# Date 2008-01-16 Time 05:39:35 PST -0800 (1200490775.33 s)
#phil __OFF__

Command line arguments: "../825.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26004
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 825

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 47.8686, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.33, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.8686, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9429 1.95157
Completeness in resolution range: 0.917432
Completeness with d_max=infinity: 0.914733

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9429
                             d_min =   1.9516

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.8686, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9429 1.95157
Completeness in resolution range: 0.917432
Completeness with d_max=infinity: 0.914733

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9433 -  4.1768 [2247/2276]  2024   223   9.9%
  bin  2:  4.1768 -  3.3273 [2143/2166]  1930   213   9.9%
  bin  3:  3.3273 -  2.9102 [2112/2137]  1897   215  10.2%
  bin  4:  2.9102 -  2.6457 [2107/2133]  1902   205   9.7%
  bin  5:  2.6457 -  2.4570 [2096/2130]  1884   212  10.1%
  bin  6:  2.4570 -  2.3127 [2077/2105]  1874   203   9.8%
  bin  7:  2.3127 -  2.1973 [2067/2103]  1857   210  10.2%
  bin  8:  2.1973 -  2.1019 [2058/2100]  1851   207  10.1%
  bin  9:  2.1019 -  2.0212 [1992/2090]  1793   199  10.0%
  bin 10:  2.0212 -  1.9516 [ 690/2112]   618    72  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_825/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.48 -     2.17: 23
        2.17 -     2.85: 1124
        2.85 -     3.53: 4386
        3.53 -     4.22: 9315
        4.22 -     4.90: 13527
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   TYR A 214 " - " O   HOH Z 204 "  1.484 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.497 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.519 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.563 3.040 -x+1/2,-y+1,z-1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.601 3.120 -x+1/2,-y+1,z-1/2
  ... (remaining 28370 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_825/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_825/model_refine_001.geo

CPU time processing inputs: 8.96


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 47.8686 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4621   r_free= 0.4536   ksol= 0.00   Bsol= 0.00   scale= 0.895    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.275892                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6590 0.99   1457  164 0.3648 0.3743      6.5525      6.5531|
|  2:  4.6590 -  3.7167 0.99   1390  151 0.3983 0.3991      6.8058      6.8194|
|  3:  3.7167 -  3.2524 0.99   1383  151 0.4289 0.3981      6.6453      6.6515|
|  4:  3.2524 -  2.9576 0.98   1342  157 0.4481 0.4406      6.5021      6.4823|
|  5:  2.9576 -  2.7470 0.99   1369  149 0.4776 0.4414      6.3457      6.3071|
|  6:  2.7470 -  2.5859 0.99   1345  154 0.4984 0.4517      6.2649      6.1563|
|  7:  2.5859 -  2.4570 0.98   1351  142 0.4873 0.4697      6.2375      6.1935|
|  8:  2.4570 -  2.3505 0.98   1320  142 0.5187 0.5352      6.1416      6.2114|
|  9:  2.3505 -  2.2603 0.99   1343  152 0.5326 0.5077      6.1339      6.1183|
| 10:  2.2603 -  2.1826 0.99   1339  154 0.5055 0.5337      6.0801      6.1039|
| 11:  2.1826 -  2.1145 0.97   1321  142 0.5248 0.5561      6.0195      6.0122|
| 12:  2.1145 -  2.0542 0.98   1309  144 0.5104 0.5548      5.9295      5.9901|
| 13:  2.0542 -  2.0003 0.80   1080  128 0.5266 0.4408      5.8769      5.8329|
| 14:  2.0003 -  1.9516 0.21    281   29 0.5854 0.4816      5.8136      5.7102|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9433 -  4.6590  1457   164  0.70  34.30   0.83     0.73      71475.25|
|  2:  4.6590 -  3.7167  1390   151  0.70  34.99   0.91     0.80     100853.08|
|  3:  3.7167 -  3.2524  1383   151  0.61  43.17   0.91     0.79     107817.07|
|  4:  3.2524 -  2.9576  1342   157  0.53  49.67   0.92     0.73      95870.86|
|  5:  2.9576 -  2.7470  1369   149  0.48  53.82   0.88     0.68      74709.82|
|  6:  2.7470 -  2.5859  1345   154  0.45  55.82   0.89     0.64      62870.81|
|  7:  2.5859 -  2.4570  1351   142  0.44  56.98   0.92     0.59      58108.16|
|  8:  2.4570 -  2.3505  1320   142  0.35  64.06   0.88     0.53      59490.03|
|  9:  2.3505 -  2.2603  1343   152  0.31  66.54   0.91     0.48      56735.98|
| 10:  2.2603 -  2.1826  1339   154  0.28  69.39   0.96     0.42      54866.04|
| 11:  2.1826 -  2.1145  1321   142  0.25  71.69   0.92     0.37      50257.25|
| 12:  2.1145 -  2.0542  1309   144  0.20  75.17   0.94     0.33      48249.13|
| 13:  2.0542 -  2.0003  1080   128  0.21  74.08   0.92     0.35      41104.56|
| 14:  2.0003 -  1.9516   281    29  0.25  71.17   0.87     0.42      33958.36|
|alpha:            min =        0.33 max =            0.80 mean =         0.57|
|beta:             min =    33958.36 max =       107817.07 mean =     68015.32|
|figures of merit: min =        0.00 max =            1.00 mean =         0.43|
|phase err.(work): min =        0.00 max =           89.99 mean =        57.33|
|phase err.(test): min =        0.00 max =           89.95 mean =        57.53|
|-----------------------------------------------------------------------------|

