# Date 2008-01-16 Time 05:19:21 PST -0800 (1200489561.33 s)
#phil __OFF__

Command line arguments: "../687.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 31999
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 687

-------------------------------------------------------------------------------
  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, 47.3993, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.3993, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.994 2.00046
Completeness in resolution range: 0.976861
Completeness with d_max=infinity: 0.973754

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9940
                             d_min =   2.0005

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, 47.3993, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.994 2.00046
Completeness in resolution range: 0.976861
Completeness with d_max=infinity: 0.973754

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9944 -  4.2796 [2104/2131]  1894   210  10.0%
  bin  2:  4.2796 -  3.4100 [2026/2042]  1823   203  10.0%
  bin  3:  3.4100 -  2.9828 [1993/2012]  1792   201  10.1%
  bin  4:  2.9828 -  2.7118 [1975/2005]  1782   193   9.8%
  bin  5:  2.7118 -  2.5184 [1963/1982]  1764   199  10.1%
  bin  6:  2.5184 -  2.3706 [1955/1980]  1757   198  10.1%
  bin  7:  2.3706 -  2.2522 [1952/1986]  1764   188   9.6%
  bin  8:  2.2522 -  2.1545 [1938/1969]  1741   197  10.2%
  bin  9:  2.1545 -  2.0718 [1923/1964]  1728   195  10.1%
  bin 10:  2.0718 -  2.0005 [1760/1982]  1585   175   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_687/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 9
        2.42 -     3.04: 2178
        3.04 -     3.66: 4648
        3.66 -     4.28: 8975
        4.28 -     4.90: 12343
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.094 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.339 3.040 -x+1/2,-y+1,z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 28148 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_687/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_687/model_refine_001.geo

