# Date 2008-01-16 Time 05:07:33 PST -0800 (1200488853.76 s)
#phil __OFF__

Command line arguments: "../603.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25640
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 603

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 48.1033, 88.1178, 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: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 48.1033, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0676 1.9908
Completeness in resolution range: 0.93508
Completeness with d_max=infinity: 0.932232

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0676
                             d_min =   1.9908

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 48.1033, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0676 1.9908
Completeness in resolution range: 0.93508
Completeness with d_max=infinity: 0.932232

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0680 -  4.2598 [2199/2227]  1976   223  10.1%
  bin  2:  4.2598 -  3.3938 [2111/2134]  1900   211  10.0%
  bin  3:  3.3938 -  2.9685 [2072/2097]  1867   205   9.9%
  bin  4:  2.9685 -  2.6988 [2080/2096]  1870   210  10.1%
  bin  5:  2.6988 -  2.5063 [2021/2058]  1818   203  10.0%
  bin  6:  2.5063 -  2.3591 [2060/2094]  1857   203   9.9%
  bin  7:  2.3591 -  2.2414 [2028/2065]  1826   202  10.0%
  bin  8:  2.2414 -  2.1441 [2014/2056]  1808   206  10.2%
  bin  9:  2.1441 -  2.0618 [2031/2070]  1839   192   9.5%
  bin 10:  2.0618 -  1.9908 [ 973/2052]   869   104  10.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_603/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.62 -     2.28: 16
        2.28 -     2.93: 1519
        2.93 -     3.59: 4395
        3.59 -     4.24: 9033
        4.24 -     4.90: 12822
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.620 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.949 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.949 3.040 -x+1,y+1/2,-z+1/2
  " NH2 ARG A  24 " - " OG  SER A  95 "  1.968 3.120 -x+1,y+1/2,-z+1/2
  ... (remaining 27780 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_603/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_603/model_refine_001.geo

CPU time processing inputs: 9.10


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 48.10325 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4725   r_free= 0.4646   ksol= 0.00   Bsol= 0.00   scale= 0.869    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.286173                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0680 -  4.7511 0.99   1431  159 0.3799 0.3800      6.5783      6.5685|
|  2:  4.7511 -  3.7909 0.99   1377  152 0.4219 0.4544      6.8569      6.9009|
|  3:  3.7909 -  3.3175 0.99   1342  151 0.4599 0.4232      6.6973      6.6238|
|  4:  3.3175 -  3.0168 0.99   1339  142 0.4645 0.4428      6.5238      6.4926|
|  5:  3.0168 -  2.8021 0.98   1328  151 0.5058 0.4435      6.3658      6.3805|
|  6:  2.8021 -  2.6378 0.99   1319  147 0.5066 0.5019      6.2816      6.1656|
|  7:  2.6378 -  2.5063 0.99   1295  150 0.4891 0.4528      6.2259      6.1344|
|  8:  2.5063 -  2.3977 0.99   1333  140 0.5066 0.5156      6.1737      6.1623|
|  9:  2.3977 -  2.3057 0.99   1313  149 0.5030 0.4914      6.1037      6.1919|
| 10:  2.3057 -  2.2264 0.98   1300  142 0.5175 0.4829      6.0895      6.0594|
| 11:  2.2264 -  2.1570 0.98   1299  147 0.5244 0.5198      6.0345      6.0241|
| 12:  2.1570 -  2.0955 1.00   1303  152 0.5068 0.5462      5.9411       5.985|
| 13:  2.0955 -  2.0405 0.95   1264  126 0.5266 0.5657      5.8769      5.8568|
| 14:  2.0405 -  1.9908 0.30    387   51 0.4700 0.4282      5.8816      5.6924|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0680 -  4.7511  1431   159  0.69  35.11   0.81     0.71      73981.78|
|  2:  4.7511 -  3.7909  1377   152  0.69  36.09   0.88     0.77     109503.78|
|  3:  3.7909 -  3.3175  1342   151  0.59  44.30   0.86     0.76     114153.01|
|  4:  3.3175 -  3.0168  1339   142  0.51  50.98   0.88     0.68      98688.04|
|  5:  3.0168 -  2.8021  1328   151  0.45  56.19   0.86     0.61      75665.08|
|  6:  2.8021 -  2.6378  1319   147  0.42  58.60   0.87     0.57      65468.52|
|  7:  2.6378 -  2.5063  1295   150  0.42  58.57   0.90     0.55      59589.29|
|  8:  2.5063 -  2.3977  1333   140  0.40  59.93   0.89     0.55      54997.51|
|  9:  2.3977 -  2.3057  1313   149  0.39  60.34   0.89     0.57      51511.63|
| 10:  2.3057 -  2.2264  1300   142  0.40  59.99   0.90     0.58      45605.46|
| 11:  2.2264 -  2.1570  1299   147  0.35  63.89   0.91     0.53      46249.73|
| 12:  2.1570 -  2.0955  1303   152  0.29  68.12   0.90     0.45      45276.34|
| 13:  2.0955 -  2.0405  1264   126  0.24  72.34   0.88     0.37      41200.74|
| 14:  2.0405 -  1.9908   387    51  0.30  67.78   1.00     0.36      29617.06|
|alpha:            min =        0.36 max =            0.77 mean =         0.59|
|beta:             min =    29617.06 max =       114153.01 mean =     67432.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           90.00 mean =        55.70|
|phase err.(test): min =        0.00 max =           89.97 mean =        56.07|
|-----------------------------------------------------------------------------|

