# Date 2008-01-16 Time 05:57:46 PST -0800 (1200491866.17 s)
#phil __OFF__

Command line arguments: "../948.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4517
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 948

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 47.8686, 85.0941, 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: 3.25, 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: (70.9525, 47.8686, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0395 1.97144
Completeness in resolution range: 0.931789
Completeness with d_max=infinity: 0.929005

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0395
                             d_min =   1.9714

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.8686, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0395 1.97144
Completeness in resolution range: 0.931789
Completeness with d_max=infinity: 0.929005

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0399 -  4.2190 [2212/2241]  1993   219   9.9%
  bin  2:  4.2190 -  3.3611 [2111/2134]  1900   211  10.0%
  bin  3:  3.3611 -  2.9398 [2093/2118]  1880   213  10.2%
  bin  4:  2.9398 -  2.6727 [2072/2088]  1869   203   9.8%
  bin  5:  2.6727 -  2.4820 [2062/2106]  1853   209  10.1%
  bin  6:  2.4820 -  2.3362 [2052/2080]  1851   201   9.8%
  bin  7:  2.3362 -  2.2196 [2025/2061]  1821   204  10.1%
  bin  8:  2.2196 -  2.1233 [2023/2065]  1821   202  10.0%
  bin  9:  2.1233 -  2.0417 [2030/2075]  1827   203  10.0%
  bin 10:  2.0417 -  1.9714 [ 909/2055]   815    94  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_948/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.61 -     2.27: 16
        2.27 -     2.93: 1513
        2.93 -     3.58: 4449
        3.58 -     4.24: 9132
        4.24 -     4.90: 13050
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.609 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.637 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.743 3.040 -x+1/2,-y+1,z+1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.777 3.040 -x+1/2,-y+1,z-1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28155 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_948/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_948/model_refine_001.geo