CPU time processing inputs: 9.06


============================ 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 47.3993 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2610   r_free= 0.2515   ksol= 0.00   Bsol= 0.00   scale= 0.989    |
|                                                                             |
| 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:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.884193                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7728 0.99   1373  153 0.2616 0.2647      6.2793      6.2467|
|  2:  4.7728 -  3.8087 0.99   1308  146 0.2002 0.1946      6.2327      6.2084|
|  3:  3.8087 -  3.3333 0.99   1294  143 0.2134 0.2104      6.1396      6.1975|
|  4:  3.3333 -  3.0313 0.99   1286  139 0.2422 0.2073      6.0916      5.9201|
|  5:  3.0313 -  2.8156 0.99   1262  142 0.2535 0.2119      5.9228      5.8009|
|  6:  2.8156 -  2.6505 0.99   1273  144 0.2647 0.2540      5.8743      5.8543|
|  7:  2.6505 -  2.5184 0.99   1259  139 0.2671 0.2459      5.8244      5.7171|
|  8:  2.5184 -  2.4093 0.98   1258  142 0.2768 0.2911      5.8151      5.8863|
|  9:  2.4093 -  2.3169 0.98   1252  137 0.2797 0.2644      5.7561      5.7327|
| 10:  2.3169 -  2.2372 0.99   1247  137 0.2989 0.2909      5.8212      5.7061|
| 11:  2.2372 -  2.1674 0.99   1261  144 0.2849 0.2887      5.6836      5.7399|
| 12:  2.1674 -  2.1057 0.97   1243  131 0.2903 0.2665      5.6713      5.6502|
| 13:  2.1057 -  2.0504 0.99   1233  139 0.3078 0.3047      5.6243      5.6185|
| 14:  2.0504 -  2.0005 0.85   1081  123 0.2916 0.3038      5.5213      5.5382|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9944 -  4.7728  1373   153  0.80  24.99   0.87     0.81      38873.17|
|  2:  4.7728 -  3.8087  1308   146  0.88  18.48   0.99     0.93      32430.82|
|  3:  3.8087 -  3.3333  1294   143  0.87  18.97   1.00     0.98      26199.84|
|  4:  3.3333 -  3.0313  1286   139  0.87  19.99   1.00     0.98      20999.58|
|  5:  3.0313 -  2.8156  1262   142  0.83  23.47   1.02     0.96      17967.61|
|  6:  2.8156 -  2.6505  1273   144  0.81  25.35   1.02     0.96      16932.67|
|  7:  2.6505 -  2.5184  1259   139  0.81  26.07   1.03     0.96      16174.37|
|  8:  2.5184 -  2.4093  1258   142  0.80  26.74   1.04     0.98      15818.68|
|  9:  2.4093 -  2.3169  1252   137  0.79  27.70   1.06     0.98      14426.88|
| 10:  2.3169 -  2.2372  1247   137  0.79  27.52   1.06     0.99      13548.81|
| 11:  2.2372 -  2.1674  1261   144  0.78  28.32   1.07     1.02      13030.83|
| 12:  2.1674 -  2.1057  1243   131  0.78  28.56   1.07     1.02      12663.60|
| 13:  2.1057 -  2.0504  1233   139  0.77  29.90   1.06     1.01      11983.69|
| 14:  2.0504 -  2.0005  1081   123  0.75  31.92   1.07     0.99      10912.71|
|alpha:            min =        0.81 max =            1.02 mean =         0.97|
|beta:             min =    10912.71 max =        38873.17 mean =     18995.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.81|
|phase err.(work): min =        0.00 max =           89.85 mean =        25.45|
|phase err.(test): min =        0.00 max =           89.85 mean =        25.47|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.994267              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.895   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.426030              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.710   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        7 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      188 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1990 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1852 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2796 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4601 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4374 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5609 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6734 |
|-----------------------------------------------------------------------------|
|-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 |        0.160 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.115    4.900  1.806 |       0.138 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.027)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2610   r_free= 0.2515   ksol= 0.00   Bsol= 0.00   scale= 0.989    |
|                                                                             |
| 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:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.884193                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2432   r_free= 0.2340   ksol= 0.31   Bsol= 50.00   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.23,1.45,-1.62,0.00,-0.00,-0.00); trace/3= -1.13                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.849493                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.853014              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.976   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.244829              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.689   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2432      final r-factor (work) = 0.1527          |
| start r-factor (free) = 0.2340      final r-factor (free) = 0.1697          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5392 = 2.85 * 0.50 * 5.8737 + 1.00 * 0.1603                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9726 = 2.85 * 0.50 * 5.5391 + 1.00 * 0.0710                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1527      final r-factor (work) = 0.1383          |
| start r-factor (free) = 0.1697      final r-factor (free) = 0.1706          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3623 = 0.24 * 1.00 * 5.5391 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3033 = 0.24 * 1.00 * 5.2912 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.027)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.57    72.35   16.79    None  None   None       |
|    all(noH): 2823   0      1.57    72.35   16.79    None  None   None       |
|    Sol.    : 438    0      6.04    68.75   37.90    None  None   None       |
|    Mac.    : 2385   0      1.57    72.35   12.91    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.572 -   8.650:  648   |   5:    36.961 -  44.039:  121        |
|      1:     8.650 -  15.728: 1264   |   6:    44.039 -  51.116:   89        |
|      2:    15.728 -  22.806:  372   |   7:    51.116 -  58.194:   69        |
|      3:    22.806 -  29.883:  120   |   8:    58.194 -  65.272:   23        |
|      4:    29.883 -  36.961:  111   |   9:    65.272 -  72.350:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1383 r_free = 0.1706             target_work(ml) = 5.297         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1378 r_free = 0.1703             target_work(ml) = 5.295         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1378   r_free= 0.1703   ksol= 0.31   Bsol= 50.00   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.23,1.45,-1.62,0.00,-0.00,-0.00); trace/3= -1.13                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.295142                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1364   r_free= 0.1681   ksol= 0.32   Bsol= 55.92   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.19,-1.16,-1.63,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.282862                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.079800              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.454   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.145355              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.494  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1364      final r-factor (work) = 0.1169          |
| start r-factor (free) = 0.1681      final r-factor (free) = 0.1540          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5750 = 2.08 * 0.50 * 5.2928 + 1.00 * 0.0710                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4771 = 2.08 * 0.50 * 5.2091 + 1.00 * 0.0601                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1169      final r-factor (work) = 0.1152          |
| start r-factor (free) = 0.1540      final r-factor (free) = 0.1514          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7650 = 0.15 * 1.00 * 5.2091 + 1.00 * 0.0078                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7555 = 0.15 * 1.00 * 5.1494 + 1.00 * 0.0070                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.027)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.17    74.17   16.48    None  None   None       |
|    all(noH): 2823   0      2.17    74.17   16.48    None  None   None       |
|    Sol.    : 438    0      5.39    67.51   36.98    None  None   None       |
|    Mac.    : 2385   0      2.17    74.17   12.72    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:     2.173 -   9.373:  851   |   5:    38.172 -  45.372:  119        |
|      1:     9.373 -  16.573: 1159   |   6:    45.372 -  52.572:   79        |
|      2:    16.573 -  23.773:  308   |   7:    52.572 -  59.772:   59        |
|      3:    23.773 -  30.972:  120   |   8:    59.772 -  66.972:   10        |
|      4:    30.972 -  38.172:  115   |   9:    66.972 -  74.172:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1152 r_free = 0.1514             target_work(ml) = 5.143         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1151 r_free = 0.1513             target_work(ml) = 5.143         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1151   r_free= 0.1513   ksol= 0.32   Bsol= 55.92   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.19,-1.16,-1.63,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.142671                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1148   r_free= 0.1511   ksol= 0.33   Bsol= 55.92   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-1.66,-1.30,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.140017                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.198903              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 147.731  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.675390              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.375  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1148      final r-factor (work) = 0.1081          |
| start r-factor (free) = 0.1511      final r-factor (free) = 0.1525          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2945 = 3.20 * 0.50 * 5.1483 + 1.00 * 0.0601                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2516 = 3.20 * 0.50 * 5.1107 + 1.00 * 0.0773                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1081      final r-factor (work) = 0.1065          |
| start r-factor (free) = 0.1525      final r-factor (free) = 0.1533          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4587 = 0.68 * 1.00 * 5.1107 + 1.00 * 0.0070                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4524 = 0.68 * 1.00 * 5.0991 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.027)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.68    80.60   16.65    None  None   None       |
|    all(noH): 2823   0      0.68    80.60   16.65    None  None   None       |
|    Sol.    : 438    0      5.93    68.18   38.45    None  None   None       |
|    Mac.    : 2385   0      0.68    80.60   12.65    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.677 -   8.669:  738   |   5:    40.637 -  48.629:  102        |
|      1:     8.669 -  16.661: 1270   |   6:    48.629 -  56.621:   93        |
|      2:    16.661 -  24.653:  319   |   7:    56.621 -  64.613:   43        |
|      3:    24.653 -  32.645:  126   |   8:    64.613 -  72.605:   10        |
