# Date 2008-01-16 Time 04:15:13 PST -0800 (1200485713.26 s)
#phil __OFF__

Command line arguments: "../242.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 28072
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 242

-------------------------------------------------------------------------------
  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: (69.1963, 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: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 45.7567, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.728 1.95037
Completeness in resolution range: 0.976228
Completeness with d_max=infinity: 0.973221

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7280
                             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: (69.1963, 45.7567, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.728 1.95037
Completeness in resolution range: 0.976228
Completeness with d_max=infinity: 0.973221

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7284 -  4.1731 [2099/2124]  1889   210  10.0%
  bin  2:  4.1731 -  3.3248 [2032/2052]  1829   203  10.0%
  bin  3:  3.3248 -  2.9082 [1997/2016]  1795   202  10.1%
  bin  4:  2.9082 -  2.6440 [1974/2004]  1780   194   9.8%
  bin  5:  2.6440 -  2.4554 [1978/1997]  1781   197  10.0%
  bin  6:  2.4554 -  2.3112 [1956/1981]  1761   195  10.0%
  bin  7:  2.3112 -  2.1959 [1945/1973]  1745   200  10.3%
  bin  8:  2.1959 -  2.1006 [1950/1986]  1756   194   9.9%
  bin  9:  2.1006 -  2.0199 [1927/1969]  1740   187   9.7%
  bin 10:  2.0199 -  1.9504 [1731/1964]  1554   177  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_242/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: 0.14 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:
        0.99 -     1.78: 11
        1.78 -     2.56: 122
        2.56 -     3.34: 4135
        3.34 -     4.12: 9732
        4.12 -     4.90: 15339
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  0.994 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.171 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.202 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.480 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.526 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 29334 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_242/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_242/model_refine_001.geo