============================== 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 = 14.384371             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.875   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.942573              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.315   (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 |  1.484 -  1.826:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.826 -  2.168:       14 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.168 -  2.509:       39 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.509 -  2.851:     1085 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.851 -  3.192:     1956 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.192 -  3.534:     2430 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.534 -  3.875:     4659 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.875 -  4.217:     4656 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.217 -  4.558:     6146 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.558 -  4.900:     7381 |
|-----------------------------------------------------------------------------|
|-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 |        0.196 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.484 |       0.675 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.850)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4621   r_free= 0.4536   ksol= 0.00   Bsol= 0.00   scale= 0.895    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.275892                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4520   r_free= 0.4423   ksol= 0.30   Bsol= 20.00   scale= 0.936   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,3.45,1.87,0.00,0.00,0.00); trace/3= 0.82                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.269000                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.507429             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.778   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.231802              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.061   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4520      final r-factor (work) = 0.3460          |
| start r-factor (free) = 0.4423      final r-factor (free) = 0.3794          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.2534 = 11.51 * 0.50 * 6.2668 + 1.00 * 0.1960                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.4745 = 11.51 * 0.50 * 6.1379 + 1.00 * 0.1585                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3460      final r-factor (work) = 0.3143          |
| start r-factor (free) = 0.3794      final r-factor (free) = 0.3893          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5668 = 1.23 * 1.00 * 6.1379 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4327 = 1.23 * 1.00 * 6.0187 + 1.00 * 0.0188                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.850)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.58   19.02    None  None   None       |
|    all(noH): 2823   0      0.00    99.58   19.02    None  None   None       |
|    Sol.    : 438    0      0.00    99.58   39.44    None  None   None       |
|    Mac.    : 2385   0      0.00    98.47   15.27    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.958:  925   |   5:    49.789 -  59.747:   90        |
|      1:     9.958 -  19.916:  907   |   6:    59.747 -  69.704:   37        |
|      2:    19.916 -  29.873:  461   |   7:    69.704 -  79.662:   29        |
|      3:    29.873 -  39.831:  234   |   8:    79.662 -  89.620:    6        |
|      4:    39.831 -  49.789:  131   |   9:    89.620 -  99.578:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3143 r_free = 0.3893             target_work(ml) = 6.026         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3138 r_free = 0.3897             target_work(ml) = 6.025         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3138   r_free= 0.3897   ksol= 0.30   Bsol= 20.00   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,3.45,1.87,0.00,0.00,0.00); trace/3= 0.82                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.025439                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3105   r_free= 0.3858   ksol= 0.32   Bsol= 53.16   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.81,1.26,-0.10,0.00,-0.00,-0.00); trace/3= -0.22                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.022206                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.637837              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.206   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.668734              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.851  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3105      final r-factor (work) = 0.2371          |
| start r-factor (free) = 0.3858      final r-factor (free) = 0.2964          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.1361 = 7.64 * 0.50 * 6.0168 + 1.00 * 0.1585                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.7432 = 7.64 * 0.50 * 5.9324 + 1.00 * 0.0877                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2371      final r-factor (work) = 0.2162          |
| start r-factor (free) = 0.2964      final r-factor (free) = 0.2769          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9859 = 0.67 * 1.00 * 5.9324 + 1.00 * 0.0187                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8606 = 0.67 * 1.00 * 5.7535 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.850)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.88   18.60    None  None   None       |
|    all(noH): 2823   0      0.00    98.88   18.60    None  None   None       |
|    Sol.    : 438    0      4.46    98.88   42.47    None  None   None       |
|    Mac.    : 2385   0      0.00    97.49   14.22    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.888:  991   |   5:    49.441 -  59.330:   92        |
|      1:     9.888 -  19.777:  995   |   6:    59.330 -  69.218:   52        |
|      2:    19.777 -  29.665:  341   |   7:    69.218 -  79.106:   23        |
|      3:    29.665 -  39.553:  168   |   8:    79.106 -  88.994:   19        |
|      4:    39.553 -  49.441:  138   |   9:    88.994 -  98.883:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2162 r_free = 0.2769             target_work(ml) = 5.722         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2160 r_free = 0.2769             target_work(ml) = 5.721         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2160   r_free= 0.2769   ksol= 0.32   Bsol= 53.16   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.81,1.26,-0.10,0.00,-0.00,-0.00); trace/3= -0.22                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.720849                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2157   r_free= 0.2762   ksol= 0.32   Bsol= 55.90   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.81,0.04,-1.00,0.00,-0.00,-0.00); trace/3= -0.93                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.718197                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.136929              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.014  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.226072              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.979  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2157      final r-factor (work) = 0.1594          |
| start r-factor (free) = 0.2762      final r-factor (free) = 0.2059          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.7421 = 6.14 * 0.50 * 5.7535 + 1.00 * 0.0877                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.2809 = 6.14 * 0.50 * 5.6073 + 1.00 * 0.0750                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1594      final r-factor (work) = 0.1446          |
| start r-factor (free) = 0.2059      final r-factor (free) = 0.1873          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2808 = 0.23 * 1.00 * 5.6073 + 1.00 * 0.0131                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2299 = 0.23 * 1.00 * 5.4012 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.850)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.51    94.21   17.63    None  None   None       |
|    all(noH): 2823   0      1.51    94.21   17.63    None  None   None       |
|    Sol.    : 438    0      5.85    94.21   41.74    None  None   None       |
|    Mac.    : 2385   0      1.51    88.85   13.20    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:     1.514 -  10.784: 1197   |   5:    47.860 -  57.129:  115        |
|      1:    10.784 -  20.053:  955   |   6:    57.129 -  66.399:   40        |
|      2:    20.053 -  29.322:  224   |   7:    66.399 -  75.668:   31        |
|      3:    29.322 -  38.591:  129   |   8:    75.668 -  84.937:   12        |
|      4:    38.591 -  47.860:  116   |   9:    84.937 -  94.206:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1446 r_free = 0.1873             target_work(ml) = 5.349         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1444 r_free = 0.1872             target_work(ml) = 5.348         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1444   r_free= 0.1872   ksol= 0.32   Bsol= 55.90   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.81,0.04,-1.00,0.00,-0.00,-0.00); trace/3= -0.93                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.348059                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1441   r_free= 0.1871   ksol= 0.33   Bsol= 55.90   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-1.26,-1.84,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.350728                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.241452              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.990  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.243558              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.885  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1441      final r-factor (work) = 0.1250          |
| start r-factor (free) = 0.1871      final r-factor (free) = 0.1686          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8401 = 3.24 * 0.50 * 5.4081 + 1.00 * 0.0750                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6437 = 3.24 * 0.50 * 5.2900 + 1.00 * 0.0701                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1250      final r-factor (work) = 0.1208          |
