# Date 2008-01-16 Time 03:49:18 PST -0800 (1200484158.28 s)
#phil __OFF__

Command line arguments: "../59.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29073
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 59

-------------------------------------------------------------------------------
  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: (68.4938, 46.93, 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: 3.32, per 1000 atoms: 1.18


================================== 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: (68.4938, 46.93, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6999 1.95073
Completeness in resolution range: 0.94373
Completeness with d_max=infinity: 0.940829

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.6999
                             d_min =   1.9507

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: (68.4938, 46.93, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6999 1.95073
Completeness in resolution range: 0.94373
Completeness with d_max=infinity: 0.940829

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7003 -  4.1737 [2191/2219]  1968   223  10.2%
  bin  2:  4.1737 -  3.3254 [2074/2097]  1870   204   9.8%
  bin  3:  3.3254 -  2.9087 [2074/2096]  1866   208  10.0%
  bin  4:  2.9087 -  2.6445 [2044/2063]  1839   205  10.0%
  bin  5:  2.6445 -  2.4559 [2021/2050]  1816   205  10.1%
  bin  6:  2.4559 -  2.3116 [2025/2067]  1827   198   9.8%
  bin  7:  2.3116 -  2.1963 [2005/2041]  1806   199   9.9%
  bin  8:  2.1963 -  2.1009 [2010/2050]  1808   202  10.0%
  bin  9:  2.1009 -  2.0203 [2017/2046]  1820   197   9.8%
  bin 10:  2.0203 -  1.9507 [1128/2028]  1010   118  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_59/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.18 -     1.92: 13
        1.92 -     2.67: 123
        2.67 -     3.41: 4491
        3.41 -     4.16: 9562
        4.16 -     4.90: 14611
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.180 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.299 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.476 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.517 3.040 -x+1,y-1/2,-z+1/2
  " NE2 GLN A  55 " - " O   ASN A 285 "  1.679 3.120 -x+1,y-1/2,-z+1/2
  ... (remaining 28795 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_59/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_59/model_refine_001.geo

CPU time processing inputs: 8.97


============================ 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 = 68.49375 46.93 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: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3448   r_free= 0.3452   ksol= 0.00   Bsol= 0.00   scale= 0.971    |
|                                                                             |
| 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:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.110443                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7003 -  4.6549 0.99   1413  157 0.3011 0.2996       6.406       6.448|
|  2:  4.6549 -  3.7143 0.99   1368  153 0.2764 0.2578      6.5054      6.5129|
|  3:  3.7143 -  3.2506 0.99   1338  149 0.3004 0.3008      6.4125      6.5207|
|  4:  3.2506 -  2.9560 0.99   1316  141 0.3153 0.3574      6.2901      6.3626|
|  5:  2.9560 -  2.7456 0.98   1312  146 0.3445 0.3484      6.1618      6.1851|
|  6:  2.7456 -  2.5847 0.98   1309  149 0.3700 0.3927      6.1073      6.0115|
|  7:  2.5847 -  2.4559 0.99   1303  150 0.3671 0.3167      6.0729      5.9951|
|  8:  2.4559 -  2.3494 0.99   1326  140 0.3772 0.3720      6.0232      6.0433|
|  9:  2.3494 -  2.2593 0.98   1285  147 0.3921 0.4242      5.9923      6.0715|
| 10:  2.2593 -  2.1816 0.98   1300  139 0.3765 0.3768      5.9637      5.9053|
| 11:  2.1816 -  2.1136 0.98   1286  147 0.3937 0.3968       5.909      5.9132|
| 12:  2.1136 -  2.0533 0.99   1283  143 0.3968 0.3836      5.8559       5.881|
| 13:  2.0533 -  1.9994 0.97   1275  133 0.3991 0.4023      5.7767      5.7004|
| 14:  1.9994 -  1.9507 0.40    516   65 0.4567 0.4496      5.8326      5.6838|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7003 -  4.6549  1413   157  0.76  28.53   0.87     0.77      49876.64|
|  2:  4.6549 -  3.7143  1368   153  0.80  26.13   0.98     0.90      60737.54|
|  3:  3.7143 -  3.2506  1338   149  0.75  30.61   1.00     0.93      61037.61|
|  4:  3.2506 -  2.9560  1316   141  0.71  34.16   1.00     0.91      52558.77|
|  5:  2.9560 -  2.7456  1312   146  0.67  38.34   0.99     0.88      42921.51|
|  6:  2.7456 -  2.5847  1309   149  0.66  38.87   0.96     0.88      36260.58|
|  7:  2.5847 -  2.4559  1303   150  0.68  37.73   1.00     0.90      32853.67|
|  8:  2.4559 -  2.3494  1326   140  0.66  39.19   1.01     0.89      29576.71|
|  9:  2.3494 -  2.2593  1285   147  0.65  40.15   1.01     0.90      28718.00|
| 10:  2.2593 -  2.1816  1300   139  0.65  40.16   1.04     0.90      26228.79|
| 11:  2.1816 -  2.1136  1286   147  0.64  41.08   1.02     0.92      24824.78|
| 12:  2.1136 -  2.0533  1283   143  0.63  41.60   1.06     0.92      22600.33|
| 13:  2.0533 -  1.9994  1275   133  0.59  44.88   1.04     0.86      21275.64|
| 14:  1.9994 -  1.9507   516    65  0.57  46.95   0.99     0.74      19492.82|
|alpha:            min =        0.74 max =            0.93 mean =         0.88|
|beta:             min =    19492.82 max =        61037.61 mean =     37397.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.68|
|phase err.(work): min =        0.00 max =           89.97 mean =        37.19|
|phase err.(test): min =        0.00 max =           89.99 mean =        36.94|
|-----------------------------------------------------------------------------|

