# Date 2008-01-16 Time 04:32:54 PST -0800 (1200486774.66 s)
#phil __OFF__

Command line arguments: "../362.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21754
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 362

-------------------------------------------------------------------------------
  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: (69.1963, 48.1033, 88.5498, 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: 3.29, per 1000 atoms: 1.17


================================== 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: (69.1963, 48.1033, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0762 1.97096
Completeness in resolution range: 0.91324
Completeness with d_max=infinity: 0.910523

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0762
                             d_min =   1.9710

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: (69.1963, 48.1033, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0762 1.97096
Completeness in resolution range: 0.91324
Completeness with d_max=infinity: 0.910523

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0766 -  4.2182 [2245/2273]  2015   230  10.2%
  bin  2:  4.2182 -  3.3603 [2168/2191]  1950   218  10.1%
  bin  3:  3.3603 -  2.9391 [2136/2161]  1933   203   9.5%
  bin  4:  2.9391 -  2.6720 [2110/2127]  1893   217  10.3%
  bin  5:  2.6720 -  2.4814 [2092/2135]  1881   211  10.1%
  bin  6:  2.4814 -  2.3357 [2107/2135]  1900   207   9.8%
  bin  7:  2.3357 -  2.2191 [2063/2099]  1862   201   9.7%
  bin  8:  2.2191 -  2.1228 [2090/2132]  1880   210  10.0%
  bin  9:  2.1228 -  2.0412 [1990/2092]  1794   196   9.8%
  bin 10:  2.0412 -  1.9710 [ 588/2105]   522    66  11.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_362/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:
        1.53 -     2.21: 21
        2.21 -     2.88: 1270
        2.88 -     3.55: 4382
        3.55 -     4.23: 9069
        4.23 -     4.90: 13170
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.535 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.570 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.574 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.636 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.720 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27907 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_362/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_362/model_refine_001.geo

