# Date 2008-01-16 Time 04:01:26 PST -0800 (1200484886.44 s)
#phil __OFF__

Command line arguments: "../140.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 8852
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 140

-------------------------------------------------------------------------------
  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: (68.845, 45.9914, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 45.9914, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.831 1.96048
Completeness in resolution range: 0.952448
Completeness with d_max=infinity: 0.94954

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8310
                             d_min =   1.9605

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: (68.845, 45.9914, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.831 1.96048
Completeness in resolution range: 0.952448
Completeness with d_max=infinity: 0.94954

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8314 -  4.1948 [2167/2191]  1948   219  10.1%
  bin  2:  4.1948 -  3.3421 [2068/2088]  1861   207  10.0%
  bin  3:  3.3421 -  2.9233 [2053/2072]  1854   199   9.7%
  bin  4:  2.9233 -  2.6577 [2008/2038]  1800   208  10.4%
  bin  5:  2.6577 -  2.4681 [2039/2058]  1835   204  10.0%
  bin  6:  2.4681 -  2.3232 [1995/2020]  1796   199  10.0%
  bin  7:  2.3232 -  2.2073 [2005/2033]  1810   195   9.7%
  bin  8:  2.2073 -  2.1115 [1981/2017]  1775   206  10.4%
  bin  9:  2.1115 -  2.0304 [1983/2025]  1792   191   9.6%
  bin 10:  2.0304 -  1.9605 [1290/2025]  1159   131  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_140/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.35 -     2.06: 23
        2.06 -     2.77: 578
        2.77 -     3.48: 4616
        3.48 -     4.19: 9538
        4.19 -     4.90: 14010
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.355 3.040 -x+1,y-1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.453 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.472 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.627 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.724 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28760 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_140/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_140/model_refine_001.geo

CPU time processing inputs: 9.13


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 45.9914 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


============================= ml refinement start =============================


   ----------structure factors based statistics (before refinement)----------  


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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4682   r_free= 0.4650   ksol= 0.00   Bsol= 0.00   scale= 0.902    |
|                                                                             |
| 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:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.275893                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8314 -  4.6787 0.99   1406  154 0.3679 0.3544      6.5542       6.517|
|  2:  4.6787 -  3.7331 0.99   1351  152 0.3916 0.3908      6.7696      6.7763|
|  3:  3.7331 -  3.2670 0.99   1308  148 0.4446 0.4151      6.6864      6.6855|
|  4:  3.2670 -  2.9709 0.99   1338  140 0.4591 0.5011      6.5258       6.576|
|  5:  2.9709 -  2.7594 0.99   1286  153 0.5030 0.4260      6.3612      6.3503|
|  6:  2.7594 -  2.5976 0.99   1312  139 0.5003 0.5381      6.2736       6.195|
|  7:  2.5976 -  2.4681 0.99   1297  151 0.5114 0.4904      6.2343      6.1479|
|  8:  2.4681 -  2.3611 0.98   1284  136 0.5269 0.5309      6.1923      6.2081|
|  9:  2.3611 -  2.2706 0.98   1278  145 0.5098 0.5488      6.1086      6.1993|
| 10:  2.2706 -  2.1925 1.00   1295  142 0.5254 0.4947      6.1085      6.0709|
| 11:  2.1925 -  2.1241 0.98   1269  146 0.5096 0.5437       6.029       6.045|
| 12:  2.1241 -  2.0636 0.98   1278  137 0.5222 0.4997      5.9633      6.0173|
| 13:  2.0636 -  2.0094 0.96   1245  136 0.5111 0.5175      5.8921      5.8183|
| 14:  2.0094 -  1.9605 0.53    683   80 0.5261 0.5053      5.9044      5.7914|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8314 -  4.6787  1406   154  0.72  32.95   0.82     0.77      68463.47|
|  2:  4.6787 -  3.7331  1351   152  0.70  35.36   0.92     0.81     108436.40|
|  3:  3.7331 -  3.2670  1308   148  0.58  45.45   0.92     0.76     118803.92|
|  4:  3.2670 -  2.9709  1338   140  0.48  53.40   0.91     0.67     111368.95|
|  5:  2.9709 -  2.7594  1286   153  0.43  57.79   0.89     0.61      80988.15|
|  6:  2.7594 -  2.5976  1312   139  0.42  58.63   0.89     0.59      68283.76|
|  7:  2.5976 -  2.4681  1297   151  0.41  59.40   0.92     0.56      60238.90|
|  8:  2.4681 -  2.3611  1284   136  0.37  62.50   0.90     0.52      57872.98|
|  9:  2.3611 -  2.2706  1278   145  0.35  63.47   0.93     0.51      54226.03|
| 10:  2.2706 -  2.1925  1295   142  0.35  63.62   0.93     0.52      48928.05|
| 11:  2.1925 -  2.1241  1269   146  0.35  63.79   0.95     0.56      48251.65|
| 12:  2.1241 -  2.0636  1278   137  0.33  65.23   0.94     0.54      43490.16|
| 13:  2.0636 -  2.0094  1245   136  0.31  67.25   0.96     0.49      38373.11|
| 14:  2.0094 -  1.9605   683    80  0.30  67.76   0.99     0.41      31123.07|
|alpha:            min =        0.41 max =            0.81 mean =         0.60|
|beta:             min =    31123.07 max =       118803.92 mean =     68737.85|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           89.99 mean =        56.23|
|phase err.(test): min =        0.00 max =           89.80 mean =        56.38|
|-----------------------------------------------------------------------------|

