# Date 2008-01-16 Time 05:47:17 PST -0800 (1200491237.35 s)
#phil __OFF__

Command line arguments: "../876.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 28719
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 876

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 46.2261, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.2261, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1439 1.97329
Completeness in resolution range: 0.942912
Completeness with d_max=infinity: 0.940107

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1439
                             d_min =   1.9733

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.2261, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1439 1.97329
Completeness in resolution range: 0.942912
Completeness with d_max=infinity: 0.940107

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1444 -  4.2235 [2185/2210]  1965   220  10.1%
  bin  2:  4.2235 -  3.3644 [2099/2119]  1892   207   9.9%
  bin  3:  3.3644 -  2.9426 [2073/2092]  1866   207  10.0%
  bin  4:  2.9426 -  2.6752 [2048/2078]  1839   209  10.2%
  bin  5:  2.6752 -  2.4844 [2033/2052]  1837   196   9.6%
  bin  6:  2.4844 -  2.3384 [2030/2055]  1819   211  10.4%
  bin  7:  2.3384 -  2.2217 [2022/2050]  1818   204  10.1%
  bin  8:  2.2217 -  2.1253 [2004/2040]  1805   199   9.9%
  bin  9:  2.1253 -  2.0437 [2005/2047]  1812   193   9.6%
  bin 10:  2.0437 -  1.9733 [1090/2032]   977   113  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_876/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 26
        2.42 -     3.04: 2178
        3.04 -     3.66: 4698
        3.66 -     4.28: 9013
        4.28 -     4.90: 12305
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.115 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  2.148 3.040 x,y+1,z
  " O   HOH Z 324 " - " O   HOH Z 374 "  2.193 3.040 -x,y-1/2,-z+1/2
  ... (remaining 28215 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_876/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_876/model_refine_001.geo

CPU time processing inputs: 9.27


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 46.22605 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3892   r_free= 0.3834   ksol= 0.00   Bsol= 0.00   scale= 0.938    |
|                                                                             |
| 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:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.178840                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1444 -  4.7112 0.99   1413  157 0.3198 0.3009      6.4414      6.3669|
|  2:  4.7112 -  3.7582 0.99   1364  153 0.3168 0.2931      6.6262      6.5318|
|  3:  3.7582 -  3.2887 0.99   1344  144 0.3303 0.3076      6.4809      6.5036|
|  4:  3.2887 -  2.9905 0.99   1325  151 0.3710 0.4156      6.3891      6.4573|
|  5:  2.9905 -  2.7776 0.99   1325  149 0.4115 0.3543       6.253      6.2037|
|  6:  2.7776 -  2.6147 0.99   1315  144 0.4014 0.4053      6.1435      6.1085|
|  7:  2.6147 -  2.4844 0.99   1313  141 0.4178 0.4019      6.1539      6.1118|
|  8:  2.4844 -  2.3766 0.98   1288  149 0.4373 0.4426      6.0905      6.1203|
|  9:  2.3766 -  2.2855 0.98   1297  146 0.4360 0.4368      6.0456      6.0631|
| 10:  2.2855 -  2.2068 1.00   1302  146 0.4523 0.4530      6.0385      5.9788|
| 11:  2.2068 -  2.1380 0.98   1312  141 0.4512 0.4933      5.9886      6.0093|
| 12:  2.1380 -  2.0771 0.98   1270  139 0.4599 0.4607      5.9059      5.9461|
| 13:  2.0771 -  2.0225 0.99   1282  142 0.4591 0.4591      5.8166      5.7645|
| 14:  2.0225 -  1.9733 0.36    480   57 0.4973 0.5116      5.8565      5.8528|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1444 -  4.7112  1413   157  0.78  26.59   0.85     0.82      45420.69|
|  2:  4.7112 -  3.7582  1364   153  0.81  25.20   0.94     0.90      59386.83|
|  3:  3.7582 -  3.2887  1344   144  0.74  31.68   0.98     0.91      65191.76|
|  4:  3.2887 -  2.9905  1325   151  0.68  36.87   0.95     0.86      60585.20|
|  5:  2.9905 -  2.7776  1325   149  0.61  43.00   0.94     0.82      50866.71|
|  6:  2.7776 -  2.6147  1315   144  0.61  43.27   0.95     0.79      43429.92|
|  7:  2.6147 -  2.4844  1313   141  0.58  45.71   0.96     0.76      42836.63|
|  8:  2.4844 -  2.3766  1288   149  0.55  47.86   0.95     0.74      39580.99|
|  9:  2.3766 -  2.2855  1297   146  0.55  47.99   0.98     0.76      37349.66|
| 10:  2.2855 -  2.2068  1302   146  0.56  47.48   0.98     0.77      32909.18|
| 11:  2.2068 -  2.1380  1312   141  0.53  49.86   0.99     0.77      34364.72|
| 12:  2.1380 -  2.0771  1270   139  0.49  53.31   0.98     0.72      32945.74|
| 13:  2.0771 -  2.0225  1282   142  0.44  57.01   0.98     0.68      30539.04|
| 14:  2.0225 -  1.9733   480    57  0.48  53.79   0.97     0.67      24996.80|
|alpha:            min =        0.67 max =            0.91 mean =         0.79|
|beta:             min =    24996.80 max =        65191.76 mean =     43912.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.61|
|phase err.(work): min =        0.00 max =           89.96 mean =        42.83|
|phase err.(test): min =        0.00 max =           89.88 mean =        42.90|
|-----------------------------------------------------------------------------|