============================== 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 = 4.944803              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.862   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.795184              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.410   (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 |  1.180 -  1.552:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.552 -  1.924:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.924 -  2.296:       24 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.296 -  2.668:       99 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.668 -  3.040:     2155 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.040 -  3.412:     2336 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.412 -  3.784:     4086 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.784 -  4.156:     5476 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.156 -  4.528:     6514 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.528 -  4.900:     8097 |
|-----------------------------------------------------------------------------|
|-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 |        0.217 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.180 |       1.019 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.467)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3448   r_free= 0.3452   ksol= 0.00   Bsol= 0.00   scale= 0.971    |
|                                                                             |
| 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:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.110443                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3303   r_free= 0.3325   ksol= 0.31   Bsol= 28.45   scale= 0.977   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.79,-2.86,-1.35,-0.00,-0.00,-0.00); trace/3= -0.81                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.089534                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.496647              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.699   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.417748              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.124   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3303      final r-factor (work) = 0.2110          |
| start r-factor (free) = 0.3325      final r-factor (free) = 0.2349          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.9333 = 4.50 * 0.50 * 6.1007 + 1.00 * 0.2169                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.2189 = 4.50 * 0.50 * 5.8420 + 1.00 * 0.0841                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2110      final r-factor (work) = 0.1917          |
| start r-factor (free) = 0.2349      final r-factor (free) = 0.2397          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4466 = 0.42 * 1.00 * 5.8420 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3489 = 0.42 * 1.00 * 5.5971 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.467)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.33   17.61    None  None   None       |
|    all(noH): 2823   0      0.00    81.33   17.61    None  None   None       |
|    Sol.    : 438    0      6.54    75.97   39.57    None  None   None       |
|    Mac.    : 2385   0      0.00    81.33   13.58    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.133:  606   |   5:    40.664 -  48.797:  122        |
|      1:     8.133 -  16.266: 1234   |   6:    48.797 -  56.930:   79        |
|      2:    16.266 -  24.399:  430   |   7:    56.930 -  65.063:   48        |
|      3:    24.399 -  32.531:  149   |   8:    65.063 -  73.195:   17        |
|      4:    32.531 -  40.664:  132   |   9:    73.195 -  81.328:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1917 r_free = 0.2397             target_work(ml) = 5.606         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1914 r_free = 0.2394             target_work(ml) = 5.605         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1914   r_free= 0.2394   ksol= 0.31   Bsol= 28.45   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.79,-2.86,-1.35,-0.00,-0.00,-0.00); trace/3= -0.81                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.605371                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1859   r_free= 0.2354   ksol= 0.30   Bsol= 30.19   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,-2.76,-1.64,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.583821                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.917807              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.756   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.198694              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.558   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1859      final r-factor (work) = 0.1418          |
| start r-factor (free) = 0.2354      final r-factor (free) = 0.1841          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4483 = 1.92 * 0.50 * 5.5940 + 1.00 * 0.0841                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2965 = 1.92 * 0.50 * 5.4705 + 1.00 * 0.0508                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1418      final r-factor (work) = 0.1348          |
| start r-factor (free) = 0.1841      final r-factor (free) = 0.1760          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0975 = 0.20 * 1.00 * 5.4705 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0634 = 0.20 * 1.00 * 5.3095 + 1.00 * 0.0084                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.467)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.35   17.28    None  None   None       |
|    all(noH): 2823   0      0.00    89.35   17.28    None  None   None       |
|    Sol.    : 438    0      5.83    76.91   38.82    None  None   None       |
|    Mac.    : 2385   0      0.00    89.35   13.32    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.935:  696   |   5:    44.674 -  53.609:  125        |
|      1:     8.935 -  17.870: 1357   |   6:    53.609 -  62.543:   50        |
|      2:    17.870 -  26.804:  289   |   7:    62.543 -  71.478:   20        |
|      3:    26.804 -  35.739:  139   |   8:    71.478 -  80.413:    5        |
|      4:    35.739 -  44.674:  140   |   9:    80.413 -  89.348:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1348 r_free = 0.1760             target_work(ml) = 5.288         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1346 r_free = 0.1759             target_work(ml) = 5.287         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1346   r_free= 0.1759   ksol= 0.30   Bsol= 30.19   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,-2.76,-1.64,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.287121                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1343   r_free= 0.1745   ksol= 0.31   Bsol= 35.36   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.98,-2.49,-1.58,-0.00,-0.00,-0.00); trace/3= -2.35                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.282642                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.815405              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.998  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.147861              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.103   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1343      final r-factor (work) = 0.1176          |
| start r-factor (free) = 0.1745      final r-factor (free) = 0.1581          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8689 = 1.82 * 0.50 * 5.3080 + 1.00 * 0.0508                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7907 = 1.82 * 0.50 * 5.2196 + 1.00 * 0.0528                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1176      final r-factor (work) = 0.1160          |
| start r-factor (free) = 0.1581      final r-factor (free) = 0.1562          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7797 = 0.15 * 1.00 * 5.2196 + 1.00 * 0.0079                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7708 = 0.15 * 1.00 * 5.1643 + 1.00 * 0.0072                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.467)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.56   16.97    None  None   None       |
|    all(noH): 2823   0      0.00    90.56   16.97    None  None   None       |
|    Sol.    : 438    0      4.65    74.18   37.90    None  None   None       |
|    Mac.    : 2385   0      0.00    90.56   13.12    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 -   9.056:  685   |   5:    45.282 -  54.338:  109        |
|      1:     9.056 -  18.113: 1416   |   6:    54.338 -  63.394:   37        |
|      2:    18.113 -  27.169:  272   |   7:    63.394 -  72.451:   14        |
|      3:    27.169 -  36.225:  132   |   8:    72.451 -  81.507:    3        |
|      4:    36.225 -  45.282:  153   |   9:    81.507 -  90.563:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1160 r_free = 0.1562             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1159 r_free = 0.1560             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1159   r_free= 0.1560   ksol= 0.31   Bsol= 35.36   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.98,-2.49,-1.58,-0.00,-0.00,-0.00); trace/3= -2.35                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.157339                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1159   r_free= 0.1560   ksol= 0.32   Bsol= 36.58   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.26,-2.48,-1.57,-0.00,-0.00,-0.00); trace/3= -2.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.156997                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.311052              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 138.455  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.220688              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 109.046  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1159      final r-factor (work) = 0.1093          |
| start r-factor (free) = 0.1560      final r-factor (free) = 0.1529          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0194 = 2.31 * 0.50 * 5.1635 + 1.00 * 0.0528                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9909 = 2.31 * 0.50 * 5.1313 + 1.00 * 0.0615                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1093      final r-factor (work) = 0.1082          |
| start r-factor (free) = 0.1529      final r-factor (free) = 0.1526          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1399 = 0.22 * 1.00 * 5.1313 + 1.00 * 0.0074                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1357 = 0.22 * 1.00 * 5.1142 + 1.00 * 0.0070                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.467)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.40    90.90   16.86    None  None   None       |
