# Date 2008-01-16 Time 05:46:52 PST -0800 (1200491212.04 s)
#phil __OFF__

Command line arguments: "../874.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 28024
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 874

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 46.2261, 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: 2.76, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.2261, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1028 1.97313
Completeness in resolution range: 0.951939
Completeness with d_max=infinity: 0.949125

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1028
                             d_min =   1.9731

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.2261, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1028 1.97313
Completeness in resolution range: 0.951939
Completeness with d_max=infinity: 0.949125

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1033 -  4.2229 [2163/2189]  1947   216  10.0%
  bin  2:  4.2229 -  3.3640 [2069/2089]  1863   206  10.0%
  bin  3:  3.3640 -  2.9424 [2060/2079]  1851   209  10.1%
  bin  4:  2.9424 -  2.6750 [2024/2054]  1822   202  10.0%
  bin  5:  2.6750 -  2.4841 [2020/2039]  1824   196   9.7%
  bin  6:  2.4841 -  2.3382 [2007/2032]  1796   211  10.5%
  bin  7:  2.3382 -  2.2215 [2003/2031]  1806   197   9.8%
  bin  8:  2.2215 -  2.1251 [1991/2027]  1794   197   9.9%
  bin  9:  2.1251 -  2.0435 [1971/2013]  1774   197  10.0%
  bin 10:  2.0435 -  1.9731 [1281/2025]  1153   128  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_874/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: 0.12 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:
        1.81 -     2.42: 26
        2.42 -     3.04: 2190
        3.04 -     3.66: 4718
        3.66 -     4.28: 9072
        4.28 -     4.90: 12332
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.050 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  2.148 3.040 x,y+1,z
  " O   HOH Z 204 " - " O   HOH Z 296 "  2.188 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28333 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_874/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_874/model_refine_001.geo

CPU time processing inputs: 7.88


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 46.22605 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: 1.97 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3579   r_free= 0.3538   ksol= 0.00   Bsol= 0.00   scale= 0.955    |
|                                                                             |
| 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:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.134934                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1033 -  4.7104 0.99   1402  157 0.3075 0.2988      6.4059       6.368|
|  2:  4.7104 -  3.7578 0.99   1346  150 0.2885 0.2779      6.5654      6.4717|
|  3:  3.7578 -  3.2884 0.99   1331  143 0.3052 0.2773      6.4329      6.4991|
|  4:  3.2884 -  2.9902 0.99   1321  152 0.3385 0.3686      6.3431       6.379|
|  5:  2.9902 -  2.7773 0.99   1313  147 0.3759 0.3217      6.2111      6.1549|
|  6:  2.7773 -  2.6145 0.99   1304  137 0.3666 0.3774      6.1098      6.0925|
|  7:  2.6145 -  2.4841 0.99   1290  143 0.3797 0.3735      6.1047      6.0823|
|  8:  2.4841 -  2.3764 0.98   1273  145 0.3953 0.3988      6.0423      6.0584|
|  9:  2.3764 -  2.2853 0.98   1276  150 0.3895 0.3989      6.0079      6.0222|
| 10:  2.2853 -  2.2067 1.00   1304  148 0.4058 0.3876      5.9887      5.9171|
| 11:  2.2067 -  2.1379 0.98   1291  133 0.4056 0.4405      5.9469      5.9955|
| 12:  2.1379 -  2.0769 0.98   1259  140 0.4237 0.4227      5.8978      5.9336|
| 13:  2.0769 -  2.0224 0.99   1281  140 0.4185 0.4290      5.7884      5.7295|
| 14:  2.0224 -  1.9731 0.49    639   74 0.4586 0.4722      5.8168      5.8159|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1033 -  4.7104  1402   157  0.78  26.71   0.85     0.82      45610.10|
|  2:  4.7104 -  3.7578  1346   150  0.82  24.23   0.95     0.91      54808.02|
|  3:  3.7578 -  3.2884  1331   143  0.76  29.70   0.99     0.93      58011.43|
|  4:  3.2884 -  2.9902  1321   152  0.72  34.01   0.98     0.90      53503.95|
|  5:  2.9902 -  2.7773  1313   147  0.65  39.44   0.95     0.86      45284.10|
|  6:  2.7773 -  2.6145  1304   137  0.65  39.61   0.97     0.85      39098.49|
|  7:  2.6145 -  2.4841  1290   143  0.64  41.06   0.99     0.83      36581.91|
|  8:  2.4841 -  2.3764  1273   145  0.62  42.30   0.98     0.83      33246.55|
|  9:  2.3764 -  2.2853  1276   150  0.63  41.39   1.00     0.84      30359.56|
| 10:  2.2853 -  2.2067  1304   148  0.63  41.76   1.01     0.87      27297.41|
| 11:  2.2067 -  2.1379  1291   133  0.61  43.34   1.03     0.87      28067.78|
| 12:  2.1379 -  2.0769  1259   140  0.57  46.35   1.00     0.82      26993.69|
| 13:  2.0769 -  2.0224  1281   140  0.51  51.87   1.02     0.75      26259.19|
| 14:  2.0224 -  1.9731   639    74  0.49  53.09   1.00     0.68      24279.65|
|alpha:            min =        0.68 max =            0.93 mean =         0.85|
|beta:             min =    24279.65 max =        58011.43 mean =     38529.37|
|figures of merit: min =        0.00 max =            1.00 mean =         0.66|
|phase err.(work): min =        0.00 max =           89.96 mean =        38.95|
|phase err.(test): min =        0.00 max =           89.97 mean =        38.92|
|-----------------------------------------------------------------------------|

============================== 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 = 3.725476              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.238   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.062657              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.967   (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 |  1.806 -  2.115:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       23 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      199 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1991 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1872 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2846 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4655 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4417 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5631 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6701 |
|-----------------------------------------------------------------------------|
|-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 |   4.111    4.900  1.806 |       0.207 |              |
|-----------------------------------------------------------------------------|