CPU time processing inputs: 9.15


============================ 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 = 69.19625 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 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5059   r_free= 0.5119   ksol= 0.00   Bsol= 0.00   scale= 0.885    |
|                                                                             |
| 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:   0.92 A                  |
| x-ray target function (ml) for work reflections: 6.305312                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7284 -  4.6543 0.99   1372  152 0.4232 0.4262      6.6375        6.65|
|  2:  4.6543 -  3.7138 0.99   1316  146 0.4629 0.4550      6.8733      6.8683|
|  3:  3.7138 -  3.2501 0.99   1286  144 0.4970 0.4830      6.7542      6.8104|
|  4:  3.2501 -  2.9555 0.99   1279  144 0.4957 0.4762      6.5794      6.5377|
|  5:  2.9555 -  2.7451 0.99   1281  141 0.5358 0.5141      6.4095      6.3953|
|  6:  2.7451 -  2.5842 0.99   1271  139 0.5412 0.5902      6.3193      6.2689|
|  7:  2.5842 -  2.4554 0.99   1269  140 0.5254 0.5207      6.2554      6.2423|
|  8:  2.4554 -  2.3490 0.98   1256  143 0.5375 0.5370      6.2167      6.1781|
|  9:  2.3490 -  2.2589 0.98   1246  136 0.5510 0.5789      6.1333      6.1825|
| 10:  2.2589 -  2.1812 1.00   1246  142 0.5205 0.5470      6.1283      6.1573|
| 11:  2.1812 -  2.1132 0.97   1257  137 0.5420 0.5607      6.0559      6.0647|
| 12:  2.1132 -  2.0529 0.98   1235  138 0.5231 0.5329      5.9938      6.0255|
| 13:  2.0529 -  1.9990 0.99   1245  142 0.5192 0.5497      5.9013      5.8836|
| 14:  1.9990 -  1.9504 0.84   1071  115 0.5415 0.4739       5.865      5.7618|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7284 -  4.6543  1372   152  0.62  41.32   0.81     0.68      97054.90|
|  2:  4.6543 -  3.7138  1316   146  0.61  42.91   0.88     0.73     146622.77|
|  3:  3.7138 -  3.2501  1286   144  0.49  52.84   0.91     0.69     154944.49|
|  4:  3.2501 -  2.9555  1279   144  0.37  61.78   0.91     0.54     135742.53|
|  5:  2.9555 -  2.7451  1281   141  0.25  71.14   0.87     0.37     104374.88|
|  6:  2.7451 -  2.5842  1271   139  0.16  78.14   0.88     0.22      90285.71|
|  7:  2.5842 -  2.4554  1269   140  0.11  81.49   0.89     0.16      81423.58|
|  8:  2.4554 -  2.3490  1256   143  0.13  80.24   0.94     0.20      73685.64|
|  9:  2.3490 -  2.2589  1246   136  0.17  77.47   0.89     0.25      65541.36|
| 10:  2.2589 -  2.1812  1246   142  0.22  73.23   0.95     0.33      57798.52|
| 11:  2.1812 -  2.1132  1257   137  0.22  73.89   0.97     0.35      53579.62|
| 12:  2.1132 -  2.0529  1235   138  0.26  70.64   0.99     0.42      47622.49|
| 13:  2.0529 -  1.9990  1245   142  0.32  66.19   0.95     0.51      38082.24|
| 14:  1.9990 -  1.9504  1071   115  0.44  56.69   0.98     0.64      25495.34|
|alpha:            min =        0.16 max =            0.73 mean =         0.44|
|beta:             min =    25495.34 max =       154944.49 mean =     84962.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.31|
|phase err.(work): min =        0.00 max =           90.00 mean =        66.13|
|phase err.(test): min =        0.00 max =           89.93 mean =        66.30|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.757898             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.300   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.362496              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.185   (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 |  0.994 -  1.385:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.385 -  1.775:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.775 -  2.166:       35 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.166 -  2.557:       87 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.557 -  2.947:     1695 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  2.947 -  3.338:     2440 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.338 -  3.728:     3924 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.728 -  4.119:     5808 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.119 -  4.509:     6741 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.509 -  4.900:     8598 |
|-----------------------------------------------------------------------------|
|-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 |        0.237 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.105    4.900  0.994 |       1.374 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.113)------------------------------------------|
|    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 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5059   r_free= 0.5119   ksol= 0.00   Bsol= 0.00   scale= 0.885    |
|                                                                             |
| 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:   0.92 A                  |
| x-ray target function (ml) for work reflections: 6.305312                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4979   r_free= 0.5002   ksol= 0.35   Bsol= 7.31   scale= 0.902    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.64,0.68,1.21,0.00,0.00,0.00); trace/3= -0.25                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.92 A                  |
| x-ray target function (ml) for work reflections: 6.302683                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.224647             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.294   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.223711              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.034   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4979      final r-factor (work) = 0.4544          |
| start r-factor (free) = 0.5002      final r-factor (free) = 0.4789          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.5944 = 11.22 * 0.50 * 6.2999 + 1.00 * 0.2372                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.2213 = 11.22 * 0.50 * 6.2581 + 1.00 * 0.0989                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4544      final r-factor (work) = 0.4176          |
| start r-factor (free) = 0.4789      final r-factor (free) = 0.4828          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.9223 = 2.22 * 1.00 * 6.2581 + 1.00 * 0.0061                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.8448 = 2.22 * 1.00 * 6.2134 + 1.00 * 0.0281                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.113)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.88   21.03    None  None   None       |
|    all(noH): 2823   0      0.00    98.88   21.03    None  None   None       |
|    Sol.    : 438    0      0.00    98.88   30.82    None  None   None       |
|    Mac.    : 2385   0      0.00    94.41   19.23    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.889:  736   |   5:    49.442 -  59.331:   97        |
|      1:     9.889 -  19.777:  818   |   6:    59.331 -  69.219:   41        |
|      2:    19.777 -  29.665:  590   |   7:    69.219 -  79.108:   17        |
|      3:    29.665 -  39.554:  320   |   8:    79.108 -  88.996:    8        |
|      4:    39.554 -  49.442:  191   |   9:    88.996 -  98.885:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4176 r_free = 0.4828             target_work(ml) = 6.218         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4174 r_free = 0.4833             target_work(ml) = 6.218         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4174   r_free= 0.4833   ksol= 0.35   Bsol= 7.31   scale= 0.975    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.64,0.68,1.21,0.00,0.00,0.00); trace/3= -0.25                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.218107                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4168   r_free= 0.4823   ksol= 0.35   Bsol= 27.16   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.59,1.37,1.82,0.00,0.00,0.00); trace/3= 0.87                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.219733                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 23.201806             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.280  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.057453              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.546  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4168      final r-factor (work) = 0.3691          |
| start r-factor (free) = 0.4823      final r-factor (free) = 0.4490          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 72.2276 = 23.20 * 0.50 * 6.2175 + 1.00 * 0.0991                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 71.8317 = 23.20 * 0.50 * 6.1797 + 1.00 * 0.1416                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3691      final r-factor (work) = 0.3567          |
| start r-factor (free) = 0.4490      final r-factor (free) = 0.4405          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5629 = 1.06 * 1.00 * 6.1797 + 1.00 * 0.0282                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5026 = 1.06 * 1.00 * 6.1334 + 1.00 * 0.0168                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.113)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.17  18.95    None  None   None       |
|    all(noH): 2823   0      0.00    109.17  18.95    None  None   None       |
|    Sol.    : 438    0      0.00    109.17  28.72    None  None   None       |
|    Mac.    : 2385   0      0.00    91.76   17.15    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 -  10.918:  864   |   5:    54.588 -  65.505:   39        |
|      1:    10.918 -  21.835: 1025   |   6:    65.505 -  76.422:   13        |
|      2:    21.835 -  32.753:  553   |   7:    76.422 -  87.340:    5        |
|      3:    32.753 -  43.670:  231   |   8:    87.340 -  98.257:    2        |
|      4:    43.670 -  54.588:   90   |   9:    98.257 - 109.175:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3567 r_free = 0.4405             target_work(ml) = 6.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3565 r_free = 0.4410             target_work(ml) = 6.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3565   r_free= 0.4410   ksol= 0.35   Bsol= 27.16   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.59,1.37,1.82,0.00,0.00,0.00); trace/3= 0.87                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.123675                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3574   r_free= 0.4385   ksol= 0.33   Bsol= 35.05   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.01,1.06,1.49,0.00,0.00,0.00); trace/3= 0.85                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.121988                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.202492             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.911   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.356060              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 155.420  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3574      final r-factor (work) = 0.3049          |
| start r-factor (free) = 0.4385      final r-factor (free) = 0.3880          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.7075 = 14.20 * 0.50 * 6.1350 + 1.00 * 0.1416                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.2565 = 14.20 * 0.50 * 6.0774 + 1.00 * 0.0992                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3049      final r-factor (work) = 0.2826          |
| start r-factor (free) = 0.3880      final r-factor (free) = 0.3750          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2581 = 1.36 * 1.00 * 6.0774 + 1.00 * 0.0168                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1329 = 1.36 * 1.00 * 5.9830 + 1.00 * 0.0195                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.113)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    122.22  18.51    None  None   None       |
|    all(noH): 2823   0      0.00    122.22  18.51    None  None   None       |
|    Sol.    : 438    0      0.00    122.22  34.41    None  None   None       |
|    Mac.    : 2385   0      0.00    106.21  15.58    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 -  12.222: 1166   |   5:    61.110 -  73.333:   40        |
|      1:    12.222 -  24.444:  904   |   6:    73.333 -  85.555:    5        |
|      2:    24.444 -  36.666:  407   |   7:    85.555 -  97.777:    2        |
|      3:    36.666 -  48.888:  199   |   8:    97.777 - 109.999:    3        |
