# Date 2008-01-16 Time 05:41:27 PST -0800 (1200490887.20 s)
#phil __OFF__

Command line arguments: "../836.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 11739
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 836

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 48.1033, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 48.1033, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9851 1.95163
Completeness in resolution range: 0.913325
Completeness with d_max=infinity: 0.91065

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9851
                             d_min =   1.9516

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 48.1033, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9851 1.95163
Completeness in resolution range: 0.913325
Completeness with d_max=infinity: 0.91065

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9855 -  4.1772 [2256/2285]  2032   224   9.9%
  bin  2:  4.1772 -  3.3275 [2156/2179]  1940   216  10.0%
  bin  3:  3.3275 -  2.9104 [2128/2153]  1916   212  10.0%
  bin  4:  2.9104 -  2.6459 [2105/2138]  1898   207   9.8%
  bin  5:  2.6459 -  2.4571 [2107/2134]  1892   215  10.2%
  bin  6:  2.4571 -  2.3128 [2086/2114]  1883   203   9.7%
  bin  7:  2.3128 -  2.1973 [2075/2111]  1866   209  10.1%
  bin  8:  2.1973 -  2.1019 [2076/2118]  1866   210  10.1%
  bin  9:  2.1019 -  2.0212 [1958/2097]  1760   198  10.1%
  bin 10:  2.0212 -  1.9516 [ 642/2119]   577    65  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_836/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.30 -     2.02: 19
        2.02 -     2.74: 296
        2.74 -     3.46: 4579
        3.46 -     4.18: 9430
        4.18 -     4.90: 14012
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   TYR A 214 " - " O   HOH Z 204 "  1.303 3.040 -x+1/2,-y+1,z-1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.339 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.422 3.040 -x+1/2,-y+1,z+1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.468 3.120 -x+1/2,-y+1,z-1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.469 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28331 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_836/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_836/model_refine_001.geo

CPU time processing inputs: 9.07


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 48.10325 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4791   r_free= 0.4667   ksol= 0.00   Bsol= 0.00   scale= 0.880    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.293239                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9855 -  4.6595 0.99   1462  164 0.3894 0.4052       6.602      6.6112|
|  2:  4.6595 -  3.7170 0.99   1402  154 0.4281 0.4214      6.8502      6.8435|
|  3:  3.7170 -  3.2526 0.99   1379  150 0.4538 0.4158      6.6743      6.6812|
|  4:  3.2526 -  2.9577 0.98   1365  160 0.4740 0.4582      6.5296      6.4939|
|  5:  2.9577 -  2.7471 0.99   1368  148 0.5033 0.4616      6.3721      6.3218|
|  6:  2.7471 -  2.5860 0.99   1347  156 0.5199 0.4598       6.283      6.1681|
|  7:  2.5860 -  2.4571 0.98   1355  142 0.4955 0.4812      6.2376      6.2023|
|  8:  2.4571 -  2.3506 0.98   1336  143 0.5243 0.5368      6.1501      6.2162|
|  9:  2.3506 -  2.2604 0.98   1329  151 0.5402 0.5130      6.1353      6.1047|
| 10:  2.2604 -  2.1826 0.99   1359  154 0.5085 0.5342      6.0793      6.1262|
| 11:  2.1826 -  2.1146 0.98   1308  143 0.5248 0.5530      6.0192      5.9849|
| 12:  2.1146 -  2.0543 0.97   1345  140 0.5095 0.5390      5.9227      5.9887|
| 13:  2.0543 -  2.0003 0.76   1007  126 0.5314 0.4267      5.8722      5.8286|
| 14:  2.0003 -  1.9516 0.20    268   28 0.5910 0.4825       5.821      5.7241|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9855 -  4.6595  1462   164  0.66  37.61   0.82     0.70      84132.86|
|  2:  4.6595 -  3.7170  1402   154  0.67  37.95   0.89     0.76     115210.65|
|  3:  3.7170 -  3.2526  1379   150  0.57  46.54   0.90     0.75     120859.32|
|  4:  3.2526 -  2.9577  1365   160  0.49  52.71   0.89     0.69     105016.15|
|  5:  2.9577 -  2.7471  1368   148  0.44  56.60   0.86     0.64      80330.81|
|  6:  2.7471 -  2.5860  1347   156  0.43  57.45   0.88     0.61      65663.93|
|  7:  2.5860 -  2.4571  1355   142  0.42  58.53   0.92     0.56      59521.60|
|  8:  2.4571 -  2.3506  1336   143  0.34  64.48   0.88     0.51      60044.23|
|  9:  2.3506 -  2.2604  1329   151  0.31  66.60   0.90     0.48      56434.48|
| 10:  2.2604 -  2.1826  1359   154  0.29  68.24   0.95     0.45      54444.69|
| 11:  2.1826 -  2.1146  1308   143  0.27  69.92   0.92     0.40      49202.99|
| 12:  2.1146 -  2.0543  1345   140  0.23  73.03   0.94     0.39      47479.11|
| 13:  2.0543 -  2.0003  1007   126  0.25  71.23   0.92     0.41      39230.63|
| 14:  2.0003 -  1.9516   268    28  0.29  67.96   0.86     0.49      32331.83|
|alpha:            min =        0.39 max =            0.76 mean =         0.57|
|beta:             min =    32331.83 max =       120859.32 mean =     72554.24|
|figures of merit: min =        0.00 max =            1.00 mean =         0.42|
|phase err.(work): min =        0.00 max =           89.98 mean =        58.16|
|phase err.(test): min =        0.00 max =           89.96 mean =        58.20|
|-----------------------------------------------------------------------------|

============================== 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 = 18.503907             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.100   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.224910              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.198   (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 |  1.303 -  1.663:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.663 -  2.022:       13 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.022 -  2.382:       33 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.382 -  2.742:      263 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.742 -  3.101:     2311 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.101 -  3.461:     2268 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.461 -  3.821:     4272 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.821 -  4.181:     5158 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.181 -  4.540:     6309 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.540 -  4.900:     7703 |
|-----------------------------------------------------------------------------|
|-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 |        0.207 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.303 |       0.839 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.887)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4791   r_free= 0.4667   ksol= 0.00   Bsol= 0.00   scale= 0.880    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.293239                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4696   r_free= 0.4555   ksol= 0.30   Bsol= 20.00   scale= 0.918   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.95,3.77,1.23,0.00,0.00,0.00); trace/3= 0.68                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.288519                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.017394             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.784   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.384621              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.040   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4696      final r-factor (work) = 0.3832          |
| start r-factor (free) = 0.4555      final r-factor (free) = 0.4244          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 47.4024 = 15.02 * 0.50 * 6.2854 + 1.00 * 0.2074                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 46.6163 = 15.02 * 0.50 * 6.1852 + 1.00 * 0.1738                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3832      final r-factor (work) = 0.3541          |
| start r-factor (free) = 0.4244      final r-factor (free) = 0.4289          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.5703 = 1.38 * 1.00 * 6.1852 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.5015 = 1.38 * 1.00 * 6.1209 + 1.00 * 0.0264                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.887)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.54  18.08    None  None   None       |
|    all(noH): 2823   0      0.00    115.54  18.08    None  None   None       |
|    Sol.    : 438    0      0.00    70.85   36.48    None  None   None       |
|    Mac.    : 2385   0      0.00    115.54  14.70    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 -  11.554: 1058   |   5:    57.770 -  69.325:   19        |
|      1:    11.554 -  23.108:  956   |   6:    69.325 -  80.879:    1        |
|      2:    23.108 -  34.662:  461   |   7:    80.879 -  92.433:    0        |
