest distance to " O   HOH Z  47 " =    2.209
peak=    3.297 closest distance to " O   HOH Z 189 " =    2.561
peak=    3.294 closest distance to " CB  VAL A 265 " =    1.214
peak=    3.294 closest distance to " CD  ARG A 195 " =    0.875
peak=    3.286 closest distance to " O   HOH Z   1 " =    2.652
peak=    3.286 closest distance to " CB  ASN A 148 " =    1.903
peak=    3.285 closest distance to " CB  GLU A  46 " =    0.996
peak=    3.284 closest distance to " O   HOH Z 171 " =    2.109
peak=    3.283 closest distance to " CG2BVAL A  72 " =    1.654
peak=    3.281 closest distance to " CB  THR A  31 " =    1.730
peak=    3.280 closest distance to " O   HOH Z 426 " =    1.422
peak=    3.280 closest distance to " O   HOH Z  88 " =    3.281
peak=    3.270 closest distance to " CA  LEU A  83 " =    1.272
peak=    3.270 closest distance to " O   GLU A   2 " =    1.674
peak=    3.263 closest distance to " O   HOH Z 411 " =    1.681
peak=    3.261 closest distance to " O   HOH Z 199 " =    1.647
peak=    3.258 closest distance to " CA  THR A  42 " =    1.030
peak=    3.252 closest distance to " CB  TYR A 169 " =    0.992
peak=    3.247 closest distance to " O   HOH Z 193 " =    1.762
peak=    3.241 closest distance to " CB  ASN A 215 " =    1.202
peak=    3.237 closest distance to " O   HOH Z 272 " =    1.865
peak=    3.228 closest distance to " CA  MET A 105 " =    1.074
peak=    3.225 closest distance to " CB  TYR A 116 " =    0.892
peak=    3.219 closest distance to " CB  ALA A   9 " =    1.616
peak=    3.216 closest distance to " O   HOH Z 162 " =    1.652
peak=    3.213 closest distance to " O   ALA A 100 " =    1.868
peak=    3.211 closest distance to " O   HOH Z 285 " =    1.433
peak=    3.211 closest distance to " O   HOH Z 402 " =    2.935
peak=    3.204 closest distance to " CA  GLY A 241 " =    0.926
peak=    3.201 closest distance to " CG  LEU A 167 " =    1.144
peak=    3.194 closest distance to " O   HOH Z 305 " =    3.630
peak=    3.191 closest distance to " CA  ALA A 233 " =    1.764
peak=    3.190 closest distance to " O   HOH Z  85 " =    1.330
peak=    3.187 closest distance to " CG  GLU A  37 " =    0.922
peak=    3.181 closest distance to " CB  PRO A  90 " =    1.154
peak=    3.171 closest distance to " OG  SER A 245 " =    1.558
peak=    3.171 closest distance to " CD  LYS A 119 " =    1.718
peak=    3.166 closest distance to " N   ALA A 158 " =    1.445
peak=    3.163 closest distance to " O   HOH Z 219 " =    5.193
peak=    3.162 closest distance to " CA  ASN A 215 " =    1.072
peak=    3.160 closest distance to " O   HOH Z  65 " =    0.973
peak=    3.156 closest distance to " CB  ASP A 298 " =    1.200
peak=    3.155 closest distance to " O   HOH Z 130 " =    2.390
peak=    3.153 closest distance to " CZ3 TRP A  85 " =    0.941
peak=    3.151 closest distance to " CA  ALA A 100 " =    1.048
peak=    3.151 closest distance to " O   HOH Z 313 " =    1.848
peak=    3.151 closest distance to " O   HOH Z 240 " =    2.768
peak=    3.146 closest distance to " O   TRP A 274 " =    1.808
peak=    3.144 closest distance to " O   HOH Z 294 " =    1.494
peak=    3.143 closest distance to " CA  THR A 221 " =    1.415
peak=    3.133 closest distance to " CD  GLU A 152 " =    0.806
peak=    3.133 closest distance to " O   HOH Z 419 " =    1.650
peak=    3.126 closest distance to " CA  SER A  87 " =    1.032
peak=    3.124 closest distance to " CG  GLN A  11 " =    1.444
peak=    3.122 closest distance to " O   HOH Z  63 " =    2.094
peak=    3.121 closest distance to " OE1 GLN A  58 " =    3.422
peak=    3.120 closest distance to " N   ASP A 162 " =    1.204
peak=    3.120 closest distance to " O   HOH Z 406 " =    2.812
peak=    3.117 closest distance to " N   TYR A 116 " =    1.615