| start r-factor (free) = 0.1686      final r-factor (free) = 0.1672          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2972 = 0.24 * 1.00 * 5.2900 + 1.00 * 0.0088                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2797 = 0.24 * 1.00 * 5.2192 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.850)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.31    92.43   17.33    None  None   None       |
|    all(noH): 2823   0      2.31    92.43   17.33    None  None   None       |
|    Sol.    : 438    0      5.64    92.43   41.20    None  None   None       |
|    Mac.    : 2385   0      2.31    89.09   12.95    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:     2.315 -  11.327: 1315   |   5:    47.375 -  56.387:   98        |
|      1:    11.327 -  20.339:  876   |   6:    56.387 -  65.399:   42        |
|      2:    20.339 -  29.351:  208   |   7:    65.399 -  74.411:   32        |
|      3:    29.351 -  38.363:  121   |   8:    74.411 -  83.423:   13        |
|      4:    38.363 -  47.375:  112   |   9:    83.423 -  92.435:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1208 r_free = 0.1672             target_work(ml) = 5.214         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1207 r_free = 0.1672             target_work(ml) = 5.214         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1207   r_free= 0.1672   ksol= 0.33   Bsol= 55.90   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-1.26,-1.84,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.213792                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1210   r_free= 0.1671   ksol= 0.33   Bsol= 55.90   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.52,-1.58,-2.01,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.215423                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.528891              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 145.783  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.179602              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 155.328  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1210      final r-factor (work) = 0.1208          |
| start r-factor (free) = 0.1671      final r-factor (free) = 0.1657          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0606 = 1.53 * 0.50 * 5.2201 + 1.00 * 0.0701                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0399 = 1.53 * 0.50 * 5.2173 + 1.00 * 0.0515                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1208      final r-factor (work) = 0.1207          |
| start r-factor (free) = 0.1657      final r-factor (free) = 0.1659          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9455 = 0.18 * 1.00 * 5.2173 + 1.00 * 0.0084                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9438 = 0.18 * 1.00 * 5.2120 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.850)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.31    90.07   16.94    None  None   None       |
|    all(noH): 2823   0      2.31    90.07   16.94    None  None   None       |
|    Sol.    : 438    0      5.51    90.07   39.67    None  None   None       |
|    Mac.    : 2385   0      2.31    87.75   12.77    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:     2.308 -  11.085: 1271   |   5:    46.190 -  54.966:   91        |
|      1:    11.085 -  19.861:  925   |   6:    54.966 -  63.742:   42        |
|      2:    19.861 -  28.637:  206   |   7:    63.742 -  72.518:   27        |
|      3:    28.637 -  37.413:  117   |   8:    72.518 -  81.295:   10        |
|      4:    37.413 -  46.190:  126   |   9:    81.295 -  90.071:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1207 r_free = 0.1659             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1206 r_free = 0.1658             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1206   r_free= 0.1658   ksol= 0.33   Bsol= 55.90   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.52,-1.58,-2.01,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.211233                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6590 0.99   1457  164 0.1007 0.1289      5.3956       5.562|
|  2:  4.6590 -  3.7167 0.99   1390  151 0.0903 0.1073      5.4639      5.6426|
|  3:  3.7167 -  3.2524 0.99   1383  151 0.1133 0.1731      5.5227      5.9169|
|  4:  3.2524 -  2.9576 0.98   1342  157 0.1393 0.1649      5.5334      5.6512|
|  5:  2.9576 -  2.7470 0.99   1369  149 0.1439 0.1932      5.3866      5.5511|
|  6:  2.7470 -  2.5859 0.99   1345  154 0.1351 0.2037      5.2755      5.5089|
|  7:  2.5859 -  2.4570 0.98   1351  142 0.1320 0.1804      5.2251      5.4034|
|  8:  2.4570 -  2.3505 0.98   1320  142 0.1343 0.1828      5.1513      5.3692|
|  9:  2.3505 -  2.2603 0.99   1343  152 0.1258 0.1930      5.0776      5.3038|
| 10:  2.2603 -  2.1826 0.99   1339  154 0.1232 0.1768      5.0186      5.2706|
| 11:  2.1826 -  2.1145 0.97   1321  142 0.1177 0.1862      4.9445      5.2343|
| 12:  2.1145 -  2.0542 0.98   1309  144 0.1246 0.1815      4.9031      5.1343|
| 13:  2.0542 -  2.0003 0.80   1080  128 0.1219 0.1782      4.8228      5.0601|
| 14:  2.0003 -  1.9516 0.21    281   29 0.1244 0.1829       4.726      4.9714|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9433 -  4.6590  1457   164  0.94   8.85   0.97     0.95       6972.93|
|  2:  4.6590 -  3.7167  1390   151  0.95   8.27   1.01     0.99       9135.79|
|  3:  3.7167 -  3.2524  1383   151  0.93  12.26   1.02     1.01      11304.30|
|  4:  3.2524 -  2.9576  1342   157  0.91  15.42   1.00     0.98      11695.43|
|  5:  2.9576 -  2.7470  1369   149  0.89  17.63   0.99     0.96       9432.62|
|  6:  2.7470 -  2.5859  1345   154  0.89  17.24   0.98     0.96       8020.90|
|  7:  2.5859 -  2.4570  1351   142  0.90  16.39   0.98     0.94       6882.96|
|  8:  2.4570 -  2.3505  1320   142  0.89  17.86   0.99     0.96       6437.88|
|  9:  2.3505 -  2.2603  1343   152  0.89  17.00   0.99     0.96       5510.54|
| 10:  2.2603 -  2.1826  1339   154  0.90  16.22   0.99     0.95       4871.62|
| 11:  2.1826 -  2.1145  1321   142  0.90  16.34   0.99     0.95       4359.28|
| 12:  2.1145 -  2.0542  1309   144  0.90  16.62   0.99     0.97       4095.74|
| 13:  2.0542 -  2.0003  1080   128  0.89  17.22   0.99     0.97       3553.94|
| 14:  2.0003 -  1.9516   281    29  0.89  17.08   0.98     0.94       2903.13|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2903.13 max =        11695.43 mean =      7111.93|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.90 mean =        15.11|
|phase err.(test): min =        0.00 max =           89.97 mean =        14.63|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1206   r_free= 0.1658   ksol= 0.33   Bsol= 55.82   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-1.50,-1.88,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.211277                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1206   r_free= 0.1658   ksol= 0.33   Bsol= 55.82   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-1.50,-1.88,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.211277                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6590 0.99   1457  164 0.1007 0.1289      5.3958      5.5623|
|  2:  4.6590 -  3.7167 0.99   1390  151 0.0903 0.1073      5.4641      5.6427|
|  3:  3.7167 -  3.2524 0.99   1383  151 0.1133 0.1731      5.5228       5.917|
|  4:  3.2524 -  2.9576 0.98   1342  157 0.1393 0.1649      5.5335      5.6512|
|  5:  2.9576 -  2.7470 0.99   1369  149 0.1439 0.1932      5.3865      5.5509|
|  6:  2.7470 -  2.5859 0.99   1345  154 0.1351 0.2036      5.2754      5.5087|
|  7:  2.5859 -  2.4570 0.98   1351  142 0.1320 0.1804      5.2251      5.4034|
|  8:  2.4570 -  2.3505 0.98   1320  142 0.1343 0.1828      5.1512      5.3693|
|  9:  2.3505 -  2.2603 0.99   1343  152 0.1258 0.1930      5.0775      5.3038|
| 10:  2.2603 -  2.1826 0.99   1339  154 0.1232 0.1768      5.0188      5.2708|
| 11:  2.1826 -  2.1145 0.97   1321  142 0.1177 0.1862      4.9445      5.2342|
| 12:  2.1145 -  2.0542 0.98   1309  144 0.1246 0.1816      4.9032      5.1347|
| 13:  2.0542 -  2.0003 0.80   1080  128 0.1219 0.1782      4.8228      5.0598|
| 14:  2.0003 -  1.9516 0.21    281   29 0.1244 0.1830       4.726       4.971|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9433 -  4.6590  1457   164  0.94   8.86   0.97     0.95       6976.48|
|  2:  4.6590 -  3.7167  1390   151  0.95   8.28   1.01     0.99       9138.90|
|  3:  3.7167 -  3.2524  1383   151  0.93  12.26   1.02     1.01      11307.30|
|  4:  3.2524 -  2.9576  1342   157  0.91  15.42   1.00     0.98      11696.21|
|  5:  2.9576 -  2.7470  1369   149  0.89  17.62   0.99     0.96       9429.62|
|  6:  2.7470 -  2.5859  1345   154  0.89  17.24   0.98     0.96       8017.43|
|  7:  2.5859 -  2.4570  1351   142  0.90  16.39   0.98     0.95       6881.12|
|  8:  2.4570 -  2.3505  1320   142  0.89  17.86   1.00     0.96       6437.42|
|  9:  2.3505 -  2.2603  1343   152  0.89  17.00   1.00     0.96       5512.48|
| 10:  2.2603 -  2.1826  1339   154  0.90  16.23   0.99     0.95       4872.73|
| 11:  2.1826 -  2.1145  1321   142  0.90  16.35   0.99     0.95       4359.91|
| 12:  2.1145 -  2.0542  1309   144  0.90  16.63   0.99     0.97       4097.39|
| 13:  2.0542 -  2.0003  1080   128  0.89  17.22   0.99     0.98       3553.84|
| 14:  2.0003 -  1.9516   281    29  0.89  17.08   0.98     0.94       2901.41|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2901.41 max =        11696.21 mean =      7112.46|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.90 mean =        15.11|
|phase err.(test): min =        0.00 max =           89.97 mean =        14.63|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.850)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.22    89.99   16.86    None  None   None       |
|    all(noH): 2823   0      2.22    89.99   16.86    None  None   None       |
|    Sol.    : 438    0      5.42    89.99   39.58    None  None   None       |
|    Mac.    : 2385   0      2.22    87.67   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:     2.225 -  11.001: 1271   |   5:    46.106 -  54.882:   91        |
|      1:    11.001 -  19.777:  925   |   6:    54.882 -  63.658:   42        |
|      2:    19.777 -  28.553:  206   |   7:    63.658 -  72.435:   27        |
|      3:    28.553 -  37.330:  117   |   8:    72.435 -  81.211:   10        |
|      4:    37.330 -  46.106:  126   |   9:    81.211 -  89.987:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 341         
Filter by distance & map next to the model:
   mapped sites are within: 0.517 - 5.966
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 337 from: 341
   mapped sites are within: 0.717 - 5.966