============================== 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 = 9.769265              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.563   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.389433              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.201   (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 |  1.620 -  1.948:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.948 -  2.276:       14 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.276 -  2.604:       37 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.604 -  2.932:     1482 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.932 -  3.260:     1884 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.260 -  3.588:     2511 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.588 -  3.916:     4673 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.916 -  4.244:     4360 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.244 -  4.572:     5814 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.572 -  4.900:     7008 |
|-----------------------------------------------------------------------------|
|-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 |        0.170 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.620 |       0.250 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.273)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4725   r_free= 0.4646   ksol= 0.00   Bsol= 0.00   scale= 0.869    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.286173                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4628   r_free= 0.4533   ksol= 0.29   Bsol= 36.47   scale= 0.913   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.80,4.20,2.52,0.00,0.00,0.00); trace/3= 0.98                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.280038                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.291205              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.978   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.222404              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.793   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4628      final r-factor (work) = 0.3807          |
| start r-factor (free) = 0.4533      final r-factor (free) = 0.4083          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.1902 = 8.29 * 0.50 * 6.2766 + 1.00 * 0.1698                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.7340 = 8.29 * 0.50 * 6.1771 + 1.00 * 0.1262                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3807      final r-factor (work) = 0.3503          |
| start r-factor (free) = 0.4083      final r-factor (free) = 0.4193          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5568 = 1.22 * 1.00 * 6.1771 + 1.00 * 0.0058                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4867 = 1.22 * 1.00 * 6.1080 + 1.00 * 0.0203                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.273)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.26  19.21    None  None   None       |
|    all(noH): 2823   0      0.00    110.26  19.21    None  None   None       |
|    Sol.    : 438    0      0.00    110.26  37.18    None  None   None       |
|    Mac.    : 2385   0      0.00    87.09   15.91    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 -  11.026:  974   |   5:    55.130 -  66.155:   54        |
|      1:    11.026 -  22.052:  936   |   6:    66.155 -  77.181:   29        |
|      2:    22.052 -  33.078:  480   |   7:    77.181 -  88.207:   14        |
|      3:    33.078 -  44.104:  224   |   8:    88.207 -  99.233:    2        |
|      4:    44.104 -  55.130:  109   |   9:    99.233 - 110.259:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3503 r_free = 0.4193             target_work(ml) = 6.111         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3500 r_free = 0.4185             target_work(ml) = 6.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3500   r_free= 0.4185   ksol= 0.29   Bsol= 36.47   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.80,4.20,2.52,0.00,0.00,0.00); trace/3= 0.98                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.110228                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3492   r_free= 0.4174   ksol= 0.30   Bsol= 50.24   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.76,2.51,1.42,0.00,0.00,0.00); trace/3= 0.72                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.112644                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.447818              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.380   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.565144              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.268  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3492      final r-factor (work) = 0.2975          |
| start r-factor (free) = 0.4174      final r-factor (free) = 0.3630          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.8244 = 6.45 * 0.50 * 6.1101 + 1.00 * 0.1262                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.6021 = 6.45 * 0.50 * 6.0545 + 1.00 * 0.0830                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2975      final r-factor (work) = 0.2886          |
| start r-factor (free) = 0.3630      final r-factor (free) = 0.3569          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4419 = 0.57 * 1.00 * 6.0545 + 1.00 * 0.0202                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4159 = 0.57 * 1.00 * 5.9831 + 1.00 * 0.0346                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.273)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.01  18.29    None  None   None       |
|    all(noH): 2823   0      0.00    112.01  18.29    None  None   None       |
|    Sol.    : 438    0      0.00    112.01  36.10    None  None   None       |
|    Mac.    : 2385   0      0.00    84.98   15.02    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 -  11.201: 1082   |   5:    56.004 -  67.205:   50        |
|      1:    11.201 -  22.402:  941   |   6:    67.205 -  78.405:   22        |
|      2:    22.402 -  33.602:  446   |   7:    78.405 -  89.606:    8        |
|      3:    33.602 -  44.803:  173   |   8:    89.606 - 100.807:    2        |
|      4:    44.803 -  56.004:   98   |   9:   100.807 - 112.008:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2886 r_free = 0.3569             target_work(ml) = 5.978         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2884 r_free = 0.3571             target_work(ml) = 5.978         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2884   r_free= 0.3571   ksol= 0.30   Bsol= 50.24   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.76,2.51,1.42,0.00,0.00,0.00); trace/3= 0.72                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 5.977945                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2886   r_free= 0.3565   ksol= 0.32   Bsol= 67.82   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.64,1.96,0.84,0.00,0.00,0.00); trace/3= 0.38                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 5.978836                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.480047              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.426   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.958807              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.822   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2886      final r-factor (work) = 0.2251          |
| start r-factor (free) = 0.3565      final r-factor (free) = 0.2766          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.4530 = 8.48 * 0.50 * 5.9835 + 1.00 * 0.0830                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.0334 = 8.48 * 0.50 * 5.8806 + 1.00 * 0.0995                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2251      final r-factor (work) = 0.1993          |
| start r-factor (free) = 0.2766      final r-factor (free) = 0.2603          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 29.1746 = 4.96 * 1.00 * 5.8806 + 1.00 * 0.0139                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 28.1923 = 4.96 * 1.00 * 5.6809 + 1.00 * 0.0216                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.273)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    126.44  19.85    None  None   None       |
|    all(noH): 2823   0      0.00    126.44  19.85    None  None   None       |
|    Sol.    : 438    0      2.65    126.44  49.24    None  None   None       |
|    Mac.    : 2385   0      0.00    119.01  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 -  12.644: 1420   |   5:    63.219 -  75.863:   84        |
|      1:    12.644 -  25.288:  781   |   6:    75.863 -  88.507:   48        |
|      2:    25.288 -  37.932:  222   |   7:    88.507 - 101.151:   26        |
|      3:    37.932 -  50.575:  130   |   8:   101.151 - 113.794:   10        |
|      4:    50.575 -  63.219:   96   |   9:   113.794 - 126.438:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1993 r_free = 0.2603             target_work(ml) = 5.652         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1992 r_free = 0.2604             target_work(ml) = 5.652         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1992   r_free= 0.2604   ksol= 0.32   Bsol= 67.82   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.64,1.96,0.84,0.00,0.00,0.00); trace/3= 0.38                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.651810                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1986   r_free= 0.2594   ksol= 0.34   Bsol= 92.00   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.79,0.37,0.27,0.00,0.00,0.00); trace/3= -0.38                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.650514                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.389200              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.922   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.158285              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.896  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1986      final r-factor (work) = 0.1676          |
| start r-factor (free) = 0.2594      final r-factor (free) = 0.2199          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7303 = 3.39 * 0.50 * 5.6832 + 1.00 * 0.0995                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5246 = 3.39 * 0.50 * 5.5823 + 1.00 * 0.0649                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1676      final r-factor (work) = 0.1636          |
