# Date 2008-01-16 Time 04:14:21 PST -0800 (1200485661.35 s)
#phil __OFF__

Command line arguments: "../234.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27556
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 234

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.845, 48.1033, 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: 3.34, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 48.1033, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0137 1.9607
Completeness in resolution range: 0.935348
Completeness with d_max=infinity: 0.932543

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0137
                             d_min =   1.9607

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 48.1033, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0137 1.9607
Completeness in resolution range: 0.935348
Completeness with d_max=infinity: 0.932543

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0141 -  4.1964 [2204/2233]  1980   224  10.2%
  bin  2:  4.1964 -  3.3429 [2107/2130]  1897   210  10.0%
  bin  3:  3.3429 -  2.9238 [2076/2101]  1871   205   9.9%
  bin  4:  2.9238 -  2.6581 [2056/2083]  1852   204   9.9%
  bin  5:  2.6581 -  2.4685 [2050/2083]  1840   210  10.2%
  bin  6:  2.4685 -  2.3235 [2052/2080]  1858   194   9.5%
  bin  7:  2.3235 -  2.2075 [2034/2070]  1826   208  10.2%
  bin  8:  2.2075 -  2.1117 [2009/2051]  1808   201  10.0%
  bin  9:  2.1117 -  2.0306 [1964/2044]  1769   195   9.9%
  bin 10:  2.0306 -  1.9607 [1037/2068]   929   108  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_234/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:
        1.14 -     1.90: 13
        1.90 -     2.65: 111
        2.65 -     3.40: 4369
        3.40 -     4.15: 9411
        4.15 -     4.90: 14582
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.144 3.040 -x+1,y+1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.426 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.515 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.587 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  69 " - " O   HOH Z 357 "  1.663 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28481 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_234/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_234/model_refine_001.geo

CPU time processing inputs: 9.22


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 48.10325 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: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4721   r_free= 0.4633   ksol= 0.00   Bsol= 0.00   scale= 0.890    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.283195                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0141 -  4.6808 0.99   1429  159 0.3867 0.4193      6.5936        6.65|
|  2:  4.6808 -  3.7341 0.99   1367  151 0.4172 0.4162      6.8301      6.8237|
|  3:  3.7341 -  3.2677 0.99   1361  151 0.4452 0.4201      6.6767      6.7185|
|  4:  3.2677 -  2.9714 0.98   1314  146 0.4573 0.4148      6.5109      6.4329|
|  5:  2.9714 -  2.7598 0.99   1343  150 0.5010 0.4666      6.3679      6.3365|
|  6:  2.7598 -  2.5980 0.99   1330  146 0.5067 0.4801      6.2831       6.143|
|  7:  2.5980 -  2.4685 0.98   1296  150 0.5140 0.4591      6.2435      6.1874|
|  8:  2.4685 -  2.3615 0.98   1328  137 0.5091 0.5445      6.1687      6.2129|
|  9:  2.3615 -  2.2709 0.99   1301  147 0.5450 0.5220      6.1242      6.1436|
| 10:  2.2709 -  2.1928 0.99   1306  139 0.4980 0.5242      6.0996       6.119|
| 11:  2.1928 -  2.1244 0.97   1320  150 0.5104 0.5350      6.0141      6.0402|
| 12:  2.1244 -  2.0638 0.98   1266  149 0.5050 0.4521      5.9417      5.9553|
| 13:  2.0638 -  2.0096 0.89   1176  129 0.5027 0.5100       5.867      5.8276|
| 14:  2.0096 -  1.9607 0.38    493   55 0.5230 0.5760      5.8522      5.7174|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0141 -  4.6808  1429   159  0.63  40.05   0.82     0.66      90698.08|
|  2:  4.6808 -  3.7341  1367   151  0.68  37.34   0.90     0.77     115534.71|
|  3:  3.7341 -  3.2677  1361   151  0.60  44.22   0.92     0.80     114883.29|
|  4:  3.2677 -  2.9714  1314   146  0.55  47.75   0.91     0.75      90881.53|
|  5:  2.9714 -  2.7598  1343   150  0.48  53.67   0.87     0.69      73272.16|
|  6:  2.7598 -  2.5980  1330   146  0.45  56.02   0.90     0.61      62699.78|
|  7:  2.5980 -  2.4685  1296   150  0.40  60.13   0.88     0.55      62822.72|
|  8:  2.4685 -  2.3615  1328   137  0.34  64.18   0.90     0.50      60084.32|
|  9:  2.3615 -  2.2709  1301   147  0.32  65.78   0.90     0.50      56719.33|
| 10:  2.2709 -  2.1928  1306   139  0.36  63.13   0.95     0.51      49063.82|
| 11:  2.1928 -  2.1244  1320   150  0.38  61.56   0.94     0.59      43949.46|
| 12:  2.1244 -  2.0638  1266   149  0.37  62.43   0.93     0.59      40581.77|
| 13:  2.0638 -  2.0096  1176   129  0.33  65.48   0.98     0.51      36207.74|
| 14:  2.0096 -  1.9607   493    55  0.24  72.30   0.93     0.32      31713.29|
|alpha:            min =        0.32 max =            0.80 mean =         0.61|
|beta:             min =    31713.29 max =       115534.71 mean =     68734.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           89.99 mean =        55.69|
|phase err.(test): min =        0.00 max =           89.99 mean =        55.53|
|-----------------------------------------------------------------------------|