============================== 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 = 7.904176              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.155   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.281469              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.760   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       24 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      200 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1978 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1864 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2834 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4618 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4395 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5626 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6679 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.165 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.806 |       0.205 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.942)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3892   r_free= 0.3834   ksol= 0.00   Bsol= 0.00   scale= 0.938    |
|                                                                             |
| 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:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.178840                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3785   r_free= 0.3784   ksol= 0.33   Bsol= 48.96   scale= 0.964   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.86,1.67,0.07,0.00,0.00,0.00); trace/3= -0.04                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.166997                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.823351              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.234   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.643397              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.497   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3785      final r-factor (work) = 0.2243          |
| start r-factor (free) = 0.3784      final r-factor (free) = 0.2544          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.1924 = 6.82 * 0.50 * 6.1635 + 1.00 * 0.1647                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.3162 = 6.82 * 0.50 * 5.9280 + 1.00 * 0.0917                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2243      final r-factor (work) = 0.2039          |
| start r-factor (free) = 0.2544      final r-factor (free) = 0.2638          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8201 = 0.64 * 1.00 * 5.9280 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6521 = 0.64 * 1.00 * 5.6571 + 1.00 * 0.0124                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.942)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.41   17.64    None  None   None       |
|    all(noH): 2823   0      0.00    91.41   17.64    None  None   None       |
|    Sol.    : 438    0      3.99    91.41   41.49    None  None   None       |
|    Mac.    : 2385   0      0.00    77.90   13.26    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 -   9.141:  824   |   5:    45.705 -  54.846:  106        |
|      1:     9.141 -  18.282: 1168   |   6:    54.846 -  63.987:   63        |
|      2:    18.282 -  27.423:  335   |   7:    63.987 -  73.128:   28        |
|      3:    27.423 -  36.564:  162   |   8:    73.128 -  82.268:   11        |
|      4:    36.564 -  45.705:  124   |   9:    82.268 -  91.409:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2039 r_free = 0.2638             target_work(ml) = 5.671         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2037 r_free = 0.2634             target_work(ml) = 5.670         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2037   r_free= 0.2634   ksol= 0.33   Bsol= 48.96   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.86,1.67,0.07,0.00,0.00,0.00); trace/3= -0.04                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.669746                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2020   r_free= 0.2607   ksol= 0.34   Bsol= 67.86   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-1.33,-0.79,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.664503                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.537657              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.486   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.196586              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.420  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2020      final r-factor (work) = 0.1526          |
| start r-factor (free) = 0.2607      final r-factor (free) = 0.2028          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2825 = 2.54 * 0.50 * 5.6673 + 1.00 * 0.0917                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0911 = 2.54 * 0.50 * 5.5465 + 1.00 * 0.0536                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1526      final r-factor (work) = 0.1439          |
| start r-factor (free) = 0.2028      final r-factor (free) = 0.1901          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1027 = 0.20 * 1.00 * 5.5465 + 1.00 * 0.0124                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3614 = 0.20 * 1.00 * 5.3877 + 1.00 * 0.3023                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.942)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.09   17.38    None  None   None       |
|    all(noH): 2823   0      0.00    90.09   17.38    None  None   None       |
|    Sol.    : 438    0      6.19    90.09   40.82    None  None   None       |
|    Mac.    : 2385   0      0.00    77.34   13.08    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 -   9.009:  735   |   5:    45.047 -  54.056:  104        |
|      1:     9.009 -  18.019: 1326   |   6:    54.056 -  63.066:   64        |
|      2:    18.019 -  27.028:  290   |   7:    63.066 -  72.075:   27        |
|      3:    27.028 -  36.038:  141   |   8:    72.075 -  81.084:   11        |
|      4:    36.038 -  45.047:  123   |   9:    81.084 -  90.094:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1439 r_free = 0.1901             target_work(ml) = 5.358         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1438 r_free = 0.1901             target_work(ml) = 5.357         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1438   r_free= 0.1901   ksol= 0.34   Bsol= 67.86   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-1.33,-0.79,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.357300                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1437   r_free= 0.1896   ksol= 0.33   Bsol= 59.94   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.41,-2.26,-0.90,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.354535                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.875895              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.598  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.476069              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.274   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1437      final r-factor (work) = 0.1252          |
| start r-factor (free) = 0.1896      final r-factor (free) = 0.1697          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1057 = 1.88 * 0.50 * 5.3864 + 1.00 * 0.0536                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0184 = 1.88 * 0.50 * 5.2943 + 1.00 * 0.0527                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1252      final r-factor (work) = 0.1197          |
| start r-factor (free) = 0.1697      final r-factor (free) = 0.1658          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.5277 = 3.48 * 1.00 * 5.2943 + 1.00 * 0.1244                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.1282 = 3.48 * 1.00 * 5.2120 + 1.00 * 0.0108                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.942)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.92   17.75    None  None   None       |
|    all(noH): 2823   0      0.00    93.92   17.75    None  None   None       |
|    Sol.    : 438    0      6.03    93.92   43.18    None  None   None       |
|    Mac.    : 2385   0      0.00    89.34   13.08    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 -   9.392:  920   |   5:    46.962 -  56.354:   99        |
|      1:     9.392 -  18.785: 1188   |   6:    56.354 -  65.746:   71        |
|      2:    18.785 -  28.177:  246   |   7:    65.746 -  75.138:   37        |
|      3:    28.177 -  37.569:  136   |   8:    75.138 -  84.531:   18        |
|      4:    37.569 -  46.962:  102   |   9:    84.531 -  93.923:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1197 r_free = 0.1658             target_work(ml) = 5.202         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1196 r_free = 0.1659             target_work(ml) = 5.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1196   r_free= 0.1659   ksol= 0.33   Bsol= 59.94   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.41,-2.26,-0.90,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.201599                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1196   r_free= 0.1657   ksol= 0.32   Bsol= 61.08   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.31,-2.42,-0.89,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.201135                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.433060              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.968  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.405844              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.883  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1196      final r-factor (work) = 0.1167          |
| start r-factor (free) = 0.1657      final r-factor (free) = 0.1632          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7869 = 1.43 * 0.50 * 5.2116 + 1.00 * 0.0527                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7673 = 1.43 * 0.50 * 5.1897 + 1.00 * 0.0487                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1167      final r-factor (work) = 0.1159          |