CPU time processing inputs: 9.33


============================ 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 = 69.19625 48.10325 88.54975 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: 1.97 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5006   r_free= 0.4999   ksol= 0.00   Bsol= 0.00   scale= 0.852    |
|                                                                             |
| 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:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.306600                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0766 -  4.7052 0.99   1461  161 0.4053 0.4088      6.6247      6.6264|
|  2:  4.7052 -  3.7536 0.99   1416  156 0.4605 0.4906      6.8899      6.9402|
|  3:  3.7536 -  3.2847 0.99   1368  156 0.4917 0.4786      6.7135      6.6823|
|  4:  3.2847 -  2.9869 0.99   1382  147 0.5014 0.4596      6.5372      6.5136|
|  5:  2.9869 -  2.7743 0.99   1352  152 0.5293 0.5198      6.3713      6.3996|
|  6:  2.7743 -  2.6116 0.99   1365  154 0.5371 0.5425      6.2888      6.1942|
|  7:  2.6116 -  2.4814 0.98   1328  153 0.5212 0.4719      6.2272      6.1623|
|  8:  2.4814 -  2.3738 0.98   1357  145 0.5453 0.5328      6.1778      6.1904|
|  9:  2.3738 -  2.2828 0.99   1340  146 0.5324 0.5482      6.1086      6.1932|
| 10:  2.2828 -  2.2042 0.98   1353  146 0.5380 0.5472      6.0988      6.0994|
| 11:  2.2042 -  2.1355 0.97   1313  156 0.5382 0.5320      6.0022      6.0194|
| 12:  2.1355 -  2.0746 0.99   1335  149 0.5308 0.5617      5.9552      5.9407|
| 13:  2.0746 -  2.0201 0.76   1029  108 0.5360 0.5884      5.8706      5.8312|
| 14:  2.0201 -  1.9710 0.18    231   30 0.4854 0.4430       5.938       5.685|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0766 -  4.7052  1461   161  0.66  37.43   0.80     0.68      82403.52|
|  2:  4.7052 -  3.7536  1416   156  0.64  40.56   0.87     0.73     130167.61|
|  3:  3.7536 -  3.2847  1368   156  0.51  50.88   0.85     0.69     138567.66|
|  4:  3.2847 -  2.9869  1382   147  0.41  59.12   0.87     0.57     119691.64|
|  5:  2.9869 -  2.7743  1352   152  0.33  65.04   0.84     0.49      92575.19|
|  6:  2.7743 -  2.6116  1365   154  0.31  66.97   0.86     0.45      78268.67|
|  7:  2.6116 -  2.4814  1328   153  0.30  67.45   0.87     0.42      70972.89|
|  8:  2.4814 -  2.3738  1357   145  0.28  68.87   0.86     0.41      63382.73|
|  9:  2.3738 -  2.2828  1340   146  0.27  69.70   0.88     0.42      60705.70|
| 10:  2.2828 -  2.2042  1353   146  0.28  69.01   0.89     0.41      52922.19|
| 11:  2.2042 -  2.1355  1313   156  0.23  72.62   0.88     0.37      52333.22|
| 12:  2.1355 -  2.0746  1335   149  0.17  77.18   0.90     0.28      49684.30|
| 13:  2.0746 -  2.0201  1029   108  0.12  81.19   0.89     0.20      44929.24|
| 14:  2.0201 -  1.9710   231    30  0.13  79.94   1.02     0.16      32886.93|
|alpha:            min =        0.16 max =            0.73 mean =         0.48|
|beta:             min =    32886.93 max =       138567.66 mean =     80190.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.35|
|phase err.(work): min =        0.00 max =           89.98 mean =        63.13|
|phase err.(test): min =        0.00 max =           90.00 mean =        63.25|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 22.428958             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.393   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.396395              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.752   (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 |  1.535 -  1.871:       11 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.871 -  2.208:       10 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.208 -  2.544:       38 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.544 -  2.881:     1232 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.881 -  3.217:     1872 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.217 -  3.554:     2510 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.554 -  3.890:     4613 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.890 -  4.227:     4456 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.227 -  4.563:     5975 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.563 -  4.900:     7195 |
|-----------------------------------------------------------------------------|
|-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 |        0.191 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.535 |       0.561 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.130)------------------------------------------|
|    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: 1.97 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5006   r_free= 0.4999   ksol= 0.00   Bsol= 0.00   scale= 0.852    |
|                                                                             |
| 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:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.306600                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4942   r_free= 0.4904   ksol= 0.30   Bsol= 50.00   scale= 0.895   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.97,2.97,2.94,0.00,0.00,0.00); trace/3= 0.98                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.303106                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 18.037723             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.797   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.062164              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.267   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4942      final r-factor (work) = 0.4057          |
| start r-factor (free) = 0.4904      final r-factor (free) = 0.4398          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 57.0181 = 18.04 * 0.50 * 6.3010 + 1.00 * 0.1906                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 56.2402 = 18.04 * 0.50 * 6.2171 + 1.00 * 0.1692                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4057      final r-factor (work) = 0.3681          |
| start r-factor (free) = 0.4398      final r-factor (free) = 0.4458          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.8266 = 2.06 * 1.00 * 6.2171 + 1.00 * 0.0060                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.6971 = 2.06 * 1.00 * 6.1441 + 1.00 * 0.0270                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.130)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    116.86  20.93    None  None   None       |
|    all(noH): 2823   0      0.00    116.86  20.93    None  None   None       |
|    Sol.    : 438    0      0.00    116.86  39.62    None  None   None       |
|    Mac.    : 2385   0      0.00    106.42  17.49    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.686: 1011   |   5:    58.430 -  70.116:   67        |
|      1:    11.686 -  23.372:  816   |   6:    70.116 -  81.802:   43        |
|      2:    23.372 -  35.058:  487   |   7:    81.802 -  93.488:   10        |
|      3:    35.058 -  46.744:  258   |   8:    93.488 - 105.174:    1        |
|      4:    46.744 -  58.430:  128   |   9:   105.174 - 116.860:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3681 r_free = 0.4458             target_work(ml) = 6.145         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3680 r_free = 0.4458             target_work(ml) = 6.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3680   r_free= 0.4458   ksol= 0.30   Bsol= 50.00   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.97,2.97,2.94,0.00,0.00,0.00); trace/3= 0.98                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.144888                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3666   r_free= 0.4444   ksol= 0.31   Bsol= 55.51   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.01,2.16,2.17,0.00,0.00,0.00); trace/3= 1.11                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.146493                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 18.319315             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.277  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.684586              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.446  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3666      final r-factor (work) = 0.2990          |
| start r-factor (free) = 0.4444      final r-factor (free) = 0.3676          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 56.4733 = 18.32 * 0.50 * 6.1469 + 1.00 * 0.1696                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 55.8337 = 18.32 * 0.50 * 6.0811 + 1.00 * 0.1327                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2990      final r-factor (work) = 0.2767          |
| start r-factor (free) = 0.3676      final r-factor (free) = 0.3497          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1905 = 0.68 * 1.00 * 6.0811 + 1.00 * 0.0275                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0967 = 0.68 * 1.00 * 5.9519 + 1.00 * 0.0221                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.130)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.07  19.68    None  None   None       |
|    all(noH): 2823   0      0.00    114.07  19.68    None  None   None       |
|    Sol.    : 438    0      0.00    114.07  39.72    None  None   None       |
|    Mac.    : 2385   0      0.00    103.34  16.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.407: 1048   |   5:    57.035 -  68.442:   65        |
|      1:    11.407 -  22.814:  901   |   6:    68.442 -  79.849:   28        |
|      2:    22.814 -  34.221:  442   |   7:    79.849 -  91.256:   11        |
|      3:    34.221 -  45.628:  223   |   8:    91.256 - 102.663:    2        |
|      4:    45.628 -  57.035:  101   |   9:   102.663 - 114.070:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2767 r_free = 0.3497             target_work(ml) = 5.929         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2765 r_free = 0.3499             target_work(ml) = 5.929         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2765   r_free= 0.3499   ksol= 0.31   Bsol= 55.51   scale= 1.042   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.01,2.16,2.17,0.00,0.00,0.00); trace/3= 1.11                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.929022                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2758   r_free= 0.3492   ksol= 0.34   Bsol= 72.60   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.82,0.70,0.60,0.00,0.00,0.00); trace/3= -0.17                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.929710                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.306710              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.266  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.327109              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.491   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2758      final r-factor (work) = 0.2321          |
| start r-factor (free) = 0.3492      final r-factor (free) = 0.2926          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.9253 = 5.31 * 0.50 * 5.9519 + 1.00 * 0.1327                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.6428 = 5.31 * 0.50 * 5.8694 + 1.00 * 0.0691                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2321      final r-factor (work) = 0.2205          |
| start r-factor (free) = 0.2926      final r-factor (free) = 0.2791          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9391 = 0.33 * 1.00 * 5.8694 + 1.00 * 0.0192                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8940 = 0.33 * 1.00 * 5.7589 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.130)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.60  18.47    None  None   None       |
|    all(noH): 2823   0      0.00    107.60  18.47    None  None   None       |
|    Sol.    : 438    0      3.34    107.60  40.49    None  None   None       |
|    Mac.    : 2385   0      0.00    89.94   14.43    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.760: 1056   |   5:    53.798 -  64.558:   71        |
|      1:    10.760 -  21.519: 1019   |   6:    64.558 -  75.318:   30        |
|      2:    21.519 -  32.279:  303   |   7:    75.318 -  86.077:   11        |
|      3:    32.279 -  43.039:  207   |   8:    86.077 -  96.837:    2        |