peak=    3.116 closest distance to " CG2 ILE A 234 " =    0.975
peak=    3.115 closest distance to " O   HOH Z 298 " =    2.366
peak=    3.113 closest distance to " CB  MET A 105 " =    1.150
peak=    3.106 closest distance to " O   HOH Z  19 " =    1.391
peak=    3.095 closest distance to " O   HOH Z 414 " =    1.743
peak=    3.093 closest distance to " ND2 ASN A 249 " =    0.893
peak=    3.091 closest distance to " O   HOH Z 420 " =    5.550
peak=    3.085 closest distance to " CB  ARG A 139 " =    0.944
peak=    3.085 closest distance to " NH2BARG A 190 " =    1.886
peak=    3.084 closest distance to " CD1 LEU A 228 " =    1.593
peak=    3.082 closest distance to " O   HOH Z 394 " =    3.784
peak=    3.080 closest distance to " CE3 TRP A 150 " =    1.043
peak=    3.079 closest distance to " CG1 VAL A 153 " =    1.066
peak=    3.072 closest distance to " O   HOH Z   9 " =    2.491
peak=    3.071 closest distance to " O   THR A 251 " =    1.164
peak=    3.064 closest distance to " CG  ARG A 138 " =    1.155
peak=    3.063 closest distance to " O   HOH Z 150 " =    1.411
peak=    3.060 closest distance to " CB  ASN A 127 " =    0.829
peak=    3.048 closest distance to " C   TYR A 214 " =    1.513

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 220         
Filter by distance & map next to the model:
   mapped sites are within: 0.983 - 5.548
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 217 from: 220
   mapped sites are within: 0.983 - 5.548

peak=   -4.697 closest distance to " O   HOH Z 266 " =    5.125
peak=   -4.500 closest distance to " CD  GLN A  58 " =    1.008
peak=   -4.419 closest distance to " CD  ARG A 156 " =    2.065
peak=   -4.381 closest distance to " O   HOH Z   5 " =    1.638
peak=   -4.372 closest distance to " SG  CYS A 254 " =    3.428
peak=   -4.313 closest distance to " CD1 LEU A 101 " =    2.439
peak=   -4.298 closest distance to " OXT GLY A 302 " =    3.003
peak=   -4.150 closest distance to " C   ILE A 239 " =    2.185
peak=   -4.135 closest distance to " CB  PRO A 243 " =    2.715
peak=   -4.133 closest distance to " O   VAL A  67 " =    2.802
peak=   -4.119 closest distance to " CG1 VAL A 112 " =    2.595
peak=   -4.111 closest distance to " CA  VAL A  67 " =    3.032
peak=   -4.106 closest distance to " CG  ASP A 132 " =    2.396
peak=   -4.105 closest distance to " CD2 LEU A 237 " =    2.679
peak=   -4.091 closest distance to " CG2 ILE A  49 " =    2.720
peak=   -4.043 closest distance to " C   HIS A 108 " =    1.115
peak=   -4.034 closest distance to " O   HOH Z  13 " =    1.745
peak=   -3.968 closest distance to " O   HOH Z 196 " =    2.068
peak=   -3.955 closest distance to " CB  ALA A 184 " =    2.368
peak=   -3.953 closest distance to " CH2 TRP A 179 " =    1.278
peak=   -3.951 closest distance to " CD1 PHE A  59 " =    2.037
peak=   -3.939 closest distance to " O   HOH Z 166 " =    1.656
peak=   -3.937 closest distance to " CA  ASP A 298 " =    1.034
peak=   -3.927 closest distance to " O   HOH Z 348 " =    2.312
peak=   -3.874 closest distance to " O   ALA A  34 " =    2.335
peak=   -3.864 closest distance to " OG BSER A 134 " =    1.394
peak=   -3.856 closest distance to " OG  SER A  97 " =    2.223
peak=   -3.848 closest distance to " O   HOH Z 210 " =    0.983
peak=   -3.848 closest distance to " CG  GLU A  53 " =    1.520
peak=   -3.832 closest distance to " O   PHE A 218 " =    1.497
peak=   -3.830 closest distance to " CD1 LEU A  25 " =    2.457
peak=   -3.820 closest distance to " O   PRO A 198 " =    1.351
peak=   -3.804 closest distance to " CD  GLN A 223 " =    1.414
peak=   -3.791 closest distance to " O   HOH Z 283 " =    2.236
peak=   -3.786 closest distance to " NE2 GLN A  88 " =    1.850