|      4:    48.888 -  61.110:   96   |   9:   109.999 - 122.221:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2826 r_free = 0.3750             target_work(ml) = 5.964         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2825 r_free = 0.3755             target_work(ml) = 5.965         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2825   r_free= 0.3755   ksol= 0.33   Bsol= 35.05   scale= 1.052   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.01,1.06,1.49,0.00,0.00,0.00); trace/3= 0.85                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 5.964529                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2824   r_free= 0.3745   ksol= 0.32   Bsol= 35.05   scale= 1.042   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.00,0.40,0.95,0.00,0.00,0.00); trace/3= 0.45                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 5.960993                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.821463              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.641  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.551229              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.128  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2824      final r-factor (work) = 0.2437          |
| start r-factor (free) = 0.3745      final r-factor (free) = 0.3273          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.5112 = 5.82 * 0.50 * 5.9820 + 1.00 * 0.0992                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.2694 = 5.82 * 0.50 * 5.9061 + 1.00 * 0.0782                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2437      final r-factor (work) = 0.2262          |
| start r-factor (free) = 0.3273      final r-factor (free) = 0.3015          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2753 = 0.55 * 1.00 * 5.9061 + 1.00 * 0.0197                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2118 = 0.55 * 1.00 * 5.8037 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.113)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.85  17.43    None  None   None       |
|    all(noH): 2823   0      0.00    115.85  17.43    None  None   None       |
|    Sol.    : 438    0      1.75    115.85  38.86    None  None   None       |
|    Mac.    : 2385   0      0.00    110.73  13.50    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 -  11.585: 1338   |   5:    57.926 -  69.511:   54        |
|      1:    11.585 -  23.170:  835   |   6:    69.511 -  81.096:   11        |
|      2:    23.170 -  34.755:  265   |   7:    81.096 -  92.681:    3        |
|      3:    34.755 -  46.341:  191   |   8:    92.681 - 104.266:    0        |
|      4:    46.341 -  57.926:  122   |   9:   104.266 - 115.851:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2262 r_free = 0.3015             target_work(ml) = 5.765         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2258 r_free = 0.3007             target_work(ml) = 5.764         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2258   r_free= 0.3007   ksol= 0.32   Bsol= 35.05   scale= 1.051   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.00,0.40,0.95,0.00,0.00,0.00); trace/3= 0.45                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.763505                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2261   r_free= 0.2998   ksol= 0.32   Bsol= 35.05   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.63,-0.37,0.27,-0.00,0.00,0.00); trace/3= -0.24                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.762074                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.098929              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.312   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.243675              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.040  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2261      final r-factor (work) = 0.1868          |
| start r-factor (free) = 0.2998      final r-factor (free) = 0.2463          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0712 = 3.10 * 0.50 * 5.8041 + 1.00 * 0.0780                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8618 = 3.10 * 0.50 * 5.6808 + 1.00 * 0.0595                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1868      final r-factor (work) = 0.1750          |
| start r-factor (free) = 0.2463      final r-factor (free) = 0.2277          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3968 = 0.24 * 1.00 * 5.6808 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3783 = 0.24 * 1.00 * 5.5558 + 1.00 * 0.0245                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.113)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.39  16.78    None  None   None       |
|    all(noH): 2823   0      0.00    109.39  16.78    None  None   None       |
|    Sol.    : 438    0      3.78    109.39  40.38    None  None   None       |
|    Mac.    : 2385   0      0.00    103.69  12.45    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 -  10.939: 1427   |   5:    54.694 -  65.633:   65        |
|      1:    10.939 -  21.878:  781   |   6:    65.633 -  76.571:   27        |
|      2:    21.878 -  32.816:  222   |   7:    76.571 -  87.510:    3        |
|      3:    32.816 -  43.755:  163   |   8:    87.510 -  98.449:    1        |
|      4:    43.755 -  54.694:  131   |   9:    98.449 - 109.388:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1750 r_free = 0.2277             target_work(ml) = 5.523         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1747 r_free = 0.2270             target_work(ml) = 5.521         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1747   r_free= 0.2270   ksol= 0.32   Bsol= 35.05   scale= 1.041   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.63,-0.37,0.27,-0.00,0.00,0.00); trace/3= -0.24                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.521379                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7284 -  4.6543 0.99   1372  152 0.1207 0.1668      5.5739      5.7632|
|  2:  4.6543 -  3.7138 0.99   1316  146 0.1265 0.1722      5.8034      6.1096|
|  3:  3.7138 -  3.2501 0.99   1286  144 0.1647 0.2019      5.8856      6.1539|
|  4:  3.2501 -  2.9555 0.99   1279  144 0.1942 0.2462      5.8659      6.0182|
|  5:  2.9555 -  2.7451 0.99   1281  141 0.2088 0.2551      5.7268      5.8815|
|  6:  2.7451 -  2.5842 0.99   1271  139 0.1902 0.2575      5.5876      5.7339|
|  7:  2.5842 -  2.4554 0.99   1269  140 0.1970 0.2451      5.5383       5.717|
|  8:  2.4554 -  2.3490 0.98   1256  143 0.1929 0.2610      5.4863      5.7401|
|  9:  2.3490 -  2.2589 0.98   1246  136 0.1952 0.2518      5.4526      5.6277|
| 10:  2.2589 -  2.1812 1.00   1246  142 0.1849 0.2687      5.3862      5.6236|
| 11:  2.1812 -  2.1132 0.97   1257  137 0.1883 0.2546      5.3368      5.5881|
| 12:  2.1132 -  2.0529 0.98   1235  138 0.1805 0.2160      5.2475      5.4384|
| 13:  2.0529 -  1.9990 0.99   1245  142 0.1801 0.2558      5.1672      5.4349|
| 14:  1.9990 -  1.9504 0.84   1071  115 0.1902 0.2386       5.137      5.2753|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7284 -  4.6543  1372   152  0.91  12.77   0.98     0.97      11743.38|
|  2:  4.6543 -  3.7138  1316   146  0.91  13.38   1.06     1.05      18119.05|
|  3:  3.7138 -  3.2501  1286   144  0.87  19.05   1.07     1.05      24087.26|
|  4:  3.2501 -  2.9555  1279   144  0.84  22.08   1.06     1.01      23771.32|
|  5:  2.9555 -  2.7451  1281   141  0.83  23.70   1.03     0.94      17115.46|
|  6:  2.7451 -  2.5842  1271   139  0.83  23.49   1.03     0.99      14687.95|
|  7:  2.5842 -  2.4554  1269   140  0.82  24.55   1.04     1.01      13620.23|
|  8:  2.4554 -  2.3490  1256   143  0.82  24.86   1.04     0.99      12417.32|
|  9:  2.3490 -  2.2589  1246   136  0.82  24.66   1.05     1.01      11917.19|
| 10:  2.2589 -  2.1812  1246   142  0.83  24.16   1.05     0.98      10116.45|
| 11:  2.1812 -  2.1132  1257   137  0.82  24.65   1.08     1.05       9361.43|
| 12:  2.1132 -  2.0529  1235   138  0.84  22.97   1.06     1.02       7885.40|
| 13:  2.0529 -  1.9990  1245   142  0.83  23.84   1.06     1.02       6847.49|
| 14:  1.9990 -  1.9504  1071   115  0.83  23.71   1.05     0.97       5928.09|
|alpha:            min =        0.94 max =            1.05 mean =         1.00|
|beta:             min =     5928.09 max =        24087.26 mean =     13536.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.84|
|phase err.(work): min =        0.00 max =           89.90 mean =        21.88|
|phase err.(test): min =        0.00 max =           89.89 mean =        20.96|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1746   r_free= 0.2262   ksol= 0.32   Bsol= 35.06   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.32,-1.27,-0.32,-0.00,-0.00,-0.00); trace/3= -0.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.519212                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1746   r_free= 0.2262   ksol= 0.32   Bsol= 35.06   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.32,-1.27,-0.32,-0.00,-0.00,-0.00); trace/3= -0.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.519212                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7284 -  4.6543 0.99   1372  152 0.1218 0.1608       5.555      5.7166|
|  2:  4.6543 -  3.7138 0.99   1316  146 0.1285 0.1732      5.8031      6.1211|
|  3:  3.7138 -  3.2501 0.99   1286  144 0.1646 0.2000      5.8851      6.1479|
|  4:  3.2501 -  2.9555 0.99   1279  144 0.1937 0.2473      5.8644      6.0179|
|  5:  2.9555 -  2.7451 0.99   1281  141 0.2083 0.2546      5.7258      5.8817|
|  6:  2.7451 -  2.5842 0.99   1271  139 0.1903 0.2575      5.5866      5.7328|
|  7:  2.5842 -  2.4554 0.99   1269  140 0.1970 0.2448      5.5381      5.7157|
|  8:  2.4554 -  2.3490 0.98   1256  143 0.1926 0.2612      5.4864      5.7428|
|  9:  2.3490 -  2.2589 0.98   1246  136 0.1945 0.2514      5.4517      5.6263|
| 10:  2.2589 -  2.1812 1.00   1246  142 0.1849 0.2690      5.3859       5.624|
| 11:  2.1812 -  2.1132 0.97   1257  137 0.1881 0.2547      5.3351      5.5885|
| 12:  2.1132 -  2.0529 0.98   1235  138 0.1802 0.2146      5.2464      5.4366|
| 13:  2.0529 -  1.9990 0.99   1245  142 0.1798 0.2551      5.1665       5.433|
| 14:  1.9990 -  1.9504 0.84   1071  115 0.1898 0.2391      5.1364      5.2762|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7284 -  4.6543  1372   152  0.92  11.93   0.98     0.96      10443.45|
|  2:  4.6543 -  3.7138  1316   146  0.92  12.90   1.05     1.04      17120.19|
|  3:  3.7138 -  3.2501  1286   144  0.87  18.97   1.05     1.03      24063.80|
|  4:  3.2501 -  2.9555  1279   144  0.84  21.98   1.04     0.99      23549.65|
|  5:  2.9555 -  2.7451  1281   141  0.83  23.67   1.00     0.92      17104.39|
|  6:  2.7451 -  2.5842  1271   139  0.83  23.43   1.00     0.96      14649.63|
|  7:  2.5842 -  2.4554  1269   140  0.82  24.58   1.01     0.99      13641.22|
|  8:  2.4554 -  2.3490  1256   143  0.82  24.87   1.00     0.96      12438.94|
|  9:  2.3490 -  2.2589  1246   136  0.82  24.66   1.01     0.98      11927.38|
| 10:  2.2589 -  2.1812  1246   142  0.83  24.12   1.01     0.95      10088.68|
| 11:  2.1812 -  2.1132  1257   137  0.82  24.62   1.04     1.01       9327.17|
| 12:  2.1132 -  2.0529  1235   138  0.84  22.92   1.01     0.98       7860.81|
| 13:  2.0529 -  1.9990  1245   142  0.83  23.81   1.02     0.97       6835.53|
| 14:  1.9990 -  1.9504  1071   115  0.83  23.71   1.00     0.93       5931.08|
|alpha:            min =        0.92 max =            1.04 mean =         0.98|
|beta:             min =     5931.08 max =        24063.80 mean =     13336.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.84|
|phase err.(work): min =        0.00 max =           89.99 mean =        21.75|
|phase err.(test): min =        0.00 max =           89.84 mean =        20.83|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.113)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.39  16.78    None  None   None       |
|    all(noH): 2823   0      0.00    109.39  16.78    None  None   None       |
|    Sol.    : 438    0      3.78    109.39  40.38    None  None   None       |
|    Mac.    : 2385   0      0.00    103.69  12.45    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.942: 1427   |   5:    54.697 -  65.636:   65        |
|      1:    10.942 -  21.881:  781   |   6:    65.636 -  76.574:   27        |
|      2:    21.881 -  32.819:  222   |   7:    76.574 -  87.513:    3        |
|      3:    32.819 -  43.758:  163   |   8:    87.513 -  98.452:    1        |
|      4:    43.758 -  54.697:  131   |   9:    98.452 - 109.391:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 345         
Filter by distance & map next to the model:
   mapped sites are within: 0.595 - 5.809
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 342 from: 345
   mapped sites are within: 0.753 - 5.809