peak=    5.586 closest distance to " CB  SER A  63 " =    1.236
peak=    5.509 closest distance to " NH2 ARG A  56 " =    2.303
peak=    5.423 closest distance to " CG  PRO A  54 " =    1.306
peak=    5.367 closest distance to " CG  PRO A  90 " =    1.250
peak=    5.353 closest distance to " CG  PRO A 198 " =    1.319
peak=    5.314 closest distance to " CB  GLN A 223 " =    1.426
peak=    5.048 closest distance to " O   HOH Z  11 " =    1.414
peak=    4.990 closest distance to " O   HOH Z 124 " =    1.572
peak=    4.836 closest distance to " CB  SER A   3 " =    1.375
peak=    4.822 closest distance to " CG  PRO A 213 " =    1.310
peak=    4.819 closest distance to " O   PRO A 198 " =    1.558
peak=    4.803 closest distance to " O   HOH Z  15 " =    2.053
peak=    4.756 closest distance to " O   HOH Z 132 " =    1.377
peak=    4.724 closest distance to " O   HOH Z  40 " =    1.951
peak=    4.668 closest distance to " CG  PRO A 280 " =    0.734
peak=    4.637 closest distance to " CB  ARG A 275 " =    0.927
peak=    4.602 closest distance to " O   HOH Z 154 " =    1.546
peak=    4.578 closest distance to " CA  TYR A  30 " =    1.014
peak=    4.565 closest distance to " O   HOH Z 389 " =    1.913
peak=    4.542 closest distance to " O   HOH Z  80 " =    1.835
peak=    4.539 closest distance to " O   HOH Z 142 " =    1.553
peak=    4.531 closest distance to " CB  GLU A 128 " =    1.143
peak=    4.530 closest distance to " O   HOH Z 234 " =    3.749
peak=    4.520 closest distance to " O   HOH Z 134 " =    1.933
peak=    4.513 closest distance to " O   HOH Z 247 " =    1.428
peak=    4.476 closest distance to " O   HOH Z 209 " =    2.376
peak=    4.465 closest distance to " O   HOH Z 211 " =    1.421
peak=    4.398 closest distance to " O   HOH Z 133 " =    1.769
peak=    4.390 closest distance to " CB  PRO A 198 " =    1.003
peak=    4.339 closest distance to " O   HOH Z 193 " =    1.992
peak=    4.317 closest distance to " O   SER A  87 " =    2.099
peak=    4.305 closest distance to " N   ASN A  39 " =    1.270
peak=    4.278 closest distance to " O   HOH Z 196 " =    1.458
peak=    4.270 closest distance to " O   HOH Z 236 " =    1.992
peak=    4.269 closest distance to " CB  GLN A 183 " =    1.295
peak=    4.267 closest distance to " O   HOH Z 126 " =    1.700
peak=    4.264 closest distance to " O   HOH Z  43 " =    1.665
peak=    4.261 closest distance to " O   HOH Z 154 " =    2.421
peak=    4.238 closest distance to " O   HOH Z 163 " =    1.637
peak=    4.236 closest distance to " O   HOH Z 272 " =    1.932
peak=    4.233 closest distance to " O   HOH Z 403 " =    1.777
peak=    4.232 closest distance to " CB  GLU A 152 " =    1.147
peak=    4.225 closest distance to " CG1 ILE A  33 " =    1.258
peak=    4.199 closest distance to " CB  LEU A 228 " =    1.140
peak=    4.199 closest distance to " O   HOH Z  48 " =    1.618
peak=    4.197 closest distance to " CB  PRO A  54 " =    0.804
peak=    4.193 closest distance to " CB  ARG A 190 " =    1.674
peak=    4.188 closest distance to " NH2 ARG A 156 " =    1.208
peak=    4.169 closest distance to " O   HOH Z 108 " =    1.539
peak=    4.164 closest distance to " NZ  LYS A  76 " =    1.241
peak=    4.162 closest distance to " O   HOH Z  97 " =    1.886
peak=    4.154 closest distance to " OD2 ASP A 286 " =    2.844
peak=    4.148 closest distance to " O   HOH Z 214 " =    1.193
peak=    4.136 closest distance to " CG  PRO A 243 " =    1.144
peak=    4.118 closest distance to " OE1 GLN A  11 " =    1.888
peak=    4.113 closest distance to " O   HOH Z 260 " =    1.378
peak=    4.106 closest distance to " O   HOH Z 298 " =    1.903
peak=    4.083 closest distance to " CB  SER A 141 " =    1.030
peak=    4.076 closest distance to " CB  VAL A 202 " =    1.479
peak=    4.064 closest distance to " CB  TYR A 169 " =    0.921
peak=    4.057 closest distance to " O   HOH Z 326 " =    1.531
peak=    4.047 closest distance to " O   HOH Z 426 " =    1.433
peak=    4.044 closest distance to " CA  ASP A 191 " =    0.830
peak=    4.029 closest distance to " NZ  LYS A 117 " =    3.224
peak=    4.010 closest distance to " O   HOH Z 368 " =    2.048
peak=    4.010 closest distance to " CG  ARG A  66 " =    2.706
peak=    4.005 closest distance to " CB  ARG A  79 " =    1.325
peak=    4.002 closest distance to " CA  ALA A  21 " =    1.275
peak=    4.000 closest distance to " O   HOH Z 316 " =    3.030
peak=    3.998 closest distance to " O   HOH Z 411 " =    3.333
peak=    3.998 closest distance to " O   HOH Z 232 " =    2.391
peak=    3.990 closest distance to " O   HOH Z  63 " =    2.031
peak=    3.976 closest distance to " CB  GLU A 277 " =    3.599
peak=    3.968 closest distance to " O   HOH Z 189 " =    1.967
peak=    3.958 closest distance to " CB  TRP A 179 " =    1.259
peak=    3.945 closest distance to " O   HOH Z  30 " =    1.760
peak=    3.944 closest distance to " NH2BARG A 145 " =    2.004
peak=    3.920 closest distance to " O   HOH Z  20 " =    1.830
peak=    3.912 closest distance to " O   HOH Z 210 " =    1.217
peak=    3.909 closest distance to " O   HOH Z 371 " =    3.304
peak=    3.886 closest distance to " CA  GLN A 223 " =    0.877
peak=    3.883 closest distance to " O   HOH Z 369 " =    2.132
peak=    3.871 closest distance to " O   HOH Z  67 " =    1.934
peak=    3.865 closest distance to " O   HOH Z 374 " =    2.540
peak=    3.861 closest distance to " O   HOH Z 132 " =    2.603
peak=    3.858 closest distance to " CG2 THR A 221 " =    1.020
peak=    3.857 closest distance to " CA  ARG A  36 " =    1.130
peak=    3.852 closest distance to " O   HOH Z 358 " =    2.045
peak=    3.838 closest distance to " OD1 ASN A  69 " =    2.509
peak=    3.822 closest distance to " CA  THR A 221 " =    0.941
peak=    3.818 closest distance to " O   HOH Z 203 " =    1.811
peak=    3.813 closest distance to " O   HOH Z  61 " =    1.503
peak=    3.812 closest distance to " O   HOH Z 313 " =    1.962
peak=    3.808 closest distance to " O   HOH Z  88 " =    3.416
peak=    3.770 closest distance to " O   HOH Z  39 " =    1.414
peak=    3.764 closest distance to " O   HOH Z 402 " =    1.524
peak=    3.763 closest distance to " O   HOH Z  44 " =    1.795
peak=    3.760 closest distance to " O   HOH Z 279 " =    2.121
peak=    3.758 closest distance to " O   HOH Z 145 " =    1.780
peak=    3.753 closest distance to " CD2 LEU A 297 " =    0.884
peak=    3.751 closest distance to " CB  ASN A 148 " =    1.226
peak=    3.750 closest distance to " O   HOH Z 227 " =    1.781
peak=    3.744 closest distance to " OD1 ASP A 238 " =    0.869
peak=    3.742 closest distance to " CB  GLN A  58 " =    0.855
peak=    3.733 closest distance to " O   HOH Z 108 " =    2.051
peak=    3.730 closest distance to " O   HOH Z 423 " =    1.896
peak=    3.719 closest distance to " CB  ARG A 139 " =    0.843
peak=    3.719 closest distance to " O   HOH Z 147 " =    1.741
peak=    3.717 closest distance to " O   HOH Z 132 " =    1.804
peak=    3.709 closest distance to " NH1 ARG A 269 " =    0.812
peak=    3.699 closest distance to " CA  ASP A 140 " =    1.152
peak=    3.692 closest distance to " NZ  LYS A 119 " =    1.730
