# Date 2008-01-16 Time 05:18:41 PST -0800 (1200489521.24 s)
#phil __OFF__

Command line arguments: "../678.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 17847
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 678

-------------------------------------------------------------------------------
  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: (70.25, 47.1647, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.1647, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0342 2.00058
Completeness in resolution range: 0.972545
Completeness with d_max=infinity: 0.969465

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0342
                             d_min =   2.0006

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: (70.25, 47.1647, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0342 2.00058
Completeness in resolution range: 0.972545
Completeness with d_max=infinity: 0.969465

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0346 -  4.2801 [2117/2141]  1903   214  10.1%
  bin  2:  4.2801 -  3.4103 [2037/2056]  1836   201   9.9%
  bin  3:  3.4103 -  2.9830 [2007/2026]  1808   199   9.9%
  bin  4:  2.9830 -  2.7120 [1981/2011]  1777   204  10.3%
  bin  5:  2.7120 -  2.5186 [1983/2002]  1787   196   9.9%
  bin  6:  2.5186 -  2.3707 [1964/1989]  1769   195   9.9%
  bin  7:  2.3707 -  2.2524 [1953/1981]  1758   195  10.0%
  bin  8:  2.2524 -  2.1546 [1945/1981]  1750   195  10.0%
  bin  9:  2.1546 -  2.0719 [1929/1971]  1735   194  10.1%
  bin 10:  2.0719 -  2.0006 [1673/1984]  1507   166   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_678/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 12
        2.42 -     3.04: 2181
        3.04 -     3.66: 4602
        3.66 -     4.28: 8967
        4.28 -     4.90: 12307
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.046 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.155 3.040 -x+1,y-1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.239 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28064 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_678/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_678/model_refine_001.geo

CPU time processing inputs: 9.07


============================ 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 = 70.25 47.16465 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: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2575   r_free= 0.2444   ksol= 0.00   Bsol= 0.00   scale= 0.990    |
|                                                                             |
| 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:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.837579                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0346 -  4.7734 0.99   1380  153 0.2520 0.2513      6.2557      6.1969|
|  2:  4.7734 -  3.8091 0.99   1311  149 0.1932 0.1723      6.1767      6.1425|
|  3:  3.8091 -  3.3336 0.99   1306  145 0.2182 0.2073      6.1268      6.1262|
|  4:  3.3336 -  3.0315 0.99   1289  136 0.2313 0.2458      6.0083      6.0518|
|  5:  3.0315 -  2.8158 0.99   1268  144 0.2618 0.2030         5.9      5.7278|
|  6:  2.8158 -  2.6507 0.99   1276  145 0.2608 0.2664      5.8185      5.7929|
|  7:  2.6507 -  2.5186 0.99   1281  142 0.2678 0.2531      5.7778      5.7711|
|  8:  2.5186 -  2.4094 0.98   1261  136 0.2774 0.2415      5.7777      5.6946|
|  9:  2.4094 -  2.3170 0.98   1252  143 0.2712 0.2609      5.7055       5.639|
| 10:  2.3170 -  2.2373 0.99   1262  136 0.2898 0.2421       5.731      5.5467|
| 11:  2.2373 -  2.1676 0.98   1261  142 0.2864 0.2585      5.6711      5.5916|
| 12:  2.1676 -  2.1058 0.97   1230  139 0.2937 0.3011      5.6213      5.7669|
| 13:  2.1058 -  2.0505 1.00   1262  137 0.2938 0.2728      5.5364      5.4991|
| 14:  2.0505 -  2.0006 0.78    991  112 0.2917 0.2875      5.4682      5.4455|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0346 -  4.7734  1380   153  0.82  23.61   0.87     0.83      35081.81|
|  2:  4.7734 -  3.8091  1311   149  0.88  17.53   0.99     0.93      29168.84|
|  3:  3.8091 -  3.3336  1306   145  0.88  17.97   1.00     0.97      23891.74|
|  4:  3.3336 -  3.0315  1289   136  0.87  19.70   1.01     0.97      20237.46|
|  5:  3.0315 -  2.8158  1268   144  0.83  23.55   1.03     0.95      16496.03|
|  6:  2.8158 -  2.6507  1276   145  0.83  23.88   1.01     0.95      14721.81|
|  7:  2.6507 -  2.5186  1281   142  0.82  24.78   1.03     0.97      13586.90|
|  8:  2.5186 -  2.4094  1261   136  0.83  24.04   1.03     0.99      12745.99|
|  9:  2.4094 -  2.3170  1252   143  0.83  24.20   1.06     1.01      11313.74|
| 10:  2.3170 -  2.2373  1262   136  0.82  24.56   1.09     1.01      10473.74|
| 11:  2.2373 -  2.1676  1261   142  0.83  24.50   1.06     1.03      10398.95|
| 12:  2.1676 -  2.1058  1230   139  0.81  25.88   1.07     1.04      10497.67|
| 13:  2.1058 -  2.0505  1262   137  0.80  27.04   1.07     1.04       9628.88|
| 14:  2.0505 -  2.0006   991   112  0.79  27.50   1.08     1.01       8045.03|
|alpha:            min =        0.83 max =            1.04 mean =         0.98|
|beta:             min =     8045.03 max =        35081.81 mean =     16486.31|
|figures of merit: min =        0.00 max =            1.00 mean =         0.83|
|phase err.(work): min =        0.00 max =           89.91 mean =        23.38|
|phase err.(test): min =        0.00 max =           88.50 mean =        22.88|
|-----------------------------------------------------------------------------|