| start r-factor (free) = 0.1632      final r-factor (free) = 0.1627          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3067 = 1.41 * 1.00 * 5.1897 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2934 = 1.41 * 1.00 * 5.1801 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.942)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.56   17.56    None  None   None       |
|    all(noH): 2823   0      0.00    93.56   17.56    None  None   None       |
|    Sol.    : 438    0      5.60    93.56   42.78    None  None   None       |
|    Mac.    : 2385   0      0.00    93.29   12.93    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 -   9.356:  933   |   5:    46.780 -  56.135:   91        |
|      1:     9.356 -  18.712: 1176   |   6:    56.135 -  65.491:   74        |
|      2:    18.712 -  28.068:  249   |   7:    65.491 -  74.847:   33        |
|      3:    28.068 -  37.424:  139   |   8:    74.847 -  84.203:   24        |
|      4:    37.424 -  46.780:   98   |   9:    84.203 -  93.559:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1159 r_free = 0.1627             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1158 r_free = 0.1627             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1627   ksol= 0.32   Bsol= 61.08   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.31,-2.42,-0.89,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.179807                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1161   r_free= 0.1626   ksol= 0.32   Bsol= 61.95   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-2.38,-0.76,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.180538                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.669901              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 153.015  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.286286              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.205  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1161      final r-factor (work) = 0.1101          |
| start r-factor (free) = 0.1626      final r-factor (free) = 0.1602          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9652 = 2.67 * 0.50 * 5.1811 + 1.00 * 0.0487                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9490 = 2.67 * 0.50 * 5.1571 + 1.00 * 0.0645                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1101      final r-factor (work) = 0.1102          |
| start r-factor (free) = 0.1602      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4874 = 0.29 * 1.00 * 5.1571 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4830 = 0.29 * 1.00 * 5.1493 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.942)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.66    91.34   16.80    None  None   None       |
|    all(noH): 2823   0      0.66    91.34   16.80    None  None   None       |
|    Sol.    : 438    0      6.01    87.24   39.66    None  None   None       |
|    Mac.    : 2385   0      0.66    91.34   12.61    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:     0.663 -   9.731: 1039   |   5:    46.000 -  55.067:   87        |
|      1:     9.731 -  18.798: 1104   |   6:    55.067 -  64.134:   51        |
|      2:    18.798 -  27.865:  231   |   7:    64.134 -  73.201:   28        |
|      3:    27.865 -  36.932:  141   |   8:    73.201 -  82.268:   11        |
|      4:    36.932 -  46.000:  127   |   9:    82.268 -  91.336:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1102 r_free = 0.1572             target_work(ml) = 5.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1101 r_free = 0.1571             target_work(ml) = 5.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1101   r_free= 0.1571   ksol= 0.32   Bsol= 61.95   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-2.38,-0.76,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.140083                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1444 -  4.7112 0.99   1413  157 0.0941 0.1247      5.3425      5.5343|
|  2:  4.7112 -  3.7582 0.99   1364  153 0.0833 0.1116      5.4179      5.6156|
|  3:  3.7582 -  3.2887 0.99   1344  144 0.1051 0.1540       5.467      5.8387|
|  4:  3.2887 -  2.9905 0.99   1325  151 0.1207 0.1691      5.4512      5.6152|
|  5:  2.9905 -  2.7776 0.99   1325  149 0.1328 0.1736      5.3169      5.5705|
|  6:  2.7776 -  2.6147 0.99   1315  144 0.1186 0.1842      5.1823      5.4613|
|  7:  2.6147 -  2.4844 0.99   1313  141 0.1238 0.1576      5.1546         5.3|
|  8:  2.4844 -  2.3766 0.98   1288  149 0.1177 0.1618      5.0648      5.3146|
|  9:  2.3766 -  2.2855 0.98   1297  146 0.1180 0.1794      5.0394      5.3313|
| 10:  2.2855 -  2.2068 1.00   1302  146 0.1120 0.1667      4.9361      5.1765|
| 11:  2.2068 -  2.1380 0.98   1312  141 0.1074 0.1849      4.9234      5.3235|
| 12:  2.1380 -  2.0771 0.98   1270  139 0.1139 0.1599      4.8582       5.105|
| 13:  2.0771 -  2.0225 0.99   1282  142 0.1108 0.1705      4.7778      5.0206|
| 14:  2.0225 -  1.9733 0.36    480   57 0.1035 0.1508      4.6702      4.8817|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1444 -  4.7112  1413   157  0.94   8.75   0.97     0.95       6634.06|
|  2:  4.7112 -  3.7582  1364   153  0.95   7.71   1.01     1.00       8798.21|
|  3:  3.7582 -  3.2887  1344   144  0.93  11.27   1.02     1.01      10335.52|
|  4:  3.2887 -  2.9905  1325   151  0.91  14.29   1.01     0.98      10539.29|
|  5:  2.9905 -  2.7776  1325   149  0.90  15.98   1.00     0.98       8222.10|
|  6:  2.7776 -  2.6147  1315   144  0.90  15.73   0.99     0.96       6740.20|
|  7:  2.6147 -  2.4844  1313   141  0.91  15.11   0.99     0.96       6033.48|
|  8:  2.4844 -  2.3766  1288   149  0.91  15.45   0.98     0.96       5272.98|
|  9:  2.3766 -  2.2855  1297   146  0.91  15.71   0.99     0.95       5060.17|
| 10:  2.2855 -  2.2068  1302   146  0.90  15.58   0.99     0.97       4256.95|
| 11:  2.2068 -  2.1380  1312   141  0.91  15.47   0.98     0.93       4163.90|
| 12:  2.1380 -  2.0771  1270   139  0.91  15.56   1.00     1.00       3846.09|
| 13:  2.0771 -  2.0225  1282   142  0.90  16.50   0.99     0.98       3367.85|
| 14:  2.0225 -  1.9733   480    57  0.92  14.27   0.97     0.94       2632.27|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2632.27 max =        10539.29 mean =      6337.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.03|
|phase err.(test): min =        0.00 max =           88.71 mean =        13.48|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1100   r_free= 0.1571   ksol= 0.33   Bsol= 61.93   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,-2.30,-0.60,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.140167                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1100   r_free= 0.1571   ksol= 0.33   Bsol= 61.93   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,-2.30,-0.60,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.140167                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1444 -  4.7112 0.99   1413  157 0.0941 0.1248      5.3441      5.5354|
|  2:  4.7112 -  3.7582 0.99   1364  153 0.0833 0.1116       5.418      5.6153|
|  3:  3.7582 -  3.2887 0.99   1344  144 0.1051 0.1540      5.4668      5.8388|
|  4:  3.2887 -  2.9905 0.99   1325  151 0.1207 0.1692      5.4512      5.6152|
|  5:  2.9905 -  2.7776 0.99   1325  149 0.1328 0.1735      5.3168      5.5703|
|  6:  2.7776 -  2.6147 0.99   1315  144 0.1186 0.1842      5.1822      5.4611|
|  7:  2.6147 -  2.4844 0.99   1313  141 0.1239 0.1577      5.1548      5.3003|
|  8:  2.4844 -  2.3766 0.98   1288  149 0.1178 0.1618      5.0648      5.3144|
|  9:  2.3766 -  2.2855 0.98   1297  146 0.1180 0.1793      5.0393      5.3309|
| 10:  2.2855 -  2.2068 1.00   1302  146 0.1120 0.1669      4.9362      5.1776|
| 11:  2.2068 -  2.1380 0.98   1312  141 0.1073 0.1849      4.9237      5.3239|
| 12:  2.1380 -  2.0771 0.98   1270  139 0.1139 0.1598      4.8581      5.1051|
| 13:  2.0771 -  2.0225 0.99   1282  142 0.1108 0.1702      4.7774      5.0193|
| 14:  2.0225 -  1.9733 0.36    480   57 0.1035 0.1508      4.6693      4.8811|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1444 -  4.7112  1413   157  0.94   8.77   0.97     0.95       6657.75|
|  2:  4.7112 -  3.7582  1364   153  0.95   7.72   1.01     1.00       8809.48|
|  3:  3.7582 -  3.2887  1344   144  0.93  11.27   1.02     1.02      10333.27|
|  4:  3.2887 -  2.9905  1325   151  0.91  14.30   1.01     0.98      10538.30|
|  5:  2.9905 -  2.7776  1325   149  0.90  15.98   1.00     0.98       8218.58|
|  6:  2.7776 -  2.6147  1315   144  0.90  15.73   0.99     0.97       6738.31|
|  7:  2.6147 -  2.4844  1313   141  0.91  15.11   0.99     0.96       6034.44|
|  8:  2.4844 -  2.3766  1288   149  0.91  15.45   0.99     0.97       5271.25|
|  9:  2.3766 -  2.2855  1297   146  0.91  15.71   1.00     0.96       5059.54|
| 10:  2.2855 -  2.2068  1302   146  0.90  15.59   1.00     0.97       4260.49|
| 11:  2.2068 -  2.1380  1312   141  0.91  15.48   0.98     0.94       4169.34|
| 12:  2.1380 -  2.0771  1270   139  0.91  15.57   1.01     1.00       3848.11|
| 13:  2.0771 -  2.0225  1282   142  0.90  16.50   1.00     0.98       3364.48|
| 14:  2.0225 -  1.9733   480    57  0.92  14.25   0.97     0.95       2626.55|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2626.55 max =        10538.30 mean =      6340.24|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.03|
|phase err.(test): min =        0.00 max =           88.70 mean =        13.49|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.942)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.64    91.31   16.78    None  None   None       |
|    all(noH): 2823   0      0.64    91.31   16.78    None  None   None       |
|    Sol.    : 438    0      5.99    87.22   39.64    None  None   None       |
|    Mac.    : 2385   0      0.64    91.31   12.58    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:     0.642 -   9.709: 1039   |   5:    45.978 -  55.045:   87        |
|      1:     9.709 -  18.776: 1104   |   6:    55.045 -  64.112:   51        |
|      2:    18.776 -  27.843:  231   |   7:    64.112 -  73.179:   28        |
|      3:    27.843 -  36.910:  141   |   8:    73.179 -  82.246:   11        |
|      4:    36.910 -  45.978:  127   |   9:    82.246 -  91.314:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 315         
Filter by distance & map next to the model:
   mapped sites are within: 0.583 - 4.695
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 312 from: 315
   mapped sites are within: 0.700 - 4.695

