# Date 2008-01-16 Time 04:03:29 PST -0800 (1200485009.21 s)
#phil __OFF__

Command line arguments: "../161.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21983
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 161

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.845, 46.4607, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 46.4607, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8121 1.96077
Completeness in resolution range: 0.948436
Completeness with d_max=infinity: 0.945506

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8121
                             d_min =   1.9608

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 46.4607, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8121 1.96077
Completeness in resolution range: 0.948436
Completeness with d_max=infinity: 0.945506

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8125 -  4.1954 [2176/2203]  1956   220  10.1%
  bin  2:  4.1954 -  3.3426 [2070/2086]  1864   206  10.0%
  bin  3:  3.3426 -  2.9237 [2065/2084]  1859   206  10.0%
  bin  4:  2.9237 -  2.6581 [2041/2071]  1836   205  10.0%
  bin  5:  2.6581 -  2.4685 [2007/2026]  1808   199   9.9%
  bin  6:  2.4685 -  2.3235 [2026/2051]  1820   206  10.2%
  bin  7:  2.3235 -  2.2076 [2014/2048]  1820   194   9.6%
  bin  8:  2.2076 -  2.1118 [1987/2018]  1780   207  10.4%
  bin  9:  2.1118 -  2.0307 [1981/2022]  1790   191   9.6%
  bin 10:  2.0307 -  1.9608 [1222/2045]  1097   125  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_161/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.59 -     2.25: 22
        2.25 -     2.92: 1508
        2.92 -     3.58: 4553
        3.58 -     4.24: 9323
        4.24 -     4.90: 13260
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.593 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.624 3.120 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.640 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.688 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.731 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28661 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_161/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_161/model_refine_001.geo

CPU time processing inputs: 9.11


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 46.4607 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3925   r_free= 0.3860   ksol= 0.00   Bsol= 0.00   scale= 0.950    |
|                                                                             |
| 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:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.175868                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8125 -  4.6792 0.99   1411  156 0.3086 0.2993      6.4212      6.3907|
|  2:  4.6792 -  3.7336 0.99   1355  152 0.3033 0.3062       6.562      6.5809|
|  3:  3.7336 -  3.2674 0.99   1324  147 0.3502 0.3464      6.5069      6.5488|
|  4:  3.2674 -  2.9713 0.99   1328  142 0.3740 0.4109       6.381      6.4768|
|  5:  2.9713 -  2.7598 0.99   1308  151 0.3998 0.3674      6.2262      6.1795|
|  6:  2.7598 -  2.5980 0.99   1311  142 0.4176 0.4492      6.1613      6.1164|
|  7:  2.5980 -  2.4685 0.99   1286  146 0.4221 0.3501      6.1407      5.9899|
|  8:  2.4685 -  2.3615 0.98   1290  145 0.4424 0.4417      6.1108      6.1399|
|  9:  2.3615 -  2.2709 0.98   1308  140 0.4611 0.4472      6.0516      6.0883|
| 10:  2.2709 -  2.1928 0.98   1298  144 0.4602 0.4017      6.0631      5.9566|
| 11:  2.1928 -  2.1244 0.99   1271  148 0.4582 0.4658      5.9749      5.9877|
| 12:  2.1244 -  2.0639 0.97   1277  135 0.4655 0.4474      5.9238      5.9667|
| 13:  2.0639 -  2.0097 0.98   1276  138 0.4706 0.4821      5.8453       5.774|
| 14:  2.0097 -  1.9608 0.45    587   73 0.4715 0.4541      5.8525      5.7183|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8125 -  4.6792  1411   156  0.77  27.67   0.86     0.80      48005.80|
|  2:  4.6792 -  3.7336  1355   152  0.80  26.55   0.97     0.89      66102.44|
|  3:  3.7336 -  3.2674  1324   147  0.73  33.18   0.98     0.90      70084.20|
|  4:  3.2674 -  2.9713  1328   142  0.67  37.95   0.97     0.86      63614.45|
|  5:  2.9713 -  2.7598  1308   151  0.62  42.62   0.96     0.82      49834.78|
|  6:  2.7598 -  2.5980  1311   142  0.61  43.08   0.94     0.81      42334.21|
|  7:  2.5980 -  2.4685  1286   146  0.62  42.65   0.98     0.81      38228.77|
|  8:  2.4685 -  2.3615  1290   145  0.59  45.26   0.97     0.79      36488.37|
|  9:  2.3615 -  2.2709  1308   140  0.57  46.21   0.96     0.80      35194.10|
| 10:  2.2709 -  2.1928  1298   144  0.57  46.66   1.00     0.80      32506.61|
| 11:  2.1928 -  2.1244  1271   148  0.55  48.09   0.97     0.83      31975.65|
| 12:  2.1244 -  2.0639  1277   135  0.53  49.67   0.99     0.80      29890.81|
| 13:  2.0639 -  2.0097  1276   138  0.49  53.21   1.00     0.74      27685.56|
| 14:  2.0097 -  1.9608   587    73  0.48  53.81   1.02     0.64      24073.91|
|alpha:            min =        0.64 max =            0.90 mean =         0.81|
|beta:             min =    24073.91 max =        70084.20 mean =     43561.54|
|figures of merit: min =        0.00 max =            1.00 mean =         0.62|
|phase err.(work): min =        0.00 max =           89.97 mean =        41.97|
|phase err.(test): min =        0.00 max =           89.96 mean =        41.84|
|-----------------------------------------------------------------------------|

