# Date 2008-01-16 Time 04:24:10 PST -0800 (1200486250.85 s)
#phil __OFF__

Command line arguments: "../298.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29824
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 298

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 46.93, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.76, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 46.93, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7486 1.96121
Completeness in resolution range: 0.963599
Completeness with d_max=infinity: 0.960575

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7486
                             d_min =   1.9612

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 46.93, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7486 1.96121
Completeness in resolution range: 0.963599
Completeness with d_max=infinity: 0.960575

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7490 -  4.1959 [2133/2161]  1921   212   9.9%
  bin  2:  4.1959 -  3.3432 [2042/2061]  1836   206  10.1%
  bin  3:  3.3432 -  2.9243 [2029/2049]  1828   201   9.9%
  bin  4:  2.9243 -  2.6586 [2006/2031]  1807   199   9.9%
  bin  5:  2.6586 -  2.4690 [1992/2011]  1789   203  10.2%
  bin  6:  2.4690 -  2.3241 [1977/2024]  1785   192   9.7%
  bin  7:  2.3241 -  2.2081 [1976/2008]  1774   202  10.2%
  bin  8:  2.2081 -  2.1122 [1957/1993]  1758   199  10.2%
  bin  9:  2.1122 -  2.0311 [1959/1988]  1766   193   9.9%
  bin 10:  2.0311 -  1.9612 [1518/2003]  1366   152  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_298/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.35 -     2.06: 16
        2.06 -     2.77: 513
        2.77 -     3.48: 4621
        3.48 -     4.19: 9535
        4.19 -     4.90: 14118
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.346 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.508 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.694 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.780 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28798 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_298/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_298/model_refine_001.geo

CPU time processing inputs: 7.77


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 46.93 84.6622 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: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3760   r_free= 0.3749   ksol= 0.00   Bsol= 0.00   scale= 0.961    |
|                                                                             |
| 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:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.150908                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7490 -  4.6796 0.99   1382  155 0.3121 0.3189      6.4275      6.4473|
|  2:  4.6796 -  3.7342 0.99   1338  146 0.3090 0.2847      6.5838      6.5542|
|  3:  3.7342 -  3.2680 0.99   1310  150 0.3229 0.3335      6.4642      6.6061|
|  4:  3.2680 -  2.9719 0.99   1304  140 0.3457 0.3785      6.3398      6.3828|
|  5:  2.9719 -  2.7604 0.99   1285  142 0.3815 0.3670      6.2259      6.1862|
|  6:  2.7604 -  2.5985 0.98   1286  143 0.4058 0.4180      6.1489         6.1|
|  7:  2.5985 -  2.4690 0.99   1276  145 0.4021 0.3515      6.1311      6.0345|
|  8:  2.4690 -  2.3620 0.98   1275  136 0.4069 0.3867      6.0832      6.1259|
|  9:  2.3620 -  2.2714 0.98   1285  146 0.4378 0.4326      6.0381      6.0645|
| 10:  2.2714 -  2.1933 0.97   1237  138 0.4121 0.4562      6.0078      6.0487|
| 11:  2.1933 -  2.1249 0.99   1275  145 0.4428 0.4569      5.9664      6.0296|
| 12:  2.1249 -  2.0643 0.98   1272  132 0.4241 0.3956      5.9039      5.9096|
| 13:  2.0643 -  2.0101 0.97   1241  144 0.4386 0.4596      5.8099      5.8204|
| 14:  2.0101 -  1.9612 0.68    864   97 0.4644 0.4344      5.7972      5.6603|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7490 -  4.6796  1382   155  0.75  30.06   0.86     0.77      54300.93|
|  2:  4.6796 -  3.7342  1338   146  0.79  27.27   0.96     0.89      67452.09|
|  3:  3.7342 -  3.2680  1310   150  0.73  32.60   0.99     0.92      69171.71|
|  4:  3.2680 -  2.9719  1304   140  0.68  36.93   1.00     0.89      60888.41|
|  5:  2.9719 -  2.7604  1285   142  0.63  41.16   0.96     0.86      49565.31|
|  6:  2.7604 -  2.5985  1286   143  0.62  42.65   0.96     0.84      42444.10|
|  7:  2.5985 -  2.4690  1276   145  0.63  41.52   0.97     0.85      39349.20|
|  8:  2.4690 -  2.3620  1275   136  0.60  44.12   0.99     0.82      37164.03|
|  9:  2.3620 -  2.2714  1285   146  0.56  47.53   1.01     0.79      35587.47|
| 10:  2.2714 -  2.1933  1237   138  0.56  47.66   1.03     0.76      33648.63|
| 11:  2.1933 -  2.1249  1275   145  0.54  49.04   1.02     0.78      31430.46|
| 12:  2.1249 -  2.0643  1272   132  0.56  47.45   1.05     0.82      28727.07|
| 13:  2.0643 -  2.0101  1241   144  0.54  48.88   1.01     0.80      25100.71|
| 14:  2.0101 -  1.9612   864    97  0.55  48.60   1.00     0.74      20509.74|
|alpha:            min =        0.74 max =            0.92 mean =         0.83|
|beta:             min =    20509.74 max =        69171.71 mean =     43336.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.63|
|phase err.(work): min =        0.00 max =           89.99 mean =        41.49|
|phase err.(test): min =        0.00 max =           89.34 mean =        41.37|
|-----------------------------------------------------------------------------|