|    all(noH): 2823   0      2.40    90.90   16.86    None  None   None       |
|    Sol.    : 438    0      4.37    72.96   37.86    None  None   None       |
|    Mac.    : 2385   0      2.40    90.90   13.00    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:     2.397 -  11.248: 1277   |   5:    46.650 -  55.501:  101        |
|      1:    11.248 -  20.098:  929   |   6:    55.501 -  64.351:   27        |
|      2:    20.098 -  28.949:  191   |   7:    64.351 -  73.202:   14        |
|      3:    28.949 -  37.799:  129   |   8:    73.202 -  82.052:    2        |
|      4:    37.799 -  46.650:  151   |   9:    82.052 -  90.903:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1082 r_free = 0.1526             target_work(ml) = 5.114         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1081 r_free = 0.1526             target_work(ml) = 5.114         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1526   ksol= 0.32   Bsol= 36.58   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.26,-2.48,-1.57,-0.00,-0.00,-0.00); trace/3= -2.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.113947                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1078   r_free= 0.1520   ksol= 0.32   Bsol= 38.10   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.23,-2.37,-1.44,-0.00,-0.00,-0.00); trace/3= -2.35                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.112427                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.918879              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.158  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.713597              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.021  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1078      final r-factor (work) = 0.1050          |
| start r-factor (free) = 0.1520      final r-factor (free) = 0.1526          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5243 = 2.92 * 0.50 * 5.1135 + 1.00 * 0.0615                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5120 = 2.92 * 0.50 * 5.1010 + 1.00 * 0.0674                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1050      final r-factor (work) = 0.1042          |
| start r-factor (free) = 0.1526      final r-factor (free) = 0.1535          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6472 = 0.71 * 1.00 * 5.1010 + 1.00 * 0.0071                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6459 = 0.71 * 1.00 * 5.0977 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.467)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.55    92.08   16.95    None  None   None       |
|    all(noH): 2823   0      1.55    92.08   16.95    None  None   None       |
|    Sol.    : 438    0      5.82    73.43   38.82    None  None   None       |
|    Mac.    : 2385   0      1.55    92.08   12.93    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.555 -  10.607: 1155   |   5:    46.819 -  55.872:  107        |
|      1:    10.607 -  19.660: 1028   |   6:    55.872 -  64.924:   42        |
|      2:    19.660 -  28.713:  203   |   7:    64.924 -  73.977:   14        |
|      3:    28.713 -  37.766:  137   |   8:    73.977 -  83.030:    4        |
|      4:    37.766 -  46.819:  131   |   9:    83.030 -  92.083:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1042 r_free = 0.1535             target_work(ml) = 5.102         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1041 r_free = 0.1535             target_work(ml) = 5.102         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1041   r_free= 0.1535   ksol= 0.32   Bsol= 38.10   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.23,-2.37,-1.44,-0.00,-0.00,-0.00); trace/3= -2.35                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.102022                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7003 -  4.6549 0.99   1413  157 0.0944 0.1281      5.3476      5.5414|
|  2:  4.6549 -  3.7143 0.99   1368  153 0.0806 0.1083      5.3925      5.6037|
|  3:  3.7143 -  3.2506 0.99   1338  149 0.0997 0.1504      5.4247       5.808|
|  4:  3.2506 -  2.9560 0.99   1316  141 0.1118 0.1491      5.3898      5.5603|
|  5:  2.9560 -  2.7456 0.98   1312  146 0.1189 0.1582       5.251      5.4776|
|  6:  2.7456 -  2.5847 0.98   1309  149 0.1159 0.1987      5.1642      5.4393|
|  7:  2.5847 -  2.4559 0.99   1303  150 0.1132 0.1523      5.1042       5.316|
|  8:  2.4559 -  2.3494 0.99   1326  140 0.1069 0.1588      5.0292      5.2398|
|  9:  2.3494 -  2.2593 0.98   1285  147 0.1107 0.1862      4.9803      5.3295|
| 10:  2.2593 -  2.1816 0.98   1300  139 0.1021 0.1664       4.909      5.1387|
| 11:  2.1816 -  2.1136 0.98   1286  147 0.1045 0.1668      4.8745      5.2101|
| 12:  2.1136 -  2.0533 0.99   1283  143 0.1024 0.1710      4.8173      5.1731|
| 13:  2.0533 -  1.9994 0.97   1275  133 0.1037 0.1590      4.7446      4.9388|
| 14:  1.9994 -  1.9507 0.40    516   65 0.1016 0.1824      4.6817      4.9426|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7003 -  4.6549  1413   157  0.94   8.81   0.98     0.96       6759.69|
|  2:  4.6549 -  3.7143  1368   153  0.95   7.71   1.03     1.02       8544.53|
|  3:  3.7143 -  3.2506  1338   149  0.94  10.93   1.03     1.03       9704.00|
|  4:  3.2506 -  2.9560  1316   141  0.93  12.78   1.02     1.01       9470.75|
|  5:  2.9560 -  2.7456  1312   146  0.91  15.13   1.00     0.97       7532.36|
|  6:  2.7456 -  2.5847  1309   149  0.90  15.78   0.98     0.96       6555.99|
|  7:  2.5847 -  2.4559  1303   150  0.91  14.69   0.99     0.95       5618.64|
|  8:  2.4559 -  2.3494  1326   140  0.91  14.71   1.00     0.98       5174.16|
|  9:  2.3494 -  2.2593  1285   147  0.91  14.99   1.00     0.96       4536.14|
| 10:  2.2593 -  2.1816  1300   139  0.91  15.14   1.00     0.97       4219.33|
| 11:  2.1816 -  2.1136  1286   147  0.91  15.48   1.00     0.97       4021.53|
| 12:  2.1136 -  2.0533  1283   143  0.91  14.76   1.01     1.01       3619.33|
| 13:  2.0533 -  1.9994  1275   133  0.91  15.44   1.00     0.98       3164.66|
| 14:  1.9994 -  1.9507   516    65  0.91  15.38   0.98     0.94       2689.74|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2689.74 max =         9704.00 mean =      6006.03|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.56|
|phase err.(test): min =        0.00 max =           89.35 mean =        13.22|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1041   r_free= 0.1535   ksol= 0.32   Bsol= 38.90   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.02,-2.12,-1.18,-0.00,-0.00,-0.00); trace/3= -2.11                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.102115                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.70 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1041   r_free= 0.1535   ksol= 0.32   Bsol= 38.90   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.02,-2.12,-1.18,-0.00,-0.00,-0.00); trace/3= -2.11                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.102115                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7003 -  4.6549 0.99   1413  157 0.0945 0.1283      5.3495      5.5436|
|  2:  4.6549 -  3.7143 0.99   1368  153 0.0807 0.1083      5.3933      5.6034|
|  3:  3.7143 -  3.2506 0.99   1338  149 0.0997 0.1504      5.4246      5.8081|
|  4:  3.2506 -  2.9560 0.99   1316  141 0.1117 0.1490      5.3896      5.5599|
|  5:  2.9560 -  2.7456 0.98   1312  146 0.1189 0.1581      5.2508      5.4775|
|  6:  2.7456 -  2.5847 0.98   1309  149 0.1159 0.1986      5.1639      5.4385|
|  7:  2.5847 -  2.4559 0.99   1303  150 0.1132 0.1522       5.104      5.3158|
|  8:  2.4559 -  2.3494 0.99   1326  140 0.1069 0.1587      5.0288      5.2391|
|  9:  2.3494 -  2.2593 0.98   1285  147 0.1107 0.1862      4.9803      5.3296|
| 10:  2.2593 -  2.1816 0.98   1300  139 0.1021 0.1664       4.909      5.1384|
| 11:  2.1816 -  2.1136 0.98   1286  147 0.1045 0.1668      4.8745      5.2102|
| 12:  2.1136 -  2.0533 0.99   1283  143 0.1024 0.1711      4.8172      5.1734|
| 13:  2.0533 -  1.9994 0.97   1275  133 0.1037 0.1590      4.7445      4.9385|
| 14:  1.9994 -  1.9507 0.40    516   65 0.1016 0.1824      4.6816      4.9426|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7003 -  4.6549  1413   157  0.94   8.84   0.98     0.96       6791.54|
|  2:  4.6549 -  3.7143  1368   153  0.95   7.72   1.03     1.02       8561.58|
|  3:  3.7143 -  3.2506  1338   149  0.94  10.93   1.04     1.03       9701.18|
|  4:  3.2506 -  2.9560  1316   141  0.93  12.78   1.02     1.01       9466.50|
|  5:  2.9560 -  2.7456  1312   146  0.91  15.13   1.00     0.98       7528.62|
|  6:  2.7456 -  2.5847  1309   149  0.90  15.78   0.99     0.96       6552.01|
|  7:  2.5847 -  2.4559  1303   150  0.91  14.68   0.99     0.96       5612.85|
|  8:  2.4559 -  2.3494  1326   140  0.91  14.71   1.01     0.99       5168.64|
|  9:  2.3494 -  2.2593  1285   147  0.91  14.99   1.01     0.97       4532.65|
| 10:  2.2593 -  2.1816  1300   139  0.91  15.14   1.01     0.98       4218.96|
| 11:  2.1816 -  2.1136  1286   147  0.91  15.49   1.01     0.98       4020.40|
| 12:  2.1136 -  2.0533  1283   143  0.91  14.78   1.02     1.02       3619.29|
| 13:  2.0533 -  1.9994  1275   133  0.91  15.44   1.01     0.99       3164.78|
| 14:  1.9994 -  1.9507   516    65  0.91  15.38   0.99     0.95       2690.11|
|alpha:            min =        0.95 max =            1.03 mean =         0.99|
|beta:             min =     2690.11 max =         9701.18 mean =      6007.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.94 mean =        13.56|
|phase err.(test): min =        0.00 max =           89.40 mean =        13.23|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.467)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.50    92.03   16.89    None  None   None       |
|    all(noH): 2823   0      1.50    92.03   16.89    None  None   None       |
|    Sol.    : 438    0      5.76    73.38   38.76    None  None   None       |
|    Mac.    : 2385   0      1.50    92.03   12.87    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.499 -  10.552: 1155   |   5:    46.763 -  55.816:  107        |
|      1:    10.552 -  19.605: 1028   |   6:    55.816 -  64.869:   42        |
|      2:    19.605 -  28.658:  203   |   7:    64.869 -  73.922:   14        |
|      3:    28.658 -  37.711:  137   |   8:    73.922 -  82.975:    4        |
|      4:    37.711 -  46.763:  131   |   9:    82.975 -  92.028:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 264         
Filter by distance & map next to the model:
   mapped sites are within: 0.661 - 5.444
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 262 from: 264
   mapped sites are within: 0.709 - 5.444

