# Date 2008-01-16 Time 04:08:58 PST -0800 (1200485338.27 s)
#phil __OFF__

Command line arguments: "../195.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25273
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 195

-------------------------------------------------------------------------------
  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: (68.845, 47.1647, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 47.1647, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8332 1.96086
Completeness in resolution range: 0.930638
Completeness with d_max=infinity: 0.927817

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8332
                             d_min =   1.9609

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: (68.845, 47.1647, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8332 1.96086
Completeness in resolution range: 0.930638
Completeness with d_max=infinity: 0.927817

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8336 -  4.1957 [2214/2242]  1991   223  10.1%
  bin  2:  4.1957 -  3.3428 [2115/2138]  1900   215  10.2%
  bin  3:  3.3428 -  2.9239 [2091/2113]  1888   203   9.7%
  bin  4:  2.9239 -  2.6582 [2085/2104]  1876   209  10.0%
  bin  5:  2.6582 -  2.4686 [2054/2083]  1839   215  10.5%
  bin  6:  2.4686 -  2.3237 [2047/2089]  1846   201   9.8%
  bin  7:  2.3237 -  2.2077 [2041/2077]  1847   194   9.5%
  bin  8:  2.2077 -  2.1119 [2042/2083]  1827   215  10.5%
  bin  9:  2.1119 -  2.0308 [2031/2059]  1837   194   9.6%
  bin 10:  2.0308 -  1.9609 [ 869/2061]   779    90  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_195/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.42 -     2.11: 14
        2.11 -     2.81: 801
        2.81 -     3.51: 4483
        3.51 -     4.20: 9331
        4.20 -     4.90: 13749
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.416 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.427 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.553 3.120 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.644 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.651 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28373 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_195/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_195/model_refine_001.geo

CPU time processing inputs: 9.14


============================ 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 = 68.845 47.16465 87.68585 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 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3822   r_free= 0.3774   ksol= 0.00   Bsol= 0.00   scale= 0.945    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.158750                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8336 -  4.6796 0.99   1438  158 0.2977 0.3093      6.4048       6.417|
|  2:  4.6796 -  3.7338 0.99   1387  155 0.2991 0.2898      6.5499      6.5585|
|  3:  3.7338 -  3.2676 0.99   1349  151 0.3475 0.3278      6.4908        6.49|
|  4:  3.2676 -  2.9715 0.99   1350  143 0.3647 0.3922      6.3467      6.4155|
|  5:  2.9715 -  2.7599 0.99   1325  154 0.4006 0.3733      6.2215      6.2123|
|  6:  2.7599 -  2.5981 0.98   1331  147 0.4049 0.4470      6.1463      6.0921|
|  7:  2.5981 -  2.4686 0.99   1314  157 0.4059 0.3499      6.1058      5.9997|
|  8:  2.4686 -  2.3616 0.99   1335  137 0.4410 0.4127      6.0882      6.0598|
|  9:  2.3616 -  2.2710 0.98   1325  144 0.4390 0.4142      6.0369      6.0548|
| 10:  2.2710 -  2.1929 0.98   1297  144 0.4415 0.4301      6.0214      5.9726|
| 11:  2.1929 -  2.1246 0.98   1304  155 0.4523 0.4606      5.9404      5.9556|
| 12:  2.1246 -  2.0640 0.99   1318  145 0.4460 0.4392      5.8844      5.9137|
| 13:  2.0640 -  2.0098 0.91   1221  122 0.4573 0.4774      5.8199      5.7959|
| 14:  2.0098 -  1.9609 0.26    336   47 0.4578 0.4349      5.8576      5.6764|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8336 -  4.6796  1438   158  0.77  28.23   0.86     0.78      49064.17|
|  2:  4.6796 -  3.7338  1387   155  0.80  26.16   0.97     0.88      63073.57|
|  3:  3.7338 -  3.2676  1349   151  0.74  32.13   0.95     0.89      65028.45|
|  4:  3.2676 -  2.9715  1350   143  0.67  37.64   0.96     0.84      58853.90|
|  5:  2.9715 -  2.7599  1325   154  0.61  42.88   0.95     0.80      48682.56|
|  6:  2.7599 -  2.5981  1331   147  0.61  43.12   0.95     0.79      42087.69|
|  7:  2.5981 -  2.4686  1314   157  0.62  42.12   0.97     0.82      36754.50|
|  8:  2.4686 -  2.3616  1335   137  0.62  42.23   0.97     0.84      32240.43|
|  9:  2.3616 -  2.2710  1325   144  0.63  42.08   0.97     0.85      30083.61|
| 10:  2.2710 -  2.1929  1297   144  0.61  43.39   0.98     0.82      28604.90|
| 11:  2.1929 -  2.1246  1304   155  0.56  47.73   0.98     0.82      31197.94|
| 12:  2.1246 -  2.0640  1318   145  0.51  51.56   1.01     0.78      30929.44|
| 13:  2.0640 -  2.0098  1221   122  0.49  53.45   0.97     0.75      28429.48|
| 14:  2.0098 -  1.9609   336    47  0.54  49.10   1.01     0.70      22207.47|
|alpha:            min =        0.70 max =            0.89 mean =         0.82|
|beta:             min =    22207.47 max =        65028.45 mean =     41840.93|
|figures of merit: min =        0.00 max =            1.00 mean =         0.63|
|phase err.(work): min =        0.00 max =           89.98 mean =        40.89|
|phase err.(test): min =        0.00 max =           89.57 mean =        40.86|
|-----------------------------------------------------------------------------|

