# Date 2008-01-16 Time 05:41:01 PST -0800 (1200490861.26 s)
#phil __OFF__

Command line arguments: "../832.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25695
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 832

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 47.8686, 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: 2.75, per 1000 atoms: 0.97


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.8686, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0892 2.01057
Completeness in resolution range: 0.967406
Completeness with d_max=infinity: 0.964358

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0892
                             d_min =   2.0106

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.8686, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0892 2.01057
Completeness in resolution range: 0.967406
Completeness with d_max=infinity: 0.964358

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0896 -  4.3013 [2125/2152]  1912   213  10.0%
  bin  2:  4.3013 -  3.4272 [2036/2052]  1833   203  10.0%
  bin  3:  3.4272 -  2.9979 [2027/2046]  1825   202  10.0%
  bin  4:  2.9979 -  2.7255 [1993/2023]  1795   198   9.9%
  bin  5:  2.7255 -  2.5312 [1984/2003]  1785   199  10.0%
  bin  6:  2.5312 -  2.3825 [1970/2006]  1773   197  10.0%
  bin  7:  2.3825 -  2.2636 [1964/1997]  1766   198  10.1%
  bin  8:  2.2636 -  2.1654 [1950/1984]  1755   195  10.0%
  bin  9:  2.1654 -  2.0823 [1939/1967]  1744   195  10.1%
  bin 10:  2.0823 -  2.0106 [1601/2019]  1442   159   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_832/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: 0.12 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:
        1.80 -     2.42: 13
        2.42 -     3.04: 2126
        3.04 -     3.66: 4566
        3.66 -     4.28: 8854
        4.28 -     4.90: 12279
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.797 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 343 " - " O   HOH Z 277 "  2.017 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  2.017 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.145 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27833 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_832/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_832/model_refine_001.geo

CPU time processing inputs: 7.93


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 47.8686 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: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4066   r_free= 0.3931   ksol= 0.00   Bsol= 0.00   scale= 0.913    |
|                                                                             |
| 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:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.211984                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0896 -  4.7971 0.99   1379  153 0.3238 0.3355      6.4532      6.4269|
|  2:  4.7971 -  3.8281 0.99   1325  149 0.3409 0.3468      6.7123      6.7276|
|  3:  3.8281 -  3.3502 0.99   1309  146 0.3713 0.3458      6.5878      6.5126|
|  4:  3.3502 -  3.0466 0.99   1291  136 0.3930 0.3841      6.4486      6.3754|
|  5:  3.0466 -  2.8298 0.99   1285  145 0.4233 0.3599      6.3083      6.2696|
|  6:  2.8298 -  2.6639 0.99   1278  145 0.4329 0.4300      6.2155      6.1202|
|  7:  2.6639 -  2.5312 0.99   1283  141 0.4381 0.3967      6.1789      6.0697|
|  8:  2.5312 -  2.4214 0.98   1266  142 0.4403 0.4087      6.1294      6.1191|
|  9:  2.4214 -  2.3286 0.98   1272  143 0.4495 0.4502       6.059      6.0956|
| 10:  2.3286 -  2.2485 0.98   1248  135 0.4669 0.4186       6.081      5.9814|
| 11:  2.2485 -  2.1784 1.00   1262  146 0.4518 0.4249       6.003      6.0137|
| 12:  2.1784 -  2.1163 0.97   1261  134 0.4610 0.4769      5.9333      6.0193|
| 13:  2.1163 -  2.0607 0.98   1260  141 0.4730 0.4447      5.8657      5.8392|
| 14:  2.0607 -  2.0106 0.72    911  103 0.4409 0.5142      5.8114      5.7505|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0896 -  4.7971  1379   153  0.74  30.68   0.84     0.77      57789.04|
|  2:  4.7971 -  3.8281  1325   149  0.78  28.50   0.93     0.84      73569.02|
|  3:  3.8281 -  3.3502  1309   146  0.72  33.88   0.92     0.85      74928.18|
|  4:  3.3502 -  3.0466  1291   136  0.67  37.93   0.92     0.81      65235.34|
|  5:  3.0466 -  2.8298  1285   145  0.60  43.68   0.92     0.76      52891.51|
|  6:  2.8298 -  2.6639  1278   145  0.58  45.45   0.92     0.74      45962.60|
|  7:  2.6639 -  2.5312  1283   141  0.57  46.28   0.94     0.73      41633.31|
|  8:  2.5312 -  2.4214  1266   142  0.57  46.94   0.94     0.74      40180.05|
|  9:  2.4214 -  2.3286  1272   143  0.55  48.43   0.93     0.75      37472.73|
| 10:  2.3286 -  2.2485  1248   135  0.55  48.10   0.95     0.75      34954.00|
| 11:  2.2485 -  2.1784  1262   146  0.53  49.70   0.96     0.74      34107.49|
| 12:  2.1784 -  2.1163  1261   134  0.47  54.34   0.96     0.68      34627.25|
| 13:  2.1163 -  2.0607  1260   141  0.42  58.78   0.92     0.59      33077.34|
| 14:  2.0607 -  2.0106   911   103  0.36  62.78   0.97     0.48      28543.72|
|alpha:            min =        0.48 max =            0.85 mean =         0.74|
|beta:             min =    28543.72 max =        74928.18 mean =     47426.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.59|
|phase err.(work): min =        0.00 max =           89.98 mean =        44.84|
|phase err.(test): min =        0.00 max =           89.69 mean =        45.15|
|-----------------------------------------------------------------------------|