|      4:    32.645 -  40.637:  119   |   9:    72.605 -  80.597:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1065 r_free = 0.1533             target_work(ml) = 5.105         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1065 r_free = 0.1534             target_work(ml) = 5.105         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1065   r_free= 0.1534   ksol= 0.33   Bsol= 55.92   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-1.66,-1.30,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.104633                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1065   r_free= 0.1528   ksol= 0.32   Bsol= 55.92   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.47,-1.66,-1.06,-0.00,-0.00,-0.00); trace/3= -1.73                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.105264                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.253126              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 155.146  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.498106              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.736  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1065      final r-factor (work) = 0.1080          |
| start r-factor (free) = 0.1528      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8230 = 2.25 * 0.50 * 5.1002 + 1.00 * 0.0773                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8223 = 2.25 * 0.50 * 5.1113 + 1.00 * 0.0641                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1080      final r-factor (work) = 0.1076          |
| start r-factor (free) = 0.1549      final r-factor (free) = 0.1560          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.7771 = 2.50 * 1.00 * 5.1113 + 1.00 * 0.0085                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.7886 = 2.50 * 1.00 * 5.1153 + 1.00 * 0.0100                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.027)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.66   16.77    None  None   None       |
|    all(noH): 2823   0      0.00    89.66   16.77    None  None   None       |
|    Sol.    : 438    0      5.61    74.52   39.56    None  None   None       |
|    Mac.    : 2385   0      0.00    89.66   12.58    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.966:  882   |   5:    44.830 -  53.796:  106        |
|      1:     8.966 -  17.932: 1213   |   6:    53.796 -  62.762:   72        |
|      2:    17.932 -  26.898:  265   |   7:    62.762 -  71.728:   29        |
|      3:    26.898 -  35.864:  133   |   8:    71.728 -  80.694:    5        |
|      4:    35.864 -  44.830:  114   |   9:    80.694 -  89.660:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1076 r_free = 0.1560             target_work(ml) = 5.121         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1075 r_free = 0.1560             target_work(ml) = 5.121         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1075   r_free= 0.1560   ksol= 0.32   Bsol= 55.92   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.47,-1.66,-1.06,-0.00,-0.00,-0.00); trace/3= -1.73                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.120775                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1074   r_free= 0.1559   ksol= 0.32   Bsol= 55.92   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-1.47,-0.81,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.120824                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.981998              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 166.048  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 6.157948              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.943  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1074      final r-factor (work) = 0.1081          |
| start r-factor (free) = 0.1559      final r-factor (free) = 0.1577          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1345 = 1.98 * 0.50 * 5.1165 + 1.00 * 0.0641                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1367 = 1.98 * 0.50 * 5.1235 + 1.00 * 0.0592                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1081      final r-factor (work) = 0.1081          |
| start r-factor (free) = 0.1577      final r-factor (free) = 0.1588          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 31.5604 = 6.16 * 1.00 * 5.1235 + 1.00 * 0.0099                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 31.5823 = 6.16 * 1.00 * 5.1269 + 1.00 * 0.0111                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.027)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.50  16.76    None  None   None       |
|    all(noH): 2823   0      0.00    105.50  16.76    None  None   None       |
|    Sol.    : 438    0      5.37    89.80   40.03    None  None   None       |
|    Mac.    : 2385   0      0.00    105.50  12.49    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 -  10.550: 1302   |   5:    52.750 -  63.300:   86        |
|      1:    10.550 -  21.100:  930   |   6:    63.300 -  73.850:   38        |
|      2:    21.100 -  31.650:  203   |   7:    73.850 -  84.400:    7        |
|      3:    31.650 -  42.200:  135   |   8:    84.400 -  94.950:    3        |
|      4:    42.200 -  52.750:  115   |   9:    94.950 - 105.499:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1081 r_free = 0.1588             target_work(ml) = 5.132         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1081 r_free = 0.1588             target_work(ml) = 5.132         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1588   ksol= 0.32   Bsol= 55.92   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-1.47,-0.81,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.131858                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7728 0.99   1373  153 0.0966 0.1265      5.3735      5.5096|
|  2:  4.7728 -  3.8087 0.99   1308  146 0.0820 0.1070      5.4129      5.6111|
|  3:  3.8087 -  3.3333 0.99   1294  143 0.0999 0.1502      5.4468      5.8747|
|  4:  3.3333 -  3.0313 0.99   1286  139 0.1162 0.1533      5.4389      5.5918|
|  5:  3.0313 -  2.8156 0.99   1262  142 0.1267 0.1804      5.3158      5.5512|
|  6:  2.8156 -  2.6505 0.99   1273  144 0.1192 0.1751      5.2178      5.4395|
|  7:  2.6505 -  2.5184 0.99   1259  139 0.1207 0.1691       5.144      5.3906|
|  8:  2.5184 -  2.4093 0.98   1258  142 0.1117 0.1756      5.0719      5.3522|
|  9:  2.4093 -  2.3169 0.98   1252  137 0.1121 0.1722       5.012      5.2662|
| 10:  2.3169 -  2.2372 0.99   1247  137 0.1080 0.1862      4.9766      5.2693|
| 11:  2.2372 -  2.1674 0.99   1261  144 0.1131 0.1814       4.941       5.277|
| 12:  2.1674 -  2.1057 0.97   1243  131 0.1103 0.1685         4.9      5.2236|
| 13:  2.1057 -  2.0504 0.99   1233  139 0.1095 0.1758      4.8041      5.0747|
| 14:  2.0504 -  2.0005 0.85   1081  123 0.1020 0.1815      4.6632      4.9886|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9944 -  4.7728  1373   153  0.94   9.36   0.97     0.94       7299.64|
|  2:  4.7728 -  3.8087  1308   146  0.95   7.92   1.01     0.99       8881.95|
|  3:  3.8087 -  3.3333  1294   143  0.94  10.84   1.02     1.01      10031.84|
|  4:  3.3333 -  3.0313  1286   139  0.92  13.20   1.01     0.99      10201.03|
|  5:  3.0313 -  2.8156  1262   142  0.90  15.60   1.00     0.97       8387.48|
|  6:  2.8156 -  2.6505  1273   144  0.90  16.06   0.98     0.94       7213.14|
|  7:  2.6505 -  2.5184  1259   139  0.91  15.45   0.98     0.96       6134.10|
|  8:  2.5184 -  2.4093  1258   142  0.91  14.81   0.98     0.96       5440.47|
|  9:  2.4093 -  2.3169  1252   137  0.91  15.30   0.99     0.95       4900.65|
| 10:  2.3169 -  2.2372  1247   137  0.90  15.68   0.98     0.94       4622.47|
| 11:  2.2372 -  2.1674  1261   144  0.90  16.40   0.98     0.95       4458.77|
| 12:  2.1674 -  2.1057  1243   131  0.91  15.40   0.99     0.97       4187.94|
| 13:  2.1057 -  2.0504  1233   139  0.91  15.61   0.98     0.97       3496.34|
| 14:  2.0504 -  2.0005  1081   123  0.91  14.91   0.96     0.92       2601.60|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2601.60 max =        10201.03 mean =      6348.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.94 mean =        13.97|
|phase err.(test): min =        0.00 max =           89.94 mean =        13.57|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1079   r_free= 0.1587   ksol= 0.32   Bsol= 54.91   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,-1.25,-0.55,-0.00,-0.00,-0.00); trace/3= -1.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.131843                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1079   r_free= 0.1587   ksol= 0.32   Bsol= 54.91   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,-1.25,-0.55,-0.00,-0.00,-0.00); trace/3= -1.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.131843                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7728 0.99   1373  153 0.0965 0.1266      5.3726      5.5096|
|  2:  4.7728 -  3.8087 0.99   1308  146 0.0821 0.1069      5.4133      5.6109|
|  3:  3.8087 -  3.3333 0.99   1294  143 0.0999 0.1503      5.4469      5.8752|
|  4:  3.3333 -  3.0313 0.99   1286  139 0.1163 0.1534      5.4389      5.5921|
|  5:  3.0313 -  2.8156 0.99   1262  142 0.1267 0.1804      5.3159      5.5508|
|  6:  2.8156 -  2.6505 0.99   1273  144 0.1192 0.1750      5.2178      5.4393|
|  7:  2.6505 -  2.5184 0.99   1259  139 0.1207 0.1691      5.1441       5.391|
|  8:  2.5184 -  2.4093 0.98   1258  142 0.1117 0.1756      5.0721      5.3523|
|  9:  2.4093 -  2.3169 0.98   1252  137 0.1120 0.1720      5.0121      5.2661|
| 10:  2.3169 -  2.2372 0.99   1247  137 0.1080 0.1863      4.9767      5.2697|
| 11:  2.2372 -  2.1674 0.99   1261  144 0.1132 0.1815      4.9411      5.2771|
| 12:  2.1674 -  2.1057 0.97   1243  131 0.1102 0.1685      4.8999      5.2236|
| 13:  2.1057 -  2.0504 0.99   1233  139 0.1095 0.1758      4.8039      5.0747|
| 14:  2.0504 -  2.0005 0.85   1081  123 0.1020 0.1814      4.6631      4.9884|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9944 -  4.7728  1373   153  0.94   9.36   0.97     0.94       7289.49|
|  2:  4.7728 -  3.8087  1308   146  0.95   7.92   1.01     1.00       8882.46|
|  3:  3.8087 -  3.3333  1294   143  0.94  10.85   1.03     1.02      10037.19|
|  4:  3.3333 -  3.0313  1286   139  0.92  13.21   1.01     1.00      10201.93|
|  5:  3.0313 -  2.8156  1262   142  0.90  15.60   1.00     0.98       8386.26|
|  6:  2.8156 -  2.6505  1273   144  0.90  16.06   0.99     0.95       7211.81|
|  7:  2.6505 -  2.5184  1259   139  0.91  15.45   0.99     0.97       6134.48|
|  8:  2.5184 -  2.4093  1258   142  0.91  14.81   0.99     0.97       5441.33|
|  9:  2.4093 -  2.3169  1252   137  0.91  15.31   1.00     0.96       4902.42|
| 10:  2.3169 -  2.2372  1247   137  0.90  15.68   1.00     0.95       4622.80|
| 11:  2.2372 -  2.1674  1261   144  0.90  16.40   1.00     0.96       4459.15|
| 12:  2.1674 -  2.1057  1243   131  0.91  15.40   1.00     0.99       4188.17|
| 13:  2.1057 -  2.0504  1233   139  0.91  15.61   1.00     0.98       3494.95|
| 14:  2.0504 -  2.0005  1081   123  0.91  14.91   0.97     0.94       2599.60|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2599.60 max =        10201.93 mean =      6348.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.85 mean =        13.97|
|phase err.(test): min =        0.00 max =           89.93 mean =        13.57|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.027)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.50  16.77    None  None   None       |
|    all(noH): 2823   0      0.00    105.50  16.77    None  None   None       |
|    Sol.    : 438    0      5.37    89.81   40.03    None  None   None       |
|    Mac.    : 2385   0      0.00    105.50  12.49    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.553: 1302   |   5:    52.753 -  63.303:   86        |
|      1:    10.553 -  21.103:  930   |   6:    63.303 -  73.853:   38        |
|      2:    21.103 -  31.653:  203   |   7:    73.853 -  84.403:    7        |
|      3:    31.653 -  42.203:  135   |   8:    84.403 -  94.952:    3        |
|      4:    42.203 -  52.753:  115   |   9:    94.952 - 105.502:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 295         
Filter by distance & map next to the model:
   mapped sites are within: 0.464 - 4.777
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 288 from: 295
   mapped sites are within: 0.727 - 4.777