| start r-factor (free) = 0.2199      final r-factor (free) = 0.2020          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9053 = 0.16 * 1.00 * 5.5823 + 1.00 * 0.0217                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9041 = 0.16 * 1.00 * 5.4941 + 1.00 * 0.0345                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.273)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.63  17.70    None  None   None       |
|    all(noH): 2823   0      0.00    113.63  17.70    None  None   None       |
|    Sol.    : 438    0      4.26    113.63  43.01    None  None   None       |
|    Mac.    : 2385   0      0.00    104.12  13.05    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 -  11.363: 1376   |   5:    56.814 -  68.176:   69        |
|      1:    11.363 -  22.725:  873   |   6:    68.176 -  79.539:   40        |
|      2:    22.725 -  34.088:  196   |   7:    79.539 -  90.902:   16        |
|      3:    34.088 -  45.451:  144   |   8:    90.902 - 102.264:    6        |
|      4:    45.451 -  56.814:   98   |   9:   102.264 - 113.627:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1636 r_free = 0.2020             target_work(ml) = 5.457         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1633 r_free = 0.2017             target_work(ml) = 5.455         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1633   r_free= 0.2017   ksol= 0.34   Bsol= 92.00   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.79,0.37,0.27,0.00,0.00,0.00); trace/3= -0.38                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.455488                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1632   r_free= 0.2011   ksol= 0.34   Bsol= 78.03   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,-0.43,-0.06,-0.00,-0.00,-0.00); trace/3= -0.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.455800                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.254985              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.219  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.242402              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.493   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1632      final r-factor (work) = 0.1367          |
| start r-factor (free) = 0.2011      final r-factor (free) = 0.1789          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0058 = 3.25 * 0.50 * 5.4937 + 1.00 * 0.0649                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8227 = 3.25 * 0.50 * 5.3743 + 1.00 * 0.0761                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1367      final r-factor (work) = 0.1301          |
| start r-factor (free) = 0.1789      final r-factor (free) = 0.1801          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7484 = 1.24 * 1.00 * 5.3743 + 1.00 * 0.0714                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5815 = 1.24 * 1.00 * 5.2867 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.273)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.46  17.78    None  None   None       |
|    all(noH): 2823   0      0.00    115.46  17.78    None  None   None       |
|    Sol.    : 438    0      2.51    115.46  45.28    None  None   None       |
|    Mac.    : 2385   0      0.00    102.78  12.73    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.546: 1440   |   5:    57.728 -  69.273:   79        |
|      1:    11.546 -  23.091:  833   |   6:    69.273 -  80.819:   44        |
|      2:    23.091 -  34.637:  172   |   7:    80.819 -  92.364:   19        |
|      3:    34.637 -  46.182:  111   |   8:    92.364 - 103.910:    7        |
|      4:    46.182 -  57.728:  114   |   9:   103.910 - 115.455:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1301 r_free = 0.1801             target_work(ml) = 5.285         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1300 r_free = 0.1800             target_work(ml) = 5.284         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1300   r_free= 0.1800   ksol= 0.34   Bsol= 78.03   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,-0.43,-0.06,-0.00,-0.00,-0.00); trace/3= -0.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.284150                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0680 -  4.7511 0.99   1431  159 0.1010 0.1329      5.4233      5.6099|
|  2:  4.7511 -  3.7909 0.99   1377  152 0.0914 0.1101      5.4916      5.6665|
|  3:  3.7909 -  3.3175 0.99   1342  151 0.1214 0.1763      5.5933      5.9703|
|  4:  3.3175 -  3.0168 0.99   1339  142 0.1426 0.1806      5.5688      5.7245|
|  5:  3.0168 -  2.8021 0.98   1328  151 0.1602 0.1811      5.4794      5.6078|
|  6:  2.8021 -  2.6378 0.99   1319  147 0.1493 0.2375      5.3702      5.6161|
|  7:  2.6378 -  2.5063 0.99   1295  150 0.1480 0.1974      5.3232      5.5434|
|  8:  2.5063 -  2.3977 0.99   1333  140 0.1451 0.2053      5.2593      5.4651|
|  9:  2.3977 -  2.3057 0.99   1313  149 0.1460 0.2210      5.1965      5.4902|
| 10:  2.3057 -  2.2264 0.98   1300  142 0.1377 0.1884      5.1165      5.2732|
| 11:  2.2264 -  2.1570 0.98   1299  147 0.1352 0.2197      5.0654       5.427|
| 12:  2.1570 -  2.0955 1.00   1303  152 0.1301 0.1776      4.9739      5.1978|
| 13:  2.0955 -  2.0405 0.95   1264  126 0.1333 0.1915       4.899      5.1254|
| 14:  2.0405 -  1.9908 0.30    387   51 0.1232 0.2080      4.8637       5.097|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0680 -  4.7511  1431   159  0.94   9.77   0.96     0.93       7866.34|
|  2:  4.7511 -  3.7909  1377   152  0.95   8.94   1.01     0.99      10173.23|
|  3:  3.7909 -  3.3175  1342   151  0.92  13.13   1.02     1.02      12760.88|
|  4:  3.3175 -  3.0168  1339   142  0.90  16.04   1.01     0.99      12847.96|
|  5:  3.0168 -  2.8021  1328   151  0.88  18.86   1.00     0.98      11243.92|
|  6:  2.8021 -  2.6378  1319   147  0.87  19.36   0.98     0.95       9647.02|
|  7:  2.6378 -  2.5063  1295   150  0.88  18.97   1.00     0.97       8844.66|
|  8:  2.5063 -  2.3977  1333   140  0.87  19.31   0.99     0.94       7915.73|
|  9:  2.3977 -  2.3057  1313   149  0.87  19.20   0.99     0.93       6744.77|
| 10:  2.3057 -  2.2264  1300   142  0.87  19.74   0.98     0.94       6250.57|
| 11:  2.2264 -  2.1570  1299   147  0.88  19.05   0.99     0.93       5641.64|
| 12:  2.1570 -  2.0955  1303   152  0.89  17.86   0.99     0.98       4817.17|
| 13:  2.0955 -  2.0405  1264   126  0.88  18.97   0.97     0.95       4202.61|
| 14:  2.0405 -  1.9908   387    51  0.89  17.48   0.95     0.89       3664.37|
|alpha:            min =        0.89 max =            1.02 mean =         0.96|
|beta:             min =     3664.37 max =        12847.96 mean =      8313.82|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.87 mean =        16.78|
|phase err.(test): min =        0.00 max =           89.00 mean =        16.10|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1305   r_free= 0.1799   ksol= 0.33   Bsol= 77.92   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-0.66,0.02,-0.00,0.00,0.00); trace/3= -0.90                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.285134                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1305   r_free= 0.1799   ksol= 0.33   Bsol= 77.92   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-0.66,0.02,-0.00,0.00,0.00); trace/3= -0.90                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.285134                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0680 -  4.7511 0.99   1431  159 0.1028 0.1338      5.4326      5.6101|
|  2:  4.7511 -  3.7909 0.99   1377  152 0.0919 0.1078      5.4956      5.6641|
|  3:  3.7909 -  3.3175 0.99   1342  151 0.1215 0.1762      5.5932      5.9725|
|  4:  3.3175 -  3.0168 0.99   1339  142 0.1432 0.1809      5.5709       5.726|
|  5:  3.0168 -  2.8021 0.98   1328  151 0.1604 0.1808      5.4795       5.607|
|  6:  2.8021 -  2.6378 0.99   1319  147 0.1490 0.2365      5.3686      5.6124|
|  7:  2.6378 -  2.5063 0.99   1295  150 0.1480 0.1979      5.3226      5.5442|
|  8:  2.5063 -  2.3977 0.99   1333  140 0.1449 0.2057      5.2595      5.4669|
|  9:  2.3977 -  2.3057 0.99   1313  149 0.1458 0.2212      5.1965      5.4906|
| 10:  2.3057 -  2.2264 0.98   1300  142 0.1376 0.1889      5.1163      5.2731|
| 11:  2.2264 -  2.1570 0.98   1299  147 0.1351 0.2195      5.0644      5.4264|
| 12:  2.1570 -  2.0955 1.00   1303  152 0.1301 0.1777      4.9736      5.1986|
| 13:  2.0955 -  2.0405 0.95   1264  126 0.1336 0.1908      4.8988      5.1226|
| 14:  2.0405 -  1.9908 0.30    387   51 0.1231 0.2077      4.8647      5.0976|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0680 -  4.7511  1431   159  0.93   9.80   0.96     0.93       7837.58|
|  2:  4.7511 -  3.7909  1377   152  0.95   8.90   1.01     0.99      10123.24|
|  3:  3.7909 -  3.3175  1342   151  0.92  13.08   1.02     1.02      12700.77|
|  4:  3.3175 -  3.0168  1339   142  0.90  16.08   1.01     0.99      12907.65|
|  5:  3.0168 -  2.8021  1328   151  0.88  18.84   1.00     0.98      11224.48|
|  6:  2.8021 -  2.6378  1319   147  0.87  19.32   0.98     0.95       9622.56|
|  7:  2.6378 -  2.5063  1295   150  0.88  18.97   1.00     0.97       8834.44|
|  8:  2.5063 -  2.3977  1333   140  0.87  19.32   0.99     0.94       7930.51|
|  9:  2.3977 -  2.3057  1313   149  0.87  19.21   0.99     0.93       6755.18|
| 10:  2.3057 -  2.2264  1300   142  0.87  19.74   0.98     0.94       6252.22|
| 11:  2.2264 -  2.1570  1299   147  0.88  19.03   0.99     0.93       5637.78|
| 12:  2.1570 -  2.0955  1303   152  0.89  17.84   0.99     0.98       4812.43|
| 13:  2.0955 -  2.0405  1264   126  0.88  18.94   0.97     0.95       4191.95|
| 14:  2.0405 -  1.9908   387    51  0.89  17.48   0.95     0.89       3653.89|
|alpha:            min =        0.89 max =            1.02 mean =         0.96|
|beta:             min =     3653.89 max =        12907.65 mean =      8303.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.99 mean =        16.78|
|phase err.(test): min =        0.00 max =           89.03 mean =        16.09|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.273)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.46  17.78    None  None   None       |
|    all(noH): 2823   0      0.00    115.46  17.78    None  None   None       |
|    Sol.    : 438    0      2.52    115.46  45.28    None  None   None       |
|    Mac.    : 2385   0      0.00    102.79  12.73    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  11.549: 1440   |   5:    57.731 -  69.276:   79        |
|      1:    11.549 -  23.094:  833   |   6:    69.276 -  80.822:   44        |
|      2:    23.094 -  34.640:  172   |   7:    80.822 -  92.367:   19        |
|      3:    34.640 -  46.185:  111   |   8:    92.367 - 103.913:    7        |
|      4:    46.185 -  57.731:  114   |   9:   103.913 - 115.458:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 320         
Filter by distance & map next to the model:
   mapped sites are within: 0.452 - 5.654
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 316 from: 320
   mapped sites are within: 0.743 - 5.654