peak=    5.926 closest distance to " O   HOH Z 142 " =    1.712
peak=    5.678 closest distance to " CB  ARG A 275 " =    0.963
peak=    5.561 closest distance to " NE2 GLN A  11 " =    1.104
peak=    5.172 closest distance to " O   HOH Z 126 " =    1.903
peak=    5.021 closest distance to " NH2 ARG A  56 " =    2.087
peak=    4.899 closest distance to " CB  SER A  63 " =    1.113
peak=    4.840 closest distance to " CB  GLN A 183 " =    1.287
peak=    4.714 closest distance to " CG  PRO A  54 " =    1.177
peak=    4.708 closest distance to " O   HOH Z  78 " =    1.845
peak=    4.681 closest distance to " CB  GLN A 223 " =    1.506
peak=    4.672 closest distance to " O   HOH Z 209 " =    2.259
peak=    4.666 closest distance to " O   HOH Z 272 " =    1.810
peak=    4.603 closest distance to " C   PRO A 198 " =    1.456
peak=    4.572 closest distance to " O   HOH Z 232 " =    2.390
peak=    4.568 closest distance to " CB  GLU A 152 " =    1.187
peak=    4.532 closest distance to " O   SER A  87 " =    2.216
peak=    4.491 closest distance to " O   HOH Z 369 " =    2.117
peak=    4.483 closest distance to " CD2 TRP A 179 " =    1.387
peak=    4.454 closest distance to " O   HOH Z  97 " =    2.426
peak=    4.441 closest distance to " O   HOH Z 193 " =    1.734
peak=    4.428 closest distance to " CG  PRO A 213 " =    1.225
peak=    4.407 closest distance to " CA  TYR A  30 " =    0.916
peak=    4.407 closest distance to " CB  ARG A  79 " =    1.351
peak=    4.404 closest distance to " O   HOH Z 427 " =    2.828
peak=    4.383 closest distance to " CB  ASN A 148 " =    1.525
peak=    4.374 closest distance to " O   HOH Z 298 " =    1.791
peak=    4.312 closest distance to " O   HOH Z  54 " =    1.749
peak=    4.308 closest distance to " O   HOH Z 287 " =    1.988
peak=    4.307 closest distance to " O   HOH Z 402 " =    1.447
peak=    4.292 closest distance to " ND2 ASN A 187 " =    1.438
peak=    4.252 closest distance to " O   HOH Z 316 " =    3.027
peak=    4.240 closest distance to " O   HOH Z 392 " =    2.778
peak=    4.223 closest distance to " O   HOH Z 327 " =    1.591
peak=    4.223 closest distance to " O   HOH Z 346 " =    1.671
peak=    4.218 closest distance to " O   HOH Z 250 " =    1.472
peak=    4.186 closest distance to " O   HOH Z 234 " =    3.521
peak=    4.174 closest distance to " O   HOH Z  97 " =    1.930
peak=    4.167 closest distance to " O   HOH Z 128 " =    1.892
peak=    4.153 closest distance to " O   HOH Z  43 " =    2.003
peak=    4.117 closest distance to " O   HOH Z 126 " =    2.027
peak=    4.114 closest distance to " O   HOH Z 368 " =    1.991
peak=    4.103 closest distance to " CG  ARG A  66 " =    2.632
peak=    4.100 closest distance to " O   HOH Z 303 " =    2.149
peak=    4.072 closest distance to " CB  VAL A 265 " =    1.234
peak=    4.069 closest distance to " OE1 GLU A   2 " =    2.227
peak=    4.065 closest distance to " CB  PRO A  54 " =    0.942
peak=    4.052 closest distance to " O   HOH Z 203 " =    1.731
peak=    4.051 closest distance to " O   HOH Z  59 " =    1.909
peak=    4.048 closest distance to " O   HOH Z 423 " =    1.977
peak=    4.024 closest distance to " CB  ARG A 190 " =    1.688
peak=    4.020 closest distance to " CB  SER A  26 " =    1.629
peak=    4.011 closest distance to " O   HOH Z  15 " =    2.273
peak=    4.011 closest distance to " O   HOH Z 403 " =    1.742
peak=    4.003 closest distance to " O   HOH Z  40 " =    1.684
peak=    3.992 closest distance to " CG1 ILE A  33 " =    1.194
peak=    3.979 closest distance to " O   HOH Z 245 " =    1.365
peak=    3.960 closest distance to " NZ  LYS A 117 " =    3.007
peak=    3.949 closest distance to " NH2BARG A 145 " =    1.991
peak=    3.947 closest distance to " O   HOH Z  44 " =    1.860
peak=    3.905 closest distance to " O   HOH Z 389 " =    1.846
peak=    3.859 closest distance to " O   HOH Z 417 " =    3.268
peak=    3.857 closest distance to " O   HOH Z  61 " =    1.533
peak=    3.854 closest distance to " O   HOH Z  68 " =    2.134
peak=    3.839 closest distance to " O   HOH Z 416 " =    2.650
peak=    3.825 closest distance to " CG  GLN A  77 " =    2.147
peak=    3.815 closest distance to " O   HOH Z 344 " =    3.088
peak=    3.790 closest distance to " O   HOH Z 144 " =    2.096
peak=    3.787 closest distance to " CA  ALA A  21 " =    1.115
peak=    3.787 closest distance to " O   HOH Z 158 " =    3.004
peak=    3.781 closest distance to " CB  SER A   3 " =    1.210
peak=    3.771 closest distance to " O   HOH Z  61 " =    1.645
peak=    3.769 closest distance to " O   HOH Z 189 " =    1.945
peak=    3.759 closest distance to " O   HOH Z 128 " =    2.142
peak=    3.756 closest distance to " O   HOH Z 265 " =    2.237
peak=    3.749 closest distance to " O   HOH Z 365 " =    2.746
peak=    3.746 closest distance to " OG BSER A 164 " =    2.090
peak=    3.743 closest distance to " O   HOH Z 284 " =    2.979
peak=    3.741 closest distance to " O   HOH Z 299 " =    4.223
peak=    3.738 closest distance to " CB  TRP A 266 " =    1.031
peak=    3.738 closest distance to " CA  ALA A  84 " =    1.240
peak=    3.730 closest distance to " O   HOH Z 425 " =    2.092
peak=    3.730 closest distance to " CB  VAL A 202 " =    1.558
peak=    3.728 closest distance to " O   HOH Z  88 " =    2.635
peak=    3.717 closest distance to " O   HOH Z 132 " =    2.623
peak=    3.709 closest distance to " OD1 ASN A  69 " =    2.598
peak=    3.698 closest distance to " CG  PRO A 243 " =    1.073
peak=    3.688 closest distance to " N   HIS A 108 " =    1.868
peak=    3.687 closest distance to " N   ASN A  39 " =    1.195
peak=    3.686 closest distance to " OD2 ASP A 286 " =    2.689
peak=    3.681 closest distance to " O   HOH Z 173 " =    2.048
peak=    3.680 closest distance to " CG  PRO A  90 " =    1.146
peak=    3.669 closest distance to " CD  ARG A 269 " =    0.936
peak=    3.668 closest distance to " O   HOH Z   1 " =    2.057
peak=    3.665 closest distance to " O   HOH Z  80 " =    1.688
peak=    3.662 closest distance to " CB  GLU A 277 " =    3.458
peak=    3.655 closest distance to " CB  TYR A 169 " =    0.795
peak=    3.649 closest distance to " CA  ASN A 215 " =    1.063
peak=    3.644 closest distance to " O   HOH Z  49 " =    2.127
peak=    3.636 closest distance to " O   HOH Z 286 " =    2.192
peak=    3.623 closest distance to " O   HOH Z 305 " =    3.516
peak=    3.620 closest distance to " O   HOH Z 406 " =    1.554
peak=    3.619 closest distance to " CG2 ILE A 120 " =    1.108
peak=    3.611 closest distance to " CG AARG A 275 " =    1.091
peak=    3.599 closest distance to " CG2 ILE A  20 " =    1.369
peak=    3.593 closest distance to " CB  GLU A 128 " =    1.069
peak=    3.587 closest distance to " CB  THR A  31 " =    1.695
peak=    3.586 closest distance to " O   HOH Z 357 " =    1.870
peak=    3.586 closest distance to " O   HOH Z  10 " =    1.867
peak=    3.586 closest distance to " O   HOH Z 180 " =    2.259
peak=    3.581 closest distance to " O   HOH Z 361 " =    3.617
peak=    3.579 closest distance to " O  BHOH Z 338 " =    2.399
peak=    3.573 closest distance to " CB  ASP A 140 " =    1.030
peak=    3.571 closest distance to " CA  MET A  40 " =    1.090
peak=    3.569 closest distance to " O   HOH Z 337 " =    3.402
peak=    3.550 closest distance to " CG  PRO A 198 " =    1.253
peak=    3.549 closest distance to " O   HOH Z 342 " =    0.865
peak=    3.547 closest distance to " O   HOH Z 227 " =    1.570
peak=    3.545 closest distance to " O   HOH Z 433 " =    1.871
peak=    3.545 closest distance to " CG  MET A 185 " =    1.072
peak=    3.542 closest distance to " CG  LYS A  76 " =    0.995
peak=    3.539 closest distance to " O   HOH Z 132 " =    2.320
peak=    3.536 closest distance to " O   HOH Z 426 " =    1.489
peak=    3.533 closest distance to " CB  TRP A 179 " =    1.183
peak=    3.527 closest distance to " CD1 ILE A 106 " =    0.908
peak=    3.524 closest distance to " O   HOH Z 214 " =    2.142
peak=    3.520 closest distance to " N   ARG A 156 " =    1.312
peak=    3.508 closest distance to " O   HOH Z 411 " =    3.775
peak=    3.504 closest distance to " CG1BVAL A  72 " =    1.549
peak=    3.503 closest distance to " O   HOH Z 380 " =    1.916
peak=    3.501 closest distance to " NH1AARG A 145 " =    1.163
peak=    3.499 closest distance to " O   ALA A   1 " =    1.675
