# Date 2008-01-16 Time 05:22:18 PST -0800 (1200489738.64 s)
#phil __OFF__

Command line arguments: "../704.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 15688
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 704

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 47.8686, 84.2302, 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: 3.33, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.8686, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9212 1.95156
Completeness in resolution range: 0.921792
Completeness with d_max=infinity: 0.919067

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9212
                             d_min =   1.9516

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.8686, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9212 1.95156
Completeness in resolution range: 0.921792
Completeness with d_max=infinity: 0.919067

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9216 -  4.1767 [2236/2265]  2013   223  10.0%
  bin  2:  4.1767 -  3.3272 [2133/2156]  1921   212   9.9%
  bin  3:  3.3272 -  2.9102 [2102/2127]  1892   210  10.0%
  bin  4:  2.9102 -  2.6457 [2096/2122]  1889   207   9.9%
  bin  5:  2.6457 -  2.4570 [2098/2132]  1888   210  10.0%
  bin  6:  2.4570 -  2.3127 [2060/2088]  1856   204   9.9%
  bin  7:  2.3127 -  2.1972 [2048/2084]  1841   207  10.1%
  bin  8:  2.1972 -  2.1019 [2055/2097]  1848   207  10.1%
  bin  9:  2.1019 -  2.0212 [1987/2077]  1790   197   9.9%
  bin 10:  2.0212 -  1.9516 [ 774/2103]   692    82  10.6%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_704/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:
        1.45 -     2.14: 23
        2.14 -     2.83: 971
        2.83 -     3.52: 4406
        3.52 -     4.21: 9361
        4.21 -     4.90: 13709
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.447 3.040 -x+1/2,-y+1,z+1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.502 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.508 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.616 3.040 -x+1/2,-y+1,z-1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.703 3.120 -x+1/2,-y+1,z-1/2
  ... (remaining 28465 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_704/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_704/model_refine_001.geo

CPU time processing inputs: 9.60


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 47.8686 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4602   r_free= 0.4522   ksol= 0.00   Bsol= 0.00   scale= 0.898    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.274711                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9216 -  4.6588 0.99   1451  163 0.3663 0.3757      6.5541      6.5639|
|  2:  4.6588 -  3.7166 0.99   1382  149 0.3984 0.4012      6.8053      6.7739|
|  3:  3.7166 -  3.2524 0.99   1379  152 0.4247 0.3994      6.6441       6.702|
|  4:  3.2524 -  2.9575 0.98   1344  155 0.4443 0.4225      6.4985      6.4677|
|  5:  2.9575 -  2.7470 0.99   1350  150 0.4760 0.4414       6.349      6.3037|
|  6:  2.7470 -  2.5859 0.99   1351  150 0.4926 0.4507      6.2614      6.1526|
|  7:  2.5859 -  2.4570 0.98   1346  143 0.4898 0.4640      6.2419      6.2033|
|  8:  2.4570 -  2.3505 0.98   1306  145 0.5127 0.5492      6.1379      6.1975|
|  9:  2.3505 -  2.2603 0.99   1338  149 0.5302 0.5074      6.1399       6.134|
| 10:  2.2603 -  2.1825 0.99   1313  150 0.5016 0.5220      6.0861      6.1105|
| 11:  2.1825 -  2.1145 0.97   1326  145 0.5218 0.5596      6.0172       6.002|
| 12:  2.1145 -  2.0542 0.98   1300  144 0.5063 0.5396      5.9371      5.9935|
| 13:  2.0542 -  2.0003 0.85   1123  131 0.5252 0.4643      5.8707      5.8386|
| 14:  2.0003 -  1.9516 0.23    321   33 0.5744 0.4531      5.8188      5.6979|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9216 -  4.6588  1451   163  0.69  34.95   0.83     0.72      73242.00|
|  2:  4.6588 -  3.7166  1382   149  0.71  34.83   0.91     0.80     100609.90|
|  3:  3.7166 -  3.2524  1379   152  0.61  42.58   0.92     0.80     105720.86|
|  4:  3.2524 -  2.9575  1344   155  0.54  48.62   0.92     0.75      92818.82|
|  5:  2.9575 -  2.7470  1350   150  0.49  52.78   0.88     0.69      73125.17|
|  6:  2.7470 -  2.5859  1351   150  0.46  55.43   0.90     0.65      62819.84|
|  7:  2.5859 -  2.4570  1346   143  0.44  56.98   0.92     0.59      58314.36|
|  8:  2.4570 -  2.3505  1306   145  0.35  64.12   0.88     0.52      59389.31|
|  9:  2.3505 -  2.2603  1338   149  0.31  66.60   0.92     0.47      56507.66|
| 10:  2.2603 -  2.1825  1313   150  0.27  70.01   0.97     0.41      55508.77|
| 11:  2.1825 -  2.1145  1326   145  0.24  72.38   0.93     0.36      51058.98|
| 12:  2.1145 -  2.0542  1300   144  0.20  75.35   0.95     0.33      48721.53|
| 13:  2.0542 -  2.0003  1123   131  0.21  74.54   0.93     0.34      40951.97|
| 14:  2.0003 -  1.9516   321    33  0.24  71.80   0.87     0.39      34263.23|
|alpha:            min =        0.33 max =            0.80 mean =         0.57|
|beta:             min =    34263.23 max =       105720.86 mean =     67612.97|
|figures of merit: min =        0.00 max =            1.00 mean =         0.43|
|phase err.(work): min =        0.00 max =           90.00 mean =        57.36|
|phase err.(test): min =        0.00 max =           89.97 mean =        57.53|
|-----------------------------------------------------------------------------|