============================== 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 = 2.774360              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.563   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.384154              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.727   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       10 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      176 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2005 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1825 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2777 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4616 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4351 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5630 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6677 |
|-----------------------------------------------------------------------------|
|-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 |        0.161 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.806 |       0.144 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.071)------------------------------------------|
|    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: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2575   r_free= 0.2444   ksol= 0.00   Bsol= 0.00   scale= 0.990    |
|                                                                             |
| 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:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.837579                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2403   r_free= 0.2282   ksol= 0.32   Bsol= 55.61   scale= 0.978   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.38,-1.82,0.54,-0.00,0.00,0.00); trace/3= -1.55                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.800770                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.550060              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.434   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.219184              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.710   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2403      final r-factor (work) = 0.1441          |
| start r-factor (free) = 0.2282      final r-factor (free) = 0.1627          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5970 = 2.55 * 0.50 * 5.8319 + 1.00 * 0.1612                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0359 = 2.55 * 0.50 * 5.4707 + 1.00 * 0.0606                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1441      final r-factor (work) = 0.1358          |
| start r-factor (free) = 0.1627      final r-factor (free) = 0.1613          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2072 = 0.22 * 1.00 * 5.4707 + 1.00 * 0.0081                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3863 = 0.22 * 1.00 * 5.2573 + 1.00 * 0.2340                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.071)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.27   16.17    None  None   None       |
|    all(noH): 2823   0      0.00    79.27   16.17    None  None   None       |
|    Sol.    : 438    0      7.04    62.79   37.00    None  None   None       |
|    Mac.    : 2385   0      0.00    79.27   12.35    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.927:  392   |   5:    39.633 -  47.559:  104        |
|      1:     7.927 -  15.853: 1613   |   6:    47.559 -  55.486:   73        |
|      2:    15.853 -  23.780:  335   |   7:    55.486 -  63.412:   35        |
|      3:    23.780 -  31.706:  147   |   8:    63.412 -  71.339:    0        |
|      4:    31.706 -  39.633:  123   |   9:    71.339 -  79.265:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1358 r_free = 0.1613             target_work(ml) = 5.256         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1352 r_free = 0.1611             target_work(ml) = 5.254         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1352   r_free= 0.1611   ksol= 0.32   Bsol= 55.61   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.38,-1.82,0.54,-0.00,0.00,0.00); trace/3= -1.55                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.254019                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1348   r_free= 0.1599   ksol= 0.33   Bsol= 60.16   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.25,-2.39,-0.89,-0.00,-0.00,-0.00); trace/3= -2.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.250546                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.386365              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.705  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.323324              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.346   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1348      final r-factor (work) = 0.1218          |
| start r-factor (free) = 0.1599      final r-factor (free) = 0.1496          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7087 = 1.39 * 0.50 * 5.2629 + 1.00 * 0.0606                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6565 = 1.39 * 0.50 * 5.1957 + 1.00 * 0.0549                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1218      final r-factor (work) = 0.1153          |
| start r-factor (free) = 0.1496      final r-factor (free) = 0.1526          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9042 = 1.32 * 1.00 * 5.1957 + 1.00 * 0.0287                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8019 = 1.32 * 1.00 * 5.1329 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.071)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.83    80.74   17.12    None  None   None       |
|    all(noH): 2823   0      0.83    80.74   17.12    None  None   None       |
|    Sol.    : 438    0      1.83    75.18   40.04    None  None   None       |
|    Mac.    : 2385   0      0.83    80.74   12.91    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.826 -   8.817:  734   |   5:    40.784 -  48.776:   98        |
|      1:     8.817 -  16.809: 1292   |   6:    48.776 -  56.767:   87        |
|      2:    16.809 -  24.801:  298   |   7:    56.767 -  64.759:   60        |
|      3:    24.801 -  32.792:  119   |   8:    64.759 -  72.750:   25        |
|      4:    32.792 -  40.784:  106   |   9:    72.750 -  80.742:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1153 r_free = 0.1526             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1152 r_free = 0.1524             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1152   r_free= 0.1524   ksol= 0.33   Bsol= 60.16   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.25,-2.39,-0.89,-0.00,-0.00,-0.00); trace/3= -2.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.144944                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1523   ksol= 0.33   Bsol= 60.16   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.73,-2.09,-0.83,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.144451                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.210082              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 140.613  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.168434              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.482  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1150      final r-factor (work) = 0.1141          |
| start r-factor (free) = 0.1523      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.1615 = 1.21 * 0.50 * 5.1344 + 1.00 * 0.0550                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.1596 = 1.21 * 0.50 * 5.1403 + 1.00 * 0.0496                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1141      final r-factor (work) = 0.1149          |
| start r-factor (free) = 0.1561      final r-factor (free) = 0.1547          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8753 = 0.17 * 1.00 * 5.1403 + 1.00 * 0.0095                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8755 = 0.17 * 1.00 * 5.1531 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.071)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.24    79.10   16.44    None  None   None       |
|    all(noH): 2823   0      1.24    79.10   16.44    None  None   None       |
|    Sol.    : 438    0      3.21    72.06   37.30    None  None   None       |
|    Mac.    : 2385   0      1.24    79.10   12.61    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.238 -   9.024:  798   |   5:    40.169 -  47.955:   93        |
|      1:     9.024 -  16.810: 1227   |   6:    47.955 -  55.741:   79        |
|      2:    16.810 -  24.597:  310   |   7:    55.741 -  63.527:   35        |
|      3:    24.597 -  32.383:  121   |   8:    63.527 -  71.313:   13        |
|      4:    32.383 -  40.169:  144   |   9:    71.313 -  79.099:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1149 r_free = 0.1547             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1148 r_free = 0.1547             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1148   r_free= 0.1547   ksol= 0.33   Bsol= 60.16   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.73,-2.09,-0.83,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.149642                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1547   ksol= 0.32   Bsol= 55.45   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-1.95,-0.73,-0.00,-0.00,-0.00); trace/3= -1.73                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.149779                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.337338              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 155.268  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.108300              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.735  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1147      final r-factor (work) = 0.1132          |
| start r-factor (free) = 0.1547      final r-factor (free) = 0.1547          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4956 = 1.34 * 0.50 * 5.1536 + 1.00 * 0.0496                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4899 = 1.34 * 0.50 * 5.1425 + 1.00 * 0.0513                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1132      final r-factor (work) = 0.1145          |