|      4:    43.039 -  53.798:  123   |   9:    96.837 - 107.597:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2205 r_free = 0.2791             target_work(ml) = 5.736         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2204 r_free = 0.2788             target_work(ml) = 5.735         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2204   r_free= 0.2788   ksol= 0.34   Bsol= 72.60   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.82,0.70,0.60,0.00,0.00,0.00); trace/3= -0.17                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.735330                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2202   r_free= 0.2785   ksol= 0.33   Bsol= 77.98   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-0.77,-0.55,-0.00,-0.00,-0.00); trace/3= -1.41                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.735102                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.369672              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.225  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.742321              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.715  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2202      final r-factor (work) = 0.1664          |
| start r-factor (free) = 0.2785      final r-factor (free) = 0.2140          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.4226 = 6.37 * 0.50 * 5.7628 + 1.00 * 0.0691                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.0114 = 6.37 * 0.50 * 5.6271 + 1.00 * 0.0899                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1664      final r-factor (work) = 0.1507          |
| start r-factor (free) = 0.2140      final r-factor (free) = 0.2037          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1874 = 0.74 * 1.00 * 5.6271 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0450 = 0.74 * 1.00 * 5.4320 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.130)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.35  18.79    None  None   None       |
|    all(noH): 2823   0      0.00    104.35  18.79    None  None   None       |
|    Sol.    : 438    0      4.61    104.35  46.04    None  None   None       |
|    Mac.    : 2385   0      0.00    91.32   13.78    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.435: 1049   |   5:    52.173 -  62.607:  101        |
|      1:    10.435 -  20.869: 1090   |   6:    62.607 -  73.042:   76        |
|      2:    20.869 -  31.304:  227   |   7:    73.042 -  83.477:   28        |
|      3:    31.304 -  41.738:  131   |   8:    83.477 -  93.911:    7        |
|      4:    41.738 -  52.173:  112   |   9:    93.911 - 104.346:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1507 r_free = 0.2037             target_work(ml) = 5.408         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1506 r_free = 0.2036             target_work(ml) = 5.408         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1506   r_free= 0.2036   ksol= 0.33   Bsol= 77.98   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-0.77,-0.55,-0.00,-0.00,-0.00); trace/3= -1.41                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.408265                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1510   r_free= 0.2034   ksol= 0.34   Bsol= 77.63   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.19,-1.41,-0.79,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.409666                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.288060              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.201  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.691256              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.926  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1510      final r-factor (work) = 0.1365          |
| start r-factor (free) = 0.2034      final r-factor (free) = 0.1865          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0239 = 3.29 * 0.50 * 5.4340 + 1.00 * 0.0903                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9023 = 3.29 * 0.50 * 5.3713 + 1.00 * 0.0717                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1365      final r-factor (work) = 0.1326          |
| start r-factor (free) = 0.1865      final r-factor (free) = 0.1854          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.0967 = 1.69 * 1.00 * 5.3713 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.9988 = 1.69 * 1.00 * 5.3123 + 1.00 * 0.0143                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.130)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.24  19.01    None  None   None       |
|    all(noH): 2823   0      0.00    111.24  19.01    None  None   None       |
|    Sol.    : 438    0      2.18    111.24  48.75    None  None   None       |
|    Mac.    : 2385   0      0.00    103.27  13.55    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.124: 1220   |   5:    55.621 -  66.745:   78        |
|      1:    11.124 -  22.248:  992   |   6:    66.745 -  77.869:   61        |
|      2:    22.248 -  33.372:  206   |   7:    77.869 -  88.993:   44        |
|      3:    33.372 -  44.497:   98   |   8:    88.993 - 100.117:   14        |
|      4:    44.497 -  55.621:  105   |   9:   100.117 - 111.241:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1326 r_free = 0.1854             target_work(ml) = 5.307         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1326 r_free = 0.1854             target_work(ml) = 5.307         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1326   r_free= 0.1854   ksol= 0.34   Bsol= 77.63   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.19,-1.41,-0.79,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.306628                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0766 -  4.7052 0.99   1461  161 0.1013 0.1400      5.4505      5.6582|
|  2:  4.7052 -  3.7536 0.99   1416  156 0.0884 0.1041      5.4865      5.6551|
|  3:  3.7536 -  3.2847 0.99   1368  156 0.1258 0.1817        5.61      5.9647|
|  4:  3.2847 -  2.9869 0.99   1382  147 0.1498 0.2020      5.5987      5.7932|
|  5:  2.9869 -  2.7743 0.99   1352  152 0.1637 0.1986      5.5245      5.6874|
|  6:  2.7743 -  2.6116 0.99   1365  154 0.1569 0.2476      5.4042      5.6538|
|  7:  2.6116 -  2.4814 0.98   1328  153 0.1527 0.1962      5.3471       5.526|
|  8:  2.4814 -  2.3738 0.98   1357  145 0.1504 0.2234      5.2893      5.5256|
|  9:  2.3738 -  2.2828 0.99   1340  146 0.1384 0.2089      5.1759      5.4387|
| 10:  2.2828 -  2.2042 0.98   1353  146 0.1415 0.2099      5.1201      5.3215|
| 11:  2.2042 -  2.1355 0.97   1313  156 0.1369 0.2065       5.036      5.3843|
| 12:  2.1355 -  2.0746 0.99   1335  149 0.1317 0.1761      4.9929      5.1931|
| 13:  2.0746 -  2.0201 0.76   1029  108 0.1256 0.2097      4.8804      5.1632|
| 14:  2.0201 -  1.9710 0.18    231   30 0.1230 0.1959      4.8701      5.0122|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0766 -  4.7052  1461   161  0.93  10.31   0.96     0.92       8600.67|
|  2:  4.7052 -  3.7536  1416   156  0.95   9.13   1.01     0.99      10533.78|
|  3:  3.7536 -  3.2847  1368   156  0.92  13.25   1.03     1.04      13107.93|
|  4:  3.2847 -  2.9869  1382   147  0.89  17.60   1.01     1.00      14101.57|
|  5:  2.9869 -  2.7743  1352   152  0.86  20.08   1.00     0.99      13069.22|
|  6:  2.7743 -  2.6116  1365   154  0.86  20.82   0.98     0.94      10561.65|
|  7:  2.6116 -  2.4814  1328   153  0.87  20.16   0.99     0.95       9567.48|
|  8:  2.4814 -  2.3738  1357   145  0.86  20.94   1.00     0.94       8699.42|
|  9:  2.3738 -  2.2828  1340   146  0.87  19.31   0.97     0.91       6850.64|
| 10:  2.2828 -  2.2042  1353   146  0.87  19.73   0.99     0.95       6240.89|
| 11:  2.2042 -  2.1355  1313   156  0.88  18.93   0.98     0.92       5271.78|
| 12:  2.1355 -  2.0746  1335   149  0.88  18.81   0.99     0.99       5070.88|
| 13:  2.0746 -  2.0201  1029   108  0.87  19.37   0.97     0.95       4255.74|
| 14:  2.0201 -  1.9710   231    30  0.89  16.49   0.95     0.89       3500.45|
|alpha:            min =        0.89 max =            1.04 mean =         0.96|
|beta:             min =     3500.45 max =        14101.57 mean =      8962.08|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.96 mean =        17.44|
|phase err.(test): min =        0.00 max =           89.61 mean =        16.69|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1325   r_free= 0.1854   ksol= 0.34   Bsol= 80.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.02,-1.47,-0.61,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.306806                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1325   r_free= 0.1854   ksol= 0.34   Bsol= 80.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.02,-1.47,-0.61,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.306806                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0766 -  4.7052 0.99   1461  161 0.1014 0.1403      5.4514      5.6607|
|  2:  4.7052 -  3.7536 0.99   1416  156 0.0886 0.1044      5.4882      5.6573|
|  3:  3.7536 -  3.2847 0.99   1368  156 0.1259 0.1818       5.611      5.9648|
|  4:  3.2847 -  2.9869 0.99   1382  147 0.1497 0.2019      5.5984       5.793|
|  5:  2.9869 -  2.7743 0.99   1352  152 0.1637 0.1985      5.5238      5.6857|
|  6:  2.7743 -  2.6116 0.99   1365  154 0.1567 0.2473      5.4033      5.6526|
|  7:  2.6116 -  2.4814 0.98   1328  153 0.1526 0.1964      5.3465       5.526|
|  8:  2.4814 -  2.3738 0.98   1357  145 0.1504 0.2231      5.2893      5.5253|
|  9:  2.3738 -  2.2828 0.99   1340  146 0.1384 0.2094      5.1762      5.4403|
| 10:  2.2828 -  2.2042 0.98   1353  146 0.1413 0.2102      5.1199      5.3222|
| 11:  2.2042 -  2.1355 0.97   1313  156 0.1369 0.2066       5.036      5.3842|
| 12:  2.1355 -  2.0746 0.99   1335  149 0.1318 0.1761       4.993      5.1935|
| 13:  2.0746 -  2.0201 0.76   1029  108 0.1258 0.2095      4.8807      5.1611|
| 14:  2.0201 -  1.9710 0.18    231   30 0.1226 0.1958      4.8713      5.0152|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0766 -  4.7052  1461   161  0.93  10.33   0.96     0.92       8616.70|
|  2:  4.7052 -  3.7536  1416   156  0.95   9.15   1.01     0.99      10568.75|
|  3:  3.7536 -  3.2847  1368   156  0.92  13.28   1.04     1.04      13158.87|
|  4:  3.2847 -  2.9869  1382   147  0.89  17.61   1.02     1.00      14107.59|
|  5:  2.9869 -  2.7743  1352   152  0.86  20.06   1.01     0.99      13043.02|
|  6:  2.7743 -  2.6116  1365   154  0.86  20.79   0.98     0.94      10540.91|
|  7:  2.6116 -  2.4814  1328   153  0.87  20.15   0.99     0.96       9554.99|
|  8:  2.4814 -  2.3738  1357   145  0.86  20.95   1.00     0.95       8703.07|
|  9:  2.3738 -  2.2828  1340   146  0.87  19.33   0.97     0.91       6857.69|
| 10:  2.2828 -  2.2042  1353   146  0.87  19.74   0.99     0.95       6244.61|
| 11:  2.2042 -  2.1355  1313   156  0.88  18.94   0.99     0.93       5274.05|
| 12:  2.1355 -  2.0746  1335   149  0.88  18.81   1.00     1.00       5074.16|
| 13:  2.0746 -  2.0201  1029   108  0.87  19.38   0.98     0.95       4254.02|
| 14:  2.0201 -  1.9710   231    30  0.89  16.50   0.96     0.90       3498.57|
|alpha:            min =        0.90 max =            1.04 mean =         0.96|
|beta:             min =     3498.57 max =        14107.59 mean =      8967.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.94 mean =        17.45|
|phase err.(test): min =        0.00 max =           89.65 mean =        16.69|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.130)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.24  19.02    None  None   None       |
|    all(noH): 2823   0      0.00    111.24  19.02    None  None   None       |
|    Sol.    : 438    0      2.19    111.24  48.75    None  None   None       |
|    Mac.    : 2385   0      0.00    103.27  13.55    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  11.127: 1220   |   5:    55.624 -  66.748:   78        |
|      1:    11.127 -  22.251:  992   |   6:    66.748 -  77.872:   61        |
|      2:    22.251 -  33.375:  206   |   7:    77.872 -  88.996:   44        |
|      3:    33.375 -  44.499:   98   |   8:    88.996 - 100.120:   14        |
|      4:    44.499 -  55.624:  105   |   9:   100.120 - 111.244:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 319         
Filter by distance & map next to the model:
   mapped sites are within: 0.529 - 4.497
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 315 from: 319
   mapped sites are within: 0.765 - 4.497

