# Date 2008-01-16 Time 05:02:07 PST -0800 (1200488527.96 s)
#phil __OFF__

Command line arguments: "../567.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4960
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 567

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 47.3993, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.31, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.3993, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9592 1.99061
Completeness in resolution range: 0.96322
Completeness with d_max=infinity: 0.960198

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9592
                             d_min =   1.9906

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.3993, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9592 1.99061
Completeness in resolution range: 0.96322
Completeness with d_max=infinity: 0.960198

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9596 -  4.2587 [2143/2170]  1928   215  10.0%
  bin  2:  4.2587 -  3.3933 [2041/2057]  1837   204  10.0%
  bin  3:  3.3933 -  2.9681 [2040/2059]  1838   202   9.9%
  bin  4:  2.9681 -  2.6985 [1995/2025]  1793   202  10.1%
  bin  5:  2.6985 -  2.5060 [1992/2011]  1791   201  10.1%
  bin  6:  2.5060 -  2.3589 [1977/2013]  1785   192   9.7%
  bin  7:  2.3589 -  2.2412 [1986/2019]  1785   201  10.1%
  bin  8:  2.2412 -  2.1439 [1953/1988]  1755   198  10.1%
  bin  9:  2.1439 -  2.0616 [1951/1978]  1758   193   9.9%
  bin 10:  2.0616 -  1.9906 [1511/2017]  1360   151  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_567/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 13
        2.42 -     3.04: 2176
        3.04 -     3.66: 4654
        3.66 -     4.28: 8979
        4.28 -     4.90: 12321
  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
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.208 3.040 -x+1,y-1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.228 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.257 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28138 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_567/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_567/model_refine_001.geo

CPU time processing inputs: 9.72


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 47.3993 86.82195 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: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2871   r_free= 0.2777   ksol= 0.00   Bsol= 0.00   scale= 0.982    |
|                                                                             |
| 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:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.947589                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9596 -  4.7496 0.99   1387  153 0.2651 0.2729      6.2923       6.274|
|  2:  4.7496 -  3.7901 0.99   1328  150 0.2182 0.1969      6.2998      6.2561|
|  3:  3.7901 -  3.3170 0.99   1318  149 0.2450 0.2310      6.2294      6.2384|
|  4:  3.3170 -  3.0164 0.99   1297  136 0.2704 0.2586      6.1324       6.025|
|  5:  3.0164 -  2.8017 0.99   1289  145 0.2956 0.2440       6.009      5.8996|
|  6:  2.8017 -  2.6375 0.99   1291  145 0.2969 0.2988      5.9398      5.8818|
|  7:  2.6375 -  2.5060 0.99   1277  146 0.2905 0.2814      5.8817      5.8138|
|  8:  2.5060 -  2.3974 0.98   1291  137 0.3122 0.3312       5.874       5.941|
|  9:  2.3974 -  2.3055 0.98   1261  144 0.3119 0.2952      5.8085      5.7268|
| 10:  2.3055 -  2.2262 0.98   1256  134 0.3278 0.2889      5.8529      5.6906|
| 11:  2.2262 -  2.1568 1.00   1279  150 0.3238 0.3240      5.7649       5.784|
| 12:  2.1568 -  2.0953 0.97   1268  133 0.3338 0.3517      5.7301      5.8241|
| 13:  2.0953 -  2.0403 0.98   1257  139 0.3447 0.3242      5.6766      5.6323|
| 14:  2.0403 -  1.9906 0.66    831   98 0.3286 0.3653      5.5836      5.6287|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9596 -  4.7496  1387   153  0.79  25.77   0.87     0.80      40981.61|
|  2:  4.7496 -  3.7901  1328   150  0.87  19.37   0.99     0.92      35911.06|
|  3:  3.7901 -  3.3170  1318   149  0.86  20.95   1.00     0.97      30515.60|
|  4:  3.3170 -  3.0164  1297   136  0.84  22.64   0.99     0.96      25838.83|
|  5:  3.0164 -  2.8017  1289   145  0.79  27.27   1.01     0.93      22376.05|
|  6:  2.8017 -  2.6375  1291   145  0.78  28.72   1.01     0.93      20847.23|
|  7:  2.6375 -  2.5060  1277   146  0.78  28.93   1.03     0.93      19340.55|
|  8:  2.5060 -  2.3974  1291   137  0.77  29.44   1.02     0.96      18312.64|
|  9:  2.3974 -  2.3055  1261   144  0.77  29.52   1.04     0.97      16231.79|
| 10:  2.3055 -  2.2262  1256   134  0.77  29.71   1.06     0.98      15200.56|
| 11:  2.2262 -  2.1568  1279   150  0.76  30.92   1.05     1.00      15073.19|
| 12:  2.1568 -  2.0953  1268   133  0.74  32.39   1.06     1.00      15608.64|
| 13:  2.0953 -  2.0403  1257   139  0.72  34.43   1.04     0.97      14950.72|
| 14:  2.0403 -  1.9906   831    98  0.69  36.40   1.06     0.91      13073.81|
|alpha:            min =        0.80 max =            1.00 mean =         0.94|
|beta:             min =    13073.81 max =        40981.61 mean =     22158.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.78|
|phase err.(work): min =        0.00 max =           89.98 mean =        28.04|
|phase err.(test): min =        0.00 max =           89.98 mean =        28.23|
|-----------------------------------------------------------------------------|