peak=    5.784 closest distance to " NH2 ARG A  56 " =    2.316
peak=    5.441 closest distance to " CB  GLN A 223 " =    1.406
peak=    5.031 closest distance to " CG  PRO A 213 " =    1.208
peak=    5.003 closest distance to " CB  ARG A 275 " =    0.952
peak=    4.967 closest distance to " CB  GLN A 183 " =    1.264
peak=    4.890 closest distance to " O   HOH Z 232 " =    2.346
peak=    4.771 closest distance to " CB  SER A  63 " =    1.197
peak=    4.733 closest distance to " CG  PRO A  90 " =    1.130
peak=    4.711 closest distance to " CA  TYR A  30 " =    0.932
peak=    4.645 closest distance to " O   HOH Z 126 " =    1.825
peak=    4.631 closest distance to " CG  PRO A 198 " =    1.248
peak=    4.583 closest distance to " C   PRO A 198 " =    1.503
peak=    4.567 closest distance to " O   HOH Z 142 " =    1.575
peak=    4.481 closest distance to " NE2 GLN A  11 " =    1.020
peak=    4.475 closest distance to " CB  TYR A 169 " =    0.776
peak=    4.435 closest distance to " O   HOH Z 298 " =    1.862
peak=    4.412 closest distance to " O   HOH Z  15 " =    2.158
peak=    4.403 closest distance to " O   HOH Z  78 " =    1.655
peak=    4.356 closest distance to " O   HOH Z 203 " =    1.747
peak=    4.353 closest distance to " CB  ARG A  79 " =    1.372
peak=    4.351 closest distance to " CB  ARG A 190 " =    1.695
peak=    4.345 closest distance to " CB  ASN A 148 " =    1.419
peak=    4.328 closest distance to " O   HOH Z 427 " =    3.050
peak=    4.316 closest distance to " CB  LEU A 228 " =    1.104
peak=    4.307 closest distance to " O   HOH Z 261 " =    2.165
peak=    4.288 closest distance to " OD1 ASN A  69 " =    2.487
peak=    4.253 closest distance to " CB  GLU A 152 " =    1.140
peak=    4.240 closest distance to " O   HOH Z 369 " =    2.197
peak=    4.171 closest distance to " O   HOH Z 234 " =    3.689
peak=    4.145 closest distance to " CZ  PHE A 218 " =    1.079
peak=    4.142 closest distance to " CD2 LEU A 297 " =    0.879
peak=    4.142 closest distance to " O   HOH Z 303 " =    2.153
peak=    4.142 closest distance to " O   HOH Z 236 " =    2.156
peak=    4.131 closest distance to " O   HOH Z 250 " =    1.461
peak=    4.130 closest distance to " CB  GLU A 277 " =    3.650
peak=    4.106 closest distance to " ND2 ASN A 187 " =    1.380
peak=    4.096 closest distance to " O   HOH Z  40 " =    1.777
peak=    4.095 closest distance to " CG  ARG A  66 " =    2.462
peak=    4.077 closest distance to " NZ  LYS A 117 " =    3.272
peak=    4.073 closest distance to " O   HOH Z 189 " =    2.343
peak=    4.065 closest distance to " O   HOH Z 158 " =    3.084
peak=    4.026 closest distance to " O   HOH Z 209 " =    2.275
peak=    4.025 closest distance to " O   HOH Z 193 " =    1.801
peak=    4.002 closest distance to " O   HOH Z  19 " =    2.275
peak=    3.984 closest distance to " CA  ARG A  36 " =    1.091
peak=    3.984 closest distance to " CB  GLU A 128 " =    1.102
peak=    3.963 closest distance to " CD  ARG A 269 " =    0.960
peak=    3.957 closest distance to " CB  SER A   3 " =    1.293
peak=    3.954 closest distance to " O   HOH Z 346 " =    1.737
peak=    3.948 closest distance to " O   HOH Z 403 " =    1.692
peak=    3.939 closest distance to " CB  VAL A 265 " =    1.216
peak=    3.921 closest distance to " CG2 ILE A 120 " =    1.057
peak=    3.919 closest distance to " O   HOH Z 316 " =    3.144
peak=    3.902 closest distance to " O   HOH Z  43 " =    1.913
peak=    3.900 closest distance to " O   HOH Z  61 " =    1.562
peak=    3.900 closest distance to " C   ILE A 106 " =    1.904
peak=    3.892 closest distance to " CA  ASN A 176 " =    1.245
peak=    3.888 closest distance to " CD1 LEU A 300 " =    1.216
peak=    3.878 closest distance to " O   HOH Z  54 " =    2.367
peak=    3.876 closest distance to " CG  PRO A 243 " =    1.082
peak=    3.848 closest distance to " O   HOH Z 368 " =    2.050
peak=    3.847 closest distance to " CG1 ILE A  33 " =    1.256
peak=    3.844 closest distance to " CB  TRP A 266 " =    1.002
peak=    3.842 closest distance to " CE  LYS A  76 " =    0.859
peak=    3.837 closest distance to " CB  ASP A 140 " =    0.951
peak=    3.832 closest distance to " O   HOH Z 197 " =    2.903
peak=    3.823 closest distance to " O   HOH Z 147 " =    1.800
peak=    3.819 closest distance to " CA  ALA A  21 " =    1.242
peak=    3.815 closest distance to " O   HOH Z 423 " =    1.995
peak=    3.813 closest distance to " OG BSER A 164 " =    2.273
peak=    3.796 closest distance to " CA  ASN A 215 " =    1.147
peak=    3.794 closest distance to " CB  ARG A  79 " =    0.985
peak=    3.793 closest distance to " O   HOH Z 180 " =    2.170
peak=    3.790 closest distance to " CA  ARG A 195 " =    1.260
peak=    3.757 closest distance to " O   HOH Z 214 " =    2.086
peak=    3.756 closest distance to " CG2 VAL A 257 " =    0.857
peak=    3.754 closest distance to " CD BLYS A 290 " =    1.020
peak=    3.738 closest distance to " O   HOH Z 402 " =    1.390
peak=    3.737 closest distance to " O   HOH Z 128 " =    2.052
peak=    3.730 closest distance to " OD2 ASP A 286 " =    2.860
peak=    3.729 closest distance to " O   SER A  87 " =    2.297
peak=    3.716 closest distance to " CG1BVAL A  72 " =    1.727
peak=    3.713 closest distance to " O   HOH Z  97 " =    1.917
peak=    3.704 closest distance to " CB  VAL A 202 " =    1.527
peak=    3.702 closest distance to " O   HOH Z 272 " =    1.858
peak=    3.697 closest distance to " O   HOH Z 108 " =    2.740
peak=    3.684 closest distance to " O   HOH Z 126 " =    1.616
peak=    3.678 closest distance to " O   HOH Z  59 " =    2.147
peak=    3.668 closest distance to " O   HOH Z 426 " =    1.573
peak=    3.664 closest distance to " O   HOH Z  21 " =    1.814
peak=    3.664 closest distance to " O   HOH Z 133 " =    2.548
peak=    3.660 closest distance to " ND2 ASN A 249 " =    1.905
peak=    3.657 closest distance to " CD2 TRP A 179 " =    1.388
peak=    3.653 closest distance to " O   HOH Z 371 " =    3.308
peak=    3.649 closest distance to " O   HOH Z  66 " =    2.061
peak=    3.646 closest distance to " CB  TRP A 179 " =    1.379
peak=    3.643 closest distance to " O   HOH Z 172 " =    3.891
peak=    3.624 closest distance to " CB  TYR A 169 " =    0.874
peak=    3.624 closest distance to " CA  THR A 221 " =    0.984
peak=    3.623 closest distance to " O   HOH Z  63 " =    2.033
peak=    3.618 closest distance to " O   HOH Z 132 " =    2.604
peak=    3.613 closest distance to " O  BHOH Z 338 " =    2.395
peak=    3.610 closest distance to " CB  ASN A  39 " =    0.851
peak=    3.604 closest distance to " NE2 GLN A  77 " =    3.326
peak=    3.597 closest distance to " CD1 LEU A  96 " =    0.740
peak=    3.584 closest distance to " CA  ALA A  51 " =    0.898
peak=    3.584 closest distance to " NH2BARG A 145 " =    2.163
peak=    3.582 closest distance to " O   HOH Z 280 " =    2.916
peak=    3.579 closest distance to " O   HOH Z 344 " =    3.195
peak=    3.578 closest distance to " CA  MET A 105 " =    1.052
peak=    3.577 closest distance to " NH2 ARG A 156 " =    1.185
peak=    3.574 closest distance to " CB  ALA A 291 " =    1.329
peak=    3.569 closest distance to " O   HOH Z 291 " =    1.554
peak=    3.564 closest distance to " O   HOH Z 411 " =    3.835
peak=    3.560 closest distance to " CD1 ILE A 106 " =    0.837
peak=    3.559 closest distance to " CA  ALA A 160 " =    0.872
peak=    3.558 closest distance to " O   HOH Z   1 " =    2.067
peak=    3.558 closest distance to " CE1 TYR A 186 " =    1.296
peak=    3.552 closest distance to " OG1 THR A 294 " =    2.386
peak=    3.552 closest distance to " CD  ARG A 159 " =    0.749
peak=    3.541 closest distance to " O   HOH Z 361 " =    3.691
peak=    3.530 closest distance to " NH1AARG A 145 " =    1.233
peak=    3.510 closest distance to " O   HOH Z 305 " =    3.638
peak=    3.510 closest distance to " O   HOH Z  66 " =    2.106
peak=    3.506 closest distance to " CB  MET A  47 " =    0.985
peak=    3.497 closest distance to " O   HOH Z  44 " =    1.773
peak=    3.497 closest distance to " CD  LYS A 166 " =    1.321
peak=    3.497 closest distance to " O   HOH Z 425 " =    1.980
peak=    3.486 closest distance to " O   HOH Z 403 " =    1.330
peak=    3.482 closest distance to " O   HOH Z 406 " =    1.496
peak=    3.477 closest distance to " O   HOH Z 337 " =    3.644
peak=    3.476 closest distance to " CB  SER A 212 " =    1.080
peak=    3.471 closest distance to " O   HOH Z 245 " =    1.295
peak=    3.470 closest distance to " CG2 VAL A 197 " =    1.126
peak=    3.470 closest distance to " O   HOH Z 185 " =    1.754
peak=    3.466 closest distance to " CA  ASP A 140 " =    1.158
peak=    3.465 closest distance to " O   HOH Z 261 " =    1.511
peak=    3.465 closest distance to " N   ARG A 156 " =    1.388
peak=    3.461 closest distance to " O   HOH Z 183 " =    1.431
peak=    3.460 closest distance to " O   THR A 220 " =    1.231
peak=    3.453 closest distance to " O   THR A 251 " =    1.118
peak=    3.450 closest distance to " O   HOH Z 135 " =    1.703
peak=    3.447 closest distance to " ND2 ASN A 110 " =    1.631
peak=    3.447 closest distance to " N   ASN A  39 " =    1.377