peak=    9.325 closest distance to " O  BHOH Z  74 " =    1.235
peak=    7.919 closest distance to " O   HOH Z 255 " =    1.511
peak=    7.010 closest distance to " O   HOH Z 178 " =    1.295
peak=    6.791 closest distance to " O   HOH Z 117 " =    1.715
peak=    6.273 closest distance to " O   HOH Z  69 " =    2.339
peak=    5.743 closest distance to " O   HOH Z 210 " =    1.575
peak=    5.586 closest distance to " O   HOH Z 248 " =    1.606
peak=    5.441 closest distance to " O   HOH Z 124 " =    1.239
peak=    5.348 closest distance to " O   HOH Z  54 " =    1.827
peak=    5.343 closest distance to " O   GLN A  11 " =    1.008
peak=    4.934 closest distance to " O   HOH Z  65 " =    1.164
peak=    4.841 closest distance to " CA  TYR A  30 " =    0.959
peak=    4.787 closest distance to " CG  PRO A  54 " =    1.379
peak=    4.778 closest distance to " CZ3 TRP A 266 " =    1.172
peak=    4.754 closest distance to " O   HOH Z  49 " =    1.709
peak=    4.682 closest distance to " CD2 TRP A 179 " =    1.310
peak=    4.622 closest distance to " O   HOH Z 404 " =    1.358
peak=    4.586 closest distance to " O   HOH Z  67 " =    1.236
peak=    4.555 closest distance to " O   HOH Z 412 " =    3.532
peak=    4.552 closest distance to " O   HOH Z 394 " =    1.614
peak=    4.508 closest distance to " OE1 GLN A  55 " =    1.480
peak=    4.437 closest distance to " O   HOH Z 403 " =    2.252
peak=    4.431 closest distance to " CA  ARG A  36 " =    1.082
peak=    4.425 closest distance to " O   HOH Z 277 " =    1.379
peak=    4.377 closest distance to " O   PRO A 198 " =    1.588
peak=    4.362 closest distance to " O   HOH Z 431 " =    1.269
peak=    4.361 closest distance to " O   HOH Z 425 " =    1.639
peak=    4.346 closest distance to " CZ  PHE A 218 " =    1.219
peak=    4.327 closest distance to " CB  ASN A  39 " =    0.778
peak=    4.269 closest distance to " O   HOH Z 406 " =    1.852
peak=    4.213 closest distance to " O   HOH Z  43 " =    2.189
peak=    4.196 closest distance to " O   HOH Z 147 " =    1.407
peak=    4.166 closest distance to " CG2 VAL A 197 " =    1.245
peak=    4.154 closest distance to " O   HOH Z 128 " =    1.732
peak=    4.126 closest distance to " O   HOH Z  97 " =    1.361
peak=    4.112 closest distance to " CB  TRP A 179 " =    1.284
peak=    4.106 closest distance to " CB  SER A  63 " =    1.092
peak=    4.105 closest distance to " O   HOH Z 130 " =    2.606
peak=    4.103 closest distance to " CB  GLN A 223 " =    1.399
peak=    4.102 closest distance to " O   HOH Z 132 " =    2.863
peak=    4.087 closest distance to " O   HOH Z 113 " =    1.821
peak=    4.075 closest distance to " O   HOH Z 437 " =    2.082
peak=    4.075 closest distance to " O   HOH Z  40 " =    2.063
peak=    4.065 closest distance to " O   HOH Z 433 " =    1.676
peak=    4.062 closest distance to " CB  GLN A 183 " =    1.310
peak=    4.035 closest distance to " CG  PRO A  90 " =    1.463
peak=    4.024 closest distance to " CB  ASN A 148 " =    1.478
peak=    4.016 closest distance to " O   HOH Z 189 " =    2.852
peak=    4.014 closest distance to " O   HOH Z 368 " =    2.184
peak=    4.013 closest distance to " CA  ALA A 100 " =    1.090
peak=    4.006 closest distance to " O   HOH Z 362 " =    3.220
peak=    3.999 closest distance to " CG2BVAL A  41 " =    0.909
peak=    3.991 closest distance to " CB  ARG A 275 " =    0.861
peak=    3.990 closest distance to " CD  ARG A 159 " =    0.841
peak=    3.980 closest distance to " O   HOH Z 287 " =    1.628
peak=    3.979 closest distance to " O   ASN A  74 " =    1.862
peak=    3.973 closest distance to " CG1AVAL A 121 " =    0.800
peak=    3.967 closest distance to " O   HOH Z 272 " =    1.427
peak=    3.933 closest distance to " CD1 LEU A  96 " =    0.861
peak=    3.910 closest distance to " CB  GLU A 152 " =    1.140
peak=    3.904 closest distance to " O   HOH Z  63 " =    1.708
peak=    3.900 closest distance to " CG  GLN A  11 " =    1.086
peak=    3.895 closest distance to " O   HOH Z 176 " =    1.897
peak=    3.867 closest distance to " NE2 GLN A  11 " =    1.171
peak=    3.865 closest distance to " CG  GLN A  58 " =    1.125
peak=    3.863 closest distance to " O   HOH Z 193 " =    1.472
peak=    3.858 closest distance to " CB  THR A  52 " =    0.809
peak=    3.857 closest distance to " O   HOH Z   9 " =    1.294
peak=    3.849 closest distance to " O   HOH Z 126 " =    1.649
peak=    3.849 closest distance to " CA  GLU A 152 " =    0.924
peak=    3.843 closest distance to " O   HOH Z 298 " =    2.018
peak=    3.839 closest distance to " O   HOH Z  35 " =    2.016
peak=    3.836 closest distance to " CD  ARG A 195 " =    1.160
peak=    3.823 closest distance to " CA  ARG A 195 " =    1.170
peak=    3.818 closest distance to " O   HOH Z 346 " =    1.519
peak=    3.817 closest distance to " CG2AVAL A 121 " =    2.055
peak=    3.812 closest distance to " O   HOH Z 402 " =    1.574
peak=    3.807 closest distance to " O   HOH Z 299 " =    3.849
peak=    3.804 closest distance to " O   HOH Z 142 " =    2.505
peak=    3.797 closest distance to " CB  ARG A 190 " =    1.820
peak=    3.791 closest distance to " CZ  PHE A  38 " =    1.106
peak=    3.789 closest distance to " CG  ARG A 138 " =    1.370
peak=    3.778 closest distance to " CB  ASN A 285 " =    0.925
peak=    3.777 closest distance to " O   HOH Z 234 " =    3.576
peak=    3.773 closest distance to " O   HOH Z 336 " =    1.893
peak=    3.768 closest distance to " ND2 ASN A 249 " =    0.942
peak=    3.762 closest distance to " CB  ARG A  79 " =    0.902
peak=    3.729 closest distance to " CD2 TYR A  68 " =    0.866
peak=    3.718 closest distance to " O   HOH Z 278 " =    0.990
peak=    3.711 closest distance to " O   HOH Z 116 " =    1.440
peak=    3.707 closest distance to " CD  PRO A  54 " =    1.145
peak=    3.702 closest distance to " O   THR A 220 " =    1.174
peak=    3.702 closest distance to " O   HOH Z 134 " =    2.159
peak=    3.701 closest distance to " O   HOH Z 369 " =    1.978
peak=    3.701 closest distance to " CB  GLU A  37 " =    0.899
peak=    3.696 closest distance to " O   HOH Z 193 " =    1.974
peak=    3.696 closest distance to " NH2 ARG A 156 " =    1.062
peak=    3.696 closest distance to " OD1 ASN A 301 " =    1.173
peak=    3.692 closest distance to " CD2 TRP A  85 " =    1.239
peak=    3.685 closest distance to " O   HOH Z 331 " =    1.198
peak=    3.685 closest distance to " O   ALA A 165 " =    1.399
peak=    3.683 closest distance to " CB  GLU A 128 " =    1.065
peak=    3.681 closest distance to " O   HOH Z  80 " =    2.175
peak=    3.678 closest distance to " O   HOH Z  88 " =    3.664
peak=    3.673 closest distance to " CA  ALA A 160 " =    0.926
peak=    3.672 closest distance to " O   HOH Z 414 " =    1.661
peak=    3.671 closest distance to " NZ  LYS A 117 " =    2.899
peak=    3.670 closest distance to " O   HOH Z 301 " =    1.422
peak=    3.658 closest distance to " CB  SER A  26 " =    1.774
peak=    3.656 closest distance to " NE2 GLN A  77 " =    3.080
peak=    3.647 closest distance to " CA  ARG A 156 " =    1.032
peak=    3.643 closest distance to " CG  PRO A 243 " =    1.063
peak=    3.626 closest distance to " CA  ASN A 215 " =    1.008
peak=    3.618 closest distance to " CA  ASN A 217 " =    1.232
peak=    3.618 closest distance to " O   HOH Z 284 " =    2.977
peak=    3.614 closest distance to " CB  LEU A  83 " =    0.765
peak=    3.613 closest distance to " CD1 ILE A 199 " =    1.335
peak=    3.609 closest distance to " CD2 LEU A 297 " =    0.957
peak=    3.594 closest distance to " CB  MET A 105 " =    0.887
peak=    3.592 closest distance to " O  BHOH Z 338 " =    1.102
peak=    3.592 closest distance to " O   HOH Z 369 " =    1.543
peak=    3.590 closest distance to " CD  LYS A 166 " =    1.514
peak=    3.588 closest distance to " O   HOH Z 251 " =    1.626
peak=    3.586 closest distance to " O   HOH Z 287 " =    2.123
peak=    3.584 closest distance to " O   HOH Z 366 " =    2.393
peak=    3.579 closest distance to " CA  ALA A  51 " =    1.058
peak=    3.579 closest distance to " O   HOH Z 195 " =    1.181
peak=    3.576 closest distance to " O   HOH Z 298 " =    4.403
peak=    3.575 closest distance to " CB  PHE A 204 " =    0.903
peak=    3.573 closest distance to " CB  PRO A  54 " =    0.954
peak=    3.571 closest distance to " CB  GLU A 277 " =    3.897
peak=    3.569 closest distance to " CE1 HIS A  81 " =    1.544
peak=    3.569 closest distance to " CB  ALA A 114 " =    0.772
peak=    3.567 closest distance to " CB  GLU A 236 " =    1.305
peak=    3.552 closest distance to " CG1 ILE A  20 " =    1.260
peak=    3.551 closest distance to " O   GLY A  91 " =    1.152
peak=    3.543 closest distance to " O   HOH Z 358 " =    1.327
peak=    3.542 closest distance to " O   HOH Z 144 " =    1.810
peak=    3.528 closest distance to " O   HOH Z 313 " =    1.709
peak=    3.526 closest distance to " O   HOH Z 401 " =    1.046
peak=    3.523 closest distance to " CB  ARG A 269 " =    1.199
peak=    3.512 closest distance to " O   HOH Z  63 " =    2.054
peak=    3.508 closest distance to " CB  ASN A 187 " =    1.343
peak=    3.506 closest distance to " CG AARG A 275 " =    1.159
peak=    3.505 closest distance to " CD  LYS A 119 " =    1.724
peak=    3.503 closest distance to " CB  MET A  40 " =    1.020
peak=    3.494 closest distance to " OG BSER A 164 " =    2.240
peak=    3.494 closest distance to " O   HOH Z  26 " =    1.159
peak=    3.492 closest distance to " O   HOH Z 393 " =    3.448
peak=    3.492 closest distance to " O   HOH Z 132 " =    2.929
peak=    3.478 closest distance to " CA  PRO A 198 " =    1.179
peak=    3.477 closest distance to " O   HOH Z 345 " =    1.578
peak=    3.474 closest distance to " O   SER A  87 " =    2.279
peak=    3.472 closest distance to " CB  PRO A  90 " =    1.042
peak=    3.469 closest distance to " CA  LEU A  83 " =    1.356
peak=    3.463 closest distance to " O   HOH Z 213 " =    1.736
peak=    3.459 closest distance to " CG1 ILE A  33 " =    1.225
peak=    3.457 closest distance to " O   HOH Z  20 " =    1.798