============================== 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 = 5.696070              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.523   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.097998              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.856   (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 |  1.346 -  1.702:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.702 -  2.057:       13 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.057 -  2.412:       30 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.412 -  2.768:      483 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.768 -  3.123:     2264 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.123 -  3.479:     2357 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.479 -  3.834:     4512 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.834 -  4.189:     5023 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.189 -  4.545:     6387 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.545 -  4.900:     7731 |
|-----------------------------------------------------------------------------|
|-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 |        0.187 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.346 |       0.577 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.477)------------------------------------------|
|    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: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3760   r_free= 0.3749   ksol= 0.00   Bsol= 0.00   scale= 0.961    |
|                                                                             |
| 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:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.150908                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3626   r_free= 0.3605   ksol= 0.32   Bsol= 21.03   scale= 0.973   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.24,-2.91,2.46,-0.00,0.00,0.00); trace/3= -0.56                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.133839                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.825985              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.420   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.545865              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.804   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3626      final r-factor (work) = 0.2213          |
| start r-factor (free) = 0.3605      final r-factor (free) = 0.2393          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.9976 = 4.83 * 0.50 * 6.1378 + 1.00 * 0.1871                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.3117 = 4.83 * 0.50 * 5.8973 + 1.00 * 0.0817                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2213      final r-factor (work) = 0.2013          |
| start r-factor (free) = 0.2393      final r-factor (free) = 0.2487          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2253 = 0.55 * 1.00 * 5.8973 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0816 = 0.55 * 1.00 * 5.6258 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.477)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.03   17.83    None  None   None       |
|    all(noH): 2823   0      0.00    84.03   17.83    None  None   None       |
|    Sol.    : 438    0      7.47    74.34   40.06    None  None   None       |
|    Mac.    : 2385   0      0.00    84.03   13.75    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 -   8.403:  640   |   5:    42.015 -  50.418:  142        |
|      1:     8.403 -  16.806: 1231   |   6:    50.418 -  58.821:   72        |
|      2:    16.806 -  25.209:  390   |   7:    58.821 -  67.224:   36        |
|      3:    25.209 -  33.612:  168   |   8:    67.224 -  75.627:   19        |
|      4:    33.612 -  42.015:  124   |   9:    75.627 -  84.030:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2013 r_free = 0.2487             target_work(ml) = 5.640         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2010 r_free = 0.2486             target_work(ml) = 5.639         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2010   r_free= 0.2486   ksol= 0.32   Bsol= 21.03   scale= 1.042   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.24,-2.91,2.46,-0.00,0.00,0.00); trace/3= -0.56                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.639115                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1961   r_free= 0.2442   ksol= 0.32   Bsol= 30.83   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.71,-2.77,-0.75,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.623892                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.532525              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.402   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.227677              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.289  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1961      final r-factor (work) = 0.1395          |
| start r-factor (free) = 0.2442      final r-factor (free) = 0.1847          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0264 = 3.53 * 0.50 * 5.6304 + 1.00 * 0.0817                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7428 = 3.53 * 0.50 * 5.4820 + 1.00 * 0.0601                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1395      final r-factor (work) = 0.1281          |
| start r-factor (free) = 0.1847      final r-factor (free) = 0.1720          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2586 = 0.23 * 1.00 * 5.4820 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2108 = 0.23 * 1.00 * 5.2844 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.477)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.08   17.26    None  None   None       |
|    all(noH): 2823   0      0.00    86.08   17.26    None  None   None       |
|    Sol.    : 438    0      6.00    75.09   39.27    None  None   None       |
|    Mac.    : 2385   0      0.00    86.08   13.22    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 -   8.608:  615   |   5:    43.041 -  51.649:  128        |
|      1:     8.608 -  17.217: 1401   |   6:    51.649 -  60.258:   66        |
|      2:    17.217 -  25.825:  311   |   7:    60.258 -  68.866:   29        |
|      3:    25.825 -  34.433:  123   |   8:    68.866 -  77.474:    8        |
|      4:    34.433 -  43.041:  141   |   9:    77.474 -  86.082:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1281 r_free = 0.1720             target_work(ml) = 5.243         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1278 r_free = 0.1718             target_work(ml) = 5.241         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1278   r_free= 0.1718   ksol= 0.32   Bsol= 30.83   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.71,-2.77,-0.75,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.241057                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1279   r_free= 0.1699   ksol= 0.32   Bsol= 33.38   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,-2.44,-1.55,-0.00,-0.00,-0.00); trace/3= -2.30                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.235342                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.208644              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.592  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.589420              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.107  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1279      final r-factor (work) = 0.1114          |
| start r-factor (free) = 0.1699      final r-factor (free) = 0.1552          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5367 = 3.21 * 0.50 * 5.2837 + 1.00 * 0.0601                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3722 = 3.21 * 0.50 * 5.1768 + 1.00 * 0.0669                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1114      final r-factor (work) = 0.1083          |
| start r-factor (free) = 0.1552      final r-factor (free) = 0.1547          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0590 = 0.59 * 1.00 * 5.1768 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0254 = 0.59 * 1.00 * 5.1187 + 1.00 * 0.0084                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.477)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.79   17.28    None  None   None       |
|    all(noH): 2823   0      0.00    89.79   17.28    None  None   None       |
|    Sol.    : 438    0      3.63    80.64   39.92    None  None   None       |
|    Mac.    : 2385   0      0.00    89.79   13.12    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 -   8.979:  735   |   5:    44.895 -  53.874:  121        |
|      1:     8.979 -  17.958: 1345   |   6:    53.874 -  62.853:   63        |
|      2:    17.958 -  26.937:  270   |   7:    62.853 -  71.832:   22        |
|      3:    26.937 -  35.916:  126   |   8:    71.832 -  80.811:   10        |
|      4:    35.916 -  44.895:  128   |   9:    80.811 -  89.790:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1083 r_free = 0.1547             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1082 r_free = 0.1546             target_work(ml) = 5.115         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1082   r_free= 0.1546   ksol= 0.32   Bsol= 33.38   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,-2.44,-1.55,-0.00,-0.00,-0.00); trace/3= -2.30                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.115120                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1546   ksol= 0.32   Bsol= 34.38   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-2.29,-1.69,-0.00,-0.00,-0.00); trace/3= -2.29                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.114669                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.023756              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 147.099  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.326963              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.751  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1081      final r-factor (work) = 0.1075          |
| start r-factor (free) = 0.1546      final r-factor (free) = 0.1538          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2460 = 2.02 * 0.50 * 5.1183 + 1.00 * 0.0669                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2313 = 2.02 * 0.50 * 5.1141 + 1.00 * 0.0565                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1075      final r-factor (work) = 0.1072          |