|      3:    34.662 -  46.216:  217   |   8:    92.433 - 103.987:    0        |
|      4:    46.216 -  57.770:  110   |   9:   103.987 - 115.541:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3541 r_free = 0.4289             target_work(ml) = 6.123         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3539 r_free = 0.4290             target_work(ml) = 6.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3539   r_free= 0.4290   ksol= 0.30   Bsol= 20.00   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.95,3.77,1.23,0.00,0.00,0.00); trace/3= 0.68                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.122547                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3522   r_free= 0.4256   ksol= 0.33   Bsol= 54.82   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.34,2.09,0.27,0.00,0.00,0.00); trace/3= 0.34                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.122630                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.099200             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.413  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.366006              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 113.582  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3522      final r-factor (work) = 0.2741          |
| start r-factor (free) = 0.4256      final r-factor (free) = 0.3363          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 49.4549 = 16.10 * 0.50 * 6.1222 + 1.00 * 0.1735                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 48.7478 = 16.10 * 0.50 * 6.0386 + 1.00 * 0.1399                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2741      final r-factor (work) = 0.2477          |
| start r-factor (free) = 0.3363      final r-factor (free) = 0.3250          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2705 = 1.37 * 1.00 * 6.0386 + 1.00 * 0.0218                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0384 = 1.37 * 1.00 * 5.8709 + 1.00 * 0.0187                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.887)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.76  19.24    None  None   None       |
|    all(noH): 2823   0      0.00    109.76  19.24    None  None   None       |
|    Sol.    : 438    0      2.75    109.76  42.65    None  None   None       |
|    Mac.    : 2385   0      0.00    91.82   14.94    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 -  10.976: 1129   |   5:    54.880 -  65.856:   88        |
|      1:    10.976 -  21.952:  882   |   6:    65.856 -  76.832:   43        |
|      2:    21.952 -  32.928:  332   |   7:    76.832 -  87.808:   17        |
|      3:    32.928 -  43.904:  185   |   8:    87.808 -  98.784:   15        |
|      4:    43.904 -  54.880:  131   |   9:    98.784 - 109.760:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2477 r_free = 0.3250             target_work(ml) = 5.855         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2476 r_free = 0.3245             target_work(ml) = 5.855         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2476   r_free= 0.3245   ksol= 0.33   Bsol= 54.82   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.34,2.09,0.27,0.00,0.00,0.00); trace/3= 0.34                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.854902                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2470   r_free= 0.3233   ksol= 0.32   Bsol= 59.41   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.99,1.13,-0.35,0.00,-0.00,-0.00); trace/3= -0.07                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.851059                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.971543              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.100  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.235804              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.558  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2470      final r-factor (work) = 0.2069          |
| start r-factor (free) = 0.3233      final r-factor (free) = 0.2673          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.7320 = 4.97 * 0.50 * 5.8703 + 1.00 * 0.1399                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.4521 = 4.97 * 0.50 * 5.7875 + 1.00 * 0.0657                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2069      final r-factor (work) = 0.1966          |
| start r-factor (free) = 0.2673      final r-factor (free) = 0.2438          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3833 = 0.24 * 1.00 * 5.7875 + 1.00 * 0.0186                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3444 = 0.24 * 1.00 * 5.6620 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.887)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.45   17.51    None  None   None       |
|    all(noH): 2823   0      0.00    98.45   17.51    None  None   None       |
|    Sol.    : 438    0      5.12    98.45   40.40    None  None   None       |
|    Mac.    : 2385   0      0.00    86.78   13.30    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.845: 1084   |   5:    49.224 -  59.068:   79        |
|      1:     9.845 -  19.690:  982   |   6:    59.068 -  68.913:   44        |
|      2:    19.690 -  29.534:  291   |   7:    68.913 -  78.758:   13        |
|      3:    29.534 -  39.379:  169   |   8:    78.758 -  88.603:   17        |
|      4:    39.379 -  49.224:  142   |   9:    88.603 -  98.447:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1966 r_free = 0.2438             target_work(ml) = 5.624         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1964 r_free = 0.2436             target_work(ml) = 5.623         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1964   r_free= 0.2436   ksol= 0.32   Bsol= 59.41   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.99,1.13,-0.35,0.00,-0.00,-0.00); trace/3= -0.07                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.623273                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1964   r_free= 0.2429   ksol= 0.32   Bsol= 57.32   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.74,0.13,-1.18,0.00,-0.00,-0.00); trace/3= -0.93                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.624494                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.731531              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.752  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.630368              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.149  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1964      final r-factor (work) = 0.1498          |
| start r-factor (free) = 0.2429      final r-factor (free) = 0.1926          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.4666 = 4.73 * 0.50 * 5.6645 + 1.00 * 0.0657                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.1077 = 4.73 * 0.50 * 5.5085 + 1.00 * 0.0759                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1498      final r-factor (work) = 0.1370          |
| start r-factor (free) = 0.1926      final r-factor (free) = 0.1856          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4816 = 0.63 * 1.00 * 5.5085 + 1.00 * 0.0093                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3776 = 0.63 * 1.00 * 5.3398 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.887)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.75    100.96  17.80    None  None   None       |
|    all(noH): 2823   0      0.75    100.96  17.80    None  None   None       |
|    Sol.    : 438    0      4.47    95.74   44.99    None  None   None       |
|    Mac.    : 2385   0      0.75    100.96  12.80    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:     0.751 -  10.772: 1295   |   5:    50.856 -  60.878:  104        |
|      1:    10.772 -  20.793:  897   |   6:    60.878 -  70.899:   54        |
|      2:    20.793 -  30.814:  200   |   7:    70.899 -  80.920:   31        |
|      3:    30.814 -  40.835:  107   |   8:    80.920 -  90.941:   18        |
|      4:    40.835 -  50.856:  109   |   9:    90.941 - 100.962:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1370 r_free = 0.1856             target_work(ml) = 5.318         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1368 r_free = 0.1855             target_work(ml) = 5.318         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1368   r_free= 0.1855   ksol= 0.32   Bsol= 57.32   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.74,0.13,-1.18,0.00,-0.00,-0.00); trace/3= -0.93                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.317719                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1370   r_free= 0.1863   ksol= 0.33   Bsol= 60.51   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,-0.64,-1.48,-0.00,-0.00,-0.00); trace/3= -1.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.320503                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.613881              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 127.653  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.245647              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.956  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1370      final r-factor (work) = 0.1271          |