============================== 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 = 12.430580             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.665   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.282580              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.219   (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 |  1.797 -  2.107:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.107 -  2.418:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.418 -  2.728:      162 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.728 -  3.038:     1964 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.038 -  3.348:     1828 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.348 -  3.659:     2738 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.659 -  3.969:     4584 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.969 -  4.279:     4270 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.279 -  4.590:     5578 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.590 -  4.900:     6701 |
|-----------------------------------------------------------------------------|
|-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 |        0.164 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.115    4.900  1.797 |       0.164 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.292)------------------------------------------|
|    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: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4066   r_free= 0.3931   ksol= 0.00   Bsol= 0.00   scale= 0.913    |
|                                                                             |
| 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:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.211984                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3948   r_free= 0.3812   ksol= 0.30   Bsol= 50.00   scale= 0.944   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.39,4.75,-0.12,0.00,-0.00,-0.00); trace/3= 0.41                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.196387                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.192472             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.427   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.661735              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.074   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3948      final r-factor (work) = 0.2451          |
| start r-factor (free) = 0.3812      final r-factor (free) = 0.2665          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.8454 = 11.19 * 0.50 * 6.1973 + 1.00 * 0.1636                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.5442 = 11.19 * 0.50 * 5.9646 + 1.00 * 0.1652                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2451      final r-factor (work) = 0.2220          |
| start r-factor (free) = 0.2665      final r-factor (free) = 0.2760          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9533 = 0.66 * 1.00 * 5.9646 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8149 = 0.66 * 1.00 * 5.7310 + 1.00 * 0.0225                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.292)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.75   17.60    None  None   None       |
|    all(noH): 2823   0      0.00    90.75   17.60    None  None   None       |
|    Sol.    : 438    0      4.66    90.75   41.11    None  None   None       |
|    Mac.    : 2385   0      0.00    80.44   13.28    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 -   9.075:  894   |   5:    45.376 -  54.451:   99        |
|      1:     9.075 -  18.150: 1090   |   6:    54.451 -  63.526:   62        |
|      2:    18.150 -  27.226:  324   |   7:    63.526 -  72.602:   39        |
|      3:    27.226 -  36.301:  180   |   8:    72.602 -  81.677:   19        |
|      4:    36.301 -  45.376:  111   |   9:    81.677 -  90.752:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2220 r_free = 0.2760             target_work(ml) = 5.739         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2217 r_free = 0.2765             target_work(ml) = 5.739         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2217   r_free= 0.2765   ksol= 0.30   Bsol= 50.00   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.39,4.75,-0.12,0.00,-0.00,-0.00); trace/3= 0.41                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.739000                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2182   r_free= 0.2725   ksol= 0.33   Bsol= 79.70   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,0.88,-0.32,0.00,-0.00,-0.00); trace/3= -0.59                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.728762                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.785330              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.828   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.637657              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.558   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2182      final r-factor (work) = 0.1737          |
| start r-factor (free) = 0.2725      final r-factor (free) = 0.2131          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1410 = 2.79 * 0.50 * 5.7270 + 1.00 * 0.1652                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9002 = 2.79 * 0.50 * 5.6323 + 1.00 * 0.0564                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1737      final r-factor (work) = 0.1626          |
| start r-factor (free) = 0.2131      final r-factor (free) = 0.2053          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6091 = 0.64 * 1.00 * 5.6323 + 1.00 * 0.0176                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5030 = 0.64 * 1.00 * 5.4727 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.292)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.69   17.97    None  None   None       |
|    all(noH): 2823   0      0.00    99.69   17.97    None  None   None       |
|    Sol.    : 438    0      5.25    97.80   44.21    None  None   None       |
|    Mac.    : 2385   0      0.00    99.69   13.15    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 -   9.969: 1122   |   5:    49.845 -  59.815:   93        |
|      1:     9.969 -  19.938:  998   |   6:    59.815 -  69.784:   66        |
|      2:    19.938 -  29.907:  245   |   7:    69.784 -  79.753:   34        |
|      3:    29.907 -  39.876:  142   |   8:    79.753 -  89.722:   19        |
|      4:    39.876 -  49.845:   96   |   9:    89.722 -  99.691:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1626 r_free = 0.2053             target_work(ml) = 5.459         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1625 r_free = 0.2053             target_work(ml) = 5.459         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1625   r_free= 0.2053   ksol= 0.33   Bsol= 79.70   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,0.88,-0.32,0.00,-0.00,-0.00); trace/3= -0.59                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.458743                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1625   r_free= 0.2051   ksol= 0.33   Bsol= 81.32   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-0.23,-0.45,-0.00,-0.00,-0.00); trace/3= -0.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.457638                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.418437              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.296  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.392272              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.050  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1625      final r-factor (work) = 0.1344          |
| start r-factor (free) = 0.2051      final r-factor (free) = 0.1790          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6749 = 2.42 * 0.50 * 5.4729 + 1.00 * 0.0570                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5557 = 2.42 * 0.50 * 5.3701 + 1.00 * 0.0621                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1344      final r-factor (work) = 0.1292          |
| start r-factor (free) = 0.1790      final r-factor (free) = 0.1725          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1198 = 0.39 * 1.00 * 5.3701 + 1.00 * 0.0132                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0813 = 0.39 * 1.00 * 5.2761 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.292)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.58  17.33    None  None   None       |
|    all(noH): 2823   0      0.00    100.58  17.33    None  None   None       |
|    Sol.    : 438    0      4.71    98.04   43.36    None  None   None       |
|    Mac.    : 2385   0      0.00    100.58  12.55    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.058: 1188   |   5:    50.290 -  60.348:   89        |
|      1:    10.058 -  20.116: 1010   |   6:    60.348 -  70.406:   65        |
|      2:    20.116 -  30.174:  195   |   7:    70.406 -  80.464:   29        |
|      3:    30.174 -  40.232:  130   |   8:    80.464 -  90.522:   13        |
|      4:    40.232 -  50.290:   96   |   9:    90.522 - 100.579:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1292 r_free = 0.1725             target_work(ml) = 5.257         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1291 r_free = 0.1725             target_work(ml) = 5.256         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1291   r_free= 0.1725   ksol= 0.33   Bsol= 81.32   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-0.23,-0.45,-0.00,-0.00,-0.00); trace/3= -0.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.256305                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1294   r_free= 0.1721   ksol= 0.33   Bsol= 76.75   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-0.59,-0.18,-0.00,-0.00,-0.00); trace/3= -0.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.256715                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.772117              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.348  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.209600              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.924  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1294      final r-factor (work) = 0.1188          |
| start r-factor (free) = 0.1721      final r-factor (free) = 0.1646          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3760 = 2.77 * 0.50 * 5.2768 + 1.00 * 0.0621                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3077 = 2.77 * 0.50 * 5.2192 + 1.00 * 0.0736                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1188      final r-factor (work) = 0.1169          |