| start r-factor (free) = 0.1547      final r-factor (free) = 0.1545          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5645 = 0.11 * 1.00 * 5.1425 + 1.00 * 0.0075                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5642 = 0.11 * 1.00 * 5.1489 + 1.00 * 0.0065                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.071)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.76    76.65   16.03    None  None   None       |
|    all(noH): 2823   0      1.76    76.65   16.03    None  None   None       |
|    Sol.    : 438    0      4.45    69.64   35.83    None  None   None       |
|    Mac.    : 2385   0      1.76    76.65   12.40    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:     1.763 -   9.252:  883   |   5:    39.209 -  46.698:   93        |
|      1:     9.252 -  16.741: 1171   |   6:    46.698 -  54.187:   81        |
|      2:    16.741 -  24.230:  294   |   7:    54.187 -  61.676:   27        |
|      3:    24.230 -  31.720:  121   |   8:    61.676 -  69.166:   12        |
|      4:    31.720 -  39.209:  138   |   9:    69.166 -  76.655:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1145 r_free = 0.1545             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1144 r_free = 0.1546             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1144   r_free= 0.1546   ksol= 0.32   Bsol= 55.45   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-1.95,-0.73,-0.00,-0.00,-0.00); trace/3= -1.73                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.148510                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1144   r_free= 0.1546   ksol= 0.32   Bsol= 55.45   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-1.92,-0.68,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.148512                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.372921              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 165.240  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.930637              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.321  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1144      final r-factor (work) = 0.1102          |
| start r-factor (free) = 0.1546      final r-factor (free) = 0.1547          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1604 = 2.37 * 0.50 * 5.1490 + 1.00 * 0.0513                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1529 = 2.37 * 0.50 * 5.1304 + 1.00 * 0.0659                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1102      final r-factor (work) = 0.1084          |
| start r-factor (free) = 0.1547      final r-factor (free) = 0.1558          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.9115 = 1.93 * 1.00 * 5.1304 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.8884 = 1.93 * 1.00 * 5.1169 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.071)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.76   16.56    None  None   None       |
|    all(noH): 2823   0      0.00    86.76   16.56    None  None   None       |
|    Sol.    : 438    0      5.73    74.37   38.98    None  None   None       |
|    Mac.    : 2385   0      0.00    86.76   12.45    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.676:  818   |   5:    43.380 -  52.057:  104        |
|      1:     8.676 -  17.352: 1265   |   6:    52.057 -  60.733:   71        |
|      2:    17.352 -  26.028:  275   |   7:    60.733 -  69.409:   36        |
|      3:    26.028 -  34.704:  128   |   8:    69.409 -  78.085:    9        |
|      4:    34.704 -  43.380:  113   |   9:    78.085 -  86.761:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1084 r_free = 0.1558             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1084 r_free = 0.1558             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1084   r_free= 0.1558   ksol= 0.32   Bsol= 55.45   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-1.92,-0.68,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.122292                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0346 -  4.7734 0.99   1380  153 0.1006 0.1310      5.4048       5.525|
|  2:  4.7734 -  3.8091 0.99   1311  149 0.0839 0.1110      5.4298      5.6288|
|  3:  3.8091 -  3.3336 0.99   1306  145 0.1032 0.1494      5.4637      5.8417|
|  4:  3.3336 -  3.0315 0.99   1289  136 0.1165 0.1505      5.4224      5.5623|
|  5:  3.0315 -  2.8158 0.99   1268  144 0.1293 0.1687      5.3084      5.5226|
|  6:  2.8158 -  2.6507 0.99   1276  145 0.1152 0.1866      5.1876       5.456|
|  7:  2.6507 -  2.5186 0.99   1281  142 0.1219 0.1616      5.1414      5.3287|
|  8:  2.5186 -  2.4094 0.98   1261  136 0.1121 0.1690       5.053      5.3501|
|  9:  2.4094 -  2.3170 0.98   1252  143 0.1122 0.1777      5.0074      5.2926|
| 10:  2.3170 -  2.2373 0.99   1262  136 0.1088 0.1707      4.9469      5.1954|
| 11:  2.2373 -  2.1676 0.98   1261  142 0.1101 0.1697      4.9257      5.1963|
| 12:  2.1676 -  2.1058 0.97   1230  139 0.1092 0.1641      4.8613      5.2181|
| 13:  2.1058 -  2.0505 1.00   1262  137 0.1040 0.1715      4.7628      5.0488|
| 14:  2.0505 -  2.0006 0.78    991  112 0.0956 0.1747      4.6235      4.9449|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0346 -  4.7734  1380   153  0.94   9.50   0.97     0.94       7547.61|
|  2:  4.7734 -  3.8091  1311   149  0.95   7.85   1.00     0.99       8986.67|
|  3:  3.8091 -  3.3336  1306   145  0.94  10.90   1.01     1.01      10043.60|
|  4:  3.3336 -  3.0315  1289   136  0.93  12.86   1.00     0.98       9633.32|
|  5:  3.0315 -  2.8158  1268   144  0.90  15.36   0.99     0.96       7972.07|
|  6:  2.8158 -  2.6507  1276   145  0.91  15.40   0.98     0.95       6768.04|
|  7:  2.6507 -  2.5186  1281   142  0.91  15.19   0.98     0.95       5944.53|
|  8:  2.5186 -  2.4094  1261   136  0.92  14.36   0.98     0.96       5092.60|
|  9:  2.4094 -  2.3170  1252   143  0.91  15.04   0.99     0.95       4828.51|
| 10:  2.3170 -  2.2373  1262   136  0.90  15.56   0.98     0.94       4279.79|
| 11:  2.2373 -  2.1676  1261   142  0.91  15.56   0.98     0.95       4302.11|
| 12:  2.1676 -  2.1058  1230   139  0.91  15.17   0.99     0.98       3840.91|
| 13:  2.1058 -  2.0505  1262   137  0.91  15.16   0.98     0.96       3230.64|
| 14:  2.0505 -  2.0006   991   112  0.92  13.92   0.95     0.91       2395.73|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2395.73 max =        10043.60 mean =      6157.67|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.85 mean =        13.65|
|phase err.(test): min =        0.00 max =           89.70 mean =        13.18|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1082   r_free= 0.1557   ksol= 0.32   Bsol= 55.93   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-1.62,-0.42,-0.00,-0.00,-0.00); trace/3= -1.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.122283                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1082   r_free= 0.1557   ksol= 0.32   Bsol= 55.93   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-1.62,-0.42,-0.00,-0.00,-0.00); trace/3= -1.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.122283                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0346 -  4.7734 0.99   1380  153 0.1006 0.1313      5.4049      5.5258|
|  2:  4.7734 -  3.8091 0.99   1311  149 0.0840 0.1111       5.431      5.6294|
|  3:  3.8091 -  3.3336 0.99   1306  145 0.1033 0.1494      5.4639      5.8419|
|  4:  3.3336 -  3.0315 0.99   1289  136 0.1164 0.1504       5.422      5.5622|
|  5:  3.0315 -  2.8158 0.99   1268  144 0.1292 0.1686      5.3078      5.5219|
|  6:  2.8158 -  2.6507 0.99   1276  145 0.1151 0.1866      5.1872      5.4558|
|  7:  2.6507 -  2.5186 0.99   1281  142 0.1219 0.1616      5.1413      5.3286|
|  8:  2.5186 -  2.4094 0.98   1261  136 0.1121 0.1689      5.0531      5.3499|
|  9:  2.4094 -  2.3170 0.98   1252  143 0.1122 0.1778      5.0074      5.2926|
| 10:  2.3170 -  2.2373 0.99   1262  136 0.1088 0.1707       4.947      5.1952|
| 11:  2.2373 -  2.1676 0.98   1261  142 0.1101 0.1695      4.9255      5.1956|
| 12:  2.1676 -  2.1058 0.97   1230  139 0.1092 0.1639      4.8611      5.2176|
| 13:  2.1058 -  2.0505 1.00   1262  137 0.1040 0.1715      4.7627      5.0487|
| 14:  2.0505 -  2.0006 0.78    991  112 0.0956 0.1747      4.6236       4.945|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0346 -  4.7734  1380   153  0.94   9.51   0.97     0.94       7558.41|
|  2:  4.7734 -  3.8091  1311   149  0.95   7.86   1.01     0.99       9000.20|
|  3:  3.8091 -  3.3336  1306   145  0.94  10.91   1.02     1.01      10049.93|
|  4:  3.3336 -  3.0315  1289   136  0.93  12.85   1.00     0.99       9625.15|
|  5:  3.0315 -  2.8158  1268   144  0.90  15.36   1.00     0.97       7963.98|
|  6:  2.8158 -  2.6507  1276   145  0.91  15.39   0.99     0.96       6761.54|
|  7:  2.6507 -  2.5186  1281   142  0.91  15.19   0.99     0.96       5942.32|
|  8:  2.5186 -  2.4094  1261   136  0.92  14.37   0.99     0.97       5092.93|
|  9:  2.4094 -  2.3170  1252   143  0.91  15.05   1.00     0.97       4830.28|
| 10:  2.3170 -  2.2373  1262   136  0.90  15.56   0.99     0.95       4278.34|
| 11:  2.2373 -  2.1676  1261   142  0.91  15.55   0.99     0.96       4298.83|
| 12:  2.1676 -  2.1058  1230   139  0.91  15.16   1.01     0.99       3838.70|
| 13:  2.1058 -  2.0505  1262   137  0.91  15.16   1.00     0.98       3229.69|
| 14:  2.0505 -  2.0006   991   112  0.92  13.92   0.97     0.93       2395.64|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2395.64 max =        10049.93 mean =      6157.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.77 mean =        13.65|
|phase err.(test): min =        0.00 max =           89.81 mean =        13.19|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.071)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.76   16.57    None  None   None       |
|    all(noH): 2823   0      0.00    86.76   16.57    None  None   None       |
|    Sol.    : 438    0      5.74    74.37   38.98    None  None   None       |
|    Mac.    : 2385   0      0.00    86.76   12.45    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   8.679:  818   |   5:    43.383 -  52.059:  104        |
|      1:     8.679 -  17.355: 1265   |   6:    52.059 -  60.736:   71        |
|      2:    17.355 -  26.031:  275   |   7:    60.736 -  69.412:   36        |
|      3:    26.031 -  34.707:  128   |   8:    69.412 -  78.088:    9        |
|      4:    34.707 -  43.383:  113   |   9:    78.088 -  86.764:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 279         
Filter by distance & map next to the model:
   mapped sites are within: 0.484 - 4.924
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 274 from: 279
   mapped sites are within: 0.701 - 4.924