peak=    3.446 closest distance to " CG2 THR A 221 " =    1.186
peak=    3.445 closest distance to " ND1 HIS A  81 " =    1.617
peak=    3.445 closest distance to " CB  THR A  31 " =    1.772
peak=    3.443 closest distance to " CA  MET A  40 " =    1.081
peak=    3.441 closest distance to " O   HOH Z 285 " =    2.988
peak=    3.440 closest distance to " O   HOH Z 391 " =    2.952
peak=    3.440 closest distance to " O   HOH Z 357 " =    2.014
peak=    3.437 closest distance to " O   HOH Z  54 " =    1.714
peak=    3.437 closest distance to " CG2 ILE A  20 " =    1.377
peak=    3.436 closest distance to " O   HOH Z 173 " =    2.016
peak=    3.433 closest distance to " O   HOH Z 327 " =    1.669
peak=    3.430 closest distance to " CB  SER A 141 " =    1.006
peak=    3.426 closest distance to " O   HOH Z 421 " =    1.826
peak=    3.424 closest distance to " CA  ALA A 291 " =    0.815
peak=    3.423 closest distance to " CG  GLN A  58 " =    2.697
peak=    3.423 closest distance to " CB  ALA A 248 " =    1.289
peak=    3.416 closest distance to " O   ALA A 165 " =    1.483
peak=    3.408 closest distance to " O   HOH Z 437 " =    1.265
peak=    3.403 closest distance to " O   HOH Z 299 " =    4.484
peak=    3.400 closest distance to " CG1 VAL A 153 " =    0.965
peak=    3.399 closest distance to " O   HOH Z 163 " =    1.873
peak=    3.396 closest distance to " CB  GLU A  46 " =    0.995
peak=    3.390 closest distance to " CB  SER A  26 " =    1.735
peak=    3.390 closest distance to " CB  ILE A 120 " =    1.289
peak=    3.388 closest distance to " CA  THR A 264 " =    0.918
peak=    3.386 closest distance to " O   HOH Z 279 " =    2.253
peak=    3.375 closest distance to " CB  ASN A 215 " =    1.200
peak=    3.373 closest distance to " CB  GLN A  89 " =    1.346
peak=    3.372 closest distance to " O   HOH Z 290 " =    0.932
peak=    3.371 closest distance to " O   HOH Z 359 " =    1.485
peak=    3.370 closest distance to " CD  LYS A 119 " =    1.273
peak=    3.366 closest distance to " CB  ARG A 139 " =    0.874
peak=    3.366 closest distance to " O   HOH Z 353 " =    2.733
peak=    3.365 closest distance to " CD  GLU A 152 " =    0.727
peak=    3.364 closest distance to " O   ASN A  74 " =    1.539
peak=    3.359 closest distance to " CG1 ILE A 151 " =    0.976
peak=    3.357 closest distance to " CB  TYR A 116 " =    0.769
peak=    3.354 closest distance to " CB  GLN A  88 " =    1.189
peak=    3.353 closest distance to " CA  LYS A 117 " =    1.236
peak=    3.350 closest distance to " O   HOH Z 193 " =    2.129
peak=    3.350 closest distance to " O   HOH Z 148 " =    3.292
peak=    3.348 closest distance to " O   HOH Z 417 " =    2.894
peak=    3.348 closest distance to " O   TRP A 274 " =    1.896
peak=    3.345 closest distance to " OE1 GLU A   2 " =    2.225
peak=    3.343 closest distance to " O   HOH Z  10 " =    1.798
peak=    3.342 closest distance to " CZ2 TRP A 179 " =    1.634
peak=    3.330 closest distance to " O   HOH Z 193 " =    1.633
peak=    3.327 closest distance to " O   HOH Z 383 " =    1.897
peak=    3.324 closest distance to " O   HOH Z 393 " =    3.254
peak=    3.321 closest distance to " N   ASN A 127 " =    1.265
peak=    3.319 closest distance to " O   HOH Z  97 " =    2.537
peak=    3.314 closest distance to " CB  LEU A 143 " =    1.123
peak=    3.311 closest distance to " O   HOH Z 365 " =    2.866
peak=    3.309 closest distance to " O   HOH Z 258 " =    2.104
peak=    3.309 closest distance to " CD1AILE A 234 " =    0.920
peak=    3.305 closest distance to " CZ  PHE A  38 " =    1.303
peak=    3.305 closest distance to " CA  ALA A 248 " =    1.200
peak=    3.302 closest distance to " CA  ASP A 162 " =    1.107
peak=    3.300 closest distance to " CB  SER A  62 " =    0.798
peak=    3.295 closest distance to " CB  ASN A 142 " =    1.149
peak=    3.292 closest distance to " O   HOH Z 325 " =    2.487
peak=    3.290 closest distance to " O   HOH Z 336 " =    1.668
peak=    3.289 closest distance to " CA  ALA A 154 " =    0.958
peak=    3.288 closest distance to " CB  ALA A  34 " =    1.056
peak=    3.285 closest distance to " CA  LEU A  83 " =    1.323
peak=    3.285 closest distance to " CA  ASN A 217 " =    1.186
peak=    3.283 closest distance to " O   HOH Z  61 " =    1.473
peak=    3.282 closest distance to " O   HOH Z  80 " =    1.577
peak=    3.281 closest distance to " CB  ALA A   1 " =    4.777
peak=    3.280 closest distance to " O   HOH Z 163 " =    1.513
peak=    3.278 closest distance to " O   HOH Z  68 " =    1.676
peak=    3.265 closest distance to " OG  SER A  22 " =    2.646
peak=    3.262 closest distance to " O   HOH Z 199 " =    1.543
peak=    3.259 closest distance to " O   HOH Z 345 " =    1.552
peak=    3.257 closest distance to " O   ASP A 124 " =    1.125
peak=    3.253 closest distance to " CG BARG A 275 " =    1.381
peak=    3.248 closest distance to " CB  SER A 216 " =    0.864
peak=    3.245 closest distance to " O   HOH Z 128 " =    2.277
peak=    3.242 closest distance to " N   TYR A 116 " =    1.571
peak=    3.238 closest distance to " CB  PHE A  16 " =    0.992
peak=    3.238 closest distance to " OG BSER A 134 " =    2.898
peak=    3.237 closest distance to " CZ3 TRP A 266 " =    1.099
peak=    3.235 closest distance to " CD2 HIS A  81 " =    1.114
peak=    3.234 closest distance to " ND2 ASN A 249 " =    0.861
peak=    3.227 closest distance to " O   HOH Z 422 " =    2.644
peak=    3.221 closest distance to " CB  SER A  62 " =    1.244
peak=    3.220 closest distance to " CA  ASN A  74 " =    1.302
peak=    3.215 closest distance to " CA  ALA A 158 " =    1.237
peak=    3.214 closest distance to " CG  LEU A 167 " =    1.185
peak=    3.212 closest distance to " O   HOH Z 248 " =    1.640
peak=    3.212 closest distance to " CB  HIS A 108 " =    0.809
peak=    3.212 closest distance to " N   GLY A  98 " =    1.130
peak=    3.211 closest distance to " C   TYR A 214 " =    1.472
peak=    3.206 closest distance to " O   HOH Z 417 " =    2.023
peak=    3.205 closest distance to " NZ  LYS A  48 " =    1.304
peak=    3.203 closest distance to " CA  ALA A  84 " =    1.294
peak=    3.198 closest distance to " O   HOH Z  85 " =    2.223
peak=    3.197 closest distance to " CD  GLU A 236 " =    1.063
peak=    3.191 closest distance to " O   HOH Z  88 " =    3.296
peak=    3.191 closest distance to " CG  MET A 185 " =    1.153
peak=    3.190 closest distance to " CB  SER A 273 " =    0.861
peak=    3.189 closest distance to " O   HOH Z 234 " =    1.835
peak=    3.188 closest distance to " CA  MET A 188 " =    0.955
peak=    3.187 closest distance to " CA  SER A 146 " =    1.676
peak=    3.182 closest distance to " CA  ALA A 295 " =    1.103
peak=    3.180 closest distance to " O   HOH Z 295 " =    1.460
peak=    3.177 closest distance to " O   ALA A 158 " =    1.201
peak=    3.175 closest distance to " CB  MET A  40 " =    0.799
peak=    3.174 closest distance to " O   HOH Z 345 " =    3.182
peak=    3.171 closest distance to " ND1 HIS A  86 " =    1.838
peak=    3.168 closest distance to " CB  GLN A 103 " =    0.836
peak=    3.166 closest distance to " CB  MET A 113 " =    1.837
peak=    3.163 closest distance to " O   HOH Z 271 " =    2.349
peak=    3.160 closest distance to " CA  SER A  87 " =    1.094
peak=    3.160 closest distance to " O   HOH Z 171 " =    2.058
peak=    3.158 closest distance to " O   HOH Z 250 " =    1.495
peak=    3.155 closest distance to " CD  ARG A  66 " =    2.382
peak=    3.153 closest distance to " CA  GLY A  80 " =    0.947
peak=    3.153 closest distance to " O   HOH Z  20 " =    1.463
peak=    3.152 closest distance to " O   HOH Z 329 " =    3.861
peak=    3.150 closest distance to " O   HOH Z 273 " =    2.871
peak=    3.146 closest distance to " CE  LYS A  48 " =    1.025
peak=    3.145 closest distance to " CG  GLN A  11 " =    1.560
peak=    3.141 closest distance to " O   HOH Z 261 " =    2.191
peak=    3.141 closest distance to " CG2BVAL A  41 " =    0.841
peak=    3.139 closest distance to " CG  GLU A  37 " =    0.863
peak=    3.133 closest distance to " CD2 TYR A  30 " =    1.390
peak=    3.133 closest distance to " CA  ASP A 191 " =    0.814
peak=    3.127 closest distance to " CB  GLN A 278 " =    0.906
peak=    3.123 closest distance to " O   HOH Z 407 " =    2.691
peak=    3.121 closest distance to " CB  ALA A 114 " =    1.058
peak=    3.120 closest distance to " O   HOH Z 313 " =    1.904
peak=    3.110 closest distance to " O   HOH Z  88 " =    1.953
peak=    3.105 closest distance to " O   HOH Z 152 " =    1.954
peak=    3.104 closest distance to " CB  GLN A 205 " =    1.100
peak=    3.095 closest distance to " CG  LYS A  76 " =    0.971
peak=    3.089 closest distance to " CD1 ILE A 199 " =    0.993
peak=    3.088 closest distance to " CB  ALA A   9 " =    1.575
peak=    3.087 closest distance to " OH  TYR A  30 " =    1.130
peak=    3.078 closest distance to " NE2 GLN A  58 " =    2.974
peak=    3.071 closest distance to " CA  ALA A 233 " =    1.448
peak=    3.067 closest distance to " O   HOH Z 409 " =    3.182
peak=    3.039 closest distance to " O   HOH Z 371 " =    1.560
peak=    3.014 closest distance to " CA  ASP A 191 " =    1.000