peak=    3.455 closest distance to " N   SER A 164 " =    1.024
peak=    3.449 closest distance to " O   HOH Z 214 " =    1.616
peak=    3.449 closest distance to " O   HOH Z 176 " =    2.323
peak=    3.448 closest distance to " CA  THR A 246 " =    1.084
peak=    3.446 closest distance to " CA  SER A  26 " =    1.023
peak=    3.441 closest distance to " CB  ARG A  79 " =    1.156
peak=    3.437 closest distance to " CA  SER A  12 " =    1.355
peak=    3.430 closest distance to " O   HOH Z 316 " =    2.886
peak=    3.429 closest distance to " O   HOH Z 209 " =    2.572
peak=    3.422 closest distance to " O   ILE A 151 " =    0.979
peak=    3.421 closest distance to " O   HOH Z 199 " =    1.426
peak=    3.421 closest distance to " O   THR A 182 " =    1.563
peak=    3.420 closest distance to " CB  VAL A 265 " =    1.171
peak=    3.416 closest distance to " O   HOH Z 313 " =    2.001
peak=    3.414 closest distance to " O   HOH Z   1 " =    2.768
peak=    3.413 closest distance to " CE  LYS A  76 " =    0.873
peak=    3.405 closest distance to " O   HOH Z 343 " =    2.547
peak=    3.404 closest distance to " O   HOH Z 279 " =    1.032
peak=    3.403 closest distance to " CA  ALA A  21 " =    1.393
peak=    3.400 closest distance to " O   HOH Z 149 " =    2.240
peak=    3.399 closest distance to " CB  SER A  62 " =    0.880
peak=    3.396 closest distance to " O   ASP A 191 " =    1.521
peak=    3.394 closest distance to " O   HOH Z 196 " =    1.390
peak=    3.391 closest distance to " OE1 GLN A 223 " =    2.307
peak=    3.390 closest distance to " O   HOH Z  78 " =    1.742
peak=    3.387 closest distance to " CA  CYS A 260 " =    1.515
peak=    3.387 closest distance to " CA  MET A 105 " =    1.273
peak=    3.386 closest distance to " O   HOH Z 371 " =    2.316
peak=    3.386 closest distance to " CD2 LEU A 297 " =    1.062
peak=    3.382 closest distance to " CA  VAL A 112 " =    1.181
peak=    3.382 closest distance to " NH2AARG A 145 " =    1.069
peak=    3.378 closest distance to " O   HOH Z 371 " =    2.164
peak=    3.375 closest distance to " CB  LEU A   5 " =    1.145
peak=    3.372 closest distance to " O   ASP A 200 " =    1.555
peak=    3.371 closest distance to " CB  ALA A 248 " =    1.403
peak=    3.371 closest distance to " O   HOH Z  43 " =    1.314
peak=    3.370 closest distance to " CB  SER A 273 " =    0.898
peak=    3.370 closest distance to " CA  ASP A 162 " =    1.104
peak=    3.369 closest distance to " CB  ASP A 191 " =    1.272
peak=    3.368 closest distance to " N   THR A  52 " =    1.116
peak=    3.364 closest distance to " O   ASP A 124 " =    1.762
peak=    3.363 closest distance to " O   HOH Z 238 " =    3.795
peak=    3.358 closest distance to " O   HOH Z 427 " =    3.227
peak=    3.358 closest distance to " CA  ALA A 295 " =    1.028
peak=    3.357 closest distance to " O   HOH Z 264 " =    1.618
peak=    3.355 closest distance to " NH1AARG A 145 " =    1.351
peak=    3.354 closest distance to " O   HOH Z 421 " =    2.041
peak=    3.349 closest distance to " CB  ASN A 142 " =    1.071
peak=    3.348 closest distance to " O   HOH Z 112 " =    1.177
peak=    3.340 closest distance to " O   HOH Z 417 " =    2.117
peak=    3.339 closest distance to " O   HOH Z 240 " =    2.653
peak=    3.332 closest distance to " O   HOH Z 423 " =    1.849
peak=    3.331 closest distance to " O   HOH Z 258 " =    1.997
peak=    3.331 closest distance to " OG  SER A 135 " =    1.296
peak=    3.328 closest distance to " OG BSER A 258 " =    2.978
peak=    3.324 closest distance to " O   HOH Z  47 " =    2.458
peak=    3.322 closest distance to " CA  ALA A 154 " =    1.149
peak=    3.319 closest distance to " OG BSER A  99 " =    2.944
peak=    3.319 closest distance to " CB  SER A 141 " =    1.224
peak=    3.318 closest distance to " O   HOH Z  88 " =    3.026
peak=    3.317 closest distance to " O   HOH Z 290 " =    1.096
peak=    3.316 closest distance to " N   TYR A 247 " =    1.304
peak=    3.316 closest distance to " CB  TYR A 247 " =    0.924
peak=    3.314 closest distance to " CB  ASP A 140 " =    0.972
peak=    3.313 closest distance to " O   HOH Z 247 " =    1.393
peak=    3.313 closest distance to " CD1 LEU A 167 " =    1.024
peak=    3.310 closest distance to " O   HOH Z 340 " =    1.260
peak=    3.310 closest distance to " CB  SER A  32 " =    1.193
peak=    3.305 closest distance to " O   HOH Z 209 " =    2.209
peak=    3.303 closest distance to " O   HOH Z 142 " =    1.450
peak=    3.303 closest distance to " O   HOH Z 193 " =    1.468
peak=    3.300 closest distance to " O   HOH Z  39 " =    1.134
peak=    3.295 closest distance to " CB  VAL A 202 " =    1.440
peak=    3.288 closest distance to " O   THR A 251 " =    1.282
peak=    3.285 closest distance to " CE1 TYR A 186 " =    1.159
peak=    3.277 closest distance to " O   HOH Z 417 " =    1.130
peak=    3.272 closest distance to " CB  PRO A 198 " =    1.266
peak=    3.265 closest distance to " CB  GLN A  89 " =    1.320
peak=    3.263 closest distance to " NE2 GLN A  58 " =    3.358
peak=    3.260 closest distance to " CZ3 TRP A  85 " =    1.028
peak=    3.258 closest distance to " O   HOH Z 106 " =    2.063
peak=    3.257 closest distance to " CG  MET A 188 " =    0.940
peak=    3.250 closest distance to " OE2 GLU A  53 " =    1.356
peak=    3.247 closest distance to " O   HOH Z 310 " =    1.934
peak=    3.244 closest distance to " CA  ARG A 195 " =    1.516
peak=    3.242 closest distance to " OH  TYR A  68 " =    0.963
peak=    3.241 closest distance to " O   TYR A 116 " =    1.423
peak=    3.238 closest distance to " OG  SER A 146 " =    0.893
peak=    3.237 closest distance to " CG2 THR A 221 " =    1.229
peak=    3.235 closest distance to " CB  PHE A 283 " =    0.891
peak=    3.234 closest distance to " CD  ARG A 139 " =    1.181
peak=    3.231 closest distance to " CD2 LEU A  83 " =    1.505
peak=    3.230 closest distance to " CG2 VAL A 268 " =    0.902
peak=    3.229 closest distance to " CG1 VAL A 153 " =    1.195
peak=    3.228 closest distance to " CB  PRO A 243 " =    1.102
peak=    3.224 closest distance to " O   HOH Z  76 " =    1.069
peak=    3.221 closest distance to " N   HIS A 108 " =    1.743
peak=    3.219 closest distance to " CG1 ILE A 120 " =    1.116
peak=    3.215 closest distance to " O   MET A 113 " =    1.555
peak=    3.210 closest distance to " O   HOH Z 365 " =    2.385
peak=    3.208 closest distance to " O  BHOH Z 338 " =    2.126
peak=    3.202 closest distance to " O   HOH Z 279 " =    2.174
peak=    3.201 closest distance to " OD1 ASN A 217 " =    1.608
peak=    3.199 closest distance to " O   HOH Z 200 " =    3.260
peak=    3.197 closest distance to " O   HOH Z 368 " =    4.497
peak=    3.196 closest distance to " C   ALA A 299 " =    1.049
peak=    3.192 closest distance to " CA  ALA A 158 " =    1.636
peak=    3.190 closest distance to " O   HOH Z 359 " =    1.630
peak=    3.190 closest distance to " CB  ASP A 124 " =    0.891
peak=    3.187 closest distance to " O   HOH Z 258 " =    1.631
peak=    3.182 closest distance to " CD1 ILE A 199 " =    1.986
peak=    3.181 closest distance to " CD  PRO A 213 " =    1.342
peak=    3.180 closest distance to " O   HOH Z 394 " =    3.900
peak=    3.179 closest distance to " CG2 THR A 220 " =    1.002
peak=    3.178 closest distance to " O   HOH Z 392 " =    0.964
peak=    3.177 closest distance to " N   ALA A   1 " =    2.167
peak=    3.175 closest distance to " CB  PHE A  16 " =    1.166
peak=    3.173 closest distance to " CD2 LEU A 255 " =    1.649
peak=    3.172 closest distance to " ND2 ASN A 187 " =    1.403
peak=    3.171 closest distance to " CB  TRP A 266 " =    1.095
peak=    3.167 closest distance to " CA  ARG A 102 " =    1.119
peak=    3.164 closest distance to " CA  ASN A 209 " =    1.201
peak=    3.159 closest distance to " CG  GLN A  77 " =    0.819
peak=    3.157 closest distance to " CD  GLN A  58 " =    1.117
peak=    3.154 closest distance to " CD  GLN A 194 " =    1.645
peak=    3.153 closest distance to " CB  TRP A 179 " =    1.891
peak=    3.153 closest distance to " O   HOH Z 407 " =    1.969
peak=    3.152 closest distance to " O   HOH Z 297 " =    1.073
peak=    3.151 closest distance to " OG  SER A 245 " =    1.419
peak=    3.150 closest distance to " O   HOH Z 365 " =    1.484
peak=    3.143 closest distance to " CE1 TYR A  30 " =    1.147
peak=    3.143 closest distance to " O   HOH Z 163 " =    2.109
peak=    3.132 closest distance to " O   ASN A 284 " =    1.843
peak=    3.131 closest distance to " O   HOH Z 214 " =    2.875
peak=    3.130 closest distance to " O   HOH Z 265 " =    2.116
peak=    3.130 closest distance to " CB  ALA A 291 " =    0.955
peak=    3.129 closest distance to " CD  ARG A 269 " =    0.936
peak=    3.129 closest distance to " CB  ARG A 156 " =    0.888
peak=    3.128 closest distance to " CG1BVAL A  72 " =    1.724
peak=    3.124 closest distance to " CA  SER A  32 " =    1.674
peak=    3.120 closest distance to " NZ  LYS A 117 " =    0.874
peak=    3.110 closest distance to " O   HOH Z 435 " =    2.813
peak=    3.106 closest distance to " N   SER A 271 " =    1.074
peak=    3.102 closest distance to " O   HOH Z 282 " =    2.265
peak=    3.092 closest distance to " CA  ALA A 129 " =    1.190
peak=    3.091 closest distance to " CA  VAL A 197 " =    1.076
peak=    3.089 closest distance to " CD1 LEU A 300 " =    1.046
peak=    3.085 closest distance to " CG2 THR A  42 " =    1.029
peak=    3.083 closest distance to " O   HOH Z 232 " =    2.579
peak=    3.074 closest distance to " CA  ASP A 140 " =    1.689
peak=    3.071 closest distance to " O   HOH Z  54 " =    2.034
peak=    3.070 closest distance to " CB  GLN A  58 " =    1.064
peak=    3.068 closest distance to " CA  TYR A 116 " =    1.459
peak=    3.064 closest distance to " N   CYS A 260 " =    1.051
peak=    3.058 closest distance to " OG1 THR A 294 " =    4.004
peak=    3.043 closest distance to " CB  PRO A  54 " =    1.364
peak=    3.033 closest distance to " O   HOH Z 221 " =    1.050

