# Date 2008-01-16 Time 04:09:33 PST -0800 (1200485373.94 s)
#phil __OFF__

Command line arguments: "../205.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25458
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 205

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.845, 47.3993, 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: 2.74, per 1000 atoms: 0.97


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 47.3993, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8556 1.96084
Completeness in resolution range: 0.929975
Completeness with d_max=infinity: 0.927158

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8556
                             d_min =   1.9608

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 47.3993, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8556 1.96084
Completeness in resolution range: 0.929975
Completeness with d_max=infinity: 0.927158

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8560 -  4.1957 [2213/2241]  1990   223  10.1%
  bin  2:  4.1957 -  3.3428 [2118/2141]  1902   216  10.2%
  bin  3:  3.3428 -  2.9239 [2085/2110]  1883   202   9.7%
  bin  4:  2.9239 -  2.6582 [2089/2105]  1876   213  10.2%
  bin  5:  2.6582 -  2.4686 [2037/2076]  1829   208  10.2%
  bin  6:  2.4686 -  2.3236 [2068/2100]  1865   203   9.8%
  bin  7:  2.3236 -  2.2077 [2043/2080]  1843   200   9.8%
  bin  8:  2.2077 -  2.1118 [2037/2079]  1829   208  10.2%
  bin  9:  2.1118 -  2.0308 [2017/2056]  1822   195   9.7%
  bin 10:  2.0308 -  1.9608 [ 882/2076]   791    91  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_205/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: 0.11 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:
        1.34 -     2.05: 13
        2.05 -     2.76: 468
        2.76 -     3.48: 4564
        3.48 -     4.19: 9366
        4.19 -     4.90: 13949
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.341 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.508 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.550 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.612 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.744 3.120 -x+1,y+1/2,-z+1/2
  ... (remaining 28355 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_205/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_205/model_refine_001.geo

