# Date 2008-01-16 Time 05:12:47 PST -0800 (1200489167.29 s)
#phil __OFF__

Command line arguments: "../638.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29272
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 638

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 46.4607, 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: (70.25, 46.4607, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8895 1.95116
Completeness in resolution range: 0.949171
Completeness with d_max=infinity: 0.946329

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8895
                             d_min =   1.9512

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.4607, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8895 1.95116
Completeness in resolution range: 0.949171
Completeness with d_max=infinity: 0.946329

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8899 -  4.1757 [2168/2197]  1954   214   9.9%
  bin  2:  4.1757 -  3.3265 [2075/2091]  1865   210  10.1%
  bin  3:  3.3265 -  2.9096 [2047/2066]  1841   206  10.1%
  bin  4:  2.9096 -  2.6452 [2047/2077]  1849   198   9.7%
  bin  5:  2.6452 -  2.4565 [2038/2057]  1834   204  10.0%
  bin  6:  2.4565 -  2.3122 [2014/2050]  1806   208  10.3%
  bin  7:  2.3122 -  2.1968 [1988/2021]  1787   201  10.1%
  bin  8:  2.1968 -  2.1014 [2004/2038]  1808   196   9.8%
  bin  9:  2.1014 -  2.0207 [1982/2010]  1781   201  10.1%
  bin 10:  2.0207 -  1.9512 [1226/2031]  1105   121   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_638/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.71 -     2.35: 34
        2.35 -     2.99: 1915
        2.99 -     3.63: 4702
        3.63 -     4.26: 9264
        4.26 -     4.90: 12878
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.715 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.722 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.773 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.786 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28788 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_638/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_638/model_refine_001.geo

CPU time processing inputs: 9.09


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.4607 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 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4115   r_free= 0.4117   ksol= 0.00   Bsol= 0.00   scale= 0.940    |
|                                                                             |
| 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:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.213668                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8899 -  4.6576 0.99   1403  157 0.3385 0.3348      6.4808      6.4962|
|  2:  4.6576 -  3.7158 0.99   1359  145 0.3437 0.3220      6.6866      6.6142|
|  3:  3.7158 -  3.2517 0.99   1321  154 0.3788 0.4111      6.5746      6.7221|
|  4:  3.2517 -  2.9569 0.99   1332  147 0.3765 0.3908        6.43      6.4239|
|  5:  2.9569 -  2.7464 0.99   1313  143 0.4243 0.3864       6.292      6.2392|
|  6:  2.7464 -  2.5853 0.99   1299  145 0.4409 0.4717      6.2141      6.2359|
|  7:  2.5853 -  2.4565 0.99   1316  141 0.4359 0.4050      6.1762      6.1393|
|  8:  2.4565 -  2.3500 0.98   1274  151 0.4528 0.4368      6.1203      6.1254|
|  9:  2.3500 -  2.2598 0.98   1301  149 0.4480 0.4165      6.0742      6.0304|
| 10:  2.2598 -  2.1821 0.98   1279  133 0.4608 0.4867      6.0421      6.0886|
| 11:  2.1821 -  2.1141 1.00   1278  141 0.4739 0.5275      6.0119      6.0421|
| 12:  2.1141 -  2.0538 0.97   1266  139 0.4697 0.4624      5.9218      5.9697|
| 13:  2.0538 -  1.9998 0.98   1286  143 0.4763 0.4664      5.8505      5.7845|
| 14:  1.9998 -  1.9512 0.46    603   71 0.5108 0.4656       5.845      5.7481|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8899 -  4.6576  1403   157  0.74  30.57   0.85     0.78      56206.07|
|  2:  4.6576 -  3.7158  1359   145  0.76  29.93   0.94     0.87      81215.78|
|  3:  3.7158 -  3.2517  1321   154  0.68  37.07   0.96     0.88      86899.90|
|  4:  3.2517 -  2.9569  1332   147  0.62  42.34   0.98     0.83      78195.76|
|  5:  2.9569 -  2.7464  1313   143  0.56  47.34   0.93     0.77      61780.46|
|  6:  2.7464 -  2.5853  1299   145  0.54  48.95   0.93     0.73      53699.76|
|  7:  2.5853 -  2.4565  1316   141  0.54  48.80   0.97     0.73      48226.84|
|  8:  2.4565 -  2.3500  1274   151  0.52  50.49   0.94     0.75      43650.07|
|  9:  2.3500 -  2.2598  1301   149  0.53  50.16   0.99     0.74      39826.08|
| 10:  2.2598 -  2.1821  1279   133  0.50  52.40   0.99     0.72      38973.53|
| 11:  2.1821 -  2.1141  1278   141  0.45  55.82   1.00     0.68      38768.22|
| 12:  2.1141 -  2.0538  1266   139  0.45  56.58   1.01     0.69      36326.82|
| 13:  2.0538 -  1.9998  1286   143  0.44  57.04   0.98     0.68      30507.93|
| 14:  1.9998 -  1.9512   603    71  0.47  54.61   0.96     0.65      24141.47|
|alpha:            min =        0.65 max =            0.88 mean =         0.76|
|beta:             min =    24141.47 max =        86899.90 mean =     52700.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.56|
|phase err.(work): min =        0.00 max =           89.99 mean =        46.78|
|phase err.(test): min =        0.00 max =           89.80 mean =        46.93|
|-----------------------------------------------------------------------------|