peak=    3.687 closest distance to " O   HOH Z 394 " =    1.577
peak=    3.681 closest distance to " CG2BVAL A  41 " =    0.974
peak=    3.678 closest distance to " OE1 GLU A   2 " =    2.141
peak=    3.676 closest distance to " O   HOH Z 118 " =    1.635
peak=    3.667 closest distance to " CG AARG A 275 " =    0.978
peak=    3.664 closest distance to " O   HOH Z 344 " =    2.934
peak=    3.664 closest distance to " O   HOH Z 207 " =    2.238
peak=    3.651 closest distance to " O   HOH Z 261 " =    2.025
peak=    3.648 closest distance to " O   HOH Z 434 " =    1.526
peak=    3.646 closest distance to " CD  LYS A 119 " =    1.424
peak=    3.640 closest distance to " CB  PRO A  54 " =    1.318
peak=    3.639 closest distance to " ND2 ASN A 187 " =    1.628
peak=    3.638 closest distance to " CB  SER A  62 " =    0.828
peak=    3.632 closest distance to " O   HOH Z  78 " =    2.040
peak=    3.632 closest distance to " CG1 VAL A 153 " =    1.116
peak=    3.623 closest distance to " O   HOH Z 280 " =    2.670
peak=    3.611 closest distance to " O   HOH Z   4 " =    1.918
peak=    3.610 closest distance to " NH2AARG A 145 " =    2.194
peak=    3.609 closest distance to " O   HOH Z 215 " =    1.410
peak=    3.609 closest distance to " CD  ARG A 269 " =    0.971
peak=    3.598 closest distance to " NH2AARG A 190 " =    1.473
peak=    3.598 closest distance to " O   HOH Z 128 " =    2.152
peak=    3.597 closest distance to " O   HOH Z 128 " =    2.142
peak=    3.595 closest distance to " O   HOH Z 193 " =    2.284
peak=    3.592 closest distance to " O   TRP A 274 " =    1.743
peak=    3.591 closest distance to " O   GLY A 211 " =    1.320
peak=    3.585 closest distance to " CG1BVAL A  72 " =    1.670
peak=    3.580 closest distance to " CB  GLN A 194 " =    0.890
peak=    3.580 closest distance to " CB  MET A  47 " =    1.053
peak=    3.568 closest distance to " C   GLY A  80 " =    1.168
peak=    3.563 closest distance to " O   HOH Z 345 " =    2.917
peak=    3.557 closest distance to " OD1 ASP A 231 " =    1.935
peak=    3.554 closest distance to " O   HOH Z 408 " =    1.565
peak=    3.546 closest distance to " CA  ASP A 124 " =    0.717
peak=    3.543 closest distance to " O   HOH Z  21 " =    1.837
peak=    3.536 closest distance to " O   HOH Z  54 " =    1.737
peak=    3.534 closest distance to " O   HOH Z 336 " =    1.641
peak=    3.532 closest distance to " CA  ASP A 162 " =    1.199
peak=    3.531 closest distance to " NH1AARG A 145 " =    1.033
peak=    3.525 closest distance to " CD1 LEU A 300 " =    1.235
peak=    3.519 closest distance to " O   HOH Z 215 " =    1.361
peak=    3.519 closest distance to " O   HOH Z 352 " =    1.196
peak=    3.518 closest distance to " CB  ASN A 285 " =    0.940
peak=    3.517 closest distance to " O   HOH Z  28 " =    2.361
peak=    3.515 closest distance to " CB  ALA A 291 " =    1.260
peak=    3.515 closest distance to " O   HOH Z 245 " =    1.382
peak=    3.514 closest distance to " CD  LYS A 166 " =    1.390
peak=    3.511 closest distance to " O   HOH Z 276 " =    1.392
peak=    3.505 closest distance to " CA  VAL A  41 " =    0.759
peak=    3.504 closest distance to " O   HOH Z 433 " =    1.509
peak=    3.498 closest distance to " NH2BARG A 102 " =    0.954
peak=    3.492 closest distance to " C   SER A  32 " =    1.069
peak=    3.492 closest distance to " CA  GLU A 152 " =    0.864
peak=    3.491 closest distance to " NE1 TRP A 274 " =    0.909
peak=    3.489 closest distance to " O   HOH Z 406 " =    1.585
peak=    3.489 closest distance to " O   HOH Z 173 " =    2.088
peak=    3.487 closest distance to " O   HOH Z 387 " =    2.317
peak=    3.483 closest distance to " O   HOH Z 402 " =    2.911
peak=    3.483 closest distance to " O   HOH Z 362 " =    3.456
peak=    3.479 closest distance to " O   HOH Z 357 " =    1.960
peak=    3.479 closest distance to " O   HOH Z 197 " =    2.000
peak=    3.474 closest distance to " CG2 VAL A  78 " =    0.962
peak=    3.471 closest distance to " O   HOH Z  97 " =    2.588
peak=    3.465 closest distance to " O   HOH Z 227 " =    1.789
peak=    3.462 closest distance to " O   HOH Z  47 " =    1.373
peak=    3.461 closest distance to " CA  ASN A 176 " =    1.771
peak=    3.460 closest distance to " CZ  PHE A 192 " =    0.996
peak=    3.458 closest distance to " O   GLY A  23 " =    2.416
peak=    3.457 closest distance to " O   HOH Z 102 " =    1.253
peak=    3.452 closest distance to " CB  ALA A 256 " =    1.056
peak=    3.448 closest distance to " O   HOH Z 438 " =    2.713
peak=    3.445 closest distance to " CD  ARG A 159 " =    0.842
peak=    3.436 closest distance to " O   HOH Z 291 " =    1.597
peak=    3.435 closest distance to " O   HOH Z 346 " =    1.606
peak=    3.434 closest distance to " CE  LYS A 119 " =    1.157
peak=    3.434 closest distance to " O   HOH Z 234 " =    1.804
peak=    3.434 closest distance to " CB  ASN A 187 " =    1.107
peak=    3.431 closest distance to " CA  ALA A 160 " =    0.857
peak=    3.425 closest distance to " CG  GLN A  11 " =    1.263
peak=    3.420 closest distance to " CB  ASN A 148 " =    1.859
peak=    3.417 closest distance to " CG2 THR A 220 " =    0.777
peak=    3.417 closest distance to " CB  ALA A 244 " =    0.909
peak=    3.414 closest distance to " CB  GLN A 103 " =    0.940
peak=    3.413 closest distance to " O   MET A 105 " =    1.923
peak=    3.410 closest distance to " O   HOH Z 126 " =    1.748
peak=    3.409 closest distance to " CG1 ILE A 120 " =    1.085
peak=    3.406 closest distance to " O   HOH Z 409 " =    3.063
peak=    3.405 closest distance to " CB  PHE A  16 " =    1.017
peak=    3.401 closest distance to " O   HOH Z  54 " =    2.302
peak=    3.397 closest distance to " NZ  LYS A 117 " =    1.293
peak=    3.397 closest distance to " CB  ALA A 100 " =    1.321
peak=    3.396 closest distance to " O   HOH Z 427 " =    3.014
peak=    3.396 closest distance to " NE2 GLN A  11 " =    1.049
peak=    3.389 closest distance to " O   HOH Z 174 " =    2.382
peak=    3.386 closest distance to " OG  SER A  97 " =    3.545
peak=    3.385 closest distance to " CD BLYS A 290 " =    1.131
peak=    3.384 closest distance to " CA  LEU A 282 " =    1.191
peak=    3.377 closest distance to " O   HOH Z  49 " =    1.861
peak=    3.376 closest distance to " CA  ARG A 195 " =    1.097
peak=    3.374 closest distance to " O   HOH Z 284 " =    2.908
peak=    3.366 closest distance to " CB  ILE A 199 " =    0.984
peak=    3.365 closest distance to " CG  GLN A  77 " =    0.785
peak=    3.363 closest distance to " CG2AVAL A 121 " =    2.223
peak=    3.362 closest distance to " CZ  PHE A 218 " =    1.039
peak=    3.356 closest distance to " CB  GLU A 152 " =    1.595
peak=    3.355 closest distance to " OG  SER A  62 " =    3.088
peak=    3.355 closest distance to " OE1 GLN A  58 " =    5.966
peak=    3.353 closest distance to " O   HOH Z 345 " =    1.797
peak=    3.351 closest distance to " O   HOH Z 427 " =    2.805
peak=    3.345 closest distance to " O   HOH Z 238 " =    5.329
peak=    3.343 closest distance to " O   THR A 251 " =    1.294
peak=    3.343 closest distance to " CD1 LEU A  96 " =    0.730
peak=    3.342 closest distance to " O   HOH Z 327 " =    2.515