CPU time processing inputs: 7.81


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 47.3993 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: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3886   r_free= 0.3825   ksol= 0.00   Bsol= 0.00   scale= 0.943    |
|                                                                             |
| 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: 6.168308                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8560 -  4.6797 0.99   1436  159 0.3065 0.3177      6.4175      6.4553|
|  2:  4.6797 -  3.7339 0.99   1388  154 0.3080 0.2939      6.5721      6.5617|
|  3:  3.7339 -  3.2676 0.99   1347  149 0.3495 0.3263      6.4936      6.4936|
|  4:  3.2676 -  2.9714 0.99   1351  147 0.3727 0.3751      6.3481      6.3658|
|  5:  2.9714 -  2.7599 0.98   1327  152 0.4069 0.3856      6.2323       6.226|
|  6:  2.7599 -  2.5981 0.99   1346  145 0.4103 0.4518      6.1584      6.0905|
|  7:  2.5981 -  2.4686 0.99   1285  156 0.4129 0.3741      6.1138      6.0258|
|  8:  2.4686 -  2.3616 0.99   1346  134 0.4456 0.4126      6.0906      6.0749|
|  9:  2.3616 -  2.2710 0.99   1324  151 0.4475 0.4067       6.054      6.0344|
| 10:  2.2710 -  2.1929 0.98   1318  142 0.4458 0.4231      6.0197      5.9687|
| 11:  2.1929 -  2.1245 0.98   1277  154 0.4569 0.4861      5.9624      6.0049|
| 12:  2.1245 -  2.0640 1.00   1324  143 0.4596 0.4512      5.8933      5.9183|
| 13:  2.0640 -  2.0098 0.91   1235  133 0.4661 0.5017      5.8283      5.8146|
| 14:  2.0098 -  1.9608 0.25    326   40 0.4599 0.4595      5.8548      5.6742|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8560 -  4.6797  1436   159  0.75  29.66   0.86     0.76      52990.98|
|  2:  4.6797 -  3.7339  1388   154  0.80  26.38   0.97     0.88      64233.53|
|  3:  3.7339 -  3.2676  1347   149  0.74  31.90   0.95     0.90      65175.97|
|  4:  3.2676 -  2.9714  1351   147  0.67  37.59   0.96     0.85      58195.12|
|  5:  2.9714 -  2.7599  1327   152  0.61  42.96   0.94     0.81      49678.58|
|  6:  2.7599 -  2.5981  1346   145  0.60  43.73   0.95     0.79      43704.62|
|  7:  2.5981 -  2.4686  1285   156  0.60  43.64   0.98     0.80      39066.54|
|  8:  2.4686 -  2.3616  1346   134  0.61  43.47   0.97     0.82      34268.03|
|  9:  2.3616 -  2.2710  1324   151  0.62  42.52   0.96     0.85      31111.51|
| 10:  2.2710 -  2.1929  1318   142  0.60  43.86   0.98     0.83      29370.85|
| 11:  2.1929 -  2.1245  1277   154  0.55  48.64   0.98     0.80      32012.44|
| 12:  2.1245 -  2.0640  1324   143  0.48  54.19   0.98     0.74      32997.40|
| 13:  2.0640 -  2.0098  1235   133  0.45  56.32   0.97     0.70      30345.30|
| 14:  2.0098 -  1.9608   326    40  0.53  50.01   1.00     0.67      23034.99|
|alpha:            min =        0.67 max =            0.90 mean =         0.81|
|beta:             min =    23034.99 max =        65175.97 mean =     43232.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.62|
|phase err.(work): min =        0.00 max =           90.00 mean =        41.82|
|phase err.(test): min =        0.00 max =           89.93 mean =        42.10|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.734987              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.235   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.937187              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.619   (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 |  1.341 -  1.697:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.697 -  2.053:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.053 -  2.409:       20 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.409 -  2.765:      448 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.765 -  3.121:     2219 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.121 -  3.476:     2345 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.476 -  3.832:     4411 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.832 -  4.188:     4955 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.188 -  4.544:     6298 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.544 -  4.900:     7651 |
|-----------------------------------------------------------------------------|
|-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 |        0.186 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.341 |       0.533 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.799)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3886   r_free= 0.3825   ksol= 0.00   Bsol= 0.00   scale= 0.943    |
|                                                                             |
| 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: 6.168308                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3801   r_free= 0.3733   ksol= 0.32   Bsol= 36.00   scale= 0.969   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.21,-0.05,0.27,-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: 6.155704                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.024772              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.968   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.530143              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.367   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3801      final r-factor (work) = 0.2187          |
| start r-factor (free) = 0.3733      final r-factor (free) = 0.2460          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.7449 = 6.02 * 0.50 * 6.1608 + 1.00 * 0.1864                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.8811 = 6.02 * 0.50 * 5.9072 + 1.00 * 0.0863                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2187      final r-factor (work) = 0.1994          |
| start r-factor (free) = 0.2460      final r-factor (free) = 0.2498          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1383 = 0.53 * 1.00 * 5.9072 + 1.00 * 0.0067                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0072 = 0.53 * 1.00 * 5.6275 + 1.00 * 0.0239                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.799)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.17   17.15    None  None   None       |
|    all(noH): 2823   0      0.00    87.17   17.15    None  None   None       |
|    Sol.    : 438    0      6.93    65.20   38.43    None  None   None       |
|    Mac.    : 2385   0      0.00    87.17   13.25    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 -   8.717:  760   |   5:    43.585 -  52.302:  132        |
|      1:     8.717 -  17.434: 1161   |   6:    52.302 -  61.019:   63        |
|      2:    17.434 -  26.151:  394   |   7:    61.019 -  69.736:    4        |
|      3:    26.151 -  34.868:  164   |   8:    69.736 -  78.453:    0        |
|      4:    34.868 -  43.585:  144   |   9:    78.453 -  87.170:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1994 r_free = 0.2498             target_work(ml) = 5.638         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1992 r_free = 0.2498             target_work(ml) = 5.637         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1992   r_free= 0.2498   ksol= 0.32   Bsol= 36.00   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.21,-0.05,0.27,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.637493                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1956   r_free= 0.2457   ksol= 0.33   Bsol= 56.56   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-1.53,-0.95,-0.00,-0.00,-0.00); trace/3= -1.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.629619                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.884878              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.923   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.335665              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.128   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1956      final r-factor (work) = 0.1432          |
| start r-factor (free) = 0.2457      final r-factor (free) = 0.1809          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2247 = 2.88 * 0.50 * 5.6421 + 1.00 * 0.0863                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0049 = 2.88 * 0.50 * 5.5094 + 1.00 * 0.0579                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1432      final r-factor (work) = 0.1328          |
| start r-factor (free) = 0.1809      final r-factor (free) = 0.1735          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8677 = 0.34 * 1.00 * 5.5094 + 1.00 * 0.0183                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7882 = 0.34 * 1.00 * 5.3012 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.799)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.17   17.33    None  None   None       |
|    all(noH): 2823   0      0.00    83.17   17.33    None  None   None       |
|    Sol.    : 438    0      6.22    71.92   39.95    None  None   None       |
|    Mac.    : 2385   0      0.00    83.17   13.17    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.317:  594   |   5:    41.584 -  49.901:  115        |
|      1:     8.317 -  16.634: 1381   |   6:    49.901 -  58.218:   87        |
|      2:    16.634 -  24.951:  334   |   7:    58.218 -  66.535:   48        |
|      3:    24.951 -  33.268:  127   |   8:    66.535 -  74.852:   14        |
|      4:    33.268 -  41.584:  121   |   9:    74.852 -  83.169:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1328 r_free = 0.1735             target_work(ml) = 5.278         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1326 r_free = 0.1734             target_work(ml) = 5.278         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1326   r_free= 0.1734   ksol= 0.33   Bsol= 56.56   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-1.53,-0.95,-0.00,-0.00,-0.00); trace/3= -1.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.277596                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1326   r_free= 0.1732   ksol= 0.33   Bsol= 56.56   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-1.92,-1.05,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.276817                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.528784              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.403  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.161766              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.698  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1326      final r-factor (work) = 0.1143          |
| start r-factor (free) = 0.1732      final r-factor (free) = 0.1595          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4130 = 3.53 * 0.50 * 5.3022 + 1.00 * 0.0579                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2675 = 3.53 * 0.50 * 5.2117 + 1.00 * 0.0720                               |
|-----------------------------------------------------------------------------|
| 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) = 0.1130          |
| start r-factor (free) = 0.1595      final r-factor (free) = 0.1564          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8518 = 0.16 * 1.00 * 5.2117 + 1.00 * 0.0088                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8424 = 0.16 * 1.00 * 5.1623 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.799)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.84    82.13   16.80    None  None   None       |
|    all(noH): 2823   0      1.84    82.13   16.80    None  None   None       |
|    Sol.    : 438    0      3.45    72.61   38.13    None  None   None       |
|    Mac.    : 2385   0      1.84    82.13   12.89    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:     1.839 -   9.868:  963   |   5:    41.984 -  50.013:   94        |
|      1:     9.868 -  17.897: 1135   |   6:    50.013 -  58.042:   80        |
|      2:    17.897 -  25.926:  251   |   7:    58.042 -  66.071:   30        |
|      3:    25.926 -  33.955:  130   |   8:    66.071 -  74.100:   10        |
