# Date 2008-01-16 Time 05:25:01 PST -0800 (1200489901.79 s)
#phil __OFF__

Command line arguments: "../726.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 2344
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 726

-------------------------------------------------------------------------------
  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, 45.7567, 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: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 45.7567, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9429 1.95037
Completeness in resolution range: 0.957102
Completeness with d_max=infinity: 0.954258

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9429
                             d_min =   1.9504

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, 45.7567, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9429 1.95037
Completeness in resolution range: 0.957102
Completeness with d_max=infinity: 0.954258

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9433 -  4.1743 [2143/2169]  1933   210   9.8%
  bin  2:  4.1743 -  3.3253 [2074/2094]  1865   209  10.1%
  bin  3:  3.3253 -  2.9084 [2037/2056]  1830   207  10.2%
  bin  4:  2.9084 -  2.6441 [2001/2031]  1805   196   9.8%
  bin  5:  2.6441 -  2.4555 [2030/2049]  1830   200   9.9%
  bin  6:  2.4555 -  2.3113 [1996/2021]  1788   208  10.4%
  bin  7:  2.3113 -  2.1959 [1984/2012]  1784   200  10.1%
  bin  8:  2.1959 -  2.1006 [1980/2016]  1785   195   9.8%
  bin  9:  2.1006 -  2.0199 [1969/2011]  1774   195   9.9%
  bin 10:  2.0199 -  1.9504 [1375/2008]  1236   139  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_726/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:
        1.32 -     2.04: 19
        2.04 -     2.75: 439
        2.75 -     3.47: 4720
        3.47 -     4.18: 9575
        4.18 -     4.90: 14238
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.324 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.622 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.696 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.704 3.120 -x,y-1/2,-z+1/2
  ... (remaining 28986 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_726/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_726/model_refine_001.geo

CPU time processing inputs: 9.28


============================ 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 45.75675 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= 0.4917   r_free= 0.4961   ksol= 0.00   Bsol= 0.00   scale= 0.886    |
|                                                                             |
| 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:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.299807                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6562 0.99   1398  158 0.4086 0.4260      6.6147      6.6701|
|  2:  4.6562 -  3.7145 0.99   1338  144 0.4427 0.4448      6.8635      6.8027|
|  3:  3.7145 -  3.2504 0.99   1318  143 0.4760 0.4693      6.7302       6.817|
|  4:  3.2504 -  2.9558 0.99   1314  158 0.4839 0.4650      6.5696      6.5237|
|  5:  2.9558 -  2.7453 0.99   1296  139 0.5195 0.4857      6.3896      6.3715|
|  6:  2.7453 -  2.5843 0.99   1284  145 0.5285 0.5708      6.3002      6.2959|
|  7:  2.5843 -  2.4555 0.99   1315  135 0.5087 0.4981       6.254       6.205|
|  8:  2.4555 -  2.3490 0.98   1261  151 0.5247 0.5065      6.1828      6.1801|
|  9:  2.3490 -  2.2589 0.98   1276  146 0.5317 0.5702      6.1388      6.1844|
| 10:  2.2589 -  2.1812 1.00   1289  139 0.5177 0.5325       6.101      6.1077|
| 11:  2.1812 -  2.1132 0.98   1274  136 0.5251 0.5762      6.0496      6.0681|
| 12:  2.1132 -  2.0530 0.98   1251  139 0.5251 0.5511       5.973      6.0333|
| 13:  2.0530 -  1.9990 0.98   1259  141 0.5160 0.5036      5.8837      5.8226|
| 14:  1.9990 -  1.9504 0.58    757   85 0.5582 0.4557      5.8874      5.7667|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 -  4.6562  1398   158  0.64  39.56   0.81     0.71      91701.10|
|  2:  4.6562 -  3.7145  1338   144  0.64  40.44   0.88     0.77     136102.51|
|  3:  3.7145 -  3.2504  1318   143  0.53  49.49   0.91     0.73     140433.96|
|  4:  3.2504 -  2.9558  1314   158  0.42  57.77   0.92     0.62     124792.19|
|  5:  2.9558 -  2.7453  1296   139  0.32  65.50   0.87     0.47      94493.88|
|  6:  2.7453 -  2.5843  1284   145  0.26  70.18   0.87     0.39      86448.25|
|  7:  2.5843 -  2.4555  1315   135  0.26  70.78   0.92     0.35      73977.52|
|  8:  2.4555 -  2.3490  1261   151  0.26  70.72   0.91     0.39      67846.20|
|  9:  2.3490 -  2.2589  1276   146  0.28  69.44   0.90     0.40      58915.89|
| 10:  2.2589 -  2.1812  1289   139  0.25  71.24   0.94     0.38      56121.26|
| 11:  2.1812 -  2.1132  1274   136  0.19  75.75   0.96     0.30      54686.40|
| 12:  2.1132 -  2.0530  1251   139  0.21  74.12   0.98     0.35      48923.75|
| 13:  2.0530 -  1.9990  1259   141  0.31  67.22   0.95     0.49      37625.77|
| 14:  1.9990 -  1.9504   757    85  0.48  54.29   0.95     0.72      24949.24|
|alpha:            min =        0.30 max =            0.77 mean =         0.50|
|beta:             min =    24949.24 max =       140433.96 mean =     80562.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.36|
|phase err.(work): min =        0.00 max =           90.00 mean =        62.57|
|phase err.(test): min =        0.00 max =           89.97 mean =        62.87|
|-----------------------------------------------------------------------------|