============================== 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 = 14.176989             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.409   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.048116              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.317   (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 |  1.144 -  1.520:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.520 -  1.895:       10 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.895 -  2.271:       18 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.271 -  2.646:       93 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.646 -  3.022:     2013 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.022 -  3.398:     2356 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.398 -  3.773:     3990 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.773 -  4.149:     5421 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.149 -  4.524:     6459 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.524 -  4.900:     8123 |
|-----------------------------------------------------------------------------|
|-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 |        0.202 |
| 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  1.144 |       0.765 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.709)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4721   r_free= 0.4633   ksol= 0.00   Bsol= 0.00   scale= 0.890    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.283195                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4645   r_free= 0.4521   ksol= 0.30   Bsol= 22.12   scale= 0.923   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.35,4.24,-1.28,0.00,-0.00,-0.00); trace/3= 0.54                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.275662                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.543068             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.989   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.125680              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.994   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4645      final r-factor (work) = 0.3648          |
| start r-factor (free) = 0.4521      final r-factor (free) = 0.3910          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.5663 = 12.54 * 0.50 * 6.2767 + 1.00 * 0.2015                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.8243 = 12.54 * 0.50 * 6.1676 + 1.00 * 0.1440                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3648      final r-factor (work) = 0.3361          |
| start r-factor (free) = 0.3910      final r-factor (free) = 0.3930          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9486 = 1.13 * 1.00 * 6.1676 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8670 = 1.13 * 1.00 * 6.0828 + 1.00 * 0.0197                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.709)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.96   17.85    None  None   None       |
|    all(noH): 2823   0      0.00    69.96   17.85    None  None   None       |
|    Sol.    : 438    0      0.14    69.96   36.36    None  None   None       |
|    Mac.    : 2385   0      0.00    61.31   14.45    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.996:  573   |   5:    34.980 -  41.976:  145        |
|      1:     6.996 -  13.992:  774   |   6:    41.976 -  48.972:   91        |
|      2:    13.992 -  20.988:  569   |   7:    48.972 -  55.968:   73        |
|      3:    20.988 -  27.984:  362   |   8:    55.968 -  62.964:   20        |
|      4:    27.984 -  34.980:  210   |   9:    62.964 -  69.959:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3361 r_free = 0.3930             target_work(ml) = 6.081         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3357 r_free = 0.3929             target_work(ml) = 6.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3357   r_free= 0.3929   ksol= 0.30   Bsol= 22.12   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.35,4.24,-1.28,0.00,-0.00,-0.00); trace/3= 0.54                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.080283                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3345   r_free= 0.3901   ksol= 0.30   Bsol= 37.14   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.50,2.92,-0.22,0.00,-0.00,-0.00); trace/3= 0.40                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.079726                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.988861              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.665  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 101.794294            wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.948  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3345      final r-factor (work) = 0.2799          |
| start r-factor (free) = 0.3901      final r-factor (free) = 0.3349          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.3593 = 5.99 * 0.50 * 6.0831 + 1.00 * 0.1440                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.0733 = 5.99 * 0.50 * 6.0064 + 1.00 * 0.0876                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2799      final r-factor (work) = 0.2614          |
| start r-factor (free) = 0.3349      final r-factor (free) = 0.3494          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 611.4333 = 101.79 * 1.00 * 6.0064 + 1.00 * 0.0199                           |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 600.8955 = 101.79 * 1.00 * 5.9026 + 1.00 * 0.0419                           |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.709)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    155.12  22.59    None  None   None       |
|    all(noH): 2823   0      0.00    155.12  22.59    None  None   None       |
|    Sol.    : 438    0      0.00    152.21  46.86    None  None   None       |
|    Mac.    : 2385   0      0.00    155.12  18.14    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 -  15.512: 1488   |   5:    77.559 -  93.070:   62        |
|      1:    15.512 -  31.023:  694   |   6:    93.070 - 108.582:   36        |
|      2:    31.023 -  46.535:  254   |   7:   108.582 - 124.094:   23        |
|      3:    46.535 -  62.047:  143   |   8:   124.094 - 139.605:   11        |
|      4:    62.047 -  77.559:  105   |   9:   139.605 - 155.117:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2614 r_free = 0.3494             target_work(ml) = 5.922         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2613 r_free = 0.3499             target_work(ml) = 5.922         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2613   r_free= 0.3499   ksol= 0.30   Bsol= 37.14   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.50,2.92,-0.22,0.00,-0.00,-0.00); trace/3= 0.40                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.922165                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2611   r_free= 0.3487   ksol= 0.31   Bsol= 50.13   scale= 1.045   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.38,3.04,0.99,0.00,0.00,0.00); trace/3= 1.22                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.923085                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.956671              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.779   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.211838              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.270  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2611      final r-factor (work) = 0.2278          |
| start r-factor (free) = 0.3487      final r-factor (free) = 0.3097          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.6765 = 5.96 * 0.50 * 5.9056 + 1.00 * 0.0876                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.5453 = 5.96 * 0.50 * 5.8683 + 1.00 * 0.0677                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2278      final r-factor (work) = 0.2228          |
| start r-factor (free) = 0.3097      final r-factor (free) = 0.2752          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2869 = 0.21 * 1.00 * 5.8683 + 1.00 * 0.0438                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2534 = 0.21 * 1.00 * 5.7917 + 1.00 * 0.0266                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.709)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    123.12  17.58    None  None   None       |
|    all(noH): 2823   0      0.00    123.12  17.58    None  None   None       |
|    Sol.    : 438    0      3.39    123.12  37.72    None  None   None       |
|    Mac.    : 2385   0      0.00    120.86  13.88    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 -  12.312: 1491   |   5:    61.560 -  73.873:   42        |
|      1:    12.312 -  24.624:  734   |   6:    73.873 -  86.185:   19        |
|      2:    24.624 -  36.936:  280   |   7:    86.185 -  98.497:   10        |
|      3:    36.936 -  49.248:  163   |   8:    98.497 - 110.809:    4        |
|      4:    49.248 -  61.560:   78   |   9:   110.809 - 123.121:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2228 r_free = 0.2752             target_work(ml) = 5.740         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2224 r_free = 0.2748             target_work(ml) = 5.739         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2224   r_free= 0.2748   ksol= 0.31   Bsol= 50.13   scale= 1.042   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.38,3.04,0.99,0.00,0.00,0.00); trace/3= 1.22                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.738796                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2219   r_free= 0.2737   ksol= 0.32   Bsol= 50.13   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.43,1.21,0.02,0.00,0.00,0.00); trace/3= -0.06                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.739063                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.175285              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.421  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.683821              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.901   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2219      final r-factor (work) = 0.1649          |
| start r-factor (free) = 0.2737      final r-factor (free) = 0.2079          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.0584 = 5.18 * 0.50 * 5.7932 + 1.00 * 0.0677                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.6059 = 5.18 * 0.50 * 5.6155 + 1.00 * 0.0749                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1649      final r-factor (work) = 0.1466          |