peak=    5.824 closest distance to " NH2 ARG A  56 " =    2.280
peak=    5.586 closest distance to " CB  GLN A 223 " =    1.426
peak=    5.209 closest distance to " CG  PRO A  54 " =    1.311
peak=    5.128 closest distance to " O   HOH Z 232 " =    2.372
peak=    5.101 closest distance to " CB  ARG A 275 " =    0.933
peak=    5.058 closest distance to " O   HOH Z 126 " =    1.899
peak=    4.824 closest distance to " O   HOH Z 298 " =    1.949
peak=    4.798 closest distance to " CB  SER A  63 " =    1.173
peak=    4.712 closest distance to " CB  GLN A 183 " =    1.241
peak=    4.604 closest distance to " O   HOH Z 369 " =    2.280
peak=    4.574 closest distance to " O   HOH Z  78 " =    1.735
peak=    4.568 closest distance to " C   PRO A 198 " =    1.509
peak=    4.535 closest distance to " CB  ARG A  79 " =    1.365
peak=    4.532 closest distance to " CB  GLU A 152 " =    1.202
peak=    4.519 closest distance to " CA  TYR A  30 " =    0.954
peak=    4.472 closest distance to " CB  ARG A 190 " =    1.613
peak=    4.460 closest distance to " NE2 GLN A  11 " =    1.026
peak=    4.442 closest distance to " CG  PRO A 213 " =    1.198
peak=    4.407 closest distance to " CB  PRO A  54 " =    0.905
peak=    4.372 closest distance to " O   HOH Z  15 " =    2.128
peak=    4.358 closest distance to " CB  LEU A 228 " =    1.090
peak=    4.319 closest distance to " O   HOH Z 427 " =    2.985
peak=    4.302 closest distance to " O   HOH Z 250 " =    1.511
peak=    4.289 closest distance to " O   HOH Z 303 " =    2.133
peak=    4.282 closest distance to " O   HOH Z 392 " =    3.019
peak=    4.279 closest distance to " O   HOH Z 142 " =    1.629
peak=    4.271 closest distance to " O   HOH Z  61 " =    1.647
peak=    4.261 closest distance to " CB  TYR A 169 " =    0.762
peak=    4.236 closest distance to " CB  ASN A 148 " =    1.584
peak=    4.234 closest distance to " CZ  PHE A 218 " =    1.092
peak=    4.214 closest distance to " O   HOH Z 236 " =    2.171
peak=    4.163 closest distance to " CG  PRO A 198 " =    1.273
peak=    4.161 closest distance to " O   HOH Z 346 " =    1.704
peak=    4.158 closest distance to " O   HOH Z  19 " =    2.380
peak=    4.157 closest distance to " OD1 ASN A  69 " =    2.614
peak=    4.127 closest distance to " O   HOH Z 158 " =    3.061
peak=    4.102 closest distance to " O   HOH Z 234 " =    3.759
peak=    4.090 closest distance to " ND2 ASN A 187 " =    1.425
peak=    4.075 closest distance to " O   HOH Z 209 " =    2.261
peak=    4.069 closest distance to " O   HOH Z  40 " =    1.853
peak=    4.065 closest distance to " CA  ARG A  36 " =    1.079
peak=    4.044 closest distance to " CB  TRP A 266 " =    0.976
peak=    3.998 closest distance to " CE  LYS A  76 " =    0.864
peak=    3.995 closest distance to " O   SER A  87 " =    2.254
peak=    3.991 closest distance to " CG  PRO A  90 " =    1.200
peak=    3.980 closest distance to " CB  GLU A 277 " =    3.643
peak=    3.973 closest distance to " O   HOH Z 189 " =    2.609
peak=    3.944 closest distance to " CG2 VAL A 257 " =    0.860
peak=    3.919 closest distance to " CD2 TRP A 179 " =    1.318
peak=    3.899 closest distance to " NZ  LYS A 117 " =    3.190
peak=    3.897 closest distance to " CB  ASP A 140 " =    1.028
peak=    3.881 closest distance to " O   HOH Z 403 " =    1.629
peak=    3.869 closest distance to " CB  GLU A 128 " =    1.007
peak=    3.868 closest distance to " CA  ARG A 195 " =    1.211
peak=    3.857 closest distance to " OG ASER A 258 " =    3.152
peak=    3.854 closest distance to " O   HOH Z 265 " =    2.354
peak=    3.847 closest distance to " CB  VAL A 265 " =    1.262
peak=    3.843 closest distance to " CD  ARG A 159 " =    0.759
peak=    3.840 closest distance to " CB  VAL A 202 " =    1.534
peak=    3.836 closest distance to " CA  ASN A 215 " =    1.103
peak=    3.832 closest distance to " O   HOH Z 423 " =    1.950
peak=    3.814 closest distance to " O   HOH Z 147 " =    1.830
peak=    3.811 closest distance to " O   HOH Z 402 " =    1.442
peak=    3.810 closest distance to " O   HOH Z 193 " =    1.897
peak=    3.798 closest distance to " CA  TYR A  30 " =    1.035
peak=    3.795 closest distance to " O   HOH Z 203 " =    1.635
peak=    3.794 closest distance to " O   HOH Z 126 " =    1.884
peak=    3.781 closest distance to " O   HOH Z 280 " =    2.967
peak=    3.780 closest distance to " O   HOH Z   1 " =    2.043
peak=    3.779 closest distance to " O   HOH Z 313 " =    1.937
peak=    3.753 closest distance to " CA  ALA A  51 " =    0.935
peak=    3.748 closest distance to " CD  LYS A 166 " =    1.266
peak=    3.745 closest distance to " O   HOH Z 389 " =    1.853
peak=    3.742 closest distance to " CD1 LEU A 300 " =    1.226
peak=    3.741 closest distance to " O   HOH Z 368 " =    2.127
peak=    3.736 closest distance to " CB  THR A  31 " =    1.538
peak=    3.735 closest distance to " O   HOH Z  43 " =    1.969
peak=    3.734 closest distance to " NH2 ARG A 156 " =    1.192
peak=    3.733 closest distance to " O   HOH Z 180 " =    2.171
peak=    3.729 closest distance to " O  BHOH Z 338 " =    2.281
peak=    3.725 closest distance to " CB  ASN A  39 " =    0.882
peak=    3.719 closest distance to " CB  GLU A  46 " =    1.004
peak=    3.714 closest distance to " O   HOH Z 272 " =    1.851
peak=    3.708 closest distance to " O   HOH Z 214 " =    2.108
peak=    3.701 closest distance to " O   MET A 105 " =    1.904
peak=    3.673 closest distance to " O   HOH Z 403 " =    1.428
peak=    3.656 closest distance to " O   HOH Z 128 " =    2.075
peak=    3.649 closest distance to " O   HOH Z 425 " =    1.983
peak=    3.646 closest distance to " CG2AVAL A  72 " =    1.758
peak=    3.645 closest distance to " OG BSER A 164 " =    2.351
peak=    3.642 closest distance to " CG  ARG A  66 " =    2.485
peak=    3.640 closest distance to " CD1 LEU A  96 " =    0.752
peak=    3.639 closest distance to " O   HOH Z 371 " =    3.184
peak=    3.632 closest distance to " CG  PRO A 243 " =    1.007
peak=    3.622 closest distance to " O   HOH Z 245 " =    1.275
peak=    3.617 closest distance to " CD  ARG A 269 " =    0.921
peak=    3.613 closest distance to " O   HOH Z  97 " =    2.540
peak=    3.604 closest distance to " O   HOH Z 261 " =    1.684
peak=    3.599 closest distance to " O   HOH Z 172 " =    3.677
peak=    3.597 closest distance to " CG2 ILE A 120 " =    1.073
peak=    3.593 closest distance to " OG1 THR A 294 " =    2.443
peak=    3.576 closest distance to " O   HOH Z 148 " =    3.337
peak=    3.572 closest distance to " O   HOH Z  97 " =    1.924
peak=    3.571 closest distance to " NH1AARG A 145 " =    1.277
peak=    3.571 closest distance to " N   ARG A 156 " =    1.406
peak=    3.568 closest distance to " O   HOH Z 261 " =    1.937
peak=    3.567 closest distance to " O   HOH Z 305 " =    3.593
peak=    3.550 closest distance to " CB  SER A   3 " =    1.260
peak=    3.549 closest distance to " O   HOH Z 185 " =    1.788
peak=    3.549 closest distance to " CB  ILE A 120 " =    1.290
peak=    3.547 closest distance to " CD BLYS A 290 " =    0.936
peak=    3.543 closest distance to " CB  SER A 212 " =    1.094
peak=    3.541 closest distance to " NH2BARG A 145 " =    2.111
peak=    3.527 closest distance to " O   HOH Z 291 " =    1.615
peak=    3.526 closest distance to " CG2 ILE A  20 " =    1.331
peak=    3.513 closest distance to " OD2 ASP A 286 " =    2.859
peak=    3.512 closest distance to " O   HOH Z 368 " =    3.626
peak=    3.508 closest distance to " CG  MET A 185 " =    1.129
peak=    3.503 closest distance to " CB  ARG A 139 " =    1.004
peak=    3.500 closest distance to " CB  ASN A 142 " =    1.110
peak=    3.490 closest distance to " CB  TRP A 179 " =    1.411
peak=    3.488 closest distance to " CD1 ILE A 106 " =    0.755
peak=    3.487 closest distance to " CA  THR A 221 " =    0.986
peak=    3.485 closest distance to " CB  MET A  47 " =    0.978
peak=    3.482 closest distance to " O   HOH Z 411 " =    3.899
peak=    3.478 closest distance to " CA  ALA A  21 " =    1.178
peak=    3.475 closest distance to " O   HOH Z 406 " =    1.558
peak=    3.475 closest distance to " O   HOH Z 344 " =    3.204
peak=    3.475 closest distance to " OG  SER A  22 " =    2.684
peak=    3.472 closest distance to " CZ2 TRP A 179 " =    1.756
peak=    3.471 closest distance to " CA  VAL A 125 " =    1.125
peak=    3.463 closest distance to " CA  MET A 105 " =    1.047
peak=    3.462 closest distance to " O   HOH Z  10 " =    1.748
peak=    3.455 closest distance to " CE1 TYR A 186 " =    1.348
peak=    3.455 closest distance to " CB  ALA A 291 " =    1.275
peak=    3.451 closest distance to " CG1 ILE A  33 " =    1.200
peak=    3.448 closest distance to " O   HOH Z 166 " =    3.954