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.833 - 5.693
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 204
   mapped sites are within: 0.833 - 5.693

peak=   -4.914 closest distance to " O   HOH Z 266 " =    4.921
peak=   -4.463 closest distance to " CD  ARG A 156 " =    2.039
peak=   -4.437 closest distance to " C   HIS A 108 " =    1.078
peak=   -4.344 closest distance to " O   HOH Z 377 " =    2.099
peak=   -4.290 closest distance to " SG  CYS A 254 " =    3.489
peak=   -4.280 closest distance to " O   VAL A  67 " =    2.714
peak=   -4.276 closest distance to " CD  GLN A  58 " =    1.074
peak=   -4.266 closest distance to " CB  PRO A 243 " =    2.651
peak=   -4.247 closest distance to " O   HOH Z 198 " =    2.104
peak=   -4.182 closest distance to " OE1 GLN A 223 " =    2.053
peak=   -4.176 closest distance to " O   HOH Z 231 " =    2.330
peak=   -4.166 closest distance to " CB  ALA A 161 " =    2.554
peak=   -4.124 closest distance to " OXT GLY A 302 " =    2.861
peak=   -4.077 closest distance to " O   HOH Z  10 " =    1.534
peak=   -4.059 closest distance to " O   HOH Z 196 " =    1.969
peak=   -3.975 closest distance to " OG BSER A 134 " =    1.274
peak=   -3.952 closest distance to " O   HOH Z 114 " =    3.206
peak=   -3.919 closest distance to " CE2 TYR A  30 " =    2.700
peak=   -3.893 closest distance to " O   HOH Z 292 " =    4.620
peak=   -3.865 closest distance to " O   HOH Z 372 " =    2.292
peak=   -3.859 closest distance to " ND2 ASN A  45 " =    1.677
peak=   -3.842 closest distance to " NE2 GLN A  88 " =    1.871
peak=   -3.827 closest distance to " ND2 ASN A  45 " =    1.062
peak=   -3.815 closest distance to " CG1 VAL A 112 " =    2.829
peak=   -3.811 closest distance to " N   ALA A  43 " =    2.731
peak=   -3.810 closest distance to " O   PRO A 198 " =    1.274
peak=   -3.801 closest distance to " O   HOH Z 126 " =    1.957
peak=   -3.787 closest distance to " CG2 ILE A 263 " =    2.315
peak=   -3.775 closest distance to " O   HOH Z  73 " =    2.289
peak=   -3.773 closest distance to " CB  ASN A  39 " =    2.372
peak=   -3.770 closest distance to " O   HOH Z  52 " =    1.351
peak=   -3.768 closest distance to " CZ3 TRP A 179 " =    1.213
peak=   -3.752 closest distance to " OG  SER A  97 " =    2.171
peak=   -3.748 closest distance to " CG  ASP A 132 " =    2.360
peak=   -3.741 closest distance to " O   HOH Z 185 " =    2.336
peak=   -3.729 closest distance to " CB  PHE A 192 " =    2.001
peak=   -3.714 closest distance to " O   HOH Z 166 " =    1.789
peak=   -3.712 closest distance to " CB  ALA A 291 " =    2.265
peak=   -3.702 closest distance to " N   ALA A 226 " =    2.060
peak=   -3.673 closest distance to " CE  MET A 105 " =    2.329
peak=   -3.667 closest distance to " CA  ASP A 298 " =    1.050
peak=   -3.656 closest distance to " CD1 LEU A 101 " =    2.379
peak=   -3.633 closest distance to " CD1 PHE A  59 " =    1.921
peak=   -3.631 closest distance to " CG1 VAL A 250 " =    2.643
peak=   -3.609 closest distance to " O   PRO A 163 " =    2.102
peak=   -3.604 closest distance to " O   HOH Z 165 " =    1.959
peak=   -3.602 closest distance to " CD  GLN A 223 " =    1.375
peak=   -3.599 closest distance to " O   HOH Z  13 " =    1.676
peak=   -3.578 closest distance to " O   HOH Z 353 " =    2.150
peak=   -3.577 closest distance to " CB  ALA A 248 " =    2.284
peak=   -3.566 closest distance to " OD1 ASN A 148 " =    1.499
peak=   -3.557 closest distance to " NH2AARG A 275 " =    5.277
peak=   -3.556 closest distance to " O   PHE A 218 " =    1.583
peak=   -3.550 closest distance to " O   HOH Z 389 " =    1.794
peak=   -3.545 closest distance to " O   HOH Z 394 " =    1.507
peak=   -3.535 closest distance to " CZ  TYR A 169 " =    1.798
peak=   -3.534 closest distance to " OG  SER A  62 " =    1.794
peak=   -3.534 closest distance to " O   HOH Z   6 " =    2.120
peak=   -3.533 closest distance to " CB  TYR A  15 " =    2.233
peak=   -3.532 closest distance to " CE3 TRP A 150 " =    2.207
peak=   -3.527 closest distance to " O   HOH Z 290 " =    1.202
peak=   -3.520 closest distance to " CG  ARG A 269 " =    2.508
peak=   -3.514 closest distance to " CB  PHE A 208 " =    2.277
peak=   -3.508 closest distance to " CA  VAL A  67 " =    2.947
peak=   -3.502 closest distance to " CG  PHE A 283 " =    2.713
peak=   -3.499 closest distance to " CD  ARG A 139 " =    1.569
peak=   -3.497 closest distance to " C   LEU A 143 " =    1.083
peak=   -3.493 closest distance to " O   HOH Z 435 " =    2.723
peak=   -3.493 closest distance to " O   HOH Z 166 " =    1.619
peak=   -3.490 closest distance to " OD2 ASP A 171 " =    1.800
peak=   -3.485 closest distance to " O   HOH Z 252 " =    3.888
peak=   -3.481 closest distance to " O   HOH Z  38 " =    1.542
peak=   -3.478 closest distance to " O   HOH Z 211 " =    1.615
peak=   -3.478 closest distance to " CD1 LEU A  25 " =    2.474
peak=   -3.475 closest distance to " CG  GLU A 277 " =    1.126
peak=   -3.474 closest distance to " O   SER A 210 " =    1.992
peak=   -3.473 closest distance to " CD  ARG A 195 " =    5.146
peak=   -3.472 closest distance to " O   HOH Z 311 " =    3.671
peak=   -3.459 closest distance to " O   HOH Z  43 " =    1.571
peak=   -3.455 closest distance to " O   HOH Z 407 " =    3.046
peak=   -3.455 closest distance to " OD1 ASP A 171 " =    1.538
peak=   -3.448 closest distance to " CB  ALA A  43 " =    2.622
peak=   -3.436 closest distance to " CB  ASP A 286 " =    1.877
peak=   -3.436 closest distance to " CB  ALA A 248 " =    2.125
peak=   -3.434 closest distance to " OD2 ASP A 191 " =    1.484
peak=   -3.429 closest distance to " CD1 LEU A 228 " =    2.221
peak=   -3.418 closest distance to " CA  GLY A 241 " =    3.143
peak=   -3.417 closest distance to " OD1 ASN A 187 " =    1.633
peak=   -3.408 closest distance to " CG1 VAL A 112 " =    2.578
peak=   -3.406 closest distance to " OE1 GLN A  88 " =    1.137
peak=   -3.406 closest distance to " O   HOH Z 243 " =    2.049
peak=   -3.399 closest distance to " CG  ASP A 231 " =    0.833
peak=   -3.395 closest distance to " CB  ALA A 291 " =    2.330
peak=   -3.394 closest distance to " O   HOH Z  93 " =    2.214
peak=   -3.389 closest distance to " O   HOH Z  60 " =    2.388
peak=   -3.387 closest distance to " O   HOH Z 322 " =    1.642
peak=   -3.386 closest distance to " O   HOH Z 351 " =    1.530
peak=   -3.382 closest distance to " CE2 PHE A  61 " =    2.565
peak=   -3.377 closest distance to " O   ALA A  10 " =    1.679
peak=   -3.377 closest distance to " CD2 TYR A 293 " =    2.032