peak=    3.498 closest distance to " O   HOH Z 345 " =    3.047
peak=    3.492 closest distance to " CB  ASN A 110 " =    1.063
peak=    3.488 closest distance to " CE  LYS A 119 " =    1.074
peak=    3.479 closest distance to " CD2 LEU A 297 " =    0.925
peak=    3.473 closest distance to " O   HOH Z  85 " =    1.375
peak=    3.473 closest distance to " O   HOH Z 147 " =    1.758
peak=    3.473 closest distance to " CB  ALA A 248 " =    1.432
peak=    3.472 closest distance to " CA  ARG A  36 " =    0.961
peak=    3.469 closest distance to " CA  ALA A 291 " =    0.810
peak=    3.466 closest distance to " CG2 VAL A 257 " =    0.839
peak=    3.458 closest distance to " O   HOH Z  94 " =    1.981
peak=    3.456 closest distance to " CA  ASN A 176 " =    1.150
peak=    3.453 closest distance to " N   PHE A 130 " =    1.287
peak=    3.451 closest distance to " CB  ALA A 291 " =    1.257
peak=    3.445 closest distance to " O   HOH Z 124 " =    1.267
peak=    3.435 closest distance to " O   HOH Z  47 " =    1.571
peak=    3.435 closest distance to " O   HOH Z  19 " =    2.122
peak=    3.434 closest distance to " CB  ARG A 139 " =    1.071
peak=    3.430 closest distance to " O   HOH Z  21 " =    1.787
peak=    3.426 closest distance to " O   HOH Z 273 " =    2.615
peak=    3.419 closest distance to " O   HOH Z 291 " =    1.435
peak=    3.414 closest distance to " CA  ALA A  51 " =    0.890
peak=    3.412 closest distance to " O   HOH Z 261 " =    1.619
peak=    3.401 closest distance to " O   HOH Z 380 " =    2.006
peak=    3.399 closest distance to " O   HOH Z 371 " =    1.517
peak=    3.395 closest distance to " CB  GLN A  88 " =    1.212
peak=    3.393 closest distance to " CB  LEU A 228 " =    1.153
peak=    3.391 closest distance to " CB  ILE A 120 " =    1.311
peak=    3.389 closest distance to " CB  ASN A  39 " =    0.808
peak=    3.385 closest distance to " O   HOH Z 248 " =    1.549
peak=    3.384 closest distance to " CA  LYS A 117 " =    1.221
peak=    3.383 closest distance to " O   HOH Z  40 " =    2.642
peak=    3.381 closest distance to " N   TYR A 116 " =    1.591
peak=    3.374 closest distance to " OE2 GLU A  53 " =    2.085
peak=    3.374 closest distance to " O   HOH Z 371 " =    3.347
peak=    3.371 closest distance to " O   HOH Z 236 " =    1.438
peak=    3.368 closest distance to " O  BHOH Z  74 " =    1.412
peak=    3.367 closest distance to " O   HOH Z 193 " =    2.026
peak=    3.364 closest distance to " O   HOH Z 207 " =    1.668
peak=    3.362 closest distance to " CD  GLN A 194 " =    1.428
peak=    3.360 closest distance to " CG2 THR A 294 " =    1.489
peak=    3.358 closest distance to " O   HOH Z  71 " =    2.147
peak=    3.355 closest distance to " OG  SER A  62 " =    2.773
peak=    3.353 closest distance to " O   HOH Z 109 " =    1.070
peak=    3.352 closest distance to " O   HOH Z 172 " =    3.656
peak=    3.352 closest distance to " CZ  PHE A 218 " =    1.050
peak=    3.346 closest distance to " CB  HIS A 108 " =    0.865
peak=    3.346 closest distance to " O   HOH Z   3 " =    1.755
peak=    3.345 closest distance to " O   HOH Z 267 " =    2.024
peak=    3.338 closest distance to " CB  LYS A 290 " =    1.016
peak=    3.337 closest distance to " NE2 GLN A  73 " =    3.780
peak=    3.334 closest distance to " O   HOH Z 353 " =    2.554
peak=    3.326 closest distance to " O   HOH Z  85 " =    2.422
peak=    3.325 closest distance to " CA  SER A 146 " =    1.799
peak=    3.325 closest distance to " NH2 ARG A 219 " =    1.912
peak=    3.323 closest distance to " CD2 HIS A  81 " =    1.097
peak=    3.322 closest distance to " O   HOH Z 148 " =    3.263
peak=    3.321 closest distance to " CE  LYS A  76 " =    0.820
peak=    3.319 closest distance to " CB  TYR A 169 " =    0.968
peak=    3.318 closest distance to " CA  ARG A 195 " =    1.301
peak=    3.313 closest distance to " O   HOH Z  89 " =    2.141
peak=    3.310 closest distance to " O   HOH Z 359 " =    1.412
peak=    3.310 closest distance to " O   HOH Z  63 " =    2.285
peak=    3.309 closest distance to " O   HOH Z  35 " =    2.449
peak=    3.302 closest distance to " CG2BVAL A  41 " =    0.815
peak=    3.288 closest distance to " O   HOH Z 421 " =    1.825
peak=    3.287 closest distance to " CG  ARG A 269 " =    1.238
peak=    3.286 closest distance to " CA  ASP A 162 " =    1.052
peak=    3.284 closest distance to " O   HOH Z 261 " =    2.291
peak=    3.281 closest distance to " CB  TYR A 116 " =    0.810
peak=    3.278 closest distance to " CD  LYS A 166 " =    1.220
peak=    3.271 closest distance to " O   HOH Z 251 " =    1.575
peak=    3.270 closest distance to " O   HOH Z 255 " =    1.658
peak=    3.269 closest distance to " O   HOH Z 185 " =    1.738
peak=    3.263 closest distance to " O   HOH Z 336 " =    1.696
peak=    3.262 closest distance to " O   HOH Z 250 " =    1.547
peak=    3.257 closest distance to " O   HOH Z   9 " =    2.143
peak=    3.257 closest distance to " CG  LEU A 167 " =    1.293
peak=    3.243 closest distance to " CB  ASN A 215 " =    1.096
peak=    3.239 closest distance to " O   HOH Z 435 " =    1.792
peak=    3.238 closest distance to " CD  LYS A  76 " =    1.706
peak=    3.238 closest distance to " O   HOH Z 334 " =    1.286
peak=    3.228 closest distance to " NH2AARG A 190 " =    1.895
peak=    3.225 closest distance to " O   HOH Z  88 " =    2.455
peak=    3.222 closest distance to " O   HOH Z 234 " =    2.122
peak=    3.209 closest distance to " CG  LYS A 119 " =    1.145
peak=    3.209 closest distance to " N   ASP A 162 " =    1.191
peak=    3.201 closest distance to " O   HOH Z  64 " =    2.190
peak=    3.196 closest distance to " CA  ARG A 159 " =    1.288
peak=    3.189 closest distance to " CG  MET A 113 " =    1.024
peak=    3.187 closest distance to " O   HOH Z 329 " =    3.881
peak=    3.184 closest distance to " CA  ASP A 140 " =    1.091
peak=    3.177 closest distance to " CB  ALA A  34 " =    1.092
peak=    3.177 closest distance to " CA  ILE A 234 " =    0.950
peak=    3.169 closest distance to " O   HOH Z 126 " =    1.511
peak=    3.166 closest distance to " O   HOH Z 409 " =    3.108
peak=    3.158 closest distance to " O   HOH Z 291 " =    1.663
peak=    3.158 closest distance to " O   HOH Z 393 " =    3.301
peak=    3.157 closest distance to " OE1 GLU A 236 " =    1.360
peak=    3.157 closest distance to " O   HOH Z 286 " =    2.283
peak=    3.147 closest distance to " CB  ASN A 285 " =    0.984
peak=    3.145 closest distance to " CB  GLU A  46 " =    1.036
peak=    3.140 closest distance to " CA  ASP A 231 " =    1.832
peak=    3.137 closest distance to " O   HOH Z 279 " =    2.175
peak=    3.137 closest distance to " O   HOH Z 345 " =    1.533
peak=    3.135 closest distance to " CB  SER A  62 " =    1.447
peak=    3.133 closest distance to " OG  SER A  22 " =    2.564
peak=    3.133 closest distance to " CB  ALA A 114 " =    1.150
peak=    3.133 closest distance to " OG  SER A  62 " =    3.535
peak=    3.131 closest distance to " ND1 HIS A  81 " =    1.566
peak=    3.118 closest distance to " O   HOH Z 332 " =    1.511
peak=    3.116 closest distance to " CA  ALA A 158 " =    1.417
peak=    3.115 closest distance to " CG  ARG A  66 " =    0.942
peak=    3.113 closest distance to " O   HOH Z 430 " =    5.444
peak=    3.113 closest distance to " OG BSER A 134 " =    2.878
peak=    3.113 closest distance to " CB  LEU A 255 " =    0.721
peak=    3.111 closest distance to " O   HOH Z 368 " =    2.742
peak=    3.110 closest distance to " CB  ARG A 156 " =    1.064
peak=    3.110 closest distance to " O   HOH Z 102 " =    1.274
peak=    3.108 closest distance to " O   HOH Z 109 " =    1.980
peak=    3.107 closest distance to " O   HOH Z 112 " =    2.647
peak=    3.105 closest distance to " CB  GLN A 278 " =    0.849
peak=    3.100 closest distance to " CG2 VAL A 202 " =    1.152
peak=    3.087 closest distance to " CB  VAL A 126 " =    1.183
peak=    3.086 closest distance to " CA  MET A 105 " =    1.003
peak=    3.080 closest distance to " CA  ARG A 275 " =    1.902
peak=    3.074 closest distance to " CG2 VAL A 197 " =    1.078
peak=    3.074 closest distance to " CB  MET A  47 " =    1.152
peak=    3.066 closest distance to " CE AMET A  47 " =    1.371
peak=    3.062 closest distance to " CA  GLY A  80 " =    0.709
peak=    3.057 closest distance to " CA  ALA A 299 " =    0.890

