# Date 2008-01-16 Time 05:25:43 PST -0800 (1200489943.80 s)
#phil __OFF__

Command line arguments: "../732.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 3601
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 732

-------------------------------------------------------------------------------
  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: (70.6012, 45.7567, 86.822, 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: 3.30, per 1000 atoms: 1.17


================================== 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: (70.6012, 45.7567, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0689 1.95362
Completeness in resolution range: 0.934099
Completeness with d_max=infinity: 0.931435

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0689
                             d_min =   1.9536

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: (70.6012, 45.7567, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0689 1.95362
Completeness in resolution range: 0.934099
Completeness with d_max=infinity: 0.931435

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0694 -  4.1818 [2202/2229]  1981   221  10.0%
  bin  2:  4.1818 -  3.3310 [2121/2141]  1909   212  10.0%
  bin  3:  3.3310 -  2.9134 [2089/2108]  1882   207   9.9%
  bin  4:  2.9134 -  2.6486 [2065/2095]  1854   211  10.2%
  bin  5:  2.6486 -  2.4596 [2064/2083]  1867   197   9.5%
  bin  6:  2.4596 -  2.3152 [2060/2085]  1847   213  10.3%
  bin  7:  2.3152 -  2.1996 [2032/2060]  1824   208  10.2%
  bin  8:  2.1996 -  2.1041 [2019/2055]  1818   201  10.0%
  bin  9:  2.1041 -  2.0233 [2024/2066]  1828   196   9.7%
  bin 10:  2.0233 -  1.9536 [ 913/2049]   820    93  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_732/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.68 -     2.32: 29
        2.32 -     2.97: 1787
        2.97 -     3.61: 4610
        3.61 -     4.26: 9242
        4.26 -     4.90: 12827
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.718 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.740 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  ... (remaining 28490 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_732/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_732/model_refine_001.geo

CPU time processing inputs: 9.44


============================ 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 = 70.60125 45.75675 86.82195 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: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4227   r_free= 0.4183   ksol= 0.00   Bsol= 0.00   scale= 0.917    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.245393                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.6649 0.99   1426  158 0.3630 0.3664      6.5478      6.5531|
|  2:  4.6649 -  3.7210 0.99   1383  155 0.3654 0.3322      6.7678      6.6923|
|  3:  3.7210 -  3.2561 0.99   1347  144 0.3878 0.3946      6.6297      6.6484|
|  4:  3.2561 -  2.9608 0.99   1346  156 0.4170 0.4340      6.4922      6.5209|
|  5:  2.9608 -  2.7500 0.99   1333  150 0.4472 0.4153      6.3224      6.3172|
|  6:  2.7500 -  2.5887 0.99   1333  148 0.4439 0.4603      6.2274      6.1776|
|  7:  2.5887 -  2.4596 0.99   1325  137 0.4497 0.4134      6.1953      6.1157|
|  8:  2.4596 -  2.3530 0.98   1302  154 0.4592 0.4710      6.1326      6.1629|
|  9:  2.3530 -  2.2627 0.98   1303  143 0.4496 0.5110       6.083      6.1566|
| 10:  2.2627 -  2.1849 1.00   1329  152 0.4637 0.4592      6.0564      6.0402|
| 11:  2.1849 -  2.1167 0.98   1310  137 0.4533 0.4402      5.9874      5.9943|
| 12:  2.1167 -  2.0564 0.98   1289  147 0.4530 0.4403      5.9008      5.9388|
| 13:  2.0564 -  2.0024 0.96   1253  136 0.4696 0.4444      5.8461      5.7739|
| 14:  2.0024 -  1.9536 0.27    351   42 0.5378 0.4908      5.8927      5.8302|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0694 -  4.6649  1426   158  0.71  33.57   0.83     0.76      70055.86|
|  2:  4.6649 -  3.7210  1383   155  0.73  32.62   0.91     0.84      95242.12|
|  3:  3.7210 -  3.2561  1347   144  0.63  41.02   0.95     0.83     100839.08|
|  4:  3.2561 -  2.9608  1346   156  0.56  47.36   0.94     0.75      92116.55|
|  5:  2.9608 -  2.7500  1333   150  0.49  52.57   0.91     0.70      71693.58|
|  6:  2.7500 -  2.5887  1333   148  0.48  53.39   0.92     0.67      60400.78|
|  7:  2.5887 -  2.4596  1325   137  0.47  54.16   0.96     0.65      54831.53|
|  8:  2.4596 -  2.3530  1302   154  0.44  56.48   0.94     0.63      51025.17|
|  9:  2.3530 -  2.2627  1303   143  0.45  56.24   0.96     0.64      47314.00|
| 10:  2.2627 -  2.1849  1329   152  0.47  54.78   0.97     0.67      40709.93|
| 11:  2.1849 -  2.1167  1310   137  0.46  55.12   1.01     0.69      38786.64|
| 12:  2.1167 -  2.0564  1289   147  0.47  54.90   0.99     0.71      34421.03|
| 13:  2.0564 -  2.0024  1253   136  0.45  56.07   0.99     0.72      29640.74|
| 14:  2.0024 -  1.9536   351    42  0.53  49.81   1.01     0.74      21681.37|
|alpha:            min =        0.63 max =            0.84 mean =         0.71|
|beta:             min =    21681.37 max =       100839.08 mean =     60254.67|
|figures of merit: min =        0.00 max =            1.00 mean =         0.53|
|phase err.(work): min =        0.00 max =           89.99 mean =        49.65|
|phase err.(test): min =        0.00 max =           89.95 mean =        49.81|
|-----------------------------------------------------------------------------|