============================== 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 = 17.407301             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.721   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.526084              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.695   (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 |  1.355 -  1.709:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.709 -  2.064:       19 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.064 -  2.418:       42 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.418 -  2.773:      536 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.773 -  3.127:     2222 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.127 -  3.482:     2394 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.482 -  3.836:     4537 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.836 -  4.191:     5001 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.191 -  4.545:     6340 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.545 -  4.900:     7670 |
|-----------------------------------------------------------------------------|
|-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 |        0.200 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.106    4.900  1.355 |       0.772 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.479)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4682   r_free= 0.4650   ksol= 0.00   Bsol= 0.00   scale= 0.902    |
|                                                                             |
| 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:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.275893                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4601   r_free= 0.4576   ksol= 0.34   Bsol= 24.56   scale= 0.942   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.11,1.67,1.16,0.00,0.00,0.00); trace/3= 0.58                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.270460                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.423746             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.447   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.259799              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.306   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4601      final r-factor (work) = 0.3294          |
| start r-factor (free) = 0.4576      final r-factor (free) = 0.3712          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.2599 = 13.42 * 0.50 * 6.2664 + 1.00 * 0.2004                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.3334 = 13.42 * 0.50 * 6.1354 + 1.00 * 0.1536                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3294      final r-factor (work) = 0.2977          |
| start r-factor (free) = 0.3712      final r-factor (free) = 0.3861          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7357 = 1.26 * 1.00 * 6.1354 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5747 = 1.26 * 1.00 * 5.9892 + 1.00 * 0.0295                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.479)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.29   18.72    None  None   None       |
|    all(noH): 2823   0      0.00    97.29   18.72    None  None   None       |
|    Sol.    : 438    0      2.30    97.29   38.79    None  None   None       |
|    Mac.    : 2385   0      0.00    97.20   15.03    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.729:  848   |   5:    48.647 -  58.376:   96        |
|      1:     9.729 -  19.459:  968   |   6:    58.376 -  68.106:   42        |
|      2:    19.459 -  29.188:  475   |   7:    68.106 -  77.835:   18        |
|      3:    29.188 -  38.918:  220   |   8:    77.835 -  87.564:    1        |
|      4:    38.918 -  48.647:  153   |   9:    87.564 -  97.294:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2977 r_free = 0.3861             target_work(ml) = 6.008         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2971 r_free = 0.3863             target_work(ml) = 6.009         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2971   r_free= 0.3863   ksol= 0.34   Bsol= 24.56   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.11,1.67,1.16,0.00,0.00,0.00); trace/3= 0.58                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.008563                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2958   r_free= 0.3840   ksol= 0.34   Bsol= 52.91   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.68,0.07,0.67,0.00,0.00,0.00); trace/3= -0.31                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.004332                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.091638              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.648   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.317422              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 106.122  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2958      final r-factor (work) = 0.2354          |
| start r-factor (free) = 0.3840      final r-factor (free) = 0.3063          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.3875 = 7.09 * 0.50 * 5.9884 + 1.00 * 0.1538                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.1028 = 7.09 * 0.50 * 5.9299 + 1.00 * 0.0765                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2354      final r-factor (work) = 0.2180          |
| start r-factor (free) = 0.3063      final r-factor (free) = 0.2888          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.8357 = 1.32 * 1.00 * 5.9299 + 1.00 * 0.0235                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6159 = 1.32 * 1.00 * 5.7679 + 1.00 * 0.0171                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.479)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.11  18.88    None  None   None       |
|    all(noH): 2823   0      0.00    108.11  18.88    None  None   None       |
|    Sol.    : 438    0      2.77    108.11  43.13    None  None   None       |
|    Mac.    : 2385   0      0.00    88.77   14.43    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.811: 1105   |   5:    54.053 -  64.863:   88        |
|      1:    10.811 -  21.621:  922   |   6:    64.863 -  75.674:   46        |
|      2:    21.621 -  32.432:  326   |   7:    75.674 -  86.484:   22        |
|      3:    32.432 -  43.242:  195   |   8:    86.484 -  97.295:    4        |
|      4:    43.242 -  54.053:  114   |   9:    97.295 - 108.105:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2180 r_free = 0.2888             target_work(ml) = 5.740         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2179 r_free = 0.2884             target_work(ml) = 5.739         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2179   r_free= 0.2884   ksol= 0.34   Bsol= 52.91   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.68,0.07,0.67,0.00,0.00,0.00); trace/3= -0.31                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.739211                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2181   r_free= 0.2878   ksol= 0.33   Bsol= 55.45   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.65,-0.40,0.75,-0.00,0.00,0.00); trace/3= -0.43                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.737638                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.027847              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.131  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.930164              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.380  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2181      final r-factor (work) = 0.1784          |
| start r-factor (free) = 0.2878      final r-factor (free) = 0.2375          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8089 = 3.03 * 0.50 * 5.7680 + 1.00 * 0.0765                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6189 = 3.03 * 0.50 * 5.6556 + 1.00 * 0.0569                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1784      final r-factor (work) = 0.1629          |
| start r-factor (free) = 0.2375      final r-factor (free) = 0.2228          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.9332 = 1.93 * 1.00 * 5.6556 + 1.00 * 0.0171                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.6650 = 1.93 * 1.00 * 5.5175 + 1.00 * 0.0153                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.479)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.57  18.32    None  None   None       |
|    all(noH): 2823   0      0.00    110.57  18.32    None  None   None       |
|    Sol.    : 438    0      5.12    110.57  46.35    None  None   None       |
|    Mac.    : 2385   0      0.00    95.59   13.17    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 -  11.057: 1316   |   5:    55.285 -  66.343:  100        |
|      1:    11.057 -  22.114:  861   |   6:    66.343 -  77.400:   62        |
|      2:    22.114 -  33.171:  206   |   7:    77.400 -  88.457:   19        |
|      3:    33.171 -  44.228:  139   |   8:    88.457 -  99.514:    7        |
|      4:    44.228 -  55.285:  112   |   9:    99.514 - 110.571:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1629 r_free = 0.2228             target_work(ml) = 5.484         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1628 r_free = 0.2227             target_work(ml) = 5.484         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1628   r_free= 0.2227   ksol= 0.33   Bsol= 55.45   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.65,-0.40,0.75,-0.00,0.00,0.00); trace/3= -0.43                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.484003                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1631   r_free= 0.2229   ksol= 0.32   Bsol= 55.45   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-1.17,0.49,-0.00,0.00,0.00); trace/3= -0.83                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.482850                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.045534              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.901  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.898955              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.861  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1631      final r-factor (work) = 0.1417          |
| start r-factor (free) = 0.2229      final r-factor (free) = 0.1967          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7014 = 2.05 * 0.50 * 5.5189 + 1.00 * 0.0569                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6000 = 2.05 * 0.50 * 5.4253 + 1.00 * 0.0512                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1417      final r-factor (work) = 0.1362          |