CPU time processing inputs: 9.06


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 47.8686 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4335   r_free= 0.4221   ksol= 0.00   Bsol= 0.00   scale= 0.908    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.241653                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0399 -  4.7060 0.99   1433  161 0.3406 0.3591      6.4915      6.4959|
|  2:  4.7060 -  3.7544 0.99   1374  147 0.3609 0.3727       6.752      6.7134|
|  3:  3.7544 -  3.2855 0.99   1357  156 0.4000 0.3586      6.6031      6.5826|
|  4:  3.2855 -  2.9876 0.99   1339  146 0.4137 0.4110      6.4479      6.4374|
|  5:  2.9876 -  2.7749 0.98   1336  149 0.4420 0.4334      6.3168      6.3013|
|  6:  2.7749 -  2.6122 0.99   1333  147 0.4760 0.4337      6.2465      6.1263|
|  7:  2.6122 -  2.4820 0.98   1323  149 0.4666 0.3955      6.2098      6.1293|
|  8:  2.4820 -  2.3744 0.99   1305  142 0.4907 0.4986      6.1274      6.1955|
|  9:  2.3744 -  2.2833 0.99   1333  153 0.5118 0.4769      6.1214      6.0911|
| 10:  2.2833 -  2.2048 0.98   1304  143 0.4750 0.5213      6.0621      6.1187|
| 11:  2.2048 -  2.1360 0.97   1293  138 0.5003 0.4953       6.013      5.9856|
| 12:  2.1360 -  2.0751 0.99   1308  153 0.4864 0.4995      5.9242      5.9701|
| 13:  2.0751 -  2.0206 0.92   1230  136 0.4799 0.4093      5.8457       5.787|
| 14:  2.0206 -  1.9714 0.27    362   39 0.5274 0.4715      5.8299      5.7727|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0399 -  4.7060  1433   161  0.73  31.93   0.84     0.75      63348.40|
|  2:  4.7060 -  3.7544  1374   147  0.75  30.88   0.93     0.83      81912.14|
|  3:  3.7544 -  3.2855  1357   156  0.67  38.17   0.92     0.83      87012.72|
|  4:  3.2855 -  2.9876  1339   146  0.60  43.46   0.93     0.79      77931.11|
|  5:  2.9876 -  2.7749  1336   149  0.54  48.52   0.90     0.73      64063.93|
|  6:  2.7749 -  2.6122  1333   147  0.52  50.19   0.92     0.72      53634.79|
|  7:  2.6122 -  2.4820  1323   149  0.52  50.45   0.93     0.69      48686.61|
|  8:  2.4820 -  2.3744  1305   142  0.46  55.21   0.89     0.66      48800.69|
|  9:  2.3744 -  2.2833  1333   153  0.43  57.35   0.91     0.63      47230.85|
| 10:  2.2833 -  2.2048  1304   143  0.42  58.42   0.97     0.61      46615.60|
| 11:  2.2048 -  2.1360  1293   138  0.40  59.98   0.93     0.60      42620.53|
| 12:  2.1360 -  2.0751  1308   153  0.40  60.36   0.94     0.61      38986.83|
| 13:  2.0751 -  2.0206  1230   136  0.42  58.38   0.96     0.63      31262.81|
| 14:  2.0206 -  1.9714   362    39  0.46  55.33   0.92     0.68      24452.35|
|alpha:            min =        0.60 max =            0.83 mean =         0.70|
|beta:             min =    24452.35 max =        87012.72 mean =     56045.78|
|figures of merit: min =        0.00 max =            1.00 mean =         0.53|
|phase err.(work): min =        0.00 max =           89.98 mean =        49.33|
|phase err.(test): min =        0.00 max =           89.99 mean =        49.46|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.315236             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.527   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.906088              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.372   (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 |  1.609 -  1.938:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.938 -  2.267:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.267 -  2.596:       37 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.596 -  2.925:     1476 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.925 -  3.255:     1897 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.255 -  3.584:     2552 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.584 -  3.913:     4679 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.913 -  4.242:     4453 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.242 -  4.571:     5947 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.571 -  4.900:     7103 |
|-----------------------------------------------------------------------------|
|-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 |        0.174 |
| 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  1.609 |       0.337 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.055)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4335   r_free= 0.4221   ksol= 0.00   Bsol= 0.00   scale= 0.908    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.241653                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4235   r_free= 0.4109   ksol= 0.29   Bsol= 28.03   scale= 0.948   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,4.24,0.16,0.00,0.00,0.00); trace/3= 0.75                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.231493                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.217154             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.397   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.900698              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.198   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4235      final r-factor (work) = 0.2819          |
| start r-factor (free) = 0.4109      final r-factor (free) = 0.3169          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.2325 = 12.22 * 0.50 * 6.2303 + 1.00 * 0.1740                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.0206 = 12.22 * 0.50 * 6.0385 + 1.00 * 0.1342                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2819      final r-factor (work) = 0.2579          |
| start r-factor (free) = 0.3169      final r-factor (free) = 0.3247          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4452 = 0.90 * 1.00 * 6.0385 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3059 = 0.90 * 1.00 * 5.8651 + 1.00 * 0.0232                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.055)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.55   17.31    None  None   None       |
|    all(noH): 2823   0      0.00    87.55   17.31    None  None   None       |
|    Sol.    : 438    0      2.51    69.85   38.36    None  None   None       |
|    Mac.    : 2385   0      0.00    87.55   13.45    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 -   8.755:  852   |   5:    43.773 -  52.528:  120        |
|      1:     8.755 -  17.509:  952   |   6:    52.528 -  61.283:   67        |
|      2:    17.509 -  26.264:  462   |   7:    61.283 -  70.037:    9        |
|      3:    26.264 -  35.019:  203   |   8:    70.037 -  78.792:    0        |
|      4:    35.019 -  43.773:  157   |   9:    78.792 -  87.547:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2579 r_free = 0.3247             target_work(ml) = 5.872         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2576 r_free = 0.3236             target_work(ml) = 5.870         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2576   r_free= 0.3236   ksol= 0.29   Bsol= 28.03   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,4.24,0.16,0.00,0.00,0.00); trace/3= 0.75                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.870177                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2551   r_free= 0.3215   ksol= 0.33   Bsol= 60.01   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.87,1.13,-0.95,0.00,-0.00,-0.00); trace/3= -0.56                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.866278                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.533982              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.112  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.719317              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 100.551  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2551      final r-factor (work) = 0.1863          |
| start r-factor (free) = 0.3215      final r-factor (free) = 0.2256          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.3655 = 5.53 * 0.50 * 5.8660 + 1.00 * 0.1342                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.9951 = 5.53 * 0.50 * 5.7524 + 1.00 * 0.0783                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1863      final r-factor (work) = 0.1643          |
| start r-factor (free) = 0.2256      final r-factor (free) = 0.2082          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1633 = 0.72 * 1.00 * 5.7524 + 1.00 * 0.0255                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9696 = 0.72 * 1.00 * 5.5009 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.055)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.83   17.95    None  None   None       |
|    all(noH): 2823   0      0.00    98.83   17.95    None  None   None       |
|    Sol.    : 438    0      4.51    98.83   43.76    None  None   None       |
|    Mac.    : 2385   0      0.00    96.90   13.21    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.883: 1082   |   5:    49.417 -  59.300:  103        |
|      1:     9.883 -  19.767: 1022   |   6:    59.300 -  69.184:   67        |
|      2:    19.767 -  29.650:  260   |   7:    69.184 -  79.067:   29        |
|      3:    29.650 -  39.534:  127   |   8:    79.067 -  88.950:   15        |
|      4:    39.534 -  49.417:  110   |   9:    88.950 -  98.834:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1643 r_free = 0.2082             target_work(ml) = 5.465         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1640 r_free = 0.2080             target_work(ml) = 5.464         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1640   r_free= 0.2080   ksol= 0.33   Bsol= 60.01   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.87,1.13,-0.95,0.00,-0.00,-0.00); trace/3= -0.56                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.464032                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1639   r_free= 0.2079   ksol= 0.32   Bsol= 63.73   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-0.17,-1.22,-0.00,-0.00,-0.00); trace/3= -1.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.463381                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.267417              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.960   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.200279              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.445  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1639      final r-factor (work) = 0.1304          |
| start r-factor (free) = 0.2079      final r-factor (free) = 0.1769          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.8179 = 4.27 * 0.50 * 5.5019 + 1.00 * 0.0783                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.5249 = 4.27 * 0.50 * 5.3654 + 1.00 * 0.0766                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1304      final r-factor (work) = 0.1249          |
| start r-factor (free) = 0.1769      final r-factor (free) = 0.1690          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0872 = 0.20 * 1.00 * 5.3654 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0644 = 0.20 * 1.00 * 5.2595 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.055)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.29   16.91    None  None   None       |
|    all(noH): 2823   0      0.00    92.29   16.91    None  None   None       |
|    Sol.    : 438    0      5.22    92.29   40.34    None  None   None       |
|    Mac.    : 2385   0      0.00    92.07   12.60    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.229:  941   |   5:    46.146 -  55.376:  102        |
|      1:     9.229 -  18.459: 1187   |   6:    55.376 -  64.605:   52        |
|      2:    18.459 -  27.688:  246   |   7:    64.605 -  73.834:   28        |
|      3:    27.688 -  36.917:  138   |   8:    73.834 -  83.064:    7        |
