# Date 2008-01-16 Time 05:46:15 PST -0800 (1200491175.40 s)
#phil __OFF__

Command line arguments: "../872.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 31468
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 872

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 46.2261, 85.5261, 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: 3.28, 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: (70.9525, 46.2261, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0608 1.97157
Completeness in resolution range: 0.95954
Completeness with d_max=infinity: 0.956681

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0608
                             d_min =   1.9716

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.2261, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0608 1.97157
Completeness in resolution range: 0.95954
Completeness with d_max=infinity: 0.956681

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0613 -  4.2194 [2136/2162]  1926   210   9.8%
  bin  2:  4.2194 -  3.3613 [2067/2087]  1857   210  10.2%
  bin  3:  3.3613 -  2.9400 [2032/2051]  1828   204  10.0%
  bin  4:  2.9400 -  2.6728 [2016/2046]  1815   201  10.0%
  bin  5:  2.6728 -  2.4822 [2015/2034]  1817   198   9.8%
  bin  6:  2.4822 -  2.3364 [1992/2017]  1785   207  10.4%
  bin  7:  2.3364 -  2.2198 [1976/2004]  1780   196   9.9%
  bin  8:  2.2198 -  2.1234 [1978/2014]  1781   197  10.0%
  bin  9:  2.1234 -  2.0419 [1960/2002]  1766   194   9.9%
  bin 10:  2.0419 -  1.9716 [1417/1998]  1275   142  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_872/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 33
        2.42 -     3.04: 2203
        3.04 -     3.66: 4752
        3.66 -     4.28: 9122
        4.28 -     4.90: 12378
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.918 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.075 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  2.148 3.040 x,y+1,z
  ... (remaining 28483 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_872/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_872/model_refine_001.geo

CPU time processing inputs: 9.18


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 46.22605 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


============================= ml refinement start =============================


   ----------structure factors based statistics (before refinement)----------  


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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3897   r_free= 0.3882   ksol= 0.00   Bsol= 0.00   scale= 0.946    |
|                                                                             |
| 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:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.175079                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0613 -  4.7065 0.99   1392  156 0.3197 0.3183      6.4337      6.4061|
|  2:  4.7065 -  3.7547 0.99   1338  146 0.3165 0.3093        6.62      6.5556|
|  3:  3.7547 -  3.2857 0.99   1323  144 0.3420 0.3029      6.4981      6.5825|
|  4:  3.2857 -  2.9878 0.99   1306  153 0.3626 0.4120      6.3958       6.398|
|  5:  2.9878 -  2.7751 0.99   1294  142 0.4087 0.3911      6.2557      6.2479|
|  6:  2.7751 -  2.6124 0.99   1295  142 0.4115 0.4075      6.1745      6.1442|
|  7:  2.6124 -  2.4822 0.99   1295  140 0.4185 0.4168      6.1525      6.1522|
|  8:  2.4822 -  2.3746 0.98   1254  144 0.4340 0.4073      6.0866      6.0615|
|  9:  2.3746 -  2.2835 0.98   1290  148 0.4299 0.4153      6.0445      6.0403|
| 10:  2.2835 -  2.2049 1.00   1278  138 0.4382 0.4669      6.0179      6.0388|
| 11:  2.2049 -  2.1362 0.98   1272  136 0.4517 0.4573      5.9823      6.0129|
| 12:  2.1362 -  2.0753 0.98   1250  145 0.4602 0.4779      5.9358      5.9659|
| 13:  2.0753 -  2.0208 0.99   1284  137 0.4432 0.4621       5.823      5.7564|
| 14:  2.0208 -  1.9716 0.59    759   88 0.4895 0.4594      5.8213      5.7942|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0613 -  4.7065  1392   156  0.77  28.35   0.85     0.80      50679.57|
|  2:  4.7065 -  3.7547  1338   146  0.79  26.78   0.95     0.90      65943.14|
|  3:  3.7547 -  3.2857  1323   144  0.73  33.11   0.98     0.90      70808.62|
|  4:  3.2857 -  2.9878  1306   153  0.67  38.29   0.97     0.86      66624.25|
|  5:  2.9878 -  2.7751  1294   142  0.59  44.55   0.94     0.80      55531.52|
|  6:  2.7751 -  2.6124  1295   142  0.58  45.36   0.95     0.79      48744.52|
|  7:  2.6124 -  2.4822  1295   140  0.59  45.22   0.97     0.78      43050.25|
|  8:  2.4822 -  2.3746  1254   144  0.57  46.60   0.97     0.79      39393.90|
|  9:  2.3746 -  2.2835  1290   148  0.58  45.92   0.97     0.78      35476.86|
| 10:  2.2835 -  2.2049  1278   138  0.56  47.41   1.00     0.79      33936.53|
| 11:  2.2049 -  2.1362  1272   136  0.53  49.47   1.01     0.79      33637.97|
| 12:  2.1362 -  2.0753  1250   145  0.51  51.29   0.99     0.76      31833.76|
| 13:  2.0753 -  2.0208  1284   137  0.48  54.03   1.00     0.72      28494.16|
| 14:  2.0208 -  1.9716   759    88  0.47  54.37   0.98     0.66      24058.39|
|alpha:            min =        0.66 max =            0.90 mean =         0.80|
|beta:             min =    24058.39 max =        70808.62 mean =     45726.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.61|
|phase err.(work): min =        0.00 max =           89.98 mean =        43.11|
|phase err.(test): min =        0.00 max =           89.89 mean =        43.28|
|-----------------------------------------------------------------------------|