|      4:    33.955 -  41.984:  128   |   9:    74.100 -  82.129:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1130 r_free = 0.1564             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1128 r_free = 0.1565             target_work(ml) = 5.152         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1128   r_free= 0.1565   ksol= 0.33   Bsol= 56.56   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-1.92,-1.05,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.152161                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1128   r_free= 0.1565   ksol= 0.32   Bsol= 50.81   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-1.92,-1.05,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.152364                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.400762              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.388  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.049512              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.909  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1128      final r-factor (work) = 0.1154          |
| start r-factor (free) = 0.1565      final r-factor (free) = 0.1564          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6872 = 1.40 * 0.50 * 5.1618 + 1.00 * 0.0720                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6690 = 1.40 * 0.50 * 5.1645 + 1.00 * 0.0519                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1154      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1564      final r-factor (free) = 0.1585          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4276 = 1.05 * 1.00 * 5.1645 + 1.00 * 0.0073                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4226 = 1.05 * 1.00 * 5.1576 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.799)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.68    91.68   17.27    None  None   None       |
|    all(noH): 2823   0      0.68    91.68   17.27    None  None   None       |
|    Sol.    : 438    0      0.68    86.34   40.60    None  None   None       |
|    Mac.    : 2385   0      0.85    91.68   12.98    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:     0.681 -   9.781:  980   |   5:    46.179 -  55.278:  104        |
|      1:     9.781 -  18.880: 1162   |   6:    55.278 -  64.378:   67        |
|      2:    18.880 -  27.980:  228   |   7:    64.378 -  73.477:   31        |
|      3:    27.980 -  37.079:  123   |   8:    73.477 -  82.577:    7        |
|      4:    37.079 -  46.179:  117   |   9:    82.577 -  91.676:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1138 r_free = 0.1585             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1138 r_free = 0.1585             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1585   ksol= 0.32   Bsol= 50.81   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-1.92,-1.05,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.164834                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1584   ksol= 0.32   Bsol= 52.63   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.98,-1.82,-0.86,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.164640                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.473964              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 152.469  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.210157              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.173  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1137      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1584      final r-factor (free) = 0.1587          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8530 = 1.47 * 0.50 * 5.1577 + 1.00 * 0.0519                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8550 = 1.47 * 0.50 * 5.1585 + 1.00 * 0.0533                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1121      final r-factor (work) = 0.1129          |
| start r-factor (free) = 0.1587      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0937 = 0.21 * 1.00 * 5.1585 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0929 = 0.21 * 1.00 * 5.1622 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.799)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.43    88.49   16.64    None  None   None       |
|    all(noH): 2823   0      1.43    88.49   16.64    None  None   None       |
|    Sol.    : 438    0      2.48    84.03   38.18    None  None   None       |
|    Mac.    : 2385   0      1.43    88.49   12.68    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:     1.432 -  10.138: 1090   |   5:    44.962 -  53.668:   96        |
|      1:    10.138 -  18.844: 1075   |   6:    53.668 -  62.374:   45        |
|      2:    18.844 -  27.550:  217   |   7:    62.374 -  71.080:   27        |
|      3:    27.550 -  36.256:  128   |   8:    71.080 -  79.786:    7        |
|      4:    36.256 -  44.962:  135   |   9:    79.786 -  88.491:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1129 r_free = 0.1572             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1129 r_free = 0.1572             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1129   r_free= 0.1572   ksol= 0.32   Bsol= 52.63   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.98,-1.82,-0.86,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.158054                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8560 -  4.6797 0.99   1436  159 0.1005 0.1309      5.4044      5.5688|
|  2:  4.6797 -  3.7339 0.99   1388  154 0.0861 0.1086      5.4348       5.618|
|  3:  3.7339 -  3.2676 0.99   1347  149 0.1071 0.1514      5.4629      5.8172|
|  4:  3.2676 -  2.9714 0.99   1351  147 0.1227 0.1554      5.4457      5.6082|
|  5:  2.9714 -  2.7599 0.98   1327  152 0.1312 0.1601      5.3155      5.4873|
|  6:  2.7599 -  2.5981 0.99   1346  145 0.1252 0.2113      5.2213      5.5081|
|  7:  2.5981 -  2.4686 0.99   1285  156 0.1242 0.1629      5.1621       5.364|
|  8:  2.4686 -  2.3616 0.99   1346  134 0.1163 0.1625      5.0866      5.2517|
|  9:  2.3616 -  2.2710 0.99   1324  151 0.1180 0.1886      5.0204      5.3352|
| 10:  2.2710 -  2.1929 0.98   1318  142 0.1135 0.1748      4.9493      5.1637|
| 11:  2.1929 -  2.1245 0.98   1277  154 0.1157 0.1790      4.9126      5.2585|
| 12:  2.1245 -  2.0640 1.00   1324  143 0.1174 0.1639       4.872      5.0918|
| 13:  2.0640 -  2.0098 0.91   1235  133 0.1163 0.1799      4.7913      5.0306|
| 14:  2.0098 -  1.9608 0.25    326   40 0.1068 0.1710      4.7359      4.9188|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8560 -  4.6797  1436   159  0.94   9.46   0.97     0.95       7503.77|
|  2:  4.6797 -  3.7339  1388   154  0.95   8.00   1.01     1.00       8964.98|
|  3:  3.7339 -  3.2676  1347   149  0.93  11.39   1.02     1.01      10074.22|
|  4:  3.2676 -  2.9714  1351   147  0.92  13.94   1.00     0.99      10243.21|
|  5:  2.9714 -  2.7599  1327   152  0.90  15.86   0.99     0.96       8182.96|
|  6:  2.7599 -  2.5981  1346   145  0.90  16.41   0.98     0.96       7107.84|
|  7:  2.5981 -  2.4686  1285   156  0.91  15.56   0.98     0.95       6128.56|
|  8:  2.4686 -  2.3616  1346   134  0.90  15.82   1.00     0.97       5653.07|
|  9:  2.3616 -  2.2710  1324   151  0.90  15.77   0.99     0.95       4909.63|
| 10:  2.2710 -  2.1929  1318   142  0.90  15.71   0.99     0.96       4403.99|
| 11:  2.1929 -  2.1245  1277   154  0.91  15.63   0.99     0.96       4090.04|
| 12:  2.1245 -  2.0640  1324   143  0.90  16.06   1.00     0.99       3857.06|
| 13:  2.0640 -  2.0098  1235   133  0.90  16.40   0.98     0.97       3333.86|
| 14:  2.0098 -  1.9608   326    40  0.92  13.85   0.97     0.92       2711.06|
|alpha:            min =        0.92 max =            1.01 mean =         0.97|
|beta:             min =     2711.06 max =        10243.21 mean =      6476.07|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.23|
|phase err.(test): min =        0.00 max =           88.43 mean =        13.81|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1128   r_free= 0.1570   ksol= 0.32   Bsol= 50.90   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-1.67,-0.64,-0.00,-0.00,-0.00); trace/3= -1.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.156792                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1128   r_free= 0.1570   ksol= 0.32   Bsol= 50.90   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-1.67,-0.64,-0.00,-0.00,-0.00); trace/3= -1.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.156792                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8560 -  4.6797 0.99   1436  159 0.1002 0.1270      5.3949      5.5346|
|  2:  4.6797 -  3.7339 0.99   1388  154 0.0862 0.1084      5.4292      5.6177|
|  3:  3.7339 -  3.2676 0.99   1347  149 0.1072 0.1499      5.4611      5.8049|
|  4:  3.2676 -  2.9714 0.99   1351  147 0.1229 0.1557      5.4439      5.6071|
|  5:  2.9714 -  2.7599 0.98   1327  152 0.1311 0.1606       5.315      5.4855|
|  6:  2.7599 -  2.5981 0.99   1346  145 0.1252 0.2115      5.2209      5.5072|
|  7:  2.5981 -  2.4686 0.99   1285  156 0.1243 0.1634      5.1628      5.3663|
|  8:  2.4686 -  2.3616 0.99   1346  134 0.1162 0.1626      5.0874      5.2524|
|  9:  2.3616 -  2.2710 0.99   1324  151 0.1177 0.1884      5.0205       5.335|
| 10:  2.2710 -  2.1929 0.98   1318  142 0.1135 0.1749      4.9506      5.1657|
| 11:  2.1929 -  2.1245 0.98   1277  154 0.1157 0.1793       4.913      5.2593|
| 12:  2.1245 -  2.0640 1.00   1324  143 0.1173 0.1639      4.8721      5.0919|
| 13:  2.0640 -  2.0098 0.91   1235  133 0.1163 0.1804      4.7919      5.0311|
| 14:  2.0098 -  1.9608 0.25    326   40 0.1070 0.1705      4.7362      4.9182|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8560 -  4.6797  1436   159  0.94   9.24   0.97     0.95       7137.87|
|  2:  4.6797 -  3.7339  1388   154  0.95   7.84   1.01     1.00       8706.30|
|  3:  3.7339 -  3.2676  1347   149  0.93  11.32   1.02     1.02       9970.08|
|  4:  3.2676 -  2.9714  1351   147  0.92  13.86   1.01     1.00      10150.27|
|  5:  2.9714 -  2.7599  1327   152  0.90  15.81   1.00     0.97       8137.63|
|  6:  2.7599 -  2.5981  1346   145  0.90  16.37   0.98     0.96       7098.53|
|  7:  2.5981 -  2.4686  1285   156  0.91  15.55   0.99     0.95       6132.50|
|  8:  2.4686 -  2.3616  1346   134  0.90  15.84   1.00     0.97       5667.99|
|  9:  2.3616 -  2.2710  1324   151  0.90  15.79   1.00     0.96       4922.20|
| 10:  2.2710 -  2.1929  1318   142  0.90  15.73   1.00     0.96       4413.32|
| 11:  2.1929 -  2.1245  1277   154  0.91  15.65   0.99     0.96       4098.32|
| 12:  2.1245 -  2.0640  1324   143  0.90  16.07   1.00     1.00       3863.13|
| 13:  2.0640 -  2.0098  1235   133  0.90  16.41   0.99     0.97       3338.31|
| 14:  2.0098 -  1.9608   326    40  0.92  13.86   0.98     0.93       2715.67|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2715.67 max =        10150.27 mean =      6411.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.19|
|phase err.(test): min =        0.00 max =           88.35 mean =        13.77|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.799)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.38    88.44   16.59    None  None   None       |
|    all(noH): 2823   0      1.38    88.44   16.59    None  None   None       |
|    Sol.    : 438    0      2.43    83.98   38.13    None  None   None       |
|    Mac.    : 2385   0      1.38    88.44   12.63    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:     1.381 -  10.087: 1090   |   5:    44.911 -  53.617:   96        |
|      1:    10.087 -  18.793: 1075   |   6:    53.617 -  62.323:   45        |
|      2:    18.793 -  27.499:  217   |   7:    62.323 -  71.029:   27        |
|      3:    27.499 -  36.205:  128   |   8:    71.029 -  79.735:    7        |
|      4:    36.205 -  44.911:  135   |   9:    79.735 -  88.441:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 297         
Filter by distance & map next to the model:
   mapped sites are within: 0.456 - 4.838
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 293 from: 297
   mapped sites are within: 0.709 - 4.838