peak=    6.609 closest distance to " O   HOH Z 203 " =    0.985
peak=    6.484 closest distance to " O   GLN A  11 " =    1.098
peak=    5.764 closest distance to " O   HOH Z 210 " =    1.475
peak=    5.471 closest distance to " O   HOH Z  54 " =    1.355
peak=    5.361 closest distance to " O   HOH Z  65 " =    1.208
peak=    5.358 closest distance to " O   HOH Z 117 " =    1.339
peak=    5.274 closest distance to " O   HOH Z 248 " =    1.596
peak=    5.232 closest distance to " O   HOH Z 403 " =    2.107
peak=    5.112 closest distance to " O   HOH Z  69 " =    1.487
peak=    4.793 closest distance to " O   HOH Z  49 " =    1.531
peak=    4.735 closest distance to " O   HOH Z 113 " =    1.911
peak=    4.706 closest distance to " CD2 TRP A 179 " =    1.314
peak=    4.671 closest distance to " CG  PRO A  54 " =    1.300
peak=    4.618 closest distance to " O   HOH Z 130 " =    2.699
peak=    4.599 closest distance to " O   HOH Z 431 " =    1.292
peak=    4.548 closest distance to " O   HOH Z  67 " =    1.140
peak=    4.543 closest distance to " CB  SER A  63 " =    1.191
peak=    4.537 closest distance to " CA  TYR A  30 " =    0.949
peak=    4.526 closest distance to " O   HOH Z 412 " =    3.240
peak=    4.522 closest distance to " O   HOH Z 426 " =    1.123
peak=    4.513 closest distance to " NH2 ARG A 156 " =    1.186
peak=    4.498 closest distance to " NE2 GLN A  11 " =    1.167
peak=    4.484 closest distance to " CB  GLN A 183 " =    1.246
peak=    4.470 closest distance to " OD1 ASN A 301 " =    1.061
peak=    4.425 closest distance to " CB  GLN A 223 " =    1.474
peak=    4.381 closest distance to " O   HOH Z  43 " =    2.161
peak=    4.327 closest distance to " O   HOH Z 261 " =    2.537
peak=    4.242 closest distance to " O   HOH Z 406 " =    1.721
peak=    4.236 closest distance to " CA  ARG A  36 " =    1.065
peak=    4.232 closest distance to " O   HOH Z 147 " =    1.529
peak=    4.228 closest distance to " CB  ARG A 190 " =    1.857
peak=    4.205 closest distance to " CB  SER A  62 " =    0.925
peak=    4.162 closest distance to " CD  LYS A 166 " =    1.564
peak=    4.156 closest distance to " O   HOH Z 124 " =    1.154
peak=    4.147 closest distance to " O   HOH Z  76 " =    1.204
peak=    4.131 closest distance to " CG  GLN A  58 " =    1.052
peak=    4.122 closest distance to " CB  TRP A 179 " =    1.307
peak=    4.082 closest distance to " O   PRO A 198 " =    1.550
peak=    4.075 closest distance to " CG  GLN A  77 " =    0.824
peak=    4.072 closest distance to " O   HOH Z 128 " =    1.404
peak=    4.072 closest distance to " CA  ARG A 195 " =    1.129
peak=    4.056 closest distance to " CG AARG A 275 " =    1.193
peak=    4.044 closest distance to " O   HOH Z 422 " =    0.909
peak=    4.041 closest distance to " CA  GLN A  11 " =    1.312
peak=    4.037 closest distance to " CZ  PHE A  38 " =    1.207
peak=    4.035 closest distance to " O   HOH Z 102 " =    1.397
peak=    4.035 closest distance to " CG  PRO A  90 " =    1.267
peak=    4.022 closest distance to " O   HOH Z 214 " =    1.673
peak=    4.015 closest distance to " CZ3 TRP A 266 " =    1.106
peak=    3.995 closest distance to " N   SER A 164 " =    0.981
peak=    3.966 closest distance to " CB  ARG A 275 " =    0.876
peak=    3.957 closest distance to " O   HOH Z 357 " =    2.256
peak=    3.949 closest distance to " O   HOH Z 139 " =    1.333
peak=    3.946 closest distance to " O   HOH Z 369 " =    1.829
peak=    3.945 closest distance to " CB  ASN A 285 " =    0.887
peak=    3.942 closest distance to " O   ALA A 165 " =    1.389
peak=    3.927 closest distance to " O   HOH Z 394 " =    1.755
peak=    3.924 closest distance to " O   HOH Z 403 " =    1.503
peak=    3.920 closest distance to " O   HOH Z 176 " =    1.663
peak=    3.905 closest distance to " O   HOH Z 196 " =    1.400
peak=    3.887 closest distance to " O   HOH Z 234 " =    3.712
peak=    3.885 closest distance to " O   HOH Z 134 " =    1.834
peak=    3.885 closest distance to " CE1 HIS A 115 " =    1.180
peak=    3.878 closest distance to " CD  ARG A  36 " =    0.994
peak=    3.876 closest distance to " CG2BVAL A  41 " =    0.915
peak=    3.871 closest distance to " CD  ARG A 195 " =    0.967
peak=    3.858 closest distance to " O   HOH Z  63 " =    1.805
peak=    3.857 closest distance to " O   HOH Z 132 " =    2.973
peak=    3.856 closest distance to " NH1AARG A 145 " =    1.276
peak=    3.855 closest distance to " O   HOH Z 433 " =    1.672
peak=    3.854 closest distance to " CB  ASN A  39 " =    0.789
peak=    3.849 closest distance to " CB  ALA A   1 " =    0.992
peak=    3.846 closest distance to " CA  THR A 246 " =    1.009
peak=    3.843 closest distance to " O   HOH Z  44 " =    2.080
peak=    3.840 closest distance to " CB  ASN A 148 " =    1.516
peak=    3.836 closest distance to " CG2 VAL A 197 " =    1.221
peak=    3.828 closest distance to " O   HOH Z 346 " =    1.571
peak=    3.827 closest distance to " OE1 GLN A  11 " =    2.366
peak=    3.822 closest distance to " O   HOH Z 358 " =    1.317
peak=    3.812 closest distance to " CA  ASN A 217 " =    1.272
peak=    3.804 closest distance to " O   HOH Z 154 " =    2.354
peak=    3.795 closest distance to " O   HOH Z 425 " =    1.529
peak=    3.794 closest distance to " CB  THR A  52 " =    0.864
peak=    3.793 closest distance to " O   HOH Z  80 " =    2.057
peak=    3.785 closest distance to " O   HOH Z 141 " =    1.752
peak=    3.772 closest distance to " O   HOH Z 417 " =    2.900
peak=    3.767 closest distance to " CB  GLU A 128 " =    1.113
peak=    3.765 closest distance to " O   HOH Z 298 " =    1.939
peak=    3.751 closest distance to " O   HOH Z 402 " =    1.696
peak=    3.751 closest distance to " CA  ALA A 100 " =    1.274
peak=    3.739 closest distance to " O   HOH Z 146 " =    1.687
peak=    3.738 closest distance to " CB  TYR A 169 " =    0.788
peak=    3.734 closest distance to " O   HOH Z 401 " =    1.162
peak=    3.728 closest distance to " CB  GLU A 152 " =    1.099
peak=    3.718 closest distance to " O  BHOH Z 338 " =    1.074
peak=    3.718 closest distance to " CG1AVAL A 121 " =    0.789
peak=    3.718 closest distance to " O   HOH Z 132 " =    2.695
peak=    3.716 closest distance to " NE2 GLN A  77 " =    3.128
peak=    3.711 closest distance to " O   ASP A 124 " =    1.503
peak=    3.710 closest distance to " O   HOH Z  35 " =    2.016
peak=    3.695 closest distance to " CG1 ILE A  33 " =    1.214
peak=    3.693 closest distance to " CG  PRO A 243 " =    1.135
peak=    3.686 closest distance to " O   HOH Z 189 " =    2.932
peak=    3.684 closest distance to " OE1 GLN A  88 " =    0.835
peak=    3.681 closest distance to " CB  ASN A 142 " =    1.129
peak=    3.681 closest distance to " CA  GLU A 152 " =    0.935
peak=    3.676 closest distance to " CZ  PHE A 218 " =    1.256
peak=    3.673 closest distance to " O   HOH Z 195 " =    1.295
peak=    3.671 closest distance to " O   HOH Z  88 " =    3.226
peak=    3.668 closest distance to " O   HOH Z  39 " =    1.298
peak=    3.666 closest distance to " O   HOH Z 146 " =    1.318
peak=    3.664 closest distance to " CG2 THR A 221 " =    1.129
peak=    3.663 closest distance to " CB  GLU A 277 " =    3.810
peak=    3.655 closest distance to " CB  VAL A 202 " =    1.449
peak=    3.651 closest distance to " CB  MET A 105 " =    1.242
peak=    3.638 closest distance to " O   HOH Z 394 " =    4.020
peak=    3.636 closest distance to " O   HOH Z  40 " =    1.967
peak=    3.636 closest distance to " O   HOH Z 250 " =    2.499
peak=    3.615 closest distance to " CA  TYR A 116 " =    1.399
peak=    3.608 closest distance to " O   HOH Z 301 " =    1.539
peak=    3.606 closest distance to " O   HOH Z 199 " =    1.480
peak=    3.600 closest distance to " O   HOH Z 428 " =    1.077
peak=    3.598 closest distance to " O   HOH Z 362 " =    3.287
peak=    3.594 closest distance to " CE1 TYR A 186 " =    1.279
peak=    3.589 closest distance to " O   ASN A  74 " =    1.885
peak=    3.585 closest distance to " O   HOH Z 418 " =    1.882
peak=    3.584 closest distance to " CA  ALA A 160 " =    0.928
peak=    3.579 closest distance to " O   HOH Z  48 " =    2.031
peak=    3.575 closest distance to " N   THR A  52 " =    1.121
peak=    3.571 closest distance to " CD  PRO A  54 " =    1.016
peak=    3.570 closest distance to " CA  ASN A 249 " =    1.330
peak=    3.560 closest distance to " O   HOH Z 298 " =    2.284
peak=    3.555 closest distance to " CA  GLY A 196 " =    0.999
peak=    3.554 closest distance to " O   HOH Z   7 " =    1.228
peak=    3.551 closest distance to " CB  ARG A  79 " =    1.049
peak=    3.550 closest distance to " CB  ASN A  45 " =    1.173
peak=    3.548 closest distance to " CB  MET A  40 " =    1.015
peak=    3.543 closest distance to " OE1 GLU A   2 " =    1.368
peak=    3.542 closest distance to " CE  LYS A  76 " =    0.898
peak=    3.530 closest distance to " O   HOH Z 126 " =    1.560
peak=    3.529 closest distance to " CB  GLU A  46 " =    1.042
peak=    3.528 closest distance to " CA  SER A  12 " =    1.477
peak=    3.520 closest distance to " ND2 ASN A 249 " =    2.145
peak=    3.508 closest distance to " O   HOH Z 299 " =    4.097
peak=    3.505 closest distance to " O   HOH Z 213 " =    2.224
peak=    3.502 closest distance to " O   HOH Z 316 " =    3.031
peak=    3.499 closest distance to " O   HOH Z 345 " =    1.660
peak=    3.499 closest distance to " O   HOH Z   9 " =    1.192
peak=    3.497 closest distance to " O   HOH Z  20 " =    1.843
peak=    3.490 closest distance to " O   SER A  87 " =    2.239
peak=    3.488 closest distance to " CB  PRO A  54 " =    0.936
peak=    3.488 closest distance to " O   HOH Z  48 " =    1.717
peak=    3.481 closest distance to " O   HOH Z  47 " =    2.582
peak=    3.481 closest distance to " O   HOH Z 116 " =    1.208
peak=    3.480 closest distance to " CB  SER A 141 " =    1.070
peak=    3.474 closest distance to " OE1 GLN A  58 " =    3.445
peak=    3.470 closest distance to " O   HOH Z 265 " =    1.973
peak=    3.468 closest distance to " O   HOH Z 336 " =    1.955