| start r-factor (free) = 0.1646      final r-factor (free) = 0.1642          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3247 = 1.21 * 1.00 * 5.2192 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2838 = 1.21 * 1.00 * 5.1849 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.292)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.25  17.06    None  None   None       |
|    all(noH): 2823   0      0.00    106.25  17.06    None  None   None       |
|    Sol.    : 438    0      3.67    102.57  43.08    None  None   None       |
|    Mac.    : 2385   0      0.00    106.25  12.28    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.626: 1350   |   5:    53.127 -  63.753:   93        |
|      1:    10.626 -  21.251:  888   |   6:    63.753 -  74.378:   46        |
|      2:    21.251 -  31.876:  196   |   7:    74.378 -  85.004:   21        |
|      3:    31.876 -  42.502:  119   |   8:    85.004 -  95.629:    8        |
|      4:    42.502 -  53.127:   96   |   9:    95.629 - 106.255:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1169 r_free = 0.1642             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1169 r_free = 0.1643             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1643   ksol= 0.33   Bsol= 76.75   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-0.59,-0.18,-0.00,-0.00,-0.00); trace/3= -0.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.184917                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1168   r_free= 0.1641   ksol= 0.33   Bsol= 72.22   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.55,-0.61,0.00,-0.00,0.00,0.00); trace/3= -0.72                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.184681                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.240199              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 127.496  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.531042              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.221  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1168      final r-factor (work) = 0.1165          |
| start r-factor (free) = 0.1641      final r-factor (free) = 0.1646          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8813 = 2.24 * 0.50 * 5.1850 + 1.00 * 0.0736                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8711 = 2.24 * 0.50 * 5.1841 + 1.00 * 0.0645                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1165      final r-factor (work) = 0.1162          |
| start r-factor (free) = 0.1646      final r-factor (free) = 0.1652          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.1332 = 2.53 * 1.00 * 5.1841 + 1.00 * 0.0121                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.1281 = 2.53 * 1.00 * 5.1818 + 1.00 * 0.0128                              |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.292)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.96  16.73    None  None   None       |
|    all(noH): 2823   0      0.00    112.96  16.73    None  None   None       |
|    Sol.    : 438    0      4.57    105.17  42.56    None  None   None       |
|    Mac.    : 2385   0      0.00    112.96  11.99    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.296: 1511   |   5:    56.480 -  67.776:   74        |
|      1:    11.296 -  22.592:  775   |   6:    67.776 -  79.072:   38        |
|      2:    22.592 -  33.888:  167   |   7:    79.072 -  90.368:   14        |
|      3:    33.888 -  45.184:  137   |   8:    90.368 - 101.664:    7        |
|      4:    45.184 -  56.480:   97   |   9:   101.664 - 112.960:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1162 r_free = 0.1652             target_work(ml) = 5.186         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1161 r_free = 0.1653             target_work(ml) = 5.186         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1161   r_free= 0.1653   ksol= 0.33   Bsol= 72.22   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.55,-0.61,0.00,-0.00,0.00,0.00); trace/3= -0.72                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.186167                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0896 -  4.7971 0.99   1379  153 0.0999 0.1294      5.3986      5.5362|
|  2:  4.7971 -  3.8281 0.99   1325  149 0.0840 0.1052      5.4222      5.6011|
|  3:  3.8281 -  3.3502 0.99   1309  146 0.1041 0.1469      5.4642      5.8523|
|  4:  3.3502 -  3.0466 0.99   1291  136 0.1254 0.1679      5.4885      5.6354|
|  5:  3.0466 -  2.8298 0.99   1285  145 0.1411 0.1852      5.3926      5.6034|
|  6:  2.8298 -  2.6639 0.99   1278  145 0.1335 0.2078      5.2961      5.5384|
|  7:  2.6639 -  2.5312 0.99   1283  141 0.1301 0.1762      5.2103       5.395|
|  8:  2.5312 -  2.4214 0.98   1266  142 0.1243 0.1814      5.1443      5.4133|
|  9:  2.4214 -  2.3286 0.98   1272  143 0.1216 0.1926      5.0699      5.3432|
| 10:  2.3286 -  2.2485 0.98   1248  135 0.1203 0.1855      5.0439      5.2631|
| 11:  2.2485 -  2.1784 1.00   1262  146 0.1220 0.1874      4.9922      5.3149|
| 12:  2.1784 -  2.1163 0.97   1261  134 0.1180 0.1771      4.9333      5.2346|
| 13:  2.1163 -  2.0607 0.98   1260  141 0.1179 0.1818      4.8405      5.0978|
| 14:  2.0607 -  2.0106 0.72    911  103 0.1090 0.1938      4.7261      5.0337|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0896 -  4.7971  1379   153  0.94   9.55   0.96     0.93       7683.73|
|  2:  4.7971 -  3.8281  1325   149  0.95   7.87   1.00     0.98       8770.36|
|  3:  3.8281 -  3.3502  1309   146  0.94  10.89   1.02     1.01      10131.35|
|  4:  3.3502 -  3.0466  1291   136  0.92  14.02   1.00     0.97      10894.92|
|  5:  3.0466 -  2.8298  1285   145  0.89  17.09   0.99     0.97       9604.79|
|  6:  2.8298 -  2.6639  1278   145  0.89  17.42   0.98     0.94       8274.40|
|  7:  2.6639 -  2.5312  1283   141  0.90  16.53   0.98     0.96       6945.34|
|  8:  2.5312 -  2.4214  1266   142  0.90  16.50   0.98     0.94       6168.46|
|  9:  2.4214 -  2.3286  1272   143  0.90  16.57   0.98     0.93       5430.25|
| 10:  2.3286 -  2.2485  1248   135  0.89  16.94   0.98     0.93       5170.95|
| 11:  2.2485 -  2.1784  1262   146  0.90  16.72   0.97     0.92       4704.13|
| 12:  2.1784 -  2.1163  1261   134  0.90  16.50   0.98     0.97       4481.62|
| 13:  2.1163 -  2.0607  1260   141  0.90  16.61   0.96     0.94       3694.59|
| 14:  2.0607 -  2.0106   911   103  0.90  15.92   0.94     0.89       2908.88|
|alpha:            min =        0.89 max =            1.01 mean =         0.95|
|beta:             min =     2908.88 max =        10894.92 mean =      6887.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.85|
|phase err.(test): min =        0.00 max =           88.99 mean =        14.32|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1160   r_free= 0.1651   ksol= 0.33   Bsol= 72.22   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.27,-0.43,0.28,-0.00,0.00,0.00); trace/3= -0.47                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.186301                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1160   r_free= 0.1651   ksol= 0.33   Bsol= 72.22   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.27,-0.43,0.28,-0.00,0.00,0.00); trace/3= -0.47                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.186301                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0896 -  4.7971 0.99   1379  153 0.1000 0.1296      5.3996      5.5376|
|  2:  4.7971 -  3.8281 0.99   1325  149 0.0840 0.1052      5.4229      5.6012|
|  3:  3.8281 -  3.3502 0.99   1309  146 0.1042 0.1470      5.4645      5.8528|
|  4:  3.3502 -  3.0466 0.99   1291  136 0.1253 0.1680      5.4885      5.6357|
|  5:  3.0466 -  2.8298 0.99   1285  145 0.1411 0.1852      5.3925      5.6032|
|  6:  2.8298 -  2.6639 0.99   1278  145 0.1335 0.2075      5.2958      5.5376|
|  7:  2.6639 -  2.5312 0.99   1283  141 0.1301 0.1763      5.2102      5.3953|
|  8:  2.5312 -  2.4214 0.98   1266  142 0.1243 0.1815      5.1445      5.4132|
|  9:  2.4214 -  2.3286 0.98   1272  143 0.1216 0.1925        5.07      5.3434|
| 10:  2.3286 -  2.2485 0.98   1248  135 0.1203 0.1856      5.0441      5.2636|
| 11:  2.2485 -  2.1784 1.00   1262  146 0.1220 0.1873      4.9923      5.3149|
| 12:  2.1784 -  2.1163 0.97   1261  134 0.1180 0.1770      4.9333      5.2348|
| 13:  2.1163 -  2.0607 0.98   1260  141 0.1179 0.1817      4.8404      5.0976|
| 14:  2.0607 -  2.0106 0.72    911  103 0.1091 0.1937      4.7257      5.0331|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0896 -  4.7971  1379   153  0.94   9.56   0.96     0.93       7701.85|
|  2:  4.7971 -  3.8281  1325   149  0.95   7.88   1.00     0.98       8781.94|
|  3:  3.8281 -  3.3502  1309   146  0.94  10.89   1.02     1.02      10140.07|
|  4:  3.3502 -  3.0466  1291   136  0.92  14.02   1.01     0.98      10897.78|
|  5:  3.0466 -  2.8298  1285   145  0.89  17.09   1.00     0.98       9599.96|
|  6:  2.8298 -  2.6639  1278   145  0.89  17.41   0.98     0.95       8268.30|
|  7:  2.6639 -  2.5312  1283   141  0.90  16.52   0.99     0.97       6942.21|
|  8:  2.5312 -  2.4214  1266   142  0.90  16.50   0.99     0.94       6169.14|
|  9:  2.4214 -  2.3286  1272   143  0.90  16.58   0.99     0.94       5432.90|
| 10:  2.3286 -  2.2485  1248   135  0.89  16.94   0.99     0.94       5173.28|
| 11:  2.2485 -  2.1784  1262   146  0.90  16.73   0.98     0.93       4706.05|
| 12:  2.1784 -  2.1163  1261   134  0.90  16.50   1.00     0.98       4482.99|
| 13:  2.1163 -  2.0607  1260   141  0.90  16.61   0.98     0.95       3692.15|
| 14:  2.0607 -  2.0106   911   103  0.90  15.90   0.95     0.91       2903.65|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     2903.65 max =        10897.78 mean =      6890.27|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.85|
|phase err.(test): min =        0.00 max =           88.99 mean =        14.32|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.292)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.96  16.74    None  None   None       |
|    all(noH): 2823   0      0.00    112.96  16.74    None  None   None       |
|    Sol.    : 438    0      4.57    105.17  42.56    None  None   None       |
|    Mac.    : 2385   0      0.00    112.96  11.99    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  11.299: 1511   |   5:    56.483 -  67.779:   74        |
|      1:    11.299 -  22.595:  775   |   6:    67.779 -  79.075:   38        |
|      2:    22.595 -  33.891:  167   |   7:    79.075 -  90.371:   14        |
|      3:    33.891 -  45.187:  137   |   8:    90.371 - 101.667:    7        |
|      4:    45.187 -  56.483:   97   |   9:   101.667 - 112.963:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 334         
Filter by distance & map next to the model:
   mapped sites are within: 0.607 - 4.564
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 329 from: 334
   mapped sites are within: 0.719 - 4.564