============================== 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 = 19.092185             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.865   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.937769              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.224   (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 |  1.447 -  1.792:        8 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.792 -  2.138:       15 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.138 -  2.483:       33 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.483 -  2.828:      938 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.828 -  3.173:     2008 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.173 -  3.519:     2398 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.519 -  3.864:     4645 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.864 -  4.209:     4716 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.209 -  4.555:     6222 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.555 -  4.900:     7487 |
|-----------------------------------------------------------------------------|
|-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 |        0.196 |
| 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  1.447 |       0.687 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.788)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4602   r_free= 0.4522   ksol= 0.00   Bsol= 0.00   scale= 0.898    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.274711                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4490   r_free= 0.4403   ksol= 0.30   Bsol= 20.00   scale= 0.938   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.28,3.62,2.00,0.00,0.00,0.00); trace/3= 0.78                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.266399                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.566862             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.669   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.254320              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.942   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4490      final r-factor (work) = 0.3292          |
| start r-factor (free) = 0.4403      final r-factor (free) = 0.3630          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 48.9617 = 15.57 * 0.50 * 6.2653 + 1.00 * 0.1963                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 47.8262 = 15.57 * 0.50 * 6.1233 + 1.00 * 0.1657                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3292      final r-factor (work) = 0.2999          |
| start r-factor (free) = 0.3630      final r-factor (free) = 0.3755          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6874 = 1.25 * 1.00 * 6.1233 + 1.00 * 0.0068                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5483 = 1.25 * 1.00 * 5.9767 + 1.00 * 0.0515                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.788)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    119.50  18.63    None  None   None       |
|    all(noH): 2823   0      0.00    119.50  18.63    None  None   None       |
|    Sol.    : 438    0      0.33    79.94   38.98    None  None   None       |
|    Mac.    : 2385   0      0.00    119.50  14.89    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 -  11.950: 1160   |   5:    59.750 -  71.700:   44        |
|      1:    11.950 -  23.900:  879   |   6:    71.700 -  83.650:    4        |
|      2:    23.900 -  35.850:  401   |   7:    83.650 -  95.600:    0        |
|      3:    35.850 -  47.800:  217   |   8:    95.600 - 107.550:    0        |
|      4:    47.800 -  59.750:  117   |   9:   107.550 - 119.499:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2999 r_free = 0.3755             target_work(ml) = 5.986         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2993 r_free = 0.3755             target_work(ml) = 5.985         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2993   r_free= 0.3755   ksol= 0.30   Bsol= 20.00   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.28,3.62,2.00,0.00,0.00,0.00); trace/3= 0.78                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 5.984975                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2953   r_free= 0.3707   ksol= 0.32   Bsol= 50.00   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.05,1.19,-0.14,0.00,-0.00,-0.00); trace/3= -0.34                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 5.980474                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.524858              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.124   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.923206              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.331   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2953      final r-factor (work) = 0.2285          |
| start r-factor (free) = 0.3707      final r-factor (free) = 0.2856          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.6560 = 6.52 * 0.50 * 5.9742 + 1.00 * 0.1657                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.3025 = 6.52 * 0.50 * 5.8927 + 1.00 * 0.0779                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2285      final r-factor (work) = 0.2078          |
| start r-factor (free) = 0.2856      final r-factor (free) = 0.2701          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4711 = 0.92 * 1.00 * 5.8927 + 1.00 * 0.0308                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2924 = 0.92 * 1.00 * 5.7164 + 1.00 * 0.0150                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.788)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.78  18.88    None  None   None       |
|    all(noH): 2823   0      0.00    102.78  18.88    None  None   None       |
|    Sol.    : 438    0      5.20    102.78  44.10    None  None   None       |
|    Mac.    : 2385   0      0.00    98.12   14.25    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.278: 1068   |   5:    51.391 -  61.669:   83        |
|      1:    10.278 -  20.556:  960   |   6:    61.669 -  71.947:   62        |
|      2:    20.556 -  30.835:  313   |   7:    71.947 -  82.225:   22        |
|      3:    30.835 -  41.113:  152   |   8:    82.225 -  92.503:   20        |
|      4:    41.113 -  51.391:  135   |   9:    92.503 - 102.782:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2078 r_free = 0.2701             target_work(ml) = 5.690         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2077 r_free = 0.2701             target_work(ml) = 5.689         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2077   r_free= 0.2701   ksol= 0.32   Bsol= 50.00   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.05,1.19,-0.14,0.00,-0.00,-0.00); trace/3= -0.34                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.689316                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2076   r_free= 0.2694   ksol= 0.32   Bsol= 56.37   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,0.19,-0.79,0.00,-0.00,-0.00); trace/3= -0.82                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.687198                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.672105              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.040  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.350324              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.998  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2076      final r-factor (work) = 0.1587          |
| start r-factor (free) = 0.2694      final r-factor (free) = 0.2096          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.4314 = 4.67 * 0.50 * 5.7163 + 1.00 * 0.0779                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.1135 = 4.67 * 0.50 * 5.5834 + 1.00 * 0.0704                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1587      final r-factor (work) = 0.1460          |
| start r-factor (free) = 0.2096      final r-factor (free) = 0.1910          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9713 = 0.35 * 1.00 * 5.5834 + 1.00 * 0.0153                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9217 = 0.35 * 1.00 * 5.4093 + 1.00 * 0.0267                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.788)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.18  17.96    None  None   None       |
|    all(noH): 2823   0      0.00    102.18  17.96    None  None   None       |
|    Sol.    : 438    0      6.05    102.18  43.28    None  None   None       |
|    Mac.    : 2385   0      0.00    101.18  13.30    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.218: 1096   |   5:    51.091 -  61.309:   98        |
|      1:    10.218 -  20.436: 1062   |   6:    61.309 -  71.527:   42        |
|      2:    20.436 -  30.655:  224   |   7:    71.527 -  81.745:   26        |
|      3:    30.655 -  40.873:  138   |   8:    81.745 -  91.963:   10        |
|      4:    40.873 -  51.091:  121   |   9:    91.963 - 102.182:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1460 r_free = 0.1910             target_work(ml) = 5.359         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1458 r_free = 0.1910             target_work(ml) = 5.359         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1458   r_free= 0.1910   ksol= 0.32   Bsol= 56.37   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,0.19,-0.79,0.00,-0.00,-0.00); trace/3= -0.82                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.358812                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1456   r_free= 0.1905   ksol= 0.33   Bsol= 55.92   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-1.05,-1.68,-0.00,-0.00,-0.00); trace/3= -1.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.361598                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.016800              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.526  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.464160              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.997   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1456      final r-factor (work) = 0.1303          |
| start r-factor (free) = 0.1905      final r-factor (free) = 0.1746          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5301 = 2.02 * 0.50 * 5.4142 + 1.00 * 0.0704                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4149 = 2.02 * 0.50 * 5.3145 + 1.00 * 0.0558                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1303      final r-factor (work) = 0.1278          |