peak=    6.116 closest distance to " NE2 GLN A  11 " =    1.226
peak=    5.585 closest distance to " NH2 ARG A  56 " =    2.093
peak=    5.560 closest distance to " CG  PRO A  54 " =    1.279
peak=    5.330 closest distance to " O   HOH Z 144 " =    1.796
peak=    5.157 closest distance to " O   HOH Z 232 " =    2.268
peak=    5.066 closest distance to " CB  GLN A 223 " =    1.461
peak=    5.060 closest distance to " O   HOH Z 126 " =    1.999
peak=    4.794 closest distance to " O   HOH Z 369 " =    2.116
peak=    4.783 closest distance to " O   HOH Z 298 " =    2.063
peak=    4.712 closest distance to " CB  GLN A 183 " =    1.207
peak=    4.679 closest distance to " O   HOH Z 423 " =    1.703
peak=    4.609 closest distance to " CB  SER A  63 " =    1.231
peak=    4.551 closest distance to " CB  PRO A  54 " =    0.956
peak=    4.545 closest distance to " ND2 ASN A 187 " =    1.536
peak=    4.544 closest distance to " CG  PRO A 213 " =    1.239
peak=    4.538 closest distance to " O   HOH Z 427 " =    2.795
peak=    4.517 closest distance to " C   PRO A 198 " =    1.545
peak=    4.516 closest distance to " CB  ARG A 275 " =    0.918
peak=    4.514 closest distance to " CB  ARG A 190 " =    1.561
peak=    4.509 closest distance to " CB  ASN A 148 " =    1.389
peak=    4.474 closest distance to " O   HOH Z 287 " =    2.162
peak=    4.428 closest distance to " O   HOH Z  78 " =    1.848
peak=    4.357 closest distance to " O   HOH Z 133 " =    2.433
peak=    4.324 closest distance to " CG  TRP A 179 " =    2.205
peak=    4.291 closest distance to " O   HOH Z  63 " =    1.421
peak=    4.263 closest distance to " O   HOH Z 417 " =    1.337
peak=    4.191 closest distance to " CB  ARG A  79 " =    1.453
peak=    4.136 closest distance to " CG  PRO A 198 " =    1.243
peak=    4.126 closest distance to " CB  LEU A 228 " =    1.084
peak=    4.115 closest distance to " O   HOH Z 316 " =    3.100
peak=    4.089 closest distance to " CB  GLU A 128 " =    0.987
peak=    4.074 closest distance to " O   HOH Z   1 " =    1.861
peak=    4.062 closest distance to " O   HOH Z 158 " =    3.085
peak=    4.046 closest distance to " O   HOH Z 180 " =    2.081
peak=    4.039 closest distance to " O   HOH Z 261 " =    2.155
peak=    4.035 closest distance to " CB  SER A 212 " =    1.230
peak=    4.033 closest distance to " O   HOH Z 214 " =    2.176
peak=    4.021 closest distance to " CD  ARG A  66 " =    2.198
peak=    4.001 closest distance to " CB  TRP A 266 " =    1.026
peak=    3.996 closest distance to " CB  VAL A 265 " =    1.386
peak=    3.993 closest distance to " O   HOH Z 380 " =    1.712
peak=    3.992 closest distance to " OD1 ASN A  69 " =    2.646
peak=    3.986 closest distance to " O   HOH Z   9 " =    1.982
peak=    3.986 closest distance to " O   HOH Z 419 " =    2.109
peak=    3.983 closest distance to " O   HOH Z  61 " =    1.602
peak=    3.971 closest distance to " CB  GLU A 152 " =    1.316
peak=    3.968 closest distance to " CD  ARG A 159 " =    0.755
peak=    3.966 closest distance to " CG  LEU A 167 " =    1.269
peak=    3.962 closest distance to " CB  ASN A 187 " =    1.077
peak=    3.961 closest distance to " CG  PRO A 243 " =    1.074
peak=    3.939 closest distance to " O   HOH Z 209 " =    2.270
peak=    3.936 closest distance to " O   HOH Z 425 " =    1.346
peak=    3.926 closest distance to " CA  TYR A  30 " =    0.961
peak=    3.924 closest distance to " ND1 HIS A  86 " =    1.689
peak=    3.906 closest distance to " CG  PRO A 280 " =    0.786
peak=    3.903 closest distance to " NH1AARG A 145 " =    1.263
peak=    3.895 closest distance to " CE  LYS A  76 " =    0.881
peak=    3.894 closest distance to " O   HOH Z 265 " =    2.260
peak=    3.886 closest distance to " CZ  PHE A 218 " =    1.061
peak=    3.882 closest distance to " CG2 VAL A 257 " =    0.910
peak=    3.881 closest distance to " O   HOH Z 437 " =    1.580
peak=    3.871 closest distance to " O   HOH Z  10 " =    1.780
peak=    3.865 closest distance to " O   HOH Z 234 " =    3.704
peak=    3.862 closest distance to " O   HOH Z  61 " =    1.535
peak=    3.860 closest distance to " O   HOH Z 362 " =    2.441
peak=    3.850 closest distance to " O   HOH Z 371 " =    1.966
peak=    3.848 closest distance to " O   HOH Z   1 " =    1.839
peak=    3.842 closest distance to " O   HOH Z 189 " =    2.592
peak=    3.807 closest distance to " CB  ASN A  39 " =    0.925
peak=    3.803 closest distance to " CA  ALA A 233 " =    1.152
peak=    3.795 closest distance to " O   HOH Z 368 " =    3.652
peak=    3.778 closest distance to " O   HOH Z 193 " =    1.832
peak=    3.775 closest distance to " CA  SER A  87 " =    0.974
peak=    3.773 closest distance to " O   HOH Z 272 " =    1.806
peak=    3.771 closest distance to " O   HOH Z 250 " =    1.477
peak=    3.765 closest distance to " O   HOH Z 285 " =    2.397
peak=    3.761 closest distance to " CB  GLU A 277 " =    3.621
peak=    3.758 closest distance to " NZ  LYS A 117 " =    3.076
peak=    3.742 closest distance to " CB  ASP A 124 " =    0.791
peak=    3.742 closest distance to " O   HOH Z  40 " =    1.962
peak=    3.731 closest distance to " O   HOH Z   2 " =    1.507
peak=    3.726 closest distance to " O   HOH Z 346 " =    1.660
peak=    3.715 closest distance to " CB  ASN A 142 " =    0.948
peak=    3.715 closest distance to " O   HOH Z 406 " =    1.647
peak=    3.707 closest distance to " O   HOH Z 116 " =    3.040
peak=    3.706 closest distance to " CA  PRO A  54 " =    1.345
peak=    3.703 closest distance to " O   HOH Z 132 " =    2.494
peak=    3.693 closest distance to " O   HOH Z 126 " =    1.491
peak=    3.691 closest distance to " CD2 TRP A 179 " =    1.252
peak=    3.679 closest distance to " CB  SER A 216 " =    0.854
peak=    3.670 closest distance to " O   HOH Z  21 " =    1.738
peak=    3.669 closest distance to " O   TYR A 116 " =    1.321
peak=    3.662 closest distance to " N   PHE A 130 " =    1.244
peak=    3.659 closest distance to " O   HOH Z 405 " =    1.341
peak=    3.653 closest distance to " O   SER A  87 " =    2.144
peak=    3.650 closest distance to " CD1 LEU A 300 " =    1.168
peak=    3.638 closest distance to " CG2 THR A 221 " =    1.003
peak=    3.634 closest distance to " O   HOH Z  88 " =    3.882
peak=    3.630 closest distance to " O   HOH Z 258 " =    2.087
peak=    3.625 closest distance to " O   HOH Z 365 " =    2.749
peak=    3.624 closest distance to " CA  THR A 264 " =    0.884
peak=    3.602 closest distance to " O   HOH Z 325 " =    3.943
peak=    3.600 closest distance to " O   HOH Z 391 " =    2.865
peak=    3.594 closest distance to " NH2AARG A 190 " =    1.973
peak=    3.591 closest distance to " O   ASN A 209 " =    1.390
peak=    3.590 closest distance to " CB  SER A   3 " =    1.418
peak=    3.586 closest distance to " O   HOH Z 352 " =    1.784
peak=    3.585 closest distance to " CB  TYR A 169 " =    0.755
peak=    3.585 closest distance to " O   HOH Z 327 " =    1.671
peak=    3.581 closest distance to " CB  ASP A 140 " =    0.855
peak=    3.579 closest distance to " O   HOH Z 368 " =    1.968
peak=    3.576 closest distance to " N   GLN A 278 " =    1.266
peak=    3.573 closest distance to " CB  VAL A 202 " =    1.663
peak=    3.571 closest distance to " O   HOH Z   9 " =    1.355
peak=    3.560 closest distance to " O   HOH Z 371 " =    2.862
peak=    3.558 closest distance to " CB  MET A  47 " =    1.120
peak=    3.539 closest distance to " O   HOH Z  68 " =    2.118
peak=    3.536 closest distance to " CA  TYR A 116 " =    1.334
peak=    3.534 closest distance to " CB  ALA A   1 " =    4.695
peak=    3.532 closest distance to " CA  ARG A 195 " =    1.254
peak=    3.531 closest distance to " O   HOH Z 345 " =    1.801
peak=    3.522 closest distance to " NE2 HIS A 207 " =    1.287
peak=    3.520 closest distance to " O   HOH Z  58 " =    1.653
peak=    3.515 closest distance to " O   HOH Z 386 " =    2.970
peak=    3.513 closest distance to " O   HOH Z 128 " =    2.218
peak=    3.511 closest distance to " O   HOH Z 193 " =    1.654
peak=    3.502 closest distance to " N   CYS A 260 " =    0.847
peak=    3.498 closest distance to " CG  LYS A 119 " =    1.141
peak=    3.496 closest distance to " ND2 ASN A 249 " =    0.852
peak=    3.493 closest distance to " CB  ARG A 139 " =    1.046
peak=    3.492 closest distance to " O   HOH Z 172 " =    2.840
peak=    3.487 closest distance to " CB  GLU A  46 " =    0.974
peak=    3.486 closest distance to " CA  ASN A 215 " =    1.150
peak=    3.483 closest distance to " O   HOH Z  88 " =    3.298
peak=    3.483 closest distance to " CA  ALA A 158 " =    1.136
peak=    3.481 closest distance to " CD BLYS A 290 " =    1.057
peak=    3.480 closest distance to " CG1 ILE A  33 " =    1.264
peak=    3.477 closest distance to " O   HOH Z 411 " =    3.803
peak=    3.464 closest distance to " O   HOH Z 373 " =    1.509
peak=    3.460 closest distance to " O   HOH Z 175 " =    2.181
peak=    3.454 closest distance to " O   HOH Z 422 " =    2.703
peak=    3.453 closest distance to " CB  GLN A  88 " =    1.239
peak=    3.452 closest distance to " CD  LYS A 166 " =    1.291
peak=    3.450 closest distance to " O   HOH Z   7 " =    1.369
peak=    3.449 closest distance to " CZ3 TRP A 266 " =    1.139
peak=    3.445 closest distance to " CD  ARG A 269 " =    0.906
peak=    3.445 closest distance to " O   HOH Z  44 " =    2.716
peak=    3.442 closest distance to " O   HOH Z 286 " =    2.186
peak=    3.439 closest distance to " CB  MET A  40 " =    0.830
peak=    3.438 closest distance to " O   HOH Z 368 " =    4.266
peak=    3.438 closest distance to " O   HOH Z 147 " =    1.784
peak=    3.436 closest distance to " OG BSER A 164 " =    2.372
peak=    3.434 closest distance to " N   ASN A 127 " =    1.306
peak=    3.431 closest distance to " O   HOH Z 213 " =    2.035
peak=    3.431 closest distance to " OG  SER A  62 " =    2.981
peak=    3.431 closest distance to " OG  SER A  22 " =    2.858
