# Date 2008-01-16 Time 06:30:16 PST -0800 (1200493816.67 s)
#phil __OFF__

Command line arguments: "../1171.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4498
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1171

-------------------------------------------------------------------------------
  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: (71.655, 47.3993, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 47.3993, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2108 2.00111
Completeness in resolution range: 0.959117
Completeness with d_max=infinity: 0.956214

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2108
                             d_min =   2.0011

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: (71.655, 47.3993, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2108 2.00111
Completeness in resolution range: 0.959117
Completeness with d_max=infinity: 0.956214

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2112 -  4.2822 [2140/2169]  1929   211   9.9%
  bin  2:  4.2822 -  3.4115 [2052/2068]  1845   207  10.1%
  bin  3:  3.4115 -  2.9840 [2038/2057]  1832   206  10.1%
  bin  4:  2.9840 -  2.7128 [2028/2058]  1827   201   9.9%
  bin  5:  2.7128 -  2.5193 [1999/2018]  1803   196   9.8%
  bin  6:  2.5193 -  2.3714 [1998/2023]  1792   206  10.3%
  bin  7:  2.3714 -  2.2530 [1959/1991]  1764   195  10.0%
  bin  8:  2.2530 -  2.1552 [1986/2018]  1789   197   9.9%
  bin  9:  2.1552 -  2.0725 [1986/2028]  1785   201  10.1%
  bin 10:  2.0725 -  2.0011 [1403/1994]  1264   139   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1171/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.50 -     2.18: 2
        2.18 -     2.86: 1121
        2.86 -     3.54: 4354
        3.54 -     4.22: 9120
        4.22 -     4.90: 13315
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.500 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.214 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.283 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27907 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_1171/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1171/model_refine_001.geo

CPU time processing inputs: 9.30


============================ 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 = 71.655 47.3993 86.39 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: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3563   r_free= 0.3510   ksol= 0.00   Bsol= 0.00   scale= 0.943    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.116080                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2112 -  4.7763 0.99   1388  155 0.2985 0.2938      6.3772      6.3222|
|  2:  4.7763 -  3.8107 0.99   1346  146 0.2794 0.2854       6.529      6.5077|
|  3:  3.8107 -  3.3348 0.99   1317  147 0.3067 0.2923      6.4145      6.4233|
|  4:  3.3348 -  3.0325 0.99   1313  152 0.3392 0.3022      6.3241      6.2356|
|  5:  3.0325 -  2.8166 0.99   1294  140 0.3600 0.3943      6.1719      6.2788|
|  6:  2.8166 -  2.6515 0.99   1286  146 0.3837 0.3627      6.1222      6.0666|
|  7:  2.6515 -  2.5193 0.99   1292  135 0.3866 0.3614      6.0936      6.0801|
|  8:  2.5193 -  2.4101 0.98   1268  150 0.3960 0.3906      6.0379      6.0306|
|  9:  2.4101 -  2.3177 0.98   1270  142 0.3988 0.3930      5.9976      6.0723|
| 10:  2.3177 -  2.2379 0.99   1282  136 0.4059 0.3984      5.9853      5.9612|
| 11:  2.2379 -  2.1682 0.99   1281  144 0.4214 0.4394      5.9465      6.0012|
| 12:  2.1682 -  2.1064 0.97   1246  139 0.4194 0.4205      5.8875      5.9339|
| 13:  2.1064 -  2.0510 0.99   1268  141 0.4272 0.4026      5.7997      5.7201|
| 14:  2.0510 -  2.0011 0.60    779   86 0.3983 0.4167      5.7118       5.722|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2112 -  4.7763  1388   155  0.78  26.64   0.85     0.80      43823.23|
|  2:  4.7763 -  3.8107  1346   146  0.83  23.43   0.96     0.88      50619.52|
|  3:  3.8107 -  3.3348  1317   147  0.78  28.50   0.96     0.90      52391.34|
|  4:  3.3348 -  3.0325  1313   152  0.74  32.19   0.95     0.88      48003.09|
|  5:  3.0325 -  2.8166  1294   140  0.66  38.95   0.96     0.83      42931.80|
|  6:  2.8166 -  2.6515  1286   146  0.65  40.23   0.97     0.81      37917.75|
|  7:  2.6515 -  2.5193  1292   135  0.64  40.91   0.97     0.80      35706.88|
|  8:  2.5193 -  2.4101  1268   150  0.62  42.85   0.96     0.81      34119.11|
|  9:  2.4101 -  2.3177  1270   142  0.60  44.03   0.99     0.79      32812.84|
| 10:  2.3177 -  2.2379  1282   136  0.58  45.39   0.99     0.79      31595.97|
| 11:  2.2379 -  2.1682  1281   144  0.57  46.32   0.99     0.79      29491.54|
| 12:  2.1682 -  2.1064  1246   139  0.59  45.12   0.99     0.83      27184.19|
| 13:  2.1064 -  2.0510  1268   141  0.58  45.71   0.96     0.82      22466.48|
| 14:  2.0510 -  2.0011   779    86  0.61  43.89   0.99     0.78      17719.53|
|alpha:            min =        0.78 max =            0.90 mean =         0.82|
|beta:             min =    17719.53 max =        52391.34 mean =     36915.47|
|figures of merit: min =        0.00 max =            1.00 mean =         0.66|
|phase err.(work): min =        0.00 max =           90.00 mean =        38.54|
|phase err.(test): min =        0.00 max =           89.92 mean =        38.32|
|-----------------------------------------------------------------------------|