| start r-factor (free) = 0.1863      final r-factor (free) = 0.1769          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0580 = 2.61 * 0.50 * 5.3423 + 1.00 * 0.0759                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9771 = 2.61 * 0.50 * 5.2907 + 1.00 * 0.0625                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1271      final r-factor (work) = 0.1258          |
| start r-factor (free) = 0.1769      final r-factor (free) = 0.1733          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3111 = 0.25 * 1.00 * 5.2907 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3145 = 0.25 * 1.00 * 5.2580 + 1.00 * 0.0229                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.887)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.09   17.01    None  None   None       |
|    all(noH): 2823   0      0.00    99.09   17.01    None  None   None       |
|    Sol.    : 438    0      4.84    99.09   42.00    None  None   None       |
|    Mac.    : 2385   0      0.00    97.64   12.43    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.909: 1143   |   5:    49.547 -  59.456:   81        |
|      1:     9.909 -  19.819: 1053   |   6:    59.456 -  69.365:   50        |
|      2:    19.819 -  29.728:  212   |   7:    69.365 -  79.275:   21        |
|      3:    29.728 -  39.637:  123   |   8:    79.275 -  89.184:   10        |
|      4:    39.637 -  49.547:  120   |   9:    89.184 -  99.093:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1258 r_free = 0.1733             target_work(ml) = 5.251         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1256 r_free = 0.1731             target_work(ml) = 5.250         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1256   r_free= 0.1731   ksol= 0.33   Bsol= 60.51   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,-0.64,-1.48,-0.00,-0.00,-0.00); trace/3= -1.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.250330                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9855 -  4.6595 0.99   1462  164 0.1011 0.1343      5.4119      5.5899|
|  2:  4.6595 -  3.7170 0.99   1402  154 0.0908 0.1121      5.4764      5.6763|
|  3:  3.7170 -  3.2526 0.99   1379  150 0.1172 0.1764      5.5579      5.9426|
|  4:  3.2526 -  2.9577 0.98   1365  160 0.1472 0.1880      5.5756      5.7564|
|  5:  2.9577 -  2.7471 0.99   1368  148 0.1527 0.1867      5.4373      5.5582|
|  6:  2.7471 -  2.5860 0.99   1347  156 0.1431 0.2202      5.3341      5.5635|
|  7:  2.5860 -  2.4571 0.98   1355  142 0.1400 0.1818      5.2697      5.4306|
|  8:  2.4571 -  2.3506 0.98   1336  143 0.1420 0.1907      5.1923      5.4176|
|  9:  2.3506 -  2.2604 0.98   1329  151 0.1310 0.1921      5.1036      5.3267|
| 10:  2.2604 -  2.1826 0.99   1359  154 0.1296 0.1831      5.0657      5.3266|
| 11:  2.1826 -  2.1146 0.98   1308  143 0.1229 0.1929      4.9908      5.2522|
| 12:  2.1146 -  2.0543 0.97   1345  140 0.1295 0.1963      4.9417      5.1725|
| 13:  2.0543 -  2.0003 0.76   1007  126 0.1253 0.1844      4.8526      5.1178|
| 14:  2.0003 -  1.9516 0.20    268   28 0.1219 0.1721      4.7375      4.9483|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9855 -  4.6595  1462   164  0.94   9.50   0.97     0.94       7516.11|
|  2:  4.6595 -  3.7170  1402   154  0.95   8.81   1.01     1.00       9922.10|
|  3:  3.7170 -  3.2526  1379   150  0.92  13.26   1.02     1.02      12525.99|
|  4:  3.2526 -  2.9577  1365   160  0.90  16.53   1.01     0.99      13105.33|
|  5:  2.9577 -  2.7471  1368   148  0.87  19.18   1.00     0.98      10772.02|
|  6:  2.7471 -  2.5860  1347   156  0.88  18.58   0.98     0.96       9053.47|
|  7:  2.5860 -  2.4571  1355   142  0.89  17.73   0.99     0.95       7714.29|
|  8:  2.4571 -  2.3506  1336   143  0.88  18.88   1.00     0.96       6960.99|
|  9:  2.3506 -  2.2604  1329   151  0.89  17.78   1.00     0.96       5922.52|
| 10:  2.2604 -  2.1826  1359   154  0.89  17.48   0.99     0.95       5430.08|
| 11:  2.1826 -  2.1146  1308   143  0.89  17.65   0.99     0.96       4975.52|
| 12:  2.1146 -  2.0543  1345   140  0.89  17.85   0.98     0.96       4513.01|
| 13:  2.0543 -  2.0003  1007   126  0.88  18.24   0.99     0.98       3870.44|
| 14:  2.0003 -  1.9516   268    28  0.88  17.87   0.98     0.95       3106.50|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     3106.50 max =        13105.33 mean =      7901.53|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.90 mean =        16.18|
|phase err.(test): min =        0.00 max =           89.45 mean =        15.58|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1256   r_free= 0.1730   ksol= 0.32   Bsol= 55.10   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.95,-0.82,-1.46,-0.00,-0.00,-0.00); trace/3= -1.41                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.250143                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1256   r_free= 0.1730   ksol= 0.32   Bsol= 55.10   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.95,-0.82,-1.46,-0.00,-0.00,-0.00); trace/3= -1.41                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.250143                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9855 -  4.6595 0.99   1462  164 0.1009 0.1339      5.4109       5.587|
|  2:  4.6595 -  3.7170 0.99   1402  154 0.0904 0.1114      5.4732      5.6705|
|  3:  3.7170 -  3.2526 0.99   1379  150 0.1172 0.1761      5.5556      5.9425|
|  4:  3.2526 -  2.9577 0.98   1365  160 0.1473 0.1879      5.5757      5.7559|
|  5:  2.9577 -  2.7471 0.99   1368  148 0.1528 0.1864      5.4376      5.5576|
|  6:  2.7471 -  2.5860 0.99   1347  156 0.1431 0.2201      5.3344      5.5643|
|  7:  2.5860 -  2.4571 0.98   1355  142 0.1402 0.1819      5.2704      5.4308|
|  8:  2.4571 -  2.3506 0.98   1336  143 0.1420 0.1910       5.193      5.4196|
|  9:  2.3506 -  2.2604 0.98   1329  151 0.1308 0.1923      5.1041      5.3274|
| 10:  2.2604 -  2.1826 0.99   1359  154 0.1296 0.1829      5.0665       5.327|
| 11:  2.1826 -  2.1146 0.98   1308  143 0.1229 0.1931      4.9906       5.252|
| 12:  2.1146 -  2.0543 0.97   1345  140 0.1297 0.1967      4.9426       5.174|
| 13:  2.0543 -  2.0003 0.76   1007  126 0.1252 0.1844      4.8528      5.1172|
| 14:  2.0003 -  1.9516 0.20    268   28 0.1220 0.1724      4.7376      4.9477|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9855 -  4.6595  1462   164  0.94   9.49   0.97     0.94       7499.38|
|  2:  4.6595 -  3.7170  1402   154  0.95   8.77   1.01     1.00       9853.13|
|  3:  3.7170 -  3.2526  1379   150  0.92  13.19   1.02     1.02      12428.96|
|  4:  3.2526 -  2.9577  1365   160  0.90  16.51   1.01     0.99      13090.24|
|  5:  2.9577 -  2.7471  1368   148  0.87  19.16   1.00     0.98      10755.69|
|  6:  2.7471 -  2.5860  1347   156  0.88  18.57   0.98     0.95       9050.65|
|  7:  2.5860 -  2.4571  1355   142  0.89  17.73   0.98     0.95       7717.50|
|  8:  2.4571 -  2.3506  1336   143  0.88  18.91   1.00     0.96       6977.14|
|  9:  2.3506 -  2.2604  1329   151  0.89  17.80   0.99     0.96       5941.67|
| 10:  2.2604 -  2.1826  1359   154  0.89  17.50   0.99     0.95       5439.71|
| 11:  2.1826 -  2.1146  1308   143  0.89  17.66   0.99     0.95       4977.66|
| 12:  2.1146 -  2.0543  1345   140  0.89  17.86   0.98     0.96       4520.06|
| 13:  2.0543 -  2.0003  1007   126  0.88  18.25   0.99     0.98       3872.40|
| 14:  2.0003 -  1.9516   268    28  0.88  17.87   0.98     0.94       3101.77|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     3101.77 max =        13090.24 mean =      7888.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.99 mean =        16.17|
|phase err.(test): min =        0.00 max =           89.63 mean =        15.58|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.887)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.10   17.02    None  None   None       |
|    all(noH): 2823   0      0.00    99.10   17.02    None  None   None       |
|    Sol.    : 438    0      4.85    99.10   42.00    None  None   None       |
|    Mac.    : 2385   0      0.00    97.64   12.43    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.912: 1143   |   5:    49.550 -  59.459:   81        |
|      1:     9.912 -  19.822: 1053   |   6:    59.459 -  69.368:   50        |
|      2:    19.822 -  29.731:  212   |   7:    69.368 -  79.278:   21        |
|      3:    29.731 -  39.640:  123   |   8:    79.278 -  89.187:   10        |