peak=    3.443 closest distance to " CB  TYR A 116 " =    0.743
peak=    3.434 closest distance to " O   HOH Z 353 " =    2.691
peak=    3.432 closest distance to " O   HOH Z 248 " =    1.598
peak=    3.429 closest distance to " CA  TYR A 116 " =    1.406
peak=    3.423 closest distance to " CA  ALA A 291 " =    0.808
peak=    3.421 closest distance to " CB  TYR A 169 " =    0.740
peak=    3.420 closest distance to " CB  HIS A 108 " =    0.805
peak=    3.414 closest distance to " CB  ALA A 114 " =    1.085
peak=    3.414 closest distance to " O   HOH Z 133 " =    2.543
peak=    3.414 closest distance to " CA  ASN A 217 " =    1.195
peak=    3.409 closest distance to " CG1 VAL A 153 " =    1.000
peak=    3.405 closest distance to " O   HOH Z 383 " =    2.033
peak=    3.404 closest distance to " O   HOH Z  59 " =    2.228
peak=    3.402 closest distance to " O   HOH Z 421 " =    1.866
peak=    3.402 closest distance to " O   HOH Z 250 " =    2.020
peak=    3.401 closest distance to " CA  THR A 264 " =    0.903
peak=    3.401 closest distance to " O   HOH Z 108 " =    2.860
peak=    3.399 closest distance to " O   HOH Z 359 " =    1.426
peak=    3.386 closest distance to " O   THR A 220 " =    1.279
peak=    3.384 closest distance to " O   ALA A 165 " =    1.538
peak=    3.383 closest distance to " O   HOH Z 299 " =    4.555
peak=    3.379 closest distance to " CB  SER A 141 " =    1.016
peak=    3.379 closest distance to " O   HOH Z 365 " =    2.864
peak=    3.377 closest distance to " O   HOH Z 419 " =    1.996
peak=    3.373 closest distance to " CD2 LEU A 297 " =    0.867
peak=    3.370 closest distance to " CG2 THR A 221 " =    1.123
peak=    3.367 closest distance to " N   TYR A 116 " =    1.592
peak=    3.366 closest distance to " N   PHE A 130 " =    1.253
peak=    3.356 closest distance to " CG2 ILE A 234 " =    0.810
peak=    3.354 closest distance to " O   HOH Z 213 " =    1.835
peak=    3.344 closest distance to " O   HOH Z 337 " =    3.653
peak=    3.343 closest distance to " NE2 HIS A 207 " =    1.276
peak=    3.342 closest distance to " O   HOH Z 258 " =    1.697
peak=    3.342 closest distance to " CA  ALA A  84 " =    1.215
peak=    3.338 closest distance to " CA  MET A  40 " =    1.158
peak=    3.336 closest distance to " O   HOH Z  66 " =    2.187
peak=    3.334 closest distance to " O   HOH Z 407 " =    2.609
peak=    3.333 closest distance to " CG  GLN A  11 " =    1.516
peak=    3.332 closest distance to " O   HOH Z  88 " =    3.391
peak=    3.332 closest distance to " O   HOH Z 426 " =    1.659
peak=    3.328 closest distance to " O   HOH Z 273 " =    2.901
peak=    3.328 closest distance to " CA  SER A  87 " =    1.063
peak=    3.326 closest distance to " CG2 VAL A 197 " =    1.094
peak=    3.322 closest distance to " O   HOH Z  21 " =    1.807
peak=    3.321 closest distance to " O   ASN A  74 " =    1.540
peak=    3.321 closest distance to " N   ASN A 127 " =    1.264
peak=    3.315 closest distance to " CB  PHE A 204 " =    0.701
peak=    3.312 closest distance to " CB  ALA A 242 " =    1.027
peak=    3.307 closest distance to " ND2 ASN A 249 " =    0.865
peak=    3.303 closest distance to " CG1 ILE A  49 " =    1.526
peak=    3.295 closest distance to " NE2 GLN A  77 " =    3.240
peak=    3.288 closest distance to " O   HOH Z 175 " =    2.148
peak=    3.288 closest distance to " CA  ALA A 158 " =    1.315
peak=    3.287 closest distance to " CA  ASP A 162 " =    1.038
peak=    3.284 closest distance to " O   HOH Z  80 " =    1.586
peak=    3.282 closest distance to " CG  GLU A  37 " =    0.886
peak=    3.279 closest distance to " O   TRP A 274 " =    1.887
peak=    3.274 closest distance to " O   HOH Z 417 " =    3.282
peak=    3.273 closest distance to " CB  ASN A 110 " =    1.152
peak=    3.269 closest distance to " O   HOH Z 132 " =    2.688
peak=    3.267 closest distance to " N   GLY A  98 " =    1.109
peak=    3.266 closest distance to " CZ  PHE A  38 " =    1.272
peak=    3.266 closest distance to " CB  ALA A  34 " =    0.990
peak=    3.261 closest distance to " O   HOH Z 294 " =    1.531
peak=    3.261 closest distance to " CB  ASP A 298 " =    1.176
peak=    3.260 closest distance to " CB  ASN A 215 " =    1.182
peak=    3.259 closest distance to " CB  SER A  62 " =    0.843
peak=    3.257 closest distance to " O   THR A 251 " =    1.164
peak=    3.257 closest distance to " CB  GLN A 103 " =    0.845
peak=    3.257 closest distance to " OG BSER A  99 " =    2.275
peak=    3.254 closest distance to " CG  LEU A 167 " =    1.251
peak=    3.248 closest distance to " O   HOH Z 171 " =    2.051
peak=    3.248 closest distance to " O   HOH Z 234 " =    1.944
peak=    3.248 closest distance to " CA  ASN A 252 " =    1.945
peak=    3.241 closest distance to " CB  GLN A  89 " =    1.314
peak=    3.238 closest distance to " O   HOH Z 285 " =    2.732
peak=    3.237 closest distance to " O   ASP A 124 " =    1.125
peak=    3.233 closest distance to " O   HOH Z 391 " =    2.906
peak=    3.232 closest distance to " CB  ALA A 104 " =    0.708
peak=    3.230 closest distance to " CA  LYS A 117 " =    1.247
peak=    3.227 closest distance to " O   HOH Z 285 " =    1.626
peak=    3.225 closest distance to " CA  ASN A 176 " =    1.269
peak=    3.223 closest distance to " CB  ALA A 248 " =    0.898
peak=    3.217 closest distance to " O   HOH Z  66 " =    2.237
peak=    3.212 closest distance to " NZ  LYS A  48 " =    1.259
peak=    3.210 closest distance to " CB  ALA A   1 " =    4.924
peak=    3.210 closest distance to " CD  ARG A  66 " =    2.421
peak=    3.208 closest distance to " O   HOH Z 128 " =    2.315
peak=    3.205 closest distance to " O   HOH Z 422 " =    2.675
peak=    3.204 closest distance to " O   HOH Z  88 " =    1.926
peak=    3.202 closest distance to " N   ASN A  39 " =    1.292
peak=    3.199 closest distance to " O   HOH Z 173 " =    1.873
peak=    3.197 closest distance to " O   HOH Z 409 " =    3.285
peak=    3.189 closest distance to " O   HOH Z 411 " =    1.737
peak=    3.188 closest distance to " CG2 THR A 220 " =    0.896
peak=    3.185 closest distance to " CD1AILE A 234 " =    0.897
peak=    3.183 closest distance to " CB  MET A  40 " =    0.777
peak=    3.182 closest distance to " N   VAL A 126 " =    1.373
peak=    3.179 closest distance to " O   HOH Z 193 " =    1.710
peak=    3.178 closest distance to " CG  MET A 185 " =    1.002
peak=    3.177 closest distance to " O   HOH Z 188 " =    2.064
peak=    3.177 closest distance to " O   HOH Z 132 " =    3.146
peak=    3.176 closest distance to " CE  LYS A  48 " =    1.055
peak=    3.169 closest distance to " OH  TYR A 116 " =    1.059
peak=    3.169 closest distance to " CB  ALA A   9 " =    1.520
peak=    3.169 closest distance to " CA  ILE A 234 " =    0.957
peak=    3.167 closest distance to " CA  ALA A 154 " =    0.968
peak=    3.164 closest distance to " C   TYR A 214 " =    1.477
peak=    3.162 closest distance to " O   HOH Z 329 " =    4.016
peak=    3.156 closest distance to " O   HOH Z  62 " =    2.175
peak=    3.156 closest distance to " CG  LYS A  76 " =    0.970
peak=    3.151 closest distance to " ND1 HIS A  81 " =    1.622
peak=    3.150 closest distance to " CD  LYS A  76 " =    1.977
peak=    3.149 closest distance to " O   HOH Z  88 " =    2.609
peak=    3.145 closest distance to " O   HOH Z 345 " =    3.255
peak=    3.141 closest distance to " O   HOH Z 327 " =    1.598
peak=    3.140 closest distance to " CB  ALA A 227 " =    1.069
peak=    3.139 closest distance to " ND1 HIS A  86 " =    1.698
peak=    3.136 closest distance to " CA  ASP A 140 " =    1.175
peak=    3.129 closest distance to " N   ASP A 162 " =    1.198
peak=    3.122 closest distance to " CD  LYS A 119 " =    1.362
peak=    3.119 closest distance to " CA  ALA A 233 " =    1.453
peak=    3.113 closest distance to " CG BARG A 275 " =    1.357
peak=    3.113 closest distance to " CB  GLN A 205 " =    1.104
peak=    3.109 closest distance to " CA  ASP A 191 " =    0.866
peak=    3.106 closest distance to " CA  ARG A 159 " =    1.245
peak=    3.104 closest distance to " O   HOH Z 384 " =    2.995
peak=    3.099 closest distance to " O   HOH Z 298 " =    2.498
peak=    3.098 closest distance to " CB  ASN A 224 " =    0.980
peak=    3.095 closest distance to " O   HOH Z  88 " =    2.788
peak=    3.093 closest distance to " O   HOH Z 116 " =    1.816
peak=    3.087 closest distance to " CB  VAL A 126 " =    1.127
peak=    3.081 closest distance to " CA  LEU A 282 " =    1.049
peak=    3.054 closest distance to " CA  THR A 221 " =    1.456
peak=    3.029 closest distance to " CE ALYS A 290 " =    1.181
peak=    3.022 closest distance to " N   SER A 135 " =    1.281
peak=    3.008 closest distance to " O   SER A 164 " =    1.182