| start r-factor (free) = 0.1538      final r-factor (free) = 0.1534          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6805 = 0.33 * 1.00 * 5.1141 + 1.00 * 0.0084                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6787 = 0.33 * 1.00 * 5.1097 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.477)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.49    90.16   17.04    None  None   None       |
|    all(noH): 2823   0      1.49    90.16   17.04    None  None   None       |
|    Sol.    : 438    0      5.24    79.58   39.20    None  None   None       |
|    Mac.    : 2385   0      1.49    90.16   12.97    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:     1.485 -  10.353: 1090   |   5:    45.824 -  54.692:  115        |
|      1:    10.353 -  19.221: 1071   |   6:    54.692 -  63.560:   51        |
|      2:    19.221 -  28.089:  216   |   7:    63.560 -  72.427:   16        |
|      3:    28.089 -  36.956:  130   |   8:    72.427 -  81.295:    8        |
|      4:    36.956 -  45.824:  122   |   9:    81.295 -  90.163:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1072 r_free = 0.1534             target_work(ml) = 5.108         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1072 r_free = 0.1534             target_work(ml) = 5.108         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1072   r_free= 0.1534   ksol= 0.32   Bsol= 34.38   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-2.29,-1.69,-0.00,-0.00,-0.00); trace/3= -2.29                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.108238                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1071   r_free= 0.1534   ksol= 0.32   Bsol= 36.08   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.78,-2.12,-1.62,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.108192                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.499685              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 163.457  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.512109              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.152  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1071      final r-factor (work) = 0.1045          |
| start r-factor (free) = 0.1534      final r-factor (free) = 0.1533          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4430 = 2.50 * 0.50 * 5.1099 + 1.00 * 0.0565                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4353 = 2.50 * 0.50 * 5.0977 + 1.00 * 0.0639                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1045      final r-factor (work) = 0.1042          |
| start r-factor (free) = 0.1533      final r-factor (free) = 0.1545          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.9119 = 3.51 * 1.00 * 5.0977 + 1.00 * 0.0082                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.8985 = 3.51 * 1.00 * 5.0936 + 1.00 * 0.0094                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.477)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.72    100.60  17.14    None  None   None       |
|    all(noH): 2823   0      0.72    100.60  17.14    None  None   None       |
|    Sol.    : 438    0      5.85    84.86   40.12    None  None   None       |
|    Mac.    : 2385   0      0.72    100.60  12.92    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:     0.722 -  10.710: 1221   |   5:    50.663 -  60.652:   82        |
|      1:    10.710 -  20.698: 1001   |   6:    60.652 -  70.640:   41        |
|      2:    20.698 -  30.687:  187   |   7:    70.640 -  80.628:    9        |
|      3:    30.687 -  40.675:  135   |   8:    80.628 -  90.616:    6        |
|      4:    40.675 -  50.663:  137   |   9:    90.616 - 100.605:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1042 r_free = 0.1545             target_work(ml) = 5.099         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1042 r_free = 0.1545             target_work(ml) = 5.099         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1042   r_free= 0.1545   ksol= 0.32   Bsol= 36.08   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.78,-2.12,-1.62,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.099405                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7490 -  4.6796 0.99   1382  155 0.0970 0.1233      5.3634      5.5303|
|  2:  4.6796 -  3.7342 0.99   1338  146 0.0802 0.1096      5.3861      5.5737|
|  3:  3.7342 -  3.2680 0.99   1310  150 0.0979 0.1485      5.4149      5.8424|
|  4:  3.2680 -  2.9719 0.99   1304  140 0.1125 0.1564      5.4026      5.5937|
|  5:  2.9719 -  2.7604 0.99   1285  142 0.1155 0.1597      5.2488      5.4573|
|  6:  2.7604 -  2.5985 0.98   1286  143 0.1142 0.1808      5.1621        5.39|
|  7:  2.5985 -  2.4690 0.99   1276  145 0.1129 0.1561       5.099      5.3147|
|  8:  2.4690 -  2.3620 0.98   1275  136 0.1066 0.1707      5.0338       5.336|
|  9:  2.3620 -  2.2714 0.98   1285  146 0.1111 0.1803      4.9883      5.3155|
| 10:  2.2714 -  2.1933 0.97   1237  138 0.1045 0.1725      4.9396      5.1692|
| 11:  2.1933 -  2.1249 0.99   1275  145 0.1070 0.1775      4.9052      5.2804|
| 12:  2.1249 -  2.0643 0.98   1272  132 0.1023 0.1656      4.8295        5.13|
| 13:  2.0643 -  2.0101 0.97   1241  144 0.1046 0.1659      4.7518      5.0089|
| 14:  2.0101 -  1.9612 0.68    864   97 0.1020 0.1678      4.6561       4.897|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7490 -  4.6796  1382   155  0.94   8.82   0.99     0.96       6782.84|
|  2:  4.6796 -  3.7342  1338   146  0.96   7.58   1.03     1.02       8433.31|
|  3:  3.7342 -  3.2680  1310   150  0.94  10.66   1.04     1.03       9473.97|
|  4:  3.2680 -  2.9719  1304   140  0.93  12.81   1.02     1.01       9590.32|
|  5:  2.9719 -  2.7604  1285   142  0.91  14.62   1.00     0.98       7443.15|
|  6:  2.7604 -  2.5985  1286   143  0.91  15.36   0.99     0.95       6526.93|
|  7:  2.5985 -  2.4690  1276   145  0.91  14.84   0.99     0.96       5628.14|
|  8:  2.4690 -  2.3620  1275   136  0.92  14.40   1.00     0.98       5192.91|
|  9:  2.3620 -  2.2714  1285   146  0.91  15.12   1.01     0.97       4685.97|
| 10:  2.2714 -  2.1933  1237   138  0.91  15.20   1.00     0.97       4369.61|
| 11:  2.1933 -  2.1249  1275   145  0.90  16.05   1.00     0.97       4230.49|
| 12:  2.1249 -  2.0643  1272   132  0.92  14.40   1.01     0.99       3665.61|
| 13:  2.0643 -  2.0101  1241   144  0.91  15.33   1.01     1.00       3183.50|
| 14:  2.0101 -  1.9612   864    97  0.91  14.75   0.99     0.96       2546.54|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2546.54 max =         9590.32 mean =      5954.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.78 mean =        13.48|
|phase err.(test): min =        0.00 max =           88.88 mean =        13.13|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1043   r_free= 0.1539   ksol= 0.32   Bsol= 39.12   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-1.94,-1.47,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.099374                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.75 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1043   r_free= 0.1539   ksol= 0.32   Bsol= 39.12   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-1.94,-1.47,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.099374                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7490 -  4.6796 0.99   1382  155 0.0960 0.1215      5.3515      5.4946|
|  2:  4.6796 -  3.7342 0.99   1338  146 0.0813 0.1094      5.3889      5.5789|
|  3:  3.7342 -  3.2680 0.99   1310  150 0.0985 0.1489      5.4221      5.8405|
|  4:  3.2680 -  2.9719 0.99   1304  140 0.1127 0.1562      5.4047      5.5937|
|  5:  2.9719 -  2.7604 0.99   1285  142 0.1160 0.1603      5.2527      5.4614|
|  6:  2.7604 -  2.5985 0.98   1286  143 0.1141 0.1799      5.1633      5.3884|
|  7:  2.5985 -  2.4690 0.99   1276  145 0.1131 0.1568      5.0996      5.3159|
|  8:  2.4690 -  2.3620 0.98   1275  136 0.1067 0.1710      5.0329      5.3339|
|  9:  2.3620 -  2.2714 0.98   1285  146 0.1108 0.1807      4.9865      5.3172|
| 10:  2.2714 -  2.1933 0.97   1237  138 0.1039 0.1720       4.939      5.1663|
| 11:  2.1933 -  2.1249 0.99   1275  145 0.1065 0.1778      4.9051      5.2828|
| 12:  2.1249 -  2.0643 0.98   1272  132 0.1021 0.1656      4.8288      5.1325|
| 13:  2.0643 -  2.0101 0.97   1241  144 0.1044 0.1662      4.7511      5.0079|
| 14:  2.0101 -  1.9612 0.68    864   97 0.1021 0.1667      4.6552      4.8945|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7490 -  4.6796  1382   155  0.94   8.38   0.99     0.96       6350.34|
|  2:  4.6796 -  3.7342  1338   146  0.96   7.45   1.03     1.02       8255.66|
|  3:  3.7342 -  3.2680  1310   150  0.94  10.73   1.04     1.04       9579.63|
|  4:  3.2680 -  2.9719  1304   140  0.93  12.84   1.02     1.01       9595.02|
|  5:  2.9719 -  2.7604  1285   142  0.91  14.71   1.01     0.98       7493.11|
|  6:  2.7604 -  2.5985  1286   143  0.90  15.44   0.99     0.96       6565.52|
|  7:  2.5985 -  2.4690  1276   145  0.91  14.83   1.00     0.97       5629.22|
|  8:  2.4690 -  2.3620  1275   136  0.92  14.38   1.01     0.99       5176.64|
|  9:  2.3620 -  2.2714  1285   146  0.91  15.11   1.01     0.98       4670.48|
| 10:  2.2714 -  2.1933  1237   138  0.91  15.22   1.01     0.98       4375.85|
| 11:  2.1933 -  2.1249  1275   145  0.90  16.07   1.01     0.98       4234.05|
| 12:  2.1249 -  2.0643  1272   132  0.92  14.40   1.02     1.00       3665.59|
| 13:  2.0643 -  2.0101  1241   144  0.91  15.31   1.02     1.01       3179.97|
| 14:  2.0101 -  1.9612   864    97  0.91  14.70   1.00     0.96       2538.04|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2538.04 max =         9595.02 mean =      5919.07|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.45|
|phase err.(test): min =        0.00 max =           89.87 mean =        13.12|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.477)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.70    100.58  17.11    None  None   None       |
|    all(noH): 2823   0      0.70    100.58  17.11    None  None   None       |
|    Sol.    : 438    0      5.83    84.83   40.09    None  None   None       |
|    Mac.    : 2385   0      0.70    100.58  12.89    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.698 -  10.686: 1221   |   5:    50.639 -  60.628:   82        |
|      1:    10.686 -  20.674: 1001   |   6:    60.628 -  70.616:   41        |
|      2:    20.674 -  30.663:  187   |   7:    70.616 -  80.604:    9        |
|      3:    30.663 -  40.651:  135   |   8:    80.604 -  90.592:    6        |
|      4:    40.651 -  50.639:  137   |   9:    90.592 - 100.581:    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)= 291         
Filter by distance & map next to the model:
   mapped sites are within: 0.394 - 4.511
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 288 from: 291
   mapped sites are within: 0.762 - 4.511