peak=    5.881 closest distance to " O   HOH Z 210 " =    1.155
peak=    5.833 closest distance to " O   HOH Z 113 " =    2.356
peak=    5.600 closest distance to " CB  GLN A 223 " =    1.368
peak=    5.111 closest distance to " CG  PRO A  54 " =    1.345
peak=    4.953 closest distance to " CG  PRO A 280 " =    0.862
peak=    4.894 closest distance to " CB  GLN A 183 " =    1.313
peak=    4.876 closest distance to " CB  SER A  63 " =    1.223
peak=    4.851 closest distance to " CB  ARG A 190 " =    1.709
peak=    4.778 closest distance to " CG  PRO A 213 " =    1.189
peak=    4.728 closest distance to " O   HOH Z 232 " =    2.338
peak=    4.713 closest distance to " CG  PRO A 198 " =    1.201
peak=    4.598 closest distance to " CB  GLU A 128 " =    1.151
peak=    4.543 closest distance to " C   PRO A 198 " =    1.550
peak=    4.531 closest distance to " CD  ARG A 269 " =    0.990
peak=    4.528 closest distance to " CA  TYR A  30 " =    0.922
peak=    4.484 closest distance to " O   HOH Z  43 " =    1.983
peak=    4.478 closest distance to " CB  ARG A 275 " =    0.956
peak=    4.437 closest distance to " O   HOH Z 433 " =    1.587
peak=    4.436 closest distance to " CB  PRO A  54 " =    0.900
peak=    4.412 closest distance to " O   HOH Z 234 " =    3.868
peak=    4.399 closest distance to " O   HOH Z 298 " =    1.988
peak=    4.396 closest distance to " CZ  PHE A 218 " =    1.112
peak=    4.386 closest distance to " CA  ALA A  51 " =    0.985
peak=    4.363 closest distance to " O   HOH Z 189 " =    2.577
peak=    4.332 closest distance to " O   HOH Z 134 " =    1.622
peak=    4.299 closest distance to " O   HOH Z  49 " =    0.928
peak=    4.294 closest distance to " CA  ARG A 195 " =    1.218
peak=    4.259 closest distance to " O   HOH Z 403 " =    1.720
peak=    4.230 closest distance to " CB  ARG A  79 " =    1.315
peak=    4.220 closest distance to " O   HOH Z  15 " =    2.303
peak=    4.195 closest distance to " O   HOH Z 369 " =    2.270
peak=    4.175 closest distance to " O   HOH Z  44 " =    2.221
peak=    4.118 closest distance to " O   HOH Z 412 " =    3.601
peak=    4.112 closest distance to " O   HOH Z 423 " =    1.864
peak=    4.104 closest distance to " CB  VAL A 202 " =    1.514
peak=    4.054 closest distance to " O   HOH Z 402 " =    1.529
peak=    4.032 closest distance to " CB  TYR A 169 " =    0.838
peak=    4.002 closest distance to " NH2 ARG A 156 " =    1.200
peak=    4.002 closest distance to " CB  ASN A 148 " =    1.407
peak=    3.991 closest distance to " CD2 TRP A 179 " =    1.325
peak=    3.988 closest distance to " CB  ASP A 140 " =    0.969
peak=    3.957 closest distance to " CA  ARG A  36 " =    1.094
peak=    3.956 closest distance to " CD  LYS A 166 " =    1.328
peak=    3.952 closest distance to " CG  PRO A 243 " =    1.094
peak=    3.952 closest distance to " CB  GLU A 152 " =    1.098
peak=    3.944 closest distance to " CG  ARG A  66 " =    2.574
peak=    3.938 closest distance to " CA  ALA A  21 " =    1.303
peak=    3.922 closest distance to " O   HOH Z 133 " =    2.685
peak=    3.918 closest distance to " CZ3 TRP A 266 " =    1.113
peak=    3.907 closest distance to " CA  ALA A 160 " =    0.916
peak=    3.901 closest distance to " CB  LEU A 228 " =    1.094
peak=    3.899 closest distance to " O   HOH Z  40 " =    1.957
peak=    3.898 closest distance to " O   HOH Z 368 " =    2.211
peak=    3.896 closest distance to " CG1 ILE A  33 " =    1.169
peak=    3.886 closest distance to " CB  TRP A 266 " =    1.024
peak=    3.876 closest distance to " CD2 LEU A 297 " =    0.949
peak=    3.875 closest distance to " O   HOH Z 203 " =    1.876
peak=    3.875 closest distance to " O   HOH Z  21 " =    1.852
peak=    3.873 closest distance to " C   ILE A 106 " =    1.904
peak=    3.858 closest distance to " NZ  LYS A 117 " =    3.092
peak=    3.844 closest distance to " O   HOH Z 287 " =    1.901
peak=    3.837 closest distance to " CE  LYS A  76 " =    0.788
peak=    3.833 closest distance to " CB  GLU A 277 " =    3.761
peak=    3.820 closest distance to " O   HOH Z 271 " =    2.643
peak=    3.815 closest distance to " O   SER A  87 " =    2.280
peak=    3.813 closest distance to " O   ASN A  74 " =    1.596
peak=    3.796 closest distance to " CD1 LEU A  96 " =    0.774
peak=    3.794 closest distance to " O   HOH Z  19 " =    1.651
peak=    3.791 closest distance to " O   HOH Z  20 " =    1.597
peak=    3.789 closest distance to " O   HOH Z  97 " =    2.020
peak=    3.785 closest distance to " O   HOH Z 280 " =    2.980
peak=    3.778 closest distance to " O   ALA A 165 " =    1.410
peak=    3.776 closest distance to " O   HOH Z 265 " =    2.111
peak=    3.772 closest distance to " O   HOH Z 126 " =    1.567
peak=    3.770 closest distance to " O   HOH Z 357 " =    2.144
peak=    3.770 closest distance to " NE2 GLN A  11 " =    1.002
peak=    3.755 closest distance to " O   THR A 251 " =    1.173
peak=    3.751 closest distance to " CZ  PHE A  38 " =    1.230
peak=    3.750 closest distance to " CB  ASN A  39 " =    0.855
peak=    3.748 closest distance to " O   HOH Z  80 " =    1.835
peak=    3.731 closest distance to " CA  ASN A 176 " =    1.798
peak=    3.730 closest distance to " N   CYS A 260 " =    0.820
peak=    3.727 closest distance to " ND2 ASN A 249 " =    2.037
peak=    3.722 closest distance to " O   HOH Z 128 " =    2.166
peak=    3.719 closest distance to " O   HOH Z 362 " =    3.464
peak=    3.719 closest distance to " CB  MET A  40 " =    0.886
peak=    3.718 closest distance to " O   HOH Z  59 " =    2.503
peak=    3.716 closest distance to " CA  PRO A  54 " =    1.364
peak=    3.714 closest distance to " O   HOH Z 285 " =    2.850
peak=    3.710 closest distance to " O   HOH Z 176 " =    1.623
peak=    3.700 closest distance to " O   HOH Z 258 " =    2.078
peak=    3.698 closest distance to " OG BSER A 164 " =    2.389
peak=    3.698 closest distance to " OD1 ASN A  69 " =    2.567
peak=    3.694 closest distance to " O   HOH Z 196 " =    1.372
peak=    3.693 closest distance to " O   THR A 220 " =    1.103
peak=    3.690 closest distance to " CA  ALA A 295 " =    1.125
peak=    3.678 closest distance to " O   HOH Z 303 " =    2.330
peak=    3.671 closest distance to " NE2 GLN A  77 " =    3.377
peak=    3.670 closest distance to " O   HOH Z 374 " =    2.894
peak=    3.663 closest distance to " O   HOH Z 142 " =    1.535
peak=    3.661 closest distance to " NH2BARG A 145 " =    2.171
peak=    3.656 closest distance to " O   HOH Z 418 " =    1.527
peak=    3.656 closest distance to " O   HOH Z 346 " =    1.601
peak=    3.656 closest distance to " O   HOH Z 158 " =    3.055
peak=    3.648 closest distance to " O   HOH Z 316 " =    3.113
peak=    3.644 closest distance to " O   HOH Z 126 " =    2.191
peak=    3.638 closest distance to " N   ASN A  39 " =    1.299
peak=    3.633 closest distance to " CD1 LEU A 300 " =    1.126
peak=    3.628 closest distance to " O   HOH Z 383 " =    2.259
peak=    3.625 closest distance to " CG1 VAL A 153 " =    1.059
peak=    3.619 closest distance to " N   ILE A  33 " =    1.016
peak=    3.615 closest distance to " O   HOH Z  61 " =    1.549
peak=    3.613 closest distance to " O   HOH Z 427 " =    3.147
peak=    3.609 closest distance to " O   HOH Z  44 " =    1.786
peak=    3.605 closest distance to " O   HOH Z 214 " =    2.568
peak=    3.600 closest distance to " O   HOH Z 279 " =    2.201
peak=    3.597 closest distance to " O   HOH Z 425 " =    1.352
peak=    3.595 closest distance to " NH1AARG A 145 " =    1.393
peak=    3.592 closest distance to " O   HOH Z  63 " =    1.887
peak=    3.587 closest distance to " CB  LEU A  83 " =    0.892
peak=    3.587 closest distance to " CA  ASP A 191 " =    0.916
peak=    3.586 closest distance to " O   HOH Z 291 " =    1.486
peak=    3.582 closest distance to " NZ  LYS A  48 " =    1.269
peak=    3.579 closest distance to " CG  GLU A  37 " =    0.858
peak=    3.576 closest distance to " O   HOH Z 132 " =    2.806
peak=    3.574 closest distance to " CB  VAL A 265 " =    1.237
peak=    3.564 closest distance to " O   HOH Z  68 " =    1.830
peak=    3.563 closest distance to " CA  ASP A 162 " =    1.155
peak=    3.558 closest distance to " O   HOH Z 391 " =    3.008
peak=    3.557 closest distance to " ND2 ASN A 187 " =    1.379
peak=    3.553 closest distance to " CB  TRP A 179 " =    1.426
peak=    3.544 closest distance to " CA  GLU A 152 " =    0.882
peak=    3.542 closest distance to " CB  SER A  62 " =    0.839
peak=    3.530 closest distance to " O   HOH Z 361 " =    2.542
peak=    3.528 closest distance to " CG2BVAL A  41 " =    0.880
peak=    3.523 closest distance to " O   HOH Z 245 " =    1.287
peak=    3.518 closest distance to " O   HOH Z 193 " =    1.934
peak=    3.514 closest distance to " CB  ALA A 291 " =    1.227
peak=    3.511 closest distance to " O   HOH Z 406 " =    1.599
peak=    3.507 closest distance to " CA  SER A  87 " =    1.098
peak=    3.505 closest distance to " O   HOH Z 403 " =    1.477
peak=    3.499 closest distance to " O   HOH Z 353 " =    2.797
peak=    3.494 closest distance to " O   HOH Z 180 " =    2.220
peak=    3.493 closest distance to " O   HOH Z 125 " =    4.031
peak=    3.491 closest distance to " O   HOH Z 294 " =    1.505
peak=    3.486 closest distance to " CA  VAL A 125 " =    1.325
peak=    3.470 closest distance to " CB  SER A  28 " =    1.070
peak=    3.470 closest distance to " CA  MET A 105 " =    1.090
peak=    3.460 closest distance to " O   ALA A 158 " =    1.161
peak=    3.460 closest distance to " NE2 HIS A 115 " =    1.024
peak=    3.459 closest distance to " O   HOH Z 147 " =    1.795
peak=    3.459 closest distance to " CB  TYR A 116 " =    0.962
peak=    3.456 closest distance to " CB  SER A   3 " =    1.390
peak=    3.451 closest distance to " O   HOH Z   1 " =    2.740
peak=    3.447 closest distance to " CB  GLU A  46 " =    1.002
peak=    3.446 closest distance to " CG2 THR A 221 " =    1.153
peak=    3.443 closest distance to " O   HOH Z 426 " =    1.525
peak=    3.438 closest distance to " O   TYR A 116 " =    1.360
peak=    3.437 closest distance to " OG BSER A 134 " =    2.885
peak=    3.437 closest distance to " CB  TYR A 247 " =    0.925
peak=    3.434 closest distance to " OE1 GLN A  11 " =    2.043
peak=    3.434 closest distance to " O   HOH Z 371 " =    2.907
peak=    3.431 closest distance to " CG  GLN A  58 " =    2.593
peak=    3.430 closest distance to " O   HOH Z  48 " =    1.863
peak=    3.429 closest distance to " OD2 ASP A 298 " =    3.898