============================== 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 = 10.341542             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.708   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.786664              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.715   (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 |  1.681 -  2.003:       11 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.003 -  2.325:       18 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.325 -  2.647:       77 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.647 -  2.969:     1710 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.969 -  3.290:     1923 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.290 -  3.612:     2687 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.612 -  3.934:     4773 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.934 -  4.256:     4469 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.256 -  4.578:     5836 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.578 -  4.900:     6991 |
|-----------------------------------------------------------------------------|
|-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 |        0.184 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.681 |       0.512 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.677)------------------------------------------|
|    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: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4227   r_free= 0.4183   ksol= 0.00   Bsol= 0.00   scale= 0.917    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.245393                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4100   r_free= 0.4086   ksol= 0.36   Bsol= 49.64   scale= 0.934   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.96,3.38,-1.39,0.00,-0.00,-0.00); trace/3= -0.32                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.234809                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.122781              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.626   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.998491              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.598   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4100      final r-factor (work) = 0.3444          |
| start r-factor (free) = 0.4086      final r-factor (free) = 0.3846          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.6227 = 9.12 * 0.50 * 6.2346 + 1.00 * 0.1842                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.0962 = 9.12 * 0.50 * 6.1336 + 1.00 * 0.1187                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3444      final r-factor (work) = 0.3158          |
| start r-factor (free) = 0.3846      final r-factor (free) = 0.3909          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1303 = 1.00 * 1.00 * 6.1336 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0645 = 1.00 * 1.00 * 6.0575 + 1.00 * 0.0161                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.677)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.93   17.94    None  None   None       |
|    all(noH): 2823   0      0.00    91.93   17.94    None  None   None       |
|    Sol.    : 438    0      1.87    91.93   34.64    None  None   None       |
|    Mac.    : 2385   0      0.00    78.50   14.87    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.193:  805   |   5:    45.964 -  55.156:   72        |
|      1:     9.193 -  18.386:  949   |   6:    55.156 -  64.349:   42        |
|      2:    18.386 -  27.578:  543   |   7:    64.349 -  73.542:   15        |
|      3:    27.578 -  36.771:  247   |   8:    73.542 -  82.735:    3        |
|      4:    36.771 -  45.964:  145   |   9:    82.735 -  91.927:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3158 r_free = 0.3909             target_work(ml) = 6.061         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3155 r_free = 0.3912             target_work(ml) = 6.060         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3155   r_free= 0.3912   ksol= 0.36   Bsol= 49.64   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.96,3.38,-1.39,0.00,-0.00,-0.00); trace/3= -0.32                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.060363                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3152   r_free= 0.3891   ksol= 0.36   Bsol= 71.44   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.65,0.92,-0.58,0.00,-0.00,-0.00); trace/3= -0.44                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.060336                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.889732             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.961  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.451445              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.384  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3152      final r-factor (work) = 0.2515          |
| start r-factor (free) = 0.3891      final r-factor (free) = 0.3207          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.1087 = 10.89 * 0.50 * 6.0589 + 1.00 * 0.1187                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.6390 = 10.89 * 0.50 * 5.9736 + 1.00 * 0.1134                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2515      final r-factor (work) = 0.2347          |
| start r-factor (free) = 0.3207      final r-factor (free) = 0.3110          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7128 = 0.45 * 1.00 * 5.9736 + 1.00 * 0.0160                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6685 = 0.45 * 1.00 * 5.8355 + 1.00 * 0.0341                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.677)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.35   17.87    None  None   None       |
|    all(noH): 2823   0      0.00    91.35   17.87    None  None   None       |
|    Sol.    : 438    0      0.88    91.35   37.03    None  None   None       |
|    Mac.    : 2385   0      0.00    79.70   14.35    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 -   9.135:  811   |   5:    45.673 -  54.808:   89        |
|      1:     9.135 -  18.269: 1013   |   6:    54.808 -  63.943:   37        |
|      2:    18.269 -  27.404:  457   |   7:    63.943 -  73.077:   15        |
|      3:    27.404 -  36.539:  233   |   8:    73.077 -  82.212:    2        |
|      4:    36.539 -  45.673:  164   |   9:    82.212 -  91.347:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2347 r_free = 0.3110             target_work(ml) = 5.818         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2345 r_free = 0.3108             target_work(ml) = 5.817         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2345   r_free= 0.3108   ksol= 0.36   Bsol= 71.44   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.65,0.92,-0.58,0.00,-0.00,-0.00); trace/3= -0.44                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.817155                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2339   r_free= 0.3088   ksol= 0.34   Bsol= 64.99   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.52,-0.85,-0.35,-0.00,-0.00,-0.00); trace/3= -0.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.812360                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.103881              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.608  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.835551              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.378   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2339      final r-factor (work) = 0.2007          |
| start r-factor (free) = 0.3088      final r-factor (free) = 0.2585          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1681 = 3.10 * 0.50 * 5.8344 + 1.00 * 0.1134                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9752 = 3.10 * 0.50 * 5.7476 + 1.00 * 0.0553                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2007      final r-factor (work) = 0.1858          |
| start r-factor (free) = 0.2585      final r-factor (free) = 0.2460          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0808 = 0.84 * 1.00 * 5.7476 + 1.00 * 0.2784                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7092 = 0.84 * 1.00 * 5.6207 + 1.00 * 0.0129                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.677)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.84   18.22    None  None   None       |
|    all(noH): 2823   0      0.00    95.84   18.22    None  None   None       |
|    Sol.    : 438    0      5.34    95.84   42.66    None  None   None       |
|    Mac.    : 2385   0      0.00    86.54   13.74    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 -   9.584:  932   |   5:    47.920 -  57.504:  112        |
|      1:     9.584 -  19.168: 1068   |   6:    57.504 -  67.088:   78        |
|      2:    19.168 -  28.752:  301   |   7:    67.088 -  76.672:   13        |
|      3:    28.752 -  38.336:  163   |   8:    76.672 -  86.255:    3        |
|      4:    38.336 -  47.920:  150   |   9:    86.255 -  95.839:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1858 r_free = 0.2460             target_work(ml) = 5.601         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1856 r_free = 0.2457             target_work(ml) = 5.600         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1856   r_free= 0.2457   ksol= 0.34   Bsol= 64.99   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.52,-0.85,-0.35,-0.00,-0.00,-0.00); trace/3= -0.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.600252                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1856   r_free= 0.2453   ksol= 0.33   Bsol= 59.81   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,-1.79,-0.65,-0.00,-0.00,-0.00); trace/3= -1.48                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.598835                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.853818              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.088  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.931854              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.212  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1856      final r-factor (work) = 0.1471          |
| start r-factor (free) = 0.2453      final r-factor (free) = 0.2019          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8879 = 3.85 * 0.50 * 5.6218 + 1.00 * 0.0553                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6633 = 3.85 * 0.50 * 5.5020 + 1.00 * 0.0614                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1471      final r-factor (work) = 0.1356          |