============================== 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 = 5.699796              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.382   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.318572              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.673   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       29 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      204 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1999 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1898 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2854 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4672 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4450 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5641 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6737 |
|-----------------------------------------------------------------------------|
|-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 |        0.165 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.806 |       0.231 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.738)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3897   r_free= 0.3882   ksol= 0.00   Bsol= 0.00   scale= 0.946    |
|                                                                             |
| 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:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.175079                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3784   r_free= 0.3802   ksol= 0.33   Bsol= 34.93   scale= 0.968   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.58,1.83,-0.72,0.00,-0.00,-0.00); trace/3= -0.16                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.162579                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.880058              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.503   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.649733              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.456   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3784      final r-factor (work) = 0.2410          |
| start r-factor (free) = 0.3802      final r-factor (free) = 0.2718          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.2001 = 4.88 * 0.50 * 6.1618 + 1.00 * 0.1652                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.6010 = 4.88 * 0.50 * 5.9480 + 1.00 * 0.0876                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2410      final r-factor (work) = 0.2207          |
| start r-factor (free) = 0.2718      final r-factor (free) = 0.2821          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8707 = 0.65 * 1.00 * 5.9480 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7364 = 0.65 * 1.00 * 5.7320 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.738)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.90   17.58    None  None   None       |
|    all(noH): 2823   0      0.00    83.90   17.58    None  None   None       |
|    Sol.    : 438    0      5.40    83.90   40.16    None  None   None       |
|    Mac.    : 2385   0      0.00    74.44   13.44    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 -   8.390:  711   |   5:    41.948 -  50.337:  111        |
|      1:     8.390 -  16.779: 1150   |   6:    50.337 -  58.727:   83        |
|      2:    16.779 -  25.169:  400   |   7:    58.727 -  67.116:   35        |
|      3:    25.169 -  33.558:  189   |   8:    67.116 -  75.506:   17        |
|      4:    33.558 -  41.948:  123   |   9:    75.506 -  83.895:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2207 r_free = 0.2821             target_work(ml) = 5.746         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2205 r_free = 0.2823             target_work(ml) = 5.746         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2205   r_free= 0.2823   ksol= 0.33   Bsol= 34.93   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.58,1.83,-0.72,0.00,-0.00,-0.00); trace/3= -0.16                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.745570                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2190   r_free= 0.2789   ksol= 0.33   Bsol= 48.95   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.08,-1.15,-1.37,-0.00,-0.00,-0.00); trace/3= -1.53                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.739957                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.472331              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.169   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.216121              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.965  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2190      final r-factor (work) = 0.1553          |
| start r-factor (free) = 0.2789      final r-factor (free) = 0.2044          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0503 = 3.47 * 0.50 * 5.7383 + 1.00 * 0.0876                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7844 = 3.47 * 0.50 * 5.6022 + 1.00 * 0.0581                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1553      final r-factor (work) = 0.1424          |
| start r-factor (free) = 0.2044      final r-factor (free) = 0.1888          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2229 = 0.22 * 1.00 * 5.6022 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1718 = 0.22 * 1.00 * 5.3861 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.738)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.74    78.97   17.01    None  None   None       |
|    all(noH): 2823   0      1.74    78.97   17.01    None  None   None       |
|    Sol.    : 438    0      6.31    78.97   39.06    None  None   None       |
|    Mac.    : 2385   0      1.74    77.35   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:     1.739 -   9.463:  862   |   5:    40.356 -  48.079:  103        |
|      1:     9.463 -  17.186: 1147   |   6:    48.079 -  55.802:   88        |
|      2:    17.186 -  24.909:  308   |   7:    55.802 -  63.526:   38        |
|      3:    24.909 -  32.633:  128   |   8:    63.526 -  71.249:   14        |
|      4:    32.633 -  40.356:  128   |   9:    71.249 -  78.972:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1424 r_free = 0.1888             target_work(ml) = 5.345         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1423 r_free = 0.1889             target_work(ml) = 5.345         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1423   r_free= 0.1889   ksol= 0.33   Bsol= 48.95   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.08,-1.15,-1.37,-0.00,-0.00,-0.00); trace/3= -1.53                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.344798                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1423   r_free= 0.1885   ksol= 0.33   Bsol= 47.14   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-2.17,-1.40,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.342149                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.666180              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.162  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.245578              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.824  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1423      final r-factor (work) = 0.1249          |
| start r-factor (free) = 0.1885      final r-factor (free) = 0.1680          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5449 = 1.67 * 0.50 * 5.3860 + 1.00 * 0.0579                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4489 = 1.67 * 0.50 * 5.2849 + 1.00 * 0.0461                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1249      final r-factor (work) = 0.1217          |
| start r-factor (free) = 0.1680      final r-factor (free) = 0.1639          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3056 = 0.25 * 1.00 * 5.2849 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2876 = 0.25 * 1.00 * 5.2113 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.738)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.90    81.12   16.92    None  None   None       |
|    all(noH): 2823   0      0.90    81.12   16.92    None  None   None       |
|    Sol.    : 438    0      5.37    77.58   39.19    None  None   None       |
|    Mac.    : 2385   0      0.90    81.12   12.83    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:     0.903 -   8.925:  746   |   5:    41.012 -  49.034:  112        |
|      1:     8.925 -  16.947: 1272   |   6:    49.034 -  57.056:   84        |
|      2:    16.947 -  24.969:  309   |   7:    57.056 -  65.078:   37        |
|      3:    24.969 -  32.991:  137   |   8:    65.078 -  73.100:   13        |
|      4:    32.991 -  41.012:  108   |   9:    73.100 -  81.121:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1217 r_free = 0.1639             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1216 r_free = 0.1640             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1216   r_free= 0.1640   ksol= 0.33   Bsol= 47.14   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-2.17,-1.40,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.200040                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1215   r_free= 0.1639   ksol= 0.33   Bsol= 47.14   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.49,-1.51,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.199613                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.909531              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.063  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.082958              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.811  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1215      final r-factor (work) = 0.1130          |
| start r-factor (free) = 0.1639      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0217 = 1.91 * 0.50 * 5.2113 + 1.00 * 0.0461                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9866 = 1.91 * 0.50 * 5.1660 + 1.00 * 0.0543                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1130      final r-factor (work) = 0.1111          |
| start r-factor (free) = 0.1561      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6024 = 1.08 * 1.00 * 5.1660 + 1.00 * 0.0078                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5684 = 1.08 * 1.00 * 5.1332 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.738)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.01   17.19    None  None   None       |