============================== 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 = 3.898632              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.335   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.979742              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.807   (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 |  1.593 -  1.924:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.924 -  2.255:       13 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.255 -  2.585:       63 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.585 -  2.916:     1445 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.916 -  3.247:     1921 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.247 -  3.577:     2632 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.577 -  3.908:     4747 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.908 -  4.239:     4576 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.239 -  4.569:     6078 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.569 -  4.900:     7182 |
|-----------------------------------------------------------------------------|
|-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 |        0.185 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.593 |       0.530 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.577)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3925   r_free= 0.3860   ksol= 0.00   Bsol= 0.00   scale= 0.950    |
|                                                                             |
| 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:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.175868                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3829   r_free= 0.3761   ksol= 0.33   Bsol= 30.83   scale= 0.978   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.08,-0.15,0.21,-0.00,0.00,0.00); trace/3= 0.05                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.162502                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.277809              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.032   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.557668              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.487   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3829      final r-factor (work) = 0.2557          |
| start r-factor (free) = 0.3761      final r-factor (free) = 0.2864          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2872 = 3.28 * 0.50 * 6.1642 + 1.00 * 0.1846                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8288 = 3.28 * 0.50 * 5.9480 + 1.00 * 0.0805                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2557      final r-factor (work) = 0.2321          |
| start r-factor (free) = 0.2864      final r-factor (free) = 0.2987          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3230 = 0.56 * 1.00 * 5.9480 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2262 = 0.56 * 1.00 * 5.7643 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.577)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.24   17.70    None  None   None       |
|    all(noH): 2823   0      0.00    76.24   17.70    None  None   None       |
|    Sol.    : 438    0      4.11    75.07   38.68    None  None   None       |
|    Mac.    : 2385   0      0.00    76.24   13.85    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.624:  556   |   5:    38.118 -  45.742:  113        |
|      1:     7.624 -  15.247: 1093   |   6:    45.742 -  53.366:   92        |
|      2:    15.247 -  22.871:  514   |   7:    53.366 -  60.989:   55        |
|      3:    22.871 -  30.495:  234   |   8:    60.989 -  68.613:   32        |
|      4:    30.495 -  38.118:  128   |   9:    68.613 -  76.236:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2321 r_free = 0.2987             target_work(ml) = 5.781         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2319 r_free = 0.2987             target_work(ml) = 5.781         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2319   r_free= 0.2987   ksol= 0.33   Bsol= 30.83   scale= 1.044   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.08,-0.15,0.21,-0.00,0.00,0.00); trace/3= 0.05                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.780701                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2301   r_free= 0.2951   ksol= 0.33   Bsol= 46.76   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-1.64,-0.67,-0.00,-0.00,-0.00); trace/3= -1.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.776250                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.351030              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.876   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.174385              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.637  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2301      final r-factor (work) = 0.1616          |
| start r-factor (free) = 0.2951      final r-factor (free) = 0.2112          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7504 = 3.35 * 0.50 * 5.7713 + 1.00 * 0.0805                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5120 = 3.35 * 0.50 * 5.6400 + 1.00 * 0.0621                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1616      final r-factor (work) = 0.1491          |
| start r-factor (free) = 0.2112      final r-factor (free) = 0.1939          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9951 = 0.17 * 1.00 * 5.6400 + 1.00 * 0.0116                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9520 = 0.17 * 1.00 * 5.4185 + 1.00 * 0.0070                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.577)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.81    77.63   17.07    None  None   None       |
|    all(noH): 2823   0      0.81    77.63   17.07    None  None   None       |
|    Sol.    : 438    0      5.60    70.18   37.98    None  None   None       |
|    Mac.    : 2385   0      0.81    77.63   13.23    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:     0.809 -   8.491:  597   |   5:    39.219 -  46.901:  114        |
|      1:     8.491 -  16.173: 1311   |   6:    46.901 -  54.583:   85        |
|      2:    16.173 -  23.855:  372   |   7:    54.583 -  62.265:   46        |
|      3:    23.855 -  31.537:  148   |   8:    62.265 -  69.947:   12        |
|      4:    31.537 -  39.219:  135   |   9:    69.947 -  77.629:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1491 r_free = 0.1939             target_work(ml) = 5.377         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1489 r_free = 0.1936             target_work(ml) = 5.375         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1489   r_free= 0.1936   ksol= 0.33   Bsol= 46.76   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-1.64,-0.67,-0.00,-0.00,-0.00); trace/3= -1.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.375296                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1488   r_free= 0.1937   ksol= 0.32   Bsol= 46.76   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.00,-2.36,-0.89,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.373654                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.173781              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.551  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.146352              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.199  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1488      final r-factor (work) = 0.1245          |
| start r-factor (free) = 0.1937      final r-factor (free) = 0.1655          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9535 = 2.17 * 0.50 * 5.4204 + 1.00 * 0.0621                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8072 = 2.17 * 0.50 * 5.2935 + 1.00 * 0.0538                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1245      final r-factor (work) = 0.1208          |
| start r-factor (free) = 0.1655      final r-factor (free) = 0.1609          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7817 = 0.15 * 1.00 * 5.2935 + 1.00 * 0.0070                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7679 = 0.15 * 1.00 * 5.2006 + 1.00 * 0.0068                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.577)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.49    80.43   16.87    None  None   None       |
|    all(noH): 2823   0      1.49    80.43   16.87    None  None   None       |
|    Sol.    : 438    0      5.26    69.62   37.90    None  None   None       |
|    Mac.    : 2385   0      1.49    80.43   13.01    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:     1.493 -   9.386:  790   |   5:    40.960 -  48.853:  112        |
|      1:     9.386 -  17.280: 1245   |   6:    48.853 -  56.747:   81        |
|      2:    17.280 -  25.173:  301   |   7:    56.747 -  64.640:   27        |
|      3:    25.173 -  33.067:  124   |   8:    64.640 -  72.534:   10        |
|      4:    33.067 -  40.960:  131   |   9:    72.534 -  80.427:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1208 r_free = 0.1609             target_work(ml) = 5.189         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1207 r_free = 0.1608             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1207   r_free= 0.1608   ksol= 0.32   Bsol= 46.76   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.00,-2.36,-0.89,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.188061                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1206   r_free= 0.1611   ksol= 0.33   Bsol= 46.76   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.27,-2.62,-1.05,-0.00,-0.00,-0.00); trace/3= -2.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.188070                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.382526              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.879  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.329951              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 157.628  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1206      final r-factor (work) = 0.1098          |
| start r-factor (free) = 0.1611      final r-factor (free) = 0.1539          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8495 = 3.38 * 0.50 * 5.2007 + 1.00 * 0.0538                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7736 = 3.38 * 0.50 * 5.1454 + 1.00 * 0.0713                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1098      final r-factor (work) = 0.1079          |