============================== 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 = 7.743822              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.173   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.488690              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.495   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.715 -  2.033:       14 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.033 -  2.352:       20 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.352 -  2.670:      103 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.670 -  2.989:     1812 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.989 -  3.307:     1932 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.307 -  3.626:     2770 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.626 -  3.944:     4777 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.944 -  4.263:     4487 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.263 -  4.581:     5885 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.581 -  4.900:     6993 |
|-----------------------------------------------------------------------------|
|-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 |        0.177 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.715 |       0.430 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    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 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4115   r_free= 0.4117   ksol= 0.00   Bsol= 0.00   scale= 0.940    |
|                                                                             |
| 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:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.213668                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3978   r_free= 0.3968   ksol= 0.33   Bsol= 26.64   scale= 0.958   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.28,-0.70,3.10,-0.00,0.00,0.00); trace/3= -0.30                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.205964                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.991291              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.261   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.730385              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.505   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3978      final r-factor (work) = 0.2679          |
| start r-factor (free) = 0.3968      final r-factor (free) = 0.2966          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.7498 = 5.99 * 0.50 * 6.1999 + 1.00 * 0.1772                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.0748 = 5.99 * 0.50 * 5.9990 + 1.00 * 0.1040                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2679      final r-factor (work) = 0.2453          |
| start r-factor (free) = 0.2966      final r-factor (free) = 0.3029          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3875 = 0.73 * 1.00 * 5.9990 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2613 = 0.73 * 1.00 * 5.8162 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.80   17.86    None  None   None       |
|    all(noH): 2823   0      0.00    84.80   17.86    None  None   None       |
|    Sol.    : 438    0      1.94    82.61   40.75    None  None   None       |
|    Mac.    : 2385   0      0.00    84.80   13.65    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.480:  728   |   5:    42.398 -  50.878:  112        |
|      1:     8.480 -  16.959: 1104   |   6:    50.878 -  59.358:   68        |
|      2:    16.959 -  25.439:  413   |   7:    59.358 -  67.838:   42        |
|      3:    25.439 -  33.919:  196   |   8:    67.838 -  76.317:   20        |
|      4:    33.919 -  42.398:  133   |   9:    76.317 -  84.797:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2453 r_free = 0.3029             target_work(ml) = 5.825         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2451 r_free = 0.3031             target_work(ml) = 5.824         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2451   r_free= 0.3031   ksol= 0.33   Bsol= 26.64   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.28,-0.70,3.10,-0.00,0.00,0.00); trace/3= -0.30                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.823889                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2421   r_free= 0.3002   ksol= 0.33   Bsol= 40.43   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-1.83,0.04,-0.00,0.00,0.00); trace/3= -1.41                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.816374                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.861625              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.241   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.201909              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.805  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2421      final r-factor (work) = 0.1720          |
| start r-factor (free) = 0.3002      final r-factor (free) = 0.2225          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.3306 = 3.86 * 0.50 * 5.8145 + 1.00 * 0.1040                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0506 = 3.86 * 0.50 * 5.6918 + 1.00 * 0.0609                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1720      final r-factor (work) = 0.1580          |
| start r-factor (free) = 0.2225      final r-factor (free) = 0.2045          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1623 = 0.20 * 1.00 * 5.6918 + 1.00 * 0.0131                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1136 = 0.20 * 1.00 * 5.4788 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.33    79.62   17.07    None  None   None       |
|    all(noH): 2823   0      1.33    79.62   17.07    None  None   None       |
|    Sol.    : 438    0      5.91    75.24   39.02    None  None   None       |
|    Mac.    : 2385   0      1.33    79.62   13.04    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.332 -   9.160:  793   |   5:    40.475 -  48.304:   99        |
|      1:     9.160 -  16.989: 1182   |   6:    48.304 -  56.133:   83        |
|      2:    16.989 -  24.818:  327   |   7:    56.133 -  63.962:   34        |
|      3:    24.818 -  32.647:  143   |   8:    63.962 -  71.791:   19        |
|      4:    32.647 -  40.475:  137   |   9:    71.791 -  79.619:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1580 r_free = 0.2045             target_work(ml) = 5.436         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1577 r_free = 0.2045             target_work(ml) = 5.435         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1577   r_free= 0.2045   ksol= 0.33   Bsol= 40.43   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-1.83,0.04,-0.00,0.00,0.00); trace/3= -1.41                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.435198                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1574   r_free= 0.2035   ksol= 0.33   Bsol= 40.43   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,-2.33,-1.22,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.429501                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.439367              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.720  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.221051              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.042  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1574      final r-factor (work) = 0.1288          |
| start r-factor (free) = 0.2035      final r-factor (free) = 0.1692          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7432 = 2.44 * 0.50 * 5.4789 + 1.00 * 0.0606                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5697 = 2.44 * 0.50 * 5.3437 + 1.00 * 0.0521                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1288      final r-factor (work) = 0.1232          |
| start r-factor (free) = 0.1692      final r-factor (free) = 0.1641          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1886 = 0.22 * 1.00 * 5.3437 + 1.00 * 0.0073                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1618 = 0.22 * 1.00 * 5.2225 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.76    81.50   17.03    None  None   None       |
|    all(noH): 2823   0      1.76    81.50   17.03    None  None   None       |
|    Sol.    : 438    0      5.51    75.05   39.56    None  None   None       |
|    Mac.    : 2385   0      1.76    81.50   12.89    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.758 -   9.732:  933   |   5:    41.630 -  49.604:  107        |
|      1:     9.732 -  17.707: 1132   |   6:    49.604 -  57.579:   81        |
|      2:    17.707 -  25.681:  268   |   7:    57.579 -  65.553:   41        |
|      3:    25.681 -  33.655:  125   |   8:    65.553 -  73.528:   14        |
|      4:    33.655 -  41.630:  118   |   9:    73.528 -  81.502:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1232 r_free = 0.1641             target_work(ml) = 5.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1231 r_free = 0.1639             target_work(ml) = 5.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1231   r_free= 0.1639   ksol= 0.33   Bsol= 40.43   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,-2.33,-1.22,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.203678                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1235   r_free= 0.1646   ksol= 0.32   Bsol= 40.43   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.61,-2.52,-1.77,-0.00,-0.00,-0.00); trace/3= -2.30                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.205267                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.853348              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.024  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.342259              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.326  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1235      final r-factor (work) = 0.1142          |
| start r-factor (free) = 0.1646      final r-factor (free) = 0.1560          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8927 = 1.85 * 0.50 * 5.2236 + 1.00 * 0.0521                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8448 = 1.85 * 0.50 * 5.1696 + 1.00 * 0.0542                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1142      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1560      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7768 = 0.34 * 1.00 * 5.1696 + 1.00 * 0.0074                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7655 = 0.34 * 1.00 * 5.1351 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.67    85.94   16.97    None  None   None       |