peak=    5.668 closest distance to " NH2 ARG A  56 " =    2.267
peak=    5.333 closest distance to " CB  ARG A 275 " =    0.941
peak=    5.327 closest distance to " CG  PRO A  54 " =    1.287
peak=    4.990 closest distance to " CG  PRO A  90 " =    1.263
peak=    4.808 closest distance to " CB  SER A  63 " =    1.131
peak=    4.769 closest distance to " CB  GLN A 223 " =    1.400
peak=    4.738 closest distance to " CG  PRO A 213 " =    1.304
peak=    4.720 closest distance to " CG  PRO A 198 " =    1.215
peak=    4.695 closest distance to " O   HOH Z 232 " =    2.373
peak=    4.693 closest distance to " O   HOH Z 126 " =    1.887
peak=    4.629 closest distance to " CB  GLU A 152 " =    1.185
peak=    4.605 closest distance to " O   HOH Z 298 " =    1.759
peak=    4.560 closest distance to " O   HOH Z 403 " =    1.683
peak=    4.552 closest distance to " CB  GLN A 183 " =    1.247
peak=    4.518 closest distance to " O   HOH Z  43 " =    2.085
peak=    4.491 closest distance to " ND2 ASN A 187 " =    1.564
peak=    4.459 closest distance to " CB  PRO A  54 " =    1.033
peak=    4.459 closest distance to " CB  ARG A  79 " =    1.333
peak=    4.419 closest distance to " O   HOH Z 402 " =    1.439
peak=    4.408 closest distance to " O   HOH Z  40 " =    1.953
peak=    4.390 closest distance to " CA  TYR A  30 " =    0.872
peak=    4.377 closest distance to " O   HOH Z 234 " =    3.691
peak=    4.330 closest distance to " O   HOH Z 250 " =    1.525
peak=    4.329 closest distance to " CG  PRO A 243 " =    1.126
peak=    4.328 closest distance to " O   HOH Z  44 " =    2.006
peak=    4.317 closest distance to " O   HOH Z 369 " =    2.324
peak=    4.316 closest distance to " O   SER A  87 " =    2.177
peak=    4.288 closest distance to " CD2 TRP A 179 " =    1.325
peak=    4.255 closest distance to " O   HOH Z  97 " =    2.007
peak=    4.237 closest distance to " O   HOH Z 287 " =    1.909
peak=    4.218 closest distance to " O   HOH Z 406 " =    1.640
peak=    4.215 closest distance to " NH2BARG A 145 " =    2.088
peak=    4.198 closest distance to " O  BHOH Z  74 " =    1.229
peak=    4.187 closest distance to " C   PRO A 198 " =    1.523
peak=    4.183 closest distance to " O   HOH Z 189 " =    2.578
peak=    4.159 closest distance to " CB  ARG A 190 " =    1.691
peak=    4.156 closest distance to " NE2 GLN A  11 " =    1.187
peak=    4.149 closest distance to " O   HOH Z 209 " =    2.233
peak=    4.142 closest distance to " CB  ARG A  79 " =    0.913
peak=    4.135 closest distance to " CZ  PHE A 218 " =    1.085
peak=    4.090 closest distance to " O   HOH Z  63 " =    1.900
peak=    4.079 closest distance to " O   HOH Z 346 " =    1.586
peak=    4.079 closest distance to " NZ  LYS A 117 " =    3.078
peak=    4.075 closest distance to " CG2 ILE A 120 " =    1.234
peak=    4.060 closest distance to " O   HOH Z 142 " =    1.650
peak=    4.052 closest distance to " O   HOH Z 272 " =    1.880
peak=    4.044 closest distance to " O   HOH Z  15 " =    2.190
peak=    4.039 closest distance to " CB  ASN A 148 " =    1.416
peak=    4.038 closest distance to " CD  ARG A 269 " =    1.033
peak=    4.035 closest distance to " O   HOH Z 128 " =    2.245
peak=    3.971 closest distance to " CB  VAL A 265 " =    1.210
peak=    3.968 closest distance to " O   HOH Z 227 " =    1.668
peak=    3.967 closest distance to " O   HOH Z  59 " =    2.208
peak=    3.963 closest distance to " O   HOH Z 126 " =    1.710
peak=    3.955 closest distance to " O   HOH Z 361 " =    3.618
peak=    3.953 closest distance to " O   HOH Z 193 " =    1.827
peak=    3.941 closest distance to " CG  ARG A  66 " =    2.633
peak=    3.940 closest distance to " N   ASN A  39 " =    1.258
peak=    3.899 closest distance to " O   HOH Z 368 " =    1.970
peak=    3.896 closest distance to " CD2 LEU A 297 " =    0.950
peak=    3.891 closest distance to " CB  GLU A 277 " =    3.595
peak=    3.879 closest distance to " O   HOH Z 128 " =    1.918
peak=    3.874 closest distance to " CB  SER A 141 " =    1.065
peak=    3.872 closest distance to " CA  ARG A  36 " =    0.989
peak=    3.845 closest distance to " CB  TRP A 179 " =    1.323
peak=    3.837 closest distance to " O   HOH Z 389 " =    1.836
peak=    3.836 closest distance to " CB  SER A   3 " =    1.256
peak=    3.832 closest distance to " CD  LYS A 166 " =    1.308
peak=    3.830 closest distance to " O   HOH Z 109 " =    1.484
peak=    3.825 closest distance to " O   HOH Z 291 " =    1.519
peak=    3.822 closest distance to " CG1BVAL A  72 " =    1.714
peak=    3.815 closest distance to " CA  ASN A 176 " =    1.166
peak=    3.800 closest distance to " CB  TYR A 169 " =    0.709
peak=    3.788 closest distance to " O   HOH Z 265 " =    2.232
peak=    3.788 closest distance to " O   HOH Z 423 " =    1.999
peak=    3.744 closest distance to " O   HOH Z  61 " =    1.598
peak=    3.733 closest distance to " CG2 VAL A 257 " =    0.793
peak=    3.729 closest distance to " O   HOH Z  88 " =    2.743
peak=    3.726 closest distance to " CG AARG A 275 " =    1.169
peak=    3.726 closest distance to " O   HOH Z 298 " =    2.318
peak=    3.726 closest distance to " O   HOH Z 248 " =    1.611
peak=    3.724 closest distance to " O   HOH Z 132 " =    2.712
peak=    3.714 closest distance to " CB  ASN A  39 " =    0.837
peak=    3.713 closest distance to " N   ARG A 156 " =    1.397
peak=    3.704 closest distance to " O   HOH Z 421 " =    1.752
peak=    3.704 closest distance to " O   HOH Z 303 " =    2.200
peak=    3.689 closest distance to " CG1 ILE A  33 " =    1.255
peak=    3.685 closest distance to " O   HOH Z 353 " =    2.677
peak=    3.684 closest distance to " O   HOH Z 327 " =    1.632
peak=    3.671 closest distance to " CG  MET A 185 " =    1.068
peak=    3.669 closest distance to " O   HOH Z 203 " =    1.831
peak=    3.657 closest distance to " CZ3 TRP A 266 " =    1.087
peak=    3.657 closest distance to " O   HOH Z  78 " =    1.638
peak=    3.653 closest distance to " O   HOH Z 173 " =    2.082
peak=    3.653 closest distance to " O   HOH Z 180 " =    2.216
peak=    3.650 closest distance to " O   HOH Z 316 " =    3.093
peak=    3.644 closest distance to " NH1AARG A 145 " =    1.321
peak=    3.643 closest distance to " CB  GLU A  46 " =    1.033
peak=    3.643 closest distance to " O   HOH Z 214 " =    2.311
peak=    3.643 closest distance to " O   HOH Z 365 " =    2.721
peak=    3.642 closest distance to " CA  ALA A  51 " =    0.905
peak=    3.640 closest distance to " CA  ALA A  84 " =    1.137
peak=    3.640 closest distance to " O   HOH Z  96 " =    2.120
peak=    3.634 closest distance to " CB  VAL A 202 " =    1.485
peak=    3.634 closest distance to " CB  SER A  26 " =    1.783
peak=    3.629 closest distance to " O   ASN A  74 " =    1.467
peak=    3.628 closest distance to " O   HOH Z  85 " =    1.364
peak=    3.622 closest distance to " O   HOH Z 251 " =    1.602
peak=    3.611 closest distance to " CB  TRP A 266 " =    1.016
peak=    3.604 closest distance to " O   HOH Z 148 " =    3.376
peak=    3.597 closest distance to " O   HOH Z 245 " =    1.416
peak=    3.594 closest distance to " O   HOH Z 427 " =    2.919
peak=    3.591 closest distance to " O   HOH Z 185 " =    1.807
peak=    3.586 closest distance to " CG2 ILE A  20 " =    1.394
peak=    3.585 closest distance to " N   ALA A   1 " =    2.988
peak=    3.583 closest distance to " CA  ALA A  21 " =    1.137
peak=    3.580 closest distance to " O   HOH Z 261 " =    1.945
peak=    3.576 closest distance to " OG BSER A 164 " =    2.194
peak=    3.574 closest distance to " O   HOH Z 102 " =    1.260
peak=    3.572 closest distance to " CA  ASN A 215 " =    1.023
peak=    3.563 closest distance to " O   HOH Z  97 " =    2.253
peak=    3.562 closest distance to " CE  LYS A  76 " =    0.893
peak=    3.556 closest distance to " O   HOH Z 337 " =    3.654
peak=    3.555 closest distance to " O   HOH Z 286 " =    2.185
peak=    3.554 closest distance to " CZ  PHE A  38 " =    1.251
peak=    3.548 closest distance to " O   HOH Z 345 " =    2.925
peak=    3.535 closest distance to " O   HOH Z  54 " =    1.660
peak=    3.534 closest distance to " CG  LEU A 167 " =    1.196
peak=    3.530 closest distance to " O   HOH Z 411 " =    3.827
peak=    3.524 closest distance to " O   HOH Z 163 " =    2.032
peak=    3.516 closest distance to " N   PHE A 130 " =    1.262
peak=    3.515 closest distance to " O   HOH Z 313 " =    1.930
peak=    3.514 closest distance to " CG  GLU A  37 " =    0.922
peak=    3.508 closest distance to " O   HOH Z 158 " =    2.984
peak=    3.508 closest distance to " CB  THR A  31 " =    1.509
peak=    3.508 closest distance to " CA  ARG A 195 " =    1.255
peak=    3.505 closest distance to " CA  ALA A 248 " =    1.480
peak=    3.505 closest distance to " O   HOH Z 357 " =    2.062
peak=    3.496 closest distance to " CG2BVAL A  41 " =    0.859
peak=    3.496 closest distance to " O   HOH Z 371 " =    3.144
peak=    3.495 closest distance to " ND2 ASN A 249 " =    0.901
peak=    3.488 closest distance to " O   HOH Z  21 " =    1.871
peak=    3.487 closest distance to " CE  LYS A 119 " =    1.165
peak=    3.485 closest distance to " O   HOH Z 273 " =    2.918
peak=    3.480 closest distance to " CB  GLN A  89 " =    1.412
peak=    3.480 closest distance to " CD  LYS A  76 " =    2.035
peak=    3.473 closest distance to " O   HOH Z 325 " =    2.307