| start r-factor (free) = 0.2019      final r-factor (free) = 0.1904          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.6457 = 3.93 * 1.00 * 5.5020 + 1.00 * 0.0127                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.0803 = 3.93 * 1.00 * 5.3581 + 1.00 * 0.0132                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.677)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.72  18.46    None  None   None       |
|    all(noH): 2823   0      0.00    102.72  18.46    None  None   None       |
|    Sol.    : 438    0      2.30    102.72  47.15    None  None   None       |
|    Mac.    : 2385   0      0.00    95.83   13.19    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:     0.000 -  10.272: 1134   |   5:    51.361 -  61.633:   97        |
|      1:    10.272 -  20.544: 1000   |   6:    61.633 -  71.906:   72        |
|      2:    20.544 -  30.817:  240   |   7:    71.906 -  82.178:   46        |
|      3:    30.817 -  41.089:  119   |   8:    82.178 -  92.450:   14        |
|      4:    41.089 -  51.361:   95   |   9:    92.450 - 102.722:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1356 r_free = 0.1904             target_work(ml) = 5.325         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1356 r_free = 0.1902             target_work(ml) = 5.324         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1356   r_free= 0.1902   ksol= 0.33   Bsol= 59.81   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,-1.79,-0.65,-0.00,-0.00,-0.00); trace/3= -1.48                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.324234                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1360   r_free= 0.1901   ksol= 0.32   Bsol= 59.81   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-2.18,-0.66,-0.00,-0.00,-0.00); trace/3= -1.60                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.323330                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.919446              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.276  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.968507              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.626  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1360      final r-factor (work) = 0.1217          |
| start r-factor (free) = 0.1901      final r-factor (free) = 0.1768          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5628 = 3.92 * 0.50 * 5.3586 + 1.00 * 0.0614                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4151 = 3.92 * 0.50 * 5.2816 + 1.00 * 0.0646                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1217      final r-factor (work) = 0.1179          |
| start r-factor (free) = 0.1768      final r-factor (free) = 0.1719          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.6917 = 2.97 * 1.00 * 5.2816 + 1.00 * 0.0131                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.5138 = 2.97 * 1.00 * 5.2220 + 1.00 * 0.0124                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.677)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.20  17.99    None  None   None       |
|    all(noH): 2823   0      0.00    104.20  17.99    None  None   None       |
|    Sol.    : 438    0      2.29    103.58  46.17    None  None   None       |
|    Mac.    : 2385   0      0.00    104.20  12.81    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 -  10.420: 1229   |   5:    52.101 -  62.521:   86        |
|      1:    10.420 -  20.841:  957   |   6:    62.521 -  72.942:   57        |
|      2:    20.841 -  31.261:  222   |   7:    72.942 -  83.362:   41        |
|      3:    31.261 -  41.681:  111   |   8:    83.362 -  93.782:   14        |
|      4:    41.681 -  52.101:   97   |   9:    93.782 - 104.202:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1179 r_free = 0.1719             target_work(ml) = 5.208         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1178 r_free = 0.1719             target_work(ml) = 5.208         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1178   r_free= 0.1719   ksol= 0.32   Bsol= 59.81   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-2.18,-0.66,-0.00,-0.00,-0.00); trace/3= -1.60                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.207538                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.6649 0.99   1426  158 0.0950 0.1369       5.366      5.6176|
|  2:  4.6649 -  3.7210 0.99   1383  155 0.0823 0.1139      5.4331      5.6626|
|  3:  3.7210 -  3.2561 0.99   1347  144 0.1106 0.1590      5.5127      5.8343|
|  4:  3.2561 -  2.9608 0.99   1346  156 0.1335 0.1887      5.5269      5.7191|
|  5:  2.9608 -  2.7500 0.99   1333  150 0.1429 0.1925      5.3974      5.6486|
|  6:  2.7500 -  2.5887 0.99   1333  148 0.1313 0.2036      5.2644      5.5165|
|  7:  2.5887 -  2.4596 0.99   1325  137 0.1306 0.1806      5.2127      5.4009|
|  8:  2.4596 -  2.3530 0.98   1302  154 0.1255 0.1770      5.1251      5.3938|
|  9:  2.3530 -  2.2627 0.98   1303  143 0.1286 0.1950      5.0963      5.3748|
| 10:  2.2627 -  2.1849 1.00   1329  152 0.1182 0.1864       5.007       5.257|
| 11:  2.1849 -  2.1167 0.98   1310  137 0.1209 0.2038      5.0113      5.4135|
| 12:  2.1167 -  2.0564 0.98   1289  147 0.1272 0.1915       4.965       5.192|
| 13:  2.0564 -  2.0024 0.96   1253  136 0.1209 0.1805      4.8504       5.075|
| 14:  2.0024 -  1.9536 0.27    351   42 0.1048 0.1662      4.6986      5.0142|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0694 -  4.6649  1426   158  0.94   9.62   0.97     0.95       7574.69|
|  2:  4.6649 -  3.7210  1383   155  0.95   8.26   1.02     1.01       9579.62|
|  3:  3.7210 -  3.2561  1347   144  0.93  12.40   1.05     1.04      11683.73|
|  4:  3.2561 -  2.9608  1346   156  0.90  15.98   1.02     1.00      12543.04|
|  5:  2.9608 -  2.7500  1333   150  0.89  17.65   1.01     0.98       9934.97|
|  6:  2.7500 -  2.5887  1333   148  0.88  18.19   1.00     0.97       8246.40|
|  7:  2.5887 -  2.4596  1325   137  0.89  16.82   1.00     0.96       7079.75|
|  8:  2.4596 -  2.3530  1302   154  0.89  17.20   1.00     0.98       6120.44|
|  9:  2.3530 -  2.2627  1303   143  0.89  17.15   1.00     0.95       5691.97|
| 10:  2.2627 -  2.1849  1329   152  0.89  17.10   1.00     0.97       5058.72|
| 11:  2.1849 -  2.1167  1310   137  0.89  18.00   0.99     0.94       5169.22|
| 12:  2.1167 -  2.0564  1289   147  0.88  18.31   1.01     1.00       4914.83|
| 13:  2.0564 -  2.0024  1253   136  0.88  18.59   1.00     0.98       4006.52|
| 14:  2.0024 -  1.9536   351    42  0.91  15.02   0.99     0.96       2903.34|
|alpha:            min =        0.94 max =            1.04 mean =         0.98|
|beta:             min =     2903.34 max =        12543.04 mean =      7461.27|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.69|
|phase err.(test): min =        0.00 max =           89.79 mean =        15.21|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1178   r_free= 0.1718   ksol= 0.32   Bsol= 54.24   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.86,-2.23,-0.57,-0.00,-0.00,-0.00); trace/3= -1.55                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.207435                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1178   r_free= 0.1718   ksol= 0.32   Bsol= 54.24   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.86,-2.23,-0.57,-0.00,-0.00,-0.00); trace/3= -1.55                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.207435                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.6649 0.99   1426  158 0.0947 0.1370      5.3662      5.6178|
|  2:  4.6649 -  3.7210 0.99   1383  155 0.0820 0.1137      5.4316      5.6602|
|  3:  3.7210 -  3.2561 0.99   1347  144 0.1104 0.1588      5.5111      5.8317|
|  4:  3.2561 -  2.9608 0.99   1346  156 0.1335 0.1890      5.5267      5.7197|
|  5:  2.9608 -  2.7500 0.99   1333  150 0.1429 0.1927      5.3974      5.6492|
|  6:  2.7500 -  2.5887 0.99   1333  148 0.1313 0.2035      5.2647      5.5166|
|  7:  2.5887 -  2.4596 0.99   1325  137 0.1306 0.1807      5.2135      5.4019|
|  8:  2.4596 -  2.3530 0.98   1302  154 0.1256 0.1773      5.1258      5.3949|
|  9:  2.3530 -  2.2627 0.98   1303  143 0.1286 0.1945      5.0968      5.3734|
| 10:  2.2627 -  2.1849 1.00   1329  152 0.1182 0.1869      5.0072       5.259|
| 11:  2.1849 -  2.1167 0.98   1310  137 0.1207 0.2038      5.0113      5.4141|
| 12:  2.1167 -  2.0564 0.98   1289  147 0.1271 0.1911       4.965      5.1918|
| 13:  2.0564 -  2.0024 0.96   1253  136 0.1209 0.1801        4.85       5.074|
| 14:  2.0024 -  1.9536 0.27    351   42 0.1049 0.1662      4.6977      5.0126|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0694 -  4.6649  1426   158  0.94   9.62   0.97     0.95       7579.63|
|  2:  4.6649 -  3.7210  1383   155  0.95   8.25   1.03     1.01       9562.10|
|  3:  3.7210 -  3.2561  1347   144  0.93  12.38   1.05     1.04      11637.72|
|  4:  3.2561 -  2.9608  1346   156  0.90  15.97   1.02     1.00      12518.81|
|  5:  2.9608 -  2.7500  1333   150  0.89  17.65   1.01     0.98       9934.73|
|  6:  2.7500 -  2.5887  1333   148  0.88  18.20   1.00     0.97       8254.79|
|  7:  2.5887 -  2.4596  1325   137  0.89  16.84   1.00     0.96       7094.71|
|  8:  2.4596 -  2.3530  1302   154  0.89  17.21   1.00     0.98       6129.34|
|  9:  2.3530 -  2.2627  1303   143  0.89  17.17   1.00     0.96       5698.25|
| 10:  2.2627 -  2.1849  1329   152  0.89  17.12   1.00     0.97       5064.71|
| 11:  2.1849 -  2.1167  1310   137  0.88  18.02   0.99     0.94       5178.01|
| 12:  2.1167 -  2.0564  1289   147  0.88  18.32   1.01     1.00       4918.08|
| 13:  2.0564 -  2.0024  1253   136  0.88  18.59   1.00     0.99       4003.76|
| 14:  2.0024 -  1.9536   351    42  0.91  14.99   0.99     0.96       2896.58|
|alpha:            min =        0.94 max =            1.04 mean =         0.98|
|beta:             min =     2896.58 max =        12518.81 mean =      7458.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.70|
|phase err.(test): min =        0.00 max =           89.85 mean =        15.20|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.677)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.21  17.99    None  None   None       |
|    all(noH): 2823   0      0.00    104.21  17.99    None  None   None       |
|    Sol.    : 438    0      2.29    103.59  46.18    None  None   None       |
|    Mac.    : 2385   0      0.00    104.21  12.82    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.423: 1229   |   5:    52.104 -  62.524:   86        |
|      1:    10.423 -  20.843:  957   |   6:    62.524 -  72.945:   57        |
|      2:    20.843 -  31.264:  222   |   7:    72.945 -  83.365:   41        |
|      3:    31.264 -  41.684:  111   |   8:    83.365 -  93.785:   14        |
|      4:    41.684 -  52.104:   97   |   9:    93.785 - 104.205:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 335         
Filter by distance & map next to the model:
   mapped sites are within: 0.411 - 4.182
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 330 from: 335
   mapped sites are within: 0.724 - 4.182