| start r-factor (free) = 0.2079      final r-factor (free) = 0.1949          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8587 = 0.68 * 1.00 * 5.6155 + 1.00 * 0.0187                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7093 = 0.68 * 1.00 * 5.4067 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.709)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.36    117.96  17.51    None  None   None       |
|    all(noH): 2823   0      0.36    117.96  17.51    None  None   None       |
|    Sol.    : 438    0      5.32    117.96  42.99    None  None   None       |
|    Mac.    : 2385   0      0.36    115.39  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:     0.362 -  12.121: 1563   |   5:    59.159 -  70.918:   67        |
|      1:    12.121 -  23.881:  699   |   6:    70.918 -  82.678:   26        |
|      2:    23.881 -  35.640:  180   |   7:    82.678 -  94.437:   14        |
|      3:    35.640 -  47.399:  149   |   8:    94.437 - 106.197:    7        |
|      4:    47.399 -  59.159:  115   |   9:   106.197 - 117.956:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1466 r_free = 0.1949             target_work(ml) = 5.371         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1465 r_free = 0.1947             target_work(ml) = 5.370         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1465   r_free= 0.1947   ksol= 0.32   Bsol= 50.13   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.43,1.21,0.02,0.00,0.00,0.00); trace/3= -0.06                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.370244                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1464   r_free= 0.1946   ksol= 0.32   Bsol= 53.99   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,0.07,-0.46,0.00,-0.00,-0.00); trace/3= -0.82                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.370606                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.801070              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.411  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.543137              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.939  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1464      final r-factor (work) = 0.1341          |
| start r-factor (free) = 0.1946      final r-factor (free) = 0.1848          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9483 = 1.80 * 0.50 * 5.4117 + 1.00 * 0.0749                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8557 = 1.80 * 0.50 * 5.3330 + 1.00 * 0.0531                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1341      final r-factor (work) = 0.1311          |
| start r-factor (free) = 0.1848      final r-factor (free) = 0.1816          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9086 = 0.54 * 1.00 * 5.3330 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8873 = 0.54 * 1.00 * 5.2940 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.709)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.62    114.04  17.19    None  None   None       |
|    all(noH): 2823   0      0.62    114.04  17.19    None  None   None       |
|    Sol.    : 438    0      4.99    114.04  43.05    None  None   None       |
|    Mac.    : 2385   0      0.62    109.40  12.44    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:     0.624 -  11.965: 1582   |   5:    57.331 -  68.673:   78        |
|      1:    11.965 -  23.307:  700   |   6:    68.673 -  80.015:   30        |
|      2:    23.307 -  34.648:  165   |   7:    80.015 -  91.356:   16        |
|      3:    34.648 -  45.990:  130   |   8:    91.356 - 102.698:    8        |
|      4:    45.990 -  57.331:  109   |   9:   102.698 - 114.039:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1311 r_free = 0.1816             target_work(ml) = 5.283         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1311 r_free = 0.1815             target_work(ml) = 5.283         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1311   r_free= 0.1815   ksol= 0.32   Bsol= 53.99   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,0.07,-0.46,0.00,-0.00,-0.00); trace/3= -0.82                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.283117                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0141 -  4.6808 0.99   1429  159 0.1015 0.1430      5.4266      5.6143|
|  2:  4.6808 -  3.7341 0.99   1367  151 0.0941 0.1172      5.5223      5.7329|
|  3:  3.7341 -  3.2677 0.99   1361  151 0.1239 0.1761      5.6024      5.9135|
|  4:  3.2677 -  2.9714 0.98   1314  146 0.1471 0.1869      5.5967      5.7563|
|  5:  2.9714 -  2.7598 0.99   1343  150 0.1595 0.1968      5.4806      5.6299|
|  6:  2.7598 -  2.5980 0.99   1330  146 0.1502 0.2380      5.3742      5.5943|
|  7:  2.5980 -  2.4685 0.98   1296  150 0.1437 0.1828      5.2939      5.4632|
|  8:  2.4685 -  2.3615 0.98   1328  137 0.1441 0.2038      5.2351      5.4803|
|  9:  2.3615 -  2.2709 0.99   1301  147 0.1399 0.2123      5.1532      5.4208|
| 10:  2.2709 -  2.1928 0.99   1306  139 0.1394 0.1865      5.1424      5.2919|
| 11:  2.1928 -  2.1244 0.97   1320  150 0.1316 0.2182      5.0319      5.3775|
| 12:  2.1244 -  2.0638 0.98   1266  149 0.1393 0.1906      4.9956      5.2244|
| 13:  2.0638 -  2.0096 0.89   1176  129 0.1301 0.1934      4.9059      5.1676|
| 14:  2.0096 -  1.9607 0.38    493   55 0.1280 0.2170      4.8303      5.0629|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0141 -  4.6808  1429   159  0.93  10.13   0.97     0.94       8167.28|
|  2:  4.6808 -  3.7341  1367   151  0.95   9.14   1.02     1.01      10877.44|
|  3:  3.7341 -  3.2677  1361   151  0.92  13.57   1.03     1.02      13182.16|
|  4:  3.2677 -  2.9714  1314   146  0.90  16.25   1.02     1.01      13272.76|
|  5:  2.9714 -  2.7598  1343   150  0.87  19.21   1.01     0.98      11363.91|
|  6:  2.7598 -  2.5980  1330   146  0.87  19.05   0.98     0.93       9321.00|
|  7:  2.5980 -  2.4685  1296   150  0.89  18.02   1.00     0.96       7953.47|
|  8:  2.4685 -  2.3615  1328   137  0.88  18.49   1.01     0.98       7450.82|
|  9:  2.3615 -  2.2709  1301   147  0.88  18.72   1.00     0.94       6328.35|
| 10:  2.2709 -  2.1928  1306   139  0.87  19.03   1.00     0.96       6319.55|
| 11:  2.1928 -  2.1244  1320   150  0.88  18.43   1.00     0.96       5307.03|
| 12:  2.1244 -  2.0638  1266   149  0.88  18.53   0.99     0.97       4910.04|
| 13:  2.0638 -  2.0096  1176   129  0.88  18.63   1.00     0.99       4256.18|
| 14:  2.0096 -  1.9607   493    55  0.88  17.89   0.97     0.92       3485.39|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     3485.39 max =        13272.76 mean =      8293.50|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           90.00 mean =        16.65|
|phase err.(test): min =        0.00 max =           89.97 mean =        16.23|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1310   r_free= 0.1815   ksol= 0.32   Bsol= 53.97   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,-0.06,-0.35,-0.00,-0.00,-0.00); trace/3= -0.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.283272                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1310   r_free= 0.1815   ksol= 0.32   Bsol= 53.97   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,-0.06,-0.35,-0.00,-0.00,-0.00); trace/3= -0.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.283272                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0141 -  4.6808 0.99   1429  159 0.1015 0.1431      5.4268      5.6147|
|  2:  4.6808 -  3.7341 0.99   1367  151 0.0941 0.1173      5.5227      5.7335|
|  3:  3.7341 -  3.2677 0.99   1361  151 0.1240 0.1761       5.603      5.9139|
|  4:  3.2677 -  2.9714 0.98   1314  146 0.1470 0.1869      5.5967      5.7565|
|  5:  2.9714 -  2.7598 0.99   1343  150 0.1595 0.1965      5.4803       5.629|
|  6:  2.7598 -  2.5980 0.99   1330  146 0.1501 0.2376      5.3737       5.593|
|  7:  2.5980 -  2.4685 0.98   1296  150 0.1436 0.1828      5.2934      5.4634|
|  8:  2.4685 -  2.3615 0.98   1328  137 0.1440 0.2041      5.2353      5.4818|
|  9:  2.3615 -  2.2709 0.99   1301  147 0.1396 0.2126      5.1532      5.4211|
| 10:  2.2709 -  2.1928 0.99   1306  139 0.1393 0.1871       5.143      5.2938|
| 11:  2.1928 -  2.1244 0.97   1320  150 0.1314 0.2182      5.0322      5.3772|
| 12:  2.1244 -  2.0638 0.98   1266  149 0.1395 0.1910      4.9965      5.2259|
| 13:  2.0638 -  2.0096 0.89   1176  129 0.1301 0.1934      4.9063      5.1666|
| 14:  2.0096 -  1.9607 0.38    493   55 0.1279 0.2171      4.8304      5.0624|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0141 -  4.6808  1429   159  0.93  10.13   0.97     0.94       8171.57|
|  2:  4.6808 -  3.7341  1367   151  0.95   9.15   1.02     1.01      10883.67|
|  3:  3.7341 -  3.2677  1361   151  0.92  13.58   1.03     1.02      13194.75|
|  4:  3.2677 -  2.9714  1314   146  0.90  16.25   1.02     1.01      13274.08|
|  5:  2.9714 -  2.7598  1343   150  0.87  19.19   1.01     0.98      11344.82|
|  6:  2.7598 -  2.5980  1330   146  0.87  19.04   0.98     0.93       9312.37|
|  7:  2.5980 -  2.4685  1296   150  0.89  18.01   1.00     0.96       7944.46|
|  8:  2.4685 -  2.3615  1328   137  0.88  18.50   1.01     0.98       7461.82|
|  9:  2.3615 -  2.2709  1301   147  0.88  18.73   1.00     0.94       6339.34|
| 10:  2.2709 -  2.1928  1306   139  0.87  19.06   1.00     0.96       6332.67|
| 11:  2.1928 -  2.1244  1320   150  0.88  18.45   1.00     0.96       5316.26|
| 12:  2.1244 -  2.0638  1266   149  0.88  18.54   0.99     0.97       4920.08|
| 13:  2.0638 -  2.0096  1176   129  0.88  18.65   1.00     0.99       4257.22|
| 14:  2.0096 -  1.9607   493    55  0.88  17.90   0.97     0.92       3482.12|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     3482.12 max =        13274.08 mean =      8296.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           90.00 mean =        16.66|
|phase err.(test): min =        0.00 max =           89.97 mean =        16.23|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.709)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.60    114.02  17.16    None  None   None       |
|    all(noH): 2823   0      0.60    114.02  17.16    None  None   None       |
|    Sol.    : 438    0      4.97    114.02  43.03    None  None   None       |
|    Mac.    : 2385   0      0.60    109.38  12.42    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:     0.603 -  11.945: 1582   |   5:    57.311 -  68.653:   78        |
|      1:    11.945 -  23.286:  700   |   6:    68.653 -  79.994:   30        |
|      2:    23.286 -  34.628:  165   |   7:    79.994 -  91.336:   16        |
|      3:    34.628 -  45.969:  130   |   8:    91.336 - 102.677:    8        |
|      4:    45.969 -  57.311:  109   |   9:   102.677 - 114.019:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 327         
Filter by distance & map next to the model:
   mapped sites are within: 0.677 - 4.422
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 323 from: 327
   mapped sites are within: 0.745 - 4.422