peak=    3.430 closest distance to " O   HOH Z 389 " =    1.860
peak=    3.425 closest distance to " NE2 GLN A  73 " =    3.810
peak=    3.423 closest distance to " CB  TYR A 169 " =    0.913
peak=    3.413 closest distance to " O   HOH Z 426 " =    1.942
peak=    3.409 closest distance to " OD1BASN A 224 " =    2.364
peak=    3.409 closest distance to " O   HOH Z 188 " =    2.232
peak=    3.398 closest distance to " CD  PRO A 243 " =    1.586
peak=    3.394 closest distance to " CD2 LEU A 297 " =    0.937
peak=    3.391 closest distance to " CB  ARG A 138 " =    0.962
peak=    3.384 closest distance to " O   HOH Z 193 " =    2.067
peak=    3.384 closest distance to " CA  SER A  95 " =    1.008
peak=    3.383 closest distance to " O   HOH Z 290 " =    1.052
peak=    3.379 closest distance to " CB  LYS A 117 " =    1.235
peak=    3.377 closest distance to " O   HOH Z 302 " =    1.782
peak=    3.376 closest distance to " CA  ILE A 234 " =    0.989
peak=    3.375 closest distance to " CB  TRP A 150 " =    1.259
peak=    3.375 closest distance to " O   HOH Z 109 " =    2.516
peak=    3.374 closest distance to " CB  ALA A  34 " =    1.048
peak=    3.369 closest distance to " CG1 VAL A 189 " =    1.779
peak=    3.368 closest distance to " O   HOH Z 132 " =    3.681
peak=    3.362 closest distance to " CB  ILE A 120 " =    1.369
peak=    3.361 closest distance to " CA  THR A 221 " =    1.000
peak=    3.360 closest distance to " O   HOH Z 305 " =    3.627
peak=    3.357 closest distance to " O  BHOH Z 338 " =    2.392
peak=    3.356 closest distance to " CD1 ILE A 263 " =    1.284
peak=    3.353 closest distance to " CA  VAL A 125 " =    1.123
peak=    3.351 closest distance to " CA  ALA A  51 " =    0.929
peak=    3.348 closest distance to " O   HOH Z 344 " =    3.094
peak=    3.346 closest distance to " O   ASN A  74 " =    1.576
peak=    3.345 closest distance to " CB  TYR A 116 " =    0.867
peak=    3.343 closest distance to " O   HOH Z 423 " =    2.194
peak=    3.337 closest distance to " O   MET A 105 " =    1.772
peak=    3.337 closest distance to " O   HOH Z 425 " =    2.033
peak=    3.337 closest distance to " O   HOH Z  53 " =    2.535
peak=    3.336 closest distance to " O   HOH Z 135 " =    1.693
peak=    3.334 closest distance to " CA  MET A  40 " =    1.193
peak=    3.334 closest distance to " CG  MET A 113 " =    1.352
peak=    3.331 closest distance to " CA  ARG A 102 " =    1.121
peak=    3.329 closest distance to " O   HOH Z   3 " =    1.930
peak=    3.327 closest distance to " CB  ASN A 110 " =    1.058
peak=    3.324 closest distance to " CG  ARG A 159 " =    0.824
peak=    3.320 closest distance to " CB  PRO A  90 " =    1.212
peak=    3.318 closest distance to " O   HOH Z 343 " =    3.377
peak=    3.317 closest distance to " CB  THR A 157 " =    1.153
peak=    3.315 closest distance to " O   HOH Z 213 " =    2.657
peak=    3.309 closest distance to " CA  TYR A  30 " =    1.058
peak=    3.304 closest distance to " CA  ASP A 124 " =    0.700
peak=    3.299 closest distance to " CA  MET A 105 " =    0.913
peak=    3.298 closest distance to " CA  ALA A 291 " =    0.846
peak=    3.297 closest distance to " CG  GLN A  89 " =    1.523
peak=    3.293 closest distance to " CA  LYS A 290 " =    1.323
peak=    3.292 closest distance to " O   HOH Z  85 " =    2.221
peak=    3.291 closest distance to " O   HOH Z 325 " =    2.438
peak=    3.290 closest distance to " NH1 ARG A 138 " =    1.076
peak=    3.290 closest distance to " CB  SER A  62 " =    1.100
peak=    3.289 closest distance to " NH2 ARG A 156 " =    1.163
peak=    3.277 closest distance to " O   HOH Z 133 " =    1.641
peak=    3.275 closest distance to " CZ3 TRP A 123 " =    1.415
peak=    3.273 closest distance to " CB  SER A 276 " =    1.091
peak=    3.272 closest distance to " CA  ASN A 217 " =    1.181
peak=    3.272 closest distance to " CA  GLU A  46 " =    0.860
peak=    3.267 closest distance to " N   ALA A   1 " =    2.050
peak=    3.266 closest distance to " CG1 ILE A 151 " =    1.120
peak=    3.261 closest distance to " NH2BARG A 145 " =    2.006
peak=    3.260 closest distance to " CB  VAL A 265 " =    1.864
peak=    3.260 closest distance to " O   HOH Z 207 " =    2.192
peak=    3.258 closest distance to " CB  LEU A 143 " =    1.132
peak=    3.257 closest distance to " O   HOH Z 409 " =    2.353
peak=    3.256 closest distance to " CA  GLY A 267 " =    1.157
peak=    3.255 closest distance to " CG2 ILE A  20 " =    1.512
peak=    3.253 closest distance to " CB  GLU A 236 " =    1.011
peak=    3.253 closest distance to " O   HOH Z 207 " =    1.833
peak=    3.250 closest distance to " O   HOH Z 238 " =    3.752
peak=    3.247 closest distance to " CB  TRP A 179 " =    1.510
peak=    3.241 closest distance to " O   HOH Z 282 " =    1.986
peak=    3.240 closest distance to " CD2 LEU A 255 " =    1.769
peak=    3.237 closest distance to " O   HOH Z 291 " =    1.533
peak=    3.232 closest distance to " CA  ALA A  21 " =    1.183
peak=    3.230 closest distance to " O   HOH Z 329 " =    3.913
peak=    3.228 closest distance to " CB  ALA A 248 " =    0.979
peak=    3.228 closest distance to " OE2 GLU A  53 " =    2.051
peak=    3.222 closest distance to " CG2 VAL A 197 " =    1.019
peak=    3.218 closest distance to " CG1 VAL A 153 " =    0.911
peak=    3.214 closest distance to " CG2 ILE A 151 " =    0.902
peak=    3.210 closest distance to " O   HOH Z  59 " =    2.035
peak=    3.206 closest distance to " O   HOH Z 188 " =    1.360
peak=    3.204 closest distance to " O   HOH Z 359 " =    1.430
peak=    3.204 closest distance to " CB  ALA A 114 " =    1.426
peak=    3.203 closest distance to " O   HOH Z 294 " =    1.489
peak=    3.198 closest distance to " N   GLU A   2 " =    1.452
peak=    3.195 closest distance to " CA  ARG A  36 " =    1.085
peak=    3.190 closest distance to " O   HOH Z  64 " =    2.320
peak=    3.189 closest distance to " CA  ASN A 127 " =    1.056
peak=    3.185 closest distance to " O   HOH Z 145 " =    2.368
peak=    3.185 closest distance to " CG2AVAL A  72 " =    1.522
peak=    3.185 closest distance to " CA  ALA A 299 " =    0.857
peak=    3.180 closest distance to " O   HOH Z  44 " =    1.619
peak=    3.177 closest distance to " CB  ALA A   9 " =    1.594
peak=    3.177 closest distance to " CB  ASN A 215 " =    1.084
peak=    3.175 closest distance to " NH1BARG A 145 " =    1.235
peak=    3.172 closest distance to " O   HOH Z 219 " =    1.890
peak=    3.172 closest distance to " ND1 HIS A  81 " =    1.676
peak=    3.171 closest distance to " O   ARG A 145 " =    1.698
peak=    3.171 closest distance to " O   HOH Z 128 " =    1.856
peak=    3.170 closest distance to " CG BARG A 275 " =    1.422
peak=    3.169 closest distance to " O   HOH Z 303 " =    3.128
peak=    3.168 closest distance to " O   HOH Z 403 " =    1.594
peak=    3.168 closest distance to " O   HOH Z 116 " =    1.758
peak=    3.161 closest distance to " N   ASN A  39 " =    1.286
peak=    3.158 closest distance to " CD1 ILE A  33 " =    1.735
peak=    3.157 closest distance to " CB  GLU A 236 " =    1.066
peak=    3.155 closest distance to " NH2 ARG A 219 " =    1.866
peak=    3.153 closest distance to " CB  SER A 210 " =    0.775
peak=    3.151 closest distance to " CG  GLN A 278 " =    1.375
peak=    3.151 closest distance to " N   ARG A 156 " =    1.315
peak=    3.149 closest distance to " O   HOH Z 148 " =    3.405
peak=    3.148 closest distance to " NE2 GLN A  58 " =    3.931
peak=    3.146 closest distance to " O   HOH Z 195 " =    1.207
peak=    3.144 closest distance to " O   HOH Z  30 " =    1.736
peak=    3.143 closest distance to " CB  GLN A 103 " =    0.857
peak=    3.142 closest distance to " CA  GLY A 136 " =    1.013
peak=    3.142 closest distance to " CG  GLN A  77 " =    2.143
peak=    3.138 closest distance to " O   HOH Z 130 " =    3.798
peak=    3.136 closest distance to " O   HOH Z 128 " =    2.068
peak=    3.134 closest distance to " OG  SER A  62 " =    2.930
peak=    3.134 closest distance to " CG BARG A 102 " =    1.899
peak=    3.133 closest distance to " O   THR A 294 " =    1.045
peak=    3.129 closest distance to " O   HOH Z 271 " =    2.479
peak=    3.121 closest distance to " CB  THR A 235 " =    1.226
peak=    3.111 closest distance to " O   HOH Z 273 " =    2.881
peak=    3.105 closest distance to " CB  ALA A 114 " =    0.869
peak=    3.102 closest distance to " N   TYR A  15 " =    0.795
peak=    3.100 closest distance to " CD1 ILE A 106 " =    0.843
peak=    3.086 closest distance to " O   HOH Z 298 " =    2.400
peak=    3.086 closest distance to " O   SER A 164 " =    1.293
peak=    3.082 closest distance to " CB  ALA A  43 " =    0.809
peak=    3.082 closest distance to " O   HOH Z 432 " =    1.692
peak=    3.078 closest distance to " O   HOH Z 358 " =    3.826
peak=    3.076 closest distance to " O   HOH Z 369 " =    1.702
peak=    3.076 closest distance to " O   HOH Z 124 " =    2.189
peak=    3.073 closest distance to " O   HOH Z 386 " =    2.988
peak=    3.073 closest distance to " N   ASP A 162 " =    1.153
peak=    3.073 closest distance to " CG BARG A 190 " =    1.082
peak=    3.072 closest distance to " CB  PHE A 204 " =    0.737
peak=    3.072 closest distance to " O   HOH Z 152 " =    2.493
peak=    3.072 closest distance to " CB  ASP A 171 " =    1.198
peak=    3.072 closest distance to " CB  SER A  99 " =    0.941
peak=    3.068 closest distance to " O   HOH Z 153 " =    1.615
peak=    3.063 closest distance to " OD1 ASN A 217 " =    1.497
peak=    3.053 closest distance to " CB  LEU A 300 " =    0.929
peak=    3.033 closest distance to " O   HOH Z 183 " =    1.401
peak=    3.032 closest distance to " CA  GLY A  35 " =    1.037
peak=    3.023 closest distance to " CB  ASP A 171 " =    0.735
peak=    3.023 closest distance to " O   HOH Z 181 " =    2.059
peak=    3.010 closest distance to " CA  ILE A 106 " =    0.823
peak=    3.009 closest distance to " O   HOH Z  43 " =    2.160

