# Date 2008-01-16 Time 06:13:26 PST -0800 (1200492806.28 s)
#phil __OFF__

Command line arguments: "../1060.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29070
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1060

-------------------------------------------------------------------------------
  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: (71.3037, 47.6339, 85.9581, 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: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.6339, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1358 1.99124
Completeness in resolution range: 0.950645
Completeness with d_max=infinity: 0.947748

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1358
                             d_min =   1.9912

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: (71.3037, 47.6339, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1358 1.99124
Completeness in resolution range: 0.950645
Completeness with d_max=infinity: 0.947748

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1362 -  4.2611 [2166/2195]  1952   214   9.9%
  bin  2:  4.2611 -  3.3947 [2070/2089]  1862   208  10.0%
  bin  3:  3.3947 -  2.9693 [2056/2076]  1849   207  10.1%
  bin  4:  2.9693 -  2.6995 [2039/2064]  1841   198   9.7%
  bin  5:  2.6995 -  2.5069 [2031/2050]  1823   208  10.2%
  bin  6:  2.5069 -  2.3597 [2003/2049]  1802   201  10.0%
  bin  7:  2.3597 -  2.2419 [1981/2014]  1781   200  10.1%
  bin  8:  2.2419 -  2.1446 [2006/2041]  1807   199   9.9%
  bin  9:  2.1446 -  2.0622 [1988/2017]  1789   199  10.0%
  bin 10:  2.0622 -  1.9912 [1249/2011]  1124   125  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1060/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:
        1.54 -     2.21: 6
        2.21 -     2.89: 1266
        2.89 -     3.56: 4408
        3.56 -     4.23: 9093
        4.23 -     4.90: 13191
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.543 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.924 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  2.028 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  2.206 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27959 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_1060/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1060/model_refine_001.geo

CPU time processing inputs: 9.10


============================ 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 = 71.30375 47.63395 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3796   r_free= 0.3712   ksol= 0.00   Bsol= 0.00   scale= 0.934    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.161071                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.7527 0.99   1404  155 0.3077 0.3208      6.4066       6.378|
|  2:  4.7527 -  3.7919 0.99   1358  148 0.2994 0.3106      6.6025      6.5808|
|  3:  3.7919 -  3.3184 0.99   1325  153 0.3316 0.3077      6.4705      6.4465|
|  4:  3.3184 -  3.0176 0.99   1323  147 0.3627 0.3379      6.3707      6.2807|
|  5:  3.0176 -  2.8028 0.99   1308  145 0.3834 0.3911      6.2284      6.2954|
|  6:  2.8028 -  2.6384 0.98   1301  144 0.4130 0.3786      6.1627      6.0666|
|  7:  2.6384 -  2.5069 0.99   1308  143 0.4153 0.3793      6.1362      6.0807|
|  8:  2.5069 -  2.3982 0.98   1281  145 0.4341 0.4224      6.0768      6.1433|
|  9:  2.3982 -  2.3062 0.98   1293  144 0.4393 0.4108      6.0493      6.0191|
| 10:  2.3062 -  2.2269 0.98   1279  136 0.4311 0.4413      6.0142      6.0324|
| 11:  2.2269 -  2.1575 0.99   1277  145 0.4415 0.4179      5.9699      5.9906|
| 12:  2.1575 -  2.0960 0.98   1271  142 0.4415 0.4791      5.9184      5.9455|
| 13:  2.0960 -  2.0409 0.97   1275  136 0.4473 0.3961      5.8247      5.7589|
| 14:  2.0409 -  1.9912 0.49    627   76 0.4171 0.4440      5.7346      5.7194|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.7527  1404   155  0.77  28.03   0.85     0.79      49311.98|
|  2:  4.7527 -  3.7919  1358   148  0.81  25.18   0.95     0.87      58531.53|
|  3:  3.7919 -  3.3184  1325   153  0.75  31.00   0.95     0.89      60722.14|
|  4:  3.3184 -  3.0176  1323   147  0.71  35.04   0.95     0.86      54654.90|
|  5:  3.0176 -  2.8028  1308   145  0.64  40.71   0.94     0.81      47496.48|
|  6:  2.8028 -  2.6384  1301   144  0.62  42.58   0.95     0.80      41325.26|
|  7:  2.6384 -  2.5069  1308   143  0.61  42.94   0.95     0.78      38828.08|
|  8:  2.5069 -  2.3982  1281   145  0.57  46.91   0.95     0.77      38269.59|
|  9:  2.3982 -  2.3062  1293   144  0.55  48.34   0.96     0.74      37150.32|
| 10:  2.3062 -  2.2269  1279   136  0.54  48.66   0.97     0.75      35303.62|
| 11:  2.2269 -  2.1575  1277   145  0.55  48.31   0.98     0.77      31887.93|
| 12:  2.1575 -  2.0960  1271   142  0.56  47.82   0.98     0.81      29208.05|
| 13:  2.0960 -  2.0409  1275   136  0.54  48.93   0.95     0.77      24852.21|
| 14:  2.0409 -  1.9912   627    76  0.55  48.21   0.98     0.73      20474.97|
|alpha:            min =        0.73 max =            0.89 mean =         0.80|
|beta:             min =    20474.97 max =        60722.14 mean =     41562.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.63|
|phase err.(work): min =        0.00 max =           89.94 mean =        41.16|
|phase err.(test): min =        0.00 max =           89.95 mean =        41.20|
|-----------------------------------------------------------------------------|