peak=   -3.783 closest distance to " O   HOH Z 111 " =    1.876
peak=   -3.778 closest distance to " CG2 ILE A 263 " =    2.271
peak=   -3.768 closest distance to " CE2 TYR A  30 " =    2.645
peak=   -3.766 closest distance to " OE1 GLN A 223 " =    2.222
peak=   -3.765 closest distance to " CD  GLN A  58 " =    1.138
peak=   -3.759 closest distance to " O   HOH Z 165 " =    1.917
peak=   -3.753 closest distance to " CZ  TYR A 169 " =    1.874
peak=   -3.739 closest distance to " CG1 VAL A  78 " =    2.774
peak=   -3.735 closest distance to " ND2 ASN A  45 " =    2.002
peak=   -3.726 closest distance to " ND2 ASN A 249 " =    2.254
peak=   -3.714 closest distance to " O   HOH Z 198 " =    2.066
peak=   -3.703 closest distance to " O   PRO A 163 " =    2.119
peak=   -3.691 closest distance to " ND2 ASN A 187 " =    1.580
peak=   -3.685 closest distance to " CE BMET A  47 " =    1.782
peak=   -3.681 closest distance to " CD  ARG A 139 " =    1.605
peak=   -3.675 closest distance to " O   HOH Z 185 " =    2.459
peak=   -3.664 closest distance to " CE3 TRP A 150 " =    2.237
peak=   -3.655 closest distance to " O   SER A 210 " =    1.841
peak=   -3.653 closest distance to " CD2 TYR A 293 " =    1.846
peak=   -3.649 closest distance to " CG2 VAL A 189 " =    2.213
peak=   -3.641 closest distance to " O   HOH Z 372 " =    2.378
peak=   -3.638 closest distance to " O   HOH Z 292 " =    4.633
peak=   -3.628 closest distance to " NE2 GLN A 223 " =    1.283
peak=   -3.623 closest distance to " N   SER A 276 " =    1.461
peak=   -3.620 closest distance to " CD  LYS A 289 " =    2.374
peak=   -3.616 closest distance to " O   HOH Z 234 " =    4.181
peak=   -3.600 closest distance to " O   HOH Z 102 " =    1.621
peak=   -3.600 closest distance to " CB  ALA A 161 " =    2.604
peak=   -3.583 closest distance to " CB  ALA A  10 " =    2.208
peak=   -3.583 closest distance to " NE2 GLN A 194 " =    1.923
peak=   -3.580 closest distance to " CB  ALA A 248 " =    2.224
peak=   -3.579 closest distance to " O   ALA A   1 " =    1.999
peak=   -3.576 closest distance to " O   HOH Z 123 " =    2.378
peak=   -3.570 closest distance to " O   HOH Z  71 " =    2.015
peak=   -3.567 closest distance to " CB  ALA A 291 " =    2.413
peak=   -3.565 closest distance to " C   SER A 206 " =    1.487
peak=   -3.564 closest distance to " O   HOH Z 150 " =    2.221
peak=   -3.559 closest distance to " OD1 ASN A 148 " =    1.530
peak=   -3.553 closest distance to " O   HOH Z 150 " =    1.195
peak=   -3.541 closest distance to " CB  PHE A 192 " =    1.961
peak=   -3.529 closest distance to " ND2 ASN A  69 " =    1.695
peak=   -3.527 closest distance to " OG BSER A 210 " =    1.326
peak=   -3.527 closest distance to " O   SER A 276 " =    1.643
peak=   -3.524 closest distance to " CE2 PHE A  61 " =    2.627
peak=   -3.521 closest distance to " N   THR A  52 " =    1.740
peak=   -3.515 closest distance to " OD1 ASP A 191 " =    1.558
peak=   -3.512 closest distance to " CB  ALA A  43 " =    2.547
peak=   -3.501 closest distance to " O   HOH Z 394 " =    1.519
peak=   -3.499 closest distance to " O   HOH Z 196 " =    1.863
peak=   -3.488 closest distance to " O   HOH Z 422 " =    1.410
peak=   -3.488 closest distance to " CB  ALA A 291 " =    2.286
peak=   -3.486 closest distance to " O   HOH Z 351 " =    1.537
peak=   -3.481 closest distance to " NE  ARG A  66 " =    4.426
peak=   -3.471 closest distance to " ND2BASN A 224 " =    1.793
peak=   -3.467 closest distance to " O   VAL A 174 " =    2.216
peak=   -3.466 closest distance to " NH2 ARG A  79 " =    2.119
peak=   -3.465 closest distance to " O   HOH Z 171 " =    2.231
peak=   -3.463 closest distance to " CB  ARG A 219 " =    2.306