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 210         
Filter by distance & map next to the model:
   mapped sites are within: 0.564 - 5.883
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 209 from: 210
   mapped sites are within: 0.735 - 5.883

peak=   -4.688 closest distance to " O   HOH Z 377 " =    1.986
peak=   -4.534 closest distance to " CB  PRO A 243 " =    2.587
peak=   -4.504 closest distance to " CD  ARG A 156 " =    2.098
peak=   -4.372 closest distance to " CD  ARG A  14 " =    3.442
peak=   -4.309 closest distance to " O   HOH Z 266 " =    5.195
peak=   -4.193 closest distance to " OG BSER A 134 " =    1.269
peak=   -4.170 closest distance to " O   HOH Z 231 " =    2.125
peak=   -4.088 closest distance to " O   HOH Z 290 " =    1.109
peak=   -4.069 closest distance to " CG  GLN A 223 " =    2.040
peak=   -4.062 closest distance to " CZ3 TRP A 179 " =    1.193
peak=   -4.027 closest distance to " CB  ALA A  43 " =    2.532
peak=   -4.022 closest distance to " O   VAL A  67 " =    2.636
peak=   -4.014 closest distance to " O   HOH Z  52 " =    1.140
peak=   -4.010 closest distance to " O   PRO A 198 " =    1.252
peak=   -3.993 closest distance to " N   ALA A  43 " =    2.572
peak=   -3.977 closest distance to " O   HOH Z 351 " =    1.560
peak=   -3.975 closest distance to " O   HOH Z 389 " =    2.003
peak=   -3.932 closest distance to " CD1 LEU A 255 " =    2.967
peak=   -3.904 closest distance to " CG1 VAL A 112 " =    2.590
peak=   -3.871 closest distance to " ND2 ASN A  45 " =    1.945
peak=   -3.862 closest distance to " O   HOH Z 185 " =    2.163
peak=   -3.850 closest distance to " ND2 ASN A 249 " =    2.182
peak=   -3.843 closest distance to " O   HOH Z  38 " =    1.476
peak=   -3.842 closest distance to " O   HOH Z 372 " =    2.537
peak=   -3.789 closest distance to " C   HIS A 108 " =    1.228
peak=   -3.769 closest distance to " O   HOH Z 407 " =    3.274
peak=   -3.754 closest distance to " CE2 PHE A 218 " =    2.443
peak=   -3.745 closest distance to " CB  ALA A 291 " =    2.205
peak=   -3.731 closest distance to " CG1 VAL A 112 " =    2.992
peak=   -3.720 closest distance to " O   HOH Z 152 " =    5.083
peak=   -3.719 closest distance to " O   TYR A 247 " =    2.843
peak=   -3.711 closest distance to " CA  GLY A  98 " =    1.860
peak=   -3.690 closest distance to " CG  MET A 105 " =    0.985
peak=   -3.685 closest distance to " CB  TRP A  85 " =    2.465
peak=   -3.672 closest distance to " O   HOH Z 313 " =    1.767
peak=   -3.667 closest distance to " N   THR A 157 " =    1.516
peak=   -3.649 closest distance to " O   HOH Z 359 " =    3.240
peak=   -3.633 closest distance to " CE  MET A 105 " =    2.516
peak=   -3.625 closest distance to " O   HOH Z 131 " =    4.118
peak=   -3.623 closest distance to " O   HOH Z 198 " =    1.955
peak=   -3.603 closest distance to " CA  GLY A 241 " =    2.274
peak=   -3.599 closest distance to " CE BMET A  47 " =    1.378
peak=   -3.598 closest distance to " ND2 ASN A  45 " =    1.302
peak=   -3.596 closest distance to " CE2 TYR A  30 " =    2.664
peak=   -3.588 closest distance to " O   HOH Z  60 " =    2.594
peak=   -3.585 closest distance to " O   PHE A 218 " =    1.508
peak=   -3.583 closest distance to " OD1 ASP A 171 " =    1.639
peak=   -3.581 closest distance to " O   HOH Z 140 " =    1.383
peak=   -3.575 closest distance to " OG BSER A 134 " =    1.725
peak=   -3.570 closest distance to " O   ILE A 109 " =    2.551
peak=   -3.569 closest distance to " CG2 THR A  18 " =    2.846
peak=   -3.566 closest distance to " OG  SER A  97 " =    2.158
peak=   -3.560 closest distance to " CA  ASP A  27 " =    2.479
peak=   -3.546 closest distance to " CB  CYS A 254 " =    2.144
peak=   -3.542 closest distance to " OD1 ASP A 191 " =    1.867
peak=   -3.541 closest distance to " O   SER A 135 " =    1.419
peak=   -3.535 closest distance to " CD2 PHE A 192 " =    2.024
peak=   -3.533 closest distance to " O   HOH Z 176 " =    0.781
peak=   -3.531 closest distance to " O   HOH Z 282 " =    0.921
peak=   -3.528 closest distance to " CB  PRO A  54 " =    2.458
peak=   -3.527 closest distance to " CA  GLY A 203 " =    2.323
peak=   -3.523 closest distance to " O   PRO A 163 " =    2.011
peak=   -3.514 closest distance to " CB  ALA A 291 " =    1.981
peak=   -3.513 closest distance to " O   HOH Z  73 " =    2.065
peak=   -3.512 closest distance to " O   PRO A 198 " =    1.371
peak=   -3.508 closest distance to " CD2 TYR A 293 " =    1.946
peak=   -3.504 closest distance to " O   HOH Z 174 " =    2.639
peak=   -3.501 closest distance to " CZ BARG A 275 " =    1.695
peak=   -3.501 closest distance to " O   HOH Z 111 " =    1.666
peak=   -3.496 closest distance to " CG2 THR A 178 " =    2.237
peak=   -3.494 closest distance to " O   ALA A  10 " =    1.631
peak=   -3.492 closest distance to " CD1 PHE A  59 " =    2.033
peak=   -3.487 closest distance to " C   ALA A 158 " =    1.552
peak=   -3.483 closest distance to " CB  PRO A 163 " =    2.507
peak=   -3.475 closest distance to " O   HOH Z 211 " =    1.488
peak=   -3.470 closest distance to " CD  GLN A  58 " =    0.974
peak=   -3.470 closest distance to " O   ARG A 145 " =    1.574
peak=   -3.468 closest distance to " O   PRO A 243 " =    2.460
peak=   -3.468 closest distance to " CB  TYR A  15 " =    2.240
peak=   -3.464 closest distance to " O   HOH Z 231 " =    1.167
peak=   -3.464 closest distance to " NH2AARG A 275 " =    5.417
peak=   -3.457 closest distance to " O   HOH Z 337 " =    1.409
peak=   -3.453 closest distance to " OXT GLY A 302 " =    3.077
peak=   -3.446 closest distance to " O   HOH Z  11 " =    1.915
peak=   -3.439 closest distance to " O   HOH Z 298 " =    2.458
peak=   -3.432 closest distance to " O   HOH Z 253 " =    3.953
peak=   -3.427 closest distance to " O   HOH Z  51 " =    1.134
peak=   -3.427 closest distance to " CD2 PHE A  61 " =    2.092
peak=   -3.424 closest distance to " O   HOH Z   9 " =    1.700
peak=   -3.424 closest distance to " O   HOH Z 191 " =    5.496
peak=   -3.423 closest distance to " OD1 ASN A 148 " =    1.599
peak=   -3.417 closest distance to " OG  SER A  87 " =    1.290
peak=   -3.416 closest distance to " CB  ASN A  39 " =    2.282
peak=   -3.408 closest distance to " O   VAL A 189 " =    2.533
peak=   -3.405 closest distance to " CD1 LEU A 101 " =    2.283
peak=   -3.404 closest distance to " O   HOH Z 357 " =    2.024
peak=   -3.393 closest distance to " C   LEU A 222 " =    0.768
peak=   -3.389 closest distance to " ND2 ASN A 187 " =    1.456
peak=   -3.387 closest distance to " CG2 ILE A 263 " =    2.314
peak=   -3.385 closest distance to " CG  PHE A 283 " =    2.650
peak=   -3.381 closest distance to " O   HOH Z 384 " =    2.848
peak=   -3.378 closest distance to " N   ASP A 171 " =    2.370