peak=    3.469 closest distance to " O   HOH Z 426 " =    1.481
peak=    3.468 closest distance to " NE2 GLN A  77 " =    3.259
peak=    3.460 closest distance to " CA  SER A  87 " =    1.001
peak=    3.455 closest distance to " O   HOH Z  62 " =    2.390
peak=    3.448 closest distance to " CB  PRO A  90 " =    0.940
peak=    3.431 closest distance to " CB  SER A  62 " =    0.931
peak=    3.427 closest distance to " N   TYR A 116 " =    1.557
peak=    3.426 closest distance to " O   HOH Z  80 " =    1.676
peak=    3.423 closest distance to " CB  ASN A 110 " =    1.048
peak=    3.423 closest distance to " O   HOH Z 126 " =    1.571
peak=    3.419 closest distance to " CA  SER A  32 " =    1.657
peak=    3.416 closest distance to " CB  PHE A  16 " =    1.092
peak=    3.408 closest distance to " O   ALA A 165 " =    1.424
peak=    3.400 closest distance to " OE1 GLU A   2 " =    2.213
peak=    3.398 closest distance to " O   HOH Z  68 " =    2.028
peak=    3.396 closest distance to " CB  ASN A 142 " =    1.065
peak=    3.396 closest distance to " CB  ALA A 114 " =    0.987
peak=    3.395 closest distance to " OD2 ASP A 298 " =    3.884
peak=    3.394 closest distance to " O  BHOH Z 338 " =    2.270
peak=    3.391 closest distance to " CA  ASN A 217 " =    1.300
peak=    3.389 closest distance to " CB  ALA A 291 " =    1.159
peak=    3.388 closest distance to " CB  PRO A 198 " =    1.077
peak=    3.377 closest distance to " CB  LEU A 228 " =    1.125
peak=    3.373 closest distance to " O   HOH Z 163 " =    1.601
peak=    3.371 closest distance to " O   HOH Z 345 " =    1.711
peak=    3.361 closest distance to " CA  ASP A 162 " =    1.099
peak=    3.360 closest distance to " O   HOH Z 285 " =    1.608
peak=    3.358 closest distance to " CD  ARG A 159 " =    0.731
peak=    3.358 closest distance to " O   GLY A  91 " =    1.562
peak=    3.353 closest distance to " CA  TRP A  85 " =    1.114
peak=    3.351 closest distance to " CG  GLN A  11 " =    1.671
peak=    3.345 closest distance to " O   HOH Z  63 " =    2.275
peak=    3.336 closest distance to " O   HOH Z  19 " =    1.672
peak=    3.335 closest distance to " O   HOH Z  48 " =    1.612
peak=    3.332 closest distance to " CA  VAL A 125 " =    1.143
peak=    3.330 closest distance to " O   HOH Z 147 " =    1.815
peak=    3.329 closest distance to " CB  TYR A 169 " =    0.827
peak=    3.329 closest distance to " CB  ILE A 120 " =    1.247
peak=    3.329 closest distance to " O   HOH Z 282 " =    1.821
peak=    3.328 closest distance to " O   HOH Z  66 " =    2.221
peak=    3.327 closest distance to " O   HOH Z 422 " =    2.618
peak=    3.325 closest distance to " O   HOH Z 344 " =    3.131
peak=    3.320 closest distance to " CB  ASN A  45 " =    1.065
peak=    3.315 closest distance to " O   HOH Z  49 " =    2.216
peak=    3.314 closest distance to " CB  ALA A 104 " =    0.743
peak=    3.313 closest distance to " O   HOH Z 427 " =    3.070
peak=    3.310 closest distance to " CA  ILE A 106 " =    0.799
peak=    3.310 closest distance to " CB  HIS A 108 " =    0.814
peak=    3.309 closest distance to " CA  TYR A 116 " =    1.441
peak=    3.300 closest distance to " O   HOH Z 305 " =    3.736
peak=    3.296 closest distance to " O   HOH Z 108 " =    2.774
peak=    3.290 closest distance to " O   THR A 220 " =    1.131
peak=    3.289 closest distance to " O   HOH Z 193 " =    2.022
peak=    3.289 closest distance to " O   HOH Z 234 " =    2.304
peak=    3.286 closest distance to " CB  LEU A  83 " =    0.791
peak=    3.280 closest distance to " O   THR A 182 " =    1.416
peak=    3.278 closest distance to " CA  MET A 105 " =    1.052
peak=    3.278 closest distance to " CA  ALA A 154 " =    0.982
peak=    3.278 closest distance to " N   HIS A 108 " =    1.825
peak=    3.276 closest distance to " O   HOH Z  47 " =    1.555
peak=    3.275 closest distance to " CB  GLN A  88 " =    1.100
peak=    3.273 closest distance to " O   HOH Z 258 " =    2.200
peak=    3.272 closest distance to " CA  ILE A 263 " =    0.980
peak=    3.272 closest distance to " O   HOH Z  30 " =    2.215
peak=    3.271 closest distance to " CB  ASP A 191 " =    1.176
peak=    3.266 closest distance to " CB  ASP A 140 " =    1.066
peak=    3.264 closest distance to " NH1 ARG A 138 " =    1.220
peak=    3.264 closest distance to " O   HOH Z 359 " =    1.575
peak=    3.261 closest distance to " O   HOH Z  89 " =    2.196
peak=    3.257 closest distance to " O   HOH Z 124 " =    1.240
peak=    3.257 closest distance to " CB  ALA A   9 " =    1.612
peak=    3.255 closest distance to " CA  ALA A 233 " =    1.334
peak=    3.249 closest distance to " OE1 GLU A 236 " =    1.127
peak=    3.248 closest distance to " OH  TYR A 116 " =    1.066
peak=    3.246 closest distance to " O   HOH Z 250 " =    1.618
peak=    3.243 closest distance to " CB  ALA A 242 " =    1.007
peak=    3.236 closest distance to " CG2 THR A 221 " =    1.071
peak=    3.233 closest distance to " CB  GLN A 103 " =    0.823
peak=    3.232 closest distance to " CB  THR A  52 " =    0.778
peak=    3.231 closest distance to " O   HOH Z 435 " =    1.816
peak=    3.230 closest distance to " CD  ARG A  66 " =    2.676
peak=    3.230 closest distance to " O   HOH Z 246 " =    1.352
peak=    3.228 closest distance to " CB  PRO A 243 " =    1.274
peak=    3.227 closest distance to " CG1 VAL A 153 " =    0.937
peak=    3.226 closest distance to " OD1 ASN A  69 " =    2.486
peak=    3.223 closest distance to " CA  LYS A 290 " =    1.155
peak=    3.221 closest distance to " O   HOH Z 299 " =    4.308
peak=    3.217 closest distance to " O   HOH Z 392 " =    2.687
peak=    3.215 closest distance to " O   HOH Z   1 " =    2.156
peak=    3.214 closest distance to " O   HOH Z 416 " =    2.921
peak=    3.209 closest distance to " O   HOH Z 213 " =    1.775
peak=    3.209 closest distance to " OE2 GLU A  53 " =    2.078
peak=    3.204 closest distance to " CB  ASN A 215 " =    1.143
peak=    3.203 closest distance to " O   HOH Z 233 " =    1.916
peak=    3.200 closest distance to " O   HOH Z 298 " =    2.103
peak=    3.196 closest distance to " O   HOH Z 329 " =    3.982
peak=    3.193 closest distance to " CB  GLN A 205 " =    1.166
peak=    3.191 closest distance to " CB  ALA A   1 " =    4.838
peak=    3.188 closest distance to " O   HOH Z 267 " =    2.023
peak=    3.187 closest distance to " O   HOH Z 285 " =    2.619
peak=    3.187 closest distance to " CG1 ILE A 120 " =    1.115
peak=    3.186 closest distance to " CD1 LEU A  96 " =    0.717
peak=    3.185 closest distance to " O   HOH Z  61 " =    1.467
peak=    3.184 closest distance to " CA  ILE A 234 " =    0.923
peak=    3.182 closest distance to " O   HOH Z  94 " =    2.410
peak=    3.178 closest distance to " O   HOH Z 425 " =    1.895
peak=    3.178 closest distance to " CA  GLY A 241 " =    0.990
peak=    3.177 closest distance to " CA  ASP A 140 " =    1.172
peak=    3.176 closest distance to " O   HOH Z 334 " =    1.394
peak=    3.175 closest distance to " O   TRP A 274 " =    1.898
peak=    3.173 closest distance to " OG BSER A 134 " =    2.743
peak=    3.165 closest distance to " CG  MET A 113 " =    1.069
peak=    3.165 closest distance to " NH2 ARG A 156 " =    1.127
peak=    3.163 closest distance to " CG BARG A 102 " =    1.714
peak=    3.162 closest distance to " O   GLY A 147 " =    1.610
peak=    3.158 closest distance to " O   HOH Z 132 " =    2.573
peak=    3.158 closest distance to " CG1 ILE A  20 " =    1.373
peak=    3.157 closest distance to " N   VAL A 265 " =    1.277
peak=    3.152 closest distance to " O   HOH Z 261 " =    2.400
peak=    3.149 closest distance to " CA  THR A 221 " =    0.959
peak=    3.148 closest distance to " O   HOH Z 207 " =    1.570
peak=    3.147 closest distance to " CD1 ILE A 199 " =    1.086
peak=    3.146 closest distance to " CA  ASP A 191 " =    0.876
peak=    3.144 closest distance to " CB  SER A 210 " =    0.818
peak=    3.143 closest distance to " CB  ARG A 139 " =    0.930
peak=    3.136 closest distance to " NE  ARG A  24 " =    0.917
peak=    3.136 closest distance to " NZ  LYS A 117 " =    1.610
peak=    3.129 closest distance to " CD  GLN A 194 " =    1.586
peak=    3.126 closest distance to " CB  ARG A 219 " =    0.926
peak=    3.114 closest distance to " CB  GLN A 278 " =    0.833
peak=    3.105 closest distance to " CB  ASN A 285 " =    1.015
peak=    3.104 closest distance to " O   HOH Z 183 " =    1.722
peak=    3.102 closest distance to " CA  ALA A 100 " =    1.028
peak=    3.101 closest distance to " O   HOH Z 162 " =    1.836
peak=    3.100 closest distance to " O   SER A 164 " =    1.089
peak=    3.097 closest distance to " CA  ALA A 160 " =    0.886
peak=    3.096 closest distance to " O   TYR A 116 " =    1.503
peak=    3.095 closest distance to " CA  GLU A 152 " =    0.888
peak=    3.092 closest distance to " NH2 ARG A  79 " =    1.358
peak=    3.091 closest distance to " CA  ASP A 124 " =    0.763
peak=    3.075 closest distance to " O   HOH Z  88 " =    1.661
peak=    3.069 closest distance to " OG BSER A 164 " =    1.974
peak=    3.067 closest distance to " CB  PHE A 283 " =    0.751
peak=    3.065 closest distance to " CZ2 TRP A 150 " =    1.036
peak=    3.053 closest distance to " O   HOH Z 152 " =    1.798
peak=    3.039 closest distance to " CB  LYS A 290 " =    1.167