============================== 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 = 3.996010              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.153   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.466859              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.643   (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:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       12 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      185 |
| 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:     1849 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2805 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4607 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4372 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5609 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6712 |
|-----------------------------------------------------------------------------|
|-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 |        0.161 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.806 |       0.147 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.005)------------------------------------------|
|    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: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2871   r_free= 0.2777   ksol= 0.00   Bsol= 0.00   scale= 0.982    |
|                                                                             |
| 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:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.947589                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2721   r_free= 0.2628   ksol= 0.32   Bsol= 47.17   scale= 0.979   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.14,0.71,-0.98,0.00,-0.00,-0.00); trace/3= -1.14                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.918180                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.722759              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.121   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.267017              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.527   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2721      final r-factor (work) = 0.1558          |
| start r-factor (free) = 0.2628      final r-factor (free) = 0.1735          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2140 = 3.72 * 0.50 * 5.9380 + 1.00 * 0.1610                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4852 = 3.72 * 0.50 * 5.5982 + 1.00 * 0.0648                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1558      final r-factor (work) = 0.1429          |
| start r-factor (free) = 0.1735      final r-factor (free) = 0.1755          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5010 = 0.27 * 1.00 * 5.5982 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4517 = 0.27 * 1.00 * 5.3154 + 1.00 * 0.0324                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.005)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    65.18   16.56    None  None   None       |
|    all(noH): 2823   0      0.00    65.18   16.56    None  None   None       |
|    Sol.    : 438    0      5.98    63.50   37.43    None  None   None       |
|    Mac.    : 2385   0      0.00    65.18   12.73    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 -   6.518:  252   |   5:    32.590 -  39.108:   93        |
|      1:     6.518 -  13.036: 1283   |   6:    39.108 -  45.626:  113        |
|      2:    13.036 -  19.554:  639   |   7:    45.626 -  52.144:   74        |
|      3:    19.554 -  26.072:  189   |   8:    52.144 -  58.662:   53        |
|      4:    26.072 -  32.590:  117   |   9:    58.662 -  65.180:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1429 r_free = 0.1755             target_work(ml) = 5.324         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1425 r_free = 0.1753             target_work(ml) = 5.323         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1425   r_free= 0.1753   ksol= 0.32   Bsol= 47.17   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.14,0.71,-0.98,0.00,-0.00,-0.00); trace/3= -1.14                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.322751                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1417   r_free= 0.1734   ksol= 0.33   Bsol= 57.53   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.28,-1.35,-1.34,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.318291                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.740094              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.135  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.222860              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.220   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1417      final r-factor (work) = 0.1215          |
| start r-factor (free) = 0.1734      final r-factor (free) = 0.1551          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6952 = 1.74 * 0.50 * 5.3222 + 1.00 * 0.0646                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6193 = 1.74 * 0.50 * 5.2456 + 1.00 * 0.0554                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1215      final r-factor (work) = 0.1172          |
| start r-factor (free) = 0.1551      final r-factor (free) = 0.1524          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1946 = 0.22 * 1.00 * 5.2456 + 1.00 * 0.0255                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1592 = 0.22 * 1.00 * 5.1667 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.005)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.71    76.17   16.69    None  None   None       |
|    all(noH): 2823   0      1.71    76.17   16.69    None  None   None       |
|    Sol.    : 438    0      5.99    69.02   38.03    None  None   None       |
|    Mac.    : 2385   0      1.71    76.17   12.77    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:     1.706 -   9.153:  807   |   5:    38.938 -  46.384:  112        |
|      1:     9.153 -  16.599: 1190   |   6:    46.384 -  53.831:   87        |
|      2:    16.599 -  24.045:  317   |   7:    53.831 -  61.277:   57        |
|      3:    24.045 -  31.492:  120   |   8:    61.277 -  68.723:   13        |
|      4:    31.492 -  38.938:  117   |   9:    68.723 -  76.170:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1172 r_free = 0.1524             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1170 r_free = 0.1524             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1170   r_free= 0.1524   ksol= 0.33   Bsol= 57.53   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.28,-1.35,-1.34,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.158839                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1168   r_free= 0.1523   ksol= 0.33   Bsol= 55.52   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.86,-1.70,-1.10,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.157526                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.015940              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.496  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.191281              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.370  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1168      final r-factor (work) = 0.1087          |
| start r-factor (free) = 0.1523      final r-factor (free) = 0.1524          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8460 = 3.02 * 0.50 * 5.1663 + 1.00 * 0.0554                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7976 = 3.02 * 0.50 * 5.1226 + 1.00 * 0.0728                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1087      final r-factor (work) = 0.1083          |
| start r-factor (free) = 0.1524      final r-factor (free) = 0.1516          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9876 = 0.19 * 1.00 * 5.1226 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9859 = 0.19 * 1.00 * 5.1149 + 1.00 * 0.0075                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.005)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.50    76.70   16.48    None  None   None       |
|    all(noH): 2823   0      1.50    76.70   16.48    None  None   None       |
|    Sol.    : 438    0      6.02    68.79   37.61    None  None   None       |
|    Mac.    : 2385   0      1.50    76.70   12.60    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:     1.499 -   9.020:  807   |   5:    39.101 -  46.622:  100        |
|      1:     9.020 -  16.540: 1209   |   6:    46.622 -  54.142:   91        |
|      2:    16.540 -  24.060:  304   |   7:    54.142 -  61.663:   53        |
|      3:    24.060 -  31.581:  127   |   8:    61.663 -  69.183:   11        |
|      4:    31.581 -  39.101:  119   |   9:    69.183 -  76.703:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1083 r_free = 0.1516             target_work(ml) = 5.113         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1083 r_free = 0.1516             target_work(ml) = 5.113         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1516   ksol= 0.33   Bsol= 55.52   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.86,-1.70,-1.10,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.112992                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1512   ksol= 0.33   Bsol= 55.52   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.66,-1.76,-0.95,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.112143                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.501239              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 161.409  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.078533              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.427  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1083      final r-factor (work) = 0.1086          |
| start r-factor (free) = 0.1512      final r-factor (free) = 0.1533          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4700 = 2.50 * 0.50 * 5.1152 + 1.00 * 0.0728                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4598 = 2.50 * 0.50 * 5.1132 + 1.00 * 0.0651                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1086      final r-factor (work) = 0.1077          |
| start r-factor (free) = 0.1533      final r-factor (free) = 0.1548          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.7487 = 3.08 * 1.00 * 5.1132 + 1.00 * 0.0074                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.7539 = 3.08 * 1.00 * 5.1142 + 1.00 * 0.0096                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.005)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.29   16.75    None  None   None       |