peak=    6.589 closest distance to " O   HOH Z 385 " =    1.306
peak=    6.325 closest distance to " NE2 GLN A  11 " =    1.394
peak=    5.994 closest distance to " O   HOH Z 431 " =    1.518
peak=    5.903 closest distance to " O   HOH Z 390 " =    1.107
peak=    5.634 closest distance to " O   HOH Z 427 " =    1.262
peak=    5.558 closest distance to " O   HOH Z  65 " =    1.449
peak=    5.545 closest distance to " O   HOH Z 417 " =    2.499
peak=    5.475 closest distance to " O   HOH Z   7 " =    1.807
peak=    5.376 closest distance to " O   HOH Z 245 " =    1.137
peak=    5.258 closest distance to " O   HOH Z 142 " =    1.914
peak=    5.204 closest distance to " O   HOH Z 287 " =    2.114
peak=    5.117 closest distance to " O   HOH Z  63 " =    1.897
peak=    5.071 closest distance to " O   HOH Z  63 " =    2.079
peak=    5.033 closest distance to " CG  PRO A  54 " =    1.341
peak=    4.999 closest distance to " O   HOH Z 427 " =    1.946
peak=    4.886 closest distance to " NH2 ARG A  56 " =    2.098
peak=    4.759 closest distance to " O   HOH Z 392 " =    1.407
peak=    4.695 closest distance to " O   HOH Z  78 " =    1.690
peak=    4.685 closest distance to " CB  GLN A 223 " =    1.541
peak=    4.609 closest distance to " O   HOH Z 139 " =    1.269
peak=    4.605 closest distance to " O   HOH Z  29 " =    1.147
peak=    4.583 closest distance to " O   HOH Z 298 " =    1.859
peak=    4.578 closest distance to " CB  PRO A  54 " =    1.057
peak=    4.552 closest distance to " O   HOH Z 222 " =    1.212
peak=    4.522 closest distance to " O   HOH Z 371 " =    2.073
peak=    4.517 closest distance to " O   HOH Z 422 " =    0.796
peak=    4.503 closest distance to " CB  GLN A 183 " =    1.178
peak=    4.488 closest distance to " O   HOH Z 380 " =    1.940
peak=    4.487 closest distance to " O   HOH Z   9 " =    1.404
peak=    4.473 closest distance to " O   HOH Z 211 " =    1.334
peak=    4.463 closest distance to " O   HOH Z 232 " =    2.283
peak=    4.462 closest distance to " O   HOH Z 236 " =    1.451
peak=    4.433 closest distance to " CA  TYR A  30 " =    1.033
peak=    4.403 closest distance to " O   HOH Z 316 " =    3.012
peak=    4.399 closest distance to " CB  ARG A 275 " =    1.045
peak=    4.395 closest distance to " CB  SER A  63 " =    1.355
peak=    4.373 closest distance to " O   HOH Z 225 " =    1.554
peak=    4.350 closest distance to " O   HOH Z 209 " =    2.276
peak=    4.332 closest distance to " CG  PRO A  90 " =    1.292
peak=    4.308 closest distance to " O   HOH Z 423 " =    1.963
peak=    4.308 closest distance to " O   HOH Z 425 " =    1.533
peak=    4.272 closest distance to " O   HOH Z 424 " =    1.217
peak=    4.263 closest distance to " O   HOH Z 133 " =    2.458
peak=    4.251 closest distance to " O   PRO A 198 " =    1.179
peak=    4.231 closest distance to " CG  PRO A 213 " =    1.257
peak=    4.221 closest distance to " O   HOH Z   2 " =    1.726
peak=    4.220 closest distance to " O   HOH Z 414 " =    1.330
peak=    4.205 closest distance to " CG  LEU A 167 " =    1.285
peak=    4.205 closest distance to " CB  ARG A 190 " =    1.690
peak=    4.197 closest distance to " O   HOH Z 352 " =    1.598
peak=    4.173 closest distance to " O   ASP A 286 " =    2.626
peak=    4.145 closest distance to " O   HOH Z 145 " =    1.772
peak=    4.139 closest distance to " O   HOH Z 214 " =    1.330
peak=    4.128 closest distance to " O   HOH Z  91 " =    2.408
peak=    4.124 closest distance to " O   HOH Z 394 " =    1.836
peak=    4.105 closest distance to " O   HOH Z 158 " =    1.177
peak=    4.094 closest distance to " O   HOH Z 371 " =    3.123
peak=    4.077 closest distance to " CB  SER A 216 " =    1.009
peak=    4.072 closest distance to " NH1AARG A 145 " =    1.174
peak=    4.050 closest distance to " N   GLU A   2 " =    1.385
peak=    4.044 closest distance to " O   HOH Z 214 " =    1.822
peak=    4.025 closest distance to " O   HOH Z 375 " =    0.853
peak=    4.023 closest distance to " CB  ASN A 148 " =    1.399
peak=    4.017 closest distance to " O   HOH Z 327 " =    1.760
peak=    3.995 closest distance to " O   HOH Z 431 " =    1.483
peak=    3.993 closest distance to " CD  ARG A  66 " =    2.169
peak=    3.992 closest distance to " CG  TRP A 179 " =    2.164
peak=    3.990 closest distance to " OG BSER A  99 " =    2.294
peak=    3.986 closest distance to " O   HOH Z 193 " =    1.680
peak=    3.974 closest distance to " O   HOH Z  30 " =    1.885
peak=    3.969 closest distance to " O   HOH Z 368 " =    3.830
peak=    3.962 closest distance to " CD  ARG A 159 " =    0.833
peak=    3.957 closest distance to " CB  LYS A 117 " =    1.214
peak=    3.947 closest distance to " OG  SER A  62 " =    3.051
peak=    3.944 closest distance to " O   HOH Z 290 " =    0.975
peak=    3.905 closest distance to " CB  TRP A 266 " =    1.066
peak=    3.903 closest distance to " CB  GLU A 277 " =    3.581
peak=    3.891 closest distance to " CA  ASN A 127 " =    1.093
peak=    3.877 closest distance to " CB  ASN A  39 " =    0.950
peak=    3.875 closest distance to " O   HOH Z  61 " =    1.553
peak=    3.873 closest distance to " O   HOH Z 437 " =    2.042
peak=    3.872 closest distance to " CG2 THR A 221 " =    1.151
peak=    3.860 closest distance to " CB  ASP A 124 " =    0.955
peak=    3.850 closest distance to " CA  ALA A 160 " =    0.867
peak=    3.848 closest distance to " O   HOH Z 112 " =    1.180
peak=    3.845 closest distance to " O   HOH Z  59 " =    1.497
peak=    3.822 closest distance to " O   HOH Z 293 " =    1.445
peak=    3.822 closest distance to " O   HOH Z 258 " =    1.951
peak=    3.796 closest distance to " O   HOH Z  88 " =    3.695
peak=    3.783 closest distance to " O   HOH Z 276 " =    1.106
peak=    3.769 closest distance to " O   HOH Z 390 " =    2.553
peak=    3.768 closest distance to " O   HOH Z 119 " =    4.182
peak=    3.764 closest distance to " O   HOH Z 389 " =    1.167
peak=    3.763 closest distance to " NE2 GLN A 278 " =    3.778
peak=    3.761 closest distance to " O   HOH Z 403 " =    1.351
peak=    3.755 closest distance to " O   HOH Z 244 " =    1.543
peak=    3.754 closest distance to " O   HOH Z  88 " =    2.829
peak=    3.750 closest distance to " OD2 ASP A 286 " =    2.736
peak=    3.750 closest distance to " CB  LEU A 228 " =    1.212
peak=    3.747 closest distance to " O   HOH Z 418 " =    1.047
peak=    3.744 closest distance to " CA  MET A 105 " =    0.904
peak=    3.741 closest distance to " O   HOH Z  68 " =    1.948
peak=    3.740 closest distance to " O   HOH Z 115 " =    1.502
peak=    3.736 closest distance to " O   HOH Z 411 " =    3.717
peak=    3.728 closest distance to " N   ALA A   1 " =    1.374
peak=    3.721 closest distance to " O   HOH Z 222 " =    2.053
peak=    3.721 closest distance to " O  BHOH Z  74 " =    1.427
peak=    3.719 closest distance to " CA  ILE A 234 " =    1.078
peak=    3.716 closest distance to " O   HOH Z 217 " =    2.888
peak=    3.715 closest distance to " CB  GLU A 128 " =    1.140
peak=    3.708 closest distance to " O   HOH Z 166 " =    1.484
peak=    3.707 closest distance to " CG  PRO A 198 " =    1.230
peak=    3.702 closest distance to " CB  VAL A 202 " =    1.645
peak=    3.701 closest distance to " O   HOH Z 122 " =    1.757
peak=    3.701 closest distance to " O   HOH Z 385 " =    3.592
peak=    3.694 closest distance to " CB  SER A   3 " =    1.324
peak=    3.691 closest distance to " O   HOH Z 195 " =    1.570
peak=    3.678 closest distance to " N   CYS A 260 " =    0.842
peak=    3.676 closest distance to " OD1 ASN A  69 " =    2.534
peak=    3.669 closest distance to " CB  SER A 276 " =    1.100
peak=    3.661 closest distance to " O   HOH Z 156 " =    3.183
peak=    3.655 closest distance to " CA  PHE A 283 " =    1.409
peak=    3.653 closest distance to " O   HOH Z  20 " =    1.515
peak=    3.643 closest distance to " O   HOH Z 425 " =    2.165
peak=    3.641 closest distance to " O   HOH Z 106 " =    3.909
peak=    3.638 closest distance to " O   HOH Z  39 " =    1.059
peak=    3.636 closest distance to " O   HOH Z 378 " =    0.844
peak=    3.629 closest distance to " O   HOH Z 359 " =    1.331
peak=    3.622 closest distance to " O   HOH Z 405 " =    1.583
peak=    3.621 closest distance to " O   HOH Z 193 " =    1.623
peak=    3.615 closest distance to " O   HOH Z   7 " =    3.218
peak=    3.609 closest distance to " O   HOH Z  17 " =    1.775
peak=    3.602 closest distance to " O   ASN A 209 " =    1.463
peak=    3.598 closest distance to " CB  GLU A 152 " =    1.307
peak=    3.593 closest distance to " NE2 GLN A  58 " =    4.119
peak=    3.588 closest distance to " O   HOH Z 155 " =    1.746
peak=    3.588 closest distance to " NE1 TRP A 274 " =    1.036
peak=    3.581 closest distance to " O   HOH Z 361 " =    1.295
peak=    3.578 closest distance to " O   HOH Z  32 " =    2.263
peak=    3.574 closest distance to " O   HOH Z 422 " =    2.455
peak=    3.565 closest distance to " OG BSER A 258 " =    0.915
peak=    3.560 closest distance to " O   HOH Z  44 " =    2.781
peak=    3.556 closest distance to " CB  VAL A 265 " =    1.333
peak=    3.555 closest distance to " O   HOH Z 158 " =    2.523
peak=    3.548 closest distance to " O   HOH Z 250 " =    1.324
peak=    3.544 closest distance to " CZ3 TRP A 266 " =    1.110
peak=    3.542 closest distance to " O   HOH Z 128 " =    2.255
peak=    3.536 closest distance to " O   HOH Z 302 " =    1.404
peak=    3.523 closest distance to " O   HOH Z 272 " =    1.788
peak=    3.518 closest distance to " O   HOH Z 362 " =    1.832
peak=    3.517 closest distance to " CA  ALA A  51 " =    1.079
peak=    3.511 closest distance to " O   HOH Z 175 " =    2.085
peak=    3.510 closest distance to " CE3 TRP A 274 " =    1.319
peak=    3.503 closest distance to " CB  THR A 157 " =    1.084
peak=    3.498 closest distance to " CA  VAL A 125 " =    1.093
peak=    3.495 closest distance to " ND1 HIS A  86 " =    1.925
peak=    3.483 closest distance to " CD  LYS A 166 " =    1.442
peak=    3.477 closest distance to " CB  ALA A 114 " =    1.478
peak=    3.476 closest distance to " CB  GLN A  89 " =    1.302
peak=    3.471 closest distance to " CA  GLY A 267 " =    1.267
peak=    3.462 closest distance to " CB  TRP A 179 " =    1.474
peak=    3.461 closest distance to " O   HOH Z  49 " =    1.396
peak=    3.458 closest distance to " CA  ALA A 180 " =    1.314
peak=    3.453 closest distance to " CB  SER A 212 " =    1.162
peak=    3.453 closest distance to " O   HOH Z 357 " =    1.931