| start r-factor (free) = 0.1746      final r-factor (free) = 0.1747          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7948 = 1.46 * 1.00 * 5.3145 + 1.00 * 0.0135                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7227 = 1.46 * 1.00 * 5.2596 + 1.00 * 0.0217                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.788)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.20  17.90    None  None   None       |
|    all(noH): 2823   0      0.00    102.20  17.90    None  None   None       |
|    Sol.    : 438    0      5.85    102.20  43.44    None  None   None       |
|    Mac.    : 2385   0      0.00    101.64  13.21    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.220: 1084   |   5:    51.098 -  61.318:   98        |
|      1:    10.220 -  20.439: 1080   |   6:    61.318 -  71.538:   45        |
|      2:    20.439 -  30.659:  217   |   7:    71.538 -  81.757:   27        |
|      3:    30.659 -  40.879:  134   |   8:    81.757 -  91.977:   10        |
|      4:    40.879 -  51.098:  122   |   9:    91.977 - 102.197:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1278 r_free = 0.1747             target_work(ml) = 5.259         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1277 r_free = 0.1747             target_work(ml) = 5.259         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1277   r_free= 0.1747   ksol= 0.33   Bsol= 55.92   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-1.05,-1.68,-0.00,-0.00,-0.00); trace/3= -1.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.259253                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1277   r_free= 0.1747   ksol= 0.32   Bsol= 55.51   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.42,-1.28,-1.74,-0.00,-0.00,-0.00); trace/3= -1.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.259108                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.743867              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.581  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.115726              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.606   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1277      final r-factor (work) = 0.1189          |
| start r-factor (free) = 0.1747      final r-factor (free) = 0.1679          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2711 = 2.74 * 0.50 * 5.2593 + 1.00 * 0.0558                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2405 = 2.74 * 0.50 * 5.2288 + 1.00 * 0.0670                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1189      final r-factor (work) = 0.1188          |
| start r-factor (free) = 0.1679      final r-factor (free) = 0.1635          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6503 = 0.12 * 1.00 * 5.2288 + 1.00 * 0.0452                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6103 = 0.12 * 1.00 * 5.2093 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.788)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.16    98.68   16.96    None  None   None       |
|    all(noH): 2823   0      2.16    98.68   16.96    None  None   None       |
|    Sol.    : 438    0      5.67    98.68   39.41    None  None   None       |
|    Mac.    : 2385   0      2.16    94.70   12.83    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.163 -  11.814: 1444   |   5:    50.421 -  60.072:   60        |
|      1:    11.814 -  21.466:  813   |   6:    60.072 -  69.724:   37        |
|      2:    21.466 -  31.117:  185   |   7:    69.724 -  79.375:   17        |
|      3:    31.117 -  40.769:  135   |   8:    79.375 -  89.027:    6        |
|      4:    40.769 -  50.421:  121   |   9:    89.027 -  98.678:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1188 r_free = 0.1635             target_work(ml) = 5.194         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1186 r_free = 0.1635             target_work(ml) = 5.194         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1186   r_free= 0.1635   ksol= 0.32   Bsol= 55.51   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.42,-1.28,-1.74,-0.00,-0.00,-0.00); trace/3= -1.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.193767                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9216 -  4.6588 0.99   1451  163 0.0969 0.1236      5.3604      5.5311|
|  2:  4.6588 -  3.7166 0.99   1382  149 0.0861 0.1086      5.4337      5.6309|
|  3:  3.7166 -  3.2524 0.99   1379  152 0.1111 0.1666      5.5051      5.9107|
|  4:  3.2524 -  2.9575 0.98   1344  155 0.1350 0.1614        5.51      5.6469|
|  5:  2.9575 -  2.7470 0.99   1350  150 0.1427 0.1900      5.3716      5.5255|
|  6:  2.7470 -  2.5859 0.99   1351  150 0.1349 0.1993      5.2691      5.4864|
|  7:  2.5859 -  2.4570 0.98   1346  143 0.1329 0.1842      5.2176      5.4297|
|  8:  2.4570 -  2.3505 0.98   1306  145 0.1335 0.1760      5.1366      5.3296|
|  9:  2.3505 -  2.2603 0.99   1338  149 0.1251 0.1849      5.0618      5.3015|
| 10:  2.2603 -  2.1825 0.99   1313  150 0.1218 0.1813      5.0078      5.2736|
| 11:  2.1825 -  2.1145 0.97   1326  145 0.1185 0.1879      4.9491      5.2247|
| 12:  2.1145 -  2.0542 0.98   1300  144 0.1211 0.1788       4.878      5.1204|
| 13:  2.0542 -  2.0003 0.85   1123  131 0.1223 0.1705      4.8147      5.0148|
| 14:  2.0003 -  1.9516 0.23    321   33 0.1258 0.1803      4.7402      5.0164|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9216 -  4.6588  1451   163  0.94   8.80   0.98     0.96       6877.34|
|  2:  4.6588 -  3.7166  1382   149  0.95   8.02   1.02     1.00       8934.67|
|  3:  3.7166 -  3.2524  1379   152  0.93  12.01   1.02     1.02      10885.05|
|  4:  3.2524 -  2.9575  1344   155  0.91  14.87   1.01     0.99      11213.96|
|  5:  2.9575 -  2.7470  1350   150  0.89  17.46   1.00     0.97       9208.77|
|  6:  2.7470 -  2.5859  1351   150  0.89  16.87   0.99     0.97       7736.33|
|  7:  2.5859 -  2.4570  1346   143  0.90  16.56   0.99     0.97       6880.44|
|  8:  2.4570 -  2.3505  1306   145  0.89  17.26   1.01     0.97       6122.70|
|  9:  2.3505 -  2.2603  1338   149  0.89  16.72   1.00     0.97       5342.20|
| 10:  2.2603 -  2.1825  1313   150  0.90  16.12   1.00     0.96       4753.03|
| 11:  2.1825 -  2.1145  1326   145  0.90  16.54   1.00     0.98       4450.08|
| 12:  2.1145 -  2.0542  1300   144  0.91  15.78   1.00     0.98       3809.18|
| 13:  2.0542 -  2.0003  1123   131  0.89  17.00   1.01     1.00       3438.35|
| 14:  2.0003 -  1.9516   321    33  0.89  17.36   0.98     0.95       2969.63|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2969.63 max =        11213.96 mean =      6897.65|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.89 mean =        14.87|
|phase err.(test): min =        0.00 max =           88.84 mean =        14.34|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1632   ksol= 0.32   Bsol= 51.23   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-1.44,-1.78,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.194898                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1632   ksol= 0.32   Bsol= 51.23   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-1.44,-1.78,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.194898                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9216 -  4.6588 0.99   1451  163 0.0972 0.1216      5.3636       5.529|
|  2:  4.6588 -  3.7166 0.99   1382  149 0.0869 0.1079      5.4387      5.6399|
|  3:  3.7166 -  3.2524 0.99   1379  152 0.1114 0.1653      5.5085      5.9062|
|  4:  3.2524 -  2.9575 0.98   1344  155 0.1354 0.1615      5.5103      5.6447|
|  5:  2.9575 -  2.7470 0.99   1350  150 0.1427 0.1899      5.3717      5.5248|
|  6:  2.7470 -  2.5859 0.99   1351  150 0.1349 0.1991      5.2691      5.4858|
|  7:  2.5859 -  2.4570 0.98   1346  143 0.1330 0.1850      5.2179      5.4325|
|  8:  2.4570 -  2.3505 0.98   1306  145 0.1334 0.1756      5.1377      5.3287|
|  9:  2.3505 -  2.2603 0.99   1338  149 0.1247 0.1844      5.0612      5.3008|
| 10:  2.2603 -  2.1825 0.99   1313  150 0.1219 0.1818      5.0079      5.2754|
| 11:  2.1825 -  2.1145 0.97   1326  145 0.1185 0.1879      4.9491      5.2241|
| 12:  2.1145 -  2.0542 0.98   1300  144 0.1211 0.1792      4.8788       5.123|
| 13:  2.0542 -  2.0003 0.85   1123  131 0.1222 0.1703      4.8155       5.014|
| 14:  2.0003 -  1.9516 0.23    321   33 0.1261 0.1799        4.74       5.013|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9216 -  4.6588  1451   163  0.94   8.78   0.97     0.95       6776.01|
|  2:  4.6588 -  3.7166  1382   149  0.95   8.11   1.01     1.00       8974.43|
|  3:  3.7166 -  3.2524  1379   152  0.93  12.06   1.02     1.02      11020.41|
|  4:  3.2524 -  2.9575  1344   155  0.91  14.85   1.01     0.98      11174.08|
|  5:  2.9575 -  2.7470  1350   150  0.89  17.43   1.00     0.97       9185.50|
|  6:  2.7470 -  2.5859  1351   150  0.89  16.88   0.98     0.96       7741.91|
|  7:  2.5859 -  2.4570  1346   143  0.90  16.59   0.99     0.96       6889.88|
|  8:  2.4570 -  2.3505  1306   145  0.89  17.28   1.00     0.96       6135.44|
|  9:  2.3505 -  2.2603  1338   149  0.89  16.74   1.00     0.96       5348.49|
| 10:  2.2603 -  2.1825  1313   150  0.90  16.10   0.99     0.96       4751.16|
| 11:  2.1825 -  2.1145  1326   145  0.90  16.54   1.00     0.97       4454.62|
| 12:  2.1145 -  2.0542  1300   144  0.91  15.79   0.99     0.97       3818.16|
| 13:  2.0542 -  2.0003  1123   131  0.89  17.00   1.00     1.00       3442.35|
| 14:  2.0003 -  1.9516   321    33  0.89  17.33   0.98     0.95       2960.36|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2960.36 max =        11174.08 mean =      6901.71|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.88|
|phase err.(test): min =        0.00 max =           88.45 mean =        14.33|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.788)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.08    98.60   16.88    None  None   None       |
|    all(noH): 2823   0      2.08    98.60   16.88    None  None   None       |
|    Sol.    : 438    0      5.59    98.60   39.33    None  None   None       |
|    Mac.    : 2385   0      2.08    94.62   12.76    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.084 -  11.736: 1444   |   5:    50.342 -  59.994:   60        |
|      1:    11.736 -  21.388:  813   |   6:    59.994 -  69.646:   37        |
|      2:    21.388 -  31.039:  185   |   7:    69.646 -  79.297:   17        |
|      3:    31.039 -  40.691:  135   |   8:    79.297 -  88.949:    6        |
|      4:    40.691 -  50.342:  121   |   9:    88.949 -  98.600:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 317         
Filter by distance & map next to the model:
   mapped sites are within: 0.553 - 5.950
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 314 from: 317
   mapped sites are within: 0.721 - 5.950