|      4:    36.917 -  46.146:  112   |   9:    83.064 -  92.293:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1249 r_free = 0.1690             target_work(ml) = 5.233         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1248 r_free = 0.1689             target_work(ml) = 5.233         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1248   r_free= 0.1689   ksol= 0.32   Bsol= 63.73   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-0.17,-1.22,-0.00,-0.00,-0.00); trace/3= -1.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.232634                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1252   r_free= 0.1688   ksol= 0.32   Bsol= 58.75   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-1.02,-1.38,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.234117                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.013560              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 133.393  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.351855              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.736   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1252      final r-factor (work) = 0.1162          |
| start r-factor (free) = 0.1688      final r-factor (free) = 0.1616          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0045 = 3.01 * 0.50 * 5.2614 + 1.00 * 0.0766                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9165 = 3.01 * 0.50 * 5.2060 + 1.00 * 0.0722                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1162      final r-factor (work) = 0.1151          |
| start r-factor (free) = 0.1616      final r-factor (free) = 0.1618          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8427 = 0.35 * 1.00 * 5.2060 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8468 = 0.35 * 1.00 * 5.1746 + 1.00 * 0.0260                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.055)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.21   16.86    None  None   None       |
|    all(noH): 2823   0      0.00    92.21   16.86    None  None   None       |
|    Sol.    : 438    0      5.26    92.21   40.30    None  None   None       |
|    Mac.    : 2385   0      0.00    92.17   12.56    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.221:  950   |   5:    46.106 -  55.327:  102        |
|      1:     9.221 -  18.442: 1183   |   6:    55.327 -  64.548:   52        |
|      2:    18.442 -  27.663:  243   |   7:    64.548 -  73.769:   27        |
|      3:    27.663 -  36.884:  136   |   8:    73.769 -  82.990:    8        |
|      4:    36.884 -  46.106:  112   |   9:    82.990 -  92.211:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1151 r_free = 0.1618             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1151 r_free = 0.1618             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1151   r_free= 0.1618   ksol= 0.32   Bsol= 58.75   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-1.02,-1.38,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.175759                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1618   ksol= 0.32   Bsol= 58.75   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-1.13,-1.29,-0.00,-0.00,-0.00); trace/3= -1.46                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.175793                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.111314              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 149.950  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.156504              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.213   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1150      final r-factor (work) = 0.1154          |
| start r-factor (free) = 0.1618      final r-factor (free) = 0.1616          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5346 = 2.11 * 0.50 * 5.1744 + 1.00 * 0.0722                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5283 = 2.11 * 0.50 * 5.1776 + 1.00 * 0.0625                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1154      final r-factor (work) = 0.1139          |
| start r-factor (free) = 0.1616      final r-factor (free) = 0.1627          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.2204 = 2.16 * 1.00 * 5.1776 + 1.00 * 0.0548                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.1593 = 2.16 * 1.00 * 5.1697 + 1.00 * 0.0108                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.055)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.06  17.03    None  None   None       |
|    all(noH): 2823   0      0.00    107.06  17.03    None  None   None       |
|    Sol.    : 438    0      5.24    97.08   41.69    None  None   None       |
|    Mac.    : 2385   0      0.00    107.06  12.51    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:     0.002 -  10.709: 1312   |   5:    53.534 -  64.240:   87        |
|      1:    10.709 -  21.415:  937   |   6:    64.240 -  74.946:   35        |
|      2:    21.415 -  32.121:  185   |   7:    74.946 -  85.652:   15        |
|      3:    32.121 -  42.827:  123   |   8:    85.652 -  96.358:    5        |
|      4:    42.827 -  53.534:  119   |   9:    96.358 - 107.065:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1139 r_free = 0.1627             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1139 r_free = 0.1627             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1627   ksol= 0.32   Bsol= 58.75   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-1.13,-1.29,-0.00,-0.00,-0.00); trace/3= -1.46                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.175057                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0399 -  4.7060 0.99   1433  161 0.0958 0.1244      5.3502       5.509|
|  2:  4.7060 -  3.7544 0.99   1374  147 0.0827 0.1066      5.4005      5.6025|
|  3:  3.7544 -  3.2855 0.99   1357  156 0.1058 0.1563      5.4617      5.8711|
|  4:  3.2855 -  2.9876 0.99   1339  146 0.1289 0.1577      5.4872      5.6245|
|  5:  2.9876 -  2.7749 0.98   1336  149 0.1401 0.1940      5.3779      5.5745|
|  6:  2.7749 -  2.6122 0.99   1333  147 0.1294 0.1951      5.2563      5.4779|
|  7:  2.6122 -  2.4820 0.98   1323  149 0.1277 0.1794      5.1938      5.4187|
|  8:  2.4820 -  2.3744 0.99   1305  142 0.1221 0.1712      5.0977      5.3117|
|  9:  2.3744 -  2.2833 0.99   1333  153 0.1187 0.1912      5.0562      5.3415|
| 10:  2.2833 -  2.2048 0.98   1304  143 0.1130 0.1786      4.9916      5.2891|
| 11:  2.2048 -  2.1360 0.97   1293  138 0.1169 0.1840      4.9437      5.2382|
| 12:  2.1360 -  2.0751 0.99   1308  153 0.1134 0.1793      4.8893      5.1515|
| 13:  2.0751 -  2.0206 0.92   1230  136 0.1177 0.1814      4.8232      5.0562|
| 14:  2.0206 -  1.9714 0.27    362   39 0.1150 0.1843      4.7134      5.0352|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0399 -  4.7060  1433   161  0.94   8.63   0.97     0.95       6643.20|
|  2:  4.7060 -  3.7544  1374   147  0.95   7.63   1.01     0.99       8284.63|
|  3:  3.7544 -  3.2855  1357   156  0.93  11.33   1.02     1.02      10110.79|
|  4:  3.2855 -  2.9876  1339   146  0.91  14.85   1.00     0.98      11177.61|
|  5:  2.9876 -  2.7749  1336   149  0.88  17.61   0.99     0.97       9442.03|
|  6:  2.7749 -  2.6122  1333   147  0.89  16.99   0.98     0.96       7819.22|
|  7:  2.6122 -  2.4820  1323   149  0.90  16.24   0.98     0.96       6740.98|
|  8:  2.4820 -  2.3744  1305   142  0.90  16.61   0.99     0.95       5859.07|
|  9:  2.3744 -  2.2833  1333   153  0.89  16.94   0.98     0.93       5369.15|
| 10:  2.2833 -  2.2048  1304   143  0.90  15.72   0.98     0.94       4797.81|
| 11:  2.2048 -  2.1360  1293   138  0.89  17.14   0.98     0.94       4528.73|
| 12:  2.1360 -  2.0751  1308   153  0.91  15.90   0.98     0.96       4121.04|
| 13:  2.0751 -  2.0206  1230   136  0.89  17.53   0.98     0.97       3717.43|
| 14:  2.0206 -  1.9714   362    39  0.88  17.52   0.96     0.92       2992.75|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     2992.75 max =        11177.61 mean =      6778.62|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.83|
|phase err.(test): min =        0.00 max =           89.92 mean =        14.21|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1627   ksol= 0.32   Bsol= 60.84   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.76,-1.03,-1.12,-0.00,-0.00,-0.00); trace/3= -1.30                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.175112                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1627   ksol= 0.32   Bsol= 60.84   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.76,-1.03,-1.12,-0.00,-0.00,-0.00); trace/3= -1.30                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.175112                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0399 -  4.7060 0.99   1433  161 0.0959 0.1244      5.3499      5.5112|
|  2:  4.7060 -  3.7544 0.99   1374  147 0.0829 0.1068      5.4028      5.6053|
|  3:  3.7544 -  3.2855 0.99   1357  156 0.1059 0.1564       5.463      5.8718|
|  4:  3.2855 -  2.9876 0.99   1339  146 0.1288 0.1578       5.487      5.6246|
|  5:  2.9876 -  2.7749 0.98   1336  149 0.1399 0.1938       5.377      5.5736|
|  6:  2.7749 -  2.6122 0.99   1333  147 0.1293 0.1948      5.2556      5.4769|
|  7:  2.6122 -  2.4820 0.98   1323  149 0.1277 0.1795      5.1934      5.4185|
|  8:  2.4820 -  2.3744 0.99   1305  142 0.1221 0.1711      5.0975      5.3109|
|  9:  2.3744 -  2.2833 0.99   1333  153 0.1186 0.1915      5.0561      5.3424|
| 10:  2.2833 -  2.2048 0.98   1304  143 0.1130 0.1785      4.9917      5.2884|
| 11:  2.2048 -  2.1360 0.97   1293  138 0.1168 0.1839      4.9435       5.238|
| 12:  2.1360 -  2.0751 0.99   1308  153 0.1134 0.1795      4.8893       5.152|
| 13:  2.0751 -  2.0206 0.92   1230  136 0.1177 0.1814       4.823       5.055|
| 14:  2.0206 -  1.9714 0.27    362   39 0.1150 0.1840      4.7134      5.0351|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0399 -  4.7060  1433   161  0.94   8.64   0.97     0.95       6650.94|
|  2:  4.7060 -  3.7544  1374   147  0.95   7.64   1.01     0.99       8320.81|
|  3:  3.7544 -  3.2855  1357   156  0.93  11.38   1.02     1.02      10161.49|
|  4:  3.2855 -  2.9876  1339   146  0.91  14.86   1.00     0.98      11181.18|
|  5:  2.9876 -  2.7749  1336   149  0.88  17.60   1.00     0.97       9429.20|
|  6:  2.7749 -  2.6122  1333   147  0.89  16.97   0.99     0.96       7804.14|
|  7:  2.6122 -  2.4820  1323   149  0.90  16.23   0.99     0.97       6732.90|
|  8:  2.4820 -  2.3744  1305   142  0.90  16.61   0.99     0.96       5856.92|
|  9:  2.3744 -  2.2833  1333   153  0.89  16.94   0.99     0.94       5370.76|
| 10:  2.2833 -  2.2048  1304   143  0.90  15.72   0.99     0.95       4797.07|
| 11:  2.2048 -  2.1360  1293   138  0.89  17.14   0.99     0.95       4526.40|
| 12:  2.1360 -  2.0751  1308   153  0.91  15.89   0.99     0.97       4120.49|
| 13:  2.0751 -  2.0206  1230   136  0.89  17.53   0.99     0.98       3715.19|
| 14:  2.0206 -  1.9714   362    39  0.88  17.51   0.97     0.93       2989.04|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2989.04 max =        11181.18 mean =      6782.99|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.83|
|phase err.(test): min =        0.00 max =           89.91 mean =        14.21|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.055)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    107.07  17.04    None  None   None       |
|    all(noH): 2823   0      0.01    107.07  17.04    None  None   None       |
|    Sol.    : 438    0      5.25    97.09   41.69    None  None   None       |
|    Mac.    : 2385   0      0.01    107.07  12.51    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:     0.005 -  10.711: 1312   |   5:    53.536 -  64.243:   87        |
|      1:    10.711 -  21.418:  937   |   6:    64.243 -  74.949:   35        |
|      2:    21.418 -  32.124:  185   |   7:    74.949 -  85.655:   15        |
|      3:    32.124 -  42.830:  123   |   8:    85.655 -  96.361:    5        |
|      4:    42.830 -  53.536:  119   |   9:    96.361 - 107.068:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 310         
Filter by distance & map next to the model:
   mapped sites are within: 0.650 - 4.238
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 306 from: 310
   mapped sites are within: 0.710 - 4.238

