# Date 2008-01-16 Time 06:51:23 PST -0800 (1200495083.30 s)
#phil __OFF__

Command line arguments: "../1310.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 28705
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1310

-------------------------------------------------------------------------------
  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: (72.0062, 47.8686, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 47.8686, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1768 1.96153
Completeness in resolution range: 0.909087
Completeness with d_max=infinity: 0.906437

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1768
                             d_min =   1.9615

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: (72.0062, 47.8686, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1768 1.96153
Completeness in resolution range: 0.909087
Completeness with d_max=infinity: 0.906437

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1772 -  4.1990 [2268/2297]  2044   224   9.9%
  bin  2:  4.1990 -  3.3446 [2157/2180]  1940   217  10.1%
  bin  3:  3.3446 -  2.9252 [2143/2168]  1924   219  10.2%
  bin  4:  2.9252 -  2.6593 [2131/2148]  1921   210   9.9%
  bin  5:  2.6593 -  2.4696 [2098/2141]  1894   204   9.7%
  bin  6:  2.4696 -  2.3245 [2104/2132]  1889   215  10.2%
  bin  7:  2.3245 -  2.2085 [2097/2133]  1882   215  10.3%
  bin  8:  2.2085 -  2.1126 [2061/2103]  1859   202   9.8%
  bin  9:  2.1126 -  2.0315 [1970/2126]  1773   197  10.0%
  bin 10:  2.0315 -  1.9615 [ 560/2120]   504    56  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1310/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.44 -     2.13: 20
        2.13 -     2.82: 890
        2.82 -     3.52: 4402
        3.52 -     4.21: 9241
        4.21 -     4.90: 13568
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.438 3.040 -x+1/2,-y+1,z+1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.508 3.120 -x+1/2,-y+1,z-1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.533 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.587 3.040 -x+1/2,-y+1,z-1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.743 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28116 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_1310/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1310/model_refine_001.geo

CPU time processing inputs: 9.12


============================ 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 = 72.00625 47.8686 84.6622 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: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4863   r_free= 0.4747   ksol= 0.00   Bsol= 0.00   scale= 0.870    |
|                                                                             |
| 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:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.292796                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1772 -  4.6842 0.99   1469  167 0.3793 0.3893      6.5722      6.5746|
|  2:  4.6842 -  3.7362 0.99   1410  155 0.4204 0.4114      6.8518      6.8621|
|  3:  3.7362 -  3.2693 0.99   1385  146 0.4692 0.4226      6.6837      6.6424|
|  4:  3.2693 -  2.9728 0.99   1376  161 0.4845 0.4738      6.5119       6.506|
|  5:  2.9728 -  2.7611 0.99   1368  150 0.5120 0.4982      6.3616      6.3534|
|  6:  2.7611 -  2.5992 0.99   1359  155 0.5284 0.5179      6.2855      6.2069|
|  7:  2.5992 -  2.4696 0.98   1356  140 0.5315 0.4796      6.2433      6.1959|
|  8:  2.4696 -  2.3625 0.98   1355  152 0.5276 0.5091      6.1422      6.1892|
|  9:  2.3625 -  2.2719 0.99   1347  153 0.5504 0.5276      6.1533      6.1238|
| 10:  2.2719 -  2.1937 0.98   1335  157 0.5373 0.5589      6.0721      6.1127|
| 11:  2.1937 -  2.1253 0.97   1337  142 0.5395 0.5659      6.0292      5.9882|
| 12:  2.1253 -  2.0647 0.98   1318  144 0.5204 0.5478      5.9311      5.9711|
| 13:  2.0647 -  2.0105 0.71    979  116 0.5293 0.4533      5.8612      5.8238|
| 14:  2.0105 -  1.9615 0.17    236   21 0.5741 0.4493      5.7818      5.8045|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1772 -  4.6842  1469   167  0.70  34.52   0.82     0.73      72576.66|
|  2:  4.6842 -  3.7362  1410   155  0.69  36.13   0.90     0.78     107881.78|
|  3:  3.7362 -  3.2693  1385   146  0.56  47.32   0.87     0.72     120375.09|
|  4:  3.2693 -  2.9728  1376   161  0.45  56.07   0.88     0.63     111494.31|
|  5:  2.9728 -  2.7611  1368   150  0.36  63.08   0.85     0.52      90573.89|
|  6:  2.7611 -  2.5992  1359   155  0.34  64.08   0.87     0.50      75784.10|
|  7:  2.5992 -  2.4696  1356   140  0.34  64.43   0.88     0.47      65102.05|
|  8:  2.4696 -  2.3625  1355   152  0.31  66.42   0.86     0.47      62654.48|
|  9:  2.3625 -  2.2719  1347   153  0.27  70.01   0.91     0.40      58232.40|
| 10:  2.2719 -  2.1937  1335   157  0.21  74.20   0.89     0.33      58418.08|
| 11:  2.1937 -  2.1253  1337   142  0.12  81.30   0.91     0.18      54989.15|
| 12:  2.1253 -  2.0647  1318   144  0.11  82.13   0.89     0.18      51610.43|
| 13:  2.0647 -  2.0105   979   116  0.18  76.74   0.91     0.29      41114.85|
| 14:  2.0105 -  1.9615   236    21  0.33  65.52   0.84     0.54      29435.39|
|alpha:            min =        0.18 max =            0.78 mean =         0.49|
|beta:             min =    29435.39 max =       120375.09 mean =     75105.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.36|
|phase err.(work): min =        0.00 max =           90.00 mean =        62.17|
|phase err.(test): min =        0.00 max =           89.90 mean =        62.13|
|-----------------------------------------------------------------------------|