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 220         
Filter by distance & map next to the model:
   mapped sites are within: 0.769 - 5.941
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 219 from: 220
   mapped sites are within: 0.769 - 5.941

peak=   -4.563 closest distance to " O   PRO A 198 " =    1.388
peak=   -4.515 closest distance to " CD2 TYR A 293 " =    1.781
peak=   -4.497 closest distance to " CD2 LEU A 237 " =    2.629
peak=   -4.390 closest distance to " CG  GLN A  58 " =    0.920
peak=   -4.263 closest distance to " CD  GLN A 223 " =    1.549
peak=   -4.254 closest distance to " CG  GLN A  11 " =    1.302
peak=   -4.248 closest distance to " O   HOH Z  67 " =    1.309
peak=   -4.226 closest distance to " CD2 PHE A  61 " =    2.023
peak=   -4.181 closest distance to " O   VAL A  67 " =    2.811
peak=   -4.134 closest distance to " O   HOH Z 150 " =    1.800
peak=   -4.087 closest distance to " CG2 ILE A  20 " =    3.023
peak=   -4.005 closest distance to " CD1 ILE A 109 " =    2.768
peak=   -4.003 closest distance to " CG  PRO A 243 " =    1.696
peak=   -4.000 closest distance to " O   HOH Z 422 " =    1.146
peak=   -3.992 closest distance to " CG2 ILE A  49 " =    2.829
peak=   -3.976 closest distance to " O   VAL A 174 " =    2.158
peak=   -3.974 closest distance to " CE2 PHE A  61 " =    2.771
peak=   -3.969 closest distance to " O   HOH Z 411 " =    5.615
peak=   -3.964 closest distance to " O   HOH Z   7 " =    1.184
peak=   -3.959 closest distance to " SG ACYS A 201 " =    1.111
peak=   -3.946 closest distance to " CD1 PHE A  59 " =    1.969
peak=   -3.941 closest distance to " CD  ARG A  14 " =    3.263
peak=   -3.928 closest distance to " O   HOH Z 374 " =    2.112
peak=   -3.927 closest distance to " CG  GLN A  58 " =    1.427
peak=   -3.895 closest distance to " CG  GLN A 103 " =    2.452
peak=   -3.882 closest distance to " CD  ARG A 156 " =    2.046
peak=   -3.861 closest distance to " O   HOH Z 377 " =    2.200
peak=   -3.810 closest distance to " C   HIS A 108 " =    1.153
peak=   -3.807 closest distance to " CB  ASN A  45 " =    2.049
peak=   -3.800 closest distance to " O   HOH Z 340 " =    1.687
peak=   -3.792 closest distance to " O   HOH Z 366 " =    1.466
peak=   -3.792 closest distance to " O   HOH Z 166 " =    1.458
peak=   -3.777 closest distance to " O   GLY A 241 " =    2.365
peak=   -3.773 closest distance to " CG2 VAL A 189 " =    2.219
peak=   -3.771 closest distance to " CG  GLU A  53 " =    1.639
peak=   -3.767 closest distance to " CD1 LEU A 101 " =    2.466
peak=   -3.761 closest distance to " ND2BASN A 224 " =    1.970
peak=   -3.749 closest distance to " CE2 TYR A  30 " =    2.729
peak=   -3.736 closest distance to " CA  ASP A 298 " =    1.112
peak=   -3.733 closest distance to " O   HOH Z 165 " =    1.841
peak=   -3.721 closest distance to " O   HOH Z 150 " =    0.794
peak=   -3.707 closest distance to " O   HOH Z 278 " =    1.052
peak=   -3.703 closest distance to " O   ASP A 107 " =    1.743
peak=   -3.678 closest distance to " CE3 TRP A 150 " =    2.243
peak=   -3.677 closest distance to " NZ  LYS A 117 " =    1.078
peak=   -3.675 closest distance to " O   HOH Z 434 " =    1.543
peak=   -3.646 closest distance to " ND2 ASN A  45 " =    2.048
peak=   -3.640 closest distance to " CG1 VAL A 112 " =    2.707
peak=   -3.638 closest distance to " O   HOH Z  52 " =    2.100
peak=   -3.634 closest distance to " CB  ALA A  43 " =    2.665
peak=   -3.628 closest distance to " CH2 TRP A 150 " =    1.136
peak=   -3.626 closest distance to " OG  SER A  97 " =    2.132
peak=   -3.624 closest distance to " O   HOH Z 388 " =    2.078
peak=   -3.613 closest distance to " CG1 VAL A 189 " =    2.374
peak=   -3.609 closest distance to " O   HOH Z 191 " =    5.941
peak=   -3.599 closest distance to " O   HOH Z 124 " =    1.484
peak=   -3.589 closest distance to " CA  GLY A 133 " =    2.038
peak=   -3.583 closest distance to " O   HOH Z 418 " =    1.260
peak=   -3.578 closest distance to " CD1 ILE A 151 " =    2.548
peak=   -3.578 closest distance to " CG2BVAL A  41 " =    2.003
peak=   -3.567 closest distance to " O   HOH Z 166 " =    1.821
peak=   -3.563 closest distance to " O   HOH Z  65 " =    1.775
peak=   -3.562 closest distance to " N   ALA A  43 " =    2.603
peak=   -3.554 closest distance to " OD2 ASP A 171 " =    1.867
peak=   -3.548 closest distance to " CB  ASP A 162 " =    1.844
peak=   -3.547 closest distance to " C   ASN A 285 " =    2.277
peak=   -3.544 closest distance to " O   HOH Z 331 " =    1.181
peak=   -3.543 closest distance to " O   LYS A  76 " =    1.832
peak=   -3.514 closest distance to " CG1 VAL A 112 " =    2.618
peak=   -3.512 closest distance to " O   HOH Z 345 " =    3.088
peak=   -3.510 closest distance to " CA  GLU A 277 " =    1.236
peak=   -3.509 closest distance to " O  BHOH Z  74 " =    0.831
peak=   -3.498 closest distance to " NE2 GLN A 223 " =    1.145
peak=   -3.487 closest distance to " O   HOH Z 222 " =    0.985
peak=   -3.483 closest distance to " O   HOH Z  56 " =    1.214
peak=   -3.479 closest distance to " O   HOH Z 109 " =    3.932
peak=   -3.478 closest distance to " O   HOH Z  90 " =    4.009
peak=   -3.473 closest distance to " O   HOH Z 109 " =    3.135
peak=   -3.471 closest distance to " O   HOH Z 216 " =    0.918
peak=   -3.459 closest distance to " O   HOH Z 155 " =    1.801
peak=   -3.457 closest distance to " CB  HIS A  86 " =    1.212
peak=   -3.443 closest distance to " CG  ARG A 269 " =    2.282
peak=   -3.441 closest distance to " CZ  PHE A  38 " =    2.148
peak=   -3.431 closest distance to " CZ  TYR A 169 " =    2.136
peak=   -3.431 closest distance to " O   HOH Z 152 " =    1.418
peak=   -3.431 closest distance to " O   HOH Z  41 " =    1.958
peak=   -3.428 closest distance to " CG  ARG A 259 " =    2.443
peak=   -3.426 closest distance to " O   HOH Z 336 " =    4.935
peak=   -3.425 closest distance to " CA  GLY A 229 " =    2.328
peak=   -3.424 closest distance to " O   HOH Z  35 " =    2.343
peak=   -3.419 closest distance to " CB  PRO A 243 " =    2.751
peak=   -3.418 closest distance to " OG  SER A  97 " =    1.797
peak=   -3.418 closest distance to " O   HOH Z 149 " =    1.715
peak=   -3.416 closest distance to " O   HOH Z  54 " =    1.991
peak=   -3.416 closest distance to " O   SER A   3 " =    0.946
peak=   -3.414 closest distance to " O   TYR A 186 " =    1.820
peak=   -3.412 closest distance to " O   HOH Z 102 " =    1.503
peak=   -3.400 closest distance to " O   SER A 146 " =    1.181
peak=   -3.393 closest distance to " CE1 TYR A 247 " =    2.772
peak=   -3.392 closest distance to " O   HOH Z 283 " =    2.284
peak=   -3.391 closest distance to " O   HOH Z 397 " =    1.149
peak=   -3.388 closest distance to " CB  TRP A  85 " =    2.542
peak=   -3.388 closest distance to " O   HOH Z   6 " =    1.505
peak=   -3.383 closest distance to " O   HOH Z 424 " =    3.084
peak=   -3.381 closest distance to " CD1 ILE A 106 " =    2.194
peak=   -3.374 closest distance to " O   HOH Z  63 " =    1.305
peak=   -3.365 closest distance to " CB  ALA A  10 " =    2.188