|    all(noH): 2823   0      0.00    93.01   17.19    None  None   None       |
|    Sol.    : 438    0      5.31    81.54   40.67    None  None   None       |
|    Mac.    : 2385   0      0.00    93.01   12.87    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.301:  895   |   5:    46.506 -  55.807:  102        |
|      1:     9.301 -  18.603: 1222   |   6:    55.807 -  65.109:   52        |
|      2:    18.603 -  27.904:  250   |   7:    65.109 -  74.410:   26        |
|      3:    27.904 -  37.205:  137   |   8:    74.410 -  83.711:   14        |
|      4:    37.205 -  46.506:  123   |   9:    83.711 -  93.012:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1111 r_free = 0.1561             target_work(ml) = 5.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1110 r_free = 0.1560             target_work(ml) = 5.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1110   r_free= 0.1560   ksol= 0.33   Bsol= 47.14   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.49,-1.51,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.133619                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1559   ksol= 0.32   Bsol= 48.54   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,-2.45,-1.42,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.134291                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.580079              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 123.137  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.520640              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.806  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1112      final r-factor (work) = 0.1108          |
| start r-factor (free) = 0.1559      final r-factor (free) = 0.1563          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1098 = 1.58 * 0.50 * 5.1332 + 1.00 * 0.0543                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1036 = 1.58 * 0.50 * 5.1332 + 1.00 * 0.0482                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1108      final r-factor (work) = 0.1106          |
| start r-factor (free) = 0.1563      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6819 = 0.52 * 1.00 * 5.1332 + 1.00 * 0.0094                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6821 = 0.52 * 1.00 * 5.1337 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.738)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.61   17.00    None  None   None       |
|    all(noH): 2823   0      0.00    93.61   17.00    None  None   None       |
|    Sol.    : 438    0      5.93    81.33   40.34    None  None   None       |
|    Mac.    : 2385   0      0.00    93.61   12.71    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.361:  943   |   5:    46.804 -  56.164:   98        |
|      1:     9.361 -  18.722: 1195   |   6:    56.164 -  65.525:   50        |
|      2:    18.722 -  28.082:  233   |   7:    65.525 -  74.886:   25        |
|      3:    28.082 -  37.443:  138   |   8:    74.886 -  84.247:   13        |
|      4:    37.443 -  46.804:  126   |   9:    84.247 -  93.607:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1106 r_free = 0.1561             target_work(ml) = 5.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1105 r_free = 0.1561             target_work(ml) = 5.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1105   r_free= 0.1561   ksol= 0.32   Bsol= 48.54   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,-2.45,-1.42,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.134156                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0613 -  4.7065 0.99   1392  156 0.0967 0.1216      5.3605      5.4998|
|  2:  4.7065 -  3.7547 0.99   1338  146 0.0851 0.1105       5.429      5.6116|
|  3:  3.7547 -  3.2857 0.99   1323  144 0.1059 0.1506      5.4687      5.8477|
|  4:  3.2857 -  2.9878 0.99   1306  153 0.1183 0.1581      5.4475      5.5883|
|  5:  2.9878 -  2.7751 0.99   1294  142 0.1344 0.1804      5.3246      5.5545|
|  6:  2.7751 -  2.6124 0.99   1295  142 0.1174 0.1701      5.1882      5.4253|
|  7:  2.6124 -  2.4822 0.99   1295  140 0.1235 0.1540      5.1509      5.3256|
|  8:  2.4822 -  2.3746 0.98   1254  144 0.1162 0.1801      5.0402      5.3627|
|  9:  2.3746 -  2.2835 0.98   1290  148 0.1146 0.1696      5.0271      5.2955|
| 10:  2.2835 -  2.2049 1.00   1278  138 0.1104 0.1699      4.9392      5.2221|
| 11:  2.2049 -  2.1362 0.98   1272  136 0.1135 0.1719       4.952      5.2684|
| 12:  2.1362 -  2.0753 0.98   1250  145 0.1082 0.1641      4.8627      5.1421|
| 13:  2.0753 -  2.0208 0.99   1284  137 0.1120 0.1830      4.7777      5.0766|
| 14:  2.0208 -  1.9716 0.59    759   88 0.1040 0.1580      4.6522      4.8888|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0613 -  4.7065  1392   156  0.94   8.61   0.98     0.95       6580.65|
|  2:  4.7065 -  3.7547  1338   146  0.95   7.70   1.02     1.01       8662.59|
|  3:  3.7547 -  3.2857  1323   144  0.94  11.07   1.03     1.03      10081.26|
|  4:  3.2857 -  2.9878  1306   153  0.92  13.57   1.01     0.99      10288.16|
|  5:  2.9878 -  2.7751  1294   142  0.90  15.85   0.99     0.97       8150.03|
|  6:  2.7751 -  2.6124  1295   142  0.91  15.36   0.99     0.97       6780.68|
|  7:  2.6124 -  2.4822  1295   140  0.91  15.17   0.99     0.97       6027.17|
|  8:  2.4822 -  2.3746  1254   144  0.91  14.98   0.98     0.96       4917.51|
|  9:  2.3746 -  2.2835  1290   148  0.91  14.97   1.00     0.97       4907.11|
| 10:  2.2835 -  2.2049  1278   138  0.91  15.20   1.00     0.96       4201.01|
| 11:  2.2049 -  2.1362  1272   136  0.90  15.99   0.98     0.93       4323.23|
| 12:  2.1362 -  2.0753  1250   145  0.91  14.78   1.01     1.00       3869.16|
| 13:  2.0753 -  2.0208  1284   137  0.91  15.83   1.00     0.98       3286.08|
| 14:  2.0208 -  1.9716   759    88  0.92  14.43   0.98     0.95       2510.22|
|alpha:            min =        0.93 max =            1.03 mean =         0.97|
|beta:             min =     2510.22 max =        10288.16 mean =      6181.67|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.93 mean =        13.75|
|phase err.(test): min =        0.00 max =           89.92 mean =        13.33|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1561   ksol= 0.32   Bsol= 48.54   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.95,-2.31,-1.23,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.134251                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1561   ksol= 0.32   Bsol= 48.54   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.95,-2.31,-1.23,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.134251                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0613 -  4.7065 0.99   1392  156 0.0967 0.1218      5.3615      5.5013|
|  2:  4.7065 -  3.7547 0.99   1338  146 0.0851 0.1105      5.4295      5.6114|
|  3:  3.7547 -  3.2857 0.99   1323  144 0.1059 0.1507      5.4687      5.8477|
|  4:  3.2857 -  2.9878 0.99   1306  153 0.1183 0.1581      5.4475      5.5884|
|  5:  2.9878 -  2.7751 0.99   1294  142 0.1344 0.1804      5.3245      5.5541|
|  6:  2.7751 -  2.6124 0.99   1295  142 0.1174 0.1700      5.1881      5.4248|
|  7:  2.6124 -  2.4822 0.99   1295  140 0.1235 0.1541       5.151      5.3258|
|  8:  2.4822 -  2.3746 0.98   1254  144 0.1162 0.1801      5.0402      5.3624|
|  9:  2.3746 -  2.2835 0.98   1290  148 0.1147 0.1696      5.0271      5.2954|
| 10:  2.2835 -  2.2049 1.00   1278  138 0.1104 0.1701      4.9394      5.2229|
| 11:  2.2049 -  2.1362 0.98   1272  136 0.1135 0.1719      4.9523      5.2687|
| 12:  2.1362 -  2.0753 0.98   1250  145 0.1082 0.1641      4.8626      5.1422|
| 13:  2.0753 -  2.0208 0.99   1284  137 0.1120 0.1830      4.7775      5.0761|
| 14:  2.0208 -  1.9716 0.59    759   88 0.1040 0.1578      4.6517      4.8879|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0613 -  4.7065  1392   156  0.94   8.63   0.98     0.95       6597.32|
|  2:  4.7065 -  3.7547  1338   146  0.95   7.72   1.02     1.01       8674.67|
|  3:  3.7547 -  3.2857  1323   144  0.94  11.08   1.03     1.03      10083.27|
|  4:  3.2857 -  2.9878  1306   153  0.92  13.57   1.01     0.99      10287.87|
|  5:  2.9878 -  2.7751  1294   142  0.90  15.85   1.00     0.98       8146.15|
|  6:  2.7751 -  2.6124  1295   142  0.91  15.36   0.99     0.97       6779.13|
|  7:  2.6124 -  2.4822  1295   140  0.91  15.17   1.00     0.97       6026.37|
|  8:  2.4822 -  2.3746  1254   144  0.91  14.98   0.99     0.96       4916.75|
|  9:  2.3746 -  2.2835  1290   148  0.91  14.97   1.01     0.98       4906.86|
| 10:  2.2835 -  2.2049  1278   138  0.91  15.20   1.00     0.97       4203.57|
| 11:  2.2049 -  2.1362  1272   136  0.90  16.00   0.99     0.94       4326.15|
| 12:  2.1362 -  2.0753  1250   145  0.91  14.79   1.02     1.01       3870.13|
| 13:  2.0753 -  2.0208  1284   137  0.91  15.82   1.01     0.99       3283.71|
| 14:  2.0208 -  1.9716   759    88  0.92  14.42   0.99     0.96       2506.28|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2506.28 max =        10287.87 mean =      6183.62|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.93 mean =        13.75|
|phase err.(test): min =        0.00 max =           89.92 mean =        13.33|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.738)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.61   17.00    None  None   None       |
|    all(noH): 2823   0      0.00    93.61   17.00    None  None   None       |
|    Sol.    : 438    0      5.93    81.33   40.34    None  None   None       |
|    Mac.    : 2385   0      0.00    93.61   12.71    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.364:  943   |   5:    46.807 -  56.167:   98        |
|      1:     9.364 -  18.724: 1195   |   6:    56.167 -  65.528:   50        |
|      2:    18.724 -  28.085:  233   |   7:    65.528 -  74.889:   25        |
|      3:    28.085 -  37.446:  138   |   8:    74.889 -  84.249:   13        |
|      4:    37.446 -  46.807:  126   |   9:    84.249 -  93.610:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 302         
Filter by distance & map next to the model:
   mapped sites are within: 0.510 - 4.551
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 297 from: 302
   mapped sites are within: 0.720 - 4.551