|    all(noH): 2823   0      0.00    86.29   16.75    None  None   None       |
|    Sol.    : 438    0      5.75    74.94   39.49    None  None   None       |
|    Mac.    : 2385   0      0.00    86.29   12.58    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.629:  778   |   5:    43.143 -  51.771:  108        |
|      1:     8.629 -  17.257: 1283   |   6:    51.771 -  60.400:   88        |
|      2:    17.257 -  25.886:  286   |   7:    60.400 -  69.028:   35        |
|      3:    25.886 -  34.514:  131   |   8:    69.028 -  77.657:    7        |
|      4:    34.514 -  43.143:  103   |   9:    77.657 -  86.285:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1077 r_free = 0.1548             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1076 r_free = 0.1549             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1076   r_free= 0.1549   ksol= 0.33   Bsol= 55.52   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.66,-1.76,-0.95,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.122393                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1075   r_free= 0.1548   ksol= 0.32   Bsol= 55.52   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-1.57,-0.72,-0.00,-0.00,-0.00); trace/3= -1.55                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.122314                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.774299              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 160.780  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 7.218877              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.112  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1075      final r-factor (work) = 0.1063          |
| start r-factor (free) = 0.1548      final r-factor (free) = 0.1559          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1607 = 2.77 * 0.50 * 5.1152 + 1.00 * 0.0651                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1676 = 2.77 * 0.50 * 5.1177 + 1.00 * 0.0686                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1063      final r-factor (work) = 0.1063          |
| start r-factor (free) = 0.1559      final r-factor (free) = 0.1566          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 36.9537 = 7.22 * 1.00 * 5.1177 + 1.00 * 0.0096                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 36.9450 = 7.22 * 1.00 * 5.1163 + 1.00 * 0.0108                              |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.005)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.09   16.76    None  None   None       |
|    all(noH): 2823   0      0.00    98.09   16.76    None  None   None       |
|    Sol.    : 438    0      5.37    84.98   40.11    None  None   None       |
|    Mac.    : 2385   0      0.00    98.09   12.47    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.810: 1145   |   5:    49.048 -  58.857:   96        |
|      1:     9.810 -  19.619: 1043   |   6:    58.857 -  68.667:   54        |
|      2:    19.619 -  29.429:  208   |   7:    68.667 -  78.476:   18        |
|      3:    29.429 -  39.238:  139   |   8:    78.476 -  88.286:    5        |
|      4:    39.238 -  49.048:  111   |   9:    88.286 -  98.095:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1063 r_free = 0.1566             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1063 r_free = 0.1566             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1063   r_free= 0.1566   ksol= 0.32   Bsol= 55.52   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-1.57,-0.72,-0.00,-0.00,-0.00); trace/3= -1.55                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.119848                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9596 -  4.7496 0.99   1387  153 0.0945 0.1264      5.3568      5.4983|
|  2:  4.7496 -  3.7901 0.99   1328  150 0.0801 0.1057       5.396      5.6034|
|  3:  3.7901 -  3.3170 0.99   1318  149 0.0997 0.1510      5.4364      5.8502|
|  4:  3.3170 -  3.0164 0.99   1297  136 0.1142 0.1511      5.4172      5.5808|
|  5:  3.0164 -  2.8017 0.99   1289  145 0.1257 0.1674      5.3017      5.5129|
|  6:  2.8017 -  2.6375 0.99   1291  145 0.1163 0.1978      5.1919      5.4747|
|  7:  2.6375 -  2.5060 0.99   1277  146 0.1168 0.1630      5.1287      5.3367|
|  8:  2.5060 -  2.3974 0.98   1291  137 0.1107 0.1635      5.0558      5.3238|
|  9:  2.3974 -  2.3055 0.98   1261  144 0.1112 0.1812      4.9975      5.2796|
| 10:  2.3055 -  2.2262 0.98   1256  134 0.1079 0.1698      4.9649      5.2003|
| 11:  2.2262 -  2.1568 1.00   1279  150 0.1099 0.1806      4.9239      5.2826|
| 12:  2.1568 -  2.0953 0.97   1268  133 0.1056 0.1651      4.8568      5.1743|
| 13:  2.0953 -  2.0403 0.98   1257  139 0.1061 0.1716      4.7688      5.0336|
| 14:  2.0403 -  1.9906 0.66    831   98 0.1000 0.1860      4.6626      5.0016|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9596 -  4.7496  1387   153  0.94   9.17   0.97     0.94       7098.51|
|  2:  4.7496 -  3.7901  1328   150  0.96   7.62   1.01     0.99       8564.41|
|  3:  3.7901 -  3.3170  1318   149  0.94  10.81   1.02     1.02       9854.00|
|  4:  3.3170 -  3.0164  1297   136  0.92  13.03   1.00     0.99       9835.60|
|  5:  3.0164 -  2.8017  1289   145  0.90  15.72   0.99     0.97       8211.41|
|  6:  2.8017 -  2.6375  1291   145  0.90  16.14   0.98     0.95       6982.28|
|  7:  2.6375 -  2.5060  1277   146  0.91  14.88   0.98     0.95       5898.79|
|  8:  2.5060 -  2.3974  1291   137  0.91  15.00   0.99     0.96       5312.15|
|  9:  2.3974 -  2.3055  1261   144  0.91  15.31   0.99     0.95       4841.88|
| 10:  2.3055 -  2.2262  1256   134  0.90  15.91   0.98     0.94       4608.53|
| 11:  2.2262 -  2.1568  1279   150  0.90  15.98   0.98     0.94       4329.48|
| 12:  2.1568 -  2.0953  1268   133  0.91  15.08   0.99     0.98       3901.45|
| 13:  2.0953 -  2.0403  1257   139  0.91  15.65   0.98     0.97       3301.81|
| 14:  2.0403 -  1.9906   831    98  0.91  14.61   0.95     0.91       2582.61|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     2582.61 max =         9854.00 mean =      6218.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.85|
|phase err.(test): min =        0.00 max =           88.99 mean =        13.36|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1061   r_free= 0.1565   ksol= 0.32   Bsol= 55.53   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-1.29,-0.43,-0.00,-0.00,-0.00); trace/3= -1.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.119961                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1061   r_free= 0.1565   ksol= 0.32   Bsol= 55.53   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-1.29,-0.43,-0.00,-0.00,-0.00); trace/3= -1.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.119961                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9596 -  4.7496 0.99   1387  153 0.0945 0.1266      5.3576      5.4996|
|  2:  4.7496 -  3.7901 0.99   1328  150 0.0802 0.1057      5.3967      5.6035|
|  3:  3.7901 -  3.3170 0.99   1318  149 0.0998 0.1510      5.4365      5.8507|
|  4:  3.3170 -  3.0164 0.99   1297  136 0.1142 0.1511      5.4171      5.5809|
|  5:  3.0164 -  2.8017 0.99   1289  145 0.1257 0.1674      5.3015      5.5125|
|  6:  2.8017 -  2.6375 0.99   1291  145 0.1162 0.1978      5.1918      5.4744|
|  7:  2.6375 -  2.5060 0.99   1277  146 0.1169 0.1630      5.1288      5.3369|
|  8:  2.5060 -  2.3974 0.98   1291  137 0.1107 0.1635      5.0559      5.3236|
|  9:  2.3974 -  2.3055 0.98   1261  144 0.1112 0.1812      4.9976      5.2797|
| 10:  2.3055 -  2.2262 0.98   1256  134 0.1079 0.1698       4.965      5.2005|
| 11:  2.2262 -  2.1568 1.00   1279  150 0.1099 0.1805      4.9239      5.2825|
| 12:  2.1568 -  2.0953 0.97   1268  133 0.1056 0.1650      4.8567       5.174|
| 13:  2.0953 -  2.0403 0.98   1257  139 0.1061 0.1716      4.7687      5.0334|
| 14:  2.0403 -  1.9906 0.66    831   98 0.1000 0.1860      4.6627      5.0014|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9596 -  4.7496  1387   153  0.94   9.18   0.97     0.94       7111.14|
|  2:  4.7496 -  3.7901  1328   150  0.96   7.63   1.01     1.00       8574.66|
|  3:  3.7901 -  3.3170  1318   149  0.94  10.81   1.03     1.02       9858.61|
|  4:  3.3170 -  3.0164  1297   136  0.92  13.03   1.01     1.00       9834.27|
|  5:  3.0164 -  2.8017  1289   145  0.90  15.71   1.00     0.97       8208.18|
|  6:  2.8017 -  2.6375  1291   145  0.90  16.14   0.99     0.96       6978.78|
|  7:  2.6375 -  2.5060  1277   146  0.91  14.88   0.99     0.96       5897.40|
|  8:  2.5060 -  2.3974  1291   137  0.91  15.00   1.00     0.97       5311.72|
|  9:  2.3974 -  2.3055  1261   144  0.91  15.32   1.00     0.96       4842.59|
| 10:  2.3055 -  2.2262  1256   134  0.90  15.91   1.00     0.96       4607.81|
| 11:  2.2262 -  2.1568  1279   150  0.90  15.98   0.99     0.96       4328.44|
| 12:  2.1568 -  2.0953  1268   133  0.91  15.08   1.01     0.99       3900.24|
| 13:  2.0953 -  2.0403  1257   139  0.91  15.65   1.00     0.98       3300.86|
| 14:  2.0403 -  1.9906   831    98  0.91  14.61   0.96     0.93       2582.43|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2582.43 max =         9858.61 mean =      6219.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.85|
|phase err.(test): min =        0.00 max =           88.99 mean =        13.36|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.005)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.10   16.76    None  None   None       |
|    all(noH): 2823   0      0.00    98.10   16.76    None  None   None       |
|    Sol.    : 438    0      5.37    84.98   40.11    None  None   None       |
|    Mac.    : 2385   0      0.00    98.10   12.48    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.813: 1145   |   5:    49.050 -  58.860:   96        |
|      1:     9.813 -  19.622: 1043   |   6:    58.860 -  68.669:   54        |
|      2:    19.622 -  29.432:  208   |   7:    68.669 -  78.479:   18        |
|      3:    29.432 -  39.241:  139   |   8:    78.479 -  88.288:    5        |
|      4:    39.241 -  49.050:  111   |   9:    88.288 -  98.098:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 279         
Filter by distance & map next to the model:
   mapped sites are within: 0.474 - 4.868
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 274 from: 279
   mapped sites are within: 0.713 - 4.868

