# Date 2008-01-16 Time 03:50:46 PST -0800 (1200484246.19 s)
#phil __OFF__

Command line arguments: "../73.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 16179
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 73

-------------------------------------------------------------------------------
  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: (68.4938, 47.1647, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 47.1647, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7905 1.95088
Completeness in resolution range: 0.925625
Completeness with d_max=infinity: 0.922834

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7905
                             d_min =   1.9509

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: (68.4938, 47.1647, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7905 1.95088
Completeness in resolution range: 0.925625
Completeness with d_max=infinity: 0.922834

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7909 -  4.1745 [2220/2248]  1997   223  10.0%
  bin  2:  4.1745 -  3.3258 [2131/2154]  1914   217  10.2%
  bin  3:  3.3258 -  2.9090 [2106/2131]  1902   204   9.7%
  bin  4:  2.9090 -  2.6447 [2088/2104]  1876   212  10.2%
  bin  5:  2.6447 -  2.4561 [2066/2105]  1854   212  10.3%
  bin  6:  2.4561 -  2.3118 [2057/2089]  1853   204   9.9%
  bin  7:  2.3118 -  2.1965 [2056/2093]  1859   197   9.6%
  bin  8:  2.1965 -  2.1011 [2053/2095]  1843   210  10.2%
  bin  9:  2.1011 -  2.0204 [2028/2067]  1832   196   9.7%
  bin 10:  2.0204 -  1.9509 [ 784/2077]   700    84  10.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_73/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:
        1.20 -     1.94: 15
        1.94 -     2.68: 132
        2.68 -     3.42: 4490
        3.42 -     4.16: 9449
        4.16 -     4.90: 14469
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.201 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.341 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.403 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.419 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.492 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28550 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_73/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_73/model_refine_001.geo