peak=    3.445 closest distance to " O   HOH Z 207 " =    2.374
peak=    3.444 closest distance to " O   HOH Z 407 " =    1.507
peak=    3.443 closest distance to " CB  TYR A 116 " =    1.044
peak=    3.438 closest distance to " CG2 VAL A 257 " =    0.864
peak=    3.438 closest distance to " CA  THR A 221 " =    1.089
peak=    3.429 closest distance to " O   HOH Z 222 " =    2.365
peak=    3.428 closest distance to " O   HOH Z 124 " =    1.374
peak=    3.427 closest distance to " O   HOH Z  92 " =    1.198
peak=    3.426 closest distance to " OE2 GLU A  53 " =    2.031
peak=    3.425 closest distance to " CE  LYS A  76 " =    0.799
peak=    3.422 closest distance to " OG  SER A  22 " =    2.848
peak=    3.420 closest distance to " O   HOH Z  44 " =    1.765
peak=    3.418 closest distance to " O   HOH Z 116 " =    2.806
peak=    3.416 closest distance to " O   HOH Z  40 " =    2.163
peak=    3.409 closest distance to " ND2 ASN A 187 " =    1.442
peak=    3.409 closest distance to " CB  TRP A 150 " =    0.932
peak=    3.406 closest distance to " O   HOH Z 346 " =    1.827
peak=    3.405 closest distance to " O   HOH Z 345 " =    1.870
peak=    3.403 closest distance to " O   HOH Z 126 " =    1.363
peak=    3.401 closest distance to " O   HOH Z 130 " =    2.109
peak=    3.397 closest distance to " O   HOH Z 344 " =    3.262
peak=    3.396 closest distance to " OG1 THR A 221 " =    1.547
peak=    3.395 closest distance to " NZ  LYS A 117 " =    1.162
peak=    3.394 closest distance to " CG1 ILE A 151 " =    1.113
peak=    3.391 closest distance to " O   HOH Z 234 " =    3.766
peak=    3.389 closest distance to " O   HOH Z   9 " =    1.915
peak=    3.389 closest distance to " O   HOH Z 146 " =    1.623
peak=    3.389 closest distance to " O   HOH Z 133 " =    1.263
peak=    3.386 closest distance to " O   HOH Z 369 " =    1.631
peak=    3.381 closest distance to " CA  ALA A 291 " =    0.889
peak=    3.380 closest distance to " O   HOH Z  61 " =    1.596
peak=    3.378 closest distance to " CA  ARG A  36 " =    1.255
peak=    3.378 closest distance to " O   HOH Z 311 " =    2.339
peak=    3.368 closest distance to " O   HOH Z  55 " =    1.683
peak=    3.364 closest distance to " CB  ALA A  10 " =    1.353
peak=    3.357 closest distance to " ND2 ASN A 249 " =    0.849
peak=    3.351 closest distance to " ND1 HIS A  81 " =    1.619
peak=    3.345 closest distance to " O   HOH Z 189 " =    2.959
peak=    3.344 closest distance to " CB  MET A 105 " =    1.377
peak=    3.342 closest distance to " CD  PRO A 243 " =    1.750
peak=    3.340 closest distance to " O   HOH Z 135 " =    1.774
peak=    3.338 closest distance to " O   HOH Z 412 " =    1.283
peak=    3.335 closest distance to " O   HOH Z 371 " =    1.926
peak=    3.335 closest distance to " CB  ALA A 114 " =    1.265
peak=    3.332 closest distance to " CE AMET A  47 " =    1.307
peak=    3.331 closest distance to " CG1BVAL A 121 " =    2.147
peak=    3.329 closest distance to " CG  GLN A  11 " =    2.079
peak=    3.325 closest distance to " O   HOH Z  97 " =    1.844
peak=    3.322 closest distance to " CB  ASN A 148 " =    2.149
peak=    3.318 closest distance to " CG  LEU A 101 " =    1.214
peak=    3.318 closest distance to " O   HOH Z 152 " =    2.012
peak=    3.318 closest distance to " O   HOH Z 288 " =    1.948
peak=    3.317 closest distance to " CB  LEU A 300 " =    0.923
peak=    3.317 closest distance to " O   HOH Z 113 " =    1.825
peak=    3.315 closest distance to " O   ASN A  74 " =    1.586
peak=    3.315 closest distance to " CA  SER A  95 " =    0.954
peak=    3.314 closest distance to " CA  ARG A 195 " =    1.411
peak=    3.312 closest distance to " CE  MET A  93 " =    1.430
peak=    3.311 closest distance to " O   HOH Z   1 " =    1.458
peak=    3.309 closest distance to " CG1 ILE A 120 " =    1.401
peak=    3.307 closest distance to " CH2 TRP A 150 " =    0.999
peak=    3.306 closest distance to " O   MET A 105 " =    1.724
peak=    3.304 closest distance to " O   HOH Z 365 " =    2.592
peak=    3.299 closest distance to " O   HOH Z 119 " =    1.526
peak=    3.294 closest distance to " CA  ASN A  74 " =    1.247
peak=    3.292 closest distance to " O   HOH Z  51 " =    1.659
peak=    3.291 closest distance to " CD2 TRP A 179 " =    1.349
peak=    3.290 closest distance to " CB  THR A  31 " =    1.597
peak=    3.290 closest distance to " CA  ASN A 215 " =    1.087
peak=    3.287 closest distance to " CB  ARG A 138 " =    0.832
peak=    3.285 closest distance to " O   HOH Z 151 " =    1.453
peak=    3.284 closest distance to " O   HOH Z 421 " =    2.906
peak=    3.284 closest distance to " CB  GLU A  46 " =    1.072
peak=    3.283 closest distance to " CG2 VAL A 197 " =    1.101
peak=    3.283 closest distance to " CB  GLN A  88 " =    1.282
peak=    3.282 closest distance to " OG BSER A 164 " =    2.124
peak=    3.280 closest distance to " N   ALA A   1 " =    2.741
peak=    3.274 closest distance to " CA  ALA A 299 " =    0.895
peak=    3.273 closest distance to " CG2 ILE A 234 " =    0.898
peak=    3.273 closest distance to " N   ILE A  33 " =    1.094
peak=    3.270 closest distance to " CD1 ILE A 263 " =    1.299
peak=    3.270 closest distance to " O   HOH Z 214 " =    3.581
peak=    3.269 closest distance to " CB  PHE A 225 " =    1.329
peak=    3.268 closest distance to " CG2 VAL A 232 " =    0.955
peak=    3.265 closest distance to " OE1 GLN A 240 " =    1.583
peak=    3.265 closest distance to " O   HOH Z 104 " =    1.375
peak=    3.264 closest distance to " O   HOH Z 108 " =    2.432
peak=    3.258 closest distance to " CZ  PHE A  38 " =    1.365
peak=    3.256 closest distance to " CB  PHE A 130 " =    1.188
peak=    3.255 closest distance to " O   HOH Z  11 " =    1.167
peak=    3.255 closest distance to " N   GLN A 278 " =    1.206
peak=    3.255 closest distance to " CB  LEU A 237 " =    0.724
peak=    3.253 closest distance to " O   HOH Z 193 " =    1.930
peak=    3.253 closest distance to " CG  GLN A  89 " =    1.470
peak=    3.251 closest distance to " O   HOH Z 261 " =    1.874
peak=    3.248 closest distance to " NZ  LYS A 119 " =    1.251
peak=    3.239 closest distance to " NZ  LYS A  48 " =    1.289
peak=    3.238 closest distance to " NZ BLYS A 290 " =    0.886
peak=    3.237 closest distance to " CE3 TRP A  85 " =    0.844
peak=    3.232 closest distance to " O   HOH Z 363 " =    1.032
peak=    3.230 closest distance to " CE3 TRP A 150 " =    1.034
peak=    3.226 closest distance to " O   HOH Z 323 " =    1.606
peak=    3.225 closest distance to " O   HOH Z  77 " =    1.293
peak=    3.223 closest distance to " O   HOH Z 389 " =    1.707
peak=    3.222 closest distance to " O   HOH Z 272 " =    2.082
peak=    3.212 closest distance to " CB  ASP A 171 " =    0.728
peak=    3.210 closest distance to " O   HOH Z 430 " =    1.824
peak=    3.209 closest distance to " O   THR A 220 " =    1.697
peak=    3.208 closest distance to " NH1BARG A 145 " =    1.236
peak=    3.207 closest distance to " CD1 LEU A 300 " =    1.076
peak=    3.205 closest distance to " O   HOH Z  50 " =    1.746
peak=    3.204 closest distance to " CB  ALA A  43 " =    0.826
peak=    3.194 closest distance to " N   SER A 271 " =    1.061
peak=    3.192 closest distance to " O   HOH Z 132 " =    2.332
peak=    3.188 closest distance to " N   VAL A 296 " =    1.782
peak=    3.188 closest distance to " ND2BASN A 224 " =    0.805
peak=    3.186 closest distance to " CG  ARG A 159 " =    0.804
peak=    3.185 closest distance to " CB  TYR A  30 " =    1.331
peak=    3.183 closest distance to " CG1 VAL A 153 " =    0.809
peak=    3.182 closest distance to " CG1 ILE A 263 " =    1.336
peak=    3.182 closest distance to " O   HOH Z 180 " =    2.269
peak=    3.182 closest distance to " CB  MET A  40 " =    0.923
peak=    3.182 closest distance to " O   HOH Z 424 " =    3.053
peak=    3.178 closest distance to " NH2AARG A 190 " =    1.714
peak=    3.177 closest distance to " O   HOH Z 235 " =    1.777
peak=    3.176 closest distance to " CB  ASP A 140 " =    0.982
peak=    3.174 closest distance to " CG2 THR A 178 " =    1.161
peak=    3.168 closest distance to " N   TYR A  15 " =    1.121
peak=    3.162 closest distance to " O  BHOH Z 338 " =    2.354
peak=    3.162 closest distance to " O   HOH Z  88 " =    2.592
peak=    3.162 closest distance to " O   HOH Z  59 " =    2.288
peak=    3.162 closest distance to " O   HOH Z 393 " =    1.230
peak=    3.162 closest distance to " O   GLY A 302 " =    2.323
peak=    3.159 closest distance to " CA  ARG A 102 " =    1.108
peak=    3.159 closest distance to " NE AARG A 275 " =    1.520
peak=    3.158 closest distance to " CA  ALA A 158 " =    1.164
peak=    3.158 closest distance to " O   HOH Z 260 " =    2.397
peak=    3.158 closest distance to " CB  ASN A 187 " =    1.002
peak=    3.158 closest distance to " O   HOH Z 358 " =    1.175
peak=    3.157 closest distance to " CA  ASN A 217 " =    1.145
peak=    3.156 closest distance to " O   HOH Z 303 " =    2.574
peak=    3.154 closest distance to " CA  ALA A 233 " =    0.904
peak=    3.151 closest distance to " CB  ASN A 215 " =    1.102
peak=    3.150 closest distance to " O   HOH Z 106 " =    2.583
peak=    3.147 closest distance to " NH2 ARG A 219 " =    1.815
peak=    3.138 closest distance to " CD2 LEU A 297 " =    1.019
peak=    3.137 closest distance to " CD1 ILE A  33 " =    1.662
peak=    3.137 closest distance to " CG1 ILE A  33 " =    1.254
peak=    3.130 closest distance to " CB  ALA A 248 " =    1.014
peak=    3.129 closest distance to " O   HOH Z 172 " =    2.189
peak=    3.127 closest distance to " O   HOH Z 402 " =    1.494
peak=    3.126 closest distance to " O   HOH Z 409 " =    2.015
peak=    3.121 closest distance to " N   SER A 134 " =    1.379
peak=    3.119 closest distance to " OE1 GLU A  37 " =    1.274
peak=    3.117 closest distance to " N   ASN A 127 " =    1.373
peak=    3.101 closest distance to " O   HOH Z 153 " =    3.785
peak=    3.099 closest distance to " CB  GLU A 236 " =    1.521
peak=    3.098 closest distance to " OD1 ASN A 217 " =    1.603
peak=    3.084 closest distance to " CB  GLU A 236 " =    1.293
peak=    3.079 closest distance to " O   HOH Z 438 " =    1.732
peak=    3.073 closest distance to " N   SER A 210 " =    1.154
peak=    3.066 closest distance to " CA  ALA A 129 " =    1.172
peak=    3.060 closest distance to " O   HOH Z  76 " =    0.835
peak=    3.050 closest distance to " O   ALA A   1 " =    1.622
peak=    3.048 closest distance to " CA  GLU A  46 " =    0.741