============================== 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 = 22.156832             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.316   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.005423              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.729   (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 |  1.438 -  1.785:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.785 -  2.131:       14 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.131 -  2.477:       33 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.477 -  2.823:      857 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.823 -  3.169:     2007 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.169 -  3.515:     2395 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.515 -  3.862:     4579 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.862 -  4.208:     4662 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.208 -  4.554:     6159 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.554 -  4.900:     7409 |
|-----------------------------------------------------------------------------|
|-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 |        0.189 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.438 |       0.551 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.145)------------------------------------------|
|    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: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4863   r_free= 0.4747   ksol= 0.00   Bsol= 0.00   scale= 0.870    |
|                                                                             |
| 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:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.292796                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4801   r_free= 0.4679   ksol= 0.28   Bsol= 30.87   scale= 0.916   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.63,2.29,0.09,0.00,0.00,0.00); trace/3= 1.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.290838                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.193440             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.391   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.717101              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.356   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4801      final r-factor (work) = 0.3685          |
| start r-factor (free) = 0.4679      final r-factor (free) = 0.4119          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 54.2339 = 17.19 * 0.50 * 6.2867 + 1.00 * 0.1888                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 53.2803 = 17.19 * 0.50 * 6.1774 + 1.00 * 0.1750                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3685      final r-factor (work) = 0.3371          |
| start r-factor (free) = 0.4119      final r-factor (free) = 0.4100          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.6138 = 1.72 * 1.00 * 6.1774 + 1.00 * 0.0066                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.5005 = 1.72 * 1.00 * 6.0775 + 1.00 * 0.0648                              |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.145)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    127.52  17.95    None  None   None       |
|    all(noH): 2823   0      0.00    127.52  17.95    None  None   None       |
|    Sol.    : 438    0      0.00    76.08   37.92    None  None   None       |
|    Mac.    : 2385   0      0.00    127.52  14.28    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.752: 1225   |   5:    63.759 -  76.511:    4        |
|      1:    12.752 -  25.504:  925   |   6:    76.511 -  89.263:    0        |
|      2:    25.504 -  38.255:  395   |   7:    89.263 - 102.015:    0        |
|      3:    38.255 -  51.007:  193   |   8:   102.015 - 114.766:    1        |
|      4:    51.007 -  63.759:   79   |   9:   114.766 - 127.518:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3371 r_free = 0.4100             target_work(ml) = 6.078         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3367 r_free = 0.4105             target_work(ml) = 6.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3367   r_free= 0.4105   ksol= 0.28   Bsol= 30.87   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.63,2.29,0.09,0.00,0.00,0.00); trace/3= 1.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.077162                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3362   r_free= 0.4088   ksol= 0.33   Bsol= 64.29   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.19,1.47,0.16,0.00,0.00,0.00); trace/3= 0.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.077645                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.159858              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.560   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.591537              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.957   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3362      final r-factor (work) = 0.2772          |
| start r-factor (free) = 0.4088      final r-factor (free) = 0.3426          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.9369 = 7.16 * 0.50 * 6.0786 + 1.00 * 0.1758                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.6178 = 7.16 * 0.50 * 6.0157 + 1.00 * 0.0821                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2772      final r-factor (work) = 0.2590          |
| start r-factor (free) = 0.3426      final r-factor (free) = 0.3381          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.6117 = 1.59 * 1.00 * 6.0157 + 1.00 * 0.0376                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.4184 = 1.59 * 1.00 * 5.9040 + 1.00 * 0.0220                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.145)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    120.52  19.97    None  None   None       |
|    all(noH): 2823   0      0.00    120.52  19.97    None  None   None       |
|    Sol.    : 438    0      1.08    120.52  44.88    None  None   None       |
|    Mac.    : 2385   0      0.00    102.34  15.40    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.052: 1226   |   5:    60.260 -  72.312:   55        |
|      1:    12.052 -  24.104:  847   |   6:    72.312 -  84.364:   52        |
|      2:    24.104 -  36.156:  300   |   7:    84.364 -  96.416:   22        |
|      3:    36.156 -  48.208:  191   |   8:    96.416 - 108.468:   10        |
|      4:    48.208 -  60.260:  117   |   9:   108.468 - 120.520:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2590 r_free = 0.3381             target_work(ml) = 5.898         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2588 r_free = 0.3380             target_work(ml) = 5.898         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2588   r_free= 0.3380   ksol= 0.33   Bsol= 64.29   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.19,1.47,0.16,0.00,0.00,0.00); trace/3= 0.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.897583                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2590   r_free= 0.3381   ksol= 0.33   Bsol= 77.35   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.07,0.98,-0.22,0.00,-0.00,-0.00); trace/3= 0.28                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.896624                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.329769              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.459   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.894880              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.132  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2590      final r-factor (work) = 0.2008          |
| start r-factor (free) = 0.3381      final r-factor (free) = 0.2628          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.6196 = 9.33 * 0.50 * 5.9031 + 1.00 * 0.0821                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.1806 = 9.33 * 0.50 * 5.8075 + 1.00 * 0.0894                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2008      final r-factor (work) = 0.1761          |
| start r-factor (free) = 0.2628      final r-factor (free) = 0.2321          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2190 = 0.89 * 1.00 * 5.8075 + 1.00 * 0.0221                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0276 = 0.89 * 1.00 * 5.6011 + 1.00 * 0.0153                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.145)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.59  18.88    None  None   None       |
|    all(noH): 2823   0      0.00    110.59  18.88    None  None   None       |
|    Sol.    : 438    0      4.93    109.88  47.72    None  None   None       |
|    Mac.    : 2385   0      0.00    110.59  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 -  11.059: 1280   |   5:    55.295 -  66.354:   95        |
|      1:    11.059 -  22.118:  870   |   6:    66.354 -  77.412:   39        |
|      2:    22.118 -  33.177:  221   |   7:    77.412 -  88.471:   35        |
|      3:    33.177 -  44.236:  141   |   8:    88.471 -  99.530:   17        |
|      4:    44.236 -  55.295:  115   |   9:    99.530 - 110.589:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1761 r_free = 0.2321             target_work(ml) = 5.536         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1760 r_free = 0.2320             target_work(ml) = 5.536         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1760   r_free= 0.2320   ksol= 0.33   Bsol= 77.35   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.07,0.98,-0.22,0.00,-0.00,-0.00); trace/3= 0.28                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.535938                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1757   r_free= 0.2322   ksol= 0.34   Bsol= 80.00   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.95,-0.37,-1.00,-0.00,-0.00,-0.00); trace/3= -0.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.537577                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.437199              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.178  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.404271              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.194  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1757      final r-factor (work) = 0.1463          |
| start r-factor (free) = 0.2322      final r-factor (free) = 0.1964          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5282 = 4.44 * 0.50 * 5.6066 + 1.00 * 0.0894                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1985 = 4.44 * 0.50 * 5.4647 + 1.00 * 0.0746                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1463      final r-factor (work) = 0.1372          |