peak=    5.258 closest distance to " CG  PRO A  54 " =    1.276
peak=    5.257 closest distance to " NH2 ARG A  56 " =    2.286
peak=    5.178 closest distance to " CB  ARG A 275 " =    0.958
peak=    5.098 closest distance to " CB  GLN A 183 " =    1.292
peak=    5.010 closest distance to " CB  GLN A 223 " =    1.406
peak=    4.912 closest distance to " O   HOH Z 232 " =    2.360
peak=    4.875 closest distance to " CB  SER A  63 " =    1.161
peak=    4.806 closest distance to " O   HOH Z 142 " =    1.600
peak=    4.719 closest distance to " CG  PRO A 213 " =    1.182
peak=    4.712 closest distance to " C   PRO A 198 " =    1.460
peak=    4.704 closest distance to " O   HOH Z 126 " =    1.860
peak=    4.642 closest distance to " NE2 GLN A  11 " =    1.035
peak=    4.622 closest distance to " CB  ARG A 190 " =    1.677
peak=    4.613 closest distance to " CA  TYR A  30 " =    0.927
peak=    4.604 closest distance to " CB  ARG A  79 " =    1.298
peak=    4.504 closest distance to " O   HOH Z  15 " =    2.147
peak=    4.414 closest distance to " O   HOH Z 298 " =    1.816
peak=    4.410 closest distance to " O   HOH Z 203 " =    1.715
peak=    4.371 closest distance to " CB  ASN A 148 " =    1.442
peak=    4.352 closest distance to " O   HOH Z  78 " =    1.608
peak=    4.345 closest distance to " CB  GLU A 152 " =    1.147
peak=    4.306 closest distance to " O   HOH Z 369 " =    2.323
peak=    4.266 closest distance to " O   HOH Z 427 " =    2.982
peak=    4.251 closest distance to " O   HOH Z 287 " =    2.115
peak=    4.250 closest distance to " CB  TYR A 169 " =    0.824
peak=    4.241 closest distance to " O   HOH Z 250 " =    1.457
peak=    4.230 closest distance to " CG  PRO A  90 " =    1.137
peak=    4.207 closest distance to " O   HOH Z 234 " =    3.698
peak=    4.199 closest distance to " NZ  LYS A 117 " =    3.254
peak=    4.184 closest distance to " O   HOH Z 193 " =    1.838
peak=    4.178 closest distance to " OD1 ASN A  69 " =    2.471
peak=    4.171 closest distance to " CB  PRO A  54 " =    0.895
peak=    4.156 closest distance to " O   HOH Z 272 " =    1.868
peak=    4.154 closest distance to " O   HOH Z 209 " =    2.262
peak=    4.128 closest distance to " O   HOH Z 158 " =    3.050
peak=    4.112 closest distance to " CG  PRO A 198 " =    1.221
peak=    4.112 closest distance to " CB  LEU A 228 " =    1.111
peak=    4.079 closest distance to " CD2 LEU A 297 " =    0.874
peak=    4.051 closest distance to " O   SER A  87 " =    2.236
peak=    4.032 closest distance to " CZ  PHE A 218 " =    1.091
peak=    4.025 closest distance to " O   HOH Z 346 " =    1.690
peak=    4.020 closest distance to " O   HOH Z 403 " =    1.687
peak=    4.018 closest distance to " O   HOH Z 280 " =    2.928
peak=    4.008 closest distance to " O   HOH Z  40 " =    1.872
peak=    3.990 closest distance to " OG ASER A 258 " =    3.134
peak=    3.980 closest distance to " CG  ARG A  66 " =    2.444
peak=    3.959 closest distance to " CB  ASP A 140 " =    1.016
peak=    3.945 closest distance to " CG1 ILE A  33 " =    1.198
peak=    3.942 closest distance to " CD2 TRP A 179 " =    1.382
peak=    3.942 closest distance to " CB  GLU A 277 " =    3.626
peak=    3.938 closest distance to " O   HOH Z 303 " =    2.183
peak=    3.937 closest distance to " CB  VAL A 265 " =    1.246
peak=    3.925 closest distance to " ND2 ASN A 187 " =    1.412
peak=    3.912 closest distance to " CA  ARG A 195 " =    1.319
peak=    3.909 closest distance to " O   HOH Z 368 " =    2.092
peak=    3.908 closest distance to " CG1BVAL A  72 " =    1.715
peak=    3.906 closest distance to " O   HOH Z  43 " =    1.914
peak=    3.903 closest distance to " O   HOH Z 189 " =    2.438
peak=    3.899 closest distance to " O   HOH Z 423 " =    2.017
peak=    3.889 closest distance to " O   HOH Z 180 " =    2.182
peak=    3.887 closest distance to " CA  ARG A  36 " =    1.101
peak=    3.860 closest distance to " CD  ARG A 269 " =    0.972
peak=    3.854 closest distance to " CB  TRP A 266 " =    0.999
peak=    3.829 closest distance to " O   HOH Z 261 " =    1.974
peak=    3.827 closest distance to " O   HOH Z  61 " =    1.564
peak=    3.819 closest distance to " O   HOH Z 265 " =    2.225
peak=    3.817 closest distance to " CE  LYS A  76 " =    0.850
peak=    3.815 closest distance to " CB  GLU A 128 " =    1.123
peak=    3.808 closest distance to " O   HOH Z 197 " =    2.895
peak=    3.806 closest distance to " O   HOH Z  63 " =    1.989
peak=    3.780 closest distance to " O   HOH Z  19 " =    2.150
peak=    3.772 closest distance to " O   HOH Z 402 " =    1.417
peak=    3.766 closest distance to " CG2 ILE A 120 " =    1.038
peak=    3.764 closest distance to " CA  ALA A  51 " =    0.918
peak=    3.762 closest distance to " O   HOH Z 128 " =    2.029
peak=    3.760 closest distance to " CA  ASN A 176 " =    1.214
peak=    3.758 closest distance to " CD  ARG A 159 " =    0.779
peak=    3.752 closest distance to " O   HOH Z  59 " =    2.235
peak=    3.738 closest distance to " O   HOH Z 214 " =    2.083
peak=    3.737 closest distance to " OG BSER A 164 " =    2.273
peak=    3.736 closest distance to " O   HOH Z 147 " =    1.821
peak=    3.735 closest distance to " C   ILE A 106 " =    1.901
peak=    3.717 closest distance to " O   HOH Z 426 " =    1.609
peak=    3.710 closest distance to " O   HOH Z 406 " =    1.543
peak=    3.705 closest distance to " O   HOH Z 291 " =    1.535
peak=    3.703 closest distance to " CB  VAL A 202 " =    1.498
peak=    3.689 closest distance to " CD  LYS A 166 " =    1.322
peak=    3.689 closest distance to " OD2 ASP A 298 " =    3.920
peak=    3.675 closest distance to " CA  ALA A  21 " =    1.211
peak=    3.673 closest distance to " O   HOH Z  97 " =    1.947
peak=    3.672 closest distance to " O   HOH Z 183 " =    1.466
peak=    3.666 closest distance to " O   HOH Z 299 " =    4.416
peak=    3.654 closest distance to " CD1 LEU A 300 " =    1.224
peak=    3.650 closest distance to " O   HOH Z  44 " =    1.741
peak=    3.649 closest distance to " CA  ASN A 215 " =    1.163
peak=    3.636 closest distance to " O   HOH Z 411 " =    3.830
peak=    3.632 closest distance to " CB  TRP A 179 " =    1.374
peak=    3.630 closest distance to " CB  SER A 212 " =    1.045
peak=    3.629 closest distance to " O   HOH Z 325 " =    2.492
peak=    3.625 closest distance to " O   HOH Z 141 " =    1.707
peak=    3.614 closest distance to " O   HOH Z 108 " =    2.760
peak=    3.613 closest distance to " ND2 ASN A 249 " =    1.904
peak=    3.613 closest distance to " O  BHOH Z 338 " =    2.295
peak=    3.602 closest distance to " NE2 GLN A  77 " =    3.247
peak=    3.599 closest distance to " O   HOH Z 361 " =    3.666
peak=    3.597 closest distance to " O   HOH Z 126 " =    1.612
peak=    3.586 closest distance to " OG1 THR A 294 " =    2.394
peak=    3.576 closest distance to " O   HOH Z 359 " =    1.493
peak=    3.574 closest distance to " CA  MET A 105 " =    1.041
peak=    3.572 closest distance to " CB  SER A   3 " =    1.277
peak=    3.566 closest distance to " NH1AARG A 145 " =    1.237
peak=    3.564 closest distance to " O   HOH Z 380 " =    1.974
peak=    3.549 closest distance to " CB  ARG A  79 " =    0.839
peak=    3.549 closest distance to " NH2BARG A 145 " =    2.160
peak=    3.548 closest distance to " CG2 VAL A 257 " =    0.841
peak=    3.547 closest distance to " O   HOH Z 245 " =    1.313
peak=    3.544 closest distance to " CG2 ILE A  20 " =    1.366
peak=    3.543 closest distance to " O   HOH Z 261 " =    1.633
peak=    3.543 closest distance to " O   HOH Z 133 " =    2.639
peak=    3.541 closest distance to " O   HOH Z 425 " =    2.000
peak=    3.537 closest distance to " OD2 ASP A 286 " =    2.840
peak=    3.535 closest distance to " O   HOH Z  21 " =    1.823
peak=    3.534 closest distance to " O   HOH Z 337 " =    3.570
peak=    3.529 closest distance to " O   HOH Z 185 " =    1.759
peak=    3.527 closest distance to " CG  PRO A 243 " =    1.053
peak=    3.518 closest distance to " O   HOH Z 279 " =    2.224
peak=    3.513 closest distance to " ND1 HIS A  81 " =    1.609
peak=    3.510 closest distance to " O   HOH Z  66 " =    1.958
peak=    3.508 closest distance to " O   HOH Z 371 " =    3.368
peak=    3.504 closest distance to " CA  THR A 221 " =    0.979
peak=    3.503 closest distance to " CA  ALA A 291 " =    0.787
peak=    3.498 closest distance to " O   HOH Z 421 " =    1.774
peak=    3.495 closest distance to " CA  ALA A 160 " =    0.870
peak=    3.494 closest distance to " CB  GLN A  89 " =    1.327
peak=    3.489 closest distance to " O   HOH Z 391 " =    2.900
peak=    3.485 closest distance to " O   HOH Z  66 " =    2.125
peak=    3.481 closest distance to " OE1 GLU A   2 " =    2.178