peak=    3.467 closest distance to " O   HOH Z 437 " =    1.776
peak=    3.465 closest distance to " O   HOH Z 246 " =    1.545
peak=    3.461 closest distance to " CA  ALA A  51 " =    1.018
peak=    3.460 closest distance to " O   THR A 251 " =    1.330
peak=    3.457 closest distance to " CG2 ILE A  20 " =    1.334
peak=    3.456 closest distance to " O   HOH Z  59 " =    2.008
peak=    3.454 closest distance to " O   HOH Z 200 " =    1.701
peak=    3.447 closest distance to " CG  ARG A 138 " =    1.486
peak=    3.444 closest distance to " CA  CYS A 260 " =    1.545
peak=    3.442 closest distance to " CG2AVAL A 121 " =    1.976
peak=    3.442 closest distance to " CA  VAL A 125 " =    1.293
peak=    3.440 closest distance to " CG1 ILE A 120 " =    1.138
peak=    3.431 closest distance to " CD1 LEU A  96 " =    0.770
peak=    3.426 closest distance to " O   HOH Z 284 " =    2.906
peak=    3.424 closest distance to " O   HOH Z   6 " =    1.210
peak=    3.419 closest distance to " CB  ALA A 114 " =    0.743
peak=    3.418 closest distance to " CG2 THR A  29 " =    1.336
peak=    3.412 closest distance to " OG BSER A 164 " =    2.122
peak=    3.411 closest distance to " O   SER A 141 " =    1.362
peak=    3.411 closest distance to " OH  TYR A 116 " =    1.253
peak=    3.408 closest distance to " CA  ASN A 176 " =    1.309
peak=    3.408 closest distance to " O   HOH Z 193 " =    1.803
peak=    3.408 closest distance to " O   HOH Z 144 " =    1.567
peak=    3.405 closest distance to " O  BHOH Z 338 " =    2.082
peak=    3.394 closest distance to " O   HOH Z 251 " =    1.520
peak=    3.393 closest distance to " CA  VAL A  41 " =    0.926
peak=    3.387 closest distance to " CA  ARG A 139 " =    1.412
peak=    3.378 closest distance to " N   HIS A 108 " =    1.782
peak=    3.378 closest distance to " CA  SER A  87 " =    1.086
peak=    3.374 closest distance to " O   GLY A  91 " =    1.143
peak=    3.364 closest distance to " CA  LEU A  83 " =    1.267
peak=    3.363 closest distance to " ND2 ASN A 249 " =    0.883
peak=    3.363 closest distance to " O   HOH Z 295 " =    1.016
peak=    3.361 closest distance to " CA  ALA A 248 " =    1.225
peak=    3.360 closest distance to " ND2 ASN A  69 " =    1.341
peak=    3.356 closest distance to " O   ASP A 200 " =    1.600
peak=    3.353 closest distance to " O   HOH Z 287 " =    2.369
peak=    3.351 closest distance to " O   HOH Z 128 " =    2.034
peak=    3.350 closest distance to " CA  ASP A 191 " =    1.269
peak=    3.346 closest distance to " CA  ALA A 158 " =    1.383
peak=    3.345 closest distance to " CG  ARG A 219 " =    1.281
peak=    3.339 closest distance to " CE1 HIS A  81 " =    1.543
peak=    3.336 closest distance to " O   HOH Z 404 " =    1.712
peak=    3.336 closest distance to " O   HOH Z 139 " =    4.810
peak=    3.334 closest distance to " CD  ARG A 159 " =    0.859
peak=    3.331 closest distance to " CB  VAL A 265 " =    1.246
peak=    3.330 closest distance to " CA  ALA A 295 " =    1.111
peak=    3.323 closest distance to " C   TYR A 214 " =    1.656
peak=    3.322 closest distance to " O   HOH Z 368 " =    2.205
peak=    3.321 closest distance to " CB  GLN A  88 " =    1.274
peak=    3.321 closest distance to " CG  PRO A 198 " =    1.142
peak=    3.321 closest distance to " O   THR A 220 " =    1.146
peak=    3.303 closest distance to " CA  CYS A 254 " =    1.437
peak=    3.303 closest distance to " NZ  LYS A 117 " =    2.918
peak=    3.302 closest distance to " O   HOH Z 209 " =    2.067
peak=    3.300 closest distance to " OG1 THR A 221 " =    1.687
peak=    3.297 closest distance to " O   HOH Z 189 " =    2.603
peak=    3.297 closest distance to " O   HOH Z 313 " =    2.023
peak=    3.291 closest distance to " CB  ALA A  71 " =    1.316
peak=    3.287 closest distance to " NH2BARG A 145 " =    1.896
peak=    3.286 closest distance to " CE  LYS A 119 " =    1.147
peak=    3.286 closest distance to " N   ASN A  39 " =    1.263
peak=    3.282 closest distance to " O   HOH Z 383 " =    2.273
peak=    3.281 closest distance to " NH1 ARG A  36 " =    1.256
peak=    3.280 closest distance to " O   HOH Z 395 " =    1.440
peak=    3.279 closest distance to " CB  PRO A 198 " =    1.260
peak=    3.274 closest distance to " CD  ARG A 269 " =    1.016
peak=    3.272 closest distance to " O  BHOH Z  74 " =    1.365
peak=    3.268 closest distance to " O   HOH Z 367 " =    1.504
peak=    3.267 closest distance to " O   HOH Z 214 " =    2.802
peak=    3.265 closest distance to " O   HOH Z 435 " =    1.900
peak=    3.264 closest distance to " CB  PRO A  90 " =    1.159
peak=    3.262 closest distance to " O   HOH Z 156 " =    2.629
peak=    3.262 closest distance to " N   GLU A  44 " =    1.428
peak=    3.258 closest distance to " O   HOH Z 435 " =    2.789
peak=    3.258 closest distance to " O   HOH Z 234 " =    1.928
peak=    3.257 closest distance to " O   HOH Z 427 " =    3.209
peak=    3.257 closest distance to " O   HOH Z 359 " =    1.579
peak=    3.254 closest distance to " O   HOH Z 216 " =    5.148
peak=    3.253 closest distance to " OG BSER A  99 " =    2.862
peak=    3.252 closest distance to " O   HOH Z 422 " =    2.698
peak=    3.249 closest distance to " CG  GLU A  37 " =    0.996
peak=    3.248 closest distance to " O   HOH Z 430 " =    5.654
peak=    3.247 closest distance to " O   HOH Z 421 " =    1.956
peak=    3.243 closest distance to " CG2 THR A 220 " =    0.830
peak=    3.243 closest distance to " CZ3 TRP A  85 " =    0.805
peak=    3.242 closest distance to " O   HOH Z  68 " =    1.846
peak=    3.238 closest distance to " N   GLY A 111 " =    1.273
peak=    3.235 closest distance to " CA  GLY A  80 " =    1.038
peak=    3.234 closest distance to " O   HOH Z 154 " =    2.944
peak=    3.232 closest distance to " CA  ASP A 149 " =    1.239
peak=    3.230 closest distance to " O   HOH Z 285 " =    1.940
peak=    3.230 closest distance to " O   HOH Z 240 " =    2.511
peak=    3.229 closest distance to " N   ALA A   1 " =    1.072
peak=    3.228 closest distance to " CA  LYS A 117 " =    1.396
peak=    3.223 closest distance to " CD  LYS A 119 " =    1.878
peak=    3.221 closest distance to " O   HOH Z 217 " =    2.876
peak=    3.221 closest distance to " O   HOH Z 327 " =    1.855
peak=    3.219 closest distance to " O   HOH Z  88 " =    2.548
peak=    3.218 closest distance to " CB  LEU A   5 " =    1.134
peak=    3.215 closest distance to " O   HOH Z 258 " =    2.231
peak=    3.212 closest distance to " OG  SER A  62 " =    2.840
peak=    3.212 closest distance to " O   HOH Z 432 " =    1.517
peak=    3.212 closest distance to " OG  SER A 245 " =    1.526
peak=    3.210 closest distance to " N   TYR A 116 " =    1.523
peak=    3.209 closest distance to " O   HOH Z 406 " =    2.573
peak=    3.207 closest distance to " N   GLY A 262 " =    1.249
peak=    3.200 closest distance to " CB  PHE A  16 " =    1.197
peak=    3.197 closest distance to " CB  TYR A 116 " =    1.195
peak=    3.196 closest distance to " CB  GLU A  37 " =    0.883
peak=    3.195 closest distance to " O   HOH Z 420 " =    5.169
peak=    3.194 closest distance to " CA  ALA A   9 " =    1.061
peak=    3.189 closest distance to " CB  PRO A 280 " =    1.215
peak=    3.187 closest distance to " OG  SER A 135 " =    1.278
peak=    3.187 closest distance to " CB  LYS A 289 " =    1.133
peak=    3.187 closest distance to " CB  PHE A 204 " =    0.871
peak=    3.187 closest distance to " CB  GLU A 175 " =    1.458
peak=    3.185 closest distance to " CG1 VAL A 153 " =    1.100
peak=    3.182 closest distance to " O   HOH Z 126 " =    2.279
peak=    3.177 closest distance to " CA  ARG A  66 " =    1.009
peak=    3.177 closest distance to " N   CYS A 260 " =    0.840
peak=    3.172 closest distance to " CB  SER A 212 " =    0.870
peak=    3.169 closest distance to " CG2 ILE A 234 " =    1.214
peak=    3.167 closest distance to " N   VAL A 126 " =    1.624
peak=    3.167 closest distance to " O   HOH Z 344 " =    3.224
peak=    3.166 closest distance to " O   HOH Z 414 " =    1.589
peak=    3.164 closest distance to " O   HOH Z 131 " =    2.576
peak=    3.156 closest distance to " O   HOH Z  61 " =    1.615
peak=    3.149 closest distance to " CE1 TYR A  30 " =    0.969
peak=    3.149 closest distance to " N   ASN A 252 " =    1.268
peak=    3.147 closest distance to " OE1 GLN A  58 " =    1.000
peak=    3.143 closest distance to " CB  LEU A  83 " =    0.787
peak=    3.142 closest distance to " ND2 ASN A 187 " =    1.525
peak=    3.135 closest distance to " CA  ASP A 140 " =    1.602
peak=    3.135 closest distance to " CG  LYS A  76 " =    1.165
peak=    3.133 closest distance to " N   ALA A 292 " =    0.993
peak=    3.130 closest distance to " CA  SER A  32 " =    1.693
peak=    3.129 closest distance to " OE1 GLN A 223 " =    3.338
peak=    3.122 closest distance to " CA  GLN A  94 " =    0.751
peak=    3.120 closest distance to " O   HOH Z 193 " =    1.962
peak=    3.112 closest distance to " N   GLU A   2 " =    0.986
peak=    3.112 closest distance to " CD  GLN A 194 " =    1.668
peak=    3.109 closest distance to " O   HOH Z  26 " =    1.061
peak=    3.108 closest distance to " CG  LEU A 237 " =    1.173
peak=    3.101 closest distance to " N   ALA A  10 " =    1.626
peak=    3.100 closest distance to " CA  THR A  82 " =    1.519
peak=    3.091 closest distance to " O   HOH Z 250 " =    1.406
peak=    3.088 closest distance to " CD2 TYR A  68 " =    0.907
peak=    3.086 closest distance to " CA  GLY A 229 " =    0.865
peak=    3.085 closest distance to " CB  ALA A  43 " =    0.940
peak=    3.075 closest distance to " O   HOH Z 343 " =    2.476
peak=    3.074 closest distance to " NE2 GLN A  58 " =    4.943
peak=    3.068 closest distance to " CB  PRO A 243 " =    1.480
peak=    3.066 closest distance to " OD2 ASP A 298 " =    3.529
peak=    3.045 closest distance to " CB  TRP A 266 " =    1.093
peak=    3.034 closest distance to " CB  ALA A 100 " =    1.246
peak=    3.033 closest distance to " NZ  LYS A 117 " =    0.860
peak=    3.010 closest distance to " O   HOH Z 428 " =    1.502