| start r-factor (free) = 0.1964      final r-factor (free) = 0.1865          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2244 = 0.40 * 1.00 * 5.4647 + 1.00 * 0.0152                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1762 = 0.40 * 1.00 * 5.3533 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.145)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.87    113.19  17.96    None  None   None       |
|    all(noH): 2823   0      0.87    113.19  17.96    None  None   None       |
|    Sol.    : 438    0      4.68    104.75  45.80    None  None   None       |
|    Mac.    : 2385   0      0.87    113.19  12.85    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:     0.868 -  12.100: 1517   |   5:    57.028 -  68.260:   74        |
|      1:    12.100 -  23.332:  750   |   6:    68.260 -  79.492:   47        |
|      2:    23.332 -  34.564:  172   |   7:    79.492 -  90.724:   21        |
|      3:    34.564 -  45.796:  123   |   8:    90.724 - 101.956:    8        |
|      4:    45.796 -  57.028:  104   |   9:   101.956 - 113.188:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1372 r_free = 0.1865             target_work(ml) = 5.326         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1371 r_free = 0.1864             target_work(ml) = 5.326         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1371   r_free= 0.1864   ksol= 0.34   Bsol= 80.00   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.95,-0.37,-1.00,-0.00,-0.00,-0.00); trace/3= -0.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.326269                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1375   r_free= 0.1870   ksol= 0.33   Bsol= 71.72   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.32,-0.89,-1.25,-0.00,-0.00,-0.00); trace/3= -1.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.328593                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.246243              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.602  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.186542              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.476  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1375      final r-factor (work) = 0.1248          |
| start r-factor (free) = 0.1870      final r-factor (free) = 0.1734          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7668 = 3.25 * 0.50 * 5.3552 + 1.00 * 0.0746                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6675 = 3.25 * 0.50 * 5.2948 + 1.00 * 0.0734                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1248      final r-factor (work) = 0.1236          |
| start r-factor (free) = 0.1734      final r-factor (free) = 0.1694          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9996 = 0.19 * 1.00 * 5.2948 + 1.00 * 0.0119                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9883 = 0.19 * 1.00 * 5.2476 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.145)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.61    109.47  17.16    None  None   None       |
|    all(noH): 2823   0      1.61    109.47  17.16    None  None   None       |
|    Sol.    : 438    0      4.54    102.57  42.61    None  None   None       |
|    Mac.    : 2385   0      1.61    109.47  12.48    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:     1.605 -  12.391: 1613   |   5:    55.537 -  66.323:   62        |
|      1:    12.391 -  23.178:  692   |   6:    66.323 -  77.109:   40        |
|      2:    23.178 -  33.964:  159   |   7:    77.109 -  87.896:   18        |
|      3:    33.964 -  44.750:  129   |   8:    87.896 -  98.682:    7        |
|      4:    44.750 -  55.537:   97   |   9:    98.682 - 109.468:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1236 r_free = 0.1694             target_work(ml) = 5.237         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1234 r_free = 0.1693             target_work(ml) = 5.236         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1234   r_free= 0.1693   ksol= 0.33   Bsol= 71.72   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.32,-0.89,-1.25,-0.00,-0.00,-0.00); trace/3= -1.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.236184                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1772 -  4.6842 0.99   1469  167 0.1007 0.1318      5.4053      5.5903|
|  2:  4.6842 -  3.7362 0.99   1410  155 0.0889 0.1094      5.4653      5.6702|
|  3:  3.7362 -  3.2693 0.99   1385  146 0.1144 0.1806      5.5214       5.941|
|  4:  3.2693 -  2.9728 0.99   1376  161 0.1455 0.1785      5.5615      5.7192|
|  5:  2.9728 -  2.7611 0.99   1368  150 0.1490 0.2011      5.4305      5.6169|
|  6:  2.7611 -  2.5992 0.99   1359  155 0.1415 0.2001      5.3102       5.488|
|  7:  2.5992 -  2.4696 0.98   1356  140 0.1359 0.1773      5.2324      5.4424|
|  8:  2.4696 -  2.3625 0.98   1355  152 0.1361 0.1786      5.1612      5.3466|
|  9:  2.3625 -  2.2719 0.99   1347  153 0.1295 0.2014      5.1029      5.3609|
| 10:  2.2719 -  2.1937 0.98   1335  157 0.1269 0.1799      5.0493      5.3074|
| 11:  2.1937 -  2.1253 0.97   1337  142 0.1244 0.1841      4.9875        5.24|
| 12:  2.1253 -  2.0647 0.98   1318  144 0.1279 0.1967      4.9319      5.1851|
| 13:  2.0647 -  2.0105 0.71    979  116 0.1287 0.1698       4.839      5.0343|
| 14:  2.0105 -  1.9615 0.17    236   21 0.1320 0.1787      4.7185      4.9387|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1772 -  4.6842  1469   167  0.94   9.56   0.97     0.95       7824.81|
|  2:  4.6842 -  3.7362  1410   155  0.95   8.55   1.00     0.99       9625.34|
|  3:  3.7362 -  3.2693  1385   146  0.92  12.97   1.02     1.02      11701.89|
|  4:  3.2693 -  2.9728  1376   161  0.89  16.84   1.00     0.97      12919.86|
|  5:  2.9728 -  2.7611  1368   150  0.87  18.79   1.00     0.97      10530.62|
|  6:  2.7611 -  2.5992  1359   155  0.88  18.07   0.99     0.96       8552.24|
|  7:  2.5992 -  2.4696  1356   140  0.89  17.30   0.99     0.96       7144.54|
|  8:  2.4696 -  2.3625  1355   152  0.89  17.67   0.99     0.96       6500.75|
|  9:  2.3625 -  2.2719  1347   153  0.88  17.99   1.00     0.96       5797.55|
| 10:  2.2719 -  2.1937  1335   157  0.89  17.18   0.98     0.94       5156.18|
| 11:  2.1937 -  2.1253  1337   142  0.89  17.02   0.99     0.95       4707.08|
| 12:  2.1253 -  2.0647  1318   144  0.89  18.04   0.99     0.98       4515.05|
| 13:  2.0647 -  2.0105   979   116  0.89  17.70   0.99     0.98       3637.79|
| 14:  2.0105 -  1.9615   236    21  0.88  17.66   0.98     0.96       2793.95|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2793.95 max =        12919.86 mean =      7642.31|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.94 mean =        15.89|
|phase err.(test): min =        0.00 max =           88.57 mean =        15.19|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1234   r_free= 0.1692   ksol= 0.32   Bsol= 61.74   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.39,-1.12,-1.30,-0.00,-0.00,-0.00); trace/3= -1.27                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.235724                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1234   r_free= 0.1692   ksol= 0.32   Bsol= 61.74   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.39,-1.12,-1.30,-0.00,-0.00,-0.00); trace/3= -1.27                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.235724                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1772 -  4.6842 0.99   1469  167 0.1003 0.1310      5.4013      5.5834|
|  2:  4.6842 -  3.7362 0.99   1410  155 0.0883 0.1086      5.4595      5.6613|
|  3:  3.7362 -  3.2693 0.99   1385  146 0.1141 0.1799      5.5182      5.9409|
|  4:  3.2693 -  2.9728 0.99   1376  161 0.1457 0.1784      5.5617      5.7189|
|  5:  2.9728 -  2.7611 0.99   1368  150 0.1492 0.2015      5.4318      5.6184|
|  6:  2.7611 -  2.5992 0.99   1359  155 0.1418 0.2002      5.3115      5.4898|
|  7:  2.5992 -  2.4696 0.98   1356  140 0.1360 0.1773      5.2336       5.443|
|  8:  2.4696 -  2.3625 0.98   1355  152 0.1361 0.1790      5.1619      5.3485|
|  9:  2.3625 -  2.2719 0.99   1347  153 0.1296 0.2016      5.1035      5.3619|
| 10:  2.2719 -  2.1937 0.98   1335  157 0.1269 0.1800      5.0499      5.3082|
| 11:  2.1937 -  2.1253 0.97   1337  142 0.1245 0.1841      4.9876      5.2397|
| 12:  2.1253 -  2.0647 0.98   1318  144 0.1280 0.1972       4.933      5.1872|
| 13:  2.0647 -  2.0105 0.71    979  116 0.1288 0.1696      4.8396      5.0335|
| 14:  2.0105 -  1.9615 0.17    236   21 0.1320 0.1782      4.7181      4.9369|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1772 -  4.6842  1469   167  0.94   9.51   0.97     0.95       7745.62|
|  2:  4.6842 -  3.7362  1410   155  0.95   8.48   1.00     0.99       9491.84|
|  3:  3.7362 -  3.2693  1385   146  0.92  12.88   1.02     1.02      11568.27|
|  4:  3.2693 -  2.9728  1376   161  0.89  16.81   1.00     0.96      12900.39|
|  5:  2.9728 -  2.7611  1368   150  0.87  18.79   0.99     0.97      10541.62|
|  6:  2.7611 -  2.5992  1359   155  0.88  18.09   0.98     0.96       8572.43|
|  7:  2.5992 -  2.4696  1356   140  0.89  17.32   0.98     0.95       7163.25|
|  8:  2.4696 -  2.3625  1355   152  0.89  17.70   0.99     0.95       6520.15|
|  9:  2.3625 -  2.2719  1347   153  0.88  18.00   1.00     0.96       5810.96|
| 10:  2.2719 -  2.1937  1335   157  0.89  17.20   0.98     0.93       5167.53|
| 11:  2.1937 -  2.1253  1337   142  0.89  17.03   0.98     0.94       4713.15|
| 12:  2.1253 -  2.0647  1318   144  0.89  18.05   0.98     0.97       4525.78|
| 13:  2.0647 -  2.0105   979   116  0.89  17.70   0.98     0.97       3639.22|
| 14:  2.0105 -  1.9615   236    21  0.88  17.64   0.97     0.95       2787.09|
|alpha:            min =        0.93 max =            1.02 mean =         0.96|
|beta:             min =     2787.09 max =        12900.39 mean =      7621.49|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.87 mean =        15.88|
|phase err.(test): min =        0.00 max =           88.45 mean =        15.18|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.145)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.55    109.41  17.10    None  None   None       |
|    all(noH): 2823   0      1.55    109.41  17.10    None  None   None       |
|    Sol.    : 438    0      4.48    102.51  42.55    None  None   None       |
|    Mac.    : 2385   0      1.55    109.41  12.43    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:     1.548 -  12.334: 1613   |   5:    55.479 -  66.266:   62        |
|      1:    12.334 -  23.120:  692   |   6:    66.266 -  77.052:   40        |
|      2:    23.120 -  33.907:  159   |   7:    77.052 -  87.838:   18        |
|      3:    33.907 -  44.693:  129   |   8:    87.838 -  98.625:    7        |
|      4:    44.693 -  55.479:   97   |   9:    98.625 - 109.411:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 361         
Filter by distance & map next to the model:
   mapped sites are within: 0.610 - 5.932
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 356 from: 361
   mapped sites are within: 0.703 - 5.932