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 220         
Filter by distance & map next to the model:
   mapped sites are within: 0.755 - 5.875
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 220 from: 220
   mapped sites are within: 0.755 - 5.875

peak=   -4.946 closest distance to " O   HOH Z 266 " =    4.889
peak=   -4.420 closest distance to " CB  PRO A 243 " =    2.652
peak=   -4.394 closest distance to " OG BSER A 134 " =    1.252
peak=   -4.342 closest distance to " C   HIS A 108 " =    1.108
peak=   -4.332 closest distance to " SG  CYS A 254 " =    3.309
peak=   -4.289 closest distance to " O   VAL A  67 " =    2.725
peak=   -4.285 closest distance to " CG  GLN A 223 " =    2.130
peak=   -4.255 closest distance to " CD  ARG A 156 " =    2.118
peak=   -4.254 closest distance to " N   ALA A 248 " =    1.758
peak=   -4.245 closest distance to " O   VAL A  67 " =    2.776
peak=   -4.242 closest distance to " N   GLN A  58 " =    1.704
peak=   -4.192 closest distance to " CG  GLN A  58 " =    1.109
peak=   -4.120 closest distance to " O   HOH Z  13 " =    1.646
peak=   -4.093 closest distance to " OXT GLY A 302 " =    2.793
peak=   -4.056 closest distance to " CB  ALA A 291 " =    2.328
peak=   -4.045 closest distance to " CD  ARG A 139 " =    1.574
peak=   -4.013 closest distance to " O   GLY A 136 " =    2.360
peak=   -4.003 closest distance to " C   ILE A 239 " =    2.171
peak=   -3.987 closest distance to " OD2 ASP A 171 " =    2.334
peak=   -3.940 closest distance to " CE2 TYR A  30 " =    2.776
peak=   -3.925 closest distance to " O   HOH Z 290 " =    1.156
peak=   -3.922 closest distance to " CG1 VAL A 112 " =    2.759
peak=   -3.903 closest distance to " O   PRO A 198 " =    1.264
peak=   -3.879 closest distance to " O   HOH Z 407 " =    2.572
peak=   -3.876 closest distance to " O   HOH Z 198 " =    1.881
peak=   -3.851 closest distance to " CB  ASN A  39 " =    2.219
peak=   -3.851 closest distance to " CE  MET A 105 " =    2.333
peak=   -3.838 closest distance to " CB  PHE A 192 " =    1.928
peak=   -3.830 closest distance to " O   HOH Z 372 " =    2.186
peak=   -3.829 closest distance to " CZ  TYR A 169 " =    1.782
peak=   -3.826 closest distance to " CD1 LEU A 101 " =    2.377
peak=   -3.826 closest distance to " O   VAL A 174 " =    2.142
peak=   -3.823 closest distance to " OD2 ASP A 191 " =    1.430
peak=   -3.813 closest distance to " N   ALA A 248 " =    2.183
peak=   -3.810 closest distance to " O   PRO A 163 " =    1.987
peak=   -3.806 closest distance to " O   PHE A 218 " =    1.666
peak=   -3.801 closest distance to " O   HOH Z 165 " =    2.054
peak=   -3.776 closest distance to " O   HOH Z 102 " =    1.693
peak=   -3.729 closest distance to " O   PRO A 198 " =    1.233
peak=   -3.724 closest distance to " CG  PHE A 283 " =    2.616
peak=   -3.713 closest distance to " CB  ALA A 161 " =    2.454
peak=   -3.712 closest distance to " O   HOH Z 362 " =    5.716
peak=   -3.703 closest distance to " O   HOH Z 185 " =    2.287
peak=   -3.699 closest distance to " C   GLN A 205 " =    1.818
peak=   -3.688 closest distance to " O   HOH Z 211 " =    1.787
peak=   -3.680 closest distance to " CB  ASP A 132 " =    2.250
peak=   -3.670 closest distance to " O   ALA A 161 " =    1.629
peak=   -3.664 closest distance to " ND2 ASN A 187 " =    1.520
peak=   -3.656 closest distance to " CA  GLY A 203 " =    2.317
peak=   -3.654 closest distance to " O   HOH Z 196 " =    1.959
peak=   -3.653 closest distance to " OG  SER A  97 " =    2.165
peak=   -3.632 closest distance to " O   HOH Z  15 " =    1.527
peak=   -3.627 closest distance to " O   HOH Z 114 " =    3.183
peak=   -3.624 closest distance to " OD1 ASP A 191 " =    1.498
peak=   -3.609 closest distance to " CD1 PHE A  59 " =    1.858
peak=   -3.599 closest distance to " O   GLN A  89 " =    1.546
peak=   -3.593 closest distance to " CB  PHE A 208 " =    2.225
peak=   -3.593 closest distance to " CG2 ILE A 263 " =    2.143
peak=   -3.590 closest distance to " N   THR A 220 " =    2.219
peak=   -3.587 closest distance to " N   ASP A 286 " =    2.279
peak=   -3.584 closest distance to " NE  ARG A 156 " =    1.891
peak=   -3.582 closest distance to " O   HOH Z  38 " =    1.626
peak=   -3.579 closest distance to " CZ3 TRP A 179 " =    1.256
peak=   -3.576 closest distance to " CA  ASP A 298 " =    1.086
peak=   -3.570 closest distance to " CB  ALA A 248 " =    2.157
peak=   -3.566 closest distance to " CB  PRO A 163 " =    2.524
peak=   -3.562 closest distance to " O   SER A  95 " =    1.508
peak=   -3.560 closest distance to " O   HOH Z 126 " =    1.908
peak=   -3.559 closest distance to " ND2 ASN A  45 " =    1.031
peak=   -3.557 closest distance to " O   HOH Z 183 " =    1.482
peak=   -3.556 closest distance to " O   HOH Z 313 " =    1.899
peak=   -3.552 closest distance to " OG  SER A   3 " =    1.677
peak=   -3.551 closest distance to " CD1 LEU A 255 " =    2.690
peak=   -3.548 closest distance to " ND2 ASN A  39 " =    1.189
peak=   -3.545 closest distance to " O   SER A 210 " =    1.959
peak=   -3.543 closest distance to " N   ALA A  43 " =    2.568
peak=   -3.540 closest distance to " CG1 VAL A 230 " =    1.874
peak=   -3.535 closest distance to " CB  ALA A 291 " =    2.251
peak=   -3.532 closest distance to " O   HOH Z 351 " =    1.486
peak=   -3.522 closest distance to " CB  ASP A 286 " =    2.095
peak=   -3.517 closest distance to " O   HOH Z  11 " =    2.074
peak=   -3.515 closest distance to " O   HOH Z 421 " =    3.198
peak=   -3.512 closest distance to " O   HOH Z 309 " =    2.596
peak=   -3.504 closest distance to " ND2 ASN A  45 " =    1.476
peak=   -3.503 closest distance to " CD1 LEU A  25 " =    2.516
peak=   -3.494 closest distance to " C   MET A 188 " =    1.491
peak=   -3.492 closest distance to " O   MET A  40 " =    2.715
peak=   -3.490 closest distance to " O   HOH Z 385 " =    2.046
peak=   -3.476 closest distance to " O   SER A 135 " =    1.507
peak=   -3.473 closest distance to " OG BSER A 134 " =    1.675
peak=   -3.467 closest distance to " O   HOH Z 389 " =    1.743
peak=   -3.462 closest distance to " CD2 LEU A 237 " =    2.508
peak=   -3.459 closest distance to " CG  GLU A   2 " =    1.956
peak=   -3.456 closest distance to " NH1 ARG A 195 " =    2.611
peak=   -3.452 closest distance to " O   HOH Z 198 " =    1.404
peak=   -3.450 closest distance to " O   HOH Z 243 " =    1.943
peak=   -3.440 closest distance to " OE1 GLN A 183 " =    1.521
peak=   -3.435 closest distance to " CB  ALA A 248 " =    2.213
peak=   -3.434 closest distance to " O   HOH Z 139 " =    5.064
peak=   -3.434 closest distance to " SG ACYS A 201 " =    2.031
peak=   -3.431 closest distance to " CG1 VAL A  78 " =    3.083
peak=   -3.430 closest distance to " C   ILE A 234 " =    1.371
peak=   -3.423 closest distance to " O   SER A  26 " =    1.187
peak=   -3.419 closest distance to " O   HOH Z 197 " =    4.976
peak=   -3.417 closest distance to " O   HOH Z 166 " =    1.480
peak=   -3.415 closest distance to " OD1 ASN A 148 " =    1.559
peak=   -3.404 closest distance to " OD1 ASP A 171 " =    1.594
peak=   -3.401 closest distance to " O   HOH Z 200 " =    4.990