|      4:    39.640 -  49.550:  120   |   9:    89.187 -  99.096:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 349         
Filter by distance & map next to the model:
   mapped sites are within: 0.629 - 5.548
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 344 from: 349
   mapped sites are within: 0.751 - 5.548

peak=    5.575 closest distance to " NH2 ARG A  56 " =    2.428
peak=    5.551 closest distance to " O   HOH Z 120 " =    1.116
peak=    5.540 closest distance to " O   HOH Z 210 " =    1.616
peak=    5.388 closest distance to " O   HOH Z 142 " =    1.599
peak=    5.293 closest distance to " CG  PRO A  54 " =    1.270
peak=    5.260 closest distance to " O   HOH Z 132 " =    1.674
peak=    5.213 closest distance to " CB  SER A  63 " =    1.260
peak=    5.187 closest distance to " O   HOH Z 352 " =    1.356
peak=    5.060 closest distance to " O   HOH Z 374 " =    1.139
peak=    5.001 closest distance to " O   HOH Z 126 " =    2.057
peak=    4.974 closest distance to " O   HOH Z 211 " =    1.611
peak=    4.919 closest distance to " O   HOH Z  15 " =    1.990
peak=    4.916 closest distance to " O   PRO A 198 " =    1.586
peak=    4.914 closest distance to " O   HOH Z 271 " =    1.809
peak=    4.836 closest distance to " CG  PRO A 198 " =    1.287
peak=    4.835 closest distance to " O   HOH Z 133 " =    1.879
peak=    4.835 closest distance to " CA  TYR A  30 " =    1.014
peak=    4.804 closest distance to " CB  GLN A 223 " =    1.439
peak=    4.787 closest distance to " CG  PRO A 280 " =    0.788
peak=    4.732 closest distance to " CG  PRO A  90 " =    1.272
peak=    4.730 closest distance to " CG  PRO A 213 " =    1.341
peak=    4.725 closest distance to " O   HOH Z 134 " =    2.295
peak=    4.687 closest distance to " O   HOH Z 433 " =    1.803
peak=    4.633 closest distance to " O   HOH Z  97 " =    1.923
peak=    4.563 closest distance to " O   HOH Z 124 " =    1.537
peak=    4.548 closest distance to " O   HOH Z 196 " =    2.196
peak=    4.492 closest distance to " O   HOH Z 247 " =    1.483
peak=    4.486 closest distance to " O   HOH Z  80 " =    2.137
peak=    4.461 closest distance to " CB  TRP A 179 " =    1.193
peak=    4.395 closest distance to " O   HOH Z  48 " =    1.840
peak=    4.387 closest distance to " CB  ARG A 275 " =    0.930
peak=    4.367 closest distance to " O   HOH Z  39 " =    1.894
peak=    4.352 closest distance to " O   HOH Z 163 " =    1.737
peak=    4.319 closest distance to " O   HOH Z 369 " =    2.109
peak=    4.306 closest distance to " CG  GLN A  77 " =    0.862
peak=    4.303 closest distance to " CB  SER A   3 " =    1.374
peak=    4.295 closest distance to " O   HOH Z 422 " =    1.070
peak=    4.283 closest distance to " O   HOH Z 234 " =    3.812
peak=    4.262 closest distance to " CB  PRO A  54 " =    0.784
peak=    4.246 closest distance to " CB  SER A 141 " =    1.052
peak=    4.244 closest distance to " O   HOH Z 350 " =    1.068
peak=    4.219 closest distance to " CB  LEU A 228 " =    1.125
peak=    4.191 closest distance to " N   ASN A  39 " =    1.271
peak=    4.186 closest distance to " CB  GLN A 183 " =    1.352
peak=    4.181 closest distance to " O   HOH Z 412 " =    3.038
peak=    4.158 closest distance to " O   HOH Z 130 " =    2.869
peak=    4.157 closest distance to " O   HOH Z  47 " =    1.578
peak=    4.129 closest distance to " O   HOH Z 326 " =    1.538
peak=    4.101 closest distance to " O   HOH Z  11 " =    1.385
peak=    4.095 closest distance to " O   HOH Z 298 " =    1.925
peak=    4.093 closest distance to " O   HOH Z 221 " =    1.346
peak=    4.090 closest distance to " O   HOH Z 389 " =    2.022
peak=    4.081 closest distance to " O   HOH Z  24 " =    1.948
peak=    4.077 closest distance to " O   HOH Z 108 " =    1.558
peak=    4.043 closest distance to " O   HOH Z 394 " =    1.645
peak=    4.036 closest distance to " CB  GLU A 152 " =    1.111
peak=    4.013 closest distance to " O   HOH Z  63 " =    2.016
peak=    4.012 closest distance to " O   HOH Z  67 " =    1.927
peak=    4.006 closest distance to " OE1 GLN A  11 " =    1.928
peak=    3.995 closest distance to " CB  SER A  62 " =    0.793
peak=    3.994 closest distance to " O   HOH Z 193 " =    1.697
peak=    3.992 closest distance to " O   HOH Z  44 " =    2.406
peak=    3.990 closest distance to " O   HOH Z 189 " =    1.850
peak=    3.985 closest distance to " CB  GLN A 194 " =    0.859
peak=    3.974 closest distance to " O   HOH Z 250 " =    2.354
peak=    3.973 closest distance to " CG2 THR A 221 " =    1.123
peak=    3.964 closest distance to " O   HOH Z 118 " =    1.971
peak=    3.958 closest distance to " O   HOH Z 156 " =    3.491
peak=    3.951 closest distance to " O   HOH Z  20 " =    1.820
peak=    3.932 closest distance to " O   HOH Z  43 " =    1.903
peak=    3.914 closest distance to " CD2 LEU A 297 " =    0.953
peak=    3.908 closest distance to " C   SER A  32 " =    1.103
peak=    3.894 closest distance to " O   ALA A 165 " =    1.204
peak=    3.880 closest distance to " CB  GLN A  58 " =    0.922
peak=    3.843 closest distance to " CB  ARG A 139 " =    1.007
peak=    3.838 closest distance to " O   HOH Z 437 " =    1.994
peak=    3.832 closest distance to " O   HOH Z  44 " =    1.784
peak=    3.832 closest distance to " O   HOH Z  61 " =    1.596
peak=    3.831 closest distance to " OD1 ASN A  60 " =    1.043
peak=    3.822 closest distance to " CB  ASN A 148 " =    1.301
peak=    3.820 closest distance to " O   HOH Z 406 " =    1.439
peak=    3.814 closest distance to " CB  ARG A  79 " =    1.368
peak=    3.813 closest distance to " CB  GLU A 128 " =    1.092
peak=    3.813 closest distance to " O   HOH Z 357 " =    1.954
peak=    3.811 closest distance to " O   HOH Z 336 " =    1.626
peak=    3.810 closest distance to " O   SER A  87 " =    2.231
peak=    3.808 closest distance to " CB  ALA A 100 " =    1.430
peak=    3.808 closest distance to " O   HOH Z   7 " =    0.984
peak=    3.807 closest distance to " CA  GLU A 152 " =    0.934
peak=    3.801 closest distance to " CE  LYS A 119 " =    1.177
peak=    3.796 closest distance to " O   HOH Z 324 " =    1.572
peak=    3.790 closest distance to " CB  TRP A 179 " =    1.580
peak=    3.789 closest distance to " CB  TYR A 169 " =    0.911
peak=    3.787 closest distance to " O   HOH Z 132 " =    2.279
peak=    3.778 closest distance to " O   HOH Z 174 " =    2.186
peak=    3.777 closest distance to " CA  ARG A  36 " =    1.046
peak=    3.768 closest distance to " CA  GLN A 223 " =    0.858
peak=    3.765 closest distance to " OG  SER A  62 " =    3.236
peak=    3.759 closest distance to " CB  VAL A 202 " =    1.520
peak=    3.759 closest distance to " O   HOH Z  78 " =    2.332
peak=    3.753 closest distance to " O   HOH Z 279 " =    2.127
peak=    3.752 closest distance to " CG1 VAL A 153 " =    1.138
peak=    3.733 closest distance to " CB  ARG A 190 " =    1.667
peak=    3.730 closest distance to " O   HOH Z 301 " =    1.588
peak=    3.728 closest distance to " O   HOH Z 374 " =    2.563
peak=    3.727 closest distance to " O   HOH Z 260 " =    1.369
peak=    3.716 closest distance to " O   HOH Z   6 " =    1.941
peak=    3.704 closest distance to " CD  LYS A 119 " =    1.422
peak=    3.699 closest distance to " CG1 ILE A  33 " =    1.209
peak=    3.697 closest distance to " O   HOH Z 331 " =    1.430
peak=    3.696 closest distance to " O   HOH Z  54 " =    1.759
peak=    3.687 closest distance to " O   HOH Z 404 " =    1.494
peak=    3.684 closest distance to " O   HOH Z 316 " =    3.034
peak=    3.674 closest distance to " CA  ALA A  21 " =    1.322
peak=    3.673 closest distance to " CG2 VAL A  78 " =    0.983
peak=    3.669 closest distance to " O   HOH Z  88 " =    3.612
peak=    3.668 closest distance to " CH2 TRP A 274 " =    2.013
peak=    3.661 closest distance to " O   HOH Z 150 " =    1.920
peak=    3.661 closest distance to " O   HOH Z 387 " =    2.419
peak=    3.660 closest distance to " O   HOH Z 128 " =    2.281
peak=    3.659 closest distance to " O   GLY A  91 " =    1.274
peak=    3.652 closest distance to " CD  ARG A 159 " =    0.841
peak=    3.646 closest distance to " O   HOH Z 362 " =    3.394
peak=    3.644 closest distance to " CB AVAL A  41 " =    0.930
peak=    3.641 closest distance to " O   HOH Z 408 " =    1.987
peak=    3.641 closest distance to " CB  GLU A 277 " =    3.682
peak=    3.632 closest distance to " O   HOH Z 245 " =    1.305
peak=    3.629 closest distance to " OD2 ASP A 286 " =    2.863
peak=    3.626 closest distance to " CD1 LEU A 300 " =    1.247
peak=    3.616 closest distance to " CB  PRO A 198 " =    0.883
peak=    3.615 closest distance to " CD2 LEU A 255 " =    1.082
peak=    3.607 closest distance to " NZ  LYS A 117 " =    3.230
peak=    3.600 closest distance to " CD BLYS A 290 " =    1.011
peak=    3.600 closest distance to " O   HOH Z 214 " =    1.054