peak=    5.806 closest distance to " CB  SER A  63 " =    1.346
peak=    5.363 closest distance to " CB  GLN A 223 " =    1.582
peak=    5.245 closest distance to " O   HOH Z 132 " =    1.495
peak=    5.130 closest distance to " NH2BARG A 102 " =    1.026
peak=    5.061 closest distance to " O   HOH Z  15 " =    2.081
peak=    4.984 closest distance to " O   HOH Z 111 " =    1.846
peak=    4.962 closest distance to " O   HOH Z 126 " =    1.860
peak=    4.830 closest distance to " CG  PRO A 213 " =    1.261
peak=    4.819 closest distance to " CG  PRO A  54 " =    1.263
peak=    4.763 closest distance to " O   HOH Z  47 " =    1.687
peak=    4.746 closest distance to " O   HOH Z 210 " =    1.202
peak=    4.740 closest distance to " CB  LEU A 228 " =    1.112
peak=    4.670 closest distance to " CG  PRO A  90 " =    1.166
peak=    4.667 closest distance to " O   HOH Z 232 " =    2.212
peak=    4.650 closest distance to " O   HOH Z 207 " =    1.995
peak=    4.642 closest distance to " O   HOH Z 425 " =    1.740
peak=    4.639 closest distance to " O   HOH Z  49 " =    0.973
peak=    4.634 closest distance to " O   HOH Z 234 " =    3.865
peak=    4.611 closest distance to " CG  PRO A 280 " =    0.890
peak=    4.600 closest distance to " O   HOH Z 163 " =    1.897
peak=    4.547 closest distance to " O   PRO A 198 " =    1.544
peak=    4.537 closest distance to " O   HOH Z 112 " =    1.574
peak=    4.536 closest distance to " O   HOH Z  11 " =    1.248
peak=    4.513 closest distance to " O   HOH Z 134 " =    1.770
peak=    4.481 closest distance to " O   HOH Z 127 " =    1.160
peak=    4.420 closest distance to " O   HOH Z 182 " =    1.220
peak=    4.403 closest distance to " O   HOH Z 214 " =    1.269
peak=    4.395 closest distance to " O   HOH Z 196 " =    1.576
peak=    4.389 closest distance to " CA  TYR A  30 " =    1.080
peak=    4.368 closest distance to " CB  PRO A  54 " =    0.786
peak=    4.323 closest distance to " CG1 ILE A  33 " =    1.252
peak=    4.303 closest distance to " O   HOH Z 118 " =    2.010
peak=    4.301 closest distance to " CB  VAL A 202 " =    1.502
peak=    4.299 closest distance to " CB  GLN A 183 " =    1.223
peak=    4.273 closest distance to " CB  ARG A 275 " =    0.843
peak=    4.270 closest distance to " CG2 THR A 221 " =    0.951
peak=    4.252 closest distance to " O   HOH Z 124 " =    1.264
peak=    4.248 closest distance to " O   HOH Z 192 " =    1.615
peak=    4.245 closest distance to " CG  PRO A 198 " =    1.321
peak=    4.216 closest distance to " O   HOH Z 394 " =    1.609
peak=    4.213 closest distance to " OD1 ASN A 217 " =    1.729
peak=    4.207 closest distance to " O   HOH Z 154 " =    1.493
peak=    4.203 closest distance to " O   HOH Z  39 " =    1.739
peak=    4.196 closest distance to " CB  GLU A 152 " =    1.171
peak=    4.196 closest distance to " CD  ARG A  66 " =    2.609
peak=    4.192 closest distance to " O   HOH Z  30 " =    1.915
peak=    4.178 closest distance to " O   HOH Z  68 " =    1.925
peak=    4.175 closest distance to " NH2 ARG A 156 " =    1.296
peak=    4.169 closest distance to " CA  GLU A 152 " =    0.913
peak=    4.156 closest distance to " O   HOH Z 411 " =    3.176
peak=    4.129 closest distance to " O   HOH Z 433 " =    1.456
peak=    4.117 closest distance to " O   HOH Z 387 " =    2.438
peak=    4.099 closest distance to " O   HOH Z 186 " =    1.174
peak=    4.078 closest distance to " CB  TRP A 179 " =    1.526
peak=    4.073 closest distance to " O   HOH Z 298 " =    1.864
peak=    4.069 closest distance to " O   HOH Z 108 " =    1.539
peak=    4.060 closest distance to " O   HOH Z 260 " =    1.441
peak=    4.057 closest distance to " O   HOH Z  80 " =    2.017
peak=    4.052 closest distance to " CB  TYR A 169 " =    0.913
peak=    4.043 closest distance to " O   HOH Z 246 " =    1.803
peak=    4.042 closest distance to " O   HOH Z 316 " =    3.058
peak=    4.037 closest distance to " O   HOH Z  39 " =    1.858
peak=    4.037 closest distance to " O   HOH Z 243 " =    1.163
peak=    4.025 closest distance to " CB  GLU A 128 " =    1.153
peak=    4.019 closest distance to " O   HOH Z 193 " =    1.946
peak=    4.016 closest distance to " OE1 GLN A  11 " =    1.965
peak=    4.000 closest distance to " CB  ASN A 148 " =    1.165
peak=    3.982 closest distance to " CA  ASP A 191 " =    0.868
peak=    3.968 closest distance to " O   HOH Z  78 " =    2.185
peak=    3.966 closest distance to " CD1 LEU A 300 " =    1.296
peak=    3.954 closest distance to " O   HOH Z 368 " =    2.110
peak=    3.954 closest distance to " O   HOH Z 403 " =    1.865
peak=    3.947 closest distance to " O   HOH Z 287 " =    2.013
peak=    3.945 closest distance to " O   HOH Z 247 " =    1.417
peak=    3.930 closest distance to " CB  SER A   3 " =    1.511
peak=    3.918 closest distance to " O   HOH Z 374 " =    2.728
peak=    3.906 closest distance to " O   HOH Z 108 " =    2.254
peak=    3.905 closest distance to " O   HOH Z 406 " =    1.547
peak=    3.903 closest distance to " CG2 VAL A  78 " =    1.044
peak=    3.900 closest distance to " O   HOH Z 104 " =    3.239
peak=    3.897 closest distance to " O   HOH Z  42 " =    1.630
peak=    3.892 closest distance to " CB  SER A 141 " =    0.973
peak=    3.887 closest distance to " O   HOH Z 389 " =    1.982
peak=    3.869 closest distance to " O   HOH Z 128 " =    2.239
peak=    3.850 closest distance to " CA  ALA A  21 " =    1.357
peak=    3.842 closest distance to " O   HOH Z  21 " =    1.901
peak=    3.839 closest distance to " O   HOH Z 404 " =    1.460
peak=    3.838 closest distance to " CG2BVAL A  41 " =    1.049
peak=    3.835 closest distance to " O   HOH Z 180 " =    2.181
peak=    3.829 closest distance to " O   HOH Z 145 " =    2.197
peak=    3.802 closest distance to " CG  PRO A 243 " =    1.100
peak=    3.800 closest distance to " CD  ARG A 269 " =    0.909
peak=    3.799 closest distance to " O   HOH Z 227 " =    1.822
peak=    3.791 closest distance to " O   HOH Z 132 " =    2.255
peak=    3.783 closest distance to " OD2 ASP A 286 " =    3.005
peak=    3.771 closest distance to " N   ASN A  39 " =    1.293
peak=    3.771 closest distance to " CA  GLY A 196 " =    0.998
peak=    3.760 closest distance to " O   HOH Z 437 " =    1.788
peak=    3.753 closest distance to " NZ  LYS A 117 " =    3.298
peak=    3.733 closest distance to " O   HOH Z 344 " =    3.145
peak=    3.733 closest distance to " O   HOH Z 116 " =    1.754
peak=    3.726 closest distance to " CD2 LEU A 255 " =    1.455
peak=    3.725 closest distance to " NH2BARG A 145 " =    1.999
peak=    3.721 closest distance to " O   HOH Z 261 " =    2.040
peak=    3.720 closest distance to " O   HOH Z 371 " =    3.063
peak=    3.709 closest distance to " CZ  PHE A 218 " =    1.170
peak=    3.708 closest distance to " O   HOH Z  20 " =    2.274
peak=    3.708 closest distance to " O   HOH Z 132 " =    1.808
peak=    3.703 closest distance to " CA  GLN A 223 " =    0.939
peak=    3.701 closest distance to " O   HOH Z 313 " =    2.052
peak=    3.701 closest distance to " O   HOH Z 357 " =    2.189
peak=    3.699 closest distance to " NH1 ARG A  56 " =    1.227
peak=    3.696 closest distance to " CB  ASP A 124 " =    0.796
peak=    3.690 closest distance to " O   HOH Z 203 " =    1.913
peak=    3.686 closest distance to " O   HOH Z 281 " =    4.008
peak=    3.681 closest distance to " CD1 TRP A 266 " =    1.097
peak=    3.679 closest distance to " CA  PRO A  54 " =    1.198
peak=    3.671 closest distance to " CB  PRO A 198 " =    0.963
peak=    3.669 closest distance to " CA  THR A 221 " =    0.923