============================== 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 = 26.882062             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.320   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.932398              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.853   (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 |  1.324 -  1.681:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.681 -  2.039:       16 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.039 -  2.397:       44 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.397 -  2.754:      395 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.754 -  3.112:     2324 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.112 -  3.470:     2396 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.470 -  3.827:     4454 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.827 -  4.185:     5121 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.185 -  4.542:     6406 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.542 -  4.900:     7832 |
|-----------------------------------------------------------------------------|
|-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 |        0.202 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.106    4.900  1.324 |       0.821 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.351)------------------------------------------|
|    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= 0.4917   r_free= 0.4961   ksol= 0.00   Bsol= 0.00   scale= 0.886    |
|                                                                             |
| 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:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.299807                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4824   r_free= 0.4854   ksol= 0.35   Bsol= 20.00   scale= 0.905   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.16,1.19,1.16,0.00,0.00,0.00); trace/3= -0.27                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.297634                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 21.353813             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.191   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.873057              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.643   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4824      final r-factor (work) = 0.3927          |
| start r-factor (free) = 0.4854      final r-factor (free) = 0.4313          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 67.3990 = 21.35 * 0.50 * 6.2936 + 1.00 * 0.2025                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 66.4735 = 21.35 * 0.50 * 6.2079 + 1.00 * 0.1919                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3927      final r-factor (work) = 0.3562          |
| start r-factor (free) = 0.4313      final r-factor (free) = 0.4471          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.6339 = 1.87 * 1.00 * 6.2079 + 1.00 * 0.0060                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.4931 = 1.87 * 1.00 * 6.1232 + 1.00 * 0.0240                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.351)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    116.87  19.13    None  None   None       |
|    all(noH): 2823   0      0.00    116.87  19.13    None  None   None       |
|    Sol.    : 438    0      0.00    116.87  33.87    None  None   None       |
|    Mac.    : 2385   0      0.00    89.47   16.42    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.687: 1042   |   5:    58.433 -  70.120:   45        |
|      1:    11.687 -  23.373:  894   |   6:    70.120 -  81.806:   15        |
|      2:    23.373 -  35.060:  493   |   7:    81.806 -  93.493:    2        |
|      3:    35.060 -  46.747:  229   |   8:    93.493 - 105.180:    1        |
|      4:    46.747 -  58.433:  101   |   9:   105.180 - 116.866:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3562 r_free = 0.4471             target_work(ml) = 6.133         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3556 r_free = 0.4465             target_work(ml) = 6.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3556   r_free= 0.4465   ksol= 0.35   Bsol= 20.00   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.16,1.19,1.16,0.00,0.00,0.00); trace/3= -0.27                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.133005                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3544   r_free= 0.4453   ksol= 0.36   Bsol= 56.93   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.75,0.37,0.55,0.00,0.00,0.00); trace/3= 0.06                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.133931                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.268513             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.127  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.702221              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.300  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3544      final r-factor (work) = 0.3123          |
| start r-factor (free) = 0.4453      final r-factor (free) = 0.3914          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.7040 = 11.27 * 0.50 * 6.1255 + 1.00 * 0.1912                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.4288 = 11.27 * 0.50 * 6.0933 + 1.00 * 0.0976                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3123      final r-factor (work) = 0.3005          |
| start r-factor (free) = 0.3914      final r-factor (free) = 0.3803          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3022 = 0.70 * 1.00 * 6.0933 + 1.00 * 0.0234                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2410 = 0.70 * 1.00 * 6.0185 + 1.00 * 0.0147                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.351)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.59  17.88    None  None   None       |
|    all(noH): 2823   0      0.00    115.59  17.88    None  None   None       |
|    Sol.    : 438    0      0.00    115.59  33.05    None  None   None       |
|    Mac.    : 2385   0      0.00    96.05   15.10    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.559: 1124   |   5:    57.795 -  69.354:   29        |
|      1:    11.559 -  23.118:  955   |   6:    69.354 -  80.913:    4        |
|      2:    23.118 -  34.677:  429   |   7:    80.913 -  92.472:    3        |
|      3:    34.677 -  46.236:  175   |   8:    92.472 - 104.031:    2        |
|      4:    46.236 -  57.795:  101   |   9:   104.031 - 115.590:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3005 r_free = 0.3803             target_work(ml) = 6.008         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3004 r_free = 0.3804             target_work(ml) = 6.008         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3004   r_free= 0.3804   ksol= 0.36   Bsol= 56.93   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.75,0.37,0.55,0.00,0.00,0.00); trace/3= 0.06                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.007686                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3008   r_free= 0.3798   ksol= 0.36   Bsol= 56.93   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.14,0.01,0.58,0.00,0.00,0.00); trace/3= 0.15                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.006687                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.065486              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.046   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.633459              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.254   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3008      final r-factor (work) = 0.2585          |
| start r-factor (free) = 0.3798      final r-factor (free) = 0.3403          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.3419 = 5.07 * 0.50 * 6.0189 + 1.00 * 0.0976                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.1478 = 5.07 * 0.50 * 5.9527 + 1.00 * 0.0712                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2585      final r-factor (work) = 0.2489          |
| start r-factor (free) = 0.3403      final r-factor (free) = 0.3364          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7874 = 0.63 * 1.00 * 5.9527 + 1.00 * 0.0166                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7577 = 0.63 * 1.00 * 5.8691 + 1.00 * 0.0398                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.351)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.27  17.70    None  None   None       |
|    all(noH): 2823   0      0.00    115.27  17.70    None  None   None       |
|    Sol.    : 438    0      0.81    115.27  34.73    None  None   None       |
|    Mac.    : 2385   0      0.00    96.38   14.57    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.527: 1159   |   5:    57.637 -  69.164:   29        |
|      1:    11.527 -  23.055:  921   |   6:    69.164 -  80.691:    4        |
|      2:    23.055 -  34.582:  410   |   7:    80.691 -  92.218:    4        |
|      3:    34.582 -  46.109:  188   |   8:    92.218 - 103.746:    2        |
|      4:    46.109 -  57.637:  105   |   9:   103.746 - 115.273:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2489 r_free = 0.3364             target_work(ml) = 5.861         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2488 r_free = 0.3363             target_work(ml) = 5.861         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2488   r_free= 0.3363   ksol= 0.36   Bsol= 56.93   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.14,0.01,0.58,0.00,0.00,0.00); trace/3= 0.15                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.861172                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2491   r_free= 0.3351   ksol= 0.34   Bsol= 43.91   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.47,-0.58,-0.00,-0.00,-0.00,-0.00); trace/3= -0.35                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.859661                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.140400              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.354  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.260920              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.950   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2491      final r-factor (work) = 0.2013          |
| start r-factor (free) = 0.3351      final r-factor (free) = 0.2685          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.0893 = 6.14 * 0.50 * 5.8687 + 1.00 * 0.0712                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.8172 = 6.14 * 0.50 * 5.7788 + 1.00 * 0.0751                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2013      final r-factor (work) = 0.1746          |