peak=    3.478 closest distance to " CG  GLN A  58 " =    2.744
peak=    3.477 closest distance to " O   HOH Z 417 " =    3.004
peak=    3.475 closest distance to " CB  THR A  31 " =    1.679
peak=    3.472 closest distance to " CA  LYS A 117 " =    1.234
peak=    3.468 closest distance to " O   HOH Z 344 " =    3.188
peak=    3.465 closest distance to " CB  ALA A 291 " =    1.326
peak=    3.461 closest distance to " O   HOH Z 132 " =    2.496
peak=    3.458 closest distance to " O   HOH Z 327 " =    1.607
peak=    3.455 closest distance to " CE1 TYR A 186 " =    1.282
peak=    3.446 closest distance to " CB  GLU A  46 " =    0.987
peak=    3.444 closest distance to " CD1 LEU A  96 " =    0.713
peak=    3.443 closest distance to " CG2 THR A 221 " =    1.174
peak=    3.439 closest distance to " O   HOH Z 353 " =    2.777
peak=    3.435 closest distance to " CB  ASN A 215 " =    1.152
peak=    3.433 closest distance to " CA  ALA A  84 " =    1.279
peak=    3.428 closest distance to " CB  ASN A  39 " =    0.859
peak=    3.414 closest distance to " CA  MET A  40 " =    1.122
peak=    3.410 closest distance to " O   HOH Z 285 " =    2.849
peak=    3.409 closest distance to " ND2 ASN A 110 " =    1.621
peak=    3.403 closest distance to " O   HOH Z 171 " =    1.876
peak=    3.400 closest distance to " CD BLYS A 290 " =    0.998
peak=    3.399 closest distance to " CB  SER A  26 " =    1.703
peak=    3.399 closest distance to " CB  GLN A  88 " =    1.191
peak=    3.388 closest distance to " O   HOH Z 407 " =    2.607
peak=    3.388 closest distance to " CB  ALA A 248 " =    1.320
peak=    3.385 closest distance to " CB  TYR A 169 " =    0.974
peak=    3.382 closest distance to " CG  MET A 185 " =    1.165
peak=    3.376 closest distance to " NH2 ARG A 156 " =    1.193
peak=    3.372 closest distance to " O   HOH Z 128 " =    2.341
peak=    3.368 closest distance to " O   HOH Z 173 " =    1.968
peak=    3.368 closest distance to " CZ2 TRP A 179 " =    1.635
peak=    3.363 closest distance to " CB  MET A  47 " =    0.970
peak=    3.361 closest distance to " O   HOH Z   1 " =    2.150
peak=    3.358 closest distance to " CB  ARG A 139 " =    0.898
peak=    3.355 closest distance to " O   HOH Z  97 " =    2.443
peak=    3.353 closest distance to " O   HOH Z 148 " =    3.330
peak=    3.350 closest distance to " CB  MET A 113 " =    1.810
peak=    3.348 closest distance to " O   HOH Z 357 " =    2.017
peak=    3.343 closest distance to " O   HOH Z 193 " =    1.613
peak=    3.342 closest distance to " O   HOH Z 417 " =    2.074
peak=    3.341 closest distance to " CA  ASP A 140 " =    1.133
peak=    3.340 closest distance to " O   HOH Z 383 " =    2.016
peak=    3.339 closest distance to " N   ARG A 156 " =    1.363
peak=    3.338 closest distance to " O   ALA A 165 " =    1.530
peak=    3.335 closest distance to " O   HOH Z 313 " =    1.867
peak=    3.334 closest distance to " O   HOH Z 403 " =    1.348
peak=    3.334 closest distance to " O   HOH Z 336 " =    1.598
peak=    3.331 closest distance to " CB  ALA A  34 " =    0.988
peak=    3.330 closest distance to " O   HOH Z 305 " =    3.628
peak=    3.327 closest distance to " O   ASN A  74 " =    1.600
peak=    3.327 closest distance to " CA  THR A 264 " =    0.936
peak=    3.320 closest distance to " O   HOH Z  88 " =    3.316
peak=    3.319 closest distance to " CB  TYR A 116 " =    0.775
peak=    3.318 closest distance to " O   HOH Z 166 " =    3.869
peak=    3.314 closest distance to " CB  SER A 141 " =    1.025
peak=    3.304 closest distance to " O   HOH Z  10 " =    1.818
peak=    3.301 closest distance to " CD  LYS A 119 " =    1.300
peak=    3.296 closest distance to " CG2 VAL A 197 " =    1.127
peak=    3.296 closest distance to " O   HOH Z 393 " =    3.293
peak=    3.295 closest distance to " O   HOH Z  85 " =    2.289
peak=    3.291 closest distance to " OG  SER A  22 " =    2.709
peak=    3.287 closest distance to " CB  GLU A 236 " =    1.078
peak=    3.285 closest distance to " CA  ASN A 217 " =    1.183
peak=    3.283 closest distance to " CG  LEU A 167 " =    1.217
peak=    3.278 closest distance to " O   HOH Z 258 " =    2.117
peak=    3.277 closest distance to " O   HOH Z 365 " =    2.873
peak=    3.276 closest distance to " CG  GLU A  37 " =    0.882
peak=    3.276 closest distance to " O   HOH Z  80 " =    1.627
peak=    3.275 closest distance to " N   ASN A 127 " =    1.258
peak=    3.270 closest distance to " CD1 ILE A 106 " =    0.858
peak=    3.262 closest distance to " O   TRP A 274 " =    1.937
peak=    3.261 closest distance to " O   HOH Z  61 " =    1.445
peak=    3.258 closest distance to " CA  ALA A 248 " =    1.232
peak=    3.257 closest distance to " CD  ARG A  66 " =    2.438
peak=    3.256 closest distance to " N   ASN A  39 " =    1.346
peak=    3.256 closest distance to " O   HOH Z  68 " =    1.658
peak=    3.256 closest distance to " O   HOH Z 248 " =    1.596
peak=    3.254 closest distance to " NZ  LYS A  48 " =    1.309
peak=    3.253 closest distance to " O   HOH Z 199 " =    1.560
peak=    3.251 closest distance to " O   HOH Z 345 " =    3.128
peak=    3.250 closest distance to " O   THR A 220 " =    1.232
peak=    3.249 closest distance to " O   HOH Z 193 " =    2.124
peak=    3.248 closest distance to " CB  ILE A 120 " =    1.282
peak=    3.241 closest distance to " O   HOH Z 273 " =    2.885
peak=    3.240 closest distance to " CB  SER A  62 " =    0.823
peak=    3.235 closest distance to " CA  TYR A 116 " =    1.384
peak=    3.234 closest distance to " CA  ALA A 295 " =    1.066
peak=    3.231 closest distance to " CA  LEU A  83 " =    1.321
peak=    3.229 closest distance to " CB  ASN A 142 " =    1.165
peak=    3.227 closest distance to " CZ  PHE A  38 " =    1.306
peak=    3.226 closest distance to " CB  HIS A 108 " =    0.831
peak=    3.219 closest distance to " O   HOH Z 329 " =    3.937
peak=    3.210 closest distance to " CB  ALA A   1 " =    4.868
peak=    3.207 closest distance to " O   HOH Z 345 " =    1.564
peak=    3.206 closest distance to " CD2 HIS A  81 " =    1.085
peak=    3.201 closest distance to " CE  LYS A  48 " =    1.033
peak=    3.199 closest distance to " N   VAL A 126 " =    1.373
peak=    3.193 closest distance to " O   ASP A 124 " =    1.115
peak=    3.192 closest distance to " CB  GLN A 103 " =    0.850
peak=    3.190 closest distance to " CB  ASN A 110 " =    1.141
peak=    3.190 closest distance to " CD  GLU A 152 " =    0.717
peak=    3.189 closest distance to " CG  LYS A  76 " =    0.988
peak=    3.189 closest distance to " ND2 ASN A 249 " =    0.885
peak=    3.176 closest distance to " CB  ALA A   9 " =    1.588
peak=    3.169 closest distance to " O   HOH Z  44 " =    3.247
peak=    3.168 closest distance to " CA  ALA A 158 " =    1.278
peak=    3.165 closest distance to " O   HOH Z 163 " =    1.508
peak=    3.165 closest distance to " O   ALA A 158 " =    1.216
peak=    3.163 closest distance to " CA  ALA A 233 " =    1.338
peak=    3.163 closest distance to " CA  SER A 146 " =    1.719
peak=    3.162 closest distance to " CD2 TYR A  30 " =    1.332
peak=    3.155 closest distance to " O   HOH Z 135 " =    1.641
peak=    3.153 closest distance to " OD1 ASN A 301 " =    1.666
peak=    3.150 closest distance to " O   HOH Z 213 " =    1.626
peak=    3.150 closest distance to " CA  ALA A 154 " =    0.982
peak=    3.149 closest distance to " CZ3 TRP A 266 " =    1.099
peak=    3.148 closest distance to " C   TYR A 214 " =    1.415
peak=    3.144 closest distance to " CB  GLN A 205 " =    1.116
peak=    3.142 closest distance to " O   HOH Z 234 " =    1.844
peak=    3.140 closest distance to " O   HOH Z 392 " =    1.987
peak=    3.140 closest distance to " O   HOH Z 422 " =    2.637
peak=    3.134 closest distance to " CD1AILE A 234 " =    0.904
peak=    3.125 closest distance to " CG2 ILE A 234 " =    0.796
peak=    3.107 closest distance to " CA  SER A  87 " =    1.087
peak=    3.104 closest distance to " O   HOH Z 419 " =    1.939
peak=    3.100 closest distance to " O   THR A 251 " =    1.108
peak=    3.093 closest distance to " CA  ARG A 159 " =    1.291
peak=    3.083 closest distance to " O   HOH Z 271 " =    2.244
peak=    3.078 closest distance to " CA  ASN A 252 " =    1.884
peak=    3.075 closest distance to " O   ALA A   1 " =    1.704
peak=    3.074 closest distance to " O   HOH Z 250 " =    1.510
peak=    3.066 closest distance to " OG BSER A  99 " =    2.369
peak=    3.063 closest distance to " CG  GLN A  11 " =    1.547
peak=    3.045 closest distance to " O   HOH Z 156 " =    3.013
peak=    3.043 closest distance to " O   HOH Z  88 " =    2.608
peak=    3.039 closest distance to " O   HOH Z 116 " =    1.782
peak=    3.016 closest distance to " CA  ASP A 191 " =    1.014