| start r-factor (free) = 0.1539      final r-factor (free) = 0.1534          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7044 = 0.33 * 1.00 * 5.1454 + 1.00 * 0.0067                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6954 = 0.33 * 1.00 * 5.1160 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.577)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.41    81.19   16.81    None  None   None       |
|    all(noH): 2823   0      1.41    81.19   16.81    None  None   None       |
|    Sol.    : 438    0      5.19    70.32   38.21    None  None   None       |
|    Mac.    : 2385   0      1.41    81.19   12.88    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:     1.412 -   9.391:  846   |   5:    41.303 -  49.281:  115        |
|      1:     9.391 -  17.369: 1206   |   6:    49.281 -  57.259:   85        |
|      2:    17.369 -  25.347:  284   |   7:    57.259 -  65.238:   25        |
|      3:    25.347 -  33.325:  122   |   8:    65.238 -  73.216:   10        |
|      4:    33.325 -  41.303:  128   |   9:    73.216 -  81.194:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1079 r_free = 0.1534             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1078 r_free = 0.1535             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1078   r_free= 0.1535   ksol= 0.33   Bsol= 46.76   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.27,-2.62,-1.05,-0.00,-0.00,-0.00); trace/3= -2.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.115539                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1078   r_free= 0.1535   ksol= 0.33   Bsol= 46.76   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.12,-2.51,-0.87,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.115563                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.768723              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 157.314  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 10.328873             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.292  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1078      final r-factor (work) = 0.1098          |
| start r-factor (free) = 0.1535      final r-factor (free) = 0.1542          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5960 = 1.77 * 0.50 * 5.1163 + 1.00 * 0.0713                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5874 = 1.77 * 0.50 * 5.1253 + 1.00 * 0.0548                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1098      final r-factor (work) = 0.1088          |
| start r-factor (free) = 0.1542      final r-factor (free) = 0.1556          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 52.9460 = 10.33 * 1.00 * 5.1253 + 1.00 * 0.0075                             |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 52.9191 = 10.33 * 1.00 * 5.1225 + 1.00 * 0.0098                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.577)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.29    94.24   17.27    None  None   None       |
|    all(noH): 2823   0      0.29    94.24   17.27    None  None   None       |
|    Sol.    : 438    0      5.86    81.44   40.72    None  None   None       |
|    Mac.    : 2385   0      0.29    94.24   12.97    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:     0.294 -   9.689:  975   |   5:    47.265 -  56.660:   87        |
|      1:     9.689 -  19.083: 1167   |   6:    56.660 -  66.054:   61        |
|      2:    19.083 -  28.477:  236   |   7:    66.054 -  75.448:   29        |
|      3:    28.477 -  37.871:  131   |   8:    75.448 -  84.842:   12        |
|      4:    37.871 -  47.265:  123   |   9:    84.842 -  94.236:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1088 r_free = 0.1556             target_work(ml) = 5.129         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1088 r_free = 0.1556             target_work(ml) = 5.129         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1088   r_free= 0.1556   ksol= 0.33   Bsol= 46.76   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.12,-2.51,-0.87,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.128792                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8125 -  4.6792 0.99   1411  156 0.0990 0.1274       5.388      5.5486|
|  2:  4.6792 -  3.7336 0.99   1355  152 0.0837 0.1111      5.4235      5.6065|
|  3:  3.7336 -  3.2674 0.99   1324  147 0.1038 0.1519      5.4535      5.8475|
|  4:  3.2674 -  2.9713 0.99   1328  142 0.1165 0.1567      5.4189      5.5907|
|  5:  2.9713 -  2.7598 0.99   1308  151 0.1255 0.1597      5.2903      5.4948|
|  6:  2.7598 -  2.5980 0.99   1311  142 0.1196 0.1922      5.1867      5.4718|
|  7:  2.5980 -  2.4685 0.99   1286  146 0.1234 0.1540      5.1583      5.2919|
|  8:  2.4685 -  2.3615 0.98   1290  145 0.1100 0.1624      5.0461      5.3008|
|  9:  2.3615 -  2.2709 0.98   1308  140 0.1152 0.1889      4.9991      5.3446|
| 10:  2.2709 -  2.1928 0.98   1298  144 0.1065 0.1610      4.9212      5.1325|
| 11:  2.1928 -  2.1244 0.99   1271  148 0.1100 0.1841      4.9122      5.3201|
| 12:  2.1244 -  2.0639 0.97   1277  135 0.1135 0.1514      4.8814      5.1225|
| 13:  2.0639 -  2.0097 0.98   1276  138 0.1052 0.1809      4.7599      5.0283|
| 14:  2.0097 -  1.9608 0.45    587   73 0.0910 0.1727      4.6217      4.9165|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8125 -  4.6792  1411   156  0.94   9.14   0.98     0.95       7180.79|
|  2:  4.6792 -  3.7336  1355   152  0.95   7.73   1.02     1.01       8911.15|
|  3:  3.7336 -  3.2674  1324   147  0.93  11.22   1.03     1.03       9972.21|
|  4:  3.2674 -  2.9713  1328   142  0.92  13.07   1.01     1.00       9756.02|
|  5:  2.9713 -  2.7598  1308   151  0.91  15.37   1.00     0.97       7931.41|
|  6:  2.7598 -  2.5980  1311   142  0.90  16.28   0.98     0.95       6857.21|
|  7:  2.5980 -  2.4685  1286   146  0.91  15.43   0.98     0.95       6095.03|
|  8:  2.4685 -  2.3615  1290   145  0.91  14.72   1.00     0.97       5191.58|
|  9:  2.3615 -  2.2709  1308   140  0.91  15.15   1.00     0.96       4694.54|
| 10:  2.2709 -  2.1928  1298   144  0.90  15.32   1.00     0.96       4174.05|
| 11:  2.1928 -  2.1244  1271   148  0.90  16.24   0.99     0.96       4326.68|
| 12:  2.1244 -  2.0639  1277   135  0.91  15.73   1.01     1.00       4024.87|
| 13:  2.0639 -  2.0097  1276   138  0.90  16.10   0.99     0.97       3272.40|
| 14:  2.0097 -  1.9608   587    73  0.93  13.13   0.98     0.94       2417.28|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2417.28 max =         9972.21 mean =      6242.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.74 mean =        13.87|
|phase err.(test): min =        0.00 max =           88.51 mean =        13.47|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1555   ksol= 0.32   Bsol= 49.37   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,-2.29,-0.68,-0.00,-0.00,-0.00); trace/3= -1.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.128618                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1555   ksol= 0.32   Bsol= 49.37   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,-2.29,-0.68,-0.00,-0.00,-0.00); trace/3= -1.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.128618                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8125 -  4.6792 0.99   1411  156 0.0989 0.1278      5.3877      5.5498|
|  2:  4.6792 -  3.7336 0.99   1355  152 0.0840 0.1113      5.4253      5.6076|
|  3:  3.7336 -  3.2674 0.99   1324  147 0.1039 0.1519      5.4543      5.8476|
|  4:  3.2674 -  2.9713 0.99   1328  142 0.1164 0.1563      5.4181      5.5889|
|  5:  2.9713 -  2.7598 0.99   1308  151 0.1253 0.1595      5.2892      5.4936|
|  6:  2.7598 -  2.5980 0.99   1311  142 0.1195 0.1920      5.1857      5.4707|
|  7:  2.5980 -  2.4685 0.99   1286  146 0.1233 0.1538      5.1575      5.2911|
|  8:  2.4685 -  2.3615 0.98   1290  145 0.1099 0.1621      5.0456      5.2997|
|  9:  2.3615 -  2.2709 0.98   1308  140 0.1152 0.1891      4.9991      5.3451|
| 10:  2.2709 -  2.1928 0.98   1298  144 0.1065 0.1609      4.9213      5.1321|
| 11:  2.1928 -  2.1244 0.99   1271  148 0.1100 0.1839       4.912      5.3197|
| 12:  2.1244 -  2.0639 0.97   1277  135 0.1134 0.1514      4.8812      5.1222|
| 13:  2.0639 -  2.0097 0.98   1276  138 0.1052 0.1810      4.7598      5.0285|
| 14:  2.0097 -  1.9608 0.45    587   73 0.0910 0.1726      4.6214      4.9156|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8125 -  4.6792  1411   156  0.94   9.13   0.98     0.95       7171.43|
|  2:  4.6792 -  3.7336  1355   152  0.95   7.73   1.03     1.01       8919.26|
|  3:  3.7336 -  3.2674  1324   147  0.93  11.22   1.04     1.03       9980.63|
|  4:  3.2674 -  2.9713  1328   142  0.92  13.05   1.02     1.01       9736.91|
|  5:  2.9713 -  2.7598  1308   151  0.91  15.35   1.00     0.98       7914.25|
|  6:  2.7598 -  2.5980  1311   142  0.90  16.26   0.99     0.96       6842.25|
|  7:  2.5980 -  2.4685  1286   146  0.91  15.41   0.99     0.95       6081.44|
|  8:  2.4685 -  2.3615  1290   145  0.91  14.72   1.00     0.98       5186.11|
|  9:  2.3615 -  2.2709  1308   140  0.91  15.15   1.01     0.97       4692.08|
| 10:  2.2709 -  2.1928  1298   144  0.90  15.32   1.01     0.97       4174.17|
| 11:  2.1928 -  2.1244  1271   148  0.90  16.23   1.00     0.97       4322.58|
| 12:  2.1244 -  2.0639  1277   135  0.91  15.72   1.02     1.01       4023.66|
| 13:  2.0639 -  2.0097  1276   138  0.90  16.09   1.01     0.98       3270.51|
| 14:  2.0097 -  1.9608   587    73  0.93  13.12   0.99     0.96       2414.81|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2414.81 max =         9980.63 mean =      6237.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.86|
|phase err.(test): min =        0.00 max =           88.47 mean =        13.46|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.577)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.29    94.23   17.27    None  None   None       |
|    all(noH): 2823   0      0.29    94.23   17.27    None  None   None       |
|    Sol.    : 438    0      5.86    81.43   40.71    None  None   None       |
|    Mac.    : 2385   0      0.29    94.23   12.96    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:     0.286 -   9.681:  975   |   5:    47.257 -  56.652:   87        |
|      1:     9.681 -  19.075: 1167   |   6:    56.652 -  66.046:   61        |
|      2:    19.075 -  28.469:  236   |   7:    66.046 -  75.440:   29        |
|      3:    28.469 -  37.863:  131   |   8:    75.440 -  84.834:   12        |
|      4:    37.863 -  47.257:  123   |   9:    84.834 -  94.228:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 292         
Filter by distance & map next to the model:
   mapped sites are within: 0.431 - 4.394
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 286 from: 292
   mapped sites are within: 0.703 - 4.394

