# Date 2008-01-16 Time 05:31:35 PST -0800 (1200490295.56 s)
#phil __OFF__

Command line arguments: "../772.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 20301
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 772

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 46.6953, 85.0941, 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: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.6953, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9858 1.97109
Completeness in resolution range: 0.958835
Completeness with d_max=infinity: 0.955934

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9858
                             d_min =   1.9711

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.6953, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9858 1.97109
Completeness in resolution range: 0.958835
Completeness with d_max=infinity: 0.955934

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9863 -  4.2180 [2140/2169]  1929   211   9.9%
  bin  2:  4.2180 -  3.3604 [2053/2069]  1846   207  10.1%
  bin  3:  3.3604 -  2.9392 [2039/2058]  1832   207  10.2%
  bin  4:  2.9392 -  2.6721 [2027/2057]  1827   200   9.9%
  bin  5:  2.6721 -  2.4815 [2000/2019]  1804   196   9.8%
  bin  6:  2.4815 -  2.3358 [2000/2025]  1793   207  10.3%
  bin  7:  2.3358 -  2.2192 [1959/1992]  1765   194   9.9%
  bin  8:  2.2192 -  2.1229 [1993/2024]  1794   199  10.0%
  bin  9:  2.1229 -  2.0414 [1982/2024]  1783   199  10.0%
  bin 10:  2.0414 -  1.9711 [1396/1993]  1257   139  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_772/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: 23
        2.42 -     3.04: 2210
        3.04 -     3.66: 4736
        3.66 -     4.28: 9094
        4.28 -     4.90: 12420
  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 113 " - " O   HOH Z 350 "  2.011 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  2.041 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  2.125 3.120 -x,y-1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 28478 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_772/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_772/model_refine_001.geo