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

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

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

|--(resolution: 1.97 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3579   r_free= 0.3538   ksol= 0.00   Bsol= 0.00   scale= 0.955    |
|                                                                             |
| 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:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.134934                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3450   r_free= 0.3447   ksol= 0.34   Bsol= 50.00   scale= 0.971   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.53,2.17,-1.78,0.00,-0.00,-0.00); trace/3= -0.38                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.117052                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.330041              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.405   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.525862              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.798   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3450      final r-factor (work) = 0.2377          |
| start r-factor (free) = 0.3447      final r-factor (free) = 0.2671          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.3527 = 3.33 * 0.50 * 6.1191 + 1.00 * 0.1642                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9096 = 3.33 * 0.50 * 5.9058 + 1.00 * 0.0764                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2377      final r-factor (work) = 0.2175          |
| start r-factor (free) = 0.2671      final r-factor (free) = 0.2793          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1116 = 0.53 * 1.00 * 5.9058 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0233 = 0.53 * 1.00 * 5.7274 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.850)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.34   17.49    None  None   None       |
|    all(noH): 2823   0      0.00    86.34   17.49    None  None   None       |
|    Sol.    : 438    0      5.59    86.34   39.42    None  None   None       |
|    Mac.    : 2385   0      0.00    71.01   13.46    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.634:  734   |   5:    43.168 -  51.802:  116        |
|      1:     8.634 -  17.267: 1171   |   6:    51.802 -  60.436:   64        |
|      2:    17.267 -  25.901:  388   |   7:    60.436 -  69.069:   24        |
|      3:    25.901 -  34.535:  180   |   8:    69.069 -  77.703:   10        |
|      4:    34.535 -  43.168:  134   |   9:    77.703 -  86.337:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2175 r_free = 0.2793             target_work(ml) = 5.743         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2173 r_free = 0.2790             target_work(ml) = 5.741         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2173   r_free= 0.2790   ksol= 0.34   Bsol= 50.00   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.53,2.17,-1.78,0.00,-0.00,-0.00); trace/3= -0.38                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.741377                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2163   r_free= 0.2754   ksol= 0.33   Bsol= 59.88   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-0.88,-1.51,-0.00,-0.00,-0.00); trace/3= -1.51                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.735725                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.262247              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.441   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.196076              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.507  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2163      final r-factor (work) = 0.1507          |
| start r-factor (free) = 0.2754      final r-factor (free) = 0.1962          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.2876 = 4.26 * 0.50 * 5.7300 + 1.00 * 0.0764                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9617 = 4.26 * 0.50 * 5.5830 + 1.00 * 0.0636                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1507      final r-factor (work) = 0.1365          |
| start r-factor (free) = 0.1962      final r-factor (free) = 0.1811          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1062 = 0.20 * 1.00 * 5.5830 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0565 = 0.20 * 1.00 * 5.3498 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.850)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.63    82.94   17.01    None  None   None       |
|    all(noH): 2823   0      1.63    82.94   17.01    None  None   None       |
|    Sol.    : 438    0      6.42    82.94   38.93    None  None   None       |
|    Mac.    : 2385   0      1.63    71.26   12.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.629 -   9.760:  911   |   5:    42.283 -  50.413:  108        |
|      1:     9.760 -  17.891: 1141   |   6:    50.413 -  58.544:   74        |
|      2:    17.891 -  26.021:  284   |   7:    58.544 -  66.675:   25        |
|      3:    26.021 -  34.152:  134   |   8:    66.675 -  74.805:   11        |
|      4:    34.152 -  42.283:  132   |   9:    74.805 -  82.936:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1365 r_free = 0.1811             target_work(ml) = 5.308         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1364 r_free = 0.1811             target_work(ml) = 5.308         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1364   r_free= 0.1811   ksol= 0.33   Bsol= 59.88   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-0.88,-1.51,-0.00,-0.00,-0.00); trace/3= -1.51                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.307914                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1361   r_free= 0.1799   ksol= 0.33   Bsol= 52.39   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.25,-2.17,-1.33,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.302162                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.797165              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.644  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.230910              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.658  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1361      final r-factor (work) = 0.1215          |
| start r-factor (free) = 0.1799      final r-factor (free) = 0.1641          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8703 = 1.80 * 0.50 * 5.3493 + 1.00 * 0.0635                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7703 = 1.80 * 0.50 * 5.2541 + 1.00 * 0.0490                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1215      final r-factor (work) = 0.1172          |
| start r-factor (free) = 0.1641      final r-factor (free) = 0.1623          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4749 = 1.23 * 1.00 * 5.2541 + 1.00 * 0.0075                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3958 = 1.23 * 1.00 * 5.1880 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.850)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.16   17.48    None  None   None       |
|    all(noH): 2823   0      0.00    89.16   17.48    None  None   None       |
|    Sol.    : 438    0      5.98    85.82   41.75    None  None   None       |
|    Mac.    : 2385   0      0.00    89.16   13.02    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.916:  771   |   5:    44.578 -  53.494:   98        |
|      1:     8.916 -  17.831: 1299   |   6:    53.494 -  62.409:   80        |
|      2:    17.831 -  26.747:  275   |   7:    62.409 -  71.325:   34        |
|      3:    26.747 -  35.662:  132   |   8:    71.325 -  80.240:   20        |
|      4:    35.662 -  44.578:  106   |   9:    80.240 -  89.156:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1172 r_free = 0.1623             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1172 r_free = 0.1623             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1172   r_free= 0.1623   ksol= 0.33   Bsol= 52.39   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.25,-2.17,-1.33,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.183016                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1171   r_free= 0.1622   ksol= 0.32   Bsol= 54.10   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.30,-2.46,-1.31,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.182151                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.973633              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.921  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.457772              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.394  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1171      final r-factor (work) = 0.1117          |
| start r-factor (free) = 0.1622      final r-factor (free) = 0.1578          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1684 = 1.97 * 0.50 * 5.1877 + 1.00 * 0.0490                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1468 = 1.97 * 0.50 * 5.1598 + 1.00 * 0.0551                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1117      final r-factor (work) = 0.1111          |
| start r-factor (free) = 0.1578      final r-factor (free) = 0.1563          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3718 = 0.46 * 1.00 * 5.1598 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3633 = 0.46 * 1.00 * 5.1424 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.850)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.16    92.07   17.19    None  None   None       |
|    all(noH): 2823   0      0.16    92.07   17.19    None  None   None       |
|    Sol.    : 438    0      5.90    86.55   40.63    None  None   None       |
|    Mac.    : 2385   0      0.16    92.07   12.89    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.157 -   9.348:  899   |   5:    46.111 -  55.302:   96        |