============================== 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 = 3.624638              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.922   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.946897              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.148   (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 |  1.500 -  1.840:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.840 -  2.180:        0 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.180 -  2.520:       19 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.520 -  2.860:     1102 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.860 -  3.200:     1911 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.200 -  3.540:     2443 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.540 -  3.880:     4584 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.880 -  4.220:     4536 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.220 -  4.560:     6055 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.560 -  4.900:     7260 |
|-----------------------------------------------------------------------------|
|-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 |        0.164 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.500 |       0.175 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.268)------------------------------------------|
|    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: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3563   r_free= 0.3510   ksol= 0.00   Bsol= 0.00   scale= 0.943    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.116080                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3452   r_free= 0.3389   ksol= 0.31   Bsol= 56.75   scale= 0.969   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.48,0.29,-1.78,0.00,-0.00,-0.00); trace/3= -0.00                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.100164                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.257156              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.127   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.518786              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.841   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3452      final r-factor (work) = 0.2333          |
| start r-factor (free) = 0.3389      final r-factor (free) = 0.2568          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1041 = 3.26 * 0.50 * 6.1035 + 1.00 * 0.1640                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6528 = 3.26 * 0.50 * 5.8818 + 1.00 * 0.0738                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2333      final r-factor (work) = 0.2163          |
| start r-factor (free) = 0.2568      final r-factor (free) = 0.2593          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0578 = 0.52 * 1.00 * 5.8818 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0016 = 0.52 * 1.00 * 5.6990 + 1.00 * 0.0450                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.268)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.96   16.73    None  None   None       |
|    all(noH): 2823   0      0.00    76.96   16.73    None  None   None       |
|    Sol.    : 438    0      5.49    64.71   37.76    None  None   None       |
|    Mac.    : 2385   0      0.00    76.96   12.87    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 -   7.697:  547   |   5:    38.482 -  46.179:  119        |
|      1:     7.697 -  15.393: 1213   |   6:    46.179 -  53.875:   85        |
|      2:    15.393 -  23.089:  509   |   7:    53.875 -  61.572:   48        |
|      3:    23.089 -  30.786:  172   |   8:    61.572 -  69.268:    4        |
|      4:    30.786 -  38.482:  125   |   9:    69.268 -  76.964:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2163 r_free = 0.2593             target_work(ml) = 5.703         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2159 r_free = 0.2588             target_work(ml) = 5.701         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2159   r_free= 0.2588   ksol= 0.31   Bsol= 56.75   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.48,0.29,-1.78,0.00,-0.00,-0.00); trace/3= -0.00                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.701093                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2144   r_free= 0.2566   ksol= 0.33   Bsol= 67.67   scale= 0.982   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.09,-1.40,-1.88,-0.00,-0.00,-0.00); trace/3= -1.46                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.699543                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.235482              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.094   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.452440              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.498   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2144      final r-factor (work) = 0.1452          |
| start r-factor (free) = 0.2566      final r-factor (free) = 0.1868          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.0120 = 5.24 * 0.50 * 5.7065 + 1.00 * 0.0738                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.5800 = 5.24 * 0.50 * 5.5403 + 1.00 * 0.0769                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1452      final r-factor (work) = 0.1304          |
| start r-factor (free) = 0.1868      final r-factor (free) = 0.1736          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5288 = 0.45 * 1.00 * 5.5403 + 1.00 * 0.0221                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4102 = 0.45 * 1.00 * 5.3060 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.268)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.83    72.18   17.10    None  None   None       |
|    all(noH): 2823   0      0.83    72.18   17.10    None  None   None       |
|    Sol.    : 438    0      4.60    72.18   40.00    None  None   None       |
|    Mac.    : 2385   0      0.83    71.69   12.90    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:     0.828 -   7.963:  568   |   5:    36.503 -  43.638:   87        |
|      1:     7.963 -  15.098: 1275   |   6:    43.638 -  50.772:   91        |
|      2:    15.098 -  22.233:  403   |   7:    50.772 -  57.907:   83        |
|      3:    22.233 -  29.368:  138   |   8:    57.907 -  65.042:   53        |
|      4:    29.368 -  36.503:  112   |   9:    65.042 -  72.177:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1304 r_free = 0.1736             target_work(ml) = 5.265         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1303 r_free = 0.1734             target_work(ml) = 5.264         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1303   r_free= 0.1734   ksol= 0.33   Bsol= 67.67   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.09,-1.40,-1.88,-0.00,-0.00,-0.00); trace/3= -1.46                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.264421                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1302   r_free= 0.1730   ksol= 0.33   Bsol= 65.30   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.73,-1.83,-1.45,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.265118                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.103605              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.921  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.460883              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.082  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1302      final r-factor (work) = 0.1204          |
| start r-factor (free) = 0.1730      final r-factor (free) = 0.1649          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6584 = 2.10 * 0.50 * 5.3066 + 1.00 * 0.0769                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5664 = 2.10 * 0.50 * 5.2360 + 1.00 * 0.0592                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1204      final r-factor (work) = 0.1179          |
| start r-factor (free) = 0.1649      final r-factor (free) = 0.1659          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6586 = 1.46 * 1.00 * 5.2360 + 1.00 * 0.0094                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6057 = 1.46 * 1.00 * 5.1985 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.268)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.18   17.48    None  None   None       |
|    all(noH): 2823   0      0.00    94.18   17.48    None  None   None       |
|    Sol.    : 438    0      0.00    88.80   42.20    None  None   None       |
|    Mac.    : 2385   0      0.00    94.18   12.94    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 -   9.418:  945   |   5:    47.088 -  56.505:   93        |
|      1:     9.418 -  18.835: 1172   |   6:    56.505 -  65.923:   78        |
|      2:    18.835 -  28.253:  247   |   7:    65.923 -  75.340:   33        |
|      3:    28.253 -  37.670:  130   |   8:    75.340 -  84.758:   10        |
|      4:    37.670 -  47.088:  107   |   9:    84.758 -  94.175:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1179 r_free = 0.1659             target_work(ml) = 5.198         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1179 r_free = 0.1659             target_work(ml) = 5.197         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1659   ksol= 0.33   Bsol= 65.30   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.73,-1.83,-1.45,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.197425                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1178   r_free= 0.1658   ksol= 0.33   Bsol= 66.09   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.76,-1.79,-1.20,-0.00,-0.00,-0.00); trace/3= -1.58                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.197210                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.669170              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 145.879  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.365161              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.950  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1178      final r-factor (work) = 0.1127          |
| start r-factor (free) = 0.1658      final r-factor (free) = 0.1643          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9974 = 2.67 * 0.50 * 5.1983 + 1.00 * 0.0599                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9811 = 2.67 * 0.50 * 5.1777 + 1.00 * 0.0711                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1127      final r-factor (work) = 0.1126          |
| start r-factor (free) = 0.1643      final r-factor (free) = 0.1625          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9020 = 0.37 * 1.00 * 5.1777 + 1.00 * 0.0113                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8978 = 0.37 * 1.00 * 5.1705 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.268)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.28    94.59   16.92    None  None   None       |