| start r-factor (free) = 0.1967      final r-factor (free) = 0.1878          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8923 = 0.90 * 1.00 * 5.4253 + 1.00 * 0.0151                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8117 = 0.90 * 1.00 * 5.3379 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.479)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.07  17.72    None  None   None       |
|    all(noH): 2823   0      0.00    109.07  17.72    None  None   None       |
|    Sol.    : 438    0      5.00    109.07  46.04    None  None   None       |
|    Mac.    : 2385   0      0.00    101.54  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:     0.000 -  10.907: 1399   |   5:    54.534 -  65.441:  102        |
|      1:    10.907 -  21.814:  814   |   6:    65.441 -  76.348:   62        |
|      2:    21.814 -  32.721:  200   |   7:    76.348 -  87.255:   23        |
|      3:    32.721 -  43.627:  116   |   8:    87.255 -  98.161:    9        |
|      4:    43.627 -  54.534:   94   |   9:    98.161 - 109.068:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1362 r_free = 0.1878             target_work(ml) = 5.313         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1361 r_free = 0.1878             target_work(ml) = 5.313         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1361   r_free= 0.1878   ksol= 0.32   Bsol= 55.45   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-1.17,0.49,-0.00,0.00,0.00); trace/3= -0.83                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.312641                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1361   r_free= 0.1878   ksol= 0.32   Bsol= 54.14   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.82,-1.27,0.51,-0.00,0.00,0.00); trace/3= -0.86                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.312441                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.533930              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.751  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.874340              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.636  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1361      final r-factor (work) = 0.1232          |
| start r-factor (free) = 0.1878      final r-factor (free) = 0.1728          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8137 = 2.53 * 0.50 * 5.3376 + 1.00 * 0.0512                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7360 = 2.53 * 0.50 * 5.2703 + 1.00 * 0.0587                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1232      final r-factor (work) = 0.1199          |
| start r-factor (free) = 0.1728      final r-factor (free) = 0.1686          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6211 = 0.87 * 1.00 * 5.2703 + 1.00 * 0.0131                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5729 = 0.87 * 1.00 * 5.2162 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.479)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.36  17.21    None  None   None       |
|    all(noH): 2823   0      0.00    108.36  17.21    None  None   None       |
|    Sol.    : 438    0      4.84    108.36  44.88    None  None   None       |
|    Mac.    : 2385   0      0.00    104.17  12.12    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.837: 1443   |   5:    54.182 -  65.019:   93        |
|      1:    10.837 -  21.673:  808   |   6:    65.019 -  75.855:   57        |
|      2:    21.673 -  32.509:  176   |   7:    75.855 -  86.692:   28        |
|      3:    32.509 -  43.346:  113   |   8:    86.692 -  97.528:    7        |
|      4:    43.346 -  54.182:   94   |   9:    97.528 - 108.365:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1199 r_free = 0.1686             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1198 r_free = 0.1686             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1198   r_free= 0.1686   ksol= 0.32   Bsol= 54.14   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.82,-1.27,0.51,-0.00,0.00,0.00); trace/3= -0.86                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.199592                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8314 -  4.6787 0.99   1406  154 0.1001 0.1364      5.4082      5.6075|
|  2:  4.6787 -  3.7331 0.99   1351  152 0.0849 0.1149      5.4504      5.6594|
|  3:  3.7331 -  3.2670 0.99   1308  148 0.1123 0.1499      5.5252      5.8367|
|  4:  3.2670 -  2.9709 0.99   1338  140 0.1313 0.1909        5.51      5.7219|
|  5:  2.9709 -  2.7594 0.99   1286  153 0.1441 0.1736      5.4047      5.6045|
|  6:  2.7594 -  2.5976 0.99   1312  139 0.1354 0.2139      5.2889      5.5384|
|  7:  2.5976 -  2.4681 0.99   1297  151 0.1416 0.1805      5.2586       5.407|
|  8:  2.4681 -  2.3611 0.98   1284  136 0.1317 0.1788      5.1652      5.4011|
|  9:  2.3611 -  2.2706 0.98   1278  145 0.1275 0.1881      5.0824       5.382|
| 10:  2.2706 -  2.1925 1.00   1295  142 0.1206 0.1729      5.0024      5.1823|
| 11:  2.1925 -  2.1241 0.98   1269  146 0.1191 0.2085       4.984      5.3395|
| 12:  2.1241 -  2.0636 0.98   1278  137 0.1300 0.1720      4.9525      5.2465|
| 13:  2.0636 -  2.0094 0.96   1245  136 0.1136 0.1865      4.7887      5.0231|
| 14:  2.0094 -  1.9605 0.53    683   80 0.0998 0.1696      4.6424      4.9401|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8314 -  4.6787  1406   154  0.93  10.21   0.98     0.95       8238.77|
|  2:  4.6787 -  3.7331  1351   152  0.95   8.24   1.03     1.01       9687.13|
|  3:  3.7331 -  3.2670  1308   148  0.93  12.16   1.05     1.05      11387.62|
|  4:  3.2670 -  2.9709  1338   140  0.91  15.01   1.03     1.01      11663.73|
|  5:  2.9709 -  2.7594  1286   153  0.89  17.19   1.02     0.99       9749.76|
|  6:  2.7594 -  2.5976  1312   139  0.88  18.13   0.99     0.95       8246.98|
|  7:  2.5976 -  2.4681  1297   151  0.89  17.33   1.00     0.96       7334.18|
|  8:  2.4681 -  2.3611  1284   136  0.90  16.76   1.01     0.98       6370.97|
|  9:  2.3611 -  2.2706  1278   145  0.90  16.17   1.00     0.95       5319.66|
| 10:  2.2706 -  2.1925  1295   142  0.89  16.86   1.01     0.98       4838.46|
| 11:  2.1925 -  2.1241  1269   146  0.89  16.91   1.00     0.97       4819.64|
| 12:  2.1241 -  2.0636  1278   137  0.89  17.39   1.02     1.03       4485.74|
| 13:  2.0636 -  2.0094  1245   136  0.90  16.18   1.00     0.98       3341.77|
| 14:  2.0094 -  1.9605   683    80  0.93  12.81   1.00     0.98       2366.20|
|alpha:            min =        0.95 max =            1.05 mean =         0.99|
|beta:             min =     2366.20 max =        11663.73 mean =      7198.69|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.83 mean =        15.11|
|phase err.(test): min =        0.00 max =           89.92 mean =        14.63|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1200   r_free= 0.1686   ksol= 0.32   Bsol= 52.79   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.82,-1.27,0.51,-0.00,0.00,0.00); trace/3= -0.86                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.198998                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1200   r_free= 0.1686   ksol= 0.32   Bsol= 52.79   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.82,-1.27,0.51,-0.00,0.00,0.00); trace/3= -0.86                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.198998                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8314 -  4.6787 0.99   1406  154 0.1005 0.1363      5.3952      5.5954|
|  2:  4.6787 -  3.7331 0.99   1351  152 0.0854 0.1153      5.4518      5.6716|
|  3:  3.7331 -  3.2670 0.99   1308  148 0.1130 0.1484      5.5309      5.8279|
|  4:  3.2670 -  2.9709 0.99   1338  140 0.1314 0.1924      5.5117      5.7293|
|  5:  2.9709 -  2.7594 0.99   1286  153 0.1440 0.1731      5.4049      5.6005|
|  6:  2.7594 -  2.5976 0.99   1312  139 0.1355 0.2135      5.2891      5.5389|
|  7:  2.5976 -  2.4681 0.99   1297  151 0.1415 0.1811      5.2585      5.4084|
|  8:  2.4681 -  2.3611 0.98   1284  136 0.1316 0.1784      5.1644      5.3983|
|  9:  2.3611 -  2.2706 0.98   1278  145 0.1272 0.1882      5.0808      5.3828|
| 10:  2.2706 -  2.1925 1.00   1295  142 0.1206 0.1728       5.002      5.1832|
| 11:  2.1925 -  2.1241 0.98   1269  146 0.1190 0.2084      4.9839      5.3394|
| 12:  2.1241 -  2.0636 0.98   1278  137 0.1298 0.1720      4.9524      5.2461|
| 13:  2.0636 -  2.0094 0.96   1245  136 0.1135 0.1865      4.7885      5.0239|
| 14:  2.0094 -  1.9605 0.53    683   80 0.0998 0.1695      4.6419      4.9395|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8314 -  4.6787  1406   154  0.93  10.05   0.98     0.95       8011.66|
|  2:  4.6787 -  3.7331  1351   152  0.95   8.23   1.03     1.02       9663.27|
|  3:  3.7331 -  3.2670  1308   148  0.93  12.26   1.05     1.05      11519.51|
|  4:  3.2670 -  2.9709  1338   140  0.91  15.01   1.03     1.01      11685.81|
|  5:  2.9709 -  2.7594  1286   153  0.89  17.17   1.02     0.99       9752.75|
|  6:  2.7594 -  2.5976  1312   139  0.88  18.13   0.99     0.95       8239.93|
|  7:  2.5976 -  2.4681  1297   151  0.89  17.32   1.00     0.96       7326.50|
|  8:  2.4681 -  2.3611  1284   136  0.90  16.76   1.01     0.98       6362.40|
|  9:  2.3611 -  2.2706  1278   145  0.90  16.15   1.00     0.95       5314.14|
| 10:  2.2706 -  2.1925  1295   142  0.89  16.86   1.01     0.98       4836.48|
| 11:  2.1925 -  2.1241  1269   146  0.89  16.92   1.00     0.97       4822.70|
| 12:  2.1241 -  2.0636  1278   137  0.89  17.41   1.02     1.03       4490.39|
| 13:  2.0636 -  2.0094  1245   136  0.90  16.18   1.00     0.98       3342.34|
| 14:  2.0094 -  1.9605   683    80  0.93  12.81   1.00     0.98       2364.53|
|alpha:            min =        0.95 max =            1.05 mean =         0.99|
|beta:             min =     2364.53 max =        11685.81 mean =      7188.70|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        15.10|
|phase err.(test): min =        0.00 max =           89.26 mean =        14.61|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.479)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.37  17.21    None  None   None       |
|    all(noH): 2823   0      0.00    108.37  17.21    None  None   None       |
|    Sol.    : 438    0      4.85    108.37  44.88    None  None   None       |
|    Mac.    : 2385   0      0.00    104.18  12.13    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.840: 1443   |   5:    54.185 -  65.022:   93        |
|      1:    10.840 -  21.676:  808   |   6:    65.022 -  75.858:   57        |
|      2:    21.676 -  32.512:  176   |   7:    75.858 -  86.695:   28        |
|      3:    32.512 -  43.349:  113   |   8:    86.695 -  97.531:    7        |
|      4:    43.349 -  54.185:   94   |   9:    97.531 - 108.368:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 311         
Filter by distance & map next to the model:
   mapped sites are within: 0.675 - 4.325
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 307 from: 311
   mapped sites are within: 0.755 - 4.325