peak=    5.811 closest distance to " O   HOH Z 111 " =    2.286
peak=    5.747 closest distance to " CB  GLN A 223 " =    1.445
peak=    5.533 closest distance to " CB  SER A  63 " =    1.264
peak=    4.856 closest distance to " O   PRO A 198 " =    1.515
peak=    4.852 closest distance to " CA  TYR A  30 " =    0.939
peak=    4.824 closest distance to " CG  PRO A 213 " =    1.241
peak=    4.765 closest distance to " O   HOH Z 232 " =    2.315
peak=    4.708 closest distance to " O   HOH Z 134 " =    1.680
peak=    4.702 closest distance to " O   HOH Z  15 " =    2.126
peak=    4.652 closest distance to " CB  GLN A 183 " =    1.304
peak=    4.619 closest distance to " O   HOH Z 126 " =    1.591
peak=    4.614 closest distance to " CB  ARG A 275 " =    0.881
peak=    4.570 closest distance to " CG  PRO A 198 " =    1.242
peak=    4.559 closest distance to " CB  GLU A 128 " =    1.193
peak=    4.452 closest distance to " O   HOH Z 234 " =    3.861
peak=    4.451 closest distance to " O   HOH Z 403 " =    1.710
peak=    4.364 closest distance to " O   HOH Z  20 " =    1.783
peak=    4.353 closest distance to " O   HOH Z  80 " =    1.740
peak=    4.348 closest distance to " O   HOH Z  97 " =    1.964
peak=    4.346 closest distance to " CA  ALA A  21 " =    1.381
peak=    4.344 closest distance to " O   HOH Z 132 " =    2.060
peak=    4.319 closest distance to " CB  ARG A  79 " =    1.398
peak=    4.298 closest distance to " OD1 ASN A  69 " =    2.574
peak=    4.283 closest distance to " CB  ARG A 190 " =    1.701
peak=    4.273 closest distance to " CG  PRO A 280 " =    0.710
peak=    4.247 closest distance to " O   HOH Z 154 " =    2.508
peak=    4.245 closest distance to " CB  SER A   3 " =    1.339
peak=    4.235 closest distance to " CG  PRO A  90 " =    1.127
peak=    4.229 closest distance to " O   HOH Z 108 " =    2.568
peak=    4.223 closest distance to " CG1 ILE A  33 " =    1.208
peak=    4.219 closest distance to " O   HOH Z 163 " =    1.615
peak=    4.212 closest distance to " CB  GLU A 152 " =    1.101
peak=    4.210 closest distance to " CB  GLU A 277 " =    3.672
peak=    4.194 closest distance to " O   HOH Z 374 " =    2.723
peak=    4.193 closest distance to " CB  LEU A 228 " =    1.177
peak=    4.190 closest distance to " O   HOH Z  43 " =    2.321
peak=    4.177 closest distance to " O   HOH Z 298 " =    1.926
peak=    4.175 closest distance to " O   HOH Z  68 " =    2.034
peak=    4.139 closest distance to " O   HOH Z 193 " =    1.824
peak=    4.139 closest distance to " CG  PRO A 243 " =    1.193
peak=    4.136 closest distance to " O   HOH Z 209 " =    2.312
peak=    4.128 closest distance to " O   HOH Z 411 " =    3.583
peak=    4.127 closest distance to " O   HOH Z 189 " =    1.994
peak=    4.111 closest distance to " CB  TYR A 169 " =    0.862
peak=    4.106 closest distance to " NE2 GLN A  11 " =    1.005
peak=    4.083 closest distance to " C   ILE A 106 " =    1.869
peak=    4.082 closest distance to " O   HOH Z  40 " =    1.955
peak=    4.074 closest distance to " CG  ARG A  66 " =    2.591
peak=    4.072 closest distance to " NH2 ARG A 156 " =    1.225
peak=    4.044 closest distance to " O   HOH Z 132 " =    1.109
peak=    4.035 closest distance to " CA  ARG A 195 " =    1.166
peak=    4.032 closest distance to " CG2 THR A 221 " =    1.083
peak=    3.997 closest distance to " O   HOH Z 352 " =    1.863
peak=    3.993 closest distance to " CB  ASN A 148 " =    1.308
peak=    3.992 closest distance to " O   HOH Z  78 " =    2.065
peak=    3.991 closest distance to " NZ  LYS A 117 " =    3.157
peak=    3.984 closest distance to " O   HOH Z 368 " =    2.108
peak=    3.963 closest distance to " NH2BARG A 145 " =    2.080
peak=    3.958 closest distance to " O   HOH Z 132 " =    2.693
peak=    3.948 closest distance to " CD1 LEU A 300 " =    1.162
peak=    3.946 closest distance to " O   HOH Z 196 " =    1.150
peak=    3.946 closest distance to " O   HOH Z 389 " =    1.934
peak=    3.936 closest distance to " O   HOH Z 124 " =    1.329
peak=    3.925 closest distance to " O   HOH Z 402 " =    1.520
peak=    3.923 closest distance to " O   SER A  87 " =    2.282
peak=    3.910 closest distance to " O   HOH Z 369 " =    2.449
peak=    3.910 closest distance to " CG2 VAL A  78 " =    0.961
peak=    3.902 closest distance to " CB  TRP A 179 " =    1.319
peak=    3.892 closest distance to " O   HOH Z 142 " =    1.531
peak=    3.868 closest distance to " CB  VAL A 202 " =    1.580
peak=    3.867 closest distance to " NH2AARG A 145 " =    2.281
peak=    3.867 closest distance to " OD2 ASP A 286 " =    2.906
peak=    3.864 closest distance to " CA  ASN A 176 " =    1.579
peak=    3.850 closest distance to " O   HOH Z 284 " =    2.846
peak=    3.847 closest distance to " O   HOH Z  21 " =    1.730
peak=    3.842 closest distance to " CA  ALA A  51 " =    0.998
peak=    3.842 closest distance to " CD  LYS A 166 " =    1.397
peak=    3.824 closest distance to " CD  ARG A 269 " =    0.991
peak=    3.818 closest distance to " O   HOH Z 154 " =    1.299
peak=    3.812 closest distance to " O   HOH Z 247 " =    1.403
peak=    3.809 closest distance to " CA  ARG A  36 " =    1.161
peak=    3.807 closest distance to " CZ  PHE A 218 " =    1.081
peak=    3.803 closest distance to " O   HOH Z 357 " =    2.076
peak=    3.795 closest distance to " O   HOH Z 279 " =    2.220
peak=    3.792 closest distance to " CG2BVAL A  41 " =    0.890
peak=    3.785 closest distance to " O   HOH Z 426 " =    1.546
peak=    3.784 closest distance to " O   HOH Z 265 " =    2.273
peak=    3.767 closest distance to " O   HOH Z  88 " =    3.478
peak=    3.764 closest distance to " CA  ASP A 191 " =    0.785
peak=    3.752 closest distance to " CA  ALA A 160 " =    0.832
peak=    3.742 closest distance to " OG BSER A 164 " =    2.348
peak=    3.742 closest distance to " O   HOH Z 406 " =    1.620
peak=    3.736 closest distance to " O   HOH Z 423 " =    1.924
peak=    3.732 closest distance to " N   ASN A  39 " =    1.293
peak=    3.730 closest distance to " CD  ARG A 159 " =    0.835
peak=    3.727 closest distance to " O   ALA A 165 " =    1.378
peak=    3.709 closest distance to " O   HOH Z  61 " =    1.502
peak=    3.704 closest distance to " O   HOH Z  54 " =    1.746
peak=    3.698 closest distance to " CB  TRP A 266 " =    0.934
peak=    3.695 closest distance to " O   HOH Z  44 " =    1.917
peak=    3.693 closest distance to " O   THR A 251 " =    1.253
peak=    3.691 closest distance to " O   HOH Z 418 " =    1.488
peak=    3.689 closest distance to " CB  SER A 141 " =    1.042
peak=    3.689 closest distance to " O   HOH Z 245 " =    1.344
peak=    3.688 closest distance to " O   HOH Z 250 " =    1.467
peak=    3.684 closest distance to " CG2 VAL A 197 " =    1.134
peak=    3.683 closest distance to " O   HOH Z 316 " =    2.993
peak=    3.681 closest distance to " O   HOH Z 272 " =    1.925
peak=    3.679 closest distance to " OG  SER A  62 " =    2.970
peak=    3.677 closest distance to " O   HOH Z 345 " =    3.037
peak=    3.670 closest distance to " O   HOH Z 133 " =    1.682
peak=    3.667 closest distance to " O   HOH Z 345 " =    1.687
peak=    3.664 closest distance to " O   HOH Z 383 " =    2.104
peak=    3.664 closest distance to " O   HOH Z 344 " =    3.136
peak=    3.663 closest distance to " O   HOH Z 236 " =    1.987
peak=    3.647 closest distance to " CD2 LEU A 255 " =    1.316
peak=    3.646 closest distance to " CB  SER A  62 " =    0.790
peak=    3.644 closest distance to " O   HOH Z 145 " =    2.236
peak=    3.643 closest distance to " C   SER A  32 " =    1.071
peak=    3.641 closest distance to " O   HOH Z 174 " =    2.491
peak=    3.639 closest distance to " O   HOH Z 261 " =    1.943
peak=    3.635 closest distance to " O   HOH Z 128 " =    2.205
peak=    3.634 closest distance to " NE2 HIS A 115 " =    0.998
peak=    3.629 closest distance to " CZ  PHE A 192 " =    0.924
peak=    3.628 closest distance to " CA  THR A 221 " =    0.934
peak=    3.627 closest distance to " CB  TYR A 116 " =    1.118
peak=    3.621 closest distance to " CE  LYS A  76 " =    0.822
peak=    3.615 closest distance to " O   HOH Z 214 " =    2.480
peak=    3.612 closest distance to " O   HOH Z 118 " =    1.553
peak=    3.605 closest distance to " O   HOH Z  19 " =    1.860
peak=    3.594 closest distance to " O   HOH Z 158 " =    2.855
peak=    3.569 closest distance to " CB  ASP A 140 " =    0.797
peak=    3.568 closest distance to " O   HOH Z 387 " =    2.520
peak=    3.566 closest distance to " O   HOH Z  47 " =    1.242
peak=    3.562 closest distance to " O   HOH Z 371 " =    3.319
peak=    3.554 closest distance to " CA  ASP A 124 " =    0.755
peak=    3.553 closest distance to " SD AMET A  47 " =    1.035
peak=    3.545 closest distance to " CA  GLU A 152 " =    0.860
peak=    3.537 closest distance to " CB  ALA A 291 " =    1.275
peak=    3.530 closest distance to " CB  ARG A 139 " =    0.758
peak=    3.529 closest distance to " CZ  PHE A  38 " =    1.367
peak=    3.524 closest distance to " O   HOH Z 147 " =    1.792
peak=    3.522 closest distance to " CG2 VAL A 257 " =    0.857
peak=    3.521 closest distance to " CD1 LEU A  96 " =    0.757
peak=    3.519 closest distance to " CG  GLN A  58 " =    2.545
peak=    3.519 closest distance to " O   TRP A 274 " =    1.895
peak=    3.518 closest distance to " CG1 VAL A 153 " =    1.058
peak=    3.516 closest distance to " O   HOH Z 368 " =    3.590
peak=    3.510 closest distance to " O   HOH Z 126 " =    1.988
peak=    3.505 closest distance to " O   HOH Z 197 " =    2.124
peak=    3.504 closest distance to " O   HOH Z 250 " =    1.779
peak=    3.502 closest distance to " O   HOH Z  49 " =    1.888
peak=    3.499 closest distance to " CB  ALA A 100 " =    1.320