|    all(noH): 2823   0      0.28    94.59   16.92    None  None   None       |
|    Sol.    : 438    0      0.46    86.23   40.10    None  None   None       |
|    Mac.    : 2385   0      0.28    94.59   12.66    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:     0.284 -   9.715: 1050   |   5:    47.438 -  56.869:   99        |
|      1:     9.715 -  19.146: 1101   |   6:    56.869 -  66.299:   58        |
|      2:    19.146 -  28.576:  231   |   7:    66.299 -  75.730:   21        |
|      3:    28.576 -  38.007:  140   |   8:    75.730 -  85.161:    9        |
|      4:    38.007 -  47.438:  110   |   9:    85.161 -  94.592:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1126 r_free = 0.1625             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1126 r_free = 0.1624             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1126   r_free= 0.1624   ksol= 0.33   Bsol= 66.09   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.76,-1.79,-1.20,-0.00,-0.00,-0.00); trace/3= -1.58                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.164969                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1125   r_free= 0.1624   ksol= 0.32   Bsol= 61.60   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.68,-1.69,-0.98,-0.00,-0.00,-0.00); trace/3= -1.45                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.165028                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.893882              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 155.250  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.146731              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.513  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1125      final r-factor (work) = 0.1141          |
| start r-factor (free) = 0.1624      final r-factor (free) = 0.1629          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9674 = 1.89 * 0.50 * 5.1707 + 1.00 * 0.0711                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9572 = 1.89 * 0.50 * 5.1717 + 1.00 * 0.0600                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1141      final r-factor (work) = 0.1160          |
| start r-factor (free) = 0.1629      final r-factor (free) = 0.1622          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7685 = 0.15 * 1.00 * 5.1717 + 1.00 * 0.0097                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7680 = 0.15 * 1.00 * 5.1827 + 1.00 * 0.0075                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.268)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.30    87.65   16.19    None  None   None       |
|    all(noH): 2823   0      1.30    87.65   16.19    None  None   None       |
|    Sol.    : 438    0      3.18    82.58   37.06    None  None   None       |
|    Mac.    : 2385   0      1.30    87.65   12.36    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:     1.297 -   9.933: 1112   |   5:    44.475 -  53.110:   89        |
|      1:     9.933 -  18.568: 1039   |   6:    53.110 -  61.746:   51        |
|      2:    18.568 -  27.204:  239   |   7:    61.746 -  70.381:   16        |
|      3:    27.204 -  35.839:  139   |   8:    70.381 -  79.017:    6        |
|      4:    35.839 -  44.475:  127   |   9:    79.017 -  87.652:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1160 r_free = 0.1622             target_work(ml) = 5.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1159 r_free = 0.1622             target_work(ml) = 5.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1159   r_free= 0.1622   ksol= 0.32   Bsol= 61.60   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.68,-1.69,-0.98,-0.00,-0.00,-0.00); trace/3= -1.45                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.180681                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2112 -  4.7763 0.99   1388  155 0.1045 0.1386      5.4313        5.58|
|  2:  4.7763 -  3.8107 0.99   1346  146 0.0897 0.1097      5.4701      5.6434|
|  3:  3.8107 -  3.3348 0.99   1317  147 0.1061 0.1542      5.4818      5.8682|
|  4:  3.3348 -  3.0325 0.99   1313  152 0.1231 0.1544      5.4803      5.5967|
|  5:  3.0325 -  2.8166 0.99   1294  140 0.1407 0.1858      5.3779      5.6104|
|  6:  2.8166 -  2.6515 0.99   1286  146 0.1288 0.1935      5.2555      5.5013|
|  7:  2.6515 -  2.5193 0.99   1292  135 0.1285 0.1674      5.2089       5.399|
|  8:  2.5193 -  2.4101 0.98   1268  150 0.1215 0.1780      5.0939      5.3651|
|  9:  2.4101 -  2.3177 0.98   1270  142 0.1222 0.1796      5.0716      5.3404|
| 10:  2.3177 -  2.2379 0.99   1282  136 0.1182 0.1866      4.9881      5.2437|
| 11:  2.2379 -  2.1682 0.99   1281  144 0.1205 0.1824       4.976      5.3023|
| 12:  2.1682 -  2.1064 0.97   1246  139 0.1125 0.1630      4.9001      5.1229|
| 13:  2.1064 -  2.0510 0.99   1268  141 0.1229 0.1854      4.8371      5.1249|
| 14:  2.0510 -  2.0011 0.60    779   86 0.1134 0.1655      4.7025      4.9125|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2112 -  4.7763  1388   155  0.94   9.67   0.97     0.94       7988.04|
|  2:  4.7763 -  3.8107  1346   146  0.95   8.28   1.00     0.98       9482.83|
|  3:  3.8107 -  3.3348  1317   147  0.93  11.56   1.01     1.00      10639.51|
|  4:  3.3348 -  3.0325  1313   152  0.92  14.12   0.99     0.97      11010.37|
|  5:  3.0325 -  2.8166  1294   140  0.89  16.91   0.99     0.96       9152.93|
|  6:  2.8166 -  2.6515  1286   146  0.90  16.65   0.97     0.95       7681.05|
|  7:  2.6515 -  2.5193  1292   135  0.90  15.86   0.99     0.95       6636.71|
|  8:  2.5193 -  2.4101  1268   150  0.90  15.80   0.98     0.97       5629.01|
|  9:  2.4101 -  2.3177  1270   142  0.91  15.74   1.00     0.96       5312.13|
| 10:  2.3177 -  2.2379  1282   136  0.90  15.78   0.98     0.94       4468.52|
| 11:  2.2379 -  2.1682  1281   144  0.89  16.90   0.99     0.95       4598.03|
| 12:  2.1682 -  2.1064  1246   139  0.92  15.04   0.99     0.98       4123.52|
| 13:  2.1064 -  2.0510  1268   141  0.89  17.00   0.98     0.98       3616.50|
| 14:  2.0510 -  2.0011   779    86  0.91  15.22   0.96     0.92       2657.04|
|alpha:            min =        0.92 max =            1.00 mean =         0.96|
|beta:             min =     2657.04 max =        11010.37 mean =      6801.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.53|
|phase err.(test): min =        0.00 max =           89.92 mean =        13.98|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1159   r_free= 0.1622   ksol= 0.32   Bsol= 58.66   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.68,-1.65,-0.88,-0.00,-0.00,-0.00); trace/3= -1.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.180756                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1159   r_free= 0.1622   ksol= 0.32   Bsol= 58.66   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.68,-1.65,-0.88,-0.00,-0.00,-0.00); trace/3= -1.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.180756                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2112 -  4.7763 0.99   1388  155 0.1043 0.1384      5.4302      5.5782|
|  2:  4.7763 -  3.8107 0.99   1346  146 0.0895 0.1094      5.4682      5.6412|
|  3:  3.8107 -  3.3348 0.99   1317  147 0.1060 0.1543      5.4809      5.8683|
|  4:  3.3348 -  3.0325 0.99   1313  152 0.1232 0.1542      5.4808      5.5966|
|  5:  3.0325 -  2.8166 0.99   1294  140 0.1409 0.1861      5.3789      5.6116|
|  6:  2.8166 -  2.6515 0.99   1286  146 0.1289 0.1934      5.2563      5.5015|
|  7:  2.6515 -  2.5193 0.99   1292  135 0.1285 0.1674      5.2092      5.3993|
|  8:  2.5193 -  2.4101 0.98   1268  150 0.1216 0.1781      5.0942      5.3653|
|  9:  2.4101 -  2.3177 0.98   1270  142 0.1223 0.1794      5.0719        5.34|
| 10:  2.3177 -  2.2379 0.99   1282  136 0.1183 0.1869      4.9886      5.2452|
| 11:  2.2379 -  2.1682 0.99   1281  144 0.1206 0.1827      4.9766       5.303|
| 12:  2.1682 -  2.1064 0.97   1246  139 0.1125 0.1631      4.9007      5.1236|
| 13:  2.1064 -  2.0510 0.99   1268  141 0.1230 0.1856      4.8374      5.1254|
| 14:  2.0510 -  2.0011 0.60    779   86 0.1135 0.1655      4.7027       4.912|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2112 -  4.7763  1388   155  0.94   9.66   0.97     0.94       7962.88|
|  2:  4.7763 -  3.8107  1346   146  0.95   8.27   1.00     0.98       9450.17|
|  3:  3.8107 -  3.3348  1317   147  0.93  11.54   1.01     1.00      10613.32|
|  4:  3.3348 -  3.0325  1313   152  0.92  14.12   0.99     0.98      11019.59|
|  5:  3.0325 -  2.8166  1294   140  0.89  16.92   0.99     0.96       9162.29|
|  6:  2.8166 -  2.6515  1286   146  0.90  16.67   0.97     0.95       7692.55|
|  7:  2.6515 -  2.5193  1292   135  0.90  15.86   0.99     0.95       6639.94|
|  8:  2.5193 -  2.4101  1268   150  0.90  15.80   0.98     0.97       5631.00|
|  9:  2.4101 -  2.3177  1270   142  0.91  15.74   1.00     0.96       5312.49|
| 10:  2.3177 -  2.2379  1282   136  0.90  15.80   0.98     0.94       4472.59|
| 11:  2.2379 -  2.1682  1281   144  0.89  16.92   0.99     0.95       4605.10|
| 12:  2.1682 -  2.1064  1246   139  0.92  15.05   0.99     0.98       4131.42|
| 13:  2.1064 -  2.0510  1268   141  0.89  17.00   0.98     0.98       3619.23|
| 14:  2.0510 -  2.0011   779    86  0.91  15.22   0.96     0.92       2656.00|
|alpha:            min =        0.92 max =            1.00 mean =         0.96|
|beta:             min =     2656.00 max =        11019.59 mean =      6799.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        14.53|
|phase err.(test): min =        0.00 max =           89.92 mean =        13.98|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.268)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.25    87.61   16.15    None  None   None       |
|    all(noH): 2823   0      1.25    87.61   16.15    None  None   None       |
|    Sol.    : 438    0      3.13    82.53   37.01    None  None   None       |
|    Mac.    : 2385   0      1.25    87.61   12.32    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:     1.251 -   9.887: 1112   |   5:    44.429 -  53.064:   89        |
|      1:     9.887 -  18.522: 1039   |   6:    53.064 -  61.700:   51        |
|      2:    18.522 -  27.158:  239   |   7:    61.700 -  70.335:   16        |
|      3:    27.158 -  35.793:  139   |   8:    70.335 -  78.971:    6        |
|      4:    35.793 -  44.429:  127   |   9:    78.971 -  87.606:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 302         
Filter by distance & map next to the model:
   mapped sites are within: 0.594 - 4.920
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 297 from: 302
   mapped sites are within: 0.714 - 4.920