peak=    6.160 closest distance to " NE2 GLN A  11 " =    1.215
peak=    5.847 closest distance to " CG  PRO A  54 " =    1.304
peak=    5.516 closest distance to " O   HOH Z 126 " =    1.986
peak=    5.446 closest distance to " NH2 ARG A  56 " =    2.095
peak=    5.324 closest distance to " CB  GLN A 223 " =    1.435
peak=    5.265 closest distance to " CG  PRO A 213 " =    1.311
peak=    5.070 closest distance to " O   HOH Z 144 " =    1.766
peak=    5.032 closest distance to " CG  PRO A  90 " =    1.119
peak=    4.931 closest distance to " CB  PRO A  54 " =    1.012
peak=    4.929 closest distance to " CB  SER A  63 " =    1.254
peak=    4.830 closest distance to " CB  ARG A 275 " =    0.922
peak=    4.823 closest distance to " CG  PRO A 198 " =    1.267
peak=    4.820 closest distance to " CB  GLU A 128 " =    1.044
peak=    4.760 closest distance to " O   HOH Z 423 " =    1.652
peak=    4.693 closest distance to " O   HOH Z 287 " =    2.077
peak=    4.680 closest distance to " O   HOH Z 232 " =    2.351
peak=    4.651 closest distance to " O   HOH Z 369 " =    2.153
peak=    4.626 closest distance to " O   HOH Z  78 " =    1.758
peak=    4.589 closest distance to " O   HOH Z 427 " =    2.705
peak=    4.580 closest distance to " O   HOH Z 298 " =    1.920
peak=    4.548 closest distance to " CB  GLN A 183 " =    1.231
peak=    4.505 closest distance to " CB  LEU A 228 " =    1.090
peak=    4.490 closest distance to " O   HOH Z 193 " =    1.864
peak=    4.477 closest distance to " O   HOH Z   9 " =    2.201
peak=    4.420 closest distance to " CG2 VAL A 257 " =    0.957
peak=    4.415 closest distance to " CA  TYR A  30 " =    0.961
peak=    4.398 closest distance to " CG  PRO A 280 " =    0.802
peak=    4.397 closest distance to " O   HOH Z 425 " =    1.316
peak=    4.379 closest distance to " CB  ASN A 148 " =    1.310
peak=    4.377 closest distance to " C   PRO A 198 " =    1.527
peak=    4.363 closest distance to " ND2 ASN A 187 " =    1.538
peak=    4.351 closest distance to " CB  SER A 216 " =    0.817
peak=    4.351 closest distance to " O   HOH Z 209 " =    2.219
peak=    4.277 closest distance to " O   HOH Z  63 " =    1.474
peak=    4.254 closest distance to " O   HOH Z 419 " =    2.157
peak=    4.240 closest distance to " CB  ASN A 187 " =    1.287
peak=    4.209 closest distance to " CG  PRO A 243 " =    1.102
peak=    4.208 closest distance to " O   HOH Z 316 " =    3.051
peak=    4.182 closest distance to " O   HOH Z   1 " =    1.909
peak=    4.171 closest distance to " O   HOH Z 217 " =    3.000
peak=    4.150 closest distance to " CB  SER A   3 " =    1.375
peak=    4.137 closest distance to " O   HOH Z 234 " =    3.695
peak=    4.123 closest distance to " O   HOH Z 132 " =    2.351
peak=    4.099 closest distance to " CG  TRP A 179 " =    2.263
peak=    4.097 closest distance to " CG  LEU A 167 " =    1.210
peak=    4.085 closest distance to " CB  GLU A 152 " =    1.402
peak=    4.078 closest distance to " CB  VAL A 265 " =    1.276
peak=    4.018 closest distance to " CB  TRP A 179 " =    1.423
peak=    3.997 closest distance to " CD  ARG A  66 " =    2.251
peak=    3.959 closest distance to " CB  ARG A 190 " =    1.642
peak=    3.942 closest distance to " O   HOH Z 371 " =    1.882
peak=    3.938 closest distance to " CA  ASN A 215 " =    1.191
peak=    3.933 closest distance to " O   HOH Z 272 " =    1.801
peak=    3.927 closest distance to " O   HOH Z 368 " =    3.643
peak=    3.923 closest distance to " CB  TRP A 266 " =    1.014
peak=    3.919 closest distance to " O   HOH Z 261 " =    1.713
peak=    3.897 closest distance to " CB  ARG A  79 " =    1.357
peak=    3.897 closest distance to " O   HOH Z 352 " =    1.760
peak=    3.891 closest distance to " CD  ARG A 159 " =    0.781
peak=    3.869 closest distance to " O   HOH Z   2 " =    1.521
peak=    3.869 closest distance to " OD1 ASN A  69 " =    2.677
peak=    3.867 closest distance to " CG1 ILE A  33 " =    1.283
peak=    3.860 closest distance to " CE  LYS A  76 " =    0.885
peak=    3.859 closest distance to " OD1BASN A 224 " =    2.260
peak=    3.856 closest distance to " ND1 HIS A  86 " =    1.788
peak=    3.851 closest distance to " CD BLYS A 290 " =    1.086
peak=    3.840 closest distance to " O   HOH Z  68 " =    2.118
peak=    3.837 closest distance to " O   HOH Z 236 " =    1.436
peak=    3.831 closest distance to " O   HOH Z 193 " =    1.675
peak=    3.827 closest distance to " CB  ARG A 139 " =    0.987
peak=    3.818 closest distance to " O   HOH Z 344 " =    3.086
peak=    3.818 closest distance to " O   HOH Z 368 " =    1.822
peak=    3.807 closest distance to " O   HOH Z 128 " =    2.160
peak=    3.803 closest distance to " O   HOH Z 207 " =    1.629
peak=    3.791 closest distance to " O   HOH Z  44 " =    1.713
peak=    3.779 closest distance to " O   HOH Z 437 " =    1.768
peak=    3.775 closest distance to " OD2 ASP A 286 " =    2.833
peak=    3.772 closest distance to " CA  THR A 264 " =    0.829
peak=    3.758 closest distance to " CB  SER A 212 " =    1.122
peak=    3.750 closest distance to " CD1 LEU A 300 " =    1.211
peak=    3.747 closest distance to " CG2 THR A 221 " =    1.032
peak=    3.745 closest distance to " O   HOH Z  61 " =    1.596
peak=    3.745 closest distance to " O   HOH Z 250 " =    1.459
peak=    3.733 closest distance to " O   HOH Z 362 " =    2.506
peak=    3.731 closest distance to " N   PHE A 130 " =    1.235
peak=    3.728 closest distance to " O   HOH Z 180 " =    2.107
peak=    3.724 closest distance to " O   HOH Z  61 " =    1.549
peak=    3.723 closest distance to " CB  ALA A  34 " =    1.058
peak=    3.721 closest distance to " O   HOH Z  10 " =    1.812
peak=    3.719 closest distance to " CA  GLY A 241 " =    3.762
peak=    3.717 closest distance to " O   HOH Z 425 " =    2.005
peak=    3.715 closest distance to " O   HOH Z   1 " =    1.782
peak=    3.680 closest distance to " NH1AARG A 145 " =    1.148
peak=    3.677 closest distance to " O   HOH Z  88 " =    3.155
peak=    3.667 closest distance to " O   HOH Z 135 " =    1.700
peak=    3.667 closest distance to " O   HOH Z 108 " =    2.064
peak=    3.667 closest distance to " O   HOH Z 175 " =    2.124
peak=    3.662 closest distance to " CB  LEU A 143 " =    1.122
peak=    3.660 closest distance to " CB  SER A  62 " =    1.162
peak=    3.653 closest distance to " O   HOH Z   3 " =    1.924
peak=    3.651 closest distance to " O   HOH Z 158 " =    3.068
peak=    3.647 closest distance to " O   SER A  87 " =    2.262
peak=    3.646 closest distance to " O   HOH Z 133 " =    1.621
peak=    3.645 closest distance to " O   HOH Z 214 " =    2.049
peak=    3.634 closest distance to " CA  ALA A  21 " =    1.163
peak=    3.629 closest distance to " CB  LYS A 117 " =    1.209
peak=    3.627 closest distance to " CB  VAL A 202 " =    1.640
peak=    3.620 closest distance to " O   HOH Z 189 " =    2.153
peak=    3.620 closest distance to " O   HOH Z  21 " =    1.698
peak=    3.614 closest distance to " O   HOH Z  64 " =    2.301
peak=    3.599 closest distance to " CZ  PHE A 218 " =    1.018
peak=    3.596 closest distance to " CA  LYS A 290 " =    1.304
peak=    3.592 closest distance to " CA  MET A  40 " =    1.065
peak=    3.577 closest distance to " O   HOH Z 409 " =    2.416
peak=    3.573 closest distance to " CD2 LEU A 255 " =    1.555
peak=    3.571 closest distance to " O   HOH Z 133 " =    2.387
peak=    3.569 closest distance to " O   HOH Z 391 " =    2.903
peak=    3.563 closest distance to " O   HOH Z   7 " =    1.153
peak=    3.547 closest distance to " CA  ALA A 233 " =    1.273
peak=    3.545 closest distance to " O   HOH Z 327 " =    1.800
peak=    3.544 closest distance to " O   HOH Z  97 " =    1.974
peak=    3.543 closest distance to " CA  ILE A 234 " =    1.013
peak=    3.540 closest distance to " O   ASN A 209 " =    1.374
peak=    3.537 closest distance to " O   HOH Z 146 " =    1.734
peak=    3.533 closest distance to " NH2BARG A 145 " =    2.014
peak=    3.532 closest distance to " CA  ALA A 158 " =    1.101
peak=    3.527 closest distance to " CB  ASN A  39 " =    0.903
peak=    3.526 closest distance to " O   HOH Z 389 " =    1.865
peak=    3.509 closest distance to " CA  SER A  87 " =    1.018
peak=    3.507 closest distance to " CD2 LEU A 297 " =    0.972
peak=    3.504 closest distance to " CB  GLU A 277 " =    3.563
peak=    3.502 closest distance to " N   GLN A 278 " =    1.101
peak=    3.501 closest distance to " O   HOH Z 217 " =    1.560
peak=    3.498 closest distance to " O   HOH Z 405 " =    1.249
peak=    3.493 closest distance to " O   HOH Z 380 " =    1.556
peak=    3.492 closest distance to " CB  ASP A 132 " =    4.046
peak=    3.484 closest distance to " O   HOH Z 261 " =    2.176
peak=    3.482 closest distance to " O   HOH Z 371 " =    2.901
peak=    3.478 closest distance to " CB  THR A 157 " =    1.107
peak=    3.474 closest distance to " CB  ASN A 142 " =    0.921
peak=    3.472 closest distance to " O   HOH Z 289 " =    1.720
peak=    3.463 closest distance to " CD  ARG A 269 " =    1.012
peak=    3.456 closest distance to " O   HOH Z 403 " =    1.631
peak=    3.455 closest distance to " O   HOH Z  40 " =    2.050
peak=    3.454 closest distance to " CG  MET A 113 " =    1.187
peak=    3.449 closest distance to " CG  ARG A 159 " =    0.813
peak=    3.446 closest distance to " CB  TYR A 116 " =    0.852
peak=    3.441 closest distance to " O   HOH Z 373 " =    1.486
peak=    3.436 closest distance to " CB  ALA A   1 " =    4.551