peak=    3.490 closest distance to " OE1 GLN A  11 " =    1.992
peak=    3.483 closest distance to " O   HOH Z  63 " =    1.954
peak=    3.479 closest distance to " CG  MET A 185 " =    1.188
peak=    3.477 closest distance to " CB  VAL A 265 " =    1.147
peak=    3.474 closest distance to " CD2 LEU A 297 " =    0.906
peak=    3.471 closest distance to " O   ASN A  74 " =    1.517
peak=    3.468 closest distance to " O   HOH Z 207 " =    2.283
peak=    3.468 closest distance to " NZ  LYS A 166 " =    3.043
peak=    3.464 closest distance to " CD1 ILE A 106 " =    0.883
peak=    3.462 closest distance to " O   HOH Z 128 " =    2.193
peak=    3.452 closest distance to " ND1 HIS A  81 " =    1.570
peak=    3.452 closest distance to " O   HOH Z   6 " =    2.073
peak=    3.451 closest distance to " O   HOH Z 425 " =    1.294
peak=    3.447 closest distance to " O   HOH Z 427 " =    2.946
peak=    3.446 closest distance to " O   VAL A  72 " =    3.267
peak=    3.441 closest distance to " CG1BVAL A  72 " =    1.683
peak=    3.441 closest distance to " C   GLY A  80 " =    1.118
peak=    3.438 closest distance to " O   HOH Z 433 " =    1.463
peak=    3.435 closest distance to " ND2 ASN A 187 " =    1.483
peak=    3.431 closest distance to " O   HOH Z  30 " =    1.619
peak=    3.431 closest distance to " O   HOH Z 419 " =    2.911
peak=    3.430 closest distance to " CA  ASP A 162 " =    1.204
peak=    3.424 closest distance to " CA  GLN A 223 " =    0.913
peak=    3.422 closest distance to " O   HOH Z 303 " =    2.125
peak=    3.421 closest distance to " CG  ARG A 219 " =    1.265
peak=    3.421 closest distance to " OG1 THR A 294 " =    2.452
peak=    3.419 closest distance to " CB  ASN A  39 " =    0.822
peak=    3.410 closest distance to " O   HOH Z 214 " =    1.165
peak=    3.406 closest distance to " O   HOH Z 358 " =    2.029
peak=    3.405 closest distance to " O   HOH Z 173 " =    2.158
peak=    3.400 closest distance to " CA  ASP A 140 " =    1.136
peak=    3.391 closest distance to " CB  SER A 216 " =    0.823
peak=    3.391 closest distance to " CD2 TRP A 179 " =    1.318
peak=    3.390 closest distance to " O   HOH Z 391 " =    3.023
peak=    3.388 closest distance to " O   HOH Z  48 " =    1.449
peak=    3.382 closest distance to " CB  ASN A 285 " =    0.905
peak=    3.379 closest distance to " CB  PRO A  54 " =    1.052
peak=    3.370 closest distance to " O   HOH Z 183 " =    1.539
peak=    3.369 closest distance to " ND2 ASN A 110 " =    1.605
peak=    3.367 closest distance to " O   ALA A 158 " =    1.222
peak=    3.364 closest distance to " O   HOH Z 313 " =    2.068
peak=    3.358 closest distance to " CG AARG A 275 " =    1.139
peak=    3.358 closest distance to " CD BLYS A 290 " =    0.962
peak=    3.355 closest distance to " CB  ALA A  71 " =    1.318
peak=    3.355 closest distance to " O   HOH Z 109 " =    2.382
peak=    3.354 closest distance to " O   HOH Z 227 " =    1.720
peak=    3.351 closest distance to " OD2 ASP A 298 " =    4.047
peak=    3.347 closest distance to " O   GLY A  57 " =    2.570
peak=    3.344 closest distance to " CA  ALA A 248 " =    1.194
peak=    3.337 closest distance to " O   HOH Z 386 " =    2.299
peak=    3.336 closest distance to " O   HOH Z 327 " =    2.232
peak=    3.334 closest distance to " CE1 TYR A 186 " =    1.277
peak=    3.334 closest distance to " O   HOH Z 365 " =    2.944
peak=    3.334 closest distance to " O   HOH Z 346 " =    1.604
peak=    3.320 closest distance to " CB  PRO A 198 " =    1.102
peak=    3.318 closest distance to " O   ASP A 124 " =    1.431
peak=    3.314 closest distance to " CA  VAL A 125 " =    1.266
peak=    3.312 closest distance to " CA  MET A  40 " =    1.065
peak=    3.311 closest distance to " CA  VAL A  41 " =    0.898
peak=    3.308 closest distance to " O   HOH Z 416 " =    2.938
peak=    3.306 closest distance to " CA  THR A 221 " =    1.305
peak=    3.305 closest distance to " O   HOH Z 437 " =    1.376
peak=    3.304 closest distance to " CG2 ILE A 120 " =    1.102
peak=    3.297 closest distance to " CB  MET A  40 " =    0.806
peak=    3.292 closest distance to " CG1 ILE A 120 " =    1.023
peak=    3.292 closest distance to " O   HOH Z 227 " =    1.602
peak=    3.288 closest distance to " O   HOH Z 263 " =    2.218
peak=    3.288 closest distance to " O   HOH Z 394 " =    1.707
peak=    3.287 closest distance to " O   HOH Z 192 " =    1.712
peak=    3.287 closest distance to " O   GLN A 278 " =    1.415
peak=    3.282 closest distance to " CB  SER A 212 " =    1.071
peak=    3.279 closest distance to " CB  TYR A 169 " =    0.839
peak=    3.278 closest distance to " N   CYS A 260 " =    0.806
peak=    3.273 closest distance to " O   HOH Z 130 " =    2.280
peak=    3.271 closest distance to " O   HOH Z 421 " =    2.059
peak=    3.270 closest distance to " CE  LYS A 119 " =    1.009
peak=    3.266 closest distance to " O   HOH Z 102 " =    1.221
peak=    3.266 closest distance to " CD1 TRP A 266 " =    1.241
peak=    3.261 closest distance to " O   HOH Z 336 " =    1.587
peak=    3.260 closest distance to " CB  PHE A  16 " =    1.008
peak=    3.260 closest distance to " O   HOH Z  97 " =    2.646
peak=    3.259 closest distance to " CA  ASN A 215 " =    1.132
peak=    3.257 closest distance to " CA  LEU A  83 " =    1.427
peak=    3.253 closest distance to " NZ  LYS A 117 " =    1.670
peak=    3.251 closest distance to " O   HOH Z 327 " =    1.679
peak=    3.248 closest distance to " O   SER A  26 " =    1.713
peak=    3.246 closest distance to " CB  MET A  47 " =    0.979
peak=    3.245 closest distance to " CA  ALA A 295 " =    1.128
peak=    3.245 closest distance to " O   HOH Z   1 " =    2.674
peak=    3.243 closest distance to " CG2 THR A 220 " =    0.783
peak=    3.239 closest distance to " CB  SER A 273 " =    0.792
peak=    3.239 closest distance to " O   HOH Z 417 " =    3.207
peak=    3.238 closest distance to " O   HOH Z 423 " =    3.389
peak=    3.236 closest distance to " OG BSER A 258 " =    3.441
peak=    3.234 closest distance to " CA  GLY A 196 " =    1.076
peak=    3.233 closest distance to " O   HOH Z 155 " =    3.065
peak=    3.228 closest distance to " CA  TYR A 116 " =    1.344
peak=    3.227 closest distance to " O   ALA A 242 " =    1.096
peak=    3.225 closest distance to " CB  ASN A 187 " =    1.132
peak=    3.223 closest distance to " O   HOH Z  66 " =    2.203
peak=    3.222 closest distance to " CG BARG A 102 " =    1.928
peak=    3.214 closest distance to " O   HOH Z 419 " =    1.609
peak=    3.209 closest distance to " CD  GLU A 152 " =    0.830
peak=    3.208 closest distance to " O   HOH Z  90 " =    3.316
peak=    3.208 closest distance to " CB  ILE A 120 " =    1.302
peak=    3.207 closest distance to " O   HOH Z 409 " =    2.893
peak=    3.207 closest distance to " CB  MET A 105 " =    1.092
peak=    3.207 closest distance to " CA  ALA A 291 " =    0.901
peak=    3.207 closest distance to " O   HOH Z 281 " =    4.238
peak=    3.206 closest distance to " O   HOH Z  22 " =    2.552
peak=    3.206 closest distance to " CA  SER A  87 " =    0.975
peak=    3.206 closest distance to " O   HOH Z 425 " =    2.168
peak=    3.205 closest distance to " O   HOH Z 116 " =    1.821
peak=    3.204 closest distance to " O   HOH Z 258 " =    2.167
peak=    3.203 closest distance to " O   HOH Z 291 " =    1.519
peak=    3.200 closest distance to " O   HOH Z 393 " =    3.521
peak=    3.192 closest distance to " OD1 ASP A 238 " =    0.824
peak=    3.192 closest distance to " CG2 ILE A 106 " =    1.016
peak=    3.189 closest distance to " O   HOH Z  48 " =    1.571
peak=    3.186 closest distance to " C   PHE A  59 " =    0.800
peak=    3.185 closest distance to " CG2AVAL A 121 " =    2.219
peak=    3.184 closest distance to " CB  LEU A  83 " =    0.827
peak=    3.182 closest distance to " O   HOH Z 438 " =    2.249
peak=    3.177 closest distance to " CA  GLU A  46 " =    0.724
peak=    3.167 closest distance to " O   HOH Z 334 " =    1.382
peak=    3.166 closest distance to " CB  TYR A  30 " =    1.474
peak=    3.164 closest distance to " O   HOH Z 299 " =    2.386
peak=    3.152 closest distance to " NH1AARG A 145 " =    1.059
peak=    3.151 closest distance to " CA  LYS A 117 " =    1.233
peak=    3.149 closest distance to " O   HOH Z  88 " =    2.856
peak=    3.142 closest distance to " NH1 ARG A  14 " =    1.309
peak=    3.142 closest distance to " O   HOH Z 162 " =    1.592
peak=    3.141 closest distance to " CB  SER A  28 " =    0.996
peak=    3.140 closest distance to " CG  GLN A  89 " =    1.417
peak=    3.134 closest distance to " O   HOH Z 148 " =    3.237
peak=    3.131 closest distance to " CA  ALA A  84 " =    1.307
peak=    3.129 closest distance to " CB  ASN A 142 " =    1.194
peak=    3.126 closest distance to " OG  SER A 245 " =    1.618
peak=    3.114 closest distance to " CE1 PHE A 225 " =    0.887
peak=    3.114 closest distance to " CB  ALA A 242 " =    0.984
peak=    3.113 closest distance to " CB  ASN A 127 " =    0.975
peak=    3.112 closest distance to " O   HOH Z 261 " =    1.606
peak=    3.106 closest distance to " CD  LYS A 119 " =    1.370
peak=    3.093 closest distance to " CA  GLU A 152 " =    1.233
peak=    3.090 closest distance to " O   HOH Z 353 " =    2.811
peak=    3.082 closest distance to " O   HOH Z  85 " =    1.998
peak=    3.061 closest distance to " O   HOH Z 197 " =    2.407
peak=    3.054 closest distance to " CA  THR A 264 " =    0.903
peak=    3.050 closest distance to " O   HOH Z 329 " =    3.649
peak=    3.031 closest distance to " CB  PRO A  54 " =    1.168
peak=    3.022 closest distance to " CA  ALA A 158 " =    1.157
peak=    3.019 closest distance to " O   HOH Z 359 " =    1.416
peak=    3.012 closest distance to " O   HOH Z 327 " =    1.780