peak=   -3.361 closest distance to " O   HOH Z 128 " =    2.327
peak=   -3.358 closest distance to " O   HOH Z 179 " =    1.916
peak=   -3.357 closest distance to " O   HOH Z   2 " =    2.077
peak=   -3.355 closest distance to " O   HOH Z 157 " =    3.680
peak=   -3.354 closest distance to " O   HOH Z 231 " =    2.066
peak=   -3.353 closest distance to " N   ARG A 259 " =    1.540
peak=   -3.351 closest distance to " CB  SER A 141 " =    2.102
peak=   -3.351 closest distance to " O   HOH Z 211 " =    1.222
peak=   -3.351 closest distance to " O   HOH Z  60 " =    1.424
peak=   -3.348 closest distance to " O   HOH Z 285 " =    1.471
peak=   -3.336 closest distance to " O   SER A 210 " =    1.756
peak=   -3.327 closest distance to " O   HOH Z 103 " =    1.728
peak=   -3.324 closest distance to " OD2 ASP A 270 " =    1.012
peak=   -3.323 closest distance to " SD  MET A 105 " =    1.047
peak=   -3.323 closest distance to " O   HOH Z 407 " =    1.037
peak=   -3.319 closest distance to " CZ  ARG A 156 " =    1.998
peak=   -3.310 closest distance to " O   HOH Z  88 " =    4.527
peak=   -3.306 closest distance to " CA  TRP A 150 " =    1.136
peak=   -3.304 closest distance to " O   HOH Z 287 " =    1.819
peak=   -3.296 closest distance to " CG  LEU A 281 " =    1.968
peak=   -3.295 closest distance to " O   HOH Z  42 " =    1.713
peak=   -3.295 closest distance to " O   VAL A 257 " =    1.472
peak=   -3.294 closest distance to " CG2 THR A  18 " =    2.886
peak=   -3.289 closest distance to " O   GLN A 240 " =    2.796
peak=   -3.288 closest distance to " O   HOH Z 387 " =    2.830
peak=   -3.287 closest distance to " CD  ARG A  79 " =    1.120
peak=   -3.287 closest distance to " O   HOH Z 198 " =    1.511
peak=   -3.280 closest distance to " SD  MET A 105 " =    2.278
peak=   -3.275 closest distance to " O   GLN A  11 " =    1.118
peak=   -3.275 closest distance to " O   HOH Z 428 " =    1.557
peak=   -3.274 closest distance to " OD1 ASP A 171 " =    1.491
peak=   -3.274 closest distance to " O   HOH Z 131 " =    4.204
peak=   -3.272 closest distance to " O   HOH Z 135 " =    2.090
peak=   -3.261 closest distance to " O   HOH Z 115 " =    1.795
peak=   -3.258 closest distance to " CD  LYS A 289 " =    2.340
peak=   -3.257 closest distance to " O   HOH Z 215 " =    2.295
peak=   -3.250 closest distance to " O   PHE A 218 " =    1.371
peak=   -3.241 closest distance to " N   ALA A 226 " =    1.968
peak=   -3.239 closest distance to " O   HOH Z   9 " =    3.142
peak=   -3.236 closest distance to " O   HOH Z 398 " =    2.246
peak=   -3.235 closest distance to " CB  ALA A   9 " =    2.609
peak=   -3.233 closest distance to " O   HOH Z 136 " =    1.227
peak=   -3.231 closest distance to " O   HOH Z  13 " =    0.982
peak=   -3.229 closest distance to " N   ILE A 120 " =    1.031
peak=   -3.229 closest distance to " N   LEU A 282 " =    2.186
peak=   -3.228 closest distance to " O   HOH Z 234 " =    4.319
peak=   -3.227 closest distance to " O   HOH Z 193 " =    1.120
peak=   -3.226 closest distance to " NH2 ARG A  79 " =    2.381
peak=   -3.223 closest distance to " CA  LYS A 289 " =    2.343
peak=   -3.219 closest distance to " CA  GLY A 203 " =    2.396
peak=   -3.216 closest distance to " O   ILE A 106 " =    1.633
peak=   -3.214 closest distance to " O   SER A 271 " =    2.002
peak=   -3.213 closest distance to " CD  GLN A  77 " =    0.935
peak=   -3.212 closest distance to " CB  ASP A 132 " =    2.539
peak=   -3.211 closest distance to " CD1 ILE A 263 " =    1.958
peak=   -3.208 closest distance to " CG  GLU A 236 " =    1.126
peak=   -3.205 closest distance to " O   ASP A 171 " =    1.067
peak=   -3.203 closest distance to " O   HOH Z 438 " =    3.042
peak=   -3.202 closest distance to " NH1 ARG A 259 " =    2.731
peak=   -3.202 closest distance to " CA  ASP A  65 " =    1.181
peak=   -3.201 closest distance to " O   ASN A 110 " =    2.533
peak=   -3.199 closest distance to " O   HOH Z 205 " =    0.769
peak=   -3.198 closest distance to " O   HOH Z  64 " =    1.514
peak=   -3.198 closest distance to " O   HOH Z 197 " =    1.863
peak=   -3.193 closest distance to " OD1 ASN A 148 " =    1.374
peak=   -3.193 closest distance to " O   HOH Z  60 " =    2.117
peak=   -3.188 closest distance to " O   GLY A  17 " =    1.012
peak=   -3.187 closest distance to " O   HOH Z 352 " =    1.637
peak=   -3.182 closest distance to " CD2 LEU A 228 " =    2.609
peak=   -3.180 closest distance to " O   ALA A   7 " =    1.598
peak=   -3.177 closest distance to " NZ  LYS A 119 " =    1.469
peak=   -3.174 closest distance to " O   HOH Z 137 " =    1.399
peak=   -3.174 closest distance to " O   HOH Z 141 " =    1.623
peak=   -3.173 closest distance to " O   SER A 273 " =    1.139
peak=   -3.171 closest distance to " O   HOH Z 114 " =    3.504
peak=   -3.171 closest distance to " CA  GLY A  57 " =    2.182
peak=   -3.170 closest distance to " CD2 LEU A 237 " =    2.484
peak=   -3.162 closest distance to " CD1 PHE A 130 " =    2.295
peak=   -3.161 closest distance to " N   ARG A 275 " =    1.584
peak=   -3.159 closest distance to " NE2 GLN A  88 " =    1.916
peak=   -3.159 closest distance to " O   HOH Z 326 " =    4.898
peak=   -3.158 closest distance to " O   HOH Z 351 " =    1.647
peak=   -3.157 closest distance to " OG  SER A  87 " =    1.754
peak=   -3.155 closest distance to " CB  SER A  62 " =    5.533
peak=   -3.148 closest distance to " O   HOH Z   5 " =    1.666
peak=   -3.147 closest distance to " O   HOH Z 189 " =    1.792
peak=   -3.146 closest distance to " CD  GLN A  88 " =    0.937
peak=   -3.145 closest distance to " CG  ARG A 219 " =    2.531
peak=   -3.144 closest distance to " OE2 GLU A 152 " =    1.581
peak=   -3.143 closest distance to " O   HOH Z  19 " =    2.335
peak=   -3.140 closest distance to " O   HOH Z 148 " =    3.781
peak=   -3.140 closest distance to " SD  MET A  93 " =    1.752
peak=   -3.139 closest distance to " CE  LYS A  76 " =    2.579
peak=   -3.137 closest distance to " O   HOH Z 196 " =    1.509
peak=   -3.133 closest distance to " OD1 ASN A  39 " =    0.986
peak=   -3.123 closest distance to " OG BSER A 134 " =    1.359
peak=   -3.117 closest distance to " O   HOH Z   6 " =    1.486
peak=   -3.116 closest distance to " CD2 HIS A 115 " =    0.979
peak=   -3.114 closest distance to " N   VAL A 197 " =    1.011
peak=   -3.114 closest distance to " CG  LEU A  83 " =    2.161
peak=   -3.105 closest distance to " NE2 GLN A 278 " =    1.625
peak=   -3.086 closest distance to " CZ  PHE A  38 " =    2.022
peak=   -3.079 closest distance to " CG  ASP A 286 " =    1.502
peak=   -3.074 closest distance to " O   HOH Z 100 " =    1.033
peak=   -3.071 closest distance to " CA  SER A 276 " =    1.529
peak=   -3.068 closest distance to " O   HOH Z 330 " =    1.212
peak=   -3.063 closest distance to " O   HOH Z 178 " =    1.774
peak=   -3.036 closest distance to " O   HOH Z  44 " =    1.868
peak=   -3.033 closest distance to " CA  GLY A 241 " =    2.934
peak=   -3.024 closest distance to " O   HOH Z 211 " =    1.337
peak=   -3.014 closest distance to " CA  GLY A 241 " =    3.334
peak=   -3.006 closest distance to " O   HOH Z 192 " =    1.628