peak=    8.451 closest distance to " O   HOH Z 138 " =    1.177
peak=    5.883 closest distance to " CB  SER A  63 " =    1.175
peak=    5.743 closest distance to " NH2 ARG A  56 " =    2.330
peak=    5.366 closest distance to " O   HOH Z 124 " =    1.538
peak=    5.177 closest distance to " O   HOH Z 132 " =    1.490
peak=    5.025 closest distance to " O   HOH Z  11 " =    1.407
peak=    4.989 closest distance to " CG  PRO A  54 " =    1.255
peak=    4.941 closest distance to " O   HOH Z  15 " =    2.088
peak=    4.770 closest distance to " O   PRO A 198 " =    1.589
peak=    4.768 closest distance to " CB  GLN A 223 " =    1.495
peak=    4.754 closest distance to " O   HOH Z 108 " =    1.553
peak=    4.750 closest distance to " O   HOH Z 134 " =    1.869
peak=    4.717 closest distance to " O   HOH Z 142 " =    1.477
peak=    4.691 closest distance to " O   HOH Z 234 " =    3.795
peak=    4.674 closest distance to " CB  SER A   3 " =    1.408
peak=    4.637 closest distance to " O   HOH Z  40 " =    1.885
peak=    4.590 closest distance to " O   HOH Z  80 " =    1.794
peak=    4.567 closest distance to " O   HOH Z 209 " =    2.410
peak=    4.559 closest distance to " O   HOH Z 389 " =    1.996
peak=    4.555 closest distance to " O   HOH Z 210 " =    1.226
peak=    4.553 closest distance to " O   HOH Z 163 " =    1.667
peak=    4.541 closest distance to " CB  GLN A 183 " =    1.270
peak=    4.538 closest distance to " O   HOH Z 133 " =    1.739
peak=    4.529 closest distance to " CA  TYR A  30 " =    1.055
peak=    4.492 closest distance to " O   HOH Z  97 " =    1.836
peak=    4.489 closest distance to " O   HOH Z 189 " =    1.936
peak=    4.478 closest distance to " O   HOH Z 411 " =    3.265
peak=    4.477 closest distance to " O   HOH Z 211 " =    1.287
peak=    4.460 closest distance to " O   SER A  87 " =    2.081
peak=    4.427 closest distance to " O   HOH Z 272 " =    1.955
peak=    4.412 closest distance to " O   HOH Z  59 " =    2.301
peak=    4.411 closest distance to " O   HOH Z  43 " =    1.642
peak=    4.384 closest distance to " CG  PRO A 213 " =    1.216
peak=    4.382 closest distance to " CG1 ILE A  33 " =    1.258
peak=    4.366 closest distance to " O   HOH Z 316 " =    2.944
peak=    4.352 closest distance to " O   HOH Z 403 " =    1.790
peak=    4.344 closest distance to " O   HOH Z  63 " =    2.165
peak=    4.307 closest distance to " OE1 GLN A  11 " =    1.952
peak=    4.293 closest distance to " O   HOH Z 193 " =    1.896
peak=    4.289 closest distance to " CB  SER A 141 " =    1.006
peak=    4.236 closest distance to " O   HOH Z 154 " =    1.566
peak=    4.231 closest distance to " O   HOH Z 433 " =    1.530
peak=    4.228 closest distance to " O   HOH Z 402 " =    1.611
peak=    4.195 closest distance to " O   HOH Z 298 " =    1.886
peak=    4.190 closest distance to " CB  ARG A 275 " =    0.893
peak=    4.188 closest distance to " O   HOH Z 236 " =    1.861
peak=    4.154 closest distance to " CG  PRO A  90 " =    1.214
peak=    4.144 closest distance to " CB  VAL A 202 " =    1.490
peak=    4.142 closest distance to " CB  GLU A 277 " =    3.586
peak=    4.130 closest distance to " CB  ARG A 190 " =    1.653
peak=    4.121 closest distance to " CB  TYR A 169 " =    0.801
peak=    4.097 closest distance to " N   ASN A  39 " =    1.349
peak=    4.086 closest distance to " O   HOH Z 352 " =    1.218
peak=    4.084 closest distance to " CA  ASP A 191 " =    0.855
peak=    4.083 closest distance to " O   HOH Z 358 " =    2.030
peak=    4.078 closest distance to " CG AARG A 275 " =    0.966
peak=    4.070 closest distance to " CB  GLU A 152 " =    1.086
peak=    4.065 closest distance to " O   HOH Z  59 " =    1.943
peak=    4.058 closest distance to " O   HOH Z 126 " =    1.709
peak=    4.035 closest distance to " O   HOH Z 118 " =    1.455
peak=    4.026 closest distance to " O   HOH Z 326 " =    1.600
peak=    4.018 closest distance to " CG  PRO A 198 " =    1.330
peak=    4.013 closest distance to " CB  ARG A  79 " =    1.388
peak=    4.008 closest distance to " O   HOH Z 368 " =    2.066
peak=    4.007 closest distance to " NH2 ARG A 156 " =    1.275
peak=    4.006 closest distance to " O   HOH Z 260 " =    1.426
peak=    3.988 closest distance to " O   HOH Z 214 " =    1.070
peak=    3.987 closest distance to " O   HOH Z  44 " =    1.916
peak=    3.984 closest distance to " O   HOH Z 371 " =    3.124
peak=    3.972 closest distance to " O   HOH Z  61 " =    1.582
peak=    3.943 closest distance to " O   HOH Z  39 " =    1.319
peak=    3.931 closest distance to " O   HOH Z 313 " =    1.915
peak=    3.930 closest distance to " O   HOH Z  66 " =    2.294
peak=    3.912 closest distance to " CB  GLU A 128 " =    1.195
peak=    3.908 closest distance to " NZ  LYS A 117 " =    1.047
peak=    3.906 closest distance to " O   HOH Z  67 " =    1.969
peak=    3.872 closest distance to " O   HOH Z 196 " =    1.326
peak=    3.859 closest distance to " O   HOH Z 426 " =    1.468
peak=    3.850 closest distance to " O   HOH Z   6 " =    2.075
peak=    3.846 closest distance to " CB  ARG A 139 " =    1.087
peak=    3.839 closest distance to " O   HOH Z 344 " =    2.877
peak=    3.824 closest distance to " NH2BARG A 145 " =    1.899
peak=    3.822 closest distance to " CA  ALA A  21 " =    1.244
peak=    3.813 closest distance to " CB  TRP A 179 " =    1.358
peak=    3.809 closest distance to " OD2 ASP A 286 " =    2.835
peak=    3.807 closest distance to " O   HOH Z  78 " =    2.095
peak=    3.789 closest distance to " CG2 THR A 221 " =    1.081
peak=    3.788 closest distance to " O   HOH Z  20 " =    1.791
peak=    3.784 closest distance to " CB  PRO A  54 " =    0.721
peak=    3.783 closest distance to " O   HOH Z 369 " =    2.084
peak=    3.781 closest distance to " CD  PRO A  54 " =    1.097
peak=    3.777 closest distance to " O   HOH Z  30 " =    1.614
peak=    3.774 closest distance to " NE2 GLN A  11 " =    1.127
peak=    3.769 closest distance to " CD  LYS A 166 " =    1.385
peak=    3.767 closest distance to " CB  ALA A 100 " =    1.308
peak=    3.763 closest distance to " O   HOH Z 374 " =    2.530
peak=    3.752 closest distance to " CG  ARG A  66 " =    2.678
peak=    3.749 closest distance to " O   HOH Z 406 " =    1.618
peak=    3.748 closest distance to " CB  LEU A 228 " =    1.204
peak=    3.747 closest distance to " CG1BVAL A  72 " =    1.737
peak=    3.741 closest distance to " O   HOH Z 128 " =    2.109
peak=    3.738 closest distance to " O   HOH Z 276 " =    1.379
peak=    3.736 closest distance to " CG  PRO A 243 " =    1.190
peak=    3.734 closest distance to " O   HOH Z 126 " =    2.270
peak=    3.719 closest distance to " O   HOH Z 402 " =    2.846
peak=    3.718 closest distance to " NZ  LYS A  76 " =    1.217
peak=    3.714 closest distance to " O   HOH Z  97 " =    2.452
peak=    3.700 closest distance to " O   HOH Z 357 " =    2.039
peak=    3.699 closest distance to " O   HOH Z 203 " =    1.733
peak=    3.695 closest distance to " O   ALA A 165 " =    1.244
peak=    3.690 closest distance to " O   HOH Z 108 " =    2.193
peak=    3.690 closest distance to " O   HOH Z 232 " =    2.353
peak=    3.688 closest distance to " O   HOH Z  48 " =    1.474
peak=    3.682 closest distance to " NZ  LYS A 117 " =    3.142
peak=    3.680 closest distance to " O   HOH Z 247 " =    1.414
peak=    3.674 closest distance to " NZ  LYS A 119 " =    1.670
peak=    3.670 closest distance to " NE AARG A 275 " =    1.316
peak=    3.662 closest distance to " CB  SER A  62 " =    0.968
peak=    3.659 closest distance to " O   HOH Z 128 " =    2.146
peak=    3.644 closest distance to " O   HOH Z  88 " =    3.429
peak=    3.633 closest distance to " CA  ASN A 176 " =    1.652
peak=    3.626 closest distance to " O   HOH Z 255 " =    1.683
peak=    3.624 closest distance to " NH2AARG A 190 " =    1.312
peak=    3.623 closest distance to " O   GLY A 211 " =    1.425
peak=    3.620 closest distance to " O   HOH Z 173 " =    2.038
peak=    3.615 closest distance to " NH2AARG A 145 " =    2.172
peak=    3.613 closest distance to " O   HOH Z 334 " =    1.565
peak=    3.609 closest distance to " O   HOH Z 287 " =    1.762
peak=    3.606 closest distance to " CA  THR A 221 " =    0.935
peak=    3.602 closest distance to " O   HOH Z  43 " =    2.421
peak=    3.596 closest distance to " OD1 ASP A 238 " =    0.860
peak=    3.592 closest distance to " O   HOH Z 362 " =    3.330
peak=    3.588 closest distance to " O   HOH Z 120 " =    0.950
peak=    3.585 closest distance to " O   HOH Z 261 " =    2.086
peak=    3.582 closest distance to " O   HOH Z 227 " =    1.841
peak=    3.578 closest distance to " O   HOH Z 394 " =    1.516
peak=    3.575 closest distance to " O   HOH Z 147 " =    1.730
peak=    3.569 closest distance to " ND2 ASN A 187 " =    1.588
peak=    3.566 closest distance to " O   HOH Z  54 " =    2.360
peak=    3.563 closest distance to " O   HOH Z 386 " =    2.249
peak=    3.561 closest distance to " CB  ASN A 148 " =    1.940
peak=    3.561 closest distance to " O   HOH Z 227 " =    1.600
peak=    3.557 closest distance to " CA  ARG A 195 " =    1.055
peak=    3.547 closest distance to " CB  ASN A 285 " =    0.922
peak=    3.543 closest distance to " CD2 LEU A 297 " =    0.866
peak=    3.542 closest distance to " O   HOH Z 132 " =    2.786
peak=    3.537 closest distance to " CB  ASN A 148 " =    1.169
peak=    3.526 closest distance to " O   HOH Z 427 " =    3.039
peak=    3.526 closest distance to " O   HOH Z 291 " =    1.607
peak=    3.526 closest distance to " O   HOH Z 284 " =    2.861
peak=    3.519 closest distance to " CG1 VAL A 153 " =    1.158
peak=    3.516 closest distance to " CA  ARG A  36 " =    1.115
peak=    3.516 closest distance to " O   HOH Z 387 " =    2.311
peak=    3.516 closest distance to " O   HOH Z 279 " =    2.002
peak=    3.515 closest distance to " CB  PRO A 198 " =    1.019
peak=    3.504 closest distance to " CD  ARG A 195 " =    0.930
peak=    3.500 closest distance to " O   HOH Z 303 " =    2.076