|    all(noH): 2823   0      1.67    85.94   16.97    None  None   None       |
|    Sol.    : 438    0      5.63    80.09   39.62    None  None   None       |
|    Mac.    : 2385   0      1.67    85.94   12.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.665 -  10.093: 1034   |   5:    43.803 -  52.230:  114        |
|      1:    10.093 -  18.520: 1098   |   6:    52.230 -  60.658:   65        |
|      2:    18.520 -  26.948:  234   |   7:    60.658 -  69.085:   29        |
|      3:    26.948 -  35.375:  122   |   8:    69.085 -  77.513:   14        |
|      4:    35.375 -  43.803:  110   |   9:    77.513 -  85.940:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1120 r_free = 0.1561             target_work(ml) = 5.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1119 r_free = 0.1559             target_work(ml) = 5.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1559   ksol= 0.32   Bsol= 40.43   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.61,-2.52,-1.77,-0.00,-0.00,-0.00); trace/3= -2.30                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.133619                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1559   ksol= 0.32   Bsol= 40.43   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-2.40,-1.79,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.133604                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.178682              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 154.480  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.245944              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.378  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1119      final r-factor (work) = 0.1083          |
| start r-factor (free) = 0.1559      final r-factor (free) = 0.1542          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6480 = 2.18 * 0.50 * 5.1351 + 1.00 * 0.0542                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6345 = 2.18 * 0.50 * 5.1195 + 1.00 * 0.0576                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1083      final r-factor (work) = 0.1075          |
| start r-factor (free) = 0.1542      final r-factor (free) = 0.1551          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3866 = 1.25 * 1.00 * 5.1195 + 1.00 * 0.0079                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3772 = 1.25 * 1.00 * 5.1112 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.75   17.05    None  None   None       |
|    all(noH): 2823   0      0.00    93.75   17.05    None  None   None       |
|    Sol.    : 438    0      6.36    83.92   40.27    None  None   None       |
|    Mac.    : 2385   0      0.00    93.75   12.79    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 -   9.375:  917   |   5:    46.876 -  56.251:  105        |
|      1:     9.375 -  18.750: 1229   |   6:    56.251 -  65.626:   50        |
|      2:    18.750 -  28.126:  231   |   7:    65.626 -  75.001:   29        |
|      3:    28.126 -  37.501:  138   |   8:    75.001 -  84.377:    9        |
|      4:    37.501 -  46.876:  113   |   9:    84.377 -  93.752:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1075 r_free = 0.1551             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1074 r_free = 0.1551             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1074   r_free= 0.1551   ksol= 0.32   Bsol= 40.43   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-2.40,-1.79,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.116284                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8899 -  4.6576 0.99   1403  157 0.0967 0.1215      5.3503      5.5151|
|  2:  4.6576 -  3.7158 0.99   1359  145 0.0826 0.1136      5.4061      5.6249|
|  3:  3.7158 -  3.2517 0.99   1321  154 0.1047 0.1511      5.4565      5.8268|
|  4:  3.2517 -  2.9569 0.99   1332  147 0.1174 0.1543      5.4358       5.592|
|  5:  2.9569 -  2.7464 0.99   1313  143 0.1244 0.1704       5.274      5.4737|
|  6:  2.7464 -  2.5853 0.99   1299  145 0.1141 0.1656      5.1535       5.391|
|  7:  2.5853 -  2.4565 0.99   1316  141 0.1170 0.1571        5.11      5.3193|
|  8:  2.4565 -  2.3500 0.98   1274  151 0.1102 0.1692      5.0147      5.3042|
|  9:  2.3500 -  2.2598 0.98   1301  149 0.1103 0.1841      4.9969      5.3022|
| 10:  2.2598 -  2.1821 0.98   1279  133 0.1079 0.1678       4.941      5.1949|
| 11:  2.1821 -  2.1141 1.00   1278  141 0.1115 0.1795      4.9259      5.2791|
| 12:  2.1141 -  2.0538 0.97   1266  139 0.1029 0.1641      4.8466      5.0776|
| 13:  2.0538 -  1.9998 0.98   1286  143 0.1127 0.1740      4.7649      5.0295|
| 14:  1.9998 -  1.9512 0.46    603   71 0.0975 0.1572      4.6207      4.9294|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8899 -  4.6576  1403   157  0.95   8.13   0.99     0.96       6210.15|
|  2:  4.6576 -  3.7158  1359   145  0.96   7.57   1.03     1.02       8455.17|
|  3:  3.7158 -  3.2517  1321   154  0.93  11.30   1.04     1.03      10085.55|
|  4:  3.2517 -  2.9569  1332   147  0.92  13.33   1.01     1.00      10064.80|
|  5:  2.9569 -  2.7464  1313   143  0.90  15.33   1.00     0.97       7638.08|
|  6:  2.7464 -  2.5853  1299   145  0.91  15.07   0.99     0.96       6375.99|
|  7:  2.5853 -  2.4565  1316   141  0.91  14.42   0.99     0.96       5557.45|
|  8:  2.4565 -  2.3500  1274   151  0.91  14.93   0.99     0.97       4890.16|
|  9:  2.3500 -  2.2598  1301   149  0.91  14.77   1.01     1.00       4772.73|
| 10:  2.2598 -  2.1821  1279   133  0.90  15.53   1.00     0.96       4311.91|
| 11:  2.1821 -  2.1141  1278   141  0.90  16.22   1.00     0.97       4347.52|
| 12:  2.1141 -  2.0538  1266   139  0.92  14.84   1.01     0.99       3883.24|
| 13:  2.0538 -  1.9998  1286   143  0.90  16.17   1.01     1.00       3187.81|
| 14:  1.9998 -  1.9512   603    71  0.92  14.23   0.99     0.96       2397.78|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2397.78 max =        10085.55 mean =      6042.52|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.62|
|phase err.(test): min =        0.00 max =           89.35 mean =        13.25|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1073   r_free= 0.1551   ksol= 0.32   Bsol= 41.83   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-2.23,-1.65,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.116260                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1073   r_free= 0.1551   ksol= 0.32   Bsol= 41.83   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-2.23,-1.65,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.116260                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8899 -  4.6576 0.99   1403  157 0.0967 0.1218      5.3517      5.5179|
|  2:  4.6576 -  3.7158 0.99   1359  145 0.0827 0.1136      5.4074       5.625|
|  3:  3.7158 -  3.2517 0.99   1321  154 0.1048 0.1512      5.4569      5.8276|
|  4:  3.2517 -  2.9569 0.99   1332  147 0.1174 0.1543      5.4357      5.5917|
|  5:  2.9569 -  2.7464 0.99   1313  143 0.1243 0.1703      5.2734      5.4724|
|  6:  2.7464 -  2.5853 0.99   1299  145 0.1141 0.1655      5.1531       5.391|
|  7:  2.5853 -  2.4565 0.99   1316  141 0.1169 0.1570      5.1097      5.3189|
|  8:  2.4565 -  2.3500 0.98   1274  151 0.1101 0.1690      5.0143      5.3032|
|  9:  2.3500 -  2.2598 0.98   1301  149 0.1103 0.1842      4.9966      5.3027|
| 10:  2.2598 -  2.1821 0.98   1279  133 0.1079 0.1677      4.9408       5.194|
| 11:  2.1821 -  2.1141 1.00   1278  141 0.1114 0.1793      4.9255      5.2789|
| 12:  2.1141 -  2.0538 0.97   1266  139 0.1029 0.1641       4.846      5.0773|
| 13:  2.0538 -  1.9998 0.98   1286  143 0.1127 0.1738      4.7645      5.0282|
| 14:  1.9998 -  1.9512 0.46    603   71 0.0975 0.1571      4.6206      4.9299|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8899 -  4.6576  1403   157  0.95   8.15   0.99     0.96       6237.27|
|  2:  4.6576 -  3.7158  1359   145  0.96   7.58   1.03     1.02       8478.19|
|  3:  3.7158 -  3.2517  1321   154  0.93  11.31   1.04     1.03      10094.01|
|  4:  3.2517 -  2.9569  1332   147  0.92  13.33   1.02     1.00      10060.80|
|  5:  2.9569 -  2.7464  1313   143  0.90  15.32   1.00     0.98       7631.16|
|  6:  2.7464 -  2.5853  1299   145  0.91  15.06   1.00     0.97       6369.89|
|  7:  2.5853 -  2.4565  1316   141  0.91  14.42   1.00     0.97       5551.63|
|  8:  2.4565 -  2.3500  1274   151  0.91  14.92   1.00     0.97       4884.92|
|  9:  2.3500 -  2.2598  1301   149  0.91  14.77   1.02     1.00       4769.18|
| 10:  2.2598 -  2.1821  1279   133  0.90  15.52   1.01     0.97       4309.29|
| 11:  2.1821 -  2.1141  1278   141  0.90  16.22   1.01     0.98       4343.91|
| 12:  2.1141 -  2.0538  1266   139  0.92  14.82   1.02     1.00       3876.92|
| 13:  2.0538 -  1.9998  1286   143  0.90  16.17   1.02     1.01       3184.55|
| 14:  1.9998 -  1.9512   603    71  0.92  14.23   1.00     0.97       2397.63|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2397.63 max =        10094.01 mean =      6043.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.61|
|phase err.(test): min =        0.00 max =           89.32 mean =        13.25|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.75   17.06    None  None   None       |
|    all(noH): 2823   0      0.00    93.75   17.06    None  None   None       |
|    Sol.    : 438    0      6.36    83.92   40.28    None  None   None       |
|    Mac.    : 2385   0      0.00    93.75   12.79    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 -   9.378:  917   |   5:    46.879 -  56.254:  105        |
|      1:     9.378 -  18.753: 1229   |   6:    56.254 -  65.629:   50        |
|      2:    18.753 -  28.129:  231   |   7:    65.629 -  75.004:   29        |
|      3:    28.129 -  37.504:  138   |   8:    75.004 -  84.380:    9        |
|      4:    37.504 -  46.879:  113   |   9:    84.380 -  93.755:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 295         
Filter by distance & map next to the model:
   mapped sites are within: 0.487 - 4.556
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 293 from: 295
   mapped sites are within: 0.714 - 4.556