peak=    3.663 closest distance to " O   SER A  87 " =    2.203
peak=    3.661 closest distance to " O   HOH Z 189 " =    2.301
peak=    3.659 closest distance to " CA  GLU A 152 " =    1.110
peak=    3.654 closest distance to " CB  TRP A 266 " =    0.984
peak=    3.653 closest distance to " OD1 ASN A  69 " =    2.397
peak=    3.652 closest distance to " O   HOH Z  22 " =    2.369
peak=    3.640 closest distance to " O   HOH Z 193 " =    2.423
peak=    3.639 closest distance to " CD  LYS A 119 " =    1.423
peak=    3.639 closest distance to " CB  ILE A 199 " =    1.062
peak=    3.633 closest distance to " O   HOH Z  54 " =    2.118
peak=    3.632 closest distance to " O   HOH Z  43 " =    1.556
peak=    3.631 closest distance to " CB  GLU A 277 " =    3.693
peak=    3.630 closest distance to " CB  ARG A 190 " =    1.772
peak=    3.625 closest distance to " O   HOH Z 272 " =    2.005
peak=    3.623 closest distance to " O   HOH Z 263 " =    2.190
peak=    3.621 closest distance to " CB  GLN A 194 " =    0.841
peak=    3.621 closest distance to " O   HOH Z 383 " =    1.906
peak=    3.619 closest distance to " CG  LEU A 167 " =    1.136
peak=    3.614 closest distance to " O   HOH Z 102 " =    1.344
peak=    3.614 closest distance to " O   HOH Z 363 " =    1.209
peak=    3.608 closest distance to " CG1 VAL A 153 " =    1.033
peak=    3.596 closest distance to " CG2 VAL A 197 " =    1.202
peak=    3.594 closest distance to " O   HOH Z 197 " =    2.087
peak=    3.593 closest distance to " O   HOH Z 174 " =    1.943
peak=    3.584 closest distance to " O   HOH Z 154 " =    2.380
peak=    3.579 closest distance to " CB  ASN A 187 " =    1.018
peak=    3.575 closest distance to " NE AARG A 275 " =    1.494
peak=    3.568 closest distance to " NH1 ARG A 138 " =    1.106
peak=    3.565 closest distance to " O   HOH Z 418 " =    1.501
peak=    3.565 closest distance to " O   HOH Z  97 " =    1.861
peak=    3.564 closest distance to " CG AARG A 275 " =    1.101
peak=    3.562 closest distance to " O   HOH Z 343 " =    2.336
peak=    3.558 closest distance to " CB  SER A 216 " =    0.827
peak=    3.552 closest distance to " O   HOH Z 332 " =    1.579
peak=    3.550 closest distance to " CD BLYS A 290 " =    1.049
peak=    3.550 closest distance to " CB  ARG A  79 " =    1.377
peak=    3.550 closest distance to " O   HOH Z 368 " =    2.614
peak=    3.548 closest distance to " O   HOH Z  47 " =    1.603
peak=    3.547 closest distance to " CA  ALA A 160 " =    0.935
peak=    3.546 closest distance to " O   HOH Z  54 " =    1.648
peak=    3.545 closest distance to " O   HOH Z 369 " =    2.219
peak=    3.544 closest distance to " CZ  PHE A 192 " =    0.926
peak=    3.541 closest distance to " O   HOH Z 292 " =    1.756
peak=    3.538 closest distance to " ND1 HIS A  81 " =    1.502
peak=    3.537 closest distance to " O   HOH Z 142 " =    1.551
peak=    3.535 closest distance to " CA  ASP A 124 " =    0.796
peak=    3.531 closest distance to " O   HOH Z 128 " =    2.343
peak=    3.529 closest distance to " CD  ARG A  66 " =    3.004
peak=    3.528 closest distance to " O   HOH Z   6 " =    2.166
peak=    3.522 closest distance to " O   HOH Z  44 " =    2.411
peak=    3.521 closest distance to " CA  ARG A 195 " =    1.120
peak=    3.520 closest distance to " O   HOH Z 184 " =    0.890
peak=    3.518 closest distance to " CB  ASP A 132 " =    3.815
peak=    3.516 closest distance to " O   HOH Z 345 " =    3.502
peak=    3.515 closest distance to " CA  ARG A  36 " =    1.142
peak=    3.514 closest distance to " O   HOH Z 135 " =    1.942
peak=    3.509 closest distance to " O   HOH Z 175 " =    3.657
peak=    3.504 closest distance to " CB  MET A  47 " =    1.044
peak=    3.492 closest distance to " O   HOH Z  19 " =    2.416
peak=    3.489 closest distance to " CD  PRO A  54 " =    1.018
peak=    3.485 closest distance to " C   SER A  32 " =    1.049
peak=    3.485 closest distance to " CG  GLN A  58 " =    2.315
peak=    3.484 closest distance to " O   GLY A  23 " =    2.383
peak=    3.482 closest distance to " CD  LYS A 166 " =    1.437
peak=    3.480 closest distance to " CD  ARG A 159 " =    0.860
peak=    3.478 closest distance to " CB  GLN A  58 " =    0.827
peak=    3.468 closest distance to " O   HOH Z  87 " =    1.926
peak=    3.466 closest distance to " ND2 ASN A 187 " =    1.553
peak=    3.462 closest distance to " CB  VAL A 265 " =    1.295
peak=    3.460 closest distance to " CB  ALA A 291 " =    1.356
peak=    3.452 closest distance to " CB  ILE A 120 " =    1.188
peak=    3.452 closest distance to " CA  GLY A 241 " =    0.748
peak=    3.446 closest distance to " O   HOH Z 211 " =    1.282
peak=    3.445 closest distance to " O   HOH Z 432 " =    1.765
peak=    3.445 closest distance to " CG  ASP A 231 " =    1.203
peak=    3.443 closest distance to " O   GLY A  91 " =    1.177
peak=    3.443 closest distance to " O   HOH Z 200 " =    1.404
peak=    3.440 closest distance to " OE1 GLN A  58 " =    1.365
peak=    3.439 closest distance to " NH2AARG A 190 " =    1.519
peak=    3.437 closest distance to " CA  ASP A 162 " =    1.149
peak=    3.434 closest distance to " NH1AARG A 145 " =    1.049
peak=    3.428 closest distance to " O   HOH Z 139 " =    3.295
peak=    3.426 closest distance to " O   HOH Z 279 " =    2.356
peak=    3.421 closest distance to " O   HOH Z 150 " =    3.371
peak=    3.419 closest distance to " CB  GLN A  88 " =    1.086
peak=    3.418 closest distance to " O   HOH Z 435 " =    1.638
peak=    3.418 closest distance to " CA  ALA A  51 " =    0.941
peak=    3.416 closest distance to " O   HOH Z 223 " =    1.055
peak=    3.412 closest distance to " CA  ILE A  33 " =    1.620
peak=    3.408 closest distance to " O   HOH Z 295 " =    1.462
peak=    3.400 closest distance to " O   THR A 251 " =    1.298
peak=    3.399 closest distance to " CD  ARG A 195 " =    0.934
peak=    3.392 closest distance to " CE1 PHE A 225 " =    1.061
peak=    3.390 closest distance to " OE1 GLN A  58 " =    5.790
peak=    3.380 closest distance to " O   HOH Z 172 " =    5.816
peak=    3.380 closest distance to " CA  ALA A 100 " =    1.081
peak=    3.377 closest distance to " CE1 HIS A 115 " =    1.030
peak=    3.377 closest distance to " CA  MET A  40 " =    1.114
peak=    3.377 closest distance to " OE1 GLN A  88 " =    0.905
peak=    3.374 closest distance to " O   HOH Z 185 " =    1.818
peak=    3.370 closest distance to " O   HOH Z 245 " =    1.343
peak=    3.367 closest distance to " N   TYR A  15 " =    0.803
peak=    3.366 closest distance to " O   GLY A  57 " =    2.534
peak=    3.364 closest distance to " N   PHE A 130 " =    1.416
peak=    3.362 closest distance to " CB  ALA A 100 " =    1.514
peak=    3.360 closest distance to " O   HOH Z 426 " =    1.525
peak=    3.358 closest distance to " CB  MET A  40 " =    0.798
peak=    3.356 closest distance to " O   HOH Z 217 " =    1.327
peak=    3.356 closest distance to " O   HOH Z 362 " =    3.313
peak=    3.348 closest distance to " CA  ILE A 106 " =    0.841
peak=    3.346 closest distance to " O   HOH Z 419 " =    2.906
peak=    3.342 closest distance to " NZ  LYS A 117 " =    1.319
peak=    3.339 closest distance to " O   HOH Z  32 " =    1.814
peak=    3.338 closest distance to " CD2 TRP A 179 " =    1.322
peak=    3.335 closest distance to " O   HOH Z 147 " =    1.785
peak=    3.327 closest distance to " CG2 VAL A 112 " =    1.467
peak=    3.326 closest distance to " CA  ALA A 295 " =    1.107
peak=    3.324 closest distance to " CD  ARG A  14 " =    1.355