peak=    3.417 closest distance to " O   HOH Z  78 " =    1.625
peak=    3.416 closest distance to " O   ASP A 191 " =    1.512
peak=    3.414 closest distance to " CD  ARG A 159 " =    0.837
peak=    3.414 closest distance to " O  BHOH Z 338 " =    2.195
peak=    3.412 closest distance to " O   HOH Z 421 " =    1.797
peak=    3.410 closest distance to " O   HOH Z 156 " =    2.652
peak=    3.408 closest distance to " O   HOH Z 369 " =    1.383
peak=    3.406 closest distance to " O   HOH Z 299 " =    4.564
peak=    3.403 closest distance to " OG  SER A 245 " =    1.641
peak=    3.394 closest distance to " CE1 TYR A 186 " =    1.266
peak=    3.391 closest distance to " O   HOH Z 386 " =    2.358
peak=    3.391 closest distance to " CD  ARG A  66 " =    2.429
peak=    3.388 closest distance to " CB  ASN A 142 " =    1.187
peak=    3.385 closest distance to " N   ASN A 127 " =    1.285
peak=    3.385 closest distance to " O   HOH Z 174 " =    2.377
peak=    3.381 closest distance to " O   HOH Z 336 " =    1.816
peak=    3.380 closest distance to " ND2 ASN A 249 " =    0.910
peak=    3.379 closest distance to " O   HOH Z 148 " =    3.323
peak=    3.377 closest distance to " CB  ALA A  43 " =    0.872
peak=    3.374 closest distance to " O   HOH Z 417 " =    3.057
peak=    3.372 closest distance to " O   HOH Z 261 " =    1.814
peak=    3.369 closest distance to " O   HOH Z 163 " =    1.566
peak=    3.368 closest distance to " CB  SER A 141 " =    1.024
peak=    3.368 closest distance to " CG2 VAL A 257 " =    0.840
peak=    3.367 closest distance to " CB  ASN A 148 " =    1.995
peak=    3.366 closest distance to " OH  TYR A 116 " =    1.139
peak=    3.365 closest distance to " CG1BVAL A  72 " =    1.924
peak=    3.362 closest distance to " O   HOH Z 345 " =    1.623
peak=    3.362 closest distance to " CG  ARG A 219 " =    1.187
peak=    3.362 closest distance to " CA  ALA A 100 " =    1.044
peak=    3.361 closest distance to " CZ  PHE A 192 " =    0.953
peak=    3.360 closest distance to " CB  ALA A 248 " =    1.291
peak=    3.358 closest distance to " O   HOH Z  30 " =    1.159
peak=    3.357 closest distance to " O   HOH Z 437 " =    1.284
peak=    3.355 closest distance to " CA  ASP A 124 " =    0.759
peak=    3.350 closest distance to " CZ3 TRP A  85 " =    0.945
peak=    3.347 closest distance to " CD BLYS A 290 " =    1.008
peak=    3.347 closest distance to " CA  ILE A 106 " =    0.844
peak=    3.347 closest distance to " CB  MET A  47 " =    0.927
peak=    3.347 closest distance to " CB  PRO A  90 " =    1.194
peak=    3.343 closest distance to " CG  GLN A  11 " =    1.292
peak=    3.329 closest distance to " OE1 GLN A  58 " =    3.774
peak=    3.326 closest distance to " CG  LEU A 167 " =    1.070
peak=    3.324 closest distance to " O   HOH Z 130 " =    2.279
peak=    3.320 closest distance to " O   HOH Z 357 " =    2.512
peak=    3.318 closest distance to " O   HOH Z 393 " =    3.263
peak=    3.317 closest distance to " CG2 THR A  29 " =    1.376
peak=    3.309 closest distance to " ND2 ASN A 301 " =    1.608
peak=    3.308 closest distance to " O   HOH Z 250 " =    1.375
peak=    3.305 closest distance to " O   HOH Z 325 " =    2.169
peak=    3.304 closest distance to " O   TRP A 274 " =    1.846
peak=    3.300 closest distance to " OE1 GLU A   2 " =    1.940
peak=    3.299 closest distance to " CG2 ILE A 120 " =    1.021
peak=    3.299 closest distance to " CB  SER A 273 " =    0.905
peak=    3.297 closest distance to " O   HOH Z 285 " =    1.611
peak=    3.295 closest distance to " O  BHOH Z  74 " =    1.338
peak=    3.295 closest distance to " O   HOH Z 344 " =    3.223
peak=    3.293 closest distance to " O   HOH Z  66 " =    2.061
peak=    3.291 closest distance to " CA  ALA A 233 " =    1.699
peak=    3.290 closest distance to " O   HOH Z 327 " =    1.750
peak=    3.290 closest distance to " CA  ALA A 154 " =    1.026
peak=    3.290 closest distance to " NH1 ARG A  14 " =    1.219
peak=    3.289 closest distance to " O   HOH Z 365 " =    2.861
peak=    3.289 closest distance to " CA  LEU A  83 " =    1.377
peak=    3.288 closest distance to " CB  GLN A  89 " =    1.194
peak=    3.287 closest distance to " O   HOH Z 124 " =    2.210
peak=    3.286 closest distance to " C   TYR A 214 " =    1.577
peak=    3.284 closest distance to " CB  ASN A 285 " =    0.906
peak=    3.284 closest distance to " CB  MET A 105 " =    0.922
peak=    3.283 closest distance to " OG  SER A  22 " =    2.849
peak=    3.280 closest distance to " CB  PRO A 198 " =    1.066
peak=    3.275 closest distance to " CE1 HIS A 108 " =    1.133
peak=    3.271 closest distance to " O   HOH Z 250 " =    1.555
peak=    3.268 closest distance to " CG2 VAL A 197 " =    1.187
peak=    3.266 closest distance to " O   HOH Z  99 " =    2.545
peak=    3.266 closest distance to " CA  ALA A 291 " =    0.787
peak=    3.263 closest distance to " CA  MET A 188 " =    1.030
peak=    3.261 closest distance to " O   ASP A 124 " =    1.276
peak=    3.259 closest distance to " CB  ALA A  71 " =    1.365
peak=    3.258 closest distance to " O   HOH Z 150 " =    1.574
peak=    3.251 closest distance to " CD1 ILE A 199 " =    1.212
peak=    3.249 closest distance to " CA  THR A 221 " =    0.903
peak=    3.249 closest distance to " CB  PHE A 204 " =    0.926
peak=    3.242 closest distance to " CA  LYS A 117 " =    1.222
peak=    3.242 closest distance to " O   HOH Z 374 " =    3.612
peak=    3.239 closest distance to " CB  GLN A 103 " =    0.908
peak=    3.238 closest distance to " O   HOH Z 247 " =    1.438
peak=    3.237 closest distance to " O   HOH Z 359 " =    1.509
peak=    3.233 closest distance to " O   HOH Z 109 " =    2.502
peak=    3.233 closest distance to " CB  ASP A 298 " =    1.259
peak=    3.230 closest distance to " CG2 ILE A  20 " =    1.355
peak=    3.229 closest distance to " CA  ASN A 217 " =    1.276
peak=    3.229 closest distance to " N   GLY A  98 " =    1.149
peak=    3.228 closest distance to " O   HOH Z 251 " =    1.546
peak=    3.226 closest distance to " CB  ARG A 269 " =    0.806
peak=    3.225 closest distance to " CB  GLN A  88 " =    1.197
peak=    3.223 closest distance to " O   HOH Z  97 " =    2.381
peak=    3.221 closest distance to " CA  GLN A  88 " =    1.404
peak=    3.220 closest distance to " CG  MET A 185 " =    1.141
peak=    3.217 closest distance to " CD  PRO A  54 " =    1.116
peak=    3.215 closest distance to " N   ASP A 132 " =    1.245
peak=    3.213 closest distance to " CB  GLU A  37 " =    0.793
peak=    3.209 closest distance to " O   HOH Z 380 " =    1.865
peak=    3.208 closest distance to " CD  GLU A 152 " =    0.837
peak=    3.208 closest distance to " O   HOH Z 173 " =    2.301
peak=    3.198 closest distance to " CG  ARG A 138 " =    1.208
peak=    3.198 closest distance to " CB  ILE A 120 " =    1.361
peak=    3.193 closest distance to " OE1 GLN A 223 " =    3.548
peak=    3.187 closest distance to " O   HOH Z 121 " =    3.784
peak=    3.185 closest distance to " CA  LEU A 101 " =    1.714
peak=    3.183 closest distance to " O   HOH Z 193 " =    1.744
peak=    3.182 closest distance to " O   HOH Z 422 " =    2.495
peak=    3.180 closest distance to " ND1 HIS A  81 " =    1.638
peak=    3.176 closest distance to " CA  SER A  32 " =    1.629
peak=    3.175 closest distance to " CB  SER A  62 " =    1.173
peak=    3.171 closest distance to " O   PHE A  61 " =    1.349
peak=    3.171 closest distance to " CG2 VAL A 126 " =    0.830
peak=    3.170 closest distance to " N   GLU A  44 " =    1.086
peak=    3.170 closest distance to " O   THR A 251 " =    1.889
peak=    3.166 closest distance to " CG2 ILE A 234 " =    0.862
peak=    3.163 closest distance to " O   HOH Z 128 " =    2.316
peak=    3.159 closest distance to " O   GLY A  91 " =    1.137
peak=    3.156 closest distance to " NH1 ARG A 269 " =    0.757
peak=    3.153 closest distance to " CB  TYR A 169 " =    0.878
peak=    3.153 closest distance to " CA  GLU A  46 " =    0.926
peak=    3.151 closest distance to " O   ALA A 242 " =    1.201
peak=    3.151 closest distance to " CA  THR A 221 " =    1.578
peak=    3.150 closest distance to " O   HOH Z  89 " =    2.174
peak=    3.146 closest distance to " N   SER A 164 " =    1.093
peak=    3.146 closest distance to " O   ASP A 200 " =    1.695
peak=    3.144 closest distance to " NH2AARG A 275 " =    3.512
peak=    3.140 closest distance to " O   HOH Z 197 " =    1.865
peak=    3.140 closest distance to " CB  ASN A 215 " =    1.179
peak=    3.138 closest distance to " CB  HIS A 108 " =    0.785
peak=    3.137 closest distance to " CA  GLY A 196 " =    1.053
peak=    3.131 closest distance to " CD1 ILE A 106 " =    0.864
peak=    3.131 closest distance to " CA  ASP A 140 " =    1.275
peak=    3.127 closest distance to " CB  SER A 212 " =    1.002
peak=    3.126 closest distance to " O   HOH Z  88 " =    3.482
peak=    3.124 closest distance to " O   HOH Z 141 " =    1.637
peak=    3.120 closest distance to " OG  SER A  62 " =    2.935
peak=    3.120 closest distance to " N   THR A  52 " =    1.079
peak=    3.116 closest distance to " O   HOH Z 416 " =    3.024
peak=    3.114 closest distance to " O   HOH Z 295 " =    1.507
peak=    3.092 closest distance to " O   HOH Z 329 " =    3.982
peak=    3.091 closest distance to " O   HOH Z 141 " =    1.632
peak=    3.082 closest distance to " O   HOH Z 248 " =    1.622
peak=    3.080 closest distance to " CG  MET A 185 " =    0.983
peak=    3.078 closest distance to " O   HOH Z 301 " =    1.964
peak=    3.075 closest distance to " O   HOH Z 381 " =    1.910
peak=    3.069 closest distance to " CZ2 TRP A 179 " =    1.781
peak=    3.065 closest distance to " NE2 GLN A  58 " =    4.415
peak=    3.061 closest distance to " CB  ALA A  34 " =    0.719
peak=    3.061 closest distance to " CE1 PHE A 218 " =    1.210
peak=    3.060 closest distance to " ND2 ASN A 110 " =    1.527
peak=    3.058 closest distance to " OD1BASN A 224 " =    2.236
peak=    3.054 closest distance to " O   HOH Z 303 " =    2.087
peak=    3.044 closest distance to " O   HOH Z 387 " =    2.855
peak=    3.042 closest distance to " O   HOH Z 327 " =    2.219
peak=    3.030 closest distance to " O   HOH Z 371 " =    3.211
peak=    3.023 closest distance to " CA  ALA A 299 " =    1.034
peak=    3.021 closest distance to " O   ASP A 124 " =    1.784
peak=    3.018 closest distance to " O   HOH Z 145 " =    2.642
peak=    3.004 closest distance to " OE1 GLN A  58 " =    3.144