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.792 - 5.727
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 204
   mapped sites are within: 0.792 - 5.727

peak=   -4.693 closest distance to " O   HOH Z 266 " =    5.329
peak=   -4.650 closest distance to " CD  GLN A  58 " =    0.981
peak=   -4.524 closest distance to " CG1 VAL A 112 " =    2.634
peak=   -4.491 closest distance to " CD  ARG A  14 " =    3.518
peak=   -4.419 closest distance to " CB  PRO A 243 " =    2.643
peak=   -4.403 closest distance to " CD  ARG A 156 " =    2.054
peak=   -4.380 closest distance to " O   VAL A  67 " =    2.762
peak=   -4.377 closest distance to " O   HOH Z 231 " =    2.224
peak=   -4.362 closest distance to " C   HIS A 108 " =    1.089
peak=   -4.313 closest distance to " OG BSER A 134 " =    1.230
peak=   -4.216 closest distance to " CG  GLN A 223 " =    2.023
peak=   -4.152 closest distance to " CG1 VAL A 112 " =    2.830
peak=   -4.103 closest distance to " CB  ALA A 161 " =    2.564
peak=   -4.099 closest distance to " O   HOH Z 377 " =    2.124
peak=   -4.081 closest distance to " O   HOH Z 198 " =    1.970
peak=   -4.040 closest distance to " CD2 PHE A 192 " =    2.021
peak=   -4.003 closest distance to " N   ALA A  43 " =    2.650
peak=   -3.989 closest distance to " O   HOH Z  73 " =    2.297
peak=   -3.944 closest distance to " ND2 ASN A  45 " =    1.827
peak=   -3.939 closest distance to " O   HOH Z 196 " =    1.994
peak=   -3.934 closest distance to " OG  SER A  97 " =    2.251
peak=   -3.926 closest distance to " CZ3 TRP A 179 " =    1.181
peak=   -3.894 closest distance to " O   HOH Z  10 " =    1.498
peak=   -3.886 closest distance to " O   HOH Z 372 " =    2.340
peak=   -3.846 closest distance to " CB  ASP A 132 " =    2.307
peak=   -3.828 closest distance to " CE2 TYR A  30 " =    2.721
peak=   -3.825 closest distance to " O   HOH Z 114 " =    3.173
peak=   -3.824 closest distance to " CA  VAL A  67 " =    2.928
peak=   -3.818 closest distance to " CD1 LEU A 101 " =    2.406
peak=   -3.816 closest distance to " CA  ASP A 298 " =    1.058
peak=   -3.804 closest distance to " CE2 PHE A  61 " =    2.613
peak=   -3.789 closest distance to " OD1 ASN A 148 " =    1.487
peak=   -3.781 closest distance to " CE  MET A 105 " =    2.477
peak=   -3.744 closest distance to " CB  ALA A 291 " =    2.412
peak=   -3.732 closest distance to " CB  ASN A  39 " =    2.391
peak=   -3.730 closest distance to " CG1 VAL A 265 " =    2.348
peak=   -3.730 closest distance to " OXT GLY A 302 " =    2.863
peak=   -3.723 closest distance to " O   HOH Z 394 " =    1.496
peak=   -3.721 closest distance to " O   HOH Z 290 " =    1.346
peak=   -3.719 closest distance to " O   PRO A 198 " =    1.300
peak=   -3.719 closest distance to " O   HOH Z 389 " =    1.862
peak=   -3.705 closest distance to " NH2AARG A 275 " =    5.267
peak=   -3.702 closest distance to " O   PRO A 163 " =    2.093
peak=   -3.697 closest distance to " CB  ALA A 291 " =    2.289
peak=   -3.696 closest distance to " NE2 GLN A  88 " =    1.901
peak=   -3.690 closest distance to " O   HOH Z 407 " =    3.155
peak=   -3.650 closest distance to " CD1 PHE A  59 " =    1.971
peak=   -3.643 closest distance to " CA  GLY A 203 " =    2.367
peak=   -3.640 closest distance to " ND2 ASN A 249 " =    2.397
peak=   -3.636 closest distance to " O   HOH Z 126 " =    1.907
peak=   -3.629 closest distance to " O   SER A 210 " =    2.031
peak=   -3.620 closest distance to " O   HOH Z 211 " =    1.567
peak=   -3.594 closest distance to " O   HOH Z 351 " =    1.515
peak=   -3.593 closest distance to " CD2 TYR A 293 " =    2.028
peak=   -3.588 closest distance to " CD  ARG A 139 " =    1.565
peak=   -3.573 closest distance to " OD1 ASP A 171 " =    1.629
peak=   -3.561 closest distance to " ND2 ASN A  45 " =    1.139
peak=   -3.551 closest distance to " O   HOH Z  13 " =    1.649
peak=   -3.544 closest distance to " CG1 VAL A 250 " =    2.663
peak=   -3.544 closest distance to " OD2 ASP A 191 " =    1.491
peak=   -3.544 closest distance to " O   HOH Z 353 " =    2.125
peak=   -3.542 closest distance to " O   HOH Z 311 " =    3.712
peak=   -3.541 closest distance to " O   HOH Z 313 " =    1.935
peak=   -3.541 closest distance to " NE2 GLN A 194 " =    1.861
peak=   -3.533 closest distance to " O   HOH Z  51 " =    1.709
peak=   -3.525 closest distance to " O   HOH Z 435 " =    2.877
peak=   -3.520 closest distance to " O   HOH Z 185 " =    2.352
peak=   -3.519 closest distance to " CG  ARG A  66 " =    2.480
peak=   -3.499 closest distance to " CZ  PHE A 155 " =    1.242
peak=   -3.482 closest distance to " CG1AVAL A  41 " =    2.815
peak=   -3.478 closest distance to " CG  GLU A 277 " =    1.150
peak=   -3.454 closest distance to " CB  ASP A 286 " =    1.807
peak=   -3.453 closest distance to " CB  ALA A  43 " =    2.598
peak=   -3.452 closest distance to " CZ  TYR A 169 " =    1.779
peak=   -3.449 closest distance to " O   ALA A  10 " =    1.737
peak=   -3.447 closest distance to " CG  GLN A  11 " =    1.704
peak=   -3.447 closest distance to " CE BMET A  47 " =    1.672
peak=   -3.447 closest distance to " O   HOH Z 292 " =    4.597
peak=   -3.446 closest distance to " O   HOH Z  60 " =    2.193
peak=   -3.429 closest distance to " O   HOH Z  44 " =    2.241
peak=   -3.426 closest distance to " CG  ARG A 269 " =    2.338
peak=   -3.424 closest distance to " O   HOH Z 357 " =    2.075
peak=   -3.420 closest distance to " O   HOH Z 166 " =    1.915
peak=   -3.405 closest distance to " CB  ALA A 248 " =    2.316
peak=   -3.405 closest distance to " CD1 ILE A 151 " =    2.431
peak=   -3.402 closest distance to " O   HOH Z 177 " =    1.751
peak=   -3.402 closest distance to " CG  HIS A  86 " =    1.088
peak=   -3.397 closest distance to " O   HOH Z 298 " =    1.340
peak=   -3.397 closest distance to " CG  ASP A 231 " =    0.792
peak=   -3.396 closest distance to " NH2 ARG A  79 " =    1.540
peak=   -3.396 closest distance to " OD2 ASP A 171 " =    2.488
peak=   -3.396 closest distance to " O   HOH Z 102 " =    1.591
peak=   -3.391 closest distance to " O   PHE A 218 " =    1.595
peak=   -3.389 closest distance to " O   HOH Z 253 " =    4.013
peak=   -3.368 closest distance to " O   HOH Z 295 " =    1.645
peak=   -3.361 closest distance to " CB  PHE A 208 " =    2.283
peak=   -3.359 closest distance to " O   ALA A  34 " =    2.465
peak=   -3.346 closest distance to " OD1 ASN A 187 " =    1.625
peak=   -3.343 closest distance to " CA  SER A  62 " =    2.696
peak=   -3.342 closest distance to " O   VAL A 189 " =    2.630