peak=    5.877 closest distance to " NH2 ARG A  56 " =    2.199
peak=    5.710 closest distance to " O   HOH Z 142 " =    1.749
peak=    5.653 closest distance to " O   HOH Z 126 " =    1.854
peak=    5.344 closest distance to " CB  ARG A 275 " =    0.939
peak=    5.174 closest distance to " CG  PRO A  54 " =    1.149
peak=    5.140 closest distance to " NE2 GLN A  11 " =    1.052
peak=    5.001 closest distance to " O   HOH Z 272 " =    1.875
peak=    4.961 closest distance to " O   HOH Z 209 " =    2.253
peak=    4.865 closest distance to " O   HOH Z 193 " =    1.665
peak=    4.843 closest distance to " CB  GLN A 223 " =    1.501
peak=    4.813 closest distance to " O   HOH Z 124 " =    1.336
peak=    4.801 closest distance to " O   HOH Z  78 " =    1.717
peak=    4.792 closest distance to " CG  PRO A 213 " =    1.224
peak=    4.788 closest distance to " CB  GLN A 183 " =    1.289
peak=    4.773 closest distance to " CB  SER A  63 " =    1.136
peak=    4.737 closest distance to " O   HOH Z 232 " =    2.398
peak=    4.708 closest distance to " C   PRO A 198 " =    1.499
peak=    4.696 closest distance to " O   HOH Z 427 " =    2.757
peak=    4.681 closest distance to " O   HOH Z 368 " =    2.028
peak=    4.624 closest distance to " O   HOH Z 298 " =    1.758
peak=    4.507 closest distance to " O   HOH Z  15 " =    2.225
peak=    4.495 closest distance to " O   HOH Z 203 " =    1.744
peak=    4.493 closest distance to " CB  GLU A 152 " =    1.222
peak=    4.457 closest distance to " O   HOH Z 183 " =    1.559
peak=    4.444 closest distance to " CA  TYR A  30 " =    0.942
peak=    4.425 closest distance to " CB  ARG A  79 " =    1.408
peak=    4.419 closest distance to " O   HOH Z  54 " =    1.728
peak=    4.394 closest distance to " O   HOH Z 403 " =    1.750
peak=    4.375 closest distance to " OD1 ASN A  69 " =    2.554
peak=    4.345 closest distance to " CB  ASN A 148 " =    1.769
peak=    4.331 closest distance to " O   HOH Z 402 " =    1.432
peak=    4.307 closest distance to " O   HOH Z 234 " =    3.602
peak=    4.303 closest distance to " CB  SER A   3 " =    1.288
peak=    4.289 closest distance to " O   HOH Z  44 " =    1.953
peak=    4.281 closest distance to " ND2 ASN A 187 " =    1.362
peak=    4.269 closest distance to " O   HOH Z  59 " =    2.005
peak=    4.242 closest distance to " O   HOH Z 189 " =    1.618
peak=    4.240 closest distance to " O   HOH Z  40 " =    1.669
peak=    4.228 closest distance to " O   HOH Z 316 " =    2.964
peak=    4.212 closest distance to " O   HOH Z 344 " =    2.978
peak=    4.189 closest distance to " O   SER A  87 " =    2.223
peak=    4.189 closest distance to " CG  ARG A  66 " =    2.736
peak=    4.178 closest distance to " NZ  LYS A 117 " =    3.128
peak=    4.172 closest distance to " O   HOH Z 303 " =    1.969
peak=    4.170 closest distance to " O   HOH Z  78 " =    2.091
peak=    4.141 closest distance to " OE1 GLU A   2 " =    2.265
peak=    4.141 closest distance to " O   HOH Z 236 " =    2.071
peak=    4.132 closest distance to " CB  TYR A 169 " =    0.838
peak=    4.114 closest distance to " O   HOH Z  97 " =    1.864
peak=    4.113 closest distance to " CG1 ILE A  33 " =    1.231
peak=    4.108 closest distance to " O   HOH Z  93 " =    2.465
peak=    4.105 closest distance to " O   HOH Z 346 " =    1.668
peak=    4.099 closest distance to " O   HOH Z  43 " =    1.902
peak=    4.089 closest distance to " OD2 ASP A 286 " =    2.725
peak=    4.021 closest distance to " O   HOH Z 144 " =    2.200
peak=    4.000 closest distance to " CB  PRO A  54 " =    0.915
peak=    4.000 closest distance to " OG BSER A 164 " =    2.223
peak=    3.978 closest distance to " O   HOH Z 407 " =    2.574
peak=    3.973 closest distance to " CB  VAL A 265 " =    1.358
peak=    3.942 closest distance to " O   HOH Z 392 " =    2.764
peak=    3.939 closest distance to " CA  ALA A  21 " =    1.134
peak=    3.923 closest distance to " CB  GLU A 128 " =    1.078
peak=    3.918 closest distance to " O   HOH Z  61 " =    1.522
peak=    3.912 closest distance to " O   HOH Z 173 " =    1.965
peak=    3.889 closest distance to " O   HOH Z 213 " =    1.726
peak=    3.881 closest distance to " CB  SER A  26 " =    1.566
peak=    3.866 closest distance to " O   HOH Z 134 " =    1.211
peak=    3.865 closest distance to " NH2BARG A 145 " =    2.011
peak=    3.863 closest distance to " CB  ARG A 190 " =    1.715
peak=    3.862 closest distance to " CG  PRO A  90 " =    1.092
peak=    3.858 closest distance to " O   MET A 105 " =    1.789
peak=    3.852 closest distance to " CD2 TRP A 179 " =    1.410
peak=    3.838 closest distance to " O   HOH Z 369 " =    2.100
peak=    3.834 closest distance to " O   HOH Z 214 " =    2.108
peak=    3.827 closest distance to " O   HOH Z  66 " =    1.939
peak=    3.825 closest distance to " O   HOH Z 128 " =    2.118
peak=    3.815 closest distance to " O   HOH Z 426 " =    1.532
peak=    3.787 closest distance to " O   HOH Z 366 " =    2.921
peak=    3.785 closest distance to " O   HOH Z 128 " =    1.971
peak=    3.782 closest distance to " CB  LEU A 228 " =    1.140
peak=    3.775 closest distance to " CB  GLU A 277 " =    3.472
peak=    3.766 closest distance to " O   HOH Z 389 " =    1.794
peak=    3.763 closest distance to " O   HOH Z 261 " =    1.594
peak=    3.744 closest distance to " O   HOH Z  61 " =    1.638
peak=    3.732 closest distance to " O   HOH Z 411 " =    3.722
peak=    3.723 closest distance to " CB  ARG A 139 " =    0.962
peak=    3.712 closest distance to " NH1BARG A 145 " =    1.236
peak=    3.709 closest distance to " O   HOH Z 132 " =    2.350
peak=    3.701 closest distance to " N   ASN A  39 " =    1.246
peak=    3.700 closest distance to " O   HOH Z 371 " =    3.313
peak=    3.700 closest distance to " O   HOH Z  50 " =    1.323
peak=    3.677 closest distance to " CG  PRO A 243 " =    1.174
peak=    3.664 closest distance to " CA  ASN A 215 " =    1.174
peak=    3.656 closest distance to " O   HOH Z  40 " =    2.655
peak=    3.648 closest distance to " O   HOH Z 207 " =    1.777
peak=    3.647 closest distance to " C   ALA A   1 " =    1.616
peak=    3.646 closest distance to " O   HOH Z 250 " =    1.584
peak=    3.640 closest distance to " CD BLYS A 290 " =    1.240
peak=    3.637 closest distance to " CB  TRP A 179 " =    1.246
peak=    3.633 closest distance to " CA  ASN A 176 " =    1.130
peak=    3.633 closest distance to " CA  MET A  40 " =    1.037
peak=    3.623 closest distance to " O   HOH Z 172 " =    3.712
peak=    3.621 closest distance to " O   HOH Z 299 " =    4.298
peak=    3.617 closest distance to " O   HOH Z 423 " =    1.984
peak=    3.615 closest distance to " CE1 TYR A 186 " =    1.253
peak=    3.615 closest distance to " O   HOH Z 227 " =    1.524
peak=    3.615 closest distance to " CG1BVAL A  72 " =    1.498
peak=    3.611 closest distance to " CD2 LEU A 297 " =    0.945
peak=    3.609 closest distance to " O   HOH Z  21 " =    1.758
peak=    3.608 closest distance to " CG  MET A 185 " =    1.163
peak=    3.601 closest distance to " O   HOH Z  10 " =    1.816
peak=    3.598 closest distance to " O   HOH Z 425 " =    2.098
peak=    3.598 closest distance to " CG2 ILE A  20 " =    1.443
peak=    3.598 closest distance to " CG2 ILE A 120 " =    1.171
peak=    3.595 closest distance to " O   HOH Z 327 " =    1.683
peak=    3.595 closest distance to " O   HOH Z 284 " =    2.837
peak=    3.586 closest distance to " O   HOH Z 180 " =    2.259
peak=    3.585 closest distance to " O   HOH Z 326 " =    1.468
peak=    3.581 closest distance to " O   HOH Z 279 " =    2.109
peak=    3.561 closest distance to " O   HOH Z   1 " =    1.908
peak=    3.561 closest distance to " O   HOH Z  88 " =    2.865
peak=    3.550 closest distance to " NZ  LYS A 119 " =    1.349
peak=    3.548 closest distance to " O   HOH Z 345 " =    3.073
peak=    3.547 closest distance to " O   HOH Z 108 " =    2.184
peak=    3.546 closest distance to " CG  PRO A 198 " =    1.151
peak=    3.545 closest distance to " O   HOH Z 250 " =    1.319
peak=    3.541 closest distance to " CB  THR A  31 " =    1.770
peak=    3.534 closest distance to " O   HOH Z 163 " =    1.873
peak=    3.531 closest distance to " O   HOH Z 261 " =    1.706
peak=    3.528 closest distance to " CG  GLN A  77 " =    2.014
peak=    3.524 closest distance to " CB  VAL A 202 " =    1.600
peak=    3.520 closest distance to " O   HOH Z 368 " =    3.707
peak=    3.519 closest distance to " CB  TRP A 266 " =    1.034
peak=    3.518 closest distance to " O   HOH Z 245 " =    1.299
peak=    3.517 closest distance to " O   HOH Z 273 " =    2.646
peak=    3.515 closest distance to " O   HOH Z 417 " =    3.105
peak=    3.500 closest distance to " O   HOH Z  66 " =    2.059
peak=    3.498 closest distance to " O   HOH Z 406 " =    1.623
peak=    3.491 closest distance to " O   HOH Z 353 " =    2.664
peak=    3.487 closest distance to " OG  SER A  62 " =    2.839
peak=    3.481 closest distance to " O   HOH Z 337 " =    3.501
peak=    3.478 closest distance to " O   HOH Z  30 " =    2.161
peak=    3.478 closest distance to " O   HOH Z 411 " =    1.692
peak=    3.472 closest distance to " CG2BVAL A  41 " =    0.799