peak=    3.593 closest distance to " NH2 ARG A 156 " =    1.247
peak=    3.593 closest distance to " CA  GLY A 196 " =    1.128
peak=    3.592 closest distance to " NH2AARG A 145 " =    2.067
peak=    3.591 closest distance to " O   HOH Z 261 " =    2.007
peak=    3.590 closest distance to " NZ  LYS A 119 " =    1.695
peak=    3.590 closest distance to " O   HOH Z 203 " =    1.687
peak=    3.590 closest distance to " CA  ASP A 191 " =    0.856
peak=    3.589 closest distance to " O   HOH Z 154 " =    1.485
peak=    3.585 closest distance to " O   GLY A 211 " =    1.361
peak=    3.583 closest distance to " CB  PHE A  16 " =    1.262
peak=    3.582 closest distance to " NE2 GLN A  11 " =    1.082
peak=    3.582 closest distance to " O   HOH Z 416 " =    1.213
peak=    3.579 closest distance to " CB  PRO A  54 " =    1.302
peak=    3.576 closest distance to " O   HOH Z 402 " =    1.667
peak=    3.576 closest distance to " O   HOH Z 428 " =    1.150
peak=    3.576 closest distance to " O   HOH Z 346 " =    1.599
peak=    3.572 closest distance to " CB  GLN A  73 " =    1.020
peak=    3.572 closest distance to " CB  ASN A 187 " =    1.197
peak=    3.571 closest distance to " O   HOH Z  93 " =    3.609
peak=    3.571 closest distance to " CA  ALA A 160 " =    0.968
peak=    3.569 closest distance to " O   HOH Z 403 " =    1.912
peak=    3.566 closest distance to " O   HOH Z  22 " =    2.398
peak=    3.561 closest distance to " CA  ALA A  51 " =    0.826
peak=    3.552 closest distance to " O   HOH Z 287 " =    1.812
peak=    3.549 closest distance to " O   HOH Z 409 " =    3.312
peak=    3.548 closest distance to " O   HOH Z 426 " =    1.427
peak=    3.545 closest distance to " O   HOH Z 195 " =    1.399
peak=    3.541 closest distance to " O   HOH Z 358 " =    1.355
peak=    3.537 closest distance to " O   HOH Z  48 " =    3.063
peak=    3.532 closest distance to " CG  ARG A  66 " =    0.843
peak=    3.521 closest distance to " O   HOH Z 431 " =    1.252
peak=    3.519 closest distance to " O   HOH Z   4 " =    1.272
peak=    3.517 closest distance to " O   HOH Z  64 " =    1.880
peak=    3.517 closest distance to " CG  GLN A  11 " =    1.308
peak=    3.514 closest distance to " CA  ARG A 195 " =    1.081
peak=    3.512 closest distance to " O   HOH Z 215 " =    1.314
peak=    3.510 closest distance to " O   HOH Z 380 " =    1.915
peak=    3.507 closest distance to " O   HOH Z 225 " =    1.981
peak=    3.502 closest distance to " CA  ASN A 176 " =    1.512
peak=    3.498 closest distance to " O   HOH Z 344 " =    2.993
peak=    3.497 closest distance to " N   SER A 164 " =    0.956
peak=    3.495 closest distance to " CA  ILE A 263 " =    0.978
peak=    3.492 closest distance to " O   HOH Z  33 " =    1.741
peak=    3.482 closest distance to " O   HOH Z 102 " =    1.263
peak=    3.478 closest distance to " O   HOH Z 334 " =    1.666
peak=    3.471 closest distance to " O   HOH Z  21 " =    1.907
peak=    3.466 closest distance to " CB  LEU A 261 " =    1.209
peak=    3.464 closest distance to " O   HOH Z 280 " =    2.306
peak=    3.462 closest distance to " O   HOH Z  28 " =    2.326
peak=    3.457 closest distance to " CB  ASN A 285 " =    0.910
peak=    3.452 closest distance to " O   HOH Z 402 " =    2.889
peak=    3.452 closest distance to " CB  ARG A 275 " =    1.244
peak=    3.451 closest distance to " O   HOH Z 432 " =    1.947
peak=    3.446 closest distance to " CB  MET A 105 " =    1.181
peak=    3.444 closest distance to " O   HOH Z 345 " =    1.850
peak=    3.441 closest distance to " NH2BARG A 145 " =    1.915
peak=    3.441 closest distance to " CD  ARG A 269 " =    0.939
peak=    3.441 closest distance to " O   HOH Z 271 " =    1.864
peak=    3.439 closest distance to " O   HOH Z 313 " =    2.159
peak=    3.439 closest distance to " O   HOH Z 403 " =    1.404
peak=    3.438 closest distance to " NH2BARG A 102 " =    0.965
peak=    3.437 closest distance to " CG1 ILE A 120 " =    1.162
peak=    3.435 closest distance to " CB  GLN A  88 " =    1.119
peak=    3.434 closest distance to " O   HOH Z  49 " =    1.245
peak=    3.434 closest distance to " O   HOH Z 142 " =    1.782
peak=    3.433 closest distance to " ND1 HIS A  81 " =    1.377
peak=    3.432 closest distance to " CG2 VAL A 197 " =    1.239
peak=    3.431 closest distance to " CA  PRO A  90 " =    0.968
peak=    3.427 closest distance to " O   HOH Z 109 " =    2.159
peak=    3.426 closest distance to " NH1AARG A 145 " =    0.996
peak=    3.422 closest distance to " O   HOH Z 272 " =    1.910
peak=    3.417 closest distance to " OD1 ASN A  69 " =    2.287
peak=    3.413 closest distance to " CG  PRO A 243 " =    1.170
peak=    3.407 closest distance to " O   HOH Z 250 " =    1.405
peak=    3.404 closest distance to " O   HOH Z 192 " =    1.554
peak=    3.402 closest distance to " CB  PRO A  90 " =    1.183
peak=    3.400 closest distance to " CG2 THR A 220 " =    0.822
peak=    3.398 closest distance to " CB  SER A 216 " =    0.829
peak=    3.395 closest distance to " CA  LYS A  48 " =    1.378
peak=    3.394 closest distance to " O   HOH Z 383 " =    1.940
peak=    3.392 closest distance to " NH1 ARG A 269 " =    0.828
peak=    3.389 closest distance to " O   HOH Z 139 " =    4.278
peak=    3.385 closest distance to " CD2 HIS A  81 " =    1.219
peak=    3.380 closest distance to " O   HOH Z 363 " =    1.138
peak=    3.379 closest distance to " CB  ASN A 148 " =    1.832
peak=    3.378 closest distance to " O   HOH Z 208 " =    1.672
peak=    3.366 closest distance to " O   HOH Z 272 " =    1.158
peak=    3.366 closest distance to " O   HOH Z 112 " =    1.527
peak=    3.365 closest distance to " CG2 VAL A 112 " =    1.556
peak=    3.364 closest distance to " CA  LEU A  83 " =    1.524
peak=    3.361 closest distance to " NZ  LYS A 117 " =    1.564
peak=    3.360 closest distance to " CA  GLN A  88 " =    1.277
peak=    3.360 closest distance to " O   HOH Z 287 " =    1.854
peak=    3.358 closest distance to " O   GLY A  23 " =    2.381
peak=    3.357 closest distance to " CB  ILE A 199 " =    1.001
peak=    3.356 closest distance to " CD1 TRP A 266 " =    1.143
peak=    3.355 closest distance to " CB  ASP A 107 " =    1.056
peak=    3.354 closest distance to " CA  ASP A 162 " =    1.286
peak=    3.354 closest distance to " O   HOH Z 132 " =    1.613
peak=    3.342 closest distance to " C   GLY A  80 " =    1.325
peak=    3.329 closest distance to " CA  ALA A 295 " =    0.986
peak=    3.329 closest distance to " O   HOH Z  39 " =    2.120
peak=    3.322 closest distance to " O   HOH Z 130 " =    1.188
peak=    3.318 closest distance to " CB  MET A  47 " =    1.011
peak=    3.316 closest distance to " O   HOH Z 358 " =    1.938
peak=    3.315 closest distance to " CA  LEU A 282 " =    1.264
peak=    3.314 closest distance to " CA  VAL A  41 " =    0.783
peak=    3.313 closest distance to " NH2AARG A 145 " =    0.899
peak=    3.310 closest distance to " CG2 ILE A 106 " =    1.194
peak=    3.310 closest distance to " CD  ARG A 195 " =    1.072
peak=    3.310 closest distance to " O   HOH Z 146 " =    1.634
peak=    3.308 closest distance to " CB  TRP A 266 " =    0.976
peak=    3.308 closest distance to " O   HOH Z 154 " =    2.399
peak=    3.304 closest distance to " O   HOH Z 345 " =    2.761
peak=    3.301 closest distance to " O   HOH Z   1 " =    3.169
peak=    3.295 closest distance to " O   HOH Z 255 " =    1.771
peak=    3.295 closest distance to " O   HOH Z 207 " =    2.342
peak=    3.294 closest distance to " O   THR A 251 " =    1.303
peak=    3.293 closest distance to " CB  ALA A  71 " =    1.328
peak=    3.284 closest distance to " OD2 ASP A 162 " =    1.151
peak=    3.281 closest distance to " N   PHE A 130 " =    1.415
peak=    3.278 closest distance to " O   HOH Z 418 " =    1.653
peak=    3.277 closest distance to " O   HOH Z 136 " =    1.235
peak=    3.272 closest distance to " CD1 LEU A 222 " =    0.798
peak=    3.271 closest distance to " O   HOH Z 368 " =    1.937
peak=    3.271 closest distance to " O  BHOH Z 338 " =    0.948
peak=    3.269 closest distance to " N   HIS A 108 " =    1.835
peak=    3.268 closest distance to " O   HOH Z 334 " =    2.688
peak=    3.268 closest distance to " O   HOH Z 423 " =    1.915
peak=    3.268 closest distance to " CA  ILE A 106 " =    0.776
peak=    3.268 closest distance to " OE1 GLN A  77 " =    1.029
peak=    3.265 closest distance to " O   HOH Z 339 " =    1.313
peak=    3.263 closest distance to " O   HOH Z 281 " =    2.378
peak=    3.252 closest distance to " CA  THR A 221 " =    0.911
peak=    3.251 closest distance to " CD1 LEU A  96 " =    0.774
peak=    3.249 closest distance to " CB  ALA A 256 " =    1.003
peak=    3.247 closest distance to " N   CYS A 260 " =    0.824
peak=    3.244 closest distance to " CA  THR A 221 " =    1.562
peak=    3.237 closest distance to " O   HOH Z 373 " =    1.620
peak=    3.235 closest distance to " CA  ASN A 127 " =    1.174