|      1:     9.348 -  18.539: 1222   |   6:    55.302 -  64.493:   58        |
|      2:    18.539 -  27.730:  242   |   7:    64.493 -  73.684:   28        |
|      3:    27.730 -  36.921:  146   |   8:    73.684 -  82.875:   14        |
|      4:    36.921 -  46.111:  113   |   9:    82.875 -  92.066:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1111 r_free = 0.1563             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1110 r_free = 0.1563             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1110   r_free= 0.1563   ksol= 0.32   Bsol= 54.10   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.30,-2.46,-1.31,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.138485                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1111   r_free= 0.1558   ksol= 0.32   Bsol= 54.10   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-2.47,-1.18,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.138192                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.915442              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 157.766  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.509428              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.920  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1111      final r-factor (work) = 0.1070          |
| start r-factor (free) = 0.1558      final r-factor (free) = 0.1552          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5518 = 2.92 * 0.50 * 5.1428 + 1.00 * 0.0551                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5328 = 2.92 * 0.50 * 5.1219 + 1.00 * 0.0665                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1070      final r-factor (work) = 0.1066          |
| start r-factor (free) = 0.1552      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6185 = 0.51 * 1.00 * 5.1219 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6155 = 0.51 * 1.00 * 5.1163 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.850)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.27    93.06   16.95    None  None   None       |
|    all(noH): 2823   0      0.27    93.06   16.95    None  None   None       |
|    Sol.    : 438    0      6.08    87.49   40.05    None  None   None       |
|    Mac.    : 2385   0      0.27    93.06   12.71    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:     0.273 -   9.552:  981   |   5:    46.667 -  55.946:   93        |
|      1:     9.552 -  18.831: 1165   |   6:    55.946 -  65.224:   54        |
|      2:    18.831 -  28.109:  229   |   7:    65.224 -  74.503:   23        |
|      3:    28.109 -  37.388:  141   |   8:    74.503 -  83.782:   14        |
|      4:    37.388 -  46.667:  120   |   9:    83.782 -  93.060:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1066 r_free = 0.1549             target_work(ml) = 5.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1066 r_free = 0.1549             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1066   r_free= 0.1549   ksol= 0.32   Bsol= 54.10   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-2.47,-1.18,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.115510                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1033 -  4.7104 0.99   1402  157 0.0934 0.1232      5.3359      5.5161|
|  2:  4.7104 -  3.7578 0.99   1346  150 0.0814 0.1094      5.4039      5.6032|
|  3:  3.7578 -  3.2884 0.99   1331  143 0.1038 0.1516      5.4526      5.8488|
|  4:  3.2884 -  2.9902 0.99   1321  152 0.1158 0.1655      5.4307      5.5948|
|  5:  2.9902 -  2.7773 0.99   1313  147 0.1289 0.1694       5.301      5.5509|
|  6:  2.7773 -  2.6145 0.99   1304  137 0.1143 0.1767      5.1727      5.4157|
|  7:  2.6145 -  2.4841 0.99   1290  143 0.1214 0.1611      5.1353      5.3377|
|  8:  2.4841 -  2.3764 0.98   1273  145 0.1101 0.1713      5.0207      5.3202|
|  9:  2.3764 -  2.2853 0.98   1276  150 0.1113 0.1662      5.0025      5.2956|
| 10:  2.2853 -  2.2067 1.00   1304  148 0.1056 0.1719      4.9121      5.1838|
| 11:  2.2067 -  2.1379 0.98   1291  133 0.1064 0.1732      4.9135      5.2389|
| 12:  2.1379 -  2.0769 0.98   1259  140 0.1061 0.1609       4.845      5.1434|
| 13:  2.0769 -  2.0224 0.99   1281  140 0.1068 0.1751      4.7562       5.024|
| 14:  2.0224 -  1.9731 0.49    639   74 0.0980 0.1532      4.6238      4.8729|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1033 -  4.7104  1402   157  0.94   8.54   0.98     0.95       6483.42|
|  2:  4.7104 -  3.7578  1346   150  0.95   7.67   1.01     1.01       8666.01|
|  3:  3.7578 -  3.2884  1331   143  0.94  11.12   1.02     1.02      10024.10|
|  4:  3.2884 -  2.9902  1321   152  0.92  13.69   1.01     0.98      10230.47|
|  5:  2.9902 -  2.7773  1313   147  0.90  15.65   0.99     0.98       8053.75|
|  6:  2.7773 -  2.6145  1304   137  0.90  15.56   0.99     0.96       6755.31|
|  7:  2.6145 -  2.4841  1290   143  0.91  15.23   0.99     0.96       5953.95|
|  8:  2.4841 -  2.3764  1273   145  0.91  14.72   0.98     0.96       4858.53|
|  9:  2.3764 -  2.2853  1276   150  0.91  14.73   1.00     0.96       4721.98|
| 10:  2.2853 -  2.2067  1304   148  0.91  15.18   0.99     0.96       4091.65|
| 11:  2.2067 -  2.1379  1291   133  0.91  15.62   0.98     0.94       4167.26|
| 12:  2.1379 -  2.0769  1259   140  0.91  15.05   1.00     1.00       3840.13|
| 13:  2.0769 -  2.0224  1281   140  0.91  15.81   0.99     0.97       3217.15|
| 14:  2.0224 -  1.9731   639    74  0.92  13.88   0.97     0.95       2421.72|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2421.72 max =        10230.47 mean =      6131.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.94 mean =        13.68|
|phase err.(test): min =        0.00 max =           89.59 mean =        13.18|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1065   r_free= 0.1549   ksol= 0.32   Bsol= 54.09   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-2.36,-0.98,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.115597                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1065   r_free= 0.1549   ksol= 0.32   Bsol= 54.09   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-2.36,-0.98,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.115597                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1033 -  4.7104 0.99   1402  157 0.0934 0.1234      5.3373      5.5178|
|  2:  4.7104 -  3.7578 0.99   1346  150 0.0814 0.1094      5.4043      5.6029|
|  3:  3.7578 -  3.2884 0.99   1331  143 0.1038 0.1516      5.4526      5.8489|
|  4:  3.2884 -  2.9902 0.99   1321  152 0.1158 0.1655      5.4307      5.5949|
|  5:  2.9902 -  2.7773 0.99   1313  147 0.1289 0.1694      5.3009      5.5506|
|  6:  2.7773 -  2.6145 0.99   1304  137 0.1142 0.1766      5.1726      5.4153|
|  7:  2.6145 -  2.4841 0.99   1290  143 0.1214 0.1612      5.1353       5.338|
|  8:  2.4841 -  2.3764 0.98   1273  145 0.1101 0.1713      5.0207      5.3198|
|  9:  2.3764 -  2.2853 0.98   1276  150 0.1114 0.1661      5.0025      5.2952|
| 10:  2.2853 -  2.2067 1.00   1304  148 0.1056 0.1722      4.9123      5.1852|
| 11:  2.2067 -  2.1379 0.98   1291  133 0.1064 0.1734      4.9138      5.2392|
| 12:  2.1379 -  2.0769 0.98   1259  140 0.1061 0.1609       4.845      5.1434|
| 13:  2.0769 -  2.0224 0.99   1281  140 0.1068 0.1749      4.7558      5.0231|
| 14:  2.0224 -  1.9731 0.49    639   74 0.0980 0.1529      4.6228      4.8715|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1033 -  4.7104  1402   157  0.94   8.56   0.98     0.95       6505.03|
|  2:  4.7104 -  3.7578  1346   150  0.95   7.68   1.02     1.01       8679.65|
|  3:  3.7578 -  3.2884  1331   143  0.94  11.12   1.03     1.02      10024.70|
|  4:  3.2884 -  2.9902  1321   152  0.92  13.69   1.01     0.99      10229.69|
|  5:  2.9902 -  2.7773  1313   147  0.90  15.65   1.00     0.98       8049.54|
|  6:  2.7773 -  2.6145  1304   137  0.90  15.56   0.99     0.97       6753.67|
|  7:  2.6145 -  2.4841  1290   143  0.91  15.23   1.00     0.97       5953.51|
|  8:  2.4841 -  2.3764  1273   145  0.91  14.72   0.99     0.96       4856.18|
|  9:  2.3764 -  2.2853  1276   150  0.91  14.72   1.00     0.97       4720.34|
| 10:  2.2853 -  2.2067  1304   148  0.91  15.18   1.00     0.97       4095.17|
| 11:  2.2067 -  2.1379  1291   133  0.91  15.64   0.99     0.95       4171.98|
| 12:  2.1379 -  2.0769  1259   140  0.91  15.06   1.01     1.00       3842.14|
| 13:  2.0769 -  2.0224  1281   140  0.91  15.80   1.00     0.98       3213.32|
| 14:  2.0224 -  1.9731   639    74  0.92  13.87   0.98     0.96       2415.75|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2415.75 max =        10229.69 mean =      6134.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.94 mean =        13.69|
|phase err.(test): min =        0.00 max =           89.59 mean =        13.18|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.850)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.27    93.05   16.94    None  None   None       |
|    all(noH): 2823   0      0.27    93.05   16.94    None  None   None       |
|    Sol.    : 438    0      6.07    87.49   40.04    None  None   None       |
|    Mac.    : 2385   0      0.27    93.05   12.70    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:     0.266 -   9.545:  981   |   5:    46.660 -  55.938:   93        |
|      1:     9.545 -  18.823: 1165   |   6:    55.938 -  65.217:   54        |
|      2:    18.823 -  28.102:  229   |   7:    65.217 -  74.496:   23        |
|      3:    28.102 -  37.381:  141   |   8:    74.496 -  83.774:   14        |
|      4:    37.381 -  46.660:  120   |   9:    83.774 -  93.053:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 299         
Filter by distance & map next to the model:
   mapped sites are within: 0.530 - 4.671
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 295 from: 299
   mapped sites are within: 0.718 - 4.671