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 222         
Filter by distance & map next to the model:
   mapped sites are within: 0.859 - 5.777
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 220 from: 222
   mapped sites are within: 0.859 - 5.777

peak=   -4.673 closest distance to " O   HOH Z 266 " =    5.253
peak=   -4.391 closest distance to " CG1 VAL A 250 " =    2.631
peak=   -4.345 closest distance to " O   HOH Z  10 " =    1.654
peak=   -4.337 closest distance to " CD  GLN A  58 " =    1.022
peak=   -4.292 closest distance to " CB  PRO A 243 " =    2.734
peak=   -4.200 closest distance to " OXT GLY A 302 " =    2.984
peak=   -4.191 closest distance to " CD  ARG A 156 " =    2.092
peak=   -4.167 closest distance to " O   HOH Z 166 " =    1.726
peak=   -4.137 closest distance to " CD1 LEU A 101 " =    2.480
peak=   -4.137 closest distance to " O   GLY A 136 " =    2.379
peak=   -4.106 closest distance to " CD  GLN A 223 " =    1.395
peak=   -4.091 closest distance to " C   HIS A 108 " =    1.078
peak=   -4.052 closest distance to " CD  ARG A  14 " =    3.458
peak=   -4.036 closest distance to " CG1 VAL A 112 " =    2.593
peak=   -4.034 closest distance to " O   HOH Z 283 " =    2.183
peak=   -3.992 closest distance to " N   ALA A  43 " =    2.667
peak=   -3.988 closest distance to " CA  ASP A 298 " =    1.067
peak=   -3.968 closest distance to " O   HOH Z 196 " =    2.494
peak=   -3.953 closest distance to " CE2 PHE A  61 " =    2.608
peak=   -3.943 closest distance to " CB  ALA A 161 " =    2.636
peak=   -3.921 closest distance to " O   PRO A 198 " =    1.319
peak=   -3.887 closest distance to " O   HOH Z 394 " =    1.583
peak=   -3.881 closest distance to " CB  PHE A 208 " =    2.337
peak=   -3.862 closest distance to " O   HOH Z  13 " =    1.831
peak=   -3.856 closest distance to " O   VAL A  67 " =    2.690
peak=   -3.853 closest distance to " CB  ALA A  10 " =    2.139
peak=   -3.839 closest distance to " CB  ALA A 291 " =    2.414
peak=   -3.837 closest distance to " O   HOH Z 377 " =    2.000
peak=   -3.832 closest distance to " ND2 ASN A  45 " =    1.919
peak=   -3.827 closest distance to " CH2 TRP A 179 " =    1.221
peak=   -3.809 closest distance to " OE1 GLN A 223 " =    2.035
peak=   -3.801 closest distance to " CB  ASP A 132 " =    2.424
peak=   -3.796 closest distance to " OG  SER A  97 " =    2.219
peak=   -3.793 closest distance to " OD1 ASN A 148 " =    1.470
peak=   -3.788 closest distance to " CD1 PHE A  59 " =    1.965
peak=   -3.758 closest distance to " CE2 TYR A  30 " =    2.666
peak=   -3.756 closest distance to " CA  VAL A  67 " =    3.041
peak=   -3.755 closest distance to " ND2 ASN A 249 " =    2.454
peak=   -3.741 closest distance to " C   SER A 206 " =    1.520
peak=   -3.733 closest distance to " O   HOH Z 185 " =    2.443
peak=   -3.720 closest distance to " CD2 TYR A 293 " =    1.916
peak=   -3.710 closest distance to " CG1 VAL A 265 " =    2.342
peak=   -3.705 closest distance to " O   HOH Z 292 " =    4.682
peak=   -3.705 closest distance to " O   PRO A 163 " =    2.151
peak=   -3.704 closest distance to " O   HOH Z 165 " =    1.933
peak=   -3.703 closest distance to " CE3 TRP A 150 " =    2.147
peak=   -3.703 closest distance to " OD1 ASP A 191 " =    1.533
peak=   -3.694 closest distance to " O   ALA A  34 " =    2.474
peak=   -3.687 closest distance to " O   HOH Z 150 " =    2.156
peak=   -3.684 closest distance to " C   ASN A 285 " =    2.414
peak=   -3.681 closest distance to " O   HOH Z 166 " =    1.956
peak=   -3.647 closest distance to " CD  ARG A 139 " =    1.578
peak=   -3.644 closest distance to " O   HOH Z   6 " =    1.403
peak=   -3.626 closest distance to " CG2 VAL A 189 " =    2.241
peak=   -3.622 closest distance to " CD1 LEU A  25 " =    2.482
peak=   -3.621 closest distance to " NE2 GLN A 194 " =    1.983
peak=   -3.613 closest distance to " ND2 ASN A 187 " =    1.686
peak=   -3.611 closest distance to " CG2 ILE A  49 " =    2.764
peak=   -3.609 closest distance to " O   HOH Z 106 " =    1.995
peak=   -3.595 closest distance to " O   HOH Z 128 " =    2.592
peak=   -3.592 closest distance to " O   HOH Z 234 " =    4.442
peak=   -3.589 closest distance to " CD2 PHE A  61 " =    2.069
peak=   -3.572 closest distance to " CD  GLN A  58 " =    1.207
peak=   -3.547 closest distance to " CB  PHE A 192 " =    1.946
peak=   -3.546 closest distance to " O   HOH Z 150 " =    1.121
peak=   -3.538 closest distance to " O   HOH Z 264 " =    1.822
peak=   -3.536 closest distance to " CG  ARG A 269 " =    2.335
peak=   -3.531 closest distance to " O   SER A 210 " =    1.861
peak=   -3.511 closest distance to " CD1 ILE A 151 " =    2.415
peak=   -3.500 closest distance to " O   HOH Z 372 " =    2.498
peak=   -3.494 closest distance to " CE BMET A  47 " =    1.914
peak=   -3.494 closest distance to " C   LEU A 143 " =    1.180
peak=   -3.491 closest distance to " NE2 GLN A 103 " =    1.847
peak=   -3.482 closest distance to " O   HOH Z 171 " =    2.206
peak=   -3.480 closest distance to " O   HOH Z  71 " =    1.926
peak=   -3.480 closest distance to " O   SER A 276 " =    1.752
peak=   -3.477 closest distance to " CG  PRO A 243 " =    1.786
peak=   -3.470 closest distance to " O   HOH Z 353 " =    2.330
peak=   -3.468 closest distance to " ND2BASN A 224 " =    1.829
peak=   -3.458 closest distance to " NE2 GLN A  88 " =    1.857
peak=   -3.457 closest distance to " O   HOH Z 198 " =    2.099
peak=   -3.456 closest distance to " O   HOH Z  19 " =    2.217
peak=   -3.455 closest distance to " ND2 ASN A  45 " =    1.117
peak=   -3.440 closest distance to " O   PHE A 218 " =    1.509
peak=   -3.435 closest distance to " O   HOH Z 111 " =    1.516
peak=   -3.435 closest distance to " N   THR A  52 " =    1.698
peak=   -3.433 closest distance to " O   ALA A  10 " =    1.727
peak=   -3.432 closest distance to " O   HOH Z 426 " =    1.719
peak=   -3.429 closest distance to " OG BSER A 134 " =    1.422
peak=   -3.429 closest distance to " CB  PHE A  16 " =    2.586
peak=   -3.428 closest distance to " CA  GLY A 133 " =    2.399
peak=   -3.428 closest distance to " O   HOH Z  52 " =    1.559
peak=   -3.427 closest distance to " CB  ALA A  43 " =    2.657
peak=   -3.426 closest distance to " CD  PRO A 213 " =    2.207
peak=   -3.422 closest distance to " O   HOH Z 396 " =    1.800
peak=   -3.421 closest distance to " O   HOH Z 377 " =    1.318
peak=   -3.418 closest distance to " CA  GLY A 241 " =    2.312
peak=   -3.412 closest distance to " CA  GLY A 241 " =    3.191
peak=   -3.411 closest distance to " O   HOH Z 150 " =    2.021
peak=   -3.404 closest distance to " OG BSER A 210 " =    2.141
peak=   -3.404 closest distance to " CG1 VAL A  78 " =    2.671
peak=   -3.400 closest distance to " NH2 ARG A  79 " =    1.554
peak=   -3.397 closest distance to " O   HOH Z 252 " =    3.903
peak=   -3.391 closest distance to " O   HOH Z 197 " =    2.005
peak=   -3.390 closest distance to " CG  GLU A  53 " =    1.553
peak=   -3.387 closest distance to " NH2 ARG A  66 " =    1.917
peak=   -3.387 closest distance to " O   HOH Z 210 " =    0.933
peak=   -3.385 closest distance to " O   HOH Z 311 " =    3.746