CPU time processing inputs: 9.36


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 46.69535 85.09415 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: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3109   r_free= 0.3126   ksol= 0.00   Bsol= 0.00   scale= 0.983    |
|                                                                             |
| 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:   0.35 A                  |
| x-ray target function (ml) for work reflections: 6.005476                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9863 -  4.7047 0.99   1388  155 0.2816 0.2786      6.3384      6.3052|
|  2:  4.7047 -  3.7536 0.99   1347  146 0.2452 0.2357      6.3874      6.3612|
|  3:  3.7536 -  3.2848 0.99   1316  147 0.2664 0.2662      6.2811      6.4131|
|  4:  3.2848 -  2.9870 0.99   1313  153 0.2715 0.2926       6.167      6.1688|
|  5:  2.9870 -  2.7744 0.99   1294  140 0.3096 0.3004      6.0569      6.0405|
|  6:  2.7744 -  2.6117 0.99   1289  145 0.3313 0.3332      6.0024      6.0183|
|  7:  2.6117 -  2.4815 0.99   1291  135 0.3273 0.3175      5.9787      5.9419|
|  8:  2.4815 -  2.3740 0.98   1267  150 0.3439 0.3368      5.9416      5.9286|
|  9:  2.3740 -  2.2829 0.98   1271  142 0.3349 0.3300      5.8821      5.8137|
| 10:  2.2829 -  2.2044 0.99   1284  137 0.3412 0.3880       5.854      5.9753|
| 11:  2.2044 -  2.1356 0.99   1282  143 0.3641 0.3561      5.8366       5.889|
| 12:  2.1356 -  2.0748 0.97   1250  139 0.3563 0.3805       5.781      5.8433|
| 13:  2.0748 -  2.0203 0.99   1268  141 0.3636 0.3582      5.6779      5.6229|
| 14:  2.0203 -  1.9711 0.60    770   86 0.3995 0.4038      5.7007      5.6307|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9863 -  4.7047  1388   155  0.80  25.24   0.87     0.81      40173.33|
|  2:  4.7047 -  3.7536  1347   146  0.85  21.50   0.98     0.93      43370.98|
|  3:  3.7536 -  3.2848  1316   147  0.81  25.16   1.01     0.97      42177.67|
|  4:  3.2848 -  2.9870  1313   153  0.79  27.54   1.02     0.96      37261.68|
|  5:  2.9870 -  2.7744  1294   140  0.74  31.91   0.99     0.94      31409.00|
|  6:  2.7744 -  2.6117  1289   145  0.73  33.35   1.00     0.93      27758.87|
|  7:  2.6117 -  2.4815  1291   135  0.74  32.45   1.02     0.94      24965.72|
|  8:  2.4815 -  2.3740  1267   150  0.72  33.86   1.00     0.95      23239.05|
|  9:  2.3740 -  2.2829  1271   142  0.72  33.70   1.05     0.94      21598.21|
| 10:  2.2829 -  2.2044  1284   137  0.69  36.20   1.05     0.94      21967.78|
| 11:  2.2044 -  2.1356  1282   143  0.68  37.90   1.07     0.93      21061.81|
| 12:  2.1356 -  2.0748  1250   139  0.68  37.48   1.07     0.96      20154.04|
| 13:  2.0748 -  2.0203  1268   141  0.65  39.85   1.06     0.91      17237.03|
| 14:  2.0203 -  1.9711   770    86  0.66  39.74   1.03     0.84      14657.68|
|alpha:            min =        0.81 max =            0.97 mean =         0.93|
|beta:             min =    14657.68 max =        43370.98 mean =     28230.60|
|figures of merit: min =        0.00 max =            1.00 mean =         0.74|
|phase err.(work): min =        0.00 max =           89.96 mean =        32.23|
|phase err.(test): min =        0.00 max =           89.30 mean =        32.31|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.218820              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.350   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.641956              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.932   (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:        3 |
| 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:      209 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2001 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1883 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2853 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4672 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4422 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5655 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6765 |
|-----------------------------------------------------------------------------|
|-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 |        0.162 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.806 |       0.189 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.759)------------------------------------------|
|    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: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3109   r_free= 0.3126   ksol= 0.00   Bsol= 0.00   scale= 0.983    |
|                                                                             |
| 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:   0.35 A                  |
| x-ray target function (ml) for work reflections: 6.005476                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2952   r_free= 0.2960   ksol= 0.32   Bsol= 35.97   scale= 0.980   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-2.23,1.15,-0.00,0.00,0.00); trace/3= -1.23                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.984046                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.398513              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.462   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.308105              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.858   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2952      final r-factor (work) = 0.1615          |
| start r-factor (free) = 0.2960      final r-factor (free) = 0.1855          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.3418 = 4.40 * 0.50 * 5.9927 + 1.00 * 0.1623                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5550 = 4.40 * 0.50 * 5.6806 + 1.00 * 0.0619                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1615      final r-factor (work) = 0.1522          |
| start r-factor (free) = 0.1855      final r-factor (free) = 0.1879          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7568 = 0.31 * 1.00 * 5.6806 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7229 = 0.31 * 1.00 * 5.3747 + 1.00 * 0.0670                               |
|-----------------------------------------------------------------------------|
| number of iterations = 4       |    number of function evaluations = 4      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.759)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.03   16.31    None  None   None       |
|    all(noH): 2823   0      0.00    78.03   16.31    None  None   None       |
|    Sol.    : 438    0      6.02    62.29   37.20    None  None   None       |
|    Mac.    : 2385   0      0.00    78.03   12.48    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.803:  401   |   5:    39.017 -  46.820:  113        |
|      1:     7.803 -  15.607: 1553   |   6:    46.820 -  54.623:   78        |
|      2:    15.607 -  23.410:  377   |   7:    54.623 -  62.426:   39        |
|      3:    23.410 -  31.213:  145   |   8:    62.426 -  70.230:    0        |
|      4:    31.213 -  39.017:  116   |   9:    70.230 -  78.033:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1522 r_free = 0.1879             target_work(ml) = 5.381         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1516 r_free = 0.1881             target_work(ml) = 5.379         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1516   r_free= 0.1881   ksol= 0.32   Bsol= 35.97   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-2.23,1.15,-0.00,0.00,0.00); trace/3= -1.23                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.378862                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1503   r_free= 0.1849   ksol= 0.33   Bsol= 43.40   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-2.74,-1.30,-0.00,-0.00,-0.00); trace/3= -2.29                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.369983                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.298915              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.084  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.426320              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.271   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1503      final r-factor (work) = 0.1212          |
| start r-factor (free) = 0.1849      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2567 = 2.30 * 0.50 * 5.3893 + 1.00 * 0.0619                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1127 = 2.30 * 0.50 * 5.2694 + 1.00 * 0.0557                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1212      final r-factor (work) = 0.1144          |
| start r-factor (free) = 0.1549      final r-factor (free) = 0.1535          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2821 = 0.43 * 1.00 * 5.2694 + 1.00 * 0.0357                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2017 = 0.43 * 1.00 * 5.1454 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.759)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.56    77.72   17.00    None  None   None       |
|    all(noH): 2823   0      1.56    77.72   17.00    None  None   None       |
|    Sol.    : 438    0      4.10    74.44   39.20    None  None   None       |
|    Mac.    : 2385   0      1.56    77.72   12.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.557 -   9.173:  774   |   5:    39.641 -  47.258:  113        |
|      1:     9.173 -  16.790: 1259   |   6:    47.258 -  54.874:   86        |
|      2:    16.790 -  24.407:  286   |   7:    54.874 -  62.491:   54        |
|      3:    24.407 -  32.024:  122   |   8:    62.491 -  70.108:   21        |
|      4:    32.024 -  39.641:  101   |   9:    70.108 -  77.725:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1144 r_free = 0.1535             target_work(ml) = 5.140         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1143 r_free = 0.1535             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1143   r_free= 0.1535   ksol= 0.33   Bsol= 43.40   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-2.74,-1.30,-0.00,-0.00,-0.00); trace/3= -2.29                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.139483                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1143   r_free= 0.1534   ksol= 0.32   Bsol= 43.40   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-2.51,-1.53,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.138300                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.726002              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.259  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.258305              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.879  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1143      final r-factor (work) = 0.1099          |
| start r-factor (free) = 0.1534      final r-factor (free) = 0.1516          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4956 = 1.73 * 0.50 * 5.1448 + 1.00 * 0.0557                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4742 = 1.73 * 0.50 * 5.1213 + 1.00 * 0.0545                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1099      final r-factor (work) = 0.1092          |
| start r-factor (free) = 0.1516      final r-factor (free) = 0.1518          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3309 = 0.26 * 1.00 * 5.1213 + 1.00 * 0.0081                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3291 = 0.26 * 1.00 * 5.1151 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.759)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.54    79.28   16.83    None  None   None       |
|    all(noH): 2823   0      1.54    79.28   16.83    None  None   None       |
|    Sol.    : 438    0      4.18    75.04   38.50    None  None   None       |
|    Mac.    : 2385   0      1.54    79.28   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:     1.540 -   9.313:  844   |   5:    40.408 -  48.182:  111        |
|      1:     9.313 -  17.087: 1189   |   6:    48.182 -  55.956:   83        |
|      2:    17.087 -  24.861:  296   |   7:    55.956 -  63.730:   44        |
|      3:    24.861 -  32.635:  131   |   8:    63.730 -  71.503:   15        |