peak=   -3.400 closest distance to " CE  MET A 105 " =    2.008
peak=   -3.398 closest distance to " CG  GLU A  53 " =    1.454
peak=   -3.392 closest distance to " N   PRO A 163 " =    1.518
peak=   -3.391 closest distance to " NE2 GLN A  88 " =    1.812
peak=   -3.390 closest distance to " CZ3 TRP A 274 " =    1.219
peak=   -3.389 closest distance to " O   HOH Z 281 " =    2.701
peak=   -3.389 closest distance to " CD2 TYR A 247 " =    2.471
peak=   -3.386 closest distance to " CA  GLY A 241 " =    2.327
peak=   -3.386 closest distance to " CG2 THR A 178 " =    2.192
peak=   -3.384 closest distance to " C   ASP A 231 " =    2.546
peak=   -3.382 closest distance to " CZ  PHE A  59 " =    1.535
peak=   -3.381 closest distance to " OD1 ASN A  39 " =    2.165
peak=   -3.380 closest distance to " OXT GLY A 302 " =    3.340
peak=   -3.380 closest distance to " CG  ASP A 231 " =    0.794
peak=   -3.373 closest distance to " O   SER A 146 " =    1.041
peak=   -3.373 closest distance to " O   HOH Z  63 " =    1.490
peak=   -3.369 closest distance to " O   ILE A 106 " =    2.029
peak=   -3.361 closest distance to " O   HOH Z 427 " =    1.408
peak=   -3.359 closest distance to " O   HOH Z  11 " =    1.751
peak=   -3.355 closest distance to " O   SER A  22 " =    2.448
peak=   -3.353 closest distance to " O   ALA A 292 " =    1.902
peak=   -3.352 closest distance to " OD1 ASP A 191 " =    1.827
peak=   -3.351 closest distance to " O   ARG A 145 " =    1.665
peak=   -3.350 closest distance to " OD1 ASN A 301 " =    1.949
peak=   -3.345 closest distance to " CD  GLN A 223 " =    0.755
peak=   -3.342 closest distance to " O   ALA A  34 " =    2.214
peak=   -3.339 closest distance to " OG1 THR A 178 " =    1.299
peak=   -3.338 closest distance to " C   LEU A 143 " =    1.036
peak=   -3.336 closest distance to " CZ2 TRP A 274 " =    1.021
peak=   -3.319 closest distance to " ND2 ASN A  60 " =    1.384
peak=   -3.318 closest distance to " O   HOH Z  10 " =    1.385
peak=   -3.315 closest distance to " O   LEU A 167 " =    1.596
peak=   -3.313 closest distance to " O   SER A   3 " =    1.024
peak=   -3.310 closest distance to " O   HOH Z 123 " =    2.278
peak=   -3.306 closest distance to " CD2 PHE A 225 " =    1.265
peak=   -3.305 closest distance to " CE3 TRP A 274 " =    2.360
peak=   -3.305 closest distance to " O   ASN A 187 " =    1.469
peak=   -3.302 closest distance to " CB  ASP A 132 " =    2.373
peak=   -3.298 closest distance to " NH2AARG A 275 " =    4.996
peak=   -3.298 closest distance to " CD  GLN A  88 " =    1.127
peak=   -3.296 closest distance to " O   HOH Z  24 " =    1.416
peak=   -3.294 closest distance to " O   HOH Z 174 " =    4.070
peak=   -3.286 closest distance to " CG  TRP A 266 " =    2.095
peak=   -3.286 closest distance to " O   HOH Z 394 " =    1.461
peak=   -3.282 closest distance to " O   TRP A  70 " =    1.458
peak=   -3.279 closest distance to " CG1 VAL A 265 " =    2.732
peak=   -3.279 closest distance to " OD2 ASP A  50 " =    1.402
peak=   -3.274 closest distance to " O  BHOH Z 338 " =    1.441
peak=   -3.273 closest distance to " O   TRP A  92 " =    1.717
peak=   -3.272 closest distance to " NH2 ARG A  66 " =    5.150
peak=   -3.270 closest distance to " NH1 ARG A  66 " =    1.150
peak=   -3.269 closest distance to " CA  GLY A 133 " =    1.864
peak=   -3.269 closest distance to " O   HOH Z 139 " =    3.050
peak=   -3.266 closest distance to " CG2 VAL A 189 " =    2.112
peak=   -3.265 closest distance to " O   HOH Z 137 " =    1.442
peak=   -3.259 closest distance to " OD1 ASN A 176 " =    1.291
peak=   -3.257 closest distance to " CG  GLU A 152 " =    1.073
peak=   -3.249 closest distance to " O   HOH Z 417 " =    2.376
peak=   -3.249 closest distance to " N   THR A  52 " =    1.758
peak=   -3.247 closest distance to " O   HOH Z 422 " =    1.550
peak=   -3.244 closest distance to " CZ  ARG A 259 " =    0.919
peak=   -3.242 closest distance to " O   HOH Z 140 " =    1.888
peak=   -3.241 closest distance to " O   ASP A 162 " =    2.120
peak=   -3.238 closest distance to " CB  GLN A  11 " =    1.957
peak=   -3.237 closest distance to " OG ASER A 134 " =    1.233
peak=   -3.231 closest distance to " C   ALA A 158 " =    1.298
peak=   -3.230 closest distance to " OG  SER A  26 " =    1.173
peak=   -3.222 closest distance to " O   HOH Z  52 " =    1.313
peak=   -3.219 closest distance to " O   HOH Z 369 " =    2.143
peak=   -3.219 closest distance to " O   HOH Z 263 " =    2.927
peak=   -3.216 closest distance to " O   HOH Z 377 " =    1.542
peak=   -3.211 closest distance to " O   HOH Z 326 " =    1.683
peak=   -3.209 closest distance to " CD2 TYR A 293 " =    1.995
peak=   -3.207 closest distance to " NE2 GLN A 194 " =    1.699
peak=   -3.206 closest distance to " O   HOH Z 251 " =    1.386
peak=   -3.204 closest distance to " O   HOH Z 166 " =    2.046
peak=   -3.201 closest distance to " CD2 PHE A  61 " =    2.324
peak=   -3.190 closest distance to " O   ALA A  51 " =    1.192
peak=   -3.188 closest distance to " O   HOH Z 397 " =    1.143
peak=   -3.187 closest distance to " O   HOH Z 265 " =    2.200
peak=   -3.179 closest distance to " O   HOH Z 256 " =    1.318
peak=   -3.176 closest distance to " CG  ASP A 162 " =    1.502
peak=   -3.169 closest distance to " OD2 ASP A  50 " =    2.211
peak=   -3.162 closest distance to " NH2 ARG A  79 " =    1.987
peak=   -3.154 closest distance to " O   HOH Z 134 " =    2.936
peak=   -3.152 closest distance to " OE2 GLU A 152 " =    1.267
peak=   -3.151 closest distance to " O   GLU A 152 " =    1.440
peak=   -3.149 closest distance to " O   SER A 146 " =    1.023
peak=   -3.143 closest distance to " CB  ASN A  39 " =    2.102
peak=   -3.139 closest distance to " O   HOH Z 311 " =    3.532
peak=   -3.129 closest distance to " O   HOH Z 234 " =    3.881
peak=   -3.128 closest distance to " O   HOH Z  43 " =    1.806
peak=   -3.126 closest distance to " CD1 ILE A 106 " =    2.236
peak=   -3.124 closest distance to " CD2 LEU A 300 " =    2.873
peak=   -3.118 closest distance to " O   HOH Z 339 " =    1.736
peak=   -3.116 closest distance to " O   HOH Z  37 " =    1.717
peak=   -3.115 closest distance to " O   HOH Z 414 " =    1.548
peak=   -3.108 closest distance to " CA  GLY A 241 " =    3.127
peak=   -3.105 closest distance to " O   HOH Z 191 " =    5.875
peak=   -3.105 closest distance to " O   HOH Z 148 " =    3.614
peak=   -3.104 closest distance to " CG  PRO A 243 " =    1.667
peak=   -3.102 closest distance to " O   HOH Z 362 " =    4.448
peak=   -3.101 closest distance to " O   HOH Z 423 " =    2.197
peak=   -3.091 closest distance to " O   ASN A  45 " =    1.827
peak=   -3.089 closest distance to " O   ALA A   1 " =    1.796
peak=   -3.087 closest distance to " OE1 GLN A 223 " =    1.882
peak=   -3.077 closest distance to " OH  TYR A 169 " =    0.963
peak=   -3.075 closest distance to " O   GLY A  75 " =    1.698
peak=   -3.072 closest distance to " CB  TRP A  85 " =    2.566
peak=   -3.065 closest distance to " N   PHE A  59 " =    1.791
peak=   -3.016 closest distance to " O   HOH Z 310 " =    3.362
peak=   -3.011 closest distance to " O   HOH Z  60 " =    1.877