peak=    5.761 closest distance to " O   HOH Z 111 " =    2.099
peak=    5.608 closest distance to " CB  GLN A 223 " =    1.424
peak=    5.296 closest distance to " CG  PRO A  54 " =    1.355
peak=    4.952 closest distance to " CB  SER A  63 " =    1.285
peak=    4.856 closest distance to " O   HOH Z 232 " =    2.241
peak=    4.836 closest distance to " CB  PRO A  54 " =    0.951
peak=    4.804 closest distance to " CB  LEU A 228 " =    1.054
peak=    4.752 closest distance to " CG  PRO A 213 " =    1.234
peak=    4.677 closest distance to " CG  PRO A  90 " =    1.169
peak=    4.672 closest distance to " CG  PRO A 198 " =    1.338
peak=    4.575 closest distance to " CB  ARG A 275 " =    0.877
peak=    4.512 closest distance to " O   HOH Z 126 " =    1.943
peak=    4.480 closest distance to " CB  GLU A 128 " =    1.065
peak=    4.460 closest distance to " CZ  PHE A 218 " =    1.074
peak=    4.451 closest distance to " C   PRO A 198 " =    1.551
peak=    4.442 closest distance to " CB  GLN A 183 " =    1.224
peak=    4.414 closest distance to " CB  GLU A 152 " =    1.150
peak=    4.411 closest distance to " CB  ASN A 148 " =    1.411
peak=    4.399 closest distance to " CG  PRO A 243 " =    1.133
peak=    4.373 closest distance to " O   HOH Z 369 " =    2.040
peak=    4.366 closest distance to " O   HOH Z 298 " =    1.945
peak=    4.358 closest distance to " NH2 ARG A 156 " =    1.189
peak=    4.356 closest distance to " CB  TRP A 266 " =    0.886
peak=    4.347 closest distance to " O   HOH Z 236 " =    1.968
peak=    4.265 closest distance to " ND2 ASN A 187 " =    1.494
peak=    4.249 closest distance to " O   HOH Z 234 " =    3.901
peak=    4.231 closest distance to " CA  TYR A  30 " =    0.937
peak=    4.227 closest distance to " CB  ASP A 124 " =    0.749
peak=    4.221 closest distance to " CB  ARG A 190 " =    1.646
peak=    4.202 closest distance to " CD1 LEU A 300 " =    1.247
peak=    4.182 closest distance to " O   HOH Z  78 " =    1.720
peak=    4.171 closest distance to " CB  ASN A 187 " =    1.136
peak=    4.162 closest distance to " CB  ARG A  79 " =    1.328
peak=    4.157 closest distance to " CA  ASP A 191 " =    0.758
peak=    4.151 closest distance to " CB  TYR A 169 " =    0.731
peak=    4.113 closest distance to " O   HOH Z  15 " =    2.010
peak=    4.110 closest distance to " O   HOH Z  21 " =    1.812
peak=    4.068 closest distance to " CZ  PHE A 192 " =    1.000
peak=    4.048 closest distance to " CB  SER A   3 " =    1.365
peak=    3.998 closest distance to " CD  ARG A 269 " =    0.925
peak=    3.994 closest distance to " O   HOH Z 261 " =    2.014
peak=    3.981 closest distance to " NH1AARG A 145 " =    1.244
peak=    3.970 closest distance to " CB  ASN A  39 " =    0.947
peak=    3.965 closest distance to " O   HOH Z 193 " =    2.081
peak=    3.949 closest distance to " O   HOH Z 368 " =    2.095
peak=    3.934 closest distance to " CB  GLU A 277 " =    3.703
peak=    3.930 closest distance to " CB  VAL A 202 " =    1.584
peak=    3.919 closest distance to " OD1 ASN A  69 " =    2.638
peak=    3.898 closest distance to " ND2 ASN A 110 " =    1.633
peak=    3.895 closest distance to " CA  THR A 264 " =    0.865
peak=    3.891 closest distance to " O   HOH Z 189 " =    2.669
peak=    3.882 closest distance to " CB  VAL A 265 " =    1.257
peak=    3.876 closest distance to " CG2 THR A 221 " =    0.934
peak=    3.871 closest distance to " CD  LYS A 166 " =    1.296
peak=    3.843 closest distance to " O   HOH Z 180 " =    2.110
peak=    3.837 closest distance to " CD  ARG A 159 " =    0.804
peak=    3.825 closest distance to " O   HOH Z 108 " =    2.638
peak=    3.823 closest distance to " O   HOH Z  40 " =    1.853
peak=    3.822 closest distance to " O   HOH Z 423 " =    1.858
peak=    3.821 closest distance to " O   HOH Z  54 " =    2.317
peak=    3.817 closest distance to " CG1 ILE A  33 " =    1.323
peak=    3.811 closest distance to " CD ALYS A 290 " =    1.051
peak=    3.799 closest distance to " O   HOH Z 272 " =    1.960
peak=    3.792 closest distance to " O   HOH Z 158 " =    3.016
peak=    3.785 closest distance to " O   HOH Z 213 " =    1.884
peak=    3.783 closest distance to " O   HOH Z 133 " =    2.256
peak=    3.776 closest distance to " CB  GLU A  46 " =    0.984
peak=    3.770 closest distance to " O   HOH Z 250 " =    1.615
peak=    3.762 closest distance to " CA  ALA A  51 " =    0.882
peak=    3.759 closest distance to " CD1 ILE A 106 " =    0.851
peak=    3.756 closest distance to " CA  ARG A 195 " =    1.215
peak=    3.741 closest distance to " O   HOH Z 214 " =    2.008
peak=    3.738 closest distance to " CB  ASP A 140 " =    0.879
peak=    3.722 closest distance to " O   MET A 105 " =    1.854
peak=    3.715 closest distance to " O   HOH Z 316 " =    3.121
peak=    3.714 closest distance to " O   HOH Z  68 " =    1.792
peak=    3.710 closest distance to " CA  THR A 221 " =    0.913
peak=    3.698 closest distance to " NE2 GLN A  11 " =    1.101
peak=    3.693 closest distance to " OD1 ASN A 217 " =    1.616
peak=    3.691 closest distance to " O   HOH Z 303 " =    2.141
peak=    3.686 closest distance to " O   HOH Z  20 " =    1.922
peak=    3.684 closest distance to " O   HOH Z  92 " =    2.520
peak=    3.683 closest distance to " CG2 VAL A 257 " =    0.929
peak=    3.678 closest distance to " CA  ASP A 124 " =    0.731
peak=    3.674 closest distance to " CA  MET A  40 " =    1.160
peak=    3.672 closest distance to " CG1BVAL A  72 " =    1.753
peak=    3.669 closest distance to " OD2 ASP A 286 " =    2.963
peak=    3.663 closest distance to " O   HOH Z 135 " =    1.760
peak=    3.661 closest distance to " CB  SER A 216 " =    0.782
peak=    3.660 closest distance to " O   HOH Z 411 " =    3.747
peak=    3.659 closest distance to " O   HOH Z 403 " =    1.713
peak=    3.656 closest distance to " O   HOH Z 346 " =    1.557
peak=    3.654 closest distance to " CB  ALA A 104 " =    0.714
peak=    3.647 closest distance to " CA  ALA A  21 " =    1.248
peak=    3.642 closest distance to " O   THR A 251 " =    1.295
peak=    3.642 closest distance to " CG1 VAL A 153 " =    0.920
peak=    3.641 closest distance to " CG  LEU A 167 " =    1.203
peak=    3.634 closest distance to " O   HOH Z 132 " =    2.689
peak=    3.633 closest distance to " O   HOH Z 344 " =    3.306
peak=    3.632 closest distance to " CG BARG A 275 " =    1.439
peak=    3.628 closest distance to " O   HOH Z 383 " =    2.038
peak=    3.625 closest distance to " O   HOH Z 193 " =    1.714
peak=    3.624 closest distance to " O   HOH Z 426 " =    1.570
peak=    3.623 closest distance to " CB  ILE A 120 " =    1.169
peak=    3.619 closest distance to " O   HOH Z 368 " =    3.665
peak=    3.618 closest distance to " CB  SER A 141 " =    0.992
peak=    3.611 closest distance to " O   HOH Z 147 " =    1.770
peak=    3.608 closest distance to " O   HOH Z  63 " =    1.912
peak=    3.606 closest distance to " O   HOH Z 406 " =    1.678
peak=    3.601 closest distance to " CB  TRP A 179 " =    1.494
peak=    3.596 closest distance to " N   ASN A  39 " =    1.310
peak=    3.594 closest distance to " O   HOH Z 197 " =    2.818
peak=    3.589 closest distance to " NH2BARG A 145 " =    2.192
peak=    3.588 closest distance to " O   HOH Z  49 " =    2.307
peak=    3.582 closest distance to " O   HOH Z 285 " =    3.048
peak=    3.578 closest distance to " CB  MET A  40 " =    0.796
peak=    3.572 closest distance to " O   HOH Z  88 " =    3.590
peak=    3.568 closest distance to " CD2 LEU A 297 " =    0.863
peak=    3.566 closest distance to " O   HOH Z 295 " =    1.480
peak=    3.559 closest distance to " CZ  PHE A 208 " =    1.160
peak=    3.555 closest distance to " O   HOH Z  62 " =    2.294
peak=    3.548 closest distance to " O   HOH Z 163 " =    1.690
peak=    3.547 closest distance to " CB  ASN A 142 " =    0.919
peak=    3.547 closest distance to " O   HOH Z 313 " =    1.839
peak=    3.546 closest distance to " O   HOH Z  97 " =    2.045
peak=    3.544 closest distance to " CA  GLN A 223 " =    0.963
peak=    3.535 closest distance to " N   ASN A 127 " =    1.274
peak=    3.534 closest distance to " N   ARG A 156 " =    1.431
peak=    3.532 closest distance to " CB  MET A  47 " =    0.977
peak=    3.528 closest distance to " O   HOH Z 281 " =    4.784
peak=    3.525 closest distance to " CA  ARG A  36 " =    1.178
peak=    3.523 closest distance to " CA  SER A  87 " =    0.971
peak=    3.521 closest distance to " ND1 HIS A  81 " =    1.687
peak=    3.520 closest distance to " O   HOH Z  66 " =    2.134
peak=    3.507 closest distance to " O   ALA A 165 " =    1.458
peak=    3.505 closest distance to " CB  SER A 212 " =    1.191
peak=    3.505 closest distance to " CG2BVAL A  41 " =    0.904
peak=    3.500 closest distance to " CA  GLU A 152 " =    0.901
peak=    3.489 closest distance to " O   HOH Z 425 " =    1.330
peak=    3.486 closest distance to " O   HOH Z 294 " =    1.595
peak=    3.479 closest distance to " O   HOH Z 171 " =    3.850
peak=    3.477 closest distance to " O   HOH Z  10 " =    1.824
peak=    3.476 closest distance to " CB  LEU A 143 " =    1.108
peak=    3.476 closest distance to " CA  ALA A 295 " =    1.125
peak=    3.473 closest distance to " ND2 ASN A 249 " =    1.966
peak=    3.466 closest distance to " CB  TYR A 169 " =    0.804
peak=    3.457 closest distance to " N   VAL A 126 " =    1.497
peak=    3.456 closest distance to " CG1 ILE A 151 " =    1.032
peak=    3.455 closest distance to " CG2 VAL A 197 " =    1.160