|      4:    32.635 -  40.408:  104   |   9:    71.503 -  79.277:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1092 r_free = 0.1518             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1091 r_free = 0.1517             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1517   ksol= 0.32   Bsol= 43.40   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-2.51,-1.53,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.115969                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1092   r_free= 0.1522   ksol= 0.32   Bsol= 43.40   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,-2.40,-1.58,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.117565                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.408777              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 148.921  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.211074              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.111  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1092      final r-factor (work) = 0.1061          |
| start r-factor (free) = 0.1522      final r-factor (free) = 0.1523          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2147 = 2.41 * 0.50 * 5.1148 + 1.00 * 0.0545                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2091 = 2.41 * 0.50 * 5.1039 + 1.00 * 0.0620                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1061      final r-factor (work) = 0.1063          |
| start r-factor (free) = 0.1523      final r-factor (free) = 0.1527          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0851 = 0.21 * 1.00 * 5.1039 + 1.00 * 0.0078                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0843 = 0.21 * 1.00 * 5.1028 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.759)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.50    80.23   16.50    None  None   None       |
|    all(noH): 2823   0      1.50    80.23   16.50    None  None   None       |
|    Sol.    : 438    0      5.79    74.65   37.23    None  None   None       |
|    Mac.    : 2385   0      1.50    80.23   12.69    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.501 -   9.374:  885   |   5:    40.865 -  48.738:  105        |
|      1:     9.374 -  17.246: 1174   |   6:    48.738 -  56.611:   69        |
|      2:    17.246 -  25.119:  284   |   7:    56.611 -  64.484:   32        |
|      3:    25.119 -  32.992:  128   |   8:    64.484 -  72.356:    7        |
|      4:    32.992 -  40.865:  133   |   9:    72.356 -  80.229:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1063 r_free = 0.1527             target_work(ml) = 5.104         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1062 r_free = 0.1527             target_work(ml) = 5.105         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1062   r_free= 0.1527   ksol= 0.32   Bsol= 43.40   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,-2.40,-1.58,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.104547                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1062   r_free= 0.1527   ksol= 0.32   Bsol= 43.40   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.30,-2.28,-1.48,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.104589                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.141706              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 166.834  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.277482              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.522  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1062      final r-factor (work) = 0.1040          |
| start r-factor (free) = 0.1527      final r-factor (free) = 0.1542          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0782 = 3.14 * 0.50 * 5.1031 + 1.00 * 0.0620                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0756 = 3.14 * 0.50 * 5.0957 + 1.00 * 0.0710                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1040      final r-factor (work) = 0.1038          |
| start r-factor (free) = 0.1542      final r-factor (free) = 0.1545          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4213 = 0.28 * 1.00 * 5.0957 + 1.00 * 0.0073                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4219 = 0.28 * 1.00 * 5.0974 + 1.00 * 0.0075                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.759)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.26    80.65   16.38    None  None   None       |
|    all(noH): 2823   0      1.26    80.65   16.38    None  None   None       |
|    Sol.    : 438    0      6.58    74.45   37.18    None  None   None       |
|    Mac.    : 2385   0      1.26    80.65   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:     1.258 -   9.198:  878   |   5:    40.955 -  48.894:  105        |
|      1:     9.198 -  17.137: 1183   |   6:    48.894 -  56.833:   70        |
|      2:    17.137 -  25.076:  284   |   7:    56.833 -  64.772:   28        |
|      3:    25.076 -  33.015:  125   |   8:    64.772 -  72.712:    7        |
|      4:    33.015 -  40.955:  137   |   9:    72.712 -  80.651:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1038 r_free = 0.1545             target_work(ml) = 5.099         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1038 r_free = 0.1545             target_work(ml) = 5.100         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1038   r_free= 0.1545   ksol= 0.32   Bsol= 43.40   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.30,-2.28,-1.48,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.099501                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9863 -  4.7047 0.99   1388  155 0.0963 0.1269      5.3615      5.5297|
|  2:  4.7047 -  3.7536 0.99   1347  146 0.0823 0.1107      5.4143      5.6139|
|  3:  3.7536 -  3.2848 0.99   1316  147 0.1005 0.1507      5.4372       5.856|
|  4:  3.2848 -  2.9870 0.99   1313  153 0.1125 0.1503      5.4195      5.5572|
|  5:  2.9870 -  2.7744 0.99   1294  140 0.1219 0.1768      5.2812      5.5533|
|  6:  2.7744 -  2.6117 0.99   1289  145 0.1125 0.1703      5.1625      5.3949|
|  7:  2.6117 -  2.4815 0.99   1291  135 0.1144 0.1587       5.113      5.3484|
|  8:  2.4815 -  2.3740 0.98   1267  150 0.1052 0.1685      4.9932      5.2942|
|  9:  2.3740 -  2.2829 0.98   1271  142 0.1070 0.1749      4.9778      5.3064|
| 10:  2.2829 -  2.2044 0.99   1284  137 0.1007 0.1681      4.8997       5.159|
| 11:  2.2044 -  2.1356 0.99   1282  143 0.1055 0.1783      4.9001      5.2852|
| 12:  2.1356 -  2.0748 0.97   1250  139 0.1005 0.1517      4.8214      5.0408|
| 13:  2.0748 -  2.0203 0.99   1268  141 0.1021 0.1769      4.7388      5.0709|
| 14:  2.0203 -  1.9711 0.60    770   86 0.0955 0.1545      4.6069      4.8557|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9863 -  4.7047  1388   155  0.94   8.96   0.98     0.95       6861.98|
|  2:  4.7047 -  3.7536  1347   146  0.95   7.74   1.02     1.01       8860.89|
|  3:  3.7536 -  3.2848  1316   147  0.93  11.20   1.02     1.01      10026.46|
|  4:  3.2848 -  2.9870  1313   153  0.92  13.49   1.01     0.99      10230.89|
|  5:  2.9870 -  2.7744  1294   140  0.90  15.62   0.99     0.97       7920.59|
|  6:  2.7744 -  2.6117  1289   145  0.91  15.44   0.98     0.95       6683.93|
|  7:  2.6117 -  2.4815  1291   135  0.91  14.60   0.99     0.96       5716.68|
|  8:  2.4815 -  2.3740  1267   150  0.92  14.34   0.99     0.97       4778.65|
|  9:  2.3740 -  2.2829  1271   142  0.92  14.28   1.01     0.99       4569.17|
| 10:  2.2829 -  2.2044  1284   137  0.91  14.52   0.99     0.95       3972.38|
| 11:  2.2044 -  2.1356  1282   143  0.90  16.05   1.00     0.97       4213.81|
| 12:  2.1356 -  2.0748  1250   139  0.92  14.09   1.00     0.98       3662.60|
| 13:  2.0748 -  2.0203  1268   141  0.91  15.66   1.01     1.00       3157.52|
| 14:  2.0203 -  1.9711   770    86  0.92  13.92   0.98     0.95       2344.59|
|alpha:            min =        0.95 max =            1.01 mean =         0.98|
|beta:             min =     2344.59 max =        10230.89 mean =      6074.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.89 mean =        13.50|
|phase err.(test): min =        0.00 max =           86.96 mean =        13.09|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1038   r_free= 0.1545   ksol= 0.32   Bsol= 43.32   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.10,-2.10,-1.31,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.099588                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1038   r_free= 0.1545   ksol= 0.32   Bsol= 43.32   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.10,-2.10,-1.31,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.099588                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9863 -  4.7047 0.99   1388  155 0.0964 0.1271      5.3624      5.5308|
|  2:  4.7047 -  3.7536 0.99   1347  146 0.0823 0.1107      5.4145      5.6136|
|  3:  3.7536 -  3.2848 0.99   1316  147 0.1005 0.1507      5.4371      5.8561|
|  4:  3.2848 -  2.9870 0.99   1313  153 0.1125 0.1503      5.4195      5.5572|
|  5:  2.9870 -  2.7744 0.99   1294  140 0.1219 0.1768      5.2811      5.5531|
|  6:  2.7744 -  2.6117 0.99   1289  145 0.1125 0.1704      5.1625      5.3951|
|  7:  2.6117 -  2.4815 0.99   1291  135 0.1144 0.1587      5.1131      5.3488|
|  8:  2.4815 -  2.3740 0.98   1267  150 0.1053 0.1685      4.9933      5.2942|
|  9:  2.3740 -  2.2829 0.98   1271  142 0.1070 0.1749      4.9778      5.3065|
| 10:  2.2829 -  2.2044 0.99   1284  137 0.1007 0.1680      4.8998      5.1589|
| 11:  2.2044 -  2.1356 0.99   1282  143 0.1055 0.1783      4.9001      5.2851|
| 12:  2.1356 -  2.0748 0.97   1250  139 0.1005 0.1518      4.8212      5.0409|
| 13:  2.0748 -  2.0203 0.99   1268  141 0.1021 0.1769      4.7387      5.0705|
| 14:  2.0203 -  1.9711 0.60    770   86 0.0955 0.1545      4.6069       4.856|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9863 -  4.7047  1388   155  0.94   8.97   0.98     0.95       6876.72|
|  2:  4.7047 -  3.7536  1347   146  0.95   7.75   1.02     1.01       8869.29|
|  3:  3.7536 -  3.2848  1316   147  0.93  11.20   1.03     1.02      10025.11|
|  4:  3.2848 -  2.9870  1313   153  0.92  13.48   1.01     0.99      10228.51|
|  5:  2.9870 -  2.7744  1294   140  0.90  15.62   1.00     0.97       7920.39|
|  6:  2.7744 -  2.6117  1289   145  0.91  15.45   0.99     0.96       6684.20|
|  7:  2.6117 -  2.4815  1291   135  0.91  14.60   0.99     0.96       5718.03|
|  8:  2.4815 -  2.3740  1267   150  0.92  14.34   1.00     0.98       4778.97|
|  9:  2.3740 -  2.2829  1271   142  0.92  14.29   1.02     0.99       4569.78|
| 10:  2.2829 -  2.2044  1284   137  0.91  14.52   1.00     0.96       3972.56|
| 11:  2.2044 -  2.1356  1282   143  0.90  16.05   1.01     0.98       4213.63|
| 12:  2.1356 -  2.0748  1250   139  0.92  14.09   1.01     0.99       3661.09|
| 13:  2.0748 -  2.0203  1268   141  0.91  15.66   1.02     1.01       3156.76|
| 14:  2.0203 -  1.9711   770    86  0.92  13.93   0.99     0.96       2344.95|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2344.95 max =        10228.51 mean =      6075.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.92 mean =        13.50|
|phase err.(test): min =        0.00 max =           86.96 mean =        13.09|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.759)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.21    80.61   16.34    None  None   None       |
|    all(noH): 2823   0      1.21    80.61   16.34    None  None   None       |
|    Sol.    : 438    0      6.54    74.41   37.14    None  None   None       |
|    Mac.    : 2385   0      1.21    80.61   12.52    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.214 -   9.153:  878   |   5:    40.910 -  48.850:  105        |
|      1:     9.153 -  17.093: 1183   |   6:    48.850 -  56.789:   70        |
|      2:    17.093 -  25.032:  284   |   7:    56.789 -  64.728:   28        |
|      3:    25.032 -  32.971:  125   |   8:    64.728 -  72.667:    7        |
|      4:    32.971 -  40.910:  137   |   9:    72.667 -  80.607:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 282         
Filter by distance & map next to the model:
   mapped sites are within: 0.413 - 4.636
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 278 from: 282
   mapped sites are within: 0.740 - 4.636