peak=    3.500 closest distance to " CA  ASP A 162 " =    1.149
peak=    3.497 closest distance to " O   HOH Z 423 " =    1.925
peak=    3.497 closest distance to " CB  GLN A 194 " =    0.848
peak=    3.495 closest distance to " O   HOH Z  49 " =    1.727
peak=    3.492 closest distance to " O   HOH Z  35 " =    2.353
peak=    3.488 closest distance to " O   HOH Z 104 " =    3.314
peak=    3.486 closest distance to " OG  SER A  62 " =    3.060
peak=    3.485 closest distance to " O   HOH Z 408 " =    1.633
peak=    3.483 closest distance to " NE1 TRP A 274 " =    0.940
peak=    3.482 closest distance to " CB  GLN A  88 " =    1.129
peak=    3.482 closest distance to " CA  GLN A 223 " =    0.799
peak=    3.481 closest distance to " O   HOH Z  54 " =    1.616
peak=    3.480 closest distance to " CG  GLN A  89 " =    1.423
peak=    3.476 closest distance to " CH2 TRP A 274 " =    1.908
peak=    3.468 closest distance to " O   HOH Z 280 " =    2.461
peak=    3.466 closest distance to " CD2 TRP A 179 " =    1.283
peak=    3.458 closest distance to " CB  ALA A 291 " =    1.119
peak=    3.443 closest distance to " OE1 GLN A  58 " =    5.950
peak=    3.443 closest distance to " CD  ARG A 269 " =    1.082
peak=    3.440 closest distance to " CG2AVAL A 121 " =    2.156
peak=    3.438 closest distance to " O   HOH Z 345 " =    1.801
peak=    3.435 closest distance to " O   HOH Z 266 " =    1.658
peak=    3.435 closest distance to " CG  GLN A  58 " =    2.271
peak=    3.433 closest distance to " OD1 ASN A  69 " =    2.555
peak=    3.431 closest distance to " CD  LYS A 119 " =    1.663
peak=    3.430 closest distance to " CE  LYS A 119 " =    1.089
peak=    3.428 closest distance to " OH  TYR A  30 " =    1.309
peak=    3.425 closest distance to " CB  GLN A  58 " =    0.774
peak=    3.424 closest distance to " O   HOH Z  21 " =    1.909
peak=    3.418 closest distance to " CB  ASN A  39 " =    0.852
peak=    3.416 closest distance to " O   HOH Z 197 " =    2.027
peak=    3.408 closest distance to " CB  ARG A 259 " =    1.915
peak=    3.407 closest distance to " CB  ILE A 199 " =    1.152
peak=    3.405 closest distance to " O   HOH Z  51 " =    1.597
peak=    3.400 closest distance to " O   HOH Z 130 " =    2.344
peak=    3.396 closest distance to " CB  ASN A 187 " =    1.051
peak=    3.396 closest distance to " O   HOH Z 126 " =    1.783
peak=    3.393 closest distance to " O   HOH Z 419 " =    2.774
peak=    3.389 closest distance to " O   HOH Z 281 " =    4.049
peak=    3.386 closest distance to " CD2 HIS A  81 " =    1.199
peak=    3.382 closest distance to " CA  LEU A 282 " =    1.111
peak=    3.380 closest distance to " CG2 VAL A 112 " =    1.466
peak=    3.377 closest distance to " O   HOH Z 250 " =    1.487
peak=    3.373 closest distance to " C   SER A  32 " =    1.057
peak=    3.369 closest distance to " O   HOH Z 162 " =    1.720
peak=    3.366 closest distance to " O   HOH Z 156 " =    2.386
peak=    3.364 closest distance to " O   HOH Z 245 " =    1.430
peak=    3.364 closest distance to " OG BSER A 210 " =    1.201
peak=    3.363 closest distance to " O   HOH Z 250 " =    1.771
peak=    3.361 closest distance to " O   HOH Z 133 " =    1.770
peak=    3.357 closest distance to " CA  VAL A  41 " =    0.733
peak=    3.355 closest distance to " O   HOH Z 427 " =    2.769
peak=    3.343 closest distance to " O   HOH Z 163 " =    2.003
peak=    3.343 closest distance to " O   HOH Z 166 " =    1.444
peak=    3.342 closest distance to " O   MET A 105 " =    1.915
peak=    3.342 closest distance to " O   HOH Z 313 " =    2.360
peak=    3.335 closest distance to " CG  GLN A  11 " =    1.162
peak=    3.334 closest distance to " O   HOH Z 279 " =    1.102
peak=    3.334 closest distance to " CA  GLY A 196 " =    1.027
peak=    3.333 closest distance to " O   SER A  26 " =    1.694
peak=    3.333 closest distance to " CA  ASP A 140 " =    1.190
peak=    3.332 closest distance to " O   HOH Z 421 " =    1.466
peak=    3.330 closest distance to " O   HOH Z  71 " =    1.194
peak=    3.327 closest distance to " O   HOH Z 409 " =    3.176
peak=    3.323 closest distance to " O   HOH Z 137 " =    1.755
peak=    3.313 closest distance to " CA  GLY A  80 " =    0.943
peak=    3.313 closest distance to " O   HOH Z 346 " =    1.534
peak=    3.312 closest distance to " O   HOH Z 301 " =    1.633
peak=    3.306 closest distance to " O   HOH Z 207 " =    2.505
peak=    3.306 closest distance to " O   HOH Z 345 " =    2.736
peak=    3.304 closest distance to " CA  ILE A 263 " =    0.974
peak=    3.300 closest distance to " CA  ALA A 160 " =    0.893
peak=    3.300 closest distance to " OD1 ASN A  60 " =    1.204
peak=    3.298 closest distance to " O   HOH Z  19 " =    1.644
peak=    3.294 closest distance to " O   HOH Z 368 " =    2.454
peak=    3.293 closest distance to " O   HOH Z 127 " =    1.160
peak=    3.290 closest distance to " CD1 LEU A 300 " =    1.267
peak=    3.282 closest distance to " CB  ALA A 244 " =    0.888
peak=    3.281 closest distance to " O   ASN A  74 " =    1.606
peak=    3.280 closest distance to " O   HOH Z 434 " =    1.578
peak=    3.280 closest distance to " O   HOH Z 365 " =    2.883
peak=    3.279 closest distance to " O   PHE A 155 " =    1.358
peak=    3.275 closest distance to " OG  SER A 245 " =    1.513
peak=    3.274 closest distance to " OG BSER A 164 " =    2.408
peak=    3.272 closest distance to " NH1 ARG A 269 " =    0.797
peak=    3.271 closest distance to " NH1AARG A 145 " =    0.994
peak=    3.271 closest distance to " O   HOH Z 145 " =    1.801
peak=    3.268 closest distance to " O   HOH Z 106 " =    1.489
peak=    3.268 closest distance to " O   HOH Z  88 " =    1.579
peak=    3.265 closest distance to " O   HOH Z 238 " =    5.334
peak=    3.263 closest distance to " O   HOH Z 263 " =    2.117
peak=    3.260 closest distance to " O   HOH Z 112 " =    1.562
peak=    3.255 closest distance to " O   HOH Z  64 " =    1.602
peak=    3.255 closest distance to " O   HOH Z 166 " =    3.123
peak=    3.248 closest distance to " O   HOH Z 438 " =    2.585
peak=    3.247 closest distance to " O   HOH Z 155 " =    2.988
peak=    3.246 closest distance to " CA  ARG A  66 " =    1.150
peak=    3.238 closest distance to " O   HOH Z 422 " =    0.772
peak=    3.235 closest distance to " O   HOH Z 157 " =    1.625
peak=    3.228 closest distance to " O   HOH Z 150 " =    1.676
peak=    3.225 closest distance to " CA  ASP A 124 " =    0.735
peak=    3.222 closest distance to " CB  MET A 105 " =    1.149
peak=    3.220 closest distance to " O   HOH Z 339 " =    1.294
peak=    3.219 closest distance to " O   HOH Z 106 " =    2.338
peak=    3.217 closest distance to " O   ALA A 158 " =    1.199
peak=    3.212 closest distance to " O   GLY A  91 " =    1.269
peak=    3.211 closest distance to " O   HOH Z 194 " =    1.817
peak=    3.210 closest distance to " CG2 ILE A 120 " =    1.183
peak=    3.200 closest distance to " O   HOH Z 337 " =    3.790
peak=    3.197 closest distance to " OG1 THR A 294 " =    2.416
peak=    3.196 closest distance to " CA  GLU A  46 " =    0.799
peak=    3.196 closest distance to " NH1BARG A 145 " =    1.106
peak=    3.195 closest distance to " CG2 VAL A 197 " =    1.149
peak=    3.192 closest distance to " O  BHOH Z 338 " =    2.265
peak=    3.188 closest distance to " CG  MET A 185 " =    1.185
peak=    3.182 closest distance to " CB  THR A  31 " =    1.777
peak=    3.176 closest distance to " O   HOH Z 215 " =    1.508
peak=    3.175 closest distance to " O   HOH Z 109 " =    3.307
peak=    3.174 closest distance to " CB  GLU A 175 " =    1.369
peak=    3.172 closest distance to " CG1BVAL A  72 " =    3.299
peak=    3.171 closest distance to " O   HOH Z   7 " =    3.058
peak=    3.169 closest distance to " N   ARG A 156 " =    1.425
peak=    3.167 closest distance to " O   HOH Z 128 " =    1.750
peak=    3.166 closest distance to " CA  TYR A 116 " =    1.445
peak=    3.164 closest distance to " CB  SER A 216 " =    0.731
peak=    3.162 closest distance to " ND1 HIS A  81 " =    1.487
peak=    3.161 closest distance to " O   HOH Z 102 " =    1.255
peak=    3.158 closest distance to " CG2 THR A 220 " =    0.773
peak=    3.157 closest distance to " OD1 ASP A 286 " =    1.474
peak=    3.152 closest distance to " O   HOH Z 299 " =    2.191
peak=    3.151 closest distance to " CB  PRO A  54 " =    1.261
peak=    3.148 closest distance to " O   HOH Z  59 " =    2.355
peak=    3.148 closest distance to " CB  LEU A 261 " =    1.236
peak=    3.147 closest distance to " OG  SER A  97 " =    3.598
peak=    3.146 closest distance to " CB  ALA A  71 " =    1.254
peak=    3.146 closest distance to " O   THR A 264 " =    1.471
peak=    3.144 closest distance to " O   HOH Z 126 " =    1.604
peak=    3.139 closest distance to " CD BLYS A 290 " =    1.191
peak=    3.133 closest distance to " CB AVAL A  41 " =    0.932
peak=    3.132 closest distance to " O   HOH Z 171 " =    2.779
peak=    3.132 closest distance to " CB  GLN A 103 " =    0.864
peak=    3.125 closest distance to " CB  TYR A 247 " =    1.053
peak=    3.119 closest distance to " CD1 ILE A  33 " =    1.732
peak=    3.115 closest distance to " CA  ALA A 158 " =    1.058
peak=    3.113 closest distance to " O   ILE A  33 " =    1.214
peak=    3.112 closest distance to " O   HOH Z 273 " =    2.746
peak=    3.108 closest distance to " O   HOH Z   4 " =    1.892
peak=    3.102 closest distance to " O   HOH Z 369 " =    1.560
peak=    3.097 closest distance to " N   SER A 135 " =    1.279
peak=    3.091 closest distance to " O   HOH Z 125 " =    2.345
peak=    3.087 closest distance to " CG1 ILE A 120 " =    1.123
peak=    3.075 closest distance to " OD2 ASP A 298 " =    4.003
peak=    3.071 closest distance to " CA  GLU A 152 " =    0.893
peak=    3.067 closest distance to " CA  LEU A  83 " =    1.532
peak=    3.062 closest distance to " O   THR A 251 " =    1.327
peak=    3.056 closest distance to " O   HOH Z 293 " =    1.826
peak=    3.028 closest distance to " NE1 TRP A 266 " =    1.756