============================== 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 = 5.248764              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.263   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.098332              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.982   (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 |  1.543 -  1.879:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.879 -  2.215:        4 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.215 -  2.550:       26 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.550 -  2.886:     1240 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.886 -  3.222:     1877 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.222 -  3.557:     2531 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.557 -  3.893:     4602 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.893 -  4.229:     4491 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.229 -  4.564:     6006 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.564 -  4.900:     7185 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.165 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.543 |       0.196 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.208)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3796   r_free= 0.3712   ksol= 0.00   Bsol= 0.00   scale= 0.934    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.161071                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3686   r_free= 0.3608   ksol= 0.29   Bsol= 37.21   scale= 0.966   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.43,3.05,-1.60,0.00,-0.00,-0.00); trace/3= 0.34                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.146062                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.676893              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.351   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.593046              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.700   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3686      final r-factor (work) = 0.2473          |
| start r-factor (free) = 0.3608      final r-factor (free) = 0.2763          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.5424 = 4.68 * 0.50 * 6.1482 + 1.00 * 0.1652                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.9527 = 4.68 * 0.50 * 5.9289 + 1.00 * 0.0884                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2473      final r-factor (work) = 0.2253          |
| start r-factor (free) = 0.2763      final r-factor (free) = 0.2794          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5222 = 0.59 * 1.00 * 5.9289 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4216 = 0.59 * 1.00 * 5.7491 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.208)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.40   17.52    None  None   None       |
|    all(noH): 2823   0      0.00    91.40   17.52    None  None   None       |
|    Sol.    : 438    0      3.53    91.40   39.84    None  None   None       |
|    Mac.    : 2385   0      0.00    83.98   13.42    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.140:  867   |   5:    45.700 -  54.840:   86        |
|      1:     9.140 -  18.280: 1110   |   6:    54.840 -  63.980:   63        |
|      2:    18.280 -  27.420:  363   |   7:    63.980 -  73.120:   36        |
|      3:    27.420 -  36.560:  165   |   8:    73.120 -  82.260:    8        |
|      4:    36.560 -  45.700:  122   |   9:    82.260 -  91.400:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2253 r_free = 0.2794             target_work(ml) = 5.754         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2250 r_free = 0.2789             target_work(ml) = 5.753         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2250   r_free= 0.2789   ksol= 0.29   Bsol= 37.21   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.43,3.05,-1.60,0.00,-0.00,-0.00); trace/3= 0.34                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.752506                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2232   r_free= 0.2764   ksol= 0.32   Bsol= 64.35   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.55,0.22,-1.54,0.00,-0.00,-0.00); trace/3= -0.96                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.748696                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.726717              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.351   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.297184              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.836  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2232      final r-factor (work) = 0.1541          |
| start r-factor (free) = 0.2764      final r-factor (free) = 0.1956          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.5582 = 5.73 * 0.50 * 5.7519 + 1.00 * 0.0884                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.1188 = 5.73 * 0.50 * 5.6043 + 1.00 * 0.0717                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1541      final r-factor (work) = 0.1384          |
| start r-factor (free) = 0.1956      final r-factor (free) = 0.1785          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6776 = 0.30 * 1.00 * 5.6043 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6002 = 0.30 * 1.00 * 5.3537 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.208)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.56    87.97   17.11    None  None   None       |
|    all(noH): 2823   0      1.56    87.97   17.11    None  None   None       |
|    Sol.    : 438    0      4.40    87.97   40.41    None  None   None       |
|    Mac.    : 2385   0      1.56    87.02   12.83    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:     1.562 -  10.203: 1109   |   5:    44.764 -  53.404:  100        |
|      1:    10.203 -  18.843: 1016   |   6:    53.404 -  62.044:   70        |
|      2:    18.843 -  27.483:  237   |   7:    62.044 -  70.685:   36        |
|      3:    27.483 -  36.124:  131   |   8:    70.685 -  79.325:   10        |
|      4:    36.124 -  44.764:  110   |   9:    79.325 -  87.965:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1384 r_free = 0.1785             target_work(ml) = 5.309         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1381 r_free = 0.1783             target_work(ml) = 5.308         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1381   r_free= 0.1783   ksol= 0.32   Bsol= 64.35   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.55,0.22,-1.54,0.00,-0.00,-0.00); trace/3= -0.96                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.308408                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1381   r_free= 0.1782   ksol= 0.33   Bsol= 65.35   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-1.10,-1.37,-0.00,-0.00,-0.00); trace/3= -1.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.307699                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.850555              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.086  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.633012              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.256  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1381      final r-factor (work) = 0.1211          |
| start r-factor (free) = 0.1782      final r-factor (free) = 0.1638          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7050 = 2.85 * 0.50 * 5.3557 + 1.00 * 0.0717                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5524 = 2.85 * 0.50 * 5.2518 + 1.00 * 0.0671                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1211      final r-factor (work) = 0.1178          |
| start r-factor (free) = 0.1638      final r-factor (free) = 0.1632          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3337 = 0.63 * 1.00 * 5.2518 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2978 = 0.63 * 1.00 * 5.1937 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.208)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.53    91.31   17.04    None  None   None       |
|    all(noH): 2823   0      0.53    91.31   17.04    None  None   None       |
|    Sol.    : 438    0      4.92    87.74   40.90    None  None   None       |
|    Mac.    : 2385   0      0.53    91.31   12.65    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:     0.529 -   9.607: 1017   |   5:    45.918 -  54.996:  103        |
|      1:     9.607 -  18.685: 1112   |   6:    54.996 -  64.074:   76        |
|      2:    18.685 -  27.763:  231   |   7:    64.074 -  73.152:   26        |
|      3:    27.763 -  36.841:  140   |   8:    73.152 -  82.229:    9        |
|      4:    36.841 -  45.918:  104   |   9:    82.229 -  91.307:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1178 r_free = 0.1632             target_work(ml) = 5.190         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1177 r_free = 0.1632             target_work(ml) = 5.190         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1177   r_free= 0.1632   ksol= 0.33   Bsol= 65.35   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-1.10,-1.37,-0.00,-0.00,-0.00); trace/3= -1.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.190208                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1177   r_free= 0.1632   ksol= 0.33   Bsol= 65.35   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.86,-1.33,-1.18,-0.00,-0.00,-0.00); trace/3= -1.45                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.189980                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.471173              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 146.632  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.045268              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.343  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1177      final r-factor (work) = 0.1136          |
| start r-factor (free) = 0.1632      final r-factor (free) = 0.1618          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4841 = 2.47 * 0.50 * 5.1935 + 1.00 * 0.0671                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4622 = 2.47 * 0.50 * 5.1760 + 1.00 * 0.0669                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1136      final r-factor (work) = 0.1127          |