============================== 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 = 5.108364              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.141   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.881213              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.656   (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 |  1.416 -  1.764:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.764 -  2.113:        7 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.113 -  2.461:       27 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.461 -  2.809:      774 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.809 -  3.158:     2077 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.158 -  3.506:     2406 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.506 -  3.855:     4583 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.855 -  4.203:     4748 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.203 -  4.552:     6226 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.552 -  4.900:     7523 |
|-----------------------------------------------------------------------------|
|-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 |        0.188 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.416 |       0.562 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.790)------------------------------------------|
|    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 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3822   r_free= 0.3774   ksol= 0.00   Bsol= 0.00   scale= 0.945    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.158750                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3723   r_free= 0.3673   ksol= 0.30   Bsol= 50.00   scale= 0.969   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.14,-2.08,2.05,-0.00,0.00,0.00); trace/3= -0.06                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.144206                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.535747              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.736   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.514979              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.380   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3723      final r-factor (work) = 0.2268          |
| start r-factor (free) = 0.3673      final r-factor (free) = 0.2557          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.1294 = 4.54 * 0.50 * 6.1472 + 1.00 * 0.1883                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.4607 = 4.54 * 0.50 * 5.9008 + 1.00 * 0.0784                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2268      final r-factor (work) = 0.2087          |
| start r-factor (free) = 0.2557      final r-factor (free) = 0.2606          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0453 = 0.51 * 1.00 * 5.9008 + 1.00 * 0.0066                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9638 = 0.51 * 1.00 * 5.6638 + 1.00 * 0.0471                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.790)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    67.71   16.90    None  None   None       |
|    all(noH): 2823   0      0.00    67.71   16.90    None  None   None       |
|    Sol.    : 438    0      6.74    63.65   38.15    None  None   None       |
|    Mac.    : 2385   0      0.00    67.71   13.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.771:  378   |   5:    33.857 -  40.628:  110        |
|      1:     6.771 -  13.543: 1127   |   6:    40.628 -  47.400:  116        |
|      2:    13.543 -  20.314:  629   |   7:    47.400 -  54.171:   69        |
|      3:    20.314 -  27.086:  227   |   8:    54.171 -  60.942:   43        |
|      4:    27.086 -  33.857:  120   |   9:    60.942 -  67.714:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2087 r_free = 0.2606             target_work(ml) = 5.673         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2084 r_free = 0.2609             target_work(ml) = 5.673         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2084   r_free= 0.2609   ksol= 0.30   Bsol= 50.00   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.14,-2.08,2.05,-0.00,0.00,0.00); trace/3= -0.06                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.673402                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2045   r_free= 0.2571   ksol= 0.33   Bsol= 56.72   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-2.49,-0.28,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.665643                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.036035              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.480   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.418936              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.577   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2045      final r-factor (work) = 0.1453          |
| start r-factor (free) = 0.2571      final r-factor (free) = 0.1838          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6953 = 3.04 * 0.50 * 5.6764 + 1.00 * 0.0784                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4636 = 3.04 * 0.50 * 5.5378 + 1.00 * 0.0571                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1453      final r-factor (work) = 0.1330          |
| start r-factor (free) = 0.1838      final r-factor (free) = 0.1762          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3470 = 0.42 * 1.00 * 5.5378 + 1.00 * 0.0270                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2314 = 0.42 * 1.00 * 5.3043 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.790)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.35   17.47    None  None   None       |
|    all(noH): 2823   0      0.00    83.35   17.47    None  None   None       |
|    Sol.    : 438    0      6.64    76.12   40.75    None  None   None       |
|    Mac.    : 2385   0      0.00    83.35   13.20    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 -   8.335:  595   |   5:    41.673 -  50.007:  101        |
|      1:     8.335 -  16.669: 1384   |   6:    50.007 -  58.342:   93        |
|      2:    16.669 -  25.004:  324   |   7:    58.342 -  66.676:   52        |
|      3:    25.004 -  33.338:  132   |   8:    66.676 -  75.011:   17        |
|      4:    33.338 -  41.673:  121   |   9:    75.011 -  83.345:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1330 r_free = 0.1762             target_work(ml) = 5.282         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1328 r_free = 0.1760             target_work(ml) = 5.281         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1328   r_free= 0.1760   ksol= 0.33   Bsol= 56.72   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-2.49,-0.28,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.281058                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1327   r_free= 0.1757   ksol= 0.33   Bsol= 56.72   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.08,-2.33,-0.69,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.279086                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.037622              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.521  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.166880              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.147  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1327      final r-factor (work) = 0.1191          |
| start r-factor (free) = 0.1757      final r-factor (free) = 0.1616          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4612 = 2.04 * 0.50 * 5.3043 + 1.00 * 0.0571                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3856 = 2.04 * 0.50 * 5.2314 + 1.00 * 0.0558                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1191      final r-factor (work) = 0.1181          |
| start r-factor (free) = 0.1616      final r-factor (free) = 0.1591          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8823 = 0.17 * 1.00 * 5.2314 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8735 = 0.17 * 1.00 * 5.1890 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.790)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.74    80.87   16.94    None  None   None       |
|    all(noH): 2823   0      1.74    80.87   16.94    None  None   None       |
|    Sol.    : 438    0      5.51    76.54   38.66    None  None   None       |
|    Mac.    : 2385   0      1.74    80.87   12.95    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:     1.742 -   9.655:  912   |   5:    41.308 -  49.221:   85        |
|      1:     9.655 -  17.568: 1156   |   6:    49.221 -  57.134:   87        |
|      2:    17.568 -  25.481:  272   |   7:    57.134 -  65.048:   39        |
|      3:    25.481 -  33.395:  124   |   8:    65.048 -  72.961:   16        |
|      4:    33.395 -  41.308:  128   |   9:    72.961 -  80.874:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1181 r_free = 0.1591             target_work(ml) = 5.182         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1179 r_free = 0.1590             target_work(ml) = 5.182         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1590   ksol= 0.33   Bsol= 56.72   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.08,-2.33,-0.69,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.181883                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1590   ksol= 0.33   Bsol= 56.72   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.16,-2.27,-0.82,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.181644                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.349288              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 146.548  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.155300              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 157.234  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1179      final r-factor (work) = 0.1124          |
| start r-factor (free) = 0.1590      final r-factor (free) = 0.1556          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1504 = 2.35 * 0.50 * 5.1885 + 1.00 * 0.0558                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1246 = 2.35 * 0.50 * 5.1604 + 1.00 * 0.0630                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1124      final r-factor (work) = 0.1123          |