peak=    3.339 closest distance to " O   HOH Z 334 " =    1.530
peak=    3.339 closest distance to " CB  SER A 216 " =    0.760
peak=    3.338 closest distance to " NE AARG A 275 " =    1.387
peak=    3.335 closest distance to " CB  TRP A 179 " =    1.561
peak=    3.333 closest distance to " CA  ILE A 263 " =    1.001
peak=    3.328 closest distance to " CA  ALA A  51 " =    0.835
peak=    3.324 closest distance to " O   HOH Z 139 " =    4.516
peak=    3.323 closest distance to " CG2 ILE A 120 " =    1.158
peak=    3.316 closest distance to " O   HOH Z 332 " =    1.532
peak=    3.314 closest distance to " O   HOH Z 250 " =    1.441
peak=    3.313 closest distance to " CB  ARG A 269 " =    1.002
peak=    3.309 closest distance to " CG2 VAL A 197 " =    1.164
peak=    3.305 closest distance to " O   HOH Z 301 " =    1.624
peak=    3.303 closest distance to " CG  GLN A  58 " =    2.298
peak=    3.301 closest distance to " CA  PRO A  90 " =    0.913
peak=    3.299 closest distance to " CA  ARG A 195 " =    1.293
peak=    3.298 closest distance to " CB  SER A 273 " =    0.816
peak=    3.297 closest distance to " O   HOH Z 156 " =    2.326
peak=    3.296 closest distance to " CB  TRP A 266 " =    0.952
peak=    3.296 closest distance to " CD  ARG A 195 " =    3.581
peak=    3.295 closest distance to " O   HOH Z  19 " =    1.757
peak=    3.295 closest distance to " CB  GLN A  73 " =    1.007
peak=    3.294 closest distance to " O   HOH Z 104 " =    3.511
peak=    3.291 closest distance to " O   ALA A   1 " =    1.440
peak=    3.289 closest distance to " CD1 TRP A 266 " =    1.250
peak=    3.287 closest distance to " O   HOH Z 144 " =    1.987
peak=    3.286 closest distance to " O   HOH Z  10 " =    1.767
peak=    3.286 closest distance to " CG2 ILE A 106 " =    1.010
peak=    3.281 closest distance to " O   HOH Z  59 " =    1.806
peak=    3.277 closest distance to " O   HOH Z 421 " =    1.687
peak=    3.276 closest distance to " O   HOH Z 194 " =    1.951
peak=    3.272 closest distance to " O   HOH Z 280 " =    2.579
peak=    3.272 closest distance to " O   HOH Z 248 " =    1.560
peak=    3.271 closest distance to " O   HOH Z 214 " =    2.206
peak=    3.270 closest distance to " OH  TYR A  30 " =    1.261
peak=    3.265 closest distance to " OG  SER A 245 " =    1.495
peak=    3.263 closest distance to " CA  VAL A 126 " =    0.958
peak=    3.263 closest distance to " OG BSER A 164 " =    2.473
peak=    3.263 closest distance to " O   HOH Z 383 " =    2.049
peak=    3.260 closest distance to " CG2 VAL A 112 " =    1.482
peak=    3.258 closest distance to " O   HOH Z 166 " =    3.216
peak=    3.252 closest distance to " O   HOH Z 419 " =    1.599
peak=    3.251 closest distance to " O   SER A  26 " =    1.692
peak=    3.243 closest distance to " CB  PRO A  90 " =    1.121
peak=    3.243 closest distance to " O   HOH Z 361 " =    2.459
peak=    3.243 closest distance to " CG2 VAL A 257 " =    0.824
peak=    3.242 closest distance to " CA  GLY A 196 " =    0.991
peak=    3.240 closest distance to " O   HOH Z 271 " =    1.276
peak=    3.240 closest distance to " O   HOH Z 127 " =    1.063
peak=    3.236 closest distance to " CD2 HIS A  81 " =    1.176
peak=    3.234 closest distance to " CA  ARG A  66 " =    1.015
peak=    3.233 closest distance to " O   HOH Z 368 " =    2.505
peak=    3.232 closest distance to " CD2 LEU A 255 " =    1.119
peak=    3.223 closest distance to " O   HOH Z 109 " =    2.394
peak=    3.219 closest distance to " CA  ALA A 248 " =    1.194
peak=    3.216 closest distance to " O   HOH Z 287 " =    1.771
peak=    3.216 closest distance to " CD  ARG A 219 " =    0.873
peak=    3.215 closest distance to " O   HOH Z 263 " =    2.070
peak=    3.213 closest distance to " CA  SER A  87 " =    0.899
peak=    3.210 closest distance to " O   HOH Z 281 " =    4.000
peak=    3.207 closest distance to " CD  ARG A 195 " =    1.010
peak=    3.207 closest distance to " OG1 THR A 294 " =    2.467
peak=    3.207 closest distance to " CD  PRO A  54 " =    1.164
peak=    3.205 closest distance to " O   HOH Z 261 " =    2.080
peak=    3.204 closest distance to " N   SER A 164 " =    0.995
peak=    3.204 closest distance to " O   HOH Z 112 " =    1.489
peak=    3.199 closest distance to " O   HOH Z 162 " =    1.759
peak=    3.199 closest distance to " O   HOH Z  22 " =    2.360
peak=    3.198 closest distance to " CG  ARG A  66 " =    1.038
peak=    3.198 closest distance to " CD1 LEU A 222 " =    0.850
peak=    3.186 closest distance to " O   GLY A  91 " =    1.327
peak=    3.186 closest distance to " NE2 HIS A 115 " =    0.861
peak=    3.185 closest distance to " CG  ARG A  66 " =    3.246
peak=    3.171 closest distance to " CA  LYS A 117 " =    1.246
peak=    3.166 closest distance to " O   HOH Z 110 " =    1.555
peak=    3.164 closest distance to " CB  LEU A 143 " =    1.103
peak=    3.162 closest distance to " O   HOH Z 185 " =    1.660
peak=    3.161 closest distance to " CB  SER A  62 " =    1.214
peak=    3.150 closest distance to " CB  MET A  40 " =    0.818
peak=    3.147 closest distance to " O   HOH Z 420 " =    2.043
peak=    3.144 closest distance to " O   HOH Z 432 " =    1.775
peak=    3.141 closest distance to " CH2 TRP A 274 " =    1.904
peak=    3.141 closest distance to " N   SER A 135 " =    1.328
peak=    3.138 closest distance to " O   HOH Z 261 " =    1.562
peak=    3.138 closest distance to " CB  THR A 157 " =    1.053
peak=    3.137 closest distance to " CB  ALA A 154 " =    1.247
peak=    3.133 closest distance to " O   HOH Z 155 " =    1.502
peak=    3.133 closest distance to " CA  GLY A 241 " =    0.909
peak=    3.132 closest distance to " CB  ASN A 127 " =    1.046
peak=    3.131 closest distance to " CD1 PHE A  59 " =    1.775
peak=    3.130 closest distance to " O   HOH Z 106 " =    2.265
peak=    3.128 closest distance to " OD2 ASP A 286 " =    3.281
peak=    3.124 closest distance to " CA  GLN A  88 " =    1.171
peak=    3.123 closest distance to " O   HOH Z 155 " =    2.836
peak=    3.122 closest distance to " O   HOH Z 126 " =    1.486
peak=    3.119 closest distance to " CA  GLU A  46 " =    0.796
peak=    3.115 closest distance to " NH1BARG A 145 " =    1.048
peak=    3.106 closest distance to " CA  ALA A 295 " =    1.082
peak=    3.105 closest distance to " CE  LYS A 193 " =    1.850
peak=    3.105 closest distance to " O   HOH Z 250 " =    1.840
peak=    3.104 closest distance to " O   HOH Z 303 " =    2.133
peak=    3.098 closest distance to " CB  ASN A  39 " =    0.830
peak=    3.089 closest distance to " CB  TYR A 247 " =    1.015
peak=    3.089 closest distance to " OG  SER A   3 " =    2.027
peak=    3.089 closest distance to " O   SER A 164 " =    1.495
peak=    3.087 closest distance to " CB  THR A  52 " =    1.215
peak=    3.082 closest distance to " CB  ALA A  71 " =    1.276
peak=    3.079 closest distance to " O   HOH Z 273 " =    3.054
peak=    3.063 closest distance to " CB  VAL A 265 " =    1.226
peak=    3.043 closest distance to " CA  ALA A 158 " =    1.059
peak=    3.033 closest distance to " O   HOH Z  61 " =    1.513
peak=    3.032 closest distance to " CD2 TRP A 179 " =    1.304