peak=   11.044 closest distance to " O  BHOH Z  74 " =    1.170
peak=    9.084 closest distance to " CB  SER A 216 " =    1.227
peak=    6.294 closest distance to " O   HOH Z 120 " =    1.209
peak=    5.348 closest distance to " O   HOH Z 102 " =    1.387
peak=    5.248 closest distance to " CA  TYR A  30 " =    0.932
peak=    5.084 closest distance to " O   HOH Z 210 " =    1.339
peak=    5.057 closest distance to " CG  PRO A 280 " =    0.789
peak=    5.055 closest distance to " O   HOH Z  46 " =    1.233
peak=    5.041 closest distance to " O   HOH Z 124 " =    1.482
peak=    5.024 closest distance to " O   HOH Z 130 " =    1.163
peak=    5.023 closest distance to " CG  ARG A  66 " =    1.183
peak=    4.939 closest distance to " O   HOH Z 159 " =    1.093
peak=    4.916 closest distance to " CB  ASN A 285 " =    1.012
peak=    4.866 closest distance to " O   HOH Z  49 " =    1.427
peak=    4.812 closest distance to " CB  ARG A 275 " =    0.935
peak=    4.775 closest distance to " CG  GLN A  77 " =    0.958
peak=    4.754 closest distance to " O   HOH Z 401 " =    1.654
peak=    4.718 closest distance to " O   HOH Z 389 " =    2.116
peak=    4.706 closest distance to " O   HOH Z 433 " =    1.777
peak=    4.703 closest distance to " O   HOH Z  80 " =    2.201
peak=    4.641 closest distance to " O   HOH Z 247 " =    1.580
peak=    4.613 closest distance to " O   ASN A 285 " =    0.893
peak=    4.586 closest distance to " CB  GLN A 223 " =    1.349
peak=    4.572 closest distance to " O   HOH Z 357 " =    1.852
peak=    4.545 closest distance to " O   PRO A 198 " =    1.601
peak=    4.526 closest distance to " O   HOH Z 193 " =    1.722
peak=    4.512 closest distance to " CB  SER A  63 " =    1.172
peak=    4.509 closest distance to " O   HOH Z 402 " =    1.653
peak=    4.504 closest distance to " NH2 ARG A  56 " =    2.338
peak=    4.497 closest distance to " O   HOH Z 134 " =    2.026
peak=    4.450 closest distance to " O   HOH Z 236 " =    1.784
peak=    4.430 closest distance to " NH1AARG A 275 " =    1.183
peak=    4.413 closest distance to " CG AARG A 275 " =    1.098
peak=    4.385 closest distance to " O   HOH Z 209 " =    2.253
peak=    4.379 closest distance to " O   HOH Z 422 " =    0.851
peak=    4.370 closest distance to " CG2 VAL A 197 " =    1.243
peak=    4.370 closest distance to " O   HOH Z 403 " =    2.152
peak=    4.330 closest distance to " CB  SER A  62 " =    0.962
peak=    4.329 closest distance to " O   HOH Z  44 " =    2.018
peak=    4.317 closest distance to " CD2 TRP A 179 " =    1.423
peak=    4.309 closest distance to " O   HOH Z 142 " =    1.535
peak=    4.296 closest distance to " CG  PRO A 198 " =    1.329
peak=    4.293 closest distance to " CB  SER A 141 " =    1.083
peak=    4.287 closest distance to " NZ  LYS A 117 " =    3.230
peak=    4.283 closest distance to " CD  ARG A 269 " =    1.087
peak=    4.248 closest distance to " O   HOH Z 214 " =    1.410
peak=    4.202 closest distance to " O   HOH Z 109 " =    1.718
peak=    4.161 closest distance to " CB AVAL A  41 " =    0.976
peak=    4.161 closest distance to " CE  LYS A 119 " =    1.147
peak=    4.154 closest distance to " CB  PRO A 213 " =    1.344
peak=    4.149 closest distance to " O   HOH Z 128 " =    1.556
peak=    4.122 closest distance to " O   HOH Z  43 " =    1.914
peak=    4.118 closest distance to " O   HOH Z  97 " =    1.415
peak=    4.114 closest distance to " O   HOH Z   7 " =    1.235
peak=    4.104 closest distance to " O   HOH Z 431 " =    1.488
peak=    4.091 closest distance to " O   HOH Z 250 " =    2.356
peak=    4.088 closest distance to " OD1 ASN A 301 " =    1.093
peak=    4.078 closest distance to " O   HOH Z  63 " =    2.008
peak=    4.056 closest distance to " O   HOH Z  52 " =    1.016
peak=    4.054 closest distance to " O   HOH Z 404 " =    1.317
peak=    4.053 closest distance to " O   GLN A  11 " =    0.978
peak=    4.045 closest distance to " NH1 ARG A  36 " =    1.131
peak=    4.040 closest distance to " O   VAL A  72 " =    1.393
peak=    4.033 closest distance to " O   HOH Z 126 " =    1.570
peak=    4.032 closest distance to " CB  ARG A 190 " =    1.823
peak=    3.999 closest distance to " O   HOH Z 132 " =    2.685
peak=    3.992 closest distance to " O   HOH Z  15 " =    2.312
peak=    3.985 closest distance to " O   HOH Z   6 " =    1.149
peak=    3.979 closest distance to " CB  GLN A  73 " =    1.189
peak=    3.973 closest distance to " O   HOH Z 414 " =    1.927
peak=    3.969 closest distance to " O   HOH Z 411 " =    3.494
peak=    3.958 closest distance to " CA  ARG A 195 " =    1.122
peak=    3.955 closest distance to " OE1 GLN A  11 " =    2.139
peak=    3.954 closest distance to " O   HOH Z 361 " =    3.132
peak=    3.951 closest distance to " CG  PRO A  90 " =    1.299
peak=    3.945 closest distance to " CB  ASN A 148 " =    1.277
peak=    3.932 closest distance to " N   ASN A  39 " =    1.182
peak=    3.922 closest distance to " O   HOH Z 189 " =    2.004
peak=    3.921 closest distance to " O   HOH Z 196 " =    1.565
peak=    3.918 closest distance to " NH2 ARG A  36 " =    1.209
peak=    3.909 closest distance to " CB  GLU A 128 " =    1.217
peak=    3.903 closest distance to " O   HOH Z 154 " =    1.688
peak=    3.898 closest distance to " CB  GLN A  58 " =    1.048
peak=    3.896 closest distance to " CG2 THR A 220 " =    0.882
peak=    3.894 closest distance to " O   HOH Z 406 " =    1.558
peak=    3.885 closest distance to " O   HOH Z 130 " =    2.437
peak=    3.872 closest distance to " O   HOH Z 371 " =    3.235
peak=    3.869 closest distance to " O   HOH Z 203 " =    1.897
peak=    3.868 closest distance to " O   HOH Z 428 " =    1.147
peak=    3.868 closest distance to " CB  PHE A  16 " =    1.150
peak=    3.867 closest distance to " O   HOH Z 163 " =    1.649
peak=    3.866 closest distance to " O   HOH Z 272 " =    1.951
peak=    3.849 closest distance to " O   HOH Z 272 " =    1.320
peak=    3.840 closest distance to " CA  SER A  12 " =    1.368
peak=    3.838 closest distance to " NH2BARG A 145 " =    2.103
peak=    3.815 closest distance to " CG1 ILE A  33 " =    1.323
peak=    3.809 closest distance to " O   HOH Z 298 " =    1.988
peak=    3.806 closest distance to " CA  VAL A  41 " =    0.921
peak=    3.784 closest distance to " O   HOH Z 234 " =    3.702
peak=    3.780 closest distance to " ND1 HIS A  81 " =    1.230
peak=    3.778 closest distance to " OE1 GLU A   2 " =    1.514
peak=    3.777 closest distance to " CB  GLN A 183 " =    1.315
peak=    3.777 closest distance to " O   HOH Z 132 " =    2.005
peak=    3.764 closest distance to " CB  PRO A  54 " =    0.745
peak=    3.758 closest distance to " CZ  PHE A 218 " =    1.048
peak=    3.747 closest distance to " NH2 ARG A 156 " =    1.093
peak=    3.741 closest distance to " CA  ARG A  66 " =    1.124
peak=    3.740 closest distance to " O   HOH Z 423 " =    3.069
peak=    3.737 closest distance to " O   HOH Z  40 " =    1.929
peak=    3.733 closest distance to " CB  VAL A 202 " =    1.427
peak=    3.726 closest distance to " O   HOH Z 112 " =    2.029
peak=    3.722 closest distance to " O   HOH Z 146 " =    1.295
peak=    3.720 closest distance to " CA  THR A  82 " =    1.779
peak=    3.708 closest distance to " O   HOH Z 435 " =    2.042
peak=    3.706 closest distance to " O   HOH Z   6 " =    2.107
peak=    3.699 closest distance to " O   HOH Z  90 " =    3.661
peak=    3.698 closest distance to " O   HOH Z   7 " =    1.171
peak=    3.697 closest distance to " O   HOH Z  48 " =    1.756
peak=    3.692 closest distance to " O   GLY A  23 " =    2.449
peak=    3.692 closest distance to " O   ARG A 275 " =    0.837
peak=    3.685 closest distance to " N   SER A 164 " =    1.008
peak=    3.682 closest distance to " O   HOH Z 380 " =    2.070
peak=    3.681 closest distance to " N   TRP A 150 " =    1.083
peak=    3.680 closest distance to " O   HOH Z 437 " =    2.078
peak=    3.679 closest distance to " O   HOH Z 291 " =    1.333
peak=    3.672 closest distance to " N   ARG A 156 " =    1.513
peak=    3.661 closest distance to " CG  PRO A 243 " =    1.160
peak=    3.661 closest distance to " O   HOH Z 315 " =    1.794
peak=    3.658 closest distance to " O   SER A  87 " =    2.187
peak=    3.655 closest distance to " CB  GLU A 175 " =    1.306
peak=    3.643 closest distance to " O   HOH Z 339 " =    1.216
peak=    3.642 closest distance to " O   HOH Z 303 " =    2.088
peak=    3.641 closest distance to " O   HOH Z  39 " =    2.089
peak=    3.640 closest distance to " CB  GLN A 194 " =    1.039
peak=    3.637 closest distance to " CB  VAL A 265 " =    1.364
peak=    3.629 closest distance to " CA  TRP A  85 " =    1.081
peak=    3.624 closest distance to " O   HOH Z  35 " =    2.012
peak=    3.618 closest distance to " O   HOH Z 427 " =    3.421
peak=    3.615 closest distance to " O   HOH Z 245 " =    1.365
peak=    3.614 closest distance to " O   HOH Z 418 " =    2.938
peak=    3.606 closest distance to " CA  GLY A  80 " =    0.881
peak=    3.604 closest distance to " O   HOH Z 365 " =    1.630
peak=    3.600 closest distance to " O   HOH Z 208 " =    1.552
peak=    3.597 closest distance to " O   HOH Z 352 " =    1.303
peak=    3.597 closest distance to " C   ILE A 106 " =    1.792
peak=    3.595 closest distance to " O   HOH Z 261 " =    2.061
peak=    3.594 closest distance to " CG2 ILE A  20 " =    1.334
peak=    3.591 closest distance to " O   HOH Z 227 " =    1.798
peak=    3.585 closest distance to " O   HOH Z 116 " =    1.094
peak=    3.583 closest distance to " CB  SER A  26 " =    1.736
peak=    3.583 closest distance to " CD  ARG A  36 " =    1.230
peak=    3.578 closest distance to " O   HOH Z 156 " =    2.545
peak=    3.578 closest distance to " O   HOH Z 289 " =    1.653
peak=    3.578 closest distance to " O   HOH Z  88 " =    3.279
peak=    3.576 closest distance to " N   ASN A 252 " =    1.098
peak=    3.570 closest distance to " CB  GLU A 277 " =    1.020
peak=    3.569 closest distance to " CD  LYS A 166 " =    1.567
peak=    3.566 closest distance to " CA  ARG A  36 " =    1.058
peak=    3.561 closest distance to " CB  THR A  52 " =    0.931
peak=    3.556 closest distance to " CD  ARG A 159 " =    0.840
peak=    3.548 closest distance to " O   HOH Z 435 " =    2.695
peak=    3.547 closest distance to " O   HOH Z  68 " =    1.977