peak=    5.952 closest distance to " NH2 ARG A  56 " =    2.210
peak=    5.477 closest distance to " O   HOH Z 126 " =    1.875
peak=    5.405 closest distance to " NE2 GLN A  11 " =    1.144
peak=    5.291 closest distance to " CB  SER A  63 " =    1.163
peak=    5.102 closest distance to " O   HOH Z 142 " =    1.722
peak=    5.002 closest distance to " CG  PRO A  54 " =    1.150
peak=    4.866 closest distance to " CB  GLN A 223 " =    1.498
peak=    4.850 closest distance to " CB  ARG A 275 " =    0.891
peak=    4.846 closest distance to " CB  GLN A 183 " =    1.199
peak=    4.768 closest distance to " C   PRO A 198 " =    1.460
peak=    4.756 closest distance to " O   HOH Z 236 " =    1.957
peak=    4.682 closest distance to " CB  GLU A 152 " =    1.193
peak=    4.656 closest distance to " O   HOH Z 232 " =    2.322
peak=    4.593 closest distance to " OD1 ASN A  69 " =    2.547
peak=    4.544 closest distance to " O   HOH Z  15 " =    2.243
peak=    4.462 closest distance to " CA  TYR A  30 " =    0.950
peak=    4.442 closest distance to " O   HOH Z  78 " =    1.698
peak=    4.431 closest distance to " CB  ARG A  79 " =    1.393
peak=    4.430 closest distance to " O   HOH Z 193 " =    1.861
peak=    4.367 closest distance to " O   HOH Z 369 " =    2.069
peak=    4.348 closest distance to " O   HOH Z 234 " =    3.714
peak=    4.337 closest distance to " ND2 ASN A 187 " =    1.519
peak=    4.331 closest distance to " CB  ASN A 148 " =    1.736
peak=    4.322 closest distance to " O   HOH Z 298 " =    1.828
peak=    4.274 closest distance to " O   HOH Z 427 " =    2.850
peak=    4.268 closest distance to " CB  SER A   3 " =    1.386
peak=    4.252 closest distance to " O   HOH Z 303 " =    2.018
peak=    4.230 closest distance to " O   HOH Z 272 " =    1.850
peak=    4.202 closest distance to " O   HOH Z 203 " =    1.843
peak=    4.158 closest distance to " O   HOH Z  61 " =    1.626
peak=    4.147 closest distance to " O   HOH Z 144 " =    2.213
peak=    4.145 closest distance to " CB  LEU A 228 " =    1.072
peak=    4.137 closest distance to " CB  TYR A 169 " =    0.772
peak=    4.115 closest distance to " CB  PRO A  54 " =    0.855
peak=    4.108 closest distance to " O   HOH Z 158 " =    3.063
peak=    4.071 closest distance to " OD2 ASP A 286 " =    2.821
peak=    4.038 closest distance to " O   HOH Z  66 " =    2.133
peak=    4.027 closest distance to " O   HOH Z  44 " =    1.763
peak=    4.025 closest distance to " O   HOH Z  10 " =    1.875
peak=    4.017 closest distance to " CA  ASN A 215 " =    1.204
peak=    3.978 closest distance to " O   HOH Z 197 " =    3.123
peak=    3.965 closest distance to " O   HOH Z 344 " =    3.117
peak=    3.961 closest distance to " O   HOH Z 346 " =    1.634
peak=    3.961 closest distance to " O   SER A  87 " =    2.289
peak=    3.946 closest distance to " O   HOH Z 368 " =    1.995
peak=    3.939 closest distance to " O   HOH Z  54 " =    1.702
peak=    3.923 closest distance to " O   HOH Z  61 " =    1.555
peak=    3.919 closest distance to " O   HOH Z 389 " =    1.910
peak=    3.907 closest distance to " O   HOH Z 425 " =    1.894
peak=    3.900 closest distance to " O   HOH Z 316 " =    3.052
peak=    3.892 closest distance to " CB  VAL A 265 " =    1.311
peak=    3.889 closest distance to " O   HOH Z 403 " =    1.649
peak=    3.879 closest distance to " O   HOH Z  59 " =    1.940
peak=    3.873 closest distance to " O   HOH Z 132 " =    2.449
peak=    3.872 closest distance to " CB  TRP A 179 " =    1.301
peak=    3.870 closest distance to " NZ  LYS A 117 " =    3.368
peak=    3.862 closest distance to " O   HOH Z 214 " =    2.029
peak=    3.851 closest distance to " CG1 ILE A  33 " =    1.246
peak=    3.828 closest distance to " O   HOH Z   6 " =    2.007
peak=    3.813 closest distance to " CG  ARG A  66 " =    2.486
peak=    3.809 closest distance to " CB  GLU A 128 " =    1.041
peak=    3.801 closest distance to " CG2 VAL A 257 " =    0.918
peak=    3.798 closest distance to " CA  THR A 264 " =    0.889
peak=    3.797 closest distance to " O   HOH Z  21 " =    1.679
peak=    3.762 closest distance to " O   HOH Z 133 " =    1.581
peak=    3.758 closest distance to " CB  TRP A 266 " =    0.935
peak=    3.753 closest distance to " O   HOH Z 423 " =    1.878
peak=    3.745 closest distance to " O   HOH Z   1 " =    1.821
peak=    3.740 closest distance to " O   HOH Z 207 " =    1.822
peak=    3.736 closest distance to " CB  SER A 216 " =    0.779
peak=    3.734 closest distance to " O   HOH Z 245 " =    1.342
peak=    3.734 closest distance to " O   HOH Z 147 " =    1.756
peak=    3.733 closest distance to " CA  ALA A  21 " =    1.164
peak=    3.732 closest distance to " O   HOH Z 327 " =    1.609
peak=    3.727 closest distance to " O   HOH Z 248 " =    1.681
peak=    3.714 closest distance to " O   HOH Z 213 " =    1.700
peak=    3.712 closest distance to " O   HOH Z 219 " =    2.063
peak=    3.711 closest distance to " O   HOH Z 273 " =    2.622
peak=    3.707 closest distance to " O   HOH Z   9 " =    2.082
peak=    3.707 closest distance to " O   HOH Z 193 " =    1.678
peak=    3.705 closest distance to " CB  ASN A 224 " =    1.078
peak=    3.701 closest distance to " CG  PRO A 243 " =    1.134
peak=    3.700 closest distance to " O   HOH Z 189 " =    2.036
peak=    3.698 closest distance to " CB  ARG A 139 " =    1.023
peak=    3.681 closest distance to " CB  ARG A 190 " =    1.683
peak=    3.673 closest distance to " CD2 TRP A 179 " =    1.350
peak=    3.669 closest distance to " O   HOH Z  97 " =    1.940
peak=    3.668 closest distance to " O   HOH Z 128 " =    2.197
peak=    3.666 closest distance to " O   HOH Z 263 " =    2.295
peak=    3.660 closest distance to " O   HOH Z 368 " =    3.555
peak=    3.655 closest distance to " O   HOH Z 128 " =    2.112
peak=    3.654 closest distance to " O   HOH Z 193 " =    2.051
peak=    3.644 closest distance to " O   HOH Z 175 " =    2.178
peak=    3.634 closest distance to " O   HOH Z  40 " =    1.776
peak=    3.633 closest distance to " O   HOH Z 406 " =    1.622
peak=    3.627 closest distance to " CE  LYS A  76 " =    0.906
peak=    3.627 closest distance to " O   HOH Z 345 " =    3.406
peak=    3.626 closest distance to " O   HOH Z  93 " =    2.489
peak=    3.625 closest distance to " O   HOH Z 337 " =    3.652
peak=    3.617 closest distance to " O   HOH Z 250 " =    1.427
peak=    3.617 closest distance to " CB  ASP A 140 " =    0.894
peak=    3.606 closest distance to " CD  ARG A 159 " =    0.767
peak=    3.605 closest distance to " CB  GLU A 277 " =    3.495
peak=    3.601 closest distance to " O   HOH Z 419 " =    1.912
peak=    3.598 closest distance to " O   HOH Z 426 " =    1.540
peak=    3.596 closest distance to " NH1AARG A 145 " =    1.112
peak=    3.589 closest distance to " O   HOH Z 305 " =    3.617
peak=    3.589 closest distance to " OD1BASN A 224 " =    2.331
peak=    3.584 closest distance to " CD2 LEU A 255 " =    1.382
peak=    3.582 closest distance to " CG  LYS A  76 " =    0.985
peak=    3.576 closest distance to " CA  ALA A 233 " =    1.144
peak=    3.576 closest distance to " O   HOH Z  85 " =    2.214
peak=    3.572 closest distance to " CA  ALA A 291 " =    0.941
peak=    3.570 closest distance to " CD1 LEU A 300 " =    1.282
peak=    3.570 closest distance to " CD BLYS A 290 " =    1.281
peak=    3.566 closest distance to " CD1 ILE A 106 " =    0.872
peak=    3.562 closest distance to " O   HOH Z  19 " =    2.483
peak=    3.557 closest distance to " O   HOH Z  88 " =    3.209
peak=    3.555 closest distance to " OG BSER A 164 " =    2.291
peak=    3.552 closest distance to " CB  GLN A  88 " =    1.237
peak=    3.551 closest distance to " NH2BARG A 145 " =    2.031
peak=    3.550 closest distance to " O   HOH Z 163 " =    1.765
peak=    3.547 closest distance to " NH1BARG A 145 " =    1.301
peak=    3.543 closest distance to " CG1BVAL A  72 " =    1.508
peak=    3.542 closest distance to " CA  THR A 221 " =    1.011
peak=    3.535 closest distance to " O   HOH Z 402 " =    1.456
peak=    3.530 closest distance to " O   MET A 105 " =    1.780
peak=    3.530 closest distance to " O   HOH Z 291 " =    1.598
peak=    3.523 closest distance to " CA  MET A  40 " =    1.122
peak=    3.522 closest distance to " O   HOH Z 209 " =    2.311
peak=    3.520 closest distance to " O   HOH Z 371 " =    3.098
peak=    3.512 closest distance to " O   HOH Z   3 " =    1.783
peak=    3.507 closest distance to " CG2 THR A 221 " =    1.208
peak=    3.499 closest distance to " O   HOH Z 407 " =    2.347
peak=    3.498 closest distance to " O   HOH Z 173 " =    1.808
peak=    3.492 closest distance to " CB  SER A 212 " =    1.067
peak=    3.488 closest distance to " ND1 HIS A  86 " =    1.743
peak=    3.484 closest distance to " N   ARG A 156 " =    1.268
peak=    3.483 closest distance to " CZ  PHE A 218 " =    1.036