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 218         
Filter by distance & map next to the model:
   mapped sites are within: 0.542 - 5.719
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 214 from: 218
   mapped sites are within: 0.745 - 5.719

peak=   -4.948 closest distance to " CD  GLN A  58 " =    0.909
peak=   -4.788 closest distance to " O   HOH Z 203 " =    0.745
peak=   -4.676 closest distance to " O   HOH Z 411 " =    5.527
peak=   -4.564 closest distance to " CD  GLN A 223 " =    1.436
peak=   -4.320 closest distance to " O   HOH Z 166 " =    1.424
peak=   -4.244 closest distance to " O   PRO A 198 " =    1.385
peak=   -4.240 closest distance to " CD1 PHE A  59 " =    2.068
peak=   -4.226 closest distance to " CD  ARG A  14 " =    3.390
peak=   -4.223 closest distance to " O   HOH Z 418 " =    1.149
peak=   -4.145 closest distance to " CG2 ILE A  49 " =    2.684
peak=   -4.019 closest distance to " CG  GLN A  11 " =    1.293
peak=   -4.006 closest distance to " O   HOH Z  67 " =    1.368
peak=   -3.999 closest distance to " O   HOH Z 155 " =    1.794
peak=   -3.995 closest distance to " CD2 LEU A 237 " =    2.500
peak=   -3.985 closest distance to " O   GLN A  11 " =    0.960
peak=   -3.972 closest distance to " O   VAL A  67 " =    2.963
peak=   -3.944 closest distance to " CD  GLN A  88 " =    0.950
peak=   -3.910 closest distance to " CG2 ILE A  20 " =    2.906
peak=   -3.909 closest distance to " O   HOH Z 407 " =    1.063
peak=   -3.896 closest distance to " OE1 GLN A  88 " =    1.148
peak=   -3.896 closest distance to " CE2 PHE A  61 " =    2.765
peak=   -3.883 closest distance to " CG  PRO A 243 " =    1.673
peak=   -3.875 closest distance to " CZ  TYR A 169 " =    1.998
peak=   -3.855 closest distance to " O   HOH Z   7 " =    1.119
peak=   -3.838 closest distance to " CB  PRO A 243 " =    2.898
peak=   -3.812 closest distance to " O   HOH Z 331 " =    1.196
peak=   -3.796 closest distance to " NE2 GLN A 223 " =    1.204
peak=   -3.784 closest distance to " CG  ARG A 269 " =    2.348
peak=   -3.777 closest distance to " CE3 TRP A 150 " =    2.296
peak=   -3.774 closest distance to " O   HOH Z  56 " =    1.664
peak=   -3.772 closest distance to " OD1 ASN A 301 " =    0.840
peak=   -3.756 closest distance to " O   HOH Z 392 " =    1.144
peak=   -3.755 closest distance to " CD  GLN A 223 " =    1.096
peak=   -3.740 closest distance to " CD1 LEU A 101 " =    2.479
peak=   -3.738 closest distance to " O   HOH Z 165 " =    1.846
peak=   -3.736 closest distance to " O   HOH Z 374 " =    2.049
peak=   -3.729 closest distance to " O   HOH Z 377 " =    2.145
peak=   -3.726 closest distance to " O   HOH Z 250 " =    1.880
peak=   -3.723 closest distance to " OXT GLY A 302 " =    3.015
peak=   -3.714 closest distance to " CD  ARG A 156 " =    2.062
peak=   -3.708 closest distance to " O   HOH Z 221 " =    1.036
peak=   -3.706 closest distance to " O   SER A 206 " =    1.272
peak=   -3.705 closest distance to " N   ARG A 275 " =    1.224
peak=   -3.695 closest distance to " CG2 THR A 182 " =    2.306
peak=   -3.693 closest distance to " O   HOH Z 211 " =    1.224
peak=   -3.693 closest distance to " O   HOH Z 174 " =    2.013
peak=   -3.691 closest distance to " O   HOH Z 368 " =    2.030
peak=   -3.685 closest distance to " CD2 PHE A  61 " =    2.067
peak=   -3.648 closest distance to " O   HOH Z  65 " =    1.948
peak=   -3.641 closest distance to " O   HOH Z  90 " =    3.684
peak=   -3.628 closest distance to " CA  GLU A 277 " =    1.158
peak=   -3.625 closest distance to " O   HOH Z 109 " =    3.410
peak=   -3.624 closest distance to " OD2 ASP A 298 " =    1.012
peak=   -3.622 closest distance to " O   HOH Z 234 " =    4.167
peak=   -3.613 closest distance to " C   ASN A 285 " =    2.304
peak=   -3.608 closest distance to " CG1 VAL A 112 " =    2.619
peak=   -3.607 closest distance to " CG  GLU A  53 " =    1.507
peak=   -3.606 closest distance to " CD1 ILE A 109 " =    2.855
peak=   -3.602 closest distance to " CD2 TYR A  30 " =    2.808
peak=   -3.601 closest distance to " CA  ASP A 298 " =    1.084
peak=   -3.597 closest distance to " CG  GLN A  58 " =    1.308
peak=   -3.597 closest distance to " SD  MET A 105 " =    2.368
peak=   -3.581 closest distance to " O   HOH Z 197 " =    1.848
peak=   -3.576 closest distance to " OG  SER A  97 " =    2.159
peak=   -3.569 closest distance to " CG  LEU A  83 " =    2.061
peak=   -3.567 closest distance to " O   ASP A 171 " =    0.969
peak=   -3.565 closest distance to " CA  SER A 276 " =    1.474
peak=   -3.563 closest distance to " CA  GLY A 203 " =    2.334
peak=   -3.562 closest distance to " CB  ALA A  43 " =    2.711
peak=   -3.558 closest distance to " O   HOH Z   6 " =    1.366
peak=   -3.558 closest distance to " O   HOH Z  35 " =    1.274
peak=   -3.545 closest distance to " O   HOH Z  10 " =    1.644
peak=   -3.523 closest distance to " O   ALA A  34 " =    2.445
peak=   -3.520 closest distance to " O   HOH Z 422 " =    1.370
peak=   -3.517 closest distance to " O   VAL A 174 " =    2.178
peak=   -3.514 closest distance to " CD2 TYR A 293 " =    1.817
peak=   -3.509 closest distance to " O   SER A 276 " =    1.647
peak=   -3.503 closest distance to " CG2 VAL A 189 " =    2.148
peak=   -3.500 closest distance to " CD2 HIS A 115 " =    1.005
peak=   -3.493 closest distance to " O   HOH Z 203 " =    1.151
peak=   -3.492 closest distance to " ND2 ASN A  45 " =    1.949
peak=   -3.490 closest distance to " C   VAL A 265 " =    0.866
peak=   -3.488 closest distance to " O   HOH Z 196 " =    1.704
peak=   -3.476 closest distance to " CA  GLY A 241 " =    3.395
peak=   -3.470 closest distance to " O   HOH Z 155 " =    1.947
peak=   -3.469 closest distance to " NE2 GLN A 103 " =    1.918
peak=   -3.462 closest distance to " O   HOH Z 166 " =    2.148
peak=   -3.461 closest distance to " CA  ASN A 127 " =    1.111
peak=   -3.461 closest distance to " O   HOH Z 407 " =    3.615
peak=   -3.461 closest distance to " O   HOH Z 423 " =    1.372
peak=   -3.460 closest distance to " OH  TYR A 247 " =    2.210
peak=   -3.456 closest distance to " O   SER A 273 " =    1.245
peak=   -3.455 closest distance to " CA  GLY A 241 " =    3.007
peak=   -3.453 closest distance to " CG1 VAL A 189 " =    2.522
peak=   -3.452 closest distance to " N   ALA A  43 " =    2.775
peak=   -3.441 closest distance to " CD1 ILE A 106 " =    2.219
peak=   -3.427 closest distance to " O   HOH Z 340 " =    1.597
peak=   -3.424 closest distance to " CG1 VAL A 112 " =    2.629
peak=   -3.421 closest distance to " CD1 ILE A 263 " =    1.981
peak=   -3.420 closest distance to " NE2 GLN A  94 " =    1.803
peak=   -3.414 closest distance to " CG2BVAL A 121 " =    1.335
peak=   -3.413 closest distance to " O  BHOH Z 338 " =    1.426
peak=   -3.403 closest distance to " O   HOH Z 156 " =    3.747
peak=   -3.395 closest distance to " NE2 GLN A 278 " =    1.752
peak=   -3.394 closest distance to " OG BSER A 210 " =    1.172