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 219         
Filter by distance & map next to the model:
   mapped sites are within: 0.823 - 5.950
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 219 from: 219
   mapped sites are within: 0.823 - 5.950

peak=   -4.600 closest distance to " O   HOH Z 266 " =    4.481
peak=   -4.384 closest distance to " CD  ARG A 156 " =    2.023
peak=   -4.294 closest distance to " OXT GLY A 302 " =    2.893
peak=   -4.216 closest distance to " O   HOH Z 210 " =    0.823
peak=   -4.166 closest distance to " CD1 LEU A 101 " =    2.560
peak=   -4.128 closest distance to " O   HOH Z   5 " =    1.593
peak=   -4.089 closest distance to " O   PRO A 163 " =    2.152
peak=   -4.086 closest distance to " C   HIS A 108 " =    1.082
peak=   -4.052 closest distance to " O   HOH Z  13 " =    1.700
peak=   -4.046 closest distance to " N   ALA A  43 " =    2.559
peak=   -4.009 closest distance to " O   HOH Z 292 " =    4.488
peak=   -3.990 closest distance to " O   VAL A  67 " =    2.769
peak=   -3.949 closest distance to " O   HOH Z  52 " =    1.632
peak=   -3.934 closest distance to " O   HOH Z 407 " =    3.621
peak=   -3.923 closest distance to " O   HOH Z 283 " =    2.049
peak=   -3.921 closest distance to " OG  SER A  97 " =    2.151
peak=   -3.897 closest distance to " CA  SER A 276 " =    1.463
peak=   -3.893 closest distance to " O   HOH Z 165 " =    2.040
peak=   -3.891 closest distance to " O   PRO A 198 " =    1.343
peak=   -3.885 closest distance to " CE2 TYR A  30 " =    2.656
peak=   -3.843 closest distance to " CD2 LEU A 237 " =    2.711
peak=   -3.837 closest distance to " OE1 GLN A 223 " =    1.962
peak=   -3.834 closest distance to " NH2 ARG A  66 " =    1.626
peak=   -3.820 closest distance to " CB  ALA A 291 " =    2.473
peak=   -3.810 closest distance to " O   HOH Z 166 " =    1.890
peak=   -3.810 closest distance to " CA  TYR A  68 " =    2.695
peak=   -3.767 closest distance to " CA  ASP A 298 " =    1.071
peak=   -3.764 closest distance to " C   ASN A 285 " =    2.463
peak=   -3.754 closest distance to " CD2 LEU A 300 " =    2.929
peak=   -3.749 closest distance to " O   ALA A 256 " =    1.600
peak=   -3.734 closest distance to " O   HOH Z 377 " =    2.035
peak=   -3.733 closest distance to " O   HOH Z 353 " =    2.243
peak=   -3.729 closest distance to " OG  SER A  62 " =    1.523
peak=   -3.716 closest distance to " CG  ARG A  66 " =    2.473
peak=   -3.716 closest distance to " O   HOH Z  43 " =    1.617
peak=   -3.708 closest distance to " OG ASER A 134 " =    1.238
peak=   -3.701 closest distance to " CH2 TRP A 179 " =    1.200
peak=   -3.700 closest distance to " O   SER A 210 " =    1.966
peak=   -3.694 closest distance to " CG  GLU A  53 " =    1.422
peak=   -3.686 closest distance to " CD  LYS A 289 " =    2.447
peak=   -3.682 closest distance to " CB  LEU A 167 " =    2.191
peak=   -3.672 closest distance to " ND2 ASN A  45 " =    0.998
peak=   -3.668 closest distance to " O   HOH Z 372 " =    2.518
peak=   -3.664 closest distance to " CD1 LEU A 228 " =    2.377
peak=   -3.662 closest distance to " ND2 ASN A 187 " =    1.643
peak=   -3.659 closest distance to " OD1 ASN A 148 " =    1.605
peak=   -3.652 closest distance to " O   HOH Z 166 " =    1.780
peak=   -3.650 closest distance to " ND2 ASN A  45 " =    1.326
peak=   -3.643 closest distance to " CB  PHE A 208 " =    2.297
peak=   -3.633 closest distance to " OH  TYR A 169 " =    1.031
peak=   -3.609 closest distance to " CG  ASP A 231 " =    0.885
peak=   -3.606 closest distance to " OD1 ASP A 191 " =    1.720
peak=   -3.603 closest distance to " CG  ASP A 132 " =    2.384
peak=   -3.592 closest distance to " CB  ALA A 291 " =    2.372
peak=   -3.589 closest distance to " NH2 ARG A  66 " =    5.489
peak=   -3.582 closest distance to " SG  CYS A 254 " =    3.444
peak=   -3.577 closest distance to " CD  ARG A 139 " =    1.651
peak=   -3.563 closest distance to " O   HOH Z 196 " =    2.415
peak=   -3.557 closest distance to " O   HOH Z  93 " =    1.560
peak=   -3.550 closest distance to " C   SER A 206 " =    1.558
peak=   -3.549 closest distance to " CE3 TRP A 150 " =    2.268
peak=   -3.548 closest distance to " CD  GLN A 223 " =    1.427
peak=   -3.546 closest distance to " CG1 VAL A 112 " =    2.599
peak=   -3.542 closest distance to " CB  ASN A  39 " =    2.240
peak=   -3.540 closest distance to " O   HOH Z  11 " =    1.944
peak=   -3.538 closest distance to " O   HOH Z 198 " =    2.205
peak=   -3.531 closest distance to " N   MET A 188 " =    1.911
peak=   -3.531 closest distance to " O   HOH Z 234 " =    4.297
peak=   -3.526 closest distance to " O   HOH Z  17 " =    1.391
peak=   -3.516 closest distance to " ND2 ASN A  60 " =    1.615
peak=   -3.515 closest distance to " CD1 PHE A  59 " =    1.864
peak=   -3.509 closest distance to " OD2 ASP A 171 " =    1.853
peak=   -3.495 closest distance to " O   GLY A 196 " =    1.089
peak=   -3.495 closest distance to " CD2 PHE A  59 " =    2.453
peak=   -3.492 closest distance to " O   ALA A   7 " =    1.541
peak=   -3.492 closest distance to " N   GLN A  58 " =    1.666
peak=   -3.491 closest distance to " CB  PRO A 243 " =    2.674
peak=   -3.489 closest distance to " CB  ALA A 161 " =    2.670
peak=   -3.489 closest distance to " OG BSER A 210 " =    2.228
peak=   -3.487 closest distance to " CG  PRO A 243 " =    1.734
peak=   -3.482 closest distance to " O   HOH Z 377 " =    1.281
peak=   -3.482 closest distance to " O   HOH Z 231 " =    2.261
peak=   -3.481 closest distance to " CA  GLY A 203 " =    2.241
peak=   -3.479 closest distance to " CB  CYS A 254 " =    2.470
peak=   -3.479 closest distance to " O   HOH Z  19 " =    2.248
peak=   -3.466 closest distance to " CD2 LEU A 167 " =    1.773
peak=   -3.462 closest distance to " O   HOH Z 118 " =    3.113
peak=   -3.457 closest distance to " CG2 ILE A 263 " =    2.338
peak=   -3.456 closest distance to " CD  ARG A 195 " =    5.046
peak=   -3.447 closest distance to " CG  GLN A  58 " =    1.262
peak=   -3.443 closest distance to " OE1 GLN A  58 " =    1.170
peak=   -3.442 closest distance to " OD2 ASP A 171 " =    2.384
peak=   -3.441 closest distance to " O   HOH Z 399 " =    2.247
peak=   -3.438 closest distance to " O   HOH Z  40 " =    3.041
peak=   -3.423 closest distance to " O   VAL A  67 " =    2.779
peak=   -3.423 closest distance to " O   HOH Z 185 " =    2.335
peak=   -3.417 closest distance to " O   HOH Z  71 " =    1.696
peak=   -3.411 closest distance to " CG2 THR A 182 " =    2.383
peak=   -3.404 closest distance to " O   ALA A   1 " =    2.022
peak=   -3.402 closest distance to " O   HOH Z  97 " =    1.622
peak=   -3.400 closest distance to " O   ALA A 160 " =    1.463
peak=   -3.397 closest distance to " O   HOH Z   6 " =    1.654
peak=   -3.396 closest distance to " O   HOH Z 388 " =    2.072
peak=   -3.394 closest distance to " O   HOH Z  11 " =    1.847
peak=   -3.391 closest distance to " NH2AARG A 275 " =    5.411
peak=   -3.383 closest distance to " NH1 ARG A 195 " =    2.657
peak=   -3.382 closest distance to " CE  MET A 105 " =    2.052