peak=    6.290 closest distance to " NE2 GLN A  11 " =    1.228
peak=    5.701 closest distance to " NH2 ARG A  56 " =    2.151
peak=    5.386 closest distance to " O   HOH Z 126 " =    1.957
peak=    5.270 closest distance to " O   HOH Z 144 " =    1.754
peak=    5.232 closest distance to " CG  PRO A  54 " =    1.229
peak=    5.190 closest distance to " CB  GLN A 223 " =    1.462
peak=    4.846 closest distance to " C   PRO A 198 " =    1.498
peak=    4.839 closest distance to " O   HOH Z 369 " =    2.163
peak=    4.813 closest distance to " O   HOH Z 232 " =    2.317
peak=    4.801 closest distance to " CB  SER A  63 " =    1.224
peak=    4.699 closest distance to " CB  GLN A 183 " =    1.215
peak=    4.670 closest distance to " O   HOH Z 298 " =    1.967
peak=    4.638 closest distance to " CG  PRO A 213 " =    1.233
peak=    4.556 closest distance to " O   HOH Z 427 " =    2.794
peak=    4.522 closest distance to " O   HOH Z 287 " =    2.261
peak=    4.434 closest distance to " CB  PRO A  54 " =    0.927
peak=    4.428 closest distance to " CB  LEU A 228 " =    1.070
peak=    4.413 closest distance to " CB  ARG A 275 " =    0.907
peak=    4.404 closest distance to " O   HOH Z   9 " =    2.175
peak=    4.403 closest distance to " O   HOH Z 423 " =    1.624
peak=    4.401 closest distance to " O   HOH Z  78 " =    1.806
peak=    4.369 closest distance to " O   HOH Z 419 " =    2.126
peak=    4.346 closest distance to " CB  ARG A  79 " =    1.464
peak=    4.302 closest distance to " ND2 ASN A 187 " =    1.516
peak=    4.283 closest distance to " CB  ARG A 190 " =    1.671
peak=    4.276 closest distance to " CG  TRP A 179 " =    2.235
peak=    4.276 closest distance to " O   HOH Z 133 " =    2.397
peak=    4.248 closest distance to " O   HOH Z 158 " =    3.096
peak=    4.230 closest distance to " O   HOH Z 193 " =    1.802
peak=    4.210 closest distance to " O   HOH Z   1 " =    1.950
peak=    4.199 closest distance to " CB  ASN A 148 " =    1.323
peak=    4.194 closest distance to " CD  ARG A  66 " =    2.206
peak=    4.167 closest distance to " CB  GLU A 128 " =    0.999
peak=    4.152 closest distance to " CB  GLU A 152 " =    1.293
peak=    4.105 closest distance to " CA  TYR A  30 " =    0.973
peak=    4.104 closest distance to " OD1 ASN A  69 " =    2.678
peak=    4.100 closest distance to " CB  VAL A 265 " =    1.311
peak=    4.072 closest distance to " CB  ASN A 187 " =    1.209
peak=    4.051 closest distance to " O   HOH Z 217 " =    3.134
peak=    4.037 closest distance to " O   HOH Z  63 " =    1.457
peak=    4.037 closest distance to " O   HOH Z 316 " =    3.062
peak=    4.036 closest distance to " O   HOH Z 261 " =    1.949
peak=    4.018 closest distance to " O   HOH Z 327 " =    1.644
peak=    4.016 closest distance to " O   HOH Z 250 " =    1.476
peak=    4.015 closest distance to " CA  ASN A 215 " =    1.211
peak=    4.007 closest distance to " ND1 HIS A  86 " =    1.745
peak=    3.997 closest distance to " CB  TRP A 266 " =    1.037
peak=    3.978 closest distance to " O   HOH Z 234 " =    3.682
peak=    3.959 closest distance to " O   HOH Z  61 " =    1.586
peak=    3.944 closest distance to " O   HOH Z 132 " =    2.410
peak=    3.939 closest distance to " O   HOH Z 214 " =    2.089
peak=    3.927 closest distance to " O   HOH Z 209 " =    2.299
peak=    3.914 closest distance to " CG2 VAL A 257 " =    0.896
peak=    3.911 closest distance to " O   HOH Z 193 " =    1.694
peak=    3.895 closest distance to " O   HOH Z 425 " =    1.284
peak=    3.894 closest distance to " O   HOH Z  61 " =    1.482
peak=    3.879 closest distance to " O   HOH Z 272 " =    1.813
peak=    3.877 closest distance to " O   HOH Z 180 " =    2.098
peak=    3.872 closest distance to " O   HOH Z 371 " =    1.904
peak=    3.871 closest distance to " CG  LEU A 167 " =    1.275
peak=    3.863 closest distance to " CE  LYS A  76 " =    0.871
peak=    3.862 closest distance to " CD  ARG A 159 " =    0.745
peak=    3.850 closest distance to " CB  SER A 212 " =    1.138
peak=    3.845 closest distance to " CB  GLU A 277 " =    3.584
peak=    3.841 closest distance to " CB  SER A   3 " =    1.352
peak=    3.823 closest distance to " O   HOH Z 425 " =    2.091
peak=    3.818 closest distance to " O   HOH Z 352 " =    1.839
peak=    3.799 closest distance to " O   HOH Z 346 " =    1.665
peak=    3.786 closest distance to " O   HOH Z 437 " =    1.599
peak=    3.785 closest distance to " O   SER A  87 " =    2.240
peak=    3.782 closest distance to " O   HOH Z 213 " =    1.921
peak=    3.773 closest distance to " O   HOH Z 368 " =    2.013
peak=    3.761 closest distance to " O   HOH Z 265 " =    2.295
peak=    3.758 closest distance to " CB  SER A 216 " =    0.862
peak=    3.757 closest distance to " O   HOH Z   1 " =    1.799
peak=    3.752 closest distance to " NH1AARG A 145 " =    1.187
peak=    3.744 closest distance to " O   HOH Z  10 " =    1.820
peak=    3.743 closest distance to " O   HOH Z  68 " =    2.164
peak=    3.731 closest distance to " CZ  PHE A 218 " =    1.032
peak=    3.728 closest distance to " CA  ALA A 233 " =    1.140
peak=    3.724 closest distance to " O   HOH Z 362 " =    2.441
peak=    3.715 closest distance to " O   HOH Z 175 " =    2.157
peak=    3.715 closest distance to " O   HOH Z 380 " =    1.614
peak=    3.714 closest distance to " O   HOH Z 368 " =    3.605
peak=    3.712 closest distance to " CG2 THR A 221 " =    1.035
peak=    3.710 closest distance to " CD2 TRP A 179 " =    1.295
peak=    3.708 closest distance to " O   HOH Z  21 " =    1.699
peak=    3.706 closest distance to " O   HOH Z 403 " =    1.634
peak=    3.706 closest distance to " N   PHE A 130 " =    1.209
peak=    3.704 closest distance to " CG1 ILE A  33 " =    1.178
peak=    3.701 closest distance to " O   HOH Z  40 " =    1.977
peak=    3.690 closest distance to " CB  ALA A  34 " =    1.107
peak=    3.688 closest distance to " O   HOH Z 371 " =    2.926
peak=    3.687 closest distance to " O   HOH Z 405 " =    1.220
peak=    3.683 closest distance to " CG  PRO A 198 " =    1.215
peak=    3.675 closest distance to " O   HOH Z 389 " =    1.911
peak=    3.669 closest distance to " O   HOH Z 386 " =    3.118
peak=    3.656 closest distance to " OG BSER A 164 " =    2.274
peak=    3.654 closest distance to " O   HOH Z 128 " =    2.225
peak=    3.654 closest distance to " CB  ARG A 139 " =    0.988
peak=    3.653 closest distance to " CB  TYR A 169 " =    0.744
peak=    3.653 closest distance to " CD BLYS A 290 " =    1.091
peak=    3.648 closest distance to " O   HOH Z  88 " =    3.502
peak=    3.642 closest distance to " O   HOH Z  88 " =    3.999
peak=    3.615 closest distance to " O   HOH Z 147 " =    1.791
peak=    3.614 closest distance to " CG  PRO A 243 " =    1.081
peak=    3.613 closest distance to " O   HOH Z   2 " =    1.377
peak=    3.613 closest distance to " CB  ASN A  39 " =    0.927
peak=    3.611 closest distance to " CA  SER A  87 " =    1.012
peak=    3.608 closest distance to " O   HOH Z 344 " =    3.168
peak=    3.597 closest distance to " O   HOH Z 133 " =    1.644
peak=    3.589 closest distance to " O   HOH Z 193 " =    2.048
peak=    3.589 closest distance to " O   HOH Z 426 " =    1.871
peak=    3.583 closest distance to " O   HOH Z 373 " =    1.505
peak=    3.569 closest distance to " O   HOH Z 305 " =    3.566
peak=    3.555 closest distance to " CB  ALA A   1 " =    4.671
peak=    3.551 closest distance to " CB  LYS A 117 " =    1.215
peak=    3.550 closest distance to " CB  TRP A 179 " =    1.457
peak=    3.548 closest distance to " OD2 ASP A 286 " =    2.824
peak=    3.547 closest distance to " CA  ARG A 195 " =    1.241
peak=    3.539 closest distance to " O  BHOH Z 338 " =    2.322
peak=    3.539 closest distance to " O   ASN A 209 " =    1.375
peak=    3.535 closest distance to " O   HOH Z 411 " =    3.810
peak=    3.534 closest distance to " CB  TYR A 169 " =    0.909
peak=    3.527 closest distance to " O   HOH Z 189 " =    2.357
peak=    3.523 closest distance to " O   HOH Z 365 " =    2.835
peak=    3.517 closest distance to " CD1 LEU A 300 " =    1.219
peak=    3.506 closest distance to " CB  ASN A 142 " =    0.864
peak=    3.504 closest distance to " O   MET A 105 " =    1.782
peak=    3.503 closest distance to " CB  GLN A  88 " =    1.251
peak=    3.497 closest distance to " CA  ALA A 158 " =    1.117
peak=    3.495 closest distance to " CB  ASP A 140 " =    0.898
peak=    3.491 closest distance to " O   HOH Z  58 " =    1.498
peak=    3.487 closest distance to " CA  MET A  40 " =    1.151
peak=    3.480 closest distance to " CA  ALA A  21 " =    1.142
peak=    3.477 closest distance to " O   HOH Z 213 " =    2.357
peak=    3.476 closest distance to " O   HOH Z 135 " =    1.678
peak=    3.474 closest distance to " O   HOH Z 116 " =    2.979
peak=    3.469 closest distance to " NE2 GLN A  73 " =    3.803
peak=    3.467 closest distance to " CA  THR A 264 " =    0.879
peak=    3.467 closest distance to " O   HOH Z 219 " =    2.170
peak=    3.466 closest distance to " CB  VAL A 202 " =    1.643
peak=    3.454 closest distance to " CB  ASN A 110 " =    1.126
peak=    3.454 closest distance to " O   HOH Z 409 " =    2.367
peak=    3.444 closest distance to " OG  SER A  22 " =    2.854
peak=    3.441 closest distance to " CD  LYS A 166 " =    1.251
peak=    3.438 closest distance to " CD2 LEU A 255 " =    1.566
peak=    3.431 closest distance to " O   HOH Z 422 " =    2.680