peak=   -3.452 closest distance to " O   VAL A 189 " =    2.619
peak=   -3.446 closest distance to " CD1 ILE A 151 " =    2.396
peak=   -3.437 closest distance to " O   HOH Z 252 " =    3.697
peak=   -3.433 closest distance to " CB  PHE A  16 " =    2.491
peak=   -3.431 closest distance to " O   HOH Z  15 " =    1.480
peak=   -3.428 closest distance to " N   ALA A 248 " =    2.310
peak=   -3.427 closest distance to " O   HOH Z 366 " =    1.828
peak=   -3.425 closest distance to " CA  GLY A 241 " =    2.376
peak=   -3.421 closest distance to " O   HOH Z 208 " =    1.904
peak=   -3.419 closest distance to " O   HOH Z   6 " =    1.624
peak=   -3.415 closest distance to " N   ALA A 248 " =    1.874
peak=   -3.414 closest distance to " O   HOH Z 197 " =    2.090
peak=   -3.411 closest distance to " O   ALA A  34 " =    2.120
peak=   -3.409 closest distance to " O   ASN A 187 " =    1.545
peak=   -3.392 closest distance to " CD2 TYR A 247 " =    2.372
peak=   -3.388 closest distance to " CG1 VAL A 112 " =    2.721
peak=   -3.381 closest distance to " O   SER A  26 " =    1.598
peak=   -3.377 closest distance to " O   HOH Z 264 " =    1.797
peak=   -3.374 closest distance to " O   HOH Z 200 " =    1.383
peak=   -3.370 closest distance to " O   HOH Z 407 " =    3.156
peak=   -3.369 closest distance to " CD  ARG A 195 " =    5.143
peak=   -3.366 closest distance to " CD  GLN A 223 " =    1.730
peak=   -3.362 closest distance to " CB  TRP A  85 " =    2.443
peak=   -3.358 closest distance to " OD1 ASP A 171 " =    1.587
peak=   -3.354 closest distance to " O   HOH Z 145 " =    2.663
peak=   -3.351 closest distance to " CA  SER A  62 " =    2.645
peak=   -3.348 closest distance to " O   HOH Z 177 " =    1.696
peak=   -3.348 closest distance to " O   HOH Z  52 " =    1.682
peak=   -3.348 closest distance to " CZ3 TRP A 274 " =    2.411
peak=   -3.347 closest distance to " O   HOH Z 290 " =    1.172
peak=   -3.344 closest distance to " C   ASN A 285 " =    2.344
peak=   -3.339 closest distance to " C   THR A 279 " =    1.104
peak=   -3.336 closest distance to " CG  PRO A 243 " =    1.717
peak=   -3.336 closest distance to " CG1AVAL A  41 " =    2.581
peak=   -3.336 closest distance to " CA  GLY A 133 " =    2.360
peak=   -3.335 closest distance to " O   HOH Z 154 " =    1.640
peak=   -3.335 closest distance to " CD2 PHE A 225 " =    1.300
peak=   -3.334 closest distance to " CD2 LEU A 300 " =    2.643
peak=   -3.332 closest distance to " CB  PRO A 163 " =    2.533
peak=   -3.330 closest distance to " O   HOH Z  78 " =    1.841
peak=   -3.330 closest distance to " O   HOH Z 136 " =    2.132
peak=   -3.328 closest distance to " O   ASN A 301 " =    1.319
peak=   -3.325 closest distance to " O   HOH Z 378 " =    1.285
peak=   -3.324 closest distance to " CB  ASP A 286 " =    1.903
peak=   -3.323 closest distance to " O   TRP A  92 " =    1.912
peak=   -3.317 closest distance to " OG BSER A 134 " =    1.882
peak=   -3.302 closest distance to " NH2 ARG A  66 " =    2.007
peak=   -3.292 closest distance to " CG  LEU A  83 " =    2.045
peak=   -3.291 closest distance to " C   GLY A  80 " =    2.534
peak=   -3.289 closest distance to " CA  GLY A 241 " =    3.130
peak=   -3.287 closest distance to " O   TYR A 186 " =    1.737
peak=   -3.282 closest distance to " O   HOH Z 252 " =    3.894
peak=   -3.281 closest distance to " O   HOH Z 240 " =    3.911
peak=   -3.279 closest distance to " O   HOH Z 126 " =    2.001
peak=   -3.276 closest distance to " OD1 ASN A  39 " =    2.279
peak=   -3.276 closest distance to " CG1 VAL A  78 " =    2.597
peak=   -3.275 closest distance to " O   HOH Z 174 " =    2.269
peak=   -3.273 closest distance to " O   HOH Z  63 " =    1.181