| start r-factor (free) = 0.2685      final r-factor (free) = 0.2400          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3047 = 1.26 * 1.00 * 5.7788 + 1.00 * 0.0181                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0794 = 1.26 * 1.00 * 5.6034 + 1.00 * 0.0139                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.351)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.69  17.86    None  None   None       |
|    all(noH): 2823   0      0.00    108.69  17.86    None  None   None       |
|    Sol.    : 438    0      2.97    108.69  44.39    None  None   None       |
|    Mac.    : 2385   0      0.00    104.46  12.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.869: 1310   |   5:    54.345 -  65.214:  100        |
|      1:    10.869 -  21.738:  842   |   6:    65.214 -  76.083:   56        |
|      2:    21.738 -  32.607:  232   |   7:    76.083 -  86.952:   14        |
|      3:    32.607 -  43.476:  146   |   8:    86.952 -  97.821:    2        |
|      4:    43.476 -  54.345:  118   |   9:    97.821 - 108.690:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1746 r_free = 0.2400             target_work(ml) = 5.547         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1744 r_free = 0.2394             target_work(ml) = 5.546         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1744   r_free= 0.2394   ksol= 0.34   Bsol= 43.91   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.47,-0.58,-0.00,-0.00,-0.00,-0.00); trace/3= -0.35                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.546080                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1745   r_free= 0.2388   ksol= 0.32   Bsol= 46.11   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.74,-1.30,-0.33,-0.00,-0.00,-0.00); trace/3= -0.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.543170                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.749272              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.137  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.287786              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.400  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1745      final r-factor (work) = 0.1510          |
| start r-factor (free) = 0.2388      final r-factor (free) = 0.2093          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7782 = 2.75 * 0.50 * 5.6037 + 1.00 * 0.0751                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5960 = 2.75 * 0.50 * 5.4878 + 1.00 * 0.0522                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1510      final r-factor (work) = 0.1437          |
| start r-factor (free) = 0.2093      final r-factor (free) = 0.1959          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5932 = 0.29 * 1.00 * 5.4878 + 1.00 * 0.0139                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5618 = 0.29 * 1.00 * 5.3933 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.351)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.54    99.64   16.81    None  None   None       |
|    all(noH): 2823   0      0.54    99.64   16.81    None  None   None       |
|    Sol.    : 438    0      5.01    96.92   42.48    None  None   None       |
|    Mac.    : 2385   0      0.54    99.64   12.09    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:     0.540 -  10.450: 1368   |   5:    50.091 -  60.001:   89        |
|      1:    10.450 -  20.360:  830   |   6:    60.001 -  69.912:   56        |
|      2:    20.360 -  30.271:  212   |   7:    69.912 -  79.822:   26        |
|      3:    30.271 -  40.181:  118   |   8:    79.822 -  89.732:    6        |
|      4:    40.181 -  50.091:  114   |   9:    89.732 -  99.642:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1437 r_free = 0.1959             target_work(ml) = 5.358         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1435 r_free = 0.1954             target_work(ml) = 5.357         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1435   r_free= 0.1954   ksol= 0.32   Bsol= 46.11   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.74,-1.30,-0.33,-0.00,-0.00,-0.00); trace/3= -0.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.357153                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6562 0.99   1398  158 0.1105 0.1426      5.4818      5.6637|
|  2:  4.6562 -  3.7145 0.99   1338  144 0.1043 0.1415      5.6277      5.8771|
|  3:  3.7145 -  3.2504 0.99   1318  143 0.1346 0.1774      5.6847      6.0072|
|  4:  3.2504 -  2.9558 0.99   1314  158 0.1574 0.2045      5.6937      5.8483|
|  5:  2.9558 -  2.7453 0.99   1296  139 0.1699 0.2249      5.5229      5.7542|
|  6:  2.7453 -  2.5843 0.99   1284  145 0.1609 0.2069      5.4268      5.5828|
|  7:  2.5843 -  2.4555 0.99   1315  135 0.1602 0.2030      5.3647      5.5367|
|  8:  2.4555 -  2.3490 0.98   1261  151 0.1636 0.2458      5.3195      5.6423|
|  9:  2.3490 -  2.2589 0.98   1276  146 0.1587 0.2151      5.2789      5.4453|
| 10:  2.2589 -  2.1812 1.00   1289  139 0.1501 0.2219      5.1903      5.4421|
| 11:  2.1812 -  2.1132 0.98   1274  136 0.1429 0.2335      5.1359      5.4979|
| 12:  2.1132 -  2.0530 0.98   1251  139 0.1404 0.1806      5.0612      5.2368|
| 13:  2.0530 -  1.9990 0.98   1259  141 0.1516 0.2392      5.0215      5.3267|
| 14:  1.9990 -  1.9504 0.58    757   85 0.1599 0.1910      4.9778      5.1234|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 -  4.6562  1398   158  0.92  11.22   0.98     0.96       9382.90|
|  2:  4.6562 -  3.7145  1338   144  0.93  10.72   1.04     1.02      13162.85|
|  3:  3.7145 -  3.2504  1318   143  0.91  15.09   1.06     1.05      16056.44|
|  4:  3.2504 -  2.9558  1314   158  0.88  18.29   1.04     1.01      16731.30|
|  5:  2.9558 -  2.7453  1296   139  0.87  19.73   1.01     0.98      11936.64|
|  6:  2.7453 -  2.5843  1284   145  0.87  19.86   1.01     0.98      10599.24|
|  7:  2.5843 -  2.4555  1315   135  0.86  20.31   1.02     0.98       9488.87|
|  8:  2.4555 -  2.3490  1261   151  0.85  21.19   1.01     0.97       8762.47|
|  9:  2.3490 -  2.2589  1276   146  0.86  20.77   1.02     0.97       8401.75|
| 10:  2.2589 -  2.1812  1289   139  0.86  20.40   1.03     0.98       6986.48|
| 11:  2.1812 -  2.1132  1274   136  0.86  20.38   1.03     0.98       6558.22|
| 12:  2.1132 -  2.0530  1251   139  0.87  19.42   1.03     1.00       5782.77|
| 13:  2.0530 -  1.9990  1259   141  0.86  21.17   1.02     1.00       5290.90|
| 14:  1.9990 -  1.9504   757    85  0.86  20.71   1.02     0.98       4537.71|
|alpha:            min =        0.96 max =            1.05 mean =         0.99|
|beta:             min =     4537.71 max =        16731.30 mean =      9750.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           90.00 mean =        18.37|
|phase err.(test): min =        0.00 max =           89.90 mean =        17.68|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1436   r_free= 0.1956   ksol= 0.32   Bsol= 41.16   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.96,-1.56,-0.55,-0.00,-0.00,-0.00); trace/3= -1.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.357937                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1436   r_free= 0.1956   ksol= 0.32   Bsol= 41.16   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.96,-1.56,-0.55,-0.00,-0.00,-0.00); trace/3= -1.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.357937                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6562 0.99   1398  158 0.1105 0.1427      5.4863      5.6682|
|  2:  4.6562 -  3.7145 0.99   1338  144 0.1045 0.1409      5.6301      5.8709|
|  3:  3.7145 -  3.2504 0.99   1318  143 0.1349 0.1761      5.6848      5.9981|
|  4:  3.2504 -  2.9558 0.99   1314  158 0.1572 0.2059      5.6933      5.8529|
|  5:  2.9558 -  2.7453 0.99   1296  139 0.1694 0.2262      5.5226      5.7548|
|  6:  2.7453 -  2.5843 0.99   1284  145 0.1606 0.2069      5.4273       5.584|
|  7:  2.5843 -  2.4555 0.99   1315  135 0.1604 0.2027       5.366      5.5368|
|  8:  2.4555 -  2.3490 0.98   1261  151 0.1632 0.2465      5.3192      5.6442|
|  9:  2.3490 -  2.2589 0.98   1276  146 0.1587 0.2152      5.2795      5.4449|
| 10:  2.2589 -  2.1812 1.00   1289  139 0.1501 0.2218       5.191      5.4422|
| 11:  2.1812 -  2.1132 0.98   1274  136 0.1429 0.2340      5.1366      5.4991|
| 12:  2.1132 -  2.0530 0.98   1251  139 0.1405 0.1808      5.0618      5.2376|
| 13:  2.0530 -  1.9990 0.98   1259  141 0.1517 0.2395      5.0215      5.3274|
| 14:  1.9990 -  1.9504 0.58    757   85 0.1599 0.1912      4.9778       5.124|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 -  4.6562  1398   158  0.92  11.47   0.98     0.95       9667.43|
|  2:  4.6562 -  3.7145  1338   144  0.93  10.76   1.04     1.01      13228.03|
|  3:  3.7145 -  3.2504  1318   143  0.91  15.04   1.05     1.05      15950.80|
|  4:  3.2504 -  2.9558  1314   158  0.88  18.25   1.03     1.01      16700.79|
|  5:  2.9558 -  2.7453  1296   139  0.87  19.80   1.01     0.97      12034.42|
|  6:  2.7453 -  2.5843  1284   145  0.87  19.88   1.00     0.97      10627.09|
|  7:  2.5843 -  2.4555  1315   135  0.86  20.31   1.01     0.97       9515.87|
|  8:  2.4555 -  2.3490  1261   151  0.85  21.21   1.00     0.96       8783.23|
|  9:  2.3490 -  2.2589  1276   146  0.86  20.80   1.00     0.96       8420.09|
| 10:  2.2589 -  2.1812  1289   139  0.86  20.45   1.01     0.96       7005.67|
| 11:  2.1812 -  2.1132  1274   136  0.86  20.39   1.01     0.97       6571.47|
| 12:  2.1132 -  2.0530  1251   139  0.87  19.44   1.01     0.98       5794.71|
| 13:  2.0530 -  1.9990  1259   141  0.86  21.18   1.00     0.99       5292.35|
| 14:  1.9990 -  1.9504   757    85  0.86  20.71   1.00     0.97       4536.33|
|alpha:            min =        0.95 max =            1.05 mean =         0.98|
|beta:             min =     4536.33 max =        16700.79 mean =      9784.78|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.91 mean =        18.40|
|phase err.(test): min =        0.00 max =           89.25 mean =        17.73|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.351)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.52    99.63   16.79    None  None   None       |
|    all(noH): 2823   0      0.52    99.63   16.79    None  None   None       |
|    Sol.    : 438    0      5.00    96.90   42.46    None  None   None       |
|    Mac.    : 2385   0      0.52    99.63   12.08    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:     0.522 -  10.433: 1368   |   5:    50.074 -  59.984:   89        |
|      1:    10.433 -  20.343:  830   |   6:    59.984 -  69.894:   56        |
|      2:    20.343 -  30.253:  212   |   7:    69.894 -  79.805:   26        |
|      3:    30.253 -  40.164:  118   |   8:    79.805 -  89.715:    6        |
|      4:    40.164 -  50.074:  114   |   9:    89.715 -  99.625:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 332         
Filter by distance & map next to the model:
   mapped sites are within: 0.512 - 5.682
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 329 from: 332
   mapped sites are within: 0.706 - 5.682