peak=   -3.372 closest distance to " O   HOH Z 298 " =    1.158
peak=   -3.370 closest distance to " CB  ASP A 132 " =    2.385
peak=   -3.368 closest distance to " CG1 VAL A 250 " =    2.694
peak=   -3.368 closest distance to " O   HOH Z 426 " =    1.658
peak=   -3.358 closest distance to " O   HOH Z 394 " =    1.446
peak=   -3.354 closest distance to " O   HOH Z 166 " =    1.264
peak=   -3.353 closest distance to " O   HOH Z 281 " =    2.668
peak=   -3.350 closest distance to " OH  TYR A 172 " =    1.740
peak=   -3.349 closest distance to " ND2 ASN A  60 " =    4.165
peak=   -3.348 closest distance to " CA  GLY A 241 " =    3.171
peak=   -3.347 closest distance to " CB  ALA A 131 " =    2.023
peak=   -3.329 closest distance to " O   HOH Z  43 " =    1.702
peak=   -3.328 closest distance to " NH2 ARG A  79 " =    2.017
peak=   -3.326 closest distance to " O   HOH Z  65 " =    1.258
peak=   -3.325 closest distance to " CG  TRP A 266 " =    1.706
peak=   -3.308 closest distance to " O   HOH Z 266 " =    4.951
peak=   -3.303 closest distance to " CB  ALA A   9 " =    2.396
peak=   -3.303 closest distance to " NE  ARG A  36 " =    1.979
peak=   -3.301 closest distance to " O   SER A  22 " =    2.557
peak=   -3.300 closest distance to " O   HOH Z  90 " =    2.599
peak=   -3.300 closest distance to " CA  GLY A 133 " =    2.051
peak=   -3.299 closest distance to " CB  ASP A 286 " =    2.223
peak=   -3.298 closest distance to " O   HOH Z  63 " =    1.982
peak=   -3.294 closest distance to " CD  GLN A  88 " =    0.860
peak=   -3.287 closest distance to " CA  ASP A 298 " =    1.078
peak=   -3.286 closest distance to " O   HOH Z 377 " =    0.735
peak=   -3.285 closest distance to " O   HOH Z 198 " =    1.690
peak=   -3.281 closest distance to " O   HOH Z 286 " =    1.858
peak=   -3.278 closest distance to " N   SER A 276 " =    1.304
peak=   -3.274 closest distance to " O   HOH Z 282 " =    4.750
peak=   -3.274 closest distance to " CB  ALA A 100 " =    2.225
peak=   -3.273 closest distance to " O   HOH Z 184 " =    1.847
peak=   -3.266 closest distance to " O   HOH Z 409 " =    5.883
peak=   -3.265 closest distance to " CE2 PHE A  61 " =    2.687
peak=   -3.264 closest distance to " N   ALA A 226 " =    2.112
peak=   -3.263 closest distance to " O   SER A 210 " =    1.965
peak=   -3.258 closest distance to " ND2BASN A 224 " =    1.778
peak=   -3.257 closest distance to " ND2 ASN A 285 " =    2.096
peak=   -3.256 closest distance to " O   HOH Z  10 " =    1.381
peak=   -3.253 closest distance to " CB  ALA A 248 " =    2.074
peak=   -3.252 closest distance to " O   HOH Z 368 " =    1.701
peak=   -3.251 closest distance to " O   HOH Z 275 " =    1.741
peak=   -3.247 closest distance to " O   ILE A  49 " =    1.697
peak=   -3.246 closest distance to " O   HOH Z 102 " =    1.623
peak=   -3.242 closest distance to " O   HOH Z   1 " =    1.458
peak=   -3.242 closest distance to " O   HOH Z 385 " =    2.101
peak=   -3.236 closest distance to " O   GLY A 211 " =    1.283
peak=   -3.234 closest distance to " CD  GLU A 277 " =    1.218
peak=   -3.233 closest distance to " O   HOH Z 166 " =    1.808
peak=   -3.231 closest distance to " CB  ALA A 114 " =    2.527
peak=   -3.226 closest distance to " O   HOH Z 317 " =    1.513
peak=   -3.224 closest distance to " C   ASN A 285 " =    2.367
peak=   -3.220 closest distance to " O   HOH Z  49 " =    1.292
peak=   -3.217 closest distance to " NE2 GLN A 278 " =    1.675
peak=   -3.213 closest distance to " O   HOH Z  60 " =    1.919
peak=   -3.210 closest distance to " CD2 PHE A 225 " =    1.134
peak=   -3.210 closest distance to " CD1 LEU A 228 " =    2.316
peak=   -3.206 closest distance to " OD2 ASP A 140 " =    1.605
peak=   -3.205 closest distance to " O   HOH Z 147 " =    1.707
peak=   -3.201 closest distance to " CG2 VAL A 189 " =    1.879
peak=   -3.200 closest distance to " O   HOH Z  24 " =    1.263
peak=   -3.197 closest distance to " CG  PRO A 163 " =    2.579
peak=   -3.192 closest distance to " CB  PHE A 208 " =    2.276
peak=   -3.190 closest distance to " O   HOH Z 412 " =    4.424
peak=   -3.188 closest distance to " CE3 TRP A 150 " =    2.209
peak=   -3.188 closest distance to " C   LYS A  76 " =    1.625
peak=   -3.187 closest distance to " C   ASN A 187 " =    1.902
peak=   -3.186 closest distance to " O   SER A  95 " =    1.497
peak=   -3.185 closest distance to " CD1 ILE A 239 " =    2.327
peak=   -3.185 closest distance to " C   GLY A  13 " =    0.964
peak=   -3.184 closest distance to " O   HOH Z 111 " =    1.246
peak=   -3.184 closest distance to " N   ASN A  60 " =    1.295
peak=   -3.184 closest distance to " OD1 ASN A 187 " =    1.567
peak=   -3.179 closest distance to " CB  ALA A 248 " =    2.404
peak=   -3.174 closest distance to " OE1 GLN A  88 " =    1.192
peak=   -3.172 closest distance to " C   ALA A 114 " =    2.271
peak=   -3.171 closest distance to " O   HOH Z 114 " =    0.853
peak=   -3.171 closest distance to " CG2 ILE A 151 " =    2.593
peak=   -3.169 closest distance to " CD1 ILE A 199 " =    2.627
peak=   -3.160 closest distance to " CH2 TRP A 177 " =    2.191
peak=   -3.151 closest distance to " CE3 TRP A 123 " =    1.331
peak=   -3.148 closest distance to " O   VAL A  67 " =    2.972
peak=   -3.146 closest distance to " O   ALA A 161 " =    1.649
peak=   -3.139 closest distance to " CG1 VAL A 197 " =    2.221
peak=   -3.137 closest distance to " CD1 LEU A 297 " =    2.557
peak=   -3.136 closest distance to " N   MET A 105 " =    2.538
peak=   -3.132 closest distance to " OE1 GLN A  58 " =    3.141
peak=   -3.123 closest distance to " CZ  PHE A  59 " =    1.624
peak=   -3.119 closest distance to " SD  MET A 188 " =    2.326
peak=   -3.116 closest distance to " O   HOH Z 353 " =    2.164
peak=   -3.112 closest distance to " CA  GLY A 241 " =    2.870
peak=   -3.112 closest distance to " OG  SER A 245 " =    1.319
peak=   -3.112 closest distance to " O   LYS A 181 " =    2.906
peak=   -3.111 closest distance to " O   HOH Z 352 " =    2.267
peak=   -3.109 closest distance to " O   GLN A 240 " =    2.008
peak=   -3.106 closest distance to " ND2 ASN A  60 " =    1.476
peak=   -3.102 closest distance to " CE  LYS A  76 " =    2.770
peak=   -3.100 closest distance to " O   GLN A 240 " =    2.430
peak=   -3.081 closest distance to " CZ  TYR A 169 " =    1.686
peak=   -3.077 closest distance to " OH  TYR A 247 " =    1.838
peak=   -3.070 closest distance to " CG  ARG A 269 " =    2.617
peak=   -3.060 closest distance to " N   ASP A 270 " =    1.429
peak=   -3.058 closest distance to " O   HOH Z 281 " =    2.968
peak=   -3.056 closest distance to " SG ACYS A 201 " =    1.847
peak=   -3.041 closest distance to " O   HOH Z  28 " =    1.930
peak=   -3.038 closest distance to " O   HOH Z 193 " =    1.562
peak=   -3.034 closest distance to " CA  GLY A  57 " =    2.222