peak=    3.461 closest distance to " O   HOH Z 291 " =    1.424
peak=    3.457 closest distance to " CE  LYS A  76 " =    0.896
peak=    3.450 closest distance to " O   HOH Z 286 " =    2.212
peak=    3.448 closest distance to " CB  GLN A  88 " =    1.189
peak=    3.437 closest distance to " O   HOH Z  89 " =    2.155
peak=    3.435 closest distance to " O   HOH Z 185 " =    1.635
peak=    3.418 closest distance to " O   HOH Z  48 " =    1.503
peak=    3.399 closest distance to " O   HOH Z 108 " =    1.040
peak=    3.396 closest distance to " O   HOH Z 211 " =    2.664
peak=    3.396 closest distance to " CA  ASP A 140 " =    1.090
peak=    3.395 closest distance to " O   HOH Z 158 " =    2.926
peak=    3.393 closest distance to " O   HOH Z 147 " =    1.711
peak=    3.393 closest distance to " O   HOH Z 263 " =    2.311
peak=    3.387 closest distance to " O   HOH Z  64 " =    2.169
peak=    3.384 closest distance to " CZ2 TRP A 179 " =    1.649
peak=    3.383 closest distance to " O   HOH Z 427 " =    3.066
peak=    3.378 closest distance to " CA  PHE A 283 " =    1.390
peak=    3.373 closest distance to " CA  LYS A 117 " =    1.244
peak=    3.372 closest distance to " CG2 VAL A 257 " =    0.817
peak=    3.370 closest distance to " CA  THR A 221 " =    0.952
peak=    3.364 closest distance to " O   HOH Z 313 " =    1.648
peak=    3.364 closest distance to " CG  LYS A  76 " =    1.037
peak=    3.364 closest distance to " O   HOH Z 227 " =    1.715
peak=    3.362 closest distance to " O   HOH Z 409 " =    3.036
peak=    3.362 closest distance to " O   HOH Z   3 " =    1.664
peak=    3.360 closest distance to " CB  ILE A 120 " =    1.317
peak=    3.359 closest distance to " OG1 THR A 294 " =    2.385
peak=    3.358 closest distance to " O   HOH Z  19 " =    2.244
peak=    3.357 closest distance to " O   HOH Z 417 " =    2.029
peak=    3.356 closest distance to " O   HOH Z 125 " =    2.379
peak=    3.355 closest distance to " O   HOH Z  49 " =    2.038
peak=    3.352 closest distance to " CA  ARG A  36 " =    1.064
peak=    3.351 closest distance to " NH1AARG A 145 " =    1.188
peak=    3.344 closest distance to " OG BSER A 258 " =    3.517
peak=    3.344 closest distance to " O   HOH Z 374 " =    2.480
peak=    3.342 closest distance to " O   HOH Z 425 " =    1.195
peak=    3.340 closest distance to " CA  ASP A 162 " =    1.097
peak=    3.338 closest distance to " CA  ALA A  84 " =    1.370
peak=    3.335 closest distance to " CB  ASN A  39 " =    0.858
peak=    3.334 closest distance to " NH2 ARG A 219 " =    1.929
peak=    3.332 closest distance to " O  BHOH Z 338 " =    2.373
peak=    3.332 closest distance to " CB  SER A 141 " =    1.060
peak=    3.332 closest distance to " O   HOH Z 435 " =    1.856
peak=    3.328 closest distance to " O   HOH Z 342 " =    0.777
peak=    3.327 closest distance to " CB  ALA A  34 " =    1.041
peak=    3.317 closest distance to " O   HOH Z 367 " =    3.346
peak=    3.315 closest distance to " O   HOH Z 286 " =    2.423
peak=    3.313 closest distance to " O   HOH Z 248 " =    1.662
peak=    3.313 closest distance to " CB  ALA A 291 " =    1.341
peak=    3.312 closest distance to " CD  LYS A 119 " =    1.237
peak=    3.308 closest distance to " CG2 THR A 221 " =    1.110
peak=    3.307 closest distance to " CA  THR A 264 " =    0.853
peak=    3.306 closest distance to " CG AARG A 275 " =    1.022
peak=    3.303 closest distance to " O   HOH Z 336 " =    1.713
peak=    3.301 closest distance to " O   HOH Z 193 " =    2.061
peak=    3.300 closest distance to " O   HOH Z 290 " =    0.921
peak=    3.299 closest distance to " O   HOH Z 106 " =    2.373
peak=    3.294 closest distance to " N   TYR A 116 " =    1.577
peak=    3.287 closest distance to " CA  ALA A 291 " =    0.883
peak=    3.286 closest distance to " C   TYR A 214 " =    1.457
peak=    3.283 closest distance to " CB  SER A  62 " =    0.854
peak=    3.272 closest distance to " CA  ASN A 217 " =    1.225
peak=    3.262 closest distance to " O   HOH Z 148 " =    3.117
peak=    3.261 closest distance to " O   HOH Z  44 " =    3.421
peak=    3.260 closest distance to " O   HOH Z 422 " =    2.674
peak=    3.258 closest distance to " CE AMET A  47 " =    1.392
peak=    3.258 closest distance to " O   HOH Z 421 " =    1.580
peak=    3.258 closest distance to " O   HOH Z 135 " =    1.628
peak=    3.257 closest distance to " O   HOH Z 357 " =    1.811
peak=    3.255 closest distance to " O   HOH Z 258 " =    2.252
peak=    3.250 closest distance to " CD2 HIS A  81 " =    1.097
peak=    3.248 closest distance to " CA  SER A 146 " =    1.793
peak=    3.248 closest distance to " CE  LYS A 119 " =    1.155
peak=    3.248 closest distance to " CB  ALA A 248 " =    1.371
peak=    3.247 closest distance to " N   ARG A 156 " =    1.265
peak=    3.246 closest distance to " CA  ALA A 160 " =    0.762
peak=    3.245 closest distance to " O   HOH Z 163 " =    1.622
peak=    3.244 closest distance to " CG  LEU A 167 " =    1.188
peak=    3.243 closest distance to " CB  ASN A 285 " =    0.964
peak=    3.243 closest distance to " O   HOH Z  85 " =    2.148
peak=    3.241 closest distance to " O   HOH Z 132 " =    2.432
peak=    3.234 closest distance to " O   HOH Z 392 " =    1.836
peak=    3.232 closest distance to " CB  ALA A   9 " =    1.576
peak=    3.230 closest distance to " O   HOH Z 281 " =    4.511
peak=    3.227 closest distance to " O   HOH Z 266 " =    2.037
peak=    3.223 closest distance to " O   HOH Z 214 " =    2.385
peak=    3.222 closest distance to " O   HOH Z 368 " =    2.561
peak=    3.222 closest distance to " O   HOH Z 189 " =    2.154
peak=    3.220 closest distance to " O   HOH Z  68 " =    1.525
peak=    3.219 closest distance to " O   HOH Z 189 " =    2.718
peak=    3.215 closest distance to " N   PHE A 130 " =    1.407
peak=    3.213 closest distance to " OE2 GLU A  53 " =    2.060
peak=    3.212 closest distance to " CG  MET A 185 " =    0.994
peak=    3.209 closest distance to " CB  ASN A 215 " =    1.126
peak=    3.207 closest distance to " OD1 ASP A 231 " =    1.913
peak=    3.207 closest distance to " CD1AILE A 234 " =    0.998
peak=    3.205 closest distance to " CA  ALA A  51 " =    0.901
peak=    3.202 closest distance to " CG  ARG A  66 " =    0.933
peak=    3.200 closest distance to " O   HOH Z 194 " =    1.732
peak=    3.199 closest distance to " O   ALA A 165 " =    1.384
peak=    3.199 closest distance to " CG2 VAL A  67 " =    1.076
peak=    3.195 closest distance to " N   ASP A 162 " =    1.228
peak=    3.195 closest distance to " CD2 LEU A 255 " =    1.252
peak=    3.189 closest distance to " O   HOH Z 192 " =    1.777
peak=    3.184 closest distance to " O   HOH Z  71 " =    1.051
peak=    3.178 closest distance to " CB  GLN A 278 " =    0.843
peak=    3.171 closest distance to " CB  ASP A 140 " =    0.964
peak=    3.170 closest distance to " O   HOH Z 329 " =    3.649
peak=    3.158 closest distance to " O   HOH Z 341 " =    1.900
peak=    3.157 closest distance to " CB  ASN A 110 " =    1.121
peak=    3.155 closest distance to " O   HOH Z 189 " =    1.273
peak=    3.149 closest distance to " OE1 GLN A  11 " =    1.909
peak=    3.147 closest distance to " CB  MET A  47 " =    1.063
peak=    3.146 closest distance to " CD  LYS A 166 " =    1.267
peak=    3.143 closest distance to " O   HOH Z 175 " =    2.090
peak=    3.130 closest distance to " O   HOH Z 359 " =    1.373
peak=    3.130 closest distance to " CA  ALA A 158 " =    1.281
peak=    3.123 closest distance to " ND1 HIS A  81 " =    1.498
peak=    3.123 closest distance to " CB  LEU A 255 " =    0.773
peak=    3.122 closest distance to " CG  GLU A 277 " =    2.061
peak=    3.118 closest distance to " CE  LYS A  48 " =    1.380
peak=    3.112 closest distance to " CD1 LEU A 300 " =    1.310
peak=    3.103 closest distance to " N   HIS A  86 " =    1.783
peak=    3.101 closest distance to " O   HOH Z 271 " =    2.226
peak=    3.099 closest distance to " CA  GLY A  80 " =    0.820
peak=    3.094 closest distance to " CB  THR A 279 " =    1.611
peak=    3.093 closest distance to " CD1 ILE A 106 " =    0.840
peak=    3.086 closest distance to " O   HOH Z 255 " =    1.601
peak=    3.086 closest distance to " O   HOH Z  59 " =    2.402
peak=    3.078 closest distance to " O   HOH Z  88 " =    2.363
peak=    3.076 closest distance to " O   HOH Z 236 " =    1.452
peak=    3.076 closest distance to " O   HOH Z 250 " =    1.857
peak=    3.074 closest distance to " O   HOH Z  47 " =    1.412
peak=    3.072 closest distance to " CB  TYR A 116 " =    0.801
peak=    3.067 closest distance to " CA  ILE A  33 " =    1.345
peak=    3.064 closest distance to " CB  SER A  62 " =    1.276
peak=    3.064 closest distance to " O   HOH Z 371 " =    1.558
peak=    3.063 closest distance to " O   GLY A  91 " =    1.522
peak=    3.058 closest distance to " CD2 TYR A 186 " =    1.017
peak=    3.057 closest distance to " O   HOH Z 291 " =    1.775
peak=    3.056 closest distance to " OG ASER A 134 " =    1.468
peak=    3.032 closest distance to " O   HOH Z 403 " =    1.185
peak=    3.012 closest distance to " O   HOH Z  88 " =    2.021
peak=    3.003 closest distance to " CB  VAL A 126 " =    1.160