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 212         
Filter by distance & map next to the model:
   mapped sites are within: 0.842 - 5.878
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 211 from: 212
   mapped sites are within: 0.842 - 5.878

peak=   -4.955 closest distance to " O   HOH Z 266 " =    5.004
peak=   -4.571 closest distance to " SG  CYS A 254 " =    3.420
peak=   -4.462 closest distance to " O   VAL A  67 " =    2.752
peak=   -4.457 closest distance to " CD  GLN A  58 " =    1.071
peak=   -4.428 closest distance to " CB  PRO A 243 " =    2.666
peak=   -4.398 closest distance to " C   HIS A 108 " =    1.097
peak=   -4.376 closest distance to " CD  ARG A 156 " =    2.132
peak=   -4.258 closest distance to " O   HOH Z 198 " =    2.074
peak=   -4.236 closest distance to " O   HOH Z 377 " =    2.158
peak=   -4.209 closest distance to " CG  GLN A 223 " =    2.085
peak=   -4.151 closest distance to " OXT GLY A 302 " =    2.816
peak=   -4.151 closest distance to " O   HOH Z 196 " =    2.012
peak=   -4.148 closest distance to " O   HOH Z 231 " =    2.346
peak=   -4.116 closest distance to " CB  ALA A 161 " =    2.545
peak=   -4.035 closest distance to " OG BSER A 134 " =    1.299
peak=   -4.018 closest distance to " O   HOH Z 372 " =    2.302
peak=   -3.954 closest distance to " CD1 LEU A 101 " =    2.362
peak=   -3.939 closest distance to " CG1 VAL A 112 " =    2.802
peak=   -3.928 closest distance to " O   HOH Z  10 " =    1.518
peak=   -3.927 closest distance to " N   ALA A  43 " =    2.735
peak=   -3.923 closest distance to " CA  ASP A 298 " =    1.041
peak=   -3.910 closest distance to " CG  ASP A 132 " =    2.365
peak=   -3.904 closest distance to " CZ3 TRP A 179 " =    1.203
peak=   -3.886 closest distance to " O   HOH Z 283 " =    2.333
peak=   -3.882 closest distance to " CD1 PHE A  59 " =    2.003
peak=   -3.877 closest distance to " O   HOH Z 292 " =    4.652
peak=   -3.877 closest distance to " CA  VAL A  67 " =    2.968
peak=   -3.864 closest distance to " CE2 TYR A  30 " =    2.708
peak=   -3.857 closest distance to " O   HOH Z 114 " =    3.177
peak=   -3.855 closest distance to " N   MET A 188 " =    1.960
peak=   -3.850 closest distance to " CE  MET A 105 " =    2.369
peak=   -3.847 closest distance to " NE2 GLN A  88 " =    1.852
peak=   -3.802 closest distance to " CG2 ILE A 263 " =    2.305
peak=   -3.770 closest distance to " OG  SER A  97 " =    2.206
peak=   -3.750 closest distance to " O   HOH Z 389 " =    1.833
peak=   -3.749 closest distance to " ND2 ASN A  45 " =    1.124
peak=   -3.731 closest distance to " O   HOH Z  13 " =    1.741
peak=   -3.731 closest distance to " O   SER A 210 " =    1.916
peak=   -3.716 closest distance to " CB  PHE A 208 " =    2.269
peak=   -3.706 closest distance to " CB  ALA A 291 " =    2.384
peak=   -3.704 closest distance to " ND2 ASN A  45 " =    1.758
peak=   -3.695 closest distance to " O   PRO A 198 " =    1.298
peak=   -3.682 closest distance to " O   PRO A 163 " =    2.085
peak=   -3.680 closest distance to " CG1 VAL A 112 " =    2.868
peak=   -3.679 closest distance to " CB  ALA A 248 " =    2.266
peak=   -3.677 closest distance to " O   HOH Z 211 " =    1.568
peak=   -3.675 closest distance to " O   HOH Z 166 " =    1.779
peak=   -3.673 closest distance to " O   HOH Z 353 " =    2.216
peak=   -3.665 closest distance to " CB  ALA A 291 " =    2.311
peak=   -3.665 closest distance to " O   PHE A 218 " =    1.603
peak=   -3.658 closest distance to " CG1 VAL A 250 " =    2.640
peak=   -3.657 closest distance to " O   HOH Z  52 " =    1.358
peak=   -3.655 closest distance to " O   HOH Z  60 " =    2.285
peak=   -3.645 closest distance to " CB  ASN A  39 " =    2.404
peak=   -3.631 closest distance to " CD  ARG A 139 " =    1.608
peak=   -3.629 closest distance to " O   HOH Z   6 " =    2.177
peak=   -3.611 closest distance to " CB  TYR A  15 " =    2.219
peak=   -3.608 closest distance to " CE2 PHE A  61 " =    2.536
peak=   -3.607 closest distance to " O   HOH Z 394 " =    1.503
peak=   -3.592 closest distance to " O   HOH Z 407 " =    2.976
peak=   -3.588 closest distance to " CD1 LEU A 228 " =    2.193
peak=   -3.588 closest distance to " O   HOH Z 185 " =    2.366
peak=   -3.583 closest distance to " O   HOH Z 243 " =    1.991
peak=   -3.582 closest distance to " CB  PHE A 192 " =    2.002
peak=   -3.577 closest distance to " ND2 ASN A 187 " =    1.548
peak=   -3.568 closest distance to " CD1 LEU A  25 " =    2.472
peak=   -3.559 closest distance to " N   ALA A 248 " =    1.678
peak=   -3.553 closest distance to " CA  GLY A 203 " =    2.431
peak=   -3.551 closest distance to " OD1 ASN A 148 " =    1.509
peak=   -3.528 closest distance to " O   HOH Z 165 " =    1.959
peak=   -3.500 closest distance to " CB  ASP A 286 " =    1.859
peak=   -3.495 closest distance to " NH2AARG A 275 " =    5.267
peak=   -3.491 closest distance to " OD1 ASP A 171 " =    1.594
peak=   -3.485 closest distance to " O   HOH Z 166 " =    1.611
peak=   -3.483 closest distance to " O   HOH Z 351 " =    1.504
peak=   -3.482 closest distance to " O   HOH Z  37 " =    1.861
peak=   -3.482 closest distance to " CA  GLY A 241 " =    3.178
peak=   -3.472 closest distance to " N   GLN A  58 " =    1.596
peak=   -3.470 closest distance to " NE2 GLN A 194 " =    1.779
peak=   -3.465 closest distance to " SG ACYS A 201 " =    2.033
peak=   -3.464 closest distance to " O   HOH Z 234 " =    4.139
peak=   -3.464 closest distance to " O   HOH Z 435 " =    2.723
peak=   -3.463 closest distance to " CD  ARG A 195 " =    5.189
peak=   -3.462 closest distance to " CE3 TRP A 150 " =    2.268
peak=   -3.461 closest distance to " O   HOH Z  43 " =    1.602
peak=   -3.460 closest distance to " O   HOH Z 252 " =    3.952
peak=   -3.444 closest distance to " CB  ALA A  43 " =    2.596
peak=   -3.439 closest distance to " ND2 ASN A 249 " =    2.427
peak=   -3.434 closest distance to " CD2 TYR A 247 " =    2.388
peak=   -3.433 closest distance to " CG  PHE A 283 " =    2.601
peak=   -3.429 closest distance to " CZ  TYR A 169 " =    1.813
peak=   -3.413 closest distance to " CB  ALA A 248 " =    2.143
peak=   -3.410 closest distance to " O   HOH Z 311 " =    3.691
peak=   -3.410 closest distance to " C   LEU A 143 " =    1.062
peak=   -3.409 closest distance to " OG  SER A  62 " =    1.770
peak=   -3.406 closest distance to " OG BSER A 134 " =    1.857
peak=   -3.403 closest distance to " CG  GLU A 277 " =    1.140
peak=   -3.402 closest distance to " O   HOH Z 198 " =    1.478
peak=   -3.397 closest distance to " O   HOH Z 290 " =    1.288
peak=   -3.391 closest distance to " CD  LYS A 289 " =    2.411
peak=   -3.386 closest distance to " CZ  PHE A  59 " =    1.693
peak=   -3.385 closest distance to " O   SER A 135 " =    1.476
peak=   -3.381 closest distance to " CB  TRP A  85 " =    2.569