CPU time processing inputs: 9.12


============================ 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 = 68.49375 47.16465 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3815   r_free= 0.3769   ksol= 0.00   Bsol= 0.00   scale= 0.948    |
|                                                                             |
| 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:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.164533                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7909 -  4.6560 0.99   1443  160 0.3042 0.3123      6.4205      6.4741|
|  2:  4.6560 -  3.7149 0.99   1394  154 0.3011 0.2827      6.5623       6.554|
|  3:  3.7149 -  3.2510 0.99   1361  153 0.3427 0.3384      6.4851      6.5387|
|  4:  3.2510 -  2.9564 0.99   1350  143 0.3649 0.3875      6.3506      6.4128|
|  5:  2.9564 -  2.7459 0.98   1337  154 0.3936 0.3805      6.2227      6.2419|
|  6:  2.7459 -  2.5849 0.99   1342  148 0.4019 0.4472      6.1495      6.0991|
|  7:  2.5849 -  2.4561 0.99   1316  156 0.4101 0.3277      6.1166      5.9898|
|  8:  2.4561 -  2.3496 0.99   1342  137 0.4331 0.4313      6.0792      6.0868|
|  9:  2.3496 -  2.2595 0.99   1325  147 0.4440 0.4124       6.054       6.063|
| 10:  2.2595 -  2.1818 0.98   1320  147 0.4360 0.3981      6.0143      5.9703|
| 11:  2.1818 -  2.1137 0.98   1287  155 0.4488 0.4677       5.953      5.9547|
| 12:  2.1137 -  2.0535 1.00   1339  143 0.4443 0.4444       5.875      5.9057|
| 13:  2.0535 -  1.9996 0.87   1184  125 0.4557 0.4762      5.8156      5.7988|
| 14:  1.9996 -  1.9509 0.22    290   37 0.4886 0.4904      5.9117      5.7244|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7909 -  4.6560  1443   160  0.75  29.53   0.86     0.76      52772.41|
|  2:  4.6560 -  3.7149  1394   154  0.79  27.23   0.97     0.87      66847.25|
|  3:  3.7149 -  3.2510  1361   153  0.73  33.24   0.97     0.89      69414.48|
|  4:  3.2510 -  2.9564  1350   143  0.66  39.16   0.96     0.84      62617.48|
|  5:  2.9564 -  2.7459  1337   154  0.60  44.02   0.96     0.80      51942.87|
|  6:  2.7459 -  2.5849  1342   148  0.60  43.66   0.95     0.80      43409.70|
|  7:  2.5849 -  2.4561  1316   156  0.62  42.52   0.97     0.83      37551.95|
|  8:  2.4561 -  2.3496  1342   137  0.61  43.05   0.98     0.84      33401.23|
|  9:  2.3496 -  2.2595  1325   147  0.62  42.69   0.97     0.86      31484.59|
| 10:  2.2595 -  2.1818  1320   147  0.61  43.66   0.99     0.84      29090.41|
| 11:  2.1818 -  2.1137  1287   155  0.57  46.79   0.98     0.84      30636.30|
| 12:  2.1137 -  2.0535  1339   143  0.51  51.58   1.02     0.79      30611.07|
| 13:  2.0535 -  1.9996  1184   125  0.48  54.03   0.98     0.76      28606.35|
| 14:  1.9996 -  1.9509   290    37  0.53  49.29   0.99     0.70      22556.28|
|alpha:            min =        0.70 max =            0.89 mean =         0.82|
|beta:             min =    22556.28 max =        69414.48 mean =     43745.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.63|
|phase err.(work): min =        0.00 max =           89.99 mean =        41.50|
|phase err.(test): min =        0.00 max =           89.54 mean =        41.35|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.472223              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.755   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.934163              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.578   (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 |  1.201 -  1.571:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.571 -  1.941:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.941 -  2.311:       18 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.311 -  2.681:      114 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.681 -  3.051:     2200 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.051 -  3.421:     2290 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.421 -  3.790:     4062 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.790 -  4.160:     5387 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.160 -  4.530:     6481 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.530 -  4.900:     7988 |
|-----------------------------------------------------------------------------|
|-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 |        0.214 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.201 |       0.951 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.656)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3815   r_free= 0.3769   ksol= 0.00   Bsol= 0.00   scale= 0.948    |
|                                                                             |
| 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:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.164533                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3713   r_free= 0.3678   ksol= 0.30   Bsol= 31.30   scale= 0.972   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.23,-1.98,0.38,-0.00,0.00,0.00); trace/3= -0.12                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.149592                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.899194              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.413   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.528414              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.341   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3713      final r-factor (work) = 0.2360          |
| start r-factor (free) = 0.3678      final r-factor (free) = 0.2681          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.2922 = 4.90 * 0.50 * 6.1555 + 1.00 * 0.2137                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.6001 = 4.90 * 0.50 * 5.9252 + 1.00 * 0.0859                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2360      final r-factor (work) = 0.2172          |
| start r-factor (free) = 0.2681      final r-factor (free) = 0.2723          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1374 = 0.53 * 1.00 * 5.9252 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0575 = 0.53 * 1.00 * 5.7080 + 1.00 * 0.0414                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 7      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.656)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    62.46   16.97    None  None   None       |
|    all(noH): 2823   0      0.00    62.46   16.97    None  None   None       |
|    Sol.    : 438    0      6.42    62.45   37.98    None  None   None       |
|    Mac.    : 2385   0      0.00    62.46   13.11    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 -   6.247:  316   |   5:    31.232 -  37.479:  100        |
|      1:     6.247 -  12.493: 1012   |   6:    37.479 -  43.725:  110        |
|      2:    12.493 -  18.739:  697   |   7:    43.725 -  49.972:   88        |
|      3:    18.739 -  24.986:  281   |   8:    49.972 -  56.218:   58        |
|      4:    24.986 -  31.232:  133   |   9:    56.218 -  62.465:   28        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2172 r_free = 0.2723             target_work(ml) = 5.715         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2169 r_free = 0.2724             target_work(ml) = 5.714         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2169   r_free= 0.2724   ksol= 0.30   Bsol= 31.30   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.23,-1.98,0.38,-0.00,0.00,0.00); trace/3= -0.12                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.714400                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2117   r_free= 0.2659   ksol= 0.33   Bsol= 49.37   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-2.50,-1.01,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.699583                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.794525              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.096   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.420386              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.981   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2117      final r-factor (work) = 0.1531          |
| start r-factor (free) = 0.2659      final r-factor (free) = 0.1908          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0721 = 2.79 * 0.50 * 5.7157 + 1.00 * 0.0858                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8429 = 2.79 * 0.50 * 5.5729 + 1.00 * 0.0560                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1531      final r-factor (work) = 0.1391          |
| start r-factor (free) = 0.1908      final r-factor (free) = 0.1838          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3745 = 0.42 * 1.00 * 5.5729 + 1.00 * 0.0318                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2579 = 0.42 * 1.00 * 5.3489 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.656)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.51   17.68    None  None   None       |
|    all(noH): 2823   0      0.00    82.51   17.68    None  None   None       |
|    Sol.    : 438    0      6.17    71.78   40.87    None  None   None       |
|    Mac.    : 2385   0      0.00    82.51   13.42    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.251:  560   |   5:    41.255 -  49.506:   97        |
|      1:     8.251 -  16.502: 1375   |   6:    49.506 -  57.757:   94        |
|      2:    16.502 -  24.753:  354   |   7:    57.757 -  66.008:   57        |
|      3:    24.753 -  33.004:  130   |   8:    66.008 -  74.259:   22        |
|      4:    33.004 -  41.255:  130   |   9:    74.259 -  82.510:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1391 r_free = 0.1838             target_work(ml) = 5.325         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1389 r_free = 0.1836             target_work(ml) = 5.324         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1389   r_free= 0.1836   ksol= 0.33   Bsol= 49.37   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-2.50,-1.01,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.324187                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1388   r_free= 0.1830   ksol= 0.32   Bsol= 49.37   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.14,-2.36,-1.10,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.320972                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.133179              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.152  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.200643              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.687  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1388      final r-factor (work) = 0.1180          |
| start r-factor (free) = 0.1830      final r-factor (free) = 0.1614          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4348 = 3.13 * 0.50 * 5.3484 + 1.00 * 0.0561                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2877 = 3.13 * 0.50 * 5.2491 + 1.00 * 0.0645                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1180      final r-factor (work) = 0.1159          |
| start r-factor (free) = 0.1614      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0624 = 0.20 * 1.00 * 5.2491 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0470 = 0.20 * 1.00 * 5.1801 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.656)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.61    83.55   17.19    None  None   None       |
|    all(noH): 2823   0      1.61    83.55   17.19    None  None   None       |
|    Sol.    : 438    0      6.40    72.89   39.14    None  None   None       |
|    Mac.    : 2385   0      1.61    83.55   13.16    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.615 -   9.808:  906   |   5:    42.581 -  50.775:   98        |
|      1:     9.808 -  18.001: 1180   |   6:    50.775 -  58.968:   85        |
|      2:    18.001 -  26.195:  259   |   7:    58.968 -  67.161:   30        |
|      3:    26.195 -  34.388:  119   |   8:    67.161 -  75.355:   11        |