| start r-factor (free) = 0.1556      final r-factor (free) = 0.1547          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8090 = 0.16 * 1.00 * 5.1604 + 1.00 * 0.0076                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8067 = 0.16 * 1.00 * 5.1474 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.790)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.83   16.70    None  None   None       |
|    all(noH): 2823   0      0.00    79.83   16.70    None  None   None       |
|    Sol.    : 438    0      0.00    75.91   37.97    None  None   None       |
|    Mac.    : 2385   0      2.10    79.83   12.79    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.983:  511   |   5:    39.914 -  47.896:   92        |
|      1:     7.983 -  15.965: 1450   |   6:    47.896 -  55.879:   86        |
|      2:    15.965 -  23.948:  352   |   7:    55.879 -  63.862:   42        |
|      3:    23.948 -  31.931:  140   |   8:    63.862 -  71.844:   14        |
|      4:    31.931 -  39.914:  132   |   9:    71.844 -  79.827:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1123 r_free = 0.1547             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1121 r_free = 0.1547             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1547   ksol= 0.33   Bsol= 56.72   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.16,-2.27,-0.82,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.144728                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1547   ksol= 0.33   Bsol= 56.72   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.11,-2.17,-0.76,-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: 5.144734                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.456482              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 162.273  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.347509              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.671  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1121      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1547      final r-factor (free) = 0.1556          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8114 = 1.46 * 0.50 * 5.1472 + 1.00 * 0.0630                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8054 = 1.46 * 0.50 * 5.1529 + 1.00 * 0.0528                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1138      final r-factor (work) = 0.1130          |
| start r-factor (free) = 0.1556      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7980 = 0.35 * 1.00 * 5.1529 + 1.00 * 0.0073                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7986 = 0.35 * 1.00 * 5.1521 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.790)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.06    81.27   16.74    None  None   None       |
|    all(noH): 2823   0      1.06    81.27   16.74    None  None   None       |
|    Sol.    : 438    0      1.06    76.95   38.66    None  None   None       |
|    Mac.    : 2385   0      1.48    81.27   12.72    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:     1.061 -   9.082:  822   |   5:    41.164 -  49.185:   98        |
|      1:     9.082 -  17.102: 1228   |   6:    49.185 -  57.205:   89        |
|      2:    17.102 -  25.123:  281   |   7:    57.205 -  65.226:   35        |
|      3:    25.123 -  33.144:  132   |   8:    65.226 -  73.247:   15        |
|      4:    33.144 -  41.164:  118   |   9:    73.247 -  81.267:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1130 r_free = 0.1561             target_work(ml) = 5.156         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1129 r_free = 0.1561             target_work(ml) = 5.156         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1129   r_free= 0.1561   ksol= 0.33   Bsol= 56.72   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.11,-2.17,-0.76,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.155650                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8336 -  4.6796 0.99   1438  158 0.1028 0.1313      5.4181      5.5714|
|  2:  4.6796 -  3.7338 0.99   1387  155 0.0875 0.1091      5.4437       5.613|
|  3:  3.7338 -  3.2676 0.99   1349  151 0.1079 0.1489      5.4688      5.7987|
|  4:  3.2676 -  2.9715 0.99   1350  143 0.1237 0.1499      5.4361      5.5813|
|  5:  2.9715 -  2.7599 0.99   1325  154 0.1294 0.1571      5.3011      5.4828|
|  6:  2.7599 -  2.5981 0.98   1331  147 0.1251 0.2054      5.2118       5.491|
|  7:  2.5981 -  2.4686 0.99   1314  157 0.1257 0.1644      5.1629      5.3591|
|  8:  2.4686 -  2.3616 0.99   1335  137 0.1174 0.1629      5.0867      5.2533|
|  9:  2.3616 -  2.2710 0.98   1325  144 0.1157 0.1915       5.018      5.3616|
| 10:  2.2710 -  2.1929 0.98   1297  144 0.1149 0.1688      4.9527      5.1503|
| 11:  2.1929 -  2.1246 0.98   1304  155 0.1153 0.1836      4.9137      5.2634|
| 12:  2.1246 -  2.0640 0.99   1318  145 0.1139 0.1602      4.8709      5.1009|
| 13:  2.0640 -  2.0098 0.91   1221  122 0.1082 0.1739      4.7707        5.01|
| 14:  2.0098 -  1.9609 0.26    336   47 0.0993 0.1701      4.6898      4.9253|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8336 -  4.6796  1438   158  0.94   9.39   0.97     0.95       7461.05|
|  2:  4.6796 -  3.7338  1387   155  0.95   7.96   1.01     1.00       8940.65|
|  3:  3.7338 -  3.2676  1349   151  0.93  11.36   1.02     1.02      10037.42|
|  4:  3.2676 -  2.9715  1350   143  0.92  13.38   1.00     0.99       9744.38|
|  5:  2.9715 -  2.7599  1325   154  0.90  15.51   0.99     0.97       7922.81|
|  6:  2.7599 -  2.5981  1331   147  0.90  16.30   0.97     0.95       6916.54|
|  7:  2.5981 -  2.4686  1314   157  0.90  15.60   0.98     0.95       6100.39|
|  8:  2.4686 -  2.3616  1335   137  0.91  15.70   0.99     0.96       5640.45|
|  9:  2.3616 -  2.2710  1325   144  0.90  15.89   0.99     0.95       4931.05|
| 10:  2.2710 -  2.1929  1297   144  0.90  15.75   0.99     0.95       4352.08|
| 11:  2.1929 -  2.1246  1304   155  0.90  15.76   0.99     0.95       4138.04|
| 12:  2.1246 -  2.0640  1318   145  0.90  16.05   1.00     0.99       3924.81|
| 13:  2.0640 -  2.0098  1221   122  0.90  16.12   0.98     0.97       3334.58|
| 14:  2.0098 -  1.9609   336    47  0.92  13.57   0.96     0.92       2549.25|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2549.25 max =        10037.42 mean =      6395.34|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.13|
|phase err.(test): min =        0.00 max =           89.73 mean =        13.74|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1128   r_free= 0.1557   ksol= 0.32   Bsol= 52.97   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-1.97,-0.56,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.154207                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1128   r_free= 0.1557   ksol= 0.32   Bsol= 52.97   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-1.97,-0.56,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.154207                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8336 -  4.6796 0.99   1438  158 0.1020 0.1270      5.4037      5.5307|
|  2:  4.6796 -  3.7338 0.99   1387  155 0.0876 0.1082      5.4382      5.6098|
|  3:  3.7338 -  3.2676 0.99   1349  151 0.1081 0.1481      5.4668      5.7903|
|  4:  3.2676 -  2.9715 0.99   1350  143 0.1238 0.1506      5.4349      5.5808|
|  5:  2.9715 -  2.7599 0.99   1325  154 0.1296 0.1571      5.3016      5.4795|
|  6:  2.7599 -  2.5981 0.98   1331  147 0.1253 0.2053      5.2123      5.4907|
|  7:  2.5981 -  2.4686 0.99   1314  157 0.1256 0.1643       5.164      5.3603|
|  8:  2.4686 -  2.3616 0.99   1335  137 0.1174 0.1635       5.088      5.2551|
|  9:  2.3616 -  2.2710 0.98   1325  144 0.1154 0.1917      5.0187      5.3621|
| 10:  2.2710 -  2.1929 0.98   1297  144 0.1150 0.1689      4.9538      5.1514|
| 11:  2.1929 -  2.1246 0.98   1304  155 0.1153 0.1838      4.9142      5.2643|
| 12:  2.1246 -  2.0640 0.99   1318  145 0.1138 0.1600      4.8706      5.0998|
| 13:  2.0640 -  2.0098 0.91   1221  122 0.1081 0.1741      4.7708      5.0105|
| 14:  2.0098 -  1.9609 0.26    336   47 0.0994 0.1697      4.6898      4.9249|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8336 -  4.6796  1438   158  0.94   9.06   0.98     0.95       7033.73|
|  2:  4.6796 -  3.7338  1387   155  0.95   7.76   1.01     1.00       8603.46|
|  3:  3.7338 -  3.2676  1349   151  0.93  11.27   1.02     1.02       9870.36|
|  4:  3.2676 -  2.9715  1350   143  0.92  13.29   1.01     1.00       9659.32|
|  5:  2.9715 -  2.7599  1325   154  0.90  15.48   0.99     0.97       7900.89|
|  6:  2.7599 -  2.5981  1331   147  0.90  16.28   0.98     0.96       6908.85|
|  7:  2.5981 -  2.4686  1314   157  0.90  15.61   0.99     0.95       6115.82|
|  8:  2.4686 -  2.3616  1335   137  0.91  15.74   1.00     0.97       5660.46|
|  9:  2.3616 -  2.2710  1325   144  0.90  15.92   1.00     0.96       4948.21|
| 10:  2.2710 -  2.1929  1297   144  0.90  15.78   0.99     0.95       4360.13|
| 11:  2.1929 -  2.1246  1304   155  0.90  15.77   0.99     0.96       4142.17|
| 12:  2.1246 -  2.0640  1318   145  0.90  16.05   1.00     1.00       3925.53|
| 13:  2.0640 -  2.0098  1221   122  0.90  16.13   0.99     0.98       3336.56|
| 14:  2.0098 -  1.9609   336    47  0.92  13.58   0.97     0.93       2551.77|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2551.77 max =         9870.36 mean =      6317.53|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.08|
|phase err.(test): min =        0.00 max =           89.93 mean =        13.70|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.790)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.02    81.23   16.71    None  None   None       |
|    all(noH): 2823   0      1.02    81.23   16.71    None  None   None       |
|    Sol.    : 438    0      1.02    76.91   38.62    None  None   None       |
|    Mac.    : 2385   0      1.44    81.23   12.68    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:     1.024 -   9.045:  822   |   5:    41.127 -  49.148:   98        |
|      1:     9.045 -  17.065: 1228   |   6:    49.148 -  57.169:   89        |
|      2:    17.065 -  25.086:  281   |   7:    57.169 -  65.189:   35        |
|      3:    25.086 -  33.107:  132   |   8:    65.189 -  73.210:   15        |
|      4:    33.107 -  41.127:  118   |   9:    73.210 -  81.230:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 278         
Filter by distance & map next to the model:
   mapped sites are within: 0.461 - 4.352
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 271 from: 278
   mapped sites are within: 0.708 - 4.352