peak=    6.028 closest distance to " NE2 GLN A  11 " =    1.153
peak=    5.899 closest distance to " NH2 ARG A  56 " =    2.113
peak=    5.693 closest distance to " O   HOH Z 126 " =    1.938
peak=    5.662 closest distance to " O   HOH Z 144 " =    1.738
peak=    5.307 closest distance to " CG  PRO A  54 " =    1.170
peak=    5.222 closest distance to " O   HOH Z 278 " =    1.100
peak=    5.097 closest distance to " CB  SER A  63 " =    1.243
peak=    5.095 closest distance to " O   HOH Z 193 " =    1.849
peak=    5.069 closest distance to " CB  GLN A 183 " =    1.238
peak=    4.989 closest distance to " CB  GLN A 223 " =    1.457
peak=    4.950 closest distance to " CB  ARG A 275 " =    0.910
peak=    4.911 closest distance to " O   HOH Z 232 " =    2.330
peak=    4.833 closest distance to " CG  PRO A 213 " =    1.226
peak=    4.762 closest distance to " CB  SER A   3 " =    1.392
peak=    4.698 closest distance to " O   HOH Z 108 " =    1.568
peak=    4.645 closest distance to " C   PRO A 198 " =    1.504
peak=    4.611 closest distance to " O   HOH Z 427 " =    2.690
peak=    4.594 closest distance to " O   HOH Z 260 " =    1.200
peak=    4.575 closest distance to " OD2 ASP A 286 " =    2.690
peak=    4.544 closest distance to " CB  ASN A 148 " =    1.478
peak=    4.540 closest distance to " OD1 ASN A  69 " =    2.640
peak=    4.504 closest distance to " O   HOH Z  78 " =    1.771
peak=    4.429 closest distance to " O   HOH Z 236 " =    1.430
peak=    4.309 closest distance to " CB  GLU A 152 " =    1.244
peak=    4.302 closest distance to " CA  TYR A  30 " =    0.934
peak=    4.302 closest distance to " O   HOH Z 203 " =    1.864
peak=    4.297 closest distance to " CB  LEU A 228 " =    1.099
peak=    4.289 closest distance to " CG  PRO A  90 " =    1.115
peak=    4.283 closest distance to " CB  GLU A 128 " =    1.072
peak=    4.244 closest distance to " O   HOH Z 234 " =    3.624
peak=    4.238 closest distance to " CB  PRO A  54 " =    0.961
peak=    4.236 closest distance to " CG  PRO A 198 " =    1.292
peak=    4.226 closest distance to " O   HOH Z 316 " =    3.004
peak=    4.211 closest distance to " CB  TYR A 169 " =    0.874
peak=    4.205 closest distance to " NZ  LYS A 117 " =    3.180
peak=    4.165 closest distance to " O   HOH Z 207 " =    1.684
peak=    4.139 closest distance to " ND2 ASN A 187 " =    1.538
peak=    4.126 closest distance to " O   HOH Z 371 " =    3.219
peak=    4.125 closest distance to " CB  VAL A 265 " =    1.326
peak=    4.103 closest distance to " O   HOH Z  10 " =    1.849
peak=    4.102 closest distance to " OG BSER A 164 " =    2.325
peak=    4.097 closest distance to " O   HOH Z 369 " =    2.093
peak=    4.092 closest distance to " CB  TRP A 179 " =    1.292
peak=    4.080 closest distance to " O   HOH Z 344 " =    2.909
peak=    4.069 closest distance to " O   HOH Z 298 " =    1.882
peak=    4.067 closest distance to " O   HOH Z 303 " =    2.094
peak=    4.057 closest distance to " O   HOH Z 368 " =    1.872
peak=    4.052 closest distance to " O   HOH Z 287 " =    2.004
peak=    4.048 closest distance to " NH1BARG A 145 " =    1.385
peak=    4.044 closest distance to " O   HOH Z 134 " =    1.281
peak=    4.040 closest distance to " O   HOH Z   6 " =    2.138
peak=    4.025 closest distance to " O   HOH Z  15 " =    2.202
peak=    3.992 closest distance to " O   HOH Z 263 " =    2.255
peak=    3.992 closest distance to " CG1 ILE A  33 " =    1.243
peak=    3.974 closest distance to " CB  ARG A  79 " =    1.462
peak=    3.973 closest distance to " O   HOH Z 202 " =    1.160
peak=    3.972 closest distance to " CB  ARG A 139 " =    0.985
peak=    3.959 closest distance to " O   HOH Z  97 " =    1.948
peak=    3.953 closest distance to " O   HOH Z 272 " =    1.823
peak=    3.950 closest distance to " O   HOH Z   1 " =    1.724
peak=    3.946 closest distance to " O   HOH Z 124 " =    1.301
peak=    3.945 closest distance to " O   HOH Z   3 " =    1.880
peak=    3.942 closest distance to " O   SER A  87 " =    2.235
peak=    3.937 closest distance to " O   HOH Z  21 " =    1.672
peak=    3.936 closest distance to " CG2 VAL A 257 " =    0.906
peak=    3.929 closest distance to " O   HOH Z 193 " =    1.988
peak=    3.916 closest distance to " CA  ASN A 215 " =    1.243
peak=    3.915 closest distance to " CA  ALA A  21 " =    1.109
peak=    3.902 closest distance to " O   HOH Z 128 " =    2.101
peak=    3.885 closest distance to " O   HOH Z  59 " =    1.820
peak=    3.876 closest distance to " O   HOH Z  61 " =    1.683
peak=    3.865 closest distance to " CD BLYS A 290 " =    1.267
peak=    3.853 closest distance to " O   HOH Z  73 " =    1.651
peak=    3.845 closest distance to " O   HOH Z 132 " =    2.191
peak=    3.841 closest distance to " O   HOH Z 407 " =    2.176
peak=    3.838 closest distance to " CA  GLY A 241 " =    3.742
peak=    3.815 closest distance to " O   HOH Z  61 " =    1.584
peak=    3.814 closest distance to " O   MET A 105 " =    1.774
peak=    3.792 closest distance to " O   HOH Z 284 " =    2.868
peak=    3.778 closest distance to " O   HOH Z 158 " =    3.000
peak=    3.773 closest distance to " O   HOH Z 425 " =    2.029
peak=    3.768 closest distance to " O   HOH Z  44 " =    1.882
peak=    3.761 closest distance to " CA  THR A 221 " =    0.938
peak=    3.756 closest distance to " CA  THR A 264 " =    0.848
peak=    3.749 closest distance to " CA  ASP A 124 " =    0.714
peak=    3.749 closest distance to " O   HOH Z 353 " =    2.620
peak=    3.743 closest distance to " O   HOH Z 180 " =    2.199
peak=    3.733 closest distance to " O   HOH Z 261 " =    1.701
peak=    3.730 closest distance to " O   HOH Z 368 " =    3.601
peak=    3.726 closest distance to " CB  TRP A 266 " =    1.065
peak=    3.713 closest distance to " O   HOH Z 389 " =    1.729
peak=    3.700 closest distance to " O   HOH Z  66 " =    2.096
peak=    3.698 closest distance to " CG  ARG A  66 " =    2.520
peak=    3.693 closest distance to " O   HOH Z 346 " =    1.681
peak=    3.681 closest distance to " O   HOH Z 281 " =    4.556
peak=    3.680 closest distance to " O   HOH Z  88 " =    3.048
peak=    3.679 closest distance to " NH2BARG A 145 " =    2.010
peak=    3.674 closest distance to " O   HOH Z 227 " =    1.704
peak=    3.665 closest distance to " NH1AARG A 145 " =    1.091
peak=    3.662 closest distance to " O   HOH Z 108 " =    1.874
peak=    3.655 closest distance to " O   HOH Z 426 " =    1.610
peak=    3.652 closest distance to " O   HOH Z 327 " =    1.691
peak=    3.649 closest distance to " O   HOH Z 141 " =    1.678
peak=    3.648 closest distance to " O   HOH Z 326 " =    1.429
peak=    3.645 closest distance to " O   HOH Z  43 " =    1.916
peak=    3.640 closest distance to " O   HOH Z  71 " =    1.345
peak=    3.639 closest distance to " CA  VAL A 126 " =    1.217
peak=    3.632 closest distance to " O   HOH Z  40 " =    2.011
peak=    3.630 closest distance to " O   HOH Z 250 " =    1.401
peak=    3.614 closest distance to " CB  ARG A 190 " =    1.739
peak=    3.612 closest distance to " O   HOH Z 147 " =    1.679
peak=    3.602 closest distance to " O   HOH Z 144 " =    2.270
peak=    3.599 closest distance to " O   HOH Z 194 " =    1.909
peak=    3.595 closest distance to " O   HOH Z 209 " =    2.283
peak=    3.592 closest distance to " O   HOH Z 227 " =    2.191
peak=    3.589 closest distance to " O   HOH Z 234 " =    3.766
peak=    3.585 closest distance to " O   HOH Z 132 " =    1.019
peak=    3.573 closest distance to " CD2 LEU A 255 " =    1.327
peak=    3.569 closest distance to " O   HOH Z 271 " =    2.183
peak=    3.568 closest distance to " O   HOH Z 313 " =    1.601
peak=    3.564 closest distance to " CA  MET A  40 " =    1.041
peak=    3.553 closest distance to " O   HOH Z  93 " =    2.149
peak=    3.543 closest distance to " O   HOH Z 106 " =    2.285
peak=    3.541 closest distance to " CE1 TYR A 186 " =    1.269
peak=    3.539 closest distance to " CD2 TRP A 179 " =    1.415
peak=    3.536 closest distance to " O   HOH Z 163 " =    1.809
peak=    3.522 closest distance to " OG  SER A  22 " =    2.786
peak=    3.520 closest distance to " O   HOH Z 374 " =    2.510
peak=    3.517 closest distance to " O   HOH Z 211 " =    2.343
peak=    3.516 closest distance to " O   HOH Z 125 " =    2.180
peak=    3.503 closest distance to " CG2 THR A 221 " =    1.137
peak=    3.503 closest distance to " O   HOH Z 260 " =    1.048
peak=    3.499 closest distance to " CE  LYS A  76 " =    0.868
peak=    3.493 closest distance to " O   HOH Z 402 " =    1.383
peak=    3.493 closest distance to " O   HOH Z 419 " =    1.888
peak=    3.487 closest distance to " CE AMET A  47 " =    1.321
peak=    3.486 closest distance to " CG  LEU A 167 " =    1.196
peak=    3.484 closest distance to " O   HOH Z 291 " =    1.862
peak=    3.483 closest distance to " O   HOH Z 357 " =    1.768
peak=    3.475 closest distance to " O   HOH Z 133 " =    1.489
peak=    3.469 closest distance to " CB  SER A  26 " =    1.564
peak=    3.469 closest distance to " NH2 ARG A 219 " =    1.889
peak=    3.466 closest distance to " O   HOH Z 279 " =    2.233
peak=    3.463 closest distance to " O   HOH Z 380 " =    1.989
peak=    3.460 closest distance to " OD1BASN A 224 " =    2.216
peak=    3.457 closest distance to " O   HOH Z 172 " =    3.336
peak=    3.443 closest distance to " O   HOH Z 389 " =    3.121