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.812 - 5.916
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 200 from: 200
   mapped sites are within: 0.812 - 5.916

peak=   -4.916 closest distance to " O   HOH Z 266 " =    4.427
peak=   -4.627 closest distance to " C   HIS A 108 " =    1.087
peak=   -4.403 closest distance to " CD  ARG A 156 " =    2.044
peak=   -4.390 closest distance to " O   VAL A  67 " =    2.759
peak=   -4.367 closest distance to " OXT GLY A 302 " =    2.707
peak=   -4.339 closest distance to " SG  CYS A 254 " =    3.270
peak=   -4.143 closest distance to " OG BSER A 134 " =    1.221
peak=   -4.140 closest distance to " N   ALA A 248 " =    1.630
peak=   -4.140 closest distance to " CG  GLN A 223 " =    2.159
peak=   -4.123 closest distance to " O   HOH Z  13 " =    1.545
peak=   -4.115 closest distance to " O   VAL A  67 " =    2.717
peak=   -4.107 closest distance to " CB  PRO A 243 " =    2.585
peak=   -4.042 closest distance to " CB  ALA A 161 " =    2.496
peak=   -4.036 closest distance to " O   HOH Z 377 " =    2.115
peak=   -4.030 closest distance to " O   PRO A 198 " =    1.305
peak=   -4.026 closest distance to " O   HOH Z 126 " =    1.803
peak=   -4.019 closest distance to " O   HOH Z 198 " =    1.983
peak=   -4.012 closest distance to " N   GLN A  58 " =    1.577
peak=   -3.977 closest distance to " O   HOH Z 372 " =    2.194
peak=   -3.967 closest distance to " CG1 VAL A 112 " =    2.714
peak=   -3.966 closest distance to " O   HOH Z 114 " =    2.994
peak=   -3.961 closest distance to " CB  ASN A  39 " =    2.255
peak=   -3.934 closest distance to " CZ  TYR A 169 " =    1.720
peak=   -3.901 closest distance to " CD1 PHE A 130 " =    2.290
peak=   -3.898 closest distance to " O   HOH Z 102 " =    1.578
peak=   -3.889 closest distance to " CG  GLU A   2 " =    1.992
peak=   -3.876 closest distance to " CG  PHE A 283 " =    2.649
peak=   -3.863 closest distance to " O   HOH Z 407 " =    2.777
peak=   -3.861 closest distance to " CD2 LEU A 300 " =    2.878
peak=   -3.840 closest distance to " O   PRO A 163 " =    2.006
peak=   -3.838 closest distance to " CD1 PHE A  59 " =    1.890
peak=   -3.821 closest distance to " CD  ARG A 139 " =    1.562
peak=   -3.792 closest distance to " O   HOH Z 185 " =    2.189
peak=   -3.789 closest distance to " ND2 ASN A  45 " =    0.984
peak=   -3.773 closest distance to " OD1 ASN A  39 " =    2.183
peak=   -3.762 closest distance to " O   HOH Z 290 " =    1.175
peak=   -3.753 closest distance to " O   ALA A 161 " =    1.603
peak=   -3.741 closest distance to " CD1 LEU A 228 " =    2.108
peak=   -3.741 closest distance to " CB  PHE A 192 " =    1.824
peak=   -3.704 closest distance to " O   HOH Z  11 " =    1.989
peak=   -3.703 closest distance to " O   SER A 135 " =    1.534
peak=   -3.698 closest distance to " C   ALA A 158 " =    1.199
peak=   -3.697 closest distance to " O   VAL A 174 " =    2.076
peak=   -3.696 closest distance to " CB  ALA A 291 " =    2.411
peak=   -3.692 closest distance to " O   HOH Z  43 " =    1.672
peak=   -3.681 closest distance to " CZ  PHE A  59 " =    1.541
peak=   -3.680 closest distance to " OG  SER A   3 " =    1.642
peak=   -3.680 closest distance to " O   MET A  40 " =    2.648
peak=   -3.675 closest distance to " OG  SER A  97 " =    2.011
peak=   -3.673 closest distance to " O   HOH Z 435 " =    2.677
peak=   -3.670 closest distance to " N   ASP A 286 " =    2.351
peak=   -3.654 closest distance to " CA  GLY A 203 " =    2.255
peak=   -3.647 closest distance to " O   HOH Z 166 " =    1.414
peak=   -3.625 closest distance to " O   HOH Z  47 " =    1.573
peak=   -3.620 closest distance to " O   HOH Z 198 " =    1.548
peak=   -3.607 closest distance to " CG  GLN A  58 " =    1.354
peak=   -3.603 closest distance to " OXT GLY A 302 " =    3.371
peak=   -3.602 closest distance to " CD1 LEU A 101 " =    2.343
peak=   -3.595 closest distance to " O   HOH Z 263 " =    2.921
peak=   -3.590 closest distance to " OD2 ASP A 191 " =    1.477
peak=   -3.588 closest distance to " O   HOH Z  11 " =    1.753
peak=   -3.583 closest distance to " SG ACYS A 201 " =    1.779
peak=   -3.580 closest distance to " CA  ASP A 298 " =    1.063
peak=   -3.556 closest distance to " O   TRP A  92 " =    1.665
peak=   -3.552 closest distance to " O   HOH Z 353 " =    2.230
peak=   -3.543 closest distance to " O   PHE A 218 " =    1.533
peak=   -3.541 closest distance to " O   HOH Z 193 " =    2.005
peak=   -3.536 closest distance to " ND2 ASN A 187 " =    1.506
peak=   -3.526 closest distance to " CG2 THR A 178 " =    2.159
peak=   -3.526 closest distance to " NH2 ARG A  79 " =    1.931
peak=   -3.504 closest distance to " O   HOH Z 362 " =    5.916
peak=   -3.497 closest distance to " CD2 LEU A 237 " =    2.508
peak=   -3.467 closest distance to " O   HOH Z 165 " =    2.039
peak=   -3.466 closest distance to " OG  SER A  62 " =    1.613
peak=   -3.466 closest distance to " O   HOH Z  63 " =    1.420
peak=   -3.465 closest distance to " N   HIS A 115 " =    1.805
peak=   -3.451 closest distance to " O   ASN A  45 " =    1.867
peak=   -3.436 closest distance to " CE2 TYR A  30 " =    2.818
peak=   -3.434 closest distance to " O   PRO A 198 " =    1.252
peak=   -3.433 closest distance to " CG2 ILE A 263 " =    2.143
peak=   -3.432 closest distance to " NH1 ARG A  36 " =    2.088
peak=   -3.430 closest distance to " OD1 ASP A 191 " =    1.381
peak=   -3.424 closest distance to " O   HOH Z 385 " =    1.976
peak=   -3.423 closest distance to " OG BSER A 134 " =    1.686
peak=   -3.420 closest distance to " CB  ALA A 248 " =    2.313
peak=   -3.418 closest distance to " NH2AARG A 275 " =    5.032
peak=   -3.414 closest distance to " C   PRO A  90 " =    1.535
peak=   -3.411 closest distance to " N   SER A 276 " =    1.177
peak=   -3.409 closest distance to " O   SER A 146 " =    1.071
peak=   -3.406 closest distance to " CG2 VAL A 189 " =    2.098
peak=   -3.402 closest distance to " CZ3 TRP A 179 " =    1.311
peak=   -3.396 closest distance to " O   HOH Z  93 " =    1.619
peak=   -3.393 closest distance to " NH1 ARG A 195 " =    2.600
peak=   -3.391 closest distance to " O   HOH Z 351 " =    1.514
peak=   -3.388 closest distance to " O   HOH Z  10 " =    1.394
peak=   -3.385 closest distance to " CG  ASP A 231 " =    0.812
peak=   -3.385 closest distance to " NH2 ARG A  56 " =    2.121
peak=   -3.382 closest distance to " O   ALA A  51 " =    1.311
peak=   -3.380 closest distance to " OD1 ASP A 191 " =    1.807
peak=   -3.370 closest distance to " CZ3 TRP A 274 " =    2.312
peak=   -3.368 closest distance to " O   HOH Z 250 " =    1.410
peak=   -3.365 closest distance to " CA  TYR A  68 " =    2.940
peak=   -3.364 closest distance to " NH2 ARG A  66 " =    4.714
peak=   -3.364 closest distance to " CA  GLY A  98 " =    1.916
peak=   -3.363 closest distance to " O   PRO A 243 " =    2.572
peak=   -3.361 closest distance to " OG ASER A 134 " =    1.103
peak=   -3.356 closest distance to " CZ2 TRP A 274 " =    1.025
peak=   -3.352 closest distance to " O   HOH Z 234 " =    3.907
peak=   -3.339 closest distance to " N   ALA A  43 " =    2.588
peak=   -3.336 closest distance to " CG  ASP A 132 " =    2.245
peak=   -3.336 closest distance to " O   HOH Z 417 " =    2.459
peak=   -3.334 closest distance to " OD2 ASP A  50 " =    1.407
peak=   -3.332 closest distance to " N   GLN A 122 " =    1.426
peak=   -3.332 closest distance to " CB  GLN A  11 " =    1.714
peak=   -3.331 closest distance to " O   HOH Z 197 " =    5.002
peak=   -3.325 closest distance to " O   HOH Z 326 " =    1.686
peak=   -3.323 closest distance to " OD1 ASN A 148 " =    1.598
peak=   -3.321 closest distance to " OG1 THR A 178 " =    1.273
peak=   -3.318 closest distance to " O   HOH Z 427 " =    1.463
peak=   -3.317 closest distance to " O   HOH Z  15 " =    1.556
peak=   -3.316 closest distance to " O   SER A 210 " =    1.885
peak=   -3.313 closest distance to " O   HOH Z  88 " =    4.504
peak=   -3.310 closest distance to " O   HOH Z 134 " =    2.709
peak=   -3.309 closest distance to " CB  ALA A 248 " =    1.998
peak=   -3.308 closest distance to " O   HOH Z  97 " =    1.544
peak=   -3.297 closest distance to " O   ASN A 187 " =    1.448
peak=   -3.297 closest distance to " C   LEU A 143 " =    1.041
peak=   -3.293 closest distance to " CB  ALA A 291 " =    2.230
peak=   -3.289 closest distance to " O   HOH Z  52 " =    1.508
peak=   -3.287 closest distance to " O   HOH Z 265 " =    1.976
peak=   -3.285 closest distance to " O   HOH Z 389 " =    1.818
peak=   -3.279 closest distance to " N   PRO A 163 " =    1.540
peak=   -3.273 closest distance to " O   HOH Z 150 " =    1.746
peak=   -3.268 closest distance to " CE  MET A 105 " =    2.169
peak=   -3.266 closest distance to " O   HOH Z 395 " =    5.127
peak=   -3.265 closest distance to " CG  GLU A 152 " =    1.162
peak=   -3.264 closest distance to " OE2 GLU A 152 " =    1.273
peak=   -3.260 closest distance to " O   HOH Z 265 " =    2.011
peak=   -3.258 closest distance to " CG  ASN A 301 " =    1.954
peak=   -3.256 closest distance to " O   ALA A  34 " =    2.407
peak=   -3.256 closest distance to " CA  GLY A 133 " =    1.871
peak=   -3.253 closest distance to " CG  ARG A 269 " =    2.315
peak=   -3.252 closest distance to " OD1 ASN A 176 " =    1.187
peak=   -3.251 closest distance to " O   HOH Z 116 " =    1.288
peak=   -3.251 closest distance to " O   ASN A 249 " =    1.479
peak=   -3.250 closest distance to " CB  PHE A 208 " =    2.174
peak=   -3.244 closest distance to " O   HOH Z 166 " =    1.960
peak=   -3.239 closest distance to " O   LYS A 117 " =    1.574
peak=   -3.238 closest distance to " ND2 ASN A  39 " =    1.336
peak=   -3.237 closest distance to " O   LEU A 167 " =    1.465
peak=   -3.235 closest distance to " O   ALA A 292 " =    1.932
peak=   -3.234 closest distance to " CG  PRO A 163 " =    2.539
peak=   -3.231 closest distance to " O   HOH Z 283 " =    1.930
peak=   -3.230 closest distance to " O   HOH Z 429 " =    1.978
peak=   -3.222 closest distance to " C   TRP A 274 " =    1.442
peak=   -3.222 closest distance to " O   HOH Z 313 " =    2.081
peak=   -3.219 closest distance to " OG  SER A  97 " =    1.785
peak=   -3.218 closest distance to " CD1 LEU A  25 " =    2.452
peak=   -3.217 closest distance to " CG1 VAL A 268 " =    2.447
peak=   -3.215 closest distance to " O   SER A  95 " =    1.457
peak=   -3.214 closest distance to " CB  ALA A   9 " =    2.343
peak=   -3.213 closest distance to " N   VAL A 189 " =    1.585
peak=   -3.204 closest distance to " NE2 GLN A  58 " =    1.238
peak=   -3.200 closest distance to " O   HOH Z 211 " =    1.775
peak=   -3.192 closest distance to " O   HOH Z 388 " =    1.970
peak=   -3.191 closest distance to " O   HOH Z 421 " =    3.165
peak=   -3.190 closest distance to " O   HOH Z 166 " =    1.939
peak=   -3.189 closest distance to " O   HOH Z  24 " =    1.437
peak=   -3.188 closest distance to " NE2 GLN A  88 " =    1.888
peak=   -3.182 closest distance to " O   HOH Z  60 " =    1.918
peak=   -3.182 closest distance to " O   HOH Z  90 " =    2.628
peak=   -3.179 closest distance to " O   HOH Z 281 " =    2.770
peak=   -3.177 closest distance to " OE1 GLN A  88 " =    1.132
peak=   -3.175 closest distance to " OD2 ASP A 171 " =    2.303
peak=   -3.173 closest distance to " O   HOH Z  19 " =    2.310
peak=   -3.164 closest distance to " O   HOH Z 210 " =    1.174
peak=   -3.163 closest distance to " CG  PRO A 243 " =    1.559
peak=   -3.161 closest distance to " CG1 VAL A 250 " =    2.609
peak=   -3.158 closest distance to " O   HOH Z 139 " =    2.953
peak=   -3.156 closest distance to " O   HOH Z 311 " =    3.530
peak=   -3.146 closest distance to " O   HOH Z 423 " =    2.223
peak=   -3.143 closest distance to " CB  ASP A 286 " =    2.024
peak=   -3.142 closest distance to " CE  MET A 113 " =    2.230
peak=   -3.141 closest distance to " OH  TYR A 214 " =    1.311
peak=   -3.136 closest distance to " O   HOH Z 251 " =    1.465
peak=   -3.134 closest distance to " CB  ASP A 132 " =    2.309
peak=   -3.132 closest distance to " CB  ALA A 131 " =    2.005
peak=   -3.128 closest distance to " O   HOH Z 346 " =    1.757
peak=   -3.127 closest distance to " OD1 ASP A 171 " =    1.549
peak=   -3.108 closest distance to " O   HOH Z 378 " =    1.624
peak=   -3.106 closest distance to " O   HOH Z 137 " =    1.395
peak=   -3.098 closest distance to " O   HOH Z 107 " =    1.534
peak=   -3.087 closest distance to " OE1 GLN A 194 " =    1.537
peak=   -3.081 closest distance to " CG1AVAL A  41 " =    2.801
peak=   -3.079 closest distance to " O   HOH Z 361 " =    3.505
peak=   -3.064 closest distance to " O   HOH Z 345 " =    1.767
peak=   -3.054 closest distance to " CE1 HIS A  81 " =    1.616
peak=   -3.032 closest distance to " CG  ASP A  50 " =    2.317
peak=   -3.025 closest distance to " O   HOH Z 385 " =    1.883
peak=   -3.007 closest distance to " O   HOH Z  43 " =    1.520