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 228         
Filter by distance & map next to the model:
   mapped sites are within: 0.915 - 5.861
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 228 from: 228
   mapped sites are within: 0.915 - 5.861

peak=   -4.464 closest distance to " CD  ARG A  14 " =    3.369
peak=   -4.440 closest distance to " CB  PRO A 243 " =    2.556
peak=   -4.343 closest distance to " CG1BVAL A  41 " =    2.802
peak=   -4.307 closest distance to " CA  GLY A  98 " =    1.756
peak=   -4.299 closest distance to " N   THR A 157 " =    1.528
peak=   -4.223 closest distance to " O   HOH Z 385 " =    1.391
peak=   -4.156 closest distance to " O   PRO A 198 " =    1.288
peak=   -4.128 closest distance to " OG BSER A 134 " =    1.525
peak=   -4.098 closest distance to " CB  ASP A  27 " =    2.474
peak=   -4.064 closest distance to " O   SER A  22 " =    2.685
peak=   -4.028 closest distance to " O   HOH Z 407 " =    3.143
peak=   -4.026 closest distance to " O   HOH Z 377 " =    1.900
peak=   -4.008 closest distance to " O   SER A 135 " =    1.519
peak=   -4.005 closest distance to " O   ASP A 191 " =    1.846
peak=   -3.992 closest distance to " O   HOH Z 197 " =    3.427
peak=   -3.992 closest distance to " O   PHE A 218 " =    1.352
peak=   -3.955 closest distance to " CB  ALA A 291 " =    2.121
peak=   -3.952 closest distance to " O   HOH Z 185 " =    1.951
peak=   -3.950 closest distance to " O   HOH Z  60 " =    1.948
peak=   -3.931 closest distance to " CZ2 TRP A 274 " =    0.927
peak=   -3.858 closest distance to " N   ALA A  43 " =    2.572
peak=   -3.845 closest distance to " O   ALA A  10 " =    1.702
peak=   -3.841 closest distance to " CB  ALA A 248 " =    2.042
peak=   -3.832 closest distance to " ND2 ASN A 249 " =    2.078
peak=   -3.816 closest distance to " O   HOH Z 313 " =    1.373
peak=   -3.814 closest distance to " O   HOH Z 111 " =    1.906
peak=   -3.792 closest distance to " CA  GLY A 203 " =    2.338
peak=   -3.788 closest distance to " NH2 ARG A 219 " =    1.900
peak=   -3.785 closest distance to " CB  ALA A 100 " =    1.936
peak=   -3.778 closest distance to " O   HOH Z 166 " =    1.288
peak=   -3.773 closest distance to " OG  SER A  97 " =    2.268
peak=   -3.737 closest distance to " O   HOH Z 231 " =    1.963
peak=   -3.711 closest distance to " CG1 VAL A  78 " =    2.473
peak=   -3.688 closest distance to " CB  ALA A  43 " =    2.325
peak=   -3.684 closest distance to " OG  SER A  87 " =    1.295
peak=   -3.677 closest distance to " O   HOH Z 298 " =    2.694
peak=   -3.676 closest distance to " CE2 TYR A  30 " =    2.582
peak=   -3.662 closest distance to " CA  GLY A 241 " =    2.192
peak=   -3.657 closest distance to " C   ALA A 114 " =    2.156
peak=   -3.643 closest distance to " CD2 TYR A 293 " =    1.803
peak=   -3.641 closest distance to " O   HOH Z  52 " =    1.114
peak=   -3.634 closest distance to " CG  PHE A 283 " =    2.682
peak=   -3.629 closest distance to " O   HOH Z 435 " =    3.161
peak=   -3.627 closest distance to " CB  ALA A 114 " =    2.444
peak=   -3.621 closest distance to " C   ALA A 158 " =    1.742
peak=   -3.612 closest distance to " CZ3 TRP A 179 " =    1.304
peak=   -3.612 closest distance to " CZ  PHE A  59 " =    1.494
peak=   -3.612 closest distance to " ND2 ASN A 209 " =    1.980
peak=   -3.609 closest distance to " O   HOH Z 196 " =    1.867
peak=   -3.604 closest distance to " O   HOH Z 426 " =    1.603
peak=   -3.587 closest distance to " CB  ALA A   9 " =    2.320
peak=   -3.587 closest distance to " O   ASP A 162 " =    2.256
peak=   -3.582 closest distance to " O   HOH Z 389 " =    2.136
peak=   -3.579 closest distance to " CD2 PHE A 130 " =    2.924
peak=   -3.571 closest distance to " O   HOH Z  28 " =    1.717
peak=   -3.566 closest distance to " OE1 GLN A 223 " =    2.249
peak=   -3.565 closest distance to " CB  ALA A  10 " =    2.266
peak=   -3.564 closest distance to " N   GLN A  58 " =    1.324
peak=   -3.560 closest distance to " O   GLY A  80 " =    2.464
peak=   -3.558 closest distance to " OE1 GLU A 277 " =    2.190
peak=   -3.557 closest distance to " O   HOH Z 102 " =    1.629
peak=   -3.552 closest distance to " O   HOH Z  39 " =    1.246
peak=   -3.546 closest distance to " O   HOH Z 286 " =    1.687
peak=   -3.542 closest distance to " OD2 ASP A 171 " =    1.939
peak=   -3.536 closest distance to " O   HOH Z 131 " =    4.002
peak=   -3.532 closest distance to " CD1 TRP A 179 " =    1.271
peak=   -3.531 closest distance to " O   VAL A 125 " =    2.076
peak=   -3.523 closest distance to " O   HOH Z  65 " =    1.041
peak=   -3.521 closest distance to " CG  GLN A  58 " =    1.233
peak=   -3.520 closest distance to " O   HOH Z 218 " =    3.642
peak=   -3.517 closest distance to " O   ARG A 145 " =    1.403
peak=   -3.515 closest distance to " CB  ASP A 132 " =    2.504
peak=   -3.508 closest distance to " CD  ARG A 156 " =    2.086
peak=   -3.506 closest distance to " CD1 ILE A 239 " =    2.555
peak=   -3.499 closest distance to " O   ILE A  49 " =    1.549
peak=   -3.495 closest distance to " CE3 TRP A 274 " =    2.383
peak=   -3.494 closest distance to " O   HOH Z  24 " =    1.072
peak=   -3.494 closest distance to " OG BSER A 134 " =    1.813
peak=   -3.491 closest distance to " ND2 ASN A 285 " =    2.013
peak=   -3.488 closest distance to " C   HIS A 207 " =    1.233
peak=   -3.486 closest distance to " O   HOH Z  90 " =    2.531
peak=   -3.485 closest distance to " O   HOH Z 351 " =    1.634
peak=   -3.480 closest distance to " CG  MET A 105 " =    0.936
peak=   -3.478 closest distance to " CD  ARG A 139 " =    1.686
peak=   -3.478 closest distance to " CB  TRP A  85 " =    2.494
peak=   -3.478 closest distance to " O   HOH Z  22 " =    2.879
peak=   -3.477 closest distance to " OG  SER A 206 " =    1.930
peak=   -3.469 closest distance to " O   HOH Z 211 " =    1.525
peak=   -3.468 closest distance to " ND2 ASN A 187 " =    1.423
peak=   -3.468 closest distance to " CE2 TYR A 116 " =    3.122
peak=   -3.464 closest distance to " O   PRO A 163 " =    1.920
peak=   -3.464 closest distance to " O   HOH Z 409 " =    5.777
peak=   -3.460 closest distance to " O   HOH Z  73 " =    2.363
peak=   -3.459 closest distance to " CE2 PHE A 218 " =    2.402
peak=   -3.454 closest distance to " CG  ASN A  39 " =    1.727
peak=   -3.446 closest distance to " CB  PRO A 213 " =    2.088
peak=   -3.445 closest distance to " CD  LYS A 166 " =    2.393
peak=   -3.441 closest distance to " NH2AARG A 275 " =    5.351
peak=   -3.436 closest distance to " O   HOH Z   1 " =    1.368
peak=   -3.434 closest distance to " CG2 ILE A  49 " =    2.728
peak=   -3.426 closest distance to " O   HOH Z 122 " =    2.218
peak=   -3.419 closest distance to " O   HOH Z 281 " =    2.895
peak=   -3.418 closest distance to " NH1 ARG A 195 " =    2.385
peak=   -3.411 closest distance to " O   HOH Z 143 " =    1.391
peak=   -3.398 closest distance to " CB  ASN A  39 " =    2.198
peak=   -3.388 closest distance to " O   HOH Z  22 " =    2.384
peak=   -3.385 closest distance to " O   HOH Z  68 " =    1.509
peak=   -3.385 closest distance to " CD2 LEU A  25 " =    2.055
peak=   -3.384 closest distance to " O   HOH Z 198 " =    1.885
peak=   -3.381 closest distance to " CB  GLN A  55 " =    1.217
peak=   -3.379 closest distance to " O   HOH Z 266 " =    4.728
peak=   -3.378 closest distance to " CG  GLN A 240 " =    2.238