peak=   -3.383 closest distance to " O   HOH Z 351 " =    1.605
peak=   -3.382 closest distance to " CB  ALA A   9 " =    2.605
peak=   -3.380 closest distance to " CB  TRP A  85 " =    2.411
peak=   -3.378 closest distance to " ND2 ASN A  69 " =    1.615
peak=   -3.371 closest distance to " O   HOH Z 366 " =    1.854
peak=   -3.370 closest distance to " O   HOH Z 393 " =    1.485
peak=   -3.369 closest distance to " O   HOH Z 243 " =    2.221
peak=   -3.363 closest distance to " CD  ARG A  79 " =    1.243
peak=   -3.354 closest distance to " O   SER A 271 " =    2.041
peak=   -3.353 closest distance to " O   HOH Z  37 " =    1.915
peak=   -3.347 closest distance to " O   HOH Z 275 " =    1.566
peak=   -3.347 closest distance to " NH2 ARG A 159 " =    2.302
peak=   -3.344 closest distance to " N   SER A 276 " =    1.540
peak=   -3.344 closest distance to " O   GLY A  17 " =    1.168
peak=   -3.343 closest distance to " OD2 ASP A 171 " =    1.862
peak=   -3.336 closest distance to " O   HOH Z 123 " =    2.503
peak=   -3.334 closest distance to " CZ  TYR A 169 " =    1.807
peak=   -3.329 closest distance to " CD2 PHE A 225 " =    1.318
peak=   -3.328 closest distance to " O   HOH Z  78 " =    1.928
peak=   -3.322 closest distance to " CG1 VAL A 112 " =    2.850
peak=   -3.321 closest distance to " O   HOH Z  90 " =    1.868
peak=   -3.317 closest distance to " O   HOH Z 136 " =    2.073
peak=   -3.312 closest distance to " CD  LYS A 289 " =    2.375
peak=   -3.308 closest distance to " O   HOH Z 216 " =    2.237
peak=   -3.304 closest distance to " CB  GLN A  11 " =    1.708
peak=   -3.302 closest distance to " CA  GLY A 203 " =    2.405
peak=   -3.291 closest distance to " OD1 ASN A 187 " =    1.663
peak=   -3.290 closest distance to " OG  SER A  62 " =    1.769
peak=   -3.289 closest distance to " O   HOH Z 134 " =    2.457
peak=   -3.287 closest distance to " NE  ARG A  66 " =    4.329
peak=   -3.285 closest distance to " CG1 VAL A 125 " =    2.048
peak=   -3.281 closest distance to " O   HOH Z 240 " =    3.776
peak=   -3.278 closest distance to " O   VAL A 189 " =    2.626
peak=   -3.260 closest distance to " ND2 ASN A  60 " =    1.935
peak=   -3.257 closest distance to " O   HOH Z 200 " =    1.286
peak=   -3.254 closest distance to " NH2 ARG A  79 " =    2.182
peak=   -3.249 closest distance to " O   HOH Z 154 " =    1.579
peak=   -3.248 closest distance to " CA  VAL A 197 " =    1.041
peak=   -3.247 closest distance to " CD  GLN A  88 " =    0.931
peak=   -3.241 closest distance to " NH2 ARG A  66 " =    3.847
peak=   -3.237 closest distance to " O   ALA A   1 " =    2.033
peak=   -3.232 closest distance to " CG1AVAL A 121 " =    1.604
peak=   -3.232 closest distance to " O   HOH Z 114 " =    3.587
peak=   -3.231 closest distance to " O   TRP A  92 " =    1.936
peak=   -3.226 closest distance to " CA  SER A  62 " =    2.516
peak=   -3.226 closest distance to " CD  GLU A 236 " =    1.081
peak=   -3.225 closest distance to " O   HOH Z 407 " =    3.596
peak=   -3.225 closest distance to " C   ASN A 187 " =    1.965
peak=   -3.223 closest distance to " CG  GLU A 277 " =    1.147
peak=   -3.212 closest distance to " CG2BVAL A  41 " =    1.639
peak=   -3.211 closest distance to " ND1 HIS A 115 " =    2.010
peak=   -3.210 closest distance to " O   TYR A 186 " =    1.823
peak=   -3.207 closest distance to " O   HOH Z 191 " =    5.777
peak=   -3.207 closest distance to " O   HOH Z 117 " =    4.478
peak=   -3.206 closest distance to " CG  MET A 105 " =    0.992
peak=   -3.206 closest distance to " C   ARG A  79 " =    2.619
peak=   -3.204 closest distance to " C   GLU A  46 " =    0.933
peak=   -3.202 closest distance to " CE3 TRP A  70 " =    1.841
peak=   -3.200 closest distance to " O   HOH Z 149 " =    2.007
peak=   -3.198 closest distance to " OH  TYR A 247 " =    1.821
peak=   -3.197 closest distance to " O   HOH Z 275 " =    1.799
peak=   -3.195 closest distance to " N   TYR A  68 " =    3.071
peak=   -3.195 closest distance to " CG  ASP A 231 " =    0.859
peak=   -3.189 closest distance to " O   HOH Z 102 " =    1.569
peak=   -3.187 closest distance to " OG BSER A 210 " =    1.501
peak=   -3.186 closest distance to " O   HOH Z 384 " =    2.147
peak=   -3.184 closest distance to " CH2 TRP A 150 " =    1.148
peak=   -3.183 closest distance to " CE  MET A  93 " =    1.766
peak=   -3.182 closest distance to " O   HOH Z 139 " =    3.108
peak=   -3.182 closest distance to " O   HOH Z 145 " =    2.382
peak=   -3.181 closest distance to " O   HOH Z 236 " =    1.561
peak=   -3.181 closest distance to " O   HOH Z 109 " =    3.566
peak=   -3.178 closest distance to " CE  MET A 105 " =    2.737
peak=   -3.178 closest distance to " N   ALA A 226 " =    2.054
peak=   -3.172 closest distance to " CD1 TYR A 247 " =    2.210
peak=   -3.166 closest distance to " O   HOH Z 326 " =    5.031
peak=   -3.163 closest distance to " CB  ASP A 171 " =    2.363
peak=   -3.161 closest distance to " C   ALA A 158 " =    1.363
peak=   -3.158 closest distance to " O   HOH Z 418 " =    1.347
peak=   -3.156 closest distance to " O   HOH Z 290 " =    1.199
peak=   -3.150 closest distance to " CD1 ILE A 263 " =    1.973
peak=   -3.148 closest distance to " CD2 PHE A  59 " =    2.496
peak=   -3.140 closest distance to " NE2 GLN A  58 " =    2.603
peak=   -3.137 closest distance to " O   HOH Z 351 " =    1.557
peak=   -3.136 closest distance to " O   HOH Z 251 " =    1.594
peak=   -3.132 closest distance to " O   HOH Z 189 " =    1.750
peak=   -3.130 closest distance to " CB  ALA A 291 " =    2.233
peak=   -3.124 closest distance to " CZ3 TRP A 274 " =    2.482
peak=   -3.123 closest distance to " O   SER A  95 " =    1.792
peak=   -3.122 closest distance to " O   HOH Z 292 " =    1.666
peak=   -3.122 closest distance to " O   HOH Z 114 " =    1.422
peak=   -3.118 closest distance to " OH  TYR A 169 " =    1.058
peak=   -3.114 closest distance to " O   LEU A 101 " =    1.962
peak=   -3.114 closest distance to " O   HOH Z  60 " =    2.105
peak=   -3.101 closest distance to " O   HOH Z 211 " =    1.629
peak=   -3.100 closest distance to " CB  ASP A 286 " =    1.877
peak=   -3.099 closest distance to " CG  TRP A 266 " =    1.808
peak=   -3.088 closest distance to " CG  ASN A 301 " =    2.015
peak=   -3.087 closest distance to " NE2 GLN A 223 " =    1.323
peak=   -3.085 closest distance to " CD1 LEU A 282 " =    2.776
peak=   -3.082 closest distance to " O   HOH Z 422 " =    1.540
peak=   -3.076 closest distance to " CZ  PHE A  38 " =    1.965
peak=   -3.074 closest distance to " O   HOH Z 193 " =    2.403
peak=   -3.069 closest distance to " CA  GLY A  98 " =    2.208
peak=   -3.067 closest distance to " OG BSER A 134 " =    1.995
peak=   -3.067 closest distance to " O   HOH Z 259 " =    2.026
peak=   -3.065 closest distance to " OG  SER A  63 " =    1.260
peak=   -3.053 closest distance to " SD  MET A  40 " =    1.975
peak=   -3.053 closest distance to " O   HOH Z 434 " =    2.201
peak=   -3.051 closest distance to " O   HOH Z 357 " =    2.152
peak=   -3.045 closest distance to " O   HOH Z  56 " =    1.359
peak=   -3.044 closest distance to " O   HOH Z 174 " =    2.234