peak=   -3.380 closest distance to " O   HOH Z 145 " =    1.742
peak=   -3.379 closest distance to " N   ALA A 226 " =    2.120
peak=   -3.375 closest distance to " O   TRP A  92 " =    1.909
peak=   -3.374 closest distance to " CE  MET A  93 " =    1.299
peak=   -3.373 closest distance to " CB  ALA A  43 " =    2.526
peak=   -3.370 closest distance to " CD1 TYR A 247 " =    2.082
peak=   -3.368 closest distance to " O   PHE A 218 " =    1.498
peak=   -3.365 closest distance to " CA  VAL A 197 " =    1.010
peak=   -3.363 closest distance to " OD2 ASP A  65 " =    1.748
peak=   -3.363 closest distance to " C   THR A 279 " =    1.130
peak=   -3.355 closest distance to " OD1 ASN A 187 " =    1.795
peak=   -3.353 closest distance to " O   HOH Z 103 " =    1.913
peak=   -3.353 closest distance to " CG1 VAL A 112 " =    2.663
peak=   -3.348 closest distance to " CG  LEU A  83 " =    2.007
peak=   -3.347 closest distance to " O   ALA A  34 " =    2.483
peak=   -3.344 closest distance to " CB  ALA A 248 " =    2.016
peak=   -3.343 closest distance to " O   HOH Z 275 " =    1.504
peak=   -3.340 closest distance to " O   HOH Z 290 " =    1.184
peak=   -3.335 closest distance to " ND2 ASN A 249 " =    2.178
peak=   -3.330 closest distance to " O   LEU A 167 " =    1.634
peak=   -3.328 closest distance to " ND2 ASN A  60 " =    1.740
peak=   -3.328 closest distance to " C   ALA A 158 " =    1.137
peak=   -3.324 closest distance to " O   HOH Z 311 " =    3.661
peak=   -3.324 closest distance to " O   HOH Z 252 " =    3.696
peak=   -3.317 closest distance to " OG  SER A  87 " =    1.446
peak=   -3.315 closest distance to " O   VAL A 189 " =    2.643
peak=   -3.307 closest distance to " CZ  PHE A  59 " =    1.911
peak=   -3.305 closest distance to " O   HOH Z  61 " =    1.558
peak=   -3.302 closest distance to " CE3 TRP A 274 " =    2.447
peak=   -3.296 closest distance to " NH2 ARG A  79 " =    1.965
peak=   -3.290 closest distance to " O   HOH Z 384 " =    2.340
peak=   -3.287 closest distance to " O   HOH Z  90 " =    1.946
peak=   -3.283 closest distance to " OG BSER A 134 " =    1.276
peak=   -3.282 closest distance to " O   HOH Z 396 " =    1.667
peak=   -3.282 closest distance to " O   GLY A 118 " =    2.312
peak=   -3.281 closest distance to " CB  ASP A 286 " =    2.242
peak=   -3.281 closest distance to " O   HOH Z  91 " =    1.950
peak=   -3.279 closest distance to " O   VAL A 125 " =    2.099
peak=   -3.278 closest distance to " CG  ASP A  50 " =    2.325
peak=   -3.275 closest distance to " O   HOH Z 150 " =    1.678
peak=   -3.270 closest distance to " CD2 TYR A 293 " =    1.974
peak=   -3.268 closest distance to " O   ALA A  10 " =    1.756
peak=   -3.262 closest distance to " CG  MET A 105 " =    0.878
peak=   -3.260 closest distance to " O   HOH Z 417 " =    2.746
peak=   -3.254 closest distance to " O   ASN A 301 " =    1.337
peak=   -3.253 closest distance to " O   HOH Z 252 " =    4.121
peak=   -3.248 closest distance to " CG2 VAL A 189 " =    2.212
peak=   -3.242 closest distance to " C   LEU A 143 " =    1.118
peak=   -3.239 closest distance to " CE1 TYR A 169 " =    2.340
peak=   -3.235 closest distance to " CA  GLY A  98 " =    2.183
peak=   -3.233 closest distance to " CZ  TYR A 169 " =    1.800
peak=   -3.232 closest distance to " CD  PRO A 198 " =    1.262
peak=   -3.230 closest distance to " CA  GLY A 241 " =    2.214
peak=   -3.229 closest distance to " O   HOH Z 414 " =    1.571
peak=   -3.227 closest distance to " O   HOH Z 111 " =    1.399
peak=   -3.224 closest distance to " O   HOH Z 430 " =    5.621
peak=   -3.223 closest distance to " N   ALA A 248 " =    1.790
peak=   -3.222 closest distance to " CB  TRP A  85 " =    2.400
peak=   -3.221 closest distance to " CG  LYS A 119 " =    2.969
peak=   -3.218 closest distance to " CE BMET A  47 " =    2.474
peak=   -3.213 closest distance to " ND2 ASN A  69 " =    1.469
peak=   -3.210 closest distance to " N   LEU A 281 " =    1.695
peak=   -3.209 closest distance to " O   HOH Z  38 " =    1.420
peak=   -3.205 closest distance to " OE2 GLU A   2 " =    1.586
peak=   -3.204 closest distance to " O   HOH Z 423 " =    2.377
peak=   -3.203 closest distance to " NE2 GLN A  88 " =    1.861
peak=   -3.201 closest distance to " O   HOH Z 231 " =    1.658
peak=   -3.196 closest distance to " CB  PRO A 163 " =    2.703
peak=   -3.192 closest distance to " SG ACYS A 201 " =    2.103
peak=   -3.188 closest distance to " CB  PHE A 192 " =    1.960
peak=   -3.188 closest distance to " NH2 ARG A 159 " =    2.339
peak=   -3.188 closest distance to " SG  CYS A 168 " =    1.065
peak=   -3.187 closest distance to " O   ASN A 187 " =    1.538
peak=   -3.185 closest distance to " OG BSER A 210 " =    1.272
peak=   -3.184 closest distance to " CB  TYR A  15 " =    2.291
peak=   -3.182 closest distance to " O   HOH Z 298 " =    2.875
peak=   -3.175 closest distance to " CD1 LEU A 167 " =    2.173
peak=   -3.175 closest distance to " O   SER A 135 " =    1.577
peak=   -3.173 closest distance to " O   GLY A 211 " =    1.506
peak=   -3.173 closest distance to " O   HOH Z 393 " =    1.771
peak=   -3.165 closest distance to " O   HOH Z 422 " =    1.588
peak=   -3.164 closest distance to " CB  ALA A 131 " =    2.087
peak=   -3.163 closest distance to " O   HOH Z 366 " =    1.719
peak=   -3.161 closest distance to " NH1 ARG A 195 " =    2.297
peak=   -3.160 closest distance to " O   HOH Z  25 " =    2.259
peak=   -3.158 closest distance to " OG BSER A 134 " =    1.832
peak=   -3.154 closest distance to " CD1 ILE A 263 " =    2.361
peak=   -3.154 closest distance to " CB  ALA A  10 " =    2.062
peak=   -3.153 closest distance to " CG  PHE A 283 " =    2.797
peak=   -3.152 closest distance to " N   GLY A  17 " =    1.752
peak=   -3.135 closest distance to " N   LEU A 261 " =    1.245
peak=   -3.131 closest distance to " O   HOH Z 113 " =    2.164
peak=   -3.129 closest distance to " CD  PRO A 213 " =    2.251
peak=   -3.118 closest distance to " CD1 TRP A 179 " =    1.145
peak=   -3.117 closest distance to " O   HOH Z 111 " =    2.007
peak=   -3.113 closest distance to " O   HOH Z 418 " =    1.467
peak=   -3.112 closest distance to " O   HOH Z 283 " =    5.950
peak=   -3.105 closest distance to " O   HOH Z 385 " =    3.832
peak=   -3.104 closest distance to " NE2 GLN A  58 " =    1.045
peak=   -3.102 closest distance to " CG  ARG A 259 " =    2.449
peak=   -3.097 closest distance to " O   HOH Z 171 " =    2.121
peak=   -3.096 closest distance to " CG  ARG A 269 " =    2.333
peak=   -3.088 closest distance to " O   HOH Z 174 " =    2.081
peak=   -3.085 closest distance to " O   HOH Z 389 " =    1.783
peak=   -3.081 closest distance to " O   HOH Z 280 " =    2.429
peak=   -3.070 closest distance to " CB  ALA A   9 " =    2.661
peak=   -3.065 closest distance to " O   HOH Z 422 " =    1.196
peak=   -3.054 closest distance to " O   HOH Z 191 " =    5.816
peak=   -3.041 closest distance to " CA  GLY A 133 " =    2.326
peak=   -3.034 closest distance to " O   PRO A 198 " =    1.737
peak=   -3.026 closest distance to " O   GLY A  23 " =    1.774
peak=   -3.008 closest distance to " N   MET A 105 " =    2.649