peak=    3.234 closest distance to " O   HOH Z 426 " =    3.272
peak=    3.231 closest distance to " O   HOH Z 116 " =    2.706
peak=    3.230 closest distance to " ND2 ASN A 187 " =    1.494
peak=    3.229 closest distance to " CB  ALA A  51 " =    0.751
peak=    3.228 closest distance to " O   HOH Z 147 " =    1.714
peak=    3.228 closest distance to " CD  GLU A 236 " =    1.069
peak=    3.224 closest distance to " O   HOH Z 152 " =    1.619
peak=    3.221 closest distance to " O   HOH Z 155 " =    1.541
peak=    3.221 closest distance to " ND2 ASN A  45 " =    1.369
peak=    3.220 closest distance to " O   HOH Z 250 " =    1.852
peak=    3.216 closest distance to " CG2AVAL A 121 " =    2.063
peak=    3.216 closest distance to " CE BMET A  47 " =    1.433
peak=    3.212 closest distance to " O   HOH Z 150 " =    3.470
peak=    3.209 closest distance to " CA  ASP A 124 " =    0.806
peak=    3.209 closest distance to " CG  GLN A  58 " =    2.197
peak=    3.205 closest distance to " CB  SER A 273 " =    0.757
peak=    3.202 closest distance to " O   HOH Z  59 " =    1.880
peak=    3.200 closest distance to " O   HOH Z 386 " =    2.288
peak=    3.195 closest distance to " O   ASN A  74 " =    1.595
peak=    3.192 closest distance to " O   TYR A 116 " =    1.471
peak=    3.190 closest distance to " O  BHOH Z 338 " =    2.246
peak=    3.190 closest distance to " N   THR A  52 " =    1.039
peak=    3.189 closest distance to " CD  LYS A 166 " =    1.508
peak=    3.188 closest distance to " O   HOH Z 435 " =    1.815
peak=    3.184 closest distance to " CA  ALA A 100 " =    1.463
peak=    3.182 closest distance to " CG1BVAL A 121 " =    1.314
peak=    3.182 closest distance to " OD1 ASP A 238 " =    0.914
peak=    3.181 closest distance to " N   GLY A  75 " =    1.130
peak=    3.177 closest distance to " O   HOH Z 293 " =    1.989
peak=    3.177 closest distance to " O   SER A  26 " =    1.739
peak=    3.176 closest distance to " O   HOH Z 166 " =    1.650
peak=    3.175 closest distance to " OG1 THR A 294 " =    2.471
peak=    3.175 closest distance to " OG  SER A 245 " =    1.499
peak=    3.174 closest distance to " O   HOH Z 155 " =    2.690
peak=    3.174 closest distance to " CD2 TRP A 179 " =    1.283
peak=    3.172 closest distance to " O   HOH Z  49 " =    1.750
peak=    3.169 closest distance to " O   HOH Z 211 " =    2.478
peak=    3.166 closest distance to " CA  ALA A 158 " =    1.151
peak=    3.166 closest distance to " NZ  LYS A 193 " =    1.543
peak=    3.164 closest distance to " O   HOH Z 238 " =    5.548
peak=    3.163 closest distance to " O   HOH Z 197 " =    1.964
peak=    3.160 closest distance to " CA  GLY A  75 " =    1.115
peak=    3.157 closest distance to " NZ BLYS A 290 " =    0.901
peak=    3.157 closest distance to " CA  ARG A 156 " =    0.927
peak=    3.153 closest distance to " O   HOH Z  50 " =    3.643
peak=    3.152 closest distance to " O   HOH Z 124 " =    3.068
peak=    3.145 closest distance to " O   HOH Z 275 " =    1.369
peak=    3.144 closest distance to " O   HOH Z  51 " =    1.637
peak=    3.141 closest distance to " O   HOH Z 377 " =    1.366
peak=    3.140 closest distance to " O   HOH Z  26 " =    1.330
peak=    3.139 closest distance to " O   HOH Z 343 " =    2.319
peak=    3.138 closest distance to " NH2AARG A 190 " =    1.362
peak=    3.132 closest distance to " O   HOH Z 127 " =    1.054
peak=    3.129 closest distance to " O   HOH Z 291 " =    1.573
peak=    3.125 closest distance to " O   HOH Z 135 " =    1.606
peak=    3.124 closest distance to " OG  SER A  97 " =    3.439
peak=    3.122 closest distance to " O   ILE A 151 " =    1.116
peak=    3.116 closest distance to " O   HOH Z 128 " =    2.068
peak=    3.114 closest distance to " CB  TYR A 116 " =    1.243
peak=    3.111 closest distance to " OH  TYR A  30 " =    1.415
peak=    3.100 closest distance to " CB  ASN A 127 " =    0.880
peak=    3.093 closest distance to " O   HOH Z 192 " =    1.949
peak=    3.088 closest distance to " CB  GLU A 277 " =    0.938
peak=    3.086 closest distance to " CA  CYS A 254 " =    1.589
peak=    3.086 closest distance to " O   HOH Z 339 " =    2.250
peak=    3.063 closest distance to " CG2 THR A 251 " =    1.077
peak=    3.059 closest distance to " NZ  LYS A 166 " =    2.883
peak=    3.059 closest distance to " O   HOH Z 126 " =    1.252
peak=    3.052 closest distance to " O   HOH Z 391 " =    3.005
peak=    3.049 closest distance to " CD1 PHE A  59 " =    1.685

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 221         
Filter by distance & map next to the model:
   mapped sites are within: 0.371 - 5.079
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 217 from: 221
   mapped sites are within: 0.717 - 5.079

peak=   -4.711 closest distance to " O   HOH Z  52 " =    2.091
peak=   -4.591 closest distance to " O   HOH Z 350 " =    0.851
peak=   -4.449 closest distance to " O   HOH Z 221 " =    1.020
peak=   -4.329 closest distance to " O   HOH Z 120 " =    0.806
peak=   -4.248 closest distance to " O   HOH Z 155 " =    1.305
peak=   -4.218 closest distance to " O   HOH Z 377 " =    0.848
peak=   -4.148 closest distance to " NH2 ARG A  66 " =    1.157
peak=   -4.116 closest distance to " CG2BVAL A  41 " =    2.710
peak=   -4.112 closest distance to " OG  SER A  97 " =    2.267
peak=   -4.072 closest distance to " CA  SER A 164 " =    2.011
peak=   -4.067 closest distance to " O   PRO A 198 " =    1.347
peak=   -4.055 closest distance to " O   HOH Z 290 " =    0.833
peak=   -4.028 closest distance to " CD  GLN A  77 " =    1.068
peak=   -4.016 closest distance to " CE2 TYR A  30 " =    2.716
peak=   -3.992 closest distance to " O   HOH Z 266 " =    4.402
peak=   -3.939 closest distance to " C   HIS A 108 " =    1.040
peak=   -3.935 closest distance to " CD1 TYR A 247 " =    2.310
peak=   -3.922 closest distance to " O   HOH Z 166 " =    1.866
peak=   -3.867 closest distance to " OXT GLY A 302 " =    2.643
peak=   -3.866 closest distance to " CD1 PHE A  59 " =    1.870
peak=   -3.826 closest distance to " CA  VAL A 197 " =    0.986
peak=   -3.820 closest distance to " CB  LEU A 167 " =    2.157
peak=   -3.792 closest distance to " CG2 THR A 221 " =    2.289
peak=   -3.779 closest distance to " CA  VAL A  67 " =    2.916
peak=   -3.768 closest distance to " ND2 ASN A  60 " =    1.356
peak=   -3.763 closest distance to " ND2 ASN A  45 " =    1.082
peak=   -3.761 closest distance to " O   HOH Z 396 " =    1.594
peak=   -3.760 closest distance to " O   HOH Z 109 " =    3.491
peak=   -3.753 closest distance to " OD2 ASP A 171 " =    1.825
peak=   -3.748 closest distance to " O   HOH Z 259 " =    0.956
peak=   -3.744 closest distance to " CA  SER A 276 " =    1.392
peak=   -3.742 closest distance to " OG ASER A 134 " =    1.249
peak=   -3.730 closest distance to " CA  GLY A 203 " =    2.306
peak=   -3.713 closest distance to " CG1 VAL A 112 " =    2.653
peak=   -3.684 closest distance to " CB  PHE A 208 " =    2.303
peak=   -3.658 closest distance to " CG  GLN A  58 " =    1.166
peak=   -3.651 closest distance to " NH2 ARG A  66 " =    1.242
peak=   -3.642 closest distance to " OD1 ASP A 191 " =    1.751
peak=   -3.639 closest distance to " O   HOH Z 388 " =    2.026
peak=   -3.631 closest distance to " O   HOH Z 407 " =    0.745
peak=   -3.629 closest distance to " O   HOH Z  71 " =    1.390
peak=   -3.619 closest distance to " C   ASN A 285 " =    2.494
peak=   -3.616 closest distance to " NE  ARG A 156 " =    1.803
peak=   -3.608 closest distance to " CB  SER A 146 " =    2.174
peak=   -3.607 closest distance to " O   ALA A   1 " =    2.025
peak=   -3.604 closest distance to " O   HOH Z 234 " =    4.244
peak=   -3.596 closest distance to " CG  ASP A 231 " =    0.767
peak=   -3.589 closest distance to " CD2 LEU A 300 " =    2.710
peak=   -3.577 closest distance to " CD2 PHE A  59 " =    2.341
peak=   -3.563 closest distance to " O  BHOH Z 338 " =    1.622
peak=   -3.561 closest distance to " CD  GLN A 223 " =    0.915
peak=   -3.559 closest distance to " CD  LYS A 119 " =    0.979
peak=   -3.551 closest distance to " SG  CYS A 254 " =    3.365
peak=   -3.551 closest distance to " O   HOH Z 313 " =    1.298
peak=   -3.546 closest distance to " O   HOH Z 292 " =    4.299
peak=   -3.544 closest distance to " O   HOH Z 151 " =    1.340
peak=   -3.538 closest distance to " CD1 LEU A 101 " =    2.574
peak=   -3.536 closest distance to " O   HOH Z 118 " =    3.380
peak=   -3.536 closest distance to " ND2 ASN A 187 " =    1.721
peak=   -3.530 closest distance to " O   HOH Z 146 " =    0.809
peak=   -3.520 closest distance to " O   HOH Z 165 " =    2.061
peak=   -3.513 closest distance to " O   HOH Z   7 " =    1.442
peak=   -3.505 closest distance to " CE  MET A 105 " =    2.046
peak=   -3.504 closest distance to " CE  MET A  93 " =    1.194
peak=   -3.504 closest distance to " O   HOH Z  97 " =    1.470