| start r-factor (free) = 0.1618      final r-factor (free) = 0.1628          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4203 = 1.05 * 1.00 * 5.1760 + 1.00 * 0.0100                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4110 = 1.05 * 1.00 * 5.1664 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.208)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.84   16.95    None  None   None       |
|    all(noH): 2823   0      0.00    99.84   16.95    None  None   None       |
|    Sol.    : 438    0      5.08    90.53   41.01    None  None   None       |
|    Mac.    : 2385   0      0.00    99.84   12.53    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.984: 1160   |   5:    49.918 -  59.901:   98        |
|      1:     9.984 -  19.967: 1030   |   6:    59.901 -  69.885:   52        |
|      2:    19.967 -  29.951:  209   |   7:    69.885 -  79.868:   18        |
|      3:    29.951 -  39.934:  136   |   8:    79.868 -  89.852:    5        |
|      4:    39.934 -  49.918:  111   |   9:    89.852 -  99.836:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1127 r_free = 0.1628             target_work(ml) = 5.170         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1127 r_free = 0.1629             target_work(ml) = 5.170         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1127   r_free= 0.1629   ksol= 0.33   Bsol= 65.35   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.86,-1.33,-1.18,-0.00,-0.00,-0.00); trace/3= -1.45                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.170160                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1128   r_free= 0.1625   ksol= 0.33   Bsol= 65.35   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.69,-1.29,-0.95,-0.00,-0.00,-0.00); trace/3= -1.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.171002                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.772131              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 160.537  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.525326              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.034  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1128      final r-factor (work) = 0.1106          |
| start r-factor (free) = 0.1625      final r-factor (free) = 0.1623          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2289 = 2.77 * 0.50 * 5.1671 + 1.00 * 0.0669                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2267 = 2.77 * 0.50 * 5.1629 + 1.00 * 0.0706                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1106      final r-factor (work) = 0.1106          |
| start r-factor (free) = 0.1623      final r-factor (free) = 0.1613          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7228 = 0.53 * 1.00 * 5.1629 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7212 = 0.53 * 1.00 * 5.1610 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.208)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.71  16.59    None  None   None       |
|    all(noH): 2823   0      0.00    101.71  16.59    None  None   None       |
|    Sol.    : 438    0      5.30    88.08   39.99    None  None   None       |
|    Mac.    : 2385   0      0.00    101.71  12.30    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.171: 1233   |   5:    50.854 -  61.025:   90        |
|      1:    10.171 -  20.342:  988   |   6:    61.025 -  71.196:   38        |
|      2:    20.342 -  30.513:  207   |   7:    71.196 -  81.367:   14        |
|      3:    30.513 -  40.684:  125   |   8:    81.367 -  91.538:    5        |
|      4:    40.684 -  50.854:  120   |   9:    91.538 - 101.709:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1106 r_free = 0.1613             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1106 r_free = 0.1613             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1106   r_free= 0.1613   ksol= 0.33   Bsol= 65.35   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.69,-1.29,-0.95,-0.00,-0.00,-0.00); trace/3= -1.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.158446                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.7527 0.99   1404  155 0.0967 0.1288      5.3703      5.5293|
|  2:  4.7527 -  3.7919 0.99   1358  148 0.0818 0.1063      5.4055       5.607|
|  3:  3.7919 -  3.3184 0.99   1325  153 0.1022 0.1497      5.4479      5.8527|
|  4:  3.3184 -  3.0176 0.99   1323  147 0.1215 0.1607      5.4609      5.6186|
|  5:  3.0176 -  2.8028 0.99   1308  145 0.1317 0.1821      5.3431      5.5477|
|  6:  2.8028 -  2.6384 0.98   1301  144 0.1250 0.1962       5.244      5.4798|
|  7:  2.6384 -  2.5069 0.99   1308  143 0.1231 0.1756      5.1733      5.4472|
|  8:  2.5069 -  2.3982 0.98   1281  145 0.1150 0.1684      5.0823      5.2944|
|  9:  2.3982 -  2.3062 0.98   1293  144 0.1157 0.1900      5.0415      5.3473|
| 10:  2.3062 -  2.2269 0.98   1279  136 0.1128 0.1862      4.9841      5.2755|
| 11:  2.2269 -  2.1575 0.99   1277  145 0.1154 0.1815      4.9558      5.3025|
| 12:  2.1575 -  2.0960 0.98   1271  142 0.1078 0.1646      4.8803      5.1116|
| 13:  2.0960 -  2.0409 0.97   1275  136 0.1179 0.1880       4.824      5.1315|
| 14:  2.0409 -  1.9912 0.49    627   76 0.1110 0.1774      4.7142      4.9631|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.7527  1404   155  0.94   9.19   0.97     0.94       7207.60|
|  2:  4.7527 -  3.7919  1358   148  0.95   7.82   1.00     0.99       8707.58|
|  3:  3.7919 -  3.3184  1325   153  0.93  11.19   1.01     1.01      10115.37|
|  4:  3.3184 -  3.0176  1323   147  0.91  14.22   1.00     0.98      10804.33|
|  5:  3.0176 -  2.8028  1308   145  0.89  16.78   0.99     0.96       8941.21|
|  6:  2.8028 -  2.6384  1301   144  0.89  17.10   0.98     0.96       7832.11|
|  7:  2.6384 -  2.5069  1308   143  0.90  15.80   0.98     0.95       6503.62|
|  8:  2.5069 -  2.3982  1281   145  0.90  16.14   0.98     0.96       5805.52|
|  9:  2.3982 -  2.3062  1293   144  0.90  15.91   0.98     0.94       5176.83|
| 10:  2.3062 -  2.2269  1279   136  0.90  16.28   0.98     0.94       4756.65|
| 11:  2.2269 -  2.1575  1277   145  0.89  16.88   0.98     0.94       4573.28|
| 12:  2.1575 -  2.0960  1271   142  0.91  15.28   0.98     0.96       4094.80|
| 13:  2.0960 -  2.0409  1275   136  0.89  17.33   0.98     0.97       3690.37|
| 14:  2.0409 -  1.9912   627    76  0.90  16.34   0.96     0.92       2919.92|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2919.92 max =        10804.33 mean =      6683.36|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.60|
|phase err.(test): min =        0.00 max =           89.80 mean =        14.05|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1105   r_free= 0.1612   ksol= 0.32   Bsol= 61.70   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.50,-1.14,-0.72,-0.00,-0.00,-0.00); trace/3= -1.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.158497                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1105   r_free= 0.1612   ksol= 0.32   Bsol= 61.70   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.50,-1.14,-0.72,-0.00,-0.00,-0.00); trace/3= -1.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.158497                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.7527 0.99   1404  155 0.0965 0.1288      5.3689      5.5286|
|  2:  4.7527 -  3.7919 0.99   1358  148 0.0817 0.1060      5.4043      5.6048|
|  3:  3.7919 -  3.3184 0.99   1325  153 0.1022 0.1497      5.4471      5.8527|
|  4:  3.3184 -  3.0176 0.99   1323  147 0.1216 0.1607      5.4614      5.6187|
|  5:  3.0176 -  2.8028 0.99   1308  145 0.1318 0.1824      5.3439      5.5485|
|  6:  2.8028 -  2.6384 0.98   1301  144 0.1251 0.1963      5.2445      5.4798|
|  7:  2.6384 -  2.5069 0.99   1308  143 0.1232 0.1756      5.1737      5.4476|
|  8:  2.5069 -  2.3982 0.98   1281  145 0.1150 0.1685      5.0827      5.2946|
|  9:  2.3982 -  2.3062 0.98   1293  144 0.1157 0.1897      5.0419      5.3471|
| 10:  2.3062 -  2.2269 0.98   1279  136 0.1128 0.1865      4.9847      5.2769|
| 11:  2.2269 -  2.1575 0.99   1277  145 0.1154 0.1815      4.9563      5.3028|
| 12:  2.1575 -  2.0960 0.98   1271  142 0.1078 0.1648      4.8807      5.1126|
| 13:  2.0960 -  2.0409 0.97   1275  136 0.1180 0.1881      4.8241      5.1315|
| 14:  2.0409 -  1.9912 0.49    627   76 0.1110 0.1771      4.7143       4.962|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.7527  1404   155  0.94   9.20   0.97     0.94       7196.74|
|  2:  4.7527 -  3.7919  1358   148  0.95   7.80   1.00     0.99       8688.05|
|  3:  3.7919 -  3.3184  1325   153  0.93  11.18   1.02     1.01      10094.48|
|  4:  3.3184 -  3.0176  1323   147  0.91  14.22   1.00     0.98      10809.04|
|  5:  3.0176 -  2.8028  1308   145  0.89  16.79   0.99     0.97       8945.63|
|  6:  2.8028 -  2.6384  1301   144  0.89  17.11   0.99     0.96       7837.73|
|  7:  2.6384 -  2.5069  1308   143  0.90  15.81   0.99     0.96       6505.97|
|  8:  2.5069 -  2.3982  1281   145  0.90  16.15   0.99     0.97       5809.04|
|  9:  2.3982 -  2.3062  1293   144  0.90  15.92   0.99     0.95       5179.76|
| 10:  2.3062 -  2.2269  1279   136  0.90  16.29   0.98     0.95       4761.83|
| 11:  2.2269 -  2.1575  1277   145  0.89  16.90   0.99     0.95       4578.92|
| 12:  2.1575 -  2.0960  1271   142  0.91  15.29   0.99     0.97       4100.42|
| 13:  2.0960 -  2.0409  1275   136  0.89  17.34   0.99     0.99       3691.78|
| 14:  2.0409 -  1.9912   627    76  0.90  16.34   0.97     0.93       2918.60|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2918.60 max =        10809.04 mean =      6682.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.61|
|phase err.(test): min =        0.00 max =           89.74 mean =        14.06|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.208)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.71  16.60    None  None   None       |
|    all(noH): 2823   0      0.00    101.71  16.60    None  None   None       |
|    Sol.    : 438    0      5.30    88.08   40.00    None  None   None       |
|    Mac.    : 2385   0      0.00    101.71  12.30    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.174: 1233   |   5:    50.857 -  61.028:   90        |
|      1:    10.174 -  20.345:  988   |   6:    61.028 -  71.199:   38        |
|      2:    20.345 -  30.516:  207   |   7:    71.199 -  81.370:   14        |
|      3:    30.516 -  40.687:  125   |   8:    81.370 -  91.541:    5        |
|      4:    40.687 -  50.857:  120   |   9:    91.541 - 101.712:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 312         
Filter by distance & map next to the model:
   mapped sites are within: 0.546 - 4.659
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 305 from: 312
   mapped sites are within: 0.700 - 4.659