peak=    5.673 closest distance to " CB  ARG A 275 " =    0.944
peak=    5.500 closest distance to " NH2 ARG A  56 " =    2.198
peak=    5.103 closest distance to " CG  PRO A  54 " =    1.338
peak=    4.934 closest distance to " CB  GLN A 223 " =    1.436
peak=    4.842 closest distance to " CB  PRO A  54 " =    1.023
peak=    4.829 closest distance to " O   HOH Z 126 " =    1.820
peak=    4.797 closest distance to " O   HOH Z 232 " =    2.386
peak=    4.778 closest distance to " O  BHOH Z  74 " =    1.203
peak=    4.681 closest distance to " CG  PRO A  90 " =    1.261
peak=    4.591 closest distance to " O   HOH Z  40 " =    1.830
peak=    4.580 closest distance to " CB  GLN A 183 " =    1.227
peak=    4.580 closest distance to " O   HOH Z 406 " =    1.655
peak=    4.572 closest distance to " O   HOH Z 402 " =    1.439
peak=    4.567 closest distance to " CZ  PHE A 218 " =    1.100
peak=    4.537 closest distance to " CG  PRO A 198 " =    1.268
peak=    4.532 closest distance to " O   HOH Z 369 " =    2.381
peak=    4.502 closest distance to " O   HOH Z 250 " =    1.548
peak=    4.470 closest distance to " CG  PRO A 213 " =    1.263
peak=    4.470 closest distance to " O   HOH Z 403 " =    1.791
peak=    4.470 closest distance to " CB  SER A  63 " =    1.147
peak=    4.426 closest distance to " CB  ARG A  79 " =    1.374
peak=    4.405 closest distance to " ND2 ASN A 187 " =    1.565
peak=    4.403 closest distance to " NE2 GLN A  11 " =    1.089
peak=    4.387 closest distance to " O   HOH Z 298 " =    1.809
peak=    4.386 closest distance to " O   HOH Z 287 " =    1.784
peak=    4.364 closest distance to " CD2 TRP A 179 " =    1.349
peak=    4.363 closest distance to " CG  PRO A 243 " =    1.078
peak=    4.359 closest distance to " CB  ASN A 148 " =    1.464
peak=    4.359 closest distance to " CB  ARG A 190 " =    1.706
peak=    4.355 closest distance to " CA  TYR A  30 " =    0.893
peak=    4.355 closest distance to " O   HOH Z 142 " =    1.624
peak=    4.312 closest distance to " CB  GLU A 152 " =    1.161
peak=    4.258 closest distance to " O   HOH Z  43 " =    1.993
peak=    4.248 closest distance to " O   SER A  87 " =    2.217
peak=    4.215 closest distance to " C   PRO A 198 " =    1.505
peak=    4.146 closest distance to " CG2 VAL A 257 " =    0.836
peak=    4.118 closest distance to " O   HOH Z 234 " =    3.720
peak=    4.110 closest distance to " CG2 ILE A 120 " =    1.241
peak=    4.108 closest distance to " CA  ARG A  36 " =    1.003
peak=    4.056 closest distance to " CB  GLU A  46 " =    1.035
peak=    4.053 closest distance to " O   HOH Z 346 " =    1.668
peak=    4.047 closest distance to " CB  VAL A 265 " =    1.236
peak=    4.046 closest distance to " CD  ARG A 269 " =    1.005
peak=    4.042 closest distance to " O   HOH Z 272 " =    1.864
peak=    4.014 closest distance to " O   HOH Z 189 " =    2.829
peak=    3.988 closest distance to " O   HOH Z  15 " =    2.236
peak=    3.971 closest distance to " O   HOH Z 126 " =    1.765
peak=    3.964 closest distance to " O   HOH Z  44 " =    1.984
peak=    3.949 closest distance to " O   HOH Z 209 " =    2.213
peak=    3.926 closest distance to " O   HOH Z  78 " =    1.699
peak=    3.923 closest distance to " O   HOH Z 291 " =    1.485
peak=    3.921 closest distance to " O   HOH Z 303 " =    2.134
peak=    3.911 closest distance to " O   HOH Z 248 " =    1.578
peak=    3.893 closest distance to " O   HOH Z  68 " =    2.140
peak=    3.880 closest distance to " CB  GLU A 277 " =    3.589
peak=    3.880 closest distance to " O   HOH Z 427 " =    2.991
peak=    3.878 closest distance to " CB  ASN A 110 " =    1.087
peak=    3.869 closest distance to " ND2 ASN A 249 " =    0.926
peak=    3.861 closest distance to " O   HOH Z 128 " =    1.912
peak=    3.858 closest distance to " NZ  LYS A 117 " =    3.106
peak=    3.845 closest distance to " N   TYR A 116 " =    1.578
peak=    3.839 closest distance to " O   HOH Z  97 " =    2.061
peak=    3.837 closest distance to " O   HOH Z 128 " =    2.234
peak=    3.833 closest distance to " CB  VAL A 202 " =    1.520
peak=    3.828 closest distance to " CE  LYS A  76 " =    0.922
peak=    3.825 closest distance to " CB  ASN A  39 " =    0.851
peak=    3.823 closest distance to " O   HOH Z  97 " =    2.201
peak=    3.813 closest distance to " O   HOH Z 365 " =    2.775
peak=    3.810 closest distance to " CD  LYS A 166 " =    1.310
peak=    3.797 closest distance to " CA  ARG A 195 " =    1.216
peak=    3.791 closest distance to " O   HOH Z 423 " =    1.970
peak=    3.785 closest distance to " O   HOH Z 227 " =    1.577
peak=    3.779 closest distance to " O   HOH Z  61 " =    1.665
peak=    3.773 closest distance to " O   HOH Z 368 " =    2.025
peak=    3.772 closest distance to " CB  THR A  31 " =    1.489
peak=    3.767 closest distance to " O   HOH Z 421 " =    1.711
peak=    3.766 closest distance to " O   HOH Z 313 " =    2.072
peak=    3.763 closest distance to " N   ASN A  39 " =    1.201
peak=    3.759 closest distance to " CG  ARG A  66 " =    2.584
peak=    3.742 closest distance to " O   HOH Z  59 " =    2.116
peak=    3.738 closest distance to " O   HOH Z 353 " =    2.643
peak=    3.722 closest distance to " O   HOH Z 193 " =    1.740
peak=    3.720 closest distance to " O   HOH Z 265 " =    2.192
peak=    3.716 closest distance to " O   HOH Z 261 " =    1.988
peak=    3.716 closest distance to " CG  MET A 185 " =    1.089
peak=    3.715 closest distance to " CA  ASN A 215 " =    1.027
peak=    3.714 closest distance to " O   HOH Z 368 " =    3.677
peak=    3.711 closest distance to " CB  ALA A 114 " =    1.011
peak=    3.707 closest distance to " O   HOH Z 132 " =    2.791
peak=    3.699 closest distance to " CA  SER A  87 " =    0.995
peak=    3.698 closest distance to " O   HOH Z 214 " =    2.142
peak=    3.698 closest distance to " CB  TRP A 266 " =    1.048
peak=    3.691 closest distance to " CB  PHE A 204 " =    0.765
peak=    3.690 closest distance to " O   HOH Z 180 " =    2.192
peak=    3.687 closest distance to " N   PHE A 130 " =    1.254
peak=    3.684 closest distance to " NH1AARG A 145 " =    1.311
peak=    3.684 closest distance to " CZ3 TRP A 266 " =    1.091
peak=    3.684 closest distance to " OG ASER A 258 " =    3.065
peak=    3.676 closest distance to " O   HOH Z 158 " =    3.056
peak=    3.673 closest distance to " O   THR A 220 " =    1.186
peak=    3.666 closest distance to " CG AARG A 275 " =    1.124
peak=    3.666 closest distance to " O  BHOH Z 338 " =    2.310
peak=    3.658 closest distance to " O   ASN A  74 " =    1.406
peak=    3.654 closest distance to " O   HOH Z 327 " =    1.567
peak=    3.648 closest distance to " NH2BARG A 145 " =    2.056
peak=    3.645 closest distance to " CA  ALA A  84 " =    1.191
peak=    3.642 closest distance to " O   HOH Z 251 " =    1.619
peak=    3.641 closest distance to " O   HOH Z 419 " =    2.082
peak=    3.637 closest distance to " O   HOH Z 389 " =    1.777
peak=    3.633 closest distance to " N   ARG A 156 " =    1.372
peak=    3.625 closest distance to " CD2 LEU A 297 " =    1.031
peak=    3.624 closest distance to " O   HOH Z  88 " =    2.592
peak=    3.622 closest distance to " CZ  PHE A  38 " =    1.217
peak=    3.613 closest distance to " O   HOH Z 173 " =    1.981
peak=    3.607 closest distance to " CE  LYS A 119 " =    1.175
peak=    3.600 closest distance to " CG2AVAL A  72 " =    1.689
peak=    3.597 closest distance to " O   HOH Z  19 " =    1.984
peak=    3.594 closest distance to " CA  ALA A  51 " =    0.914
peak=    3.591 closest distance to " O   HOH Z 126 " =    1.589
peak=    3.584 closest distance to " CG  GLN A  11 " =    1.572
peak=    3.575 closest distance to " O   HOH Z 280 " =    2.999
peak=    3.574 closest distance to " O   HOH Z  21 " =    1.856
peak=    3.574 closest distance to " CB  SER A   3 " =    1.147
peak=    3.571 closest distance to " O   HOH Z 392 " =    2.744
peak=    3.568 closest distance to " O   HOH Z  54 " =    1.685
peak=    3.550 closest distance to " CG  GLU A  37 " =    0.991
peak=    3.548 closest distance to " CB  SER A  26 " =    1.772
peak=    3.543 closest distance to " O   HOH Z 148 " =    3.431
peak=    3.542 closest distance to " O   HOH Z 411 " =    3.901
peak=    3.537 closest distance to " CG2AVAL A 121 " =    2.258
peak=    3.536 closest distance to " CB  HIS A 108 " =    0.848
peak=    3.536 closest distance to " CA  ILE A 234 " =    0.951
peak=    3.533 closest distance to " O   HOH Z  85 " =    1.486
peak=    3.529 closest distance to " O   HOH Z 163 " =    2.026
peak=    3.521 closest distance to " CB  ASN A 142 " =    1.079
peak=    3.521 closest distance to " CB  PRO A  90 " =    1.074