|      4:    34.388 -  42.581:  132   |   9:    75.355 -  83.548:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1159 r_free = 0.1584             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1158 r_free = 0.1583             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1583   ksol= 0.32   Bsol= 49.37   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.14,-2.36,-1.10,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.168779                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1583   ksol= 0.33   Bsol= 49.37   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.14,-2.36,-1.10,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.168857                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.759986              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 147.905  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.173293              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.261  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1158      final r-factor (work) = 0.1143          |
| start r-factor (free) = 0.1583      final r-factor (free) = 0.1557          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6226 = 1.76 * 0.50 * 5.1797 + 1.00 * 0.0645                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5988 = 1.76 * 0.50 * 5.1645 + 1.00 * 0.0541                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1143      final r-factor (work) = 0.1140          |
| start r-factor (free) = 0.1557      final r-factor (free) = 0.1552          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9027 = 0.17 * 1.00 * 5.1645 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9009 = 0.17 * 1.00 * 5.1566 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.656)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.62   16.92    None  None   None       |
|    all(noH): 2823   0      0.00    83.62   16.92    None  None   None       |
|    Sol.    : 438    0      0.00    72.31   38.17    None  None   None       |
|    Mac.    : 2385   0      1.95    83.62   13.02    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.363:  553   |   5:    41.812 -  50.175:   97        |
|      1:     8.363 -  16.725: 1438   |   6:    50.175 -  58.537:   83        |
|      2:    16.725 -  25.087:  344   |   7:    58.537 -  66.899:   26        |
|      3:    25.087 -  33.450:  132   |   8:    66.899 -  75.262:    8        |
|      4:    33.450 -  41.812:  138   |   9:    75.262 -  83.624:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1140 r_free = 0.1552             target_work(ml) = 5.156         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1139 r_free = 0.1551             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1551   ksol= 0.33   Bsol= 49.37   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.14,-2.36,-1.10,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.155328                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1551   ksol= 0.32   Bsol= 47.72   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.35,-2.34,-1.10,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.154154                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.105586              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 155.214  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.203955              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.340  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1137      final r-factor (work) = 0.1101          |
| start r-factor (free) = 0.1551      final r-factor (free) = 0.1544          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4817 = 2.11 * 0.50 * 5.1555 + 1.00 * 0.0541                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4717 = 2.11 * 0.50 * 5.1395 + 1.00 * 0.0609                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1101      final r-factor (work) = 0.1098          |
| start r-factor (free) = 0.1544      final r-factor (free) = 0.1540          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0554 = 0.20 * 1.00 * 5.1395 + 1.00 * 0.0072                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0545 = 0.20 * 1.00 * 5.1346 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.656)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.66    83.23   16.81    None  None   None       |
|    all(noH): 2823   0      1.66    83.23   16.81    None  None   None       |
|    Sol.    : 438    0      1.66    72.52   38.02    None  None   None       |
|    Mac.    : 2385   0      2.00    83.23   12.91    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.655 -   9.813:  938   |   5:    42.442 -  50.600:   97        |
|      1:     9.813 -  17.970: 1159   |   6:    50.600 -  58.757:   74        |
|      2:    17.970 -  26.127:  260   |   7:    58.757 -  66.915:   25        |
|      3:    26.127 -  34.285:  126   |   8:    66.915 -  75.072:    7        |
|      4:    34.285 -  42.442:  133   |   9:    75.072 -  83.229:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1098 r_free = 0.1540             target_work(ml) = 5.134         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1097 r_free = 0.1540             target_work(ml) = 5.134         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1097   r_free= 0.1540   ksol= 0.32   Bsol= 47.72   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.35,-2.34,-1.10,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.134106                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7909 -  4.6560 0.99   1443  160 0.0990 0.1298      5.3888      5.5576|
|  2:  4.6560 -  3.7149 0.99   1394  154 0.0845 0.1096      5.4181      5.6113|
|  3:  3.7149 -  3.2510 0.99   1361  153 0.1045 0.1497        5.44       5.792|
|  4:  3.2510 -  2.9564 0.99   1350  143 0.1208 0.1484      5.4162      5.5728|
|  5:  2.9564 -  2.7459 0.98   1337  154 0.1254 0.1517      5.2768      5.4535|
|  6:  2.7459 -  2.5849 0.99   1342  148 0.1212 0.2064      5.1839      5.4812|
|  7:  2.5849 -  2.4561 0.99   1316  156 0.1211 0.1596      5.1372      5.3394|
|  8:  2.4561 -  2.3496 0.99   1342  137 0.1152 0.1624      5.0688      5.2318|
|  9:  2.3496 -  2.2595 0.99   1325  147 0.1140 0.1793      4.9965      5.3259|
| 10:  2.2595 -  2.1818 0.98   1320  147 0.1106 0.1709        4.93      5.1779|
| 11:  2.1818 -  2.1137 0.98   1287  155 0.1108 0.1775       4.883      5.2126|
| 12:  2.1137 -  2.0535 1.00   1339  143 0.1121 0.1541      4.8455      5.0532|
| 13:  2.0535 -  1.9996 0.87   1184  125 0.1088 0.1863      4.7548      5.0414|
| 14:  1.9996 -  1.9509 0.22    290   37 0.1010 0.1460      4.7059      4.7896|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7909 -  4.6560  1443   160  0.94   9.31   0.98     0.95       7273.57|
|  2:  4.6560 -  3.7149  1394   154  0.95   7.79   1.01     1.00       8716.28|
|  3:  3.7149 -  3.2510  1361   153  0.94  11.05   1.02     1.02       9679.01|
|  4:  3.2510 -  2.9564  1350   143  0.92  13.50   1.01     1.00       9644.48|
|  5:  2.9564 -  2.7459  1337   154  0.91  15.13   0.99     0.97       7600.15|
|  6:  2.7459 -  2.5849  1342   148  0.90  15.89   0.98     0.95       6553.40|
|  7:  2.5849 -  2.4561  1316   156  0.91  15.25   0.98     0.95       5906.42|
|  8:  2.4561 -  2.3496  1342   137  0.91  15.45   1.00     0.97       5441.07|
|  9:  2.3496 -  2.2595  1325   147  0.91  15.63   1.00     0.96       4732.70|
| 10:  2.2595 -  2.1818  1320   147  0.90  15.55   0.99     0.96       4245.80|
| 11:  2.1818 -  2.1137  1287   155  0.91  15.19   0.99     0.96       3940.49|
| 12:  2.1137 -  2.0535  1339   143  0.91  15.69   1.01     1.01       3729.77|
| 13:  2.0535 -  1.9996  1184   125  0.90  15.95   0.99     0.97       3190.09|
| 14:  1.9996 -  1.9509   290    37  0.92  13.45   0.98     0.94       2650.50|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2650.50 max =         9679.01 mean =      6202.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.87|
|phase err.(test): min =        0.00 max =           89.87 mean =        13.48|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1097   r_free= 0.1540   ksol= 0.32   Bsol= 47.66   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.24,-2.18,-0.92,-0.00,-0.00,-0.00); trace/3= -2.11                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.134156                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1097   r_free= 0.1540   ksol= 0.32   Bsol= 47.66   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.24,-2.18,-0.92,-0.00,-0.00,-0.00); trace/3= -2.11                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.134156                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7909 -  4.6560 0.99   1443  160 0.0991 0.1299      5.3896      5.5583|
|  2:  4.6560 -  3.7149 0.99   1394  154 0.0845 0.1096       5.418      5.6107|
|  3:  3.7149 -  3.2510 0.99   1361  153 0.1045 0.1497      5.4395      5.7916|
|  4:  3.2510 -  2.9564 0.99   1350  143 0.1208 0.1483      5.4161      5.5726|
|  5:  2.9564 -  2.7459 0.98   1337  154 0.1254 0.1518      5.2769      5.4536|
|  6:  2.7459 -  2.5849 0.99   1342  148 0.1212 0.2065      5.1841      5.4812|
|  7:  2.5849 -  2.4561 0.99   1316  156 0.1211 0.1595      5.1372      5.3394|
|  8:  2.4561 -  2.3496 0.99   1342  137 0.1152 0.1622      5.0687      5.2315|
|  9:  2.3496 -  2.2595 0.99   1325  147 0.1140 0.1793      4.9967      5.3258|
| 10:  2.2595 -  2.1818 0.98   1320  147 0.1106 0.1710      4.9302      5.1782|
| 11:  2.1818 -  2.1137 0.98   1287  155 0.1108 0.1776      4.8833      5.2129|
| 12:  2.1137 -  2.0535 1.00   1339  143 0.1121 0.1540      4.8454       5.053|
| 13:  2.0535 -  1.9996 0.87   1184  125 0.1088 0.1864      4.7548      5.0416|
| 14:  1.9996 -  1.9509 0.22    290   37 0.1011 0.1461      4.7053      4.7892|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7909 -  4.6560  1443   160  0.94   9.32   0.98     0.95       7285.14|
|  2:  4.6560 -  3.7149  1394   154  0.95   7.79   1.02     1.00       8716.20|
|  3:  3.7149 -  3.2510  1361   153  0.94  11.05   1.02     1.02       9667.89|
|  4:  3.2510 -  2.9564  1350   143  0.92  13.50   1.01     1.01       9642.29|
|  5:  2.9564 -  2.7459  1337   154  0.91  15.13   1.00     0.97       7600.33|
|  6:  2.7459 -  2.5849  1342   148  0.90  15.89   0.98     0.95       6555.81|
|  7:  2.5849 -  2.4561  1316   156  0.91  15.25   0.99     0.96       5905.70|
|  8:  2.4561 -  2.3496  1342   137  0.91  15.45   1.00     0.97       5438.77|
|  9:  2.3496 -  2.2595  1325   147  0.91  15.63   1.00     0.96       4730.74|
| 10:  2.2595 -  2.1818  1320   147  0.90  15.56   1.00     0.97       4246.79|
| 11:  2.1818 -  2.1137  1287   155  0.91  15.19   1.00     0.97       3943.18|
| 12:  2.1137 -  2.0535  1339   143  0.91  15.70   1.01     1.01       3731.64|
| 13:  2.0535 -  1.9996  1184   125  0.90  15.96   0.99     0.98       3191.90|
| 14:  1.9996 -  1.9509   290    37  0.92  13.45   0.98     0.94       2650.74|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2650.74 max =         9667.89 mean =      6203.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.87|
|phase err.(test): min =        0.00 max =           89.87 mean =        13.48|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.656)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.60    83.17   16.75    None  None   None       |
|    all(noH): 2823   0      1.60    83.17   16.75    None  None   None       |
|    Sol.    : 438    0      1.60    72.46   37.96    None  None   None       |
|    Mac.    : 2385   0      1.94    83.17   12.85    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.596 -   9.753:  938   |   5:    42.383 -  50.541:   97        |
|      1:     9.753 -  17.911: 1159   |   6:    50.541 -  58.698:   74        |
|      2:    17.911 -  26.068:  260   |   7:    58.698 -  66.855:   25        |
|      3:    26.068 -  34.226:  126   |   8:    66.855 -  75.013:    7        |
|      4:    34.226 -  42.383:  133   |   9:    75.013 -  83.170:    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)= 286         
Filter by distance & map next to the model:
   mapped sites are within: 0.419 - 4.304
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 279 from: 286
   mapped sites are within: 0.708 - 4.304