peak=    8.291 closest distance to " O   HOH Z  86 " =    1.015
peak=    8.002 closest distance to " O   HOH Z 138 " =    1.216
peak=    7.941 closest distance to " O   HOH Z 390 " =    1.404
peak=    7.034 closest distance to " O   SER A  62 " =    1.057
peak=    6.588 closest distance to " O   HOH Z 431 " =    2.083
peak=    6.550 closest distance to " O   HOH Z 381 " =    1.337
peak=    6.501 closest distance to " O   HOH Z  61 " =    1.674
peak=    6.500 closest distance to " O   HOH Z 205 " =    1.886
peak=    6.243 closest distance to " O   HOH Z 289 " =    1.814
peak=    6.112 closest distance to " O   HOH Z 130 " =    1.317
peak=    5.907 closest distance to " O   HOH Z 385 " =    1.802
peak=    5.721 closest distance to " O   HOH Z 399 " =    0.917
peak=    5.651 closest distance to " O   HOH Z 350 " =    1.332
peak=    5.628 closest distance to " O   HOH Z 222 " =    1.793
peak=    5.565 closest distance to " OD1 ASP A  50 " =    1.219
peak=    5.491 closest distance to " O   HOH Z  97 " =    1.746
peak=    5.481 closest distance to " O   HOH Z  65 " =    1.930
peak=    5.312 closest distance to " CG  PRO A  90 " =    1.204
peak=    5.261 closest distance to " NE2 GLN A  11 " =    1.504
peak=    5.250 closest distance to " O   HOH Z 278 " =    1.741
peak=    5.225 closest distance to " NH2 ARG A  56 " =    2.060
peak=    5.186 closest distance to " O   HOH Z   7 " =    2.005
peak=    5.154 closest distance to " O   HOH Z 103 " =    1.058
peak=    5.150 closest distance to " O   HOH Z  29 " =    1.400
peak=    5.142 closest distance to " O   HOH Z 214 " =    1.696
peak=    5.141 closest distance to " O   HOH Z  78 " =    1.832
peak=    5.069 closest distance to " O   HOH Z  72 " =    1.101
peak=    4.941 closest distance to " O   PRO A 198 " =    1.350
peak=    4.916 closest distance to " O   HOH Z 117 " =    1.511
peak=    4.877 closest distance to " O   HOH Z 144 " =    2.035
peak=    4.845 closest distance to " O   HOH Z 358 " =    1.427
peak=    4.816 closest distance to " O   HOH Z 427 " =    2.069
peak=    4.813 closest distance to " O   HOH Z 363 " =    1.261
peak=    4.763 closest distance to " O   HOH Z 258 " =    1.318
peak=    4.732 closest distance to " O   HOH Z 211 " =    1.680
peak=    4.702 closest distance to " N   SER A  63 " =    0.860
peak=    4.675 closest distance to " O   HOH Z 403 " =    1.838
peak=    4.661 closest distance to " O   HOH Z  59 " =    1.483
peak=    4.632 closest distance to " O   HOH Z 276 " =    1.758
peak=    4.593 closest distance to " O   HOH Z  54 " =    1.390
peak=    4.588 closest distance to " O   HOH Z 120 " =    1.024
peak=    4.575 closest distance to " O   HOH Z 126 " =    1.946
peak=    4.564 closest distance to " O   HOH Z 389 " =    1.646
peak=    4.491 closest distance to " O   HOH Z 264 " =    1.073
peak=    4.428 closest distance to " O   HOH Z 133 " =    1.590
peak=    4.424 closest distance to " CB  ASN A 148 " =    1.340
peak=    4.405 closest distance to " CG  PRO A 213 " =    1.280
peak=    4.384 closest distance to " N   GLU A   2 " =    1.369
peak=    4.380 closest distance to " O   HOH Z 316 " =    2.870
peak=    4.379 closest distance to " O   HOH Z 400 " =    0.895
peak=    4.367 closest distance to " O   HOH Z  28 " =    1.765
peak=    4.339 closest distance to " NE2 GLN A  11 " =    1.713
peak=    4.330 closest distance to " O   HOH Z 311 " =    1.544
peak=    4.317 closest distance to " O   HOH Z 112 " =    1.560
peak=    4.309 closest distance to " NZ BLYS A 290 " =    1.123
peak=    4.296 closest distance to " O   HOH Z 417 " =    1.744
peak=    4.289 closest distance to " CB  ALA A   1 " =    1.292
peak=    4.284 closest distance to " NZ  LYS A 117 " =    1.236
peak=    4.271 closest distance to " O   HOH Z 287 " =    1.827
peak=    4.269 closest distance to " O   HOH Z 109 " =    1.839
peak=    4.263 closest distance to " O   HOH Z 245 " =    1.375
peak=    4.252 closest distance to " O   HOH Z  49 " =    1.779
peak=    4.250 closest distance to " O   HOH Z  46 " =    1.316
peak=    4.240 closest distance to " O   HOH Z 302 " =    1.631
peak=    4.229 closest distance to " O   HOH Z 105 " =    1.323
peak=    4.225 closest distance to " N   GLN A 278 " =    1.111
peak=    4.215 closest distance to " O   HOH Z 416 " =    1.482
peak=    4.207 closest distance to " O   HOH Z 414 " =    1.434
peak=    4.164 closest distance to " NH2 ARG A 219 " =    1.786
peak=    4.144 closest distance to " OE1 GLN A  77 " =    1.223
peak=    4.125 closest distance to " O   HOH Z  63 " =    1.927
peak=    4.105 closest distance to " CB  GLU A 128 " =    0.959
peak=    4.105 closest distance to " CG  PRO A 198 " =    1.410
peak=    4.103 closest distance to " OG BSER A 258 " =    1.038
peak=    4.097 closest distance to " CG  PRO A  54 " =    1.305
peak=    4.074 closest distance to " O   HOH Z   5 " =    1.617
peak=    4.073 closest distance to " CE  MET A  93 " =    1.384
peak=    4.067 closest distance to " CB  SER A 216 " =    1.041
peak=    4.064 closest distance to " CA  LEU A 282 " =    1.079
peak=    4.063 closest distance to " O   HOH Z 269 " =    1.461
peak=    4.063 closest distance to " O   HOH Z 212 " =    1.934
peak=    4.029 closest distance to " O   HOH Z 282 " =    1.906
peak=    3.998 closest distance to " O   HOH Z 427 " =    1.311
peak=    3.992 closest distance to " O   HOH Z 332 " =    1.241
peak=    3.986 closest distance to " OD1 ASN A  45 " =    1.142
peak=    3.982 closest distance to " O   HOH Z 161 " =    1.038
peak=    3.978 closest distance to " CB  PRO A  54 " =    1.034
peak=    3.975 closest distance to " O   HOH Z 424 " =    1.152
peak=    3.974 closest distance to " O   HOH Z  92 " =    1.333
peak=    3.972 closest distance to " O   HOH Z  76 " =    1.166
peak=    3.972 closest distance to " O   ALA A 165 " =    1.198
peak=    3.969 closest distance to " O   HOH Z 124 " =    1.525
peak=    3.966 closest distance to " O   ASP A 286 " =    2.330
peak=    3.949 closest distance to " O   HOH Z 139 " =    1.741
peak=    3.941 closest distance to " O   HOH Z  69 " =    2.286
peak=    3.937 closest distance to " CG  PRO A 243 " =    1.145
peak=    3.937 closest distance to " O   HOH Z  53 " =    2.392
peak=    3.933 closest distance to " O   HOH Z 247 " =    1.231
peak=    3.932 closest distance to " CD  ARG A 138 " =    0.877
peak=    3.932 closest distance to " O   HOH Z  91 " =    2.124
peak=    3.917 closest distance to " O   HOH Z 405 " =    1.595
peak=    3.917 closest distance to " O   HOH Z 250 " =    2.068
peak=    3.909 closest distance to " O   HOH Z 415 " =    1.036
peak=    3.908 closest distance to " N   ALA A   1 " =    1.410
peak=    3.900 closest distance to " O   HOH Z 134 " =    1.714
peak=    3.890 closest distance to " O   HOH Z 272 " =    1.817
peak=    3.884 closest distance to " O   HOH Z   2 " =    2.025
peak=    3.876 closest distance to " O   HOH Z   6 " =    1.829
peak=    3.872 closest distance to " O   HOH Z  39 " =    1.253
peak=    3.856 closest distance to " CB  ARG A 275 " =    1.107
peak=    3.849 closest distance to " O   HOH Z 402 " =    1.554
peak=    3.820 closest distance to " O   HOH Z 186 " =    1.344
peak=    3.815 closest distance to " CB  ALA A 104 " =    1.136
peak=    3.804 closest distance to " O   HOH Z 344 " =    1.278
peak=    3.791 closest distance to " O   HOH Z 365 " =    2.490
peak=    3.790 closest distance to " O   HOH Z 244 " =    1.470
peak=    3.785 closest distance to " O   HOH Z 132 " =    1.160
peak=    3.781 closest distance to " O   HOH Z 393 " =    1.546
peak=    3.780 closest distance to " CA  GLU A 152 " =    1.112
peak=    3.775 closest distance to " N   GLN A  73 " =    1.343
peak=    3.766 closest distance to " O   HOH Z  88 " =    2.808
peak=    3.763 closest distance to " OG BSER A  12 " =    1.088
peak=    3.761 closest distance to " O   HOH Z 269 " =    3.114
peak=    3.738 closest distance to " CB  ASP A 124 " =    1.016
peak=    3.735 closest distance to " O   HOH Z 182 " =    1.293
peak=    3.713 closest distance to " OE1 GLN A  58 " =    5.436
peak=    3.703 closest distance to " O   HOH Z 286 " =    2.487
peak=    3.701 closest distance to " O   HOH Z 157 " =    2.948
peak=    3.699 closest distance to " O   HOH Z   9 " =    1.107
peak=    3.690 closest distance to " O   HOH Z 369 " =    2.003
peak=    3.690 closest distance to " CB  GLN A 183 " =    0.966
peak=    3.686 closest distance to " NE2 GLN A  55 " =    1.057
peak=    3.682 closest distance to " O   HOH Z 298 " =    2.003
peak=    3.681 closest distance to " O   HOH Z 426 " =    1.264
peak=    3.680 closest distance to " O   HOH Z 423 " =    2.001
peak=    3.678 closest distance to " O   HOH Z 293 " =    1.322
peak=    3.666 closest distance to " CZ3 TRP A 274 " =    2.091
peak=    3.659 closest distance to " O   ASN A 217 " =    1.027
peak=    3.654 closest distance to " NE AARG A 275 " =    1.372
peak=    3.653 closest distance to " OD1 ASN A 217 " =    1.722
peak=    3.645 closest distance to " CB  SER A   3 " =    1.362
peak=    3.644 closest distance to " O   HOH Z 313 " =    2.175
peak=    3.643 closest distance to " O   HOH Z  89 " =    1.481
peak=    3.638 closest distance to " O   HOH Z 128 " =    1.800
peak=    3.637 closest distance to " O   HOH Z 193 " =    1.787
peak=    3.637 closest distance to " CG  LEU A 167 " =    1.212
peak=    3.635 closest distance to " CB  PHE A  16 " =    1.066
peak=    3.633 closest distance to " CA  SER A  62 " =    1.151
peak=    3.630 closest distance to " O   HOH Z 371 " =    3.160
peak=    3.620 closest distance to " N   TYR A  15 " =    1.156
peak=    3.609 closest distance to " O   HOH Z 352 " =    1.606
peak=    3.603 closest distance to " NH2 ARG A 269 " =    0.801
peak=    3.599 closest distance to " O   HOH Z  67 " =    1.782
peak=    3.599 closest distance to " O   HOH Z 128 " =    2.179
peak=    3.583 closest distance to " O   HOH Z 364 " =    1.553
peak=    3.577 closest distance to " O   HOH Z 171 " =    2.540
peak=    3.577 closest distance to " OG ASER A 134 " =    1.369
peak=    3.576 closest distance to " CG2 THR A 251 " =    1.690
peak=    3.570 closest distance to " CA  ARG A  36 " =    1.287
peak=    3.570 closest distance to " CZ3 TRP A 123 " =    1.256
peak=    3.570 closest distance to " O   HOH Z 166 " =    1.781
peak=    3.565 closest distance to " O   HOH Z 223 " =    0.997
peak=    3.563 closest distance to " O   HOH Z 202 " =    1.738
peak=    3.558 closest distance to " CG1BVAL A 121 " =    1.852
peak=    3.553 closest distance to " CB  ASN A 148 " =    1.810