peak=    3.521 closest distance to " CB  LEU A 228 " =    1.112
peak=    3.515 closest distance to " O   HOH Z 337 " =    3.572
peak=    3.508 closest distance to " CB  TRP A 179 " =    1.321
peak=    3.496 closest distance to " CB  ALA A 291 " =    1.176
peak=    3.495 closest distance to " O   HOH Z 325 " =    2.363
peak=    3.490 closest distance to " O   ALA A 165 " =    1.484
peak=    3.488 closest distance to " CE1 TYR A 186 " =    1.262
peak=    3.482 closest distance to " CB  GLU A 128 " =    0.986
peak=    3.481 closest distance to " OG BSER A 164 " =    2.195
peak=    3.472 closest distance to " CD1 ILE A 199 " =    1.093
peak=    3.472 closest distance to " CB  ALA A 248 " =    1.314
peak=    3.469 closest distance to " CG  LEU A 167 " =    1.254
peak=    3.462 closest distance to " CB  LEU A  83 " =    0.758
peak=    3.458 closest distance to " OG  SER A 276 " =    1.318
peak=    3.457 closest distance to " CB  GLN A  89 " =    1.368
peak=    3.453 closest distance to " CA  TYR A 116 " =    1.398
peak=    3.451 closest distance to " CG2 ILE A  20 " =    1.382
peak=    3.447 closest distance to " CB  SER A 141 " =    1.069
peak=    3.443 closest distance to " OG1 THR A 264 " =    0.763
peak=    3.440 closest distance to " O   HOH Z 298 " =    2.249
peak=    3.435 closest distance to " O   HOH Z 357 " =    2.053
peak=    3.431 closest distance to " CG1 ILE A  33 " =    1.246
peak=    3.430 closest distance to " O   HOH Z 203 " =    1.776
peak=    3.430 closest distance to " CB  GLN A 205 " =    1.118
peak=    3.430 closest distance to " O   HOH Z  88 " =    3.048
peak=    3.423 closest distance to " CA  VAL A 125 " =    1.124
peak=    3.421 closest distance to " O   HOH Z 371 " =    3.082
peak=    3.415 closest distance to " O   HOH Z 345 " =    3.066
peak=    3.411 closest distance to " O   HOH Z 273 " =    2.890
peak=    3.405 closest distance to " O   HOH Z 417 " =    3.498
peak=    3.403 closest distance to " O   HOH Z 234 " =    2.267
peak=    3.401 closest distance to " CB  TYR A 169 " =    0.782
peak=    3.401 closest distance to " CA  ALA A 154 " =    0.973
peak=    3.391 closest distance to " CA  ASN A 176 " =    1.160
peak=    3.386 closest distance to " CB  PRO A 198 " =    1.167
peak=    3.383 closest distance to " O   HOH Z 329 " =    4.061
peak=    3.377 closest distance to " CA  MET A 105 " =    1.015
peak=    3.377 closest distance to " CA  ASN A 217 " =    1.259
peak=    3.371 closest distance to " CB  SER A 210 " =    0.845
peak=    3.360 closest distance to " O   HOH Z 417 " =    1.052
peak=    3.359 closest distance to " CB  GLN A  88 " =    1.128
peak=    3.358 closest distance to " O   THR A 182 " =    1.436
peak=    3.353 closest distance to " CD  ARG A 159 " =    0.713
peak=    3.352 closest distance to " O   HOH Z 245 " =    1.348
peak=    3.342 closest distance to " O   HOH Z 299 " =    4.352
peak=    3.338 closest distance to " O   HOH Z 407 " =    2.808
peak=    3.334 closest distance to " CA  ASP A 162 " =    1.042
peak=    3.332 closest distance to " O   HOH Z  78 " =    2.188
peak=    3.327 closest distance to " CB  PRO A 243 " =    1.258
peak=    3.322 closest distance to " CA  ASN A 127 " =    1.189
peak=    3.322 closest distance to " CA  ALA A  21 " =    1.085
peak=    3.322 closest distance to " O   HOH Z 185 " =    1.834
peak=    3.321 closest distance to " CB  SER A  62 " =    0.951
peak=    3.314 closest distance to " O   HOH Z  80 " =    1.730
peak=    3.308 closest distance to " CD1AILE A 234 " =    0.927
peak=    3.305 closest distance to " OD1 ASN A  69 " =    2.551
peak=    3.303 closest distance to " CB  ILE A 120 " =    1.268
peak=    3.303 closest distance to " O   HOH Z 359 " =    1.567
peak=    3.299 closest distance to " CB  SER A 212 " =    1.190
peak=    3.298 closest distance to " OG ASER A  99 " =    1.424
peak=    3.298 closest distance to " O   HOH Z 109 " =    1.208
peak=    3.297 closest distance to " OH  TYR A 116 " =    1.078
peak=    3.294 closest distance to " O   HOH Z  78 " =    2.452
peak=    3.288 closest distance to " CB  ASP A 140 " =    1.134
peak=    3.285 closest distance to " O   HOH Z 305 " =    3.671
peak=    3.284 closest distance to " CG1 VAL A 153 " =    0.938
peak=    3.279 closest distance to " O   HOH Z  66 " =    2.171
peak=    3.277 closest distance to " O   HOH Z 132 " =    2.506
peak=    3.275 closest distance to " O   HOH Z 227 " =    2.129
peak=    3.274 closest distance to " CG2 ILE A 239 " =    0.715
peak=    3.269 closest distance to " O   HOH Z  63 " =    2.278
peak=    3.263 closest distance to " O   GLY A  91 " =    1.501
peak=    3.257 closest distance to " O   HOH Z  62 " =    2.234
peak=    3.256 closest distance to " O   HOH Z 344 " =    3.139
peak=    3.246 closest distance to " O   HOH Z  10 " =    1.769
peak=    3.243 closest distance to " O   HOH Z 213 " =    1.777
peak=    3.243 closest distance to " CB  ALA A 242 " =    0.989
peak=    3.242 closest distance to " O   HOH Z   1 " =    2.010
peak=    3.238 closest distance to " O   LEU A 228 " =    1.782
peak=    3.238 closest distance to " CA  THR A 264 " =    0.888
peak=    3.237 closest distance to " O   HOH Z 361 " =    2.466
peak=    3.236 closest distance to " O   HOH Z  47 " =    1.621
peak=    3.226 closest distance to " OG  SER A  28 " =    1.444
peak=    3.224 closest distance to " CB  ALA A 104 " =    0.738
peak=    3.221 closest distance to " O   HOH Z 172 " =    3.876
peak=    3.220 closest distance to " CA  ALA A 248 " =    1.186
peak=    3.217 closest distance to " O   HOH Z 193 " =    1.940
peak=    3.216 closest distance to " CZ2 TRP A 179 " =    1.803
peak=    3.210 closest distance to " O   HOH Z  61 " =    1.452
peak=    3.207 closest distance to " CD1 LEU A  96 " =    0.708
peak=    3.205 closest distance to " O   HOH Z  48 " =    1.572
peak=    3.203 closest distance to " CA  SER A  32 " =    1.709
peak=    3.190 closest distance to " O   HOH Z 422 " =    2.591
peak=    3.188 closest distance to " O   HOH Z 425 " =    1.916
peak=    3.185 closest distance to " N   ASP A 162 " =    1.129
peak=    3.185 closest distance to " OG  SER A  62 " =    2.705
peak=    3.182 closest distance to " CG2BVAL A  41 " =    0.864
peak=    3.181 closest distance to " O   HOH Z  94 " =    2.358
peak=    3.175 closest distance to " N   CYS A 260 " =    0.932
peak=    3.173 closest distance to " OE1 GLU A 236 " =    1.294
peak=    3.172 closest distance to " CA  GLN A  94 " =    0.731
peak=    3.167 closest distance to " CB  LEU A 300 " =    0.941
peak=    3.163 closest distance to " CB  ASN A 215 " =    1.160
peak=    3.163 closest distance to " O   HOH Z  90 " =    2.233
peak=    3.161 closest distance to " OE1 GLU A   2 " =    2.243
peak=    3.161 closest distance to " O   HOH Z 285 " =    2.389
peak=    3.160 closest distance to " CG  MET A 113 " =    1.082
peak=    3.159 closest distance to " CA  ASP A 140 " =    1.151
peak=    3.158 closest distance to " N   SER A 135 " =    1.333
peak=    3.156 closest distance to " O   HOH Z  96 " =    1.960
peak=    3.139 closest distance to " NH2BARG A 190 " =    1.652
peak=    3.137 closest distance to " CB  ASN A 285 " =    0.997
peak=    3.137 closest distance to " CA  ILE A 263 " =    1.026
peak=    3.136 closest distance to " O   HOH Z 394 " =    3.885
peak=    3.136 closest distance to " O   HOH Z 380 " =    1.948
peak=    3.134 closest distance to " CA  ASP A 124 " =    0.771
peak=    3.132 closest distance to " CA  LYS A 117 " =    1.234
peak=    3.132 closest distance to " CD1 ILE A 106 " =    0.895
peak=    3.122 closest distance to " O   HOH Z 426 " =    1.763
peak=    3.121 closest distance to " O   HOH Z 233 " =    1.750
peak=    3.121 closest distance to " CA  MET A  40 " =    1.109
peak=    3.113 closest distance to " CG  LYS A 119 " =    1.116
peak=    3.102 closest distance to " O   HOH Z   9 " =    2.052
peak=    3.101 closest distance to " N   LYS A 119 " =    1.496
peak=    3.094 closest distance to " CB  TYR A 116 " =    0.753
peak=    3.090 closest distance to " CG2 VAL A 197 " =    1.061
peak=    3.087 closest distance to " CB  THR A 279 " =    1.633
peak=    3.086 closest distance to " O   HOH Z 263 " =    1.764
peak=    3.080 closest distance to " O   HOH Z 147 " =    1.855
peak=    3.074 closest distance to " CD2 TYR A 186 " =    1.074
peak=    3.072 closest distance to " CG2 VAL A 296 " =    1.126
peak=    3.069 closest distance to " O   HOH Z   1 " =    1.540
peak=    3.067 closest distance to " O   HOH Z 433 " =    1.853
peak=    3.061 closest distance to " CA  LYS A 290 " =    1.189
peak=    3.018 closest distance to " NE AARG A 190 " =    2.037