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.404 - 5.243
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 194 from: 198
   mapped sites are within: 0.731 - 5.243

peak=   -4.344 closest distance to " O   HOH Z 290 " =    0.877
peak=   -4.306 closest distance to " O   PRO A 198 " =    1.271
peak=   -4.294 closest distance to " OXT GLY A 302 " =    2.817
peak=   -4.252 closest distance to " O   VAL A  67 " =    2.660
peak=   -4.155 closest distance to " NH2 ARG A  66 " =    1.423
peak=   -4.113 closest distance to " O   HOH Z  52 " =    1.972
peak=   -4.109 closest distance to " O   HOH Z 221 " =    1.051
peak=   -4.093 closest distance to " CD  ARG A 156 " =    1.942
peak=   -4.073 closest distance to " OG  SER A  97 " =    2.215
peak=   -4.044 closest distance to " OG ASER A 134 " =    1.400
peak=   -4.027 closest distance to " O   HOH Z 377 " =    0.910
peak=   -4.025 closest distance to " O   HOH Z 266 " =    4.250
peak=   -4.019 closest distance to " O   HOH Z 407 " =    3.581
peak=   -3.941 closest distance to " C   HIS A 108 " =    1.053
peak=   -3.930 closest distance to " O   HOH Z  93 " =    1.180
peak=   -3.920 closest distance to " CD  GLN A  58 " =    0.874
peak=   -3.919 closest distance to " CE2 TYR A  30 " =    2.688
peak=   -3.913 closest distance to " CG  ASP A  50 " =    2.545
peak=   -3.908 closest distance to " CA  SER A 276 " =    1.453
peak=   -3.902 closest distance to " O   HOH Z  13 " =    1.450
peak=   -3.891 closest distance to " O   HOH Z 166 " =    1.895
peak=   -3.887 closest distance to " O   HOH Z  71 " =    1.321
peak=   -3.860 closest distance to " OE2 GLU A   2 " =    1.333
peak=   -3.843 closest distance to " CD1 LEU A 101 " =    2.634
peak=   -3.839 closest distance to " CE  MET A 105 " =    1.895
peak=   -3.839 closest distance to " O   HOH Z  17 " =    1.104
peak=   -3.829 closest distance to " O   HOH Z  43 " =    1.919
peak=   -3.806 closest distance to " CG2 THR A   4 " =    1.828
peak=   -3.788 closest distance to " C   ALA A 158 " =    1.203
peak=   -3.786 closest distance to " CA  SER A 164 " =    1.991
peak=   -3.784 closest distance to " ND2 ASN A  45 " =    0.971
peak=   -3.767 closest distance to " CD2 LEU A 300 " =    2.856
peak=   -3.765 closest distance to " CH2 TRP A 179 " =    1.160
peak=   -3.759 closest distance to " OG  SER A  62 " =    1.308
peak=   -3.734 closest distance to " O   HOH Z  11 " =    1.620
peak=   -3.732 closest distance to " CB  LEU A 167 " =    2.171
peak=   -3.724 closest distance to " O   HOH Z 150 " =    1.284
peak=   -3.722 closest distance to " ND2 ASN A 187 " =    1.704
peak=   -3.720 closest distance to " N   ALA A  43 " =    2.586
peak=   -3.716 closest distance to " CG  ASP A 231 " =    0.785
peak=   -3.713 closest distance to " O   HOH Z 418 " =    1.313
peak=   -3.710 closest distance to " O   HOH Z 185 " =    2.366
peak=   -3.690 closest distance to " CD1 LEU A 228 " =    2.375
peak=   -3.683 closest distance to " C   SER A 206 " =    1.636
peak=   -3.681 closest distance to " O   ALA A 160 " =    1.508
peak=   -3.674 closest distance to " C   ASN A 285 " =    2.386
peak=   -3.670 closest distance to " CA  VAL A 197 " =    1.022
peak=   -3.668 closest distance to " CE  MET A  93 " =    1.095
peak=   -3.656 closest distance to " O   ALA A 256 " =    1.465
peak=   -3.654 closest distance to " CD2 LEU A 237 " =    2.513
peak=   -3.654 closest distance to " N   GLN A  58 " =    1.700
peak=   -3.647 closest distance to " CG  GLN A  58 " =    1.206
peak=   -3.641 closest distance to " CD  ARG A 139 " =    1.510
peak=   -3.638 closest distance to " ND2 ASN A  60 " =    1.291
peak=   -3.638 closest distance to " CD  PRO A 198 " =    1.192
peak=   -3.634 closest distance to " OD1 ASP A 191 " =    1.727
peak=   -3.619 closest distance to " O   HOH Z 292 " =    4.432
peak=   -3.608 closest distance to " O   HOH Z 423 " =    2.347
peak=   -3.605 closest distance to " C   THR A 279 " =    1.206
peak=   -3.583 closest distance to " CB  ALA A 291 " =    2.435
peak=   -3.578 closest distance to " CA  GLY A 203 " =    2.256
peak=   -3.576 closest distance to " SG ACYS A 201 " =    2.347
peak=   -3.572 closest distance to " O   HOH Z 234 " =    4.212
peak=   -3.569 closest distance to " CZ  TYR A 169 " =    1.821
peak=   -3.566 closest distance to " O   TRP A  92 " =    1.830
peak=   -3.564 closest distance to " CA  VAL A  67 " =    2.921
peak=   -3.562 closest distance to " O   HOH Z  91 " =    2.209
peak=   -3.548 closest distance to " CG  LYS A 193 " =    2.577
peak=   -3.548 closest distance to " CG  GLU A  53 " =    1.395
peak=   -3.534 closest distance to " CA  TRP A 274 " =    1.704
peak=   -3.527 closest distance to " CD  ARG A 195 " =    5.116
peak=   -3.525 closest distance to " CD1 TYR A 247 " =    2.264
peak=   -3.521 closest distance to " OG BSER A 134 " =    1.805
peak=   -3.516 closest distance to " CD2 PHE A  59 " =    2.492
peak=   -3.512 closest distance to " O   HOH Z 313 " =    1.045
peak=   -3.510 closest distance to " CD  GLN A  88 " =    0.731
peak=   -3.505 closest distance to " OD1 ASN A 148 " =    1.705
peak=   -3.500 closest distance to " ND2 ASN A  45 " =    1.137
peak=   -3.499 closest distance to " OG  SER A  32 " =    1.106
peak=   -3.479 closest distance to " O   HOH Z  10 " =    1.552
peak=   -3.477 closest distance to " CB  ALA A 161 " =    2.615
peak=   -3.477 closest distance to " O   HOH Z  15 " =    1.615
peak=   -3.471 closest distance to " NH1 ARG A 195 " =    2.243
peak=   -3.471 closest distance to " O   HOH Z  19 " =    2.160
peak=   -3.468 closest distance to " O   HOH Z 151 " =    1.534
peak=   -3.463 closest distance to " O   ASP A 191 " =    1.354
peak=   -3.458 closest distance to " CG1 VAL A 112 " =    2.591
peak=   -3.455 closest distance to " CD1 PHE A  59 " =    1.860
peak=   -3.450 closest distance to " O   HOH Z  92 " =    1.687
peak=   -3.446 closest distance to " CD  GLN A  88 " =    0.900
peak=   -3.444 closest distance to " O   GLY A 196 " =    1.101
peak=   -3.443 closest distance to " O   HOH Z 348 " =    2.325
peak=   -3.440 closest distance to " CB  TYR A  15 " =    2.262
peak=   -3.433 closest distance to " CA  ASP A 298 " =    1.100
peak=   -3.429 closest distance to " O   HOH Z 165 " =    2.048
peak=   -3.427 closest distance to " O   HOH Z 353 " =    2.382
peak=   -3.421 closest distance to " CB  CYS A 254 " =    2.519
peak=   -3.414 closest distance to " CD  GLN A 223 " =    0.784
peak=   -3.414 closest distance to " NH2 ARG A  66 " =    5.099
peak=   -3.410 closest distance to " CB  PRO A 163 " =    2.811
peak=   -3.403 closest distance to " O   HOH Z 259 " =    1.158
peak=   -3.394 closest distance to " NZ  LYS A 117 " =    1.545
peak=   -3.388 closest distance to " O   HOH Z 196 " =    2.576
peak=   -3.386 closest distance to " O   HOH Z 222 " =    1.247
peak=   -3.386 closest distance to " CB  ASN A  39 " =    2.211
peak=   -3.380 closest distance to " CG  LEU A  83 " =    1.964
peak=   -3.377 closest distance to " OD2 ASP A 171 " =    1.748
peak=   -3.368 closest distance to " O   HOH Z 377 " =    1.931
peak=   -3.364 closest distance to " C   LEU A 143 " =    1.313
peak=   -3.364 closest distance to " CG  ARG A 269 " =    2.277
peak=   -3.362 closest distance to " CZ  ARG A  66 " =    0.948
peak=   -3.361 closest distance to " O   HOH Z 380 " =    4.714
peak=   -3.360 closest distance to " O   HOH Z 388 " =    2.085
peak=   -3.351 closest distance to " N   LEU A 281 " =    1.877
peak=   -3.350 closest distance to " CA  GLY A 241 " =    2.251
peak=   -3.347 closest distance to " CE  MET A 105 " =    2.064
peak=   -3.345 closest distance to " NH2AARG A 275 " =    5.243
peak=   -3.342 closest distance to " OH  TYR A 169 " =    0.987
peak=   -3.340 closest distance to " O   HOH Z 283 " =    1.656
peak=   -3.333 closest distance to " CD1 LEU A  25 " =    2.473
peak=   -3.330 closest distance to " SG  CYS A 254 " =    3.137
peak=   -3.315 closest distance to " NH2 ARG A  79 " =    1.900
peak=   -3.306 closest distance to " O   HOH Z 360 " =    2.458
peak=   -3.305 closest distance to " O   HOH Z  38 " =    1.269
peak=   -3.304 closest distance to " O   GLY A 118 " =    2.150
peak=   -3.301 closest distance to " O   HOH Z 265 " =    1.920
peak=   -3.296 closest distance to " OD2 ASP A 171 " =    2.348
peak=   -3.295 closest distance to " O   THR A  18 " =    1.718
peak=   -3.294 closest distance to " O   HOH Z 148 " =    3.631
peak=   -3.293 closest distance to " CD1 PHE A 130 " =    2.257
peak=   -3.286 closest distance to " O   HOH Z 396 " =    1.784
peak=   -3.276 closest distance to " O   HOH Z  58 " =    1.082
peak=   -3.271 closest distance to " O   HOH Z 392 " =    1.477
peak=   -3.266 closest distance to " N   ALA A 226 " =    2.078
peak=   -3.262 closest distance to " O   HOH Z 351 " =    1.299
peak=   -3.260 closest distance to " O   SER A 210 " =    1.817
peak=   -3.258 closest distance to " OG  SER A 245 " =    1.000
peak=   -3.258 closest distance to " CB  PRO A 243 " =    2.565
peak=   -3.255 closest distance to " O   HOH Z  20 " =    1.372
peak=   -3.254 closest distance to " O   HOH Z 417 " =    2.708
peak=   -3.252 closest distance to " O   HOH Z 414 " =    1.348
peak=   -3.251 closest distance to " O   HOH Z 166 " =    1.996
peak=   -3.246 closest distance to " NH2 ARG A 159 " =    2.291
peak=   -3.241 closest distance to " O   HOH Z 385 " =    3.697
peak=   -3.240 closest distance to " O   ALA A   1 " =    2.018
peak=   -3.237 closest distance to " O   ALA A 161 " =    1.648
peak=   -3.234 closest distance to " NH1 ARG A 195 " =    2.593
peak=   -3.230 closest distance to " CA  GLY A  98 " =    2.206
peak=   -3.208 closest distance to " O   LEU A 167 " =    1.652
peak=   -3.205 closest distance to " O   HOH Z 423 " =    1.168
peak=   -3.202 closest distance to " CD2 LEU A 237 " =    2.672
peak=   -3.199 closest distance to " O   HOH Z  62 " =    1.013
peak=   -3.198 closest distance to " O   ALA A  10 " =    1.666
peak=   -3.195 closest distance to " CD2 LEU A 167 " =    1.670
peak=   -3.195 closest distance to " CE1 TYR A 169 " =    2.284
peak=   -3.191 closest distance to " CG  MET A 105 " =    0.882
peak=   -3.180 closest distance to " O   HOH Z 298 " =    2.796
peak=   -3.174 closest distance to " CD2 TYR A 293 " =    2.124
peak=   -3.173 closest distance to " N   MET A 188 " =    1.959
peak=   -3.170 closest distance to " O   HOH Z  39 " =    1.615
peak=   -3.167 closest distance to " O   HOH Z  25 " =    2.124
peak=   -3.167 closest distance to " NE2 GLN A 103 " =    1.638
peak=   -3.164 closest distance to " SG  CYS A 168 " =    1.115
peak=   -3.163 closest distance to " O   HOH Z  76 " =    2.069
peak=   -3.160 closest distance to " CG1 VAL A 153 " =    2.179
peak=   -3.159 closest distance to " CB  ASP A 162 " =    2.721
peak=   -3.158 closest distance to " O   ALA A  34 " =    2.574
peak=   -3.153 closest distance to " O   HOH Z  98 " =    1.758
peak=   -3.148 closest distance to " O   HOH Z  98 " =    1.816
peak=   -3.141 closest distance to " ND2 ASN A 249 " =    1.962
peak=   -3.134 closest distance to " O   HOH Z 427 " =    1.318
peak=   -3.134 closest distance to " O   VAL A 174 " =    1.992
peak=   -3.133 closest distance to " CD  LYS A 289 " =    2.532
peak=   -3.132 closest distance to " OD1 ASN A  39 " =    1.162
peak=   -3.132 closest distance to " O   HOH Z  97 " =    1.565
peak=   -3.129 closest distance to " O   PHE A 218 " =    1.451
peak=   -3.129 closest distance to " O   HOH Z 163 " =    4.897
peak=   -3.125 closest distance to " ND2 ASN A  39 " =    1.371
peak=   -3.122 closest distance to " O   HOH Z  68 " =    2.929
peak=   -3.121 closest distance to " CG1AVAL A  41 " =    2.490
peak=   -3.119 closest distance to " O   HOH Z 424 " =    2.899
peak=   -3.116 closest distance to " O   HOH Z 100 " =    0.886
peak=   -3.113 closest distance to " CG  LYS A 119 " =    2.982
peak=   -3.098 closest distance to " O   HOH Z 172 " =    5.060
peak=   -3.095 closest distance to " CG  ASP A 132 " =    2.246
peak=   -3.095 closest distance to " O   GLY A 262 " =    2.052
peak=   -3.090 closest distance to " O   HOH Z  90 " =    2.054
peak=   -3.076 closest distance to " CA  ALA A  34 " =    2.422
peak=   -3.073 closest distance to " O   ARG A 275 " =    2.201
peak=   -3.050 closest distance to " CD  GLN A 223 " =    0.821
peak=   -3.033 closest distance to " O   HOH Z 422 " =    1.408
peak=   -3.032 closest distance to " OG1 THR A  82 " =    2.164
peak=   -3.030 closest distance to " CB  PHE A 192 " =    1.963
peak=   -3.026 closest distance to " O   HOH Z 111 " =    3.335