peak=   -3.272 closest distance to " OD1 ASN A 301 " =    2.030
peak=   -3.269 closest distance to " OE1 GLN A 223 " =    2.174
peak=   -3.267 closest distance to " O   HOH Z  56 " =    1.406
peak=   -3.267 closest distance to " CD2 HIS A 207 " =    2.378
peak=   -3.260 closest distance to " CB  ALA A   9 " =    2.553
peak=   -3.257 closest distance to " NE2 GLN A  88 " =    1.077
peak=   -3.254 closest distance to " O   HOH Z 426 " =    1.760
peak=   -3.250 closest distance to " OE2 GLU A   2 " =    1.713
peak=   -3.249 closest distance to " OG BSER A 210 " =    2.288
peak=   -3.248 closest distance to " O   HOH Z 103 " =    1.912
peak=   -3.245 closest distance to " O   GLY A 196 " =    1.053
peak=   -3.240 closest distance to " O   HOH Z 275 " =    1.483
peak=   -3.237 closest distance to " NE2 GLN A  11 " =    1.781
peak=   -3.235 closest distance to " O   SER A 135 " =    1.619
peak=   -3.233 closest distance to " CZ  PHE A  38 " =    2.354
peak=   -3.231 closest distance to " O   HOH Z 418 " =    1.344
peak=   -3.228 closest distance to " ND2 ASN A  45 " =    1.217
peak=   -3.224 closest distance to " CD2 PHE A  61 " =    2.133
peak=   -3.217 closest distance to " O   HOH Z 135 " =    1.499
peak=   -3.216 closest distance to " O   HOH Z 106 " =    1.960
peak=   -3.216 closest distance to " CA  GLY A 241 " =    2.901
peak=   -3.215 closest distance to " O   HOH Z 166 " =    1.557
peak=   -3.214 closest distance to " CH2 TRP A 150 " =    1.135
peak=   -3.214 closest distance to " OD2 ASP A 171 " =    2.501
peak=   -3.209 closest distance to " O   SER A   3 " =    1.150
peak=   -3.205 closest distance to " OE1 GLN A 183 " =    1.521
peak=   -3.205 closest distance to " O   HOH Z 114 " =    3.517
peak=   -3.200 closest distance to " CD1 TRP A 179 " =    1.176
peak=   -3.198 closest distance to " CE  MET A 105 " =    2.860
peak=   -3.197 closest distance to " O   HOH Z   6 " =    1.990
peak=   -3.194 closest distance to " O   ALA A  10 " =    1.801
peak=   -3.191 closest distance to " O   HOH Z 193 " =    1.545
peak=   -3.181 closest distance to " O   HOH Z 311 " =    3.788
peak=   -3.179 closest distance to " N   ALA A 226 " =    1.987
peak=   -3.175 closest distance to " CG  ARG A 269 " =    2.292
peak=   -3.174 closest distance to " O   HOH Z 285 " =    1.294
peak=   -3.171 closest distance to " CD1 ILE A 106 " =    2.164
peak=   -3.164 closest distance to " C   ALA A 158 " =    1.402
peak=   -3.163 closest distance to " O   PRO A 198 " =    1.363
peak=   -3.161 closest distance to " OG  SER A  26 " =    1.300
peak=   -3.159 closest distance to " O   HOH Z  90 " =    1.954
peak=   -3.152 closest distance to " O   HOH Z 389 " =    1.799
peak=   -3.149 closest distance to " OD1 ASN A 249 " =    2.416
peak=   -3.146 closest distance to " O   HOH Z  40 " =    2.332
peak=   -3.141 closest distance to " O   HOH Z 281 " =    2.379
peak=   -3.126 closest distance to " CB  ASP A 132 " =    2.402
peak=   -3.116 closest distance to " CG2AVAL A  41 " =    2.969
peak=   -3.115 closest distance to " O   HOH Z 149 " =    2.140
peak=   -3.113 closest distance to " OD2 ASP A 171 " =    1.810
peak=   -3.109 closest distance to " CE3 TRP A  92 " =    2.640
peak=   -3.103 closest distance to " O   HOH Z 361 " =    3.378
peak=   -3.101 closest distance to " O   HOH Z 336 " =    4.851
peak=   -3.095 closest distance to " CZ  PHE A  38 " =    1.951
peak=   -3.094 closest distance to " O   HOH Z  11 " =    1.818
peak=   -3.083 closest distance to " O   HOH Z 211 " =    1.639
peak=   -3.080 closest distance to " O   HOH Z 423 " =    2.364
peak=   -3.079 closest distance to " O   HOH Z 396 " =    1.991
peak=   -3.074 closest distance to " NH2 ARG A  66 " =    5.548