peak=    3.546 closest distance to " CG  GLN A  11 " =    1.408
peak=    3.543 closest distance to " O   HOH Z 128 " =    1.836
peak=    3.541 closest distance to " CD2 PHE A 225 " =    0.957
peak=    3.535 closest distance to " OG  SER A  62 " =    2.812
peak=    3.535 closest distance to " O   HOH Z 146 " =    1.414
peak=    3.531 closest distance to " O   HOH Z 279 " =    2.091
peak=    3.526 closest distance to " O   SER A 273 " =    1.661
peak=    3.519 closest distance to " O  BHOH Z 338 " =    0.937
peak=    3.513 closest distance to " CA  ILE A 120 " =    1.263
peak=    3.503 closest distance to " O   HOH Z 369 " =    2.264
peak=    3.501 closest distance to " O   HOH Z  78 " =    1.626
peak=    3.497 closest distance to " O   HOH Z  53 " =    1.145
peak=    3.492 closest distance to " N   ALA A   1 " =    1.219
peak=    3.490 closest distance to " CB  GLU A   2 " =    1.084
peak=    3.489 closest distance to " O   HOH Z  61 " =    1.614
peak=    3.488 closest distance to " O   HOH Z 124 " =    3.369
peak=    3.485 closest distance to " CB  TRP A 179 " =    1.105
peak=    3.485 closest distance to " CB  ALA A 248 " =    1.459
peak=    3.479 closest distance to " CD1 TRP A 274 " =    1.074
peak=    3.478 closest distance to " O   HOH Z  20 " =    1.745
peak=    3.477 closest distance to " CD1 LEU A 167 " =    1.379
peak=    3.475 closest distance to " O   HOH Z 394 " =    1.521
peak=    3.474 closest distance to " CD  GLN A  73 " =    1.034
peak=    3.468 closest distance to " CD  ARG A  36 " =    1.158
peak=    3.459 closest distance to " CA  ALA A 100 " =    1.370
peak=    3.457 closest distance to " CA  ASN A 127 " =    1.056
peak=    3.457 closest distance to " CA  ASN A 176 " =    1.096
peak=    3.452 closest distance to " O   HOH Z 336 " =    1.578
peak=    3.452 closest distance to " NH1AARG A 275 " =    2.258
peak=    3.452 closest distance to " CE1 HIS A 108 " =    1.351
peak=    3.451 closest distance to " CE3 TRP A 274 " =    2.690
peak=    3.451 closest distance to " O   HOH Z 257 " =    2.172
peak=    3.450 closest distance to " O   HOH Z 124 " =    1.972
peak=    3.449 closest distance to " ND2 ASN A 187 " =    1.677
peak=    3.440 closest distance to " O   HOH Z 358 " =    1.998
peak=    3.437 closest distance to " O   HOH Z 365 " =    2.500
peak=    3.436 closest distance to " CB  ASN A 187 " =    1.292
peak=    3.434 closest distance to " CB  PHE A 283 " =    1.014
peak=    3.433 closest distance to " NE2 GLN A  77 " =    3.034
peak=    3.430 closest distance to " CB  SER A 273 " =    0.874
peak=    3.429 closest distance to " OD1 ASN A  60 " =    1.125
peak=    3.428 closest distance to " CB  MET A 105 " =    1.004
peak=    3.425 closest distance to " CG2 THR A  42 " =    0.864
peak=    3.417 closest distance to " O   HOH Z  89 " =    2.080
peak=    3.417 closest distance to " O   HOH Z 133 " =    1.385
peak=    3.415 closest distance to " CG2 THR A 221 " =    1.245
peak=    3.414 closest distance to " CD  ARG A 195 " =    1.094
peak=    3.408 closest distance to " O   HOH Z 427 " =    1.124
peak=    3.407 closest distance to " CA  ALA A  51 " =    0.948
peak=    3.406 closest distance to " O   HOH Z 111 " =    3.705
peak=    3.404 closest distance to " CB  VAL A 230 " =    1.062
peak=    3.398 closest distance to " NZ  LYS A 117 " =    0.821
peak=    3.396 closest distance to " O   HOH Z 344 " =    2.813
peak=    3.392 closest distance to " OG BSER A 210 " =    1.141
peak=    3.391 closest distance to " O   HOH Z 267 " =    1.878
peak=    3.386 closest distance to " O   HOH Z 427 " =    3.346
peak=    3.385 closest distance to " CA  ARG A 156 " =    1.000
peak=    3.382 closest distance to " O   HOH Z 358 " =    1.552
peak=    3.381 closest distance to " CB  PRO A 198 " =    1.348
peak=    3.378 closest distance to " O   HOH Z 425 " =    1.569
peak=    3.357 closest distance to " OG  SER A 245 " =    1.420
peak=    3.355 closest distance to " CB  GLN A  89 " =    1.300
peak=    3.355 closest distance to " CG1 VAL A 153 " =    1.244
peak=    3.348 closest distance to " CG2 VAL A  78 " =    0.900
peak=    3.348 closest distance to " O   HOH Z 173 " =    2.174
peak=    3.345 closest distance to " CA  ALA A  21 " =    1.377
peak=    3.344 closest distance to " CB  GLN A  88 " =    1.211
peak=    3.333 closest distance to " CA  THR A 294 " =    2.024
peak=    3.330 closest distance to " CB  PRO A  90 " =    1.071
peak=    3.326 closest distance to " CD1 LEU A 222 " =    0.888
peak=    3.324 closest distance to " CB  ARG A  79 " =    0.778
peak=    3.323 closest distance to " OH  TYR A  30 " =    1.228
peak=    3.314 closest distance to " O   HOH Z  59 " =    1.862
peak=    3.313 closest distance to " O   HOH Z 154 " =    2.299
peak=    3.312 closest distance to " O   GLY A  57 " =    0.989
peak=    3.312 closest distance to " CB  GLU A 152 " =    1.108
peak=    3.311 closest distance to " O   HOH Z 185 " =    1.739
peak=    3.311 closest distance to " ND2 ASN A 301 " =    1.061
peak=    3.305 closest distance to " CB  LEU A 228 " =    1.265
peak=    3.301 closest distance to " OG BSER A 212 " =    2.569
peak=    3.289 closest distance to " OE1 GLN A 194 " =    1.637
peak=    3.288 closest distance to " CB  GLU A  46 " =    1.079
peak=    3.284 closest distance to " CB  PRO A 213 " =    2.076
peak=    3.284 closest distance to " O   HOH Z 301 " =    1.420
peak=    3.282 closest distance to " CB  ALA A  71 " =    1.188
peak=    3.282 closest distance to " O   ALA A 165 " =    1.534
peak=    3.281 closest distance to " CB  ILE A 199 " =    1.126
peak=    3.273 closest distance to " CZ  PHE A  38 " =    1.302
peak=    3.273 closest distance to " CA  LEU A  83 " =    1.200
peak=    3.273 closest distance to " OE1 GLN A  73 " =    1.393
peak=    3.273 closest distance to " CD2 HIS A  81 " =    1.211
peak=    3.266 closest distance to " CB  TRP A 179 " =    1.752
peak=    3.264 closest distance to " O   HOH Z 248 " =    1.512
peak=    3.262 closest distance to " CG2 ILE A 120 " =    1.245
peak=    3.260 closest distance to " O   HOH Z 316 " =    2.585
peak=    3.259 closest distance to " CB  ALA A 256 " =    1.087
peak=    3.255 closest distance to " O   HOH Z 334 " =    1.561
peak=    3.254 closest distance to " CB  GLU A 236 " =    1.350
peak=    3.249 closest distance to " O   HOH Z 112 " =    1.438
peak=    3.242 closest distance to " O   LYS A 289 " =    0.965
peak=    3.240 closest distance to " O   HOH Z 367 " =    3.156
peak=    3.238 closest distance to " O   HOH Z 234 " =    4.031
peak=    3.237 closest distance to " CA  GLU A 152 " =    0.931
peak=    3.234 closest distance to " ND1 HIS A  81 " =    1.459
peak=    3.234 closest distance to " NH1 ARG A  36 " =    1.039
peak=    3.232 closest distance to " CA  PRO A  90 " =    0.897
peak=    3.229 closest distance to " OG BSER A 258 " =    2.726
peak=    3.226 closest distance to " CB  ARG A  79 " =    0.905
peak=    3.221 closest distance to " CA  ARG A 195 " =    1.443
peak=    3.221 closest distance to " O   HOH Z 139 " =    4.422
peak=    3.217 closest distance to " O   HOH Z  85 " =    1.983
peak=    3.200 closest distance to " CG  MET A  40 " =    2.279
peak=    3.199 closest distance to " CB  TRP A 266 " =    1.059
peak=    3.195 closest distance to " CB  ALA A 114 " =    1.268
peak=    3.194 closest distance to " O   HOH Z  80 " =    3.256
peak=    3.189 closest distance to " CG2 VAL A 268 " =    1.192
peak=    3.188 closest distance to " O   ALA A 242 " =    1.141
peak=    3.186 closest distance to " O   HOH Z 147 " =    1.773
peak=    3.186 closest distance to " O   HOH Z 403 " =    1.387
peak=    3.184 closest distance to " CG1 ILE A 120 " =    1.096
peak=    3.182 closest distance to " O   HOH Z 265 " =    1.944
peak=    3.182 closest distance to " O   HOH Z 343 " =    2.625
peak=    3.179 closest distance to " O   HOH Z 345 " =    2.569
peak=    3.178 closest distance to " O   HOH Z 250 " =    1.409
peak=    3.174 closest distance to " CA  CYS A 260 " =    1.722
peak=    3.173 closest distance to " O   GLY A  91 " =    1.245
peak=    3.170 closest distance to " CB  PRO A 243 " =    1.112
peak=    3.164 closest distance to " O   HOH Z 132 " =    1.329
peak=    3.163 closest distance to " O   HOH Z 150 " =    1.568
peak=    3.161 closest distance to " N   ASP A 286 " =    0.953
peak=    3.160 closest distance to " OD1 ASP A 171 " =    1.194
peak=    3.157 closest distance to " NZ  LYS A  48 " =    1.179
peak=    3.156 closest distance to " O   HOH Z 152 " =    1.774
peak=    3.153 closest distance to " O   HOH Z   4 " =    0.957
peak=    3.145 closest distance to " CD  LYS A 119 " =    1.967
peak=    3.142 closest distance to " O   HOH Z 109 " =    2.762
peak=    3.137 closest distance to " O   HOH Z 128 " =    2.386
peak=    3.134 closest distance to " O   HOH Z 345 " =    1.766
peak=    3.132 closest distance to " NH2AARG A 190 " =    1.352
peak=    3.126 closest distance to " CG  MET A 185 " =    1.245
peak=    3.122 closest distance to " O   HOH Z 225 " =    1.934
peak=    3.121 closest distance to " O   HOH Z 261 " =    1.537
peak=    3.117 closest distance to " O   HOH Z 195 " =    1.193
peak=    3.116 closest distance to " O   CYS A 168 " =    1.537
peak=    3.115 closest distance to " O   ASN A  74 " =    1.791
peak=    3.112 closest distance to " O   HOH Z 126 " =    2.144
peak=    3.111 closest distance to " O   HOH Z 111 " =    1.532
peak=    3.110 closest distance to " O   HOH Z  85 " =    1.380
peak=    3.109 closest distance to " CB  TYR A 247 " =    1.042
peak=    3.105 closest distance to " O   ASP A 200 " =    1.592
peak=    3.100 closest distance to " O   HOH Z 412 " =    3.477
peak=    3.095 closest distance to " CB  ASP A 286 " =    1.046
peak=    3.092 closest distance to " O   HOH Z 162 " =    1.687
peak=    3.085 closest distance to " O   HOH Z  38 " =    1.434
peak=    3.059 closest distance to " CB  ASN A 187 " =    1.504
peak=    3.057 closest distance to " OD1 ASN A  39 " =    1.078
peak=    3.055 closest distance to " O   HOH Z 373 " =    1.623
peak=    3.049 closest distance to " OE1 GLN A 223 " =    2.306
peak=    3.034 closest distance to " CG2 VAL A 257 " =    0.846
peak=    3.020 closest distance to " CB  THR A  31 " =    1.740
peak=    3.003 closest distance to " O   HOH Z 142 " =    1.792