peak=   -3.503 closest distance to " NH1 ARG A 195 " =    2.302
peak=   -3.497 closest distance to " N   ALA A  43 " =    2.750
peak=   -3.491 closest distance to " N   GLN A  58 " =    1.667
peak=   -3.484 closest distance to " O   HOH Z  93 " =    1.248
peak=   -3.484 closest distance to " OG BSER A 210 " =    2.066
peak=   -3.482 closest distance to " O   HOH Z  37 " =    1.845
peak=   -3.480 closest distance to " OG  SER A  32 " =    1.166
peak=   -3.476 closest distance to " O   GLY A 118 " =    2.271
peak=   -3.475 closest distance to " O   HOH Z 378 " =    1.180
peak=   -3.474 closest distance to " CG  PRO A 243 " =    1.534
peak=   -3.473 closest distance to " C   GLY A 133 " =    1.260
peak=   -3.470 closest distance to " CB  ASP A  50 " =    2.499
peak=   -3.467 closest distance to " O   HOH Z  91 " =    2.039
peak=   -3.463 closest distance to " O   HOH Z 150 " =    1.184
peak=   -3.462 closest distance to " O   ALA A 161 " =    1.725
peak=   -3.461 closest distance to " CD1 TRP A 179 " =    1.104
peak=   -3.461 closest distance to " OG  SER A 273 " =    2.147
peak=   -3.461 closest distance to " NH2 ARG A  79 " =    1.852
peak=   -3.454 closest distance to " ND2 ASN A  39 " =    1.253
peak=   -3.424 closest distance to " O   LEU A 300 " =    2.441
peak=   -3.421 closest distance to " CB  ARG A 156 " =    2.457
peak=   -3.419 closest distance to " OG  SER A  62 " =    1.257
peak=   -3.415 closest distance to " CB  LYS A 193 " =    2.763
peak=   -3.406 closest distance to " O   HOH Z 140 " =    0.762
peak=   -3.406 closest distance to " CD  ARG A 139 " =    1.571
peak=   -3.392 closest distance to " O   HOH Z 416 " =    0.717
peak=   -3.391 closest distance to " O   GLY A 196 " =    1.026
peak=   -3.380 closest distance to " C   ASN A 187 " =    1.981
peak=   -3.378 closest distance to " O   HOH Z  19 " =    2.213
peak=   -3.377 closest distance to " O   HOH Z 422 " =    1.329
peak=   -3.369 closest distance to " CD1 LEU A 228 " =    2.421
peak=   -3.364 closest distance to " O   ALA A  10 " =    1.769
peak=   -3.361 closest distance to " O   HOH Z 190 " =    2.136
peak=   -3.356 closest distance to " O   PHE A 218 " =    1.375
peak=   -3.355 closest distance to " O   VAL A 197 " =    1.396
peak=   -3.355 closest distance to " CD2 LEU A 237 " =    2.406
peak=   -3.348 closest distance to " C   THR A 279 " =    1.164
peak=   -3.347 closest distance to " CD1 LEU A  25 " =    2.501
peak=   -3.344 closest distance to " OH  TYR A 169 " =    0.940
peak=   -3.339 closest distance to " CE3 TRP A  92 " =    2.643
peak=   -3.338 closest distance to " O   HOH Z 352 " =    0.917
peak=   -3.338 closest distance to " CG  TRP A 266 " =    1.819
peak=   -3.337 closest distance to " CD  GLN A  88 " =    0.783
peak=   -3.336 closest distance to " CB  ALA A 291 " =    2.177
peak=   -3.333 closest distance to " O   HOH Z 377 " =    2.135
peak=   -3.330 closest distance to " OD2 ASP A 171 " =    2.170
peak=   -3.328 closest distance to " O   HOH Z  90 " =    1.833
peak=   -3.325 closest distance to " OG ASER A 164 " =    0.904
peak=   -3.321 closest distance to " O   HOH Z 434 " =    3.931
peak=   -3.316 closest distance to " CD  PRO A 198 " =    1.086
peak=   -3.315 closest distance to " O   HOH Z 185 " =    2.200
peak=   -3.314 closest distance to " O   HOH Z  78 " =    1.950
peak=   -3.314 closest distance to " CG  LEU A  83 " =    2.220
peak=   -3.312 closest distance to " O   VAL A 125 " =    2.192
peak=   -3.311 closest distance to " O   HOH Z   7 " =    1.136
peak=   -3.309 closest distance to " CB  ALA A 248 " =    1.961
peak=   -3.306 closest distance to " N   GLY A 262 " =    1.930
peak=   -3.303 closest distance to " O   SER A 146 " =    0.921
peak=   -3.298 closest distance to " O   HOH Z 426 " =    2.458
peak=   -3.297 closest distance to " O   HOH Z 380 " =    4.206
peak=   -3.295 closest distance to " O   TRP A  92 " =    1.909
peak=   -3.293 closest distance to " O   HOH Z 385 " =    3.667
peak=   -3.293 closest distance to " O   HOH Z  17 " =    0.865
peak=   -3.293 closest distance to " CE2 TRP A 274 " =    1.133
peak=   -3.292 closest distance to " C   ALA A 158 " =    1.162
peak=   -3.290 closest distance to " O   GLY A 196 " =    2.455
peak=   -3.289 closest distance to " OG1 THR A  82 " =    1.341
peak=   -3.287 closest distance to " CH2 TRP A 179 " =    1.150
peak=   -3.286 closest distance to " CB  ALA A 161 " =    2.567
peak=   -3.285 closest distance to " ND2 ASN A 215 " =    2.042
peak=   -3.282 closest distance to " O   ALA A 256 " =    1.453
peak=   -3.278 closest distance to " O   HOH Z 423 " =    2.394
peak=   -3.273 closest distance to " O   HOH Z 427 " =    1.244
peak=   -3.269 closest distance to " O   HOH Z  11 " =    1.474
peak=   -3.268 closest distance to " O   HOH Z  15 " =    1.659
peak=   -3.268 closest distance to " O   HOH Z 432 " =    1.009
peak=   -3.267 closest distance to " O   HOH Z  58 " =    1.124
peak=   -3.266 closest distance to " CG  ARG A 269 " =    2.473
peak=   -3.263 closest distance to " O   HOH Z 418 " =    1.353
peak=   -3.263 closest distance to " O   LEU A 167 " =    1.701
peak=   -3.262 closest distance to " CB  ALA A 131 " =    2.277
peak=   -3.260 closest distance to " CZ  TYR A 169 " =    1.887
peak=   -3.258 closest distance to " O   HOH Z 148 " =    3.115
peak=   -3.254 closest distance to " N   ALA A   9 " =    1.576
peak=   -3.251 closest distance to " C   SER A 206 " =    1.531
peak=   -3.243 closest distance to " CG  GLU A  53 " =    1.429
peak=   -3.242 closest distance to " O   HOH Z 100 " =    1.000
peak=   -3.240 closest distance to " O   HOH Z  64 " =    1.224
peak=   -3.239 closest distance to " NH1 ARG A 195 " =    2.716
peak=   -3.239 closest distance to " O   HOH Z  37 " =    1.584
peak=   -3.238 closest distance to " CD  GLN A  58 " =    0.894
peak=   -3.238 closest distance to " O   HOH Z 275 " =    1.563
peak=   -3.237 closest distance to " CB  CYS A 254 " =    2.587
peak=   -3.232 closest distance to " NH2AARG A 275 " =    5.079
peak=   -3.230 closest distance to " OG1 THR A  82 " =    2.191
peak=   -3.226 closest distance to " NH2 ARG A 159 " =    2.442
peak=   -3.222 closest distance to " O   SER A   3 " =    1.200
peak=   -3.222 closest distance to " O   HOH Z 396 " =    2.190
peak=   -3.214 closest distance to " O   HOH Z 367 " =    4.631
peak=   -3.209 closest distance to " CA  ASP A 298 " =    1.084
peak=   -3.207 closest distance to " O   HOH Z 231 " =    0.866
peak=   -3.202 closest distance to " O   HOH Z 318 " =    1.405
peak=   -3.200 closest distance to " OXT GLY A 302 " =    3.612
peak=   -3.192 closest distance to " C   TRP A 274 " =    1.485
peak=   -3.191 closest distance to " CB  GLN A  55 " =    1.494
peak=   -3.187 closest distance to " O   HOH Z 119 " =    2.908
peak=   -3.184 closest distance to " O   HOH Z 331 " =    1.029
peak=   -3.179 closest distance to " CG2 VAL A 296 " =    2.128
peak=   -3.174 closest distance to " CD2 LEU A 237 " =    2.616
peak=   -3.174 closest distance to " CA  GLY A 133 " =    1.759
peak=   -3.173 closest distance to " OE2 GLU A   2 " =    1.150
peak=   -3.173 closest distance to " O   HOH Z 265 " =    1.997
peak=   -3.161 closest distance to " O   HOH Z 423 " =    1.092
peak=   -3.161 closest distance to " NE2 GLN A  88 " =    2.050
peak=   -3.160 closest distance to " CG1AVAL A  41 " =    2.556
peak=   -3.160 closest distance to " O   HOH Z 115 " =    4.824
peak=   -3.155 closest distance to " CD  GLU A 236 " =    1.035
peak=   -3.155 closest distance to " O   HOH Z 166 " =    2.293
peak=   -3.153 closest distance to " O   HOH Z 171 " =    2.295
peak=   -3.150 closest distance to " O   HOH Z 399 " =    2.376
peak=   -3.147 closest distance to " O   HOH Z 384 " =    2.087
peak=   -3.142 closest distance to " O   VAL A 174 " =    2.040
peak=   -3.142 closest distance to " O   HOH Z 136 " =    1.464
peak=   -3.141 closest distance to " CD  GLN A  73 " =    0.888
peak=   -3.140 closest distance to " CG2 THR A   4 " =    1.716
peak=   -3.139 closest distance to " O   HOH Z 392 " =    1.234
peak=   -3.137 closest distance to " O   HOH Z 410 " =    2.210
peak=   -3.131 closest distance to " O   HOH Z 292 " =    3.137
peak=   -3.125 closest distance to " NE1 TRP A 266 " =    2.323
peak=   -3.123 closest distance to " O   HOH Z 210 " =    2.317
peak=   -3.121 closest distance to " CB  ALA A  43 " =    2.461
peak=   -3.121 closest distance to " CB  ASN A  39 " =    2.228
peak=   -3.115 closest distance to " CB  PRO A 243 " =    2.593
peak=   -3.104 closest distance to " CE2 TRP A  85 " =    1.004
peak=   -3.104 closest distance to " CD2 HIS A 115 " =    1.089
peak=   -3.099 closest distance to " O   HOH Z  43 " =    1.989
peak=   -3.093 closest distance to " O   HOH Z 259 " =    2.173
peak=   -3.092 closest distance to " O   HOH Z  40 " =    2.880
peak=   -3.087 closest distance to " NZ  LYS A 117 " =    1.654