peak=    5.856 closest distance to " CB  ARG A 275 " =    0.971
peak=    5.792 closest distance to " O   HOH Z 142 " =    1.785
peak=    5.582 closest distance to " NE2 GLN A  11 " =    1.140
peak=    5.473 closest distance to " NH2 ARG A  56 " =    2.145
peak=    5.424 closest distance to " CG  PRO A  54 " =    1.279
peak=    5.282 closest distance to " O   HOH Z 417 " =    1.609
peak=    5.120 closest distance to " O   HOH Z 126 " =    1.846
peak=    4.887 closest distance to " O   HOH Z 232 " =    2.403
peak=    4.766 closest distance to " CG  PRO A 213 " =    1.236
peak=    4.748 closest distance to " CB  PRO A  54 " =    1.022
peak=    4.691 closest distance to " O   HOH Z 427 " =    2.901
peak=    4.674 closest distance to " O   HOH Z 402 " =    1.429
peak=    4.619 closest distance to " O   HOH Z  78 " =    1.751
peak=    4.601 closest distance to " O   HOH Z 369 " =    2.305
peak=    4.595 closest distance to " CA  TYR A  30 " =    0.930
peak=    4.587 closest distance to " CB  GLN A 223 " =    1.490
peak=    4.513 closest distance to " O   HOH Z 287 " =    1.959
peak=    4.474 closest distance to " CG2 VAL A 257 " =    0.854
peak=    4.441 closest distance to " CB  GLN A 183 " =    1.204
peak=    4.343 closest distance to " CB  ARG A  79 " =    1.349
peak=    4.317 closest distance to " OG ASER A 258 " =    3.009
peak=    4.306 closest distance to " CB  VAL A 265 " =    1.253
peak=    4.264 closest distance to " CB  ASN A 148 " =    1.435
peak=    4.263 closest distance to " NZ  LYS A 117 " =    3.063
peak=    4.259 closest distance to " CG  PRO A 198 " =    1.229
peak=    4.253 closest distance to " CG  PRO A  90 " =    1.206
peak=    4.241 closest distance to " NZ  LYS A 119 " =    2.731
peak=    4.225 closest distance to " O   SER A  87 " =    2.169
peak=    4.223 closest distance to " O   HOH Z 303 " =    2.134
peak=    4.221 closest distance to " ND2 ASN A 187 " =    1.413
peak=    4.214 closest distance to " O   HOH Z  15 " =    2.295
peak=    4.210 closest distance to " O   HOH Z 403 " =    1.793
peak=    4.201 closest distance to " O   HOH Z 346 " =    1.694
peak=    4.197 closest distance to " CB  GLU A 152 " =    1.242
peak=    4.194 closest distance to " CG  PRO A 243 " =    1.035
peak=    4.187 closest distance to " O   HOH Z 327 " =    1.596
peak=    4.179 closest distance to " O   HOH Z 272 " =    1.851
peak=    4.177 closest distance to " O   HOH Z 209 " =    2.223
peak=    4.171 closest distance to " O   HOH Z 298 " =    1.780
peak=    4.159 closest distance to " C   PRO A 198 " =    1.458
peak=    4.140 closest distance to " CZ  PHE A 218 " =    1.040
peak=    4.122 closest distance to " O   HOH Z 250 " =    1.500
peak=    4.119 closest distance to " O   HOH Z 158 " =    3.005
peak=    4.114 closest distance to " O   HOH Z 203 " =    1.725
peak=    4.101 closest distance to " CB  SER A  63 " =    1.195
peak=    4.093 closest distance to " CD2 TRP A 179 " =    1.324
peak=    4.080 closest distance to " O   HOH Z 112 " =    1.213
peak=    4.073 closest distance to " O   HOH Z  61 " =    1.680
peak=    4.071 closest distance to " O   HOH Z 236 " =    1.381
peak=    4.033 closest distance to " O   HOH Z 371 " =    1.773
peak=    4.031 closest distance to " O   HOH Z  40 " =    1.725
peak=    4.007 closest distance to " CB  VAL A 202 " =    1.564
peak=    4.003 closest distance to " CB  ARG A 190 " =    1.719
peak=    3.971 closest distance to " CG  ARG A  66 " =    2.636
peak=    3.958 closest distance to " OG BSER A 164 " =    2.216
peak=    3.950 closest distance to " O   HOH Z 193 " =    1.702
peak=    3.945 closest distance to " CB  ARG A  79 " =    0.904
peak=    3.942 closest distance to " CB  TRP A 266 " =    1.120
peak=    3.933 closest distance to " CA  ASN A 215 " =    1.031
peak=    3.890 closest distance to " O   HOH Z 132 " =    2.239
peak=    3.887 closest distance to " O   HOH Z 188 " =    2.775
peak=    3.884 closest distance to " O   HOH Z 234 " =    3.574
peak=    3.882 closest distance to " O   HOH Z 365 " =    2.688
peak=    3.866 closest distance to " O   HOH Z 419 " =    2.268
peak=    3.865 closest distance to " O   HOH Z  97 " =    2.434
peak=    3.858 closest distance to " N   TYR A 116 " =    1.532
peak=    3.858 closest distance to " CE  LYS A  76 " =    0.878
peak=    3.843 closest distance to " N   ASN A  39 " =    1.231
peak=    3.843 closest distance to " CG2 ILE A 120 " =    1.159
peak=    3.826 closest distance to " CB  THR A  31 " =    1.607
peak=    3.824 closest distance to " O   HOH Z  44 " =    1.756
peak=    3.815 closest distance to " O   HOH Z  97 " =    1.976
peak=    3.806 closest distance to " O   HOH Z 368 " =    3.573
peak=    3.806 closest distance to " NH2AARG A 190 " =    1.921
peak=    3.791 closest distance to " O   HOH Z 173 " =    2.021
peak=    3.779 closest distance to " O   HOH Z 128 " =    2.072
peak=    3.778 closest distance to " O   HOH Z 248 " =    1.524
peak=    3.761 closest distance to " O   HOH Z 353 " =    2.575
peak=    3.753 closest distance to " O   HOH Z 193 " =    1.925
peak=    3.750 closest distance to " O   HOH Z 392 " =    2.972
peak=    3.744 closest distance to " O   HOH Z 344 " =    3.234
peak=    3.718 closest distance to " O   HOH Z 415 " =    3.637
peak=    3.705 closest distance to " CB  SER A   3 " =    1.255
peak=    3.699 closest distance to " O   HOH Z  59 " =    1.683
peak=    3.666 closest distance to " CB  GLU A  46 " =    1.063
peak=    3.650 closest distance to " O   HOH Z  61 " =    1.470
peak=    3.645 closest distance to " O   HOH Z 357 " =    1.914
peak=    3.637 closest distance to " CB  SER A  26 " =    1.707
peak=    3.630 closest distance to " OD1 ASN A  69 " =    2.458
peak=    3.629 closest distance to " CA  ARG A  36 " =    0.975
peak=    3.629 closest distance to " CB  ILE A 120 " =    1.391
peak=    3.626 closest distance to " ND2 ASN A 249 " =    0.884
peak=    3.625 closest distance to " CB  GLU A 128 " =    0.998
peak=    3.620 closest distance to " NH2BARG A 145 " =    2.043
peak=    3.606 closest distance to " CG1 ILE A  33 " =    1.184
peak=    3.604 closest distance to " O   HOH Z 265 " =    2.250
peak=    3.604 closest distance to " O   HOH Z 180 " =    2.260
peak=    3.603 closest distance to " CG1BVAL A  72 " =    1.535
peak=    3.599 closest distance to " O   HOH Z 128 " =    2.033
peak=    3.597 closest distance to " CB  ASN A 110 " =    1.089
peak=    3.597 closest distance to " CB  TYR A 169 " =    0.815
peak=    3.594 closest distance to " O   HOH Z  88 " =    2.422
peak=    3.590 closest distance to " O   HOH Z 423 " =    1.875
peak=    3.587 closest distance to " N   PHE A 130 " =    1.266
peak=    3.584 closest distance to " O   HOH Z 126 " =    1.521
peak=    3.581 closest distance to " O   HOH Z   1 " =    2.010
peak=    3.577 closest distance to " O   HOH Z   3 " =    1.983
peak=    3.574 closest distance to " CB  LEU A 228 " =    1.100
peak=    3.566 closest distance to " CA  ARG A 195 " =    1.191
peak=    3.564 closest distance to " O   HOH Z 291 " =    1.441
peak=    3.564 closest distance to " O   HOH Z 141 " =    1.653
peak=    3.562 closest distance to " O   HOH Z  88 " =    2.523
peak=    3.557 closest distance to " O   HOH Z 425 " =    1.966
peak=    3.548 closest distance to " CB  ARG A 139 " =    1.070
peak=    3.548 closest distance to " CB  GLU A 277 " =    3.530
peak=    3.545 closest distance to " O   HOH Z 233 " =    2.048
peak=    3.536 closest distance to " CB  ASP A 140 " =    1.028
peak=    3.536 closest distance to " CD2 LEU A 297 " =    0.977
peak=    3.535 closest distance to " O   HOH Z  10 " =    1.759
peak=    3.533 closest distance to " O   HOH Z 406 " =    1.532
peak=    3.533 closest distance to " C   PHE A  59 " =    0.902
peak=    3.528 closest distance to " CB  ASN A  39 " =    0.878
peak=    3.523 closest distance to " O   HOH Z   6 " =    2.160
peak=    3.518 closest distance to " O   HOH Z 245 " =    1.355
peak=    3.511 closest distance to " O   HOH Z   1 " =    1.574
peak=    3.511 closest distance to " CB  GLN A  88 " =    1.232
peak=    3.510 closest distance to " O   HOH Z  66 " =    2.118
peak=    3.506 closest distance to " NH1AARG A 145 " =    1.184
peak=    3.506 closest distance to " O   HOH Z 359 " =    1.450
peak=    3.506 closest distance to " O   HOH Z 305 " =    3.443
peak=    3.506 closest distance to " CA  ALA A  84 " =    1.257
peak=    3.494 closest distance to " CB  GLN A  89 " =    1.426
peak=    3.493 closest distance to " CB  LYS A 117 " =    1.195
peak=    3.491 closest distance to " O   HOH Z 261 " =    1.778
peak=    3.488 closest distance to " O   HOH Z 337 " =    3.484
peak=    3.488 closest distance to " CG  MET A 185 " =    1.211
peak=    3.483 closest distance to " CB  HIS A 108 " =    0.850
peak=    3.480 closest distance to " O   THR A 220 " =    1.287
peak=    3.474 closest distance to " O   HOH Z 368 " =    2.109
peak=    3.474 closest distance to " O   HOH Z 286 " =    2.348
peak=    3.471 closest distance to " CB  SER A 212 " =    1.104
peak=    3.467 closest distance to " O  BHOH Z  74 " =    1.299
peak=    3.465 closest distance to " CB  ALA A 114 " =    0.951