peak=    3.430 closest distance to " NH2BARG A 145 " =    2.083
peak=    3.430 closest distance to " O   HOH Z 391 " =    2.875
peak=    3.422 closest distance to " O   HOH Z 280 " =    3.004
peak=    3.421 closest distance to " CD2 LEU A 297 " =    0.943
peak=    3.421 closest distance to " O   HOH Z  44 " =    1.630
peak=    3.420 closest distance to " CA  LYS A 290 " =    1.353
peak=    3.419 closest distance to " O   HOH Z   3 " =    1.841
peak=    3.415 closest distance to " CA  TYR A 116 " =    1.264
peak=    3.408 closest distance to " OE1 GLN A  11 " =    2.196
peak=    3.407 closest distance to " CA  THR A 221 " =    0.965
peak=    3.406 closest distance to " CG1 VAL A 189 " =    1.876
peak=    3.402 closest distance to " OG  SER A  62 " =    2.958
peak=    3.401 closest distance to " O   HOH Z 108 " =    2.244
peak=    3.395 closest distance to " O   HOH Z 271 " =    2.519
peak=    3.393 closest distance to " O   HOH Z 417 " =    1.116
peak=    3.393 closest distance to " OD1BASN A 224 " =    2.308
peak=    3.393 closest distance to " CG  GLN A  89 " =    1.484
peak=    3.393 closest distance to " O   HOH Z  44 " =    2.911
peak=    3.393 closest distance to " O   HOH Z 146 " =    1.709
peak=    3.392 closest distance to " CG  PRO A  90 " =    1.185
peak=    3.391 closest distance to " O   HOH Z 423 " =    2.380
peak=    3.391 closest distance to " CB  THR A 157 " =    1.143
peak=    3.387 closest distance to " O   HOH Z 286 " =    2.327
peak=    3.386 closest distance to " CE1 TYR A 186 " =    1.338
peak=    3.385 closest distance to " CB  ILE A 120 " =    1.375
peak=    3.383 closest distance to " CA  ALA A  84 " =    1.482
peak=    3.383 closest distance to " N   CYS A 260 " =    0.858
peak=    3.383 closest distance to " O   HOH Z 145 " =    2.308
peak=    3.383 closest distance to " CD  PRO A 243 " =    1.610
peak=    3.382 closest distance to " O   HOH Z 285 " =    2.653
peak=    3.377 closest distance to " NH2AARG A 190 " =    1.910
peak=    3.375 closest distance to " O   HOH Z 126 " =    1.461
peak=    3.372 closest distance to " O   HOH Z 302 " =    1.815
peak=    3.370 closest distance to " O   HOH Z 172 " =    3.044
peak=    3.359 closest distance to " CG  MET A 113 " =    1.376
peak=    3.352 closest distance to " CB  GLN A  89 " =    1.418
peak=    3.348 closest distance to " O   HOH Z 287 " =    2.170
peak=    3.343 closest distance to " CB  SER A  62 " =    1.266
peak=    3.342 closest distance to " O   HOH Z 227 " =    1.771
peak=    3.336 closest distance to " O   HOH Z 291 " =    1.524
peak=    3.336 closest distance to " CB  ALA A 114 " =    1.462
peak=    3.335 closest distance to " NH2 ARG A 156 " =    1.217
peak=    3.335 closest distance to " O   HOH Z 390 " =    2.616
peak=    3.321 closest distance to " O   HOH Z 345 " =    3.392
peak=    3.316 closest distance to " O   HOH Z 345 " =    1.711
peak=    3.316 closest distance to " CB  MET A  47 " =    1.179
peak=    3.314 closest distance to " O   HOH Z  43 " =    2.190
peak=    3.314 closest distance to " CA  ALA A 291 " =    0.892
peak=    3.308 closest distance to " O   HOH Z 329 " =    3.828
peak=    3.307 closest distance to " O   HOH Z 245 " =    1.278
peak=    3.302 closest distance to " O   HOH Z 258 " =    2.273
peak=    3.302 closest distance to " O   TYR A 116 " =    1.323
peak=    3.302 closest distance to " CA  ILE A 234 " =    0.989
peak=    3.300 closest distance to " O   HOH Z 130 " =    3.810
peak=    3.299 closest distance to " N   GLN A 278 " =    1.240
peak=    3.293 closest distance to " CB  MET A  40 " =    0.790
peak=    3.293 closest distance to " NE2 HIS A 207 " =    1.393
peak=    3.290 closest distance to " O   HOH Z 325 " =    3.808
peak=    3.285 closest distance to " CA  ALA A  51 " =    0.936
peak=    3.285 closest distance to " O   HOH Z 188 " =    1.950
peak=    3.278 closest distance to " O   HOH Z  59 " =    1.938
peak=    3.277 closest distance to " CA  GLY A 267 " =    1.233
peak=    3.276 closest distance to " O   HOH Z  93 " =    2.643
peak=    3.272 closest distance to " NE2 GLN A  58 " =    3.699
peak=    3.266 closest distance to " O   HOH Z 207 " =    1.737
peak=    3.266 closest distance to " N   SER A 134 " =    1.362
peak=    3.262 closest distance to " O   HOH Z 128 " =    2.051
peak=    3.260 closest distance to " O   HOH Z 128 " =    1.926
peak=    3.259 closest distance to " CB  TYR A 116 " =    0.812
peak=    3.258 closest distance to " ND2 ASN A 249 " =    0.820
peak=    3.255 closest distance to " O   HOH Z 217 " =    1.496
peak=    3.254 closest distance to " CB  THR A  31 " =    1.713
peak=    3.253 closest distance to " ND1 HIS A  81 " =    1.610
peak=    3.252 closest distance to " O   HOH Z 109 " =    2.573
peak=    3.248 closest distance to " CA  ALA A 299 " =    0.862
peak=    3.247 closest distance to " CB  ARG A 138 " =    0.964
peak=    3.246 closest distance to " O   HOH Z 238 " =    3.730
peak=    3.245 closest distance to " CD  ARG A 219 " =    1.133
peak=    3.244 closest distance to " CG  GLN A  88 " =    1.076
peak=    3.244 closest distance to " CG2AVAL A  72 " =    1.544
peak=    3.242 closest distance to " CG2 VAL A 197 " =    1.099
peak=    3.242 closest distance to " CB  ALA A   9 " =    1.589
peak=    3.242 closest distance to " NH2AARG A 275 " =    3.595
peak=    3.239 closest distance to " O   HOH Z  97 " =    1.980
peak=    3.237 closest distance to " O   HOH Z 298 " =    2.521
peak=    3.236 closest distance to " O   HOH Z 402 " =    1.454
peak=    3.233 closest distance to " O   HOH Z 407 " =    2.268
peak=    3.232 closest distance to " O   HOH Z  66 " =    2.127
peak=    3.229 closest distance to " CA  SER A  32 " =    1.681
peak=    3.227 closest distance to " N   SER A 146 " =    1.719
peak=    3.227 closest distance to " CB  ASP A 171 " =    1.334
peak=    3.223 closest distance to " CB  LEU A 143 " =    1.111
peak=    3.223 closest distance to " O   ASN A  74 " =    1.593
peak=    3.223 closest distance to " O   HOH Z 152 " =    1.840
peak=    3.220 closest distance to " CG1 ILE A 151 " =    1.018
peak=    3.218 closest distance to " O   ALA A 165 " =    1.382
peak=    3.217 closest distance to " O   HOH Z 406 " =    1.594
peak=    3.208 closest distance to " NH2 ARG A 219 " =    1.851
peak=    3.206 closest distance to " O   HOH Z  64 " =    2.193
peak=    3.205 closest distance to " CA  GLU A  46 " =    0.832
peak=    3.202 closest distance to " CB  ALA A 248 " =    0.914
peak=    3.198 closest distance to " O   HOH Z  64 " =    2.149
peak=    3.196 closest distance to " NH1BARG A 145 " =    1.183
peak=    3.192 closest distance to " N   ARG A 156 " =    1.299
peak=    3.192 closest distance to " CA  ASN A 217 " =    1.152
peak=    3.191 closest distance to " CB  TRP A 150 " =    1.264
peak=    3.190 closest distance to " O   HOH Z 417 " =    3.626
peak=    3.186 closest distance to " O   HOH Z 211 " =    2.803
peak=    3.185 closest distance to " O   HOH Z 148 " =    3.403
peak=    3.180 closest distance to " CG  GLN A  77 " =    2.227
peak=    3.180 closest distance to " O   HOH Z 248 " =    1.646
peak=    3.177 closest distance to " OE2 GLU A  53 " =    2.147
peak=    3.174 closest distance to " CD1 ILE A 106 " =    0.890
peak=    3.170 closest distance to " CG BARG A 102 " =    1.879
peak=    3.169 closest distance to " CA  MET A 105 " =    0.948
peak=    3.163 closest distance to " OG  SER A  62 " =    3.059
peak=    3.157 closest distance to " CB  LEU A 237 " =    0.718
peak=    3.148 closest distance to " CA  GLY A 136 " =    1.048
peak=    3.146 closest distance to " CZ3 TRP A 266 " =    1.106
peak=    3.140 closest distance to " CG  LYS A  76 " =    1.000
peak=    3.139 closest distance to " CG  ARG A 159 " =    0.804
peak=    3.137 closest distance to " CG BARG A 275 " =    1.419
peak=    3.136 closest distance to " O   HOH Z  53 " =    2.559
peak=    3.134 closest distance to " CB  GLU A 236 " =    1.104
peak=    3.132 closest distance to " O   HOH Z 432 " =    1.713
peak=    3.130 closest distance to " CA  SER A  95 " =    1.038
peak=    3.129 closest distance to " N   TYR A  15 " =    0.757
peak=    3.127 closest distance to " O   HOH Z 303 " =    3.045
peak=    3.125 closest distance to " O   HOH Z 227 " =    2.019
peak=    3.124 closest distance to " NH1 ARG A 138 " =    1.036
peak=    3.115 closest distance to " O   HOH Z 266 " =    3.345
peak=    3.113 closest distance to " O   HOH Z 132 " =    3.379
peak=    3.113 closest distance to " CB  GLU A  46 " =    1.092
peak=    3.113 closest distance to " CB  HIS A 108 " =    0.759
peak=    3.106 closest distance to " CB  ALA A 291 " =    1.354
peak=    3.105 closest distance to " O   HOH Z 359 " =    1.365
peak=    3.091 closest distance to " O   HOH Z 303 " =    1.780
peak=    3.086 closest distance to " O   HOH Z 386 " =    2.803
peak=    3.084 closest distance to " OG BSER A  99 " =    2.179
peak=    3.083 closest distance to " CD  ARG A 138 " =    0.814
peak=    3.078 closest distance to " O   HOH Z  88 " =    2.001
peak=    3.075 closest distance to " CG  GLN A 278 " =    1.341
peak=    3.073 closest distance to " O   HOH Z 116 " =    1.712
peak=    3.056 closest distance to " O   HOH Z 153 " =    1.570
peak=    3.043 closest distance to " CB  VAL A 126 " =    1.092
peak=    3.018 closest distance to " CB  ASP A 132 " =    4.147
peak=    3.012 closest distance to " CB  GLU A 277 " =    3.780