peak=    6.584 closest distance to " O   HOH Z 385 " =    1.202
peak=    6.262 closest distance to " O   HOH Z 375 " =    1.746
peak=    6.082 closest distance to " O   HOH Z 245 " =    1.171
peak=    6.019 closest distance to " O   HOH Z 117 " =    1.706
peak=    5.750 closest distance to " O   HOH Z 142 " =    1.906
peak=    5.739 closest distance to " O   HOH Z 236 " =    1.608
peak=    5.597 closest distance to " NE2 GLN A  11 " =    1.225
peak=    5.535 closest distance to " O   HOH Z 422 " =    1.031
peak=    5.526 closest distance to " O   HOH Z  65 " =    1.260
peak=    5.496 closest distance to " O   HOH Z 427 " =    1.227
peak=    5.400 closest distance to " O   HOH Z 287 " =    1.950
peak=    5.385 closest distance to " O   HOH Z 417 " =    2.525
peak=    5.285 closest distance to " CG  PRO A  54 " =    1.307
peak=    5.266 closest distance to " O   HOH Z  49 " =    1.215
peak=    5.197 closest distance to " O   HOH Z  69 " =    1.191
peak=    5.186 closest distance to " O   HOH Z  39 " =    1.349
peak=    5.137 closest distance to " O   HOH Z   9 " =    1.786
peak=    5.043 closest distance to " O   HOH Z 105 " =    1.021
peak=    5.035 closest distance to " O   HOH Z 126 " =    2.111
peak=    5.001 closest distance to " O   HOH Z 222 " =    1.192
peak=    4.982 closest distance to " O   HOH Z 423 " =    1.743
peak=    4.962 closest distance to " OE1 GLN A  55 " =    2.270
peak=    4.954 closest distance to " O   HOH Z 427 " =    2.090
peak=    4.904 closest distance to " CB  PRO A  54 " =    1.074
peak=    4.872 closest distance to " O   HOH Z 419 " =    2.417
peak=    4.838 closest distance to " CB  ARG A 275 " =    1.063
peak=    4.827 closest distance to " O   HOH Z  63 " =    1.678
peak=    4.710 closest distance to " O   HOH Z 232 " =    2.334
peak=    4.698 closest distance to " O   HOH Z 352 " =    1.513
peak=    4.576 closest distance to " O   HOH Z 130 " =    1.109
peak=    4.523 closest distance to " O   HOH Z 132 " =    1.170
peak=    4.504 closest distance to " NZ  LYS A 119 " =    2.327
peak=    4.477 closest distance to " O   HOH Z 113 " =    2.103
peak=    4.467 closest distance to " O   HOH Z  40 " =    1.478
peak=    4.452 closest distance to " O   HOH Z 371 " =    1.953
peak=    4.416 closest distance to " O   HOH Z 112 " =    1.231
peak=    4.411 closest distance to " O   HOH Z  91 " =    2.469
peak=    4.406 closest distance to " CB  ASN A 148 " =    1.417
peak=    4.405 closest distance to " O   HOH Z 406 " =    1.636
peak=    4.362 closest distance to " CD  GLN A  77 " =    1.088
peak=    4.343 closest distance to " O   HOH Z   1 " =    1.703
peak=    4.341 closest distance to " CB  GLU A 277 " =    3.508
peak=    4.330 closest distance to " O   HOH Z 380 " =    1.884
peak=    4.306 closest distance to " O   HOH Z  78 " =    1.654
peak=    4.292 closest distance to " CA  TYR A  30 " =    1.022
peak=    4.261 closest distance to " CG  PRO A  90 " =    1.197
peak=    4.259 closest distance to " O   HOH Z 124 " =    1.353
peak=    4.259 closest distance to " CB  GLN A 223 " =    1.557
peak=    4.253 closest distance to " O   HOH Z 402 " =    1.496
peak=    4.250 closest distance to " O   HOH Z 425 " =    1.451
peak=    4.245 closest distance to " CG  TRP A 179 " =    2.194
peak=    4.218 closest distance to " OG ASER A 258 " =    3.025
peak=    4.206 closest distance to " CG  GLN A  58 " =    0.890
peak=    4.196 closest distance to " O   PRO A 198 " =    1.361
peak=    4.186 closest distance to " O   HOH Z 327 " =    1.762
peak=    4.175 closest distance to " O   HOH Z  24 " =    1.983
peak=    4.164 closest distance to " O   HOH Z 193 " =    1.450
peak=    4.160 closest distance to " O   HOH Z 130 " =    2.504
peak=    4.147 closest distance to " O   HOH Z 394 " =    1.852
peak=    4.141 closest distance to " CB  SER A  63 " =    1.265
peak=    4.123 closest distance to " CE  LYS A 119 " =    1.366
peak=    4.113 closest distance to " O   HOH Z 346 " =    1.605
peak=    4.103 closest distance to " CG  PRO A 213 " =    1.274
peak=    4.075 closest distance to " O   HOH Z 272 " =    1.828
peak=    4.073 closest distance to " O   HOH Z 298 " =    1.772
peak=    4.071 closest distance to " O   HOH Z 258 " =    2.017
peak=    4.064 closest distance to " CB  ARG A 190 " =    1.484
peak=    4.062 closest distance to " O   HOH Z 365 " =    2.514
peak=    4.043 closest distance to " O   HOH Z 392 " =    1.117
peak=    4.025 closest distance to " CB  THR A  31 " =    1.582
peak=    4.010 closest distance to " CB  ASP A 191 " =    1.185
peak=    4.000 closest distance to " O   HOH Z 389 " =    1.333
peak=    3.996 closest distance to " O   HOH Z  61 " =    1.592
peak=    3.992 closest distance to " O   HOH Z 145 " =    1.131
peak=    3.990 closest distance to " NH1AARG A 145 " =    1.262
peak=    3.970 closest distance to " O   HOH Z  11 " =    1.398
peak=    3.966 closest distance to " O   HOH Z 419 " =    1.760
peak=    3.954 closest distance to " NZ  LYS A 117 " =    2.831
peak=    3.951 closest distance to " CB  VAL A 265 " =    1.323
peak=    3.916 closest distance to " O   HOH Z  71 " =    1.323
peak=    3.907 closest distance to " NE2 GLN A  58 " =    4.325
peak=    3.901 closest distance to " O   HOH Z 378 " =    0.924
peak=    3.884 closest distance to " O   HOH Z 126 " =    1.443
peak=    3.872 closest distance to " CA  ASN A 127 " =    1.070
peak=    3.856 closest distance to " O   HOH Z 425 " =    2.120
peak=    3.854 closest distance to " O   HOH Z 214 " =    2.501
peak=    3.842 closest distance to " O   HOH Z  83 " =    0.961
peak=    3.841 closest distance to " CG  LYS A  76 " =    1.751
peak=    3.838 closest distance to " CB  SER A  99 " =    0.874
peak=    3.836 closest distance to " N   GLU A   2 " =    1.399
peak=    3.835 closest distance to " CB  VAL A 202 " =    1.642
peak=    3.827 closest distance to " O   HOH Z  92 " =    1.135
peak=    3.823 closest distance to " CB  ARG A  79 " =    1.357
peak=    3.818 closest distance to " OG BSER A 164 " =    2.191
peak=    3.817 closest distance to " O   HOH Z 193 " =    1.664
peak=    3.814 closest distance to " CB  ASN A 142 " =    1.044
peak=    3.807 closest distance to " CG  GLN A  11 " =    2.098
peak=    3.797 closest distance to " CA  VAL A 125 " =    1.185
peak=    3.796 closest distance to " O   HOH Z 423 " =    1.522
peak=    3.792 closest distance to " O   HOH Z 234 " =    3.441
peak=    3.784 closest distance to " NE1 TRP A 274 " =    1.020
peak=    3.770 closest distance to " NH2AARG A 190 " =    1.889
peak=    3.762 closest distance to " CB  LYS A 117 " =    1.251
peak=    3.757 closest distance to " O   HOH Z   7 " =    1.336
peak=    3.756 closest distance to " O   HOH Z 405 " =    1.509
peak=    3.740 closest distance to " CG AARG A 275 " =    1.096
peak=    3.736 closest distance to " ND2 ASN A 249 " =    0.883
peak=    3.736 closest distance to " O   HOH Z 411 " =    3.724
peak=    3.736 closest distance to " CB  SER A  62 " =    0.908
peak=    3.733 closest distance to " CG1 ILE A 120 " =    1.486
peak=    3.726 closest distance to " CG  LEU A 167 " =    1.268
peak=    3.720 closest distance to " OG  SER A 271 " =    2.662
peak=    3.717 closest distance to " CZ3 TRP A 266 " =    1.114
peak=    3.717 closest distance to " O   HOH Z 153 " =    3.619
peak=    3.714 closest distance to " CD2 TRP A 179 " =    1.308
peak=    3.706 closest distance to " CG  PRO A 198 " =    1.223
peak=    3.705 closest distance to " O   HOH Z  26 " =    1.320
peak=    3.703 closest distance to " O   HOH Z 290 " =    1.023
peak=    3.701 closest distance to " CG2 VAL A 257 " =    0.900
peak=    3.698 closest distance to " CB  PRO A  90 " =    1.043
peak=    3.691 closest distance to " O   HOH Z 368 " =    3.623
peak=    3.689 closest distance to " CG2 ILE A 120 " =    1.236
peak=    3.679 closest distance to " O   HOH Z 227 " =    2.118
peak=    3.664 closest distance to " O   HOH Z 357 " =    1.914
peak=    3.662 closest distance to " O   HOH Z 119 " =    4.170
peak=    3.654 closest distance to " O   HOH Z 244 " =    1.705
peak=    3.653 closest distance to " CB  GLN A 183 " =    1.238
peak=    3.647 closest distance to " O   HOH Z 365 " =    1.435
peak=    3.647 closest distance to " CB  GLU A 128 " =    0.994
peak=    3.647 closest distance to " N   GLN A 278 " =    1.288
peak=    3.647 closest distance to " CB  PHE A 130 " =    1.052
peak=    3.643 closest distance to " O   HOH Z 362 " =    1.915
peak=    3.643 closest distance to " O   HOH Z 437 " =    1.744
peak=    3.641 closest distance to " CB  SER A   3 " =    1.272
peak=    3.639 closest distance to " CB  LEU A 300 " =    0.992
peak=    3.638 closest distance to " O   HOH Z 286 " =    2.224
peak=    3.634 closest distance to " CB  SER A 216 " =    0.975
peak=    3.632 closest distance to " O   HOH Z 139 " =    1.015
peak=    3.628 closest distance to " O   HOH Z 368 " =    1.916
peak=    3.619 closest distance to " CB  GLN A  88 " =    1.319
peak=    3.613 closest distance to " O   HOH Z  68 " =    2.063
peak=    3.592 closest distance to " OE2 GLU A  53 " =    2.036
peak=    3.592 closest distance to " CB  ASN A  39 " =    1.023
peak=    3.567 closest distance to " N   PHE A 130 " =    1.262
peak=    3.563 closest distance to " O   HOH Z 390 " =    1.216
peak=    3.561 closest distance to " CB  ALA A 114 " =    0.890
peak=    3.559 closest distance to " O   HOH Z  59 " =    1.514
peak=    3.559 closest distance to " O   HOH Z 369 " =    1.728
peak=    3.555 closest distance to " CG  GLN A  89 " =    1.552
peak=    3.554 closest distance to " CB AVAL A  41 " =    1.174
peak=    3.548 closest distance to " O   HOH Z  44 " =    1.697
peak=    3.528 closest distance to " O   HOH Z 421 " =    1.983
peak=    3.527 closest distance to " CG2 VAL A 197 " =    1.084
peak=    3.525 closest distance to " CB  TRP A 179 " =    1.332