peak=    3.552 closest distance to " NE1 TRP A 274 " =    1.089
peak=    3.552 closest distance to " O   HOH Z 392 " =    1.328
peak=    3.550 closest distance to " CE AMET A  47 " =    1.172
peak=    3.549 closest distance to " O   HOH Z 217 " =    2.868
peak=    3.542 closest distance to " CB  TRP A 179 " =    1.412
peak=    3.542 closest distance to " CA  ASN A  74 " =    1.319
peak=    3.540 closest distance to " CB  ASP A 132 " =    3.787
peak=    3.531 closest distance to " O   HOH Z 259 " =    2.056
peak=    3.528 closest distance to " O   HOH Z 158 " =    1.384
peak=    3.526 closest distance to " O   HOH Z  88 " =    2.711
peak=    3.520 closest distance to " O   HOH Z 286 " =    2.270
peak=    3.507 closest distance to " OD2 ASP A 286 " =    2.429
peak=    3.503 closest distance to " OD1 ASP A 286 " =    1.063
peak=    3.498 closest distance to " O   HOH Z  32 " =    2.179
peak=    3.493 closest distance to " O   HOH Z 147 " =    1.497
peak=    3.483 closest distance to " N   ARG A 156 " =    1.240
peak=    3.483 closest distance to " O   HOH Z 116 " =    1.192
peak=    3.479 closest distance to " O   HOH Z  11 " =    1.381
peak=    3.477 closest distance to " CB  VAL A 202 " =    1.732
peak=    3.476 closest distance to " CD1 LEU A 228 " =    1.774
peak=    3.472 closest distance to " OG  SER A  62 " =    3.411
peak=    3.469 closest distance to " CD1 PHE A 283 " =    1.062
peak=    3.469 closest distance to " O   HOH Z 291 " =    1.588
peak=    3.467 closest distance to " CG  ASN A  60 " =    1.280
peak=    3.460 closest distance to " CA  TYR A  30 " =    1.066
peak=    3.460 closest distance to " CB  GLU A 277 " =    1.062
peak=    3.457 closest distance to " CB  SER A  63 " =    1.458
peak=    3.456 closest distance to " CG  GLN A 240 " =    3.377
peak=    3.449 closest distance to " O   HOH Z 422 " =    2.875
peak=    3.448 closest distance to " O   HOH Z  48 " =    1.641
peak=    3.448 closest distance to " CD2 TRP A 179 " =    2.158
peak=    3.446 closest distance to " OE1 GLN A 240 " =    1.868
peak=    3.438 closest distance to " O   HOH Z 132 " =    2.425
peak=    3.435 closest distance to " CA  SER A  63 " =    0.896
peak=    3.430 closest distance to " O   HOH Z 124 " =    4.305
peak=    3.429 closest distance to " CG  GLN A  77 " =    2.119
peak=    3.428 closest distance to " CD BLYS A 290 " =    1.155
peak=    3.421 closest distance to " O   HOH Z 104 " =    1.780
peak=    3.415 closest distance to " O   ALA A 242 " =    0.904
peak=    3.415 closest distance to " O   HOH Z  44 " =    1.407
peak=    3.413 closest distance to " O   HOH Z 271 " =    1.932
peak=    3.412 closest distance to " CB  ASN A  60 " =    0.831
peak=    3.409 closest distance to " CB  SER A 276 " =    1.137
peak=    3.402 closest distance to " O   HOH Z 250 " =    1.340
peak=    3.401 closest distance to " CA  ALA A  21 " =    1.180
peak=    3.399 closest distance to " O   HOH Z 126 " =    1.493
peak=    3.397 closest distance to " N   GLY A 287 " =    0.961
peak=    3.396 closest distance to " CB  LEU A 300 " =    1.035
peak=    3.393 closest distance to " N   ALA A 100 " =    0.807
peak=    3.393 closest distance to " CA  THR A 221 " =    0.889
peak=    3.392 closest distance to " O   HOH Z 110 " =    1.377
peak=    3.388 closest distance to " O   HOH Z 236 " =    1.485
peak=    3.388 closest distance to " O   HOH Z 277 " =    2.184
peak=    3.387 closest distance to " O   HOH Z 434 " =    1.607
peak=    3.386 closest distance to " O   HOH Z 371 " =    1.890
peak=    3.384 closest distance to " CA  ALA A 299 " =    1.002
peak=    3.383 closest distance to " CA  ASN A 284 " =    0.978
peak=    3.379 closest distance to " O   HOH Z 431 " =    1.348
peak=    3.377 closest distance to " CB  GLN A 223 " =    1.419
peak=    3.376 closest distance to " C   ASN A 285 " =    0.876
peak=    3.374 closest distance to " CG2 VAL A 257 " =    0.881
peak=    3.371 closest distance to " O   HOH Z 412 " =    1.824
peak=    3.370 closest distance to " N   SER A 210 " =    1.109
peak=    3.364 closest distance to " OD1 ASP A 238 " =    0.910
peak=    3.363 closest distance to " CA  GLY A 147 " =    0.937
peak=    3.361 closest distance to " CB  ARG A  79 " =    1.057
peak=    3.360 closest distance to " CD2 LEU A   5 " =    1.038
peak=    3.355 closest distance to " O   HOH Z 291 " =    1.576
peak=    3.354 closest distance to " CG2 THR A 279 " =    1.100
peak=    3.353 closest distance to " O   HOH Z 112 " =    2.261
peak=    3.353 closest distance to " O   HOH Z 134 " =    1.304
peak=    3.350 closest distance to " CG  GLN A  88 " =    1.068
peak=    3.338 closest distance to " CG AARG A 275 " =    1.217
peak=    3.335 closest distance to " CA  ALA A 160 " =    0.851
peak=    3.333 closest distance to " ND2 ASN A  69 " =    1.095
peak=    3.331 closest distance to " CB  ARG A 139 " =    0.986
peak=    3.329 closest distance to " O   HOH Z 365 " =    2.458
peak=    3.327 closest distance to " SD  MET A 188 " =    1.482
peak=    3.323 closest distance to " O   HOH Z 423 " =    1.662
peak=    3.315 closest distance to " CE  LYS A 166 " =    1.921
peak=    3.314 closest distance to " O   HOH Z 409 " =    1.722
peak=    3.306 closest distance to " CB  MET A 105 " =    1.091
peak=    3.303 closest distance to " O   HOH Z 347 " =    1.288
peak=    3.302 closest distance to " CB  ASP A 298 " =    1.127
peak=    3.300 closest distance to " O   HOH Z 108 " =    2.108
peak=    3.299 closest distance to " O   HOH Z 361 " =    3.671
peak=    3.299 closest distance to " O   HOH Z 116 " =    2.300
peak=    3.297 closest distance to " O   HOH Z 155 " =    2.389
peak=    3.294 closest distance to " N   GLY A  98 " =    1.156
peak=    3.293 closest distance to " NH2AARG A 190 " =    1.616
peak=    3.290 closest distance to " O   HOH Z 384 " =    1.466
peak=    3.289 closest distance to " CB  ASN A 215 " =    1.401
peak=    3.277 closest distance to " O   HOH Z 209 " =    1.243
peak=    3.276 closest distance to " NZ  LYS A 193 " =    2.107
peak=    3.276 closest distance to " O   HOH Z 233 " =    1.400
peak=    3.276 closest distance to " O   HOH Z 158 " =    2.431
peak=    3.273 closest distance to " CD  LYS A 166 " =    1.495
peak=    3.269 closest distance to " NH1AARG A 145 " =    0.919
peak=    3.267 closest distance to " CB  VAL A 121 " =    1.086
peak=    3.263 closest distance to " O   HOH Z  48 " =    1.665
peak=    3.262 closest distance to " O   HOH Z  15 " =    1.434
peak=    3.261 closest distance to " O   HOH Z 410 " =    1.700
peak=    3.257 closest distance to " O   HOH Z  95 " =    1.856
peak=    3.256 closest distance to " O   HOH Z 152 " =    2.230
peak=    3.248 closest distance to " CB  ASP A 140 " =    0.706
peak=    3.248 closest distance to " O   HOH Z 261 " =    2.219
peak=    3.244 closest distance to " O   HOH Z 436 " =    2.239
peak=    3.244 closest distance to " N   GLY A 241 " =    1.510
peak=    3.240 closest distance to " CA  PRO A 280 " =    1.343
peak=    3.239 closest distance to " O   HOH Z 406 " =    1.333
peak=    3.238 closest distance to " O   HOH Z 375 " =    1.139
peak=    3.236 closest distance to " CB  SER A 273 " =    0.850
peak=    3.236 closest distance to " CG  PHE A  59 " =    1.072
peak=    3.233 closest distance to " O   HOH Z  24 " =    1.769
peak=    3.227 closest distance to " CB  GLU A 152 " =    1.137
peak=    3.226 closest distance to " C   THR A  18 " =    1.241
peak=    3.223 closest distance to " O   HOH Z 145 " =    2.462
peak=    3.223 closest distance to " N   SER A  62 " =    2.319
peak=    3.222 closest distance to " CB  ALA A 244 " =    0.879
peak=    3.220 closest distance to " O   HOH Z 119 " =    1.451
peak=    3.218 closest distance to " OD1 ASN A  45 " =    1.381
peak=    3.218 closest distance to " CB  LYS A 290 " =    1.502
peak=    3.218 closest distance to " O   HOH Z  10 " =    1.774
peak=    3.213 closest distance to " O   HOH Z 145 " =    1.863
peak=    3.206 closest distance to " O   HOH Z 421 " =    1.986
peak=    3.205 closest distance to " O   HOH Z 368 " =    1.568
peak=    3.204 closest distance to " CB  SER A  12 " =    1.644
peak=    3.203 closest distance to " O   HOH Z 151 " =    1.862
peak=    3.199 closest distance to " O   HOH Z 135 " =    1.546
peak=    3.199 closest distance to " CB  ASP A 132 " =    3.784
peak=    3.196 closest distance to " CA  THR A 264 " =    0.727
peak=    3.194 closest distance to " O   HOH Z 114 " =    1.920
peak=    3.188 closest distance to " O   HOH Z 172 " =    2.023
peak=    3.188 closest distance to " CD  ARG A  66 " =    2.386
peak=    3.179 closest distance to " CE AMET A  47 " =    1.246
peak=    3.175 closest distance to " O   HOH Z 411 " =    2.987
peak=    3.170 closest distance to " O   HOH Z 326 " =    1.386
peak=    3.168 closest distance to " O   HOH Z 413 " =    1.668
peak=    3.166 closest distance to " O   HOH Z 288 " =    1.890
peak=    3.166 closest distance to " CD2 LEU A  25 " =    1.220
peak=    3.163 closest distance to " CA  ARG A 195 " =    1.384
peak=    3.156 closest distance to " CB  VAL A 230 " =    0.792
peak=    3.153 closest distance to " O   HOH Z 129 " =    0.971
peak=    3.150 closest distance to " O   HOH Z 116 " =    5.682
peak=    3.149 closest distance to " CB  TYR A 116 " =    1.211
peak=    3.146 closest distance to " O   HOH Z 425 " =    1.844
peak=    3.141 closest distance to " CG2 THR A 221 " =    1.297
peak=    3.126 closest distance to " CB  ASN A 215 " =    1.110
peak=    3.115 closest distance to " O   HOH Z  97 " =    2.036
peak=    3.100 closest distance to " O   GLU A   2 " =    0.859
peak=    3.096 closest distance to " CB  THR A 235 " =    1.194
peak=    3.095 closest distance to " CG2 THR A 220 " =    0.932
peak=    3.091 closest distance to " O   HOH Z 101 " =    0.852
peak=    3.084 closest distance to " CB  MET A  47 " =    0.970
peak=    3.078 closest distance to " O   HOH Z 213 " =    1.967
peak=    3.075 closest distance to " CA  ALA A  51 " =    1.121
peak=    3.065 closest distance to " CE3 TRP A 274 " =    1.396
peak=    3.062 closest distance to " O   HOH Z 227 " =    2.013
peak=    3.061 closest distance to " CG2 THR A 294 " =    1.110
peak=    3.054 closest distance to " OE2 GLU A 277 " =    1.710
peak=    3.047 closest distance to " CB  GLN A  11 " =    1.449
peak=    3.043 closest distance to " CA  ILE A 263 " =    1.167
peak=    3.028 closest distance to " CE  LYS A 289 " =    1.340
peak=    3.010 closest distance to " CB  ALA A 114 " =    0.799