peak=    9.269 closest distance to " O   HOH Z 399 " =    1.269
peak=    8.604 closest distance to " C   SER A  62 " =    1.235
peak=    8.444 closest distance to " O   HOH Z  86 " =    1.124
peak=    6.964 closest distance to " C   ASN A 285 " =    1.032
peak=    6.660 closest distance to " OD1 ASN A  60 " =    1.426
peak=    6.428 closest distance to " O   HOH Z 390 " =    1.561
peak=    6.394 closest distance to " C   ASN A 284 " =    0.830
peak=    6.266 closest distance to " O   HOH Z 289 " =    1.962
peak=    6.186 closest distance to " O   ASN A 285 " =    1.668
peak=    6.082 closest distance to " N   ASN A 285 " =    1.030
peak=    6.039 closest distance to " O   HOH Z 332 " =    1.295
peak=    5.909 closest distance to " O   HOH Z  65 " =    2.202
peak=    5.786 closest distance to " O   HOH Z 103 " =    1.352
peak=    5.554 closest distance to " NH2 ARG A  56 " =    2.132
peak=    5.554 closest distance to " O   HOH Z 244 " =    1.768
peak=    5.505 closest distance to " O   HOH Z  91 " =    1.304
peak=    5.417 closest distance to " CG  ASN A 110 " =    1.199
peak=    5.371 closest distance to " O   HOH Z  61 " =    1.960
peak=    5.366 closest distance to " O   HOH Z 130 " =    1.692
peak=    5.314 closest distance to " N   PHE A  59 " =    0.921
peak=    5.303 closest distance to " O   HOH Z 138 " =    1.102
peak=    5.299 closest distance to " O   HOH Z  55 " =    1.905
peak=    5.273 closest distance to " OD2 ASP A  50 " =    1.176
peak=    5.135 closest distance to " O   HOH Z 430 " =    2.284
peak=    5.127 closest distance to " O   HOH Z 375 " =    1.661
peak=    5.079 closest distance to " O   HOH Z 205 " =    1.393
peak=    5.075 closest distance to " N   GLY A 287 " =    1.004
peak=    5.056 closest distance to " OD1 ASP A 286 " =    1.262
peak=    5.006 closest distance to " O   HOH Z 120 " =    1.243
peak=    5.000 closest distance to " N   ASP A 286 " =    0.982
peak=    4.993 closest distance to " O   HOH Z 363 " =    1.393
peak=    4.983 closest distance to " O   HOH Z 116 " =    1.567
peak=    4.928 closest distance to " O   HOH Z 385 " =    1.974
peak=    4.901 closest distance to " O   HOH Z 179 " =    1.150
peak=    4.881 closest distance to " CG  PRO A  90 " =    1.240
peak=    4.799 closest distance to " O   HOH Z 137 " =    1.129
peak=    4.749 closest distance to " O   HOH Z 402 " =    1.419
peak=    4.719 closest distance to " OD1 ASN A 285 " =    1.219
peak=    4.712 closest distance to " NH2 ARG A 269 " =    1.008
peak=    4.696 closest distance to " CB  ARG A 275 " =    1.314
peak=    4.691 closest distance to " CG2 THR A 246 " =    1.129
peak=    4.673 closest distance to " O   HOH Z 214 " =    1.688
peak=    4.665 closest distance to " O   HOH Z 291 " =    1.537
peak=    4.652 closest distance to " O   HOH Z 358 " =    1.616
peak=    4.621 closest distance to " O   HOH Z 117 " =    1.673
peak=    4.593 closest distance to " O   HOH Z 381 " =    1.194
peak=    4.591 closest distance to " O   HOH Z 426 " =    1.379
peak=    4.576 closest distance to " N   LYS A 119 " =    0.903
peak=    4.557 closest distance to " O   HOH Z 278 " =    1.938
peak=    4.536 closest distance to " CB  ASN A  60 " =    0.906
peak=    4.531 closest distance to " O   HOH Z 222 " =    1.947
peak=    4.518 closest distance to " O   HOH Z 194 " =    1.804
peak=    4.515 closest distance to " O   HOH Z 429 " =    1.350
peak=    4.506 closest distance to " NE2 GLN A  11 " =    1.593
peak=    4.489 closest distance to " OD2 ASP A 270 " =    1.205
peak=    4.468 closest distance to " O   HOH Z 199 " =    1.415
peak=    4.445 closest distance to " O   ALA A 165 " =    1.108
peak=    4.437 closest distance to " O   HOH Z 165 " =    1.062
peak=    4.431 closest distance to " O   ALA A 242 " =    1.020
peak=    4.416 closest distance to " O   HOH Z 313 " =    1.414
peak=    4.413 closest distance to " N   ASN A  60 " =    1.177
peak=    4.399 closest distance to " O   HOH Z 410 " =    1.421
peak=    4.398 closest distance to " CA  ASN A 284 " =    1.201
peak=    4.385 closest distance to " O   HOH Z  53 " =    2.336
peak=    4.383 closest distance to " CB  GLN A  77 " =    0.922
peak=    4.364 closest distance to " O   HOH Z 139 " =    2.175
peak=    4.325 closest distance to " OD1 ASN A  45 " =    1.228
peak=    4.323 closest distance to " CE AMET A  47 " =    1.110
peak=    4.300 closest distance to " O   HOH Z  92 " =    1.670
peak=    4.284 closest distance to " O   PRO A 198 " =    1.541
peak=    4.280 closest distance to " OG ASER A 258 " =    2.713
peak=    4.275 closest distance to " O   HOH Z 112 " =    1.592
peak=    4.270 closest distance to " OG  SER A  22 " =    1.175
peak=    4.206 closest distance to " O   HOH Z 124 " =    1.903
peak=    4.140 closest distance to " CB  ALA A   8 " =    0.993
peak=    4.133 closest distance to " O   HOH Z 427 " =    2.034
peak=    4.124 closest distance to " O   HOH Z  69 " =    1.390
peak=    4.088 closest distance to " CB  GLN A 122 " =    1.131
peak=    4.087 closest distance to " O   HOH Z 250 " =    2.037
peak=    4.066 closest distance to " O   HOH Z 276 " =    1.970
peak=    4.063 closest distance to " O   HOH Z 182 " =    1.391
peak=    4.061 closest distance to " OG ASER A 134 " =    1.410
peak=    4.029 closest distance to " NE1 TRP A 266 " =    1.774
peak=    4.024 closest distance to " CA  ARG A 219 " =    2.159
peak=    4.023 closest distance to " N   SER A  63 " =    0.885
peak=    4.008 closest distance to " O   HOH Z 133 " =    1.509
peak=    4.006 closest distance to " O   HOH Z 402 " =    1.580
peak=    4.002 closest distance to " OG BSER A 212 " =    2.712
peak=    3.985 closest distance to " O   HOH Z 279 " =    1.234
peak=    3.981 closest distance to " O   HOH Z 311 " =    1.867
peak=    3.962 closest distance to " CZ3 TRP A  70 " =    0.987
peak=    3.937 closest distance to " CG2 VAL A 250 " =    1.045
peak=    3.924 closest distance to " O   HOH Z 366 " =    2.344
peak=    3.922 closest distance to " O   HOH Z  97 " =    2.017
peak=    3.917 closest distance to " O   HOH Z 347 " =    1.289
peak=    3.914 closest distance to " CB  ALA A 244 " =    1.092
peak=    3.912 closest distance to " O   HOH Z  49 " =    1.996
peak=    3.903 closest distance to " CB  SER A   3 " =    1.372
peak=    3.888 closest distance to " CB  SER A 210 " =    0.839
peak=    3.880 closest distance to " O   HOH Z 272 " =    1.881
peak=    3.870 closest distance to " O   HOH Z 161 " =    1.128
peak=    3.870 closest distance to " O   HOH Z 302 " =    1.829
peak=    3.869 closest distance to " O   HOH Z 407 " =    1.731
peak=    3.864 closest distance to " N   VAL A 121 " =    0.875
peak=    3.864 closest distance to " O   HOH Z 123 " =    1.598
peak=    3.859 closest distance to " O   HOH Z 212 " =    1.717
peak=    3.858 closest distance to " O   HOH Z 424 " =    1.404
peak=    3.855 closest distance to " O   HOH Z  29 " =    1.326
peak=    3.855 closest distance to " CD2 HIS A 115 " =    1.065
peak=    3.849 closest distance to " CB  ALA A   1 " =    1.263
peak=    3.832 closest distance to " O   HOH Z 138 " =    2.056
peak=    3.831 closest distance to " CG  LEU A 167 " =    1.247
peak=    3.828 closest distance to " O   HOH Z 366 " =    2.188
peak=    3.816 closest distance to " CB  MET A  47 " =    1.294