================= 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    :  0.3760 0.3749   6.150908e+00   6.156871e+00
   1_bss:  0.3626 0.3605   6.133839e+00   6.126729e+00
   1_xyz:  0.2213 0.2393   5.694388e+00   5.772582e+00
   1_adp:  0.2013 0.2487   5.639768e+00   5.804359e+00
   1_occ:  0.2010 0.2486   5.639115e+00   5.804368e+00
   2_bss:  0.1961 0.2442   5.623892e+00   5.791247e+00
   2_xyz:  0.1395 0.1847   5.322824e+00   5.528333e+00
   2_adp:  0.1281 0.1720   5.242583e+00   5.450793e+00
   2_occ:  0.1278 0.1718   5.241057e+00   5.449374e+00
   3_bss:  0.1279 0.1699   5.235342e+00   5.440613e+00
   3_xyz:  0.1114 0.1552   5.132173e+00   5.365976e+00
   3_adp:  0.1083 0.1547   5.115511e+00   5.360288e+00
   3_occ:  0.1082 0.1546   5.115120e+00   5.360016e+00
   4_bss:  0.1081 0.1546   5.114669e+00   5.359616e+00
   4_xyz:  0.1075 0.1538   5.111270e+00   5.356032e+00
   4_adp:  0.1072 0.1534   5.108441e+00   5.353884e+00
   4_occ:  0.1072 0.1534   5.108238e+00   5.353857e+00
   5_bss:  0.1071 0.1534   5.108192e+00   5.353827e+00
   5_xyz:  0.1045 0.1533   5.096375e+00   5.352338e+00
   5_adp:  0.1042 0.1545   5.099408e+00   5.360245e+00
   5_occ:  0.1042 0.1545   5.099405e+00   5.360377e+00
   5_bss:  0.1043 0.1539   5.099374e+00   5.358008e+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  21.034  -1.241  -2.906   2.464  -0.000   0.000   0.000
   1_xyz:  0.316  21.034  -1.241  -2.906   2.464  -0.000   0.000   0.000
   1_adp:  0.316  21.034  -1.241  -2.906   2.464  -0.000   0.000   0.000
   1_occ:  0.316  21.034  -1.241  -2.906   2.464  -0.000   0.000   0.000
   2_bss:  0.316  30.832  -2.706  -2.767  -0.752  -0.000  -0.000  -0.000
   2_xyz:  0.316  30.832  -2.706  -2.767  -0.752  -0.000  -0.000  -0.000
   2_adp:  0.316  30.832  -2.706  -2.767  -0.752  -0.000  -0.000  -0.000
   2_occ:  0.316  30.832  -2.706  -2.767  -0.752  -0.000  -0.000  -0.000
   3_bss:  0.315  33.382  -2.903  -2.442  -1.549  -0.000  -0.000  -0.000
   3_xyz:  0.315  33.382  -2.903  -2.442  -1.549  -0.000  -0.000  -0.000
   3_adp:  0.315  33.382  -2.903  -2.442  -1.549  -0.000  -0.000  -0.000
   3_occ:  0.315  33.382  -2.903  -2.442  -1.549  -0.000  -0.000  -0.000
   4_bss:  0.317  34.383  -2.879  -2.285  -1.692  -0.000  -0.000  -0.000
   4_xyz:  0.317  34.383  -2.879  -2.285  -1.692  -0.000  -0.000  -0.000
   4_adp:  0.317  34.383  -2.879  -2.285  -1.692  -0.000  -0.000  -0.000
   4_occ:  0.317  34.383  -2.879  -2.285  -1.692  -0.000  -0.000  -0.000
   5_bss:  0.321  36.083  -2.782  -2.123  -1.616  -0.000  -0.000  -0.000
   5_xyz:  0.321  36.083  -2.782  -2.123  -1.616  -0.000  -0.000  -0.000
   5_adp:  0.321  36.083  -2.782  -2.123  -1.616  -0.000  -0.000  -0.000
   5_occ:  0.321  36.083  -2.782  -2.123  -1.616  -0.000  -0.000  -0.000
   5_bss:  0.319  39.123  -2.615  -1.939  -1.473  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  41.475 0.6276  0.8259    43332.476
   1_bss:  39.857 0.6452  0.8339    38908.972
   1_xyz:  23.109 0.8322  1.0092    14637.714
   1_adp:  24.338 0.8188  1.0033    15736.671
   1_occ:  24.345 0.8187  1.0032    15741.616
   2_bss:  23.757 0.8246  0.9552    15113.388
   2_xyz:  17.334 0.8858  0.9930     8482.478
   2_adp:  15.535 0.9021  0.9951     7332.421
   2_occ:  15.507 0.9023  0.9950     7297.909
   3_bss:  15.306 0.9039  0.9874     7111.135
   3_xyz:  13.763 0.9163  0.9941     6028.773
   3_adp:  13.585 0.9180  0.9910     5979.460
   3_occ:  13.577 0.9181  0.9909     5972.348
   4_bss:  13.570 0.9181  0.9913     5969.867
   4_xyz:  13.413 0.9196  0.9899     5889.518
   4_adp:  13.334 0.9203  0.9857     5869.271
   4_occ:  13.332 0.9203  0.9856     5866.346
   5_bss:  13.332 0.9203  0.9897     5869.408
   5_xyz:  13.300 0.9206  0.9898     5866.855
   5_adp:  13.443 0.9195  0.9837     5951.998
   5_occ:  13.443 0.9195  0.9836     5953.230
   5_bss:  13.416 0.9196  0.9889     5918.316
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.8708e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.8708e-01
   1_xyz:   1.198  0.009  0.073 15.297  0.005  4.107   8.1650e-02
   1_adp:   1.198  0.009  0.073 15.297  0.005  4.107   8.1650e-02
   1_occ:   1.198  0.009  0.073 15.297  0.005  4.107   8.1650e-02
   2_bss:   1.198  0.009  0.073 15.297  0.005  4.107   8.1650e-02
   2_xyz:   1.044  0.006  0.070 14.558  0.004  4.108   6.0060e-02
   2_adp:   1.044  0.006  0.070 14.558  0.004  4.108   6.0060e-02
   2_occ:   1.044  0.006  0.070 14.558  0.004  4.108   6.0060e-02
   3_bss:   1.044  0.006  0.070 14.558  0.004  4.108   6.0060e-02
   3_xyz:   1.089  0.007  0.077 15.025  0.005  4.107   6.6910e-02
   3_adp:   1.089  0.007  0.077 15.025  0.005  4.107   6.6910e-02
   3_occ:   1.089  0.007  0.077 15.025  0.005  4.107   6.6910e-02
   4_bss:   1.089  0.007  0.077 15.025  0.005  4.107   6.6910e-02
   4_xyz:   0.981  0.006  0.071 14.633  0.004  4.107   5.6473e-02
   4_adp:   0.981  0.006  0.071 14.633  0.004  4.107   5.6473e-02
   4_occ:   0.981  0.006  0.071 14.633  0.004  4.107   5.6473e-02
   5_bss:   0.981  0.006  0.071 14.633  0.004  4.107   5.6473e-02
   5_xyz:   1.061  0.007  0.076 14.838  0.004  4.107   6.3936e-02
   5_adp:   1.061  0.007  0.076 14.838  0.004  4.107   6.3936e-02
   5_occ:   1.061  0.007  0.076 14.838  0.004  4.107   6.3936e-02
   5_bss:   1.061  0.007  0.076 14.838  0.004  4.107   6.3936e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.346   2.3898e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.346   2.3898e-01
   1_xyz:   8.696  0.045  0.304 86.291  0.054  2.094   8.0371e-02
   1_adp:   8.696  0.045  0.304 86.291  0.054  2.094   8.0371e-02
   1_occ:   8.696  0.045  0.304 86.291  0.054  2.094   8.0371e-02
   2_bss:   8.696  0.045  0.304 86.291  0.054  2.094   8.0371e-02
   2_xyz:   6.465  0.038  0.250 81.951  0.043  2.352   7.5077e-02
   2_adp:   6.465  0.038  0.250 81.951  0.043  2.352   7.5077e-02
   2_occ:   6.465  0.038  0.250 81.951  0.043  2.352   7.5077e-02
   3_bss:   6.465  0.038  0.250 81.951  0.043  2.352   7.5077e-02
   3_xyz:   6.788  0.041  0.249 82.953  0.041  2.286   5.5737e-02
   3_adp:   6.788  0.041  0.249 82.953  0.041  2.286   5.5737e-02
   3_occ:   6.788  0.041  0.249 82.953  0.041  2.286   5.5737e-02
   4_bss:   6.788  0.041  0.249 82.953  0.041  2.286   5.5737e-02
   4_xyz:   6.384  0.040  0.237 81.916  0.043  2.317   3.8340e-02
   4_adp:   6.384  0.040  0.237 81.916  0.043  2.317   3.8340e-02
   4_occ:   6.384  0.040  0.237 81.916  0.043  2.317   3.8340e-02
   5_bss:   6.384  0.040  0.237 81.916  0.043  2.317   3.8340e-02
   5_xyz:   6.823  0.043  0.258 82.714  0.039  2.271   4.7662e-02
   5_adp:   6.823  0.043  0.258 82.714  0.039  2.271   4.7662e-02
   5_occ:   6.823  0.043  0.258 82.714  0.039  2.271   4.7662e-02
   5_bss:   6.823  0.043  0.258 82.714  0.039  2.271   4.7662e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  84.03   0.00  17.83  84.03   0.00  13.75  74.34   7.47  40.06
   1_occ:  84.03   0.00  17.83  84.03   0.00  13.75  74.34   7.47  40.06
   2_bss:  84.03   0.00  17.83  84.03   0.00  13.75  74.34   7.47  40.06
   2_xyz:  84.03   0.00  17.83  84.03   0.00  13.75  74.34   7.47  40.06
   2_adp:  86.08   0.00  17.26  86.08   0.00  13.22  75.09   6.00  39.27
   2_occ:  86.08   0.00  17.26  86.08   0.00  13.22  75.09   6.00  39.27
   3_bss:  86.08   0.00  17.26  86.08   0.00  13.22  75.09   6.00  39.27
   3_xyz:  86.08   0.00  17.26  86.08   0.00  13.22  75.09   6.00  39.27
   3_adp:  89.79   0.00  17.28  89.79   0.00  13.12  80.64   3.63  39.92
   3_occ:  89.79   0.00  17.28  89.79   0.00  13.12  80.64   3.63  39.92
   4_bss:  89.79   0.00  17.28  89.79   0.00  13.12  80.64   3.63  39.92
   4_xyz:  89.79   0.00  17.28  89.79   0.00  13.12  80.64   3.63  39.92
   4_adp:  90.16   1.49  17.04  90.16   1.49  12.97  79.58   5.24  39.20
   4_occ:  90.16   1.49  17.04  90.16   1.49  12.97  79.58   5.24  39.20
   5_bss:  90.16   1.49  17.04  90.16   1.49  12.97  79.58   5.24  39.20
   5_xyz:  90.16   1.49  17.04  90.16   1.49  12.97  79.58   5.24  39.20
   5_adp: 100.60   0.72  17.14 100.60   0.72  12.92  84.86   5.85  40.12
   5_occ: 100.60   0.72  17.14 100.60   0.72  12.92  84.86   5.85  40.12
   5_bss: 100.58   0.70  17.11 100.58   0.70  12.89  84.83   5.83  40.09
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.793    0.012    0.347
   1_adp:    1.793    0.012    0.347
   1_occ:    1.793    0.012    0.347
   2_bss:    1.793    0.012    0.347
   2_xyz:    1.526    0.015    0.436
   2_adp:    1.526    0.015    0.436
   2_occ:    1.526    0.015    0.436
   3_bss:    1.526    0.015    0.436
   3_xyz:    1.263    0.045    0.473
   3_adp:    1.263    0.045    0.473
   3_occ:    1.263    0.045    0.473
   4_bss:    1.263    0.045    0.473
   4_xyz:    1.403    0.041    0.483
   4_adp:    1.403    0.041    0.483
   4_occ:    1.403    0.041    0.483
   5_bss:    1.403    0.041    0.483
   5_xyz:    1.366    0.052    0.491
   5_adp:    1.366    0.052    0.491
   5_occ:    1.366    0.052    0.491
   5_bss:    1.366    0.052    0.491
------------------------------------------------------------------------