peak=    3.323 closest distance to " CD2 LEU A 297 " =    0.808
peak=    3.322 closest distance to " CB  GLU A  53 " =    1.022
peak=    3.322 closest distance to " CA  LEU A  83 " =    1.590
peak=    3.320 closest distance to " CG  GLU A  37 " =    0.983
peak=    3.314 closest distance to " CD  PRO A 280 " =    1.180
peak=    3.312 closest distance to " O   HOH Z 418 " =    5.932
peak=    3.309 closest distance to " CE  LYS A 119 " =    0.969
peak=    3.305 closest distance to " O   HOH Z 420 " =    1.912
peak=    3.304 closest distance to " O   HOH Z  63 " =    1.983
peak=    3.300 closest distance to " O   HOH Z 301 " =    1.634
peak=    3.300 closest distance to " O   HOH Z 326 " =    1.364
peak=    3.298 closest distance to " O   HOH Z 244 " =    1.736
peak=    3.298 closest distance to " NE2 GLN A  11 " =    1.081
peak=    3.297 closest distance to " O   HOH Z 207 " =    1.737
peak=    3.291 closest distance to " CG2AVAL A 121 " =    2.156
peak=    3.291 closest distance to " O   ALA A 165 " =    1.304
peak=    3.286 closest distance to " N   ASN A 127 " =    1.308
peak=    3.284 closest distance to " O   HOH Z 293 " =    1.767
peak=    3.284 closest distance to " CB  MET A 105 " =    1.150
peak=    3.278 closest distance to " O   HOH Z 215 " =    1.419
peak=    3.275 closest distance to " CA  GLY A 267 " =    1.038
peak=    3.273 closest distance to " CA  TYR A 116 " =    1.433
peak=    3.267 closest distance to " O   HOH Z 424 " =    2.766
peak=    3.266 closest distance to " CD2 LEU A 300 " =    1.000
peak=    3.266 closest distance to " O   HOH Z 255 " =    1.681
peak=    3.263 closest distance to " CA  LYS A  48 " =    1.306
peak=    3.261 closest distance to " CB  GLU A 277 " =    1.047
peak=    3.258 closest distance to " O   HOH Z 174 " =    1.287
peak=    3.258 closest distance to " O   HOH Z 409 " =    2.776
peak=    3.255 closest distance to " CB  ASN A 170 " =    1.288
peak=    3.252 closest distance to " CB  THR A 235 " =    1.064
peak=    3.252 closest distance to " NZ  LYS A 193 " =    1.495
peak=    3.250 closest distance to " O   HOH Z 336 " =    1.624
peak=    3.248 closest distance to " CB  ASN A 148 " =    1.835
peak=    3.248 closest distance to " O   GLN A 278 " =    1.142
peak=    3.244 closest distance to " OG BSER A 258 " =    3.552
peak=    3.241 closest distance to " CB  TYR A  30 " =    1.160
peak=    3.240 closest distance to " O   HOH Z 303 " =    2.239
peak=    3.239 closest distance to " O   HOH Z  87 " =    2.551
peak=    3.233 closest distance to " O   HOH Z 355 " =    1.571
peak=    3.232 closest distance to " CA  SER A  87 " =    0.827
peak=    3.231 closest distance to " O   HOH Z 294 " =    1.589
peak=    3.230 closest distance to " O   HOH Z  44 " =    3.146
peak=    3.230 closest distance to " CG2 THR A  42 " =    0.882
peak=    3.230 closest distance to " O   HOH Z 150 " =    1.523
peak=    3.227 closest distance to " O   HOH Z  66 " =    2.200
peak=    3.226 closest distance to " C   VAL A 265 " =    1.184
peak=    3.225 closest distance to " CA  LYS A 117 " =    1.295
peak=    3.223 closest distance to " NZ ALYS A 290 " =    0.979
peak=    3.223 closest distance to " O   HOH Z 195 " =    1.118
peak=    3.216 closest distance to " CB  TYR A 247 " =    1.025
peak=    3.216 closest distance to " CA  GLU A  46 " =    0.819
peak=    3.215 closest distance to " O   HOH Z 427 " =    3.240
peak=    3.215 closest distance to " O   HOH Z 282 " =    2.170
peak=    3.212 closest distance to " O   HOH Z 152 " =    1.309
peak=    3.205 closest distance to " O   HOH Z 214 " =    1.957
peak=    3.204 closest distance to " O   ASN A  74 " =    1.617
peak=    3.203 closest distance to " NH1 ARG A  14 " =    1.168
peak=    3.201 closest distance to " CA  ALA A 154 " =    1.065
peak=    3.200 closest distance to " CD1 ILE A 106 " =    0.921
peak=    3.199 closest distance to " CE3 TRP A 274 " =    3.703
peak=    3.198 closest distance to " NE  ARG A 156 " =    1.076
peak=    3.192 closest distance to " O   HOH Z 217 " =    2.068
peak=    3.189 closest distance to " O   HOH Z  99 " =    2.599
peak=    3.187 closest distance to " ND2 ASN A 301 " =    1.073
peak=    3.184 closest distance to " CG  LYS A 181 " =    0.703
peak=    3.181 closest distance to " CG1BVAL A  72 " =    1.803
peak=    3.180 closest distance to " O   HOH Z 173 " =    1.970
peak=    3.177 closest distance to " OG  SER A  97 " =    3.486
peak=    3.175 closest distance to " N   THR A  52 " =    1.126
peak=    3.173 closest distance to " CZ3 TRP A  85 " =    0.983
peak=    3.172 closest distance to " CA  GLY A  75 " =    1.112
peak=    3.172 closest distance to " O   HOH Z   1 " =    2.439
peak=    3.168 closest distance to " O   HOH Z 391 " =    2.957
peak=    3.163 closest distance to " CD1 TYR A 169 " =    1.490
peak=    3.162 closest distance to " O   HOH Z 305 " =    3.683
peak=    3.161 closest distance to " CB  LEU A 143 " =    1.037
peak=    3.159 closest distance to " O   HOH Z 166 " =    1.499
peak=    3.156 closest distance to " CA  LEU A 282 " =    0.952
peak=    3.153 closest distance to " CA  GLN A  88 " =    1.478
peak=    3.153 closest distance to " O   HOH Z 276 " =    1.325
peak=    3.150 closest distance to " CB  PHE A  61 " =    0.788
peak=    3.150 closest distance to " O   HOH Z 377 " =    1.461
peak=    3.149 closest distance to " CD  GLU A 236 " =    1.143
peak=    3.146 closest distance to " CB  PHE A  16 " =    1.142
peak=    3.143 closest distance to " CA  THR A 294 " =    1.822
peak=    3.140 closest distance to " CA  ASP A 140 " =    1.326
peak=    3.137 closest distance to " O   HOH Z 186 " =    2.891
peak=    3.135 closest distance to " NH1BARG A 145 " =    1.051
peak=    3.134 closest distance to " CD  ARG A 219 " =    0.971
peak=    3.134 closest distance to " O   ASN A 209 " =    1.194
peak=    3.133 closest distance to " CB  TYR A 116 " =    1.287
peak=    3.128 closest distance to " O   TRP A 274 " =    1.726
peak=    3.127 closest distance to " NZ  LYS A 119 " =    1.491
peak=    3.124 closest distance to " O   HOH Z  78 " =    1.123
peak=    3.122 closest distance to " C   GLY A  80 " =    1.203
peak=    3.121 closest distance to " CB  LEU A 237 " =    0.813
peak=    3.117 closest distance to " O   ASN A 217 " =    1.247
peak=    3.116 closest distance to " O   MET A 105 " =    1.836
peak=    3.114 closest distance to " CB  ALA A 248 " =    0.966
peak=    3.113 closest distance to " CB  ARG A 259 " =    1.857
peak=    3.110 closest distance to " O   HOH Z 329 " =    3.601
peak=    3.110 closest distance to " O   HOH Z 284 " =    3.010
peak=    3.109 closest distance to " O   HOH Z 417 " =    3.364
peak=    3.106 closest distance to " O   HOH Z 368 " =    4.297
peak=    3.106 closest distance to " CB  LEU A  83 " =    0.792
peak=    3.098 closest distance to " CA  ALA A 158 " =    1.108
peak=    3.092 closest distance to " CA  ARG A 156 " =    0.973
peak=    3.086 closest distance to " O   HOH Z 133 " =    1.610
peak=    3.085 closest distance to " O   ASP A 124 " =    1.039
peak=    3.083 closest distance to " CB  ASP A 253 " =    1.077
peak=    3.081 closest distance to " O   HOH Z 248 " =    1.639
peak=    3.073 closest distance to " CB  ASN A  39 " =    0.834
peak=    3.069 closest distance to " CG  GLN A  77 " =    0.718
peak=    3.062 closest distance to " CB  ASN A 142 " =    1.061
peak=    3.050 closest distance to " CD1 TRP A 274 " =    1.062
peak=    3.037 closest distance to " N   ARG A 156 " =    1.415
peak=    3.032 closest distance to " O   HOH Z 327 " =    1.723
peak=    3.010 closest distance to " O   HOH Z 109 " =    2.397