peak=    3.442 closest distance to " O   HOH Z 132 " =    2.430
peak=    3.435 closest distance to " O   HOH Z   1 " =    1.641
peak=    3.432 closest distance to " CB  VAL A 202 " =    1.643
peak=    3.429 closest distance to " O   HOH Z  49 " =    1.997
peak=    3.428 closest distance to " O   HOH Z 218 " =    2.272
peak=    3.426 closest distance to " O   HOH Z 423 " =    2.688
peak=    3.424 closest distance to " CG  GLU A 277 " =    2.173
peak=    3.418 closest distance to " O   HOH Z  63 " =    2.406
peak=    3.414 closest distance to " O   HOH Z 425 " =    1.234
peak=    3.414 closest distance to " CD2 LEU A 297 " =    0.961
peak=    3.411 closest distance to " O   HOH Z  48 " =    1.399
peak=    3.401 closest distance to " N   PHE A 130 " =    1.306
peak=    3.398 closest distance to " O   HOH Z 286 " =    2.267
peak=    3.393 closest distance to " CB  SER A 216 " =    0.766
peak=    3.391 closest distance to " CG  PRO A 243 " =    1.117
peak=    3.390 closest distance to " O   HOH Z 214 " =    1.960
peak=    3.389 closest distance to " O   HOH Z 409 " =    2.548
peak=    3.389 closest distance to " O   HOH Z 173 " =    1.889
peak=    3.387 closest distance to " CB  GLN A  88 " =    1.208
peak=    3.382 closest distance to " O   HOH Z 189 " =    1.466
peak=    3.377 closest distance to " O   HOH Z 411 " =    1.742
peak=    3.377 closest distance to " CG1BVAL A  72 " =    1.441
peak=    3.377 closest distance to " CD  ARG A  66 " =    2.370
peak=    3.377 closest distance to " O   HOH Z 153 " =    1.625
peak=    3.376 closest distance to " O   HOH Z 193 " =    1.511
peak=    3.375 closest distance to " CB  ALA A 291 " =    1.421
peak=    3.369 closest distance to " O   HOH Z 276 " =    1.247
peak=    3.366 closest distance to " CD1 LEU A 300 " =    1.247
peak=    3.364 closest distance to " CB  LEU A 143 " =    1.100
peak=    3.362 closest distance to " O   HOH Z 371 " =    1.502
peak=    3.358 closest distance to " NH2AARG A 190 " =    1.282
peak=    3.351 closest distance to " NH2AARG A 275 " =    3.653
peak=    3.347 closest distance to " O   HOH Z 366 " =    3.163
peak=    3.332 closest distance to " O   HOH Z 329 " =    3.471
peak=    3.332 closest distance to " O   HOH Z  50 " =    1.502
peak=    3.331 closest distance to " CA  ARG A  56 " =    2.099
peak=    3.330 closest distance to " O   HOH Z 189 " =    1.987
peak=    3.329 closest distance to " CB  MET A  47 " =    1.158
peak=    3.328 closest distance to " O   HOH Z 368 " =    2.603
peak=    3.327 closest distance to " O   HOH Z 286 " =    2.437
peak=    3.325 closest distance to " CA  VAL A  41 " =    0.935
peak=    3.323 closest distance to " CG2 ILE A 120 " =    1.182
peak=    3.323 closest distance to " CB  ASP A 171 " =    1.029
peak=    3.322 closest distance to " O   HOH Z 437 " =    1.667
peak=    3.321 closest distance to " CG2BVAL A  41 " =    0.903
peak=    3.321 closest distance to " O   HOH Z 248 " =    1.650
peak=    3.319 closest distance to " O   HOH Z 403 " =    1.320
peak=    3.316 closest distance to " CG  MET A 185 " =    1.224
peak=    3.313 closest distance to " O   HOH Z 213 " =    1.801
peak=    3.313 closest distance to " CD  ARG A 159 " =    0.730
peak=    3.308 closest distance to " O   HOH Z 291 " =    1.567
peak=    3.308 closest distance to " CD  LYS A 166 " =    1.255
peak=    3.306 closest distance to " O   HOH Z 345 " =    3.415
peak=    3.304 closest distance to " O   HOH Z 336 " =    1.835
peak=    3.303 closest distance to " CB  LYS A 117 " =    1.167
peak=    3.301 closest distance to " N   ARG A 156 " =    1.226
peak=    3.295 closest distance to " O   HOH Z   2 " =    1.421
peak=    3.293 closest distance to " O   HOH Z 151 " =    1.561
peak=    3.292 closest distance to " O   HOH Z 188 " =    1.901
peak=    3.290 closest distance to " O   ALA A 165 " =    1.339
peak=    3.289 closest distance to " CB  THR A 157 " =    1.027
peak=    3.286 closest distance to " O   HOH Z 295 " =    1.534
peak=    3.283 closest distance to " NH2 ARG A 156 " =    1.247
peak=    3.281 closest distance to " OG BSER A  99 " =    2.192
peak=    3.278 closest distance to " O   HOH Z 266 " =    2.918
peak=    3.277 closest distance to " O   HOH Z 392 " =    1.449
peak=    3.277 closest distance to " CG1 VAL A 202 " =    1.938
peak=    3.274 closest distance to " C   ALA A 299 " =    0.947
peak=    3.274 closest distance to " O   ALA A   1 " =    1.482
peak=    3.272 closest distance to " O   HOH Z 282 " =    1.590
peak=    3.271 closest distance to " CB  GLU A 277 " =    3.483
peak=    3.271 closest distance to " O   HOH Z 258 " =    1.735
peak=    3.270 closest distance to " OG  SER A  62 " =    2.993
peak=    3.267 closest distance to " O   HOH Z  85 " =    2.150
peak=    3.267 closest distance to " CE BMET A  47 " =    1.481
peak=    3.264 closest distance to " O   HOH Z  64 " =    2.094
peak=    3.263 closest distance to " N   ASN A  39 " =    1.181
peak=    3.262 closest distance to " CA  LYS A 290 " =    1.328
peak=    3.255 closest distance to " ND1 HIS A  86 " =    1.782
peak=    3.246 closest distance to " O   HOH Z 163 " =    1.752
peak=    3.245 closest distance to " CA  GLY A  80 " =    1.030
peak=    3.242 closest distance to " CG  MET A 185 " =    1.112
peak=    3.242 closest distance to " N   TYR A  15 " =    0.967
peak=    3.236 closest distance to " O   HOH Z 409 " =    3.437
peak=    3.235 closest distance to " O   HOH Z 287 " =    1.777
peak=    3.226 closest distance to " O   HOH Z 438 " =    2.110
peak=    3.226 closest distance to " CB  ALA A  21 " =    1.750
peak=    3.219 closest distance to " O   HOH Z 115 " =    1.973
peak=    3.218 closest distance to " O   HOH Z 128 " =    2.176
peak=    3.218 closest distance to " O   HOH Z 261 " =    1.444
peak=    3.216 closest distance to " N   GLN A 278 " =    0.989
peak=    3.215 closest distance to " NE AARG A 275 " =    1.439
peak=    3.213 closest distance to " N   ASN A 127 " =    1.238
peak=    3.207 closest distance to " O   HOH Z 334 " =    1.381
peak=    3.205 closest distance to " O   HOH Z  49 " =    2.124
peak=    3.203 closest distance to " CG  MET A  93 " =    0.936
peak=    3.199 closest distance to " CD  PRO A 243 " =    1.576
peak=    3.195 closest distance to " O   HOH Z 406 " =    1.605
peak=    3.193 closest distance to " O   HOH Z 135 " =    1.573
peak=    3.191 closest distance to " O   GLY A  57 " =    2.477
peak=    3.189 closest distance to " CA  ALA A  43 " =    1.243
peak=    3.188 closest distance to " OG BSER A 258 " =    3.431
peak=    3.186 closest distance to " CG1 ILE A 151 " =    0.875
peak=    3.185 closest distance to " O   HOH Z 391 " =    3.005
peak=    3.184 closest distance to " O   HOH Z 234 " =    1.811
peak=    3.184 closest distance to " CA  ALA A 248 " =    1.387
peak=    3.177 closest distance to " CA  ILE A  33 " =    1.571
peak=    3.177 closest distance to " CB  TYR A  30 " =    1.487
peak=    3.175 closest distance to " CD  LYS A 119 " =    1.098
peak=    3.174 closest distance to " O   HOH Z 379 " =    1.862
peak=    3.174 closest distance to " O   GLY A 229 " =    1.539
peak=    3.174 closest distance to " CB  ALA A  34 " =    1.088
peak=    3.173 closest distance to " CB  THR A  31 " =    1.779
peak=    3.173 closest distance to " CG2 VAL A  67 " =    1.033
peak=    3.170 closest distance to " CA  ALA A 154 " =    1.017
peak=    3.168 closest distance to " O   HOH Z 261 " =    2.060
peak=    3.167 closest distance to " CG  MET A 113 " =    1.223
peak=    3.162 closest distance to " O   HOH Z 148 " =    3.160
peak=    3.161 closest distance to " CB  ALA A  71 " =    1.471
peak=    3.158 closest distance to " CA  ALA A  51 " =    0.984
peak=    3.158 closest distance to " CG2 ILE A  20 " =    1.552
peak=    3.157 closest distance to " CA  ALA A 233 " =    1.045
peak=    3.156 closest distance to " O   HOH Z 289 " =    1.399
peak=    3.155 closest distance to " O   HOH Z  68 " =    1.516
peak=    3.149 closest distance to " CE2 TRP A 179 " =    1.544
peak=    3.148 closest distance to " OE1 GLN A  11 " =    1.995
peak=    3.146 closest distance to " NE2 GLN A  58 " =    4.296
peak=    3.144 closest distance to " NE2 GLN A  73 " =    3.546
peak=    3.136 closest distance to " CA  ASN A 176 " =    1.181
peak=    3.133 closest distance to " CB  ASN A  39 " =    0.871
peak=    3.127 closest distance to " CD2 HIS A  81 " =    1.159
peak=    3.126 closest distance to " CB  TYR A 116 " =    0.877
peak=    3.123 closest distance to " O   HOH Z 106 " =    1.876
peak=    3.121 closest distance to " O   HOH Z 273 " =    2.921
peak=    3.119 closest distance to " CB  LEU A 255 " =    0.735
peak=    3.117 closest distance to " O   HOH Z 417 " =    3.280
peak=    3.101 closest distance to " CG  LYS A 166 " =    1.549
peak=    3.100 closest distance to " CB  GLU A 152 " =    1.410
peak=    3.078 closest distance to " N   CYS A 260 " =    0.724
peak=    3.069 closest distance to " O   HOH Z  78 " =    2.203
peak=    3.068 closest distance to " O   HOH Z 128 " =    1.661
peak=    3.068 closest distance to " CB  TRP A 179 " =    1.659
peak=    3.054 closest distance to " O   HOH Z 365 " =    2.676
peak=    3.037 closest distance to " CG  ARG A 269 " =    1.297
peak=    3.036 closest distance to " O   HOH Z 280 " =    2.564
peak=    3.007 closest distance to " O   HOH Z 213 " =    1.614