peak=    3.464 closest distance to " O   HOH Z 280 " =    2.969
peak=    3.463 closest distance to " CB  LEU A 300 " =    0.960
peak=    3.457 closest distance to " O   HOH Z 394 " =    1.648
peak=    3.455 closest distance to " O   ASN A  74 " =    1.459
peak=    3.454 closest distance to " CB  ASN A 142 " =    1.070
peak=    3.451 closest distance to " O   HOH Z 371 " =    3.015
peak=    3.451 closest distance to " O   HOH Z 407 " =    2.383
peak=    3.450 closest distance to " CE  LYS A 119 " =    1.210
peak=    3.447 closest distance to " NZ  LYS A  48 " =    1.073
peak=    3.435 closest distance to " CB  ALA A 114 " =    1.339
peak=    3.433 closest distance to " O   HOH Z  92 " =    2.486
peak=    3.429 closest distance to " O   HOH Z 389 " =    1.688
peak=    3.420 closest distance to " O   HOH Z  43 " =    1.759
peak=    3.417 closest distance to " O   HOH Z  44 " =    2.890
peak=    3.416 closest distance to " CD  ARG A 269 " =    0.980
peak=    3.415 closest distance to " CG  LEU A 167 " =    1.291
peak=    3.410 closest distance to " CA  ASN A 127 " =    1.162
peak=    3.396 closest distance to " O   HOH Z 394 " =    3.841
peak=    3.383 closest distance to " O   HOH Z 325 " =    2.443
peak=    3.379 closest distance to " O   HOH Z 380 " =    1.706
peak=    3.377 closest distance to " CG AARG A 275 " =    1.094
peak=    3.371 closest distance to " O   HOH Z 172 " =    3.245
peak=    3.369 closest distance to " CB  ASN A 215 " =    1.079
peak=    3.364 closest distance to " O   HOH Z 411 " =    3.848
peak=    3.363 closest distance to " CA  ALA A 233 " =    0.954
peak=    3.356 closest distance to " CA  PHE A 283 " =    1.275
peak=    3.354 closest distance to " O   HOH Z 336 " =    1.688
peak=    3.346 closest distance to " OG  SER A  62 " =    2.781
peak=    3.343 closest distance to " O   HOH Z 345 " =    3.249
peak=    3.330 closest distance to " CD  LYS A 166 " =    1.208
peak=    3.326 closest distance to " O   HOH Z 421 " =    1.888
peak=    3.325 closest distance to " O   HOH Z  43 " =    2.358
peak=    3.321 closest distance to " O   HOH Z  89 " =    2.087
peak=    3.320 closest distance to " CD1 ILE A 263 " =    1.386
peak=    3.314 closest distance to " O  BHOH Z 338 " =    2.353
peak=    3.313 closest distance to " O   HOH Z 214 " =    2.309
peak=    3.313 closest distance to " O   HOH Z 329 " =    4.012
peak=    3.309 closest distance to " CG2 THR A 221 " =    1.141
peak=    3.308 closest distance to " O   HOH Z 298 " =    2.538
peak=    3.303 closest distance to " OD2 ASP A 286 " =    2.749
peak=    3.299 closest distance to " NE  ARG A  56 " =    3.460
peak=    3.298 closest distance to " O   HOH Z 342 " =    0.922
peak=    3.298 closest distance to " CB  TRP A 179 " =    1.307
peak=    3.296 closest distance to " NE2 GLN A  77 " =    3.027
peak=    3.293 closest distance to " CB  SER A 273 " =    0.863
peak=    3.290 closest distance to " CG  LYS A  76 " =    1.375
peak=    3.286 closest distance to " N   ASP A 162 " =    1.077
peak=    3.286 closest distance to " O   HOH Z 185 " =    1.824
peak=    3.286 closest distance to " O   HOH Z 433 " =    2.006
peak=    3.284 closest distance to " O   HOH Z 422 " =    2.568
peak=    3.283 closest distance to " CD1 ILE A 106 " =    0.848
peak=    3.283 closest distance to " OG1 THR A 221 " =    1.273
peak=    3.283 closest distance to " CA  ASN A 217 " =    1.175
peak=    3.280 closest distance to " N   GLN A 278 " =    1.405
peak=    3.277 closest distance to " CD  ARG A  66 " =    2.531
peak=    3.275 closest distance to " O   HOH Z 257 " =    2.108
peak=    3.274 closest distance to " CA  MET A  40 " =    1.139
peak=    3.270 closest distance to " CA  MET A 105 " =    1.004
peak=    3.268 closest distance to " O   HOH Z  80 " =    2.065
peak=    3.262 closest distance to " CA  LYS A 290 " =    1.322
peak=    3.262 closest distance to " N   GLU A   2 " =    1.512
peak=    3.261 closest distance to " O   HOH Z 391 " =    2.862
peak=    3.260 closest distance to " CA  LEU A 300 " =    1.017
peak=    3.256 closest distance to " N   ARG A 156 " =    1.288
peak=    3.252 closest distance to " OG1 THR A 264 " =    0.792
peak=    3.246 closest distance to " CB  THR A  52 " =    0.730
peak=    3.245 closest distance to " O   HOH Z 373 " =    1.460
peak=    3.244 closest distance to " O   HOH Z  85 " =    2.341
peak=    3.243 closest distance to " O   HOH Z 290 " =    0.836
peak=    3.238 closest distance to " O   HOH Z 285 " =    2.434
peak=    3.237 closest distance to " O   HOH Z 109 " =    2.246
peak=    3.237 closest distance to " CE ALYS A 290 " =    1.230
peak=    3.235 closest distance to " CE AMET A  47 " =    1.438
peak=    3.233 closest distance to " CG  LYS A 119 " =    1.078
peak=    3.229 closest distance to " CB  LYS A 290 " =    1.171
peak=    3.228 closest distance to " CB  PHE A 204 " =    0.703
peak=    3.225 closest distance to " CB  THR A 157 " =    1.122
peak=    3.219 closest distance to " CA  THR A 264 " =    0.880
peak=    3.216 closest distance to " O   HOH Z 147 " =    1.768
peak=    3.214 closest distance to " CA  ASP A 162 " =    1.038
peak=    3.213 closest distance to " CZ3 TRP A 266 " =    1.090
peak=    3.208 closest distance to " CA  SER A  87 " =    1.025
peak=    3.205 closest distance to " CA  ALA A  51 " =    0.908
peak=    3.203 closest distance to " CD1 LEU A  96 " =    0.729
peak=    3.202 closest distance to " CB  TYR A 116 " =    0.801
peak=    3.201 closest distance to " CG2 ILE A  20 " =    1.476
peak=    3.197 closest distance to " CG  MET A 113 " =    0.967
peak=    3.196 closest distance to " O   HOH Z 213 " =    1.877
peak=    3.196 closest distance to " NE2 HIS A 207 " =    1.251
peak=    3.195 closest distance to " CB  SER A 216 " =    0.889
peak=    3.194 closest distance to " O   ALA A   1 " =    1.657
peak=    3.192 closest distance to " O   HOH Z  48 " =    1.524
peak=    3.190 closest distance to " O   HOH Z 213 " =    1.753
peak=    3.186 closest distance to " O   HOH Z 261 " =    1.975
peak=    3.185 closest distance to " N   ASN A 127 " =    1.282
peak=    3.185 closest distance to " O   HOH Z  66 " =    2.053
peak=    3.184 closest distance to " O   HOH Z 437 " =    1.322
peak=    3.182 closest distance to " O   HOH Z 153 " =    3.851
peak=    3.182 closest distance to " CD2 TYR A 186 " =    1.058
peak=    3.181 closest distance to " CA  VAL A 125 " =    1.059
peak=    3.181 closest distance to " N   CYS A 260 " =    0.914
peak=    3.178 closest distance to " CB  ALA A 248 " =    1.393
peak=    3.177 closest distance to " CB  SER A  62 " =    1.392
peak=    3.176 closest distance to " O   HOH Z  88 " =    2.022
peak=    3.166 closest distance to " NE  ARG A  24 " =    1.948
peak=    3.165 closest distance to " CA  THR A 221 " =    1.050
peak=    3.164 closest distance to " O   HOH Z 375 " =    1.086
peak=    3.164 closest distance to " OG BSER A  99 " =    2.390
peak=    3.162 closest distance to " CB  ALA A 291 " =    1.244
peak=    3.156 closest distance to " CB  PRO A  90 " =    1.102
peak=    3.153 closest distance to " N   HIS A  86 " =    1.836
peak=    3.152 closest distance to " O   GLN A 194 " =    1.590
peak=    3.149 closest distance to " CB  ARG A 219 " =    0.853
peak=    3.148 closest distance to " CA  ALA A 291 " =    0.769
peak=    3.148 closest distance to " CB  ALA A  34 " =    1.108
peak=    3.147 closest distance to " CD2 LEU A 261 " =    1.482
peak=    3.144 closest distance to " O   HOH Z 435 " =    1.940
peak=    3.128 closest distance to " O   HOH Z 119 " =    4.394
peak=    3.126 closest distance to " O   HOH Z 426 " =    1.926
peak=    3.125 closest distance to " O   HOH Z 234 " =    2.242
peak=    3.123 closest distance to " CA  ILE A 234 " =    1.019
peak=    3.120 closest distance to " O   HOH Z 302 " =    1.761
peak=    3.120 closest distance to " CG  GLN A  58 " =    0.969
peak=    3.116 closest distance to " O   HOH Z 423 " =    2.806
peak=    3.115 closest distance to " CG1 VAL A 126 " =    1.181
peak=    3.111 closest distance to " CG  ARG A 269 " =    1.295
peak=    3.110 closest distance to " CA  LYS A 117 " =    1.245
peak=    3.110 closest distance to " O   ARG A 145 " =    1.817
peak=    3.109 closest distance to " CD1AILE A 234 " =    0.885
peak=    3.108 closest distance to " NH1 ARG A  14 " =    1.264
peak=    3.101 closest distance to " O   HOH Z  28 " =    1.857
peak=    3.097 closest distance to " O   HOH Z 130 " =    2.163
peak=    3.097 closest distance to " O   HOH Z 299 " =    4.314
peak=    3.096 closest distance to " O   HOH Z 271 " =    2.276
peak=    3.094 closest distance to " CA  ARG A 102 " =    1.037
peak=    3.087 closest distance to " CG  LYS A  76 " =    0.898
peak=    3.085 closest distance to " O   HOH Z 219 " =    2.049
peak=    3.083 closest distance to " CG2 VAL A 197 " =    1.089
peak=    3.058 closest distance to " CA  ALA A 299 " =    0.905
peak=    3.050 closest distance to " OE2 GLU A  53 " =    2.022
peak=    3.027 closest distance to " CA  ALA A 233 " =    0.997
peak=    3.022 closest distance to " NH1BARG A 145 " =    1.288
peak=    3.014 closest distance to " O   HOH Z 409 " =    2.767