peak=    5.583 closest distance to " CB  ARG A 275 " =    0.946
peak=    5.194 closest distance to " NH2 ARG A  56 " =    2.150
peak=    5.160 closest distance to " O   HOH Z 417 " =    2.083
peak=    5.049 closest distance to " CG  PRO A  54 " =    1.257
peak=    4.945 closest distance to " O   HOH Z 126 " =    1.903
peak=    4.914 closest distance to " O   HOH Z 232 " =    2.358
peak=    4.897 closest distance to " NE2 GLN A  11 " =    1.137
peak=    4.840 closest distance to " CB  GLN A 223 " =    1.431
peak=    4.684 closest distance to " O   HOH Z 109 " =    2.384
peak=    4.629 closest distance to " CB  SER A  63 " =    1.149
peak=    4.626 closest distance to " CB  GLN A 183 " =    1.243
peak=    4.511 closest distance to " O   HOH Z 402 " =    1.419
peak=    4.509 closest distance to " CB  ARG A  79 " =    1.392
peak=    4.497 closest distance to " O   HOH Z 142 " =    1.590
peak=    4.475 closest distance to " CB  GLU A 152 " =    1.216
peak=    4.470 closest distance to " O   SER A  87 " =    2.147
peak=    4.454 closest distance to " CB  PRO A  54 " =    0.998
peak=    4.452 closest distance to " O   HOH Z 287 " =    1.964
peak=    4.415 closest distance to " ND2 ASN A 187 " =    1.544
peak=    4.403 closest distance to " CG  PRO A 213 " =    1.250
peak=    4.401 closest distance to " O   HOH Z 209 " =    2.230
peak=    4.386 closest distance to " CD2 TRP A 179 " =    1.332
peak=    4.367 closest distance to " O   HOH Z 369 " =    2.209
peak=    4.350 closest distance to " CA  TYR A  30 " =    0.911
peak=    4.349 closest distance to " CB  ASN A 148 " =    1.470
peak=    4.346 closest distance to " CG  PRO A  90 " =    1.260
peak=    4.341 closest distance to " C   PRO A 198 " =    1.504
peak=    4.295 closest distance to " O   HOH Z 250 " =    1.509
peak=    4.282 closest distance to " O   HOH Z 327 " =    1.632
peak=    4.279 closest distance to " O   HOH Z  63 " =    2.091
peak=    4.267 closest distance to " O   HOH Z 272 " =    1.905
peak=    4.244 closest distance to " O   HOH Z 298 " =    1.809
peak=    4.225 closest distance to " O   HOH Z  40 " =    1.842
peak=    4.194 closest distance to " O   HOH Z 346 " =    1.611
peak=    4.188 closest distance to " O   HOH Z 234 " =    3.610
peak=    4.184 closest distance to " O   HOH Z 193 " =    1.805
peak=    4.149 closest distance to " O   HOH Z  97 " =    1.964
peak=    4.135 closest distance to " O   HOH Z 128 " =    1.891
peak=    4.124 closest distance to " CB  ARG A 190 " =    1.699
peak=    4.091 closest distance to " O   HOH Z  15 " =    2.172
peak=    4.079 closest distance to " O   HOH Z  43 " =    2.100
peak=    4.067 closest distance to " O   HOH Z 406 " =    1.604
peak=    4.063 closest distance to " CG  PRO A 243 " =    1.051
peak=    4.059 closest distance to " O   HOH Z  54 " =    1.679
peak=    4.058 closest distance to " O   HOH Z  97 " =    2.221
peak=    4.044 closest distance to " CB  VAL A 265 " =    1.255
peak=    4.035 closest distance to " CA  ARG A  36 " =    1.011
peak=    4.026 closest distance to " O   HOH Z 128 " =    2.193
peak=    4.024 closest distance to " O   HOH Z 368 " =    2.044
peak=    4.017 closest distance to " NH2BARG A 145 " =    2.013
peak=    4.012 closest distance to " O   HOH Z 389 " =    1.843
peak=    4.009 closest distance to " CZ  PHE A 218 " =    1.131
peak=    3.986 closest distance to " CG  PRO A 198 " =    1.289
peak=    3.960 closest distance to " O   HOH Z 303 " =    2.174
peak=    3.954 closest distance to " O   HOH Z  61 " =    1.602
peak=    3.944 closest distance to " O   HOH Z  78 " =    1.750
peak=    3.942 closest distance to " O   HOH Z 427 " =    2.934
peak=    3.935 closest distance to " O   HOH Z 227 " =    1.647
peak=    3.910 closest distance to " O   HOH Z 423 " =    1.950
peak=    3.909 closest distance to " CB  VAL A 202 " =    1.496
peak=    3.904 closest distance to " NZ  LYS A 117 " =    2.951
peak=    3.886 closest distance to " CB  TRP A 266 " =    1.043
peak=    3.884 closest distance to " CB  ASN A 110 " =    1.045
peak=    3.874 closest distance to " O   HOH Z 403 " =    1.711
peak=    3.857 closest distance to " O   HOH Z 132 " =    2.608
peak=    3.851 closest distance to " CG2 VAL A 257 " =    0.821
peak=    3.849 closest distance to " O   HOH Z  44 " =    2.005
peak=    3.849 closest distance to " O   HOH Z 189 " =    2.645
peak=    3.845 closest distance to " CG  ARG A  66 " =    2.685
peak=    3.835 closest distance to " N   PHE A 130 " =    1.310
peak=    3.816 closest distance to " CA  ALA A  84 " =    1.192
peak=    3.811 closest distance to " O   HOH Z 173 " =    2.060
peak=    3.794 closest distance to " CB  THR A  31 " =    1.519
peak=    3.792 closest distance to " O   HOH Z 392 " =    2.699
peak=    3.790 closest distance to " CB  ASN A  39 " =    0.822
peak=    3.780 closest distance to " N   ASN A  39 " =    1.234
peak=    3.773 closest distance to " O   HOH Z 365 " =    2.741
peak=    3.760 closest distance to " O  BHOH Z  74 " =    1.336
peak=    3.758 closest distance to " O   HOH Z 368 " =    3.667
peak=    3.748 closest distance to " OE1 GLU A   2 " =    2.269
peak=    3.746 closest distance to " CB  GLU A  46 " =    1.040
peak=    3.744 closest distance to " O   HOH Z 203 " =    1.765
peak=    3.741 closest distance to " CG2 ILE A 120 " =    1.249
peak=    3.738 closest distance to " O   HOH Z 357 " =    1.994
peak=    3.736 closest distance to " O   HOH Z 248 " =    1.558
peak=    3.733 closest distance to " CB  GLU A 277 " =    3.547
peak=    3.733 closest distance to " CD  ARG A 269 " =    0.962
peak=    3.719 closest distance to " CA  ASN A 215 " =    0.958
peak=    3.710 closest distance to " O   HOH Z 421 " =    1.586
peak=    3.709 closest distance to " O   HOH Z 180 " =    2.228
peak=    3.707 closest distance to " O   HOH Z 291 " =    1.456
peak=    3.700 closest distance to " O   HOH Z 158 " =    3.071
peak=    3.698 closest distance to " CB  SER A  26 " =    1.758
peak=    3.697 closest distance to " OG ASER A 258 " =    3.025
peak=    3.695 closest distance to " CB  ALA A 114 " =    1.148
peak=    3.694 closest distance to " O   HOH Z  59 " =    2.109
peak=    3.687 closest distance to " O   HOH Z  85 " =    1.451
peak=    3.665 closest distance to " NH2AARG A 190 " =    2.056
peak=    3.660 closest distance to " O   HOH Z  68 " =    2.189
peak=    3.653 closest distance to " N   ARG A 156 " =    1.348
peak=    3.651 closest distance to " CD2 LEU A 297 " =    0.976
peak=    3.642 closest distance to " O   HOH Z  21 " =    1.855
peak=    3.621 closest distance to " CB  SER A   3 " =    1.255
peak=    3.619 closest distance to " O   HOH Z 280 " =    2.960
peak=    3.616 closest distance to " O   HOH Z 416 " =    2.706
peak=    3.602 closest distance to " O   HOH Z  19 " =    1.923
peak=    3.598 closest distance to " O   HOH Z  43 " =    1.104
peak=    3.596 closest distance to " O   HOH Z   1 " =    1.961
peak=    3.595 closest distance to " CD  LYS A  76 " =    1.780
peak=    3.591 closest distance to " CG AARG A 275 " =    1.113
peak=    3.586 closest distance to " O   HOH Z 425 " =    1.923
peak=    3.584 closest distance to " CG2AVAL A  72 " =    1.643
peak=    3.578 closest distance to " O   HOH Z  88 " =    2.672
peak=    3.571 closest distance to " N   TYR A 116 " =    1.598
peak=    3.569 closest distance to " CA  ALA A  51 " =    0.889
peak=    3.555 closest distance to " CB  TRP A 179 " =    1.240
peak=    3.551 closest distance to " CB  HIS A 108 " =    0.861
peak=    3.543 closest distance to " O   HOH Z 214 " =    2.176
peak=    3.534 closest distance to " O   HOH Z 245 " =    1.402
peak=    3.532 closest distance to " CG2 ILE A  20 " =    1.404
peak=    3.517 closest distance to " O   HOH Z  78 " =    2.437
peak=    3.516 closest distance to " O   HOH Z 342 " =    0.998
peak=    3.515 closest distance to " CG  MET A 185 " =    1.062
peak=    3.510 closest distance to " O   HOH Z  61 " =    1.495
peak=    3.505 closest distance to " O   HOH Z 185 " =    1.821
peak=    3.500 closest distance to " O   HOH Z 344 " =    3.102
peak=    3.498 closest distance to " O  BHOH Z 338 " =    2.257
peak=    3.496 closest distance to " CA  ASN A 176 " =    1.163
peak=    3.495 closest distance to " CB  SER A 141 " =    1.032
peak=    3.493 closest distance to " O   HOH Z 415 " =    3.600
peak=    3.492 closest distance to " CD  LYS A 166 " =    1.292
peak=    3.491 closest distance to " CA  ARG A 195 " =    1.235
peak=    3.478 closest distance to " O   HOH Z 265 " =    2.158
peak=    3.475 closest distance to " CG2AVAL A 121 " =    2.243
peak=    3.467 closest distance to " CB  GLN A  88 " =    1.115
peak=    3.465 closest distance to " CE  LYS A 119 " =    1.115
peak=    3.464 closest distance to " O   HOH Z 353 " =    2.606
peak=    3.460 closest distance to " CB  ILE A 120 " =    1.261
peak=    3.457 closest distance to " O   HOH Z 305 " =    3.666
peak=    3.442 closest distance to " CA  SER A  87 " =    1.010