peak=    3.428 closest distance to " O   HOH Z 271 " =    2.451
peak=    3.425 closest distance to " OG  SER A  62 " =    3.026
peak=    3.413 closest distance to " O   HOH Z 193 " =    2.004
peak=    3.413 closest distance to " OG BSER A 164 " =    2.328
peak=    3.409 closest distance to " O   HOH Z 130 " =    3.811
peak=    3.408 closest distance to " CB  ARG A  79 " =    0.850
peak=    3.404 closest distance to " CD  LYS A 166 " =    1.301
peak=    3.404 closest distance to " CD  PRO A 243 " =    1.600
peak=    3.400 closest distance to " CA  GLY A 267 " =    1.261
peak=    3.390 closest distance to " O   HOH Z 302 " =    1.695
peak=    3.385 closest distance to " O   HOH Z 172 " =    3.090
peak=    3.385 closest distance to " N   ASN A  39 " =    1.312
peak=    3.384 closest distance to " O   HOH Z 211 " =    2.642
peak=    3.382 closest distance to " O   HOH Z 147 " =    1.716
peak=    3.381 closest distance to " CG1BVAL A  72 " =    1.457
peak=    3.379 closest distance to " O   HOH Z 403 " =    1.328
peak=    3.378 closest distance to " O   MET A 105 " =    1.788
peak=    3.360 closest distance to " CE1 TYR A 186 " =    1.399
peak=    3.358 closest distance to " NZ  LYS A  76 " =    1.490
peak=    3.358 closest distance to " CB  MET A  40 " =    0.796
peak=    3.357 closest distance to " O  BHOH Z  74 " =    1.354
peak=    3.352 closest distance to " O   HOH Z 407 " =    2.254
peak=    3.351 closest distance to " NE AARG A 275 " =    1.371
peak=    3.350 closest distance to " O   HOH Z 227 " =    1.685
peak=    3.349 closest distance to " OG  SER A  62 " =    3.017
peak=    3.344 closest distance to " O   HOH Z 258 " =    2.299
peak=    3.341 closest distance to " CA  ALA A 154 " =    0.951
peak=    3.340 closest distance to " O   HOH Z 219 " =    2.288
peak=    3.332 closest distance to " O   HOH Z 305 " =    3.565
peak=    3.332 closest distance to " O   HOH Z 128 " =    2.047
peak=    3.332 closest distance to " NH1 ARG A  14 " =    1.055
peak=    3.327 closest distance to " O   HOH Z 386 " =    3.127
peak=    3.326 closest distance to " N   TYR A  15 " =    0.788
peak=    3.325 closest distance to " O   TYR A 116 " =    1.320
peak=    3.324 closest distance to " CB  ALA A 291 " =    1.360
peak=    3.322 closest distance to " CD2 TRP A 179 " =    1.317
peak=    3.317 closest distance to " O   HOH Z  58 " =    1.462
peak=    3.314 closest distance to " O   HOH Z 286 " =    2.362
peak=    3.310 closest distance to " O   HOH Z 329 " =    3.694
peak=    3.309 closest distance to " O  BHOH Z 338 " =    2.408
peak=    3.307 closest distance to " CA  ALA A 291 " =    0.951
peak=    3.306 closest distance to " CA  ARG A 195 " =    1.279
peak=    3.305 closest distance to " NH1BARG A 145 " =    1.166
peak=    3.304 closest distance to " CB  SER A 276 " =    1.207
peak=    3.300 closest distance to " CA  LEU A 101 " =    1.582
peak=    3.298 closest distance to " O   HOH Z 153 " =    1.596
peak=    3.295 closest distance to " O   HOH Z 365 " =    2.864
peak=    3.294 closest distance to " O   HOH Z  59 " =    1.560
peak=    3.293 closest distance to " O   HOH Z  93 " =    2.408
peak=    3.292 closest distance to " O   THR A 220 " =    1.428
peak=    3.291 closest distance to " CA  THR A 221 " =    0.953
peak=    3.288 closest distance to " CA  ALA A 160 " =    0.914
peak=    3.284 closest distance to " O   HOH Z 426 " =    1.817
peak=    3.284 closest distance to " OG  SER A  22 " =    2.822
peak=    3.281 closest distance to " CD  GLN A 240 " =    1.499
peak=    3.281 closest distance to " CG  GLU A 277 " =    2.130
peak=    3.276 closest distance to " O   HOH Z  43 " =    2.207
peak=    3.275 closest distance to " N   CYS A 260 " =    0.823
peak=    3.275 closest distance to " O   HOH Z 417 " =    1.070
peak=    3.274 closest distance to " CA  ARG A 102 " =    1.229
peak=    3.273 closest distance to " O   HOH Z 284 " =    3.119
peak=    3.272 closest distance to " O   HOH Z 116 " =    2.887
peak=    3.271 closest distance to " O   HOH Z 213 " =    2.594
peak=    3.271 closest distance to " O   HOH Z  64 " =    2.115
peak=    3.268 closest distance to " O   HOH Z 345 " =    3.461
peak=    3.267 closest distance to " NH2 ARG A 219 " =    1.863
peak=    3.266 closest distance to " CB  ASN A 110 " =    1.118
peak=    3.265 closest distance to " CA  ALA A 299 " =    0.887
peak=    3.259 closest distance to " CB  THR A  31 " =    1.766
peak=    3.258 closest distance to " CB  ILE A 120 " =    1.350
peak=    3.256 closest distance to " CG1 ILE A 151 " =    0.970
peak=    3.252 closest distance to " CG  GLN A  89 " =    1.484
peak=    3.250 closest distance to " O   HOH Z 374 " =    2.623
peak=    3.248 closest distance to " O   HOH Z 435 " =    1.942
peak=    3.248 closest distance to " NE2 GLN A  73 " =    3.631
peak=    3.244 closest distance to " CB  GLU A 152 " =    1.384
peak=    3.244 closest distance to " N   GLY A 241 " =    1.471
peak=    3.244 closest distance to " CA  ASN A 127 " =    1.036
peak=    3.244 closest distance to " N   ARG A 156 " =    1.289
peak=    3.243 closest distance to " O   HOH Z 247 " =    1.213
peak=    3.237 closest distance to " CD1 ILE A 106 " =    0.833
peak=    3.237 closest distance to " O   HOH Z  59 " =    1.934
peak=    3.236 closest distance to " CB  HIS A 108 " =    0.784
peak=    3.236 closest distance to " CA  TYR A 116 " =    1.335
peak=    3.235 closest distance to " N   SER A 134 " =    1.353
peak=    3.234 closest distance to " CD  LYS A 119 " =    1.139
peak=    3.231 closest distance to " OD1 ASP A 238 " =    1.003
peak=    3.228 closest distance to " O   HOH Z 402 " =    1.440
peak=    3.226 closest distance to " N   SER A 146 " =    1.649
peak=    3.225 closest distance to " CB  PRO A 243 " =    1.153
peak=    3.221 closest distance to " O   HOH Z 423 " =    2.251
peak=    3.219 closest distance to " O   HOH Z 128 " =    2.034
peak=    3.216 closest distance to " CA  MET A 105 " =    0.935
peak=    3.213 closest distance to " CG  GLN A  88 " =    1.063
peak=    3.213 closest distance to " NH2AARG A 190 " =    1.857
peak=    3.209 closest distance to " CB  ALA A 114 " =    0.884
peak=    3.204 closest distance to " CG1 ILE A 120 " =    1.100
peak=    3.204 closest distance to " CE AMET A  47 " =    1.405
peak=    3.203 closest distance to " O   HOH Z 207 " =    2.056
peak=    3.198 closest distance to " O   HOH Z 119 " =    1.515
peak=    3.197 closest distance to " O   HOH Z 281 " =    1.817
peak=    3.196 closest distance to " CA  ASP A 162 " =    1.127
peak=    3.194 closest distance to " O   HOH Z 291 " =    1.621
peak=    3.194 closest distance to " CA  TYR A 186 " =    1.604
peak=    3.190 closest distance to " O   HOH Z  44 " =    3.018
peak=    3.190 closest distance to " O   HOH Z 109 " =    2.636
peak=    3.189 closest distance to " O   HOH Z 188 " =    1.953
peak=    3.188 closest distance to " CD1AILE A 234 " =    0.971
peak=    3.185 closest distance to " CB  ASP A 140 " =    0.812
peak=    3.183 closest distance to " CB  ALA A 248 " =    0.938
peak=    3.182 closest distance to " NE2 GLN A  58 " =    3.400
peak=    3.181 closest distance to " O   HOH Z 422 " =    2.656
peak=    3.180 closest distance to " O   ASP A 124 " =    1.134
peak=    3.178 closest distance to " O   HOH Z  88 " =    2.731
peak=    3.178 closest distance to " CD  ARG A  14 " =    1.322
peak=    3.174 closest distance to " O   HOH Z 134 " =    1.188
peak=    3.174 closest distance to " N   ALA A 154 " =    0.947
peak=    3.170 closest distance to " O   HOH Z 227 " =    2.069
peak=    3.168 closest distance to " O   HOH Z 285 " =    1.693
peak=    3.167 closest distance to " OE2 GLU A  53 " =    2.176
peak=    3.166 closest distance to " O   HOH Z 108 " =    1.318
peak=    3.164 closest distance to " CB  VAL A 250 " =    1.038
peak=    3.162 closest distance to " O   HOH Z 245 " =    1.241
peak=    3.158 closest distance to " O   HOH Z 359 " =    1.363
peak=    3.157 closest distance to " CD  ARG A 219 " =    1.081
peak=    3.155 closest distance to " CG BARG A 102 " =    1.878
peak=    3.154 closest distance to " CG  GLN A 144 " =    0.975
peak=    3.147 closest distance to " O   HOH Z 263 " =    1.672
peak=    3.143 closest distance to " O   HOH Z 163 " =    1.861
peak=    3.137 closest distance to " ND1 HIS A  81 " =    1.619
peak=    3.136 closest distance to " OG  SER A  97 " =    3.344
peak=    3.131 closest distance to " O   HOH Z 183 " =    1.363
peak=    3.125 closest distance to " O   HOH Z 213 " =    1.941
peak=    3.122 closest distance to " CB  LEU A 255 " =    0.792
peak=    3.118 closest distance to " O   HOH Z  66 " =    2.039
peak=    3.117 closest distance to " CB  ALA A 114 " =    1.447
peak=    3.111 closest distance to " CG  GLN A 240 " =    3.445
peak=    3.107 closest distance to " CA  ALA A  51 " =    0.961
peak=    3.088 closest distance to " O   HOH Z 110 " =    1.610
peak=    3.085 closest distance to " CB  ARG A 138 " =    0.966
peak=    3.079 closest distance to " CB  LEU A 237 " =    0.720
peak=    3.078 closest distance to " CG1 VAL A 189 " =    1.805
peak=    3.077 closest distance to " O   HOH Z 298 " =    2.544
peak=    3.073 closest distance to " O   HOH Z  49 " =    1.930
peak=    3.072 closest distance to " O   HOH Z 266 " =    3.221
peak=    3.066 closest distance to " CB  GLN A  88 " =    1.298
peak=    3.016 closest distance to " O   HOH Z 115 " =    1.441
peak=    3.014 closest distance to " O   HOH Z 238 " =    3.707