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 207         
Filter by distance & map next to the model:
   mapped sites are within: 0.512 - 5.557
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 207
   mapped sites are within: 0.729 - 5.557

peak=   -5.693 closest distance to " O   SER A  62 " =    0.931
peak=   -4.716 closest distance to " O   HOH Z  60 " =    1.819
peak=   -4.644 closest distance to " CG  MET A 105 " =    0.939
peak=   -4.320 closest distance to " O   PRO A 198 " =    1.133
peak=   -4.294 closest distance to " O   HOH Z 388 " =    2.046
peak=   -4.226 closest distance to " O   HOH Z 381 " =    0.797
peak=   -4.204 closest distance to " O   HOH Z 290 " =    1.034
peak=   -4.203 closest distance to " OG  SER A  97 " =    2.232
peak=   -4.191 closest distance to " O   HOH Z 264 " =    0.850
peak=   -4.176 closest distance to " O   HOH Z  39 " =    1.265
peak=   -4.141 closest distance to " O   HOH Z 409 " =    3.082
peak=   -4.069 closest distance to " O   HOH Z  24 " =    1.187
peak=   -4.049 closest distance to " CB  CYS A 201 " =    2.290
peak=   -4.042 closest distance to " CD1 TRP A 179 " =    1.032
peak=   -4.030 closest distance to " CB  ALA A 248 " =    1.919
peak=   -4.026 closest distance to " CD  ARG A  14 " =    2.952
peak=   -4.018 closest distance to " CG  ASP A  50 " =    0.930
peak=   -4.001 closest distance to " CA  GLY A 133 " =    1.903
peak=   -4.000 closest distance to " CB  ASN A 285 " =    2.065
peak=   -3.974 closest distance to " O   TRP A  70 " =    1.332
peak=   -3.966 closest distance to " O   HOH Z 208 " =    0.895
peak=   -3.963 closest distance to " O   HOH Z 377 " =    1.575
peak=   -3.948 closest distance to " O   SER A 146 " =    1.482
peak=   -3.929 closest distance to " CG  GLN A  88 " =    0.815
peak=   -3.872 closest distance to " C   SER A  63 " =    1.095
peak=   -3.868 closest distance to " O   HOH Z 163 " =    1.456
peak=   -3.866 closest distance to " CD2 LEU A 237 " =    2.423
peak=   -3.839 closest distance to " O   HOH Z 234 " =    4.567
peak=   -3.817 closest distance to " O   HOH Z 347 " =    0.836
peak=   -3.808 closest distance to " CG  PRO A 243 " =    1.015
peak=   -3.787 closest distance to " N   GLN A  58 " =    1.154
peak=   -3.786 closest distance to " O   HOH Z  65 " =    0.807
peak=   -3.777 closest distance to " O   HOH Z 198 " =    2.332
peak=   -3.769 closest distance to " ND2 ASN A 209 " =    1.729
peak=   -3.750 closest distance to " O   HOH Z 139 " =    2.177
peak=   -3.736 closest distance to " O   HOH Z  77 " =    1.505
peak=   -3.719 closest distance to " O   HOH Z 150 " =    2.823
peak=   -3.718 closest distance to " O   ILE A  49 " =    1.396
peak=   -3.716 closest distance to " O   HOH Z 415 " =    1.108
peak=   -3.712 closest distance to " OG1 THR A 246 " =    1.764
peak=   -3.709 closest distance to " O   HOH Z 100 " =    1.613
peak=   -3.691 closest distance to " O   HOH Z 266 " =    4.291
peak=   -3.678 closest distance to " OG  SER A   3 " =    1.049
peak=   -3.669 closest distance to " O   ALA A  51 " =    1.180
peak=   -3.669 closest distance to " O   SER A 135 " =    1.595
peak=   -3.664 closest distance to " OG ASER A 134 " =    1.116
peak=   -3.657 closest distance to " O   GLY A  98 " =    2.207
peak=   -3.653 closest distance to " OD2 ASP A 140 " =    1.251
peak=   -3.624 closest distance to " CB  ASP A 162 " =    2.389
peak=   -3.619 closest distance to " O   ALA A   1 " =    1.023
peak=   -3.618 closest distance to " CA  ASP A  27 " =    2.360
peak=   -3.605 closest distance to " O   HOH Z 404 " =    1.320
peak=   -3.599 closest distance to " CB  TYR A  15 " =    2.032
peak=   -3.596 closest distance to " O   HOH Z  76 " =    1.005
peak=   -3.592 closest distance to " O   HOH Z 425 " =    0.762
peak=   -3.583 closest distance to " O   HOH Z 143 " =    1.142
peak=   -3.576 closest distance to " OH  TYR A 214 " =    1.124
peak=   -3.552 closest distance to " O   HOH Z  88 " =    2.027
peak=   -3.546 closest distance to " O   HOH Z 413 " =    4.192
peak=   -3.545 closest distance to " O   HOH Z 250 " =    1.309
peak=   -3.543 closest distance to " O   HOH Z  73 " =    1.578
peak=   -3.528 closest distance to " O   ASN A 215 " =    1.753
peak=   -3.525 closest distance to " O   HOH Z  72 " =    0.876
peak=   -3.524 closest distance to " CA  ASN A 127 " =    1.303
peak=   -3.524 closest distance to " CE3 TRP A 274 " =    2.595
peak=   -3.524 closest distance to " O   GLN A  73 " =    1.130
peak=   -3.512 closest distance to " O   HOH Z  98 " =    1.718
peak=   -3.509 closest distance to " CB  VAL A  72 " =    0.850
peak=   -3.505 closest distance to " O   ALA A 165 " =    1.220
peak=   -3.498 closest distance to " O   HOH Z  56 " =    0.729
peak=   -3.496 closest distance to " O   THR A 235 " =    1.130
peak=   -3.494 closest distance to " CG1BVAL A  72 " =    4.701
peak=   -3.486 closest distance to " O   SER A  22 " =    2.670
peak=   -3.482 closest distance to " O   HOH Z   1 " =    3.592
peak=   -3.462 closest distance to " O   HOH Z 102 " =    2.160
peak=   -3.457 closest distance to " CG BLYS A 290 " =    0.933
peak=   -3.457 closest distance to " O   ASN A 301 " =    1.654
peak=   -3.456 closest distance to " CA  SER A  63 " =    1.104
peak=   -3.449 closest distance to " N   HIS A 115 " =    1.913
peak=   -3.442 closest distance to " CD1 LEU A   5 " =    2.429
peak=   -3.437 closest distance to " O   HOH Z 372 " =    2.414
peak=   -3.429 closest distance to " O   LYS A 119 " =    0.844
peak=   -3.427 closest distance to " O   SER A  97 " =    1.277
peak=   -3.414 closest distance to " O   HOH Z 114 " =    4.315
peak=   -3.403 closest distance to " CD2 LEU A 297 " =    1.282
peak=   -3.396 closest distance to " CG  GLU A 277 " =    1.225
peak=   -3.394 closest distance to " CG  ASN A  60 " =    1.125
peak=   -3.390 closest distance to " NH2 ARG A  79 " =    1.733
peak=   -3.389 closest distance to " O   HOH Z  14 " =    1.251
peak=   -3.388 closest distance to " CD  LYS A 289 " =    2.427
peak=   -3.380 closest distance to " O   HOH Z 140 " =    4.310
peak=   -3.377 closest distance to " CZ3 TRP A 123 " =    1.707
peak=   -3.369 closest distance to " O   HOH Z 138 " =    1.106
peak=   -3.368 closest distance to " CE2 TYR A  30 " =    2.712
peak=   -3.367 closest distance to " O   ILE A 106 " =    2.052
peak=   -3.367 closest distance to " CB  PHE A 283 " =    2.325
peak=   -3.365 closest distance to " NH2AARG A 275 " =    5.557
peak=   -3.364 closest distance to " O   HOH Z 359 " =    1.559
peak=   -3.363 closest distance to " O   HOH Z 126 " =    1.660