peak=   -3.375 closest distance to " NH2 ARG A  79 " =    1.541
peak=   -3.358 closest distance to " CA  GLY A 203 " =    2.413
peak=   -3.354 closest distance to " CG2 VAL A 189 " =    2.206
peak=   -3.351 closest distance to " O   HOH Z 393 " =    1.403
peak=   -3.347 closest distance to " CD2 LEU A 300 " =    2.857
peak=   -3.346 closest distance to " ND2 ASN A 187 " =    1.559
peak=   -3.342 closest distance to " CD  LYS A 289 " =    2.450
peak=   -3.338 closest distance to " OG BSER A 134 " =    1.905
peak=   -3.334 closest distance to " CB  PHE A  16 " =    2.557
peak=   -3.331 closest distance to " CE2 PHE A 218 " =    2.415
peak=   -3.324 closest distance to " O   HOH Z 234 " =    4.105
peak=   -3.321 closest distance to " CB  GLN A  11 " =    1.804
peak=   -3.318 closest distance to " O   ALA A  34 " =    2.347
peak=   -3.317 closest distance to " O   HOH Z 102 " =    1.539
peak=   -3.312 closest distance to " C   SER A 206 " =    1.554
peak=   -3.312 closest distance to " CD2 TYR A 247 " =    2.379
peak=   -3.308 closest distance to " N   THR A  52 " =    1.715
peak=   -3.304 closest distance to " O   PRO A 198 " =    1.890
peak=   -3.300 closest distance to " O   HOH Z 177 " =    1.725
peak=   -3.298 closest distance to " CZ  PHE A  59 " =    1.683
peak=   -3.297 closest distance to " C   ALA A 158 " =    1.260
peak=   -3.293 closest distance to " OD1 ASP A 191 " =    1.644
peak=   -3.292 closest distance to " O   HOH Z 265 " =    2.229
peak=   -3.291 closest distance to " O   SER A 135 " =    1.484
peak=   -3.282 closest distance to " ND2 ASN A 249 " =    2.411
peak=   -3.274 closest distance to " O   HOH Z  37 " =    1.848
peak=   -3.274 closest distance to " CG  PRO A 243 " =    1.745
peak=   -3.274 closest distance to " O   HOH Z  51 " =    1.868
peak=   -3.273 closest distance to " CZ  PHE A 155 " =    1.234
peak=   -3.273 closest distance to " CD1 ILE A 239 " =    2.099
peak=   -3.270 closest distance to " ND2 ASN A  69 " =    1.643
peak=   -3.269 closest distance to " OE2 GLU A   2 " =    1.874
peak=   -3.266 closest distance to " O   HOH Z   6 " =    1.543
peak=   -3.266 closest distance to " O   HOH Z 139 " =    2.969
peak=   -3.261 closest distance to " O   HOH Z 377 " =    1.724
peak=   -3.260 closest distance to " O   MET A  40 " =    2.711
peak=   -3.259 closest distance to " CG1AVAL A  41 " =    2.809
peak=   -3.258 closest distance to " O   HOH Z 414 " =    1.631
peak=   -3.256 closest distance to " O   HOH Z  11 " =    1.742
peak=   -3.256 closest distance to " O   HOH Z 123 " =    2.361
peak=   -3.252 closest distance to " O   HOH Z 357 " =    2.059
peak=   -3.247 closest distance to " CD2 LEU A 237 " =    2.679
peak=   -3.247 closest distance to " O   HOH Z 198 " =    1.447
peak=   -3.237 closest distance to " O   GLU A 152 " =    1.420
peak=   -3.236 closest distance to " CG1 VAL A 125 " =    1.987
peak=   -3.234 closest distance to " OD2 ASP A 171 " =    2.417
peak=   -3.231 closest distance to " O   HOH Z 128 " =    2.503
peak=   -3.229 closest distance to " NH1 ARG A 195 " =    2.623
peak=   -3.229 closest distance to " CA  GLY A 133 " =    2.322
peak=   -3.220 closest distance to " CA  PRO A 243 " =    2.451
peak=   -3.219 closest distance to " CZ2 TRP A 274 " =    1.032
peak=   -3.218 closest distance to " O   GLY A 211 " =    1.447
peak=   -3.217 closest distance to " O   SER A  95 " =    1.647
peak=   -3.216 closest distance to " N   ALA A 248 " =    1.616
peak=   -3.216 closest distance to " CA  GLY A 133 " =    1.985
peak=   -3.213 closest distance to " N   ASP A 286 " =    2.310
peak=   -3.210 closest distance to " N   MET A 105 " =    2.611
peak=   -3.206 closest distance to " OG BSER A 210 " =    2.165
peak=   -3.204 closest distance to " CG  PRO A 163 " =    2.530
peak=   -3.202 closest distance to " NE2 GLN A 194 " =    1.786
peak=   -3.200 closest distance to " NH2 ARG A  66 " =    2.083
peak=   -3.198 closest distance to " O   LEU A 167 " =    1.473
peak=   -3.198 closest distance to " O   HOH Z 396 " =    1.770
peak=   -3.196 closest distance to " O   HOH Z 426 " =    1.579
peak=   -3.195 closest distance to " O   HOH Z 193 " =    1.814
peak=   -3.193 closest distance to " O   ALA A 161 " =    1.683
peak=   -3.192 closest distance to " CD1 ILE A 151 " =    2.353
peak=   -3.189 closest distance to " CZ3 TRP A 274 " =    2.455
peak=   -3.184 closest distance to " C   GLY A  17 " =    1.168
peak=   -3.183 closest distance to " O   LEU A 101 " =    2.105
peak=   -3.175 closest distance to " CG  GLU A  53 " =    1.512
peak=   -3.174 closest distance to " O   HOH Z 191 " =    5.693
peak=   -3.173 closest distance to " NH2BARG A 275 " =    2.259
peak=   -3.171 closest distance to " NH2 ARG A  79 " =    2.027
peak=   -3.168 closest distance to " CD1 LEU A 297 " =    2.451
peak=   -3.168 closest distance to " CB  ALA A  10 " =    2.232
peak=   -3.166 closest distance to " N   SER A 276 " =    1.358
peak=   -3.165 closest distance to " CD  GLU A 236 " =    1.073
peak=   -3.161 closest distance to " CG1 VAL A  67 " =    3.160
peak=   -3.159 closest distance to " O   HOH Z 244 " =    2.060
peak=   -3.154 closest distance to " O   HOH Z  44 " =    2.184
peak=   -3.152 closest distance to " O   VAL A 174 " =    2.084
peak=   -3.146 closest distance to " C   MET A 188 " =    1.499
peak=   -3.145 closest distance to " OG  SER A  97 " =    2.106
peak=   -3.144 closest distance to " SG ACYS A 201 " =    1.982
peak=   -3.141 closest distance to " CD2 LEU A 237 " =    2.197
peak=   -3.140 closest distance to " ND2BASN A 224 " =    1.704
peak=   -3.131 closest distance to " O   HOH Z 134 " =    2.904
peak=   -3.126 closest distance to " O   HOH Z 357 " =    2.183
peak=   -3.123 closest distance to " OG ASER A 134 " =    1.213
peak=   -3.121 closest distance to " CG  TRP A 266 " =    1.858
peak=   -3.120 closest distance to " O   HOH Z 298 " =    2.612
peak=   -3.116 closest distance to " O   HOH Z 324 " =    2.270
peak=   -3.112 closest distance to " O   HOH Z 353 " =    2.118
peak=   -3.107 closest distance to " O   ALA A 160 " =    1.576
peak=   -3.102 closest distance to " O   HOH Z 283 " =    5.581
peak=   -3.100 closest distance to " OH  TYR A 247 " =    1.813
peak=   -3.098 closest distance to " O   ALA A 292 " =    1.995
peak=   -3.089 closest distance to " CG2 ILE A  49 " =    2.805
peak=   -3.084 closest distance to " CG2BVAL A  41 " =    1.869
peak=   -3.030 closest distance to " CA  GLY A 241 " =    2.811
peak=   -3.021 closest distance to " CG  ASN A 301 " =    2.080
peak=   -3.008 closest distance to " CG1 VAL A  78 " =    2.671