peak=   -3.392 closest distance to " N   SER A 134 " =    1.233
peak=   -3.389 closest distance to " CD  ARG A  36 " =    1.011
peak=   -3.384 closest distance to " O   SER A 271 " =    2.014
peak=   -3.382 closest distance to " O   PRO A 163 " =    2.120
peak=   -3.377 closest distance to " O   HOH Z 128 " =    2.521
peak=   -3.372 closest distance to " OD2 ASP A 171 " =    1.846
peak=   -3.372 closest distance to " CZ  PHE A  38 " =    2.331
peak=   -3.368 closest distance to " O   HOH Z 423 " =    2.684
peak=   -3.367 closest distance to " CG  ARG A 259 " =    2.472
peak=   -3.366 closest distance to " CA  VAL A 197 " =    0.982
peak=   -3.365 closest distance to " O   MET A  40 " =    2.858
peak=   -3.365 closest distance to " O   HOH Z  19 " =    2.307
peak=   -3.363 closest distance to " O   HOH Z 134 " =    2.574
peak=   -3.361 closest distance to " CB  ALA A 161 " =    2.633
peak=   -3.354 closest distance to " CG  PRO A 280 " =    2.298
peak=   -3.351 closest distance to " O   HOH Z  40 " =    2.863
peak=   -3.343 closest distance to " O   HOH Z 191 " =    5.719
peak=   -3.343 closest distance to " CB  ASN A  45 " =    2.106
peak=   -3.335 closest distance to " O   HOH Z  54 " =    1.602
peak=   -3.334 closest distance to " CG  GLN A 103 " =    2.433
peak=   -3.333 closest distance to " N   ALA A 226 " =    2.128
peak=   -3.330 closest distance to " CB  SER A 210 " =    1.076
peak=   -3.328 closest distance to " CG2BVAL A  41 " =    1.541
peak=   -3.326 closest distance to " O   HOH Z 424 " =    2.948
peak=   -3.326 closest distance to " CB  ALA A  10 " =    2.169
peak=   -3.316 closest distance to " O   HOH Z 124 " =    1.646
peak=   -3.313 closest distance to " NH2 ARG A  36 " =    1.184
peak=   -3.308 closest distance to " O   HOH Z 265 " =    1.355
peak=   -3.307 closest distance to " O   HOH Z 198 " =    1.479
peak=   -3.297 closest distance to " O   HOH Z 133 " =    1.706
peak=   -3.296 closest distance to " O   HOH Z 366 " =    1.729
peak=   -3.294 closest distance to " O   HOH Z 102 " =    1.684
peak=   -3.293 closest distance to " O   HOH Z  37 " =    1.472
peak=   -3.293 closest distance to " O   HOH Z 171 " =    2.368
peak=   -3.285 closest distance to " O   HOH Z 252 " =    3.899
peak=   -3.283 closest distance to " O   SER A 210 " =    1.655
peak=   -3.282 closest distance to " NH2 ARG A  79 " =    2.228
peak=   -3.280 closest distance to " CZ  ARG A 156 " =    1.648
peak=   -3.280 closest distance to " CG  LEU A 281 " =    2.083
peak=   -3.277 closest distance to " CG  HIS A  86 " =    1.190
peak=   -3.277 closest distance to " CE1 HIS A  81 " =    1.555
peak=   -3.276 closest distance to " O   HOH Z 205 " =    0.808
peak=   -3.274 closest distance to " O   HOH Z 166 " =    1.874
peak=   -3.274 closest distance to " O   HOH Z 110 " =    1.308
peak=   -3.266 closest distance to " O   HOH Z 136 " =    2.501
peak=   -3.264 closest distance to " O   HOH Z 136 " =    0.928
peak=   -3.261 closest distance to " CB  ALA A 131 " =    2.402
peak=   -3.260 closest distance to " O   ARG A 275 " =    1.909
peak=   -3.260 closest distance to " O   HOH Z  15 " =    1.520
peak=   -3.258 closest distance to " O   PHE A 218 " =    1.415
peak=   -3.255 closest distance to " O   HOH Z  52 " =    1.927
peak=   -3.254 closest distance to " OD1 ASP A 171 " =    1.637
peak=   -3.245 closest distance to " O   HOH Z 200 " =    1.140
peak=   -3.245 closest distance to " O   LYS A  76 " =    1.449
peak=   -3.242 closest distance to " O   TRP A  92 " =    2.090
peak=   -3.242 closest distance to " CD  ARG A  79 " =    1.341
peak=   -3.239 closest distance to " O   HOH Z 185 " =    2.641
peak=   -3.238 closest distance to " O   HOH Z 290 " =    1.068
peak=   -3.231 closest distance to " O   HOH Z 336 " =    5.520
peak=   -3.230 closest distance to " O   HOH Z 149 " =    1.920
peak=   -3.230 closest distance to " O   GLY A  17 " =    1.103
peak=   -3.226 closest distance to " O   HOH Z 216 " =    1.124
peak=   -3.225 closest distance to " C   THR A 279 " =    1.104
peak=   -3.220 closest distance to " OD1 ASN A 148 " =    1.355
peak=   -3.219 closest distance to " CB  PRO A 163 " =    2.380
peak=   -3.215 closest distance to " O   HOH Z 283 " =    2.453
peak=   -3.214 closest distance to " CH2 TRP A 179 " =    1.253
peak=   -3.213 closest distance to " ND2 ASN A  60 " =    2.094
peak=   -3.212 closest distance to " NE  ARG A  66 " =    4.783
peak=   -3.211 closest distance to " O   HOH Z  19 " =    0.765
peak=   -3.207 closest distance to " NH2 ARG A  66 " =    2.072
peak=   -3.207 closest distance to " O   HOH Z  37 " =    2.106
peak=   -3.207 closest distance to " OD1 ASN A 187 " =    1.726
peak=   -3.197 closest distance to " O   HOH Z 150 " =    1.769
peak=   -3.195 closest distance to " O   HOH Z 326 " =    5.149
peak=   -3.191 closest distance to " N   TYR A  68 " =    2.874
peak=   -3.190 closest distance to " O   HOH Z 345 " =    2.947
peak=   -3.181 closest distance to " O   HOH Z 435 " =    1.753
peak=   -3.178 closest distance to " ND2 ASN A  60 " =    2.169
peak=   -3.176 closest distance to " O   HOH Z 401 " =    1.425
peak=   -3.173 closest distance to " CB  SER A 146 " =    2.106
peak=   -3.171 closest distance to " CD1 LEU A  25 " =    2.508
peak=   -3.167 closest distance to " CE3 TRP A  70 " =    1.663
peak=   -3.167 closest distance to " O   HOH Z 388 " =    2.146
peak=   -3.165 closest distance to " NH2 ARG A 159 " =    2.492
peak=   -3.163 closest distance to " O   HOH Z   2 " =    2.178
peak=   -3.162 closest distance to " CD  GLN A  77 " =    1.069
peak=   -3.159 closest distance to " NH2 ARG A  79 " =    1.780
peak=   -3.157 closest distance to " CD1 LEU A 167 " =    2.057
peak=   -3.153 closest distance to " O   HOH Z 287 " =    1.866
peak=   -3.153 closest distance to " CZ  ARG A 156 " =    1.717
peak=   -3.151 closest distance to " ND2 ASN A  60 " =    1.499
peak=   -3.150 closest distance to " O   HOH Z 351 " =    1.788
peak=   -3.149 closest distance to " O   HOH Z 109 " =    1.517
peak=   -3.145 closest distance to " O   HOH Z 151 " =    1.261
peak=   -3.143 closest distance to " CB  ALA A 291 " =    2.500
peak=   -3.140 closest distance to " CG2 ILE A 263 " =    2.219
peak=   -3.127 closest distance to " SG  CYS A 168 " =    1.156
peak=   -3.123 closest distance to " O   HOH Z 281 " =    2.348
peak=   -3.119 closest distance to " O   HOH Z 189 " =    1.678
peak=   -3.116 closest distance to " CG  PRO A 163 " =    2.528
peak=   -3.113 closest distance to " CH2 TRP A 150 " =    1.055
peak=   -3.104 closest distance to " O   HOH Z 428 " =    1.497
peak=   -3.100 closest distance to " CB  ASN A  45 " =    0.890
peak=   -3.095 closest distance to " OD2 ASP A 270 " =    0.939
peak=   -3.085 closest distance to " O   ALA A  10 " =    1.837
peak=   -3.077 closest distance to " CD1 LEU A   5 " =    2.540
peak=   -3.050 closest distance to " O   HOH Z 146 " =    1.164
peak=   -3.038 closest distance to " O   HOH Z 265 " =    1.960