peak=    5.998 closest distance to " O   HOH Z 111 " =    2.184
peak=    5.556 closest distance to " CB  GLN A 223 " =    1.448
peak=    5.405 closest distance to " CG  PRO A  54 " =    1.246
peak=    5.282 closest distance to " CB  SER A  63 " =    1.264
peak=    4.796 closest distance to " CB  GLN A 183 " =    1.297
peak=    4.689 closest distance to " CB  ARG A 275 " =    0.921
peak=    4.683 closest distance to " C   PRO A 198 " =    1.502
peak=    4.628 closest distance to " O   HOH Z 232 " =    2.363
peak=    4.628 closest distance to " CG  PRO A 213 " =    1.195
peak=    4.574 closest distance to " CA  TYR A  30 " =    0.962
peak=    4.548 closest distance to " CB  PRO A  54 " =    0.835
peak=    4.436 closest distance to " CB  ARG A 190 " =    1.711
peak=    4.433 closest distance to " O   HOH Z 369 " =    2.132
peak=    4.427 closest distance to " O   HOH Z 298 " =    1.920
peak=    4.378 closest distance to " OD1 ASN A  69 " =    2.565
peak=    4.375 closest distance to " CB  GLU A 128 " =    1.149
peak=    4.361 closest distance to " CB  LEU A 228 " =    1.088
peak=    4.310 closest distance to " O   HOH Z 126 " =    1.968
peak=    4.306 closest distance to " O   HOH Z 193 " =    1.946
peak=    4.300 closest distance to " O   HOH Z 403 " =    1.726
peak=    4.299 closest distance to " O   HOH Z  15 " =    2.146
peak=    4.276 closest distance to " CB  GLU A 152 " =    1.159
peak=    4.232 closest distance to " NH2 ARG A 156 " =    1.202
peak=    4.231 closest distance to " CB  TYR A 169 " =    0.789
peak=    4.207 closest distance to " NE2 GLN A  11 " =    1.038
peak=    4.185 closest distance to " O   HOH Z  68 " =    1.954
peak=    4.156 closest distance to " CB  ASN A 148 " =    1.382
peak=    4.154 closest distance to " CZ  PHE A 218 " =    1.113
peak=    4.147 closest distance to " O   HOH Z 265 " =    2.261
peak=    4.123 closest distance to " CB  ARG A  79 " =    1.368
peak=    4.120 closest distance to " CD1 LEU A 300 " =    1.187
peak=    4.119 closest distance to " CB  GLU A 277 " =    3.704
peak=    4.103 closest distance to " O   HOH Z 234 " =    3.818
peak=    4.079 closest distance to " O   HOH Z 236 " =    1.967
peak=    4.077 closest distance to " CG1 ILE A  33 " =    1.256
peak=    4.076 closest distance to " O   MET A 105 " =    1.894
peak=    4.059 closest distance to " CG  PRO A 198 " =    1.191
peak=    4.058 closest distance to " CB  TRP A 266 " =    0.956
peak=    4.054 closest distance to " CB  VAL A 202 " =    1.584
peak=    4.049 closest distance to " O   HOH Z  40 " =    1.839
peak=    4.047 closest distance to " CA  THR A 221 " =    0.938
peak=    4.042 closest distance to " O   HOH Z 133 " =    2.343
peak=    4.034 closest distance to " O   HOH Z 427 " =    2.995
peak=    4.003 closest distance to " CG  PRO A 243 " =    1.158
peak=    3.997 closest distance to " CG2 THR A 221 " =    0.987
peak=    3.989 closest distance to " O   HOH Z 261 " =    2.001
peak=    3.979 closest distance to " O   HOH Z 303 " =    2.107
peak=    3.978 closest distance to " CB  SER A   3 " =    1.382
peak=    3.965 closest distance to " O   HOH Z  21 " =    1.782
peak=    3.952 closest distance to " O   HOH Z 214 " =    2.080
peak=    3.947 closest distance to " O   HOH Z  20 " =    1.830
peak=    3.944 closest distance to " CA  ALA A  21 " =    1.293
peak=    3.942 closest distance to " O   HOH Z 147 " =    1.811
peak=    3.942 closest distance to " O   HOH Z 412 " =    3.738
peak=    3.941 closest distance to " CB  TRP A 179 " =    1.419
peak=    3.933 closest distance to " O   HOH Z 368 " =    2.068
peak=    3.923 closest distance to " O   HOH Z 189 " =    2.441
peak=    3.921 closest distance to " O   HOH Z  78 " =    1.651
peak=    3.909 closest distance to " CD  ARG A 269 " =    0.926
peak=    3.903 closest distance to " O   HOH Z 128 " =    2.156
peak=    3.902 closest distance to " NZ  LYS A 117 " =    3.317
peak=    3.891 closest distance to " CG  PRO A  90 " =    1.157
peak=    3.860 closest distance to " O   HOH Z 142 " =    1.516
peak=    3.859 closest distance to " O   HOH Z 134 " =    1.392
peak=    3.854 closest distance to " CD2 LEU A 297 " =    0.878
peak=    3.853 closest distance to " O   SER A  87 " =    2.267
peak=    3.818 closest distance to " O   HOH Z 163 " =    1.660
peak=    3.811 closest distance to " O   HOH Z 406 " =    1.630
peak=    3.809 closest distance to " O   HOH Z 203 " =    1.919
peak=    3.809 closest distance to " O   HOH Z 423 " =    1.959
peak=    3.808 closest distance to " O   HOH Z  19 " =    2.230
peak=    3.806 closest distance to " O   HOH Z 426 " =    1.583
peak=    3.795 closest distance to " O   HOH Z 158 " =    3.033
peak=    3.791 closest distance to " CA  ARG A 195 " =    1.225
peak=    3.790 closest distance to " O   HOH Z 316 " =    3.137
peak=    3.783 closest distance to " O   HOH Z 180 " =    2.244
peak=    3.778 closest distance to " ND1 HIS A  81 " =    1.631
peak=    3.777 closest distance to " CD  ARG A 159 " =    0.838
peak=    3.766 closest distance to " O   HOH Z  97 " =    2.034
peak=    3.764 closest distance to " NH2BARG A 145 " =    2.149
peak=    3.762 closest distance to " O   HOH Z  80 " =    1.640
peak=    3.761 closest distance to " CB  ASN A 187 " =    1.284
peak=    3.760 closest distance to " CA  ALA A  51 " =    0.976
peak=    3.752 closest distance to " CA  ALA A 160 " =    0.903
peak=    3.751 closest distance to " ND2 ASN A 187 " =    1.470
peak=    3.750 closest distance to " O   HOH Z 280 " =    3.018
peak=    3.739 closest distance to " O   HOH Z 250 " =    1.492
peak=    3.736 closest distance to " CB  VAL A 265 " =    1.236
peak=    3.717 closest distance to " OD2 ASP A 286 " =    2.924
peak=    3.714 closest distance to " CB  ASP A 140 " =    0.886
peak=    3.709 closest distance to " CB  ASN A  39 " =    0.865
peak=    3.695 closest distance to " CA  PRO A  54 " =    1.354
peak=    3.689 closest distance to " CE  LYS A  76 " =    0.836
peak=    3.685 closest distance to " CA  ARG A  36 " =    1.175
peak=    3.683 closest distance to " O   HOH Z 135 " =    1.866
peak=    3.682 closest distance to " NH1AARG A 145 " =    1.192
peak=    3.679 closest distance to " O   HOH Z 368 " =    3.678
peak=    3.677 closest distance to " CD1 ILE A 106 " =    0.908
peak=    3.677 closest distance to " O   HOH Z 272 " =    1.879
peak=    3.658 closest distance to " O   HOH Z  44 " =    2.305
peak=    3.654 closest distance to " CB  TYR A 116 " =    0.937
peak=    3.648 closest distance to " O   HOH Z  61 " =    1.557
peak=    3.630 closest distance to " CA  ASN A 176 " =    1.268
peak=    3.628 closest distance to " O   HOH Z 132 " =    2.740
peak=    3.625 closest distance to " CA  MET A  40 " =    1.135
peak=    3.620 closest distance to " O   HOH Z  43 " =    1.892
peak=    3.614 closest distance to " O   HOH Z 346 " =    1.554
peak=    3.607 closest distance to " CA  THR A 264 " =    0.917
peak=    3.605 closest distance to " O   HOH Z  63 " =    1.870
peak=    3.603 closest distance to " ND2 ASN A 110 " =    1.608
peak=    3.597 closest distance to " CA  ASP A 191 " =    0.796
peak=    3.592 closest distance to " CE1 TYR A 186 " =    1.243
peak=    3.576 closest distance to " O   HOH Z 305 " =    3.792
peak=    3.572 closest distance to " O   ALA A 158 " =    1.242
peak=    3.569 closest distance to " CD BLYS A 290 " =    1.003
peak=    3.567 closest distance to " CD  ARG A  66 " =    2.457
peak=    3.564 closest distance to " CA  ASN A 215 " =    1.163
peak=    3.558 closest distance to " CB  SER A 141 " =    0.973
peak=    3.557 closest distance to " OD1 ASN A 217 " =    1.849
peak=    3.556 closest distance to " O   ALA A 165 " =    1.421
peak=    3.556 closest distance to " O   THR A 251 " =    1.218
peak=    3.553 closest distance to " O   HOH Z   1 " =    2.265
peak=    3.547 closest distance to " CB  SER A 212 " =    1.102
peak=    3.545 closest distance to " O   HOH Z  61 " =    1.562
peak=    3.540 closest distance to " O   HOH Z 193 " =    2.205
peak=    3.534 closest distance to " CD2 TRP A 179 " =    1.317
peak=    3.529 closest distance to " OG BSER A 164 " =    2.355
peak=    3.528 closest distance to " CG2 VAL A 197 " =    1.176
peak=    3.526 closest distance to " CG2 VAL A 257 " =    0.936
peak=    3.521 closest distance to " O   HOH Z 402 " =    1.458
peak=    3.520 closest distance to " CG2BVAL A  41 " =    0.845
peak=    3.518 closest distance to " CB  TYR A 169 " =    0.876
peak=    3.512 closest distance to " O   HOH Z 295 " =    1.486
peak=    3.511 closest distance to " CZ  PHE A 192 " =    0.966
peak=    3.510 closest distance to " CA  ASP A 124 " =    0.700
peak=    3.501 closest distance to " O   HOH Z  88 " =    3.573
peak=    3.495 closest distance to " O   HOH Z 197 " =    2.691
peak=    3.493 closest distance to " O   HOH Z 383 " =    2.067
peak=    3.485 closest distance to " O   HOH Z 371 " =    3.339
peak=    3.483 closest distance to " C   SER A  32 " =    1.073
peak=    3.481 closest distance to " O   HOH Z 291 " =    1.529
peak=    3.475 closest distance to " CG1BVAL A  72 " =    1.788
peak=    3.474 closest distance to " CB  PHE A  16 " =    1.030
peak=    3.473 closest distance to " O   HOH Z 126 " =    1.552
peak=    3.470 closest distance to " CD  LYS A 166 " =    1.338
peak=    3.469 closest distance to " CB  ALA A 100 " =    1.283
peak=    3.462 closest distance to " ND2 ASN A 249 " =    1.956
peak=    3.457 closest distance to " O   HOH Z  49 " =    2.360
peak=    3.455 closest distance to " O   HOH Z 411 " =    1.829
peak=    3.455 closest distance to " O   HOH Z 281 " =    4.659
peak=    3.452 closest distance to " CB  ILE A 120 " =    1.301
peak=    3.446 closest distance to " CG  GLN A  58 " =    2.708
peak=    3.446 closest distance to " CG AARG A 275 " =    1.160