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 214         
Filter by distance & map next to the model:
   mapped sites are within: 0.438 - 5.066
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 214
   mapped sites are within: 0.718 - 5.066

peak=   -4.588 closest distance to " O   HOH Z 290 " =    0.823
peak=   -4.440 closest distance to " O   HOH Z 221 " =    1.115
peak=   -4.356 closest distance to " O   HOH Z 377 " =    0.808
peak=   -4.271 closest distance to " OXT GLY A 302 " =    2.897
peak=   -4.240 closest distance to " OG ASER A 134 " =    1.449
peak=   -4.189 closest distance to " CA  SER A 164 " =    1.992
peak=   -4.099 closest distance to " O   VAL A  67 " =    2.690
peak=   -4.092 closest distance to " CD1 LEU A 101 " =    2.581
peak=   -4.077 closest distance to " O   HOH Z 138 " =    0.791
peak=   -4.048 closest distance to " ND2 ASN A 187 " =    1.470
peak=   -4.039 closest distance to " CE2 TYR A  30 " =    2.691
peak=   -4.030 closest distance to " NH2 ARG A  79 " =    1.866
peak=   -4.028 closest distance to " O   PRO A 198 " =    1.261
peak=   -4.004 closest distance to " NH2 ARG A  66 " =    1.421
peak=   -4.001 closest distance to " O   HOH Z  13 " =    1.575
peak=   -3.997 closest distance to " OG  SER A  97 " =    2.235
peak=   -3.980 closest distance to " CH2 TRP A 179 " =    1.181
peak=   -3.969 closest distance to " O   HOH Z 266 " =    4.135
peak=   -3.960 closest distance to " O   HOH Z  71 " =    1.390
peak=   -3.928 closest distance to " O   HOH Z  11 " =    1.577
peak=   -3.914 closest distance to " CD  GLN A  58 " =    0.860
peak=   -3.910 closest distance to " O   HOH Z 166 " =    1.987
peak=   -3.902 closest distance to " O   HOH Z  17 " =    1.140
peak=   -3.893 closest distance to " CD  GLN A  88 " =    0.853
peak=   -3.883 closest distance to " O   HOH Z  52 " =    2.033
peak=   -3.883 closest distance to " CD  GLN A 223 " =    0.861
peak=   -3.882 closest distance to " CD  ARG A 156 " =    1.958
peak=   -3.880 closest distance to " O   HOH Z  93 " =    1.119
peak=   -3.880 closest distance to " CE  MET A 105 " =    1.937
peak=   -3.869 closest distance to " CG  GLN A  58 " =    1.240
peak=   -3.868 closest distance to " O   HOH Z 407 " =    3.498
peak=   -3.867 closest distance to " O   HOH Z 234 " =    4.293
peak=   -3.863 closest distance to " N   SER A 276 " =    1.382
peak=   -3.857 closest distance to " N   GLN A  58 " =    1.794
peak=   -3.851 closest distance to " C   SER A 206 " =    1.564
peak=   -3.845 closest distance to " CG  ASP A  50 " =    2.394
peak=   -3.842 closest distance to " CA  VAL A  67 " =    2.955
peak=   -3.806 closest distance to " O   HOH Z 423 " =    2.394
peak=   -3.806 closest distance to " C   HIS A 108 " =    1.150
peak=   -3.781 closest distance to " OG BSER A 134 " =    1.755
peak=   -3.709 closest distance to " CB  ALA A 291 " =    2.416
peak=   -3.703 closest distance to " CZ  TYR A 169 " =    1.868
peak=   -3.701 closest distance to " O   TRP A  92 " =    1.868
peak=   -3.695 closest distance to " CB  ASP A 162 " =    2.681
peak=   -3.684 closest distance to " ND2 ASN A  45 " =    1.023
peak=   -3.684 closest distance to " OG  SER A  62 " =    1.301
peak=   -3.682 closest distance to " C   ASN A 285 " =    2.281
peak=   -3.681 closest distance to " O   HOH Z  15 " =    1.505
peak=   -3.680 closest distance to " O   HOH Z 313 " =    1.062
peak=   -3.677 closest distance to " O   HOH Z 396 " =    1.758
peak=   -3.670 closest distance to " N   ALA A  43 " =    2.613
peak=   -3.664 closest distance to " OE2 GLU A   2 " =    1.395
peak=   -3.653 closest distance to " CD2 PHE A  59 " =    2.347
peak=   -3.650 closest distance to " O   HOH Z 388 " =    2.137
peak=   -3.645 closest distance to " O   HOH Z 292 " =    4.505
peak=   -3.644 closest distance to " CD1 TYR A 247 " =    2.219
peak=   -3.635 closest distance to " OD1 ASP A 191 " =    1.819
peak=   -3.632 closest distance to " CB  CYS A 254 " =    2.564
peak=   -3.600 closest distance to " O   HOH Z 377 " =    2.010
peak=   -3.600 closest distance to " C   ALA A 158 " =    1.244
peak=   -3.593 closest distance to " CD2 LEU A 300 " =    2.909
peak=   -3.573 closest distance to " O   HOH Z 196 " =    2.420
peak=   -3.571 closest distance to " ND2 ASN A 209 " =    1.833
peak=   -3.570 closest distance to " O   GLY A 196 " =    1.060
peak=   -3.569 closest distance to " CA  ASN A 148 " =    1.677
peak=   -3.566 closest distance to " O   HOH Z 138 " =    1.200
peak=   -3.565 closest distance to " CZ  ARG A  66 " =    1.234
peak=   -3.564 closest distance to " CG  ASP A 231 " =    0.758
peak=   -3.547 closest distance to " CB  ALA A 291 " =    2.093
peak=   -3.541 closest distance to " O   HOH Z 151 " =    1.502
peak=   -3.537 closest distance to " CD1 PHE A  59 " =    1.888
peak=   -3.536 closest distance to " C   THR A 279 " =    1.240
peak=   -3.506 closest distance to " O   HOH Z 150 " =    1.344
peak=   -3.504 closest distance to " O   HOH Z  20 " =    1.306
peak=   -3.499 closest distance to " O   PHE A 218 " =    1.402
peak=   -3.498 closest distance to " O   VAL A 174 " =    2.049
peak=   -3.494 closest distance to " CG  ARG A 269 " =    2.290
peak=   -3.488 closest distance to " CB  LYS A 193 " =    2.526
peak=   -3.487 closest distance to " CB  PHE A 208 " =    2.291
peak=   -3.478 closest distance to " CB  LEU A 167 " =    2.124
peak=   -3.475 closest distance to " OG1 THR A   4 " =    1.834
peak=   -3.471 closest distance to " O   HOH Z  10 " =    1.487
peak=   -3.469 closest distance to " CE  MET A  93 " =    1.318
peak=   -3.460 closest distance to " SG  CYS A 254 " =    3.311
peak=   -3.458 closest distance to " CG  GLU A  53 " =    1.450
peak=   -3.457 closest distance to " O   HOH Z 283 " =    1.712
peak=   -3.457 closest distance to " O   ALA A   1 " =    2.043
peak=   -3.455 closest distance to " O   SER A 146 " =    0.823
peak=   -3.449 closest distance to " CA  GLY A  98 " =    2.186
peak=   -3.444 closest distance to " CA  GLY A 203 " =    2.224
peak=   -3.442 closest distance to " O   HOH Z 418 " =    1.268
peak=   -3.436 closest distance to " O   HOH Z  19 " =    2.228
peak=   -3.435 closest distance to " O   HOH Z  43 " =    1.662
peak=   -3.432 closest distance to " O   HOH Z 118 " =    3.237
peak=   -3.410 closest distance to " CB  ALA A 161 " =    2.494
peak=   -3.406 closest distance to " O   ARG A 275 " =    2.154
peak=   -3.402 closest distance to " CG1 VAL A 112 " =    2.559
peak=   -3.400 closest distance to " CD1 LEU A  25 " =    2.418
peak=   -3.396 closest distance to " CD2 LEU A 237 " =    2.434
peak=   -3.391 closest distance to " CD  ARG A 139 " =    1.628
peak=   -3.391 closest distance to " CD1 PHE A 130 " =    2.301
peak=   -3.384 closest distance to " O   HOH Z 414 " =    1.361