peak=    3.813 closest distance to " CD1 PHE A 130 " =    0.874
peak=    3.800 closest distance to " O   HOH Z 269 " =    1.467
peak=    3.797 closest distance to " O   HOH Z   7 " =    1.829
peak=    3.795 closest distance to " CG2 THR A 246 " =    1.432
peak=    3.778 closest distance to " O   HOH Z 183 " =    1.224
peak=    3.776 closest distance to " O   PHE A  61 " =    0.802
peak=    3.768 closest distance to " O   SER A 271 " =    1.146
peak=    3.763 closest distance to " NZ  LYS A 117 " =    1.344
peak=    3.750 closest distance to " CB  ASP A 286 " =    1.006
peak=    3.746 closest distance to " CD2 LEU A  25 " =    1.236
peak=    3.743 closest distance to " NH2 ARG A  36 " =    1.181
peak=    3.734 closest distance to " O   HOH Z 178 " =    2.240
peak=    3.732 closest distance to " O   HOH Z 369 " =    1.635
peak=    3.731 closest distance to " O   HOH Z 360 " =    1.308
peak=    3.724 closest distance to " CE  MET A  93 " =    1.396
peak=    3.714 closest distance to " O   HOH Z 104 " =    1.420
peak=    3.711 closest distance to " CB  ASP A 124 " =    1.041
peak=    3.698 closest distance to " O   HOH Z 393 " =    1.719
peak=    3.695 closest distance to " CE1 PHE A 283 " =    1.069
peak=    3.692 closest distance to " O   HOH Z 211 " =    1.694
peak=    3.676 closest distance to " O   HOH Z 223 " =    1.010
peak=    3.676 closest distance to " O   HOH Z   6 " =    1.743
peak=    3.669 closest distance to " N   ALA A 100 " =    0.837
peak=    3.669 closest distance to " O   HOH Z 246 " =    1.290
peak=    3.665 closest distance to " O   HOH Z 167 " =    1.136
peak=    3.662 closest distance to " O   HOH Z 207 " =    1.590
peak=    3.662 closest distance to " CD  PRO A 243 " =    1.264
peak=    3.656 closest distance to " O   HOH Z 392 " =    1.682
peak=    3.652 closest distance to " O   HOH Z 121 " =    2.117
peak=    3.652 closest distance to " O   HOH Z 255 " =    1.093
peak=    3.638 closest distance to " CB  GLU A   2 " =    1.031
peak=    3.638 closest distance to " O   HOH Z 344 " =    1.319
peak=    3.638 closest distance to " CG  ARG A  66 " =    2.590
peak=    3.637 closest distance to " CB  THR A 235 " =    1.481
peak=    3.630 closest distance to " O   HOH Z 143 " =    2.139
peak=    3.624 closest distance to " CE  LYS A 289 " =    1.154
peak=    3.613 closest distance to " N   ASN A 285 " =    1.264
peak=    3.613 closest distance to " CB  ASP A 200 " =    1.176
peak=    3.610 closest distance to " CG  LEU A 282 " =    1.152
peak=    3.608 closest distance to " O   HOH Z 133 " =    2.309
peak=    3.603 closest distance to " NE1 TRP A  85 " =    1.173
peak=    3.588 closest distance to " O   ARG A  66 " =    1.103
peak=    3.586 closest distance to " O   HOH Z   5 " =    1.687
peak=    3.584 closest distance to " O   HOH Z  47 " =    1.624
peak=    3.570 closest distance to " O   HOH Z 199 " =    1.693
peak=    3.567 closest distance to " O   HOH Z  28 " =    2.440
peak=    3.567 closest distance to " O   HOH Z  32 " =    1.777
peak=    3.564 closest distance to " O   HOH Z 143 " =    1.634
peak=    3.560 closest distance to " N   ILE A  33 " =    1.484
peak=    3.557 closest distance to " NZ  LYS A 289 " =    1.735
peak=    3.554 closest distance to " CG  PRO A 198 " =    1.685
peak=    3.553 closest distance to " C   ASN A 215 " =    1.455
peak=    3.549 closest distance to " O   HOH Z 193 " =    1.472
peak=    3.546 closest distance to " O   HOH Z 383 " =    1.131
peak=    3.543 closest distance to " O   HOH Z  88 " =    2.411
peak=    3.542 closest distance to " O   HOH Z 185 " =    1.555
peak=    3.541 closest distance to " OE1 GLN A  58 " =    5.528
peak=    3.537 closest distance to " O   HOH Z 427 " =    1.261
peak=    3.537 closest distance to " CA  CYS A 260 " =    0.910
peak=    3.531 closest distance to " O   HOH Z  22 " =    1.631
peak=    3.530 closest distance to " O   HOH Z 363 " =    2.534
peak=    3.525 closest distance to " O   HOH Z 286 " =    1.747
peak=    3.523 closest distance to " O   HOH Z  24 " =    1.689
peak=    3.519 closest distance to " O   HOH Z 269 " =    2.816
peak=    3.518 closest distance to " CB  LYS A 166 " =    0.825
peak=    3.516 closest distance to " O   HOH Z 116 " =    5.516
peak=    3.515 closest distance to " CB  GLN A  88 " =    1.388
peak=    3.513 closest distance to " OE1 GLN A  55 " =    1.874
peak=    3.507 closest distance to " N   ARG A 275 " =    0.781
peak=    3.503 closest distance to " O   HOH Z 132 " =    1.796
peak=    3.503 closest distance to " CA  PRO A 213 " =    0.769
peak=    3.501 closest distance to " O   HOH Z 240 " =    1.957
peak=    3.499 closest distance to " CB  GLU A 152 " =    1.252
peak=    3.495 closest distance to " O   GLY A 111 " =    1.552
peak=    3.495 closest distance to " CB  ARG A 102 " =    1.040
peak=    3.494 closest distance to " C   ILE A 120 " =    1.118
peak=    3.493 closest distance to " O   HOH Z 109 " =    1.795
peak=    3.490 closest distance to " O   HOH Z 303 " =    2.159
peak=    3.489 closest distance to " N   PHE A 130 " =    1.382
peak=    3.488 closest distance to " O   HOH Z  63 " =    1.838
peak=    3.480 closest distance to " C   ALA A   1 " =    1.570
peak=    3.477 closest distance to " CE1 HIS A 115 " =    2.859
peak=    3.477 closest distance to " OD2 ASP A 140 " =    1.164
peak=    3.473 closest distance to " CB  SER A 216 " =    0.912
peak=    3.473 closest distance to " CE2 TRP A  70 " =    1.640
peak=    3.471 closest distance to " OE1 GLN A  88 " =    1.055
peak=    3.470 closest distance to " CB  ASP A 132 " =    3.685
peak=    3.467 closest distance to " O   HOH Z 261 " =    2.147
peak=    3.466 closest distance to " NE2 GLN A  55 " =    1.248
peak=    3.458 closest distance to " O   TYR A 169 " =    1.257
peak=    3.458 closest distance to " CD2 LEU A   5 " =    1.254
peak=    3.454 closest distance to " O   HOH Z 232 " =    1.309
peak=    3.453 closest distance to " CB  ALA A  10 " =    0.999
peak=    3.451 closest distance to " O   HOH Z 196 " =    1.695
peak=    3.450 closest distance to " O   HOH Z 126 " =    1.587
peak=    3.446 closest distance to " N   GLU A   2 " =    1.389
peak=    3.444 closest distance to " O   HOH Z 352 " =    1.965
peak=    3.439 closest distance to " O   GLY A 302 " =    1.343
peak=    3.437 closest distance to " N   ASN A 142 " =    1.183
peak=    3.434 closest distance to " CB  ASN A 148 " =    1.277
peak=    3.429 closest distance to " CB  SER A 276 " =    1.482
peak=    3.422 closest distance to " NZ  LYS A 289 " =    1.434
peak=    3.417 closest distance to " CG  PRO A 213 " =    1.130
peak=    3.416 closest distance to " OE1 GLN A  77 " =    0.962
peak=    3.413 closest distance to " CG2 THR A 251 " =    1.639
peak=    3.413 closest distance to " CB  ALA A 137 " =    0.984
peak=    3.413 closest distance to " CB  TRP A 123 " =    1.130
peak=    3.409 closest distance to " O   HOH Z 371 " =    2.738
peak=    3.401 closest distance to " O   HOH Z 422 " =    2.526
peak=    3.399 closest distance to " CD1 LEU A 228 " =    1.707
peak=    3.397 closest distance to " O   HOH Z 172 " =    2.008
peak=    3.395 closest distance to " CD1 TRP A 179 " =    1.132
peak=    3.394 closest distance to " CA  PHE A 130 " =    1.336
peak=    3.390 closest distance to " C   VAL A  72 " =    1.031