================= 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    :  0.3892 0.3834   6.178840e+00   6.162488e+00
   1_bss:  0.3785 0.3784   6.166997e+00   6.148646e+00
   1_xyz:  0.2243 0.2544   5.724698e+00   5.809032e+00
   1_adp:  0.2039 0.2638   5.670829e+00   5.844890e+00
   1_occ:  0.2037 0.2634   5.669746e+00   5.843857e+00
   2_bss:  0.2020 0.2607   5.664503e+00   5.835894e+00
   2_xyz:  0.1526 0.2028   5.410761e+00   5.618289e+00
   2_adp:  0.1439 0.1901   5.357868e+00   5.564038e+00
   2_occ:  0.1438 0.1901   5.357300e+00   5.563999e+00
   3_bss:  0.1437 0.1896   5.354535e+00   5.560975e+00
   3_xyz:  0.1252 0.1697   5.234471e+00   5.453310e+00
   3_adp:  0.1197 0.1658   5.201584e+00   5.431107e+00
   3_occ:  0.1196 0.1659   5.201599e+00   5.431389e+00
   4_bss:  0.1196 0.1657   5.201135e+00   5.431131e+00
   4_xyz:  0.1167 0.1632   5.183163e+00   5.419745e+00
   4_adp:  0.1159 0.1627   5.179883e+00   5.418193e+00
   4_occ:  0.1158 0.1627   5.179807e+00   5.418237e+00
   5_bss:  0.1161 0.1626   5.180538e+00   5.417202e+00
   5_xyz:  0.1101 0.1602   5.147779e+00   5.403488e+00
   5_adp:  0.1102 0.1572   5.140470e+00   5.389928e+00
   5_occ:  0.1101 0.1571   5.140083e+00   5.389428e+00
   5_bss:  0.1100 0.1571   5.140167e+00   5.389441e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.332  48.962  -1.864   1.674   0.068   0.000   0.000   0.000
   1_xyz:  0.332  48.962  -1.864   1.674   0.068   0.000   0.000   0.000
   1_adp:  0.332  48.962  -1.864   1.674   0.068   0.000   0.000   0.000
   1_occ:  0.332  48.962  -1.864   1.674   0.068   0.000   0.000   0.000
   2_bss:  0.341  67.863  -2.354  -1.329  -0.786  -0.000  -0.000  -0.000
   2_xyz:  0.341  67.863  -2.354  -1.329  -0.786  -0.000  -0.000  -0.000
   2_adp:  0.341  67.863  -2.354  -1.329  -0.786  -0.000  -0.000  -0.000
   2_occ:  0.341  67.863  -2.354  -1.329  -0.786  -0.000  -0.000  -0.000
   3_bss:  0.326  59.938  -2.415  -2.256  -0.905  -0.000  -0.000  -0.000
   3_xyz:  0.326  59.938  -2.415  -2.256  -0.905  -0.000  -0.000  -0.000
   3_adp:  0.326  59.938  -2.415  -2.256  -0.905  -0.000  -0.000  -0.000
   3_occ:  0.326  59.938  -2.415  -2.256  -0.905  -0.000  -0.000  -0.000
   4_bss:  0.322  61.080  -2.310  -2.422  -0.887  -0.000  -0.000  -0.000
   4_xyz:  0.322  61.080  -2.310  -2.422  -0.887  -0.000  -0.000  -0.000
   4_adp:  0.322  61.080  -2.310  -2.422  -0.887  -0.000  -0.000  -0.000
   4_occ:  0.322  61.080  -2.310  -2.422  -0.887  -0.000  -0.000  -0.000
   5_bss:  0.323  61.948  -2.154  -2.384  -0.756  -0.000  -0.000  -0.000
   5_xyz:  0.323  61.948  -2.154  -2.384  -0.756  -0.000  -0.000  -0.000
   5_adp:  0.323  61.948  -2.154  -2.384  -0.756  -0.000  -0.000  -0.000
   5_occ:  0.323  61.948  -2.154  -2.384  -0.756  -0.000  -0.000  -0.000
   5_bss:  0.326  61.926  -1.996  -2.299  -0.598  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  42.833 0.6100  0.7900    43909.588
   1_bss:  42.165 0.6164  0.8013    41911.244
   1_xyz:  24.543 0.8177  0.9918    16309.851
   1_adp:  25.844 0.8029  0.9796    17470.897
   1_occ:  25.832 0.8030  0.9791    17415.443
   2_bss:  25.469 0.8068  0.9355    17053.655
   2_xyz:  19.407 0.8665  0.9776    10246.531
   2_adp:  17.848 0.8820  0.9830     9208.344
   2_occ:  17.851 0.8820  0.9828     9201.570
   3_bss:  17.775 0.8826  0.9700     9121.353
   3_xyz:  15.404 0.9032  0.9795     7237.975
   3_adp:  14.905 0.9076  0.9746     6904.338
   3_occ:  14.911 0.9076  0.9745     6909.470
   4_bss:  14.903 0.9076  0.9742     6906.776
   4_xyz:  14.610 0.9103  0.9752     6726.106
   4_adp:  14.550 0.9109  0.9690     6699.550
   4_occ:  14.549 0.9109  0.9690     6699.351
   5_bss:  14.545 0.9109  0.9727     6683.200
   5_xyz:  14.265 0.9130  0.9746     6509.775
   5_adp:  13.981 0.9153  0.9708     6348.570
   5_occ:  13.972 0.9153  0.9707     6337.506
   5_bss:  13.976 0.9153  0.9746     6339.933
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6466e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6466e-01
   1_xyz:   1.289  0.010  0.087 15.771  0.006  4.110   9.1724e-02
   1_adp:   1.289  0.010  0.087 15.771  0.006  4.110   9.1724e-02
   1_occ:   1.289  0.010  0.087 15.771  0.006  4.110   9.1724e-02
   2_bss:   1.289  0.010  0.087 15.771  0.006  4.110   9.1724e-02
   2_xyz:   0.965  0.006  0.072 14.470  0.003  4.121   5.3592e-02
   2_adp:   0.965  0.006  0.072 14.470  0.003  4.121   5.3592e-02
   2_occ:   0.965  0.006  0.072 14.470  0.003  4.121   5.3592e-02
   3_bss:   0.965  0.006  0.072 14.470  0.003  4.121   5.3592e-02
   3_xyz:   0.923  0.006  0.069 14.528  0.003  4.126   5.2662e-02
   3_adp:   0.923  0.006  0.069 14.528  0.003  4.126   5.2662e-02
   3_occ:   0.923  0.006  0.069 14.528  0.003  4.126   5.2662e-02
   4_bss:   0.923  0.006  0.069 14.528  0.003  4.126   5.2662e-02
   4_xyz:   0.890  0.006  0.068 14.411  0.003  4.128   4.8712e-02
   4_adp:   0.890  0.006  0.068 14.411  0.003  4.128   4.8712e-02
   4_occ:   0.890  0.006  0.068 14.411  0.003  4.128   4.8712e-02
   5_bss:   0.890  0.006  0.068 14.411  0.003  4.128   4.8712e-02
   5_xyz:   1.040  0.008  0.079 14.803  0.004  4.132   6.4538e-02
   5_adp:   1.040  0.008  0.079 14.803  0.004  4.132   6.4538e-02
   5_occ:   1.040  0.008  0.079 14.803  0.004  4.132   6.4538e-02
   5_bss:   1.040  0.008  0.079 14.803  0.004  4.132   6.4538e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4143e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4143e-01
   1_xyz:  10.758  0.075  0.302 83.624  0.048  2.095   8.5647e-02
   1_adp:  10.758  0.075  0.302 83.624  0.048  2.095   8.5647e-02
   1_occ:  10.758  0.075  0.302 83.624  0.048  2.095   8.5647e-02
   2_bss:  10.758  0.075  0.302 83.624  0.048  2.095   8.5647e-02
   2_xyz:   7.534  0.057  0.246 81.815  0.021  2.380   4.6346e-02
   2_adp:   7.534  0.057  0.246 81.815  0.021  2.380   4.6346e-02
   2_occ:   7.534  0.057  0.246 81.815  0.021  2.380   4.6346e-02
   3_bss:   7.534  0.057  0.246 81.815  0.021  2.380   4.6346e-02
   3_xyz:   7.547  0.045  0.202 84.546  0.021  2.363   6.6254e-02
   3_adp:   7.547  0.045  0.202 84.546  0.021  2.363   6.6254e-02
   3_occ:   7.547  0.045  0.202 84.546  0.021  2.363   6.6254e-02
   4_bss:   7.547  0.045  0.202 84.546  0.021  2.363   6.6254e-02
   4_xyz:   7.637  0.052  0.198 82.666  0.028  2.384   2.8911e-02
   4_adp:   7.637  0.052  0.198 82.666  0.028  2.384   2.8911e-02
   4_occ:   7.637  0.052  0.198 82.666  0.028  2.384   2.8911e-02
   5_bss:   7.637  0.052  0.198 82.666  0.028  2.384   2.8911e-02
   5_xyz:   7.778  0.043  0.267 84.378  0.028  2.298   5.1997e-02
   5_adp:   7.778  0.043  0.267 84.378  0.028  2.298   5.1997e-02
   5_occ:   7.778  0.043  0.267 84.378  0.028  2.298   5.1997e-02
   5_bss:   7.778  0.043  0.267 84.378  0.028  2.298   5.1997e-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:  91.41   0.00  17.64  77.90   0.00  13.26  91.41   3.99  41.49
   1_occ:  91.41   0.00  17.64  77.90   0.00  13.26  91.41   3.99  41.49
   2_bss:  91.41   0.00  17.64  77.90   0.00  13.26  91.41   3.99  41.49
   2_xyz:  91.41   0.00  17.64  77.90   0.00  13.26  91.41   3.99  41.49
   2_adp:  90.09   0.00  17.38  77.34   0.00  13.08  90.09   6.19  40.82
   2_occ:  90.09   0.00  17.38  77.34   0.00  13.08  90.09   6.19  40.82
   3_bss:  90.09   0.00  17.38  77.34   0.00  13.08  90.09   6.19  40.82
   3_xyz:  90.09   0.00  17.38  77.34   0.00  13.08  90.09   6.19  40.82
   3_adp:  93.92   0.00  17.75  89.34   0.00  13.08  93.92   6.03  43.18
   3_occ:  93.92   0.00  17.75  89.34   0.00  13.08  93.92   6.03  43.18
   4_bss:  93.92   0.00  17.75  89.34   0.00  13.08  93.92   6.03  43.18
   4_xyz:  93.92   0.00  17.75  89.34   0.00  13.08  93.92   6.03  43.18
   4_adp:  93.56   0.00  17.56  93.29   0.00  12.93  93.56   5.60  42.78
   4_occ:  93.56   0.00  17.56  93.29   0.00  12.93  93.56   5.60  42.78
   5_bss:  93.56   0.00  17.56  93.29   0.00  12.93  93.56   5.60  42.78
   5_xyz:  93.56   0.00  17.56  93.29   0.00  12.93  93.56   5.60  42.78
   5_adp:  91.34   0.66  16.80  91.34   0.66  12.61  87.24   6.01  39.66
   5_occ:  91.34   0.66  16.80  91.34   0.66  12.61  87.24   6.01  39.66
   5_bss:  91.31   0.64  16.78  91.31   0.64  12.58  87.22   5.99  39.64
------------------------------------------------------------------------
 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:    1.208    0.017    0.403
   1_adp:    1.208    0.017    0.403
   1_occ:    1.208    0.017    0.403
   2_bss:    1.208    0.017    0.403
   2_xyz:    1.109    0.038    0.459
   2_adp:    1.109    0.038    0.459
   2_occ:    1.109    0.038    0.459
   3_bss:    1.109    0.038    0.459
   3_xyz:    1.145    0.045    0.521
   3_adp:    1.145    0.045    0.521
   3_occ:    1.145    0.045    0.521
   4_bss:    1.145    0.045    0.521
   4_xyz:    1.255    0.053    0.529
   4_adp:    1.255    0.053    0.529
   4_occ:    1.255    0.053    0.529
   5_bss:    1.255    0.053    0.529
   5_xyz:    1.327    0.055    0.546
   5_adp:    1.327    0.055    0.546
   5_occ:    1.327    0.055    0.546
   5_bss:    1.327    0.055    0.546
------------------------------------------------------------------------

CPU time actual refinement: 332.35


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_876/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_876/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_876/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_876/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_876/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 332.20 
  Macro-tasks:
    bulk solvent and scale       = 36.97  
    individual site refinement   = 134.40 
    weights calculation          = 30.93  
    collect and process          = 6.74   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 209.16 
  Micro-tasks:
    mask                            = 1.84   
    f_calc                          = 106.92 
    alpha_beta                      = 8.41   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 114.56 
    fmodel                         = 6.79   
    r_factors                      = 0.29   
    phase_errors                   = 10.68  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 250.91 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.754 micro seconds
Total CPU time: 5.76 minutes
from_scatterers_fft:    639 calls, 106.53 s
gradients_fft:          584 calls, 101.48 s

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

# Date 2008-01-16 Time 05:53:02 PST -0800 (1200491582.19 s)
Start R-work = 0.3892, R-free = 0.3834 (no bulk solvent and anisotropic scale)
Final R-work = 0.1328, R-free = 0.1761 (no bulk solvent and anisotropic scale)

Start R-work = 0.3785, R-free = 0.3784
Final R-work = 0.1100, R-free = 0.1571