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.685 - 5.913
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 198
   mapped sites are within: 0.750 - 5.913

peak=   -4.554 closest distance to " O   HOH Z 377 " =    1.907
peak=   -4.466 closest distance to " CB  PRO A 243 " =    2.572
peak=   -4.377 closest distance to " CD  ARG A 156 " =    2.019
peak=   -4.309 closest distance to " O   PRO A 198 " =    1.263
peak=   -4.255 closest distance to " O   HOH Z 266 " =    4.698
peak=   -4.179 closest distance to " OG BSER A 134 " =    1.239
peak=   -4.148 closest distance to " O   HOH Z 435 " =    2.939
peak=   -4.124 closest distance to " O   HOH Z 372 " =    2.485
peak=   -4.098 closest distance to " O   HOH Z 290 " =    1.140
peak=   -4.073 closest distance to " CA  GLY A  98 " =    1.902
peak=   -4.046 closest distance to " SG  CYS A 254 " =    3.417
peak=   -4.026 closest distance to " CG  GLN A 223 " =    1.962
peak=   -4.018 closest distance to " CZ3 TRP A 179 " =    1.188
peak=   -4.011 closest distance to " O   HOH Z 231 " =    2.050
peak=   -3.963 closest distance to " CG1 VAL A 112 " =    2.860
peak=   -3.957 closest distance to " O   HOH Z 389 " =    1.838
peak=   -3.943 closest distance to " C   HIS A 108 " =    1.116
peak=   -3.937 closest distance to " CZ  PHE A  59 " =    1.516
peak=   -3.936 closest distance to " ND2 ASN A  45 " =    1.025
peak=   -3.910 closest distance to " O   HOH Z 198 " =    1.991
peak=   -3.892 closest distance to " O   HOH Z 351 " =    1.537
peak=   -3.875 closest distance to " O   SER A 135 " =    1.430
peak=   -3.874 closest distance to " CE2 PHE A 218 " =    2.484
peak=   -3.836 closest distance to " O   HOH Z 185 " =    2.109
peak=   -3.803 closest distance to " N   ALA A  43 " =    2.494
peak=   -3.789 closest distance to " O   HOH Z 152 " =    5.070
peak=   -3.780 closest distance to " O   HOH Z  47 " =    1.563
peak=   -3.779 closest distance to " O   PRO A 243 " =    2.484
peak=   -3.770 closest distance to " O   HOH Z  43 " =    1.724
peak=   -3.759 closest distance to " ND2 ASN A  45 " =    1.593
peak=   -3.755 closest distance to " CB  ALA A 248 " =    1.963
peak=   -3.752 closest distance to " CB  ASP A  27 " =    2.440
peak=   -3.750 closest distance to " CG  PHE A 283 " =    2.660
peak=   -3.736 closest distance to " O   VAL A  67 " =    2.576
peak=   -3.725 closest distance to " CG  MET A 105 " =    0.938
peak=   -3.724 closest distance to " OD1 ASP A 191 " =    1.791
peak=   -3.719 closest distance to " O   HOH Z 407 " =    3.225
peak=   -3.718 closest distance to " C   ASN A 285 " =    2.482
peak=   -3.713 closest distance to " OE1 GLN A  88 " =    1.175
peak=   -3.705 closest distance to " CB  ALA A 291 " =    2.155
peak=   -3.698 closest distance to " C   ALA A 158 " =    1.411
peak=   -3.691 closest distance to " CB  CYS A 254 " =    2.149
peak=   -3.688 closest distance to " O   HOH Z 102 " =    1.620
peak=   -3.679 closest distance to " CB  TYR A  15 " =    2.129
peak=   -3.671 closest distance to " OD1 ASN A 187 " =    1.567
peak=   -3.662 closest distance to " O   HOH Z 313 " =    1.867
peak=   -3.660 closest distance to " CG  ASP A 231 " =    0.750
peak=   -3.656 closest distance to " C   LEU A 143 " =    1.289
peak=   -3.643 closest distance to " O   VAL A 189 " =    2.419
peak=   -3.634 closest distance to " O   HOH Z 385 " =    2.036
peak=   -3.622 closest distance to " O   HOH Z  60 " =    2.530
peak=   -3.618 closest distance to " O   ILE A 109 " =    2.575
peak=   -3.617 closest distance to " CB  ASN A  39 " =    2.252
peak=   -3.598 closest distance to " CE2 TYR A  30 " =    2.714
peak=   -3.597 closest distance to " O   HOH Z  52 " =    1.272
peak=   -3.595 closest distance to " O   TYR A 247 " =    2.779
peak=   -3.585 closest distance to " O   HOH Z 353 " =    2.159
peak=   -3.585 closest distance to " O   VAL A  67 " =    2.687
peak=   -3.579 closest distance to " O   ALA A 180 " =    1.257
peak=   -3.576 closest distance to " O   HOH Z  38 " =    1.570
peak=   -3.571 closest distance to " N   THR A 157 " =    1.537
peak=   -3.570 closest distance to " O   PRO A 163 " =    1.959
peak=   -3.569 closest distance to " O   HOH Z 126 " =    1.877
peak=   -3.567 closest distance to " CA  GLY A 203 " =    2.254
peak=   -3.566 closest distance to " O   HOH Z  11 " =    1.868
peak=   -3.563 closest distance to " O   HOH Z 114 " =    2.973
peak=   -3.551 closest distance to " O   HOH Z  13 " =    1.507
peak=   -3.543 closest distance to " OG  SER A  87 " =    1.320
peak=   -3.541 closest distance to " CZ BARG A 275 " =    1.714
peak=   -3.535 closest distance to " O   HOH Z  93 " =    2.422
peak=   -3.519 closest distance to " O   HOH Z 388 " =    2.015
peak=   -3.518 closest distance to " O   HOH Z 298 " =    1.220
peak=   -3.515 closest distance to " N   GLN A  58 " =    1.565
peak=   -3.513 closest distance to " O   HOH Z  65 " =    1.240
peak=   -3.512 closest distance to " CE  MET A 105 " =    2.272
peak=   -3.497 closest distance to " O   HOH Z 409 " =    5.913
peak=   -3.494 closest distance to " NH2AARG A 275 " =    5.423
peak=   -3.482 closest distance to " CD1 LEU A 228 " =    2.231
peak=   -3.476 closest distance to " O   HOH Z  90 " =    2.725
peak=   -3.457 closest distance to " CZ  TYR A 169 " =    1.658
peak=   -3.453 closest distance to " CE3 TRP A 274 " =    2.371
peak=   -3.448 closest distance to " O   PHE A 218 " =    1.449
peak=   -3.447 closest distance to " CB  ALA A 291 " =    2.175
peak=   -3.442 closest distance to " NE  ARG A  36 " =    1.968
peak=   -3.441 closest distance to " OD1 ASP A 191 " =    1.498
peak=   -3.434 closest distance to " OXT GLY A 302 " =    2.930
peak=   -3.429 closest distance to " O   HOH Z 298 " =    2.474
peak=   -3.429 closest distance to " CE3 TRP A 123 " =    1.342
peak=   -3.427 closest distance to " O   MET A  40 " =    2.771
peak=   -3.427 closest distance to " O   HOH Z 191 " =    5.516
peak=   -3.426 closest distance to " CG1 VAL A 197 " =    2.191
peak=   -3.423 closest distance to " CD  ARG A 139 " =    1.501
peak=   -3.422 closest distance to " OD1 ASP A 171 " =    1.570
peak=   -3.421 closest distance to " O   HOH Z 281 " =    2.798
peak=   -3.420 closest distance to " OD1 ASN A 148 " =    1.638
peak=   -3.419 closest distance to " CB  PHE A 192 " =    1.903
peak=   -3.418 closest distance to " O   HOH Z 345 " =    2.094