peak=   -3.380 closest distance to " N   THR A  52 " =    1.708
peak=   -3.372 closest distance to " NH2 ARG A  79 " =    1.583
peak=   -3.367 closest distance to " N   ALA A 226 " =    2.063
peak=   -3.361 closest distance to " CG2 VAL A 189 " =    2.201
peak=   -3.361 closest distance to " O   HOH Z  44 " =    2.183
peak=   -3.359 closest distance to " O   HOH Z 322 " =    1.684
peak=   -3.358 closest distance to " CG1 VAL A 112 " =    2.604
peak=   -3.342 closest distance to " CB  PHE A  16 " =    2.593
peak=   -3.338 closest distance to " CD2 TYR A 293 " =    2.027
peak=   -3.332 closest distance to " CG  ARG A 269 " =    2.516
peak=   -3.329 closest distance to " O   VAL A 174 " =    2.122
peak=   -3.329 closest distance to " C   SER A 206 " =    1.539
peak=   -3.327 closest distance to " NH2 ARG A  79 " =    2.049
peak=   -3.323 closest distance to " O   MET A  40 " =    2.729
peak=   -3.320 closest distance to " O   HOH Z 171 " =    1.980
peak=   -3.319 closest distance to " O   HOH Z 393 " =    1.412
peak=   -3.317 closest distance to " CD2 LEU A 237 " =    2.717
peak=   -3.315 closest distance to " O   HOH Z 123 " =    2.370
peak=   -3.310 closest distance to " CD1 ILE A 151 " =    2.361
peak=   -3.306 closest distance to " O   HOH Z 313 " =    1.917
peak=   -3.304 closest distance to " CG  GLU A   2 " =    1.889
peak=   -3.303 closest distance to " O   HOH Z 111 " =    1.647
peak=   -3.303 closest distance to " O   ALA A 161 " =    1.697
peak=   -3.302 closest distance to " OD2 ASP A 171 " =    2.446
peak=   -3.293 closest distance to " OD1 ASP A 191 " =    1.740
peak=   -3.292 closest distance to " O   HOH Z  63 " =    1.555
peak=   -3.290 closest distance to " NE  ARG A  66 " =    4.086
peak=   -3.290 closest distance to " CD2 LEU A 300 " =    2.761
peak=   -3.289 closest distance to " O   HOH Z  38 " =    1.539
peak=   -3.287 closest distance to " CG  PRO A 243 " =    1.840
peak=   -3.286 closest distance to " O   HOH Z   6 " =    1.543
peak=   -3.283 closest distance to " CE2 PHE A 218 " =    2.439
peak=   -3.280 closest distance to " O   HOH Z 191 " =    5.878
peak=   -3.279 closest distance to " O   HOH Z 369 " =    2.332
peak=   -3.272 closest distance to " O   HOH Z 193 " =    1.777
peak=   -3.267 closest distance to " CA  GLY A 133 " =    2.327
peak=   -3.267 closest distance to " OD1 ASN A 187 " =    1.689
peak=   -3.267 closest distance to " OG BSER A 210 " =    2.093
peak=   -3.261 closest distance to " OD2 ASP A 191 " =    1.509
peak=   -3.254 closest distance to " O   ALA A  34 " =    2.293
peak=   -3.252 closest distance to " O   HOH Z 265 " =    2.306
peak=   -3.247 closest distance to " CG1 VAL A  78 " =    2.858
peak=   -3.246 closest distance to " CG  HIS A  86 " =    1.079
peak=   -3.241 closest distance to " CD2 PHE A 225 " =    1.201
peak=   -3.241 closest distance to " CG  GLU A  53 " =    1.538
peak=   -3.239 closest distance to " O   VAL A 189 " =    2.637
peak=   -3.239 closest distance to " O   HOH Z 357 " =    2.188
peak=   -3.238 closest distance to " CA  PRO A 243 " =    2.403
peak=   -3.232 closest distance to " O   HOH Z 177 " =    1.707
peak=   -3.227 closest distance to " O   HOH Z 139 " =    3.015
peak=   -3.227 closest distance to " OE1 GLN A 223 " =    2.054
peak=   -3.222 closest distance to " O   HOH Z 102 " =    1.548
peak=   -3.220 closest distance to " NH2 ARG A 159 " =    2.333
peak=   -3.220 closest distance to " O   HOH Z  71 " =    1.898
peak=   -3.219 closest distance to " O   HOH Z  93 " =    2.217
peak=   -3.218 closest distance to " CD  GLU A 236 " =    1.069
peak=   -3.218 closest distance to " CB  PRO A 163 " =    2.436
peak=   -3.216 closest distance to " O   HOH Z 275 " =    1.500
peak=   -3.210 closest distance to " NE2 GLN A 278 " =    1.775
peak=   -3.204 closest distance to " CZ  PHE A 155 " =    1.243
peak=   -3.201 closest distance to " O   HOH Z 200 " =    3.643
peak=   -3.200 closest distance to " O   ALA A  10 " =    1.723
peak=   -3.199 closest distance to " OG  SER A  97 " =    2.060
peak=   -3.197 closest distance to " N   MET A 105 " =    2.572
peak=   -3.194 closest distance to " OD2 ASP A 171 " =    1.780
peak=   -3.193 closest distance to " CZ3 TRP A 274 " =    2.430
peak=   -3.191 closest distance to " O   HOH Z 377 " =    1.809
peak=   -3.190 closest distance to " CG  ASN A 148 " =    2.421
peak=   -3.188 closest distance to " O   HOH Z 350 " =    2.070
peak=   -3.184 closest distance to " C   ALA A 158 " =    1.315
peak=   -3.183 closest distance to " O   LEU A 101 " =    2.086
peak=   -3.181 closest distance to " CB  GLN A  11 " =    1.886
peak=   -3.175 closest distance to " N   SER A 276 " =    1.382
peak=   -3.174 closest distance to " O   HOH Z 414 " =    1.543
peak=   -3.174 closest distance to " CA  ALA A 248 " =    2.638
peak=   -3.174 closest distance to " CZ2 TRP A 274 " =    1.004
peak=   -3.171 closest distance to " NE2 GLN A  58 " =    2.531
peak=   -3.169 closest distance to " O   PRO A 198 " =    1.333
peak=   -3.169 closest distance to " CG  ASP A 231 " =    0.842
peak=   -3.163 closest distance to " CG  TRP A 266 " =    1.905
peak=   -3.162 closest distance to " O   SER A  95 " =    1.603
peak=   -3.156 closest distance to " CG1AVAL A  41 " =    2.828
peak=   -3.153 closest distance to " O   SER A  62 " =    2.141
peak=   -3.151 closest distance to " O   HOH Z 244 " =    2.016
peak=   -3.149 closest distance to " OE1 GLN A 183 " =    1.475
peak=   -3.147 closest distance to " O   HOH Z 396 " =    1.750
peak=   -3.139 closest distance to " CD2 LEU A 143 " =    2.751
peak=   -3.139 closest distance to " CG2 ILE A  49 " =    2.810
peak=   -3.136 closest distance to " O   HOH Z 134 " =    2.917
peak=   -3.132 closest distance to " OH  TYR A 247 " =    1.887
peak=   -3.130 closest distance to " CE1 TYR A 247 " =    2.769
peak=   -3.129 closest distance to " O   HOH Z 357 " =    2.052
peak=   -3.126 closest distance to " O   HOH Z 128 " =    2.617
peak=   -3.116 closest distance to " O   HOH Z 216 " =    2.130
peak=   -3.114 closest distance to " O   HOH Z 421 " =    3.325
peak=   -3.113 closest distance to " O   PRO A 198 " =    1.882
peak=   -3.101 closest distance to " NH2BARG A 275 " =    2.263
peak=   -3.098 closest distance to " CG1 VAL A 125 " =    2.017
peak=   -3.094 closest distance to " C   MET A 188 " =    1.506
peak=   -3.089 closest distance to " O   ALA A 292 " =    1.998
peak=   -3.075 closest distance to " O   ASN A 301 " =    1.362
peak=   -3.073 closest distance to " OD1 ASN A 301 " =    2.003
peak=   -3.071 closest distance to " CG  PRO A 163 " =    2.589
peak=   -3.055 closest distance to " NH1 ARG A 195 " =    2.645
peak=   -3.043 closest distance to " O   HOH Z 283 " =    5.596
peak=   -3.026 closest distance to " O   HOH Z 353 " =    2.140
peak=   -3.013 closest distance to " O   HOH Z 263 " =    3.188
peak=   -3.007 closest distance to " CA  GLY A 241 " =    2.827