peak=   -3.363 closest distance to " O   HOH Z  96 " =    1.371
peak=   -3.356 closest distance to " ND2 ASN A  45 " =    1.072
peak=   -3.351 closest distance to " C   VAL A 232 " =    1.192
peak=   -3.347 closest distance to " CG  ARG A  66 " =    1.174
peak=   -3.333 closest distance to " O   GLN A  77 " =    1.997
peak=   -3.332 closest distance to " CA  GLY A 211 " =    1.414
peak=   -3.332 closest distance to " O   VAL A 197 " =    0.972
peak=   -3.328 closest distance to " O   HOH Z 247 " =    1.012
peak=   -3.322 closest distance to " CB  PRO A 213 " =    1.613
peak=   -3.321 closest distance to " O   HOH Z  22 " =    1.327
peak=   -3.320 closest distance to " O   HOH Z 221 " =    0.936
peak=   -3.317 closest distance to " O   LEU A 297 " =    0.745
peak=   -3.316 closest distance to " OD1 ASP A 191 " =    2.002
peak=   -3.313 closest distance to " O   HOH Z 438 " =    1.024
peak=   -3.312 closest distance to " C   HIS A 108 " =    1.156
peak=   -3.310 closest distance to " OG  SER A 206 " =    1.584
peak=   -3.308 closest distance to " O   HOH Z  51 " =    0.737
peak=   -3.305 closest distance to " O   HOH Z 231 " =    0.782
peak=   -3.305 closest distance to " N   SER A  12 " =    1.088
peak=   -3.300 closest distance to " CD2 TYR A 293 " =    2.013
peak=   -3.295 closest distance to " O   HOH Z 135 " =    0.734
peak=   -3.294 closest distance to " N   ALA A   1 " =    1.183
peak=   -3.292 closest distance to " O   PRO A  54 " =    1.397
peak=   -3.292 closest distance to " O   HOH Z 385 " =    0.997
peak=   -3.292 closest distance to " O   HOH Z 298 " =    1.123
peak=   -3.290 closest distance to " C   PHE A  59 " =    1.253
peak=   -3.289 closest distance to " O   HOH Z 231 " =    1.809
peak=   -3.283 closest distance to " O   VAL A 197 " =    1.001
peak=   -3.281 closest distance to " O   HOH Z 389 " =    4.531
peak=   -3.279 closest distance to " O   PRO A 198 " =    1.064
peak=   -3.278 closest distance to " CB  ALA A 291 " =    2.149
peak=   -3.276 closest distance to " CD2 TRP A 179 " =    1.397
peak=   -3.273 closest distance to " OD1 ASP A  27 " =    1.994
peak=   -3.270 closest distance to " CZ  ARG A  36 " =    1.459
peak=   -3.268 closest distance to " OE1 GLU A 277 " =    2.409
peak=   -3.268 closest distance to " CD1 TYR A 214 " =    1.441
peak=   -3.266 closest distance to " O   HOH Z 323 " =    1.821
peak=   -3.264 closest distance to " O   HOH Z 322 " =    0.740
peak=   -3.259 closest distance to " ND2 ASN A 285 " =    1.828
peak=   -3.253 closest distance to " N   GLN A  58 " =    1.901
peak=   -3.253 closest distance to " O   HOH Z 374 " =    2.649
peak=   -3.249 closest distance to " N   GLY A 302 " =    1.521
peak=   -3.248 closest distance to " O   HOH Z  36 " =    2.624
peak=   -3.247 closest distance to " CD  LYS A 166 " =    2.535
peak=   -3.235 closest distance to " O   HOH Z  13 " =    1.276
peak=   -3.232 closest distance to " N   LEU A 282 " =    2.227
peak=   -3.230 closest distance to " NE2 GLN A  55 " =    0.735
peak=   -3.230 closest distance to " N   ALA A 248 " =    1.748
peak=   -3.230 closest distance to " O   HOH Z  97 " =    1.066
peak=   -3.227 closest distance to " N   LYS A 166 " =    1.783
peak=   -3.226 closest distance to " O   HOH Z 399 " =    0.844
peak=   -3.213 closest distance to " OG1 THR A 279 " =    1.239
peak=   -3.212 closest distance to " C   VAL A  72 " =    1.075
peak=   -3.208 closest distance to " CB  ALA A 227 " =    2.107
peak=   -3.205 closest distance to " N   ALA A 114 " =    2.271
peak=   -3.203 closest distance to " N   SER A 206 " =    2.025
peak=   -3.201 closest distance to " CA  LYS A 290 " =    1.409
peak=   -3.199 closest distance to " O   HOH Z  40 " =    3.845
peak=   -3.195 closest distance to " O   HOH Z 117 " =    0.745
peak=   -3.187 closest distance to " O   HOH Z 185 " =    2.122
peak=   -3.186 closest distance to " O   GLN A 194 " =    1.204
peak=   -3.183 closest distance to " CB  PHE A  59 " =    2.325
peak=   -3.180 closest distance to " NH1 ARG A  56 " =    2.346
peak=   -3.172 closest distance to " O   HOH Z 100 " =    1.222
peak=   -3.171 closest distance to " CB  ALA A  43 " =    1.979
peak=   -3.170 closest distance to " O   ALA A 158 " =    2.306
peak=   -3.168 closest distance to " OE2 GLU A 152 " =    2.202
peak=   -3.167 closest distance to " O   HOH Z 292 " =    3.536
peak=   -3.162 closest distance to " O   HOH Z 138 " =    0.777
peak=   -3.161 closest distance to " O   HOH Z 109 " =    3.904
peak=   -3.151 closest distance to " O   HOH Z 197 " =    3.588
peak=   -3.150 closest distance to " O   HOH Z 253 " =    1.562
peak=   -3.150 closest distance to " CG  ASP A 231 " =    0.819
peak=   -3.149 closest distance to " N   ASP A 171 " =    2.457
peak=   -3.146 closest distance to " O   GLY A 196 " =    1.014
peak=   -3.145 closest distance to " O   HOH Z 166 " =    1.079
peak=   -3.144 closest distance to " O   HOH Z 428 " =    1.944
peak=   -3.143 closest distance to " O   HOH Z 397 " =    1.450
peak=   -3.142 closest distance to " O   HOH Z 388 " =    2.063
peak=   -3.124 closest distance to " O   HOH Z 390 " =    2.376
peak=   -3.120 closest distance to " O   HOH Z  64 " =    1.220
peak=   -3.117 closest distance to " OG  SER A  63 " =    1.215
peak=   -3.117 closest distance to " O   HOH Z 426 " =    1.495
peak=   -3.110 closest distance to " O   HOH Z  68 " =    1.948
peak=   -3.101 closest distance to " O   HOH Z 143 " =    1.038
peak=   -3.100 closest distance to " O   HOH Z 364 " =    0.967
peak=   -3.100 closest distance to " OE1 GLN A  58 " =    2.532
peak=   -3.100 closest distance to " O   HOH Z 417 " =    2.350
peak=   -3.094 closest distance to " O   HOH Z 377 " =    0.742
peak=   -3.091 closest distance to " O   GLY A 229 " =    1.164
peak=   -3.086 closest distance to " CG1 VAL A 268 " =    2.309
peak=   -3.083 closest distance to " CG2AVAL A  41 " =    2.707
peak=   -3.081 closest distance to " O   ALA A  10 " =    1.525
peak=   -3.080 closest distance to " O   HOH Z 263 " =    2.818
peak=   -3.080 closest distance to " CG  ARG A 139 " =    1.154
peak=   -3.078 closest distance to " CB  TRP A  85 " =    2.098
peak=   -3.078 closest distance to " CA  GLY A 287 " =    0.824
peak=   -3.077 closest distance to " O   GLY A  80 " =    2.405
peak=   -3.041 closest distance to " CD  LYS A 289 " =    1.491
peak=   -3.037 closest distance to " O   ILE A 239 " =    1.247
peak=   -3.028 closest distance to " O   GLY A 136 " =    1.713
peak=   -3.026 closest distance to " O   HOH Z   2 " =    1.354
peak=   -3.022 closest distance to " NE  ARG A 156 " =    1.916