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.924 - 5.792
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 200 from: 200
   mapped sites are within: 0.924 - 5.792

peak=   -4.514 closest distance to " OG BSER A 134 " =    1.297
peak=   -4.444 closest distance to " CG  GLN A  58 " =    1.058
peak=   -4.422 closest distance to " CG  GLN A 223 " =    1.978
peak=   -4.404 closest distance to " O   HOH Z 377 " =    2.070
peak=   -4.362 closest distance to " C   HIS A 108 " =    1.133
peak=   -4.330 closest distance to " CD  ARG A 156 " =    2.049
peak=   -4.310 closest distance to " CD  ARG A  14 " =    3.382
peak=   -4.303 closest distance to " O   HOH Z 266 " =    5.231
peak=   -4.227 closest distance to " CB  PRO A 243 " =    2.661
peak=   -4.222 closest distance to " CG1 VAL A 112 " =    2.811
peak=   -4.208 closest distance to " CE  MET A 105 " =    2.378
peak=   -4.199 closest distance to " O   HOH Z 198 " =    1.528
peak=   -4.189 closest distance to " O   HOH Z 372 " =    2.293
peak=   -4.178 closest distance to " O   PRO A 198 " =    1.252
peak=   -4.151 closest distance to " CB  PHE A 192 " =    2.015
peak=   -4.054 closest distance to " CA  VAL A  67 " =    2.934
peak=   -4.044 closest distance to " O   VAL A  67 " =    2.617
peak=   -4.025 closest distance to " CD1 LEU A 255 " =    2.760
peak=   -3.985 closest distance to " OD2 ASP A 191 " =    1.377
peak=   -3.970 closest distance to " O   HOH Z 231 " =    2.224
peak=   -3.916 closest distance to " CB  ASN A  39 " =    2.309
peak=   -3.900 closest distance to " O   HOH Z 351 " =    1.456
peak=   -3.870 closest distance to " ND2 ASN A  45 " =    1.347
peak=   -3.831 closest distance to " CE2 TYR A  30 " =    2.754
peak=   -3.828 closest distance to " OXT GLY A 302 " =    2.853
peak=   -3.811 closest distance to " CB  ALA A 291 " =    2.185
peak=   -3.801 closest distance to " O   HOH Z 407 " =    2.668
peak=   -3.790 closest distance to " O   ALA A 161 " =    1.618
peak=   -3.761 closest distance to " CG2 ILE A 263 " =    2.228
peak=   -3.755 closest distance to " O   HOH Z 389 " =    1.956
peak=   -3.733 closest distance to " CZ3 TRP A 179 " =    1.219
peak=   -3.721 closest distance to " CG  PHE A 283 " =    2.614
peak=   -3.719 closest distance to " CD  ARG A 139 " =    1.557
peak=   -3.701 closest distance to " CZ  TYR A 169 " =    1.777
peak=   -3.700 closest distance to " O   PHE A 218 " =    1.522
peak=   -3.697 closest distance to " O   SER A  95 " =    1.446
peak=   -3.694 closest distance to " O   HOH Z 395 " =    5.111
peak=   -3.694 closest distance to " CE2 PHE A 218 " =    2.411
peak=   -3.678 closest distance to " O   HOH Z 313 " =    1.813
peak=   -3.674 closest distance to " CZ  PHE A  59 " =    1.460
peak=   -3.673 closest distance to " N   ALA A  43 " =    2.498
peak=   -3.672 closest distance to " CD2 TYR A 247 " =    2.494
peak=   -3.668 closest distance to " O   HOH Z  63 " =    1.662
peak=   -3.668 closest distance to " CD2 TYR A 293 " =    1.906
peak=   -3.667 closest distance to " CB  ALA A 161 " =    2.413
peak=   -3.663 closest distance to " O   PRO A 163 " =    1.961
peak=   -3.655 closest distance to " OD1 ASP A 171 " =    1.600
peak=   -3.647 closest distance to " CB  ALA A  43 " =    2.477
peak=   -3.619 closest distance to " N   ALA A 248 " =    1.631
peak=   -3.615 closest distance to " ND2 ASN A 249 " =    2.337
peak=   -3.613 closest distance to " CB  TRP A  85 " =    2.490
peak=   -3.610 closest distance to " O   HOH Z 185 " =    2.234
peak=   -3.609 closest distance to " NE  ARG A 156 " =    1.899
peak=   -3.591 closest distance to " NE2 GLN A 278 " =    1.681
peak=   -3.576 closest distance to " ND2 ASN A 187 " =    1.512
peak=   -3.569 closest distance to " O   HOH Z 211 " =    1.579
peak=   -3.569 closest distance to " O   HOH Z 429 " =    1.984
peak=   -3.556 closest distance to " CD2 PHE A 225 " =    1.212
peak=   -3.555 closest distance to " OG  SER A   3 " =    1.707
peak=   -3.544 closest distance to " CB  ALA A 248 " =    2.225
peak=   -3.538 closest distance to " OD1 ASN A 148 " =    1.506
peak=   -3.530 closest distance to " CE BMET A  47 " =    1.186
peak=   -3.527 closest distance to " O   HOH Z 348 " =    2.241
peak=   -3.517 closest distance to " O   PRO A 198 " =    1.266
peak=   -3.504 closest distance to " O   HOH Z 102 " =    1.653
peak=   -3.498 closest distance to " O   HOH Z 362 " =    5.753
peak=   -3.492 closest distance to " CG2 THR A 178 " =    2.254
peak=   -3.484 closest distance to " O   HOH Z  11 " =    1.772
peak=   -3.474 closest distance to " CA  ASN A 127 " =    1.372
peak=   -3.472 closest distance to " O   SER A 210 " =    2.009
peak=   -3.471 closest distance to " CZ2 TRP A 274 " =    0.924
peak=   -3.471 closest distance to " OE1 GLN A 183 " =    1.536
peak=   -3.465 closest distance to " O   HOH Z 353 " =    2.220
peak=   -3.464 closest distance to " OE2 GLU A 152 " =    1.284
peak=   -3.457 closest distance to " O   TRP A  70 " =    1.413
peak=   -3.453 closest distance to " N   GLN A  58 " =    1.663
peak=   -3.446 closest distance to " CD1 LEU A 101 " =    2.266
peak=   -3.441 closest distance to " O   HOH Z  15 " =    1.467
peak=   -3.440 closest distance to " O   SER A 135 " =    1.432
peak=   -3.439 closest distance to " O   HOH Z  13 " =    1.678
peak=   -3.438 closest distance to " O   ALA A 292 " =    1.960
peak=   -3.438 closest distance to " CB  SER A 210 " =    1.164
peak=   -3.437 closest distance to " CA  GLY A  57 " =    2.147
peak=   -3.431 closest distance to " O   HOH Z 165 " =    2.164
peak=   -3.431 closest distance to " CB  ALA A 291 " =    2.223
peak=   -3.423 closest distance to " O   HOH Z  38 " =    1.875
peak=   -3.410 closest distance to " O   HOH Z 394 " =    1.469
peak=   -3.402 closest distance to " CD1 PHE A  59 " =    2.023
peak=   -3.396 closest distance to " O   HOH Z 369 " =    2.242
peak=   -3.393 closest distance to " CB  ALA A 244 " =    2.083
peak=   -3.392 closest distance to " O   HOH Z 298 " =    1.290
peak=   -3.392 closest distance to " O   HOH Z 290 " =    1.285
peak=   -3.391 closest distance to " O   HOH Z 421 " =    3.126
peak=   -3.390 closest distance to " CE2 PHE A  61 " =    2.595
peak=   -3.388 closest distance to " CA  GLY A 203 " =    2.371
peak=   -3.387 closest distance to " CA  ASP A 298 " =    1.062
peak=   -3.386 closest distance to " N   MET A 188 " =    1.944
peak=   -3.378 closest distance to " OD2 ASP A 171 " =    2.367
peak=   -3.374 closest distance to " CB  TYR A  15 " =    2.195