peak=    3.445 closest distance to " OD2 ASP A 298 " =    3.934
peak=    3.444 closest distance to " CA  ALA A 295 " =    1.121
peak=    3.442 closest distance to " O   HOH Z  44 " =    1.743
peak=    3.440 closest distance to " NZ  LYS A 166 " =    3.110
peak=    3.435 closest distance to " CA  ASP A 162 " =    1.210
peak=    3.433 closest distance to " O   HOH Z 271 " =    3.013
peak=    3.419 closest distance to " O   HOH Z  66 " =    2.143
peak=    3.417 closest distance to " CB  SER A 216 " =    0.833
peak=    3.414 closest distance to " CG2 ILE A  20 " =    1.241
peak=    3.407 closest distance to " CG2 ILE A 120 " =    1.078
peak=    3.406 closest distance to " O   HOH Z 174 " =    2.476
peak=    3.405 closest distance to " CG  LEU A 167 " =    1.179
peak=    3.405 closest distance to " CA  ALA A 291 " =    0.881
peak=    3.403 closest distance to " OG1 THR A 294 " =    2.456
peak=    3.401 closest distance to " O   HOH Z 425 " =    1.976
peak=    3.397 closest distance to " N   ASN A  39 " =    1.389
peak=    3.397 closest distance to " N   ARG A 156 " =    1.383
peak=    3.393 closest distance to " O   HOH Z  10 " =    1.835
peak=    3.392 closest distance to " O  BHOH Z 338 " =    2.277
peak=    3.386 closest distance to " O   HOH Z 345 " =    1.688
peak=    3.386 closest distance to " O   HOH Z 391 " =    2.968
peak=    3.383 closest distance to " O   HOH Z 421 " =    1.588
peak=    3.374 closest distance to " O   HOH Z 279 " =    2.334
peak=    3.373 closest distance to " CB  ALA A 291 " =    1.313
peak=    3.372 closest distance to " OG  SER A 245 " =    1.657
peak=    3.371 closest distance to " N   ASN A 127 " =    1.259
peak=    3.365 closest distance to " CB  ARG A 139 " =    0.900
peak=    3.365 closest distance to " O   TRP A 274 " =    1.894
peak=    3.362 closest distance to " O   ASN A  74 " =    1.579
peak=    3.361 closest distance to " CB  GLN A  89 " =    1.275
peak=    3.359 closest distance to " O   HOH Z 359 " =    1.452
peak=    3.356 closest distance to " CB  GLU A  46 " =    0.980
peak=    3.354 closest distance to " O   HOH Z 171 " =    3.913
peak=    3.354 closest distance to " CA  MET A 105 " =    1.069
peak=    3.349 closest distance to " O   HOH Z 102 " =    1.269
peak=    3.345 closest distance to " NE2 GLN A  77 " =    3.416
peak=    3.340 closest distance to " ND1 HIS A  86 " =    1.822
peak=    3.333 closest distance to " O   HOH Z 245 " =    1.326
peak=    3.333 closest distance to " CA  ALA A  84 " =    1.428
peak=    3.330 closest distance to " CG1 ILE A 151 " =    1.011
peak=    3.327 closest distance to " CB  SER A  62 " =    0.746
peak=    3.325 closest distance to " O   HOH Z 299 " =    4.536
peak=    3.325 closest distance to " CB  GLN A  88 " =    1.236
peak=    3.323 closest distance to " O   HOH Z 344 " =    3.103
peak=    3.313 closest distance to " CB  ASN A 285 " =    0.874
peak=    3.311 closest distance to " CG1 VAL A 153 " =    0.997
peak=    3.310 closest distance to " NE1 TRP A 266 " =    1.372
peak=    3.307 closest distance to " CA  SER A  87 " =    1.037
peak=    3.304 closest distance to " O   HOH Z 128 " =    2.240
peak=    3.303 closest distance to " CA  GLY A 241 " =    0.740
peak=    3.302 closest distance to " NE2 HIS A 115 " =    0.965
peak=    3.302 closest distance to " O   HOH Z 247 " =    1.392
peak=    3.301 closest distance to " N   VAL A 126 " =    1.481
peak=    3.300 closest distance to " CG  LYS A  76 " =    0.991
peak=    3.299 closest distance to " O   ASN A  74 " =    2.100
peak=    3.298 closest distance to " O   HOH Z 250 " =    1.558
peak=    3.296 closest distance to " CA  LEU A  83 " =    1.472
peak=    3.292 closest distance to " O   HOH Z   6 " =    2.147
peak=    3.291 closest distance to " CG BARG A 102 " =    1.925
peak=    3.290 closest distance to " O   HOH Z 133 " =    1.667
peak=    3.289 closest distance to " O   HOH Z 374 " =    2.857
peak=    3.288 closest distance to " CB  HIS A 108 " =    0.808
peak=    3.285 closest distance to " O   HOH Z 327 " =    1.856
peak=    3.285 closest distance to " O   HOH Z 329 " =    3.746
peak=    3.283 closest distance to " CB  TRP A 150 " =    1.357
peak=    3.283 closest distance to " O   HOH Z 271 " =    2.353
peak=    3.279 closest distance to " O   HOH Z 353 " =    2.819
peak=    3.273 closest distance to " O   HOH Z 183 " =    1.496
peak=    3.273 closest distance to " CD  LYS A 119 " =    1.403
peak=    3.271 closest distance to " CB  MET A  47 " =    0.977
peak=    3.267 closest distance to " CD2 LEU A 255 " =    1.435
peak=    3.266 closest distance to " CG2 VAL A  78 " =    1.001
peak=    3.265 closest distance to " CD  ARG A  66 " =    2.456
peak=    3.264 closest distance to " O   HOH Z 392 " =    1.489
peak=    3.261 closest distance to " CD1AILE A 234 " =    0.894
peak=    3.261 closest distance to " CB  MET A 113 " =    1.844
peak=    3.261 closest distance to " CA  ALA A 158 " =    1.103
peak=    3.259 closest distance to " O   HOH Z 365 " =    2.950
peak=    3.259 closest distance to " O   HOH Z 185 " =    1.851
peak=    3.256 closest distance to " CA  ALA A 154 " =    0.992
peak=    3.254 closest distance to " O   HOH Z 141 " =    1.717
peak=    3.253 closest distance to " O   HOH Z 437 " =    1.317
peak=    3.252 closest distance to " O   HOH Z 357 " =    2.051
peak=    3.251 closest distance to " CA  VAL A 125 " =    1.114
peak=    3.246 closest distance to " O   HOH Z 425 " =    1.279
peak=    3.242 closest distance to " CB  ALA A 248 " =    0.977
peak=    3.238 closest distance to " OE1 GLN A  11 " =    1.951
peak=    3.236 closest distance to " CB  GLN A 103 " =    0.880
peak=    3.234 closest distance to " C   TYR A 214 " =    1.466
peak=    3.232 closest distance to " OG  SER A  62 " =    2.982
peak=    3.231 closest distance to " CD  ARG A 219 " =    1.028
peak=    3.229 closest distance to " CA  ASP A 140 " =    1.193
peak=    3.229 closest distance to " CB  ALA A   9 " =    1.566
peak=    3.228 closest distance to " CB  TRP A 150 " =    1.034
peak=    3.227 closest distance to " CA  ALA A 248 " =    1.187
peak=    3.222 closest distance to " O   HOH Z  59 " =    2.086
peak=    3.221 closest distance to " CG  MET A 185 " =    1.112
peak=    3.219 closest distance to " O   HOH Z 273 " =    2.879
peak=    3.219 closest distance to " O   HOH Z 227 " =    1.674
peak=    3.216 closest distance to " O   HOH Z 193 " =    1.568
peak=    3.216 closest distance to " CA  ILE A  33 " =    1.609
peak=    3.211 closest distance to " O   HOH Z 109 " =    2.808
peak=    3.210 closest distance to " O   HOH Z 313 " =    1.782
peak=    3.209 closest distance to " O   HOH Z 116 " =    1.834
peak=    3.205 closest distance to " O   HOH Z 213 " =    1.652
peak=    3.203 closest distance to " CB  LEU A  83 " =    0.811
peak=    3.202 closest distance to " CB  ARG A 259 " =    1.897
peak=    3.199 closest distance to " CG  MET A 185 " =    1.231
peak=    3.199 closest distance to " CG BARG A 275 " =    1.364
peak=    3.198 closest distance to " CG  GLU A  37 " =    0.869
peak=    3.194 closest distance to " CZ2 TRP A 179 " =    1.707
peak=    3.193 closest distance to " CB  ASN A 142 " =    1.032
peak=    3.189 closest distance to " OG  SER A  97 " =    3.549
peak=    3.187 closest distance to " O   HOH Z  97 " =    2.712
peak=    3.187 closest distance to " CA  GLU A 152 " =    0.846
peak=    3.184 closest distance to " N   ASN A 252 " =    1.307
peak=    3.179 closest distance to " CG  ARG A 219 " =    1.196
peak=    3.177 closest distance to " O   HOH Z 298 " =    2.546
peak=    3.175 closest distance to " CA  TYR A 116 " =    1.349
peak=    3.174 closest distance to " CA  MET A 188 " =    0.997
peak=    3.171 closest distance to " CB  MET A  40 " =    0.873
peak=    3.170 closest distance to " O   HOH Z 423 " =    3.259
peak=    3.168 closest distance to " O   HOH Z 387 " =    2.693
peak=    3.163 closest distance to " O   HOH Z 345 " =    3.343
peak=    3.162 closest distance to " O   HOH Z  85 " =    2.153
peak=    3.156 closest distance to " CA  ILE A 106 " =    0.835
peak=    3.155 closest distance to " O   HOH Z 234 " =    1.753
peak=    3.150 closest distance to " CB  ASN A 215 " =    1.189
peak=    3.150 closest distance to " O   HOH Z 286 " =    2.232
peak=    3.146 closest distance to " O   HOH Z 148 " =    3.209
peak=    3.146 closest distance to " CB  THR A 157 " =    1.121
peak=    3.144 closest distance to " CG ALYS A 290 " =    1.186
peak=    3.143 closest distance to " O   HOH Z 422 " =    2.688
peak=    3.139 closest distance to " CA  ALA A 233 " =    1.507
peak=    3.129 closest distance to " O   HOH Z 403 " =    1.362
peak=    3.125 closest distance to " OE1 GLU A 152 " =    0.860
peak=    3.120 closest distance to " O   HOH Z 334 " =    1.504
peak=    3.116 closest distance to " NE2 GLN A  58 " =    3.686
peak=    3.108 closest distance to " CB  SER A 273 " =    0.839
peak=    3.104 closest distance to " CB  GLU A 152 " =    1.492
peak=    3.103 closest distance to " OG  SER A  22 " =    2.810
peak=    3.103 closest distance to " O   HOH Z 227 " =    1.667
peak=    3.100 closest distance to " OD2 ASP A 200 " =    1.264
peak=    3.095 closest distance to " O   HOH Z  44 " =    3.270
peak=    3.095 closest distance to " CG2 THR A 220 " =    0.753
peak=    3.088 closest distance to " N   TYR A  15 " =    0.810
peak=    3.084 closest distance to " O   THR A 251 " =    1.849
peak=    3.054 closest distance to " CB  ALA A 104 " =    0.727
peak=    3.046 closest distance to " O   HOH Z 128 " =    1.662
peak=    3.030 closest distance to " O   GLN A 278 " =    1.547
peak=    3.029 closest distance to " CB  ARG A 138 " =    0.982
peak=    3.020 closest distance to " O   HOH Z  85 " =    1.335