================= 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    :  0.4621 0.4536   6.275892e+00   6.265611e+00
   1_bss:  0.4520 0.4423   6.269000e+00   6.251125e+00
   1_xyz:  0.3460 0.3794   6.072059e+00   6.138495e+00
   1_adp:  0.3143 0.3893   6.026210e+00   6.156313e+00
   1_occ:  0.3138 0.3897   6.025439e+00   6.156193e+00
   2_bss:  0.3105 0.3858   6.022206e+00   6.154125e+00
   2_xyz:  0.2371 0.2964   5.792015e+00   5.970276e+00
   2_adp:  0.2162 0.2769   5.721566e+00   5.911575e+00
   2_occ:  0.2160 0.2769   5.720849e+00   5.910949e+00
   3_bss:  0.2157 0.2762   5.718197e+00   5.908691e+00
   3_xyz:  0.1594 0.2059   5.442719e+00   5.655711e+00
   3_adp:  0.1446 0.1873   5.348513e+00   5.552720e+00
   3_occ:  0.1444 0.1872   5.348059e+00   5.552409e+00
   4_bss:  0.1441 0.1871   5.350728e+00   5.554426e+00
   4_xyz:  0.1250 0.1686   5.233035e+00   5.454101e+00
   4_adp:  0.1208 0.1672   5.213940e+00   5.442614e+00
   4_occ:  0.1207 0.1672   5.213792e+00   5.442897e+00
   5_bss:  0.1210 0.1671   5.215423e+00   5.443696e+00
   5_xyz:  0.1208 0.1657   5.212224e+00   5.433220e+00
   5_adp:  0.1207 0.1659   5.211498e+00   5.432504e+00
   5_occ:  0.1206 0.1658   5.211233e+00   5.432563e+00
   5_bss:  0.1206 0.1658   5.211277e+00   5.432609e+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:  0.297  20.000  -2.847   3.446   1.866   0.000   0.000   0.000
   1_xyz:  0.297  20.000  -2.847   3.446   1.866   0.000   0.000   0.000
   1_adp:  0.297  20.000  -2.847   3.446   1.866   0.000   0.000   0.000
   1_occ:  0.297  20.000  -2.847   3.446   1.866   0.000   0.000   0.000
   2_bss:  0.325  53.163  -1.807   1.259  -0.098   0.000  -0.000  -0.000
   2_xyz:  0.325  53.163  -1.807   1.259  -0.098   0.000  -0.000  -0.000
   2_adp:  0.325  53.163  -1.807   1.259  -0.098   0.000  -0.000  -0.000
   2_occ:  0.325  53.163  -1.807   1.259  -0.098   0.000  -0.000  -0.000
   3_bss:  0.324  55.904  -1.814   0.036  -0.998   0.000  -0.000  -0.000
   3_xyz:  0.324  55.904  -1.814   0.036  -0.998   0.000  -0.000  -0.000
   3_adp:  0.324  55.904  -1.814   0.036  -0.998   0.000  -0.000  -0.000
   3_occ:  0.324  55.904  -1.814   0.036  -0.998   0.000  -0.000  -0.000
   4_bss:  0.328  55.904  -2.445  -1.256  -1.839  -0.000  -0.000  -0.000
   4_xyz:  0.328  55.904  -2.445  -1.256  -1.839  -0.000  -0.000  -0.000
   4_adp:  0.328  55.904  -2.445  -1.256  -1.839  -0.000  -0.000  -0.000
   4_occ:  0.328  55.904  -2.445  -1.256  -1.839  -0.000  -0.000  -0.000
   5_bss:  0.328  55.904  -2.516  -1.582  -2.014  -0.000  -0.000  -0.000
   5_xyz:  0.328  55.904  -2.516  -1.582  -2.014  -0.000  -0.000  -0.000
   5_adp:  0.328  55.904  -2.516  -1.582  -2.014  -0.000  -0.000  -0.000
   5_occ:  0.328  55.904  -2.516  -1.582  -2.014  -0.000  -0.000  -0.000
   5_bss:  0.328  55.820  -2.384  -1.495  -1.881  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.346 0.4269  0.5748    68013.151
   1_bss:  55.794 0.4451  0.6153    63933.888
   1_xyz:  42.097 0.6169  0.8383    40782.607
   1_adp:  43.478 0.5994  0.8248    43062.354
   1_occ:  43.474 0.5994  0.8240    43037.029
   2_bss:  43.050 0.6045  0.8062    42510.559
   2_xyz:  31.544 0.7389  0.9440    24093.578
   2_adp:  28.739 0.7709  0.9572    20773.224
   2_occ:  28.727 0.7710  0.9570    20739.218
   3_bss:  28.552 0.7728  0.9352    20504.334
   3_xyz:  20.494 0.8555  0.9950    11124.599
   3_adp:  17.839 0.8816  1.0039     9132.150
   3_occ:  17.837 0.8816  1.0039     9136.704
   4_bss:  17.866 0.8814  0.9719     9216.180
   4_xyz:  15.629 0.9012  0.9806     7365.235
   4_adp:  15.331 0.9040  0.9774     7236.245
   4_occ:  15.331 0.9040  0.9773     7247.143
   5_bss:  15.357 0.9039  0.9710     7284.147
   5_xyz:  15.112 0.9060  0.9704     7094.068
   5_adp:  15.066 0.9066  0.9659     7106.831
   5_occ:  15.062 0.9066  0.9658     7112.030
   5_bss:  15.063 0.9066  0.9670     7112.560
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.9599e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.9599e-01
   1_xyz:   1.657  0.013  0.100 16.498  0.006  4.108   1.5851e-01
   1_adp:   1.657  0.013  0.100 16.498  0.006  4.108   1.5851e-01
   1_occ:   1.657  0.013  0.100 16.498  0.006  4.108   1.5851e-01
   2_bss:   1.657  0.013  0.100 16.498  0.006  4.108   1.5851e-01
   2_xyz:   1.331  0.009  0.083 14.804  0.006  4.109   8.7696e-02
   2_adp:   1.331  0.009  0.083 14.804  0.006  4.109   8.7696e-02
   2_occ:   1.331  0.009  0.083 14.804  0.006  4.109   8.7696e-02
   3_bss:   1.331  0.009  0.083 14.804  0.006  4.109   8.7696e-02
   3_xyz:   1.141  0.009  0.075 14.868  0.004  4.121   7.5046e-02
   3_adp:   1.141  0.009  0.075 14.868  0.004  4.121   7.5046e-02
   3_occ:   1.141  0.009  0.075 14.868  0.004  4.121   7.5046e-02
   4_bss:   1.141  0.009  0.075 14.868  0.004  4.121   7.5046e-02
   4_xyz:   1.121  0.008  0.078 14.725  0.004  4.113   7.0073e-02
   4_adp:   1.121  0.008  0.078 14.725  0.004  4.113   7.0073e-02
   4_occ:   1.121  0.008  0.078 14.725  0.004  4.113   7.0073e-02
   5_bss:   1.121  0.008  0.078 14.725  0.004  4.113   7.0073e-02
   5_xyz:   0.923  0.006  0.066 14.329  0.003  4.114   5.1482e-02
   5_adp:   0.923  0.006  0.066 14.329  0.003  4.114   5.1482e-02
   5_occ:   0.923  0.006  0.066 14.329  0.003  4.114   5.1482e-02
   5_bss:   0.923  0.006  0.066 14.329  0.003  4.114   5.1482e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.484   2.4248e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.484   2.4248e-01
   1_xyz:   9.960  0.104  0.457 89.713  0.033  1.891   1.7672e-01
   1_adp:   9.960  0.104  0.457 89.713  0.033  1.891   1.7672e-01
   1_occ:   9.960  0.104  0.457 89.713  0.033  1.891   1.7672e-01
   2_bss:   9.960  0.104  0.457 89.713  0.033  1.891   1.7672e-01
   2_xyz:   8.155  0.065  0.231 87.061  0.077  2.219   8.4261e-02
   2_adp:   8.155  0.065  0.231 87.061  0.077  2.219   8.4261e-02
   2_occ:   8.155  0.065  0.231 87.061  0.077  2.219   8.4261e-02
   3_bss:   8.155  0.065  0.231 87.061  0.077  2.219   8.4261e-02
   3_xyz:   7.973  0.060  0.257 81.599  0.027  2.141   6.6236e-02
   3_adp:   7.973  0.060  0.257 81.599  0.027  2.141   6.6236e-02
   3_occ:   7.973  0.060  0.257 81.599  0.027  2.141   6.6236e-02
   4_bss:   7.973  0.060  0.257 81.599  0.027  2.141   6.6236e-02
   4_xyz:   7.268  0.050  0.243 82.698  0.037  2.299   5.1572e-02
   4_adp:   7.268  0.050  0.243 82.698  0.037  2.299   5.1572e-02
   4_occ:   7.268  0.050  0.243 82.698  0.037  2.299   5.1572e-02
   5_bss:   7.268  0.050  0.243 82.698  0.037  2.299   5.1572e-02
   5_xyz:   6.869  0.041  0.208 81.323  0.032  2.407   3.5762e-02
   5_adp:   6.869  0.041  0.208 81.323  0.032  2.407   3.5762e-02
   5_occ:   6.869  0.041  0.208 81.323  0.032  2.407   3.5762e-02
   5_bss:   6.869  0.041  0.208 81.323  0.032  2.407   3.5762e-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:  99.58   0.00  19.02  98.47   0.00  15.27  99.58   0.00  39.44
   1_occ:  99.58   0.00  19.02  98.47   0.00  15.27  99.58   0.00  39.44
   2_bss:  99.58   0.00  19.02  98.47   0.00  15.27  99.58   0.00  39.44
   2_xyz:  99.58   0.00  19.02  98.47   0.00  15.27  99.58   0.00  39.44
   2_adp:  98.88   0.00  18.60  97.49   0.00  14.22  98.88   4.46  42.47
   2_occ:  98.88   0.00  18.60  97.49   0.00  14.22  98.88   4.46  42.47
   3_bss:  98.88   0.00  18.60  97.49   0.00  14.22  98.88   4.46  42.47
   3_xyz:  98.88   0.00  18.60  97.49   0.00  14.22  98.88   4.46  42.47
   3_adp:  94.21   1.51  17.63  88.85   1.51  13.20  94.21   5.85  41.74
   3_occ:  94.21   1.51  17.63  88.85   1.51  13.20  94.21   5.85  41.74
   4_bss:  94.21   1.51  17.63  88.85   1.51  13.20  94.21   5.85  41.74
   4_xyz:  94.21   1.51  17.63  88.85   1.51  13.20  94.21   5.85  41.74
   4_adp:  92.43   2.31  17.33  89.09   2.31  12.95  92.43   5.64  41.20
   4_occ:  92.43   2.31  17.33  89.09   2.31  12.95  92.43   5.64  41.20
   5_bss:  92.43   2.31  17.33  89.09   2.31  12.95  92.43   5.64  41.20
   5_xyz:  92.43   2.31  17.33  89.09   2.31  12.95  92.43   5.64  41.20
   5_adp:  90.07   2.31  16.94  87.75   2.31  12.77  90.07   5.51  39.67
   5_occ:  90.07   2.31  16.94  87.75   2.31  12.77  90.07   5.51  39.67
   5_bss:  89.99   2.22  16.86  87.67   2.22  12.68  89.99   5.42  39.58
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    2.360    0.035    0.457
   1_adp:    2.360    0.035    0.457
   1_occ:    2.360    0.035    0.457
   2_bss:    2.360    0.035    0.457
   2_xyz:    2.021    0.054    0.614
   2_adp:    2.021    0.054    0.614
   2_occ:    2.021    0.054    0.614
   3_bss:    2.021    0.054    0.614
   3_xyz:    1.885    0.059    0.758
   3_adp:    1.885    0.059    0.758
   3_occ:    1.885    0.059    0.758
   4_bss:    1.885    0.059    0.758
   4_xyz:    1.599    0.055    0.797
   4_adp:    1.599    0.055    0.797
   4_occ:    1.599    0.055    0.797
   5_bss:    1.599    0.055    0.797
   5_xyz:    1.587    0.080    0.808
   5_adp:    1.587    0.080    0.808
   5_occ:    1.587    0.080    0.808
   5_bss:    1.587    0.080    0.808
------------------------------------------------------------------------

CPU time actual refinement: 355.00


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_825/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_825/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_825/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_825/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_825/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 354.86 
  Macro-tasks:
    bulk solvent and scale       = 46.40  
    individual site refinement   = 143.06 
    weights calculation          = 29.59  
    collect and process          = 6.51   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 225.65 
  Micro-tasks:
    mask                            = 2.36   
    f_calc                          = 116.34 
    alpha_beta                      = 8.33   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 119.26 
    fmodel                         = 7.61   
    r_factors                      = 0.17   
    phase_errors                   = 11.22  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 266.74 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.073 micro seconds
Total CPU time: 6.14 minutes
from_scatterers_fft:    631 calls, 116.00 s
gradients_fft:          576 calls, 108.33 s

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

# Date 2008-01-16 Time 05:45:43 PST -0800 (1200491143.90 s)
Start R-work = 0.4621, R-free = 0.4536 (no bulk solvent and anisotropic scale)
Final R-work = 0.1435, R-free = 0.1868 (no bulk solvent and anisotropic scale)

Start R-work = 0.4520, R-free = 0.4423
Final R-work = 0.1206, R-free = 0.1658