================= 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    :  0.4335 0.4221   6.241653e+00   6.222796e+00
   1_bss:  0.4235 0.4109   6.231493e+00   6.206793e+00
   1_xyz:  0.2819 0.3169   5.919320e+00   6.009540e+00
   1_adp:  0.2579 0.3247   5.872159e+00   6.025145e+00
   1_occ:  0.2576 0.3236   5.870177e+00   6.023425e+00
   2_bss:  0.2551 0.3215   5.866278e+00   6.019543e+00
   2_xyz:  0.1863 0.2256   5.561296e+00   5.732135e+00
   2_adp:  0.1643 0.2082   5.464840e+00   5.655517e+00
   2_occ:  0.1640 0.2080   5.464032e+00   5.654383e+00
   3_bss:  0.1639 0.2079   5.463381e+00   5.653051e+00
   3_xyz:  0.1304 0.1769   5.274995e+00   5.504902e+00
   3_adp:  0.1249 0.1690   5.233085e+00   5.458851e+00
   3_occ:  0.1248 0.1689   5.232634e+00   5.458725e+00
   4_bss:  0.1252 0.1688   5.234117e+00   5.457663e+00
   4_xyz:  0.1162 0.1616   5.179049e+00   5.411096e+00
   4_adp:  0.1151 0.1618   5.175798e+00   5.412617e+00
   4_occ:  0.1151 0.1618   5.175759e+00   5.412967e+00
   5_bss:  0.1150 0.1618   5.175793e+00   5.413002e+00
   5_xyz:  0.1154 0.1616   5.177153e+00   5.411343e+00
   5_adp:  0.1139 0.1627   5.174996e+00   5.417677e+00
   5_occ:  0.1139 0.1627   5.175057e+00   5.417929e+00
   5_bss:  0.1138 0.1627   5.175112e+00   5.418141e+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:  0.293  28.034  -2.140   4.235   0.160   0.000   0.000   0.000
   1_xyz:  0.293  28.034  -2.140   4.235   0.160   0.000   0.000   0.000
   1_adp:  0.293  28.034  -2.140   4.235   0.160   0.000   0.000   0.000
   1_occ:  0.293  28.034  -2.140   4.235   0.160   0.000   0.000   0.000
   2_bss:  0.328  60.011  -1.872   1.128  -0.945   0.000  -0.000  -0.000
   2_xyz:  0.328  60.011  -1.872   1.128  -0.945   0.000  -0.000  -0.000
   2_adp:  0.328  60.011  -1.872   1.128  -0.945   0.000  -0.000  -0.000
   2_occ:  0.328  60.011  -1.872   1.128  -0.945   0.000  -0.000  -0.000
   3_bss:  0.325  63.728  -1.902  -0.172  -1.221  -0.000  -0.000  -0.000
   3_xyz:  0.325  63.728  -1.902  -0.172  -1.221  -0.000  -0.000  -0.000
   3_adp:  0.325  63.728  -1.902  -0.172  -1.221  -0.000  -0.000  -0.000
   3_occ:  0.325  63.728  -1.902  -0.172  -1.221  -0.000  -0.000  -0.000
   4_bss:  0.323  58.749  -2.059  -1.024  -1.385  -0.000  -0.000  -0.000
   4_xyz:  0.323  58.749  -2.059  -1.024  -1.385  -0.000  -0.000  -0.000
   4_adp:  0.323  58.749  -2.059  -1.024  -1.385  -0.000  -0.000  -0.000
   4_occ:  0.323  58.749  -2.059  -1.024  -1.385  -0.000  -0.000  -0.000
   5_bss:  0.323  58.749  -1.965  -1.128  -1.288  -0.000  -0.000  -0.000
   5_xyz:  0.323  58.749  -1.965  -1.128  -1.288  -0.000  -0.000  -0.000
   5_adp:  0.323  58.749  -1.965  -1.128  -1.288  -0.000  -0.000  -0.000
   5_occ:  0.323  58.749  -1.965  -1.128  -1.288  -0.000  -0.000  -0.000
   5_bss:  0.321  60.837  -1.762  -1.034  -1.116  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.341 0.5299  0.7003    56043.562
   1_bss:  48.283 0.5413  0.7320    52409.430
   1_xyz:  33.819 0.7151  0.9237    27855.934
   1_adp:  34.628 0.7053  0.9039    29028.667
   1_occ:  34.531 0.7063  0.9042    28828.961
   2_bss:  34.141 0.7108  0.8732    28399.139
   2_xyz:  22.779 0.8330  0.9736    13361.347
   2_adp:  20.365 0.8578  0.9807    11369.345
   2_occ:  20.343 0.8580  0.9809    11346.922
   3_bss:  20.278 0.8588  0.9637    11309.801
   3_xyz:  16.759 0.8910  0.9822     8063.309
   3_adp:  15.678 0.9009  0.9822     7459.020
   3_occ:  15.673 0.9010  0.9822     7461.383
   4_bss:  15.666 0.9010  0.9693     7462.608
   4_xyz:  14.617 0.9099  0.9720     6725.627
   4_adp:  14.621 0.9100  0.9688     6761.690
   4_occ:  14.624 0.9100  0.9687     6767.090
   5_bss:  14.626 0.9100  0.9699     6767.807
   5_xyz:  14.621 0.9099  0.9696     6714.395
   5_adp:  14.760 0.9088  0.9624     6774.261
   5_occ:  14.766 0.9087  0.9623     6778.383
   5_bss:  14.767 0.9087  0.9678     6782.756
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.7398e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.7398e-01
   1_xyz:   1.634  0.013  0.098 16.343  0.007  4.120   1.3422e-01
   1_adp:   1.634  0.013  0.098 16.343  0.007  4.120   1.3422e-01
   1_occ:   1.634  0.013  0.098 16.343  0.007  4.120   1.3422e-01
   2_bss:   1.634  0.013  0.098 16.343  0.007  4.120   1.3422e-01
   2_xyz:   1.198  0.009  0.079 14.865  0.005  4.115   7.8341e-02
   2_adp:   1.198  0.009  0.079 14.865  0.005  4.115   7.8341e-02
   2_occ:   1.198  0.009  0.079 14.865  0.005  4.115   7.8341e-02
   3_bss:   1.198  0.009  0.079 14.865  0.005  4.115   7.8341e-02
   3_xyz:   1.135  0.010  0.078 15.101  0.005  4.112   7.6635e-02
   3_adp:   1.135  0.010  0.078 15.101  0.005  4.112   7.6635e-02
   3_occ:   1.135  0.010  0.078 15.101  0.005  4.112   7.6635e-02
   4_bss:   1.135  0.010  0.078 15.101  0.005  4.112   7.6635e-02
   4_xyz:   1.109  0.009  0.080 15.070  0.005  4.118   7.2221e-02
   4_adp:   1.109  0.009  0.080 15.070  0.005  4.118   7.2221e-02
   4_occ:   1.109  0.009  0.080 15.070  0.005  4.118   7.2221e-02
   5_bss:   1.109  0.009  0.080 15.070  0.005  4.118   7.2221e-02
   5_xyz:   1.024  0.008  0.075 14.771  0.004  4.118   6.2526e-02
   5_adp:   1.024  0.008  0.075 14.771  0.004  4.118   6.2526e-02
   5_occ:   1.024  0.008  0.075 14.771  0.004  4.118   6.2526e-02
   5_bss:   1.024  0.008  0.075 14.771  0.004  4.118   6.2526e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.609   2.4248e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.609   2.4248e-01
   1_xyz:  10.674  0.097  0.417 86.536  0.038  2.138   9.4569e-02
   1_adp:  10.674  0.097  0.417 86.536  0.038  2.138   9.4569e-02
   1_occ:  10.674  0.097  0.417 86.536  0.038  2.138   9.4569e-02
   2_bss:  10.674  0.097  0.417 86.536  0.038  2.138   9.4569e-02
   2_xyz:   7.821  0.057  0.222 84.965  0.041  2.287   1.0353e-01
   2_adp:   7.821  0.057  0.222 84.965  0.041  2.287   1.0353e-01
   2_occ:   7.821  0.057  0.222 84.965  0.041  2.287   1.0353e-01
   3_bss:   7.821  0.057  0.222 84.965  0.041  2.287   1.0353e-01
   3_xyz:   8.259  0.061  0.242 81.635  0.036  2.291   6.2709e-02
   3_adp:   8.259  0.061  0.242 81.635  0.036  2.291   6.2709e-02
   3_occ:   8.259  0.061  0.242 81.635  0.036  2.291   6.2709e-02
   4_bss:   8.259  0.061  0.242 81.635  0.036  2.291   6.2709e-02
   4_xyz:   8.009  0.044  0.273 82.840  0.036  2.319   5.3770e-02
   4_adp:   8.009  0.044  0.273 82.840  0.036  2.319   5.3770e-02
   4_occ:   8.009  0.044  0.273 82.840  0.036  2.319   5.3770e-02
   5_bss:   8.009  0.044  0.273 82.840  0.036  2.319   5.3770e-02
   5_xyz:   7.572  0.039  0.248 81.603  0.034  2.361   4.2737e-02
   5_adp:   7.572  0.039  0.248 81.603  0.034  2.361   4.2737e-02
   5_occ:   7.572  0.039  0.248 81.603  0.034  2.361   4.2737e-02
   5_bss:   7.572  0.039  0.248 81.603  0.034  2.361   4.2737e-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:  87.55   0.00  17.31  87.55   0.00  13.45  69.85   2.51  38.36
   1_occ:  87.55   0.00  17.31  87.55   0.00  13.45  69.85   2.51  38.36
   2_bss:  87.55   0.00  17.31  87.55   0.00  13.45  69.85   2.51  38.36
   2_xyz:  87.55   0.00  17.31  87.55   0.00  13.45  69.85   2.51  38.36
   2_adp:  98.83   0.00  17.95  96.90   0.00  13.21  98.83   4.51  43.76
   2_occ:  98.83   0.00  17.95  96.90   0.00  13.21  98.83   4.51  43.76
   3_bss:  98.83   0.00  17.95  96.90   0.00  13.21  98.83   4.51  43.76
   3_xyz:  98.83   0.00  17.95  96.90   0.00  13.21  98.83   4.51  43.76
   3_adp:  92.29   0.00  16.91  92.07   0.00  12.60  92.29   5.22  40.34
   3_occ:  92.29   0.00  16.91  92.07   0.00  12.60  92.29   5.22  40.34
   4_bss:  92.29   0.00  16.91  92.07   0.00  12.60  92.29   5.22  40.34
   4_xyz:  92.29   0.00  16.91  92.07   0.00  12.60  92.29   5.22  40.34
   4_adp:  92.21   0.00  16.86  92.17   0.00  12.56  92.21   5.26  40.30
   4_occ:  92.21   0.00  16.86  92.17   0.00  12.56  92.21   5.26  40.30
   5_bss:  92.21   0.00  16.86  92.17   0.00  12.56  92.21   5.26  40.30
   5_xyz:  92.21   0.00  16.86  92.17   0.00  12.56  92.21   5.26  40.30
   5_adp: 107.06   0.00  17.03 107.06   0.00  12.51  97.08   5.24  41.69
   5_occ: 107.06   0.00  17.03 107.06   0.00  12.51  97.08   5.24  41.69
   5_bss: 107.07   0.01  17.04 107.07   0.01  12.51  97.09   5.25  41.69
------------------------------------------------------------------------
 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:    1.606    0.040    0.483
   1_adp:    1.606    0.040    0.483
   1_occ:    1.606    0.040    0.483
   2_bss:    1.606    0.040    0.483
   2_xyz:    1.278    0.069    0.601
   2_adp:    1.278    0.069    0.601
   2_occ:    1.278    0.069    0.601
   3_bss:    1.278    0.069    0.601
   3_xyz:    1.417    0.065    0.685
   3_adp:    1.417    0.065    0.685
   3_occ:    1.417    0.065    0.685
   4_bss:    1.417    0.065    0.685
   4_xyz:    1.350    0.066    0.715
   4_adp:    1.350    0.066    0.715
   4_occ:    1.350    0.066    0.715
   5_bss:    1.350    0.066    0.715
   5_xyz:    1.359    0.045    0.720
   5_adp:    1.359    0.045    0.720
   5_occ:    1.359    0.045    0.720
   5_bss:    1.359    0.045    0.720
------------------------------------------------------------------------

CPU time actual refinement: 348.97


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_948/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_948/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_948/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_948/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_948/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 348.82 
  Macro-tasks:
    bulk solvent and scale       = 37.72  
    individual site refinement   = 153.59 
    weights calculation          = 29.08  
    collect and process          = 6.55   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 227.05 
  Micro-tasks:
    mask                            = 1.81   
    f_calc                          = 113.21 
    alpha_beta                      = 8.44   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 124.83 
    fmodel                         = 6.55   
    r_factors                      = 0.18   
    phase_errors                   = 10.96  
    foms                           = 0.34   
    TOTAL for micro-tasks          = 267.48 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.794 micro seconds
Total CPU time: 6.04 minutes
from_scatterers_fft:    681 calls, 112.83 s
gradients_fft:          626 calls, 109.98 s

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

# Date 2008-01-16 Time 06:03:47 PST -0800 (1200492227.88 s)
Start R-work = 0.4335, R-free = 0.4221 (no bulk solvent and anisotropic scale)
Final R-work = 0.1334, R-free = 0.1795 (no bulk solvent and anisotropic scale)

Start R-work = 0.4235, R-free = 0.4109
Final R-work = 0.1138, R-free = 0.1627