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 217         
Filter by distance & map next to the model:
   mapped sites are within: 0.866 - 5.420
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 216 from: 217
   mapped sites are within: 0.866 - 5.420

peak=   -4.640 closest distance to " O   HOH Z 266 " =    4.809
peak=   -4.478 closest distance to " CD  ARG A 156 " =    2.065
peak=   -4.352 closest distance to " O   HOH Z  10 " =    1.592
peak=   -4.298 closest distance to " CB  PRO A 243 " =    2.645
peak=   -4.264 closest distance to " CG1 VAL A 250 " =    2.711
peak=   -4.189 closest distance to " O   HOH Z 372 " =    2.522
peak=   -4.057 closest distance to " O   VAL A  67 " =    2.720
peak=   -4.030 closest distance to " O   HOH Z  52 " =    1.591
peak=   -4.026 closest distance to " OG  SER A  97 " =    2.219
peak=   -4.017 closest distance to " N   ALA A  43 " =    2.645
peak=   -3.999 closest distance to " O   HOH Z 377 " =    2.020
peak=   -3.993 closest distance to " CB  ALA A 161 " =    2.667
peak=   -3.976 closest distance to " OE1 GLN A 223 " =    1.961
peak=   -3.939 closest distance to " CD  ARG A  14 " =    3.487
peak=   -3.923 closest distance to " O   HOH Z 290 " =    1.189
peak=   -3.916 closest distance to " OXT GLY A 302 " =    2.923
peak=   -3.896 closest distance to " O   HOH Z 196 " =    2.143
peak=   -3.882 closest distance to " CD1 PHE A  59 " =    1.918
peak=   -3.880 closest distance to " O   HOH Z 353 " =    2.281
peak=   -3.870 closest distance to " CD1 PHE A 130 " =    2.334
peak=   -3.867 closest distance to " O   HOH Z  73 " =    2.295
peak=   -3.856 closest distance to " CG1 VAL A 112 " =    2.586
peak=   -3.826 closest distance to " O   PRO A 163 " =    2.158
peak=   -3.825 closest distance to " ND2 ASN A  45 " =    1.799
peak=   -3.804 closest distance to " O   HOH Z 198 " =    2.457
peak=   -3.797 closest distance to " CD1 LEU A 101 " =    2.515
peak=   -3.789 closest distance to " CE2 TYR A  30 " =    2.726
peak=   -3.789 closest distance to " O   PRO A 198 " =    1.335
peak=   -3.785 closest distance to " O   HOH Z 292 " =    4.651
peak=   -3.774 closest distance to " CZ3 TRP A 179 " =    1.196
peak=   -3.768 closest distance to " CG2 ILE A 263 " =    2.360
peak=   -3.751 closest distance to " OG BSER A 134 " =    1.344
peak=   -3.747 closest distance to " CB  ASP A 132 " =    2.376
peak=   -3.746 closest distance to " CA  ASP A 298 " =    1.068
peak=   -3.743 closest distance to " C   HIS A 108 " =    1.124
peak=   -3.730 closest distance to " OG BSER A 134 " =    1.900
peak=   -3.712 closest distance to " ND2 ASN A  45 " =    1.062
peak=   -3.704 closest distance to " CD  GLN A  58 " =    1.088
peak=   -3.702 closest distance to " C   ASN A 187 " =    1.924
peak=   -3.701 closest distance to " CD2 LEU A 300 " =    2.865
peak=   -3.701 closest distance to " C   ASN A 285 " =    2.526
peak=   -3.682 closest distance to " NH2AARG A 275 " =    5.420
peak=   -3.662 closest distance to " CG  GLU A  53 " =    1.499
peak=   -3.644 closest distance to " O   HOH Z 394 " =    1.490
peak=   -3.631 closest distance to " CB  ALA A 291 " =    2.345
peak=   -3.630 closest distance to " CD1 LEU A 228 " =    2.340
peak=   -3.625 closest distance to " OD1 ASN A 148 " =    1.558
peak=   -3.613 closest distance to " O   HOH Z 211 " =    1.600
peak=   -3.610 closest distance to " O   HOH Z 407 " =    3.462
peak=   -3.609 closest distance to " CD2 TYR A 293 " =    2.027
peak=   -3.603 closest distance to " O   HOH Z 118 " =    3.308
peak=   -3.598 closest distance to " C   SER A 206 " =    1.492
peak=   -3.597 closest distance to " NH2 ARG A  66 " =    1.942
peak=   -3.594 closest distance to " O   HOH Z 166 " =    1.738
peak=   -3.581 closest distance to " O   HOH Z  13 " =    1.675
peak=   -3.580 closest distance to " CD2 PHE A  61 " =    2.494
peak=   -3.579 closest distance to " O   VAL A  67 " =    2.817
peak=   -3.567 closest distance to " CA  GLY A 203 " =    2.309
peak=   -3.565 closest distance to " OD1 ASP A 191 " =    1.700
peak=   -3.557 closest distance to " CG  ARG A 269 " =    2.402
peak=   -3.557 closest distance to " C   ALA A 158 " =    1.352
peak=   -3.552 closest distance to " O   HOH Z  38 " =    1.390
peak=   -3.530 closest distance to " CB  ASN A  39 " =    2.299
peak=   -3.523 closest distance to " CD  ARG A 139 " =    1.572
peak=   -3.523 closest distance to " O   HOH Z 377 " =    1.455
peak=   -3.522 closest distance to " CG  ARG A  66 " =    2.348
peak=   -3.518 closest distance to " NE1 TRP A 266 " =    2.273
peak=   -3.517 closest distance to " O   HOH Z 393 " =    1.479
peak=   -3.513 closest distance to " SG  CYS A 168 " =    1.097
peak=   -3.503 closest distance to " O   VAL A 125 " =    2.332
peak=   -3.502 closest distance to " O   HOH Z  43 " =    1.580
peak=   -3.500 closest distance to " ND2 ASN A  60 " =    1.399
peak=   -3.497 closest distance to " O   HOH Z  19 " =    2.201
peak=   -3.494 closest distance to " ND2 ASN A 249 " =    2.418
peak=   -3.483 closest distance to " O   HOH Z 311 " =    3.725
peak=   -3.472 closest distance to " CE3 TRP A 274 " =    2.550
peak=   -3.472 closest distance to " O   HOH Z 185 " =    2.430
peak=   -3.470 closest distance to " O   VAL A 189 " =    2.628
peak=   -3.458 closest distance to " O   SER A 210 " =    2.036
peak=   -3.450 closest distance to " O   HOH Z 252 " =    4.053
peak=   -3.449 closest distance to " OD2 ASP A 171 " =    1.824
peak=   -3.449 closest distance to " O   HOH Z 111 " =    1.978
peak=   -3.444 closest distance to " CB  ALA A  43 " =    2.540
peak=   -3.443 closest distance to " N   SER A 276 " =    1.478
peak=   -3.443 closest distance to " NE2 GLN A  88 " =    1.873
peak=   -3.443 closest distance to " O   HOH Z 426 " =    1.647
peak=   -3.442 closest distance to " CA  GLY A 241 " =    3.102
peak=   -3.430 closest distance to " O   HOH Z 111 " =    1.392
peak=   -3.428 closest distance to " OG  SER A  62 " =    1.655
peak=   -3.423 closest distance to " CG2 ILE A  49 " =    2.665
peak=   -3.422 closest distance to " O   HOH Z 166 " =    1.641
peak=   -3.417 closest distance to " NE2 GLN A 103 " =    1.774
peak=   -3.416 closest distance to " CG  TRP A 266 " =    1.771
peak=   -3.412 closest distance to " NH2 ARG A  79 " =    1.982
peak=   -3.411 closest distance to " N   ALA A 226 " =    2.120
peak=   -3.410 closest distance to " O   HOH Z 234 " =    4.272
peak=   -3.409 closest distance to " CB  PRO A 163 " =    2.575
peak=   -3.407 closest distance to " O   HOH Z 103 " =    1.845
peak=   -3.402 closest distance to " CG2 VAL A 189 " =    2.224
peak=   -3.401 closest distance to " O   HOH Z 165 " =    1.914
peak=   -3.400 closest distance to " SG ACYS A 201 " =    2.064
peak=   -3.396 closest distance to " O   HOH Z 348 " =    2.285
peak=   -3.386 closest distance to " OG ASER A 134 " =    1.291
peak=   -3.381 closest distance to " O   HOH Z 298 " =    2.694
peak=   -3.375 closest distance to " CG  ASP A 231 " =    0.866
peak=   -3.373 closest distance to " ND2 ASN A 187 " =    1.689