================= 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    :  0.4725 0.4646   6.286173e+00   6.265791e+00
   1_bss:  0.4628 0.4533   6.280038e+00   6.255201e+00
   1_xyz:  0.3807 0.4083   6.154710e+00   6.190383e+00
   1_adp:  0.3503 0.4193   6.110896e+00   6.201702e+00
   1_occ:  0.3500 0.4185   6.110228e+00   6.201667e+00
   2_bss:  0.3492 0.4174   6.112644e+00   6.203854e+00
   2_xyz:  0.2975 0.3630   5.991239e+00   6.119850e+00
   2_adp:  0.2886 0.3569   5.977963e+00   6.107995e+00
   2_occ:  0.2884 0.3571   5.977945e+00   6.108843e+00
   3_bss:  0.2886 0.3565   5.978836e+00   6.108726e+00
   3_xyz:  0.2251 0.2766   5.740179e+00   5.907654e+00
   3_adp:  0.1993 0.2603   5.652412e+00   5.850894e+00
   3_occ:  0.1992 0.2604   5.651810e+00   5.850470e+00
   4_bss:  0.1986 0.2594   5.650514e+00   5.849165e+00
   4_xyz:  0.1676 0.2199   5.497417e+00   5.709753e+00
   4_adp:  0.1636 0.2020   5.456682e+00   5.635851e+00
   4_occ:  0.1633 0.2017   5.455488e+00   5.635409e+00
   5_bss:  0.1632 0.2011   5.455800e+00   5.634527e+00
   5_xyz:  0.1367 0.1789   5.313394e+00   5.519408e+00
   5_adp:  0.1301 0.1801   5.284517e+00   5.511827e+00
   5_occ:  0.1300 0.1800   5.284150e+00   5.511522e+00
   5_bss:  0.1305 0.1799   5.285134e+00   5.511349e+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:  0.286  36.467  -3.795   4.203   2.519   0.000   0.000   0.000
   1_xyz:  0.286  36.467  -3.795   4.203   2.519   0.000   0.000   0.000
   1_adp:  0.286  36.467  -3.795   4.203   2.519   0.000   0.000   0.000
   1_occ:  0.286  36.467  -3.795   4.203   2.519   0.000   0.000   0.000
   2_bss:  0.296  50.239  -1.756   2.506   1.422   0.000   0.000   0.000
   2_xyz:  0.296  50.239  -1.756   2.506   1.422   0.000   0.000   0.000
   2_adp:  0.296  50.239  -1.756   2.506   1.422   0.000   0.000   0.000
   2_occ:  0.296  50.239  -1.756   2.506   1.422   0.000   0.000   0.000
   3_bss:  0.321  67.819  -1.640   1.956   0.840   0.000   0.000   0.000
   3_xyz:  0.321  67.819  -1.640   1.956   0.840   0.000   0.000   0.000
   3_adp:  0.321  67.819  -1.640   1.956   0.840   0.000   0.000   0.000
   3_occ:  0.321  67.819  -1.640   1.956   0.840   0.000   0.000   0.000
   4_bss:  0.340  91.998  -1.794   0.368   0.273   0.000   0.000   0.000
   4_xyz:  0.340  91.998  -1.794   0.368   0.273   0.000   0.000   0.000
   4_adp:  0.340  91.998  -1.794   0.368   0.273   0.000   0.000   0.000
   4_occ:  0.340  91.998  -1.794   0.368   0.273   0.000   0.000   0.000
   5_bss:  0.335  78.025  -2.143  -0.428  -0.056  -0.000  -0.000  -0.000
   5_xyz:  0.335  78.025  -2.143  -0.428  -0.056  -0.000  -0.000  -0.000
   5_adp:  0.335  78.025  -2.143  -0.428  -0.056  -0.000  -0.000  -0.000
   5_occ:  0.335  78.025  -2.143  -0.428  -0.056  -0.000  -0.000  -0.000
   5_bss:  0.331  77.916  -2.064  -0.661   0.024  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.734 0.4489  0.5906    67421.597
   1_bss:  54.485 0.4636  0.6317    64387.716
   1_xyz:  47.694 0.5482  0.7316    50234.599
   1_adp:  48.315 0.5403  0.7278    51841.086
   1_occ:  48.318 0.5403  0.7269    51774.252
   2_bss:  48.124 0.5429  0.7287    51826.370
   2_xyz:  40.365 0.6378  0.8424    38479.000
   2_adp:  39.370 0.6500  0.8433    37122.797
   2_occ:  39.391 0.6498  0.8424    37188.472
   3_bss:  39.317 0.6507  0.8340    37146.518
   3_xyz:  28.822 0.7699  0.9558    20453.710
   3_adp:  26.465 0.7956  0.9536    17762.999
   3_occ:  26.449 0.7958  0.9536    17740.503
   4_bss:  26.291 0.7975  0.9318    17613.941
   4_xyz:  21.944 0.8419  0.9589    12524.935
   4_adp:  19.638 0.8655  0.9693    10789.987
   4_occ:  19.614 0.8657  0.9695    10773.317
   5_bss:  19.577 0.8661  0.9535    10737.268
   5_xyz:  16.954 0.8900  0.9672     8413.636
   5_adp:  16.730 0.8921  0.9608     8316.325
   5_occ:  16.716 0.8923  0.9608     8312.954
   5_bss:  16.707 0.8923  0.9599     8302.980
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6979e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6979e-01
   1_xyz:   1.575  0.011  0.098 15.721  0.006  4.111   1.2619e-01
   1_adp:   1.575  0.011  0.098 15.721  0.006  4.111   1.2619e-01
   1_occ:   1.575  0.011  0.098 15.721  0.006  4.111   1.2619e-01
   2_bss:   1.575  0.011  0.098 15.721  0.006  4.111   1.2619e-01
   2_xyz:   1.257  0.009  0.086 14.800  0.004  4.110   8.2984e-02
   2_adp:   1.257  0.009  0.086 14.800  0.004  4.110   8.2984e-02
   2_occ:   1.257  0.009  0.086 14.800  0.004  4.110   8.2984e-02
   3_bss:   1.257  0.009  0.086 14.800  0.004  4.110   8.2984e-02
   3_xyz:   1.305  0.011  0.087 15.308  0.006  4.111   9.9540e-02
   3_adp:   1.305  0.011  0.087 15.308  0.006  4.111   9.9540e-02
   3_occ:   1.305  0.011  0.087 15.308  0.006  4.111   9.9540e-02
   4_bss:   1.305  0.011  0.087 15.308  0.006  4.111   9.9540e-02
   4_xyz:   1.057  0.008  0.077 14.521  0.004  4.126   6.4927e-02
   4_adp:   1.057  0.008  0.077 14.521  0.004  4.126   6.4927e-02
   4_occ:   1.057  0.008  0.077 14.521  0.004  4.126   6.4927e-02
   5_bss:   1.057  0.008  0.077 14.521  0.004  4.126   6.4927e-02
   5_xyz:   1.139  0.010  0.081 14.744  0.004  4.117   7.6098e-02
   5_adp:   1.139  0.010  0.081 14.744  0.004  4.117   7.6098e-02
   5_occ:   1.139  0.010  0.081 14.744  0.004  4.117   7.6098e-02
   5_bss:   1.139  0.010  0.081 14.744  0.004  4.117   7.6098e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.620   2.4462e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.620   2.4462e-01
   1_xyz:   9.216  0.079  0.405 82.191  0.040  1.822   8.5106e-02
   1_adp:   9.216  0.079  0.405 82.191  0.040  1.822   8.5106e-02
   1_occ:   9.216  0.079  0.405 82.191  0.040  1.822   8.5106e-02
   2_bss:   9.216  0.079  0.405 82.191  0.040  1.822   8.5106e-02
   2_xyz:   8.193  0.050  0.291 81.163  0.019  2.243   9.2748e-02
   2_adp:   8.193  0.050  0.291 81.163  0.019  2.243   9.2748e-02
   2_occ:   8.193  0.050  0.291 81.163  0.019  2.243   9.2748e-02
   3_bss:   8.193  0.050  0.291 81.163  0.019  2.243   9.2748e-02
   3_xyz:   8.503  0.086  0.260 87.124  0.044  2.165   1.2174e-01
   3_adp:   8.503  0.086  0.260 87.124  0.044  2.165   1.2174e-01
   3_occ:   8.503  0.086  0.260 87.124  0.044  2.165   1.2174e-01
   4_bss:   8.503  0.086  0.260 87.124  0.044  2.165   1.2174e-01
   4_xyz:   7.361  0.054  0.235 81.187  0.039  2.299   5.8799e-02
   4_adp:   7.361  0.054  0.235 81.187  0.039  2.299   5.8799e-02
   4_occ:   7.361  0.054  0.235 81.187  0.039  2.299   5.8799e-02
   5_bss:   7.361  0.054  0.235 81.187  0.039  2.299   5.8799e-02
   5_xyz:   8.480  0.054  0.264 83.098  0.042  2.238   5.7116e-02
   5_adp:   8.480  0.054  0.264 83.098  0.042  2.238   5.7116e-02
   5_occ:   8.480  0.054  0.264 83.098  0.042  2.238   5.7116e-02
   5_bss:   8.480  0.054  0.264 83.098  0.042  2.238   5.7116e-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: 110.26   0.00  19.21  87.09   0.00  15.91 110.26   0.00  37.18
   1_occ: 110.26   0.00  19.21  87.09   0.00  15.91 110.26   0.00  37.18
   2_bss: 110.26   0.00  19.21  87.09   0.00  15.91 110.26   0.00  37.18
   2_xyz: 110.26   0.00  19.21  87.09   0.00  15.91 110.26   0.00  37.18
   2_adp: 112.01   0.00  18.29  84.98   0.00  15.02 112.01   0.00  36.10
   2_occ: 112.01   0.00  18.29  84.98   0.00  15.02 112.01   0.00  36.10
   3_bss: 112.01   0.00  18.29  84.98   0.00  15.02 112.01   0.00  36.10
   3_xyz: 112.01   0.00  18.29  84.98   0.00  15.02 112.01   0.00  36.10
   3_adp: 126.44   0.00  19.85 119.01   0.00  14.45 126.44   2.65  49.24
   3_occ: 126.44   0.00  19.85 119.01   0.00  14.45 126.44   2.65  49.24
   4_bss: 126.44   0.00  19.85 119.01   0.00  14.45 126.44   2.65  49.24
   4_xyz: 126.44   0.00  19.85 119.01   0.00  14.45 126.44   2.65  49.24
   4_adp: 113.63   0.00  17.70 104.12   0.00  13.05 113.63   4.26  43.01
   4_occ: 113.63   0.00  17.70 104.12   0.00  13.05 113.63   4.26  43.01
   5_bss: 113.63   0.00  17.70 104.12   0.00  13.05 113.63   4.26  43.01
   5_xyz: 113.63   0.00  17.70 104.12   0.00  13.05 113.63   4.26  43.01
   5_adp: 115.46   0.00  17.78 102.78   0.00  12.73 115.46   2.51  45.28
   5_occ: 115.46   0.00  17.78 102.78   0.00  12.73 115.46   2.51  45.28
   5_bss: 115.46   0.00  17.78 102.79   0.00  12.73 115.46   2.52  45.28
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.815    0.021    0.347
   1_adp:    1.815    0.021    0.347
   1_occ:    1.815    0.021    0.347
   2_bss:    1.815    0.021    0.347
   2_xyz:    1.400    0.038    0.476
   2_adp:    1.400    0.038    0.476
   2_occ:    1.400    0.038    0.476
   3_bss:    1.400    0.038    0.476
   3_xyz:    1.576    0.074    0.729
   3_adp:    1.576    0.074    0.729
   3_occ:    1.576    0.074    0.729
   4_bss:    1.576    0.074    0.729
   4_xyz:    1.616    0.093    0.781
   4_adp:    1.616    0.093    0.781
   4_occ:    1.616    0.093    0.781
   5_bss:    1.616    0.093    0.781
   5_xyz:    1.657    0.041    0.848
   5_adp:    1.657    0.041    0.848
   5_occ:    1.657    0.041    0.848
   5_bss:    1.657    0.041    0.848
------------------------------------------------------------------------

CPU time actual refinement: 344.76


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_603/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_603/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_603/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_603/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_603/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 344.60 
  Macro-tasks:
    bulk solvent and scale       = 47.01  
    individual site refinement   = 138.45 
    weights calculation          = 28.58  
    collect and process          = 6.31   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 220.43 
  Micro-tasks:
    mask                            = 2.94   
    f_calc                          = 109.21 
    alpha_beta                      = 8.14   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 117.66 
    fmodel                         = 7.78   
    r_factors                      = 0.25   
    phase_errors                   = 10.40  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 257.72 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.913 micro seconds
Total CPU time: 5.97 minutes
from_scatterers_fft:    644 calls, 108.99 s
gradients_fft:          589 calls, 104.78 s

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

# Date 2008-01-16 Time 05:13:31 PST -0800 (1200489211.52 s)
Start R-work = 0.4725, R-free = 0.4646 (no bulk solvent and anisotropic scale)
Final R-work = 0.1485, R-free = 0.1957 (no bulk solvent and anisotropic scale)

Start R-work = 0.4628, R-free = 0.4533
Final R-work = 0.1305, R-free = 0.1799