peak=   -3.374 closest distance to " O   ASN A 301 " =    1.389
peak=   -3.364 closest distance to " OG  SER A  26 " =    1.213
peak=   -3.358 closest distance to " O   VAL A  67 " =    2.516
peak=   -3.355 closest distance to " OG  SER A  63 " =    1.377
peak=   -3.352 closest distance to " N   VAL A 232 " =    2.178
peak=   -3.349 closest distance to " O   HOH Z  49 " =    1.227
peak=   -3.345 closest distance to " O   HOH Z 352 " =    1.927
peak=   -3.343 closest distance to " O   HOH Z 429 " =    1.796
peak=   -3.343 closest distance to " CB  ALA A 227 " =    2.346
peak=   -3.340 closest distance to " O   HOH Z 147 " =    1.264
peak=   -3.334 closest distance to " CB  TYR A  15 " =    2.185
peak=   -3.334 closest distance to " O   HOH Z 323 " =    2.091
peak=   -3.330 closest distance to " O   HOH Z 200 " =    3.617
peak=   -3.326 closest distance to " O   HOH Z 114 " =    0.988
peak=   -3.324 closest distance to " O   HOH Z 337 " =    1.485
peak=   -3.324 closest distance to " CG2 ILE A 151 " =    2.482
peak=   -3.324 closest distance to " NE  ARG A  36 " =    1.828
peak=   -3.314 closest distance to " OH  TYR A 172 " =    1.803
peak=   -3.307 closest distance to " ND2 ASN A  60 " =    4.180
peak=   -3.306 closest distance to " O   LEU A 300 " =    2.226
peak=   -3.305 closest distance to " CA  GLY A 133 " =    1.883
peak=   -3.304 closest distance to " O   SER A  62 " =    2.418
peak=   -3.303 closest distance to " O   HOH Z 289 " =    1.688
peak=   -3.301 closest distance to " CG1 VAL A 250 " =    2.634
peak=   -3.298 closest distance to " N   LEU A 282 " =    2.133
peak=   -3.289 closest distance to " O   VAL A 197 " =    1.817
peak=   -3.282 closest distance to " O   HOH Z 298 " =    1.087
peak=   -3.281 closest distance to " O   LEU A 261 " =    1.243
peak=   -3.281 closest distance to " O   HOH Z 265 " =    1.986
peak=   -3.279 closest distance to " O   HOH Z 393 " =    2.810
peak=   -3.276 closest distance to " O   HOH Z 348 " =    1.881
peak=   -3.275 closest distance to " CG2 VAL A 232 " =    2.040
peak=   -3.275 closest distance to " O   HOH Z 275 " =    1.598
peak=   -3.272 closest distance to " CG2BVAL A  72 " =    1.598
peak=   -3.272 closest distance to " OG  SER A 273 " =    1.975
peak=   -3.269 closest distance to " O   HOH Z  43 " =    1.752
peak=   -3.262 closest distance to " CG  LEU A 281 " =    1.836
peak=   -3.256 closest distance to " O   HOH Z 174 " =    2.805
peak=   -3.253 closest distance to " O   HOH Z  88 " =    1.705
peak=   -3.253 closest distance to " O   TRP A  70 " =    1.450
peak=   -3.249 closest distance to " OE1 GLN A 223 " =    2.232
peak=   -3.249 closest distance to " O   GLU A 152 " =    1.416
peak=   -3.248 closest distance to " CB  PRO A  90 " =    1.541
peak=   -3.248 closest distance to " CG  TRP A  85 " =    0.942
peak=   -3.245 closest distance to " CG  GLN A  58 " =    0.915
peak=   -3.238 closest distance to " OD2 ASP A 191 " =    1.573
peak=   -3.236 closest distance to " CB  CYS A 201 " =    2.030
peak=   -3.235 closest distance to " O   HOH Z 292 " =    1.580
peak=   -3.232 closest distance to " OG ASER A 134 " =    1.287
peak=   -3.232 closest distance to " OG  SER A 245 " =    1.368
peak=   -3.232 closest distance to " C   HIS A 108 " =    1.237
peak=   -3.228 closest distance to " O   HOH Z 318 " =    1.659
peak=   -3.228 closest distance to " O   HOH Z 166 " =    1.920
peak=   -3.226 closest distance to " O   HOH Z 359 " =    1.451
peak=   -3.220 closest distance to " O   HOH Z 108 " =    1.946
peak=   -3.219 closest distance to " N   ASP A 171 " =    2.387
peak=   -3.218 closest distance to " O   HOH Z 350 " =    2.100
peak=   -3.218 closest distance to " O   ALA A 180 " =    1.236
peak=   -3.207 closest distance to " O   ALA A   1 " =    1.313
peak=   -3.206 closest distance to " O   HOH Z  64 " =    1.631
peak=   -3.206 closest distance to " NH2 ARG A  79 " =    2.077
peak=   -3.205 closest distance to " CA  GLY A 241 " =    3.012
peak=   -3.205 closest distance to " O   HOH Z  53 " =    1.728
peak=   -3.202 closest distance to " O   HOH Z 132 " =    5.052
peak=   -3.201 closest distance to " O   HOH Z 251 " =    1.179
peak=   -3.200 closest distance to " O   HOH Z 336 " =    5.861
peak=   -3.191 closest distance to " CG  PRO A 163 " =    2.659
peak=   -3.185 closest distance to " O   HOH Z 389 " =    1.206
peak=   -3.185 closest distance to " CG  ARG A 269 " =    2.459
peak=   -3.181 closest distance to " CG  GLN A 278 " =    2.316
peak=   -3.179 closest distance to " O   HOH Z  60 " =    2.214
peak=   -3.177 closest distance to " CA  ASN A 148 " =    1.754
peak=   -3.173 closest distance to " CG2 ILE A  20 " =    2.610
peak=   -3.171 closest distance to " CG1BVAL A  72 " =    2.163
peak=   -3.170 closest distance to " CB  PHE A 130 " =    1.219
peak=   -3.169 closest distance to " O   THR A  82 " =    1.287
peak=   -3.166 closest distance to " N   ALA A 295 " =    1.442
peak=   -3.161 closest distance to " O   VAL A 174 " =    2.338
peak=   -3.156 closest distance to " CE BMET A  47 " =    1.250
peak=   -3.156 closest distance to " OD2 ASP A 132 " =    2.125
peak=   -3.155 closest distance to " OE1 GLN A  58 " =    2.946
peak=   -3.155 closest distance to " CG2 VAL A 189 " =    1.863
peak=   -3.148 closest distance to " O   HOH Z  77 " =    1.711
peak=   -3.148 closest distance to " O   HOH Z 201 " =    2.163
peak=   -3.147 closest distance to " O   HOH Z 155 " =    1.108
peak=   -3.147 closest distance to " O   HOH Z  11 " =    1.770
peak=   -3.146 closest distance to " O   HOH Z 105 " =    2.863
peak=   -3.140 closest distance to " O   HOH Z 140 " =    1.385
peak=   -3.140 closest distance to " O   HOH Z 418 " =    1.603
peak=   -3.139 closest distance to " CG1 VAL A 197 " =    1.977
peak=   -3.136 closest distance to " O   ALA A  51 " =    1.287
peak=   -3.135 closest distance to " CE1 PHE A  59 " =    2.118
peak=   -3.135 closest distance to " NE2 GLN A  77 " =    2.291
peak=   -3.135 closest distance to " N   ASN A  60 " =    1.174
peak=   -3.130 closest distance to " O   HOH Z 139 " =    2.976
peak=   -3.128 closest distance to " CG1BVAL A  41 " =    2.711
peak=   -3.127 closest distance to " O   HOH Z  51 " =    1.019
peak=   -3.127 closest distance to " CG1 VAL A 125 " =    2.258
peak=   -3.127 closest distance to " CB  SER A 245 " =    2.401
peak=   -3.121 closest distance to " CG1 VAL A 265 " =    2.293
peak=   -3.120 closest distance to " O   HOH Z 198 " =    1.978
peak=   -3.110 closest distance to " CZ  TYR A 169 " =    1.820
peak=   -3.110 closest distance to " O   HOH Z 213 " =    1.513
peak=   -3.106 closest distance to " N   ALA A   1 " =    1.401
peak=   -3.102 closest distance to " O   HOH Z 103 " =    1.702
peak=   -3.097 closest distance to " O   ALA A  84 " =    1.636
peak=   -3.096 closest distance to " O   HOH Z 231 " =    1.248
peak=   -3.091 closest distance to " CB  ALA A 131 " =    1.854
peak=   -3.085 closest distance to " CB  PHE A 192 " =    1.640
peak=   -3.074 closest distance to " O   HOH Z  56 " =    1.619
peak=   -3.071 closest distance to " N   ASP A 270 " =    1.379
peak=   -3.070 closest distance to " CG  TRP A 266 " =    1.709
peak=   -3.053 closest distance to " OG  SER A  32 " =    1.259
peak=   -3.049 closest distance to " O   HOH Z 297 " =    2.344
peak=   -3.041 closest distance to " O   HOH Z 295 " =    2.004
peak=   -3.029 closest distance to " CE  MET A 105 " =    2.271