peak=   -3.373 closest distance to " OH  TYR A 247 " =    2.186
peak=   -3.361 closest distance to " O   HOH Z 389 " =    1.863
peak=   -3.360 closest distance to " O   HOH Z 177 " =    1.686
peak=   -3.357 closest distance to " O   HOH Z 241 " =    1.273
peak=   -3.356 closest distance to " O   ALA A  10 " =    1.731
peak=   -3.353 closest distance to " CG1 VAL A 112 " =    2.830
peak=   -3.351 closest distance to " CB  ALA A 291 " =    2.278
peak=   -3.345 closest distance to " C   LEU A 143 " =    1.132
peak=   -3.344 closest distance to " CA  GLY A 133 " =    2.284
peak=   -3.337 closest distance to " O   HOH Z   6 " =    1.577
peak=   -3.334 closest distance to " O   HOH Z  11 " =    1.894
peak=   -3.330 closest distance to " CH2 TRP A 177 " =    2.101
peak=   -3.328 closest distance to " O   PHE A 218 " =    1.592
peak=   -3.328 closest distance to " CD  PRO A 213 " =    2.255
peak=   -3.327 closest distance to " CD  ARG A 195 " =    5.092
peak=   -3.326 closest distance to " CZ  PHE A  59 " =    1.853
peak=   -3.319 closest distance to " O   HOH Z 243 " =    2.163
peak=   -3.318 closest distance to " N   GLN A  58 " =    1.599
peak=   -3.317 closest distance to " O   HOH Z 123 " =    2.447
peak=   -3.316 closest distance to " O   HOH Z  11 " =    2.173
peak=   -3.312 closest distance to " NE2 GLN A  58 " =    1.142
peak=   -3.310 closest distance to " C   ILE A 234 " =    1.318
peak=   -3.310 closest distance to " CZ  TYR A 169 " =    1.809
peak=   -3.307 closest distance to " O   HOH Z 193 " =    1.525
peak=   -3.306 closest distance to " O   HOH Z 128 " =    2.507
peak=   -3.306 closest distance to " CE  MET A 105 " =    2.060
peak=   -3.305 closest distance to " O   HOH Z  71 " =    1.648
peak=   -3.305 closest distance to " O   HOH Z 252 " =    3.969
peak=   -3.303 closest distance to " NH1 ARG A 195 " =    2.611
peak=   -3.299 closest distance to " O   ASN A 301 " =    1.411
peak=   -3.298 closest distance to " CE  MET A  93 " =    1.244
peak=   -3.295 closest distance to " CB  TRP A  85 " =    2.430
peak=   -3.295 closest distance to " CG1 VAL A 112 " =    2.951
peak=   -3.295 closest distance to " NH2 ARG A  79 " =    1.570
peak=   -3.292 closest distance to " O   HOH Z 351 " =    1.554
peak=   -3.290 closest distance to " O   HOH Z  60 " =    2.720
peak=   -3.287 closest distance to " OD1 ASN A 187 " =    1.672
peak=   -3.286 closest distance to " CG1 VAL A 197 " =    2.298
peak=   -3.283 closest distance to " CB  ASP A 286 " =    2.212
peak=   -3.282 closest distance to " CD2 PHE A  59 " =    2.561
peak=   -3.280 closest distance to " OD2 ASP A  65 " =    1.836
peak=   -3.279 closest distance to " CG  PRO A 163 " =    2.496
peak=   -3.279 closest distance to " CD  LYS A 289 " =    2.434
peak=   -3.279 closest distance to " N   MET A 105 " =    2.843
peak=   -3.278 closest distance to " CB  PHE A  16 " =    2.653
peak=   -3.277 closest distance to " CB  ALA A 248 " =    2.059
peak=   -3.276 closest distance to " O   ALA A   1 " =    1.935
peak=   -3.272 closest distance to " O   HOH Z  90 " =    1.817
peak=   -3.271 closest distance to " CA  GLY A 241 " =    2.312
peak=   -3.269 closest distance to " O   HOH Z 198 " =    1.459
peak=   -3.264 closest distance to " CD2 LEU A 167 " =    1.854
peak=   -3.259 closest distance to " OG BSER A 210 " =    2.142
peak=   -3.256 closest distance to " O   HOH Z 256 " =    2.392
peak=   -3.253 closest distance to " CD1 TRP A 179 " =    1.102
peak=   -3.253 closest distance to " O   GLY A 211 " =    1.481
peak=   -3.245 closest distance to " CD2 PHE A 225 " =    1.255
peak=   -3.245 closest distance to " O   HOH Z 435 " =    2.624
peak=   -3.238 closest distance to " N   ALA A 248 " =    1.682
peak=   -3.238 closest distance to " O   HOH Z  51 " =    1.575
peak=   -3.237 closest distance to " O   HOH Z 275 " =    1.539
peak=   -3.235 closest distance to " CG  PHE A 283 " =    2.834
peak=   -3.231 closest distance to " CE3 TRP A 150 " =    2.064
peak=   -3.230 closest distance to " NH2 ARG A 159 " =    2.385
peak=   -3.228 closest distance to " O   HOH Z 350 " =    1.995
peak=   -3.228 closest distance to " N   THR A 157 " =    1.590
peak=   -3.226 closest distance to " CD  GLU A 236 " =    1.025
peak=   -3.225 closest distance to " O   HOH Z 264 " =    1.839
peak=   -3.224 closest distance to " O   HOH Z  88 " =    2.154
peak=   -3.215 closest distance to " O   HOH Z 423 " =    2.374
peak=   -3.209 closest distance to " CE BMET A  47 " =    2.348
peak=   -3.208 closest distance to " CG  MET A 105 " =    0.918
peak=   -3.204 closest distance to " CG  GLU A 277 " =    1.141
peak=   -3.203 closest distance to " CD1 ILE A 239 " =    2.087
peak=   -3.202 closest distance to " O   HOH Z 265 " =    2.240
peak=   -3.200 closest distance to " O   GLY A 196 " =    1.129
peak=   -3.194 closest distance to " O   HOH Z 436 " =    1.509
peak=   -3.193 closest distance to " OE2 GLU A   2 " =    1.745
peak=   -3.188 closest distance to " OD1 ASP A 171 " =    1.522
peak=   -3.185 closest distance to " CE3 TRP A  70 " =    1.861
peak=   -3.181 closest distance to " O   HOH Z 396 " =    1.702
peak=   -3.180 closest distance to " O   HOH Z 139 " =    2.930
peak=   -3.179 closest distance to " C   ALA A   8 " =    1.634
peak=   -3.173 closest distance to " ND2BASN A 224 " =    1.716
peak=   -3.167 closest distance to " O   HOH Z 421 " =    3.304
peak=   -3.166 closest distance to " CB  ALA A 248 " =    2.395
peak=   -3.160 closest distance to " CG  ASN A 301 " =    1.972
peak=   -3.160 closest distance to " O   HOH Z 281 " =    2.535
peak=   -3.157 closest distance to " CB  ALA A  10 " =    2.163
peak=   -3.156 closest distance to " CB  CYS A 254 " =    2.461
peak=   -3.156 closest distance to " CZ  PHE A  38 " =    2.327
peak=   -3.154 closest distance to " CB  TYR A  15 " =    2.271
peak=   -3.154 closest distance to " CE2 PHE A 218 " =    2.463
peak=   -3.152 closest distance to " O   ALA A  34 " =    2.564
peak=   -3.149 closest distance to " C   GLY A  17 " =    1.258
peak=   -3.144 closest distance to " O   ARG A  24 " =    2.157
peak=   -3.129 closest distance to " O   HOH Z 323 " =    1.403
peak=   -3.126 closest distance to " CD  GLN A  88 " =    0.870
peak=   -3.111 closest distance to " O   HOH Z 176 " =    1.005
peak=   -3.099 closest distance to " O   HOH Z 357 " =    2.094
peak=   -3.096 closest distance to " CD2 TYR A 247 " =    2.375
peak=   -3.096 closest distance to " ND2 ASN A  60 " =    1.763
peak=   -3.087 closest distance to " CD1 ILE A 151 " =    2.308
peak=   -3.086 closest distance to " O   HOH Z  61 " =    1.595
peak=   -3.086 closest distance to " OD2 ASP A  50 " =    2.244
peak=   -3.070 closest distance to " O   GLY A 203 " =    2.381
peak=   -3.058 closest distance to " CG2 THR A 221 " =    2.263
peak=   -3.040 closest distance to " CG2 ILE A  20 " =    2.878
peak=   -3.034 closest distance to " O   HOH Z 357 " =    2.060
peak=   -3.031 closest distance to " O   SER A 164 " =    2.001
peak=   -3.024 closest distance to " CA  GLY A 241 " =    2.814