peak=    3.387 closest distance to " O   HOH Z 185 " =    1.413
peak=    3.384 closest distance to " OG1 THR A 246 " =    1.263
peak=    3.381 closest distance to " O   HOH Z 128 " =    1.246
peak=    3.380 closest distance to " O   HOH Z 419 " =    1.812
peak=    3.371 closest distance to " CB  LEU A   5 " =    1.195
peak=    3.368 closest distance to " N   GLY A 196 " =    1.177
peak=    3.368 closest distance to " O   HOH Z 329 " =    1.878
peak=    3.367 closest distance to " O   HOH Z 361 " =    3.256
peak=    3.366 closest distance to " CA  ASN A  74 " =    1.442
peak=    3.366 closest distance to " CG2 VAL A 257 " =    1.152
peak=    3.362 closest distance to " CE1 TYR A  68 " =    1.108
peak=    3.362 closest distance to " CA  ARG A  36 " =    1.255
peak=    3.361 closest distance to " CA  LEU A 282 " =    1.161
peak=    3.358 closest distance to " O   LYS A 289 " =    2.245
peak=    3.356 closest distance to " OG1 THR A 182 " =    1.384
peak=    3.349 closest distance to " O   HOH Z  39 " =    1.253
peak=    3.346 closest distance to " O   HOH Z 434 " =    5.809
peak=    3.339 closest distance to " O   HOH Z 414 " =    1.619
peak=    3.336 closest distance to " O   HOH Z  59 " =    1.700
peak=    3.332 closest distance to " CG2 VAL A 232 " =    1.064
peak=    3.324 closest distance to " CG2 THR A 294 " =    1.235
peak=    3.322 closest distance to " O   HOH Z 422 " =    1.727
peak=    3.312 closest distance to " O   HOH Z   1 " =    2.510
peak=    3.310 closest distance to " O   HOH Z 257 " =    1.440
peak=    3.309 closest distance to " O   HOH Z 350 " =    1.200
peak=    3.304 closest distance to " CA  PHE A  59 " =    0.870
peak=    3.302 closest distance to " CG  ASP A 238 " =    0.872
peak=    3.299 closest distance to " OG  SER A   3 " =    1.148
peak=    3.297 closest distance to " O   HOH Z 388 " =    1.157
peak=    3.290 closest distance to " CG2 ILE A  20 " =    1.224
peak=    3.288 closest distance to " CB  ARG A  66 " =    0.753
peak=    3.287 closest distance to " O   HOH Z 293 " =    1.435
peak=    3.287 closest distance to " NH1AARG A 145 " =    0.898
peak=    3.285 closest distance to " CB  MET A  93 " =    1.554
peak=    3.285 closest distance to " O   HOH Z 433 " =    1.477
peak=    3.283 closest distance to " CG1 ILE A 120 " =    1.114
peak=    3.281 closest distance to " O   ASP A 286 " =    1.983
peak=    3.280 closest distance to " CG2 ILE A 120 " =    1.171
peak=    3.279 closest distance to " OE1 GLN A 194 " =    1.308
peak=    3.278 closest distance to " N   GLY A  98 " =    1.344
peak=    3.270 closest distance to " CE1 PHE A  16 " =    0.951
peak=    3.267 closest distance to " N   ILE A  20 " =    1.069
peak=    3.266 closest distance to " O   HOH Z 353 " =    1.622
peak=    3.261 closest distance to " CG2 VAL A  78 " =    1.038
peak=    3.260 closest distance to " CG  LYS A 119 " =    1.167
peak=    3.260 closest distance to " CB  PHE A 225 " =    1.326
peak=    3.257 closest distance to " O   HOH Z  89 " =    1.609
peak=    3.253 closest distance to " CZ  PHE A  59 " =    0.918
peak=    3.253 closest distance to " O   HOH Z 258 " =    1.006
peak=    3.253 closest distance to " CA  SER A 273 " =    0.799
peak=    3.250 closest distance to " O   HOH Z 412 " =    1.509
peak=    3.244 closest distance to " O   HOH Z 361 " =    2.456
peak=    3.242 closest distance to " O   HOH Z  48 " =    2.757
peak=    3.239 closest distance to " O   HOH Z 270 " =    1.703
peak=    3.238 closest distance to " CB  GLN A 223 " =    1.716
peak=    3.238 closest distance to " CB  ALA A 131 " =    1.638
peak=    3.236 closest distance to " OD1 ASN A  69 " =    1.028
peak=    3.230 closest distance to " CA  PRO A 280 " =    1.190
peak=    3.228 closest distance to " O   HOH Z  40 " =    2.284
peak=    3.226 closest distance to " CB  ALA A 180 " =    0.964
peak=    3.224 closest distance to " O   HOH Z  76 " =    1.253
peak=    3.221 closest distance to " CB  VAL A 126 " =    1.089
peak=    3.220 closest distance to " N   PHE A  61 " =    0.914
peak=    3.217 closest distance to " CG  LEU A 255 " =    1.106
peak=    3.217 closest distance to " CB  SER A 245 " =    1.267
peak=    3.211 closest distance to " O   HOH Z 178 " =    1.322
peak=    3.203 closest distance to " CB  VAL A 202 " =    1.501
peak=    3.202 closest distance to " O   HOH Z 359 " =    1.627
peak=    3.202 closest distance to " CA  ASN A 127 " =    0.804
peak=    3.201 closest distance to " C   ALA A 180 " =    0.975
peak=    3.201 closest distance to " CD  LYS A 181 " =    1.722
peak=    3.200 closest distance to " O   LYS A 119 " =    0.860
peak=    3.199 closest distance to " O   HOH Z  59 " =    1.905
peak=    3.198 closest distance to " O   HOH Z 241 " =    1.536
peak=    3.196 closest distance to " OG BSER A 258 " =    0.976
peak=    3.194 closest distance to " OE2 GLU A 236 " =    1.700
peak=    3.194 closest distance to " CB  ASN A 187 " =    2.180
peak=    3.192 closest distance to " O   HOH Z 276 " =    2.317
peak=    3.183 closest distance to " O   HOH Z 246 " =    1.509
peak=    3.181 closest distance to " O   HOH Z 326 " =    1.266
peak=    3.178 closest distance to " CA  LEU A  25 " =    0.972
peak=    3.176 closest distance to " OD1 ASN A 285 " =    1.302
peak=    3.174 closest distance to " CD  LYS A 166 " =    1.174
peak=    3.173 closest distance to " CB  ALA A 104 " =    1.317
peak=    3.172 closest distance to " CB  GLU A 128 " =    1.111
peak=    3.168 closest distance to " CD2 LEU A 300 " =    0.908
peak=    3.165 closest distance to " CG2 THR A  29 " =    1.190
peak=    3.163 closest distance to " N   ALA A 160 " =    0.908
peak=    3.162 closest distance to " NH2BARG A 145 " =    1.888
peak=    3.158 closest distance to " O   HOH Z 139 " =    2.747
peak=    3.157 closest distance to " O   HOH Z 117 " =    2.949
peak=    3.150 closest distance to " O   HOH Z 258 " =    1.878
peak=    3.147 closest distance to " O   PHE A  59 " =    2.534
peak=    3.145 closest distance to " O   HOH Z 193 " =    2.005
peak=    3.143 closest distance to " O   HOH Z 217 " =    1.828
peak=    3.142 closest distance to " OD1 ASN A 170 " =    1.631
peak=    3.141 closest distance to " CA  MET A  40 " =    1.132
peak=    3.137 closest distance to " O   HOH Z 334 " =    1.576
peak=    3.127 closest distance to " O   HOH Z 119 " =    1.633
peak=    3.125 closest distance to " O   HOH Z 211 " =    2.802
peak=    3.102 closest distance to " O   HOH Z  49 " =    2.559
peak=    3.099 closest distance to " CD  PRO A 163 " =    3.580
peak=    3.089 closest distance to " O   HOH Z 209 " =    1.523
peak=    3.087 closest distance to " CG  LYS A 117 " =    1.089
peak=    3.085 closest distance to " CB  PRO A 243 " =    1.143
peak=    3.082 closest distance to " CE1 TYR A  30 " =    0.920
peak=    3.075 closest distance to " O  BHOH Z  74 " =    1.037
peak=    3.071 closest distance to " CA  ASN A 173 " =    0.953
peak=    3.069 closest distance to " O   HOH Z 408 " =    2.153
peak=    3.060 closest distance to " CB  HIS A 108 " =    0.897
peak=    3.050 closest distance to " O   HOH Z 282 " =    1.627
peak=    3.048 closest distance to " N   GLY A 111 " =    1.341
peak=    3.043 closest distance to " CA  LYS A 181 " =    2.109
peak=    3.024 closest distance to " O   HOH Z 189 " =    1.863