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 199         
Filter by distance & map next to the model:
   mapped sites are within: 0.605 - 5.943
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 199
   mapped sites are within: 0.786 - 5.943

peak=   -4.792 closest distance to " CG  GLN A  58 " =    1.044
peak=   -4.590 closest distance to " C   HIS A 108 " =    1.125
peak=   -4.516 closest distance to " O   HOH Z 266 " =    5.197
peak=   -4.364 closest distance to " O   HOH Z 290 " =    0.983
peak=   -4.346 closest distance to " CD  ARG A  14 " =    3.404
peak=   -4.268 closest distance to " OG BSER A 134 " =    1.307
peak=   -4.152 closest distance to " CG2 ILE A  49 " =    2.717
peak=   -4.137 closest distance to " OXT GLY A 302 " =    2.885
peak=   -4.120 closest distance to " CB  PRO A 243 " =    2.688
peak=   -4.116 closest distance to " CB  ALA A 184 " =    2.363
peak=   -4.087 closest distance to " O   HOH Z 377 " =    1.981
peak=   -4.063 closest distance to " CG  GLN A 223 " =    1.958
peak=   -4.021 closest distance to " O   PRO A 198 " =    1.238
peak=   -4.016 closest distance to " O   VAL A  67 " =    2.636
peak=   -3.990 closest distance to " N   ALA A 248 " =    1.732
peak=   -3.972 closest distance to " CZ3 TRP A 179 " =    1.279
peak=   -3.950 closest distance to " CD1 LEU A  25 " =    2.532
peak=   -3.942 closest distance to " O   HOH Z 198 " =    1.439
peak=   -3.930 closest distance to " CD  ARG A 156 " =    2.090
peak=   -3.925 closest distance to " O   HOH Z 351 " =    1.488
peak=   -3.907 closest distance to " O   HOH Z   6 " =    2.147
peak=   -3.898 closest distance to " CD2 PHE A 192 " =    2.143
peak=   -3.883 closest distance to " OG  SER A  97 " =    2.203
peak=   -3.873 closest distance to " O   PRO A 163 " =    2.085
peak=   -3.862 closest distance to " O   VAL A 174 " =    2.177
peak=   -3.841 closest distance to " CG1 VAL A 112 " =    2.763
peak=   -3.827 closest distance to " CE2 TYR A  30 " =    2.745
peak=   -3.816 closest distance to " CB  ALA A 161 " =    2.485
peak=   -3.811 closest distance to " CA  VAL A  67 " =    2.900
peak=   -3.792 closest distance to " CD1 LEU A 101 " =    2.454
peak=   -3.788 closest distance to " CD2 TYR A 293 " =    2.003
peak=   -3.736 closest distance to " ND2 ASN A  45 " =    1.146
peak=   -3.728 closest distance to " ND2 ASN A 187 " =    1.530
peak=   -3.716 closest distance to " CZ  ARG A  66 " =    1.175
peak=   -3.701 closest distance to " O   HOH Z 165 " =    1.891
peak=   -3.694 closest distance to " CG1AVAL A  41 " =    2.563
peak=   -3.688 closest distance to " CZ  TYR A 169 " =    1.828
peak=   -3.671 closest distance to " OD1 ASN A 148 " =    1.483
peak=   -3.654 closest distance to " CB  ALA A 248 " =    2.267
peak=   -3.654 closest distance to " N   THR A  52 " =    1.721
peak=   -3.633 closest distance to " O   SER A  95 " =    1.563
peak=   -3.630 closest distance to " CB  PHE A 208 " =    2.283
peak=   -3.625 closest distance to " CA  GLY A 241 " =    2.415
peak=   -3.620 closest distance to " CB  ASN A  39 " =    2.286
peak=   -3.618 closest distance to " O   PHE A 218 " =    1.580
peak=   -3.615 closest distance to " N   SER A 212 " =    2.114
peak=   -3.613 closest distance to " O   HOH Z 369 " =    2.300
peak=   -3.599 closest distance to " CA  ASP A 298 " =    1.083
peak=   -3.597 closest distance to " CZ3 TRP A 274 " =    2.364
peak=   -3.595 closest distance to " CE  MET A 105 " =    2.414
peak=   -3.595 closest distance to " O   HOH Z 113 " =    1.960
peak=   -3.572 closest distance to " OE1 GLN A 183 " =    1.576
peak=   -3.569 closest distance to " CG  GLN A  11 " =    1.740
peak=   -3.560 closest distance to " O   HOH Z 196 " =    1.914
peak=   -3.556 closest distance to " O   HOH Z 394 " =    1.493
peak=   -3.551 closest distance to " CE2 PHE A  61 " =    2.621
peak=   -3.543 closest distance to " CD1 PHE A  59 " =    1.977
peak=   -3.543 closest distance to " O   GLY A  80 " =    2.438
peak=   -3.533 closest distance to " O   HOH Z  43 " =    1.371
peak=   -3.533 closest distance to " NE2 GLN A 194 " =    1.909
peak=   -3.532 closest distance to " OD2 ASP A 171 " =    2.391
peak=   -3.530 closest distance to " O   HOH Z 183 " =    1.501
peak=   -3.526 closest distance to " O   HOH Z 185 " =    2.440
peak=   -3.522 closest distance to " O   HOH Z 166 " =    1.852
peak=   -3.511 closest distance to " CG  ASP A 132 " =    2.320
peak=   -3.498 closest distance to " CZ  TYR A 172 " =    1.917
peak=   -3.490 closest distance to " O   HOH Z  15 " =    1.543
peak=   -3.487 closest distance to " O   HOH Z 197 " =    2.180
peak=   -3.485 closest distance to " O   HOH Z 114 " =    3.265
peak=   -3.482 closest distance to " O   ALA A  34 " =    2.291
peak=   -3.481 closest distance to " NE2 GLN A  88 " =    0.991
peak=   -3.477 closest distance to " O   HOH Z 102 " =    1.630
peak=   -3.474 closest distance to " O   HOH Z  10 " =    1.505
peak=   -3.472 closest distance to " CA  GLY A 241 " =    3.239
peak=   -3.468 closest distance to " O   HOH Z 395 " =    5.142
peak=   -3.464 closest distance to " O   HOH Z 407 " =    2.804
peak=   -3.459 closest distance to " NH2 ARG A  79 " =    1.606
peak=   -3.454 closest distance to " N   GLN A  58 " =    1.611
peak=   -3.442 closest distance to " ND2 ASN A  39 " =    1.095
peak=   -3.441 closest distance to " N   THR A 220 " =    2.299
peak=   -3.435 closest distance to " NE2 GLN A 278 " =    1.898
peak=   -3.425 closest distance to " O   ALA A  10 " =    1.766
peak=   -3.424 closest distance to " CD2 LEU A 237 " =    2.522
peak=   -3.424 closest distance to " OD1 ASP A 191 " =    1.420
peak=   -3.421 closest distance to " O   HOH Z 422 " =    1.369
peak=   -3.416 closest distance to " CD2 TYR A 247 " =    2.442
peak=   -3.413 closest distance to " N   ALA A  43 " =    2.618
peak=   -3.408 closest distance to " OD2 ASP A 191 " =    1.447
peak=   -3.404 closest distance to " O   HOH Z 264 " =    1.668
peak=   -3.388 closest distance to " O   TRP A  92 " =    1.946
peak=   -3.385 closest distance to " C   SER A 206 " =    1.533
peak=   -3.385 closest distance to " CG1 VAL A  67 " =    3.046
peak=   -3.375 closest distance to " O   GLY A 196 " =    1.087
peak=   -3.369 closest distance to " CD  ARG A  79 " =    1.201
peak=   -3.367 closest distance to " O   HOH Z 377 " =    1.587
peak=   -3.367 closest distance to " CG  GLU A  53 " =    1.507
peak=   -3.366 closest distance to " O   HOH Z 283 " =    2.312
peak=   -3.363 closest distance to " OD1 ASP A 171 " =    1.505
peak=   -3.358 closest distance to " O   HOH Z 211 " =    1.508
peak=   -3.357 closest distance to " CG2 ILE A 263 " =    2.210
peak=   -3.355 closest distance to " CB  PRO A 163 " =    2.519
peak=   -3.355 closest distance to " O   PRO A 198 " =    1.280
peak=   -3.351 closest distance to " CE1 TYR A 247 " =    2.738
peak=   -3.351 closest distance to " CG  LEU A  83 " =    2.001
peak=   -3.346 closest distance to " C   THR A 279 " =    1.155
peak=   -3.346 closest distance to " O   ILE A 106 " =    1.844
peak=   -3.341 closest distance to " CG  GLU A 152 " =    0.899
peak=   -3.341 closest distance to " O   HOH Z  13 " =    1.676
peak=   -3.338 closest distance to " CD1 ILE A 106 " =    2.228
peak=   -3.337 closest distance to " CG1 VAL A 112 " =    2.567
peak=   -3.336 closest distance to " O   VAL A 189 " =    1.827
peak=   -3.330 closest distance to " O   HOH Z  88 " =    4.541
peak=   -3.329 closest distance to " OG BSER A 134 " =    1.904
peak=   -3.327 closest distance to " O   HOH Z   6 " =    1.565
peak=   -3.322 closest distance to " SG ACYS A 201 " =    2.215
peak=   -3.320 closest distance to " O   HOH Z  38 " =    1.682
peak=   -3.314 closest distance to " O   HOH Z 193 " =    1.639
peak=   -3.313 closest distance to " N   ASP A 286 " =    2.163
peak=   -3.306 closest distance to " CE3 TRP A 150 " =    2.223
peak=   -3.304 closest distance to " CG  PHE A 283 " =    2.547
peak=   -3.303 closest distance to " CD  PRO A 243 " =    2.038
peak=   -3.303 closest distance to " O   LEU A 167 " =    1.549
peak=   -3.302 closest distance to " ND2 ASN A 249 " =    2.312
peak=   -3.297 closest distance to " CE BMET A  47 " =    1.508
peak=   -3.294 closest distance to " CB  TRP A  85 " =    2.469
peak=   -3.294 closest distance to " C   ILE A 234 " =    1.274
peak=   -3.289 closest distance to " O   HOH Z 174 " =    3.722
peak=   -3.289 closest distance to " CG  PRO A 243 " =    1.749
peak=   -3.287 closest distance to " CB  ALA A 291 " =    2.214
peak=   -3.281 closest distance to " OD1 ASN A 301 " =    1.980
peak=   -3.276 closest distance to " O   HOH Z 301 " =    2.324
peak=   -3.276 closest distance to " O   HOH Z 394 " =    1.142
peak=   -3.273 closest distance to " O   HOH Z 116 " =    1.399
peak=   -3.273 closest distance to " NH2AARG A 275 " =    5.034
peak=   -3.262 closest distance to " CD  GLU A  44 " =    1.106
peak=   -3.262 closest distance to " O   HOH Z  60 " =    1.719
peak=   -3.260 closest distance to " CD  GLN A 223 " =    1.290
peak=   -3.259 closest distance to " O   HOH Z 281 " =    2.616
peak=   -3.257 closest distance to " O   HOH Z 364 " =    5.137
peak=   -3.253 closest distance to " O   HOH Z 372 " =    2.287
peak=   -3.252 closest distance to " O   HOH Z 243 " =    1.945
peak=   -3.246 closest distance to " O   HOH Z  63 " =    1.580
peak=   -3.245 closest distance to " O   HOH Z  37 " =    1.788
peak=   -3.244 closest distance to " N   ALA A 226 " =    1.906
peak=   -3.236 closest distance to " OD1 ASN A  39 " =    2.238
peak=   -3.226 closest distance to " CG  GLU A 277 " =    1.258
peak=   -3.224 closest distance to " O   HOH Z  19 " =    2.358
peak=   -3.221 closest distance to " CD1 LEU A 255 " =    2.727
peak=   -3.218 closest distance to " O   HOH Z 154 " =    1.859
peak=   -3.218 closest distance to " OE1 GLN A 223 " =    2.004
peak=   -3.218 closest distance to " CA  TYR A  68 " =    3.058
peak=   -3.214 closest distance to " O   HOH Z  71 " =    2.097
peak=   -3.213 closest distance to " O   HOH Z 139 " =    3.236
peak=   -3.212 closest distance to " O   VAL A 189 " =    2.632
peak=   -3.209 closest distance to " CG2 VAL A 296 " =    1.919
peak=   -3.198 closest distance to " CB  ALA A 291 " =    2.391
peak=   -3.194 closest distance to " O   HOH Z 389 " =    1.853
peak=   -3.185 closest distance to " CH2 TRP A 150 " =    1.092
peak=   -3.181 closest distance to " O   HOH Z 421 " =    3.769
peak=   -3.181 closest distance to " O   GLN A  94 " =    2.238
peak=   -3.174 closest distance to " O   HOH Z 198 " =    1.484
peak=   -3.173 closest distance to " O   HOH Z 111 " =    3.658
peak=   -3.171 closest distance to " CD  GLN A  11 " =    0.943
peak=   -3.168 closest distance to " O   GLU A 152 " =    1.365
peak=   -3.167 closest distance to " NH2 ARG A  66 " =    5.747
peak=   -3.165 closest distance to " CD2 LEU A 237 " =    2.146
peak=   -3.163 closest distance to " C   LEU A 143 " =    0.987
peak=   -3.163 closest distance to " O   HOH Z 234 " =    3.985
peak=   -3.156 closest distance to " O   HOH Z 414 " =    1.479
peak=   -3.152 closest distance to " CD2 LEU A 237 " =    2.644
peak=   -3.147 closest distance to " C   ALA A 158 " =    1.400
peak=   -3.142 closest distance to " ND2 ASN A  69 " =    1.641
peak=   -3.142 closest distance to " O   HOH Z 265 " =    2.350
peak=   -3.142 closest distance to " CD  GLN A 223 " =    0.880
peak=   -3.139 closest distance to " OD1 ASN A  74 " =    0.786
peak=   -3.135 closest distance to " SD  MET A 105 " =    0.976
peak=   -3.133 closest distance to " O   HOH Z 423 " =    2.396
peak=   -3.133 closest distance to " N   SER A 276 " =    1.266
peak=   -3.130 closest distance to " O   MET A  40 " =    2.945
peak=   -3.129 closest distance to " O   ALA A 227 " =    1.465
peak=   -3.125 closest distance to " O   HOH Z 362 " =    5.943
peak=   -3.125 closest distance to " CG  ASP A 231 " =    0.837
peak=   -3.122 closest distance to " NH1 ARG A 195 " =    2.606
peak=   -3.121 closest distance to " CD1 LEU A 228 " =    2.147
peak=   -3.117 closest distance to " ND2 ASN A  45 " =    1.458
peak=   -3.116 closest distance to " O   HOH Z 126 " =    1.973
peak=   -3.115 closest distance to " O   HOH Z 200 " =    4.924
peak=   -3.113 closest distance to " OH  TYR A 169 " =    0.940
peak=   -3.112 closest distance to " O   SER A 276 " =    1.671
peak=   -3.112 closest distance to " CD  ARG A 139 " =    1.596
peak=   -3.103 closest distance to " O   HOH Z 174 " =    2.300
peak=   -3.099 closest distance to " CG2 THR A 178 " =    2.306
peak=   -3.087 closest distance to " O   HOH Z 105 " =    2.300
peak=   -3.082 closest distance to " CZ  PHE A  38 " =    2.001
peak=   -3.067 closest distance to " O   HOH Z 323 " =    1.285
peak=   -3.040 closest distance to " CB  ASP A 286 " =    1.806