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 189         
Filter by distance & map next to the model:
   mapped sites are within: 0.471 - 5.925
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 188 from: 189
   mapped sites are within: 0.742 - 5.925

peak=   -5.021 closest distance to " CG  GLN A  58 " =    1.025
peak=   -4.528 closest distance to " C   HIS A 108 " =    1.082
peak=   -4.464 closest distance to " CD  ARG A  14 " =    3.413
peak=   -4.365 closest distance to " OG BSER A 134 " =    1.304
peak=   -4.346 closest distance to " O   HOH Z 198 " =    1.310
peak=   -4.333 closest distance to " O   HOH Z 266 " =    5.411
peak=   -4.327 closest distance to " CG2 ILE A  49 " =    2.738
peak=   -4.321 closest distance to " O   PRO A 198 " =    1.258
peak=   -4.268 closest distance to " CB  PRO A 243 " =    2.715
peak=   -4.153 closest distance to " CD  ARG A 156 " =    2.122
peak=   -4.114 closest distance to " N   ALA A 248 " =    1.707
peak=   -4.109 closest distance to " O   HOH Z 377 " =    2.091
peak=   -4.102 closest distance to " O   HOH Z 290 " =    1.093
peak=   -4.033 closest distance to " OG  SER A  97 " =    2.222
peak=   -4.029 closest distance to " O   HOH Z 231 " =    2.327
peak=   -4.002 closest distance to " CG1 VAL A 112 " =    2.792
peak=   -3.955 closest distance to " OXT GLY A 302 " =    2.886
peak=   -3.948 closest distance to " CD1 LEU A 101 " =    2.411
peak=   -3.939 closest distance to " CA  VAL A  67 " =    2.945
peak=   -3.932 closest distance to " CB  PHE A 192 " =    2.060
peak=   -3.931 closest distance to " CG  GLN A 223 " =    2.146
peak=   -3.925 closest distance to " O   VAL A  67 " =    2.674
peak=   -3.915 closest distance to " CD2 TYR A 293 " =    1.978
peak=   -3.894 closest distance to " CE  MET A 105 " =    2.471
peak=   -3.882 closest distance to " CE2 TYR A  30 " =    2.786
peak=   -3.882 closest distance to " O   HOH Z 351 " =    1.431
peak=   -3.831 closest distance to " CZ3 TRP A 179 " =    1.253
peak=   -3.826 closest distance to " CB  ASN A  39 " =    2.326
peak=   -3.807 closest distance to " CD1 LEU A  25 " =    2.554
peak=   -3.755 closest distance to " NH2 ARG A  66 " =    1.188
peak=   -3.741 closest distance to " O   HOH Z   6 " =    2.039
peak=   -3.728 closest distance to " O   ILE A 109 " =    2.541
peak=   -3.721 closest distance to " O   HOH Z 165 " =    1.951
peak=   -3.695 closest distance to " O   SER A 210 " =    2.008
peak=   -3.690 closest distance to " O   HOH Z 211 " =    1.472
peak=   -3.679 closest distance to " O   PRO A 163 " =    2.022
peak=   -3.671 closest distance to " N   THR A  52 " =    1.727
peak=   -3.667 closest distance to " O   HOH Z 185 " =    2.376
peak=   -3.658 closest distance to " O   VAL A 174 " =    2.174
peak=   -3.626 closest distance to " CD1 ILE A 239 " =    2.344
peak=   -3.622 closest distance to " O   HOH Z 348 " =    2.235
peak=   -3.618 closest distance to " CA  GLY A 241 " =    2.388
peak=   -3.609 closest distance to " CG  GLN A  11 " =    1.709
peak=   -3.608 closest distance to " OD2 ASP A 191 " =    1.430
peak=   -3.607 closest distance to " CZ  TYR A 169 " =    1.822
peak=   -3.601 closest distance to " O   HOH Z 394 " =    1.492
peak=   -3.594 closest distance to " O   HOH Z 196 " =    1.929
peak=   -3.590 closest distance to " ND2 ASN A 249 " =    2.323
peak=   -3.583 closest distance to " CA  ASP A 298 " =    1.084
peak=   -3.578 closest distance to " CE2 PHE A  61 " =    2.629
peak=   -3.578 closest distance to " ND2 ASN A  45 " =    1.123
peak=   -3.572 closest distance to " O   HOH Z 372 " =    2.204
peak=   -3.567 closest distance to " ND2 ASN A 187 " =    1.500
peak=   -3.566 closest distance to " O   ALA A  10 " =    1.778
peak=   -3.536 closest distance to " O   HOH Z 102 " =    1.677
peak=   -3.513 closest distance to " OD2 ASP A 171 " =    2.392
peak=   -3.506 closest distance to " O   HOH Z 407 " =    2.741
peak=   -3.499 closest distance to " O   HOH Z   6 " =    1.507
peak=   -3.493 closest distance to " O   HOH Z  15 " =    1.502
peak=   -3.490 closest distance to " CG  GLU A 277 " =    1.283
peak=   -3.489 closest distance to " CG1 VAL A 112 " =    2.621
peak=   -3.484 closest distance to " O   PHE A 218 " =    1.603
peak=   -3.481 closest distance to " CA  GLY A 241 " =    3.236
peak=   -3.481 closest distance to " CD  PRO A 243 " =    2.087
peak=   -3.477 closest distance to " OD1 ASP A 171 " =    1.500
peak=   -3.477 closest distance to " CB  ALA A  43 " =    2.352
peak=   -3.472 closest distance to " CB  ALA A 248 " =    2.260
peak=   -3.468 closest distance to " NE2 GLN A 278 " =    1.674
peak=   -3.467 closest distance to " CG1 VAL A  67 " =    3.079
peak=   -3.465 closest distance to " O   HOH Z 183 " =    1.621
peak=   -3.463 closest distance to " N   ASP A 286 " =    2.186
peak=   -3.458 closest distance to " CD  ARG A 195 " =    5.165
peak=   -3.458 closest distance to " O   ALA A 292 " =    2.115
peak=   -3.455 closest distance to " O   HOH Z 166 " =    2.036
peak=   -3.454 closest distance to " O   SER A  95 " =    1.551
peak=   -3.433 closest distance to " O   HOH Z 429 " =    2.215
peak=   -3.429 closest distance to " O   HOH Z 374 " =    1.952
peak=   -3.424 closest distance to " CG  GLU A  53 " =    1.462
peak=   -3.424 closest distance to " O   HOH Z 281 " =    2.657
peak=   -3.423 closest distance to " CE3 TRP A 150 " =    2.202
peak=   -3.421 closest distance to " O   HOH Z 353 " =    2.236
peak=   -3.419 closest distance to " CG  PHE A 283 " =    2.567
peak=   -3.418 closest distance to " CG2 ILE A 263 " =    2.217
peak=   -3.414 closest distance to " ND2 ASN A  45 " =    1.754
peak=   -3.404 closest distance to " OE1 GLN A 183 " =    1.570
peak=   -3.400 closest distance to " CE BMET A  47 " =    1.391
peak=   -3.398 closest distance to " N   ALA A  43 " =    2.546
peak=   -3.395 closest distance to " O   HOH Z  63 " =    1.601
peak=   -3.373 closest distance to " O   HOH Z 421 " =    3.453
peak=   -3.373 closest distance to " CB  ASP A 132 " =    2.297
peak=   -3.372 closest distance to " O   HOH Z 193 " =    1.468
peak=   -3.365 closest distance to " OD1 ASN A 148 " =    1.418