peak=   -3.416 closest distance to " CD1 LEU A 101 " =    2.329
peak=   -3.409 closest distance to " O   ALA A 161 " =    1.477
peak=   -3.402 closest distance to " O   HOH Z 193 " =    1.930
peak=   -3.399 closest distance to " CA  GLY A 241 " =    2.225
peak=   -3.394 closest distance to " CG  GLN A  88 " =    0.816
peak=   -3.393 closest distance to " CE1 TYR A 169 " =    2.480
peak=   -3.392 closest distance to " CD1 PHE A  59 " =    1.873
peak=   -3.372 closest distance to " NH1AARG A 275 " =    1.788
peak=   -3.368 closest distance to " CB  TRP A  85 " =    2.390
peak=   -3.365 closest distance to " O   TRP A  70 " =    1.418
peak=   -3.362 closest distance to " O   HOH Z 377 " =    0.987
peak=   -3.361 closest distance to " OD2 ASP A 171 " =    2.037
peak=   -3.357 closest distance to " OD2 ASP A 191 " =    1.511
peak=   -3.355 closest distance to " O   GLY A 211 " =    1.342
peak=   -3.352 closest distance to " O   HOH Z 184 " =    1.870
peak=   -3.347 closest distance to " O   HOH Z 198 " =    1.590
peak=   -3.346 closest distance to " O   HOH Z 211 " =    1.519
peak=   -3.338 closest distance to " O   HOH Z  24 " =    1.359
peak=   -3.337 closest distance to " O   SER A  95 " =    1.457
peak=   -3.336 closest distance to " O   SER A  22 " =    2.502
peak=   -3.336 closest distance to " O   HOH Z 111 " =    2.141
peak=   -3.330 closest distance to " OG  SER A  97 " =    2.125
peak=   -3.330 closest distance to " CA  GLY A 133 " =    1.975
peak=   -3.322 closest distance to " O   VAL A 174 " =    2.194
peak=   -3.316 closest distance to " CB  SER A 245 " =    2.260
peak=   -3.314 closest distance to " ND2 ASN A 249 " =    2.267
peak=   -3.311 closest distance to " CB  ALA A  43 " =    2.441
peak=   -3.306 closest distance to " OG BSER A 134 " =    1.627
peak=   -3.303 closest distance to " O   HOH Z 140 " =    1.712
peak=   -3.300 closest distance to " OD2 ASP A  50 " =    1.601
peak=   -3.298 closest distance to " O   ASN A 249 " =    1.397
peak=   -3.294 closest distance to " O   HOH Z  98 " =    2.347
peak=   -3.291 closest distance to " CD  GLN A  58 " =    1.158
peak=   -3.289 closest distance to " O   HOH Z 282 " =    1.202
peak=   -3.280 closest distance to " O   SER A   3 " =    1.166
peak=   -3.275 closest distance to " N   SER A 212 " =    1.832
peak=   -3.274 closest distance to " O   GLY A  17 " =    1.214
peak=   -3.265 closest distance to " NH1 ARG A 195 " =    2.667
peak=   -3.263 closest distance to " CG2 THR A 178 " =    2.170
peak=   -3.262 closest distance to " CB  PRO A 163 " =    2.520
peak=   -3.256 closest distance to " O   HOH Z  63 " =    1.869
peak=   -3.255 closest distance to " N   ARG A  14 " =    1.008
peak=   -3.252 closest distance to " O   HOH Z   1 " =    1.487
peak=   -3.250 closest distance to " O   ALA A  34 " =    2.497
peak=   -3.247 closest distance to " O   HOH Z 174 " =    2.542
peak=   -3.245 closest distance to " O   HOH Z 359 " =    3.331
peak=   -3.237 closest distance to " CG  PRO A 163 " =    2.464
peak=   -3.236 closest distance to " N   ALA A 248 " =    1.482
peak=   -3.236 closest distance to " CB  ALA A 131 " =    1.995
peak=   -3.233 closest distance to " O   PRO A 198 " =    1.258
peak=   -3.225 closest distance to " O   HOH Z 266 " =    4.446
peak=   -3.223 closest distance to " O   HOH Z 292 " =    1.539
peak=   -3.222 closest distance to " O   HOH Z 111 " =    1.180
peak=   -3.219 closest distance to " CD  GLN A 223 " =    1.313
peak=   -3.218 closest distance to " O   HOH Z 322 " =    1.610
peak=   -3.208 closest distance to " CG1 VAL A 250 " =    2.620
peak=   -3.207 closest distance to " CG2 VAL A 232 " =    2.072
peak=   -3.204 closest distance to " OG  SER A 245 " =    1.180
peak=   -3.202 closest distance to " CD  LYS A 289 " =    2.380
peak=   -3.195 closest distance to " CB  ALA A   7 " =    2.030
peak=   -3.189 closest distance to " CB  ALA A 244 " =    2.066
peak=   -3.185 closest distance to " O   HOH Z 222 " =    1.164
peak=   -3.181 closest distance to " O   HOH Z 309 " =    2.405
peak=   -3.181 closest distance to " O   HOH Z 417 " =    2.855
peak=   -3.181 closest distance to " O   HOH Z  90 " =    1.804
peak=   -3.177 closest distance to " NH2 ARG A  79 " =    1.919
peak=   -3.177 closest distance to " O   ALA A  10 " =    1.673
peak=   -3.175 closest distance to " O   HOH Z 263 " =    5.070
peak=   -3.174 closest distance to " CG  TRP A 266 " =    1.815
peak=   -3.162 closest distance to " CD2 TYR A 293 " =    1.918
peak=   -3.159 closest distance to " CD2 PHE A  61 " =    2.070
peak=   -3.159 closest distance to " O   ILE A  49 " =    1.727
peak=   -3.156 closest distance to " CB  ASP A 286 " =    2.178
peak=   -3.155 closest distance to " CB  ILE A  33 " =    2.906
peak=   -3.150 closest distance to " O   HOH Z 324 " =    2.071
peak=   -3.145 closest distance to " O   HOH Z 250 " =    1.418
peak=   -3.143 closest distance to " CG  GLU A 152 " =    1.345
peak=   -3.142 closest distance to " O   HOH Z  60 " =    2.052
peak=   -3.141 closest distance to " OXT GLY A 302 " =    3.424
peak=   -3.140 closest distance to " O   HOH Z 418 " =    1.626
peak=   -3.135 closest distance to " NE BARG A 102 " =    2.410
peak=   -3.134 closest distance to " O   HOH Z 352 " =    1.943
peak=   -3.130 closest distance to " O   GLY A  80 " =    2.293
peak=   -3.124 closest distance to " CG2 ILE A 263 " =    2.322
peak=   -3.123 closest distance to " O   HOH Z 166 " =    1.338
peak=   -3.122 closest distance to " CE  MET A  93 " =    1.150
peak=   -3.113 closest distance to " O   HOH Z 263 " =    2.893
peak=   -3.112 closest distance to " O   HOH Z 114 " =    0.781
peak=   -3.102 closest distance to " O   HOH Z  28 " =    1.952
peak=   -3.099 closest distance to " OH  TYR A 214 " =    1.192
peak=   -3.095 closest distance to " CB  ASP A 132 " =    2.313
peak=   -3.095 closest distance to " ND2BASN A 224 " =    1.718
peak=   -3.087 closest distance to " CZ3 TRP A 123 " =    1.761
peak=   -3.081 closest distance to " CG  GLU A 277 " =    1.213
peak=   -3.066 closest distance to " CD1 TYR A 247 " =    2.636
peak=   -3.059 closest distance to " ND2 ASN A 215 " =    2.275
peak=   -3.055 closest distance to " O   HOH Z 417 " =    2.559
peak=   -3.051 closest distance to " O   LEU A 101 " =    2.630
peak=   -3.040 closest distance to " O   HOH Z  51 " =    1.345
peak=   -3.009 closest distance to " O   HOH Z 318 " =    1.918