================= 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    :  0.3886 0.3825   6.168308e+00   6.153068e+00
   1_bss:  0.3801 0.3733   6.155704e+00   6.138725e+00
   1_xyz:  0.2187 0.2460   5.686800e+00   5.786540e+00
   1_adp:  0.1994 0.2498   5.637683e+00   5.813083e+00
   1_occ:  0.1992 0.2498   5.637493e+00   5.813730e+00
   2_bss:  0.1956 0.2457   5.629619e+00   5.804153e+00
   2_xyz:  0.1432 0.1809   5.338575e+00   5.526330e+00
   2_adp:  0.1328 0.1735   5.278242e+00   5.479644e+00
   2_occ:  0.1326 0.1734   5.277596e+00   5.479299e+00
   3_bss:  0.1326 0.1732   5.276817e+00   5.476512e+00
   3_xyz:  0.1143 0.1595   5.166468e+00   5.396687e+00
   3_adp:  0.1130 0.1564   5.152637e+00   5.378808e+00
   3_occ:  0.1128 0.1565   5.152161e+00   5.378707e+00
   4_bss:  0.1128 0.1565   5.152364e+00   5.379090e+00
   4_xyz:  0.1154 0.1564   5.165953e+00   5.383716e+00
   4_adp:  0.1138 0.1585   5.164913e+00   5.395207e+00
   4_occ:  0.1138 0.1585   5.164834e+00   5.395299e+00
   5_bss:  0.1137 0.1584   5.164640e+00   5.395044e+00
   5_xyz:  0.1121 0.1587   5.158738e+00   5.396366e+00
   5_adp:  0.1129 0.1572   5.158061e+00   5.389075e+00
   5_occ:  0.1129 0.1572   5.158054e+00   5.389307e+00
   5_bss:  0.1128 0.1570   5.156792e+00   5.385736e+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:  0.316  35.998  -0.213  -0.047   0.272  -0.000   0.000   0.000
   1_xyz:  0.316  35.998  -0.213  -0.047   0.272  -0.000   0.000   0.000
   1_adp:  0.316  35.998  -0.213  -0.047   0.272  -0.000   0.000   0.000
   1_occ:  0.316  35.998  -0.213  -0.047   0.272  -0.000   0.000   0.000
   2_bss:  0.331  56.561  -2.590  -1.527  -0.947  -0.000  -0.000  -0.000
   2_xyz:  0.331  56.561  -2.590  -1.527  -0.947  -0.000  -0.000  -0.000
   2_adp:  0.331  56.561  -2.590  -1.527  -0.947  -0.000  -0.000  -0.000
   2_occ:  0.331  56.561  -2.590  -1.527  -0.947  -0.000  -0.000  -0.000
   3_bss:  0.327  56.561  -3.098  -1.917  -1.047  -0.000  -0.000  -0.000
   3_xyz:  0.327  56.561  -3.098  -1.917  -1.047  -0.000  -0.000  -0.000
   3_adp:  0.327  56.561  -3.098  -1.917  -1.047  -0.000  -0.000  -0.000
   3_occ:  0.327  56.561  -3.098  -1.917  -1.047  -0.000  -0.000  -0.000
   4_bss:  0.324  50.806  -3.098  -1.917  -1.047  -0.000  -0.000  -0.000
   4_xyz:  0.324  50.806  -3.098  -1.917  -1.047  -0.000  -0.000  -0.000
   4_adp:  0.324  50.806  -3.098  -1.917  -1.047  -0.000  -0.000  -0.000
   4_occ:  0.324  50.806  -3.098  -1.917  -1.047  -0.000  -0.000  -0.000
   5_bss:  0.321  52.627  -2.983  -1.823  -0.857  -0.000  -0.000  -0.000
   5_xyz:  0.321  52.627  -2.983  -1.823  -0.857  -0.000  -0.000  -0.000
   5_adp:  0.321  52.627  -2.983  -1.823  -0.857  -0.000  -0.000  -0.000
   5_occ:  0.321  52.627  -2.983  -1.823  -0.857  -0.000  -0.000  -0.000
   5_bss:  0.321  50.899  -2.831  -1.674  -0.644  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  41.847 0.6225  0.8089    43229.830
   1_bss:  40.929 0.6318  0.8272    40461.064
   1_xyz:  24.148 0.8211  1.0030    15565.019
   1_adp:  24.986 0.8118  0.9958    16379.580
   1_occ:  25.025 0.8114  0.9952    16416.409
   2_bss:  24.695 0.8145  0.9396    15920.779
   2_xyz:  17.325 0.8859  0.9854     8431.880
   2_adp:  16.169 0.8967  0.9862     7732.275
   2_occ:  16.157 0.8968  0.9862     7721.868
   3_bss:  16.100 0.8972  0.9741     7651.982
   3_xyz:  14.523 0.9104  0.9792     6554.147
   3_adp:  14.146 0.9137  0.9759     6401.229
   3_occ:  14.146 0.9137  0.9757     6391.952
   4_bss:  14.158 0.9136  0.9755     6394.583
   4_xyz:  14.111 0.9143  0.9756     6395.034
   4_adp:  14.319 0.9127  0.9692     6511.299
   4_occ:  14.319 0.9127  0.9691     6509.589
   5_bss:  14.314 0.9127  0.9737     6504.374
   5_xyz:  14.318 0.9127  0.9736     6539.016
   5_adp:  14.181 0.9137  0.9694     6475.154
   5_occ:  14.186 0.9137  0.9693     6475.151
   5_bss:  14.147 0.9140  0.9735     6410.318
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.8637e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.8637e-01
   1_xyz:   1.250  0.010  0.077 15.052  0.005  4.111   8.6337e-02
   1_adp:   1.250  0.010  0.077 15.052  0.005  4.111   8.6337e-02
   1_occ:   1.250  0.010  0.077 15.052  0.005  4.111   8.6337e-02
   2_bss:   1.250  0.010  0.077 15.052  0.005  4.111   8.6337e-02
   2_xyz:   1.016  0.006  0.070 14.454  0.004  4.123   5.7890e-02
   2_adp:   1.016  0.006  0.070 14.454  0.004  4.123   5.7890e-02
   2_occ:   1.016  0.006  0.070 14.454  0.004  4.123   5.7890e-02
   3_bss:   1.016  0.006  0.070 14.454  0.004  4.123   5.7890e-02
   3_xyz:   1.118  0.009  0.082 14.896  0.005  4.128   7.2019e-02
   3_adp:   1.118  0.009  0.082 14.896  0.005  4.128   7.2019e-02
   3_occ:   1.118  0.009  0.082 14.896  0.005  4.128   7.2019e-02
   4_bss:   1.118  0.009  0.082 14.896  0.005  4.128   7.2019e-02
   4_xyz:   0.926  0.006  0.071 14.447  0.004  4.112   5.1875e-02
   4_adp:   0.926  0.006  0.071 14.447  0.004  4.112   5.1875e-02
   4_occ:   0.926  0.006  0.071 14.447  0.004  4.112   5.1875e-02
   5_bss:   0.926  0.006  0.071 14.447  0.004  4.112   5.1875e-02
   5_xyz:   0.951  0.006  0.073 14.377  0.003  4.113   5.3331e-02
   5_adp:   0.951  0.006  0.073 14.377  0.003  4.113   5.3331e-02
   5_occ:   0.951  0.006  0.073 14.377  0.003  4.113   5.3331e-02
   5_bss:   0.951  0.006  0.073 14.377  0.003  4.113   5.3331e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.341   2.4185e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.341   2.4185e-01
   1_xyz:   8.045  0.062  0.307 84.258  0.033  2.230   8.3457e-02
   1_adp:   8.045  0.062  0.307 84.258  0.033  2.230   8.3457e-02
   1_occ:   8.045  0.062  0.307 84.258  0.033  2.230   8.3457e-02
   2_bss:   8.045  0.062  0.307 84.258  0.033  2.230   8.3457e-02
   2_xyz:   7.141  0.038  0.212 80.579  0.043  2.313   5.7549e-02
   2_adp:   7.141  0.038  0.212 80.579  0.043  2.313   5.7549e-02
   2_occ:   7.141  0.038  0.212 80.579  0.043  2.313   5.7549e-02
   3_bss:   7.141  0.038  0.212 80.579  0.043  2.313   5.7549e-02
   3_xyz:   7.811  0.050  0.281 83.714  0.036  2.281   6.2370e-02
   3_adp:   7.811  0.050  0.281 83.714  0.036  2.281   6.2370e-02
   3_occ:   7.811  0.050  0.281 83.714  0.036  2.281   6.2370e-02
   4_bss:   7.811  0.050  0.281 83.714  0.036  2.281   6.2370e-02
   4_xyz:   6.760  0.043  0.221 82.137  0.037  2.395   3.1951e-02
   4_adp:   6.760  0.043  0.221 82.137  0.037  2.395   3.1951e-02
   4_occ:   6.760  0.043  0.221 82.137  0.037  2.395   3.1951e-02
   5_bss:   6.760  0.043  0.221 82.137  0.037  2.395   3.1951e-02
   5_xyz:   6.926  0.043  0.227 82.490  0.029  2.375   3.7649e-02
   5_adp:   6.926  0.043  0.227 82.490  0.029  2.375   3.7649e-02
   5_occ:   6.926  0.043  0.227 82.490  0.029  2.375   3.7649e-02
   5_bss:   6.926  0.043  0.227 82.490  0.029  2.375   3.7649e-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:  87.17   0.00  17.15  87.17   0.00  13.25  65.20   6.93  38.43
   1_occ:  87.17   0.00  17.15  87.17   0.00  13.25  65.20   6.93  38.43
   2_bss:  87.17   0.00  17.15  87.17   0.00  13.25  65.20   6.93  38.43
   2_xyz:  87.17   0.00  17.15  87.17   0.00  13.25  65.20   6.93  38.43
   2_adp:  83.17   0.00  17.33  83.17   0.00  13.17  71.92   6.22  39.95
   2_occ:  83.17   0.00  17.33  83.17   0.00  13.17  71.92   6.22  39.95
   3_bss:  83.17   0.00  17.33  83.17   0.00  13.17  71.92   6.22  39.95
   3_xyz:  83.17   0.00  17.33  83.17   0.00  13.17  71.92   6.22  39.95
   3_adp:  82.13   1.84  16.80  82.13   1.84  12.89  72.61   3.45  38.13
   3_occ:  82.13   1.84  16.80  82.13   1.84  12.89  72.61   3.45  38.13
   4_bss:  82.13   1.84  16.80  82.13   1.84  12.89  72.61   3.45  38.13
   4_xyz:  82.13   1.84  16.80  82.13   1.84  12.89  72.61   3.45  38.13
   4_adp:  91.68   0.68  17.27  91.68   0.85  12.98  86.34   0.68  40.60
   4_occ:  91.68   0.68  17.27  91.68   0.85  12.98  86.34   0.68  40.60
   5_bss:  91.68   0.68  17.27  91.68   0.85  12.98  86.34   0.68  40.60
   5_xyz:  91.68   0.68  17.27  91.68   0.85  12.98  86.34   0.68  40.60
   5_adp:  88.49   1.43  16.64  88.49   1.43  12.68  84.03   2.48  38.18
   5_occ:  88.49   1.43  16.64  88.49   1.43  12.68  84.03   2.48  38.18
   5_bss:  88.44   1.38  16.59  88.44   1.38  12.63  83.98   2.43  38.13
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.794    0.018    0.390
   1_adp:    1.794    0.018    0.390
   1_occ:    1.794    0.018    0.390
   2_bss:    1.794    0.018    0.390
   2_xyz:    1.714    0.028    0.462
   2_adp:    1.714    0.028    0.462
   2_occ:    1.714    0.028    0.462
   3_bss:    1.714    0.028    0.462
   3_xyz:    1.559    0.029    0.514
   3_adp:    1.559    0.029    0.514
   3_occ:    1.559    0.029    0.514
   4_bss:    1.559    0.029    0.514
   4_xyz:    1.504    0.038    0.519
   4_adp:    1.504    0.038    0.519
   4_occ:    1.504    0.038    0.519
   5_bss:    1.504    0.038    0.519
   5_xyz:    1.479    0.024    0.529
   5_adp:    1.479    0.024    0.529
   5_occ:    1.479    0.024    0.529
   5_bss:    1.479    0.024    0.529
------------------------------------------------------------------------