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 201         
Filter by distance & map next to the model:
   mapped sites are within: 0.611 - 5.071
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 201
   mapped sites are within: 0.795 - 5.071

peak=   -4.644 closest distance to " O   HOH Z 266 " =    4.252
peak=   -4.503 closest distance to " CB  PRO A 243 " =    2.564
peak=   -4.340 closest distance to " O   HOH Z 198 " =    2.068
peak=   -4.337 closest distance to " CD  ARG A 156 " =    1.955
peak=   -4.301 closest distance to " SG  CYS A 254 " =    3.202
peak=   -4.249 closest distance to " O   HOH Z 377 " =    2.022
peak=   -4.244 closest distance to " O   PRO A 198 " =    1.311
peak=   -4.201 closest distance to " O   VAL A 153 " =    2.372
peak=   -4.197 closest distance to " N   GLN A  58 " =    1.710
peak=   -4.126 closest distance to " C   HIS A 108 " =    1.114
peak=   -4.053 closest distance to " O   HOH Z 388 " =    1.827
peak=   -4.041 closest distance to " CG  GLN A 223 " =    1.983
peak=   -4.029 closest distance to " O   HOH Z  13 " =    1.401
peak=   -4.026 closest distance to " O   VAL A  67 " =    2.650
peak=   -4.011 closest distance to " CB  TYR A  15 " =    2.163
peak=   -3.993 closest distance to " O   HOH Z 231 " =    2.001
peak=   -3.971 closest distance to " OXT GLY A 302 " =    2.720
peak=   -3.941 closest distance to " CZ  PHE A  59 " =    1.552
peak=   -3.932 closest distance to " CG  LYS A 193 " =    2.289
peak=   -3.927 closest distance to " O   HOH Z  43 " =    1.708
peak=   -3.923 closest distance to " O   HOH Z  98 " =    1.929
peak=   -3.921 closest distance to " O   PRO A 163 " =    1.928
peak=   -3.910 closest distance to " O   VAL A  67 " =    2.741
peak=   -3.886 closest distance to " CD  ARG A 139 " =    1.496
peak=   -3.869 closest distance to " CE3 TRP A 274 " =    2.322
peak=   -3.867 closest distance to " N   ASP A 286 " =    2.412
peak=   -3.866 closest distance to " CB  ALA A 291 " =    2.382
peak=   -3.858 closest distance to " C   ALA A 158 " =    1.238
peak=   -3.850 closest distance to " O   HOH Z 290 " =    1.125
peak=   -3.830 closest distance to " O   HOH Z 407 " =    3.109
peak=   -3.808 closest distance to " O   HOH Z 395 " =    5.071
peak=   -3.796 closest distance to " N   ALA A 248 " =    1.581
peak=   -3.782 closest distance to " O   ILE A 109 " =    2.551
peak=   -3.778 closest distance to " CB  ASN A  39 " =    2.168
peak=   -3.770 closest distance to " ND2 ASN A  45 " =    0.916
peak=   -3.769 closest distance to " OD1 ASP A 191 " =    1.857
peak=   -3.767 closest distance to " O   HOH Z 385 " =    2.036
peak=   -3.765 closest distance to " OG BSER A 134 " =    1.211
peak=   -3.761 closest distance to " O   HOH Z 185 " =    2.163
peak=   -3.761 closest distance to " CA  GLY A 203 " =    2.232
peak=   -3.760 closest distance to " CZ  TYR A 169 " =    1.683
peak=   -3.749 closest distance to " CD1 LEU A 228 " =    2.201
peak=   -3.738 closest distance to " O   SER A 135 " =    1.487
peak=   -3.733 closest distance to " O   HOH Z  24 " =    1.280
peak=   -3.729 closest distance to " C   ASP A 231 " =    2.560
peak=   -3.728 closest distance to " CE  MET A 105 " =    2.126
peak=   -3.726 closest distance to " O   ALA A 161 " =    1.551
peak=   -3.720 closest distance to " CG  PHE A 283 " =    2.610
peak=   -3.702 closest distance to " O   HOH Z  93 " =    1.852
peak=   -3.701 closest distance to " O   HOH Z 435 " =    2.661
peak=   -3.700 closest distance to " CD1 PHE A  59 " =    1.840
peak=   -3.683 closest distance to " CE2 TYR A  30 " =    2.903
peak=   -3.681 closest distance to " CE2 PHE A 218 " =    2.526
peak=   -3.667 closest distance to " CZ3 TRP A 179 " =    1.279
peak=   -3.663 closest distance to " CG  ASP A 231 " =    0.795
peak=   -3.644 closest distance to " O   HOH Z  60 " =    2.255
peak=   -3.631 closest distance to " O   HOH Z 102 " =    1.690
peak=   -3.630 closest distance to " N   MET A 188 " =    1.899
peak=   -3.629 closest distance to " CG1 VAL A 112 " =    2.853
peak=   -3.619 closest distance to " C   LEU A 143 " =    1.195
peak=   -3.613 closest distance to " N   ALA A  43 " =    2.387
peak=   -3.610 closest distance to " CD1 LEU A 101 " =    2.343
peak=   -3.609 closest distance to " CA  SER A 146 " =    2.268
peak=   -3.608 closest distance to " N   HIS A 115 " =    1.724
peak=   -3.606 closest distance to " CA  GLY A 133 " =    1.946
peak=   -3.604 closest distance to " CB  ALA A 291 " =    2.166
peak=   -3.604 closest distance to " O   HOH Z  11 " =    1.800
peak=   -3.598 closest distance to " OG  SER A  97 " =    1.996
peak=   -3.589 closest distance to " O   HOH Z 385 " =    1.840
peak=   -3.589 closest distance to " O   HOH Z  88 " =    1.937
peak=   -3.583 closest distance to " O   PRO A 198 " =    1.283
peak=   -3.562 closest distance to " OD1 ASN A 187 " =    1.702
peak=   -3.560 closest distance to " OXT GLY A 302 " =    3.476
peak=   -3.556 closest distance to " O   HOH Z 198 " =    1.482
peak=   -3.545 closest distance to " O   HOH Z 263 " =    2.948
peak=   -3.541 closest distance to " CB  ASP A  27 " =    2.387
peak=   -3.540 closest distance to " NH1 ARG A 195 " =    2.570
peak=   -3.534 closest distance to " O   HOH Z  47 " =    1.516
peak=   -3.528 closest distance to " O   HOH Z 166 " =    1.308
peak=   -3.522 closest distance to " CB  ASP A 132 " =    2.274
peak=   -3.516 closest distance to " O   TRP A  70 " =    1.508
peak=   -3.514 closest distance to " CB  ALA A 248 " =    1.931
peak=   -3.482 closest distance to " O   HOH Z  11 " =    1.971
peak=   -3.480 closest distance to " NH2 ARG A  79 " =    1.815
peak=   -3.477 closest distance to " SG ACYS A 201 " =    1.937
peak=   -3.475 closest distance to " O   HOH Z 114 " =    2.803
peak=   -3.473 closest distance to " O   HOH Z  88 " =    2.401
peak=   -3.471 closest distance to " ND2 ASN A 187 " =    1.521
peak=   -3.462 closest distance to " O   ALA A  51 " =    1.293
peak=   -3.444 closest distance to " OD1 ASP A 171 " =    1.527
peak=   -3.443 closest distance to " CB  ASP A 149 " =    2.012
peak=   -3.439 closest distance to " O   HOH Z  52 " =    1.399
peak=   -3.437 closest distance to " CG  PRO A 163 " =    2.510
peak=   -3.435 closest distance to " O   HOH Z 389 " =    1.826
peak=   -3.433 closest distance to " N   THR A 157 " =    1.497
peak=   -3.422 closest distance to " OD2 ASP A 171 " =    2.058
peak=   -3.422 closest distance to " O   SER A 146 " =    0.967
peak=   -3.413 closest distance to " CB  ALA A  43 " =    2.319