peak=    3.440 closest distance to " CA  ALA A  21 " =    1.110
peak=    3.439 closest distance to " NE2 GLN A  77 " =    3.127
peak=    3.438 closest distance to " O   HOH Z 273 " =    2.785
peak=    3.436 closest distance to " O   HOH Z 148 " =    3.353
peak=    3.431 closest distance to " ND2 ASN A 249 " =    0.923
peak=    3.431 closest distance to " O   HOH Z  62 " =    2.289
peak=    3.428 closest distance to " O   ALA A 165 " =    1.496
peak=    3.423 closest distance to " O   HOH Z  10 " =    1.801
peak=    3.422 closest distance to " O   HOH Z  80 " =    1.690
peak=    3.421 closest distance to " CB  ASP A 140 " =    1.043
peak=    3.418 closest distance to " NH1AARG A 145 " =    1.270
peak=    3.416 closest distance to " O   HOH Z 298 " =    2.255
peak=    3.415 closest distance to " O   HOH Z 380 " =    1.937
peak=    3.415 closest distance to " O   HOH Z 359 " =    1.581
peak=    3.414 closest distance to " O   HOH Z 345 " =    3.013
peak=    3.408 closest distance to " O   ASN A  74 " =    1.684
peak=    3.404 closest distance to " O   HOH Z 261 " =    1.933
peak=    3.403 closest distance to " CB  ALA A 248 " =    1.287
peak=    3.403 closest distance to " CB  TYR A 169 " =    0.803
peak=    3.398 closest distance to " CB  LEU A  83 " =    0.767
peak=    3.397 closest distance to " CB  ALA A 291 " =    1.165
peak=    3.395 closest distance to " O   HOH Z  47 " =    1.665
peak=    3.395 closest distance to " O   HOH Z 380 " =    2.054
peak=    3.395 closest distance to " O   HOH Z 433 " =    1.871
peak=    3.391 closest distance to " CB  GLU A 128 " =    1.025
peak=    3.385 closest distance to " O   HOH Z  88 " =    2.800
peak=    3.385 closest distance to " CG2BVAL A  41 " =    0.853
peak=    3.385 closest distance to " O   HOH Z 233 " =    1.980
peak=    3.385 closest distance to " O   HOH Z 172 " =    3.903
peak=    3.376 closest distance to " CG  GLN A  77 " =    2.113
peak=    3.367 closest distance to " O   HOH Z 126 " =    1.542
peak=    3.366 closest distance to " CB  PRO A  90 " =    1.074
peak=    3.358 closest distance to " CB  THR A  52 " =    0.748
peak=    3.357 closest distance to " O   HOH Z 337 " =    3.542
peak=    3.356 closest distance to " O   HOH Z  66 " =    2.173
peak=    3.354 closest distance to " O   HOH Z 371 " =    3.123
peak=    3.352 closest distance to " CG  GLN A  11 " =    1.749
peak=    3.352 closest distance to " O   HOH Z 166 " =    3.927
peak=    3.351 closest distance to " O   HOH Z 234 " =    2.211
peak=    3.348 closest distance to " O   GLY A  91 " =    1.520
peak=    3.345 closest distance to " CB  LYS A 290 " =    0.996
peak=    3.343 closest distance to " O   HOH Z 345 " =    1.588
peak=    3.342 closest distance to " O   HOH Z 332 " =    1.483
peak=    3.342 closest distance to " O   HOH Z 187 " =    2.256
peak=    3.341 closest distance to " O   HOH Z 147 " =    1.790
peak=    3.340 closest distance to " O   HOH Z  89 " =    2.182
peak=    3.335 closest distance to " CG1 ILE A  33 " =    1.196
peak=    3.333 closest distance to " OG BSER A 164 " =    2.152
peak=    3.332 closest distance to " CG  LEU A 167 " =    1.266
peak=    3.324 closest distance to " O   HOH Z 183 " =    1.740
peak=    3.321 closest distance to " CA  ALA A 248 " =    1.174
peak=    3.321 closest distance to " O   HOH Z 250 " =    2.075
peak=    3.315 closest distance to " O   HOH Z 299 " =    4.304
peak=    3.311 closest distance to " CA  MET A  40 " =    1.136
peak=    3.306 closest distance to " CA  ASP A 162 " =    1.062
peak=    3.305 closest distance to " O   HOH Z  30 " =    2.316
peak=    3.301 closest distance to " O   HOH Z  63 " =    2.208
peak=    3.296 closest distance to " CB  ASN A 142 " =    1.120
peak=    3.296 closest distance to " O   HOH Z 325 " =    2.402
peak=    3.294 closest distance to " CG  LYS A 119 " =    1.125
peak=    3.288 closest distance to " CG  GLU A  37 " =    0.972
peak=    3.288 closest distance to " N   CYS A 260 " =    0.985
peak=    3.287 closest distance to " O   HOH Z 188 " =    1.368
peak=    3.282 closest distance to " O   HOH Z 411 " =    3.868
peak=    3.281 closest distance to " OH  TYR A 116 " =    1.100
peak=    3.265 closest distance to " O   HOH Z 250 " =    1.568
peak=    3.261 closest distance to " CE  LYS A  76 " =    0.881
peak=    3.261 closest distance to " OE1 GLU A 236 " =    1.347
peak=    3.259 closest distance to " O   HOH Z 102 " =    1.251
peak=    3.258 closest distance to " CG1 ILE A  49 " =    1.411
peak=    3.254 closest distance to " O   HOH Z 193 " =    1.986
peak=    3.247 closest distance to " OG ASER A  99 " =    1.403
peak=    3.244 closest distance to " CD  ARG A 159 " =    0.708
peak=    3.243 closest distance to " CA  ALA A 233 " =    1.237
peak=    3.242 closest distance to " O   HOH Z  94 " =    2.199
peak=    3.241 closest distance to " CB  ARG A 139 " =    1.163
peak=    3.238 closest distance to " CE1 TYR A 186 " =    1.275
peak=    3.235 closest distance to " CA  ASN A 217 " =    1.243
peak=    3.232 closest distance to " CB  SER A  62 " =    0.978
peak=    3.232 closest distance to " OD2 ASP A 286 " =    2.804
peak=    3.228 closest distance to " CA  TYR A 116 " =    1.424
peak=    3.228 closest distance to " CB  SER A  62 " =    1.375
peak=    3.225 closest distance to " OD1 ASN A  69 " =    2.621
peak=    3.219 closest distance to " O   HOH Z 426 " =    1.516
peak=    3.218 closest distance to " O   HOH Z 427 " =    3.178
peak=    3.217 closest distance to " O   HOH Z 132 " =    2.390
peak=    3.217 closest distance to " CA  ILE A 234 " =    0.940
peak=    3.217 closest distance to " O   ALA A   1 " =    1.664
peak=    3.210 closest distance to " O   THR A 220 " =    1.156
peak=    3.210 closest distance to " OG1 THR A 264 " =    0.831
peak=    3.209 closest distance to " CA  SER A  32 " =    1.689
peak=    3.208 closest distance to " CB  ASN A  45 " =    1.128
peak=    3.206 closest distance to " CD  GLN A 194 " =    1.517
peak=    3.201 closest distance to " O   HOH Z 285 " =    2.548
peak=    3.199 closest distance to " N   LYS A 119 " =    1.414
peak=    3.193 closest distance to " CD1 ILE A 106 " =    0.897
peak=    3.189 closest distance to " CA  ASP A 124 " =    0.756
peak=    3.183 closest distance to " CG2 VAL A 197 " =    1.028
peak=    3.176 closest distance to " CA  VAL A 125 " =    1.050
peak=    3.176 closest distance to " N   ASP A 162 " =    1.099
peak=    3.175 closest distance to " O   HOH Z  89 " =    1.878
peak=    3.175 closest distance to " CB  ASP A 191 " =    1.134
peak=    3.173 closest distance to " CB  ASN A 285 " =    1.003
peak=    3.170 closest distance to " O   HOH Z 109 " =    2.032
peak=    3.170 closest distance to " OG  SER A 245 " =    1.561
peak=    3.170 closest distance to " N   SER A 135 " =    1.322
peak=    3.169 closest distance to " CB  PRO A 243 " =    1.457
peak=    3.167 closest distance to " NZ  LYS A  48 " =    1.174
peak=    3.165 closest distance to " CG  LYS A  76 " =    1.003
peak=    3.161 closest distance to " O   HOH Z 329 " =    3.948
peak=    3.153 closest distance to " CB  GLN A 205 " =    1.165
peak=    3.153 closest distance to " O   HOH Z 257 " =    2.214
peak=    3.153 closest distance to " O   HOH Z 428 " =    3.895
peak=    3.152 closest distance to " CB  GLN A 103 " =    0.848
peak=    3.151 closest distance to " CB  PRO A 198 " =    1.256
peak=    3.150 closest distance to " O   HOH Z 419 " =    1.919
peak=    3.144 closest distance to " CB  LEU A 300 " =    0.969
peak=    3.140 closest distance to " CA  ARG A 159 " =    1.285
peak=    3.139 closest distance to " O   HOH Z  88 " =    3.089
peak=    3.136 closest distance to " CB  LEU A 228 " =    1.110
peak=    3.132 closest distance to " CD  LYS A 119 " =    1.720
peak=    3.132 closest distance to " CB  ASN A 215 " =    1.134
peak=    3.129 closest distance to " O   HOH Z 361 " =    2.432
peak=    3.118 closest distance to " O   HOH Z 293 " =    1.824
peak=    3.113 closest distance to " CZ  PHE A  38 " =    1.212
peak=    3.110 closest distance to " C   TYR A 214 " =    1.511
peak=    3.106 closest distance to " CG2 THR A 294 " =    1.679
peak=    3.104 closest distance to " O   HOH Z 313 " =    1.522
peak=    3.104 closest distance to " CZ2 TRP A 179 " =    1.803
peak=    3.101 closest distance to " CD1 ILE A 199 " =    1.150
peak=    3.088 closest distance to " O   HOH Z  85 " =    2.328
peak=    3.086 closest distance to " CD  ARG A  66 " =    2.670
peak=    3.086 closest distance to " CA  LYS A 117 " =    1.217
peak=    3.082 closest distance to " O   HOH Z  35 " =    2.440
peak=    3.076 closest distance to " O   HOH Z  48 " =    1.580
peak=    3.073 closest distance to " CD1AILE A 234 " =    0.924
peak=    3.054 closest distance to " NE AARG A 190 " =    2.016
peak=    3.044 closest distance to " CA  MET A 105 " =    1.024
peak=    3.025 closest distance to " CB  ARG A 219 " =    0.967