peak=   -3.340 closest distance to " CE2 PHE A 218 " =    2.437
peak=   -3.333 closest distance to " CA  GLY A 241 " =    3.255
peak=   -3.328 closest distance to " O   HOH Z   6 " =    1.404
peak=   -3.327 closest distance to " O   HOH Z 134 " =    2.942
peak=   -3.323 closest distance to " C   LEU A 143 " =    1.011
peak=   -3.323 closest distance to " CD1 ILE A 239 " =    2.261
peak=   -3.317 closest distance to " CD  ARG A 195 " =    5.202
peak=   -3.311 closest distance to " NE2 GLN A 278 " =    1.764
peak=   -3.304 closest distance to " C   MET A 188 " =    1.425
peak=   -3.303 closest distance to " O   HOH Z  38 " =    1.502
peak=   -3.301 closest distance to " CB  TRP A  85 " =    2.577
peak=   -3.300 closest distance to " O   HOH Z 243 " =    1.983
peak=   -3.299 closest distance to " NH2BARG A 275 " =    2.094
peak=   -3.297 closest distance to " CG2 ILE A  49 " =    2.750
peak=   -3.297 closest distance to " SD  MET A 188 " =    2.111
peak=   -3.296 closest distance to " N   ALA A 248 " =    1.657
peak=   -3.296 closest distance to " CG1 VAL A 125 " =    1.910
peak=   -3.290 closest distance to " ND2 ASN A 187 " =    1.555
peak=   -3.284 closest distance to " O   HOH Z 421 " =    3.219
peak=   -3.281 closest distance to " O   HOH Z  11 " =    1.726
peak=   -3.280 closest distance to " O   HOH Z  37 " =    1.732
peak=   -3.272 closest distance to " CG2 VAL A 189 " =    2.152
peak=   -3.271 closest distance to " CB  ALA A 248 " =    2.197
peak=   -3.271 closest distance to " N   THR A 157 " =    1.566
peak=   -3.268 closest distance to " O   HOH Z 426 " =    1.594
peak=   -3.265 closest distance to " CB  TYR A  15 " =    2.167
peak=   -3.260 closest distance to " OG BSER A 134 " =    1.811
peak=   -3.260 closest distance to " O   HOH Z 123 " =    2.337
peak=   -3.260 closest distance to " O   LEU A 167 " =    1.500
peak=   -3.259 closest distance to " O   LEU A 101 " =    2.182
peak=   -3.250 closest distance to " CE3 TRP A 150 " =    2.210
peak=   -3.248 closest distance to " CB  PRO A 163 " =    2.446
peak=   -3.248 closest distance to " CG  PHE A 283 " =    2.573
peak=   -3.240 closest distance to " CG1 VAL A  67 " =    3.055
peak=   -3.240 closest distance to " O   HOH Z 322 " =    1.287
peak=   -3.239 closest distance to " OD2 ASP A  50 " =    2.093
peak=   -3.234 closest distance to " O   HOH Z  71 " =    2.181
peak=   -3.232 closest distance to " O   HOH Z 191 " =    5.727
peak=   -3.230 closest distance to " CG  LEU A  83 " =    1.974
peak=   -3.230 closest distance to " O   VAL A 189 " =    1.591
peak=   -3.229 closest distance to " O   GLN A 240 " =    2.459
peak=   -3.228 closest distance to " CD  GLU A 236 " =    1.057
peak=   -3.226 closest distance to " NH2 ARG A 159 " =    2.380
peak=   -3.217 closest distance to " N   ALA A 226 " =    2.073
peak=   -3.213 closest distance to " O   SER A 135 " =    1.477
peak=   -3.208 closest distance to " N   THR A  52 " =    1.680
peak=   -3.205 closest distance to " SG ACYS A 201 " =    1.931
peak=   -3.204 closest distance to " CD2 PHE A 225 " =    1.137
peak=   -3.203 closest distance to " O   HOH Z  43 " =    1.620
peak=   -3.201 closest distance to " O   HOH Z 414 " =    1.554
peak=   -3.197 closest distance to " C   SER A 206 " =    1.491
peak=   -3.197 closest distance to " O   HOH Z 198 " =    1.497
peak=   -3.194 closest distance to " O   HOH Z 317 " =    1.523
peak=   -3.192 closest distance to " OE1 GLN A  88 " =    1.146
peak=   -3.189 closest distance to " C   ALA A 158 " =    1.322
peak=   -3.183 closest distance to " O   PRO A  90 " =    1.817
peak=   -3.182 closest distance to " CG  TRP A 266 " =    1.941
peak=   -3.182 closest distance to " CD  PRO A 213 " =    2.180
peak=   -3.182 closest distance to " CD1 LEU A  83 " =    2.616
peak=   -3.175 closest distance to " CG1 VAL A 197 " =    2.305
peak=   -3.174 closest distance to " OH  TYR A 247 " =    1.901
peak=   -3.174 closest distance to " CD2 LEU A 237 " =    2.752
peak=   -3.171 closest distance to " O   HOH Z 322 " =    1.710
peak=   -3.170 closest distance to " NH1 ARG A  36 " =    2.037
peak=   -3.168 closest distance to " OG  SER A  62 " =    1.786
peak=   -3.168 closest distance to " O   GLY A 211 " =    1.403
peak=   -3.167 closest distance to " CD1 ILE A 199 " =    2.522
peak=   -3.165 closest distance to " O   HOH Z  76 " =    1.954
peak=   -3.164 closest distance to " O   SER A  95 " =    1.642
peak=   -3.162 closest distance to " CB  PHE A  16 " =    2.608
peak=   -3.161 closest distance to " CD1 LEU A   5 " =    2.494
peak=   -3.156 closest distance to " O   HOH Z 262 " =    2.888
peak=   -3.154 closest distance to " ND2BASN A 224 " =    1.786
peak=   -3.153 closest distance to " O   ARG A  24 " =    2.127
peak=   -3.151 closest distance to " CG  PRO A 163 " =    2.590
peak=   -3.150 closest distance to " CD2 HIS A 207 " =    2.416
peak=   -3.146 closest distance to " O   HOH Z  52 " =    1.422
peak=   -3.146 closest distance to " CA  GLY A 241 " =    2.345
peak=   -3.144 closest distance to " O   GLY A  17 " =    1.111
peak=   -3.140 closest distance to " OD2 ASP A 171 " =    1.817
peak=   -3.139 closest distance to " O   HOH Z 171 " =    1.944
peak=   -3.138 closest distance to " O   ILE A 106 " =    1.938
peak=   -3.136 closest distance to " O   HOH Z 166 " =    1.592
peak=   -3.133 closest distance to " O   ALA A 161 " =    1.779
peak=   -3.129 closest distance to " CA  GLY A 133 " =    2.325
peak=   -3.127 closest distance to " O   HOH Z  85 " =    2.215
peak=   -3.119 closest distance to " O   HOH Z 393 " =    1.343
peak=   -3.113 closest distance to " NH1 ARG A 195 " =    2.611
peak=   -3.111 closest distance to " CG2 THR A 221 " =    2.289
peak=   -3.110 closest distance to " CE3 TRP A 274 " =    2.512
peak=   -3.109 closest distance to " ND2 ASN A  60 " =    1.318
peak=   -3.108 closest distance to " OE2 GLU A 152 " =    1.251
peak=   -3.093 closest distance to " O   PRO A 198 " =    1.330
peak=   -3.090 closest distance to " OE2 GLU A   2 " =    1.845
peak=   -3.069 closest distance to " O   HOH Z 193 " =    1.810
peak=   -3.067 closest distance to " O   HOH Z 234 " =    4.215
peak=   -3.061 closest distance to " CD1 TRP A  70 " =    1.081
peak=   -3.051 closest distance to " O   HOH Z 353 " =    2.117
peak=   -3.047 closest distance to " CD1 TYR A 247 " =    2.741
peak=   -3.040 closest distance to " CD1 LEU A 228 " =    2.250
peak=   -3.018 closest distance to " O   HOH Z 236 " =    1.526
peak=   -3.011 closest distance to " O   HOH Z 350 " =    1.860
peak=   -3.001 closest distance to " CD1 LEU A 255 " =    2.693