================= 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    :  0.2871 0.2777   5.947589e+00   5.912295e+00
   1_bss:  0.2721 0.2628   5.918180e+00   5.874665e+00
   1_xyz:  0.1558 0.1735   5.377802e+00   5.474017e+00
   1_adp:  0.1429 0.1755   5.323914e+00   5.495353e+00
   1_occ:  0.1425 0.1753   5.322751e+00   5.495109e+00
   2_bss:  0.1417 0.1734   5.318291e+00   5.487342e+00
   2_xyz:  0.1215 0.1551   5.187424e+00   5.380833e+00
   2_adp:  0.1172 0.1524   5.159009e+00   5.364085e+00
   2_occ:  0.1170 0.1524   5.158839e+00   5.364300e+00
   3_bss:  0.1168 0.1523   5.157526e+00   5.363489e+00
   3_xyz:  0.1087 0.1524   5.117379e+00   5.356925e+00
   3_adp:  0.1083 0.1516   5.112913e+00   5.353163e+00
   3_occ:  0.1083 0.1516   5.112992e+00   5.353542e+00
   4_bss:  0.1083 0.1512   5.112143e+00   5.351151e+00
   4_xyz:  0.1086 0.1533   5.120696e+00   5.365262e+00
   4_adp:  0.1077 0.1548   5.122276e+00   5.374975e+00
   4_occ:  0.1076 0.1549   5.122393e+00   5.375330e+00
   5_bss:  0.1075 0.1548   5.122314e+00   5.375282e+00
   5_xyz:  0.1063 0.1559   5.118714e+00   5.377307e+00
   5_adp:  0.1063 0.1566   5.119757e+00   5.380834e+00
   5_occ:  0.1063 0.1566   5.119848e+00   5.381128e+00
   5_bss:  0.1061 0.1565   5.119961e+00   5.381208e+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:  0.316  47.169  -3.139   0.711  -0.982   0.000  -0.000  -0.000
   1_xyz:  0.316  47.169  -3.139   0.711  -0.982   0.000  -0.000  -0.000
   1_adp:  0.316  47.169  -3.139   0.711  -0.982   0.000  -0.000  -0.000
   1_occ:  0.316  47.169  -3.139   0.711  -0.982   0.000  -0.000  -0.000
   2_bss:  0.327  57.531  -3.280  -1.353  -1.345  -0.000  -0.000  -0.000
   2_xyz:  0.327  57.531  -3.280  -1.353  -1.345  -0.000  -0.000  -0.000
   2_adp:  0.327  57.531  -3.280  -1.353  -1.345  -0.000  -0.000  -0.000
   2_occ:  0.327  57.531  -3.280  -1.353  -1.345  -0.000  -0.000  -0.000
   3_bss:  0.326  55.522  -2.861  -1.695  -1.095  -0.000  -0.000  -0.000
   3_xyz:  0.326  55.522  -2.861  -1.695  -1.095  -0.000  -0.000  -0.000
   3_adp:  0.326  55.522  -2.861  -1.695  -1.095  -0.000  -0.000  -0.000
   3_occ:  0.326  55.522  -2.861  -1.695  -1.095  -0.000  -0.000  -0.000
   4_bss:  0.326  55.522  -2.661  -1.764  -0.946  -0.000  -0.000  -0.000
   4_xyz:  0.326  55.522  -2.661  -1.764  -0.946  -0.000  -0.000  -0.000
   4_adp:  0.326  55.522  -2.661  -1.764  -0.946  -0.000  -0.000  -0.000
   4_occ:  0.326  55.522  -2.661  -1.764  -0.946  -0.000  -0.000  -0.000
   5_bss:  0.322  55.522  -2.372  -1.568  -0.717  -0.000  -0.000  -0.000
   5_xyz:  0.322  55.522  -2.372  -1.568  -0.717  -0.000  -0.000  -0.000
   5_adp:  0.322  55.522  -2.372  -1.568  -0.717  -0.000  -0.000  -0.000
   5_occ:  0.322  55.522  -2.372  -1.568  -0.717  -0.000  -0.000  -0.000
   5_bss:  0.321  55.525  -2.058  -1.294  -0.429  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  28.057 0.7828  0.9449    22157.133
   1_bss:  26.802 0.7944  0.9210    19051.517
   1_xyz:  15.910 0.8996  0.9982     7582.483
   1_adp:  16.434 0.8946  0.9919     7843.816
   1_occ:  16.436 0.8946  0.9915     7835.489
   2_bss:  16.246 0.8963  0.9646     7719.407
   2_xyz:  13.986 0.9151  0.9716     6186.291
   2_adp:  13.606 0.9182  0.9668     5992.046
   2_occ:  13.611 0.9181  0.9666     5994.373
   3_bss:  13.590 0.9183  0.9712     5987.975
   3_xyz:  13.403 0.9198  0.9736     5967.062
   3_adp:  13.287 0.9208  0.9690     5935.839
   3_occ:  13.294 0.9208  0.9690     5939.824
   4_bss:  13.257 0.9211  0.9721     5892.795
   4_xyz:  13.480 0.9194  0.9708     6056.766
   4_adp:  13.687 0.9178  0.9623     6136.760
   4_occ:  13.691 0.9178  0.9622     6139.847
   5_bss:  13.689 0.9178  0.9705     6137.915
   5_xyz:  13.724 0.9175  0.9708     6181.597
   5_adp:  13.796 0.9170  0.9625     6214.529
   5_occ:  13.798 0.9169  0.9624     6217.348
   5_bss:  13.800 0.9169  0.9726     6218.497
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6101e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6101e-01
   1_xyz:   1.065  0.008  0.070 15.060  0.004  4.119   6.4820e-02
   1_adp:   1.065  0.008  0.070 15.060  0.004  4.119   6.4820e-02
   1_occ:   1.065  0.008  0.070 15.060  0.004  4.119   6.4820e-02
   2_bss:   1.065  0.008  0.070 15.060  0.004  4.119   6.4820e-02
   2_xyz:   0.967  0.007  0.072 14.549  0.004  4.123   5.5394e-02
   2_adp:   0.967  0.007  0.072 14.549  0.004  4.123   5.5394e-02
   2_occ:   0.967  0.007  0.072 14.549  0.004  4.123   5.5394e-02
   3_bss:   0.967  0.007  0.072 14.549  0.004  4.123   5.5394e-02
   3_xyz:   1.094  0.010  0.084 14.915  0.005  4.128   7.2812e-02
   3_adp:   1.094  0.010  0.084 14.915  0.005  4.128   7.2812e-02
   3_occ:   1.094  0.010  0.084 14.915  0.005  4.128   7.2812e-02
   4_bss:   1.094  0.010  0.084 14.915  0.005  4.128   7.2812e-02
   4_xyz:   1.038  0.009  0.081 14.654  0.004  4.129   6.5116e-02
   4_adp:   1.038  0.009  0.081 14.654  0.004  4.129   6.5116e-02
   4_occ:   1.038  0.009  0.081 14.654  0.004  4.129   6.5116e-02
   5_bss:   1.038  0.009  0.081 14.654  0.004  4.129   6.5116e-02
   5_xyz:   1.070  0.009  0.083 14.720  0.004  4.130   6.8587e-02
   5_adp:   1.070  0.009  0.083 14.720  0.004  4.130   6.8587e-02
   5_occ:   1.070  0.009  0.083 14.720  0.004  4.130   6.8587e-02
   5_bss:   1.070  0.009  0.083 14.720  0.004  4.130   6.8587e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4191e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4191e-01
   1_xyz:   7.276  0.045  0.258 83.794  0.034  2.319   7.4181e-02
   1_adp:   7.276  0.045  0.258 83.794  0.034  2.319   7.4181e-02
   1_occ:   7.276  0.045  0.258 83.794  0.034  2.319   7.4181e-02
   2_bss:   7.276  0.045  0.258 83.794  0.034  2.319   7.4181e-02
   2_xyz:   6.835  0.038  0.222 82.396  0.042  2.392   4.1109e-02
   2_adp:   6.835  0.038  0.222 82.396  0.042  2.392   4.1109e-02
   2_occ:   6.835  0.038  0.222 82.396  0.042  2.392   4.1109e-02
   3_bss:   6.835  0.038  0.222 82.396  0.042  2.392   4.1109e-02
   3_xyz:   7.943  0.053  0.294 82.730  0.038  2.312   5.9726e-02
   3_adp:   7.943  0.053  0.294 82.730  0.038  2.312   5.9726e-02
   3_occ:   7.943  0.053  0.294 82.730  0.038  2.312   5.9726e-02
   4_bss:   7.943  0.053  0.294 82.730  0.038  2.312   5.9726e-02
   4_xyz:   7.622  0.052  0.265 82.454  0.041  2.342   4.9480e-02
   4_adp:   7.622  0.052  0.265 82.454  0.041  2.342   4.9480e-02
   4_occ:   7.622  0.052  0.265 82.454  0.041  2.342   4.9480e-02
   5_bss:   7.622  0.052  0.265 82.454  0.041  2.342   4.9480e-02
   5_xyz:   7.663  0.054  0.277 82.521  0.038  2.325   5.2177e-02
   5_adp:   7.663  0.054  0.277 82.521  0.038  2.325   5.2177e-02
   5_occ:   7.663  0.054  0.277 82.521  0.038  2.325   5.2177e-02
   5_bss:   7.663  0.054  0.277 82.521  0.038  2.325   5.2177e-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:  65.18   0.00  16.56  65.18   0.00  12.73  63.50   5.98  37.43
   1_occ:  65.18   0.00  16.56  65.18   0.00  12.73  63.50   5.98  37.43
   2_bss:  65.18   0.00  16.56  65.18   0.00  12.73  63.50   5.98  37.43
   2_xyz:  65.18   0.00  16.56  65.18   0.00  12.73  63.50   5.98  37.43
   2_adp:  76.17   1.71  16.69  76.17   1.71  12.77  69.02   5.99  38.03
   2_occ:  76.17   1.71  16.69  76.17   1.71  12.77  69.02   5.99  38.03
   3_bss:  76.17   1.71  16.69  76.17   1.71  12.77  69.02   5.99  38.03
   3_xyz:  76.17   1.71  16.69  76.17   1.71  12.77  69.02   5.99  38.03
   3_adp:  76.70   1.50  16.48  76.70   1.50  12.60  68.79   6.02  37.61
   3_occ:  76.70   1.50  16.48  76.70   1.50  12.60  68.79   6.02  37.61
   4_bss:  76.70   1.50  16.48  76.70   1.50  12.60  68.79   6.02  37.61
   4_xyz:  76.70   1.50  16.48  76.70   1.50  12.60  68.79   6.02  37.61
   4_adp:  86.29   0.00  16.75  86.29   0.00  12.58  74.94   5.75  39.49
   4_occ:  86.29   0.00  16.75  86.29   0.00  12.58  74.94   5.75  39.49
   5_bss:  86.29   0.00  16.75  86.29   0.00  12.58  74.94   5.75  39.49
   5_xyz:  86.29   0.00  16.75  86.29   0.00  12.58  74.94   5.75  39.49
   5_adp:  98.09   0.00  16.76  98.09   0.00  12.47  84.98   5.37  40.11
   5_occ:  98.09   0.00  16.76  98.09   0.00  12.47  84.98   5.37  40.11
   5_bss:  98.10   0.00  16.76  98.10   0.00  12.48  84.98   5.37  40.11
------------------------------------------------------------------------
 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:    0.835    0.028    0.279
   1_adp:    0.835    0.028    0.279
   1_occ:    0.835    0.028    0.279
   2_bss:    0.835    0.028    0.279
   2_xyz:    0.784    0.035    0.315
   2_adp:    0.784    0.035    0.315
   2_occ:    0.784    0.035    0.315
   3_bss:    0.784    0.035    0.315
   3_xyz:    0.849    0.025    0.341
   3_adp:    0.849    0.025    0.341
   3_occ:    0.849    0.025    0.341
   4_bss:    0.849    0.025    0.341
   4_xyz:    0.914    0.028    0.352
   4_adp:    0.914    0.028    0.352
   4_occ:    0.914    0.028    0.352
   5_bss:    0.914    0.028    0.352
   5_xyz:    0.974    0.013    0.356
   5_adp:    0.974    0.013    0.356
   5_occ:    0.974    0.013    0.356
   5_bss:    0.974    0.013    0.356
------------------------------------------------------------------------

CPU time actual refinement: 326.57


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_567/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_567/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_567/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_567/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_567/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 326.42 
  Macro-tasks:
    bulk solvent and scale       = 38.56  
    individual site refinement   = 136.67 
    weights calculation          = 29.57  
    collect and process          = 6.55   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 211.46 
  Micro-tasks:
    mask                            = 1.16   
    f_calc                          = 103.43 
    alpha_beta                      = 7.91   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 113.42 
    fmodel                         = 6.32   
    r_factors                      = 0.21   
    phase_errors                   = 10.96  
    foms                           = 0.19   
    TOTAL for micro-tasks          = 244.73 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.590 micro seconds
Total CPU time: 5.67 minutes
from_scatterers_fft:    651 calls, 103.02 s
gradients_fft:          596 calls,  99.36 s

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

# Date 2008-01-16 Time 05:07:47 PST -0800 (1200488867.89 s)
Start R-work = 0.2871, R-free = 0.2777 (no bulk solvent and anisotropic scale)
Final R-work = 0.1274, R-free = 0.1734 (no bulk solvent and anisotropic scale)

Start R-work = 0.2721, R-free = 0.2628
Final R-work = 0.1061, R-free = 0.1565