================= 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    :  0.3796 0.3712   6.161071e+00   6.144373e+00
   1_bss:  0.3686 0.3608   6.146062e+00   6.123768e+00
   1_xyz:  0.2473 0.2763   5.810649e+00   5.893861e+00
   1_adp:  0.2253 0.2794   5.753561e+00   5.910072e+00
   1_occ:  0.2250 0.2789   5.752506e+00   5.909202e+00
   2_bss:  0.2232 0.2764   5.748696e+00   5.904859e+00
   2_xyz:  0.1541 0.1956   5.402316e+00   5.603948e+00
   2_adp:  0.1384 0.1785   5.309177e+00   5.519615e+00
   2_occ:  0.1381 0.1783   5.308408e+00   5.519059e+00
   3_bss:  0.1381 0.1782   5.307699e+00   5.515980e+00
   3_xyz:  0.1211 0.1638   5.206402e+00   5.434201e+00
   3_adp:  0.1178 0.1632   5.190230e+00   5.426220e+00
   3_occ:  0.1177 0.1632   5.190208e+00   5.426355e+00
   4_bss:  0.1177 0.1632   5.189980e+00   5.426158e+00
   4_xyz:  0.1136 0.1618   5.170943e+00   5.416586e+00
   4_adp:  0.1127 0.1628   5.170081e+00   5.420257e+00
   4_occ:  0.1127 0.1629   5.170160e+00   5.420588e+00
   5_bss:  0.1128 0.1625   5.171002e+00   5.420570e+00
   5_xyz:  0.1106 0.1623   5.161828e+00   5.418380e+00
   5_adp:  0.1106 0.1613   5.158379e+00   5.413548e+00
   5_occ:  0.1106 0.1613   5.158446e+00   5.413818e+00
   5_bss:  0.1105 0.1612   5.158497e+00   5.413859e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.293  37.208  -0.430   3.045  -1.596   0.000  -0.000  -0.000
   1_xyz:  0.293  37.208  -0.430   3.045  -1.596   0.000  -0.000  -0.000
   1_adp:  0.293  37.208  -0.430   3.045  -1.596   0.000  -0.000  -0.000
   1_occ:  0.293  37.208  -0.430   3.045  -1.596   0.000  -0.000  -0.000
   2_bss:  0.322  64.345  -1.550   0.217  -1.541   0.000  -0.000  -0.000
   2_xyz:  0.322  64.345  -1.550   0.217  -1.541   0.000  -0.000  -0.000
   2_adp:  0.322  64.345  -1.550   0.217  -1.541   0.000  -0.000  -0.000
   2_occ:  0.322  64.345  -1.550   0.217  -1.541   0.000  -0.000  -0.000
   3_bss:  0.327  65.352  -1.935  -1.105  -1.375  -0.000  -0.000  -0.000
   3_xyz:  0.327  65.352  -1.935  -1.105  -1.375  -0.000  -0.000  -0.000
   3_adp:  0.327  65.352  -1.935  -1.105  -1.375  -0.000  -0.000  -0.000
   3_occ:  0.327  65.352  -1.935  -1.105  -1.375  -0.000  -0.000  -0.000
   4_bss:  0.327  65.352  -1.861  -1.325  -1.179  -0.000  -0.000  -0.000
   4_xyz:  0.327  65.352  -1.861  -1.325  -1.179  -0.000  -0.000  -0.000
   4_adp:  0.327  65.352  -1.861  -1.325  -1.179  -0.000  -0.000  -0.000
   4_occ:  0.327  65.352  -1.861  -1.325  -1.179  -0.000  -0.000  -0.000
   5_bss:  0.327  65.352  -1.686  -1.286  -0.953  -0.000  -0.000  -0.000
   5_xyz:  0.327  65.352  -1.686  -1.286  -0.953  -0.000  -0.000  -0.000
   5_adp:  0.327  65.352  -1.686  -1.286  -0.953  -0.000  -0.000  -0.000
   5_occ:  0.327  65.352  -1.686  -1.286  -0.953  -0.000  -0.000  -0.000
   5_bss:  0.321  61.699  -1.499  -1.139  -0.724  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  41.168 0.6308  0.7993    41562.655
   1_bss:  40.271 0.6397  0.8218    38679.634
   1_xyz:  28.105 0.7795  0.9582    20131.666
   1_adp:  28.676 0.7725  0.9445    20858.495
   1_occ:  28.656 0.7727  0.9444    20807.069
   2_bss:  28.353 0.7760  0.9084    20480.980
   2_xyz:  19.200 0.8680  0.9782     9891.833
   2_adp:  16.952 0.8895  0.9811     8286.112
   2_occ:  16.935 0.8896  0.9811     8273.946
   3_bss:  16.872 0.8902  0.9644     8243.544
   3_xyz:  15.049 0.9061  0.9718     6927.668
   3_adp:  14.814 0.9084  0.9666     6848.651
   3_occ:  14.815 0.9084  0.9665     6852.324
   4_bss:  14.809 0.9084  0.9674     6850.719
   4_xyz:  14.580 0.9104  0.9680     6704.552
   4_adp:  14.650 0.9099  0.9608     6768.565
   4_occ:  14.655 0.9099  0.9607     6773.934
   5_bss:  14.687 0.9096  0.9656     6786.990
   5_xyz:  14.651 0.9098  0.9655     6737.113
   5_adp:  14.542 0.9107  0.9596     6679.311
   5_occ:  14.547 0.9107  0.9596     6683.663
   5_bss:  14.551 0.9106  0.9660     6682.705
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6520e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6520e-01
   1_xyz:   1.298  0.010  0.080 15.359  0.005  4.116   8.8399e-02
   1_adp:   1.298  0.010  0.080 15.359  0.005  4.116   8.8399e-02
   1_occ:   1.298  0.010  0.080 15.359  0.005  4.116   8.8399e-02
   2_bss:   1.298  0.010  0.080 15.359  0.005  4.116   8.8399e-02
   2_xyz:   1.116  0.009  0.079 14.709  0.004  4.135   7.1658e-02
   2_adp:   1.116  0.009  0.079 14.709  0.004  4.135   7.1658e-02
   2_occ:   1.116  0.009  0.079 14.709  0.004  4.135   7.1658e-02
   3_bss:   1.116  0.009  0.079 14.709  0.004  4.135   7.1658e-02
   3_xyz:   1.057  0.009  0.078 14.732  0.004  4.115   6.7101e-02
   3_adp:   1.057  0.009  0.078 14.732  0.004  4.115   6.7101e-02
   3_occ:   1.057  0.009  0.078 14.732  0.004  4.115   6.7101e-02
   4_bss:   1.057  0.009  0.078 14.732  0.004  4.115   6.7101e-02
   4_xyz:   1.057  0.009  0.078 14.704  0.004  4.118   6.6897e-02
   4_adp:   1.057  0.009  0.078 14.704  0.004  4.118   6.6897e-02
   4_occ:   1.057  0.009  0.078 14.704  0.004  4.118   6.6897e-02
   5_bss:   1.057  0.009  0.078 14.704  0.004  4.118   6.6897e-02
   5_xyz:   1.086  0.010  0.081 14.739  0.004  4.120   7.0622e-02
   5_adp:   1.086  0.010  0.081 14.739  0.004  4.120   7.0622e-02
   5_occ:   1.086  0.010  0.081 14.739  0.004  4.120   7.0622e-02
   5_bss:   1.086  0.010  0.081 14.739  0.004  4.120   7.0622e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.543   2.4337e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.543   2.4337e-01
   1_xyz:  10.016  0.060  0.371 87.020  0.022  2.116   9.1252e-02
   1_adp:  10.016  0.060  0.371 87.020  0.022  2.116   9.1252e-02
   1_occ:  10.016  0.060  0.371 87.020  0.022  2.116   9.1252e-02
   2_bss:  10.016  0.060  0.371 87.020  0.022  2.116   9.1252e-02
   2_xyz:   7.355  0.071  0.265 87.007  0.038  2.200   7.2801e-02
   2_adp:   7.355  0.071  0.265 87.007  0.038  2.200   7.2801e-02
   2_occ:   7.355  0.071  0.265 87.007  0.038  2.200   7.2801e-02
   3_bss:   7.355  0.071  0.265 87.007  0.038  2.200   7.2801e-02
   3_xyz:   7.567  0.048  0.244 83.890  0.041  2.305   4.7548e-02
   3_adp:   7.567  0.048  0.244 83.890  0.041  2.305   4.7548e-02
   3_occ:   7.567  0.048  0.244 83.890  0.041  2.305   4.7548e-02
   4_bss:   7.567  0.048  0.244 83.890  0.041  2.305   4.7548e-02
   4_xyz:   7.640  0.047  0.261 82.190  0.041  2.327   4.6454e-02
   4_adp:   7.640  0.047  0.261 82.190  0.041  2.327   4.6454e-02
   4_occ:   7.640  0.047  0.261 82.190  0.041  2.327   4.6454e-02
   5_bss:   7.640  0.047  0.261 82.190  0.041  2.327   4.6454e-02
   5_xyz:   7.772  0.046  0.249 82.319  0.039  2.329   5.0460e-02
   5_adp:   7.772  0.046  0.249 82.319  0.039  2.329   5.0460e-02
   5_occ:   7.772  0.046  0.249 82.319  0.039  2.329   5.0460e-02
   5_bss:   7.772  0.046  0.249 82.319  0.039  2.329   5.0460e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  91.40   0.00  17.52  83.98   0.00  13.42  91.40   3.53  39.84
   1_occ:  91.40   0.00  17.52  83.98   0.00  13.42  91.40   3.53  39.84
   2_bss:  91.40   0.00  17.52  83.98   0.00  13.42  91.40   3.53  39.84
   2_xyz:  91.40   0.00  17.52  83.98   0.00  13.42  91.40   3.53  39.84
   2_adp:  87.97   1.56  17.11  87.02   1.56  12.83  87.97   4.40  40.41
   2_occ:  87.97   1.56  17.11  87.02   1.56  12.83  87.97   4.40  40.41
   3_bss:  87.97   1.56  17.11  87.02   1.56  12.83  87.97   4.40  40.41
   3_xyz:  87.97   1.56  17.11  87.02   1.56  12.83  87.97   4.40  40.41
   3_adp:  91.31   0.53  17.04  91.31   0.53  12.65  87.74   4.92  40.90
   3_occ:  91.31   0.53  17.04  91.31   0.53  12.65  87.74   4.92  40.90
   4_bss:  91.31   0.53  17.04  91.31   0.53  12.65  87.74   4.92  40.90
   4_xyz:  91.31   0.53  17.04  91.31   0.53  12.65  87.74   4.92  40.90
   4_adp:  99.84   0.00  16.95  99.84   0.00  12.53  90.53   5.08  41.01
   4_occ:  99.84   0.00  16.95  99.84   0.00  12.53  90.53   5.08  41.01
   5_bss:  99.84   0.00  16.95  99.84   0.00  12.53  90.53   5.08  41.01
   5_xyz:  99.84   0.00  16.95  99.84   0.00  12.53  90.53   5.08  41.01
   5_adp: 101.71   0.00  16.59 101.71   0.00  12.30  88.08   5.30  39.99
   5_occ: 101.71   0.00  16.59 101.71   0.00  12.30  88.08   5.30  39.99
   5_bss: 101.71   0.00  16.60 101.71   0.00  12.30  88.08   5.30  40.00
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.659    0.017    0.330
   1_adp:    1.659    0.017    0.330
   1_occ:    1.659    0.017    0.330
   2_bss:    1.659    0.017    0.330
   2_xyz:    1.030    0.022    0.490
   2_adp:    1.030    0.022    0.490
   2_occ:    1.030    0.022    0.490
   3_bss:    1.030    0.022    0.490
   3_xyz:    1.051    0.021    0.528
   3_adp:    1.051    0.021    0.528
   3_occ:    1.051    0.021    0.528
   4_bss:    1.051    0.021    0.528
   4_xyz:    1.058    0.063    0.551
   4_adp:    1.058    0.063    0.551
   4_occ:    1.058    0.063    0.551
   5_bss:    1.058    0.063    0.551
   5_xyz:    1.131    0.071    0.563
   5_adp:    1.131    0.071    0.563
   5_occ:    1.131    0.071    0.563
   5_bss:    1.131    0.071    0.563
------------------------------------------------------------------------

CPU time actual refinement: 330.20


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1060/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_1060/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1060/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1060/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1060/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 330.05 
  Macro-tasks:
    bulk solvent and scale       = 40.64  
    individual site refinement   = 134.91 
    weights calculation          = 28.56  
    collect and process          = 6.57   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 210.79 
  Micro-tasks:
    mask                            = 1.74   
    f_calc                          = 104.05 
    alpha_beta                      = 8.34   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 113.57 
    fmodel                         = 6.72   
    r_factors                      = 0.11   
    phase_errors                   = 11.02  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 247.02 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.636 micro seconds
Total CPU time: 5.72 minutes
from_scatterers_fft:    664 calls, 103.72 s
gradients_fft:          609 calls,  99.68 s

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

# Date 2008-01-16 Time 06:19:08 PST -0800 (1200493148.21 s)
Start R-work = 0.3796, R-free = 0.3712 (no bulk solvent and anisotropic scale)
Final R-work = 0.1298, R-free = 0.1777 (no bulk solvent and anisotropic scale)

Start R-work = 0.3686, R-free = 0.3608
Final R-work = 0.1105, R-free = 0.1612