peak=   -3.409 closest distance to " N   SER A 276 " =    1.185
peak=   -3.409 closest distance to " NH1AARG A 275 " =    1.741
peak=   -3.407 closest distance to " O   HOH Z 353 " =    2.076
peak=   -3.391 closest distance to " CD2 LEU A 300 " =    2.796
peak=   -3.389 closest distance to " OH  TYR A 214 " =    1.257
peak=   -3.387 closest distance to " O   HOH Z 311 " =    3.524
peak=   -3.375 closest distance to " N   GLN A 122 " =    1.434
peak=   -3.372 closest distance to " O   HOH Z  10 " =    1.401
peak=   -3.370 closest distance to " O   HOH Z  90 " =    2.552
peak=   -3.366 closest distance to " OD1 ASP A 191 " =    1.348
peak=   -3.366 closest distance to " O   HOH Z 298 " =    1.205
peak=   -3.360 closest distance to " O   HOH Z 351 " =    1.580
peak=   -3.356 closest distance to " O   PHE A 218 " =    1.532
peak=   -3.354 closest distance to " O   HOH Z 313 " =    1.967
peak=   -3.344 closest distance to " OD1 ASN A 148 " =    1.648
peak=   -3.342 closest distance to " CB  PRO A 163 " =    2.574
peak=   -3.338 closest distance to " O   HOH Z 438 " =    1.168
peak=   -3.333 closest distance to " O   TRP A  92 " =    1.680
peak=   -3.329 closest distance to " O   HOH Z 348 " =    1.822
peak=   -3.324 closest distance to " CD  GLN A  88 " =    0.866
peak=   -3.324 closest distance to " OD1 ASP A 200 " =    1.304
peak=   -3.321 closest distance to " CB  ALA A  51 " =    1.869
peak=   -3.316 closest distance to " C   TRP A 274 " =    1.517
peak=   -3.315 closest distance to " CD2 LEU A 300 " =    3.110
peak=   -3.306 closest distance to " O   HOH Z 137 " =    1.420
peak=   -3.306 closest distance to " O   HOH Z 137 " =    1.463
peak=   -3.303 closest distance to " OG ASER A 134 " =    1.008
peak=   -3.298 closest distance to " O   HOH Z 317 " =    2.522
peak=   -3.297 closest distance to " OD1 ASN A 176 " =    1.232
peak=   -3.296 closest distance to " O   HOH Z 193 " =    1.546
peak=   -3.285 closest distance to " O   HOH Z  63 " =    1.430
peak=   -3.276 closest distance to " CE  LYS A  76 " =    2.915
peak=   -3.273 closest distance to " ND2 ASN A 252 " =    1.520
peak=   -3.267 closest distance to " NH2BARG A 275 " =    1.963
peak=   -3.262 closest distance to " O   VAL A 174 " =    2.103
peak=   -3.261 closest distance to " O   HOH Z 211 " =    1.531
peak=   -3.258 closest distance to " CA  ASP A 298 " =    1.033
peak=   -3.258 closest distance to " O   HOH Z 120 " =    2.244
peak=   -3.257 closest distance to " O   GLY A 211 " =    1.314
peak=   -3.253 closest distance to " O   HOH Z   3 " =    1.921
peak=   -3.250 closest distance to " OD2 ASP A 191 " =    1.430
peak=   -3.247 closest distance to " N   GLN A  58 " =    1.246
peak=   -3.243 closest distance to " OG BSER A 134 " =    1.634
peak=   -3.243 closest distance to " O   HOH Z 148 " =    3.237
peak=   -3.241 closest distance to " CB  ILE A  33 " =    2.887
peak=   -3.241 closest distance to " O   HOH Z  60 " =    1.899
peak=   -3.237 closest distance to " O   HOH Z 423 " =    1.120
peak=   -3.236 closest distance to " C   PRO A  90 " =    1.483
peak=   -3.234 closest distance to " N   SER A 212 " =    1.906
peak=   -3.226 closest distance to " O   ASN A 249 " =    1.453
peak=   -3.225 closest distance to " CG2 ILE A 263 " =    2.281
peak=   -3.221 closest distance to " O   HOH Z  97 " =    1.651
peak=   -3.216 closest distance to " CG  GLU A 152 " =    1.379
peak=   -3.214 closest distance to " CB  TRP A  85 " =    2.531
peak=   -3.204 closest distance to " CG1 VAL A 197 " =    2.148
peak=   -3.203 closest distance to " CB  CYS A 254 " =    2.327
peak=   -3.201 closest distance to " CE  MET A  93 " =    1.140
peak=   -3.196 closest distance to " CD  GLN A  58 " =    1.351
peak=   -3.193 closest distance to " CG  MET A 105 " =    0.934
peak=   -3.187 closest distance to " O   SER A  22 " =    2.385
peak=   -3.183 closest distance to " OG1 THR A 178 " =    1.181
peak=   -3.182 closest distance to " N   ALA A 114 " =    2.401
peak=   -3.180 closest distance to " O   HOH Z 281 " =    2.925
peak=   -3.173 closest distance to " O   GLY A  80 " =    2.426
peak=   -3.172 closest distance to " O   HOH Z 369 " =    2.222
peak=   -3.165 closest distance to " CA  GLY A 241 " =    3.329
peak=   -3.162 closest distance to " O   ALA A 180 " =    1.237
peak=   -3.160 closest distance to " OG  SER A  87 " =    1.239
peak=   -3.159 closest distance to " O   VAL A 197 " =    1.262
peak=   -3.158 closest distance to " CB  ALA A 244 " =    1.989
peak=   -3.151 closest distance to " CB  ALA A 248 " =    2.354
peak=   -3.150 closest distance to " CG  LEU A  83 " =    1.850
peak=   -3.149 closest distance to " O   HOH Z 359 " =    3.181
peak=   -3.149 closest distance to " OE1 GLN A 223 " =    1.796
peak=   -3.148 closest distance to " O   HOH Z 168 " =    1.728
peak=   -3.137 closest distance to " OG  SER A  62 " =    1.531
peak=   -3.132 closest distance to " OG  SER A 245 " =    1.101
peak=   -3.130 closest distance to " O   HOH Z 436 " =    1.212
peak=   -3.124 closest distance to " O   HOH Z 210 " =    1.148
peak=   -3.120 closest distance to " O   HOH Z 310 " =    3.302
peak=   -3.119 closest distance to " O   PRO A 243 " =    2.521
peak=   -3.116 closest distance to " O   HOH Z 417 " =    2.441
peak=   -3.110 closest distance to " CG2 VAL A 189 " =    1.983
peak=   -3.109 closest distance to " O   HOH Z 371 " =    1.624
peak=   -3.108 closest distance to " O   HOH Z 234 " =    3.931
peak=   -3.099 closest distance to " C   LEU A   5 " =    0.995
peak=   -3.099 closest distance to " O   MET A  40 " =    2.691
peak=   -3.097 closest distance to " O   HOH Z 193 " =    1.818
peak=   -3.092 closest distance to " ND2 ASN A  39 " =    1.469
peak=   -3.091 closest distance to " O   ASP A 231 " =    2.467
peak=   -3.089 closest distance to " CE3 TRP A 123 " =    1.291
peak=   -3.089 closest distance to " O   HOH Z 378 " =    1.789
peak=   -3.085 closest distance to " NH2 ARG A 159 " =    2.448
peak=   -3.081 closest distance to " N   GLN A  77 " =    1.632
peak=   -3.080 closest distance to " OG ASER A 216 " =    0.987
peak=   -3.078 closest distance to " O   HOH Z 361 " =    3.401
peak=   -3.071 closest distance to " O   HOH Z 236 " =    1.899
peak=   -3.070 closest distance to " NH1 ARG A  56 " =    2.511
peak=   -3.064 closest distance to " O   HOH Z 385 " =    1.602
peak=   -3.015 closest distance to " CE  LYS A  76 " =    2.785
peak=   -3.009 closest distance to " OG  SER A   3 " =    1.284