CPU time actual refinement: 282.76


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_298/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_298/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_298/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_298/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_298/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 282.63 
  Macro-tasks:
    bulk solvent and scale       = 35.24  
    individual site refinement   = 118.79 
    weights calculation          = 24.22  
    collect and process          = 5.41   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 183.75 
  Micro-tasks:
    mask                            = 1.49   
    f_calc                          = 89.60  
    alpha_beta                      = 6.84   
    target                          = 0.96   
    gradients_wrt_atomic_parameters = 97.66  
    fmodel                         = 5.97   
    r_factors                      = 0.18   
    phase_errors                   = 8.92   
    foms                           = 0.19   
    TOTAL for micro-tasks          = 211.81 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 3.948 micro seconds
Total CPU time: 4.90 minutes
from_scatterers_fft:    659 calls, 89.28 s
gradients_fft:          604 calls, 85.72 s

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

# Date 2008-01-16 Time 04:29:03 PST -0800 (1200486543.65 s)
Start R-work = 0.3760, R-free = 0.3749 (no bulk solvent and anisotropic scale)
Final R-work = 0.1298, R-free = 0.1749 (no bulk solvent and anisotropic scale)

Start R-work = 0.3626, R-free = 0.3605
Final R-work = 0.1043, R-free = 0.1539