peak=   -3.357 closest distance to " CZ3 TRP A 274 " =    2.396
peak=   -3.356 closest distance to " NE2 GLN A  88 " =    1.059
peak=   -3.355 closest distance to " CZ  PHE A 155 " =    1.070
peak=   -3.352 closest distance to " O   ILE A 106 " =    1.792
peak=   -3.351 closest distance to " O   HOH Z  43 " =    1.410
peak=   -3.350 closest distance to " O   TRP A  92 " =    1.936
peak=   -3.349 closest distance to " NH2 ARG A  79 " =    1.584
peak=   -3.334 closest distance to " O   HOH Z  38 " =    1.740
peak=   -3.329 closest distance to " CG1AVAL A  41 " =    2.524
peak=   -3.327 closest distance to " CD  ARG A  79 " =    1.169
peak=   -3.326 closest distance to " O   HOH Z  60 " =    1.763
peak=   -3.325 closest distance to " ND2 ASN A  45 " =    1.161
peak=   -3.315 closest distance to " CA  ILE A 263 " =    1.090
peak=   -3.313 closest distance to " CD1 ILE A 106 " =    2.262
peak=   -3.309 closest distance to " NH2AARG A 275 " =    5.040
peak=   -3.308 closest distance to " O   HOH Z 191 " =    5.925
peak=   -3.307 closest distance to " CD1 LEU A 255 " =    2.687
peak=   -3.306 closest distance to " O   VAL A 189 " =    2.623
peak=   -3.304 closest distance to " O   HOH Z  13 " =    1.667
peak=   -3.298 closest distance to " O   HOH Z 357 " =    2.125
peak=   -3.297 closest distance to " O   HOH Z 233 " =    2.466
peak=   -3.289 closest distance to " CD  ARG A 139 " =    1.573
peak=   -3.289 closest distance to " CD  GLN A 223 " =    0.742
peak=   -3.287 closest distance to " OG BSER A 134 " =    1.841
peak=   -3.283 closest distance to " CD  GLN A 223 " =    1.136
peak=   -3.281 closest distance to " CD1 PHE A  59 " =    1.954
peak=   -3.281 closest distance to " O   HOH Z 174 " =    2.347
peak=   -3.279 closest distance to " CD2 LEU A 237 " =    2.542
peak=   -3.279 closest distance to " O   HOH Z 111 " =    3.790
peak=   -3.276 closest distance to " ND2 ASN A  60 " =    4.130
peak=   -3.273 closest distance to " O   VAL A 189 " =    1.716
peak=   -3.271 closest distance to " O   HOH Z 139 " =    3.276
peak=   -3.267 closest distance to " CB  ALA A 291 " =    2.331
peak=   -3.267 closest distance to " O   ALA A  34 " =    2.198
peak=   -3.263 closest distance to " O   HOH Z 200 " =    4.815
peak=   -3.261 closest distance to " O   HOH Z 106 " =    1.854
peak=   -3.256 closest distance to " O   HOH Z 114 " =    3.226
peak=   -3.256 closest distance to " CG  TRP A 266 " =    2.025
peak=   -3.254 closest distance to " O   GLY A  80 " =    2.348
peak=   -3.253 closest distance to " O   ALA A 227 " =    1.518
peak=   -3.249 closest distance to " O   LEU A 167 " =    1.486
peak=   -3.247 closest distance to " CZ  TYR A 172 " =    1.910
peak=   -3.245 closest distance to " C   SER A 206 " =    1.554
peak=   -3.242 closest distance to " O   HOH Z 113 " =    1.714
peak=   -3.241 closest distance to " OD1 ASN A 301 " =    1.878
peak=   -3.239 closest distance to " O   HOH Z 313 " =    2.008
peak=   -3.239 closest distance to " O   HOH Z 362 " =    5.838
peak=   -3.237 closest distance to " CA  GLY A 203 " =    2.318
peak=   -3.236 closest distance to " O   HOH Z 243 " =    2.000
peak=   -3.228 closest distance to " OE1 GLU A  44 " =    1.144
peak=   -3.226 closest distance to " CG  ASP A 231 " =    0.814
peak=   -3.222 closest distance to " CB  ALA A 291 " =    2.149
peak=   -3.219 closest distance to " C   LEU A 143 " =    0.983
peak=   -3.218 closest distance to " N   GLN A  58 " =    1.710
peak=   -3.213 closest distance to " CB  ASP A 286 " =    1.793
peak=   -3.210 closest distance to " CG1 VAL A 125 " =    1.953
peak=   -3.208 closest distance to " O   LYS A  76 " =    2.049
peak=   -3.206 closest distance to " O   HOH Z 369 " =    2.271
peak=   -3.199 closest distance to " O   HOH Z 283 " =    2.503
peak=   -3.199 closest distance to " O   GLN A  89 " =    1.503
peak=   -3.192 closest distance to " CB  TRP A  85 " =    2.564
peak=   -3.190 closest distance to " O   HOH Z 301 " =    2.422
peak=   -3.188 closest distance to " CG2 THR A  18 " =    2.916
peak=   -3.183 closest distance to " C   MET A 188 " =    1.460
peak=   -3.176 closest distance to " O   HOH Z 126 " =    1.969
peak=   -3.173 closest distance to " O   HOH Z  88 " =    2.708
peak=   -3.173 closest distance to " O   HOH Z 171 " =    2.055
peak=   -3.169 closest distance to " OD1 ASP A 191 " =    1.465
peak=   -3.165 closest distance to " O   GLU A 152 " =    1.548
peak=   -3.157 closest distance to " O   GLU A 152 " =    1.341
peak=   -3.154 closest distance to " O   HOH Z  10 " =    1.495
peak=   -3.151 closest distance to " O   TRP A  70 " =    1.500
peak=   -3.150 closest distance to " O   HOH Z  37 " =    1.738
peak=   -3.143 closest distance to " O   HOH Z 414 " =    1.554
peak=   -3.135 closest distance to " CD2 LEU A 237 " =    2.132
peak=   -3.134 closest distance to " O   HOH Z  71 " =    2.382
peak=   -3.131 closest distance to " CB  SER A 210 " =    1.129
peak=   -3.126 closest distance to " O   SER A   3 " =    0.984
peak=   -3.112 closest distance to " CG  ARG A 269 " =    2.220
peak=   -3.107 closest distance to " O   HOH Z 405 " =    2.595
peak=   -3.106 closest distance to " O   HOH Z 110 " =    1.368
peak=   -3.104 closest distance to " O   HOH Z 198 " =    1.576
peak=   -3.102 closest distance to " CB  HIS A  86 " =    1.129
peak=   -3.099 closest distance to " O   PRO A 198 " =    1.253
peak=   -3.098 closest distance to " N   PHE A  59 " =    1.817
peak=   -3.086 closest distance to " ND2 ASN A  60 " =    1.289
peak=   -3.082 closest distance to " CG2 THR A 178 " =    2.348
peak=   -3.077 closest distance to " OG  SER A   3 " =    1.692
peak=   -3.072 closest distance to " O   HOH Z 134 " =    3.195
peak=   -3.071 closest distance to " OH  TYR A 169 " =    0.933
peak=   -3.061 closest distance to " O   HOH Z 265 " =    2.364
peak=   -3.056 closest distance to " NE2 GLN A  88 " =    1.768
peak=   -3.053 closest distance to " C   GLY A  17 " =    1.013
peak=   -3.047 closest distance to " O   HOH Z 150 " =    2.048
peak=   -3.034 closest distance to " O   HOH Z  89 " =    2.742
peak=   -3.031 closest distance to " CD2 LEU A 237 " =    2.356