peak=   -3.369 closest distance to " O   HOH Z 131 " =    4.080
peak=   -3.365 closest distance to " O   VAL A 174 " =    2.229
peak=   -3.360 closest distance to " O   VAL A 189 " =    2.645
peak=   -3.354 closest distance to " ND2 ASN A  60 " =    4.080
peak=   -3.349 closest distance to " CG  PRO A 243 " =    1.663
peak=   -3.346 closest distance to " O   HOH Z 183 " =    1.589
peak=   -3.340 closest distance to " CB  ASP A 286 " =    2.270
peak=   -3.339 closest distance to " OD1 ASP A 191 " =    1.678
peak=   -3.339 closest distance to " NH2AARG A 275 " =    5.095
peak=   -3.337 closest distance to " O   HOH Z 123 " =    2.280
peak=   -3.329 closest distance to " O   ASN A  45 " =    1.900
peak=   -3.326 closest distance to " OG  SER A  97 " =    2.149
peak=   -3.325 closest distance to " O   HOH Z 359 " =    3.211
peak=   -3.323 closest distance to " O   SER A  22 " =    2.443
peak=   -3.322 closest distance to " O   HOH Z 166 " =    2.174
peak=   -3.318 closest distance to " CA  GLY A 241 " =    2.272
peak=   -3.316 closest distance to " O   HOH Z 351 " =    1.671
peak=   -3.313 closest distance to " C   ALA A 114 " =    2.244
peak=   -3.313 closest distance to " CB  ASP A 132 " =    2.382
peak=   -3.310 closest distance to " CE3 TRP A 274 " =    2.246
peak=   -3.307 closest distance to " O   HOH Z 317 " =    1.476
peak=   -3.305 closest distance to " CG1 VAL A  78 " =    2.803
peak=   -3.302 closest distance to " CG2 ILE A  49 " =    2.757
peak=   -3.301 closest distance to " O   HOH Z 137 " =    1.397
peak=   -3.301 closest distance to " O   ALA A  10 " =    1.616
peak=   -3.300 closest distance to " CD2 PHE A  61 " =    2.389
peak=   -3.299 closest distance to " O   HOH Z 114 " =    2.988
peak=   -3.295 closest distance to " CB  GLN A  11 " =    1.847
peak=   -3.285 closest distance to " CB  ASP A 286 " =    1.690
peak=   -3.282 closest distance to " CB  ALA A   7 " =    2.065
peak=   -3.280 closest distance to " O   HOH Z 243 " =    2.035
peak=   -3.275 closest distance to " O   HOH Z 298 " =    2.414
peak=   -3.272 closest distance to " O   HOH Z 393 " =    3.402
peak=   -3.271 closest distance to " O   VAL A 125 " =    2.103
peak=   -3.270 closest distance to " O   GLU A 152 " =    1.363
peak=   -3.266 closest distance to " CB  ASP A 132 " =    2.228
peak=   -3.257 closest distance to " O   MET A  40 " =    2.804
peak=   -3.255 closest distance to " ND2 ASN A  39 " =    1.274
peak=   -3.255 closest distance to " O   HOH Z 256 " =    1.395
peak=   -3.251 closest distance to " O   HOH Z  90 " =    2.370
peak=   -3.250 closest distance to " O   HOH Z 385 " =    1.862
peak=   -3.245 closest distance to " O   ASN A 252 " =    1.324
peak=   -3.242 closest distance to " CD2 LEU A 237 " =    2.750
peak=   -3.239 closest distance to " O   ARG A 145 " =    1.464
peak=   -3.235 closest distance to " O   HOH Z  37 " =    1.672
peak=   -3.233 closest distance to " O   HOH Z 253 " =    3.706
peak=   -3.232 closest distance to " O   HOH Z 263 " =    2.989
peak=   -3.218 closest distance to " CA  GLY A 133 " =    1.929
peak=   -3.215 closest distance to " O   GLN A  89 " =    1.474
peak=   -3.211 closest distance to " O   HOH Z 191 " =    5.792
peak=   -3.208 closest distance to " N   ASP A 286 " =    2.238
peak=   -3.208 closest distance to " O   LYS A  76 " =    1.724
peak=   -3.205 closest distance to " O   HOH Z   6 " =    1.449
peak=   -3.204 closest distance to " O   HOH Z  60 " =    1.821
peak=   -3.204 closest distance to " O   GLY A  80 " =    2.415
peak=   -3.199 closest distance to " O   HOH Z 174 " =    2.532
peak=   -3.199 closest distance to " OD2 ASP A  50 " =    1.529
peak=   -3.190 closest distance to " CG  GLU A 152 " =    1.254
peak=   -3.190 closest distance to " CB  PRO A 163 " =    2.441
peak=   -3.187 closest distance to " CG  TRP A 266 " =    1.989
peak=   -3.181 closest distance to " CG  GLU A 277 " =    1.372
peak=   -3.181 closest distance to " OE1 GLN A  88 " =    1.081
peak=   -3.179 closest distance to " CG1 VAL A 230 " =    1.999
peak=   -3.175 closest distance to " SG ACYS A 201 " =    1.692
peak=   -3.173 closest distance to " CB  GLN A  55 " =    1.260
peak=   -3.172 closest distance to " NH1 ARG A 195 " =    2.661
peak=   -3.169 closest distance to " O   ALA A  34 " =    2.156
peak=   -3.163 closest distance to " O   GLN A 240 " =    1.928
peak=   -3.163 closest distance to " OG  SER A  63 " =    1.168
peak=   -3.160 closest distance to " O   HOH Z 140 " =    1.680
peak=   -3.160 closest distance to " CA  GLY A 241 " =    3.214
peak=   -3.158 closest distance to " O   HOH Z 357 " =    2.098
peak=   -3.156 closest distance to " O   HOH Z  24 " =    1.316
peak=   -3.155 closest distance to " OG  SER A  97 " =    1.666
peak=   -3.152 closest distance to " O   HOH Z 288 " =    1.229
peak=   -3.136 closest distance to " CG1 VAL A 197 " =    2.133
peak=   -3.128 closest distance to " OD1 ASN A 301 " =    1.875
peak=   -3.125 closest distance to " O   ALA A 180 " =    1.016
peak=   -3.122 closest distance to " O   HOH Z  73 " =    2.451
peak=   -3.119 closest distance to " CD1 LEU A   5 " =    2.368
peak=   -3.116 closest distance to " O   HOH Z  60 " =    2.306
peak=   -3.116 closest distance to " O   HOH Z 166 " =    1.489
peak=   -3.115 closest distance to " O   TRP A  92 " =    1.794
peak=   -3.112 closest distance to " CB  CYS A 201 " =    2.605
peak=   -3.106 closest distance to " O   HOH Z 281 " =    2.799
peak=   -3.102 closest distance to " O   ALA A 180 " =    1.189
peak=   -3.096 closest distance to " O   HOH Z 250 " =    1.328
peak=   -3.090 closest distance to " CD  GLN A  77 " =    1.347
peak=   -3.089 closest distance to " C   ALA A 158 " =    1.452
peak=   -3.088 closest distance to " CG1AVAL A  41 " =    2.561
peak=   -3.075 closest distance to " NE2 GLN A 223 " =    1.340
peak=   -3.074 closest distance to " N   PHE A  59 " =    1.818
peak=   -3.069 closest distance to " CG1 VAL A 197 " =    2.248
peak=   -3.069 closest distance to " O   HOH Z   3 " =    2.037
peak=   -3.063 closest distance to " O   HOH Z 371 " =    1.704
peak=   -3.049 closest distance to " O   HOH Z 318 " =    1.851
peak=   -3.049 closest distance to " O   HOH Z 389 " =    1.418
peak=   -3.045 closest distance to " N   ALA A 226 " =    1.897
peak=   -3.040 closest distance to " CA  GLY A  57 " =    2.148
peak=   -3.038 closest distance to " CG  ARG A 269 " =    2.219
peak=   -3.012 closest distance to " O   PRO A 163 " =    1.290