================= 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    :  0.3448 0.3452   6.110443e+00   6.111669e+00
   1_bss:  0.3303 0.3325   6.089534e+00   6.090295e+00
   1_xyz:  0.2110 0.2349   5.665870e+00   5.760026e+00
   1_adp:  0.1917 0.2397   5.605972e+00   5.781454e+00
   1_occ:  0.1914 0.2394   5.605371e+00   5.781308e+00
   2_bss:  0.1859 0.2354   5.583821e+00   5.763828e+00
   2_xyz:  0.1418 0.1841   5.334480e+00   5.529100e+00
   2_adp:  0.1348 0.1760   5.287935e+00   5.484236e+00
   2_occ:  0.1346 0.1759   5.287121e+00   5.483660e+00
   3_bss:  0.1343 0.1745   5.282642e+00   5.476110e+00
   3_xyz:  0.1176 0.1581   5.171509e+00   5.386727e+00
   3_adp:  0.1160 0.1562   5.158142e+00   5.374091e+00
   3_occ:  0.1159 0.1560   5.157339e+00   5.373413e+00
   4_bss:  0.1159 0.1560   5.156997e+00   5.372946e+00
   4_xyz:  0.1093 0.1529   5.118993e+00   5.352846e+00
   4_adp:  0.1082 0.1526   5.114081e+00   5.351508e+00
   4_occ:  0.1081 0.1526   5.113947e+00   5.351690e+00
   5_bss:  0.1078 0.1520   5.112427e+00   5.349216e+00
   5_xyz:  0.1050 0.1526   5.102549e+00   5.353496e+00
   5_adp:  0.1042 0.1535   5.102047e+00   5.359436e+00
   5_occ:  0.1041 0.1535   5.102022e+00   5.359566e+00
   5_bss:  0.1041 0.1535   5.102115e+00   5.359556e+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:  0.314  28.446   1.792  -2.861  -1.352  -0.000  -0.000  -0.000
   1_xyz:  0.314  28.446   1.792  -2.861  -1.352  -0.000  -0.000  -0.000
   1_adp:  0.314  28.446   1.792  -2.861  -1.352  -0.000  -0.000  -0.000
   1_occ:  0.314  28.446   1.792  -2.861  -1.352  -0.000  -0.000  -0.000
   2_bss:  0.302  30.195  -2.003  -2.757  -1.636  -0.000  -0.000  -0.000
   2_xyz:  0.302  30.195  -2.003  -2.757  -1.636  -0.000  -0.000  -0.000
   2_adp:  0.302  30.195  -2.003  -2.757  -1.636  -0.000  -0.000  -0.000
   2_occ:  0.302  30.195  -2.003  -2.757  -1.636  -0.000  -0.000  -0.000
   3_bss:  0.314  35.364  -2.984  -2.486  -1.585  -0.000  -0.000  -0.000
   3_xyz:  0.314  35.364  -2.984  -2.486  -1.585  -0.000  -0.000  -0.000
   3_adp:  0.314  35.364  -2.984  -2.486  -1.585  -0.000  -0.000  -0.000
   3_occ:  0.314  35.364  -2.984  -2.486  -1.585  -0.000  -0.000  -0.000
   4_bss:  0.318  36.575  -3.256  -2.481  -1.565  -0.000  -0.000  -0.000
   4_xyz:  0.318  36.575  -3.256  -2.481  -1.565  -0.000  -0.000  -0.000
   4_adp:  0.318  36.575  -3.256  -2.481  -1.565  -0.000  -0.000  -0.000
   4_occ:  0.318  36.575  -3.256  -2.481  -1.565  -0.000  -0.000  -0.000
   5_bss:  0.318  38.100  -3.232  -2.368  -1.437  -0.000  -0.000  -0.000
   5_xyz:  0.318  38.100  -3.232  -2.368  -1.437  -0.000  -0.000  -0.000
   5_adp:  0.318  38.100  -3.232  -2.368  -1.437  -0.000  -0.000  -0.000
   5_occ:  0.318  38.100  -3.232  -2.368  -1.437  -0.000  -0.000  -0.000
   5_bss:  0.320  38.900  -3.023  -2.116  -1.182  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  37.169 0.6797  0.8839    37394.627
   1_bss:  35.976 0.6920  0.8795    33971.122
   1_xyz:  22.860 0.8344  1.0011    14315.752
   1_adp:  23.656 0.8255  0.9980    14881.681
   1_occ:  23.672 0.8253  0.9978    14903.680
   2_bss:  23.012 0.8316  0.9552    14126.169
   2_xyz:  17.136 0.8878  0.9884     8377.305
   2_adp:  16.047 0.8980  0.9926     7769.855
   2_occ:  16.035 0.8981  0.9926     7756.887
   3_bss:  15.890 0.8993  0.9845     7619.086
   3_xyz:  14.157 0.9135  0.9897     6327.116
   3_adp:  13.864 0.9160  0.9885     6220.898
   3_occ:  13.855 0.9161  0.9884     6207.468
   4_bss:  13.853 0.9161  0.9852     6203.583
   4_xyz:  13.444 0.9193  0.9861     5936.930
   4_adp:  13.395 0.9198  0.9825     5924.886
   4_occ:  13.395 0.9198  0.9824     5923.629
   5_bss:  13.362 0.9200  0.9857     5881.013
   5_xyz:  13.411 0.9198  0.9856     5957.405
   5_adp:  13.522 0.9189  0.9802     6004.637
   5_occ:  13.523 0.9189  0.9802     6005.293
   5_bss:  13.527 0.9189  0.9867     6006.872
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   2.1685e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   2.1685e-01
   1_xyz:   1.214  0.010  0.077 15.130  0.005  4.107   8.4148e-02
   1_adp:   1.214  0.010  0.077 15.130  0.005  4.107   8.4148e-02
   1_occ:   1.214  0.010  0.077 15.130  0.005  4.107   8.4148e-02
   2_bss:   1.214  0.010  0.077 15.130  0.005  4.107   8.4148e-02
   2_xyz:   0.943  0.005  0.066 14.246  0.004  4.117   5.0828e-02
   2_adp:   0.943  0.005  0.066 14.246  0.004  4.117   5.0828e-02
   2_occ:   0.943  0.005  0.066 14.246  0.004  4.117   5.0828e-02
   3_bss:   0.943  0.005  0.066 14.246  0.004  4.117   5.0828e-02
   3_xyz:   0.953  0.005  0.068 14.510  0.004  4.108   5.2777e-02
   3_adp:   0.953  0.005  0.068 14.510  0.004  4.108   5.2777e-02
   3_occ:   0.953  0.005  0.068 14.510  0.004  4.108   5.2777e-02
   4_bss:   0.953  0.005  0.068 14.510  0.004  4.108   5.2777e-02
   4_xyz:   1.029  0.007  0.074 14.746  0.004  4.108   6.1506e-02
   4_adp:   1.029  0.007  0.074 14.746  0.004  4.108   6.1506e-02
   4_occ:   1.029  0.007  0.074 14.746  0.004  4.108   6.1506e-02
   5_bss:   1.029  0.007  0.074 14.746  0.004  4.108   6.1506e-02
   5_xyz:   1.088  0.008  0.078 14.872  0.005  4.108   6.7380e-02
   5_adp:   1.088  0.008  0.078 14.872  0.005  4.108   6.7380e-02
   5_occ:   1.088  0.008  0.078 14.872  0.005  4.108   6.7380e-02
   5_bss:   1.088  0.008  0.078 14.872  0.005  4.108   6.7380e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.180   2.4184e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.180   2.4184e-01
   1_xyz:   8.339  0.067  0.288 82.777  0.044  2.082   8.4631e-02
   1_adp:   8.339  0.067  0.288 82.777  0.044  2.082   8.4631e-02
   1_occ:   8.339  0.067  0.288 82.777  0.044  2.082   8.4631e-02
   2_bss:   8.339  0.067  0.288 82.777  0.044  2.082   8.4631e-02
   2_xyz:   7.119  0.034  0.199 80.523  0.041  2.336   6.2527e-02
   2_adp:   7.119  0.034  0.199 80.523  0.041  2.336   6.2527e-02
   2_occ:   7.119  0.034  0.199 80.523  0.041  2.336   6.2527e-02
   3_bss:   7.119  0.034  0.199 80.523  0.041  2.336   6.2527e-02
   3_xyz:   7.033  0.042  0.203 83.158  0.035  2.343   3.3755e-02
   3_adp:   7.033  0.042  0.203 83.158  0.035  2.343   3.3755e-02
   3_occ:   7.033  0.042  0.203 83.158  0.035  2.343   3.3755e-02
   4_bss:   7.033  0.042  0.203 83.158  0.035  2.343   3.3755e-02
   4_xyz:   6.907  0.046  0.239 82.551  0.044  2.305   5.3907e-02
   4_adp:   6.907  0.046  0.239 82.551  0.044  2.305   5.3907e-02
   4_occ:   6.907  0.046  0.239 82.551  0.044  2.305   5.3907e-02
   5_bss:   6.907  0.046  0.239 82.551  0.044  2.305   5.3907e-02
   5_xyz:   7.125  0.050  0.258 83.790  0.043  2.301   5.6544e-02
   5_adp:   7.125  0.050  0.258 83.790  0.043  2.301   5.6544e-02
   5_occ:   7.125  0.050  0.258 83.790  0.043  2.301   5.6544e-02
   5_bss:   7.125  0.050  0.258 83.790  0.043  2.301   5.6544e-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:  81.33   0.00  17.61  81.33   0.00  13.58  75.97   6.54  39.57
   1_occ:  81.33   0.00  17.61  81.33   0.00  13.58  75.97   6.54  39.57
   2_bss:  81.33   0.00  17.61  81.33   0.00  13.58  75.97   6.54  39.57
   2_xyz:  81.33   0.00  17.61  81.33   0.00  13.58  75.97   6.54  39.57
   2_adp:  89.35   0.00  17.28  89.35   0.00  13.32  76.91   5.83  38.82
   2_occ:  89.35   0.00  17.28  89.35   0.00  13.32  76.91   5.83  38.82
   3_bss:  89.35   0.00  17.28  89.35   0.00  13.32  76.91   5.83  38.82
   3_xyz:  89.35   0.00  17.28  89.35   0.00  13.32  76.91   5.83  38.82
   3_adp:  90.56   0.00  16.97  90.56   0.00  13.12  74.18   4.65  37.90
   3_occ:  90.56   0.00  16.97  90.56   0.00  13.12  74.18   4.65  37.90
   4_bss:  90.56   0.00  16.97  90.56   0.00  13.12  74.18   4.65  37.90
   4_xyz:  90.56   0.00  16.97  90.56   0.00  13.12  74.18   4.65  37.90
   4_adp:  90.90   2.40  16.86  90.90   2.40  13.00  72.96   4.37  37.86
   4_occ:  90.90   2.40  16.86  90.90   2.40  13.00  72.96   4.37  37.86
   5_bss:  90.90   2.40  16.86  90.90   2.40  13.00  72.96   4.37  37.86
   5_xyz:  90.90   2.40  16.86  90.90   2.40  13.00  72.96   4.37  37.86
   5_adp:  92.08   1.55  16.95  92.08   1.55  12.93  73.43   5.82  38.82
   5_occ:  92.08   1.55  16.95  92.08   1.55  12.93  73.43   5.82  38.82
   5_bss:  92.03   1.50  16.89  92.03   1.50  12.87  73.38   5.76  38.76
------------------------------------------------------------------------
 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:    2.301    0.014    0.327
   1_adp:    2.301    0.014    0.327
   1_occ:    2.301    0.014    0.327
   2_bss:    2.301    0.014    0.327
   2_xyz:    1.865    0.014    0.382
   2_adp:    1.865    0.014    0.382
   2_occ:    1.865    0.014    0.382
   3_bss:    1.865    0.014    0.382
   3_xyz:    1.469    0.006    0.430
   3_adp:    1.469    0.006    0.430
   3_occ:    1.469    0.006    0.430
   4_bss:    1.469    0.006    0.430
   4_xyz:    1.233    0.020    0.447
   4_adp:    1.233    0.020    0.447
   4_occ:    1.233    0.020    0.447
   5_bss:    1.233    0.020    0.447
   5_xyz:    1.328    0.004    0.457
   5_adp:    1.328    0.004    0.457
   5_occ:    1.328    0.004    0.457
   5_bss:    1.328    0.004    0.457
------------------------------------------------------------------------

CPU time actual refinement: 360.80


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_59/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_59/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_59/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_59/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_59/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 360.65 
  Macro-tasks:
    bulk solvent and scale       = 39.91  
    individual site refinement   = 160.78 
    weights calculation          = 29.84  
    collect and process          = 6.74   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 237.35 
  Micro-tasks:
    mask                            = 1.74   
    f_calc                          = 118.81 
    alpha_beta                      = 8.43   
    target                          = 1.24   
    gradients_wrt_atomic_parameters = 124.31 
    fmodel                         = 7.13   
    r_factors                      = 0.14   
    phase_errors                   = 12.01  
    foms                           = 0.20   
    TOTAL for micro-tasks          = 274.01 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.899 micro seconds
Total CPU time: 6.23 minutes
from_scatterers_fft:    690 calls, 118.33 s
gradients_fft:          635 calls, 111.29 s

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

# Date 2008-01-16 Time 03:55:32 PST -0800 (1200484532.43 s)
Start R-work = 0.3448, R-free = 0.3452 (no bulk solvent and anisotropic scale)
Final R-work = 0.1318, R-free = 0.1750 (no bulk solvent and anisotropic scale)

Start R-work = 0.3303, R-free = 0.3325
Final R-work = 0.1041, R-free = 0.1535