CPU time actual refinement: 277.62


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_205/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_205/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_205/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_205/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_205/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 277.50 
  Macro-tasks:
    bulk solvent and scale       = 32.10  
    individual site refinement   = 117.62 
    weights calculation          = 24.14  
    collect and process          = 5.42   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 179.36 
  Micro-tasks:
    mask                            = 1.51   
    f_calc                          = 89.09  
    alpha_beta                      = 6.91   
    target                          = 1.01   
    gradients_wrt_atomic_parameters = 97.31  
    fmodel                         = 5.10   
    r_factors                      = 0.14   
    phase_errors                   = 8.97   
    foms                           = 0.26   
    TOTAL for micro-tasks          = 210.30 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 3.910 micro seconds
Total CPU time: 4.81 minutes
from_scatterers_fft:    646 calls, 88.79 s
gradients_fft:          591 calls, 85.39 s

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

# Date 2008-01-16 Time 04:14:21 PST -0800 (1200485661.78 s)
Start R-work = 0.3886, R-free = 0.3825 (no bulk solvent and anisotropic scale)
Final R-work = 0.1366, R-free = 0.1760 (no bulk solvent and anisotropic scale)

Start R-work = 0.3801, R-free = 0.3733
Final R-work = 0.1128, R-free = 0.1570