peak=   -3.383 closest distance to " O   HOH Z 165 " =    2.102
peak=   -3.382 closest distance to " ND2 ASN A  60 " =    1.341
peak=   -3.382 closest distance to " CB  PRO A 163 " =    2.830
peak=   -3.372 closest distance to " O   HOH Z 259 " =    1.221
peak=   -3.370 closest distance to " CA  TRP A 274 " =    1.640
peak=   -3.365 closest distance to " O   HOH Z  38 " =    1.322
peak=   -3.364 closest distance to " O   HOH Z 417 " =    2.565
peak=   -3.363 closest distance to " C   LEU A 143 " =    1.286
peak=   -3.361 closest distance to " O   HOH Z 412 " =    4.881
peak=   -3.360 closest distance to " CG2 THR A 221 " =    2.344
peak=   -3.360 closest distance to " O   HOH Z  92 " =    1.575
peak=   -3.358 closest distance to " CE2 TRP A 274 " =    1.209
peak=   -3.357 closest distance to " O   ASP A 191 " =    1.327
peak=   -3.349 closest distance to " O   HOH Z 132 " =    1.362
peak=   -3.348 closest distance to " CG  LEU A  83 " =    1.961
peak=   -3.346 closest distance to " CA  VAL A 197 " =    0.959
peak=   -3.341 closest distance to " CB  ALA A 131 " =    2.260
peak=   -3.340 closest distance to " O   HOH Z 166 " =    2.062
peak=   -3.339 closest distance to " CB  ARG A 219 " =    2.335
peak=   -3.338 closest distance to " CD2 LEU A 237 " =    2.670
peak=   -3.332 closest distance to " CA  GLY A 241 " =    2.282
peak=   -3.332 closest distance to " O   ALA A 256 " =    1.486
peak=   -3.330 closest distance to " NE1 TRP A 177 " =    1.893
peak=   -3.320 closest distance to " NH1 ARG A 195 " =    2.548
peak=   -3.318 closest distance to " O   HOH Z  97 " =    1.311
peak=   -3.310 closest distance to " O   GLY A 118 " =    2.233
peak=   -3.310 closest distance to " CB  ALA A 248 " =    1.925
peak=   -3.307 closest distance to " NE2 GLN A 103 " =    1.615
peak=   -3.304 closest distance to " OG1 THR A  82 " =    2.228
peak=   -3.301 closest distance to " NZ  LYS A 117 " =    1.573
peak=   -3.293 closest distance to " OG1 THR A 178 " =    1.168
peak=   -3.292 closest distance to " O   HOH Z 140 " =    0.718
peak=   -3.292 closest distance to " CD1 LEU A 228 " =    2.402
peak=   -3.292 closest distance to " O   LEU A 167 " =    1.664
peak=   -3.286 closest distance to " N   MET A 188 " =    1.922
peak=   -3.285 closest distance to " OD1 ASP A 171 " =    1.662
peak=   -3.283 closest distance to " O   HOH Z  90 " =    2.104
peak=   -3.278 closest distance to " OG  SER A  32 " =    1.226
peak=   -3.267 closest distance to " OD1 ASN A 176 " =    1.089
peak=   -3.266 closest distance to " O   PRO A 198 " =    1.254
peak=   -3.264 closest distance to " O   HOH Z  78 " =    1.972
peak=   -3.253 closest distance to " O   HOH Z  76 " =    2.036
peak=   -3.251 closest distance to " CG  ASP A 132 " =    2.297
peak=   -3.250 closest distance to " CA  ASP A 298 " =    1.103
peak=   -3.245 closest distance to " O   LEU A 222 " =    1.274
peak=   -3.241 closest distance to " O   HOH Z  98 " =    1.848
peak=   -3.237 closest distance to " O   HOH Z 185 " =    2.273
peak=   -3.237 closest distance to " O   HOH Z 281 " =    2.781
peak=   -3.236 closest distance to " O   HOH Z 360 " =    2.361
peak=   -3.234 closest distance to " NH2 ARG A  66 " =    5.058
peak=   -3.233 closest distance to " O   HOH Z 420 " =    2.823
peak=   -3.233 closest distance to " O   HOH Z  39 " =    1.574
peak=   -3.229 closest distance to " ND2 ASN A  39 " =    1.307
peak=   -3.226 closest distance to " CB  PRO A 243 " =    2.562
peak=   -3.222 closest distance to " C   ALA A 242 " =    1.938
peak=   -3.216 closest distance to " O   SER A 210 " =    1.824
peak=   -3.215 closest distance to " CD2 HIS A 115 " =    1.017
peak=   -3.215 closest distance to " O   HOH Z 236 " =    1.766
peak=   -3.213 closest distance to " O   HOH Z 222 " =    1.519
peak=   -3.211 closest distance to " CD  ARG A 195 " =    5.066
peak=   -3.209 closest distance to " O   HOH Z 100 " =    0.836
peak=   -3.209 closest distance to " C   GLU A  46 " =    1.196
peak=   -3.208 closest distance to " N   LEU A 281 " =    1.828
peak=   -3.206 closest distance to " CB  ASN A  39 " =    2.303
peak=   -3.205 closest distance to " N   ALA A 226 " =    2.095
peak=   -3.204 closest distance to " CD  GLN A  58 " =    1.230
peak=   -3.201 closest distance to " O   HOH Z 424 " =    3.036
peak=   -3.192 closest distance to " O   SER A  26 " =    1.257
peak=   -3.185 closest distance to " O   HOH Z 423 " =    1.069
peak=   -3.184 closest distance to " CD1 TRP A 179 " =    1.080
peak=   -3.183 closest distance to " O   ASN A 187 " =    1.508
peak=   -3.182 closest distance to " OD2 ASP A 171 " =    2.439
peak=   -3.172 closest distance to " OD2 ASP A 171 " =    1.770
peak=   -3.166 closest distance to " O   HOH Z 352 " =    0.853
peak=   -3.161 closest distance to " OG  SER A   3 " =    1.368
peak=   -3.159 closest distance to " CG  GLU A 152 " =    0.945
peak=   -3.159 closest distance to " CB  PHE A  59 " =    2.567
peak=   -3.158 closest distance to " CG1AVAL A  41 " =    2.523
peak=   -3.150 closest distance to " CE3 TRP A 274 " =    2.574
peak=   -3.150 closest distance to " CG1 VAL A 197 " =    1.742
peak=   -3.150 closest distance to " O   HOH Z 264 " =    1.929
peak=   -3.148 closest distance to " CE3 TRP A 150 " =    2.243
peak=   -3.142 closest distance to " O   ALA A  34 " =    2.599
peak=   -3.136 closest distance to " N   ALA A 248 " =    1.732
peak=   -3.133 closest distance to " O   ASN A 301 " =    1.260
peak=   -3.132 closest distance to " C   GLY A  80 " =    2.468
peak=   -3.131 closest distance to " O   VAL A 125 " =    2.035
peak=   -3.129 closest distance to " O   HOH Z  37 " =    1.555
peak=   -3.124 closest distance to " N   GLN A  77 " =    1.426
peak=   -3.122 closest distance to " CG  GLU A 152 " =    2.492
peak=   -3.121 closest distance to " CH2 TRP A 150 " =    1.219
peak=   -3.118 closest distance to " CB  TRP A  85 " =    2.432
peak=   -3.108 closest distance to " CG  TRP A 266 " =    1.726
peak=   -3.105 closest distance to " SG ACYS A 201 " =    2.358
peak=   -3.098 closest distance to " O   HOH Z 280 " =    1.919
peak=   -3.093 closest distance to " NH1 ARG A  66 " =    3.961
peak=   -3.087 closest distance to " O   HOH Z  39 " =    1.524
peak=   -3.082 closest distance to " O   HOH Z 427 " =    1.361
peak=   -3.072 closest distance to " O   HOH Z  63 " =    0.959
peak=   -3.063 closest distance to " O   HOH Z 111 " =    3.365
peak=   -3.058 closest distance to " N   GLY A 133 " =    1.713
peak=   -3.049 closest distance to " O   SER A 135 " =    1.473
peak=   -3.040 closest distance to " O   SER A 276 " =    1.642
peak=   -3.022 closest distance to " O   GLY A  23 " =    1.781
peak=   -3.000 closest distance to " O   SER A 146 " =    0.935