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 216         
Filter by distance & map next to the model:
   mapped sites are within: 0.718 - 5.964
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 216 from: 216
   mapped sites are within: 0.718 - 5.964

peak=   -4.626 closest distance to " O   HOH Z  52 " =    1.040
peak=   -4.571 closest distance to " C   HIS A 108 " =    1.033
peak=   -4.519 closest distance to " O   HOH Z 266 " =    4.683
peak=   -4.380 closest distance to " O   HOH Z 120 " =    1.138
peak=   -4.271 closest distance to " CB  LEU A 167 " =    2.163
peak=   -4.237 closest distance to " O   GLN A  11 " =    0.939
peak=   -4.228 closest distance to " CD1 PHE A  59 " =    1.879
peak=   -4.192 closest distance to " CG  PRO A 243 " =    1.721
peak=   -4.138 closest distance to " O  BHOH Z 338 " =    1.588
peak=   -4.119 closest distance to " CD2 LEU A 237 " =    2.269
peak=   -4.115 closest distance to " NH2 ARG A  36 " =    1.083
peak=   -4.085 closest distance to " CG2 ILE A  49 " =    2.576
peak=   -4.083 closest distance to " O   HOH Z 196 " =    1.846
peak=   -4.081 closest distance to " C   THR A 279 " =    1.163
peak=   -4.027 closest distance to " O   HOH Z  13 " =    1.716
peak=   -4.022 closest distance to " CA  VAL A  67 " =    2.973
peak=   -4.011 closest distance to " SG  CYS A 254 " =    3.275
peak=   -4.008 closest distance to " CD  GLN A 223 " =    1.744
peak=   -3.980 closest distance to " O   HOH Z 424 " =    1.351
peak=   -3.966 closest distance to " O   PRO A 198 " =    1.396
peak=   -3.964 closest distance to " O   HOH Z 422 " =    1.206
peak=   -3.943 closest distance to " OXT GLY A 302 " =    2.859
peak=   -3.917 closest distance to " O   HOH Z   7 " =    0.958
peak=   -3.903 closest distance to " O   PHE A 218 " =    1.412
peak=   -3.884 closest distance to " NE2 GLN A 223 " =    1.121
peak=   -3.879 closest distance to " CD  GLN A  58 " =    1.148
peak=   -3.878 closest distance to " O   HOH Z 391 " =    1.182
peak=   -3.863 closest distance to " O   HOH Z 165 " =    1.781
peak=   -3.855 closest distance to " O   HOH Z 210 " =    0.860
peak=   -3.853 closest distance to " O   HOH Z  56 " =    0.999
peak=   -3.852 closest distance to " CA  GLY A 133 " =    1.980
peak=   -3.805 closest distance to " O   HOH Z 418 " =    1.379
peak=   -3.799 closest distance to " CA  SER A 164 " =    1.942
peak=   -3.794 closest distance to " CB  SER A  28 " =    1.090
peak=   -3.725 closest distance to " O   HOH Z 326 " =    4.923
peak=   -3.719 closest distance to " CG  MET A  93 " =    2.453
peak=   -3.708 closest distance to " CG  ASP A 162 " =    1.412
peak=   -3.695 closest distance to " O   TYR A  15 " =    1.660
peak=   -3.693 closest distance to " N   ALA A  43 " =    2.590
peak=   -3.683 closest distance to " O   HOH Z 196 " =    1.737
peak=   -3.669 closest distance to " OD1 ASN A 301 " =    0.838
peak=   -3.662 closest distance to " O   HOH Z 234 " =    4.114
peak=   -3.651 closest distance to " C   ILE A 239 " =    2.258
peak=   -3.644 closest distance to " O   HOH Z 424 " =    3.404
peak=   -3.635 closest distance to " O   HOH Z 197 " =    1.861
peak=   -3.630 closest distance to " O   HOH Z 233 " =    2.439
peak=   -3.624 closest distance to " O   VAL A 174 " =    1.938
peak=   -3.620 closest distance to " O   HOH Z 423 " =    2.356
peak=   -3.607 closest distance to " ND2 ASN A  69 " =    1.523
peak=   -3.605 closest distance to " OG  SER A  32 " =    0.989
peak=   -3.602 closest distance to " O   TRP A  92 " =    2.006
peak=   -3.595 closest distance to " O   ALA A  34 " =    2.352
peak=   -3.555 closest distance to " O   HOH Z  37 " =    1.477
peak=   -3.550 closest distance to " CG2 THR A 182 " =    2.264
peak=   -3.547 closest distance to " CG2 VAL A 189 " =    2.238
peak=   -3.543 closest distance to " C   GLY A  91 " =    1.129
peak=   -3.537 closest distance to " O   SER A  95 " =    1.679
peak=   -3.532 closest distance to " CA  GLU A 277 " =    1.205
peak=   -3.529 closest distance to " O   HOH Z 109 " =    2.905
peak=   -3.525 closest distance to " ND2 ASN A  39 " =    1.186
peak=   -3.525 closest distance to " O   HOH Z  71 " =    1.928
peak=   -3.521 closest distance to " C   ASN A 285 " =    2.388
peak=   -3.520 closest distance to " CD1 TRP A 179 " =    1.107
peak=   -3.518 closest distance to " O   HOH Z  15 " =    1.619
peak=   -3.510 closest distance to " N   VAL A  72 " =    1.386
peak=   -3.507 closest distance to " CA  GLY A 203 " =    2.059
peak=   -3.502 closest distance to " CD2 PHE A  61 " =    2.048
peak=   -3.500 closest distance to " ND2 ASN A  60 " =    1.198
peak=   -3.498 closest distance to " CG  GLU A  53 " =    1.164
peak=   -3.487 closest distance to " CE  MET A 105 " =    1.975
peak=   -3.485 closest distance to " N   ASP A 272 " =    1.261
peak=   -3.485 closest distance to " O   HOH Z 401 " =    0.891
peak=   -3.480 closest distance to " CD  GLU A 236 " =    1.019
peak=   -3.480 closest distance to " O   HOH Z 221 " =    1.133
peak=   -3.469 closest distance to " CG2BVAL A  41 " =    2.734
peak=   -3.467 closest distance to " NH2 ARG A  79 " =    2.198
peak=   -3.451 closest distance to " CD2 TYR A  30 " =    2.792
peak=   -3.448 closest distance to " CD  ARG A 156 " =    1.995
peak=   -3.446 closest distance to " O   HOH Z  29 " =    1.552
peak=   -3.443 closest distance to " C   VAL A 265 " =    0.921
peak=   -3.442 closest distance to " O   HOH Z 140 " =    1.378
peak=   -3.439 closest distance to " O   ASN A 187 " =    1.516
peak=   -3.430 closest distance to " CA  VAL A 197 " =    0.969
peak=   -3.426 closest distance to " O   THR A  52 " =    1.846
peak=   -3.421 closest distance to " O   ASP A 171 " =    1.019
peak=   -3.421 closest distance to " N   ARG A 275 " =    0.972
peak=   -3.418 closest distance to " OE2 GLU A 277 " =    4.068
peak=   -3.418 closest distance to " O   HOH Z 159 " =    0.838
peak=   -3.414 closest distance to " CB  PRO A 213 " =    1.496
peak=   -3.410 closest distance to " O   HOH Z 222 " =    1.260
peak=   -3.408 closest distance to " O   HOH Z 176 " =    1.557
peak=   -3.406 closest distance to " O   HOH Z 159 " =    1.061
peak=   -3.398 closest distance to " O   HOH Z  41 " =    1.969
peak=   -3.396 closest distance to " CB  ALA A 161 " =    2.545
peak=   -3.384 closest distance to " O   HOH Z 407 " =    1.531
peak=   -3.370 closest distance to " NH2 ARG A  66 " =    1.488
peak=   -3.369 closest distance to " O   MET A  40 " =    2.630
peak=   -3.367 closest distance to " CG  GLN A  11 " =    1.252
peak=   -3.367 closest distance to " O   HOH Z 130 " =    1.392
peak=   -3.366 closest distance to " CG  PRO A 163 " =    1.460
peak=   -3.361 closest distance to " O   HOH Z 174 " =    2.231
peak=   -3.359 closest distance to " O   HOH Z 287 " =    2.182
peak=   -3.356 closest distance to " O   HOH Z 151 " =    1.388
peak=   -3.353 closest distance to " CA  TYR A  68 " =    2.676
peak=   -3.353 closest distance to " O   HOH Z 130 " =    1.953
peak=   -3.349 closest distance to " OD1 ASP A 272 " =    1.402