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 212         
Filter by distance & map next to the model:
   mapped sites are within: 0.234 - 5.849
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 194 from: 212
   mapped sites are within: 0.711 - 5.849

peak=   -5.238 closest distance to " O   SER A  62 " =    0.796
peak=   -4.991 closest distance to " O   ASN A 285 " =    0.987
peak=   -4.905 closest distance to " N   ASN A  60 " =    1.000
peak=   -4.848 closest distance to " CG  ASP A  50 " =    0.956
peak=   -4.531 closest distance to " O   HOH Z  86 " =    0.711
peak=   -4.363 closest distance to " N   ALA A  64 " =    1.050
peak=   -4.332 closest distance to " N   ASN A 285 " =    1.071
peak=   -4.277 closest distance to " SD  MET A 105 " =    2.109
peak=   -4.256 closest distance to " O   HOH Z  91 " =    2.423
peak=   -4.235 closest distance to " C   ASN A 285 " =    0.849
peak=   -4.172 closest distance to " CB  ASN A 285 " =    1.597
peak=   -4.167 closest distance to " CB  PHE A  59 " =    1.198
peak=   -4.151 closest distance to " O   LYS A 119 " =    0.767
peak=   -4.136 closest distance to " CG1BVAL A  72 " =    1.766
peak=   -4.103 closest distance to " O   HOH Z 234 " =    4.555
peak=   -4.064 closest distance to " SG  CYS A 254 " =    3.106
peak=   -4.053 closest distance to " O   LYS A  76 " =    0.885
peak=   -4.017 closest distance to " CE1 PHE A  16 " =    1.472
peak=   -3.982 closest distance to " O   PHE A  61 " =    0.804
peak=   -3.977 closest distance to " O   HOH Z 290 " =    0.744
peak=   -3.962 closest distance to " O   PRO A 198 " =    1.080
peak=   -3.959 closest distance to " O   SER A  22 " =    1.112
peak=   -3.957 closest distance to " CB  ASN A  60 " =    1.166
peak=   -3.940 closest distance to " N   ASN A 284 " =    0.999
peak=   -3.932 closest distance to " CB  ARG A  66 " =    1.753
peak=   -3.916 closest distance to " N   ARG A 275 " =    0.842
peak=   -3.901 closest distance to " O   HOH Z 415 " =    4.197
peak=   -3.872 closest distance to " O   HOH Z 244 " =    0.944
peak=   -3.835 closest distance to " O   HOH Z 156 " =    2.213
peak=   -3.833 closest distance to " O   HOH Z 350 " =    0.835
peak=   -3.816 closest distance to " CG  MET A 105 " =    0.884
peak=   -3.807 closest distance to " O   ASP A 286 " =    1.028
peak=   -3.802 closest distance to " NH2AARG A 275 " =    5.389
peak=   -3.795 closest distance to " CZ  ARG A  36 " =    1.389
peak=   -3.794 closest distance to " N   GLN A  58 " =    1.221
peak=   -3.787 closest distance to " N   LYS A 119 " =    0.760
peak=   -3.775 closest distance to " CD  PRO A  90 " =    1.696
peak=   -3.774 closest distance to " O   HOH Z  29 " =    0.715
peak=   -3.767 closest distance to " N   PHE A  59 " =    1.097
peak=   -3.763 closest distance to " ND2 ASN A  69 " =    1.135
peak=   -3.758 closest distance to " N   GLN A  58 " =    2.189
peak=   -3.745 closest distance to " CG  GLN A  55 " =    1.008
peak=   -3.736 closest distance to " O   VAL A 125 " =    2.140
peak=   -3.731 closest distance to " CB  ASN A 285 " =    1.221
peak=   -3.729 closest distance to " N   ASN A 127 " =    1.361
peak=   -3.723 closest distance to " OD2 ASP A 270 " =    0.839
peak=   -3.721 closest distance to " O   TYR A 214 " =    0.944
peak=   -3.720 closest distance to " ND2 ASN A 110 " =    1.178
peak=   -3.708 closest distance to " CD2 TYR A 293 " =    2.025
peak=   -3.706 closest distance to " O   HOH Z  24 " =    0.906
peak=   -3.700 closest distance to " C   ASN A 284 " =    0.962
peak=   -3.698 closest distance to " ND2 ASN A 110 " =    1.221
peak=   -3.692 closest distance to " CG  PRO A 243 " =    0.904
peak=   -3.689 closest distance to " O   HOH Z 264 " =    0.784
peak=   -3.678 closest distance to " O   HOH Z  69 " =    1.554
peak=   -3.675 closest distance to " O   HOH Z 138 " =    0.879
peak=   -3.663 closest distance to " O   HOH Z 135 " =    0.719
peak=   -3.655 closest distance to " O   HOH Z 347 " =    0.841
peak=   -3.650 closest distance to " CB  VAL A 125 " =    1.372
peak=   -3.635 closest distance to " O   HOH Z  60 " =    0.911
peak=   -3.631 closest distance to " C   ASP A 124 " =    1.189
peak=   -3.624 closest distance to " CA  GLY A 133 " =    1.944
peak=   -3.600 closest distance to " OG1 THR A 246 " =    2.163
peak=   -3.598 closest distance to " O   HOH Z 101 " =    1.144
peak=   -3.595 closest distance to " O   HOH Z 246 " =    1.834
peak=   -3.591 closest distance to " CD1 TRP A 179 " =    0.872
peak=   -3.585 closest distance to " O   HOH Z 337 " =    1.468
peak=   -3.583 closest distance to " O   HOH Z 381 " =    1.042
peak=   -3.569 closest distance to " OG  SER A   3 " =    1.125
peak=   -3.565 closest distance to " OD2 ASP A 253 " =    0.735
peak=   -3.558 closest distance to " OG ASER A 134 " =    0.882
peak=   -3.557 closest distance to " CG  GLN A  73 " =    1.212
peak=   -3.551 closest distance to " CA  TYR A  68 " =    2.747
peak=   -3.550 closest distance to " CB  ALA A 248 " =    1.991
peak=   -3.537 closest distance to " C   ASP A 124 " =    1.988
peak=   -3.534 closest distance to " O   GLN A  77 " =    1.672
peak=   -3.533 closest distance to " O   HOH Z 247 " =    0.820
peak=   -3.518 closest distance to " O   HOH Z  72 " =    0.809
peak=   -3.516 closest distance to " O   HOH Z 163 " =    1.743
peak=   -3.515 closest distance to " N   SER A 210 " =    0.923
peak=   -3.506 closest distance to " O   SER A 135 " =    1.728
peak=   -3.499 closest distance to " O   GLY A 136 " =    1.377
peak=   -3.494 closest distance to " N   ILE A  33 " =    1.751
peak=   -3.489 closest distance to " O   HOH Z 100 " =    0.815
peak=   -3.484 closest distance to " SG  CYS A 168 " =    1.292
peak=   -3.476 closest distance to " O   HOH Z 150 " =    2.980
peak=   -3.473 closest distance to " CB  ASN A 252 " =    2.001
peak=   -3.472 closest distance to " N   HIS A 115 " =    1.829
peak=   -3.464 closest distance to " O   HOH Z  37 " =    1.931
peak=   -3.464 closest distance to " O   PHE A 218 " =    1.126
peak=   -3.463 closest distance to " O   HOH Z 305 " =    1.198
peak=   -3.455 closest distance to " O   HOH Z 426 " =    1.755
peak=   -3.449 closest distance to " CG  PRO A 213 " =    0.876
peak=   -3.444 closest distance to " O   HOH Z  82 " =    1.413
peak=   -3.436 closest distance to " NE1 TRP A  70 " =    1.140
peak=   -3.436 closest distance to " ND2 ASN A 285 " =    1.001
peak=   -3.435 closest distance to " O   HOH Z  52 " =    0.937
peak=   -3.434 closest distance to " ND2 ASN A 285 " =    1.444
peak=   -3.434 closest distance to " CE2 TRP A 274 " =    1.038
peak=   -3.433 closest distance to " CD1 LEU A  25 " =    2.082
peak=   -3.424 closest distance to " CG1BVAL A  72 " =    4.896
peak=   -3.423 closest distance to " N   ASN A 284 " =    0.870
peak=   -3.422 closest distance to " OG1 THR A 294 " =    2.333
peak=   -3.421 closest distance to " O   HOH Z  98 " =    1.508
peak=   -3.418 closest distance to " O   HOH Z 117 " =    1.174
peak=   -3.416 closest distance to " O   ASN A 284 " =    0.937
peak=   -3.411 closest distance to " O   HOH Z  73 " =    1.478
peak=   -3.396 closest distance to " OG  SER A 206 " =    1.332
peak=   -3.393 closest distance to " O   HOH Z  13 " =    1.475
peak=   -3.391 closest distance to " O   HOH Z 256 " =    0.951
peak=   -3.387 closest distance to " CG  PRO A 213 " =    1.414
peak=   -3.386 closest distance to " OD2 ASP A 272 " =    1.149
peak=   -3.384 closest distance to " O   HOH Z 316 " =    2.062
peak=   -3.383 closest distance to " O   LYS A  76 " =    1.403
peak=   -3.382 closest distance to " CZ  PHE A  16 " =    0.976
peak=   -3.377 closest distance to " CE1 HIS A 115 " =    1.296
peak=   -3.374 closest distance to " CE3 TRP A 274 " =    2.496
peak=   -3.367 closest distance to " OH  TYR A  30 " =    0.882
peak=   -3.367 closest distance to " O   HOH Z 397 " =    1.397
peak=   -3.365 closest distance to " O   PRO A  54 " =    1.298
peak=   -3.360 closest distance to " OG  SER A  97 " =    2.421
peak=   -3.353 closest distance to " CB  ALA A 291 " =    2.142
peak=   -3.351 closest distance to " O   HOH Z 286 " =    4.027
peak=   -3.348 closest distance to " O   SER A 276 " =    1.466
peak=   -3.348 closest distance to " N   ALA A   1 " =    1.091
peak=   -3.343 closest distance to " CG  GLN A  88 " =    0.979
peak=   -3.337 closest distance to " O   HOH Z 207 " =    1.509
peak=   -3.333 closest distance to " N   SER A 206 " =    1.722
peak=   -3.333 closest distance to " O   HOH Z  39 " =    0.944
peak=   -3.332 closest distance to " OD2 ASP A 191 " =    1.349
peak=   -3.331 closest distance to " N   GLY A  98 " =    1.627
peak=   -3.326 closest distance to " CB  ASN A 249 " =    1.796
peak=   -3.324 closest distance to " O   LEU A 101 " =    1.055
peak=   -3.320 closest distance to " CG2 ILE A 120 " =    1.285
peak=   -3.319 closest distance to " N   ALA A  19 " =    1.924
peak=   -3.316 closest distance to " ND2 ASN A 173 " =    1.777
peak=   -3.315 closest distance to " CA  SER A  63 " =    1.024
peak=   -3.312 closest distance to " OG  SER A  62 " =    0.965
peak=   -3.306 closest distance to " O   HOH Z  88 " =    1.665
peak=   -3.303 closest distance to " CD  GLU A 277 " =    0.954
peak=   -3.303 closest distance to " CD1 PHE A  59 " =    0.957
peak=   -3.301 closest distance to " O   HOH Z 278 " =    1.230
peak=   -3.301 closest distance to " O   ALA A  51 " =    1.358
peak=   -3.298 closest distance to " CA  ASN A  60 " =    1.123
peak=   -3.288 closest distance to " C   ASP A 231 " =    2.151
peak=   -3.285 closest distance to " O   HOH Z 154 " =    1.430
peak=   -3.284 closest distance to " CB  ALA A 161 " =    1.301
peak=   -3.281 closest distance to " O   HOH Z 126 " =    1.826
peak=   -3.277 closest distance to " CD  PRO A 198 " =    1.482
peak=   -3.273 closest distance to " O   HOH Z 409 " =    2.983
peak=   -3.273 closest distance to " O   HOH Z 377 " =    0.733
peak=   -3.267 closest distance to " OD2 ASP A  27 " =    1.150
peak=   -3.267 closest distance to " O   HOH Z 266 " =    4.370
peak=   -3.262 closest distance to " O   HIS A 115 " =    1.331
peak=   -3.244 closest distance to " O   HOH Z 170 " =    5.849
peak=   -3.237 closest distance to " O   HOH Z  60 " =    1.939
peak=   -3.237 closest distance to " CG2 THR A  31 " =    2.274
peak=   -3.229 closest distance to " N   PHE A  61 " =    1.300
peak=   -3.227 closest distance to " O   ALA A 165 " =    1.074
peak=   -3.227 closest distance to " CB  PRO A 213 " =    2.192
peak=   -3.221 closest distance to " CD1 PHE A 283 " =    2.438
peak=   -3.220 closest distance to " O   HOH Z 350 " =    1.929
peak=   -3.220 closest distance to " CG2 THR A 246 " =    1.434
peak=   -3.212 closest distance to " CB  PHE A  61 " =    1.126
peak=   -3.204 closest distance to " OD1 ASP A  50 " =    0.923
peak=   -3.193 closest distance to " NE2 GLN A  58 " =    3.663
peak=   -3.192 closest distance to " C   ASP A 286 " =    1.172
peak=   -3.181 closest distance to " NH1 ARG A 259 " =    0.869
peak=   -3.169 closest distance to " O   HOH Z   6 " =    2.378
peak=   -3.164 closest distance to " O   HOH Z 406 " =    0.845
peak=   -3.163 closest distance to " O   HOH Z 251 " =    1.279
peak=   -3.162 closest distance to " O   HOH Z 178 " =    1.339
peak=   -3.161 closest distance to " O   HOH Z 391 " =    1.147
peak=   -3.158 closest distance to " N   THR A 157 " =    1.871
peak=   -3.151 closest distance to " N   THR A 246 " =    0.883
peak=   -3.142 closest distance to " O   HOH Z  68 " =    1.940
peak=   -3.136 closest distance to " O   HOH Z 139 " =    2.096
peak=   -3.121 closest distance to " O   ASP A 270 " =    1.854
peak=   -3.114 closest distance to " N   THR A 220 " =    1.622
peak=   -3.111 closest distance to " O   HOH Z 156 " =    2.495
peak=   -3.108 closest distance to " C   SER A 288 " =    0.853
peak=   -3.108 closest distance to " SD  MET A 105 " =    2.435
peak=   -3.103 closest distance to " O   HOH Z 148 " =    1.047
peak=   -3.096 closest distance to " CA  ASN A 217 " =    1.523
peak=   -3.089 closest distance to " O   HOH Z 412 " =    5.013
peak=   -3.083 closest distance to " C   ASN A  69 " =    1.011
peak=   -3.081 closest distance to " O   THR A 235 " =    1.124
peak=   -3.073 closest distance to " C   THR A 251 " =    1.751
peak=   -3.064 closest distance to " OG BSER A  99 " =    1.695
peak=   -3.058 closest distance to " O   HOH Z 166 " =    1.534
peak=   -3.052 closest distance to " CB  SER A  62 " =    4.286
peak=   -3.045 closest distance to " O   ALA A  10 " =    1.337
peak=   -3.040 closest distance to " OD2 ASP A 253 " =    0.817
peak=   -3.038 closest distance to " CB  ALA A 248 " =    2.199