peak=    3.482 closest distance to " O   HOH Z 295 " =    1.527
peak=    3.482 closest distance to " CB  VAL A 202 " =    1.600
peak=    3.478 closest distance to " CD2 LEU A 297 " =    0.833
peak=    3.470 closest distance to " O   HOH Z 199 " =    1.520
peak=    3.453 closest distance to " O   HOH Z 380 " =    2.042
peak=    3.452 closest distance to " O   HOH Z 410 " =    1.909
peak=    3.435 closest distance to " CE BLYS A 290 " =    1.163
peak=    3.434 closest distance to " CA  ALA A  84 " =    1.385
peak=    3.431 closest distance to " O   HOH Z 258 " =    1.710
peak=    3.429 closest distance to " CB  ASN A  39 " =    0.879
peak=    3.428 closest distance to " CB  ILE A 120 " =    1.241
peak=    3.416 closest distance to " O   HOH Z 299 " =    4.394
peak=    3.410 closest distance to " O   HOH Z 180 " =    2.123
peak=    3.402 closest distance to " O   HOH Z  43 " =    2.017
peak=    3.394 closest distance to " O   HOH Z 281 " =    4.153
peak=    3.393 closest distance to " O   HOH Z 280 " =    3.019
peak=    3.390 closest distance to " O   HOH Z 263 " =    1.692
peak=    3.388 closest distance to " CG  LEU A 167 " =    1.255
peak=    3.385 closest distance to " CA  ARG A 195 " =    1.217
peak=    3.382 closest distance to " CB  ASN A 142 " =    0.952
peak=    3.380 closest distance to " O   HOH Z  40 " =    1.850
peak=    3.380 closest distance to " O   HOH Z 292 " =    1.649
peak=    3.375 closest distance to " O   HOH Z 144 " =    1.855
peak=    3.373 closest distance to " O   HOH Z 267 " =    2.074
peak=    3.372 closest distance to " CB  ALA A 291 " =    1.409
peak=    3.371 closest distance to " O   HOH Z 411 " =    3.931
peak=    3.367 closest distance to " O   HOH Z 148 " =    3.193
peak=    3.364 closest distance to " O   HOH Z  89 " =    2.196
peak=    3.363 closest distance to " O   HOH Z 423 " =    2.966
peak=    3.361 closest distance to " O   HOH Z 417 " =    3.196
peak=    3.348 closest distance to " N   TRP A 177 " =    1.750
peak=    3.337 closest distance to " CG  PRO A 198 " =    1.343
peak=    3.337 closest distance to " CB  LEU A 143 " =    1.097
peak=    3.336 closest distance to " O   HOH Z 353 " =    2.678
peak=    3.336 closest distance to " O   HOH Z 172 " =    3.266
peak=    3.336 closest distance to " CB  LEU A 255 " =    0.748
peak=    3.332 closest distance to " CZ2 TRP A 179 " =    1.673
peak=    3.331 closest distance to " O   HOH Z 261 " =    2.182
peak=    3.331 closest distance to " CB  ALA A   9 " =    1.546
peak=    3.328 closest distance to " O   HOH Z 437 " =    1.545
peak=    3.324 closest distance to " CA  ASP A 162 " =    1.046
peak=    3.323 closest distance to " O   HOH Z  44 " =    3.175
peak=    3.321 closest distance to " NH2 ARG A 156 " =    1.167
peak=    3.320 closest distance to " O   HOH Z 329 " =    3.778
peak=    3.320 closest distance to " CA  ALA A  51 " =    0.949
peak=    3.320 closest distance to " O   HOH Z 234 " =    1.715
peak=    3.318 closest distance to " O   HOH Z 433 " =    1.795
peak=    3.317 closest distance to " O   HOH Z 411 " =    1.751
peak=    3.316 closest distance to " CB  SER A  26 " =    1.535
peak=    3.313 closest distance to " O   HOH Z 366 " =    3.114
peak=    3.312 closest distance to " OG  SER A  22 " =    2.711
peak=    3.310 closest distance to " CG2 ILE A 120 " =    1.258
peak=    3.309 closest distance to " CB  THR A 157 " =    1.082
peak=    3.304 closest distance to " ND1 HIS A  81 " =    1.629
peak=    3.300 closest distance to " CA  ALA A  43 " =    1.265
peak=    3.299 closest distance to " CG  MET A 185 " =    1.123
peak=    3.298 closest distance to " CG BARG A 275 " =    1.491
peak=    3.295 closest distance to " CB  ALA A 233 " =    1.399
peak=    3.288 closest distance to " CA  ALA A 158 " =    1.163
peak=    3.285 closest distance to " CG  GLN A  89 " =    1.459
peak=    3.283 closest distance to " CB  MET A  40 " =    0.858
peak=    3.283 closest distance to " O   HOH Z  50 " =    1.501
peak=    3.280 closest distance to " O   HOH Z 280 " =    1.891
peak=    3.280 closest distance to " O   HOH Z 326 " =    1.478
peak=    3.278 closest distance to " CD  LYS A 119 " =    1.351
peak=    3.278 closest distance to " CA  ASP A 140 " =    1.149
peak=    3.277 closest distance to " O   HOH Z 319 " =    2.190
peak=    3.274 closest distance to " CD  LYS A 166 " =    1.195
peak=    3.274 closest distance to " O   HOH Z 286 " =    2.234
peak=    3.271 closest distance to " O   HOH Z 166 " =    3.765
peak=    3.268 closest distance to " OE1 GLN A  11 " =    2.147
peak=    3.267 closest distance to " CB  GLN A  89 " =    1.324
peak=    3.264 closest distance to " O   HOH Z 359 " =    1.448
peak=    3.261 closest distance to " CB  ALA A   1 " =    4.636
peak=    3.259 closest distance to " CA  PHE A 283 " =    1.256
peak=    3.258 closest distance to " O   HOH Z 409 " =    2.803
peak=    3.258 closest distance to " O   HOH Z 302 " =    1.958
peak=    3.256 closest distance to " CB  ALA A  34 " =    1.104
peak=    3.250 closest distance to " O   HOH Z 374 " =    2.587
peak=    3.247 closest distance to " O   GLY A  57 " =    2.550
peak=    3.245 closest distance to " CG  GLU A 277 " =    2.197
peak=    3.240 closest distance to " O  BHOH Z 338 " =    2.298
peak=    3.229 closest distance to " O   HOH Z   1 " =    1.657
peak=    3.228 closest distance to " O   HOH Z 116 " =    1.734
peak=    3.226 closest distance to " CB  ALA A  71 " =    1.350
peak=    3.223 closest distance to " CG  MET A 185 " =    1.042
peak=    3.215 closest distance to " CB  TRP A 150 " =    1.345
peak=    3.215 closest distance to " CB  LYS A 290 " =    1.016
peak=    3.212 closest distance to " O   HOH Z 435 " =    1.878
peak=    3.208 closest distance to " O   HOH Z  96 " =    2.004
peak=    3.205 closest distance to " O   HOH Z 125 " =    2.308
peak=    3.197 closest distance to " NH2AARG A 190 " =    1.219
peak=    3.194 closest distance to " O   PRO A  90 " =    1.345
peak=    3.193 closest distance to " N   SER A 134 " =    1.367
peak=    3.192 closest distance to " O   HOH Z  66 " =    2.150
peak=    3.191 closest distance to " CA  ALA A 248 " =    1.251
peak=    3.184 closest distance to " O   HOH Z 257 " =    2.273
peak=    3.177 closest distance to " OG  SER A 206 " =    1.351
peak=    3.177 closest distance to " CG  PRO A 213 " =    1.023
peak=    3.176 closest distance to " O   TRP A 274 " =    1.865
peak=    3.170 closest distance to " OG  SER A  97 " =    3.575
peak=    3.169 closest distance to " O   HOH Z 133 " =    2.467
peak=    3.169 closest distance to " O   HOH Z 108 " =    2.297
peak=    3.168 closest distance to " CA  VAL A 126 " =    1.115
peak=    3.161 closest distance to " CG2BVAL A  41 " =    0.790
peak=    3.161 closest distance to " CA  SER A  87 " =    0.965
peak=    3.161 closest distance to " CB  ASN A 215 " =    1.066
peak=    3.159 closest distance to " O   HOH Z  49 " =    2.129
peak=    3.156 closest distance to " O   HOH Z  71 " =    2.327
peak=    3.155 closest distance to " CB  SER A  62 " =    1.261
peak=    3.155 closest distance to " CB  ASP A 171 " =    0.740
peak=    3.149 closest distance to " OG1 THR A 294 " =    2.455
peak=    3.148 closest distance to " CB  GLN A 278 " =    0.844
peak=    3.147 closest distance to " CB  ASP A 171 " =    1.036
peak=    3.145 closest distance to " O   HOH Z 345 " =    1.737
peak=    3.139 closest distance to " O   HOH Z 171 " =    2.036
peak=    3.137 closest distance to " OG1 THR A 294 " =    1.637
peak=    3.132 closest distance to " O   HOH Z 371 " =    1.702
peak=    3.124 closest distance to " CA  ILE A  33 " =    1.468
peak=    3.120 closest distance to " CG  PRO A  90 " =    1.078
peak=    3.119 closest distance to " O   HOH Z 383 " =    1.764
peak=    3.118 closest distance to " O   HOH Z  49 " =    2.687
peak=    3.117 closest distance to " CB  TYR A 116 " =    0.836
peak=    3.116 closest distance to " O   HOH Z 227 " =    1.605
peak=    3.110 closest distance to " O   HOH Z 391 " =    2.965
peak=    3.093 closest distance to " O   HOH Z 357 " =    1.761
peak=    3.092 closest distance to " N   SER A 135 " =    1.301
peak=    3.088 closest distance to " O   HOH Z  59 " =    2.464
peak=    3.087 closest distance to " CB  ASN A 110 " =    1.154
peak=    3.078 closest distance to " O   ALA A   1 " =    1.639
peak=    3.075 closest distance to " O   HOH Z 286 " =    2.452
peak=    3.073 closest distance to " O   HOH Z 256 " =    1.472
peak=    3.071 closest distance to " O   HOH Z 152 " =    1.714
peak=    3.052 closest distance to " O   HOH Z 336 " =    1.845
peak=    3.048 closest distance to " O   HOH Z 255 " =    1.599
peak=    3.047 closest distance to " O   HOH Z 303 " =    1.602
peak=    3.037 closest distance to " CB  ARG A 190 " =    1.081
peak=    3.033 closest distance to " CB  ARG A 138 " =    0.981
peak=    3.005 closest distance to " CB  MET A  47 " =    1.211