================= 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    :  0.4227 0.4183   6.245393e+00   6.237350e+00
   1_bss:  0.4100 0.4086   6.234809e+00   6.225636e+00
   1_xyz:  0.3444 0.3846   6.103933e+00   6.172609e+00
   1_adp:  0.3158 0.3909   6.060869e+00   6.181286e+00
   1_occ:  0.3155 0.3912   6.060363e+00   6.181466e+00
   2_bss:  0.3152 0.3891   6.060336e+00   6.181877e+00
   2_xyz:  0.2515 0.3207   5.866056e+00   6.023070e+00
   2_adp:  0.2347 0.3110   5.817664e+00   5.993445e+00
   2_occ:  0.2345 0.3108   5.817155e+00   5.993550e+00
   3_bss:  0.2339 0.3088   5.812360e+00   5.989155e+00
   3_xyz:  0.2007 0.2585   5.659895e+00   5.849059e+00
   3_adp:  0.1858 0.2460   5.601003e+00   5.809123e+00
   3_occ:  0.1856 0.2457   5.600252e+00   5.808162e+00
   4_bss:  0.1856 0.2453   5.598835e+00   5.805580e+00
   4_xyz:  0.1471 0.2019   5.390604e+00   5.626086e+00
   4_adp:  0.1356 0.1904   5.324536e+00   5.568821e+00
   4_occ:  0.1356 0.1902   5.324234e+00   5.568454e+00
   5_bss:  0.1360 0.1901   5.323330e+00   5.567029e+00
   5_xyz:  0.1217 0.1768   5.232605e+00   5.490594e+00
   5_adp:  0.1179 0.1719   5.207707e+00   5.464814e+00
   5_occ:  0.1178 0.1719   5.207538e+00   5.464652e+00
   5_bss:  0.1178 0.1718   5.207435e+00   5.464509e+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:  0.356  49.635  -2.964   3.384  -1.393   0.000  -0.000  -0.000
   1_xyz:  0.356  49.635  -2.964   3.384  -1.393   0.000  -0.000  -0.000
   1_adp:  0.356  49.635  -2.964   3.384  -1.393   0.000  -0.000  -0.000
   1_occ:  0.356  49.635  -2.964   3.384  -1.393   0.000  -0.000  -0.000
   2_bss:  0.356  71.440  -1.654   0.917  -0.576   0.000  -0.000  -0.000
   2_xyz:  0.356  71.440  -1.654   0.917  -0.576   0.000  -0.000  -0.000
   2_adp:  0.356  71.440  -1.654   0.917  -0.576   0.000  -0.000  -0.000
   2_occ:  0.356  71.440  -1.654   0.917  -0.576   0.000  -0.000  -0.000
   3_bss:  0.344  64.988  -1.515  -0.851  -0.349  -0.000  -0.000  -0.000
   3_xyz:  0.344  64.988  -1.515  -0.851  -0.349  -0.000  -0.000  -0.000
   3_adp:  0.344  64.988  -1.515  -0.851  -0.349  -0.000  -0.000  -0.000
   3_occ:  0.344  64.988  -1.515  -0.851  -0.349  -0.000  -0.000  -0.000
   4_bss:  0.329  59.814  -1.983  -1.793  -0.649  -0.000  -0.000  -0.000
   4_xyz:  0.329  59.814  -1.983  -1.793  -0.649  -0.000  -0.000  -0.000
   4_adp:  0.329  59.814  -1.983  -1.793  -0.649  -0.000  -0.000  -0.000
   4_occ:  0.329  59.814  -1.983  -1.793  -0.649  -0.000  -0.000  -0.000
   5_bss:  0.322  59.814  -1.945  -2.185  -0.665  -0.000  -0.000  -0.000
   5_xyz:  0.322  59.814  -1.945  -2.185  -0.665  -0.000  -0.000  -0.000
   5_adp:  0.322  59.814  -1.945  -2.185  -0.665  -0.000  -0.000  -0.000
   5_occ:  0.322  59.814  -1.945  -2.185  -0.665  -0.000  -0.000  -0.000
   5_bss:  0.315  54.245  -1.862  -2.231  -0.571  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.666 0.5267  0.7139    60255.477
   1_bss:  49.181 0.5316  0.7162    58142.070
   1_xyz:  44.018 0.5940  0.7839    45853.921
   1_adp:  44.482 0.5880  0.7788    46807.290
   1_occ:  44.544 0.5872  0.7776    46921.575
   2_bss:  44.089 0.5927  0.7835    46275.749
   2_xyz:  34.177 0.7099  0.9159    28750.742
   2_adp:  32.394 0.7307  0.9283    26453.865
   2_occ:  32.380 0.7308  0.9282    26433.638
   3_bss:  32.072 0.7339  0.9166    25887.560
   3_xyz:  25.964 0.8008  0.9716    17569.715
   3_adp:  24.499 0.8165  0.9734    15876.900
   3_occ:  24.467 0.8168  0.9732    15826.764
   4_bss:  24.396 0.8174  0.9542    15714.548
   4_xyz:  19.713 0.8635  0.9827    10523.189
   4_adp:  18.153 0.8787  0.9800     9342.759
   4_occ:  18.144 0.8788  0.9799     9331.397
   5_bss:  18.102 0.8791  0.9758     9285.344
   5_xyz:  16.252 0.8957  0.9842     7826.826
   5_adp:  15.643 0.9013  0.9793     7467.123
   5_occ:  15.643 0.9013  0.9792     7461.662
   5_bss:  15.646 0.9013  0.9807     7459.190
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.8423e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.8423e-01
   1_xyz:   1.477  0.011  0.100 15.858  0.006  4.106   1.1868e-01
   1_adp:   1.477  0.011  0.100 15.858  0.006  4.106   1.1868e-01
   1_occ:   1.477  0.011  0.100 15.858  0.006  4.106   1.1868e-01
   2_bss:   1.477  0.011  0.100 15.858  0.006  4.106   1.1868e-01
   2_xyz:   1.392  0.011  0.096 15.308  0.006  4.104   1.1336e-01
   2_adp:   1.392  0.011  0.096 15.308  0.006  4.104   1.1336e-01
   2_occ:   1.392  0.011  0.096 15.308  0.006  4.104   1.1336e-01
   3_bss:   1.392  0.011  0.096 15.308  0.006  4.104   1.1336e-01
   3_xyz:   0.949  0.006  0.066 14.240  0.003  4.111   5.5313e-02
   3_adp:   0.949  0.006  0.066 14.240  0.003  4.111   5.5313e-02
   3_occ:   0.949  0.006  0.066 14.240  0.003  4.111   5.5313e-02
   4_bss:   0.949  0.006  0.066 14.240  0.003  4.111   5.5313e-02
   4_xyz:   1.006  0.007  0.073 14.564  0.004  4.108   6.1441e-02
   4_adp:   1.006  0.007  0.073 14.564  0.004  4.108   6.1441e-02
   4_occ:   1.006  0.007  0.073 14.564  0.004  4.108   6.1441e-02
   5_bss:   1.006  0.007  0.073 14.564  0.004  4.108   6.1441e-02
   5_xyz:   1.042  0.007  0.076 14.592  0.004  4.112   6.4614e-02
   5_adp:   1.042  0.007  0.076 14.592  0.004  4.112   6.4614e-02
   5_occ:   1.042  0.007  0.076 14.592  0.004  4.112   6.4614e-02
   5_bss:   1.042  0.007  0.076 14.592  0.004  4.112   6.4614e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.681   2.4051e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.681   2.4051e-01
   1_xyz:   8.705  0.084  0.364 84.521  0.040  2.039   1.0214e-01
   1_adp:   8.705  0.084  0.364 84.521  0.040  2.039   1.0214e-01
   1_occ:   8.705  0.084  0.364 84.521  0.040  2.039   1.0214e-01
   2_bss:   8.705  0.084  0.364 84.521  0.040  2.039   1.0214e-01
   2_xyz:   8.532  0.046  0.302 78.565  0.048  1.930   1.2317e-01
   2_adp:   8.532  0.046  0.302 78.565  0.048  1.930   1.2317e-01
   2_occ:   8.532  0.046  0.302 78.565  0.048  1.930   1.2317e-01
   3_bss:   8.532  0.046  0.302 78.565  0.048  1.930   1.2317e-01
   3_xyz:   6.947  0.053  0.247 78.103  0.017  2.343   5.6660e-02
   3_adp:   6.947  0.053  0.247 78.103  0.017  2.343   5.6660e-02
   3_occ:   6.947  0.053  0.247 78.103  0.017  2.343   5.6660e-02
   4_bss:   6.947  0.053  0.247 78.103  0.017  2.343   5.6660e-02
   4_xyz:   6.601  0.045  0.219 80.831  0.038  2.320   7.2868e-02
   4_adp:   6.601  0.045  0.219 80.831  0.038  2.320   7.2868e-02
   4_occ:   6.601  0.045  0.219 80.831  0.038  2.320   7.2868e-02
   5_bss:   6.601  0.045  0.219 80.831  0.038  2.320   7.2868e-02
   5_xyz:   7.000  0.044  0.258 81.448  0.041  2.315   7.0581e-02
   5_adp:   7.000  0.044  0.258 81.448  0.041  2.315   7.0581e-02
   5_occ:   7.000  0.044  0.258 81.448  0.041  2.315   7.0581e-02
   5_bss:   7.000  0.044  0.258 81.448  0.041  2.315   7.0581e-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:  91.93   0.00  17.94  78.50   0.00  14.87  91.93   1.87  34.64
   1_occ:  91.93   0.00  17.94  78.50   0.00  14.87  91.93   1.87  34.64
   2_bss:  91.93   0.00  17.94  78.50   0.00  14.87  91.93   1.87  34.64
   2_xyz:  91.93   0.00  17.94  78.50   0.00  14.87  91.93   1.87  34.64
   2_adp:  91.35   0.00  17.87  79.70   0.00  14.35  91.35   0.88  37.03
   2_occ:  91.35   0.00  17.87  79.70   0.00  14.35  91.35   0.88  37.03
   3_bss:  91.35   0.00  17.87  79.70   0.00  14.35  91.35   0.88  37.03
   3_xyz:  91.35   0.00  17.87  79.70   0.00  14.35  91.35   0.88  37.03
   3_adp:  95.84   0.00  18.22  86.54   0.00  13.74  95.84   5.34  42.66
   3_occ:  95.84   0.00  18.22  86.54   0.00  13.74  95.84   5.34  42.66
   4_bss:  95.84   0.00  18.22  86.54   0.00  13.74  95.84   5.34  42.66
   4_xyz:  95.84   0.00  18.22  86.54   0.00  13.74  95.84   5.34  42.66
   4_adp: 102.72   0.00  18.46  95.83   0.00  13.19 102.72   2.30  47.15
   4_occ: 102.72   0.00  18.46  95.83   0.00  13.19 102.72   2.30  47.15
   5_bss: 102.72   0.00  18.46  95.83   0.00  13.19 102.72   2.30  47.15
   5_xyz: 102.72   0.00  18.46  95.83   0.00  13.19 102.72   2.30  47.15
   5_adp: 104.20   0.00  17.99 104.20   0.00  12.81 103.58   2.29  46.17
   5_occ: 104.20   0.00  17.99 104.20   0.00  12.81 103.58   2.29  46.17
   5_bss: 104.21   0.00  17.99 104.21   0.00  12.82 103.59   2.29  46.18
------------------------------------------------------------------------
 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:    1.604    0.011    0.309
   1_adp:    1.604    0.011    0.309
   1_occ:    1.604    0.011    0.309
   2_bss:    1.604    0.011    0.309
   2_xyz:    1.518    0.048    0.545
   2_adp:    1.518    0.048    0.545
   2_occ:    1.518    0.048    0.545
   3_bss:    1.518    0.048    0.545
   3_xyz:    1.711    0.041    0.627
   3_adp:    1.711    0.041    0.627
   3_occ:    1.711    0.041    0.627
   4_bss:    1.711    0.041    0.627
   4_xyz:    1.563    0.062    0.721
   4_adp:    1.563    0.062    0.721
   4_occ:    1.563    0.062    0.721
   5_bss:    1.563    0.062    0.721
   5_xyz:    1.618    0.021    0.750
   5_adp:    1.618    0.021    0.750
   5_occ:    1.618    0.021    0.750
   5_bss:    1.618    0.021    0.750
------------------------------------------------------------------------

CPU time actual refinement: 343.59


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_732/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_732/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_732/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_732/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_732/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 343.42 
  Macro-tasks:
    bulk solvent and scale       = 37.42  
    individual site refinement   = 146.15 
    weights calculation          = 29.04  
    collect and process          = 6.07   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 218.78 
  Micro-tasks:
    mask                            = 2.46   
    f_calc                          = 113.32 
    alpha_beta                      = 8.48   
    target                          = 1.21   
    gradients_wrt_atomic_parameters = 121.90 
    fmodel                         = 6.60   
    r_factors                      = 0.20   
    phase_errors                   = 10.61  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 265.05 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.893 micro seconds
Total CPU time: 5.96 minutes
from_scatterers_fft:    633 calls, 112.91 s
gradients_fft:          578 calls, 108.68 s

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

# Date 2008-01-16 Time 05:31:41 PST -0800 (1200490301.12 s)
Start R-work = 0.4227, R-free = 0.4183 (no bulk solvent and anisotropic scale)
Final R-work = 0.1383, R-free = 0.1875 (no bulk solvent and anisotropic scale)

Start R-work = 0.4100, R-free = 0.4086
Final R-work = 0.1178, R-free = 0.1718