peak=    3.452 closest distance to " CA  ALA A 154 " =    0.949
peak=    3.445 closest distance to " O   HOH Z 172 " =    3.824
peak=    3.444 closest distance to " O   TRP A 274 " =    1.831
peak=    3.441 closest distance to " CE  LYS A  76 " =    0.891
peak=    3.441 closest distance to " O   HOH Z 273 " =    2.710
peak=    3.441 closest distance to " O   HOH Z 193 " =    2.136
peak=    3.438 closest distance to " O   HOH Z 402 " =    1.459
peak=    3.435 closest distance to " O   HOH Z 234 " =    1.821
peak=    3.434 closest distance to " O   HOH Z 134 " =    1.432
peak=    3.429 closest distance to " O   HOH Z   1 " =    2.317
peak=    3.420 closest distance to " O   HOH Z 427 " =    3.160
peak=    3.416 closest distance to " CD  ARG A  66 " =    2.390
peak=    3.409 closest distance to " O   HOH Z 280 " =    3.012
peak=    3.408 closest distance to " CB  ALA A 242 " =    0.830
peak=    3.401 closest distance to " O   HOH Z 263 " =    1.714
peak=    3.400 closest distance to " NE1 TRP A 266 " =    1.389
peak=    3.395 closest distance to " CB  ALA A 291 " =    1.108
peak=    3.391 closest distance to " N   GLY A  98 " =    1.160
peak=    3.389 closest distance to " NZ  LYS A 117 " =    3.323
peak=    3.387 closest distance to " CG2 ILE A 120 " =    1.082
peak=    3.386 closest distance to " CB  ALA A   9 " =    1.580
peak=    3.385 closest distance to " CG  GLU A  37 " =    0.917
peak=    3.383 closest distance to " O   HOH Z 291 " =    1.568
peak=    3.382 closest distance to " CA  ALA A 158 " =    1.054
peak=    3.381 closest distance to " CB  ALA A 248 " =    1.028
peak=    3.377 closest distance to " O   HOH Z 128 " =    2.289
peak=    3.376 closest distance to " CG2 THR A 220 " =    0.860
peak=    3.376 closest distance to " CA  GLY A 241 " =    0.726
peak=    3.374 closest distance to " CE1 TYR A 186 " =    1.262
peak=    3.373 closest distance to " O  BHOH Z 338 " =    2.423
peak=    3.370 closest distance to " CD  ARG A 219 " =    1.020
peak=    3.368 closest distance to " O   HOH Z  44 " =    2.214
peak=    3.367 closest distance to " O   HOH Z   4 " =    1.891
peak=    3.366 closest distance to " CB  GLN A  88 " =    1.237
peak=    3.359 closest distance to " CA  ASN A 215 " =    1.201
peak=    3.352 closest distance to " CB  LYS A 193 " =    0.960
peak=    3.349 closest distance to " CG AARG A 275 " =    1.231
peak=    3.345 closest distance to " O   HOH Z  68 " =    2.234
peak=    3.344 closest distance to " CB  GLN A 103 " =    0.858
peak=    3.325 closest distance to " O   HOH Z 128 " =    2.159
peak=    3.325 closest distance to " CG BARG A 102 " =    1.889
peak=    3.324 closest distance to " O   HOH Z 305 " =    3.739
peak=    3.323 closest distance to " O   HOH Z 281 " =    3.957
peak=    3.320 closest distance to " O   HOH Z 133 " =    1.725
peak=    3.319 closest distance to " CB  PRO A 198 " =    1.017
peak=    3.316 closest distance to " CA  GLN A  88 " =    1.330
peak=    3.316 closest distance to " O   HOH Z 245 " =    1.347
peak=    3.313 closest distance to " O   HOH Z 247 " =    1.466
peak=    3.312 closest distance to " O   SER A  87 " =    2.330
peak=    3.312 closest distance to " O   HOH Z  80 " =    1.627
peak=    3.309 closest distance to " ND1 HIS A  86 " =    1.728
peak=    3.309 closest distance to " CB  TYR A 116 " =    0.922
peak=    3.307 closest distance to " CA  ASP A 140 " =    1.282
peak=    3.307 closest distance to " O   HOH Z 327 " =    2.047
peak=    3.306 closest distance to " OG  SER A  28 " =    1.538
peak=    3.296 closest distance to " CA  ILE A 106 " =    0.851
peak=    3.290 closest distance to " O   HOH Z 411 " =    1.824
peak=    3.288 closest distance to " CA  ASP A 162 " =    1.098
peak=    3.287 closest distance to " O   ALA A 158 " =    1.306
peak=    3.285 closest distance to " CB  GLU A 236 " =    0.866
peak=    3.285 closest distance to " CG2 VAL A  78 " =    0.999
peak=    3.284 closest distance to " O   HOH Z 391 " =    2.958
peak=    3.280 closest distance to " CD1AILE A 234 " =    0.972
peak=    3.279 closest distance to " CA  VAL A  41 " =    0.814
peak=    3.276 closest distance to " CE1 HIS A 115 " =    1.013
peak=    3.276 closest distance to " O   HOH Z 421 " =    1.752
peak=    3.273 closest distance to " N   TYR A  15 " =    0.724
peak=    3.272 closest distance to " CG  ARG A 159 " =    0.961
peak=    3.268 closest distance to " O   HOH Z  88 " =    1.787
peak=    3.267 closest distance to " CA  ILE A  33 " =    1.633
peak=    3.267 closest distance to " CD  LYS A 119 " =    1.463
peak=    3.266 closest distance to " CD2 LEU A 255 " =    1.554
peak=    3.264 closest distance to " CZ  PHE A  38 " =    1.302
peak=    3.262 closest distance to " N   SER A 135 " =    1.339
peak=    3.257 closest distance to " O   TYR A 116 " =    1.276
peak=    3.253 closest distance to " O   HOH Z 298 " =    2.584
peak=    3.250 closest distance to " CA  ALA A 160 " =    0.950
peak=    3.246 closest distance to " NH1 ARG A 138 " =    1.093
peak=    3.245 closest distance to " O   THR A 220 " =    1.233
peak=    3.240 closest distance to " O   HOH Z 148 " =    3.253
peak=    3.237 closest distance to " CB  ALA A 100 " =    1.296
peak=    3.237 closest distance to " O   HOH Z 109 " =    2.832
peak=    3.236 closest distance to " O   HOH Z 350 " =    1.624
peak=    3.231 closest distance to " O   HOH Z 185 " =    1.900
peak=    3.230 closest distance to " CA  MET A 105 " =    1.017
peak=    3.230 closest distance to " O   HOH Z 142 " =    1.550
peak=    3.227 closest distance to " O   HOH Z 371 " =    3.250
peak=    3.225 closest distance to " O   HOH Z 352 " =    1.944
peak=    3.224 closest distance to " C   TYR A 214 " =    1.490
peak=    3.220 closest distance to " O   THR A 251 " =    2.020
peak=    3.214 closest distance to " O   HOH Z 425 " =    1.998
peak=    3.210 closest distance to " CB  ALA A  34 " =    0.992
peak=    3.206 closest distance to " O   HOH Z 116 " =    1.858
peak=    3.203 closest distance to " CB  ALA A 248 " =    1.220
peak=    3.200 closest distance to " O   LEU A 300 " =    1.493
peak=    3.197 closest distance to " CB  ALA A 114 " =    1.147
peak=    3.193 closest distance to " O   HOH Z 419 " =    3.175
peak=    3.187 closest distance to " CG2 ILE A 151 " =    0.717
peak=    3.186 closest distance to " OG  SER A 276 " =    1.223
peak=    3.185 closest distance to " CG  MET A 185 " =    1.221
peak=    3.182 closest distance to " O   HOH Z 175 " =    3.656
peak=    3.180 closest distance to " CA  GLY A 267 " =    0.972
peak=    3.180 closest distance to " CB  GLU A 152 " =    1.487
peak=    3.177 closest distance to " O   HOH Z  61 " =    1.579
peak=    3.175 closest distance to " O   HOH Z 188 " =    2.280
peak=    3.175 closest distance to " O   HOH Z 329 " =    3.693
peak=    3.174 closest distance to " CA  ALA A 233 " =    1.501
peak=    3.174 closest distance to " ND2 ASN A 209 " =    1.681
peak=    3.169 closest distance to " O   HOH Z 392 " =    2.104
peak=    3.166 closest distance to " CG  LYS A  76 " =    0.970
peak=    3.158 closest distance to " CB  MET A 113 " =    1.848
peak=    3.157 closest distance to " OD1 ASP A 171 " =    1.155
peak=    3.156 closest distance to " NE2 HIS A 207 " =    1.284
peak=    3.156 closest distance to " CB  GLN A  89 " =    1.200
peak=    3.156 closest distance to " O   HOH Z 345 " =    1.853
peak=    3.154 closest distance to " O   HOH Z  97 " =    2.677
peak=    3.152 closest distance to " CD2 TRP A 179 " =    1.312
peak=    3.151 closest distance to " O   HOH Z 387 " =    3.004
peak=    3.151 closest distance to " O   HOH Z 409 " =    3.259
peak=    3.146 closest distance to " O   HOH Z 432 " =    1.622
peak=    3.146 closest distance to " N   GLN A 278 " =    0.904
peak=    3.145 closest distance to " O   ASN A 209 " =    1.321
peak=    3.144 closest distance to " CA  ALA A  84 " =    1.372
peak=    3.143 closest distance to " O   HOH Z 403 " =    1.365
peak=    3.135 closest distance to " OG  SER A  22 " =    2.752
peak=    3.131 closest distance to " CB  HIS A 108 " =    0.797
peak=    3.129 closest distance to " CB  SER A 210 " =    0.819
peak=    3.128 closest distance to " CA  THR A  42 " =    0.887
peak=    3.128 closest distance to " CB  TRP A 150 " =    1.400
peak=    3.125 closest distance to " CG  MET A 185 " =    1.043
peak=    3.123 closest distance to " CA  TYR A 116 " =    1.410
peak=    3.123 closest distance to " CG  GLN A  11 " =    1.162
peak=    3.121 closest distance to " O   HOH Z 248 " =    1.639
peak=    3.117 closest distance to " NZ ALYS A 290 " =    1.055
peak=    3.113 closest distance to " OG BSER A 134 " =    2.971
peak=    3.110 closest distance to " NH2AARG A 275 " =    3.676
peak=    3.108 closest distance to " OG BSER A 164 " =    2.431
peak=    3.106 closest distance to " O   HOH Z 302 " =    2.029
peak=    3.103 closest distance to " CB  PRO A 163 " =    4.167
peak=    3.099 closest distance to " O   HOH Z 218 " =    4.920
peak=    3.096 closest distance to " OG  SER A 206 " =    1.274
peak=    3.093 closest distance to " CB  PHE A 283 " =    0.748
peak=    3.080 closest distance to " CB  ARG A 138 " =    1.062
peak=    3.079 closest distance to " CG2 ILE A  20 " =    1.283
peak=    3.072 closest distance to " CZ2 TRP A 179 " =    1.750
peak=    3.071 closest distance to " O   HOH Z 384 " =    2.847
peak=    3.057 closest distance to " O   HOH Z 327 " =    1.850
peak=    3.036 closest distance to " O   HOH Z 353 " =    2.706