================= 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    :  0.4066 0.3931   6.211984e+00   6.178816e+00
   1_bss:  0.3948 0.3812   6.196387e+00   6.159164e+00
   1_xyz:  0.2451 0.2665   5.794943e+00   5.876556e+00
   1_adp:  0.2220 0.2760   5.739425e+00   5.896367e+00
   1_occ:  0.2217 0.2765   5.739000e+00   5.896084e+00
   2_bss:  0.2182 0.2725   5.728762e+00   5.886988e+00
   2_xyz:  0.1737 0.2131   5.505780e+00   5.673963e+00
   2_adp:  0.1626 0.2053   5.459185e+00   5.641020e+00
   2_occ:  0.1625 0.2053   5.458743e+00   5.640945e+00
   3_bss:  0.1625 0.2051   5.457638e+00   5.639552e+00
   3_xyz:  0.1344 0.1790   5.294657e+00   5.507175e+00
   3_adp:  0.1292 0.1725   5.256669e+00   5.471395e+00
   3_occ:  0.1291 0.1725   5.256305e+00   5.471195e+00
   4_bss:  0.1294 0.1721   5.256715e+00   5.470065e+00
   4_xyz:  0.1188 0.1646   5.192982e+00   5.425338e+00
   4_adp:  0.1169 0.1642   5.184968e+00   5.422968e+00
   4_occ:  0.1169 0.1643   5.184917e+00   5.423240e+00
   5_bss:  0.1168 0.1641   5.184681e+00   5.423085e+00
   5_xyz:  0.1165 0.1646   5.185727e+00   5.425401e+00
   5_adp:  0.1162 0.1652   5.186180e+00   5.429392e+00
   5_occ:  0.1161 0.1653   5.186167e+00   5.429636e+00
   5_bss:  0.1160 0.1651   5.186301e+00   5.429754e+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:  0.299  50.000  -3.390   4.754  -0.121   0.000  -0.000  -0.000
   1_xyz:  0.299  50.000  -3.390   4.754  -0.121   0.000  -0.000  -0.000
   1_adp:  0.299  50.000  -3.390   4.754  -0.121   0.000  -0.000  -0.000
   1_occ:  0.299  50.000  -3.390   4.754  -0.121   0.000  -0.000  -0.000
   2_bss:  0.331  79.703  -2.336   0.878  -0.323   0.000  -0.000  -0.000
   2_xyz:  0.331  79.703  -2.336   0.878  -0.323   0.000  -0.000  -0.000
   2_adp:  0.331  79.703  -2.336   0.878  -0.323   0.000  -0.000  -0.000
   2_occ:  0.331  79.703  -2.336   0.878  -0.323   0.000  -0.000  -0.000
   3_bss:  0.333  81.317  -2.122  -0.231  -0.446  -0.000  -0.000  -0.000
   3_xyz:  0.333  81.317  -2.122  -0.231  -0.446  -0.000  -0.000  -0.000
   3_adp:  0.333  81.317  -2.122  -0.231  -0.446  -0.000  -0.000  -0.000
   3_occ:  0.333  81.317  -2.122  -0.231  -0.446  -0.000  -0.000  -0.000
   4_bss:  0.331  76.750  -1.800  -0.595  -0.177  -0.000  -0.000  -0.000
   4_xyz:  0.331  76.750  -1.800  -0.595  -0.177  -0.000  -0.000  -0.000
   4_adp:  0.331  76.750  -1.800  -0.595  -0.177  -0.000  -0.000  -0.000
   4_occ:  0.331  76.750  -1.800  -0.595  -0.177  -0.000  -0.000  -0.000
   5_bss:  0.325  72.218  -1.554  -0.613   0.000  -0.000   0.000   0.000
   5_xyz:  0.325  72.218  -1.554  -0.613   0.000  -0.000   0.000   0.000
   5_adp:  0.325  72.218  -1.554  -0.613   0.000  -0.000   0.000   0.000
   5_occ:  0.325  72.218  -1.554  -0.613   0.000  -0.000   0.000   0.000
   5_bss:  0.325  72.221  -1.266  -0.430   0.276  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  44.871 0.5855  0.7360    47422.645
   1_bss:  43.915 0.5956  0.7596    44337.569
   1_xyz:  27.866 0.7814  0.9485    19306.498
   1_adp:  28.763 0.7707  0.9269    20200.304
   1_occ:  28.779 0.7705  0.9263    20202.916
   2_bss:  28.132 0.7778  0.9071    19646.222
   2_xyz:  20.924 0.8522  0.9650    11562.400
   2_adp:  19.843 0.8634  0.9601    10787.522
   2_occ:  19.844 0.8633  0.9600    10783.098
   3_bss:  19.755 0.8642  0.9501    10721.448
   3_xyz:  16.691 0.8920  0.9654     8026.800
   3_adp:  15.767 0.9005  0.9588     7528.556
   3_occ:  15.758 0.9006  0.9588     7527.831
   4_bss:  15.749 0.9006  0.9619     7516.974
   4_xyz:  14.805 0.9085  0.9681     6844.561
   4_adp:  14.707 0.9095  0.9596     6822.091
   4_occ:  14.710 0.9095  0.9595     6824.128
   5_bss:  14.706 0.9096  0.9643     6820.342
   5_xyz:  14.722 0.9095  0.9625     6837.387
   5_adp:  14.796 0.9089  0.9505     6884.412
   5_occ:  14.797 0.9089  0.9504     6886.929
   5_bss:  14.799 0.9089  0.9589     6889.244
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.115   1.6357e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.115   1.6357e-01
   1_xyz:   1.672  0.016  0.102 15.767  0.007  4.125   1.6517e-01
   1_adp:   1.672  0.016  0.102 15.767  0.007  4.125   1.6517e-01
   1_occ:   1.672  0.016  0.102 15.767  0.007  4.125   1.6517e-01
   2_bss:   1.672  0.016  0.102 15.767  0.007  4.125   1.6517e-01
   2_xyz:   0.970  0.007  0.070 14.789  0.004  4.137   5.6362e-02
   2_adp:   0.970  0.007  0.070 14.789  0.004  4.137   5.6362e-02
   2_occ:   0.970  0.007  0.070 14.789  0.004  4.137   5.6362e-02
   3_bss:   0.970  0.007  0.070 14.789  0.004  4.137   5.6362e-02
   3_xyz:   1.033  0.008  0.076 14.611  0.003  4.125   6.2107e-02
   3_adp:   1.033  0.008  0.076 14.611  0.003  4.125   6.2107e-02
   3_occ:   1.033  0.008  0.076 14.611  0.003  4.125   6.2107e-02
   4_bss:   1.033  0.008  0.076 14.611  0.003  4.125   6.2107e-02
   4_xyz:   1.111  0.010  0.081 14.818  0.004  4.117   7.3562e-02
   4_adp:   1.111  0.010  0.081 14.818  0.004  4.117   7.3562e-02
   4_occ:   1.111  0.010  0.081 14.818  0.004  4.117   7.3562e-02
   5_bss:   1.111  0.010  0.081 14.818  0.004  4.117   7.3562e-02
   5_xyz:   1.036  0.009  0.078 14.591  0.003  4.118   6.4467e-02
   5_adp:   1.036  0.009  0.078 14.591  0.003  4.118   6.4467e-02
   5_occ:   1.036  0.009  0.078 14.591  0.003  4.118   6.4467e-02
   5_bss:   1.036  0.009  0.078 14.591  0.003  4.118   6.4467e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.797   2.4407e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.797   2.4407e-01
   1_xyz:   9.884  0.130  0.290 87.694  0.038  2.133   3.3059e-01
   1_adp:   9.884  0.130  0.290 87.694  0.038  2.133   3.3059e-01
   1_occ:   9.884  0.130  0.290 87.694  0.038  2.133   3.3059e-01
   2_bss:   9.884  0.130  0.290 87.694  0.038  2.133   3.3059e-01
   2_xyz:   7.644  0.037  0.241 81.843  0.052  2.302   4.0383e-02
   2_adp:   7.644  0.037  0.241 81.843  0.052  2.302   4.0383e-02
   2_occ:   7.644  0.037  0.241 81.843  0.052  2.302   4.0383e-02
   3_bss:   7.644  0.037  0.241 81.843  0.052  2.302   4.0383e-02
   3_xyz:   7.541  0.051  0.240 81.417  0.030  2.308   5.6998e-02
   3_adp:   7.541  0.051  0.240 81.417  0.030  2.308   5.6998e-02
   3_occ:   7.541  0.051  0.240 81.417  0.030  2.308   5.6998e-02
   4_bss:   7.541  0.051  0.240 81.417  0.030  2.308   5.6998e-02
   4_xyz:   8.092  0.047  0.291 82.053  0.034  2.343   7.3740e-02
   4_adp:   8.092  0.047  0.291 82.053  0.034  2.343   7.3740e-02
   4_occ:   8.092  0.047  0.291 82.053  0.034  2.343   7.3740e-02
   5_bss:   8.092  0.047  0.291 82.053  0.034  2.343   7.3740e-02
   5_xyz:   7.866  0.047  0.264 80.863  0.032  2.381   4.2088e-02
   5_adp:   7.866  0.047  0.264 80.863  0.032  2.381   4.2088e-02
   5_occ:   7.866  0.047  0.264 80.863  0.032  2.381   4.2088e-02
   5_bss:   7.866  0.047  0.264 80.863  0.032  2.381   4.2088e-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:  90.75   0.00  17.60  80.44   0.00  13.28  90.75   4.66  41.11
   1_occ:  90.75   0.00  17.60  80.44   0.00  13.28  90.75   4.66  41.11
   2_bss:  90.75   0.00  17.60  80.44   0.00  13.28  90.75   4.66  41.11
   2_xyz:  90.75   0.00  17.60  80.44   0.00  13.28  90.75   4.66  41.11
   2_adp:  99.69   0.00  17.97  99.69   0.00  13.15  97.80   5.25  44.21
   2_occ:  99.69   0.00  17.97  99.69   0.00  13.15  97.80   5.25  44.21
   3_bss:  99.69   0.00  17.97  99.69   0.00  13.15  97.80   5.25  44.21
   3_xyz:  99.69   0.00  17.97  99.69   0.00  13.15  97.80   5.25  44.21
   3_adp: 100.58   0.00  17.33 100.58   0.00  12.55  98.04   4.71  43.36
   3_occ: 100.58   0.00  17.33 100.58   0.00  12.55  98.04   4.71  43.36
   4_bss: 100.58   0.00  17.33 100.58   0.00  12.55  98.04   4.71  43.36
   4_xyz: 100.58   0.00  17.33 100.58   0.00  12.55  98.04   4.71  43.36
   4_adp: 106.25   0.00  17.06 106.25   0.00  12.28 102.57   3.67  43.08
   4_occ: 106.25   0.00  17.06 106.25   0.00  12.28 102.57   3.67  43.08
   5_bss: 106.25   0.00  17.06 106.25   0.00  12.28 102.57   3.67  43.08
   5_xyz: 106.25   0.00  17.06 106.25   0.00  12.28 102.57   3.67  43.08
   5_adp: 112.96   0.00  16.73 112.96   0.00  11.99 105.17   4.57  42.56
   5_occ: 112.96   0.00  16.73 112.96   0.00  11.99 105.17   4.57  42.56
   5_bss: 112.96   0.00  16.74 112.96   0.00  11.99 105.17   4.57  42.56
------------------------------------------------------------------------
 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:    1.418    0.043    0.509
   1_adp:    1.418    0.043    0.509
   1_occ:    1.418    0.043    0.509
   2_bss:    1.418    0.043    0.509
   2_xyz:    1.132    0.051    0.532
   2_adp:    1.132    0.051    0.532
   2_occ:    1.132    0.051    0.532
   3_bss:    1.132    0.051    0.532
   3_xyz:    1.268    0.076    0.614
   3_adp:    1.268    0.076    0.614
   3_occ:    1.268    0.076    0.614
   4_bss:    1.268    0.076    0.614
   4_xyz:    1.302    0.054    0.640
   4_adp:    1.302    0.054    0.640
   4_occ:    1.302    0.054    0.640
   5_bss:    1.302    0.054    0.640
   5_xyz:    1.267    0.084    0.652
   5_adp:    1.267    0.084    0.652
   5_occ:    1.267    0.084    0.652
   5_bss:    1.267    0.084    0.652
------------------------------------------------------------------------

CPU time actual refinement: 291.15


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_832/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_832/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_832/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_832/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_832/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 291.02 
  Macro-tasks:
    bulk solvent and scale       = 46.52  
    individual site refinement   = 113.27 
    weights calculation          = 24.97  
    collect and process          = 5.58   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 190.44 
  Micro-tasks:
    mask                            = 1.49   
    f_calc                          = 87.71  
    alpha_beta                      = 6.93   
    target                          = 0.99   
    gradients_wrt_atomic_parameters = 95.63  
    fmodel                         = 7.65   
    r_factors                      = 0.35   
    phase_errors                   = 9.07   
    foms                           = 0.21   
    TOTAL for micro-tasks          = 210.03 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.100 micro seconds
Total CPU time: 5.04 minutes
from_scatterers_fft:    645 calls, 87.42 s
gradients_fft:          590 calls, 83.94 s

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

# Date 2008-01-16 Time 05:46:03 PST -0800 (1200491163.83 s)
Start R-work = 0.4066, R-free = 0.3931 (no bulk solvent and anisotropic scale)
Final R-work = 0.1327, R-free = 0.1794 (no bulk solvent and anisotropic scale)

Start R-work = 0.3948, R-free = 0.3812
Final R-work = 0.1160, R-free = 0.1651