================= 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    :  0.4115 0.4117   6.213668e+00   6.212760e+00
   1_bss:  0.3978 0.3968   6.205964e+00   6.188341e+00
   1_xyz:  0.2679 0.2966   5.875335e+00   5.966252e+00
   1_adp:  0.2453 0.3029   5.824637e+00   5.985017e+00
   1_occ:  0.2451 0.3031   5.823889e+00   5.984265e+00
   2_bss:  0.2421 0.3002   5.816374e+00   5.978500e+00
   2_xyz:  0.1720 0.2225   5.516102e+00   5.710131e+00
   2_adp:  0.1580 0.2045   5.436037e+00   5.632656e+00
   2_occ:  0.1577 0.2045   5.435198e+00   5.632066e+00
   3_bss:  0.1574 0.2035   5.429501e+00   5.625647e+00
   3_xyz:  0.1288 0.1692   5.242964e+00   5.455132e+00
   3_adp:  0.1232 0.1641   5.204611e+00   5.418080e+00
   3_occ:  0.1231 0.1639   5.203678e+00   5.417038e+00
   4_bss:  0.1235 0.1646   5.205267e+00   5.419688e+00
   4_xyz:  0.1142 0.1560   5.144104e+00   5.370835e+00
   4_adp:  0.1120 0.1561   5.134159e+00   5.367806e+00
   4_occ:  0.1119 0.1559   5.133619e+00   5.367363e+00
   5_bss:  0.1119 0.1559   5.133604e+00   5.367444e+00
   5_xyz:  0.1083 0.1542   5.115161e+00   5.360476e+00
   5_adp:  0.1075 0.1551   5.116353e+00   5.368213e+00
   5_occ:  0.1074 0.1551   5.116284e+00   5.368296e+00
   5_bss:  0.1073 0.1551   5.116260e+00   5.368237e+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:  0.330  26.635  -3.284  -0.700   3.097  -0.000   0.000   0.000
   1_xyz:  0.330  26.635  -3.284  -0.700   3.097  -0.000   0.000   0.000
   1_adp:  0.330  26.635  -3.284  -0.700   3.097  -0.000   0.000   0.000
   1_occ:  0.330  26.635  -3.284  -0.700   3.097  -0.000   0.000   0.000
   2_bss:  0.328  40.430  -2.443  -1.830   0.036  -0.000   0.000   0.000
   2_xyz:  0.328  40.430  -2.443  -1.830   0.036  -0.000   0.000   0.000
   2_adp:  0.328  40.430  -2.443  -1.830   0.036  -0.000   0.000   0.000
   2_occ:  0.328  40.430  -2.443  -1.830   0.036  -0.000   0.000   0.000
   3_bss:  0.328  40.430  -2.482  -2.333  -1.218  -0.000  -0.000  -0.000
   3_xyz:  0.328  40.430  -2.482  -2.333  -1.218  -0.000  -0.000  -0.000
   3_adp:  0.328  40.430  -2.482  -2.333  -1.218  -0.000  -0.000  -0.000
   3_occ:  0.328  40.430  -2.482  -2.333  -1.218  -0.000  -0.000  -0.000
   4_bss:  0.323  40.430  -2.606  -2.515  -1.771  -0.000  -0.000  -0.000
   4_xyz:  0.323  40.430  -2.606  -2.515  -1.771  -0.000  -0.000  -0.000
   4_adp:  0.323  40.430  -2.606  -2.515  -1.771  -0.000  -0.000  -0.000
   4_occ:  0.323  40.430  -2.606  -2.515  -1.771  -0.000  -0.000  -0.000
   5_bss:  0.323  40.430  -2.457  -2.403  -1.793  -0.000  -0.000  -0.000
   5_xyz:  0.323  40.430  -2.457  -2.403  -1.793  -0.000  -0.000  -0.000
   5_adp:  0.323  40.430  -2.457  -2.403  -1.793  -0.000  -0.000  -0.000
   5_occ:  0.323  40.430  -2.457  -2.403  -1.793  -0.000  -0.000  -0.000
   5_bss:  0.324  41.826  -2.255  -2.232  -1.648  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.795 0.5620  0.7554    52698.885
   1_bss:  44.963 0.5822  0.7738    47613.626
   1_xyz:  30.744 0.7504  0.9487    24139.046
   1_adp:  31.873 0.7367  0.9349    25235.753
   1_occ:  31.896 0.7364  0.9344    25221.756
   2_bss:  31.445 0.7414  0.9062    24726.604
   2_xyz:  22.073 0.8411  0.9875    12947.844
   2_adp:  19.645 0.8657  0.9989    10931.050
   2_occ:  19.636 0.8658  0.9986    10908.827
   3_bss:  19.426 0.8675  0.9778    10672.118
   3_xyz:  15.447 0.9025  0.9953     7240.321
   3_adp:  14.623 0.9098  0.9965     6770.826
   3_occ:  14.593 0.9100  0.9964     6752.532
   4_bss:  14.641 0.9097  0.9858     6834.530
   4_xyz:  13.723 0.9170  0.9879     6100.577
   4_adp:  13.614 0.9181  0.9839     6082.151
   4_occ:  13.600 0.9182  0.9838     6074.508
   5_bss:  13.602 0.9182  0.9867     6077.317
   5_xyz:  13.448 0.9194  0.9880     5973.881
   5_adp:  13.581 0.9184  0.9831     6043.482
   5_occ:  13.580 0.9184  0.9830     6042.449
   5_bss:  13.578 0.9184  0.9894     6043.523
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.7720e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.7720e-01
   1_xyz:   1.350  0.010  0.084 15.949  0.006  4.106   1.0396e-01
   1_adp:   1.350  0.010  0.084 15.949  0.006  4.106   1.0396e-01
   1_occ:   1.350  0.010  0.084 15.949  0.006  4.106   1.0396e-01
   2_bss:   1.350  0.010  0.084 15.949  0.006  4.106   1.0396e-01
   2_xyz:   1.038  0.007  0.070 14.381  0.004  4.115   6.0877e-02
   2_adp:   1.038  0.007  0.070 14.381  0.004  4.115   6.0877e-02
   2_occ:   1.038  0.007  0.070 14.381  0.004  4.115   6.0877e-02
   3_bss:   1.038  0.007  0.070 14.381  0.004  4.115   6.0877e-02
   3_xyz:   0.938  0.005  0.066 14.404  0.004  4.109   5.2083e-02
   3_adp:   0.938  0.005  0.066 14.404  0.004  4.109   5.2083e-02
   3_occ:   0.938  0.005  0.066 14.404  0.004  4.109   5.2083e-02
   4_bss:   0.938  0.005  0.066 14.404  0.004  4.109   5.2083e-02
   4_xyz:   0.956  0.006  0.069 14.563  0.004  4.108   5.4222e-02
   4_adp:   0.956  0.006  0.069 14.563  0.004  4.108   5.4222e-02
   4_occ:   0.956  0.006  0.069 14.563  0.004  4.108   5.4222e-02
   5_bss:   0.956  0.006  0.069 14.563  0.004  4.108   5.4222e-02
   5_xyz:   0.987  0.006  0.070 14.593  0.004  4.107   5.7605e-02
   5_adp:   0.987  0.006  0.070 14.593  0.004  4.107   5.7605e-02
   5_occ:   0.987  0.006  0.070 14.593  0.004  4.107   5.7605e-02
   5_bss:   0.987  0.006  0.070 14.593  0.004  4.107   5.7605e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.715   2.3830e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.715   2.3830e-01
   1_xyz:   9.626  0.058  0.360 89.346  0.042  2.202   8.3261e-02
   1_adp:   9.626  0.058  0.360 89.346  0.042  2.202   8.3261e-02
   1_occ:   9.626  0.058  0.360 89.346  0.042  2.202   8.3261e-02
   2_bss:   9.626  0.058  0.360 89.346  0.042  2.202   8.3261e-02
   2_xyz:   6.539  0.072  0.235 82.853  0.037  2.402   6.8890e-02
   2_adp:   6.539  0.072  0.235 82.853  0.037  2.402   6.8890e-02
   2_occ:   6.539  0.072  0.235 82.853  0.037  2.402   6.8890e-02
   3_bss:   6.539  0.072  0.235 82.853  0.037  2.402   6.8890e-02
   3_xyz:   6.674  0.042  0.245 83.604  0.033  2.343   3.8755e-02
   3_adp:   6.674  0.042  0.245 83.604  0.033  2.343   3.8755e-02
   3_occ:   6.674  0.042  0.245 83.604  0.033  2.343   3.8755e-02
   4_bss:   6.674  0.042  0.245 83.604  0.033  2.343   3.8755e-02
   4_xyz:   6.648  0.034  0.213 85.239  0.039  2.324   3.6433e-02
   4_adp:   6.648  0.034  0.213 85.239  0.039  2.324   3.6433e-02
   4_occ:   6.648  0.034  0.213 85.239  0.039  2.324   3.6433e-02
   5_bss:   6.648  0.034  0.213 85.239  0.039  2.324   3.6433e-02
   5_xyz:   6.310  0.035  0.225 83.296  0.040  2.277   4.7311e-02
   5_adp:   6.310  0.035  0.225 83.296  0.040  2.277   4.7311e-02
   5_occ:   6.310  0.035  0.225 83.296  0.040  2.277   4.7311e-02
   5_bss:   6.310  0.035  0.225 83.296  0.040  2.277   4.7311e-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:  84.80   0.00  17.86  84.80   0.00  13.65  82.61   1.94  40.75
   1_occ:  84.80   0.00  17.86  84.80   0.00  13.65  82.61   1.94  40.75
   2_bss:  84.80   0.00  17.86  84.80   0.00  13.65  82.61   1.94  40.75
   2_xyz:  84.80   0.00  17.86  84.80   0.00  13.65  82.61   1.94  40.75
   2_adp:  79.62   1.33  17.07  79.62   1.33  13.04  75.24   5.91  39.02
   2_occ:  79.62   1.33  17.07  79.62   1.33  13.04  75.24   5.91  39.02
   3_bss:  79.62   1.33  17.07  79.62   1.33  13.04  75.24   5.91  39.02
   3_xyz:  79.62   1.33  17.07  79.62   1.33  13.04  75.24   5.91  39.02
   3_adp:  81.50   1.76  17.03  81.50   1.76  12.89  75.05   5.51  39.56
   3_occ:  81.50   1.76  17.03  81.50   1.76  12.89  75.05   5.51  39.56
   4_bss:  81.50   1.76  17.03  81.50   1.76  12.89  75.05   5.51  39.56
   4_xyz:  81.50   1.76  17.03  81.50   1.76  12.89  75.05   5.51  39.56
   4_adp:  85.94   1.67  16.97  85.94   1.67  12.81  80.09   5.63  39.62
   4_occ:  85.94   1.67  16.97  85.94   1.67  12.81  80.09   5.63  39.62
   5_bss:  85.94   1.67  16.97  85.94   1.67  12.81  80.09   5.63  39.62
   5_xyz:  85.94   1.67  16.97  85.94   1.67  12.81  80.09   5.63  39.62
   5_adp:  93.75   0.00  17.05  93.75   0.00  12.79  83.92   6.36  40.27
   5_occ:  93.75   0.00  17.05  93.75   0.00  12.79  83.92   6.36  40.27
   5_bss:  93.75   0.00  17.06  93.75   0.00  12.79  83.92   6.36  40.28
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.878    0.021    0.392
   1_adp:    1.878    0.021    0.392
   1_occ:    1.878    0.021    0.392
   2_bss:    1.878    0.021    0.392
   2_xyz:    1.297    0.033    0.500
   2_adp:    1.297    0.033    0.500
   2_occ:    1.297    0.033    0.500
   3_bss:    1.297    0.033    0.500
   3_xyz:    1.239    0.044    0.561
   3_adp:    1.239    0.044    0.561
   3_occ:    1.239    0.044    0.561
   4_bss:    1.239    0.044    0.561
   4_xyz:    1.323    0.025    0.588
   4_adp:    1.323    0.025    0.588
   4_occ:    1.323    0.025    0.588
   5_bss:    1.323    0.025    0.588
   5_xyz:    1.327    0.014    0.601
   5_adp:    1.327    0.014    0.601
   5_occ:    1.327    0.014    0.601
   5_bss:    1.327    0.014    0.601
------------------------------------------------------------------------

CPU time actual refinement: 344.97


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_638/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_638/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_638/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_638/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_638/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 344.81 
  Macro-tasks:
    bulk solvent and scale       = 37.03  
    individual site refinement   = 143.92 
    weights calculation          = 30.55  
    collect and process          = 6.61   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 218.22 
  Micro-tasks:
    mask                            = 1.87   
    f_calc                          = 113.40 
    alpha_beta                      = 8.27   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 121.27 
    fmodel                         = 6.67   
    r_factors                      = 0.16   
    phase_errors                   = 11.05  
    foms                           = 0.17   
    TOTAL for micro-tasks          = 264.02 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.895 micro seconds
Total CPU time: 5.97 minutes
from_scatterers_fft:    643 calls, 113.06 s
gradients_fft:          588 calls, 107.91 s

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

# Date 2008-01-16 Time 05:18:46 PST -0800 (1200489526.50 s)
Start R-work = 0.4115, R-free = 0.4117 (no bulk solvent and anisotropic scale)
Final R-work = 0.1326, R-free = 0.1756 (no bulk solvent and anisotropic scale)

Start R-work = 0.3978, R-free = 0.3968
Final R-work = 0.1073, R-free = 0.1551