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 201         
Filter by distance & map next to the model:
   mapped sites are within: 0.717 - 5.899
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 201
   mapped sites are within: 0.717 - 5.899

peak=   -4.691 closest distance to " O   HOH Z 377 " =    2.128
peak=   -4.663 closest distance to " CB  PRO A 243 " =    2.560
peak=   -4.562 closest distance to " CD  ARG A 156 " =    2.066
peak=   -4.508 closest distance to " O   HOH Z 266 " =    4.979
peak=   -4.230 closest distance to " OG BSER A 134 " =    1.281
peak=   -4.221 closest distance to " SG  CYS A 254 " =    3.386
peak=   -4.182 closest distance to " O   HOH Z 435 " =    2.915
peak=   -4.154 closest distance to " CG  GLN A 223 " =    2.003
peak=   -4.112 closest distance to " O   VAL A  67 " =    2.631
peak=   -4.101 closest distance to " CG1 VAL A 112 " =    2.846
peak=   -4.075 closest distance to " O   HOH Z 372 " =    2.486
peak=   -4.052 closest distance to " O   HOH Z 231 " =    2.150
peak=   -4.029 closest distance to " O   HOH Z 389 " =    1.898
peak=   -4.017 closest distance to " O   PRO A 198 " =    1.299
peak=   -3.958 closest distance to " O   HOH Z 185 " =    2.107
peak=   -3.932 closest distance to " ND2 ASN A  45 " =    1.847
peak=   -3.922 closest distance to " CZ3 TRP A 179 " =    1.185
peak=   -3.922 closest distance to " CB  ALA A  43 " =    2.482
peak=   -3.914 closest distance to " C   HIS A 108 " =    1.196
peak=   -3.898 closest distance to " N   ALA A  43 " =    2.633
peak=   -3.895 closest distance to " O   HOH Z 351 " =    1.561
peak=   -3.894 closest distance to " O   HOH Z 290 " =    1.259
peak=   -3.881 closest distance to " O   HOH Z 407 " =    3.212
peak=   -3.869 closest distance to " O   HOH Z  38 " =    1.485
peak=   -3.843 closest distance to " O   PRO A 198 " =    1.324
peak=   -3.837 closest distance to " CA  GLY A  98 " =    1.870
peak=   -3.836 closest distance to " CD  ARG A 195 " =    5.191
peak=   -3.798 closest distance to " ND2 ASN A  45 " =    1.225
peak=   -3.789 closest distance to " O   HOH Z 198 " =    2.041
peak=   -3.762 closest distance to " CB  ALA A 291 " =    2.060
peak=   -3.747 closest distance to " O   HOH Z 313 " =    1.848
peak=   -3.720 closest distance to " CE2 PHE A 218 " =    2.417
peak=   -3.719 closest distance to " CE  MET A 105 " =    2.299
peak=   -3.709 closest distance to " O   HOH Z  60 " =    2.462
peak=   -3.709 closest distance to " OG  SER A  87 " =    1.331
peak=   -3.700 closest distance to " O   VAL A 189 " =    2.541
peak=   -3.673 closest distance to " O   ILE A 109 " =    2.544
peak=   -3.651 closest distance to " CB  TRP A  85 " =    2.447
peak=   -3.646 closest distance to " OD1 ASP A 171 " =    1.601
peak=   -3.643 closest distance to " CZ BARG A 275 " =    1.656
peak=   -3.638 closest distance to " CG  MET A 105 " =    0.955
peak=   -3.616 closest distance to " OD1 ASP A 191 " =    1.908
peak=   -3.609 closest distance to " CG  PHE A 283 " =    2.635
peak=   -3.608 closest distance to " CA  GLY A 203 " =    2.270
peak=   -3.607 closest distance to " CB  ALA A 291 " =    2.159
peak=   -3.594 closest distance to " CE2 TYR A  30 " =    2.715
peak=   -3.592 closest distance to " O   VAL A  67 " =    2.793
peak=   -3.592 closest distance to " CB  PHE A 192 " =    1.980
peak=   -3.588 closest distance to " OG BSER A 134 " =    1.633
peak=   -3.578 closest distance to " CZ  TYR A 169 " =    1.570
peak=   -3.574 closest distance to " O   HOH Z 198 " =    1.582
peak=   -3.574 closest distance to " O   HOH Z  52 " =    1.212
peak=   -3.564 closest distance to " NE  ARG A  36 " =    1.886
peak=   -3.560 closest distance to " O   HOH Z 359 " =    3.289
peak=   -3.558 closest distance to " NH2AARG A 275 " =    5.433
peak=   -3.555 closest distance to " CZ  PHE A  59 " =    1.567
peak=   -3.548 closest distance to " O   HOH Z 114 " =    3.022
peak=   -3.547 closest distance to " O   PRO A 243 " =    2.457
peak=   -3.545 closest distance to " O   SER A 135 " =    1.450
peak=   -3.544 closest distance to " CB  ASN A  39 " =    2.249
peak=   -3.542 closest distance to " O   HOH Z  13 " =    1.702
peak=   -3.539 closest distance to " O   ARG A 145 " =    1.560
peak=   -3.538 closest distance to " C   LEU A 222 " =    0.717
peak=   -3.538 closest distance to " CB  CYS A 254 " =    2.231
peak=   -3.532 closest distance to " OD1 ASN A 148 " =    1.592
peak=   -3.530 closest distance to " C   ALA A 158 " =    1.492
peak=   -3.521 closest distance to " O   PHE A 218 " =    1.528
peak=   -3.516 closest distance to " CG1 VAL A 197 " =    2.165
peak=   -3.513 closest distance to " N   THR A 157 " =    1.482
peak=   -3.512 closest distance to " ND2 ASN A 249 " =    2.122
peak=   -3.501 closest distance to " C   ASN A 187 " =    1.869
peak=   -3.497 closest distance to " CG2 THR A  18 " =    2.863
peak=   -3.495 closest distance to " OD1 ASP A 191 " =    1.574
peak=   -3.493 closest distance to " O   HOH Z 298 " =    2.451
peak=   -3.483 closest distance to " CD1 LEU A 101 " =    2.309
peak=   -3.483 closest distance to " CA  GLY A 241 " =    2.211
peak=   -3.483 closest distance to " O   HOH Z  43 " =    1.734
peak=   -3.482 closest distance to " O   PRO A 163 " =    1.954
peak=   -3.481 closest distance to " CD2 LEU A 237 " =    2.812
peak=   -3.478 closest distance to " O   HOH Z 348 " =    1.833
peak=   -3.472 closest distance to " CD1 PHE A  59 " =    1.959
peak=   -3.467 closest distance to " O   HOH Z 351 " =    1.693
peak=   -3.466 closest distance to " CD  GLN A  58 " =    1.063
peak=   -3.462 closest distance to " O   HOH Z  11 " =    1.887
peak=   -3.439 closest distance to " CD  ARG A 139 " =    1.540
peak=   -3.438 closest distance to " CB  PRO A 163 " =    2.466
peak=   -3.437 closest distance to " CB  ALA A 248 " =    2.374
peak=   -3.432 closest distance to " OG  SER A  97 " =    2.177
peak=   -3.431 closest distance to " O   HOH Z 131 " =    4.140
peak=   -3.431 closest distance to " O   HOH Z 292 " =    1.565
peak=   -3.426 closest distance to " CB  ALA A 131 " =    1.989
peak=   -3.423 closest distance to " O   HOH Z 211 " =    1.508
peak=   -3.417 closest distance to " OD1 ASN A 187 " =    1.645
peak=   -3.409 closest distance to " O   HOH Z 111 " =    1.892
peak=   -3.406 closest distance to " CG  PRO A 163 " =    2.537
peak=   -3.403 closest distance to " CB  ASP A  27 " =    2.447
peak=   -3.401 closest distance to " O   HOH Z 102 " =    1.591
peak=   -3.393 closest distance to " CB  ASP A 286 " =    2.245
peak=   -3.386 closest distance to " O   HOH Z 298 " =    1.260
peak=   -3.382 closest distance to " CB  TYR A  15 " =    2.175
peak=   -3.377 closest distance to " O   HOH Z 409 " =    5.899
peak=   -3.376 closest distance to " O   HOH Z  73 " =    2.176
peak=   -3.376 closest distance to " O   HOH Z 140 " =    1.632
peak=   -3.374 closest distance to " O   HOH Z 281 " =    2.682
peak=   -3.372 closest distance to " CD2 PHE A 225 " =    1.148
peak=   -3.369 closest distance to " CB  ALA A 248 " =    1.985
peak=   -3.369 closest distance to " O   SER A  95 " =    1.487
peak=   -3.367 closest distance to " CG2 THR A 178 " =    2.201
peak=   -3.365 closest distance to " NH2 ARG A  79 " =    1.955
peak=   -3.356 closest distance to " O   HOH Z  90 " =    2.685
peak=   -3.356 closest distance to " CG  TRP A 266 " =    1.754
peak=   -3.352 closest distance to " O   HOH Z 345 " =    2.116
peak=   -3.350 closest distance to " O   GLY A  17 " =    1.163
peak=   -3.344 closest distance to " OXT GLY A 302 " =    3.071
peak=   -3.343 closest distance to " O   HOH Z 253 " =    3.985
peak=   -3.340 closest distance to " O   HOH Z  51 " =    1.140
peak=   -3.337 closest distance to " O   HOH Z 266 " =    4.747
peak=   -3.337 closest distance to " O   HOH Z  63 " =    1.980
peak=   -3.333 closest distance to " CA  GLY A 133 " =    2.035
peak=   -3.332 closest distance to " CG  ASP A 231 " =    0.730
peak=   -3.330 closest distance to " N   ASP A 286 " =    2.361
peak=   -3.326 closest distance to " C   LEU A 143 " =    1.263
peak=   -3.322 closest distance to " O   HOH Z 353 " =    2.145
peak=   -3.320 closest distance to " CB  ASP A 132 " =    2.350
peak=   -3.317 closest distance to " O   HOH Z  65 " =    1.278
peak=   -3.315 closest distance to " O   ALA A  10 " =    1.656
peak=   -3.313 closest distance to " O   GLY A 211 " =    1.363
peak=   -3.311 closest distance to " CD2 PHE A  61 " =    2.068
peak=   -3.308 closest distance to " O   HOH Z 384 " =    2.751
peak=   -3.304 closest distance to " O   HOH Z 191 " =    5.540
peak=   -3.304 closest distance to " O   HOH Z 196 " =    2.289
peak=   -3.298 closest distance to " CG1 VAL A 250 " =    2.637
peak=   -3.298 closest distance to " O   ALA A 180 " =    1.204
peak=   -3.295 closest distance to " O   HOH Z 174 " =    2.569
peak=   -3.288 closest distance to " O   HOH Z 166 " =    1.288
peak=   -3.287 closest distance to " N   SER A 212 " =    1.997
peak=   -3.283 closest distance to " CD1 LEU A 228 " =    2.255
peak=   -3.282 closest distance to " CB  PRO A  54 " =    2.420
peak=   -3.271 closest distance to " O   SER A  22 " =    2.501
peak=   -3.268 closest distance to " CE3 TRP A 274 " =    2.378
peak=   -3.268 closest distance to " CE1 PHE A  59 " =    2.118
peak=   -3.263 closest distance to " SD  MET A 188 " =    2.329
peak=   -3.262 closest distance to " OG  SER A 245 " =    1.268
peak=   -3.261 closest distance to " NH1AARG A 275 " =    1.816
peak=   -3.261 closest distance to " N   ASP A 171 " =    2.351
peak=   -3.246 closest distance to " O   HOH Z 263 " =    3.124
peak=   -3.245 closest distance to " CG  GLU A 152 " =    1.254
peak=   -3.245 closest distance to " O   HOH Z 337 " =    1.559
peak=   -3.244 closest distance to " ND2 ASN A 187 " =    1.472
peak=   -3.243 closest distance to " O   HOH Z  10 " =    1.417
peak=   -3.243 closest distance to " O   HOH Z 385 " =    2.126
peak=   -3.241 closest distance to " O   GLN A 240 " =    2.005
peak=   -3.240 closest distance to " CE1 TYR A 169 " =    2.550
peak=   -3.234 closest distance to " O   HOH Z 189 " =    1.830
peak=   -3.225 closest distance to " C   GLY A  13 " =    1.036
peak=   -3.223 closest distance to " O   HOH Z 352 " =    2.253
peak=   -3.221 closest distance to " NE2 GLN A 278 " =    1.756
peak=   -3.220 closest distance to " N   MET A 105 " =    2.555
peak=   -3.218 closest distance to " O   HOH Z  90 " =    1.796
peak=   -3.207 closest distance to " OE1 GLN A  58 " =    3.083
peak=   -3.207 closest distance to " O   HOH Z 282 " =    1.271
peak=   -3.199 closest distance to " CG  GLN A  88 " =    0.833
peak=   -3.198 closest distance to " O   HOH Z 426 " =    1.659
peak=   -3.197 closest distance to " OD2 ASP A 171 " =    2.091
peak=   -3.193 closest distance to " CG2 ILE A 263 " =    2.275
peak=   -3.181 closest distance to " O   HOH Z 394 " =    1.427
peak=   -3.179 closest distance to " ND2 ASN A  60 " =    1.437
peak=   -3.177 closest distance to " N   ALA A 248 " =    1.511
peak=   -3.173 closest distance to " O   HOH Z 350 " =    1.293
peak=   -3.173 closest distance to " O   HOH Z 111 " =    1.288
peak=   -3.171 closest distance to " CD1 ILE A 199 " =    2.625
peak=   -3.170 closest distance to " O   HOH Z 348 " =    2.261
peak=   -3.169 closest distance to " O   ALA A 161 " =    1.596
peak=   -3.164 closest distance to " CG1 VAL A 268 " =    2.422
peak=   -3.160 closest distance to " CG2 THR A 157 " =    2.192
peak=   -3.156 closest distance to " ND2BASN A 224 " =    1.776
peak=   -3.154 closest distance to " OD2 ASP A 171 " =    1.761
peak=   -3.148 closest distance to " O   ALA A  34 " =    2.417
peak=   -3.146 closest distance to " O   HOH Z 414 " =    2.424
peak=   -3.145 closest distance to " O   HOH Z 168 " =    1.811
peak=   -3.141 closest distance to " O   HOH Z 377 " =    0.939
peak=   -3.134 closest distance to " OH  TYR A 214 " =    1.237
peak=   -3.131 closest distance to " O   HOH Z 409 " =    4.497
peak=   -3.131 closest distance to " NH1 ARG A 195 " =    2.670
peak=   -3.128 closest distance to " CB  ALA A 114 " =    2.539
peak=   -3.113 closest distance to " CE  LYS A  76 " =    2.817
peak=   -3.107 closest distance to " CE3 TRP A 123 " =    1.319
peak=   -3.100 closest distance to " OH  TYR A 247 " =    1.830
peak=   -3.091 closest distance to " N   SER A 276 " =    1.271
peak=   -3.090 closest distance to " OXT GLY A 302 " =    3.370
peak=   -3.086 closest distance to " CD1 LEU A 297 " =    2.560
peak=   -3.080 closest distance to " O   HOH Z 256 " =    1.499
peak=   -3.080 closest distance to " O   HOH Z 282 " =    4.800
peak=   -3.072 closest distance to " N   GLN A  58 " =    2.087
peak=   -3.071 closest distance to " CG2 VAL A 189 " =    1.896
peak=   -3.062 closest distance to " C   LYS A  76 " =    1.627
peak=   -3.060 closest distance to " O   HOH Z 412 " =    4.419
peak=   -3.059 closest distance to " O   HOH Z 114 " =    0.832
peak=   -3.055 closest distance to " C   ALA A 114 " =    2.249
peak=   -3.049 closest distance to " CD2 TYR A 293 " =    1.919
peak=   -3.015 closest distance to " O   HOH Z 417 " =    2.779