================= 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    :  0.3822 0.3774   6.158750e+00   6.145304e+00
   1_bss:  0.3723 0.3673   6.144206e+00   6.128812e+00
   1_xyz:  0.2268 0.2557   5.719358e+00   5.819382e+00
   1_adp:  0.2087 0.2606   5.673308e+00   5.844038e+00
   1_occ:  0.2084 0.2609   5.673402e+00   5.844840e+00
   2_bss:  0.2045 0.2571   5.665643e+00   5.838154e+00
   2_xyz:  0.1453 0.1838   5.349908e+00   5.534461e+00
   2_adp:  0.1330 0.1762   5.281915e+00   5.489210e+00
   2_occ:  0.1328 0.1760   5.281058e+00   5.488548e+00
   3_bss:  0.1327 0.1757   5.279086e+00   5.484869e+00
   3_xyz:  0.1191 0.1616   5.191416e+00   5.409841e+00
   3_adp:  0.1181 0.1591   5.182426e+00   5.395917e+00
   3_occ:  0.1179 0.1590   5.181883e+00   5.395646e+00
   4_bss:  0.1179 0.1590   5.181644e+00   5.395377e+00
   4_xyz:  0.1124 0.1556   5.148159e+00   5.375362e+00
   4_adp:  0.1123 0.1547   5.145562e+00   5.371457e+00
   4_occ:  0.1121 0.1547   5.144728e+00   5.370836e+00
   5_bss:  0.1121 0.1547   5.144734e+00   5.370799e+00
   5_xyz:  0.1138 0.1556   5.157416e+00   5.379347e+00
   5_adp:  0.1130 0.1561   5.155615e+00   5.384519e+00
   5_occ:  0.1129 0.1561   5.155650e+00   5.384634e+00
   5_bss:  0.1128 0.1557   5.154207e+00   5.380494e+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:  0.300  50.000  -0.144  -2.080   2.048  -0.000   0.000   0.000
   1_xyz:  0.300  50.000  -0.144  -2.080   2.048  -0.000   0.000   0.000
   1_adp:  0.300  50.000  -0.144  -2.080   2.048  -0.000   0.000   0.000
   1_occ:  0.300  50.000  -0.144  -2.080   2.048  -0.000   0.000   0.000
   2_bss:  0.329  56.719  -2.588  -2.486  -0.282  -0.000  -0.000  -0.000
   2_xyz:  0.329  56.719  -2.588  -2.486  -0.282  -0.000  -0.000  -0.000
   2_adp:  0.329  56.719  -2.588  -2.486  -0.282  -0.000  -0.000  -0.000
   2_occ:  0.329  56.719  -2.588  -2.486  -0.282  -0.000  -0.000  -0.000
   3_bss:  0.326  56.719  -3.077  -2.334  -0.694  -0.000  -0.000  -0.000
   3_xyz:  0.326  56.719  -3.077  -2.334  -0.694  -0.000  -0.000  -0.000
   3_adp:  0.326  56.719  -3.077  -2.334  -0.694  -0.000  -0.000  -0.000
   3_occ:  0.326  56.719  -3.077  -2.334  -0.694  -0.000  -0.000  -0.000
   4_bss:  0.326  56.719  -3.159  -2.269  -0.815  -0.000  -0.000  -0.000
   4_xyz:  0.326  56.719  -3.159  -2.269  -0.815  -0.000  -0.000  -0.000
   4_adp:  0.326  56.719  -3.159  -2.269  -0.815  -0.000  -0.000  -0.000
   4_occ:  0.326  56.719  -3.159  -2.269  -0.815  -0.000  -0.000  -0.000
   5_bss:  0.326  56.719  -3.108  -2.167  -0.755  -0.000  -0.000  -0.000
   5_xyz:  0.326  56.719  -3.108  -2.167  -0.755  -0.000  -0.000  -0.000
   5_adp:  0.326  56.719  -3.108  -2.167  -0.755  -0.000  -0.000  -0.000
   5_occ:  0.326  56.719  -3.108  -2.167  -0.755  -0.000  -0.000  -0.000
   5_bss:  0.322  52.969  -2.939  -1.967  -0.565  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  40.890 0.6343  0.8203    41838.512
   1_bss:  39.669 0.6472  0.8417    38682.671
   1_xyz:  25.073 0.8118  0.9956    16722.771
   1_adp:  25.958 0.8019  0.9881    17596.693
   1_occ:  26.010 0.8013  0.9874    17653.224
   2_bss:  25.680 0.8045  0.9313    17242.156
   2_xyz:  17.440 0.8851  0.9827     8586.431
   2_adp:  16.315 0.8954  0.9833     7889.265
   2_occ:  16.295 0.8956  0.9833     7873.985
   3_bss:  16.218 0.8962  0.9741     7795.265
   3_xyz:  14.729 0.9087  0.9783     6712.791
   3_adp:  14.447 0.9113  0.9744     6595.840
   3_occ:  14.442 0.9114  0.9743     6584.700
   4_bss:  14.436 0.9114  0.9727     6581.175
   4_xyz:  13.994 0.9150  0.9749     6310.031
   4_adp:  13.907 0.9158  0.9714     6277.043
   4_occ:  13.895 0.9159  0.9714     6265.973
   5_bss:  13.897 0.9158  0.9738     6265.893
   5_xyz:  14.006 0.9152  0.9730     6369.895
   5_adp:  14.087 0.9145  0.9680     6395.825
   5_occ:  14.088 0.9145  0.9678     6394.653
   5_bss:  14.040 0.9148  0.9729     6316.872
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.8828e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.8828e-01
   1_xyz:   1.193  0.008  0.075 14.982  0.005  4.111   7.8403e-02
   1_adp:   1.193  0.008  0.075 14.982  0.005  4.111   7.8403e-02
   1_occ:   1.193  0.008  0.075 14.982  0.005  4.111   7.8403e-02
   2_bss:   1.193  0.008  0.075 14.982  0.005  4.111   7.8403e-02
   2_xyz:   1.009  0.006  0.071 14.598  0.004  4.123   5.7107e-02
   2_adp:   1.009  0.006  0.071 14.598  0.004  4.123   5.7107e-02
   2_occ:   1.009  0.006  0.071 14.598  0.004  4.123   5.7107e-02
   3_bss:   1.009  0.006  0.071 14.598  0.004  4.123   5.7107e-02
   3_xyz:   0.974  0.007  0.074 14.597  0.004  4.127   5.5796e-02
   3_adp:   0.974  0.007  0.074 14.597  0.004  4.127   5.5796e-02
   3_occ:   0.974  0.007  0.074 14.597  0.004  4.127   5.5796e-02
   4_bss:   0.974  0.007  0.074 14.597  0.004  4.127   5.5796e-02
   4_xyz:   1.036  0.008  0.078 14.648  0.004  4.111   6.2992e-02
   4_adp:   1.036  0.008  0.078 14.648  0.004  4.111   6.2992e-02
   4_occ:   1.036  0.008  0.078 14.648  0.004  4.111   6.2992e-02
   5_bss:   1.036  0.008  0.078 14.648  0.004  4.111   6.2992e-02
   5_xyz:   0.937  0.006  0.073 14.426  0.004  4.111   5.2792e-02
   5_adp:   0.937  0.006  0.073 14.426  0.004  4.111   5.2792e-02
   5_occ:   0.937  0.006  0.073 14.426  0.004  4.111   5.2792e-02
   5_bss:   0.937  0.006  0.073 14.426  0.004  4.111   5.2792e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.416   2.4185e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.416   2.4185e-01
   1_xyz:   8.215  0.051  0.309 83.635  0.046  2.162   8.1124e-02
   1_adp:   8.215  0.051  0.309 83.635  0.046  2.162   8.1124e-02
   1_occ:   8.215  0.051  0.309 83.635  0.046  2.162   8.1124e-02
   2_bss:   8.215  0.051  0.309 83.635  0.046  2.162   8.1124e-02
   2_xyz:   6.868  0.035  0.245 81.787  0.038  2.310   4.2179e-02
   2_adp:   6.868  0.035  0.245 81.787  0.038  2.310   4.2179e-02
   2_occ:   6.868  0.035  0.245 81.787  0.038  2.310   4.2179e-02
   3_bss:   6.868  0.035  0.245 81.787  0.038  2.310   4.2179e-02
   3_xyz:   6.897  0.044  0.238 83.759  0.032  2.315   3.8053e-02
   3_adp:   6.897  0.044  0.238 83.759  0.032  2.315   3.8053e-02
   3_occ:   6.897  0.044  0.238 83.759  0.032  2.315   3.8053e-02
   4_bss:   6.897  0.044  0.238 83.759  0.032  2.315   3.8053e-02
   4_xyz:   7.372  0.050  0.259 83.060  0.038  2.343   4.4402e-02
   4_adp:   7.372  0.050  0.259 83.060  0.038  2.343   4.4402e-02
   4_occ:   7.372  0.050  0.259 83.060  0.038  2.343   4.4402e-02
   5_bss:   7.372  0.050  0.259 83.060  0.038  2.343   4.4402e-02
   5_xyz:   6.677  0.045  0.228 83.163  0.035  2.407   3.3186e-02
   5_adp:   6.677  0.045  0.228 83.163  0.035  2.407   3.3186e-02
   5_occ:   6.677  0.045  0.228 83.163  0.035  2.407   3.3186e-02
   5_bss:   6.677  0.045  0.228 83.163  0.035  2.407   3.3186e-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:  67.71   0.00  16.90  67.71   0.00  13.00  63.65   6.74  38.15
   1_occ:  67.71   0.00  16.90  67.71   0.00  13.00  63.65   6.74  38.15
   2_bss:  67.71   0.00  16.90  67.71   0.00  13.00  63.65   6.74  38.15
   2_xyz:  67.71   0.00  16.90  67.71   0.00  13.00  63.65   6.74  38.15
   2_adp:  83.35   0.00  17.47  83.35   0.00  13.20  76.12   6.64  40.75
   2_occ:  83.35   0.00  17.47  83.35   0.00  13.20  76.12   6.64  40.75
   3_bss:  83.35   0.00  17.47  83.35   0.00  13.20  76.12   6.64  40.75
   3_xyz:  83.35   0.00  17.47  83.35   0.00  13.20  76.12   6.64  40.75
   3_adp:  80.87   1.74  16.94  80.87   1.74  12.95  76.54   5.51  38.66
   3_occ:  80.87   1.74  16.94  80.87   1.74  12.95  76.54   5.51  38.66
   4_bss:  80.87   1.74  16.94  80.87   1.74  12.95  76.54   5.51  38.66
   4_xyz:  80.87   1.74  16.94  80.87   1.74  12.95  76.54   5.51  38.66
   4_adp:  79.83   0.00  16.70  79.83   2.10  12.79  75.91   0.00  37.97
   4_occ:  79.83   0.00  16.70  79.83   2.10  12.79  75.91   0.00  37.97
   5_bss:  79.83   0.00  16.70  79.83   2.10  12.79  75.91   0.00  37.97
   5_xyz:  79.83   0.00  16.70  79.83   2.10  12.79  75.91   0.00  37.97
   5_adp:  81.27   1.06  16.74  81.27   1.48  12.72  76.95   1.06  38.66
   5_occ:  81.27   1.06  16.74  81.27   1.48  12.72  76.95   1.06  38.66
   5_bss:  81.23   1.02  16.71  81.23   1.44  12.68  76.91   1.02  38.62
------------------------------------------------------------------------
 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:    1.708    0.018    0.350
   1_adp:    1.708    0.018    0.350
   1_occ:    1.708    0.018    0.350
   2_bss:    1.708    0.018    0.350
   2_xyz:    1.632    0.007    0.445
   2_adp:    1.632    0.007    0.445
   2_occ:    1.632    0.007    0.445
   3_bss:    1.632    0.007    0.445
   3_xyz:    1.547    0.043    0.482
   3_adp:    1.547    0.043    0.482
   3_occ:    1.547    0.043    0.482
   4_bss:    1.547    0.043    0.482
   4_xyz:    1.378    0.046    0.498
   4_adp:    1.378    0.046    0.498
   4_occ:    1.378    0.046    0.498
   5_bss:    1.378    0.046    0.498
   5_xyz:    1.357    0.058    0.502
   5_adp:    1.357    0.058    0.502
   5_occ:    1.357    0.058    0.502
   5_bss:    1.357    0.058    0.502
------------------------------------------------------------------------

CPU time actual refinement: 342.08


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_195/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_195/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_195/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_195/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_195/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 341.94 
  Macro-tasks:
    bulk solvent and scale       = 38.46  
    individual site refinement   = 145.42 
    weights calculation          = 30.78  
    collect and process          = 6.84   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 221.63 
  Micro-tasks:
    mask                            = 1.82   
    f_calc                          = 108.47 
    alpha_beta                      = 8.41   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 119.04 
    fmodel                         = 7.01   
    r_factors                      = 0.30   
    phase_errors                   = 11.12  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 257.64 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.777 micro seconds
Total CPU time: 5.92 minutes
from_scatterers_fft:    660 calls, 108.17 s
gradients_fft:          605 calls, 104.90 s

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

# Date 2008-01-16 Time 04:14:52 PST -0800 (1200485692.56 s)
Start R-work = 0.3822, R-free = 0.3774 (no bulk solvent and anisotropic scale)
Final R-work = 0.1372, R-free = 0.1755 (no bulk solvent and anisotropic scale)

Start R-work = 0.3723, R-free = 0.3673
Final R-work = 0.1128, R-free = 0.1557