peak=   -3.073 closest distance to " NH2 ARG A  66 " =    1.182
peak=   -3.069 closest distance to " O   HOH Z 156 " =    3.550
peak=   -3.059 closest distance to " CB  SER A  62 " =    5.498
peak=   -3.052 closest distance to " O   HOH Z 434 " =    2.601
peak=   -3.049 closest distance to " O   HOH Z 392 " =    1.444
peak=   -3.045 closest distance to " O   HOH Z 377 " =    2.053
peak=   -3.025 closest distance to " O   HOH Z 166 " =    1.345
peak=   -3.017 closest distance to " O   HOH Z 236 " =    1.637

================= 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    :  0.4210 0.4081   6.228192e+00   6.196777e+00
   1_bss:  0.4104 0.3958   6.216413e+00   6.180196e+00
   1_xyz:  0.2997 0.3224   5.981220e+00   6.032787e+00
   1_adp:  0.2733 0.3363   5.930522e+00   6.056968e+00
   1_occ:  0.2732 0.3364   5.930022e+00   6.057115e+00
   2_bss:  0.2721 0.3341   5.928605e+00   6.056238e+00
   2_xyz:  0.1999 0.2422   5.635066e+00   5.794800e+00
   2_adp:  0.1816 0.2245   5.561096e+00   5.732548e+00
   2_occ:  0.1813 0.2246   5.560370e+00   5.732519e+00
   3_bss:  0.1807 0.2232   5.557944e+00   5.729041e+00
   3_xyz:  0.1383 0.1807   5.317337e+00   5.523207e+00
   3_adp:  0.1282 0.1736   5.260341e+00   5.480285e+00
   3_occ:  0.1282 0.1738   5.260486e+00   5.480558e+00
   4_bss:  0.1286 0.1741   5.262291e+00   5.480952e+00
   4_xyz:  0.1219 0.1677   5.222509e+00   5.446944e+00
   4_adp:  0.1199 0.1667   5.210081e+00   5.437614e+00
   4_occ:  0.1199 0.1667   5.209941e+00   5.437552e+00
   5_bss:  0.1199 0.1667   5.209961e+00   5.437676e+00
   5_xyz:  0.1121 0.1624   5.161180e+00   5.407058e+00
   5_adp:  0.1112 0.1616   5.155494e+00   5.403070e+00
   5_occ:  0.1112 0.1616   5.155175e+00   5.403017e+00
   5_bss:  0.1110 0.1615   5.155344e+00   5.403186e+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:  0.296  35.629  -2.793   4.577   0.005   0.000   0.000   0.000
   1_xyz:  0.296  35.629  -2.793   4.577   0.005   0.000   0.000   0.000
   1_adp:  0.296  35.629  -2.793   4.577   0.005   0.000   0.000   0.000
   1_occ:  0.296  35.629  -2.793   4.577   0.005   0.000   0.000   0.000
   2_bss:  0.317  59.174  -2.330   1.852  -0.232   0.000  -0.000  -0.000
   2_xyz:  0.317  59.174  -2.330   1.852  -0.232   0.000  -0.000  -0.000
   2_adp:  0.317  59.174  -2.330   1.852  -0.232   0.000  -0.000  -0.000
   2_occ:  0.317  59.174  -2.330   1.852  -0.232   0.000  -0.000  -0.000
   3_bss:  0.322  60.518  -2.438  -0.135  -0.435  -0.000  -0.000  -0.000
   3_xyz:  0.322  60.518  -2.438  -0.135  -0.435  -0.000  -0.000  -0.000
   3_adp:  0.322  60.518  -2.438  -0.135  -0.435  -0.000  -0.000  -0.000
   3_occ:  0.322  60.518  -2.438  -0.135  -0.435  -0.000  -0.000  -0.000
   4_bss:  0.330  66.357  -2.464  -0.852  -0.490  -0.000  -0.000  -0.000
   4_xyz:  0.330  66.357  -2.464  -0.852  -0.490  -0.000  -0.000  -0.000
   4_adp:  0.330  66.357  -2.464  -0.852  -0.490  -0.000  -0.000  -0.000
   4_occ:  0.330  66.357  -2.464  -0.852  -0.490  -0.000  -0.000  -0.000
   5_bss:  0.327  65.997  -2.286  -0.937  -0.340  -0.000  -0.000  -0.000
   5_xyz:  0.327  65.997  -2.286  -0.937  -0.340  -0.000  -0.000  -0.000
   5_adp:  0.327  65.997  -2.286  -0.937  -0.340  -0.000  -0.000  -0.000
   5_occ:  0.327  65.997  -2.286  -0.937  -0.340  -0.000  -0.000  -0.000
   5_bss:  0.324  63.956  -1.993  -0.773  -0.071  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.307 0.5679  0.7326    50505.017
   1_bss:  45.211 0.5797  0.7632    47092.817
   1_xyz:  35.007 0.7018  0.8940    29626.370
   1_adp:  36.373 0.6852  0.8726    31759.105
   1_occ:  36.414 0.6847  0.8717    31774.411
   2_bss:  36.015 0.6895  0.8567    31369.619
   2_xyz:  24.873 0.8115  0.9686    15321.814
   2_adp:  22.637 0.8354  0.9743    13330.503