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.292 - 5.536
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 194 from: 200
   mapped sites are within: 0.753 - 5.536

peak=   -4.729 closest distance to " O   HOH Z 290 " =    1.018
peak=   -4.370 closest distance to " CB  PRO A 243 " =    2.632
peak=   -4.254 closest distance to " O   VAL A  67 " =    2.632
peak=   -4.221 closest distance to " O   HOH Z 266 " =    5.065
peak=   -4.168 closest distance to " CZ3 TRP A 179 " =    1.142
peak=   -4.100 closest distance to " O   HOH Z  10 " =    1.596
peak=   -4.055 closest distance to " CD  GLN A 223 " =    1.298
peak=   -4.038 closest distance to " CD  ARG A 156 " =    2.087
peak=   -4.034 closest distance to " N   ALA A  43 " =    2.619
peak=   -4.030 closest distance to " CB  ALA A 161 " =    2.624
peak=   -4.026 closest distance to " CE2 TYR A  30 " =    2.823
peak=   -4.009 closest distance to " O   PRO A 198 " =    1.268
peak=   -3.989 closest distance to " CG1 VAL A 112 " =    2.601
peak=   -3.963 closest distance to " O   HOH Z  52 " =    1.558
peak=   -3.957 closest distance to " O   HOH Z  38 " =    1.167
peak=   -3.902 closest distance to " O   HOH Z 118 " =    3.458
peak=   -3.875 closest distance to " CG1 VAL A 250 " =    2.720
peak=   -3.872 closest distance to " O   HOH Z 394 " =    1.500
peak=   -3.852 closest distance to " O   HOH Z 372 " =    2.489
peak=   -3.841 closest distance to " NH2AARG A 275 " =    5.536
peak=   -3.834 closest distance to " OD1 ASN A 148 " =    1.620
peak=   -3.822 closest distance to " CD  GLN A  58 " =    0.997
peak=   -3.813 closest distance to " CA  GLY A 241 " =    3.152
peak=   -3.795 closest distance to " OG  SER A  97 " =    2.275
peak=   -3.793 closest distance to " CG  ARG A 269 " =    2.432
peak=   -3.773 closest distance to " CD2 TYR A 293 " =    2.033
peak=   -3.755 closest distance to " CA  GLY A 241 " =    2.372
peak=   -3.755 closest distance to " ND2 ASN A  45 " =    1.287
peak=   -3.746 closest distance to " O   HOH Z 241 " =    1.134
peak=   -3.743 closest distance to " ND2 ASN A  45 " =    1.014
peak=   -3.730 closest distance to " O   HOH Z  73 " =    2.243
peak=   -3.724 closest distance to " O   HOH Z 377 " =    0.836
peak=   -3.714 closest distance to " NE2 GLN A 103 " =    1.842
peak=   -3.710 closest distance to " O   HOH Z 377 " =    1.832
peak=   -3.699 closest distance to " C   HIS A 108 " =    1.112
peak=   -3.697 closest distance to " CD1 LEU A 228 " =    2.449
peak=   -3.695 closest distance to " CD1 PHE A  59 " =    1.892
peak=   -3.693 closest distance to " C   ASN A 285 " =    2.546
peak=   -3.684 closest distance to " O   HOH Z 185 " =    2.461
peak=   -3.675 closest distance to " CG  GLU A  53 " =    1.360
peak=   -3.670 closest distance to " O   HOH Z  43 " =    1.505
peak=   -3.654 closest distance to " O   PRO A 163 " =    2.148
peak=   -3.651 closest distance to " CD  ARG A  14 " =    3.326
peak=   -3.643 closest distance to " O   HOH Z 389 " =    1.913
peak=   -3.639 closest distance to " O   HOH Z 231 " =    2.190
peak=   -3.635 closest distance to " C   ALA A 158 " =    1.390
peak=   -3.634 closest distance to " O   HOH Z 196 " =    2.070
peak=   -3.631 closest distance to " CG  MET A 105 " =    0.946
peak=   -3.624 closest distance to " CD2 LEU A 300 " =    2.922
peak=   -3.618 closest distance to " O   HOH Z 176 " =    0.797
peak=   -3.613 closest distance to " O   HOH Z 353 " =    2.190
peak=   -3.612 closest distance to " NH2 ARG A  66 " =    1.966
peak=   -3.606 closest distance to " CD2 PHE A  61 " =    2.518
peak=   -3.605 closest distance to " NH2 ARG A  79 " =    1.543
peak=   -3.598 closest distance to " CG  ARG A  66 " =    2.396
peak=   -3.582 closest distance to " O   HOH Z 128 " =    2.519
peak=   -3.579 closest distance to " N   ALA A 226 " =    2.156
peak=   -3.574 closest distance to " O   GLY A 211 " =    1.453
peak=   -3.569 closest distance to " CD1 LEU A 101 " =    2.488
peak=   -3.551 closest distance to " C   ASN A 187 " =    1.908
peak=   -3.535 closest distance to " CB  ALA A 291 " =    2.155
peak=   -3.520 closest distance to " O   HOH Z 407 " =    3.570
peak=   -3.513 closest distance to " O   HOH Z 351 " =    1.595
peak=   -3.508 closest distance to " CD1 ILE A 239 " =    2.058
peak=   -3.507 closest distance to " CG1 VAL A 265 " =    2.417
peak=   -3.504 closest distance to " OXT GLY A 302 " =    2.949
peak=   -3.495 closest distance to " O   ALA A  10 " =    1.730
peak=   -3.472 closest distance to " C   SER A 206 " =    1.470
peak=   -3.467 closest distance to " O   HOH Z 426 " =    1.704
peak=   -3.467 closest distance to " ND2 ASN A  60 " =    1.357
peak=   -3.458 closest distance to " CG  ASP A 231 " =    0.773
peak=   -3.456 closest distance to " NE1 TRP A 266 " =    2.331
peak=   -3.449 closest distance to " CG  LEU A 101 " =    2.513
peak=   -3.440 closest distance to " CB  LEU A  83 " =    2.383
peak=   -3.440 closest distance to " O   HOH Z  60 " =    2.533
peak=   -3.434 closest distance to " CD1 ILE A 151 " =    2.375
peak=   -3.428 closest distance to " CZ  TYR A 169 " =    1.780
peak=   -3.428 closest distance to " CD  ARG A  79 " =    1.132
peak=   -3.426 closest distance to " O   VAL A 189 " =    2.625
peak=   -3.422 closest distance to " CB  ASN A  39 " =    2.207
peak=   -3.422 closest distance to " O   HOH Z 311 " =    3.779
peak=   -3.422 closest distance to " O   HOH Z 435 " =    2.772
peak=   -3.412 closest distance to " N   SER A 212 " =    1.988
peak=   -3.409 closest distance to " CD2 PHE A  59 " =    2.626
peak=   -3.408 closest distance to " CB  ALA A  43 " =    2.603
peak=   -3.407 closest distance to " O   HOH Z 393 " =    1.390
peak=   -3.388 closest distance to " CA  ASP A 298 " =    1.113
peak=   -3.381 closest distance to " CG1 VAL A 112 " =    2.895
peak=   -3.379 closest distance to " O   HOH Z 177 " =    1.657
peak=   -3.378 closest distance to " NH1 ARG A 195 " =    2.577
peak=   -3.378 closest distance to " OG BSER A 134 " =    1.902
peak=   -3.376 closest distance to " O   HOH Z 166 " =    1.781
peak=   -3.375 closest distance to " O   HOH Z  37 " =    1.935
peak=   -3.374 closest distance to " O   HOH Z 222 " =    1.245
peak=   -3.371 closest distance to " CG1 VAL A 197 " =    2.322
peak=   -3.369 closest distance to " O   HOH Z 232 " =    1.722