peak=   -3.349 closest distance to " O   ARG A  79 " =    0.870
peak=   -3.347 closest distance to " CD  GLN A  58 " =    0.967
peak=   -3.345 closest distance to " OG  SER A 141 " =    2.061
peak=   -3.344 closest distance to " O   HOH Z 109 " =    5.735
peak=   -3.343 closest distance to " SD  MET A  93 " =    1.614
peak=   -3.340 closest distance to " N   THR A 235 " =    1.215
peak=   -3.339 closest distance to " O   HOH Z 130 " =    0.800
peak=   -3.339 closest distance to " CB  GLN A  73 " =    1.000
peak=   -3.338 closest distance to " OD2 ASP A 298 " =    1.003
peak=   -3.333 closest distance to " O   HOH Z 195 " =    3.330
peak=   -3.329 closest distance to " O   HOH Z 290 " =    0.885
peak=   -3.319 closest distance to " OG1 THR A  82 " =    1.339
peak=   -3.317 closest distance to " O   HOH Z 118 " =    4.553
peak=   -3.316 closest distance to " O   HOH Z 150 " =    1.891
peak=   -3.313 closest distance to " O   HOH Z 139 " =    5.333
peak=   -3.313 closest distance to " CD1 ILE A 106 " =    2.050
peak=   -3.312 closest distance to " CA  SER A 288 " =    1.053
peak=   -3.309 closest distance to " CB  ALA A  43 " =    2.620
peak=   -3.309 closest distance to " CD  GLN A  88 " =    0.894
peak=   -3.306 closest distance to " O   HOH Z 250 " =    1.464
peak=   -3.306 closest distance to " CA  ALA A 114 " =    1.047
peak=   -3.302 closest distance to " O   HOH Z 392 " =    1.483
peak=   -3.300 closest distance to " CA  SER A 276 " =    1.376
peak=   -3.298 closest distance to " O   HOH Z 145 " =    2.311
peak=   -3.296 closest distance to " OXT GLY A 302 " =    3.338
peak=   -3.296 closest distance to " C   ASN A 148 " =    1.785
peak=   -3.296 closest distance to " NE2 GLN A  88 " =    1.003
peak=   -3.288 closest distance to " CD2 HIS A 115 " =    1.029
peak=   -3.286 closest distance to " O   HOH Z   6 " =    1.566
peak=   -3.283 closest distance to " O   HOH Z 191 " =    5.964
peak=   -3.281 closest distance to " OD2 ASP A 171 " =    1.722
peak=   -3.278 closest distance to " CE1 TYR A 247 " =    2.438
peak=   -3.272 closest distance to " CD1 LEU A  96 " =    2.039
peak=   -3.271 closest distance to " CA  LEU A 143 " =    1.103
peak=   -3.269 closest distance to " CD2 PHE A  59 " =    2.372
peak=   -3.265 closest distance to " O   HOH Z 396 " =    1.481
peak=   -3.263 closest distance to " O   HOH Z 166 " =    1.371
peak=   -3.262 closest distance to " O   HOH Z 348 " =    2.384
peak=   -3.257 closest distance to " O   HOH Z 426 " =    1.626
peak=   -3.252 closest distance to " O   HOH Z 126 " =    1.643
peak=   -3.250 closest distance to " CE3 TRP A  70 " =    1.748
peak=   -3.247 closest distance to " OD2 ASP A 171 " =    2.246
peak=   -3.247 closest distance to " CE  MET A  93 " =    1.204
peak=   -3.247 closest distance to " NE1 TRP A 177 " =    1.983
peak=   -3.243 closest distance to " NH2 ARG A  66 " =    5.445
peak=   -3.242 closest distance to " O   HOH Z 388 " =    2.063
peak=   -3.234 closest distance to " O   HOH Z 423 " =    1.243
peak=   -3.233 closest distance to " O   HOH Z 397 " =    1.220
peak=   -3.230 closest distance to " O   HOH Z 377 " =    1.052
peak=   -3.226 closest distance to " O   HOH Z 403 " =    1.028
peak=   -3.222 closest distance to " N   GLY A  17 " =    1.573
peak=   -3.220 closest distance to " O   HOH Z 171 " =    2.355
peak=   -3.220 closest distance to " N   ASN A 215 " =    1.636
peak=   -3.220 closest distance to " O   HOH Z  38 " =    1.364
peak=   -3.219 closest distance to " CB  ALA A 248 " =    2.190
peak=   -3.217 closest distance to " O   HOH Z  18 " =    1.205
peak=   -3.210 closest distance to " C   TYR A  30 " =    1.032
peak=   -3.209 closest distance to " N   LEU A 237 " =    1.762
peak=   -3.207 closest distance to " O   HOH Z 309 " =    1.136
peak=   -3.207 closest distance to " N   ALA A 248 " =    1.878
peak=   -3.205 closest distance to " O   HOH Z 146 " =    1.433
peak=   -3.202 closest distance to " O   HOH Z 139 " =    3.213
peak=   -3.201 closest distance to " CG1 VAL A 112 " =    2.511
peak=   -3.197 closest distance to " OD1 ASN A 173 " =    1.414
peak=   -3.188 closest distance to " O   HOH Z 135 " =    1.584
peak=   -3.187 closest distance to " O   HOH Z 422 " =    0.921
peak=   -3.183 closest distance to " CD2 PHE A 192 " =    2.092
peak=   -3.181 closest distance to " O   HOH Z 384 " =    1.823
peak=   -3.175 closest distance to " CB  ASP A 132 " =    2.321
peak=   -3.175 closest distance to " C   SER A 206 " =    1.519
peak=   -3.173 closest distance to " O   HOH Z 345 " =    3.049
peak=   -3.172 closest distance to " OG  SER A  87 " =    1.675
peak=   -3.172 closest distance to " O   HOH Z 368 " =    2.039
peak=   -3.171 closest distance to " CD  LYS A 289 " =    2.332
peak=   -3.170 closest distance to " CG1 VAL A 112 " =    2.501
peak=   -3.169 closest distance to " O   HOH Z 102 " =    1.585
peak=   -3.165 closest distance to " O   HOH Z 311 " =    3.117
peak=   -3.158 closest distance to " OD1 ASP A 191 " =    1.395
peak=   -3.154 closest distance to " O   MET A  47 " =    2.635
peak=   -3.152 closest distance to " O   HOH Z  11 " =    1.554
peak=   -3.151 closest distance to " N   SER A 134 " =    1.178
peak=   -3.151 closest distance to " OG  SER A  97 " =    2.188
peak=   -3.142 closest distance to " O   GLY A  75 " =    1.719
peak=   -3.141 closest distance to " O   ALA A   1 " =    2.227
peak=   -3.139 closest distance to " O   HOH Z 427 " =    0.942
peak=   -3.137 closest distance to " O   GLY A 241 " =    2.124
peak=   -3.136 closest distance to " N   MET A 188 " =    2.150
peak=   -3.132 closest distance to " O   HOH Z 424 " =    1.406
peak=   -3.132 closest distance to " O   HOH Z 111 " =    3.784
peak=   -3.130 closest distance to " C   ALA A 158 " =    1.016
peak=   -3.125 closest distance to " CD  PRO A 213 " =    2.271
peak=   -3.121 closest distance to " O   HOH Z   2 " =    2.506
peak=   -3.114 closest distance to " CG1BVAL A  72 " =    1.990
peak=   -3.113 closest distance to " O   HOH Z 186 " =    0.941
peak=   -3.106 closest distance to " CH2 TRP A 150 " =    0.997
peak=   -3.106 closest distance to " SD  MET A  40 " =    2.010
peak=   -3.100 closest distance to " CD2 PHE A 225 " =    1.425
peak=   -3.098 closest distance to " O   HOH Z 299 " =    1.989
peak=   -3.093 closest distance to " O   GLY A  80 " =    2.409
peak=   -3.077 closest distance to " O   SER A 273 " =    1.047
peak=   -3.077 closest distance to " CG  GLU A   2 " =    1.737
peak=   -3.076 closest distance to " O   HOH Z 135 " =    2.107
peak=   -3.074 closest distance to " OD1 ASN A 176 " =    1.367
peak=   -3.073 closest distance to " OH  TYR A 169 " =    0.923
peak=   -3.072 closest distance to " CA  ASP A  65 " =    1.450
peak=   -3.068 closest distance to " O   HOH Z  46 " =    0.718
peak=   -3.065 closest distance to " CG  GLN A 103 " =    2.235
peak=   -3.056 closest distance to " N   ALA A 226 " =    1.898
peak=   -3.056 closest distance to " O   HOH Z 250 " =    1.549
peak=   -3.054 closest distance to " O   GLU A 152 " =    1.253