================= 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    :  0.4917 0.4961   6.299807e+00   6.296779e+00
   1_bss:  0.4824 0.4854   6.297634e+00   6.287793e+00
   1_xyz:  0.3927 0.4313   6.167487e+00   6.228408e+00
   1_adp:  0.3562 0.4471   6.133494e+00   6.238123e+00
   1_occ:  0.3556 0.4465   6.133005e+00   6.237608e+00
   2_bss:  0.3544 0.4453   6.133931e+00   6.237211e+00
   2_xyz:  0.3123 0.3914   6.028395e+00   6.169184e+00
   2_adp:  0.3005 0.3803   6.007978e+00   6.153595e+00
   2_occ:  0.3004 0.3804   6.007686e+00   6.153278e+00
   3_bss:  0.3008 0.3798   6.006687e+00   6.151920e+00
   3_xyz:  0.2585 0.3403   5.886011e+00   6.054929e+00
   3_adp:  0.2489 0.3364   5.861368e+00   6.042581e+00
   3_occ:  0.2488 0.3363   5.861172e+00   6.042539e+00
   4_bss:  0.2491 0.3351   5.859661e+00   6.040229e+00
   4_xyz:  0.2013 0.2685   5.664415e+00   5.869563e+00
   4_adp:  0.1746 0.2400   5.547247e+00   5.780851e+00
   4_occ:  0.1744 0.2394   5.546080e+00   5.779567e+00
   5_bss:  0.1745 0.2388   5.543170e+00   5.777204e+00
   5_xyz:  0.1510 0.2093   5.408671e+00   5.649437e+00
   5_adp:  0.1437 0.1959   5.358414e+00   5.588647e+00
   5_occ:  0.1435 0.1954   5.357153e+00   5.587888e+00
   5_bss:  0.1436 0.1956   5.357937e+00   5.587969e+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:  0.345  20.001  -3.160   1.186   1.158   0.000   0.000   0.000
   1_xyz:  0.345  20.001  -3.160   1.186   1.158   0.000   0.000   0.000
   1_adp:  0.345  20.001  -3.160   1.186   1.158   0.000   0.000   0.000
   1_occ:  0.345  20.001  -3.160   1.186   1.158   0.000   0.000   0.000
   2_bss:  0.361  56.934  -0.746   0.367   0.555   0.000   0.000   0.000
   2_xyz:  0.361  56.934  -0.746   0.367   0.555   0.000   0.000   0.000
   2_adp:  0.361  56.934  -0.746   0.367   0.555   0.000   0.000   0.000
   2_occ:  0.361  56.934  -0.746   0.367   0.555   0.000   0.000   0.000
   3_bss:  0.361  56.934  -0.143   0.011   0.584   0.000   0.000   0.000
   3_xyz:  0.361  56.934  -0.143   0.011   0.584   0.000   0.000   0.000
   3_adp:  0.361  56.934  -0.143   0.011   0.584   0.000   0.000   0.000
   3_occ:  0.361  56.934  -0.143   0.011   0.584   0.000   0.000   0.000
   4_bss:  0.337  43.905  -0.471  -0.579  -0.002  -0.000  -0.000  -0.000
   4_xyz:  0.337  43.905  -0.471  -0.579  -0.002  -0.000  -0.000  -0.000
   4_adp:  0.337  43.905  -0.471  -0.579  -0.002  -0.000  -0.000  -0.000
   4_occ:  0.337  43.905  -0.471  -0.579  -0.002  -0.000  -0.000  -0.000
   5_bss:  0.321  46.110  -0.744  -1.297  -0.328  -0.000  -0.000  -0.000
   5_xyz:  0.321  46.110  -0.744  -1.297  -0.328  -0.000  -0.000  -0.000
   5_adp:  0.321  46.110  -0.744  -1.297  -0.328  -0.000  -0.000  -0.000
   5_occ:  0.321  46.110  -0.744  -1.297  -0.328  -0.000  -0.000  -0.000
   5_bss:  0.316  41.160  -0.961  -1.556  -0.554  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  62.604 0.3601  0.5019    80564.254
   1_bss:  61.289 0.3759  0.5220    76684.104
   1_xyz:  50.234 0.5171  0.7038    56782.064
   1_adp:  52.318 0.4900  0.6659    59487.842
   1_occ:  52.313 0.4900  0.6655    59467.302
   2_bss:  52.217 0.4912  0.6784    59424.688
   2_xyz:  43.974 0.5938  0.8150    44933.917
   2_adp:  42.061 0.6176  0.8284    42562.027
   2_occ:  42.092 0.6171  0.8273    42498.058
   3_bss:  42.023 0.6177  0.8301    42222.562
   3_xyz:  35.422 0.6963  0.9185    31471.827
   3_adp:  34.439 0.7080  0.9217    30428.910
   3_occ:  34.446 0.7079  0.9209    30448.815
   4_bss:  34.347 0.7088  0.9048    30147.204
   4_xyz:  27.087 0.7890  0.9752    18997.890
   4_adp:  23.824 0.8235  0.9818    15206.532
   4_occ:  23.783 0.8239  0.9818    15133.273
   5_bss:  23.686 0.8247  0.9665    14990.087
   5_xyz:  20.107 0.8601  0.9872    11107.691
   5_adp:  18.336 0.8778  0.9895     9797.283
   5_occ:  18.300 0.8781  0.9894     9752.313
   5_bss:  18.334 0.8778  0.9802     9786.938
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.106   2.0246e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.106   2.0246e-01
   1_xyz:   1.903  0.014  0.130 17.414  0.007  4.108   1.9187e-01
   1_adp:   1.903  0.014  0.130 17.414  0.007  4.108   1.9187e-01
   1_occ:   1.903  0.014  0.130 17.414  0.007  4.108   1.9187e-01
   2_bss:   1.903  0.014  0.130 17.414  0.007  4.108   1.9187e-01
   2_xyz:   1.251  0.009  0.084 15.503  0.005  4.103   9.7646e-02
   2_adp:   1.251  0.009  0.084 15.503  0.005  4.103   9.7646e-02
   2_occ:   1.251  0.009  0.084 15.503  0.005  4.103   9.7646e-02
   3_bss:   1.251  0.009  0.084 15.503  0.005  4.103   9.7646e-02
   3_xyz:   1.103  0.008  0.070 14.732  0.004  4.109   7.1160e-02
   3_adp:   1.103  0.008  0.070 14.732  0.004  4.109   7.1160e-02
   3_occ:   1.103  0.008  0.070 14.732  0.004  4.109   7.1160e-02
   4_bss:   1.103  0.008  0.070 14.732  0.004  4.109   7.1160e-02
   4_xyz:   1.161  0.008  0.076 14.809  0.004  4.103   7.5144e-02
   4_adp:   1.161  0.008  0.076 14.809  0.004  4.103   7.5144e-02
   4_occ:   1.161  0.008  0.076 14.809  0.004  4.103   7.5144e-02
   5_bss:   1.161  0.008  0.076 14.809  0.004  4.103   7.5144e-02
   5_xyz:   0.914  0.005  0.062 14.338  0.003  4.107   5.2184e-02
   5_adp:   0.914  0.005  0.062 14.338  0.003  4.107   5.2184e-02
   5_occ:   0.914  0.005  0.062 14.338  0.003  4.107   5.2184e-02
   5_bss:   0.914  0.005  0.062 14.338  0.003  4.107   5.2184e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.324   2.3829e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.324   2.3829e-01
   1_xyz:  11.766  0.087  0.473 88.794  0.057  1.800   1.2525e-01
   1_adp:  11.766  0.087  0.473 88.794  0.057  1.800   1.2525e-01
   1_occ:  11.766  0.087  0.473 88.794  0.057  1.800   1.2525e-01
   2_bss:  11.766  0.087  0.473 88.794  0.057  1.800   1.2525e-01
   2_xyz:   8.796  0.070  0.272 82.576  0.056  2.155   1.7563e-01
   2_adp:   8.796  0.070  0.272 82.576  0.056  2.155   1.7563e-01
   2_occ:   8.796  0.070  0.272 82.576  0.056  2.155   1.7563e-01
   3_bss:   8.796  0.070  0.272 82.576  0.056  2.155   1.7563e-01
   3_xyz:   7.388  0.063  0.272 81.378  0.023  2.180   6.9778e-02
   3_adp:   7.388  0.063  0.272 81.378  0.023  2.180   6.9778e-02
   3_occ:   7.388  0.063  0.272 81.378  0.023  2.180   6.9778e-02
   4_bss:   7.388  0.063  0.272 81.378  0.023  2.180   6.9778e-02
   4_xyz:   7.370  0.055  0.259 78.480  0.028  2.104   6.5202e-02
   4_adp:   7.370  0.055  0.259 78.480  0.028  2.104   6.5202e-02
   4_occ:   7.370  0.055  0.259 78.480  0.028  2.104   6.5202e-02
   5_bss:   7.370  0.055  0.259 78.480  0.028  2.104   6.5202e-02
   5_xyz:   6.795  0.048  0.224 78.707  0.028  2.388   3.8759e-02
   5_adp:   6.795  0.048  0.224 78.707  0.028  2.388   3.8759e-02
   5_occ:   6.795  0.048  0.224 78.707  0.028  2.388   3.8759e-02
   5_bss:   6.795  0.048  0.224 78.707  0.028  2.388   3.8759e-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: 116.87   0.00  19.13  89.47   0.00  16.42 116.87   0.00  33.87
   1_occ: 116.87   0.00  19.13  89.47   0.00  16.42 116.87   0.00  33.87
   2_bss: 116.87   0.00  19.13  89.47   0.00  16.42 116.87   0.00  33.87
   2_xyz: 116.87   0.00  19.13  89.47   0.00  16.42 116.87   0.00  33.87
   2_adp: 115.59   0.00  17.88  96.05   0.00  15.10 115.59   0.00  33.05
   2_occ: 115.59   0.00  17.88  96.05   0.00  15.10 115.59   0.00  33.05
   3_bss: 115.59   0.00  17.88  96.05   0.00  15.10 115.59   0.00  33.05
   3_xyz: 115.59   0.00  17.88  96.05   0.00  15.10 115.59   0.00  33.05
   3_adp: 115.27   0.00  17.70  96.38   0.00  14.57 115.27   0.81  34.73
   3_occ: 115.27   0.00  17.70  96.38   0.00  14.57 115.27   0.81  34.73
   4_bss: 115.27   0.00  17.70  96.38   0.00  14.57 115.27   0.81  34.73
   4_xyz: 115.27   0.00  17.70  96.38   0.00  14.57 115.27   0.81  34.73
   4_adp: 108.69   0.00  17.86 104.46   0.00  12.98 108.69   2.97  44.39
   4_occ: 108.69   0.00  17.86 104.46   0.00  12.98 108.69   2.97  44.39
   5_bss: 108.69   0.00  17.86 104.46   0.00  12.98 108.69   2.97  44.39
   5_xyz: 108.69   0.00  17.86 104.46   0.00  12.98 108.69   2.97  44.39
   5_adp:  99.64   0.54  16.81  99.64   0.54  12.09  96.92   5.01  42.48
   5_occ:  99.64   0.54  16.81  99.64   0.54  12.09  96.92   5.01  42.48
   5_bss:  99.63   0.52  16.79  99.63   0.52  12.08  96.90   5.00  42.46
------------------------------------------------------------------------
 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:    2.067    0.038    0.450
   1_adp:    2.067    0.038    0.450
   1_occ:    2.067    0.038    0.450
   2_bss:    2.067    0.038    0.450
   2_xyz:    1.690    0.043    0.573
   2_adp:    1.690    0.043    0.573
   2_occ:    1.690    0.043    0.573
   3_bss:    1.690    0.043    0.573
   3_xyz:    1.675    0.072    0.693
   3_adp:    1.675    0.072    0.693
   3_occ:    1.675    0.072    0.693
   4_bss:    1.675    0.072    0.693
   4_xyz:    1.857    0.071    0.847
   4_adp:    1.857    0.071    0.847
   4_occ:    1.857    0.071    0.847
   5_bss:    1.857    0.071    0.847
   5_xyz:    1.873    0.079    0.891
   5_adp:    1.873    0.079    0.891
   5_occ:    1.873    0.079    0.891
   5_bss:    1.873    0.079    0.891
------------------------------------------------------------------------

CPU time actual refinement: 361.74


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_726/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_726/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_726/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_726/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_726/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 361.59 
  Macro-tasks:
    bulk solvent and scale       = 43.91  
    individual site refinement   = 148.72 
    weights calculation          = 30.68  
    collect and process          = 6.48   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 229.90 
  Micro-tasks:
    mask                            = 3.07   
    f_calc                          = 118.17 
    alpha_beta                      = 8.41   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 125.80 
    fmodel                         = 7.71   
    r_factors                      = 0.21   
    phase_errors                   = 10.06  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 274.84 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.138 micro seconds
Total CPU time: 6.26 minutes
from_scatterers_fft:    646 calls, 117.85 s
gradients_fft:          591 calls, 112.76 s

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

# Date 2008-01-16 Time 05:31:16 PST -0800 (1200490276.43 s)
Start R-work = 0.4917, R-free = 0.4961 (no bulk solvent and anisotropic scale)
Final R-work = 0.1603, R-free = 0.2116 (no bulk solvent and anisotropic scale)

Start R-work = 0.4824, R-free = 0.4854
Final R-work = 0.1436, R-free = 0.1956