================= 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    :  0.5059 0.5119   6.305312e+00   6.300063e+00
   1_bss:  0.4979 0.5002   6.302683e+00   6.289048e+00
   1_xyz:  0.4544 0.4789   6.250659e+00   6.271972e+00
   1_adp:  0.4176 0.4828   6.217879e+00   6.274406e+00
   1_occ:  0.4174 0.4833   6.218107e+00   6.275197e+00
   2_bss:  0.4168 0.4823   6.219733e+00   6.276717e+00
   2_xyz:  0.3691 0.4490   6.141707e+00   6.244246e+00
   2_adp:  0.3567 0.4405   6.123718e+00   6.234975e+00
   2_occ:  0.3565 0.4410   6.123675e+00   6.235174e+00
   3_bss:  0.3574 0.4385   6.121988e+00   6.232662e+00
   3_xyz:  0.3049 0.3880   6.011522e+00   6.153044e+00
   3_adp:  0.2826 0.3750   5.964403e+00   6.131959e+00
   3_occ:  0.2825 0.3755   5.964529e+00   6.132292e+00
   4_bss:  0.2824 0.3745   5.960993e+00   6.129297e+00
   4_xyz:  0.2437 0.3273   5.830277e+00   6.020832e+00
   4_adp:  0.2262 0.3015   5.765151e+00   5.958190e+00
   4_occ:  0.2258 0.3007   5.763505e+00   5.956017e+00
   5_bss:  0.2261 0.2998   5.762074e+00   5.953898e+00
   5_xyz:  0.1868 0.2463   5.585296e+00   5.795825e+00
   5_adp:  0.1750 0.2277   5.523094e+00   5.733342e+00
   5_occ:  0.1747 0.2270   5.521379e+00   5.730855e+00
   5_bss:  0.1746 0.2262   5.519212e+00   5.727403e+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:  0.354   7.314  -2.643   0.684   1.213   0.000   0.000   0.000
   1_xyz:  0.354   7.314  -2.643   0.684   1.213   0.000   0.000   0.000
   1_adp:  0.354   7.314  -2.643   0.684   1.213   0.000   0.000   0.000
   1_occ:  0.354   7.314  -2.643   0.684   1.213   0.000   0.000   0.000
   2_bss:  0.350  27.158  -0.594   1.369   1.824   0.000   0.000   0.000
   2_xyz:  0.350  27.158  -0.594   1.369   1.824   0.000   0.000   0.000
   2_adp:  0.350  27.158  -0.594   1.369   1.824   0.000   0.000   0.000
   2_occ:  0.350  27.158  -0.594   1.369   1.824   0.000   0.000   0.000
   3_bss:  0.329  35.054  -0.007   1.063   1.490   0.000   0.000   0.000
   3_xyz:  0.329  35.054  -0.007   1.063   1.490   0.000   0.000   0.000
   3_adp:  0.329  35.054  -0.007   1.063   1.490   0.000   0.000   0.000
   3_occ:  0.329  35.054  -0.007   1.063   1.490   0.000   0.000   0.000
   4_bss:  0.321  35.054  -0.003   0.396   0.950   0.000   0.000   0.000
   4_xyz:  0.321  35.054  -0.003   0.396   0.950   0.000   0.000   0.000
   4_adp:  0.321  35.054  -0.003   0.396   0.950   0.000   0.000   0.000
   4_occ:  0.321  35.054  -0.003   0.396   0.950   0.000   0.000   0.000
   5_bss:  0.321  35.054  -0.625  -0.369   0.266  -0.000   0.000   0.000
   5_xyz:  0.321  35.054  -0.625  -0.369   0.266  -0.000   0.000   0.000
   5_adp:  0.321  35.054  -0.625  -0.369   0.266  -0.000   0.000   0.000
   5_occ:  0.321  35.054  -0.625  -0.369   0.266  -0.000   0.000   0.000
   5_bss:  0.321  35.057  -1.320  -1.275  -0.325  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  66.143 0.3139  0.4363    84970.038
   1_bss:  65.092 0.3262  0.4522    80912.538
   1_xyz:  59.899 0.3933  0.5382    72824.587
   1_adp:  61.481 0.3724  0.5147    75258.792
   1_occ:  61.706 0.3695  0.5105    75683.363
   2_bss:  61.762 0.3688  0.5345    76116.859
   2_xyz:  53.052 0.4813  0.7042    62441.696
   2_adp:  50.816 0.5101  0.7338    59292.771
   2_occ:  50.841 0.5097  0.7330    59320.562
   3_bss:  50.604 0.5124  0.7366    58582.164
   3_xyz:  42.780 0.6086  0.8648    43255.440
   3_adp:  40.048 0.6419  0.8817    39547.868
   3_occ:  40.081 0.6415  0.8810    39593.340
   4_bss:  39.926 0.6430  0.8695    39055.319
   4_xyz:  33.636 0.7158  0.9482    28246.736
   4_adp:  30.015 0.7576  0.9679    23703.651
   4_occ:  29.914 0.7588  0.9690    23586.480
   5_bss:  29.779 0.7601  0.9453    23339.790
   5_xyz:  23.956 0.8224  0.9951    15638.820
   5_adp:  21.844 0.8446  1.0040    13633.359
   5_occ:  21.786 0.8452  1.0039    13537.451
   5_bss:  21.658 0.8461  0.9774    13337.369
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.105   2.3725e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.105   2.3725e-01
   1_xyz:   1.299  0.010  0.087 15.462  0.005  4.103   9.8853e-02
   1_adp:   1.299  0.010  0.087 15.462  0.005  4.103   9.8853e-02
   1_occ:   1.299  0.010  0.087 15.462  0.005  4.103   9.8853e-02
   2_bss:   1.299  0.010  0.087 15.462  0.005  4.103   9.8853e-02
   2_xyz:   1.484  0.012  0.091 16.387  0.006  4.098   1.4165e-01
   2_adp:   1.484  0.012  0.091 16.387  0.006  4.098   1.4165e-01
   2_occ:   1.484  0.012  0.091 16.387  0.006  4.098   1.4165e-01
   3_bss:   1.484  0.012  0.091 16.387  0.006  4.098   1.4165e-01
   3_xyz:   1.294  0.010  0.086 15.881  0.005  4.097   9.9236e-02
   3_adp:   1.294  0.010  0.086 15.881  0.005  4.097   9.9236e-02
   3_occ:   1.294  0.010  0.086 15.881  0.005  4.097   9.9236e-02
   4_bss:   1.294  0.010  0.086 15.881  0.005  4.097   9.9236e-02
   4_xyz:   1.067  0.008  0.073 14.797  0.004  4.107   7.8222e-02
   4_adp:   1.067  0.008  0.073 14.797  0.004  4.107   7.8222e-02
   4_occ:   1.067  0.008  0.073 14.797  0.004  4.107   7.8222e-02
   5_bss:   1.067  0.008  0.073 14.797  0.004  4.107   7.8222e-02
   5_xyz:   0.954  0.007  0.067 14.614  0.003  4.104   5.9510e-02
   5_adp:   0.954  0.007  0.067 14.614  0.003  4.104   5.9510e-02
   5_occ:   0.954  0.007  0.067 14.614  0.003  4.104   5.9510e-02
   5_bss:   0.954  0.007  0.067 14.614  0.003  4.104   5.9510e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  0.994   2.3864e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  0.994   2.3864e-01
   1_xyz:   9.793  0.055  0.498 80.342  0.041  1.975   7.9068e-02
   1_adp:   9.793  0.055  0.498 80.342  0.041  1.975   7.9068e-02
   1_occ:   9.793  0.055  0.498 80.342  0.041  1.975   7.9068e-02
   2_bss:   9.793  0.055  0.498 80.342  0.041  1.975   7.9068e-02
   2_xyz:   9.126  0.083  0.324 80.456  0.025  2.121   2.2077e-01
   2_adp:   9.126  0.083  0.324 80.456  0.025  2.121   2.2077e-01
   2_occ:   9.126  0.083  0.324 80.456  0.025  2.121   2.2077e-01
   3_bss:   9.126  0.083  0.324 80.456  0.025  2.121   2.2077e-01
   3_xyz:   8.949  0.085  0.330 79.080  0.018  2.156   7.7198e-02
   3_adp:   8.949  0.085  0.330 79.080  0.018  2.156   7.7198e-02
   3_occ:   8.949  0.085  0.330 79.080  0.018  2.156   7.7198e-02
   4_bss:   8.949  0.085  0.330 79.080  0.018  2.156   7.7198e-02
   4_xyz:   7.593  0.061  0.252 70.071  0.015  2.279   1.5413e-01
   4_adp:   7.593  0.061  0.252 70.071  0.015  2.279   1.5413e-01
   4_occ:   7.593  0.061  0.252 70.071  0.015  2.279   1.5413e-01
   5_bss:   7.593  0.061  0.252 70.071  0.015  2.279   1.5413e-01
   5_xyz:   8.347  0.053  0.238 73.801  0.017  2.309   5.2524e-02
   5_adp:   8.347  0.053  0.238 73.801  0.017  2.309   5.2524e-02
   5_occ:   8.347  0.053  0.238 73.801  0.017  2.309   5.2524e-02
   5_bss:   8.347  0.053  0.238 73.801  0.017  2.309   5.2524e-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:  98.88   0.00  21.03  94.41   0.00  19.23  98.88   0.00  30.82
   1_occ:  98.88   0.00  21.03  94.41   0.00  19.23  98.88   0.00  30.82
   2_bss:  98.88   0.00  21.03  94.41   0.00  19.23  98.88   0.00  30.82
   2_xyz:  98.88   0.00  21.03  94.41   0.00  19.23  98.88   0.00  30.82
   2_adp: 109.17   0.00  18.95  91.76   0.00  17.15 109.17   0.00  28.72
   2_occ: 109.17   0.00  18.95  91.76   0.00  17.15 109.17   0.00  28.72
   3_bss: 109.17   0.00  18.95  91.76   0.00  17.15 109.17   0.00  28.72
   3_xyz: 109.17   0.00  18.95  91.76   0.00  17.15 109.17   0.00  28.72
   3_adp: 122.22   0.00  18.51 106.21   0.00  15.58 122.22   0.00  34.41
   3_occ: 122.22   0.00  18.51 106.21   0.00  15.58 122.22   0.00  34.41
   4_bss: 122.22   0.00  18.51 106.21   0.00  15.58 122.22   0.00  34.41
   4_xyz: 122.22   0.00  18.51 106.21   0.00  15.58 122.22   0.00  34.41
   4_adp: 115.85   0.00  17.43 110.73   0.00  13.50 115.85   1.75  38.86
   4_occ: 115.85   0.00  17.43 110.73   0.00  13.50 115.85   1.75  38.86
   5_bss: 115.85   0.00  17.43 110.73   0.00  13.50 115.85   1.75  38.86
   5_xyz: 115.85   0.00  17.43 110.73   0.00  13.50 115.85   1.75  38.86
   5_adp: 109.39   0.00  16.78 103.69   0.00  12.45 109.39   3.78  40.38
   5_occ: 109.39   0.00  16.78 103.69   0.00  12.45 109.39   3.78  40.38
   5_bss: 109.39   0.00  16.78 103.69   0.00  12.45 109.39   3.78  40.38
------------------------------------------------------------------------
 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:    2.136    0.012    0.233
   1_adp:    2.136    0.012    0.233
   1_occ:    2.136    0.012    0.233
   2_bss:    2.136    0.012    0.233
   2_xyz:    2.027    0.017    0.493
   2_adp:    2.027    0.017    0.493
   2_occ:    2.027    0.017    0.493
   3_bss:    2.027    0.017    0.493
   3_xyz:    2.021    0.074    0.675
   3_adp:    2.021    0.074    0.675
   3_occ:    2.021    0.074    0.675
   4_bss:    2.021    0.074    0.675
   4_xyz:    2.046    0.095    0.787
   4_adp:    2.046    0.095    0.787
   4_occ:    2.046    0.095    0.787
   5_bss:    2.046    0.095    0.787
   5_xyz:    2.172    0.080    0.894
   5_adp:    2.172    0.080    0.894
   5_occ:    2.172    0.080    0.894
   5_bss:    2.172    0.080    0.894
------------------------------------------------------------------------

CPU time actual refinement: 337.52


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_242/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_242/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_242/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_242/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_242/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 337.36 
  Macro-tasks:
    bulk solvent and scale       = 42.40  
    individual site refinement   = 137.61 
    weights calculation          = 30.41  
    collect and process          = 6.24   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 216.78 
  Micro-tasks:
    mask                            = 2.96   
    f_calc                          = 106.97 
    alpha_beta                      = 8.21   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 115.25 
    fmodel                         = 7.40   
    r_factors                      = 0.17   
    phase_errors                   = 9.59   
    foms                           = 0.32   
    TOTAL for micro-tasks          = 252.01 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.850 micro seconds
Total CPU time: 5.85 minutes
from_scatterers_fft:    622 calls, 106.64 s
gradients_fft:          567 calls, 102.71 s

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

# Date 2008-01-16 Time 04:21:03 PST -0800 (1200486063.56 s)
Start R-work = 0.5059, R-free = 0.5119 (no bulk solvent and anisotropic scale)
Final R-work = 0.1909, R-free = 0.2415 (no bulk solvent and anisotropic scale)

Start R-work = 0.4979, R-free = 0.5002
Final R-work = 0.1746, R-free = 0.2262