peak=    3.523 closest distance to " OG  SER A  62 " =    2.916
peak=    3.517 closest distance to " O   HOH Z 248 " =    1.657
peak=    3.514 closest distance to " CA  ALA A  51 " =    1.029
peak=    3.513 closest distance to " CA  PHE A 283 " =    1.301
peak=    3.512 closest distance to " O   HOH Z 293 " =    1.438
peak=    3.512 closest distance to " O   HOH Z 119 " =    1.393
peak=    3.510 closest distance to " O   HOH Z 215 " =    1.484
peak=    3.507 closest distance to " CB  ALA A 114 " =    1.491
peak=    3.505 closest distance to " O   HOH Z 128 " =    1.995
peak=    3.497 closest distance to " O   HOH Z 116 " =    1.137
peak=    3.491 closest distance to " O   HOH Z 216 " =    4.107
peak=    3.489 closest distance to " O   HOH Z 116 " =    2.721
peak=    3.484 closest distance to " O   HOH Z 218 " =    1.654
peak=    3.476 closest distance to " ND2 ASN A 187 " =    1.366
peak=    3.468 closest distance to " O   HOH Z 194 " =    2.409
peak=    3.464 closest distance to " O   HOH Z 130 " =    2.243
peak=    3.463 closest distance to " O   HOH Z 143 " =    1.337
peak=    3.459 closest distance to " O   HOH Z  32 " =    1.988
peak=    3.457 closest distance to " CB  ASN A 215 " =    1.062
peak=    3.455 closest distance to " O   HOH Z 173 " =    1.816
peak=    3.454 closest distance to " O   HOH Z 359 " =    1.401
peak=    3.454 closest distance to " CA  ARG A 195 " =    1.314
peak=    3.452 closest distance to " CE3 TRP A 150 " =    1.072
peak=    3.448 closest distance to " CG  PRO A 243 " =    1.108
peak=    3.445 closest distance to " O   HOH Z 434 " =    1.321
peak=    3.442 closest distance to " O   HOH Z 282 " =    2.166
peak=    3.438 closest distance to " O   HOH Z 305 " =    3.622
peak=    3.423 closest distance to " NZ  LYS A 166 " =    1.048
peak=    3.420 closest distance to " O   HOH Z 207 " =    2.374
peak=    3.417 closest distance to " O   HOH Z 193 " =    1.013
peak=    3.416 closest distance to " O   HOH Z  93 " =    2.341
peak=    3.412 closest distance to " NZ  LYS A 117 " =    1.269
peak=    3.411 closest distance to " CD  PRO A 243 " =    1.779
peak=    3.403 closest distance to " O   HOH Z  32 " =    1.820
peak=    3.392 closest distance to " O   ASN A  74 " =    1.762
peak=    3.387 closest distance to " O   HOH Z 386 " =    1.269
peak=    3.385 closest distance to " O   HOH Z 198 " =    1.344
peak=    3.383 closest distance to " O   HOH Z 203 " =    1.458
peak=    3.383 closest distance to " CB  GLU A 152 " =    1.304
peak=    3.382 closest distance to " OG BSER A  99 " =    2.444
peak=    3.382 closest distance to " CG  LYS A 119 " =    1.037
peak=    3.379 closest distance to " CB  SER A 276 " =    1.263
peak=    3.378 closest distance to " O   HOH Z 132 " =    1.796
peak=    3.377 closest distance to " CA  ALA A 129 " =    1.269
peak=    3.376 closest distance to " O   HOH Z  48 " =    1.670
peak=    3.373 closest distance to " O   HOH Z 215 " =    1.630
peak=    3.372 closest distance to " CB  ASP A 140 " =    0.996
peak=    3.370 closest distance to " O   HOH Z 414 " =    1.207
peak=    3.365 closest distance to " CA  ALA A 291 " =    0.867
peak=    3.360 closest distance to " CB  ASN A 148 " =    1.940
peak=    3.345 closest distance to " CB  ASN A 110 " =    0.983
peak=    3.344 closest distance to " CB  ASP A 107 " =    1.012
peak=    3.342 closest distance to " OD1 ASN A  69 " =    2.513
peak=    3.342 closest distance to " O   HOH Z  22 " =    2.012
peak=    3.341 closest distance to " O   HOH Z  43 " =    1.335
peak=    3.339 closest distance to " OE1 GLU A   2 " =    1.702
peak=    3.339 closest distance to " CB  HIS A 108 " =    0.810
peak=    3.335 closest distance to " CB  ARG A 156 " =    1.291
peak=    3.333 closest distance to " O   HOH Z 403 " =    1.220
peak=    3.330 closest distance to " CD  ARG A 269 " =    0.951
peak=    3.329 closest distance to " O   HOH Z   1 " =    1.488
peak=    3.324 closest distance to " O   HOH Z 276 " =    1.145
peak=    3.324 closest distance to " NE2 GLN A  73 " =    3.728
peak=    3.324 closest distance to " O   HOH Z 146 " =    1.482
peak=    3.323 closest distance to " ND1 HIS A  81 " =    1.435
peak=    3.322 closest distance to " O   HOH Z 153 " =    1.588
peak=    3.316 closest distance to " N   ILE A  33 " =    1.123
peak=    3.315 closest distance to " O   HOH Z 393 " =    1.374
peak=    3.308 closest distance to " O   HOH Z  61 " =    1.608
peak=    3.303 closest distance to " O  BHOH Z 338 " =    2.296
peak=    3.302 closest distance to " CB  TRP A 266 " =    1.162
peak=    3.298 closest distance to " ND2BASN A 224 " =    0.775
peak=    3.292 closest distance to " CA  ARG A  36 " =    1.031
peak=    3.290 closest distance to " CB  ARG A 219 " =    0.872
peak=    3.289 closest distance to " CA  ASP A 124 " =    0.772
peak=    3.289 closest distance to " O   HOH Z  85 " =    2.345
peak=    3.286 closest distance to " O   HOH Z  90 " =    4.009
peak=    3.285 closest distance to " O   HOH Z 189 " =    2.796
peak=    3.284 closest distance to " O   HOH Z  83 " =    1.043
peak=    3.282 closest distance to " O   HOH Z  76 " =    0.889
peak=    3.282 closest distance to " CB  ARG A  79 " =    0.761
peak=    3.280 closest distance to " O  BHOH Z  74 " =    1.512
peak=    3.266 closest distance to " CA  ARG A 156 " =    1.030
peak=    3.260 closest distance to " O   HOH Z 422 " =    2.194
peak=    3.259 closest distance to " O   HOH Z  97 " =    1.913
peak=    3.258 closest distance to " O   HOH Z 371 " =    1.758
peak=    3.249 closest distance to " O   HOH Z 303 " =    1.695
peak=    3.248 closest distance to " N   CYS A 260 " =    0.922
peak=    3.245 closest distance to " O   HOH Z 323 " =    1.553
peak=    3.242 closest distance to " CB  SER A 212 " =    1.226
peak=    3.240 closest distance to " O   HOH Z 261 " =    1.697
peak=    3.238 closest distance to " CA  SER A  32 " =    1.657
peak=    3.237 closest distance to " CG2BVAL A  41 " =    0.755
peak=    3.230 closest distance to " O   HOH Z 251 " =    1.122
peak=    3.230 closest distance to " NH2BARG A 145 " =    1.881
peak=    3.230 closest distance to " CE  LYS A  76 " =    0.858
peak=    3.228 closest distance to " O   HOH Z 272 " =    2.149
peak=    3.228 closest distance to " CA  ASN A 215 " =    1.022
peak=    3.228 closest distance to " CA  ALA A 160 " =    1.130
peak=    3.227 closest distance to " CG2 VAL A 232 " =    1.029
peak=    3.227 closest distance to " O   HOH Z 296 " =    1.052
peak=    3.225 closest distance to " O   HOH Z  80 " =    1.865
peak=    3.224 closest distance to " CG2 ILE A  20 " =    1.725
peak=    3.222 closest distance to " CB  ALA A 131 " =    1.798
peak=    3.215 closest distance to " O   THR A 220 " =    1.259
peak=    3.212 closest distance to " O   HOH Z  77 " =    1.301
peak=    3.211 closest distance to " OG1 THR A 221 " =    1.174
peak=    3.205 closest distance to " CZ  PHE A  38 " =    1.299
peak=    3.202 closest distance to " CG  GLU A  37 " =    1.051
peak=    3.202 closest distance to " O   HOH Z 344 " =    3.096
peak=    3.200 closest distance to " CB  ASN A 285 " =    1.073
peak=    3.199 closest distance to " CA  LEU A  83 " =    1.569
peak=    3.198 closest distance to " N   ALA A   1 " =    3.177
peak=    3.196 closest distance to " CG2 ILE A 234 " =    1.142
peak=    3.192 closest distance to " N   TYR A  15 " =    1.263
peak=    3.186 closest distance to " O   HOH Z 303 " =    2.548
peak=    3.181 closest distance to " O   HOH Z 128 " =    2.836
peak=    3.178 closest distance to " CB  ASP A 124 " =    0.937
peak=    3.178 closest distance to " O   HOH Z 371 " =    3.102
peak=    3.171 closest distance to " O   HOH Z 188 " =    2.738
peak=    3.169 closest distance to " NH1 ARG A  14 " =    1.130
peak=    3.165 closest distance to " OD1BASN A 224 " =    2.137
peak=    3.164 closest distance to " N   ASN A 127 " =    1.377
peak=    3.163 closest distance to " O   HOH Z 213 " =    1.518
peak=    3.163 closest distance to " O   GLY A 302 " =    2.254
peak=    3.158 closest distance to " O   HOH Z 148 " =    3.423
peak=    3.156 closest distance to " O   HOH Z 343 " =    3.035
peak=    3.151 closest distance to " O   HOH Z  44 " =    2.814
peak=    3.150 closest distance to " CB  ALA A   1 " =    0.951
peak=    3.150 closest distance to " O   HOH Z  47 " =    1.784
peak=    3.144 closest distance to " O   HOH Z 172 " =    2.524
peak=    3.143 closest distance to " O   THR A 182 " =    1.551
peak=    3.140 closest distance to " O   HOH Z 299 " =    4.132
peak=    3.134 closest distance to " O   HOH Z  88 " =    2.625
peak=    3.134 closest distance to " CB  SER A  62 " =    1.199
peak=    3.126 closest distance to " CB  ASN A 176 " =    1.146
peak=    3.126 closest distance to " CD  LYS A 166 " =    1.354
peak=    3.124 closest distance to " CB  PRO A 243 " =    1.223
peak=    3.115 closest distance to " O   HOH Z 109 " =    1.019
peak=    3.113 closest distance to " O   HOH Z 248 " =    2.233
peak=    3.111 closest distance to " NE2 GLN A  73 " =    1.576
peak=    3.110 closest distance to " O   HOH Z 394 " =    3.662
peak=    3.106 closest distance to " OE2 GLU A  44 " =    1.134
peak=    3.099 closest distance to " CB  GLN A 223 " =    1.698
peak=    3.083 closest distance to " O   HOH Z  40 " =    1.953
peak=    3.081 closest distance to " O   HOH Z 267 " =    1.975
peak=    3.080 closest distance to " ND1 HIS A  86 " =    1.877
peak=    3.080 closest distance to " CA  ALA A 233 " =    0.943
peak=    3.067 closest distance to " NH1 ARG A  66 " =    1.557
peak=    3.060 closest distance to " O   HOH Z 188 " =    1.448
peak=    3.051 closest distance to " CG2 ILE A  20 " =    1.184
peak=    3.044 closest distance to " O   HOH Z   3 " =    2.583
peak=    3.042 closest distance to " O   HOH Z 222 " =    2.067