================= 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    :  0.3579 0.3538   6.134934e+00   6.123971e+00
   1_bss:  0.3450 0.3447   6.117052e+00   6.104564e+00
   1_xyz:  0.2377 0.2671   5.791775e+00   5.866871e+00
   1_adp:  0.2175 0.2793   5.742500e+00   5.899248e+00
   1_occ:  0.2173 0.2790   5.741377e+00   5.898433e+00
   2_bss:  0.2163 0.2754   5.735725e+00   5.889134e+00
   2_xyz:  0.1507 0.1962   5.395204e+00   5.598436e+00
   2_adp:  0.1365 0.1811   5.308308e+00   5.521381e+00
   2_occ:  0.1364 0.1811   5.307914e+00   5.521197e+00
   3_bss:  0.1361 0.1799   5.302162e+00   5.514348e+00
   3_xyz:  0.1215 0.1641   5.206051e+00   5.427964e+00
   3_adp:  0.1172 0.1623   5.182916e+00   5.416208e+00
   3_occ:  0.1172 0.1623   5.183016e+00   5.416572e+00
   4_bss:  0.1171 0.1622   5.182151e+00   5.415890e+00
   4_xyz:  0.1117 0.1578   5.144423e+00   5.390473e+00
   4_adp:  0.1111 0.1563   5.138554e+00   5.383402e+00
   4_occ:  0.1110 0.1563   5.138485e+00   5.383376e+00
   5_bss:  0.1111 0.1558   5.138192e+00   5.381244e+00
   5_xyz:  0.1070 0.1552   5.118023e+00   5.376536e+00
   5_adp:  0.1066 0.1549   5.115410e+00   5.374087e+00
   5_occ:  0.1066 0.1549   5.115510e+00   5.374326e+00
   5_bss:  0.1065 0.1549   5.115597e+00   5.374366e+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:  0.343  50.000  -1.535   2.171  -1.780   0.000  -0.000  -0.000
   1_xyz:  0.343  50.000  -1.535   2.171  -1.780   0.000  -0.000  -0.000
   1_adp:  0.343  50.000  -1.535   2.171  -1.780   0.000  -0.000  -0.000
   1_occ:  0.343  50.000  -1.535   2.171  -1.780   0.000  -0.000  -0.000
   2_bss:  0.329  59.878  -2.145  -0.877  -1.509  -0.000  -0.000  -0.000
   2_xyz:  0.329  59.878  -2.145  -0.877  -1.509  -0.000  -0.000  -0.000
   2_adp:  0.329  59.878  -2.145  -0.877  -1.509  -0.000  -0.000  -0.000
   2_occ:  0.329  59.878  -2.145  -0.877  -1.509  -0.000  -0.000  -0.000
   3_bss:  0.325  52.390  -2.245  -2.169  -1.330  -0.000  -0.000  -0.000
   3_xyz:  0.325  52.390  -2.245  -2.169  -1.330  -0.000  -0.000  -0.000
   3_adp:  0.325  52.390  -2.245  -2.169  -1.330  -0.000  -0.000  -0.000
   3_occ:  0.325  52.390  -2.245  -2.169  -1.330  -0.000  -0.000  -0.000
   4_bss:  0.321  54.099  -2.303  -2.459  -1.310  -0.000  -0.000  -0.000
   4_xyz:  0.321  54.099  -2.303  -2.459  -1.310  -0.000  -0.000  -0.000
   4_adp:  0.321  54.099  -2.303  -2.459  -1.310  -0.000  -0.000  -0.000
   4_occ:  0.321  54.099  -2.303  -2.459  -1.310  -0.000  -0.000  -0.000
   5_bss:  0.321  54.099  -2.192  -2.473  -1.179  -0.000  -0.000  -0.000
   5_xyz:  0.321  54.099  -2.192  -2.473  -1.179  -0.000  -0.000  -0.000
   5_adp:  0.321  54.099  -2.192  -2.473  -1.179  -0.000  -0.000  -0.000
   5_occ:  0.321  54.099  -2.192  -2.473  -1.179  -0.000  -0.000  -0.000
   5_bss:  0.323  54.092  -2.008  -2.357  -0.982  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  38.949 0.6576  0.8456    38528.117
   1_bss:  38.121 0.6656  0.8457    36015.114
   1_xyz:  26.220 0.8005  0.9690    18624.085
   1_adp:  27.723 0.7834  0.9544    20201.143
   1_occ:  27.713 0.7834  0.9541    20155.532
   2_bss:  27.183 0.7890  0.9245    19577.864
   2_xyz:  18.953 0.8708  0.9870     9821.606
   2_adp:  16.961 0.8899  0.9939     8462.392
   2_occ:  16.962 0.8899  0.9936     8452.828
   3_bss:  16.777 0.8914  0.9802     8280.391
   3_xyz:  14.811 0.9083  0.9855     6886.958
   3_adp:  14.526 0.9109  0.9803     6713.568
   3_occ:  14.529 0.9108  0.9802     6715.793
   4_bss:  14.511 0.9110  0.9766     6704.961
   4_xyz:  13.990 0.9151  0.9794     6339.775
   4_adp:  13.833 0.9165  0.9759     6255.998
   4_occ:  13.832 0.9165  0.9758     6254.800
   5_bss:  13.809 0.9166  0.9785     6218.250
   5_xyz:  13.691 0.9176  0.9782     6165.681
   5_adp:  13.631 0.9181  0.9722     6132.593
   5_occ:  13.633 0.9180  0.9721     6131.538
   5_bss:  13.637 0.9180  0.9776     6133.782
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6423e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6423e-01
   1_xyz:   1.152  0.009  0.077 15.116  0.005  4.109   7.6376e-02
   1_adp:   1.152  0.009  0.077 15.116  0.005  4.109   7.6376e-02
   1_occ:   1.152  0.009  0.077 15.116  0.005  4.109   7.6376e-02
   2_bss:   1.152  0.009  0.077 15.116  0.005  4.109   7.6376e-02
   2_xyz:   1.053  0.007  0.076 14.509  0.004  4.119   6.3594e-02
   2_adp:   1.053  0.007  0.076 14.509  0.004  4.119   6.3594e-02
   2_occ:   1.053  0.007  0.076 14.509  0.004  4.119   6.3594e-02
   3_bss:   1.053  0.007  0.076 14.509  0.004  4.119   6.3594e-02
   3_xyz:   0.880  0.005  0.067 14.450  0.003  4.117   4.9047e-02
   3_adp:   0.880  0.005  0.067 14.450  0.003  4.117   4.9047e-02
   3_occ:   0.880  0.005  0.067 14.450  0.003  4.117   4.9047e-02
   4_bss:   0.880  0.005  0.067 14.450  0.003  4.117   4.9047e-02
   4_xyz:   0.953  0.007  0.073 14.513  0.004  4.119   5.5062e-02
   4_adp:   0.953  0.007  0.073 14.513  0.004  4.119   5.5062e-02
   4_occ:   0.953  0.007  0.073 14.513  0.004  4.119   5.5062e-02
   5_bss:   0.953  0.007  0.073 14.513  0.004  4.119   5.5062e-02
   5_xyz:   1.043  0.009  0.079 14.800  0.004  4.121   6.6513e-02
   5_adp:   1.043  0.009  0.079 14.800  0.004  4.121   6.6513e-02
   5_occ:   1.043  0.009  0.079 14.800  0.004  4.121   6.6513e-02
   5_bss:   1.043  0.009  0.079 14.800  0.004  4.121   6.6513e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4064e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4064e-01
   1_xyz:   8.329  0.046  0.289 85.064  0.046  2.132   7.8468e-02
   1_adp:   8.329  0.046  0.289 85.064  0.046  2.132   7.8468e-02
   1_occ:   8.329  0.046  0.289 85.064  0.046  2.132   7.8468e-02
   2_bss:   8.329  0.046  0.289 85.064  0.046  2.132   7.8468e-02
   2_xyz:   8.501  0.045  0.232 82.982  0.040  2.307   9.2094e-02
   2_adp:   8.501  0.045  0.232 82.982  0.040  2.307   9.2094e-02
   2_occ:   8.501  0.045  0.232 82.982  0.040  2.307   9.2094e-02
   3_bss:   8.501  0.045  0.232 82.982  0.040  2.307   9.2094e-02
   3_xyz:   7.485  0.042  0.207 85.177  0.035  2.352   3.5332e-02
   3_adp:   7.485  0.042  0.207 85.177  0.035  2.352   3.5332e-02
   3_occ:   7.485  0.042  0.207 85.177  0.035  2.352   3.5332e-02
   4_bss:   7.485  0.042  0.207 85.177  0.035  2.352   3.5332e-02
   4_xyz:   7.596  0.039  0.216 84.326  0.035  2.319   3.9226e-02
   4_adp:   7.596  0.039  0.216 84.326  0.035  2.319   3.9226e-02
   4_occ:   7.596  0.039  0.216 84.326  0.035  2.319   3.9226e-02
   5_bss:   7.596  0.039  0.216 84.326  0.035  2.319   3.9226e-02
   5_xyz:   7.286  0.051  0.259 84.849  0.038  2.257   5.5349e-02
   5_adp:   7.286  0.051  0.259 84.849  0.038  2.257   5.5349e-02
   5_occ:   7.286  0.051  0.259 84.849  0.038  2.257   5.5349e-02
   5_bss:   7.286  0.051  0.259 84.849  0.038  2.257   5.5349e-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:  86.34   0.00  17.49  71.01   0.00  13.46  86.34   5.59  39.42
   1_occ:  86.34   0.00  17.49  71.01   0.00  13.46  86.34   5.59  39.42
   2_bss:  86.34   0.00  17.49  71.01   0.00  13.46  86.34   5.59  39.42
   2_xyz:  86.34   0.00  17.49  71.01   0.00  13.46  86.34   5.59  39.42
   2_adp:  82.94   1.63  17.01  71.26   1.63  12.98  82.94   6.42  38.93
   2_occ:  82.94   1.63  17.01  71.26   1.63  12.98  82.94   6.42  38.93
   3_bss:  82.94   1.63  17.01  71.26   1.63  12.98  82.94   6.42  38.93
   3_xyz:  82.94   1.63  17.01  71.26   1.63  12.98  82.94   6.42  38.93
   3_adp:  89.16   0.00  17.48  89.16   0.00  13.02  85.82   5.98  41.75
   3_occ:  89.16   0.00  17.48  89.16   0.00  13.02  85.82   5.98  41.75
   4_bss:  89.16   0.00  17.48  89.16   0.00  13.02  85.82   5.98  41.75
   4_xyz:  89.16   0.00  17.48  89.16   0.00  13.02  85.82   5.98  41.75
   4_adp:  92.07   0.16  17.19  92.07   0.16  12.89  86.55   5.90  40.63
   4_occ:  92.07   0.16  17.19  92.07   0.16  12.89  86.55   5.90  40.63
   5_bss:  92.07   0.16  17.19  92.07   0.16  12.89  86.55   5.90  40.63
   5_xyz:  92.07   0.16  17.19  92.07   0.16  12.89  86.55   5.90  40.63
   5_adp:  93.06   0.27  16.95  93.06   0.27  12.71  87.49   6.08  40.05
   5_occ:  93.06   0.27  16.95  93.06   0.27  12.71  87.49   6.08  40.05
   5_bss:  93.05   0.27  16.94  93.05   0.27  12.70  87.49   6.07  40.04
------------------------------------------------------------------------
 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:    1.482    0.017    0.276
   1_adp:    1.482    0.017    0.276
   1_occ:    1.482    0.017    0.276
   2_bss:    1.482    0.017    0.276
   2_xyz:    1.130    0.034    0.439
   2_adp:    1.130    0.034    0.439
   2_occ:    1.130    0.034    0.439
   3_bss:    1.130    0.034    0.439
   3_xyz:    0.979    0.034    0.469
   3_adp:    0.979    0.034    0.469
   3_occ:    0.979    0.034    0.469
   4_bss:    0.979    0.034    0.469
   4_xyz:    1.111    0.044    0.490
   4_adp:    1.111    0.044    0.490
   4_occ:    1.111    0.044    0.490
   5_bss:    1.111    0.044    0.490
   5_xyz:    1.180    0.048    0.502
   5_adp:    1.180    0.048    0.502
   5_occ:    1.180    0.048    0.502
   5_bss:    1.180    0.048    0.502
------------------------------------------------------------------------