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 201         
Filter by distance & map next to the model:
   mapped sites are within: 0.764 - 5.749
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 200 from: 201
   mapped sites are within: 0.764 - 5.749

peak=   -4.748 closest distance to " O   HOH Z 266 " =    4.568
peak=   -4.677 closest distance to " CB  PRO A 243 " =    2.600
peak=   -4.422 closest distance to " O   VAL A  67 " =    2.728
peak=   -4.357 closest distance to " CD  ARG A 156 " =    2.011
peak=   -4.302 closest distance to " O   HOH Z 372 " =    2.384
peak=   -4.277 closest distance to " O   HOH Z 290 " =    1.206
peak=   -4.247 closest distance to " O   ILE A 109 " =    2.577
peak=   -4.218 closest distance to " CG  GLN A 223 " =    1.747
peak=   -4.187 closest distance to " CB  PRO A 280 " =    2.155
peak=   -4.126 closest distance to " C   HIS A 108 " =    1.133
peak=   -4.079 closest distance to " SG  CYS A 254 " =    3.310
peak=   -4.058 closest distance to " O   HOH Z 198 " =    2.132
peak=   -4.030 closest distance to " CA  VAL A  67 " =    2.705
peak=   -4.021 closest distance to " CD  ARG A 139 " =    1.528
peak=   -4.021 closest distance to " CG1 VAL A 112 " =    2.767
peak=   -4.015 closest distance to " N   ALA A  43 " =    2.509
peak=   -4.014 closest distance to " O   HOH Z 389 " =    1.849
peak=   -3.945 closest distance to " CG  ASP A 231 " =    0.764
peak=   -3.931 closest distance to " O   HOH Z 353 " =    2.216
peak=   -3.924 closest distance to " CD1 PHE A  59 " =    1.885
peak=   -3.921 closest distance to " OG BSER A 134 " =    1.269
peak=   -3.907 closest distance to " O   HOH Z 126 " =    1.854
peak=   -3.891 closest distance to " O   HOH Z 231 " =    2.194
peak=   -3.886 closest distance to " CD1 LEU A 228 " =    2.229
peak=   -3.869 closest distance to " O   HOH Z 185 " =    2.200
peak=   -3.843 closest distance to " CE2 TYR A  30 " =    2.782
peak=   -3.823 closest distance to " CZ3 TRP A 179 " =    1.062
peak=   -3.799 closest distance to " O   HOH Z 435 " =    2.775
peak=   -3.798 closest distance to " CG  PHE A 283 " =    2.754
peak=   -3.776 closest distance to " CB  ALA A 291 " =    2.405
peak=   -3.762 closest distance to " O   HOH Z 114 " =    3.038
peak=   -3.759 closest distance to " ND2 ASN A  45 " =    1.754
peak=   -3.755 closest distance to " CE  MET A 105 " =    2.229
peak=   -3.750 closest distance to " CD  GLN A  58 " =    1.056
peak=   -3.744 closest distance to " OD1 ASP A 171 " =    1.627
peak=   -3.737 closest distance to " CZ  TYR A 169 " =    1.681
peak=   -3.737 closest distance to " O   PRO A 163 " =    2.052
peak=   -3.735 closest distance to " CB  PRO A 163 " =    2.541
peak=   -3.731 closest distance to " CE2 PHE A 218 " =    2.461
peak=   -3.727 closest distance to " O   HOH Z 198 " =    1.278
peak=   -3.725 closest distance to " O   HOH Z 313 " =    2.029
peak=   -3.722 closest distance to " O   HOH Z  43 " =    1.558
peak=   -3.720 closest distance to " O   ARG A 145 " =    1.584
peak=   -3.718 closest distance to " O   HOH Z  10 " =    1.456
peak=   -3.711 closest distance to " N   GLN A  58 " =    1.677
peak=   -3.709 closest distance to " O   PRO A 198 " =    1.302
peak=   -3.679 closest distance to " OG  SER A  97 " =    2.163
peak=   -3.662 closest distance to " NH1 ARG A 195 " =    2.522
peak=   -3.658 closest distance to " CD2 LEU A 300 " =    2.916
peak=   -3.644 closest distance to " CD1 LEU A 101 " =    2.347
peak=   -3.635 closest distance to " CG2 ILE A 263 " =    2.251
peak=   -3.633 closest distance to " C   ALA A 158 " =    1.282
peak=   -3.629 closest distance to " CD2 PHE A 192 " =    2.108
peak=   -3.617 closest distance to " O   HOH Z 351 " =    1.442
peak=   -3.612 closest distance to " N   SER A 212 " =    2.070
peak=   -3.607 closest distance to " N   ASP A 286 " =    2.458
peak=   -3.602 closest distance to " O   PRO A 198 " =    1.247
peak=   -3.602 closest distance to " O   HOH Z 311 " =    3.617
peak=   -3.600 closest distance to " OXT GLY A 302 " =    2.720
peak=   -3.588 closest distance to " O   HOH Z 111 " =    2.191
peak=   -3.586 closest distance to " NH2 ARG A  79 " =    1.916
peak=   -3.574 closest distance to " O   HOH Z 407 " =    3.053
peak=   -3.570 closest distance to " O   HOH Z 211 " =    1.712
peak=   -3.570 closest distance to " O   HOH Z 196 " =    2.080
peak=   -3.569 closest distance to " CZ  PHE A  59 " =    1.557
peak=   -3.561 closest distance to " CB  ALA A 291 " =    2.219
peak=   -3.557 closest distance to " OG BSER A 134 " =    1.656
peak=   -3.543 closest distance to " O   VAL A 189 " =    2.554
peak=   -3.542 closest distance to " NH2AARG A 275 " =    5.325
peak=   -3.542 closest distance to " N   ALA A 248 " =    1.566
peak=   -3.539 closest distance to " ND2 ASN A  45 " =    1.047
peak=   -3.539 closest distance to " O   HOH Z  13 " =    1.518
peak=   -3.535 closest distance to " SG ACYS A 201 " =    1.843
peak=   -3.532 closest distance to " CB  CYS A 201 " =    2.642
peak=   -3.497 closest distance to " O   SER A 135 " =    1.506
peak=   -3.489 closest distance to " CB  TYR A  15 " =    2.169
peak=   -3.487 closest distance to " CA  GLY A 203 " =    2.170
peak=   -3.475 closest distance to " OG  SER A  62 " =    1.447
peak=   -3.471 closest distance to " CB  ASN A  39 " =    2.219
peak=   -3.464 closest distance to " O   HOH Z  11 " =    1.745
peak=   -3.458 closest distance to " CG  GLU A 152 " =    1.067
peak=   -3.457 closest distance to " CD1 LEU A 297 " =    2.368
peak=   -3.451 closest distance to " O   LYS A 117 " =    1.672
peak=   -3.430 closest distance to " O   SER A  95 " =    1.452
peak=   -3.429 closest distance to " CG  ARG A 269 " =    2.622
peak=   -3.419 closest distance to " O   TRP A  70 " =    1.574
peak=   -3.418 closest distance to " OG  SER A   3 " =    1.702
peak=   -3.417 closest distance to " C   LEU A 143 " =    1.086
peak=   -3.412 closest distance to " O   HOH Z 385 " =    1.920
peak=   -3.407 closest distance to " O   HOH Z 395 " =    5.180
peak=   -3.403 closest distance to " O   HOH Z  38 " =    1.587
peak=   -3.403 closest distance to " CA  GLY A  98 " =    1.934
peak=   -3.402 closest distance to " O   GLY A 196 " =    1.092
peak=   -3.400 closest distance to " N   THR A 235 " =    1.345
peak=   -3.395 closest distance to " NH2BARG A 275 " =    1.882
peak=   -3.392 closest distance to " CB  ALA A 248 " =    2.024
peak=   -3.387 closest distance to " O   HOH Z 193 " =    1.938
peak=   -3.381 closest distance to " O   HOH Z 417 " =    2.428