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 213         
Filter by distance & map next to the model:
   mapped sites are within: 0.602 - 5.694
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 210 from: 213
   mapped sites are within: 0.729 - 5.694

peak=   -4.293 closest distance to " NH2 ARG A  66 " =    1.319
peak=   -4.273 closest distance to " CG  GLN A  58 " =    1.080
peak=   -4.271 closest distance to " O   HOH Z 266 " =    4.531
peak=   -4.260 closest distance to " O   HOH Z 290 " =    0.915
peak=   -4.158 closest distance to " CD1 PHE A  59 " =    1.915
peak=   -4.145 closest distance to " CG  ASP A 231 " =    0.758
peak=   -4.127 closest distance to " O   HOH Z 231 " =    1.946
peak=   -4.108 closest distance to " N   ALA A  43 " =    2.582
peak=   -4.086 closest distance to " O   HOH Z  13 " =    1.588
peak=   -4.079 closest distance to " O   HOH Z  19 " =    1.967
peak=   -4.055 closest distance to " O   HOH Z 166 " =    1.794
peak=   -4.048 closest distance to " C   ASN A 285 " =    2.608
peak=   -4.020 closest distance to " O   HOH Z  17 " =    1.243
peak=   -4.000 closest distance to " ND2 ASN A  45 " =    0.875
peak=   -3.994 closest distance to " O   HOH Z 377 " =    1.787
peak=   -3.993 closest distance to " O   HOH Z 377 " =    0.845
peak=   -3.981 closest distance to " O   HOH Z 109 " =    3.752
peak=   -3.969 closest distance to " CH2 TRP A 179 " =    1.133
peak=   -3.948 closest distance to " O   HOH Z 434 " =    4.234
peak=   -3.928 closest distance to " O   HOH Z  97 " =    1.518
peak=   -3.927 closest distance to " O   HOH Z 210 " =    0.781
peak=   -3.914 closest distance to " OD2 ASP A 171 " =    2.258
peak=   -3.911 closest distance to " CD2 PHE A  59 " =    2.434
peak=   -3.910 closest distance to " OG  SER A  97 " =    2.253
peak=   -3.909 closest distance to " O   HOH Z   5 " =    1.561
peak=   -3.909 closest distance to " CD2 LEU A 300 " =    3.373
peak=   -3.903 closest distance to " N   GLN A  58 " =    1.486
peak=   -3.887 closest distance to " O   HOH Z 231 " =    1.389
peak=   -3.883 closest distance to " O   HOH Z  52 " =    1.664
peak=   -3.868 closest distance to " CD  GLN A  88 " =    1.000
peak=   -3.847 closest distance to " CE2 TYR A  30 " =    2.692
peak=   -3.814 closest distance to " O   HOH Z 184 " =    1.334
peak=   -3.813 closest distance to " CG1 VAL A 112 " =    2.606
peak=   -3.808 closest distance to " O   GLY A 118 " =    2.309
peak=   -3.802 closest distance to " CD  ARG A 156 " =    1.999
peak=   -3.802 closest distance to " O   GLY A 196 " =    1.134
peak=   -3.794 closest distance to " O   HOH Z 213 " =    1.345
peak=   -3.794 closest distance to " OG1 THR A  82 " =    1.925
peak=   -3.792 closest distance to " CA  VAL A  67 " =    2.850
peak=   -3.789 closest distance to " CG  ARG A 269 " =    2.329
peak=   -3.775 closest distance to " CB  CYS A 254 " =    2.477
peak=   -3.743 closest distance to " O   HOH Z 259 " =    0.806
peak=   -3.734 closest distance to " O   HOH Z  38 " =    0.952
peak=   -3.730 closest distance to " CD2 LEU A 237 " =    2.533
peak=   -3.727 closest distance to " CD1 LEU A 228 " =    2.542
peak=   -3.722 closest distance to " O   HOH Z  43 " =    1.581
peak=   -3.719 closest distance to " SG ACYS A 201 " =    2.312
peak=   -3.715 closest distance to " CB  LEU A 167 " =    2.189
peak=   -3.714 closest distance to " C   ALA A 158 " =    1.200
peak=   -3.713 closest distance to " CD2 LEU A 143 " =    2.523
peak=   -3.701 closest distance to " O   HOH Z 426 " =    1.802
peak=   -3.673 closest distance to " CZ  ARG A  66 " =    1.032
peak=   -3.662 closest distance to " O   HOH Z 221 " =    1.251
peak=   -3.661 closest distance to " O   HOH Z  71 " =    1.307
peak=   -3.660 closest distance to " O   HOH Z 185 " =    2.517
peak=   -3.652 closest distance to " OE2 GLU A   2 " =    1.414
peak=   -3.634 closest distance to " CB  ARG A 219 " =    2.317
peak=   -3.630 closest distance to " O   HOH Z  94 " =    1.955
peak=   -3.630 closest distance to " CG  ARG A  66 " =    2.431
peak=   -3.623 closest distance to " CG2 THR A 221 " =    2.296
peak=   -3.619 closest distance to " O   VAL A  67 " =    2.800
peak=   -3.615 closest distance to " O   ILE A 109 " =    2.741
peak=   -3.610 closest distance to " CD  GLN A 223 " =    0.916
peak=   -3.597 closest distance to " O   HOH Z 308 " =    1.586
peak=   -3.588 closest distance to " O   HOH Z 252 " =    4.132
peak=   -3.585 closest distance to " O   HOH Z 283 " =    1.833
peak=   -3.583 closest distance to " CE  MET A  93 " =    1.171
peak=   -3.581 closest distance to " OH  TYR A 169 " =    1.047
peak=   -3.579 closest distance to " CA  ASN A 127 " =    1.156
peak=   -3.577 closest distance to " OG ASER A 134 " =    1.469
peak=   -3.570 closest distance to " OE1 GLN A  88 " =    0.934
peak=   -3.569 closest distance to " OXT GLY A 302 " =    2.848
peak=   -3.568 closest distance to " C   ASN A 187 " =    1.865
peak=   -3.563 closest distance to " CG  GLU A  53 " =    1.427
peak=   -3.544 closest distance to " O   HOH Z 221 " =    1.396
peak=   -3.539 closest distance to " O   HOH Z 325 " =    1.761
peak=   -3.538 closest distance to " CA  ASN A 148 " =    1.700
peak=   -3.534 closest distance to " O   HOH Z 111 " =    1.197
peak=   -3.525 closest distance to " O   PRO A 198 " =    1.317
peak=   -3.502 closest distance to " CA  GLY A 241 " =    2.258
peak=   -3.500 closest distance to " CA  TRP A 274 " =    1.581
peak=   -3.496 closest distance to " O   PRO A 163 " =    2.138
peak=   -3.488 closest distance to " CG  ASP A  50 " =    2.117
peak=   -3.479 closest distance to " O   HOH Z  91 " =    1.994
peak=   -3.476 closest distance to " CB  SER A 134 " =    1.898
peak=   -3.475 closest distance to " N   ALA A 226 " =    2.083
peak=   -3.469 closest distance to " OD1 ASP A 191 " =    1.635
peak=   -3.465 closest distance to " O   HOH Z 150 " =    1.751
peak=   -3.465 closest distance to " O   HOH Z 351 " =    1.429
peak=   -3.457 closest distance to " OD2 ASP A 171 " =    1.893
peak=   -3.446 closest distance to " CA  GLY A 133 " =    2.348
peak=   -3.446 closest distance to " CB  TYR A  15 " =    2.318
peak=   -3.436 closest distance to " CD  ARG A 139 " =    1.712
peak=   -3.427 closest distance to " CA  TYR A  68 " =    2.640
peak=   -3.416 closest distance to " O   HOH Z 313 " =    1.161
peak=   -3.410 closest distance to " O   HOH Z  11 " =    1.529
peak=   -3.404 closest distance to " O   HOH Z 422 " =    0.987
peak=   -3.396 closest distance to " O   HOH Z 384 " =    2.136
peak=   -3.394 closest distance to " O   HOH Z 103 " =    1.851
peak=   -3.390 closest distance to " O   HOH Z  48 " =    0.795
peak=   -3.383 closest distance to " CA  VAL A 232 " =    2.454
peak=   -3.379 closest distance to " O   HOH Z 150 " =    1.204
peak=   -3.379 closest distance to " CG  MET A  93 " =    2.552
peak=   -3.376 closest distance to " CB  PRO A 243 " =    2.653
peak=   -3.374 closest distance to " O   HOH Z  53 " =    1.364
peak=   -3.372 closest distance to " O   HOH Z 148 " =    3.456
peak=   -3.371 closest distance to " NH2 ARG A  66 " =    5.524
peak=   -3.370 closest distance to " O   HOH Z 275 " =    1.534
peak=   -3.363 closest distance to " O   HOH Z 388 " =    1.982
peak=   -3.363 closest distance to " C   HIS A 108 " =    1.152
peak=   -3.357 closest distance to " CD2 LEU A 237 " =    2.492
peak=   -3.354 closest distance to " SG  CYS A 168 " =    0.904
peak=   -3.351 closest distance to " CG  ASP A 298 " =    0.895
peak=   -3.347 closest distance to " O   HOH Z 102 " =    0.875
peak=   -3.347 closest distance to " O   HOH Z 243 " =    1.732
peak=   -3.346 closest distance to " CE1 TYR A 247 " =    2.442
peak=   -3.345 closest distance to " O   HOH Z 312 " =    1.521
peak=   -3.334 closest distance to " O   HOH Z 292 " =    4.217
peak=   -3.329 closest distance to " O   HOH Z 234 " =    4.329
peak=   -3.327 closest distance to " CG  ARG A 219 " =    2.329
peak=   -3.320 closest distance to " CG  MET A 105 " =    0.941
peak=   -3.319 closest distance to " CB  ALA A 227 " =    2.357
peak=   -3.317 closest distance to " O   HOH Z 241 " =    0.976
peak=   -3.314 closest distance to " O   HOH Z 396 " =    1.630
peak=   -3.313 closest distance to " CG  LYS A 193 " =    2.641
peak=   -3.312 closest distance to " O   HOH Z 423 " =    1.947
peak=   -3.311 closest distance to " O   VAL A 174 " =    2.152
peak=   -3.309 closest distance to " O   HOH Z  98 " =    1.967
peak=   -3.306 closest distance to " CB  ARG A 219 " =    2.413
peak=   -3.304 closest distance to " OD2 ASP A  65 " =    1.969
peak=   -3.301 closest distance to " O   HOH Z 418 " =    1.509
peak=   -3.301 closest distance to " O   HOH Z 380 " =    4.603
peak=   -3.299 closest distance to " OG  SER A  63 " =    1.280
peak=   -3.295 closest distance to " CD2 LEU A 167 " =    1.808
peak=   -3.292 closest distance to " CG  TRP A 266 " =    1.747
peak=   -3.278 closest distance to " CD  ARG A 195 " =    5.191
peak=   -3.276 closest distance to " CG  LEU A  83 " =    2.048
peak=   -3.273 closest distance to " O   HOH Z  39 " =    1.942
peak=   -3.273 closest distance to " O   HOH Z 141 " =    1.896
peak=   -3.271 closest distance to " CB  ALA A 131 " =    2.307
peak=   -3.270 closest distance to " NZ  LYS A 119 " =    1.413
peak=   -3.267 closest distance to " CB  ALA A 248 " =    1.965
peak=   -3.264 closest distance to " O   HOH Z 407 " =    0.829
peak=   -3.264 closest distance to " CG2 VAL A 189 " =    0.914
peak=   -3.263 closest distance to " O   LEU A 101 " =    2.493
peak=   -3.262 closest distance to " O   TRP A  92 " =    1.870
peak=   -3.259 closest distance to " O   PHE A 218 " =    1.452
peak=   -3.252 closest distance to " CZ3 TRP A  92 " =    1.042
peak=   -3.250 closest distance to " O   HOH Z  58 " =    0.901
peak=   -3.248 closest distance to " CE  MET A 105 " =    2.023
peak=   -3.246 closest distance to " O   HOH Z 389 " =    2.086
peak=   -3.242 closest distance to " CB  ALA A 291 " =    2.188
peak=   -3.241 closest distance to " O   HOH Z 414 " =    1.316
peak=   -3.241 closest distance to " CH2 TRP A 177 " =    2.079
peak=   -3.234 closest distance to " OG  SER A  26 " =    1.273
peak=   -3.228 closest distance to " OE1 GLN A  88 " =    1.166
peak=   -3.226 closest distance to " O   HOH Z 371 " =    1.647
peak=   -3.223 closest distance to " CG  ARG A 259 " =    2.695
peak=   -3.217 closest distance to " O   HOH Z 298 " =    2.932
peak=   -3.216 closest distance to " O   HOH Z 165 " =    2.106
peak=   -3.215 closest distance to " CA  SER A 276 " =    1.488
peak=   -3.206 closest distance to " OG  SER A  87 " =    1.471
peak=   -3.205 closest distance to " CA  GLY A 241 " =    3.019
peak=   -3.201 closest distance to " CD  LYS A 289 " =    2.407
peak=   -3.198 closest distance to " N   LEU A 261 " =    1.322
peak=   -3.193 closest distance to " O   LEU A 143 " =    1.421
peak=   -3.192 closest distance to " OE1 GLN A  94 " =    2.416
peak=   -3.190 closest distance to " CD  ARG A 159 " =    1.172
peak=   -3.186 closest distance to " C   SER A 206 " =    1.459
peak=   -3.179 closest distance to " CB  ALA A  10 " =    1.974
peak=   -3.179 closest distance to " O   VAL A 125 " =    2.101
peak=   -3.176 closest distance to " O   HOH Z 348 " =    2.238
peak=   -3.172 closest distance to " O   HOH Z 385 " =    4.052
peak=   -3.171 closest distance to " CD2 TRP A 274 " =    2.343
peak=   -3.169 closest distance to " CA  PRO A 198 " =    1.113
peak=   -3.165 closest distance to " O   ASN A 301 " =    1.448
peak=   -3.164 closest distance to " O   ALA A 160 " =    1.447
peak=   -3.164 closest distance to " C   SER A 271 " =    1.212
peak=   -3.164 closest distance to " O   HOH Z 132 " =    1.485
peak=   -3.161 closest distance to " O   SER A 210 " =    1.945
peak=   -3.159 closest distance to " OG  SER A  62 " =    1.551
peak=   -3.158 closest distance to " O   HOH Z 151 " =    1.556
peak=   -3.153 closest distance to " CD1 TYR A 247 " =    2.186
peak=   -3.147 closest distance to " CG2 THR A   4 " =    1.892
peak=   -3.141 closest distance to " O   HOH Z 236 " =    1.702
peak=   -3.135 closest distance to " OG  SER A 245 " =    0.975
peak=   -3.129 closest distance to " CA  ASP A 298 " =    1.045
peak=   -3.126 closest distance to " NE2 GLN A  88 " =    1.903
peak=   -3.123 closest distance to " O   HOH Z 118 " =    0.896
peak=   -3.117 closest distance to " CB  ASN A 170 " =    2.180
peak=   -3.114 closest distance to " O   HOH Z 390 " =    2.322
peak=   -3.114 closest distance to " O   HOH Z 424 " =    2.817
peak=   -3.106 closest distance to " O   GLY A  80 " =    2.192
peak=   -3.101 closest distance to " OG1 THR A  82 " =    1.469
peak=   -3.101 closest distance to " O   HOH Z 399 " =    2.335
peak=   -3.099 closest distance to " O   HOH Z  90 " =    1.878
peak=   -3.096 closest distance to " O   VAL A 197 " =    1.412
peak=   -3.088 closest distance to " O   MET A  47 " =    2.486
peak=   -3.083 closest distance to " O   HOH Z 186 " =    1.147
peak=   -3.081 closest distance to " CG  PRO A 163 " =    2.239
peak=   -3.079 closest distance to " NE2 GLN A  58 " =    0.729
peak=   -3.070 closest distance to " O   HOH Z 427 " =    1.427
peak=   -3.068 closest distance to " ND2 ASN A  60 " =    1.774
peak=   -3.068 closest distance to " O   HOH Z 267 " =    1.403
peak=   -3.066 closest distance to " CB  PRO A 163 " =    2.807
peak=   -3.066 closest distance to " O   GLN A 194 " =    1.269
peak=   -3.065 closest distance to " CG1 VAL A 153 " =    2.158
peak=   -3.048 closest distance to " CE  MET A 105 " =    2.235
peak=   -3.036 closest distance to " O   HOH Z 253 " =    1.392
peak=   -3.031 closest distance to " O   HOH Z 430 " =    5.694