================= 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    :  0.4602 0.4522   6.274711e+00   6.264089e+00
   1_bss:  0.4490 0.4403   6.266399e+00   6.248881e+00
   1_xyz:  0.3292 0.3630   6.032009e+00   6.103688e+00
   1_adp:  0.2999 0.3755   5.986145e+00   6.124805e+00
   1_occ:  0.2993 0.3755   5.984975e+00   6.123894e+00
   2_bss:  0.2953 0.3707   5.980474e+00   6.120780e+00
   2_xyz:  0.2285 0.2856   5.757366e+00   5.936996e+00
   2_adp:  0.2078 0.2701   5.689550e+00   5.886437e+00
   2_occ:  0.2077 0.2701   5.689316e+00   5.886347e+00
   3_bss:  0.2076 0.2694   5.687198e+00   5.885026e+00
   3_xyz:  0.1587 0.2096   5.443391e+00   5.663387e+00
   3_adp:  0.1460 0.1910   5.359049e+00   5.566817e+00
   3_occ:  0.1458 0.1910   5.358812e+00   5.566825e+00
   4_bss:  0.1456 0.1905   5.361598e+00   5.568900e+00
   4_xyz:  0.1303 0.1746   5.268245e+00   5.484374e+00
   4_adp:  0.1278 0.1747   5.259494e+00   5.481900e+00
   4_occ:  0.1277 0.1747   5.259253e+00   5.482156e+00
   5_bss:  0.1277 0.1747   5.259108e+00   5.482089e+00
   5_xyz:  0.1189 0.1679   5.205986e+00   5.442296e+00
   5_adp:  0.1188 0.1635   5.193921e+00   5.417207e+00
   5_occ:  0.1186 0.1635   5.193767e+00   5.417888e+00
   5_bss:  0.1190 0.1632   5.194898e+00   5.418033e+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:  0.300  20.000  -3.278   3.616   1.995   0.000   0.000   0.000
   1_xyz:  0.300  20.000  -3.278   3.616   1.995   0.000   0.000   0.000
   1_adp:  0.300  20.000  -3.278   3.616   1.995   0.000   0.000   0.000
   1_occ:  0.300  20.000  -3.278   3.616   1.995   0.000   0.000   0.000
   2_bss:  0.324  50.001  -2.053   1.186  -0.140   0.000  -0.000  -0.000
   2_xyz:  0.324  50.001  -2.053   1.186  -0.140   0.000  -0.000  -0.000
   2_adp:  0.324  50.001  -2.053   1.186  -0.140   0.000  -0.000  -0.000
   2_occ:  0.324  50.001  -2.053   1.186  -0.140   0.000  -0.000  -0.000
   3_bss:  0.324  56.366  -1.882   0.194  -0.786   0.000  -0.000  -0.000
   3_xyz:  0.324  56.366  -1.882   0.194  -0.786   0.000  -0.000  -0.000
   3_adp:  0.324  56.366  -1.882   0.194  -0.786   0.000  -0.000  -0.000
   3_occ:  0.324  56.366  -1.882   0.194  -0.786   0.000  -0.000  -0.000
   4_bss:  0.327  55.921  -2.443  -1.053  -1.676  -0.000  -0.000  -0.000
   4_xyz:  0.327  55.921  -2.443  -1.053  -1.676  -0.000  -0.000  -0.000
   4_adp:  0.327  55.921  -2.443  -1.053  -1.676  -0.000  -0.000  -0.000
   4_occ:  0.327  55.921  -2.443  -1.053  -1.676  -0.000  -0.000  -0.000
   5_bss:  0.325  55.505  -2.420  -1.276  -1.737  -0.000  -0.000  -0.000
   5_xyz:  0.325  55.505  -2.420  -1.276  -1.737  -0.000  -0.000  -0.000
   5_adp:  0.325  55.505  -2.420  -1.276  -1.737  -0.000  -0.000  -0.000
   5_occ:  0.325  55.505  -2.420  -1.276  -1.737  -0.000  -0.000  -0.000
   5_bss:  0.322  51.230  -2.448  -1.441  -1.776  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.376 0.4265  0.5738    67609.654
   1_bss:  55.508 0.4489  0.6194    63220.927
   1_xyz:  39.617 0.6468  0.8694    36616.375
   1_adp:  41.117 0.6279  0.8519    38934.111
   1_occ:  41.059 0.6286  0.8518    38851.333
   2_bss:  40.538 0.6349  0.8320    38218.350
   2_xyz:  29.876 0.7577  0.9512    22030.486
   2_adp:  27.562 0.7836  0.9578    19438.353
   2_occ:  27.567 0.7836  0.9575    19432.396
   3_bss:  27.426 0.7849  0.9425    19258.012
   3_xyz:  20.719 0.8534  0.9925    11440.756
   3_adp:  18.169 0.8786  1.0058     9418.968
   3_occ:  18.169 0.8786  1.0057     9422.402
   4_bss:  18.192 0.8785  0.9747     9496.275
   4_xyz:  16.286 0.8956  0.9818     7894.682
   4_adp:  16.181 0.8968  0.9794     7896.035
   4_occ:  16.181 0.8969  0.9795     7901.813
   5_bss:  16.177 0.8969  0.9767     7900.176
   5_xyz:  15.381 0.9035  0.9795     7223.045
   5_adp:  14.811 0.9085  0.9788     6878.748
   5_occ:  14.819 0.9084  0.9787     6897.501
   5_bss:  14.829 0.9083  0.9731     6901.523
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.9625e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.9625e-01
   1_xyz:   1.746  0.014  0.105 16.770  0.007  4.107   1.6571e-01
   1_adp:   1.746  0.014  0.105 16.770  0.007  4.107   1.6571e-01
   1_occ:   1.746  0.014  0.105 16.770  0.007  4.107   1.6571e-01
   2_bss:   1.746  0.014  0.105 16.770  0.007  4.107   1.6571e-01
   2_xyz:   1.241  0.008  0.080 14.870  0.005  4.109   7.7853e-02
   2_adp:   1.241  0.008  0.080 14.870  0.005  4.109   7.7853e-02
   2_occ:   1.241  0.008  0.080 14.870  0.005  4.109   7.7853e-02
   3_bss:   1.241  0.008  0.080 14.870  0.005  4.109   7.7853e-02
   3_xyz:   1.090  0.008  0.069 14.975  0.004  4.118   7.0412e-02
   3_adp:   1.090  0.008  0.069 14.975  0.004  4.118   7.0412e-02
   3_occ:   1.090  0.008  0.069 14.975  0.004  4.118   7.0412e-02
   4_bss:   1.090  0.008  0.069 14.975  0.004  4.118   7.0412e-02
   4_xyz:   0.983  0.006  0.068 14.431  0.004  4.112   5.5774e-02
   4_adp:   0.983  0.006  0.068 14.431  0.004  4.112   5.5774e-02
   4_occ:   0.983  0.006  0.068 14.431  0.004  4.112   5.5774e-02
   5_bss:   0.983  0.006  0.068 14.431  0.004  4.112   5.5774e-02
   5_xyz:   1.091  0.008  0.075 14.782  0.004  4.115   6.6971e-02
   5_adp:   1.091  0.008  0.075 14.782  0.004  4.115   6.6971e-02
   5_occ:   1.091  0.008  0.075 14.782  0.004  4.115   6.6971e-02
   5_bss:   1.091  0.008  0.075 14.782  0.004  4.115   6.6971e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.447   2.4183e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.447   2.4183e-01
   1_xyz:  10.155  0.107  0.476 88.194  0.030  2.023   1.2620e-01
   1_adp:  10.155  0.107  0.476 88.194  0.030  2.023   1.2620e-01
   1_occ:  10.155  0.107  0.476 88.194  0.030  2.023   1.2620e-01
   2_bss:  10.155  0.107  0.476 88.194  0.030  2.023   1.2620e-01
   2_xyz:   8.236  0.053  0.219 86.948  0.077  2.259   7.6221e-02
   2_adp:   8.236  0.053  0.219 86.948  0.077  2.259   7.6221e-02
   2_occ:   8.236  0.053  0.219 86.948  0.077  2.259   7.6221e-02
   3_bss:   8.236  0.053  0.219 86.948  0.077  2.259   7.6221e-02
   3_xyz:   7.672  0.060  0.225 83.743  0.023  2.308   1.0491e-01
   3_adp:   7.672  0.060  0.225 83.743  0.023  2.308   1.0491e-01
   3_occ:   7.672  0.060  0.225 83.743  0.023  2.308   1.0491e-01
   4_bss:   7.672  0.060  0.225 83.743  0.023  2.308   1.0491e-01
   4_xyz:   7.078  0.038  0.221 81.448  0.038  2.363   4.6551e-02
   4_adp:   7.078  0.038  0.221 81.448  0.038  2.363   4.6551e-02
   4_occ:   7.078  0.038  0.221 81.448  0.038  2.363   4.6551e-02
   5_bss:   7.078  0.038  0.221 81.448  0.038  2.363   4.6551e-02
   5_xyz:   7.674  0.045  0.238 81.985  0.031  2.314   5.8802e-02
   5_adp:   7.674  0.045  0.238 81.985  0.031  2.314   5.8802e-02
   5_occ:   7.674  0.045  0.238 81.985  0.031  2.314   5.8802e-02
   5_bss:   7.674  0.045  0.238 81.985  0.031  2.314   5.8802e-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: 119.50   0.00  18.63 119.50   0.00  14.89  79.94   0.33  38.98
   1_occ: 119.50   0.00  18.63 119.50   0.00  14.89  79.94   0.33  38.98
   2_bss: 119.50   0.00  18.63 119.50   0.00  14.89  79.94   0.33  38.98
   2_xyz: 119.50   0.00  18.63 119.50   0.00  14.89  79.94   0.33  38.98
   2_adp: 102.78   0.00  18.88  98.12   0.00  14.25 102.78   5.20  44.10
   2_occ: 102.78   0.00  18.88  98.12   0.00  14.25 102.78   5.20  44.10
   3_bss: 102.78   0.00  18.88  98.12   0.00  14.25 102.78   5.20  44.10
   3_xyz: 102.78   0.00  18.88  98.12   0.00  14.25 102.78   5.20  44.10
   3_adp: 102.18   0.00  17.96 101.18   0.00  13.30 102.18   6.05  43.28
   3_occ: 102.18   0.00  17.96 101.18   0.00  13.30 102.18   6.05  43.28
   4_bss: 102.18   0.00  17.96 101.18   0.00  13.30 102.18   6.05  43.28
   4_xyz: 102.18   0.00  17.96 101.18   0.00  13.30 102.18   6.05  43.28
   4_adp: 102.20   0.00  17.90 101.64   0.00  13.21 102.20   5.85  43.44
   4_occ: 102.20   0.00  17.90 101.64   0.00  13.21 102.20   5.85  43.44
   5_bss: 102.20   0.00  17.90 101.64   0.00  13.21 102.20   5.85  43.44
   5_xyz: 102.20   0.00  17.90 101.64   0.00  13.21 102.20   5.85  43.44
   5_adp:  98.68   2.16  16.96  94.70   2.16  12.83  98.68   5.67  39.41
   5_occ:  98.68   2.16  16.96  94.70   2.16  12.83  98.68   5.67  39.41
   5_bss:  98.60   2.08  16.88  94.62   2.08  12.76  98.60   5.59  39.33
------------------------------------------------------------------------
 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:    2.184    0.026    0.496
   1_adp:    2.184    0.026    0.496
   1_occ:    2.184    0.026    0.496
   2_bss:    2.184    0.026    0.496
   2_xyz:    1.697    0.035    0.612
   2_adp:    1.697    0.035    0.612
   2_occ:    1.697    0.035    0.612
   3_bss:    1.697    0.035    0.612
   3_xyz:    1.571    0.090    0.738
   3_adp:    1.571    0.090    0.738
   3_occ:    1.571    0.090    0.738
   4_bss:    1.571    0.090    0.738
   4_xyz:    1.585    0.041    0.775
   4_adp:    1.585    0.041    0.775
   4_occ:    1.585    0.041    0.775
   5_bss:    1.585    0.041    0.775
   5_xyz:    1.596    0.058    0.802
   5_adp:    1.596    0.058    0.802
   5_occ:    1.596    0.058    0.802
   5_bss:    1.596    0.058    0.802
------------------------------------------------------------------------

CPU time actual refinement: 357.00


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_704/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_704/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_704/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_704/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_704/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 356.86 
  Macro-tasks:
    bulk solvent and scale       = 45.66  
    individual site refinement   = 148.04 
    weights calculation          = 29.92  
    collect and process          = 6.53   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 230.27 
  Micro-tasks:
    mask                            = 2.45   
    f_calc                          = 113.99 
    alpha_beta                      = 8.09   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 123.09 
    fmodel                         = 7.27   
    r_factors                      = 0.22   
    phase_errors                   = 10.28  
    foms                           = 0.34   
    TOTAL for micro-tasks          = 266.90 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.065 micro seconds
Total CPU time: 6.18 minutes
from_scatterers_fft:    650 calls, 113.67 s
gradients_fft:          595 calls, 109.92 s

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

# Date 2008-01-16 Time 05:28:28 PST -0800 (1200490108.26 s)
Start R-work = 0.4602, R-free = 0.4522 (no bulk solvent and anisotropic scale)
Final R-work = 0.1420, R-free = 0.1850 (no bulk solvent and anisotropic scale)

Start R-work = 0.4490, R-free = 0.4403
Final R-work = 0.1190, R-free = 0.1632