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 212         
Filter by distance & map next to the model:
   mapped sites are within: 0.851 - 5.162
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 212 from: 212
   mapped sites are within: 0.851 - 5.162

peak=   -4.589 closest distance to " O   HOH Z  69 " =    1.719
peak=   -4.505 closest distance to " O   PRO A 198 " =    1.146
peak=   -4.223 closest distance to " O   HOH Z  24 " =    1.073
peak=   -4.215 closest distance to " SG  CYS A 254 " =    3.399
peak=   -4.169 closest distance to " O   HOH Z 131 " =    4.011
peak=   -4.164 closest distance to " OG BSER A 134 " =    1.374
peak=   -4.122 closest distance to " O   HOH Z 385 " =    1.389
peak=   -4.086 closest distance to " CB  ALA A  43 " =    2.401
peak=   -4.075 closest distance to " O   HOH Z 100 " =    1.162
peak=   -4.064 closest distance to " O   HOH Z 387 " =    2.429
peak=   -4.031 closest distance to " O   SER A  22 " =    2.560
peak=   -4.014 closest distance to " O   HOH Z 276 " =    1.378
peak=   -4.006 closest distance to " O   HOH Z 185 " =    1.862
peak=   -3.947 closest distance to " O   HOH Z 377 " =    2.126
peak=   -3.940 closest distance to " O   ALA A  10 " =    1.616
peak=   -3.936 closest distance to " O   HOH Z 231 " =    2.068
peak=   -3.876 closest distance to " O   HOH Z 195 " =    1.849
peak=   -3.848 closest distance to " CD2 TYR A 293 " =    1.800
peak=   -3.843 closest distance to " O   HOH Z 286 " =    1.495
peak=   -3.838 closest distance to " NE2 GLN A  55 " =    1.283
peak=   -3.821 closest distance to " CB  GLN A  55 " =    1.341
peak=   -3.809 closest distance to " O   HOH Z 211 " =    1.361
peak=   -3.797 closest distance to " O   HOH Z  39 " =    1.321
peak=   -3.780 closest distance to " CG2 ILE A  20 " =    2.819
peak=   -3.764 closest distance to " O   HOH Z 351 " =    1.584
peak=   -3.758 closest distance to " O   HOH Z  60 " =    1.922
peak=   -3.757 closest distance to " O   PHE A 218 " =    1.390
peak=   -3.754 closest distance to " O   MET A  40 " =    2.841
peak=   -3.748 closest distance to " CZ  PHE A  59 " =    1.407
peak=   -3.747 closest distance to " O   HOH Z 147 " =    1.126
peak=   -3.743 closest distance to " CD1 ILE A 239 " =    2.505
peak=   -3.739 closest distance to " CG2 ILE A  49 " =    2.716
peak=   -3.738 closest distance to " O   PRO A 163 " =    1.217
peak=   -3.720 closest distance to " O   ILE A  49 " =    1.609
peak=   -3.715 closest distance to " C   HIS A 108 " =    1.186
peak=   -3.710 closest distance to " N   THR A 157 " =    1.535
peak=   -3.696 closest distance to " O   HOH Z 298 " =    2.572
peak=   -3.688 closest distance to " CA  GLY A  98 " =    1.717
peak=   -3.681 closest distance to " O   VAL A  67 " =    2.614
peak=   -3.678 closest distance to " O   HOH Z 372 " =    2.424
peak=   -3.661 closest distance to " O   ASP A 191 " =    1.948
peak=   -3.653 closest distance to " CA  GLY A 133 " =    1.918
peak=   -3.645 closest distance to " CD  ARG A 156 " =    1.963
peak=   -3.644 closest distance to " OXT GLY A 302 " =    3.150
peak=   -3.641 closest distance to " O   GLU A 152 " =    1.412
peak=   -3.634 closest distance to " OD1 ASN A 187 " =    1.688
peak=   -3.632 closest distance to " N   GLN A  58 " =    1.172
peak=   -3.623 closest distance to " CA  GLY A 241 " =    2.218
peak=   -3.620 closest distance to " O   HOH Z 313 " =    1.546
peak=   -3.619 closest distance to " OG  SER A  63 " =    1.387
peak=   -3.616 closest distance to " CE BMET A  47 " =    1.073
peak=   -3.614 closest distance to " CG  MET A 105 " =    0.974
peak=   -3.609 closest distance to " CD1 LEU A 101 " =    2.223
peak=   -3.605 closest distance to " O   HOH Z 348 " =    1.964
peak=   -3.605 closest distance to " O   HOH Z  37 " =    1.568
peak=   -3.596 closest distance to " CG  GLN A  88 " =    0.851
peak=   -3.590 closest distance to " CZ2 TRP A 274 " =    0.987
peak=   -3.589 closest distance to " O   HOH Z 123 " =    2.505
peak=   -3.585 closest distance to " O   HOH Z 150 " =    2.221
peak=   -3.584 closest distance to " O   SER A 135 " =    1.455
peak=   -3.576 closest distance to " OE1 GLN A 223 " =    2.143
peak=   -3.565 closest distance to " CB  ALA A 291 " =    2.185
peak=   -3.560 closest distance to " OG  SER A  97 " =    2.277
peak=   -3.531 closest distance to " CD1 LEU A 255 " =    2.792
peak=   -3.518 closest distance to " CG1BVAL A  72 " =    2.174
peak=   -3.515 closest distance to " OD2 ASP A 171 " =    2.264
peak=   -3.511 closest distance to " O   HOH Z 198 " =    1.299
peak=   -3.507 closest distance to " CB  ASN A  45 " =    1.984
peak=   -3.505 closest distance to " CD  GLN A  77 " =    1.160
peak=   -3.503 closest distance to " N   HIS A 207 " =    1.285
peak=   -3.491 closest distance to " OE2 GLU A 152 " =    1.230
peak=   -3.489 closest distance to " OD1 ASN A 301 " =    1.909
peak=   -3.488 closest distance to " CE2 TYR A  30 " =    2.744
peak=   -3.478 closest distance to " CB  SER A 210 " =    1.122
peak=   -3.475 closest distance to " CG  GLN A  58 " =    0.910
peak=   -3.472 closest distance to " O   HOH Z 266 " =    4.930
peak=   -3.462 closest distance to " O   ARG A 219 " =    1.755
peak=   -3.459 closest distance to " CD2 LEU A 237 " =    2.674
peak=   -3.456 closest distance to " O   HOH Z 426 " =    1.591
peak=   -3.450 closest distance to " O   HOH Z 429 " =    1.803
peak=   -3.450 closest distance to " CZ  TYR A 169 " =    1.806
peak=   -3.445 closest distance to " CB  PHE A 192 " =    1.871
peak=   -3.439 closest distance to " O   HOH Z 201 " =    1.899
peak=   -3.434 closest distance to " N   ALA A   1 " =    3.055
peak=   -3.434 closest distance to " CD2 PHE A  61 " =    1.989
peak=   -3.425 closest distance to " CG2BVAL A  72 " =    1.655
peak=   -3.425 closest distance to " OE1 GLN A 183 " =    1.538
peak=   -3.423 closest distance to " OH  TYR A 172 " =    1.806
peak=   -3.420 closest distance to " O   HOH Z   5 " =    1.359
peak=   -3.408 closest distance to " C   ALA A 114 " =    2.062
peak=   -3.404 closest distance to " O   HOH Z 105 " =    1.294
peak=   -3.403 closest distance to " O   TRP A  70 " =    1.403
peak=   -3.395 closest distance to " CB  PRO A 213 " =    2.157
peak=   -3.394 closest distance to " C   GLN A  58 " =    2.020
peak=   -3.391 closest distance to " NE  ARG A  36 " =    1.898
peak=   -3.390 closest distance to " O   HOH Z 238 " =    1.090
peak=   -3.387 closest distance to " OG  SER A  87 " =    1.667
peak=   -3.385 closest distance to " O   HOH Z 158 " =    1.674
peak=   -3.383 closest distance to " O   VAL A 125 " =    2.098
peak=   -3.382 closest distance to " O   HOH Z 428 " =    2.713
peak=   -3.381 closest distance to " CZ  PHE A  38 " =    2.484
peak=   -3.373 closest distance to " OD2 ASP A 191 " =    1.381
peak=   -3.370 closest distance to " O   HOH Z  11 " =    1.672
peak=   -3.369 closest distance to " CE3 TRP A 274 " =    2.230