================= 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    :  0.4863 0.4747   6.292796e+00   6.281964e+00
   1_bss:  0.4801 0.4679   6.290838e+00   6.274908e+00
   1_xyz:  0.3685 0.4119   6.118957e+00   6.193861e+00
   1_adp:  0.3371 0.4100   6.078027e+00   6.194253e+00
   1_occ:  0.3367 0.4105   6.077162e+00   6.194260e+00
   2_bss:  0.3362 0.4088   6.077645e+00   6.192477e+00
   2_xyz:  0.2772 0.3426   5.929727e+00   6.086718e+00
   2_adp:  0.2590 0.3381   5.897950e+00   6.077704e+00
   2_occ:  0.2588 0.3380   5.897583e+00   6.077280e+00
   3_bss:  0.2590 0.3381   5.896624e+00   6.077511e+00
   3_xyz:  0.2008 0.2628   5.652584e+00   5.864247e+00
   3_adp:  0.1761 0.2321   5.536323e+00   5.755541e+00
   3_occ:  0.1760 0.2320   5.535938e+00   5.755057e+00
   4_bss:  0.1757 0.2322   5.537577e+00   5.754952e+00
   4_xyz:  0.1463 0.1964   5.374899e+00   5.607307e+00
   4_adp:  0.1372 0.1865   5.326450e+00   5.559359e+00
   4_occ:  0.1371 0.1864   5.326269e+00   5.559307e+00
   5_bss:  0.1375 0.1870   5.328593e+00   5.560564e+00
   5_xyz:  0.1248 0.1734   5.249663e+00   5.482824e+00
   5_adp:  0.1236 0.1694   5.236598e+00   5.462407e+00
   5_occ:  0.1234 0.1693   5.236184e+00   5.462145e+00
   5_bss:  0.1234 0.1692   5.235724e+00   5.461471e+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:  0.277  30.868   0.633   2.294   0.090   0.000   0.000   0.000
   1_xyz:  0.277  30.868   0.633   2.294   0.090   0.000   0.000   0.000
   1_adp:  0.277  30.868   0.633   2.294   0.090   0.000   0.000   0.000
   1_occ:  0.277  30.868   0.633   2.294   0.090   0.000   0.000   0.000
   2_bss:  0.333  64.288   0.192   1.471   0.161   0.000   0.000   0.000
   2_xyz:  0.333  64.288   0.192   1.471   0.161   0.000   0.000   0.000
   2_adp:  0.333  64.288   0.192   1.471   0.161   0.000   0.000   0.000
   2_occ:  0.333  64.288   0.192   1.471   0.161   0.000   0.000   0.000
   3_bss:  0.334  77.350   0.067   0.983  -0.223   0.000  -0.000  -0.000
   3_xyz:  0.334  77.350   0.067   0.983  -0.223   0.000  -0.000  -0.000
   3_adp:  0.334  77.350   0.067   0.983  -0.223   0.000  -0.000  -0.000
   3_occ:  0.334  77.350   0.067   0.983  -0.223   0.000  -0.000  -0.000
   4_bss:  0.340  80.001  -0.947  -0.366  -0.997  -0.000  -0.000  -0.000
   4_xyz:  0.340  80.001  -0.947  -0.366  -0.997  -0.000  -0.000  -0.000
   4_adp:  0.340  80.001  -0.947  -0.366  -0.997  -0.000  -0.000  -0.000
   4_occ:  0.340  80.001  -0.947  -0.366  -0.997  -0.000  -0.000  -0.000
   5_bss:  0.333  71.725  -1.317  -0.889  -1.246  -0.000  -0.000  -0.000
   5_xyz:  0.333  71.725  -1.317  -0.889  -1.246  -0.000  -0.000  -0.000
   5_adp:  0.333  71.725  -1.317  -0.889  -1.246  -0.000  -0.000  -0.000
   5_occ:  0.333  71.725  -1.317  -0.889  -1.246  -0.000  -0.000  -0.000
   5_bss:  0.322  61.741  -1.390  -1.115  -1.305  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  62.163 0.3642  0.4861    75100.827
   1_bss:  61.486 0.3712  0.5148    72371.033
   1_xyz:  47.636 0.5478  0.7580    49662.147
   1_adp:  47.965 0.5431  0.7489    49834.289
   1_occ:  47.967 0.5431  0.7475    49807.259
   2_bss:  47.825 0.5447  0.7419    49518.863
   2_xyz:  38.169 0.6624  0.8812    33871.336
   2_adp:  37.132 0.6750  0.8843    32807.056
   2_occ:  37.113 0.6753  0.8843    32778.524
   3_bss:  37.050 0.6759  0.8738    32680.338
   3_xyz:  27.257 0.7856  0.9736    18262.565
   3_adp:  23.207 0.8289  0.9860    14171.365
   3_occ:  23.199 0.8290  0.9858    14157.452
   4_bss:  23.175 0.8293  0.9519    14167.551
   4_xyz:  19.276 0.8674  0.9758    10063.401
   4_adp:  17.962 0.8805  0.9771     9193.539
   4_occ:  17.958 0.8805  0.9770     9191.627
   5_bss:  17.996 0.8802  0.9645     9232.614
   5_xyz:  16.280 0.8956  0.9712     7857.347
   5_adp:  15.827 0.8998  0.9673     7648.074
   5_occ:  15.818 0.8999  0.9673     7642.578
   5_bss:  15.806 0.9000  0.9616     7621.802
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.8885e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.8885e-01
   1_xyz:   1.750  0.015  0.109 16.392  0.007  4.106   1.7503e-01
   1_adp:   1.750  0.015  0.109 16.392  0.007  4.106   1.7503e-01
   1_occ:   1.750  0.015  0.109 16.392  0.007  4.106   1.7503e-01
   2_bss:   1.750  0.015  0.109 16.392  0.007  4.106   1.7503e-01
   2_xyz:   1.272  0.008  0.082 14.602  0.005  4.126   8.2133e-02
   2_adp:   1.272  0.008  0.082 14.602  0.005  4.126   8.2133e-02
   2_occ:   1.272  0.008  0.082 14.602  0.005  4.126   8.2133e-02
   3_bss:   1.272  0.008  0.082 14.602  0.005  4.126   8.2133e-02
   3_xyz:   1.281  0.010  0.084 14.859  0.004  4.119   8.9434e-02
   3_adp:   1.281  0.010  0.084 14.859  0.004  4.119   8.9434e-02
   3_occ:   1.281  0.010  0.084 14.859  0.004  4.119   8.9434e-02
   4_bss:   1.281  0.010  0.084 14.859  0.004  4.119   8.9434e-02
   4_xyz:   1.156  0.009  0.079 14.670  0.004  4.133   7.4628e-02
   4_adp:   1.156  0.009  0.079 14.670  0.004  4.133   7.4628e-02
   4_occ:   1.156  0.009  0.079 14.670  0.004  4.133   7.4628e-02
   5_bss:   1.156  0.009  0.079 14.670  0.004  4.133   7.4628e-02
   5_xyz:   1.139  0.010  0.080 14.612  0.004  4.116   7.3427e-02
   5_adp:   1.139  0.010  0.080 14.612  0.004  4.116   7.3427e-02
   5_occ:   1.139  0.010  0.080 14.612  0.004  4.116   7.3427e-02
   5_bss:   1.139  0.010  0.080 14.612  0.004  4.116   7.3427e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.438   2.4371e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.438   2.4371e-01
   1_xyz:  10.446  0.084  0.388 87.535  0.034  1.978   1.3587e-01
   1_adp:  10.446  0.084  0.388 87.535  0.034  1.978   1.3587e-01
   1_occ:  10.446  0.084  0.388 87.535  0.034  1.978   1.3587e-01
   2_bss:  10.446  0.084  0.388 87.535  0.034  1.978   1.3587e-01
   2_xyz:   7.903  0.042  0.230 79.792  0.055  2.274   9.3022e-02
   2_adp:   7.903  0.042  0.230 79.792  0.055  2.274   9.3022e-02
   2_occ:   7.903  0.042  0.230 79.792  0.055  2.274   9.3022e-02
   3_bss:   7.903  0.042  0.230 79.792  0.055  2.274   9.3022e-02
   3_xyz:   9.019  0.063  0.316 78.992  0.021  2.158   9.8710e-02
   3_adp:   9.019  0.063  0.316 78.992  0.021  2.158   9.8710e-02
   3_occ:   9.019  0.063  0.316 78.992  0.021  2.158   9.8710e-02
   4_bss:   9.019  0.063  0.316 78.992  0.021  2.158   9.8710e-02
   4_xyz:   8.435  0.055  0.257 88.682  0.044  2.251   5.1355e-02
   4_adp:   8.435  0.055  0.257 88.682  0.044  2.251   5.1355e-02
   4_occ:   8.435  0.055  0.257 88.682  0.044  2.251   5.1355e-02
   5_bss:   8.435  0.055  0.257 88.682  0.044  2.251   5.1355e-02
   5_xyz:   8.645  0.056  0.248 81.579  0.035  2.326   4.9025e-02
   5_adp:   8.645  0.056  0.248 81.579  0.035  2.326   4.9025e-02
   5_occ:   8.645  0.056  0.248 81.579  0.035  2.326   4.9025e-02
   5_bss:   8.645  0.056  0.248 81.579  0.035  2.326   4.9025e-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: 127.52   0.00  17.95 127.52   0.00  14.28  76.08   0.00  37.92
   1_occ: 127.52   0.00  17.95 127.52   0.00  14.28  76.08   0.00  37.92
   2_bss: 127.52   0.00  17.95 127.52   0.00  14.28  76.08   0.00  37.92
   2_xyz: 127.52   0.00  17.95 127.52   0.00  14.28  76.08   0.00  37.92
   2_adp: 120.52   0.00  19.97 102.34   0.00  15.40 120.52   1.08  44.88
   2_occ: 120.52   0.00  19.97 102.34   0.00  15.40 120.52   1.08  44.88
   3_bss: 120.52   0.00  19.97 102.34   0.00  15.40 120.52   1.08  44.88
   3_xyz: 120.52   0.00  19.97 102.34   0.00  15.40 120.52   1.08  44.88
   3_adp: 110.59   0.00  18.88 110.59   0.00  13.58 109.88   4.93  47.72
   3_occ: 110.59   0.00  18.88 110.59   0.00  13.58 109.88   4.93  47.72
   4_bss: 110.59   0.00  18.88 110.59   0.00  13.58 109.88   4.93  47.72
   4_xyz: 110.59   0.00  18.88 110.59   0.00  13.58 109.88   4.93  47.72
   4_adp: 113.19   0.87  17.96 113.19   0.87  12.85 104.75   4.68  45.80
   4_occ: 113.19   0.87  17.96 113.19   0.87  12.85 104.75   4.68  45.80
   5_bss: 113.19   0.87  17.96 113.19   0.87  12.85 104.75   4.68  45.80
   5_xyz: 113.19   0.87  17.96 113.19   0.87  12.85 104.75   4.68  45.80
   5_adp: 109.47   1.61  17.16 109.47   1.61  12.48 102.57   4.54  42.61
   5_occ: 109.47   1.61  17.16 109.47   1.61  12.48 102.57   4.54  42.61
   5_bss: 109.41   1.55  17.10 109.41   1.55  12.43 102.51   4.48  42.55
------------------------------------------------------------------------
 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:    2.281    0.022    0.448
   1_adp:    2.281    0.022    0.448
   1_occ:    2.281    0.022    0.448
   2_bss:    2.281    0.022    0.448
   2_xyz:    2.167    0.032    0.570
   2_adp:    2.167    0.032    0.570
   2_occ:    2.167    0.032    0.570
   3_bss:    2.167    0.032    0.570
   3_xyz:    1.987    0.069    0.777
   3_adp:    1.987    0.069    0.777
   3_occ:    1.987    0.069    0.777
   4_bss:    1.987    0.069    0.777
   4_xyz:    1.763    0.124    0.834
   4_adp:    1.763    0.124    0.834
   4_occ:    1.763    0.124    0.834
   5_bss:    1.763    0.124    0.834
   5_xyz:    1.551    0.124    0.874
   5_adp:    1.551    0.124    0.874
   5_occ:    1.551    0.124    0.874
   5_bss:    1.551    0.124    0.874
------------------------------------------------------------------------

CPU time actual refinement: 367.24


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1310/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_1310/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1310/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1310/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1310/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 367.10 
  Macro-tasks:
    bulk solvent and scale       = 49.65  
    individual site refinement   = 151.78 
    weights calculation          = 30.63  
    collect and process          = 6.41   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 238.59 
  Micro-tasks:
    mask                            = 2.55   
    f_calc                          = 118.03 
    alpha_beta                      = 8.51   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 126.26 
    fmodel                         = 8.10   
    r_factors                      = 0.28   
    phase_errors                   = 10.03  
    foms                           = 0.20   
    TOTAL for micro-tasks          = 275.15 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.187 micro seconds
Total CPU time: 6.34 minutes
from_scatterers_fft:    637 calls, 117.65 s
gradients_fft:          582 calls, 113.30 s

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

# Date 2008-01-16 Time 06:57:43 PST -0800 (1200495463.18 s)
Start R-work = 0.4863, R-free = 0.4747 (no bulk solvent and anisotropic scale)
Final R-work = 0.1419, R-free = 0.1870 (no bulk solvent and anisotropic scale)

Start R-work = 0.4801, R-free = 0.4679
Final R-work = 0.1234, R-free = 0.1692