================= 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    :  0.4721 0.4633   6.283195e+00   6.269155e+00
   1_bss:  0.4645 0.4521   6.275662e+00   6.259424e+00
   1_xyz:  0.3648 0.3910   6.129572e+00   6.171338e+00
   1_adp:  0.3361 0.3930   6.081209e+00   6.173811e+00
   1_occ:  0.3357 0.3929   6.080283e+00   6.173368e+00
   2_bss:  0.3345 0.3901   6.079726e+00   6.172818e+00
   2_xyz:  0.2799 0.3349   5.937664e+00   6.063337e+00
   2_adp:  0.2614 0.3494   5.922249e+00   6.089620e+00
   2_occ:  0.2613 0.3499   5.922165e+00   6.089915e+00
   3_bss:  0.2611 0.3487   5.923085e+00   6.089819e+00
   3_xyz:  0.2278 0.3097   5.789914e+00   5.990422e+00
   3_adp:  0.2228 0.2752   5.739609e+00   5.896705e+00
   3_occ:  0.2224 0.2748   5.738796e+00   5.896242e+00
   4_bss:  0.2219 0.2737   5.739063e+00   5.894668e+00
   4_xyz:  0.1649 0.2079   5.464047e+00   5.649738e+00
   4_adp:  0.1466 0.1949   5.370921e+00   5.581204e+00
   4_occ:  0.1465 0.1947   5.370244e+00   5.580730e+00
   5_bss:  0.1464 0.1946   5.370606e+00   5.580264e+00
   5_xyz:  0.1341 0.1848   5.304368e+00   5.525507e+00
   5_adp:  0.1311 0.1816   5.283271e+00   5.505868e+00
   5_occ:  0.1311 0.1815   5.283117e+00   5.505779e+00
   5_bss:  0.1310 0.1815   5.283272e+00   5.506025e+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:  0.304  22.120  -1.348   4.239  -1.275   0.000  -0.000  -0.000
   1_xyz:  0.304  22.120  -1.348   4.239  -1.275   0.000  -0.000  -0.000
   1_adp:  0.304  22.120  -1.348   4.239  -1.275   0.000  -0.000  -0.000
   1_occ:  0.304  22.120  -1.348   4.239  -1.275   0.000  -0.000  -0.000
   2_bss:  0.301  37.145  -1.496   2.918  -0.216   0.000  -0.000  -0.000
   2_xyz:  0.301  37.145  -1.496   2.918  -0.216   0.000  -0.000  -0.000
   2_adp:  0.301  37.145  -1.496   2.918  -0.216   0.000  -0.000  -0.000
   2_occ:  0.301  37.145  -1.496   2.918  -0.216   0.000  -0.000  -0.000
   3_bss:  0.312  50.131  -0.384   3.036   0.995   0.000   0.000   0.000
   3_xyz:  0.312  50.131  -0.384   3.036   0.995   0.000   0.000   0.000
   3_adp:  0.312  50.131  -0.384   3.036   0.995   0.000   0.000   0.000
   3_occ:  0.312  50.131  -0.384   3.036   0.995   0.000   0.000   0.000
   4_bss:  0.317  50.131  -1.427   1.212   0.024   0.000   0.000   0.000
   4_xyz:  0.317  50.131  -1.427   1.212   0.024   0.000   0.000   0.000
   4_adp:  0.317  50.131  -1.427   1.212   0.024   0.000   0.000   0.000
   4_occ:  0.317  50.131  -1.427   1.212   0.024   0.000   0.000   0.000
   5_bss:  0.324  53.990  -2.069   0.075  -0.464   0.000  -0.000  -0.000
   5_xyz:  0.324  53.990  -2.069   0.075  -0.464   0.000  -0.000  -0.000
   5_adp:  0.324  53.990  -2.069   0.075  -0.464   0.000  -0.000  -0.000
   5_occ:  0.324  53.990  -2.069   0.075  -0.464   0.000  -0.000  -0.000
   5_bss:  0.324  53.970  -1.996  -0.058  -0.354  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.678 0.4503  0.6117    68726.933
   1_bss:  54.496 0.4642  0.6443    65403.076
   1_xyz:  45.568 0.5744  0.7709    46236.278
   1_adp:  44.956 0.5819  0.7770    45659.815
   1_occ:  44.918 0.5823  0.7757    45446.531
   2_bss:  44.600 0.5862  0.7799    44962.031
   2_xyz:  36.953 0.6777  0.8846    32039.631
   2_adp:  38.672 0.6573  0.8400    34926.860
   2_occ:  38.669 0.6573  0.8399    34947.588
   3_bss:  38.657 0.6575  0.8644    34907.110
   3_xyz:  33.040 0.7225  0.9390    25996.459
   3_adp:  28.051 0.7796  0.9844    20329.791
   3_occ:  28.012 0.7801  0.9851    20305.221
   4_bss:  27.902 0.7811  0.9431    20163.353
   4_xyz:  20.205 0.8594  0.9960    11081.314
   4_adp:  18.418 0.8766  0.9969     9622.274
   4_occ:  18.404 0.8767  0.9971     9613.457
   5_bss:  18.379 0.8770  0.9709     9588.823
   5_xyz:  17.103 0.8887  0.9763     8573.015
   5_adp:  16.609 0.8933  0.9726     8293.996
   5_occ:  16.609 0.8933  0.9726     8292.413
   5_bss:  16.615 0.8933  0.9727     8295.543
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   2.0150e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   2.0150e-01
   1_xyz:   1.671  0.012  0.098 16.269  0.007  4.102   1.4401e-01
   1_adp:   1.671  0.012  0.098 16.269  0.007  4.102   1.4401e-01
   1_occ:   1.671  0.012  0.098 16.269  0.007  4.102   1.4401e-01
   2_bss:   1.671  0.012  0.098 16.269  0.007  4.102   1.4401e-01
   2_xyz:   1.261  0.010  0.082 15.085  0.006  4.106   8.7635e-02
   2_adp:   1.261  0.010  0.082 15.085  0.006  4.106   8.7635e-02
   2_occ:   1.261  0.010  0.082 15.085  0.006  4.106   8.7635e-02
   3_bss:   1.261  0.010  0.082 15.085  0.006  4.106   8.7635e-02
   3_xyz:   1.097  0.007  0.074 14.754  0.004  4.111   6.7660e-02
   3_adp:   1.097  0.007  0.074 14.754  0.004  4.111   6.7660e-02
   3_occ:   1.097  0.007  0.074 14.754  0.004  4.111   6.7660e-02
   4_bss:   1.097  0.007  0.074 14.754  0.004  4.111   6.7660e-02
   4_xyz:   1.151  0.008  0.074 15.005  0.005  4.111   7.4869e-02
   4_adp:   1.151  0.008  0.074 15.005  0.005  4.111   7.4869e-02
   4_occ:   1.151  0.008  0.074 15.005  0.005  4.111   7.4869e-02
   5_bss:   1.151  0.008  0.074 15.005  0.005  4.111   7.4869e-02
   5_xyz:   0.943  0.006  0.065 14.547  0.004  4.116   5.3107e-02
   5_adp:   0.943  0.006  0.065 14.547  0.004  4.116   5.3107e-02
   5_occ:   0.943  0.006  0.065 14.547  0.004  4.116   5.3107e-02
   5_bss:   0.943  0.006  0.065 14.547  0.004  4.116   5.3107e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.144   2.4229e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.144   2.4229e-01
   1_xyz:   9.036  0.077  0.475 89.347  0.061  1.891   1.0557e-01
   1_adp:   9.036  0.077  0.475 89.347  0.061  1.891   1.0557e-01
   1_occ:   9.036  0.077  0.475 89.347  0.061  1.891   1.0557e-01
   2_bss:   9.036  0.077  0.475 89.347  0.061  1.891   1.0557e-01
   2_xyz:   8.306  0.083  0.306 83.285  0.046  2.257   1.3224e-01
   2_adp:   8.306  0.083  0.306 83.285  0.046  2.257   1.3224e-01
   2_occ:   8.306  0.083  0.306 83.285  0.046  2.257   1.3224e-01
   3_bss:   8.306  0.083  0.306 83.285  0.046  2.257   1.3224e-01
   3_xyz:   6.573  0.049  0.354 86.335  0.038  2.272   4.5790e-02
   3_adp:   6.573  0.049  0.354 86.335  0.038  2.272   4.5790e-02
   3_occ:   6.573  0.049  0.354 86.335  0.038  2.272   4.5790e-02
   4_bss:   6.573  0.049  0.354 86.335  0.038  2.272   4.5790e-02
   4_xyz:   7.994  0.050  0.248 79.904  0.038  2.225   6.5828e-02
   4_adp:   7.994  0.050  0.248 79.904  0.038  2.225   6.5828e-02
   4_occ:   7.994  0.050  0.248 79.904  0.038  2.225   6.5828e-02
   5_bss:   7.994  0.050  0.248 79.904  0.038  2.225   6.5828e-02
   5_xyz:   6.696  0.039  0.208 80.085  0.030  2.307   3.1971e-02
   5_adp:   6.696  0.039  0.208 80.085  0.030  2.307   3.1971e-02
   5_occ:   6.696  0.039  0.208 80.085  0.030  2.307   3.1971e-02
   5_bss:   6.696  0.039  0.208 80.085  0.030  2.307   3.1971e-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:  69.96   0.00  17.85  61.31   0.00  14.45  69.96   0.14  36.36
   1_occ:  69.96   0.00  17.85  61.31   0.00  14.45  69.96   0.14  36.36
   2_bss:  69.96   0.00  17.85  61.31   0.00  14.45  69.96   0.14  36.36
   2_xyz:  69.96   0.00  17.85  61.31   0.00  14.45  69.96   0.14  36.36
   2_adp: 155.12   0.00  22.59 155.12   0.00  18.14 152.21   0.00  46.86
   2_occ: 155.12   0.00  22.59 155.12   0.00  18.14 152.21   0.00  46.86
   3_bss: 155.12   0.00  22.59 155.12   0.00  18.14 152.21   0.00  46.86
   3_xyz: 155.12   0.00  22.59 155.12   0.00  18.14 152.21   0.00  46.86
   3_adp: 123.12   0.00  17.58 120.86   0.00  13.88 123.12   3.39  37.72
   3_occ: 123.12   0.00  17.58 120.86   0.00  13.88 123.12   3.39  37.72
   4_bss: 123.12   0.00  17.58 120.86   0.00  13.88 123.12   3.39  37.72
   4_xyz: 123.12   0.00  17.58 120.86   0.00  13.88 123.12   3.39  37.72
   4_adp: 117.96   0.36  17.51 115.39   0.36  12.83 117.96   5.32  42.99
   4_occ: 117.96   0.36  17.51 115.39   0.36  12.83 117.96   5.32  42.99
   5_bss: 117.96   0.36  17.51 115.39   0.36  12.83 117.96   5.32  42.99
   5_xyz: 117.96   0.36  17.51 115.39   0.36  12.83 117.96   5.32  42.99
   5_adp: 114.04   0.62  17.19 109.40   0.62  12.44 114.04   4.99  43.05
   5_occ: 114.04   0.62  17.19 109.40   0.62  12.44 114.04   4.99  43.05
   5_bss: 114.02   0.60  17.16 109.38   0.60  12.42 114.02   4.97  43.03
------------------------------------------------------------------------
 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:    2.523    0.025    0.396
   1_adp:    2.523    0.025    0.396
   1_occ:    2.523    0.025    0.396
   2_bss:    2.523    0.025    0.396
   2_xyz:    2.264    0.034    0.529
   2_adp:    2.264    0.034    0.529
   2_occ:    2.264    0.034    0.529
   3_bss:    2.264    0.034    0.529
   3_xyz:    2.298    0.028    0.669
   3_adp:    2.298    0.028    0.669
   3_occ:    2.298    0.028    0.669
   4_bss:    2.298    0.028    0.669
   4_xyz:    2.179    0.064    0.802
   4_adp:    2.179    0.064    0.802
   4_occ:    2.179    0.064    0.802
   5_bss:    2.179    0.064    0.802
   5_xyz:    2.106    0.063    0.832
   5_adp:    2.106    0.063    0.832
   5_occ:    2.106    0.063    0.832
   5_bss:    2.106    0.063    0.832
------------------------------------------------------------------------

CPU time actual refinement: 348.82


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_234/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_234/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_234/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_234/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_234/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 348.67 
  Macro-tasks:
    bulk solvent and scale       = 44.60  
    individual site refinement   = 141.65 
    weights calculation          = 29.89  
    collect and process          = 6.60   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 222.86 
  Micro-tasks:
    mask                            = 2.40   
    f_calc                          = 111.35 
    alpha_beta                      = 8.47   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 119.14 
    fmodel                         = 7.53   
    r_factors                      = 0.27   
    phase_errors                   = 10.44  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 261.01 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.996 micro seconds
Total CPU time: 6.04 minutes
from_scatterers_fft:    636 calls, 110.96 s
gradients_fft:          581 calls, 106.48 s

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

# Date 2008-01-16 Time 04:20:24 PST -0800 (1200486024.00 s)
Start R-work = 0.4721, R-free = 0.4633 (no bulk solvent and anisotropic scale)
Final R-work = 0.1497, R-free = 0.1978 (no bulk solvent and anisotropic scale)

Start R-work = 0.4645, R-free = 0.4521
Final R-work = 0.1310, R-free = 0.1815