peak=   -3.365 closest distance to " O   PRO A 198 " =    1.170
peak=   -3.361 closest distance to " CD2 PHE A 225 " =    1.082
peak=   -3.361 closest distance to " O   ALA A   1 " =    1.730
peak=   -3.357 closest distance to " CD  PRO A 243 " =    2.036
peak=   -3.355 closest distance to " O   HOH Z  28 " =    1.762
peak=   -3.349 closest distance to " O   HOH Z 359 " =    3.266
peak=   -3.347 closest distance to " CE  MET A 105 " =    2.520
peak=   -3.344 closest distance to " N   ASN A 127 " =    1.247
peak=   -3.343 closest distance to " O   HOH Z 102 " =    1.508
peak=   -3.339 closest distance to " ND2 ASN A 285 " =    2.104
peak=   -3.335 closest distance to " CD2 HIS A 207 " =    2.225
peak=   -3.327 closest distance to " O   HOH Z 374 " =    1.802
peak=   -3.319 closest distance to " O   HOH Z  26 " =    0.914
peak=   -3.316 closest distance to " O   HOH Z  97 " =    1.160
peak=   -3.315 closest distance to " NH2 ARG A 219 " =    1.865
peak=   -3.313 closest distance to " O   HOH Z   1 " =    1.218
peak=   -3.312 closest distance to " O   ASN A 187 " =    1.534
peak=   -3.310 closest distance to " O   HOH Z 346 " =    1.678
peak=   -3.305 closest distance to " O   HOH Z 166 " =    1.872
peak=   -3.304 closest distance to " OG  SER A  97 " =    1.619
peak=   -3.296 closest distance to " CB  ALA A 291 " =    2.300
peak=   -3.290 closest distance to " O   HOH Z 421 " =    2.655
peak=   -3.290 closest distance to " O   HOH Z 351 " =    1.671
peak=   -3.289 closest distance to " O   HOH Z 393 " =    5.037
peak=   -3.280 closest distance to " O   HOH Z 278 " =    1.344
peak=   -3.277 closest distance to " O   GLY A  80 " =    2.404
peak=   -3.276 closest distance to " O   SER A  95 " =    1.494
peak=   -3.274 closest distance to " O   ALA A 161 " =    1.733
peak=   -3.273 closest distance to " O   HOH Z 213 " =    1.480
peak=   -3.268 closest distance to " O   HOH Z 427 " =    1.422
peak=   -3.262 closest distance to " O   HOH Z 263 " =    3.107
peak=   -3.259 closest distance to " CB  ASP A  27 " =    2.322
peak=   -3.259 closest distance to " O   HOH Z 179 " =    1.801
peak=   -3.257 closest distance to " O   HOH Z 281 " =    4.691
peak=   -3.257 closest distance to " CE2 PHE A 218 " =    2.371
peak=   -3.256 closest distance to " CB  SER A 245 " =    2.220
peak=   -3.254 closest distance to " C   ALA A 158 " =    1.505
peak=   -3.251 closest distance to " O   HOH Z 165 " =    2.455
peak=   -3.249 closest distance to " O   HOH Z  49 " =    0.981
peak=   -3.246 closest distance to " CG2 ILE A 151 " =    2.565
peak=   -3.244 closest distance to " O   HOH Z 126 " =    1.602
peak=   -3.239 closest distance to " O   PRO A 163 " =    1.789
peak=   -3.238 closest distance to " O   HOH Z  90 " =    2.296
peak=   -3.238 closest distance to " N   LYS A 166 " =    1.888
peak=   -3.236 closest distance to " O   HOH Z  52 " =    1.121
peak=   -3.235 closest distance to " OG  SER A 245 " =    1.475
peak=   -3.235 closest distance to " OE1 GLU A 277 " =    1.936
peak=   -3.231 closest distance to " O   HOH Z  40 " =    1.621
peak=   -3.226 closest distance to " O   HOH Z 435 " =    3.179
peak=   -3.222 closest distance to " N   MET A 188 " =    1.940
peak=   -3.219 closest distance to " N   ALA A 248 " =    1.667
peak=   -3.216 closest distance to " O   HOH Z 412 " =    3.250
peak=   -3.214 closest distance to " SG ACYS A 201 " =    1.253
peak=   -3.213 closest distance to " CG  PHE A 283 " =    2.676
peak=   -3.210 closest distance to " N   VAL A 232 " =    1.999
peak=   -3.209 closest distance to " N   PHE A  59 " =    1.917
peak=   -3.208 closest distance to " O   HOH Z 151 " =    1.428
peak=   -3.208 closest distance to " CG2 THR A 178 " =    2.000
peak=   -3.206 closest distance to " O   HOH Z 298 " =    1.187
peak=   -3.202 closest distance to " CD1 TRP A 179 " =    1.302
peak=   -3.202 closest distance to " O   HOH Z 389 " =    1.262
peak=   -3.201 closest distance to " CG2 VAL A 189 " =    1.915
peak=   -3.192 closest distance to " OD2 ASP A  27 " =    1.422
peak=   -3.189 closest distance to " CE2 PHE A  61 " =    2.674
peak=   -3.188 closest distance to " O   HOH Z 369 " =    2.156
peak=   -3.187 closest distance to " CD  PRO A 213 " =    2.099
peak=   -3.187 closest distance to " O   HOH Z 236 " =    1.478
peak=   -3.186 closest distance to " CG  LEU A  83 " =    2.303
peak=   -3.175 closest distance to " OG BSER A 134 " =    1.828
peak=   -3.173 closest distance to " O   LYS A  76 " =    1.783
peak=   -3.172 closest distance to " NE2 GLN A 278 " =    1.520
peak=   -3.169 closest distance to " O   TYR A 186 " =    1.530
peak=   -3.157 closest distance to " CA  SER A  26 " =    0.958
peak=   -3.154 closest distance to " OD2 ASP A 171 " =    1.615
peak=   -3.149 closest distance to " CH2 TRP A 179 " =    1.338
peak=   -3.144 closest distance to " O   HOH Z 414 " =    1.319
peak=   -3.143 closest distance to " O   HOH Z 134 " =    4.119
peak=   -3.140 closest distance to " NZ  LYS A 166 " =    1.375
peak=   -3.140 closest distance to " O   HOH Z 216 " =    1.441
peak=   -3.139 closest distance to " C   ARG A 195 " =    1.640
peak=   -3.137 closest distance to " CG  GLU A 128 " =    1.583
peak=   -3.136 closest distance to " O   HOH Z 290 " =    1.026
peak=   -3.136 closest distance to " CG  GLN A 278 " =    1.908
peak=   -3.135 closest distance to " O   HOH Z  64 " =    1.679
peak=   -3.135 closest distance to " ND2 ASN A  69 " =    1.593
peak=   -3.128 closest distance to " O   HOH Z 407 " =    2.561
peak=   -3.126 closest distance to " CG2 THR A  52 " =    3.043
peak=   -3.125 closest distance to " O   HOH Z 244 " =    1.749
peak=   -3.123 closest distance to " OE1 GLN A  58 " =    5.162
peak=   -3.120 closest distance to " O   SER A 210 " =    1.894
peak=   -3.120 closest distance to " OD1 ASP A 171 " =    1.622
peak=   -3.118 closest distance to " O   VAL A 174 " =    2.199
peak=   -3.115 closest distance to " OD1 ASN A 148 " =    1.501
peak=   -3.114 closest distance to " O   ASP A 298 " =    1.738
peak=   -3.111 closest distance to " O   HOH Z 251 " =    1.038
peak=   -3.107 closest distance to " O   HOH Z 140 " =    1.216
peak=   -3.102 closest distance to " O   ASN A 249 " =    1.669
peak=   -3.101 closest distance to " CG2AVAL A  41 " =    2.889
peak=   -3.095 closest distance to " O   HOH Z 288 " =    1.335
peak=   -3.092 closest distance to " OG  SER A  63 " =    1.229
peak=   -3.078 closest distance to " CG2BVAL A  41 " =    1.046
peak=   -3.073 closest distance to " O   HOH Z  63 " =    2.585
peak=   -3.071 closest distance to " N   SER A 276 " =    1.265
peak=   -3.063 closest distance to " O   HOH Z  88 " =    1.574
peak=   -3.057 closest distance to " O   HOH Z 253 " =    3.447
peak=   -3.050 closest distance to " O   HOH Z 423 " =    1.431
peak=   -3.044 closest distance to " N   ARG A 159 " =    2.064
peak=   -3.014 closest distance to " NE2 GLN A  55 " =    1.018