   2_occ:  22.628 0.8355  0.9742    13321.782
   3_bss:  22.438 0.8374  0.9509    13139.070
   3_xyz:  17.206 0.8870  0.9817     8280.705
   3_adp:  16.191 0.8963  0.9777     7693.528
   3_occ:  16.205 0.8962  0.9775     7701.612
   4_bss:  16.205 0.8962  0.9689     7709.015
   4_xyz:  15.418 0.9034  0.9702     7202.921
   4_adp:  15.207 0.9053  0.9615     7136.589
   4_occ:  15.206 0.9053  0.9614     7134.289
   5_bss:  15.207 0.9053  0.9644     7134.805
   5_xyz:  14.615 0.9099  0.9693     6723.120
   5_adp:  14.521 0.9108  0.9616     6659.873
   5_occ:  14.517 0.9109  0.9615     6656.555
   5_bss:  14.521 0.9108  0.9699     6657.653
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6628e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6628e-01
   1_xyz:   1.360  0.010  0.083 15.019  0.005  4.110   9.5252e-02
   1_adp:   1.360  0.010  0.083 15.019  0.005  4.110   9.5252e-02
   1_occ:   1.360  0.010  0.083 15.019  0.005  4.110   9.5252e-02
   2_bss:   1.360  0.010  0.083 15.019  0.005  4.110   9.5252e-02
   2_xyz:   1.257  0.009  0.083 14.391  0.005  4.110   8.3260e-02
   2_adp:   1.257  0.009  0.083 14.391  0.005  4.110   8.3260e-02
   2_occ:   1.257  0.009  0.083 14.391  0.005  4.110   8.3260e-02
   3_bss:   1.257  0.009  0.083 14.391  0.005  4.110   8.3260e-02
   3_xyz:   1.117  0.009  0.075 14.642  0.004  4.122   7.2117e-02
   3_adp:   1.117  0.009  0.075 14.642  0.004  4.122   7.2117e-02
   3_occ:   1.117  0.009  0.075 14.642  0.004  4.122   7.2117e-02
   4_bss:   1.117  0.009  0.075 14.642  0.004  4.122   7.2117e-02
   4_xyz:   0.994  0.007  0.074 14.355  0.004  4.115   5.7511e-02
   4_adp:   0.994  0.007  0.074 14.355  0.004  4.115   5.7511e-02
   4_occ:   0.994  0.007  0.074 14.355  0.004  4.115   5.7511e-02
   5_bss:   0.994  0.007  0.074 14.355  0.004  4.115   5.7511e-02
   5_xyz:   1.173  0.011  0.085 14.780  0.004  4.119   8.1471e-02
   5_adp:   1.173  0.011  0.085 14.780  0.004  4.119   8.1471e-02
   5_occ:   1.173  0.011  0.085 14.780  0.004  4.119   8.1471e-02
   5_bss:   1.173  0.011  0.085 14.780  0.004  4.119   8.1471e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4252e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4252e-01
   1_xyz:   8.752  0.064  0.394 85.423  0.019  2.091   9.5062e-02
   1_adp:   8.752  0.064  0.394 85.423  0.019  2.091   9.5062e-02
   1_occ:   8.752  0.064  0.394 85.423  0.019  2.091   9.5062e-02
   2_bss:   8.752  0.064  0.394 85.423  0.019  2.091   9.5062e-02
   2_xyz:   7.396  0.044  0.272 84.916  0.035  2.242   1.2223e-01
   2_adp:   7.396  0.044  0.272 84.916  0.035  2.242   1.2223e-01
   2_occ:   7.396  0.044  0.272 84.916  0.035  2.242   1.2223e-01
   3_bss:   7.396  0.044  0.272 84.916  0.035  2.242   1.2223e-01
   3_xyz:   8.480  0.063  0.246 83.124  0.030  2.264   5.8476e-02
   3_adp:   8.480  0.063  0.246 83.124  0.030  2.264   5.8476e-02
   3_occ:   8.480  0.063  0.246 83.124  0.030  2.264   5.8476e-02
   4_bss:   8.480  0.063  0.246 83.124  0.030  2.264   5.8476e-02
   4_xyz:   7.068  0.041  0.238 81.856  0.031  2.416   5.6659e-02
   4_adp:   7.068  0.041  0.238 81.856  0.031  2.416   5.6659e-02
   4_occ:   7.068  0.041  0.238 81.856  0.031  2.416   5.6659e-02
   5_bss:   7.068  0.041  0.238 81.856  0.031  2.416   5.6659e-02
   5_xyz:   8.714  0.050  0.308 82.244  0.033  2.289   8.0199e-02
   5_adp:   8.714  0.050  0.308 82.244  0.033  2.289   8.0199e-02
   5_occ:   8.714  0.050  0.308 82.244  0.033  2.289   8.0199e-02
   5_bss:   8.714  0.050  0.308 82.244  0.033  2.289   8.0199e-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:  88.33   0.00  17.73  73.09   0.00  14.16  88.33   1.12  37.14
   1_occ:  88.33   0.00  17.73  73.09   0.00  14.16  88.33   1.12  37.14