================= 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    :  0.5006 0.4999   6.306600e+00   6.296982e+00
   1_bss:  0.4942 0.4904   6.303106e+00   6.292997e+00
   1_xyz:  0.4057 0.4398   6.186552e+00   6.233109e+00
   1_adp:  0.3681 0.4458   6.144961e+00   6.240138e+00
   1_occ:  0.3680 0.4458   6.144888e+00   6.241026e+00
   2_bss:  0.3666 0.4444   6.146493e+00   6.242025e+00
   2_xyz:  0.2990 0.3676   5.977658e+00   6.126130e+00
   2_adp:  0.2767 0.3497   5.929014e+00   6.088266e+00
   2_occ:  0.2765 0.3499   5.929022e+00   6.088972e+00
   3_bss:  0.2758 0.3492   5.929710e+00   6.088193e+00
   3_xyz:  0.2321 0.2926   5.780036e+00   5.959196e+00
   3_adp:  0.2205 0.2791   5.736113e+00   5.917735e+00
   3_occ:  0.2204 0.2788   5.735330e+00   5.917020e+00
   4_bss:  0.2202 0.2785   5.735102e+00   5.916416e+00
   4_xyz:  0.1664 0.2140   5.479312e+00   5.685227e+00
   4_adp:  0.1507 0.2037   5.408428e+00   5.633494e+00
   4_occ:  0.1506 0.2036   5.408265e+00   5.633771e+00
   5_bss:  0.1510 0.2034   5.409666e+00   5.633907e+00
   5_xyz:  0.1365 0.1865   5.326574e+00   5.553023e+00
   5_adp:  0.1326 0.1854   5.306793e+00   5.538505e+00
   5_occ:  0.1326 0.1854   5.306628e+00   5.538441e+00
   5_bss:  0.1325 0.1854   5.306806e+00   5.538684e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  50.000  -2.974   2.969   2.940   0.000   0.000   0.000
   1_xyz:  0.300  50.000  -2.974   2.969   2.940   0.000   0.000   0.000
   1_adp:  0.300  50.000  -2.974   2.969   2.940   0.000   0.000   0.000
   1_occ:  0.300  50.000  -2.974   2.969   2.940   0.000   0.000   0.000
   2_bss:  0.313  55.512  -1.005   2.161   2.166   0.000   0.000   0.000
   2_xyz:  0.313  55.512  -1.005   2.161   2.166   0.000   0.000   0.000
   2_adp:  0.313  55.512  -1.005   2.161   2.166   0.000   0.000   0.000
   2_occ:  0.313  55.512  -1.005   2.161   2.166   0.000   0.000   0.000
   3_bss:  0.336  72.604  -1.821   0.704   0.603   0.000   0.000   0.000
   3_xyz:  0.336  72.604  -1.821   0.704   0.603   0.000   0.000   0.000
   3_adp:  0.336  72.604  -1.821   0.704   0.603   0.000   0.000   0.000
   3_occ:  0.336  72.604  -1.821   0.704   0.603   0.000   0.000   0.000
   4_bss:  0.333  77.978  -2.919  -0.768  -0.548  -0.000  -0.000  -0.000
   4_xyz:  0.333  77.978  -2.919  -0.768  -0.548  -0.000  -0.000  -0.000
   4_adp:  0.333  77.978  -2.919  -0.768  -0.548  -0.000  -0.000  -0.000
   4_occ:  0.333  77.978  -2.919  -0.768  -0.548  -0.000  -0.000  -0.000
   5_bss:  0.336  77.633  -3.190  -1.411  -0.787  -0.000  -0.000  -0.000
   5_xyz:  0.336  77.633  -3.190  -1.411  -0.787  -0.000  -0.000  -0.000
   5_adp:  0.336  77.633  -3.190  -1.411  -0.787  -0.000  -0.000  -0.000
   5_occ:  0.336  77.633  -3.190  -1.411  -0.787  -0.000  -0.000  -0.000
   5_bss:  0.338  80.003  -3.016  -1.471  -0.611  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  63.142 0.3527  0.4754    80183.704
   1_bss:  61.494 0.3734  0.5262    77841.718
   1_xyz:  52.499 0.4879  0.6744    59345.318
   1_adp:  52.721 0.4848  0.6800    60393.105
   1_occ:  52.754 0.4844  0.6784    60528.260
   2_bss:  52.602 0.4864  0.6867    60477.555
   2_xyz:  41.087 0.6283  0.8748    39544.089
   2_adp:  38.194 0.6634  0.9062    35098.237
   2_occ:  38.251 0.6627  0.9050    35160.526
   3_bss:  38.137 0.6641  0.8692    35093.956
   3_xyz:  30.868 0.7476  0.9476    23751.956
   3_adp:  28.626 0.7731  0.9579    21219.736
   3_occ:  28.600 0.7734  0.9580    21155.245
   4_bss:  28.498 0.7744  0.9189    21056.462
   4_xyz:  20.967 0.8519  0.9717    11926.425
   4_adp:  19.670 0.8646  0.9696    10891.576
   4_occ:  19.674 0.8646  0.9695    10901.643
   5_bss:  19.683 0.8646  0.9570    10913.604
   5_xyz:  17.668 0.8836  0.9656     9105.334
   5_adp:  17.367 0.8864  0.9596     8963.434
   5_occ:  17.365 0.8864  0.9595     8961.119
   5_bss:  17.371 0.8863  0.9630     8966.514
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.9065e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.9065e-01
   1_xyz:   1.778  0.013  0.112 16.462  0.007  4.101   1.6918e-01
   1_adp:   1.778  0.013  0.112 16.462  0.007  4.101   1.6918e-01
   1_occ:   1.778  0.013  0.112 16.462  0.007  4.101   1.6918e-01
   2_bss:   1.778  0.013  0.112 16.462  0.007  4.101   1.6918e-01
   2_xyz:   1.555  0.012  0.102 15.989  0.006  4.107   1.3269e-01
   2_adp:   1.555  0.012  0.102 15.989  0.006  4.107   1.3269e-01
   2_occ:   1.555  0.012  0.102 15.989  0.006  4.107   1.3269e-01
   3_bss:   1.555  0.012  0.102 15.989  0.006  4.107   1.3269e-01
   3_xyz:   1.061  0.008  0.073 14.896  0.004  4.109   6.9112e-02
   3_adp:   1.061  0.008  0.073 14.896  0.004  4.109   6.9112e-02
   3_occ:   1.061  0.008  0.073 14.896  0.004  4.109   6.9112e-02
   4_bss:   1.061  0.008  0.073 14.896  0.004  4.109   6.9112e-02
   4_xyz:   1.257  0.011  0.086 14.997  0.004  4.132   8.9938e-02
   4_adp:   1.257  0.011  0.086 14.997  0.004  4.132   8.9938e-02
   4_occ:   1.257  0.011  0.086 14.997  0.004  4.132   8.9938e-02
   5_bss:   1.257  0.011  0.086 14.997  0.004  4.132   8.9938e-02
   5_xyz:   1.118  0.009  0.081 14.725  0.004  4.130   7.1747e-02
   5_adp:   1.118  0.009  0.081 14.725  0.004  4.130   7.1747e-02
   5_occ:   1.118  0.009  0.081 14.725  0.004  4.130   7.1747e-02
   5_bss:   1.118  0.009  0.081 14.725  0.004  4.130   7.1747e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.535   2.4512e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.535   2.4512e-01
   1_xyz:  11.474  0.101  0.382 80.749  0.049  1.731   1.0567e-01
   1_adp:  11.474  0.101  0.382 80.749  0.049  1.731   1.0567e-01
   1_occ:  11.474  0.101  0.382 80.749  0.049  1.731   1.0567e-01
   2_bss:  11.474  0.101  0.382 80.749  0.049  1.731   1.0567e-01
   2_xyz:  11.127  0.071  0.348 84.771  0.038  2.136   1.0269e-01
   2_adp:  11.127  0.071  0.348 84.771  0.038  2.136   1.0269e-01
   2_occ:  11.127  0.071  0.348 84.771  0.038  2.136   1.0269e-01
   3_bss:  11.127  0.071  0.348 84.771  0.038  2.136   1.0269e-01
   3_xyz:   6.270  0.064  0.278 86.270  0.050  2.200   5.5100e-02
   3_adp:   6.270  0.064  0.278 86.270  0.050  2.200   5.5100e-02
   3_occ:   6.270  0.064  0.278 86.270  0.050  2.200   5.5100e-02
   4_bss:   6.270  0.064  0.278 86.270  0.050  2.200   5.5100e-02
   4_xyz:   8.758  0.057  0.265 83.947  0.034  2.160   7.3834e-02
   4_adp:   8.758  0.057  0.265 83.947  0.034  2.160   7.3834e-02
   4_occ:   8.758  0.057  0.265 83.947  0.034  2.160   7.3834e-02
   5_bss:   8.758  0.057  0.265 83.947  0.034  2.160   7.3834e-02
   5_xyz:   8.054  0.049  0.261 83.759  0.042  2.140   7.2755e-02
   5_adp:   8.054  0.049  0.261 83.759  0.042  2.140   7.2755e-02
   5_occ:   8.054  0.049  0.261 83.759  0.042  2.140   7.2755e-02
   5_bss:   8.054  0.049  0.261 83.759  0.042  2.140   7.2755e-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: 116.86   0.00  20.93 106.42   0.00  17.49 116.86   0.00  39.62
   1_occ: 116.86   0.00  20.93 106.42   0.00  17.49 116.86   0.00  39.62
   2_bss: 116.86   0.00  20.93 106.42   0.00  17.49 116.86   0.00  39.62
   2_xyz: 116.86   0.00  20.93 106.42   0.00  17.49 116.86   0.00  39.62
   2_adp: 114.07   0.00  19.68 103.34   0.00  16.00 114.07   0.00  39.72
   2_occ: 114.07   0.00  19.68 103.34   0.00  16.00 114.07   0.00  39.72
   3_bss: 114.07   0.00  19.68 103.34   0.00  16.00 114.07   0.00  39.72
   3_xyz: 114.07   0.00  19.68 103.34   0.00  16.00 114.07   0.00  39.72
   3_adp: 107.60   0.00  18.47  89.94   0.00  14.43 107.60   3.34  40.49
   3_occ: 107.60   0.00  18.47  89.94   0.00  14.43 107.60   3.34  40.49
   4_bss: 107.60   0.00  18.47  89.94   0.00  14.43 107.60   3.34  40.49
   4_xyz: 107.60   0.00  18.47  89.94   0.00  14.43 107.60   3.34  40.49
   4_adp: 104.35   0.00  18.79  91.32   0.00  13.78 104.35   4.61  46.04
   4_occ: 104.35   0.00  18.79  91.32   0.00  13.78 104.35   4.61  46.04
   5_bss: 104.35   0.00  18.79  91.32   0.00  13.78 104.35   4.61  46.04
   5_xyz: 104.35   0.00  18.79  91.32   0.00  13.78 104.35   4.61  46.04
   5_adp: 111.24   0.00  19.01 103.27   0.00  13.55 111.24   2.18  48.75
   5_occ: 111.24   0.00  19.01 103.27   0.00  13.55 111.24   2.18  48.75
   5_bss: 111.24   0.00  19.02 103.27   0.00  13.55 111.24   2.19  48.75
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    2.608    0.027    0.428
   1_adp:    2.608    0.027    0.428
   1_occ:    2.608    0.027    0.428
   2_bss:    2.608    0.027    0.428
   2_xyz:    2.278    0.035    0.684
   2_adp:    2.278    0.035    0.684
   2_occ:    2.278    0.035    0.684
   3_bss:    2.278    0.035    0.684
   3_xyz:    2.116    0.066    0.774
   3_adp:    2.116    0.066    0.774
   3_occ:    2.116    0.066    0.774
   4_bss:    2.116    0.066    0.774
   4_xyz:    1.789    0.083    0.916
   4_adp:    1.789    0.083    0.916
   4_occ:    1.789    0.083    0.916
   5_bss:    1.789    0.083    0.916
   5_xyz:    1.676    0.098    0.945
   5_adp:    1.676    0.098    0.945
   5_occ:    1.676    0.098    0.945
   5_bss:    1.676    0.098    0.945
------------------------------------------------------------------------

CPU time actual refinement: 357.01


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_362/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_362/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_362/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_362/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_362/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 356.84 
  Macro-tasks:
    bulk solvent and scale       = 48.93  
    individual site refinement   = 148.04 
    weights calculation          = 29.76  
    collect and process          = 6.23   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 233.07 
  Micro-tasks:
    mask                            = 2.43   
    f_calc                          = 113.23 
    alpha_beta                      = 8.17   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 122.72 
    fmodel                         = 7.99   
    r_factors                      = 0.15   
    phase_errors                   = 9.93   
    foms                           = 0.22   
    TOTAL for micro-tasks          = 265.97 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.010 micro seconds
Total CPU time: 6.17 minutes
from_scatterers_fft:    653 calls, 112.79 s
gradients_fft:          598 calls, 109.31 s

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

# Date 2008-01-16 Time 04:39:05 PST -0800 (1200487145.01 s)
Start R-work = 0.5006, R-free = 0.4999 (no bulk solvent and anisotropic scale)
Final R-work = 0.1548, R-free = 0.2027 (no bulk solvent and anisotropic scale)

Start R-work = 0.4942, R-free = 0.4904
Final R-work = 0.1325, R-free = 0.1854