peak=   -3.374 closest distance to " O   ALA A 161 " =    1.612
peak=   -3.369 closest distance to " O   HOH Z  52 " =    1.289
peak=   -3.364 closest distance to " CD1 ILE A 239 " =    2.092
peak=   -3.358 closest distance to " CD2 LEU A 237 " =    2.730
peak=   -3.354 closest distance to " CA  GLY A 133 " =    2.056
peak=   -3.346 closest distance to " OD1 ASN A 148 " =    1.683
peak=   -3.345 closest distance to " CB  ASP A 132 " =    2.349
peak=   -3.345 closest distance to " NH2 ARG A  79 " =    1.700
peak=   -3.343 closest distance to " CG1 VAL A 230 " =    1.948
peak=   -3.341 closest distance to " CD2 PHE A  61 " =    2.454
peak=   -3.340 closest distance to " O   PHE A 218 " =    1.664
peak=   -3.333 closest distance to " OE1 GLN A 223 " =    1.904
peak=   -3.332 closest distance to " CA  GLY A 241 " =    2.995
peak=   -3.332 closest distance to " O   HOH Z  60 " =    2.466
peak=   -3.331 closest distance to " O   HOH Z 317 " =    2.431
peak=   -3.328 closest distance to " OD1 ASN A 176 " =    1.282
peak=   -3.328 closest distance to " CB  ASP A 286 " =    2.225
peak=   -3.325 closest distance to " CB  TRP A  85 " =    2.529
peak=   -3.321 closest distance to " CG1 VAL A 197 " =    2.185
peak=   -3.320 closest distance to " CB  ALA A   1 " =    2.654
peak=   -3.317 closest distance to " O   HOH Z 359 " =    3.119
peak=   -3.317 closest distance to " CB  ALA A 248 " =    2.384
peak=   -3.316 closest distance to " N   PHE A  59 " =    2.115
peak=   -3.312 closest distance to " CE  LYS A  76 " =    2.875
peak=   -3.301 closest distance to " O   MET A  40 " =    2.769
peak=   -3.295 closest distance to " O   HOH Z   6 " =    1.487
peak=   -3.295 closest distance to " C   MET A 188 " =    1.415
peak=   -3.293 closest distance to " O   GLY A  80 " =    2.500
peak=   -3.292 closest distance to " CG  GLU A   2 " =    1.902
peak=   -3.288 closest distance to " CG1 VAL A 250 " =    2.678
peak=   -3.288 closest distance to " OH  TYR A 214 " =    1.239
peak=   -3.288 closest distance to " OG1 THR A 178 " =    1.276
peak=   -3.280 closest distance to " O   HOH Z 200 " =    4.706
peak=   -3.271 closest distance to " ND2 ASN A 249 " =    2.236
peak=   -3.270 closest distance to " O   HOH Z 316 " =    1.781
peak=   -3.269 closest distance to " O   HOH Z 348 " =    2.239
peak=   -3.269 closest distance to " NZ  LYS A 119 " =    3.432
peak=   -3.266 closest distance to " O   HOH Z 210 " =    1.059
peak=   -3.260 closest distance to " O   ALA A   1 " =    1.833
peak=   -3.258 closest distance to " OD2 ASP A 171 " =    2.249
peak=   -3.254 closest distance to " CD2 TYR A 247 " =    2.481
peak=   -3.248 closest distance to " CG  ASP A 132 " =    2.283
peak=   -3.247 closest distance to " O   HOH Z 166 " =    1.394
peak=   -3.247 closest distance to " CG  GLN A  88 " =    0.835
peak=   -3.243 closest distance to " OD1 ASP A 191 " =    1.506
peak=   -3.243 closest distance to " O   LEU A 101 " =    2.765
peak=   -3.241 closest distance to " N   GLN A 122 " =    1.418
peak=   -3.240 closest distance to " OG  SER A  87 " =    1.335
peak=   -3.235 closest distance to " O   HOH Z 385 " =    1.915
peak=   -3.233 closest distance to " CG1 VAL A 112 " =    2.603
peak=   -3.231 closest distance to " CA  ASP A 298 " =    1.076
peak=   -3.229 closest distance to " CG2 VAL A 189 " =    2.019
peak=   -3.226 closest distance to " O   VAL A 174 " =    2.020
peak=   -3.224 closest distance to " O   HOH Z 137 " =    1.439
peak=   -3.224 closest distance to " O   HOH Z 281 " =    2.723
peak=   -3.222 closest distance to " O   HOH Z 323 " =    1.313
peak=   -3.220 closest distance to " O   SER A  22 " =    2.388
peak=   -3.217 closest distance to " O   HOH Z  44 " =    2.230
peak=   -3.213 closest distance to " O   HOH Z 348 " =    1.844
peak=   -3.202 closest distance to " O   HOH Z  22 " =    2.613
peak=   -3.195 closest distance to " CG  ARG A  66 " =    2.368
peak=   -3.192 closest distance to " NE  ARG A  36 " =    1.872
peak=   -3.188 closest distance to " CG  ASN A 301 " =    1.906
peak=   -3.186 closest distance to " O   ALA A  51 " =    1.366
peak=   -3.178 closest distance to " OXT GLY A 302 " =    3.418
peak=   -3.176 closest distance to " O   HOH Z 322 " =    1.323
peak=   -3.172 closest distance to " O   HOH Z 388 " =    2.012
peak=   -3.163 closest distance to " CG  TRP A 266 " =    1.772
peak=   -3.160 closest distance to " O   HOH Z  73 " =    2.348
peak=   -3.157 closest distance to " N   ALA A 226 " =    2.043
peak=   -3.156 closest distance to " O   HOH Z 241 " =    1.421
peak=   -3.153 closest distance to " O   HOH Z 111 " =    1.595
peak=   -3.151 closest distance to " OE1 GLN A  88 " =    1.262
peak=   -3.148 closest distance to " CE  MET A  93 " =    1.228
peak=   -3.147 closest distance to " NH1 ARG A  36 " =    2.003
peak=   -3.146 closest distance to " OG BSER A 210 " =    2.119
peak=   -3.145 closest distance to " CA  TYR A  30 " =    2.894
peak=   -3.123 closest distance to " OD2 ASP A 171 " =    1.762
peak=   -3.123 closest distance to " O   GLN A 240 " =    2.024
peak=   -3.122 closest distance to " O   HOH Z 377 " =    0.782
peak=   -3.118 closest distance to " O   HOH Z  71 " =    2.360
peak=   -3.113 closest distance to " CG2 THR A 221 " =    2.224
peak=   -3.111 closest distance to " O   HOH Z 436 " =    1.283
peak=   -3.111 closest distance to " O   HOH Z 222 " =    1.153
peak=   -3.111 closest distance to " O   HOH Z 263 " =    3.007
peak=   -3.109 closest distance to " O   HOH Z  51 " =    1.472
peak=   -3.105 closest distance to " O   HOH Z  11 " =    2.063
peak=   -3.105 closest distance to " OD2 ASP A  50 " =    1.524
peak=   -3.090 closest distance to " O   ASN A 249 " =    1.470
peak=   -3.086 closest distance to " O   HOH Z 168 " =    1.814
peak=   -3.084 closest distance to " O   HOH Z 414 " =    1.719
peak=   -3.083 closest distance to " CD2 TYR A 293 " =    2.042
peak=   -3.080 closest distance to " O   HOH Z 174 " =    2.991
peak=   -3.080 closest distance to " CE3 TRP A 274 " =    2.388
peak=   -3.075 closest distance to " O   ALA A 292 " =    1.940
peak=   -3.070 closest distance to " OD1AASN A 224 " =    1.738
peak=   -3.053 closest distance to " O   HOH Z 176 " =    0.815
peak=   -3.050 closest distance to " O   LYS A 289 " =    3.034
peak=   -3.047 closest distance to " CE  LYS A  76 " =    2.837
peak=   -3.046 closest distance to " CA  GLY A 241 " =    2.752
peak=   -3.045 closest distance to " ND2 ASN A  60 " =    1.505
peak=   -3.040 closest distance to " O   HOH Z 283 " =    5.749