   2_bss:  88.33   0.00  17.73  73.09   0.00  14.16  88.33   1.12  37.14
   2_xyz:  88.33   0.00  17.73  73.09   0.00  14.16  88.33   1.12  37.14
   2_adp:  87.96   0.00  17.37  73.87   0.00  13.35  87.96   4.88  39.28
   2_occ:  87.96   0.00  17.37  73.87   0.00  13.35  87.96   4.88  39.28
   3_bss:  87.96   0.00  17.37  73.87   0.00  13.35  87.96   4.88  39.28
   3_xyz:  87.96   0.00  17.37  73.87   0.00  13.35  87.96   4.88  39.28
   3_adp:  88.33   0.00  17.38  88.07   0.00  12.86  88.33   5.59  41.98
   3_occ:  88.33   0.00  17.38  88.07   0.00  12.86  88.33   5.59  41.98
   4_bss:  88.33   0.00  17.38  88.07   0.00  12.86  88.33   5.59  41.98
   4_xyz:  88.33   0.00  17.38  88.07   0.00  12.86  88.33   5.59  41.98
   4_adp:  92.91   0.00  17.12  92.91   0.00  12.56  87.71   0.00  41.98
   4_occ:  92.91   0.00  17.12  92.91   0.00  12.56  87.71   0.00  41.98
   5_bss:  92.91   0.00  17.12  92.91   0.00  12.56  87.71   0.00  41.98
   5_xyz:  92.91   0.00  17.12  92.91   0.00  12.56  87.71   0.00  41.98
   5_adp: 104.33   0.00  16.95 104.33   0.00  12.37  96.32   0.00  41.94
   5_occ: 104.33   0.00  16.95 104.33   0.00  12.37  96.32   0.00  41.94
   5_bss: 104.34   0.00  16.96 104.34   0.00  12.37  96.33   0.00  41.94
------------------------------------------------------------------------
 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:    1.710    0.020    0.332
   1_adp:    1.710    0.020    0.332
   1_occ:    1.710    0.020    0.332
   2_bss:    1.710    0.020    0.332
   2_xyz:    1.240    0.027    0.517
   2_adp:    1.240    0.027    0.517
   2_occ:    1.240    0.027    0.517
   3_bss:    1.240    0.027    0.517
   3_xyz:    1.264    0.053    0.624
   3_adp:    1.264    0.053    0.624
   3_occ:    1.264    0.053    0.624
   4_bss:    1.264    0.053    0.624
   4_xyz:    1.316    0.081    0.655
   4_adp:    1.316    0.081    0.655
   4_occ:    1.316    0.081    0.655
   5_bss:    1.316    0.081    0.655
   5_xyz:    1.264    0.075    0.672
   5_adp:    1.264    0.075    0.672
   5_occ:    1.264    0.075    0.672
   5_bss:    1.264    0.075    0.672
------------------------------------------------------------------------

CPU time actual refinement: 332.84


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_469/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_469/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_469/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_469/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_469/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 332.69 
  Macro-tasks:
    bulk solvent and scale       = 39.33  
    individual site refinement   = 132.78 
    weights calculation          = 29.42  
    collect and process          = 6.58   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 208.25 
  Micro-tasks:
    mask                            = 1.77   
    f_calc                          = 106.18 
    alpha_beta                      = 8.21   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 114.28 
    fmodel                         = 6.95   
    r_factors                      = 0.16   
    phase_errors                   = 10.89  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 249.89 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.769 micro seconds
Total CPU time: 5.77 minutes
from_scatterers_fft:    646 calls, 105.86 s
gradients_fft:          591 calls, 101.51 s

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

# Date 2008-01-16 Time 04:54:30 PST -0800 (1200488070.53 s)
Start R-work = 0.4210, R-free = 0.4081 (no bulk solvent and anisotropic scale)
Final R-work = 0.1308, R-free = 0.1766 (no bulk solvent and anisotropic scale)

Start R-work = 0.4104, R-free = 0.3958
Final R-work = 0.1110, R-free = 0.1615