peak=   -3.359 closest distance to " OG  SER A  62 " =    1.622
peak=   -3.359 closest distance to " CG  PHE A 283 " =    2.867
peak=   -3.358 closest distance to " CD  ARG A 139 " =    1.632
peak=   -3.355 closest distance to " CB  ILE A  20 " =    2.905
peak=   -3.354 closest distance to " CG  TRP A 266 " =    1.806
peak=   -3.353 closest distance to " CB  ASP A 286 " =    2.128
peak=   -3.349 closest distance to " O   HOH Z  13 " =    1.422
peak=   -3.345 closest distance to " CG  GLU A 152 " =    0.873
peak=   -3.345 closest distance to " CE BMET A  47 " =    2.157
peak=   -3.342 closest distance to " CG1 VAL A 125 " =    1.969
peak=   -3.337 closest distance to " OD2 ASP A 171 " =    1.892
peak=   -3.337 closest distance to " ND2 ASN A 249 " =    2.437
peak=   -3.335 closest distance to " O   HOH Z 313 " =    1.144
peak=   -3.335 closest distance to " CD  GLN A  88 " =    0.986
peak=   -3.334 closest distance to " CH2 TRP A 177 " =    2.182
peak=   -3.331 closest distance to " CG2 ILE A  49 " =    2.848
peak=   -3.328 closest distance to " O   HOH Z 114 " =    1.477
peak=   -3.325 closest distance to " CD  PRO A 213 " =    2.178
peak=   -3.320 closest distance to " CG  GLU A 277 " =    1.132
peak=   -3.318 closest distance to " N   THR A  18 " =    1.293
peak=   -3.317 closest distance to " O   HOH Z  19 " =    2.284
peak=   -3.316 closest distance to " OE1 GLN A  88 " =    1.195
peak=   -3.313 closest distance to " CE3 TRP A 150 " =    1.977
peak=   -3.311 closest distance to " O   TYR A 247 " =    2.878
peak=   -3.308 closest distance to " SG  CYS A 254 " =    3.228
peak=   -3.308 closest distance to " C   LEU A 143 " =    1.153
peak=   -3.300 closest distance to " NE2 GLN A 194 " =    1.861
peak=   -3.298 closest distance to " O   HOH Z 198 " =    0.770
peak=   -3.298 closest distance to " N   SER A   3 " =    2.041
peak=   -3.295 closest distance to " CE  MET A 105 " =    2.231
peak=   -3.293 closest distance to " CB  TRP A  85 " =    2.442
peak=   -3.292 closest distance to " CD  ARG A 195 " =    5.132
peak=   -3.289 closest distance to " O   GLY A 196 " =    1.239
peak=   -3.287 closest distance to " SG  CYS A 168 " =    1.096
peak=   -3.287 closest distance to " OD1 ASP A 191 " =    1.577
peak=   -3.279 closest distance to " CG2 VAL A 189 " =    2.178
peak=   -3.277 closest distance to " CA  GLY A 203 " =    2.379
peak=   -3.277 closest distance to " O   VAL A  67 " =    2.722
peak=   -3.275 closest distance to " CB  PRO A 163 " =    2.616
peak=   -3.273 closest distance to " CB  ALA A   9 " =    2.657
peak=   -3.272 closest distance to " O   HOH Z 396 " =    1.838
peak=   -3.272 closest distance to " O   HOH Z 243 " =    1.996
peak=   -3.269 closest distance to " CE  MET A  93 " =    1.478
peak=   -3.267 closest distance to " O   HOH Z 292 " =    4.644
peak=   -3.254 closest distance to " SD BMET A  47 " =    0.995
peak=   -3.253 closest distance to " O   HOH Z 111 " =    2.039
peak=   -3.251 closest distance to " ND2BASN A 224 " =    1.791
peak=   -3.249 closest distance to " CG  LEU A  83 " =    1.980
peak=   -3.245 closest distance to " O   HOH Z 252 " =    4.194
peak=   -3.244 closest distance to " O   HOH Z 298 " =    2.610
peak=   -3.241 closest distance to " OD1 ASP A 171 " =    1.507
peak=   -3.240 closest distance to " O   HOH Z 275 " =    1.583
peak=   -3.240 closest distance to " OG BSER A 134 " =    1.311
peak=   -3.239 closest distance to " CG2 THR A 221 " =    2.211
peak=   -3.236 closest distance to " CB  ARG A  79 " =    2.637
peak=   -3.234 closest distance to " O   HOH Z 417 " =    2.597
peak=   -3.232 closest distance to " O   HOH Z  71 " =    1.407
peak=   -3.230 closest distance to " CD2 LEU A 167 " =    1.868
peak=   -3.227 closest distance to " O   HOH Z 211 " =    1.590
peak=   -3.221 closest distance to " CA  GLY A 241 " =    2.821
peak=   -3.220 closest distance to " O   HOH Z  76 " =    1.980
peak=   -3.218 closest distance to " NH2 ARG A  79 " =    1.962
peak=   -3.214 closest distance to " CB  ALA A 291 " =    2.303
peak=   -3.211 closest distance to " O   HOH Z 193 " =    2.156
peak=   -3.204 closest distance to " O   LEU A 101 " =    2.861
peak=   -3.201 closest distance to " CD1 LEU A   5 " =    2.557
peak=   -3.200 closest distance to " O   HOH Z 234 " =    4.488
peak=   -3.190 closest distance to " N   THR A 157 " =    1.654
peak=   -3.187 closest distance to " CZ  ARG A  66 " =    1.036
peak=   -3.184 closest distance to " O   HOH Z  88 " =    2.599
peak=   -3.183 closest distance to " CD1 TRP A 179 " =    0.905
peak=   -3.183 closest distance to " O   HOH Z 166 " =    1.649
peak=   -3.182 closest distance to " C   GLY A  13 " =    0.892
peak=   -3.169 closest distance to " CA  SER A 135 " =    1.282
peak=   -3.165 closest distance to " CD  GLN A  55 " =    0.771
peak=   -3.160 closest distance to " CE3 TRP A  70 " =    1.867
peak=   -3.155 closest distance to " O   HOH Z  51 " =    1.495
peak=   -3.152 closest distance to " OD2 ASP A  50 " =    2.257
peak=   -3.150 closest distance to " O   HOH Z 198 " =    1.266
peak=   -3.147 closest distance to " C   MET A 188 " =    1.533
peak=   -3.147 closest distance to " O   HOH Z 323 " =    1.299
peak=   -3.147 closest distance to " O   HOH Z 371 " =    1.997
peak=   -3.146 closest distance to " ND2 ASN A  60 " =    1.904
peak=   -3.134 closest distance to " O   HOH Z 390 " =    2.283
peak=   -3.133 closest distance to " OG BSER A 210 " =    2.184
peak=   -3.130 closest distance to " O   HOH Z 380 " =    4.805
peak=   -3.123 closest distance to " CG  PRO A 163 " =    2.390
peak=   -3.122 closest distance to " CB  PRO A  54 " =    2.563
peak=   -3.119 closest distance to " O   HOH Z 398 " =    0.753
peak=   -3.114 closest distance to " CB  ASP A 132 " =    2.315
peak=   -3.112 closest distance to " O   HOH Z 106 " =    2.036
peak=   -3.094 closest distance to " O   GLY A 203 " =    2.398
peak=   -3.085 closest distance to " O   ALA A   7 " =    1.711
peak=   -3.080 closest distance to " CZ  ARG A 259 " =    0.798
peak=   -3.077 closest distance to " CB  ALA A 248 " =    2.511
peak=   -3.073 closest distance to " O   HOH Z 259 " =    2.166
peak=   -3.043 closest distance to " OD1 ASN A 249 " =    2.217
peak=   -3.029 closest distance to " CG2BVAL A  41 " =    1.785