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.407 - 5.939
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 205
   mapped sites are within: 0.719 - 5.939

peak=   -4.703 closest distance to " CG  GLN A  58 " =    1.017
peak=   -4.607 closest distance to " O   HOH Z 266 " =    5.219
peak=   -4.570 closest distance to " C   HIS A 108 " =    1.131
peak=   -4.460 closest distance to " CD  ARG A  14 " =    3.430
peak=   -4.458 closest distance to " OG BSER A 134 " =    1.339
peak=   -4.265 closest distance to " CB  PRO A 243 " =    2.696
peak=   -4.245 closest distance to " O   HOH Z 290 " =    1.071
peak=   -4.234 closest distance to " CA  VAL A  67 " =    2.928
peak=   -4.167 closest distance to " O   HOH Z 198 " =    1.288
peak=   -4.143 closest distance to " CG1 VAL A 112 " =    2.735
peak=   -4.082 closest distance to " CD  ARG A 156 " =    2.078
peak=   -4.075 closest distance to " CD1 LEU A 101 " =    2.422
peak=   -4.053 closest distance to " N   ALA A 248 " =    1.778
peak=   -4.036 closest distance to " OXT GLY A 302 " =    2.844
peak=   -4.017 closest distance to " O   HOH Z 377 " =    2.171
peak=   -4.009 closest distance to " O   PRO A 198 " =    1.255
peak=   -3.998 closest distance to " O   HOH Z 231 " =    2.379
peak=   -3.994 closest distance to " O   VAL A  67 " =    2.593
peak=   -3.990 closest distance to " CG  GLN A 223 " =    2.191
peak=   -3.963 closest distance to " CZ3 TRP A 179 " =    1.244
peak=   -3.941 closest distance to " CZ  TYR A 169 " =    1.849
peak=   -3.927 closest distance to " O   HOH Z 351 " =    1.444
peak=   -3.859 closest distance to " CB  PHE A 192 " =    2.044
peak=   -3.857 closest distance to " CE  MET A 105 " =    2.395
peak=   -3.836 closest distance to " CD1 LEU A  25 " =    2.545
peak=   -3.830 closest distance to " OD2 ASP A 171 " =    2.324
peak=   -3.829 closest distance to " O   VAL A 174 " =    2.200
peak=   -3.786 closest distance to " CB  ASN A  39 " =    2.306
peak=   -3.755 closest distance to " ND2 ASN A 187 " =    1.531
peak=   -3.750 closest distance to " CE2 TYR A  30 " =    2.720
peak=   -3.744 closest distance to " O   PRO A 163 " =    2.025
peak=   -3.733 closest distance to " CZ  ARG A  66 " =    1.141
peak=   -3.728 closest distance to " N   GLN A  58 " =    1.713
peak=   -3.719 closest distance to " O   HOH Z 183 " =    1.432
peak=   -3.711 closest distance to " O   HOH Z 211 " =    1.559
peak=   -3.706 closest distance to " O   HOH Z 165 " =    1.939
peak=   -3.701 closest distance to " O   HOH Z 185 " =    2.394
peak=   -3.681 closest distance to " O   HOH Z  13 " =    1.640
peak=   -3.675 closest distance to " O   HOH Z 372 " =    2.257
peak=   -3.656 closest distance to " O   HOH Z   6 " =    2.162
peak=   -3.643 closest distance to " O   HOH Z 139 " =    5.138
peak=   -3.633 closest distance to " O   HOH Z 102 " =    1.752
peak=   -3.630 closest distance to " CG  ASP A 132 " =    2.263
peak=   -3.627 closest distance to " CA  GLY A 241 " =    3.205
peak=   -3.617 closest distance to " OG  SER A  97 " =    2.202
peak=   -3.610 closest distance to " O   SER A 210 " =    1.969
peak=   -3.609 closest distance to " O   PHE A 218 " =    1.640
peak=   -3.604 closest distance to " CG1 VAL A  67 " =    3.130
peak=   -3.591 closest distance to " O   GLY A 241 " =    2.339
peak=   -3.589 closest distance to " O   HOH Z 313 " =    1.916
peak=   -3.575 closest distance to " CB  ALA A 161 " =    2.440
peak=   -3.575 closest distance to " CB  ALA A 291 " =    2.221
peak=   -3.567 closest distance to " O   ALA A 161 " =    1.677
peak=   -3.567 closest distance to " N   THR A  52 " =    1.747
peak=   -3.563 closest distance to " O   HOH Z 429 " =    2.180
peak=   -3.558 closest distance to " CD2 TYR A 293 " =    1.964
peak=   -3.557 closest distance to " CB  PHE A 208 " =    2.246
peak=   -3.555 closest distance to " O   HOH Z 435 " =    2.610
peak=   -3.535 closest distance to " NE2 GLN A 194 " =    1.912
peak=   -3.513 closest distance to " CD1 PHE A  59 " =    2.030
peak=   -3.504 closest distance to " CG2 ILE A 263 " =    2.170
peak=   -3.504 closest distance to " O   HOH Z 394 " =    1.433
peak=   -3.491 closest distance to " O   HOH Z 421 " =    3.402
peak=   -3.489 closest distance to " O   HOH Z  63 " =    1.556
peak=   -3.489 closest distance to " CB  ASP A 286 " =    1.801
peak=   -3.489 closest distance to " CG  PHE A 283 " =    2.558
peak=   -3.485 closest distance to " CB  ALA A 248 " =    2.315
peak=   -3.479 closest distance to " CA  ASP A 298 " =    1.100
peak=   -3.477 closest distance to " O   HOH Z 362 " =    5.864
peak=   -3.471 closest distance to " O   HOH Z 166 " =    1.946
peak=   -3.471 closest distance to " OG BSER A 134 " =    1.830
peak=   -3.466 closest distance to " O   HOH Z 196 " =    2.014
peak=   -3.465 closest distance to " O   HOH Z 109 " =    2.079
peak=   -3.463 closest distance to " CG  GLU A 277 " =    1.271
peak=   -3.460 closest distance to " CD2 TYR A 247 " =    2.453
peak=   -3.460 closest distance to " O   HOH Z 243 " =    2.002
peak=   -3.458 closest distance to " O   HOH Z  42 " =    0.719
peak=   -3.458 closest distance to " O   HOH Z 174 " =    3.912
peak=   -3.456 closest distance to " OD2 ASP A 191 " =    1.422
peak=   -3.454 closest distance to " ND2 ASN A  45 " =    1.088
peak=   -3.449 closest distance to " O   HOH Z  38 " =    1.649
peak=   -3.442 closest distance to " N   THR A 220 " =    2.287
peak=   -3.439 closest distance to " CB  PRO A 163 " =    2.443
peak=   -3.437 closest distance to " O   PRO A 198 " =    1.231
peak=   -3.435 closest distance to " C   GLN A 205 " =    1.807
peak=   -3.422 closest distance to " OD1 ASP A 171 " =    1.530
peak=   -3.413 closest distance to " CE BMET A  47 " =    1.401
peak=   -3.406 closest distance to " CD  ARG A 139 " =    1.569
peak=   -3.399 closest distance to " CE3 TRP A 274 " =    2.466
peak=   -3.397 closest distance to " O   SER A  95 " =    1.522
peak=   -3.393 closest distance to " O   HOH Z 281 " =    2.720
peak=   -3.392 closest distance to " N   GLY A  23 " =    2.328
peak=   -3.387 closest distance to " OD1 ASN A 301 " =    1.917
peak=   -3.386 closest distance to " O   HOH Z 114 " =    3.282
peak=   -3.384 closest distance to " O   HOH Z  15 " =    1.520
peak=   -3.378 closest distance to " CD  GLN A  88 " =    1.047
peak=   -3.375 closest distance to " SG ACYS A 201 " =    2.061
peak=   -3.374 closest distance to " O   HOH Z  43 " =    1.484
peak=   -3.362 closest distance to " O   ALA A  34 " =    2.316
peak=   -3.358 closest distance to " O   GLN A  94 " =    2.187