================= 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    :  0.3925 0.3860   6.175868e+00   6.157279e+00
   1_bss:  0.3829 0.3761   6.162502e+00   6.138006e+00
   1_xyz:  0.2557 0.2864   5.830789e+00   5.904522e+00
   1_adp:  0.2321 0.2987   5.781076e+00   5.945478e+00
   1_occ:  0.2319 0.2987   5.780701e+00   5.945586e+00
   2_bss:  0.2301 0.2951   5.776250e+00   5.941677e+00
   2_xyz:  0.1616 0.2112   5.455202e+00   5.658528e+00
   2_adp:  0.1491 0.1939   5.376632e+00   5.570831e+00
   2_occ:  0.1489 0.1936   5.375296e+00   5.569743e+00
   3_bss:  0.1488 0.1937   5.373654e+00   5.567226e+00
   3_xyz:  0.1245 0.1655   5.215833e+00   5.425517e+00
   3_adp:  0.1208 0.1609   5.188650e+00   5.401852e+00
   3_occ:  0.1207 0.1608   5.188061e+00   5.401488e+00
   4_bss:  0.1206 0.1611   5.188070e+00   5.401237e+00
   4_xyz:  0.1098 0.1539   5.124424e+00   5.365857e+00
   4_adp:  0.1079 0.1534   5.115771e+00   5.364105e+00
   4_occ:  0.1078 0.1535   5.115539e+00   5.363992e+00
   5_bss:  0.1078 0.1535   5.115563e+00   5.363977e+00
   5_xyz:  0.1098 0.1542   5.128401e+00   5.370480e+00
   5_adp:  0.1088 0.1556   5.128969e+00   5.379487e+00
   5_occ:  0.1088 0.1556   5.128792e+00   5.379379e+00
   5_bss:  0.1087 0.1555   5.128618e+00   5.379084e+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:  0.329  30.830   0.084  -0.147   0.207  -0.000   0.000   0.000
   1_xyz:  0.329  30.830   0.084  -0.147   0.207  -0.000   0.000   0.000
   1_adp:  0.329  30.830   0.084  -0.147   0.207  -0.000   0.000   0.000
   1_occ:  0.329  30.830   0.084  -0.147   0.207  -0.000   0.000   0.000
   2_bss:  0.332  46.759  -2.107  -1.638  -0.670  -0.000  -0.000  -0.000
   2_xyz:  0.332  46.759  -2.107  -1.638  -0.670  -0.000  -0.000  -0.000
   2_adp:  0.332  46.759  -2.107  -1.638  -0.670  -0.000  -0.000  -0.000
   2_occ:  0.332  46.759  -2.107  -1.638  -0.670  -0.000  -0.000  -0.000
   3_bss:  0.321  46.759  -2.997  -2.365  -0.887  -0.000  -0.000  -0.000
   3_xyz:  0.321  46.759  -2.997  -2.365  -0.887  -0.000  -0.000  -0.000
   3_adp:  0.321  46.759  -2.997  -2.365  -0.887  -0.000  -0.000  -0.000
   3_occ:  0.321  46.759  -2.997  -2.365  -0.887  -0.000  -0.000  -0.000
   4_bss:  0.326  46.759  -3.266  -2.618  -1.050  -0.000  -0.000  -0.000
   4_xyz:  0.326  46.759  -3.266  -2.618  -1.050  -0.000  -0.000  -0.000
   4_adp:  0.326  46.759  -3.266  -2.618  -1.050  -0.000  -0.000  -0.000
   4_occ:  0.326  46.759  -3.266  -2.618  -1.050  -0.000  -0.000  -0.000
   5_bss:  0.325  46.759  -3.124  -2.512  -0.874  -0.000  -0.000  -0.000
   5_xyz:  0.325  46.759  -3.124  -2.512  -0.874  -0.000  -0.000  -0.000
   5_adp:  0.325  46.759  -3.124  -2.512  -0.874  -0.000  -0.000  -0.000
   5_occ:  0.325  46.759  -3.124  -2.512  -0.874  -0.000  -0.000  -0.000
   5_bss:  0.323  49.369  -2.903  -2.294  -0.675  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  41.953 0.6216  0.8134    43556.311
   1_bss:  40.695 0.6349  0.8365    40257.100
   1_xyz:  27.810 0.7828  0.9844    20645.918
   1_adp:  29.698 0.7609  0.9667    22806.569
   1_occ:  29.720 0.7607  0.9661    22827.773
   2_bss:  29.411 0.7639  0.9184    22368.689
   2_xyz:  20.367 0.8574  0.9932    11257.279
   2_adp:  18.030 0.8805  1.0042     9481.348
   2_occ:  18.008 0.8807  1.0040     9447.421
   3_bss:  17.906 0.8815  0.9818     9349.981
   3_xyz:  14.971 0.9066  0.9906     6927.473
   3_adp:  14.416 0.9114  0.9877     6634.752
   3_occ:  14.409 0.9115  0.9876     6625.661
   4_bss:  14.403 0.9115  0.9794     6628.126
   4_xyz:  13.649 0.9176  0.9829     6114.923
   4_adp:  13.598 0.9181  0.9780     6080.070
   4_occ:  13.593 0.9182  0.9779     6076.932
   5_bss:  13.594 0.9182  0.9829     6076.752
   5_xyz:  13.666 0.9178  0.9822     6170.486
   5_adp:  13.833 0.9165  0.9752     6244.340
   5_occ:  13.830 0.9165  0.9751     6241.627
   5_bss:  13.822 0.9166  0.9825     6236.142
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.8461e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.8461e-01
   1_xyz:   1.197  0.009  0.076 15.021  0.005  4.107   8.0546e-02
   1_adp:   1.197  0.009  0.076 15.021  0.005  4.107   8.0546e-02
   1_occ:   1.197  0.009  0.076 15.021  0.005  4.107   8.0546e-02
   2_bss:   1.197  0.009  0.076 15.021  0.005  4.107   8.0546e-02
   2_xyz:   1.070  0.007  0.077 14.606  0.004  4.117   6.2117e-02
   2_adp:   1.070  0.007  0.077 14.606  0.004  4.117   6.2117e-02
   2_occ:   1.070  0.007  0.077 14.606  0.004  4.117   6.2117e-02
   3_bss:   1.070  0.007  0.077 14.606  0.004  4.117   6.2117e-02
   3_xyz:   0.953  0.006  0.069 14.636  0.004  4.110   5.3762e-02
   3_adp:   0.953  0.006  0.069 14.636  0.004  4.110   5.3762e-02
   3_occ:   0.953  0.006  0.069 14.636  0.004  4.110   5.3762e-02
   4_bss:   0.953  0.006  0.069 14.636  0.004  4.110   5.3762e-02
   4_xyz:   1.115  0.008  0.083 15.123  0.005  4.112   7.1349e-02
   4_adp:   1.115  0.008  0.083 15.123  0.005  4.112   7.1349e-02
   4_occ:   1.115  0.008  0.083 15.123  0.005  4.112   7.1349e-02
   5_bss:   1.115  0.008  0.083 15.123  0.005  4.112   7.1349e-02
   5_xyz:   0.953  0.006  0.073 14.596  0.004  4.108   5.4777e-02
   5_adp:   0.953  0.006  0.073 14.596  0.004  4.108   5.4777e-02
   5_occ:   0.953  0.006  0.073 14.596  0.004  4.108   5.4777e-02
   5_bss:   0.953  0.006  0.073 14.596  0.004  4.108   5.4777e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.593   2.3958e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.593   2.3958e-01
   1_xyz:   8.689  0.046  0.301 86.103  0.045  2.071   8.0760e-02
   1_adp:   8.689  0.046  0.301 86.103  0.045  2.071   8.0760e-02
   1_occ:   8.689  0.046  0.301 86.103  0.045  2.071   8.0760e-02
   2_bss:   8.689  0.046  0.301 86.103  0.045  2.071   8.0760e-02
   2_xyz:   7.174  0.040  0.275 83.724  0.043  2.353   5.0981e-02
   2_adp:   7.174  0.040  0.275 83.724  0.043  2.353   5.0981e-02
   2_occ:   7.174  0.040  0.275 83.724  0.043  2.353   5.0981e-02
   3_bss:   7.174  0.040  0.275 83.724  0.043  2.353   5.0981e-02
   3_xyz:   6.737  0.046  0.221 83.097  0.033  2.329   3.5692e-02
   3_adp:   6.737  0.046  0.221 83.097  0.033  2.329   3.5692e-02
   3_occ:   6.737  0.046  0.221 83.097  0.033  2.329   3.5692e-02
   4_bss:   6.737  0.046  0.221 83.097  0.033  2.329   3.5692e-02
   4_xyz:   7.161  0.051  0.276 84.226  0.036  2.252   5.6804e-02
   4_adp:   7.161  0.051  0.276 84.226  0.036  2.252   5.6804e-02
   4_occ:   7.161  0.051  0.276 84.226  0.036  2.252   5.6804e-02
   5_bss:   7.161  0.051  0.276 84.226  0.036  2.252   5.6804e-02
   5_xyz:   6.645  0.047  0.232 83.726  0.042  2.351   4.1929e-02
   5_adp:   6.645  0.047  0.232 83.726  0.042  2.351   4.1929e-02
   5_occ:   6.645  0.047  0.232 83.726  0.042  2.351   4.1929e-02
   5_bss:   6.645  0.047  0.232 83.726  0.042  2.351   4.1929e-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:  76.24   0.00  17.70  76.24   0.00  13.85  75.07   4.11  38.68
   1_occ:  76.24   0.00  17.70  76.24   0.00  13.85  75.07   4.11  38.68
   2_bss:  76.24   0.00  17.70  76.24   0.00  13.85  75.07   4.11  38.68
   2_xyz:  76.24   0.00  17.70  76.24   0.00  13.85  75.07   4.11  38.68
   2_adp:  77.63   0.81  17.07  77.63   0.81  13.23  70.18   5.60  37.98
   2_occ:  77.63   0.81  17.07  77.63   0.81  13.23  70.18   5.60  37.98
   3_bss:  77.63   0.81  17.07  77.63   0.81  13.23  70.18   5.60  37.98
   3_xyz:  77.63   0.81  17.07  77.63   0.81  13.23  70.18   5.60  37.98
   3_adp:  80.43   1.49  16.87  80.43   1.49  13.01  69.62   5.26  37.90
   3_occ:  80.43   1.49  16.87  80.43   1.49  13.01  69.62   5.26  37.90
   4_bss:  80.43   1.49  16.87  80.43   1.49  13.01  69.62   5.26  37.90
   4_xyz:  80.43   1.49  16.87  80.43   1.49  13.01  69.62   5.26  37.90
   4_adp:  81.19   1.41  16.81  81.19   1.41  12.88  70.32   5.19  38.21
   4_occ:  81.19   1.41  16.81  81.19   1.41  12.88  70.32   5.19  38.21
   5_bss:  81.19   1.41  16.81  81.19   1.41  12.88  70.32   5.19  38.21
   5_xyz:  81.19   1.41  16.81  81.19   1.41  12.88  70.32   5.19  38.21
   5_adp:  94.24   0.29  17.27  94.24   0.29  12.97  81.44   5.86  40.72
   5_occ:  94.24   0.29  17.27  94.24   0.29  12.97  81.44   5.86  40.72
   5_bss:  94.23   0.29  17.27  94.23   0.29  12.96  81.43   5.86  40.71
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.556    0.018    0.284
   1_adp:    1.556    0.018    0.284
   1_occ:    1.556    0.018    0.284
   2_bss:    1.556    0.018    0.284
   2_xyz:    1.402    0.026    0.439
   2_adp:    1.402    0.026    0.439
   2_occ:    1.402    0.026    0.439
   3_bss:    1.402    0.026    0.439
   3_xyz:    1.510    0.026    0.494
   3_adp:    1.510    0.026    0.494
   3_occ:    1.510    0.026    0.494
   4_bss:    1.510    0.026    0.494
   4_xyz:    1.538    0.077    0.525
   4_adp:    1.538    0.077    0.525
   4_occ:    1.538    0.077    0.525
   5_bss:    1.538    0.077    0.525
   5_xyz:    1.512    0.076    0.529
   5_adp:    1.512    0.076    0.529
   5_occ:    1.512    0.076    0.529
   5_bss:    1.512    0.076    0.529
------------------------------------------------------------------------

CPU time actual refinement: 324.24


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_161/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_161/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_161/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_161/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_161/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 324.09 
  Macro-tasks:
    bulk solvent and scale       = 36.21  
    individual site refinement   = 134.01 
    weights calculation          = 28.52  
    collect and process          = 6.47   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 205.31 
  Micro-tasks:
    mask                            = 1.80   
    f_calc                          = 103.61 
    alpha_beta                      = 7.97   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 112.91 
    fmodel                         = 6.45   
    r_factors                      = 0.14   
    phase_errors                   = 10.96  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 245.27 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.573 micro seconds
Total CPU time: 5.63 minutes
from_scatterers_fft:    659 calls, 103.23 s
gradients_fft:          604 calls,  99.24 s

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

# Date 2008-01-16 Time 04:09:06 PST -0800 (1200485346.40 s)
Start R-work = 0.3925, R-free = 0.3860 (no bulk solvent and anisotropic scale)
Final R-work = 0.1341, R-free = 0.1755 (no bulk solvent and anisotropic scale)

Start R-work = 0.3829, R-free = 0.3761
Final R-work = 0.1087, R-free = 0.1555