================= 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    :  0.3563 0.3510   6.116080e+00   6.111733e+00
   1_bss:  0.3452 0.3389   6.100164e+00   6.091885e+00
   1_xyz:  0.2333 0.2568   5.755567e+00   5.832878e+00
   1_adp:  0.2163 0.2593   5.703109e+00   5.847036e+00
   1_occ:  0.2159 0.2588   5.701093e+00   5.845519e+00
   2_bss:  0.2144 0.2566   5.699543e+00   5.842546e+00
   2_xyz:  0.1452 0.1868   5.356749e+00   5.560734e+00
   2_adp:  0.1304 0.1736   5.264940e+00   5.489340e+00
   2_occ:  0.1303 0.1734   5.264421e+00   5.488912e+00
   3_bss:  0.1302 0.1730   5.265118e+00   5.488181e+00
   3_xyz:  0.1204 0.1649   5.208770e+00   5.440057e+00
   3_adp:  0.1179 0.1659   5.197530e+00   5.437192e+00
   3_occ:  0.1179 0.1659   5.197425e+00   5.437126e+00
   4_bss:  0.1178 0.1658   5.197210e+00   5.437070e+00
   4_xyz:  0.1127 0.1643   5.170687e+00   5.425314e+00
   4_adp:  0.1126 0.1625   5.164951e+00   5.416411e+00
   4_occ:  0.1126 0.1624   5.164969e+00   5.416641e+00
   5_bss:  0.1125 0.1624   5.165028e+00   5.416708e+00
   5_xyz:  0.1141 0.1629   5.174470e+00   5.421014e+00
   5_adp:  0.1160 0.1622   5.180652e+00   5.419117e+00
   5_occ:  0.1159 0.1622   5.180681e+00   5.419398e+00
   5_bss:  0.1159 0.1622   5.180756e+00   5.419430e+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:  0.310  56.750   1.481   0.289  -1.776   0.000  -0.000  -0.000
   1_xyz:  0.310  56.750   1.481   0.289  -1.776   0.000  -0.000  -0.000
   1_adp:  0.310  56.750   1.481   0.289  -1.776   0.000  -0.000  -0.000
   1_occ:  0.310  56.750   1.481   0.289  -1.776   0.000  -0.000  -0.000
   2_bss:  0.330  67.666  -1.091  -1.405  -1.877  -0.000  -0.000  -0.000
   2_xyz:  0.330  67.666  -1.091  -1.405  -1.877  -0.000  -0.000  -0.000
   2_adp:  0.330  67.666  -1.091  -1.405  -1.877  -0.000  -0.000  -0.000
   2_occ:  0.330  67.666  -1.091  -1.405  -1.877  -0.000  -0.000  -0.000
   3_bss:  0.330  65.304  -1.728  -1.835  -1.453  -0.000  -0.000  -0.000
   3_xyz:  0.330  65.304  -1.728  -1.835  -1.453  -0.000  -0.000  -0.000
   3_adp:  0.330  65.304  -1.728  -1.835  -1.453  -0.000  -0.000  -0.000
   3_occ:  0.330  65.304  -1.728  -1.835  -1.453  -0.000  -0.000  -0.000
   4_bss:  0.325  66.086  -1.760  -1.790  -1.202  -0.000  -0.000  -0.000
   4_xyz:  0.325  66.086  -1.760  -1.790  -1.202  -0.000  -0.000  -0.000
   4_adp:  0.325  66.086  -1.760  -1.790  -1.202  -0.000  -0.000  -0.000
   4_occ:  0.325  66.086  -1.760  -1.790  -1.202  -0.000  -0.000  -0.000
   5_bss:  0.319  61.597  -1.681  -1.692  -0.983  -0.000  -0.000  -0.000
   5_xyz:  0.319  61.597  -1.681  -1.692  -0.983  -0.000  -0.000  -0.000
   5_adp:  0.319  61.597  -1.681  -1.692  -0.983  -0.000  -0.000  -0.000
   5_occ:  0.319  61.597  -1.681  -1.692  -0.983  -0.000  -0.000  -0.000
   5_bss:  0.316  58.659  -1.675  -1.649  -0.876  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  38.518 0.6624  0.8245    36916.590
   1_bss:  37.533 0.6724  0.8414    34323.959
   1_xyz:  25.483 0.8075  0.9712    17057.919
   1_adp:  26.104 0.8003  0.9617    17656.608
   1_occ:  26.072 0.8005  0.9617    17563.910
   2_bss:  25.918 0.8021  0.9161    17420.704
   2_xyz:  18.105 0.8787  0.9714     9082.364
   2_adp:  16.250 0.8958  0.9742     7766.118
   2_occ:  16.239 0.8959  0.9740     7759.287
   3_bss:  16.249 0.8958  0.9666     7776.054
   3_xyz:  15.065 0.9062  0.9691     7019.434
   3_adp:  14.931 0.9077  0.9623     6983.722
   3_occ:  14.933 0.9077  0.9621     6982.022
   4_bss:  14.930 0.9077  0.9651     6980.473
   4_xyz:  14.699 0.9095  0.9673     6820.398
   4_adp:  14.481 0.9114  0.9627     6733.094
   4_occ:  14.487 0.9113  0.9626     6734.813
   5_bss:  14.489 0.9113  0.9671     6733.125
   5_xyz:  14.549 0.9110  0.9657     6785.313
   5_adp:  14.469 0.9117  0.9617     6799.829
   5_occ:  14.476 0.9117  0.9616     6802.378
   5_bss:  14.479 0.9116  0.9618     6800.089
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6403e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6403e-01
   1_xyz:   1.147  0.009  0.074 15.163  0.004  4.115   7.3770e-02
   1_adp:   1.147  0.009  0.074 15.163  0.004  4.115   7.3770e-02
   1_occ:   1.147  0.009  0.074 15.163  0.004  4.115   7.3770e-02
   2_bss:   1.147  0.009  0.074 15.163  0.004  4.115   7.3770e-02
   2_xyz:   1.117  0.010  0.081 14.690  0.004  4.137   7.6935e-02
   2_adp:   1.117  0.010  0.081 14.690  0.004  4.137   7.6935e-02
   2_occ:   1.117  0.010  0.081 14.690  0.004  4.137   7.6935e-02
   3_bss:   1.117  0.010  0.081 14.690  0.004  4.137   7.6935e-02
   3_xyz:   0.989  0.008  0.074 14.539  0.004  4.141   5.9212e-02
   3_adp:   0.989  0.008  0.074 14.539  0.004  4.141   5.9212e-02
   3_occ:   0.989  0.008  0.074 14.539  0.004  4.141   5.9212e-02
   4_bss:   0.989  0.008  0.074 14.539  0.004  4.141   5.9212e-02
   4_xyz:   1.093  0.010  0.081 14.675  0.004  4.128   7.1055e-02
   4_adp:   1.093  0.010  0.081 14.675  0.004  4.128   7.1055e-02
   4_occ:   1.093  0.010  0.081 14.675  0.004  4.128   7.1055e-02
   5_bss:   1.093  0.010  0.081 14.675  0.004  4.128   7.1055e-02
   5_xyz:   1.000  0.008  0.075 14.447  0.004  4.128   5.9962e-02
   5_adp:   1.000  0.008  0.075 14.447  0.004  4.128   5.9962e-02
   5_occ:   1.000  0.008  0.075 14.447  0.004  4.128   5.9962e-02
   5_bss:   1.000  0.008  0.075 14.447  0.004  4.128   5.9962e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.500   2.4369e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.500   2.4369e-01
   1_xyz:   7.603  0.054  0.313 88.828  0.026  2.087   7.6205e-02
   1_adp:   7.603  0.054  0.313 88.828  0.026  2.087   7.6205e-02
   1_occ:   7.603  0.054  0.313 88.828  0.026  2.087   7.6205e-02
   2_bss:   7.603  0.054  0.313 88.828  0.026  2.087   7.6205e-02
   2_xyz:   7.514  0.068  0.242 84.748  0.043  2.221   1.4875e-01
   2_adp:   7.514  0.068  0.242 84.748  0.043  2.221   1.4875e-01
   2_occ:   7.514  0.068  0.242 84.748  0.043  2.221   1.4875e-01
   3_bss:   7.514  0.068  0.242 84.748  0.043  2.221   1.4875e-01
   3_xyz:   7.757  0.046  0.238 82.816  0.042  2.368   4.1507e-02
   3_adp:   7.757  0.046  0.238 82.816  0.042  2.368   4.1507e-02
   3_occ:   7.757  0.046  0.238 82.816  0.042  2.368   4.1507e-02
   4_bss:   7.757  0.046  0.238 82.816  0.042  2.368   4.1507e-02
   4_xyz:   7.756  0.047  0.253 82.449  0.042  2.312   5.0261e-02
   4_adp:   7.756  0.047  0.253 82.449  0.042  2.312   5.0261e-02
   4_occ:   7.756  0.047  0.253 82.449  0.042  2.312   5.0261e-02
   5_bss:   7.756  0.047  0.253 82.449  0.042  2.312   5.0261e-02
   5_xyz:   7.844  0.044  0.228 82.916  0.040  2.385   3.7975e-02
   5_adp:   7.844  0.044  0.228 82.916  0.040  2.385   3.7975e-02
   5_occ:   7.844  0.044  0.228 82.916  0.040  2.385   3.7975e-02
   5_bss:   7.844  0.044  0.228 82.916  0.040  2.385   3.7975e-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:  76.96   0.00  16.73  76.96   0.00  12.87  64.71   5.49  37.76
   1_occ:  76.96   0.00  16.73  76.96   0.00  12.87  64.71   5.49  37.76
   2_bss:  76.96   0.00  16.73  76.96   0.00  12.87  64.71   5.49  37.76
   2_xyz:  76.96   0.00  16.73  76.96   0.00  12.87  64.71   5.49  37.76
   2_adp:  72.18   0.83  17.10  71.69   0.83  12.90  72.18   4.60  40.00
   2_occ:  72.18   0.83  17.10  71.69   0.83  12.90  72.18   4.60  40.00
   3_bss:  72.18   0.83  17.10  71.69   0.83  12.90  72.18   4.60  40.00
   3_xyz:  72.18   0.83  17.10  71.69   0.83  12.90  72.18   4.60  40.00
   3_adp:  94.18   0.00  17.48  94.18   0.00  12.94  88.80   0.00  42.20
   3_occ:  94.18   0.00  17.48  94.18   0.00  12.94  88.80   0.00  42.20
   4_bss:  94.18   0.00  17.48  94.18   0.00  12.94  88.80   0.00  42.20
   4_xyz:  94.18   0.00  17.48  94.18   0.00  12.94  88.80   0.00  42.20
   4_adp:  94.59   0.28  16.92  94.59   0.28  12.66  86.23   0.46  40.10
   4_occ:  94.59   0.28  16.92  94.59   0.28  12.66  86.23   0.46  40.10
   5_bss:  94.59   0.28  16.92  94.59   0.28  12.66  86.23   0.46  40.10
   5_xyz:  94.59   0.28  16.92  94.59   0.28  12.66  86.23   0.46  40.10
   5_adp:  87.65   1.30  16.19  87.65   1.30  12.36  82.58   3.18  37.06
   5_occ:  87.65   1.30  16.19  87.65   1.30  12.36  82.58   3.18  37.06
   5_bss:  87.61   1.25  16.15  87.61   1.25  12.32  82.53   3.13  37.01
------------------------------------------------------------------------
 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:    1.609    0.019    0.280
   1_adp:    1.609    0.019    0.280
   1_occ:    1.609    0.019    0.280
   2_bss:    1.609    0.019    0.280
   2_xyz:    0.935    0.021    0.443
   2_adp:    0.935    0.021    0.443
   2_occ:    0.935    0.021    0.443
   3_bss:    0.935    0.021    0.443
   3_xyz:    0.943    0.041    0.461
   3_adp:    0.943    0.041    0.461
   3_occ:    0.943    0.041    0.461
   4_bss:    0.943    0.041    0.461
   4_xyz:    0.978    0.016    0.482
   4_adp:    0.978    0.016    0.482
   4_occ:    0.978    0.016    0.482
   5_bss:    0.978    0.016    0.482
   5_xyz:    0.994    0.017    0.486
   5_adp:    0.994    0.017    0.486
   5_occ:    0.994    0.017    0.486
   5_bss:    0.994    0.017    0.486
------------------------------------------------------------------------

CPU time actual refinement: 314.53


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1171/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_1171/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1171/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1171/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1171/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 314.39 
  Macro-tasks:
    bulk solvent and scale       = 38.42  
    individual site refinement   = 125.25 
    weights calculation          = 29.77  
    collect and process          = 6.60   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 200.15 
  Micro-tasks:
    mask                            = 1.21   
    f_calc                          = 98.60  
    alpha_beta                      = 8.20   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 106.54 
    fmodel                         = 6.37   
    r_factors                      = 0.13   
    phase_errors                   = 11.11  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 233.60 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.551 micro seconds
Total CPU time: 5.47 minutes
from_scatterers_fft:    615 calls, 98.22 s
gradients_fft:          560 calls, 93.88 s

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

# Date 2008-01-16 Time 06:35:45 PST -0800 (1200494145.26 s)
Start R-work = 0.3563, R-free = 0.3510 (no bulk solvent and anisotropic scale)
Final R-work = 0.1365, R-free = 0.1798 (no bulk solvent and anisotropic scale)

Start R-work = 0.3452, R-free = 0.3389
Final R-work = 0.1159, R-free = 0.1622