CPU time actual refinement: 273.47


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_874/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_874/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_874/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_874/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_874/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 273.34 
  Macro-tasks:
    bulk solvent and scale       = 30.76  
    individual site refinement   = 115.96 
    weights calculation          = 25.19  
    collect and process          = 5.55   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 177.54 
  Micro-tasks:
    mask                            = 1.49   
    f_calc                          = 86.87  
    alpha_beta                      = 6.94   
    target                          = 1.00   
    gradients_wrt_atomic_parameters = 94.96  
    fmodel                         = 5.68   
    r_factors                      = 0.19   
    phase_errors                   = 9.05   
    foms                           = 0.22   
    TOTAL for micro-tasks          = 206.40 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 3.865 micro seconds
Total CPU time: 4.75 minutes
from_scatterers_fft:    635 calls, 86.57 s
gradients_fft:          580 calls, 83.08 s

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

# Date 2008-01-16 Time 05:51:36 PST -0800 (1200491496.35 s)
Start R-work = 0.3579, R-free = 0.3538 (no bulk solvent and anisotropic scale)
Final R-work = 0.1303, R-free = 0.1747 (no bulk solvent and anisotropic scale)

Start R-work = 0.3450, R-free = 0.3447
Final R-work = 0.1065, R-free = 0.1549