================= 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    :  0.4682 0.4650   6.275893e+00   6.264185e+00
   1_bss:  0.4601 0.4576   6.270460e+00   6.253281e+00
   1_xyz:  0.3294 0.3712   6.048073e+00   6.116837e+00
   1_adp:  0.2977 0.3861   6.008052e+00   6.145726e+00
   1_occ:  0.2971 0.3863   6.008563e+00   6.146380e+00
   2_bss:  0.2958 0.3840   6.004332e+00   6.143403e+00
   2_xyz:  0.2354 0.3063   5.802973e+00   5.982716e+00
   2_adp:  0.2180 0.2888   5.740116e+00   5.936648e+00
   2_occ:  0.2179 0.2884   5.739211e+00   5.935717e+00
   3_bss:  0.2181 0.2878   5.737638e+00   5.934964e+00
   3_xyz:  0.1784 0.2375   5.556467e+00   5.771853e+00
   3_adp:  0.1629 0.2228   5.484383e+00   5.710722e+00
   3_occ:  0.1628 0.2227   5.484003e+00   5.710190e+00
   4_bss:  0.1631 0.2229   5.482850e+00   5.708409e+00
   4_xyz:  0.1417 0.1967   5.352789e+00   5.590698e+00
   4_adp:  0.1362 0.1878   5.312916e+00   5.544922e+00
   4_occ:  0.1361 0.1878   5.312641e+00   5.544466e+00
   5_bss:  0.1361 0.1878   5.312441e+00   5.544316e+00
   5_xyz:  0.1232 0.1728   5.226718e+00   5.469179e+00
   5_adp:  0.1199 0.1686   5.199780e+00   5.441775e+00
   5_occ:  0.1198 0.1686   5.199592e+00   5.441540e+00
   5_bss:  0.1200 0.1686   5.198998e+00   5.441157e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.338  24.557  -1.105   1.671   1.161   0.000   0.000   0.000
   1_xyz:  0.338  24.557  -1.105   1.671   1.161   0.000   0.000   0.000
   1_adp:  0.338  24.557  -1.105   1.671   1.161   0.000   0.000   0.000
   1_occ:  0.338  24.557  -1.105   1.671   1.161   0.000   0.000   0.000
   2_bss:  0.340  52.909  -1.679   0.072   0.666   0.000   0.000   0.000
   2_xyz:  0.340  52.909  -1.679   0.072   0.666   0.000   0.000   0.000
   2_adp:  0.340  52.909  -1.679   0.072   0.666   0.000   0.000   0.000
   2_occ:  0.340  52.909  -1.679   0.072   0.666   0.000   0.000   0.000
   3_bss:  0.330  55.449  -1.647  -0.397   0.747  -0.000   0.000   0.000
   3_xyz:  0.330  55.449  -1.647  -0.397   0.747  -0.000   0.000   0.000
   3_adp:  0.330  55.449  -1.647  -0.397   0.747  -0.000   0.000   0.000
   3_occ:  0.330  55.449  -1.647  -0.397   0.747  -0.000   0.000   0.000
   4_bss:  0.322  55.449  -1.800  -1.175   0.488  -0.000   0.000   0.000
   4_xyz:  0.322  55.449  -1.800  -1.175   0.488  -0.000   0.000   0.000
   4_adp:  0.322  55.449  -1.800  -1.175   0.488  -0.000   0.000   0.000
   4_occ:  0.322  55.449  -1.800  -1.175   0.488  -0.000   0.000   0.000
   5_bss:  0.318  54.141  -1.821  -1.266   0.513  -0.000   0.000   0.000
   5_xyz:  0.318  54.141  -1.821  -1.266   0.513  -0.000   0.000   0.000
   5_adp:  0.318  54.141  -1.821  -1.266   0.513  -0.000   0.000   0.000
   5_occ:  0.318  54.141  -1.821  -1.266   0.513  -0.000   0.000   0.000
   5_bss:  0.318  52.793  -1.824  -1.269   0.510  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.247 0.4422  0.6048    68733.477
   1_bss:  55.084 0.4557  0.6396    65687.483
   1_xyz:  39.649 0.6475  0.8745    38785.307
   1_adp:  42.322 0.6142  0.8360    43202.288
   1_occ:  42.447 0.6127  0.8329    43358.818
   2_bss:  42.015 0.6177  0.8143    42467.528
   2_xyz:  31.914 0.7352  0.9409    25352.142
   2_adp:  29.434 0.7635  0.9464    22335.117
   2_occ:  29.394 0.7639  0.9467    22267.694
   3_bss:  29.289 0.7648  0.9431    22099.645
   3_xyz:  23.780 0.8230  0.9865    14751.727
   3_adp:  21.727 0.8445  0.9842    12865.193
   3_occ:  21.714 0.8446  0.9840    12840.088
   4_bss:  21.652 0.8451  0.9704    12764.755
   4_xyz:  18.648 0.8739  0.9873     9726.562
   4_adp:  17.433 0.8855  0.9832     8904.037
   4_occ:  17.427 0.8856  0.9831     8890.851
   5_bss:  17.424 0.8856  0.9820     8888.029
   5_xyz:  15.767 0.9001  0.9898     7566.170
   5_adp:  15.066 0.9063  0.9854     7203.973
   5_occ:  15.065 0.9063  0.9854     7198.161
   5_bss:  15.056 0.9063  0.9857     7188.208
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.106   2.0042e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.106   2.0042e-01
   1_xyz:   1.715  0.013  0.112 16.060  0.007  4.100   1.5358e-01
   1_adp:   1.715  0.013  0.112 16.060  0.007  4.100   1.5358e-01
   1_occ:   1.715  0.013  0.112 16.060  0.007  4.100   1.5358e-01
   2_bss:   1.715  0.013  0.112 16.060  0.007  4.100   1.5358e-01
   2_xyz:   1.172  0.007  0.089 15.155  0.004  4.115   7.6502e-02
   2_adp:   1.172  0.007  0.089 15.155  0.004  4.115   7.6502e-02
   2_occ:   1.172  0.007  0.089 15.155  0.004  4.115   7.6502e-02
   3_bss:   1.172  0.007  0.089 15.155  0.004  4.115   7.6502e-02
   3_xyz:   0.997  0.006  0.066 14.655  0.004  4.118   5.6855e-02
   3_adp:   0.997  0.006  0.066 14.655  0.004  4.118   5.6855e-02
   3_occ:   0.997  0.006  0.066 14.655  0.004  4.118   5.6855e-02
   4_bss:   0.997  0.006  0.066 14.655  0.004  4.118   5.6855e-02
   4_xyz:   0.926  0.005  0.066 14.386  0.003  4.108   5.1174e-02
   4_adp:   0.926  0.005  0.066 14.386  0.003  4.108   5.1174e-02
   4_occ:   0.926  0.005  0.066 14.386  0.003  4.108   5.1174e-02
   5_bss:   0.926  0.005  0.066 14.386  0.003  4.108   5.1174e-02
   5_xyz:   1.006  0.006  0.072 14.633  0.004  4.111   5.8720e-02
   5_adp:   1.006  0.006  0.072 14.633  0.004  4.111   5.8720e-02
   5_occ:   1.006  0.006  0.072 14.633  0.004  4.111   5.8720e-02
   5_bss:   1.006  0.006  0.072 14.633  0.004  4.111   5.8720e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.355   2.3996e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.355   2.3996e-01
   1_xyz:  12.054  0.071  0.417 87.918  0.062  1.969   1.2133e-01
   1_adp:  12.054  0.071  0.417 87.918  0.062  1.969   1.2133e-01
   1_occ:  12.054  0.071  0.417 87.918  0.062  1.969   1.2133e-01
   2_bss:  12.054  0.071  0.417 87.918  0.062  1.969   1.2133e-01
   2_xyz:   7.641  0.048  0.340 86.675  0.034  2.209   7.2662e-02
   2_adp:   7.641  0.048  0.340 86.675  0.034  2.209   7.2662e-02
   2_occ:   7.641  0.048  0.340 86.675  0.034  2.209   7.2662e-02
   3_bss:   7.641  0.048  0.340 86.675  0.034  2.209   7.2662e-02
   3_xyz:   7.137  0.043  0.195 84.574  0.036  2.328   4.8857e-02
   3_adp:   7.137  0.043  0.195 84.574  0.036  2.328   4.8857e-02
   3_occ:   7.137  0.043  0.195 84.574  0.036  2.328   4.8857e-02
   4_bss:   7.137  0.043  0.195 84.574  0.036  2.328   4.8857e-02
   4_xyz:   7.253  0.044  0.194 80.483  0.032  2.362   4.7907e-02
   4_adp:   7.253  0.044  0.194 80.483  0.032  2.362   4.7907e-02
   4_occ:   7.253  0.044  0.194 80.483  0.032  2.362   4.7907e-02
   5_bss:   7.253  0.044  0.194 80.483  0.032  2.362   4.7907e-02
   5_xyz:   7.063  0.044  0.245 82.068  0.037  2.291   5.5340e-02
   5_adp:   7.063  0.044  0.245 82.068  0.037  2.291   5.5340e-02
   5_occ:   7.063  0.044  0.245 82.068  0.037  2.291   5.5340e-02
   5_bss:   7.063  0.044  0.245 82.068  0.037  2.291   5.5340e-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:  97.29   0.00  18.72  97.20   0.00  15.03  97.29   2.30  38.79
   1_occ:  97.29   0.00  18.72  97.20   0.00  15.03  97.29   2.30  38.79
   2_bss:  97.29   0.00  18.72  97.20   0.00  15.03  97.29   2.30  38.79
   2_xyz:  97.29   0.00  18.72  97.20   0.00  15.03  97.29   2.30  38.79
   2_adp: 108.11   0.00  18.88  88.77   0.00  14.43 108.11   2.77  43.13
   2_occ: 108.11   0.00  18.88  88.77   0.00  14.43 108.11   2.77  43.13
   3_bss: 108.11   0.00  18.88  88.77   0.00  14.43 108.11   2.77  43.13
   3_xyz: 108.11   0.00  18.88  88.77   0.00  14.43 108.11   2.77  43.13
   3_adp: 110.57   0.00  18.32  95.59   0.00  13.17 110.57   5.12  46.35
   3_occ: 110.57   0.00  18.32  95.59   0.00  13.17 110.57   5.12  46.35
   4_bss: 110.57   0.00  18.32  95.59   0.00  13.17 110.57   5.12  46.35
   4_xyz: 110.57   0.00  18.32  95.59   0.00  13.17 110.57   5.12  46.35
   4_adp: 109.07   0.00  17.72 101.54   0.00  12.52 109.07   5.00  46.04
   4_occ: 109.07   0.00  17.72 101.54   0.00  12.52 109.07   5.00  46.04
   5_bss: 109.07   0.00  17.72 101.54   0.00  12.52 109.07   5.00  46.04
   5_xyz: 109.07   0.00  17.72 101.54   0.00  12.52 109.07   5.00  46.04
   5_adp: 108.36   0.00  17.21 104.17   0.00  12.12 108.36   4.84  44.88
   5_occ: 108.36   0.00  17.21 104.17   0.00  12.12 108.36   4.84  44.88
   5_bss: 108.37   0.00  17.21 104.18   0.00  12.13 108.37   4.85  44.88
------------------------------------------------------------------------
 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:    2.268    0.027    0.445
   1_adp:    2.268    0.027    0.445
   1_occ:    2.268    0.027    0.445
   2_bss:    2.268    0.027    0.445
   2_xyz:    2.272    0.058    0.573
   2_adp:    2.272    0.058    0.573
   2_occ:    2.272    0.058    0.573
   3_bss:    2.272    0.058    0.573
   3_xyz:    2.395    0.057    0.688
   3_adp:    2.395    0.057    0.688
   3_occ:    2.395    0.057    0.688
   4_bss:    2.395    0.057    0.688
   4_xyz:    2.539    0.021    0.731
   4_adp:    2.539    0.021    0.731
   4_occ:    2.539    0.021    0.731
   5_bss:    2.539    0.021    0.731
   5_xyz:    2.684    0.063    0.772
   5_adp:    2.684    0.063    0.772
   5_occ:    2.684    0.063    0.772
   5_bss:    2.684    0.063    0.772
------------------------------------------------------------------------

CPU time actual refinement: 357.13


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_140/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_140/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_140/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_140/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_140/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 356.97 
  Macro-tasks:
    bulk solvent and scale       = 44.61  
    individual site refinement   = 143.26 
    weights calculation          = 30.23  
    collect and process          = 6.65   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 224.85 
  Micro-tasks:
    mask                            = 2.33   
    f_calc                          = 115.05 
    alpha_beta                      = 8.50   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 123.33 
    fmodel                         = 7.31   
    r_factors                      = 0.22   
    phase_errors                   = 10.54  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 268.73 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.034 micro seconds
Total CPU time: 6.17 minutes
from_scatterers_fft:    673 calls, 114.68 s
gradients_fft:          618 calls, 109.77 s

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

# Date 2008-01-16 Time 04:07:36 PST -0800 (1200485256.65 s)
Start R-work = 0.4682, R-free = 0.4650 (no bulk solvent and anisotropic scale)
Final R-work = 0.1385, R-free = 0.1817 (no bulk solvent and anisotropic scale)

Start R-work = 0.4601, R-free = 0.4576
Final R-work = 0.1200, R-free = 0.1686