================= 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    :  0.3109 0.3126   6.005476e+00   6.012236e+00
   1_bss:  0.2952 0.2960   5.984046e+00   5.976656e+00
   1_xyz:  0.1615 0.1855   5.419735e+00   5.540059e+00
   1_adp:  0.1522 0.1879   5.381410e+00   5.559582e+00
   1_occ:  0.1516 0.1881   5.378862e+00   5.557959e+00
   2_bss:  0.1503 0.1849   5.369983e+00   5.545722e+00
   2_xyz:  0.1212 0.1549   5.176050e+00   5.376773e+00
   2_adp:  0.1144 0.1535   5.139780e+00   5.361786e+00
   2_occ:  0.1143 0.1535   5.139483e+00   5.361665e+00
   3_bss:  0.1143 0.1534   5.138300e+00   5.360689e+00
   3_xyz:  0.1099 0.1516   5.117831e+00   5.353167e+00
   3_adp:  0.1092 0.1518   5.116045e+00   5.354357e+00
   3_occ:  0.1091 0.1517   5.115969e+00   5.354480e+00
   4_bss:  0.1092 0.1522   5.117565e+00   5.356636e+00
   4_xyz:  0.1061 0.1523   5.102286e+00   5.353829e+00
   4_adp:  0.1063 0.1527   5.104487e+00   5.356285e+00
   4_occ:  0.1062 0.1527   5.104547e+00   5.356542e+00
   5_bss:  0.1062 0.1527   5.104589e+00   5.356583e+00
   5_xyz:  0.1040 0.1542   5.099110e+00   5.364124e+00
   5_adp:  0.1038 0.1545   5.099360e+00   5.366224e+00
   5_occ:  0.1038 0.1545   5.099501e+00   5.366529e+00
   5_bss:  0.1038 0.1545   5.099588e+00   5.366605e+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:  0.324  35.973  -2.601  -2.234   1.145  -0.000   0.000   0.000
   1_xyz:  0.324  35.973  -2.601  -2.234   1.145  -0.000   0.000   0.000
   1_adp:  0.324  35.973  -2.601  -2.234   1.145  -0.000   0.000   0.000
   1_occ:  0.324  35.973  -2.601  -2.234   1.145  -0.000   0.000   0.000
   2_bss:  0.327  43.402  -2.812  -2.740  -1.305  -0.000  -0.000  -0.000
   2_xyz:  0.327  43.402  -2.812  -2.740  -1.305  -0.000  -0.000  -0.000
   2_adp:  0.327  43.402  -2.812  -2.740  -1.305  -0.000  -0.000  -0.000
   2_occ:  0.327  43.402  -2.812  -2.740  -1.305  -0.000  -0.000  -0.000
   3_bss:  0.321  43.402  -2.554  -2.505  -1.530  -0.000  -0.000  -0.000
   3_xyz:  0.321  43.402  -2.554  -2.505  -1.530  -0.000  -0.000  -0.000
   3_adp:  0.321  43.402  -2.554  -2.505  -1.530  -0.000  -0.000  -0.000
   3_occ:  0.321  43.402  -2.554  -2.505  -1.530  -0.000  -0.000  -0.000
   4_bss:  0.321  43.402  -2.426  -2.399  -1.576  -0.000  -0.000  -0.000
   4_xyz:  0.321  43.402  -2.426  -2.399  -1.576  -0.000  -0.000  -0.000
   4_adp:  0.321  43.402  -2.426  -2.399  -1.576  -0.000  -0.000  -0.000
   4_occ:  0.321  43.402  -2.426  -2.399  -1.576  -0.000  -0.000  -0.000
   5_bss:  0.321  43.402  -2.298  -2.285  -1.482  -0.000  -0.000  -0.000
   5_xyz:  0.321  43.402  -2.298  -2.285  -1.482  -0.000  -0.000  -0.000
   5_adp:  0.321  43.402  -2.298  -2.285  -1.482  -0.000  -0.000  -0.000
   5_occ:  0.321  43.402  -2.298  -2.285  -1.482  -0.000  -0.000  -0.000
   5_bss:  0.322  43.324  -2.102  -2.102  -1.309  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  32.239 0.7362  0.9269    28231.402
   1_bss:  30.622 0.7519  0.9078    24431.155
   1_xyz:  17.012 0.8908  1.0086     8842.637
   1_adp:  17.512 0.8860  1.0029     9149.134
   1_occ:  17.483 0.8862  1.0028     9093.001
   2_bss:  17.155 0.8890  0.9676     8837.344
   2_xyz:  13.678 0.9175  0.9814     6201.373
   2_adp:  13.466 0.9191  0.9806     6003.404
   2_occ:  13.463 0.9192  0.9806     6000.373
   3_bss:  13.444 0.9193  0.9837     5991.362
   3_xyz:  13.248 0.9210  0.9833     5880.757
   3_adp:  13.243 0.9212  0.9797     5893.708
   3_occ:  13.245 0.9212  0.9797     5895.633
   4_bss:  13.299 0.9207  0.9815     5936.543
   4_xyz:  13.279 0.9207  0.9817     5913.178
   4_adp:  13.313 0.9205  0.9781     5943.041
   4_occ:  13.319 0.9204  0.9780     5945.403
   5_bss:  13.320 0.9204  0.9820     5946.402
   5_xyz:  13.417 0.9198  0.9812     6055.629
   5_adp:  13.453 0.9196  0.9763     6071.267
   5_occ:  13.458 0.9195  0.9762     6074.822
   5_bss:  13.460 0.9195  0.9812     6076.368
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6235e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6235e-01
   1_xyz:   1.021  0.007  0.070 15.068  0.004  4.110   6.1936e-02
   1_adp:   1.021  0.007  0.070 15.068  0.004  4.110   6.1936e-02
   1_occ:   1.021  0.007  0.070 15.068  0.004  4.110   6.1936e-02
   2_bss:   1.021  0.007  0.070 15.068  0.004  4.110   6.1936e-02
   2_xyz:   0.965  0.006  0.071 14.902  0.004  4.114   5.5703e-02
   2_adp:   0.965  0.006  0.071 14.902  0.004  4.114   5.5703e-02
   2_occ:   0.965  0.006  0.071 14.902  0.004  4.114   5.5703e-02
   3_bss:   0.965  0.006  0.071 14.902  0.004  4.114   5.5703e-02
   3_xyz:   0.932  0.006  0.071 14.890  0.004  4.114   5.4490e-02
   3_adp:   0.932  0.006  0.071 14.890  0.004  4.114   5.4490e-02
   3_occ:   0.932  0.006  0.071 14.890  0.004  4.114   5.4490e-02
   4_bss:   0.932  0.006  0.071 14.890  0.004  4.114   5.4490e-02
   4_xyz:   1.009  0.007  0.076 15.052  0.004  4.115   6.1986e-02
   4_adp:   1.009  0.007  0.076 15.052  0.004  4.115   6.1986e-02
   4_occ:   1.009  0.007  0.076 15.052  0.004  4.115   6.1986e-02
   5_bss:   1.009  0.007  0.076 15.052  0.004  4.115   6.1986e-02
   5_xyz:   1.084  0.009  0.081 15.192  0.005  4.110   7.1006e-02
   5_adp:   1.084  0.009  0.081 15.192  0.005  4.110   7.1006e-02
   5_occ:   1.084  0.009  0.081 15.192  0.005  4.110   7.1006e-02
   5_bss:   1.084  0.009  0.081 15.192  0.005  4.110   7.1006e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3970e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3970e-01
   1_xyz:   7.432  0.045  0.348 84.456  0.038  2.340   6.3583e-02
   1_adp:   7.432  0.045  0.348 84.456  0.038  2.340   6.3583e-02
   1_occ:   7.432  0.045  0.348 84.456  0.038  2.340   6.3583e-02
   2_bss:   7.432  0.045  0.348 84.456  0.038  2.340   6.3583e-02
   2_xyz:   7.227  0.032  0.229 85.046  0.039  2.317   3.9323e-02
   2_adp:   7.227  0.032  0.229 85.046  0.039  2.317   3.9323e-02
   2_occ:   7.227  0.032  0.229 85.046  0.039  2.317   3.9323e-02
   3_bss:   7.227  0.032  0.229 85.046  0.039  2.317   3.9323e-02
   3_xyz:   7.021  0.036  0.223 83.675  0.037  2.310   4.0045e-02
   3_adp:   7.021  0.036  0.223 83.675  0.037  2.310   4.0045e-02
   3_occ:   7.021  0.036  0.223 83.675  0.037  2.310   4.0045e-02
   4_bss:   7.021  0.036  0.223 83.675  0.037  2.310   4.0045e-02
   4_xyz:   6.524  0.039  0.238 83.838  0.037  2.249   4.6079e-02
   4_adp:   6.524  0.039  0.238 83.838  0.037  2.249   4.6079e-02
   4_occ:   6.524  0.039  0.238 83.838  0.037  2.249   4.6079e-02
   5_bss:   6.524  0.039  0.238 83.838  0.037  2.249   4.6079e-02
   5_xyz:   6.732  0.046  0.257 83.646  0.042  2.229   5.8325e-02
   5_adp:   6.732  0.046  0.257 83.646  0.042  2.229   5.8325e-02
   5_occ:   6.732  0.046  0.257 83.646  0.042  2.229   5.8325e-02
   5_bss:   6.732  0.046  0.257 83.646  0.042  2.229   5.8325e-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:  78.03   0.00  16.31  78.03   0.00  12.48  62.29   6.02  37.20
   1_occ:  78.03   0.00  16.31  78.03   0.00  12.48  62.29   6.02  37.20
   2_bss:  78.03   0.00  16.31  78.03   0.00  12.48  62.29   6.02  37.20
   2_xyz:  78.03   0.00  16.31  78.03   0.00  12.48  62.29   6.02  37.20
   2_adp:  77.72   1.56  17.00  77.72   1.56  12.92  74.44   4.10  39.20
   2_occ:  77.72   1.56  17.00  77.72   1.56  12.92  74.44   4.10  39.20
   3_bss:  77.72   1.56  17.00  77.72   1.56  12.92  74.44   4.10  39.20
   3_xyz:  77.72   1.56  17.00  77.72   1.56  12.92  74.44   4.10  39.20
   3_adp:  79.28   1.54  16.83  79.28   1.54  12.86  75.04   4.18  38.50
   3_occ:  79.28   1.54  16.83  79.28   1.54  12.86  75.04   4.18  38.50
   4_bss:  79.28   1.54  16.83  79.28   1.54  12.86  75.04   4.18  38.50
   4_xyz:  79.28   1.54  16.83  79.28   1.54  12.86  75.04   4.18  38.50
   4_adp:  80.23   1.50  16.50  80.23   1.50  12.69  74.65   5.79  37.23
   4_occ:  80.23   1.50  16.50  80.23   1.50  12.69  74.65   5.79  37.23
   5_bss:  80.23   1.50  16.50  80.23   1.50  12.69  74.65   5.79  37.23
   5_xyz:  80.23   1.50  16.50  80.23   1.50  12.69  74.65   5.79  37.23
   5_adp:  80.65   1.26  16.38  80.65   1.26  12.56  74.45   6.58  37.18
   5_occ:  80.65   1.26  16.38  80.65   1.26  12.56  74.45   6.58  37.18
   5_bss:  80.61   1.21  16.34  80.61   1.21  12.52  74.41   6.54  37.14
------------------------------------------------------------------------
 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:    1.079    0.007    0.297
   1_adp:    1.079    0.007    0.297
   1_occ:    1.079    0.007    0.297
   2_bss:    1.079    0.007    0.297
   2_xyz:    0.770    0.021    0.335
   2_adp:    0.770    0.021    0.335
   2_occ:    0.770    0.021    0.335
   3_bss:    0.770    0.021    0.335
   3_xyz:    0.960    0.016    0.355
   3_adp:    0.960    0.016    0.355
   3_occ:    0.960    0.016    0.355
   4_bss:    0.960    0.016    0.355
   4_xyz:    0.911    0.013    0.367
   4_adp:    0.911    0.013    0.367
   4_occ:    0.911    0.013    0.367
   5_bss:    0.911    0.013    0.367
   5_xyz:    1.114    0.032    0.375
   5_adp:    1.114    0.032    0.375
   5_occ:    1.114    0.032    0.375
   5_bss:    1.114    0.032    0.375
------------------------------------------------------------------------

CPU time actual refinement: 327.85


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_772/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_772/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_772/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_772/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_772/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 327.70 
  Macro-tasks:
    bulk solvent and scale       = 37.09  
    individual site refinement   = 135.69 
    weights calculation          = 29.33  
    collect and process          = 6.56   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 208.77 
  Micro-tasks:
    mask                            = 1.20   
    f_calc                          = 104.57 
    alpha_beta                      = 8.10   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 113.90 
    fmodel                         = 6.55   
    r_factors                      = 0.21   
    phase_errors                   = 10.98  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 246.99 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.644 micro seconds
Total CPU time: 5.69 minutes
from_scatterers_fft:    650 calls, 104.19 s
gradients_fft:          595 calls, 100.18 s

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

# Date 2008-01-16 Time 05:37:15 PST -0800 (1200490635.88 s)
Start R-work = 0.3109, R-free = 0.3126 (no bulk solvent and anisotropic scale)
Final R-work = 0.1290, R-free = 0.1739 (no bulk solvent and anisotropic scale)

Start R-work = 0.2952, R-free = 0.2960
Final R-work = 0.1038, R-free = 0.1545