================= 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    :  0.3897 0.3882   6.175079e+00   6.169322e+00
   1_bss:  0.3784 0.3802   6.162579e+00   6.151150e+00
   1_xyz:  0.2410 0.2718   5.793545e+00   5.878359e+00
   1_adp:  0.2207 0.2821   5.746222e+00   5.910841e+00
   1_occ:  0.2205 0.2823   5.745570e+00   5.910886e+00
   2_bss:  0.2190 0.2789   5.739957e+00   5.903027e+00
   2_xyz:  0.1553 0.2044   5.424238e+00   5.636908e+00
   2_adp:  0.1424 0.1888   5.345330e+00   5.560875e+00
   2_occ:  0.1423 0.1889   5.344798e+00   5.560279e+00
   3_bss:  0.1423 0.1885   5.342149e+00   5.557975e+00
   3_xyz:  0.1249 0.1680   5.224002e+00   5.447133e+00
   3_adp:  0.1217 0.1639   5.200192e+00   5.425669e+00
   3_occ:  0.1216 0.1640   5.200040e+00   5.425596e+00
   4_bss:  0.1215 0.1639   5.199613e+00   5.425258e+00
   4_xyz:  0.1130 0.1561   5.141129e+00   5.380993e+00
   4_adp:  0.1111 0.1561   5.133678e+00   5.379199e+00
   4_occ:  0.1110 0.1560   5.133619e+00   5.379270e+00
   5_bss:  0.1112 0.1559   5.134291e+00   5.378431e+00
   5_xyz:  0.1108 0.1563   5.135358e+00   5.381744e+00
   5_adp:  0.1106 0.1561   5.134281e+00   5.382090e+00
   5_occ:  0.1105 0.1561   5.134156e+00   5.382062e+00
   5_bss:  0.1104 0.1561   5.134251e+00   5.382106e+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:  0.332  34.934  -1.575   1.828  -0.718   0.000  -0.000  -0.000
   1_xyz:  0.332  34.934  -1.575   1.828  -0.718   0.000  -0.000  -0.000
   1_adp:  0.332  34.934  -1.575   1.828  -0.718   0.000  -0.000  -0.000
   1_occ:  0.332  34.934  -1.575   1.828  -0.718   0.000  -0.000  -0.000
   2_bss:  0.335  48.950  -2.079  -1.149  -1.372  -0.000  -0.000  -0.000
   2_xyz:  0.335  48.950  -2.079  -1.149  -1.372  -0.000  -0.000  -0.000
   2_adp:  0.335  48.950  -2.079  -1.149  -1.372  -0.000  -0.000  -0.000
   2_occ:  0.335  48.950  -2.079  -1.149  -1.372  -0.000  -0.000  -0.000
   3_bss:  0.327  47.140  -2.165  -2.170  -1.401  -0.000  -0.000  -0.000
   3_xyz:  0.327  47.140  -2.165  -2.170  -1.401  -0.000  -0.000  -0.000
   3_adp:  0.327  47.140  -2.165  -2.170  -1.401  -0.000  -0.000  -0.000
   3_occ:  0.327  47.140  -2.165  -2.170  -1.401  -0.000  -0.000  -0.000
   4_bss:  0.327  47.140  -2.280  -2.494  -1.513  -0.000  -0.000  -0.000
   4_xyz:  0.327  47.140  -2.280  -2.494  -1.513  -0.000  -0.000  -0.000
   4_adp:  0.327  47.140  -2.280  -2.494  -1.513  -0.000  -0.000  -0.000
   4_occ:  0.327  47.140  -2.280  -2.494  -1.513  -0.000  -0.000  -0.000
   5_bss:  0.323  48.540  -2.136  -2.447  -1.421  -0.000  -0.000  -0.000
   5_xyz:  0.323  48.540  -2.136  -2.447  -1.421  -0.000  -0.000  -0.000
   5_adp:  0.323  48.540  -2.136  -2.447  -1.421  -0.000  -0.000  -0.000
   5_occ:  0.323  48.540  -2.136  -2.447  -1.421  -0.000  -0.000  -0.000
   5_bss:  0.323  48.543  -1.952  -2.307  -1.231  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  43.125 0.6071  0.7985    45726.654
   1_bss:  42.111 0.6174  0.8091    42633.482
   1_xyz:  26.664 0.7960  0.9797    19292.427
   1_adp:  28.136 0.7791  0.9629    20836.627
   1_occ:  28.166 0.7787  0.9621    20847.085
   2_bss:  27.740 0.7831  0.9220    20316.965
   2_xyz:  19.714 0.8639  0.9848    10605.854
   2_adp:  17.634 0.8842  0.9924     9117.815
   2_occ:  17.628 0.8843  0.9922     9102.252
   3_bss:  17.538 0.8850  0.9790     9014.396
   3_xyz:  15.100 0.9059  0.9879     7099.768
   3_adp:  14.587 0.9105  0.9860     6821.748
   3_occ:  14.587 0.9105  0.9859     6820.957
   4_bss:  14.576 0.9106  0.9795     6815.298
   4_xyz:  13.702 0.9174  0.9828     6180.703
   4_adp:  13.649 0.9180  0.9781     6148.682
   4_occ:  13.650 0.9180  0.9780     6149.505
   5_bss:  13.667 0.9178  0.9814     6148.302
   5_xyz:  13.715 0.9176  0.9800     6184.477
   5_adp:  13.705 0.9177  0.9739     6184.836
   5_occ:  13.704 0.9177  0.9738     6181.941
   5_bss:  13.708 0.9177  0.9800     6183.892
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.6519e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.6519e-01
   1_xyz:   1.265  0.009  0.083 15.181  0.006  4.107   8.7631e-02
   1_adp:   1.265  0.009  0.083 15.181  0.006  4.107   8.7631e-02
   1_occ:   1.265  0.009  0.083 15.181  0.006  4.107   8.7631e-02
   2_bss:   1.265  0.009  0.083 15.181  0.006  4.107   8.7631e-02
   2_xyz:   1.003  0.007  0.070 14.258  0.004  4.115   5.8135e-02
   2_adp:   1.003  0.007  0.070 14.258  0.004  4.115   5.8135e-02
   2_occ:   1.003  0.007  0.070 14.258  0.004  4.115   5.8135e-02
   3_bss:   1.003  0.007  0.070 14.258  0.004  4.115   5.8135e-02
   3_xyz:   0.858  0.005  0.064 14.168  0.003  4.116   4.6142e-02
   3_adp:   0.858  0.005  0.064 14.168  0.003  4.116   4.6142e-02
   3_occ:   0.858  0.005  0.064 14.168  0.003  4.116   4.6142e-02
   4_bss:   0.858  0.005  0.064 14.168  0.003  4.116   4.6142e-02
   4_xyz:   0.947  0.006  0.070 14.403  0.004  4.118   5.4299e-02
   4_adp:   0.947  0.006  0.070 14.403  0.004  4.118   5.4299e-02
   4_occ:   0.947  0.006  0.070 14.403  0.004  4.118   5.4299e-02
   5_bss:   0.947  0.006  0.070 14.403  0.004  4.118   5.4299e-02
   5_xyz:   0.881  0.005  0.067 14.195  0.003  4.119   4.8177e-02
   5_adp:   0.881  0.005  0.067 14.195  0.003  4.119   4.8177e-02
   5_occ:   0.881  0.005  0.067 14.195  0.003  4.119   4.8177e-02
   5_bss:   0.881  0.005  0.067 14.195  0.003  4.119   4.8177e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3968e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3968e-01
   1_xyz:   8.464  0.052  0.376 85.977  0.043  2.188   8.6823e-02
   1_adp:   8.464  0.052  0.376 85.977  0.043  2.188   8.6823e-02
   1_occ:   8.464  0.052  0.376 85.977  0.043  2.188   8.6823e-02
   2_bss:   8.464  0.052  0.376 85.977  0.043  2.188   8.6823e-02
   2_xyz:   7.552  0.044  0.235 84.612  0.033  2.328   5.9095e-02
   2_adp:   7.552  0.044  0.235 84.612  0.033  2.328   5.9095e-02
   2_occ:   7.552  0.044  0.235 84.612  0.033  2.328   5.9095e-02
   3_bss:   7.552  0.044  0.235 84.612  0.033  2.328   5.9095e-02
   3_xyz:   7.422  0.048  0.204 84.891  0.032  2.383   3.3951e-02
   3_adp:   7.422  0.048  0.204 84.891  0.032  2.383   3.3951e-02
   3_occ:   7.422  0.048  0.204 84.891  0.032  2.383   3.3951e-02
   4_bss:   7.422  0.048  0.204 84.891  0.032  2.383   3.3951e-02
   4_xyz:   7.571  0.038  0.210 84.875  0.036  2.307   5.8671e-02
   4_adp:   7.571  0.038  0.210 84.875  0.036  2.307   5.8671e-02
   4_occ:   7.571  0.038  0.210 84.875  0.036  2.307   5.8671e-02
   5_bss:   7.571  0.038  0.210 84.875  0.036  2.307   5.8671e-02
   5_xyz:   7.228  0.040  0.205 84.228  0.032  2.373   3.0978e-02
   5_adp:   7.228  0.040  0.205 84.228  0.032  2.373   3.0978e-02
   5_occ:   7.228  0.040  0.205 84.228  0.032  2.373   3.0978e-02
   5_bss:   7.228  0.040  0.205 84.228  0.032  2.373   3.0978e-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:  83.90   0.00  17.58  74.44   0.00  13.44  83.90   5.40  40.16
   1_occ:  83.90   0.00  17.58  74.44   0.00  13.44  83.90   5.40  40.16
   2_bss:  83.90   0.00  17.58  74.44   0.00  13.44  83.90   5.40  40.16
   2_xyz:  83.90   0.00  17.58  74.44   0.00  13.44  83.90   5.40  40.16
   2_adp:  78.97   1.74  17.01  77.35   1.74  12.95  78.97   6.31  39.06
   2_occ:  78.97   1.74  17.01  77.35   1.74  12.95  78.97   6.31  39.06
   3_bss:  78.97   1.74  17.01  77.35   1.74  12.95  78.97   6.31  39.06
   3_xyz:  78.97   1.74  17.01  77.35   1.74  12.95  78.97   6.31  39.06
   3_adp:  81.12   0.90  16.92  81.12   0.90  12.83  77.58   5.37  39.19
   3_occ:  81.12   0.90  16.92  81.12   0.90  12.83  77.58   5.37  39.19
   4_bss:  81.12   0.90  16.92  81.12   0.90  12.83  77.58   5.37  39.19
   4_xyz:  81.12   0.90  16.92  81.12   0.90  12.83  77.58   5.37  39.19
   4_adp:  93.01   0.00  17.19  93.01   0.00  12.87  81.54   5.31  40.67
   4_occ:  93.01   0.00  17.19  93.01   0.00  12.87  81.54   5.31  40.67
   5_bss:  93.01   0.00  17.19  93.01   0.00  12.87  81.54   5.31  40.67
   5_xyz:  93.01   0.00  17.19  93.01   0.00  12.87  81.54   5.31  40.67
   5_adp:  93.61   0.00  17.00  93.61   0.00  12.71  81.33   5.93  40.34
   5_occ:  93.61   0.00  17.00  93.61   0.00  12.71  81.33   5.93  40.34
   5_bss:  93.61   0.00  17.00  93.61   0.00  12.71  81.33   5.93  40.34
------------------------------------------------------------------------
 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:    1.621    0.019    0.341
   1_adp:    1.621    0.019    0.341
   1_occ:    1.621    0.019    0.341
   2_bss:    1.621    0.019    0.341
   2_xyz:    1.115    0.035    0.460
   2_adp:    1.115    0.035    0.460
   2_occ:    1.115    0.035    0.460
   3_bss:    1.115    0.035    0.460
   3_xyz:    1.056    0.044    0.507
   3_adp:    1.056    0.044    0.507
   3_occ:    1.056    0.044    0.507
   4_bss:    1.056    0.044    0.507
   4_xyz:    1.148    0.036    0.535
   4_adp:    1.148    0.036    0.535
   4_occ:    1.148    0.036    0.535
   5_bss:    1.148    0.036    0.535
   5_xyz:    1.237    0.040    0.545
   5_adp:    1.237    0.040    0.545
   5_occ:    1.237    0.040    0.545
   5_bss:    1.237    0.040    0.545
------------------------------------------------------------------------

CPU time actual refinement: 328.32


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_872/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_872/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_872/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_872/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_872/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 328.17 
  Macro-tasks:
    bulk solvent and scale       = 36.67  
    individual site refinement   = 137.80 
    weights calculation          = 30.00  
    collect and process          = 6.68   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 211.25 
  Micro-tasks:
    mask                            = 1.76   
    f_calc                          = 104.92 
    alpha_beta                      = 8.44   
    target                          = 1.21   
    gradients_wrt_atomic_parameters = 113.94 
    fmodel                         = 6.74   
    r_factors                      = 0.14   
    phase_errors                   = 11.08  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 248.46 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.633 micro seconds
Total CPU time: 5.69 minutes
from_scatterers_fft:    641 calls, 104.61 s
gradients_fft:          586 calls, 100.18 s

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

# Date 2008-01-16 Time 05:51:56 PST -0800 (1200491516.77 s)
Start R-work = 0.3897, R-free = 0.3882 (no bulk solvent and anisotropic scale)
Final R-work = 0.1338, R-free = 0.1755 (no bulk solvent and anisotropic scale)

Start R-work = 0.3784, R-free = 0.3802
Final R-work = 0.1104, R-free = 0.1561