================= 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    :  0.2610 0.2515   5.884193e+00   5.852274e+00
   1_bss:  0.2432 0.2340   5.849493e+00   5.811593e+00
   1_xyz:  0.1527 0.1697   5.362235e+00   5.461989e+00
   1_adp:  0.1383 0.1706   5.296708e+00   5.475817e+00
   1_occ:  0.1378 0.1703   5.295142e+00   5.474859e+00
   2_bss:  0.1364 0.1681   5.282862e+00   5.460948e+00
   2_xyz:  0.1169 0.1540   5.158625e+00   5.370404e+00
   2_adp:  0.1152 0.1514   5.143319e+00   5.356852e+00
   2_occ:  0.1151 0.1513   5.142671e+00   5.356545e+00
   3_bss:  0.1148 0.1511   5.140017e+00   5.354705e+00
   3_xyz:  0.1081 0.1525   5.107771e+00   5.352787e+00
   3_adp:  0.1065 0.1533   5.104546e+00   5.358335e+00
   3_occ:  0.1065 0.1534   5.104633e+00   5.358708e+00
   4_bss:  0.1065 0.1528   5.105264e+00   5.358116e+00
   4_xyz:  0.1080 0.1549   5.119124e+00   5.371496e+00
   4_adp:  0.1076 0.1560   5.120745e+00   5.377722e+00
   4_occ:  0.1075 0.1560   5.120775e+00   5.377990e+00
   5_bss:  0.1074 0.1559   5.120824e+00   5.378067e+00
   5_xyz:  0.1081 0.1577   5.129059e+00   5.387700e+00
   5_adp:  0.1081 0.1588   5.131871e+00   5.393885e+00
   5_occ:  0.1081 0.1588   5.131858e+00   5.394044e+00
   5_bss:  0.1079 0.1587   5.131843e+00   5.394082e+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:  0.315  50.000  -3.232   1.449  -1.620   0.000  -0.000  -0.000
   1_xyz:  0.315  50.000  -3.232   1.449  -1.620   0.000  -0.000  -0.000
   1_adp:  0.315  50.000  -3.232   1.449  -1.620   0.000  -0.000  -0.000
   1_occ:  0.315  50.000  -3.232   1.449  -1.620   0.000  -0.000  -0.000
   2_bss:  0.325  55.916  -3.194  -1.165  -1.628  -0.000  -0.000  -0.000
   2_xyz:  0.325  55.916  -3.194  -1.165  -1.628  -0.000  -0.000  -0.000
   2_adp:  0.325  55.916  -3.194  -1.165  -1.628  -0.000  -0.000  -0.000
   2_occ:  0.325  55.916  -3.194  -1.165  -1.628  -0.000  -0.000  -0.000
   3_bss:  0.327  55.916  -2.760  -1.660  -1.301  -0.000  -0.000  -0.000
   3_xyz:  0.327  55.916  -2.760  -1.660  -1.301  -0.000  -0.000  -0.000
   3_adp:  0.327  55.916  -2.760  -1.660  -1.301  -0.000  -0.000  -0.000
   3_occ:  0.327  55.916  -2.760  -1.660  -1.301  -0.000  -0.000  -0.000
   4_bss:  0.324  55.916  -2.472  -1.656  -1.061  -0.000  -0.000  -0.000
   4_xyz:  0.324  55.916  -2.472  -1.656  -1.061  -0.000  -0.000  -0.000
   4_adp:  0.324  55.916  -2.472  -1.656  -1.061  -0.000  -0.000  -0.000
   4_occ:  0.324  55.916  -2.472  -1.656  -1.061  -0.000  -0.000  -0.000
   5_bss:  0.324  55.916  -2.183  -1.465  -0.808  -0.000  -0.000  -0.000
   5_xyz:  0.324  55.916  -2.183  -1.465  -0.808  -0.000  -0.000  -0.000
   5_adp:  0.324  55.916  -2.183  -1.465  -0.808  -0.000  -0.000  -0.000
   5_occ:  0.324  55.916  -2.183  -1.465  -0.808  -0.000  -0.000  -0.000
   5_bss:  0.319  54.910  -1.913  -1.248  -0.548  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  25.451 0.8110  0.9678    18995.642
   1_bss:  24.208 0.8221  0.9380    15955.442
   1_xyz:  15.473 0.9036  0.9980     7330.604
   1_adp:  15.835 0.8999  0.9916     7417.111
   1_occ:  15.825 0.8999  0.9914     7396.620
   2_bss:  15.482 0.9029  0.9662     7193.225
   2_xyz:  13.626 0.9180  0.9722     6015.685
   2_adp:  13.328 0.9205  0.9675     5902.894
   2_occ:  13.322 0.9205  0.9675     5896.279
   3_bss:  13.268 0.9209  0.9718     5880.905
   3_xyz:  13.166 0.9217  0.9737     5884.817
   3_adp:  13.283 0.9209  0.9672     5922.837
   3_occ:  13.291 0.9208  0.9672     5926.976
   4_bss:  13.284 0.9209  0.9733     5924.027
   4_xyz:  13.519 0.9191  0.9715     6079.188
   4_adp:  13.643 0.9182  0.9630     6132.718
   4_occ:  13.645 0.9182  0.9629     6136.626
   5_bss:  13.646 0.9182  0.9715     6138.405
   5_xyz:  13.803 0.9170  0.9711     6274.378
   5_adp:  13.929 0.9160  0.9628     6346.596
   5_occ:  13.932 0.9159  0.9627     6347.829
   5_bss:  13.932 0.9159  0.9715     6347.411
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.115   1.6033e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.115   1.6033e-01
   1_xyz:   1.045  0.009  0.071 15.151  0.004  4.114   7.0957e-02
   1_adp:   1.045  0.009  0.071 15.151  0.004  4.114   7.0957e-02
   1_occ:   1.045  0.009  0.071 15.151  0.004  4.114   7.0957e-02
   2_bss:   1.045  0.009  0.071 15.151  0.004  4.114   7.0957e-02
   2_xyz:   0.998  0.007  0.076 14.926  0.004  4.121   6.0108e-02
   2_adp:   0.998  0.007  0.076 14.926  0.004  4.121   6.0108e-02
   2_occ:   0.998  0.007  0.076 14.926  0.004  4.121   6.0108e-02
   3_bss:   0.998  0.007  0.076 14.926  0.004  4.121   6.0108e-02
   3_xyz:   1.118  0.011  0.086 15.269  0.005  4.125   7.7314e-02
   3_adp:   1.118  0.011  0.086 15.269  0.005  4.125   7.7314e-02
   3_occ:   1.118  0.011  0.086 15.269  0.005  4.125   7.7314e-02
   4_bss:   1.118  0.011  0.086 15.269  0.005  4.125   7.7314e-02
   4_xyz:   1.018  0.009  0.079 14.946  0.004  4.125   6.4092e-02
   4_adp:   1.018  0.009  0.079 14.946  0.004  4.125   6.4092e-02
   4_occ:   1.018  0.009  0.079 14.946  0.004  4.125   6.4092e-02
   5_bss:   1.018  0.009  0.079 14.946  0.004  4.125   6.4092e-02
   5_xyz:   0.983  0.008  0.077 14.796  0.004  4.126   5.9238e-02
   5_adp:   0.983  0.008  0.077 14.796  0.004  4.126   5.9238e-02
   5_occ:   0.983  0.008  0.077 14.796  0.004  4.126   5.9238e-02
   5_bss:   0.983  0.008  0.077 14.796  0.004  4.126   5.9238e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4185e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4185e-01
   1_xyz:   7.831  0.058  0.258 83.364  0.031  2.341   1.7455e-01
   1_adp:   7.831  0.058  0.258 83.364  0.031  2.341   1.7455e-01
   1_occ:   7.831  0.058  0.258 83.364  0.031  2.341   1.7455e-01
   2_bss:   7.831  0.058  0.258 83.364  0.031  2.341   1.7455e-01
   2_xyz:   7.325  0.046  0.240 83.885  0.039  2.367   3.9410e-02
   2_adp:   7.325  0.046  0.240 83.885  0.039  2.367   3.9410e-02
   2_occ:   7.325  0.046  0.240 83.885  0.039  2.367   3.9410e-02
   3_bss:   7.325  0.046  0.240 83.885  0.039  2.367   3.9410e-02
   3_xyz:   8.040  0.052  0.288 82.920  0.037  2.294   6.5330e-02
   3_adp:   8.040  0.052  0.288 82.920  0.037  2.294   6.5330e-02
   3_occ:   8.040  0.052  0.288 82.920  0.037  2.294   6.5330e-02
   4_bss:   8.040  0.052  0.288 82.920  0.037  2.294   6.5330e-02
   4_xyz:   7.291  0.048  0.253 82.734  0.040  2.364   4.7733e-02
   4_adp:   7.291  0.048  0.253 82.734  0.040  2.364   4.7733e-02
   4_occ:   7.291  0.048  0.253 82.734  0.040  2.364   4.7733e-02
   5_bss:   7.291  0.048  0.253 82.734  0.040  2.364   4.7733e-02
   5_xyz:   7.017  0.046  0.246 82.468  0.034  2.344   3.9570e-02
   5_adp:   7.017  0.046  0.246 82.468  0.034  2.344   3.9570e-02
   5_occ:   7.017  0.046  0.246 82.468  0.034  2.344   3.9570e-02
   5_bss:   7.017  0.046  0.246 82.468  0.034  2.344   3.9570e-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:  72.35   1.57  16.79  72.35   1.57  12.91  68.75   6.04  37.90
   1_occ:  72.35   1.57  16.79  72.35   1.57  12.91  68.75   6.04  37.90
   2_bss:  72.35   1.57  16.79  72.35   1.57  12.91  68.75   6.04  37.90
   2_xyz:  72.35   1.57  16.79  72.35   1.57  12.91  68.75   6.04  37.90
   2_adp:  74.17   2.17  16.48  74.17   2.17  12.72  67.51   5.39  36.98
   2_occ:  74.17   2.17  16.48  74.17   2.17  12.72  67.51   5.39  36.98
   3_bss:  74.17   2.17  16.48  74.17   2.17  12.72  67.51   5.39  36.98
   3_xyz:  74.17   2.17  16.48  74.17   2.17  12.72  67.51   5.39  36.98
   3_adp:  80.60   0.68  16.65  80.60   0.68  12.65  68.18   5.93  38.45
   3_occ:  80.60   0.68  16.65  80.60   0.68  12.65  68.18   5.93  38.45
   4_bss:  80.60   0.68  16.65  80.60   0.68  12.65  68.18   5.93  38.45
   4_xyz:  80.60   0.68  16.65  80.60   0.68  12.65  68.18   5.93  38.45
   4_adp:  89.66   0.00  16.77  89.66   0.00  12.58  74.52   5.61  39.56
   4_occ:  89.66   0.00  16.77  89.66   0.00  12.58  74.52   5.61  39.56
   5_bss:  89.66   0.00  16.77  89.66   0.00  12.58  74.52   5.61  39.56
   5_xyz:  89.66   0.00  16.77  89.66   0.00  12.58  74.52   5.61  39.56
   5_adp: 105.50   0.00  16.76 105.50   0.00  12.49  89.80   5.37  40.03
   5_occ: 105.50   0.00  16.76 105.50   0.00  12.49  89.80   5.37  40.03
   5_bss: 105.50   0.00  16.77 105.50   0.00  12.49  89.81   5.37  40.03
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    0.893    0.012    0.244
   1_adp:    0.893    0.012    0.244
   1_occ:    0.893    0.012    0.244
   2_bss:    0.893    0.012    0.244
   2_xyz:    0.703    0.039    0.287
   2_adp:    0.703    0.039    0.287
   2_occ:    0.703    0.039    0.287
   3_bss:    0.703    0.039    0.287
   3_xyz:    0.735    0.023    0.310
   3_adp:    0.735    0.023    0.310
   3_occ:    0.735    0.023    0.310
   4_bss:    0.735    0.023    0.310
   4_xyz:    0.809    0.035    0.317
   4_adp:    0.809    0.035    0.317
   4_occ:    0.809    0.035    0.317
   5_bss:    0.809    0.035    0.317
   5_xyz:    0.980    0.038    0.323
   5_adp:    0.980    0.038    0.323
   5_occ:    0.980    0.038    0.323
   5_bss:    0.980    0.038    0.323
------------------------------------------------------------------------

CPU time actual refinement: 321.58


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_687/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_687/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_687/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_687/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_687/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 321.42 
  Macro-tasks:
    bulk solvent and scale       = 38.14  
    individual site refinement   = 125.80 
    weights calculation          = 28.59  
    collect and process          = 6.49   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 199.13 
  Micro-tasks:
    mask                            = 1.15   
    f_calc                          = 102.50 
    alpha_beta                      = 7.94   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 110.78 
    fmodel                         = 6.73   
    r_factors                      = 0.16   
    phase_errors                   = 11.39  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 242.05 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.601 micro seconds
Total CPU time: 5.58 minutes
from_scatterers_fft:    659 calls, 102.23 s
gradients_fft:          604 calls,  97.76 s

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

# Date 2008-01-16 Time 05:24:54 PST -0800 (1200489894.96 s)
Start R-work = 0.2610, R-free = 0.2515 (no bulk solvent and anisotropic scale)
Final R-work = 0.1286, R-free = 0.1751 (no bulk solvent and anisotropic scale)

Start R-work = 0.2432, R-free = 0.2340
Final R-work = 0.1079, R-free = 0.1587