================= 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    :  0.2575 0.2444   5.837579e+00   5.795338e+00
   1_bss:  0.2403 0.2282   5.800770e+00   5.751325e+00
   1_xyz:  0.1441 0.1627   5.304436e+00   5.407671e+00
   1_adp:  0.1358 0.1613   5.256226e+00   5.408172e+00
   1_occ:  0.1352 0.1611   5.254019e+00   5.407701e+00
   2_bss:  0.1348 0.1599   5.250546e+00   5.400744e+00
   2_xyz:  0.1218 0.1496   5.167636e+00   5.339346e+00
   2_adp:  0.1153 0.1526   5.145166e+00   5.357666e+00
   2_occ:  0.1152 0.1524   5.144944e+00   5.357510e+00
   3_bss:  0.1150 0.1523   5.144451e+00   5.357173e+00
   3_xyz:  0.1141 0.1561   5.149817e+00   5.376829e+00
   3_adp:  0.1149 0.1547   5.149653e+00   5.371905e+00
   3_occ:  0.1148 0.1547   5.149642e+00   5.372201e+00
   4_bss:  0.1147 0.1547   5.149779e+00   5.372560e+00
   4_xyz:  0.1132 0.1547   5.143019e+00   5.373923e+00
   4_adp:  0.1145 0.1545   5.148323e+00   5.373040e+00
   4_occ:  0.1144 0.1546   5.148510e+00   5.373525e+00
   5_bss:  0.1144 0.1546   5.148512e+00   5.373535e+00
   5_xyz:  0.1102 0.1547   5.127755e+00   5.369988e+00
   5_adp:  0.1084 0.1558   5.122223e+00   5.375184e+00
   5_occ:  0.1084 0.1558   5.122292e+00   5.375367e+00
   5_bss:  0.1082 0.1557   5.122283e+00   5.375267e+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:  0.318  55.606  -3.384  -1.820   0.545  -0.000   0.000   0.000
   1_xyz:  0.318  55.606  -3.384  -1.820   0.545  -0.000   0.000   0.000
   1_adp:  0.318  55.606  -3.384  -1.820   0.545  -0.000   0.000   0.000
   1_occ:  0.318  55.606  -3.384  -1.820   0.545  -0.000   0.000   0.000
   2_bss:  0.330  60.156  -3.249  -2.389  -0.891  -0.000  -0.000  -0.000
   2_xyz:  0.330  60.156  -3.249  -2.389  -0.891  -0.000  -0.000  -0.000
   2_adp:  0.330  60.156  -3.249  -2.389  -0.891  -0.000  -0.000  -0.000
   2_occ:  0.330  60.156  -3.249  -2.389  -0.891  -0.000  -0.000  -0.000
   3_bss:  0.330  60.156  -2.727  -2.095  -0.831  -0.000  -0.000  -0.000
   3_xyz:  0.330  60.156  -2.727  -2.095  -0.831  -0.000  -0.000  -0.000
   3_adp:  0.330  60.156  -2.727  -2.095  -0.831  -0.000  -0.000  -0.000
   3_occ:  0.330  60.156  -2.727  -2.095  -0.831  -0.000  -0.000  -0.000
   4_bss:  0.324  55.453  -2.509  -1.954  -0.726  -0.000  -0.000  -0.000
   4_xyz:  0.324  55.453  -2.509  -1.954  -0.726  -0.000  -0.000  -0.000
   4_adp:  0.324  55.453  -2.509  -1.954  -0.726  -0.000  -0.000  -0.000
   4_occ:  0.324  55.453  -2.509  -1.954  -0.726  -0.000  -0.000  -0.000
   5_bss:  0.324  55.453  -2.440  -1.916  -0.684  -0.000  -0.000  -0.000
   5_xyz:  0.324  55.453  -2.440  -1.916  -0.684  -0.000  -0.000  -0.000
   5_adp:  0.324  55.453  -2.440  -1.916  -0.684  -0.000  -0.000  -0.000
   5_occ:  0.324  55.453  -2.440  -1.916  -0.684  -0.000  -0.000  -0.000
   5_bss:  0.321  55.934  -2.114  -1.621  -0.416  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  23.332 0.8330  0.9779    16486.552
   1_bss:  21.992 0.8448  0.9393    13700.699
   1_xyz:  14.361 0.9127  0.9888     6642.257
   1_adp:  14.381 0.9121  0.9850     6602.508
   1_occ:  14.370 0.9122  0.9846     6588.293
   2_bss:  14.197 0.9136  0.9647     6517.893
   2_xyz:  12.918 0.9239  0.9668     5745.893
   2_adp:  13.298 0.9209  0.9595     5861.626
   2_occ:  13.295 0.9209  0.9593     5858.554
   3_bss:  13.288 0.9210  0.9697     5858.849
   3_xyz:  13.602 0.9187  0.9692     6138.112
   3_adp:  13.481 0.9197  0.9640     6087.018
   3_occ:  13.490 0.9196  0.9639     6092.060
   4_bss:  13.498 0.9195  0.9692     6095.890
   4_xyz:  13.536 0.9192  0.9693     6125.649
   4_adp:  13.499 0.9195  0.9649     6134.410
   4_occ:  13.511 0.9194  0.9648     6140.617
   5_bss:  13.512 0.9194  0.9666     6141.062
   5_xyz:  13.456 0.9197  0.9676     6134.515
   5_adp:  13.597 0.9186  0.9607     6155.256
   5_occ:  13.599 0.9186  0.9606     6157.245
   5_bss:  13.601 0.9186  0.9709     6157.343
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6117e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6117e-01
   1_xyz:   1.012  0.008  0.072 15.009  0.004  4.119   6.0551e-02
   1_adp:   1.012  0.008  0.072 15.009  0.004  4.119   6.0551e-02
   1_occ:   1.012  0.008  0.072 15.009  0.004  4.119   6.0551e-02
   2_bss:   1.012  0.008  0.072 15.009  0.004  4.119   6.0551e-02
   2_xyz:   0.949  0.007  0.074 14.540  0.004  4.124   5.4911e-02
   2_adp:   0.949  0.007  0.074 14.540  0.004  4.124   5.4911e-02
   2_occ:   0.949  0.007  0.074 14.540  0.004  4.124   5.4911e-02
   3_bss:   0.949  0.007  0.074 14.540  0.004  4.124   5.4911e-02
   3_xyz:   0.897  0.006  0.070 14.371  0.003  4.121   4.9572e-02
   3_adp:   0.897  0.006  0.070 14.371  0.003  4.121   4.9572e-02
   3_occ:   0.897  0.006  0.070 14.371  0.003  4.121   4.9572e-02
   4_bss:   0.897  0.006  0.070 14.371  0.003  4.121   4.9572e-02
   4_xyz:   0.914  0.006  0.072 14.334  0.003  4.122   5.1275e-02
   4_adp:   0.914  0.006  0.072 14.334  0.003  4.122   5.1275e-02
   4_occ:   0.914  0.006  0.072 14.334  0.003  4.122   5.1275e-02
   5_bss:   0.914  0.006  0.072 14.334  0.003  4.122   5.1275e-02
   5_xyz:   1.038  0.009  0.081 14.602  0.004  4.125   6.5904e-02
   5_adp:   1.038  0.009  0.081 14.602  0.004  4.125   6.5904e-02
   5_occ:   1.038  0.009  0.081 14.602  0.004  4.125   6.5904e-02
   5_bss:   1.038  0.009  0.081 14.602  0.004  4.125   6.5904e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4241e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4241e-01
   1_xyz:   7.769  0.047  0.241 81.858  0.034  2.340   6.7159e-02
   1_adp:   7.769  0.047  0.241 81.858  0.034  2.340   6.7159e-02
   1_occ:   7.769  0.047  0.241 81.858  0.034  2.340   6.7159e-02
   2_bss:   7.769  0.047  0.241 81.858  0.034  2.340   6.7159e-02
   2_xyz:   6.684  0.036  0.226 83.652  0.040  2.414   3.4949e-02
   2_adp:   6.684  0.036  0.226 83.652  0.040  2.414   3.4949e-02
   2_occ:   6.684  0.036  0.226 83.652  0.040  2.414   3.4949e-02
   3_bss:   6.684  0.036  0.226 83.652  0.040  2.414   3.4949e-02
   3_xyz:   6.749  0.040  0.215 82.365  0.036  2.410   2.9828e-02
   3_adp:   6.749  0.040  0.215 82.365  0.036  2.410   2.9828e-02
   3_occ:   6.749  0.040  0.215 82.365  0.036  2.410   2.9828e-02
   4_bss:   6.749  0.040  0.215 82.365  0.036  2.410   2.9828e-02
   4_xyz:   6.662  0.040  0.224 82.850  0.034  2.404   2.9941e-02
   4_adp:   6.662  0.040  0.224 82.850  0.034  2.404   2.9941e-02
   4_occ:   6.662  0.040  0.224 82.850  0.034  2.404   2.9941e-02
   5_bss:   6.662  0.040  0.224 82.850  0.034  2.404   2.9941e-02
   5_xyz:   7.369  0.049  0.272 83.233  0.035  2.304   4.7803e-02
   5_adp:   7.369  0.049  0.272 83.233  0.035  2.304   4.7803e-02
   5_occ:   7.369  0.049  0.272 83.233  0.035  2.304   4.7803e-02
   5_bss:   7.369  0.049  0.272 83.233  0.035  2.304   4.7803e-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:  79.27   0.00  16.17  79.27   0.00  12.35  62.79   7.04  37.00
   1_occ:  79.27   0.00  16.17  79.27   0.00  12.35  62.79   7.04  37.00
   2_bss:  79.27   0.00  16.17  79.27   0.00  12.35  62.79   7.04  37.00
   2_xyz:  79.27   0.00  16.17  79.27   0.00  12.35  62.79   7.04  37.00
   2_adp:  80.74   0.83  17.12  80.74   0.83  12.91  75.18   1.83  40.04
   2_occ:  80.74   0.83  17.12  80.74   0.83  12.91  75.18   1.83  40.04
   3_bss:  80.74   0.83  17.12  80.74   0.83  12.91  75.18   1.83  40.04
   3_xyz:  80.74   0.83  17.12  80.74   0.83  12.91  75.18   1.83  40.04
   3_adp:  79.10   1.24  16.44  79.10   1.24  12.61  72.06   3.21  37.30
   3_occ:  79.10   1.24  16.44  79.10   1.24  12.61  72.06   3.21  37.30
   4_bss:  79.10   1.24  16.44  79.10   1.24  12.61  72.06   3.21  37.30
   4_xyz:  79.10   1.24  16.44  79.10   1.24  12.61  72.06   3.21  37.30
   4_adp:  76.65   1.76  16.03  76.65   1.76  12.40  69.64   4.45  35.83
   4_occ:  76.65   1.76  16.03  76.65   1.76  12.40  69.64   4.45  35.83
   5_bss:  76.65   1.76  16.03  76.65   1.76  12.40  69.64   4.45  35.83
   5_xyz:  76.65   1.76  16.03  76.65   1.76  12.40  69.64   4.45  35.83
   5_adp:  86.76   0.00  16.56  86.76   0.00  12.45  74.37   5.73  38.98
   5_occ:  86.76   0.00  16.56  86.76   0.00  12.45  74.37   5.73  38.98
   5_bss:  86.76   0.00  16.57  86.76   0.00  12.45  74.37   5.74  38.98
------------------------------------------------------------------------
 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:    0.660    0.008    0.225
   1_adp:    0.660    0.008    0.225
   1_occ:    0.660    0.008    0.225
   2_bss:    0.660    0.008    0.225
   2_xyz:    0.747    0.036    0.248
   2_adp:    0.747    0.036    0.248
   2_occ:    0.747    0.036    0.248
   3_bss:    0.747    0.036    0.248
   3_xyz:    1.013    0.030    0.263
   3_adp:    1.013    0.030    0.263
   3_occ:    1.013    0.030    0.263
   4_bss:    1.013    0.030    0.263
   4_xyz:    1.110    0.023    0.269
   4_adp:    1.110    0.023    0.269
   4_occ:    1.110    0.023    0.269
   5_bss:    1.110    0.023    0.269
   5_xyz:    1.109    0.023    0.274
   5_adp:    1.109    0.023    0.274
   5_occ:    1.109    0.023    0.274
   5_bss:    1.109    0.023    0.274
------------------------------------------------------------------------

CPU time actual refinement: 327.97


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_678/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_678/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_678/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_678/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_678/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 327.82 
  Macro-tasks:
    bulk solvent and scale       = 38.06  
    individual site refinement   = 135.65 
    weights calculation          = 29.58  
    collect and process          = 6.60   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 210.00 
  Micro-tasks:
    mask                            = 0.62   
    f_calc                          = 104.44 
    alpha_beta                      = 8.17   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 114.27 
    fmodel                         = 6.69   
    r_factors                      = 0.21   
    phase_errors                   = 11.43  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 247.21 
NUMBER OF MASK CALCS=  2
Time per interpreted Python bytecode instruction: 4.612 micro seconds
Total CPU time: 5.69 minutes
from_scatterers_fft:    657 calls, 104.06 s
gradients_fft:          602 calls, 100.25 s

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

# Date 2008-01-16 Time 05:24:22 PST -0800 (1200489862.55 s)
Start R-work = 0.2575, R-free = 0.2444 (no bulk solvent and anisotropic scale)
Final R-work = 0.1301, R-free = 0.1728 (no bulk solvent and anisotropic scale)

Start R-work = 0.2403, R-free = 0.2282
Final R-work = 0.1082, R-free = 0.1557