peak=   -3.354 closest distance to " ND2 ASN A  39 " =    1.088
peak=   -3.351 closest distance to " N   ALA A  43 " =    2.561
peak=   -3.345 closest distance to " CG  ASP A 231 " =    0.785
peak=   -3.345 closest distance to " O   HOH Z 126 " =    1.886
peak=   -3.338 closest distance to " NE2 GLN A 278 " =    1.913
peak=   -3.337 closest distance to " O   HOH Z 357 " =    2.098
peak=   -3.334 closest distance to " CG1AVAL A  41 " =    2.664
peak=   -3.332 closest distance to " NH1 ARG A 195 " =    2.594
peak=   -3.330 closest distance to " NH2AARG A 275 " =    5.045
peak=   -3.324 closest distance to " O   MET A  40 " =    2.869
peak=   -3.321 closest distance to " OH  TYR A 186 " =    2.608
peak=   -3.320 closest distance to " ND2 ASN A  45 " =    1.427
peak=   -3.320 closest distance to " O   LEU A 167 " =    1.564
peak=   -3.317 closest distance to " O   HOH Z  71 " =    2.160
peak=   -3.316 closest distance to " OE1 GLN A 183 " =    1.473
peak=   -3.313 closest distance to " O   HOH Z 389 " =    1.786
peak=   -3.311 closest distance to " O   SER A   3 " =    0.996
peak=   -3.309 closest distance to " O   HOH Z 200 " =    4.887
peak=   -3.307 closest distance to " CG1 VAL A 265 " =    2.655
peak=   -3.302 closest distance to " O   GLN A  89 " =    1.535
peak=   -3.300 closest distance to " O   HOH Z 139 " =    3.249
peak=   -3.290 closest distance to " O   HOH Z 198 " =    1.464
peak=   -3.290 closest distance to " O   ALA A 292 " =    2.206
peak=   -3.290 closest distance to " OD1 ASN A  39 " =    2.236
peak=   -3.288 closest distance to " N   ALA A 226 " =    1.921
peak=   -3.282 closest distance to " O   ALA A  10 " =    1.798
peak=   -3.281 closest distance to " ND2 ASN A 249 " =    2.328
peak=   -3.274 closest distance to " CG  GLU A  53 " =    1.537
peak=   -3.273 closest distance to " CA  GLY A 133 " =    1.944
peak=   -3.268 closest distance to " O   GLN A 240 " =    2.112
peak=   -3.264 closest distance to " C   ASP A 231 " =    2.545
peak=   -3.263 closest distance to " O   TRP A  92 " =    1.924
peak=   -3.262 closest distance to " O   ILE A 106 " =    1.919
peak=   -3.261 closest distance to " ND2 ASN A  60 " =    1.282
peak=   -3.259 closest distance to " OXT GLY A 302 " =    3.376
peak=   -3.259 closest distance to " CB  ALA A 291 " =    2.291
peak=   -3.258 closest distance to " CG2 ILE A  49 " =    2.695
peak=   -3.255 closest distance to " O   HOH Z 377 " =    1.515
peak=   -3.254 closest distance to " CD1 ILE A 106 " =    2.240
peak=   -3.254 closest distance to " O   HOH Z 191 " =    5.939
peak=   -3.252 closest distance to " O   HOH Z  88 " =    4.293
peak=   -3.247 closest distance to " CZ3 TRP A 274 " =    1.113
peak=   -3.240 closest distance to " OD1 ASN A 148 " =    1.462
peak=   -3.231 closest distance to " O   HOH Z 317 " =    1.539
peak=   -3.228 closest distance to " C   SER A 206 " =    1.554
peak=   -3.227 closest distance to " OG ASER A 134 " =    1.465
peak=   -3.219 closest distance to " OH  TYR A 172 " =    1.857
peak=   -3.215 closest distance to " NE2 GLN A  11 " =    1.855
peak=   -3.214 closest distance to " CD2 PHE A  61 " =    2.299
peak=   -3.210 closest distance to " CE3 TRP A 150 " =    2.386
peak=   -3.208 closest distance to " CG1 VAL A 250 " =    2.703
peak=   -3.205 closest distance to " C   ALA A 158 " =    1.414
peak=   -3.199 closest distance to " CG1 VAL A 112 " =    2.584
peak=   -3.197 closest distance to " OD2 ASP A  50 " =    1.452
peak=   -3.197 closest distance to " O   ASN A 187 " =    1.533
peak=   -3.192 closest distance to " O   HOH Z 174 " =    2.365
peak=   -3.190 closest distance to " CG1 VAL A 230 " =    1.966
peak=   -3.189 closest distance to " CD2 LEU A 300 " =    2.651
peak=   -3.188 closest distance to " O   HOH Z   6 " =    1.556
peak=   -3.187 closest distance to " O   HOH Z 123 " =    2.378
peak=   -3.180 closest distance to " CB  ASP A 132 " =    2.428
peak=   -3.178 closest distance to " OD2 ASP A  50 " =    2.125
peak=   -3.166 closest distance to " CB  SER A 210 " =    1.282
peak=   -3.166 closest distance to " CG  ARG A 269 " =    2.160
peak=   -3.165 closest distance to " NH2 ARG A  79 " =    2.105
peak=   -3.156 closest distance to " O   HOH Z 111 " =    3.683
peak=   -3.154 closest distance to " C   MET A 188 " =    1.523
peak=   -3.153 closest distance to " O   HOH Z 197 " =    5.128
peak=   -3.151 closest distance to " O   GLU A 152 " =    1.670
peak=   -3.147 closest distance to " CA  ASN A 127 " =    1.390
peak=   -3.147 closest distance to " OD1 ASP A 191 " =    1.603
peak=   -3.147 closest distance to " CZ  ARG A 259 " =    0.936
peak=   -3.142 closest distance to " O   HOH Z 422 " =    1.543
peak=   -3.139 closest distance to " O   HOH Z  33 " =    2.735
peak=   -3.137 closest distance to " O   HOH Z 283 " =    2.433
peak=   -3.136 closest distance to " CG  GLU A 152 " =    0.935
peak=   -3.134 closest distance to " CA  ASP A  27 " =    2.465
peak=   -3.133 closest distance to " NH2 ARG A  56 " =    1.807
peak=   -3.133 closest distance to " O   HOH Z  11 " =    1.805
peak=   -3.116 closest distance to " O   HOH Z 110 " =    1.432
peak=   -3.112 closest distance to " O   GLU A 152 " =    1.384
peak=   -3.107 closest distance to " CG  GLN A 223 " =    1.070
peak=   -3.106 closest distance to " ND2 ASN A 187 " =    0.834
peak=   -3.100 closest distance to " CA  TRP A 274 " =    1.429
peak=   -3.097 closest distance to " OH  TYR A 169 " =    0.893
peak=   -3.094 closest distance to " O   SER A 276 " =    1.675
peak=   -3.093 closest distance to " CB  TRP A  85 " =    2.571
peak=   -3.090 closest distance to " CD2 LEU A 237 " =    2.625
peak=   -3.088 closest distance to " CG2 THR A 178 " =    2.314
peak=   -3.082 closest distance to " O   HOH Z 134 " =    3.098
peak=   -3.080 closest distance to " O   HOH Z 326 " =    1.694
peak=   -3.079 closest distance to " CA  GLY A 203 " =    2.421
peak=   -3.075 closest distance to " O   HOH Z 274 " =    1.178
peak=   -3.073 closest distance to " N   PHE A  59 " =    1.741
peak=   -3.065 closest distance to " NE2 GLN A  88 " =    1.711
peak=   -3.065 closest distance to " O   HOH Z 265 " =    2.332
peak=   -3.051 closest distance to " N   ASP A 286 " =    2.029
peak=   -3.048 closest distance to " CG  GLU A   2 " =    1.978
peak=   -3.047 closest distance to " N   GLY A 196 " =    1.742
peak=   -3.046 closest distance to " O   HOH Z 193 " =    1.723
peak=   -3.044 closest distance to " CD2 LEU A 237 " =    2.332
peak=   -3.022 closest distance to " CD1 LEU A  25 " =    2.402

================= 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    :  0.3815 0.3769   6.164533e+00   6.160218e+00
   1_bss:  0.3713 0.3678   6.149592e+00   6.144997e+00
   1_xyz:  0.2360 0.2681   5.763549e+00   5.862959e+00
   1_adp:  0.2172 0.2723   5.714879e+00   5.881614e+00
   1_occ:  0.2169 0.2724   5.714400e+00   5.881371e+00
   2_bss:  0.2117 0.2659   5.699583e+00   5.867314e+00
   2_xyz:  0.1531 0.1908   5.396628e+00   5.574243e+00
   2_adp:  0.1391 0.1838   5.325145e+00   5.527092e+00
   2_occ:  0.1389 0.1836   5.324187e+00   5.526385e+00
   3_bss:  0.1388 0.1830   5.320972e+00   5.521860e+00
   3_xyz:  0.1180 0.1614   5.187581e+00   5.412186e+00
   3_adp:  0.1159 0.1584   5.169281e+00   5.390832e+00
   3_occ:  0.1158 0.1583   5.168779e+00   5.390657e+00
   4_bss:  0.1158 0.1583   5.168857e+00   5.390723e+00
   4_xyz:  0.1143 0.1557   5.157565e+00   5.379084e+00
   4_adp:  0.1140 0.1552   5.155960e+00   5.377535e+00
   4_occ:  0.1139 0.1551   5.155328e+00   5.377173e+00
   5_bss:  0.1137 0.1551   5.154154e+00   5.374733e+00
   5_xyz:  0.1101 0.1544   5.136426e+00   5.371117e+00
   5_adp:  0.1098 0.1540   5.134293e+00   5.369660e+00
   5_occ:  0.1097 0.1540   5.134106e+00   5.369693e+00
   5_bss:  0.1097 0.1540   5.134156e+00   5.369674e+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:  0.303  31.299   1.229  -1.979   0.382  -0.000   0.000   0.000
   1_xyz:  0.303  31.299   1.229  -1.979   0.382  -0.000   0.000   0.000
   1_adp:  0.303  31.299   1.229  -1.979   0.382  -0.000   0.000   0.000
   1_occ:  0.303  31.299   1.229  -1.979   0.382  -0.000   0.000   0.000
   2_bss:  0.328  49.375  -2.291  -2.503  -1.008  -0.000  -0.000  -0.000
   2_xyz:  0.328  49.375  -2.291  -2.503  -1.008  -0.000  -0.000  -0.000
   2_adp:  0.328  49.375  -2.291  -2.503  -1.008  -0.000  -0.000  -0.000
   2_occ:  0.328  49.375  -2.291  -2.503  -1.008  -0.000  -0.000  -0.000
   3_bss:  0.323  49.375  -3.142  -2.361  -1.099  -0.000  -0.000  -0.000
   3_xyz:  0.323  49.375  -3.142  -2.361  -1.099  -0.000  -0.000  -0.000
   3_adp:  0.323  49.375  -3.142  -2.361  -1.099  -0.000  -0.000  -0.000
   3_occ:  0.323  49.375  -3.142  -2.361  -1.099  -0.000  -0.000  -0.000
   4_bss:  0.326  49.374  -3.142  -2.361  -1.099  -0.000  -0.000  -0.000
   4_xyz:  0.326  49.374  -3.142  -2.361  -1.099  -0.000  -0.000  -0.000
   4_adp:  0.326  49.374  -3.142  -2.361  -1.099  -0.000  -0.000  -0.000
   4_occ:  0.326  49.374  -3.142  -2.361  -1.099  -0.000  -0.000  -0.000
   5_bss:  0.323  47.716  -3.347  -2.345  -1.103  -0.000  -0.000  -0.000
   5_xyz:  0.323  47.716  -3.347  -2.345  -1.103  -0.000  -0.000  -0.000
   5_adp:  0.323  47.716  -3.347  -2.345  -1.103  -0.000  -0.000  -0.000
   5_occ:  0.323  47.716  -3.347  -2.345  -1.103  -0.000  -0.000  -0.000
   5_bss:  0.324  47.657  -3.239  -2.178  -0.923  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  41.482 0.6275  0.8229    43741.130
   1_bss:  40.429 0.6384  0.8406    40719.108
   1_xyz:  26.478 0.7970  0.9910    18604.108
   1_adp:  27.235 0.7882  0.9872    19269.954
   1_occ:  27.255 0.7880  0.9869    19297.856
   2_bss:  26.646 0.7940  0.9300    18407.625
   2_xyz:  18.329 0.8771  0.9845     9366.931
   2_adp:  17.079 0.8890  0.9888     8587.890
   2_occ:  17.056 0.8892  0.9889     8568.606
   3_bss:  16.957 0.8899  0.9783     8439.130
   3_xyz:  14.817 0.9078  0.9850     6723.195
   3_adp:  14.389 0.9115  0.9826     6501.805
   3_occ:  14.382 0.9116  0.9825     6489.168
   4_bss:  14.384 0.9115  0.9825     6491.458
   4_xyz:  14.039 0.9147  0.9831     6315.445
   4_adp:  13.978 0.9153  0.9794     6313.616
   4_occ:  13.972 0.9154  0.9793     6302.570
   5_bss:  13.942 0.9156  0.9767     6266.215
   5_xyz:  13.857 0.9162  0.9779     6228.547
   5_adp:  13.832 0.9164  0.9752     6205.265
   5_occ:  13.829 0.9164  0.9752     6201.997
   5_bss:  13.832 0.9164  0.9783     6202.271
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   2.1370e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   2.1370e-01
   1_xyz:   1.247  0.009  0.078 15.073  0.005  4.108   8.5857e-02
   1_adp:   1.247  0.009  0.078 15.073  0.005  4.108   8.5857e-02
   1_occ:   1.247  0.009  0.078 15.073  0.005  4.108   8.5857e-02
   2_bss:   1.247  0.009  0.078 15.073  0.005  4.108   8.5857e-02
   2_xyz:   1.007  0.006  0.070 14.386  0.004  4.122   5.6026e-02
   2_adp:   1.007  0.006  0.070 14.386  0.004  4.122   5.6026e-02
   2_occ:   1.007  0.006  0.070 14.386  0.004  4.122   5.6026e-02
   3_bss:   1.007  0.006  0.070 14.386  0.004  4.122   5.6026e-02
   3_xyz:   1.068  0.008  0.077 14.743  0.004  4.118   6.4472e-02
   3_adp:   1.068  0.008  0.077 14.743  0.004  4.118   6.4472e-02
   3_occ:   1.068  0.008  0.077 14.743  0.004  4.118   6.4472e-02
   4_bss:   1.068  0.008  0.077 14.743  0.004  4.118   6.4472e-02
   4_xyz:   0.956  0.006  0.072 14.446  0.004  4.110   5.4093e-02
   4_adp:   0.956  0.006  0.072 14.446  0.004  4.110   5.4093e-02
   4_occ:   0.956  0.006  0.072 14.446  0.004  4.110   5.4093e-02
   5_bss:   0.956  0.006  0.072 14.446  0.004  4.110   5.4093e-02
   5_xyz:   1.027  0.007  0.077 14.631  0.004  4.111   6.0921e-02
   5_adp:   1.027  0.007  0.077 14.631  0.004  4.111   6.0921e-02
   5_occ:   1.027  0.007  0.077 14.631  0.004  4.111   6.0921e-02
   5_bss:   1.027  0.007  0.077 14.631  0.004  4.111   6.0921e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.201   2.4296e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.201   2.4296e-01
   1_xyz:   8.053  0.062  0.346 83.413  0.043  2.165   8.2700e-02
   1_adp:   8.053  0.062  0.346 83.413  0.043  2.165   8.2700e-02
   1_occ:   8.053  0.062  0.346 83.413  0.043  2.165   8.2700e-02
   2_bss:   8.053  0.062  0.346 83.413  0.043  2.165   8.2700e-02
   2_xyz:   6.984  0.032  0.216 79.854  0.035  2.224   4.3144e-02
   2_adp:   6.984  0.032  0.216 79.854  0.035  2.224   4.3144e-02
   2_occ:   6.984  0.032  0.216 79.854  0.035  2.224   4.3144e-02
   3_bss:   6.984  0.032  0.216 79.854  0.035  2.224   4.3144e-02
   3_xyz:   7.441  0.052  0.245 83.655  0.039  2.312   4.8752e-02
   3_adp:   7.441  0.052  0.245 83.655  0.039  2.312   4.8752e-02
   3_occ:   7.441  0.052  0.245 83.655  0.039  2.312   4.8752e-02
   4_bss:   7.441  0.052  0.245 83.655  0.039  2.312   4.8752e-02
   4_xyz:   6.532  0.045  0.235 82.244  0.037  2.387   3.4114e-02
   4_adp:   6.532  0.045  0.235 82.244  0.037  2.387   3.4114e-02
   4_occ:   6.532  0.045  0.235 82.244  0.037  2.387   3.4114e-02
   5_bss:   6.532  0.045  0.235 82.244  0.037  2.387   3.4114e-02
   5_xyz:   7.258  0.048  0.250 83.695  0.038  2.333   4.2338e-02
   5_adp:   7.258  0.048  0.250 83.695  0.038  2.333   4.2338e-02
   5_occ:   7.258  0.048  0.250 83.695  0.038  2.333   4.2338e-02
   5_bss:   7.258  0.048  0.250 83.695  0.038  2.333   4.2338e-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:  62.46   0.00  16.97  62.46   0.00  13.11  62.45   6.42  37.98
   1_occ:  62.46   0.00  16.97  62.46   0.00  13.11  62.45   6.42  37.98
   2_bss:  62.46   0.00  16.97  62.46   0.00  13.11  62.45   6.42  37.98
   2_xyz:  62.46   0.00  16.97  62.46   0.00  13.11  62.45   6.42  37.98
   2_adp:  82.51   0.00  17.68  82.51   0.00  13.42  71.78   6.17  40.87
   2_occ:  82.51   0.00  17.68  82.51   0.00  13.42  71.78   6.17  40.87
   3_bss:  82.51   0.00  17.68  82.51   0.00  13.42  71.78   6.17  40.87
   3_xyz:  82.51   0.00  17.68  82.51   0.00  13.42  71.78   6.17  40.87
   3_adp:  83.55   1.61  17.19  83.55   1.61  13.16  72.89   6.40  39.14
   3_occ:  83.55   1.61  17.19  83.55   1.61  13.16  72.89   6.40  39.14
   4_bss:  83.55   1.61  17.19  83.55   1.61  13.16  72.89   6.40  39.14
   4_xyz:  83.55   1.61  17.19  83.55   1.61  13.16  72.89   6.40  39.14
   4_adp:  83.62   0.00  16.92  83.62   1.95  13.02  72.31   0.00  38.17
   4_occ:  83.62   0.00  16.92  83.62   1.95  13.02  72.31   0.00  38.17
   5_bss:  83.62   0.00  16.92  83.62   1.95  13.02  72.31   0.00  38.17
   5_xyz:  83.62   0.00  16.92  83.62   1.95  13.02  72.31   0.00  38.17
   5_adp:  83.23   1.66  16.81  83.23   2.00  12.91  72.52   1.66  38.02
   5_occ:  83.23   1.66  16.81  83.23   2.00  12.91  72.52   1.66  38.02
   5_bss:  83.17   1.60  16.75  83.17   1.94  12.85  72.46   1.60  37.96
------------------------------------------------------------------------
 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:    2.380    0.012    0.366
   1_adp:    2.380    0.012    0.366
   1_occ:    2.380    0.012    0.366
   2_bss:    2.380    0.012    0.366
   2_xyz:    2.486    0.036    0.446
   2_adp:    2.486    0.036    0.446
   2_occ:    2.486    0.036    0.446
   3_bss:    2.486    0.036    0.446
   3_xyz:    2.560    0.044    0.497
   3_adp:    2.560    0.044    0.497
   3_occ:    2.560    0.044    0.497
   4_bss:    2.560    0.044    0.497
   4_xyz:    2.605    0.060    0.511
   4_adp:    2.605    0.060    0.511
   4_occ:    2.605    0.060    0.511
   5_bss:    2.605    0.060    0.511
   5_xyz:    2.695    0.073    0.522
   5_adp:    2.695    0.073    0.522
   5_occ:    2.695    0.073    0.522
   5_bss:    2.695    0.073    0.522
------------------------------------------------------------------------

CPU time actual refinement: 336.37


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_73/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_73/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_73/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_73/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_73/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 336.23 
  Macro-tasks:
    bulk solvent and scale       = 35.44  
    individual site refinement   = 143.69 
    weights calculation          = 29.81  
    collect and process          = 6.52   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 215.58 
  Micro-tasks:
    mask                            = 1.81   
    f_calc                          = 108.64 
    alpha_beta                      = 8.12   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 118.51 
    fmodel                         = 6.57   
    r_factors                      = 0.24   
    phase_errors                   = 10.96  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 256.27 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.694 micro seconds
Total CPU time: 5.83 minutes
from_scatterers_fft:    666 calls, 108.28 s
gradients_fft:          611 calls, 104.40 s

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

# Date 2008-01-16 Time 03:56:35 PST -0800 (1200484595.14 s)
Start R-work = 0.3815, R-free = 0.3769 (no bulk solvent and anisotropic scale)
Final R-work = 0.1368, R-free = 0.1757 (no bulk solvent and anisotropic scale)

Start R-work = 0.3713, R-free = 0.3678
Final R-work = 0.1097, R-free = 0.1540