peak=   -3.086 closest distance to " OD1 ASN A 148 " =    1.722
peak=   -3.084 closest distance to " O   HOH Z 405 " =    2.229
peak=   -3.083 closest distance to " O   HOH Z  25 " =    2.212
peak=   -3.079 closest distance to " CD  GLN A  58 " =    1.185
peak=   -3.079 closest distance to " NZ  LYS A 119 " =    1.305
peak=   -3.076 closest distance to " O   HOH Z 166 " =    2.249
peak=   -3.074 closest distance to " O   HOH Z 432 " =    1.458
peak=   -3.074 closest distance to " O   HOH Z 184 " =    1.422
peak=   -3.070 closest distance to " CB  TRP A  85 " =    2.387
peak=   -3.064 closest distance to " O   ALA A  34 " =    2.562
peak=   -3.062 closest distance to " O   HOH Z 231 " =    1.996
peak=   -3.058 closest distance to " OG ASER A  12 " =    1.577
peak=   -3.023 closest distance to " OE1 GLN A  77 " =    1.390

================= 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    :  0.4791 0.4667   6.293239e+00   6.279226e+00
   1_bss:  0.4696 0.4555   6.288519e+00   6.268895e+00
   1_xyz:  0.3832 0.4244   6.158732e+00   6.215542e+00
   1_adp:  0.3541 0.4289   6.123249e+00   6.219114e+00
   1_occ:  0.3539 0.4290   6.122547e+00   6.218828e+00
   2_bss:  0.3522 0.4256   6.122630e+00   6.218080e+00
   2_xyz:  0.2741 0.3363   5.915152e+00   6.060213e+00
   2_adp:  0.2477 0.3250   5.855475e+00   6.035385e+00
   2_occ:  0.2476 0.3245   5.854902e+00   6.034631e+00
   3_bss:  0.2470 0.3233   5.851059e+00   6.031365e+00
   3_xyz:  0.2069 0.2673   5.678504e+00   5.870943e+00
   3_adp:  0.1966 0.2438   5.624069e+00   5.796807e+00
   3_occ:  0.1964 0.2436   5.623273e+00   5.796313e+00
   4_bss:  0.1964 0.2429   5.624494e+00   5.795710e+00
   4_xyz:  0.1498 0.1926   5.381907e+00   5.580794e+00
   4_adp:  0.1370 0.1856   5.318102e+00   5.536222e+00
   4_occ:  0.1368 0.1855   5.317719e+00   5.536159e+00
   5_bss:  0.1370 0.1863   5.320503e+00   5.538308e+00
   5_xyz:  0.1271 0.1769   5.260973e+00   5.486832e+00
   5_adp:  0.1258 0.1733   5.250724e+00   5.473399e+00
   5_occ:  0.1256 0.1731   5.250330e+00   5.473670e+00
   5_bss:  0.1256 0.1730   5.250143e+00   5.473229e+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:  0.296  20.000  -2.947   3.769   1.226   0.000   0.000   0.000
   1_xyz:  0.296  20.000  -2.947   3.769   1.226   0.000   0.000   0.000
   1_adp:  0.296  20.000  -2.947   3.769   1.226   0.000   0.000   0.000
   1_occ:  0.296  20.000  -2.947   3.769   1.226   0.000   0.000   0.000
   2_bss:  0.327  54.819  -1.337   2.091   0.274   0.000   0.000   0.000
   2_xyz:  0.327  54.819  -1.337   2.091   0.274   0.000   0.000   0.000
   2_adp:  0.327  54.819  -1.337   2.091   0.274   0.000   0.000   0.000
   2_occ:  0.327  54.819  -1.337   2.091   0.274   0.000   0.000   0.000
   3_bss:  0.324  59.409  -0.989   1.126  -0.349   0.000  -0.000  -0.000
   3_xyz:  0.324  59.409  -0.989   1.126  -0.349   0.000  -0.000  -0.000
   3_adp:  0.324  59.409  -0.989   1.126  -0.349   0.000  -0.000  -0.000
   3_occ:  0.324  59.409  -0.989   1.126  -0.349   0.000  -0.000  -0.000
   4_bss:  0.324  57.316  -1.740   0.133  -1.182   0.000  -0.000  -0.000
   4_xyz:  0.324  57.316  -1.740   0.133  -1.182   0.000  -0.000  -0.000
   4_adp:  0.324  57.316  -1.740   0.133  -1.182   0.000  -0.000  -0.000
   4_occ:  0.324  57.316  -1.740   0.133  -1.182   0.000  -0.000  -0.000
   5_bss:  0.330  60.508  -1.982  -0.645  -1.479  -0.000  -0.000  -0.000
   5_xyz:  0.330  60.508  -1.982  -0.645  -1.479  -0.000  -0.000  -0.000
   5_adp:  0.330  60.508  -1.982  -0.645  -1.479  -0.000  -0.000  -0.000
   5_occ:  0.330  60.508  -1.982  -0.645  -1.479  -0.000  -0.000  -0.000
   5_bss:  0.325  55.105  -1.952  -0.817  -1.458  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.168 0.4175  0.5698    72551.502
   1_bss:  56.732 0.4345  0.6053    68569.798
   1_xyz:  49.540 0.5251  0.7245    54068.351
   1_adp:  50.215 0.5160  0.7156    54555.300
   1_occ:  50.209 0.5160  0.7139    54468.930
   2_bss:  49.788 0.5214  0.7177    53975.749
   2_xyz:  37.192 0.6742  0.8970    32049.145
   2_adp:  35.291 0.6968  0.8989    29856.066
   2_occ:  35.274 0.6970  0.8985    29804.703
   3_bss:  35.034 0.6995  0.8879    29327.859
   3_xyz:  27.470 0.7842  0.9598    18909.220
   3_adp:  24.417 0.8176  0.9749    15881.880
   3_occ:  24.396 0.8178  0.9751    15858.386
   4_bss:  24.342 0.8184  0.9468    15826.820
   4_xyz:  18.668 0.8736  0.9832     9706.036
   4_adp:  17.599 0.8839  0.9816     8964.679
   4_occ:  17.591 0.8839  0.9816     8963.777
   5_bss:  17.640 0.8836  0.9668     9045.819
   5_xyz:  16.433 0.8944  0.9723     8057.561
   5_adp:  16.125 0.8973  0.9684     7895.670
   5_occ:  16.120 0.8974  0.9683     7901.693
   5_bss:  16.113 0.8975  0.9672     7888.989
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   2.0739e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   2.0739e-01
   1_xyz:   1.771  0.014  0.108 16.896  0.006  4.108   1.7382e-01
   1_adp:   1.771  0.014  0.108 16.896  0.006  4.108   1.7382e-01
   1_occ:   1.771  0.014  0.108 16.896  0.006  4.108   1.7382e-01
   2_bss:   1.771  0.014  0.108 16.896  0.006  4.108   1.7382e-01
   2_xyz:   1.638  0.013  0.103 15.882  0.007  4.118   1.3990e-01
   2_adp:   1.638  0.013  0.103 15.882  0.007  4.118   1.3990e-01
   2_occ:   1.638  0.013  0.103 15.882  0.007  4.118   1.3990e-01
   3_bss:   1.638  0.013  0.103 15.882  0.007  4.118   1.3990e-01
   3_xyz:   1.045  0.007  0.064 14.915  0.004  4.112   6.5689e-02
   3_adp:   1.045  0.007  0.064 14.915  0.004  4.112   6.5689e-02
   3_occ:   1.045  0.007  0.064 14.915  0.004  4.112   6.5689e-02
   4_bss:   1.045  0.007  0.064 14.915  0.004  4.112   6.5689e-02
   4_xyz:   1.132  0.009  0.077 14.990  0.004  4.110   7.5881e-02
   4_adp:   1.132  0.009  0.077 14.990  0.004  4.110   7.5881e-02
   4_occ:   1.132  0.009  0.077 14.990  0.004  4.110   7.5881e-02
   5_bss:   1.132  0.009  0.077 14.990  0.004  4.110   7.5881e-02
   5_xyz:   1.035  0.007  0.072 14.661  0.004  4.116   6.2497e-02
   5_adp:   1.035  0.007  0.072 14.661  0.004  4.116   6.2497e-02
   5_occ:   1.035  0.007  0.072 14.661  0.004  4.116   6.2497e-02
   5_bss:   1.035  0.007  0.072 14.661  0.004  4.116   6.2497e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.303   2.4387e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.303   2.4387e-01
   1_xyz:   9.966  0.081  0.417 88.088  0.024  1.820   1.0605e-01
   1_adp:   9.966  0.081  0.417 88.088  0.024  1.820   1.0605e-01
   1_occ:   9.966  0.081  0.417 88.088  0.024  1.820   1.0605e-01
   2_bss:   9.966  0.081  0.417 88.088  0.024  1.820   1.0605e-01
   2_xyz:   8.460  0.099  0.382 81.120  0.042  1.957   1.1191e-01
   2_adp:   8.460  0.099  0.382 81.120  0.042  1.957   1.1191e-01
   2_occ:   8.460  0.099  0.382 81.120  0.042  1.957   1.1191e-01
   3_bss:   8.460  0.099  0.382 81.120  0.042  1.957   1.1191e-01
   3_xyz:   7.186  0.056  0.205 86.987  0.047  2.246   7.7132e-02
   3_adp:   7.186  0.056  0.205 86.987  0.047  2.246   7.7132e-02
   3_occ:   7.186  0.056  0.205 86.987  0.047  2.246   7.7132e-02
   4_bss:   7.186  0.056  0.205 86.987  0.047  2.246   7.7132e-02
   4_xyz:   7.613  0.064  0.239 82.145  0.042  2.214   6.0157e-02
   4_adp:   7.613  0.064  0.239 82.145  0.042  2.214   6.0157e-02
   4_occ:   7.613  0.064  0.239 82.145  0.042  2.214   6.0157e-02
   5_bss:   7.613  0.064  0.239 82.145  0.042  2.214   6.0157e-02
   5_xyz:   7.443  0.056  0.238 83.071  0.031  2.372   5.9536e-02
   5_adp:   7.443  0.056  0.238 83.071  0.031  2.372   5.9536e-02
   5_occ:   7.443  0.056  0.238 83.071  0.031  2.372   5.9536e-02
   5_bss:   7.443  0.056  0.238 83.071  0.031  2.372   5.9536e-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: 115.54   0.00  18.08 115.54   0.00  14.70  70.85   0.00  36.48
   1_occ: 115.54   0.00  18.08 115.54   0.00  14.70  70.85   0.00  36.48
   2_bss: 115.54   0.00  18.08 115.54   0.00  14.70  70.85   0.00  36.48
   2_xyz: 115.54   0.00  18.08 115.54   0.00  14.70  70.85   0.00  36.48
   2_adp: 109.76   0.00  19.24  91.82   0.00  14.94 109.76   2.75  42.65
   2_occ: 109.76   0.00  19.24  91.82   0.00  14.94 109.76   2.75  42.65
   3_bss: 109.76   0.00  19.24  91.82   0.00  14.94 109.76   2.75  42.65
   3_xyz: 109.76   0.00  19.24  91.82   0.00  14.94 109.76   2.75  42.65
   3_adp:  98.45   0.00  17.51  86.78   0.00  13.30  98.45   5.12  40.40
   3_occ:  98.45   0.00  17.51  86.78   0.00  13.30  98.45   5.12  40.40
   4_bss:  98.45   0.00  17.51  86.78   0.00  13.30  98.45   5.12  40.40
   4_xyz:  98.45   0.00  17.51  86.78   0.00  13.30  98.45   5.12  40.40
   4_adp: 100.96   0.75  17.80 100.96   0.75  12.80  95.74   4.47  44.99
   4_occ: 100.96   0.75  17.80 100.96   0.75  12.80  95.74   4.47  44.99
   5_bss: 100.96   0.75  17.80 100.96   0.75  12.80  95.74   4.47  44.99
   5_xyz: 100.96   0.75  17.80 100.96   0.75  12.80  95.74   4.47  44.99
   5_adp:  99.09   0.00  17.01  97.64   0.00  12.43  99.09   4.84  42.00
   5_occ:  99.09   0.00  17.01  97.64   0.00  12.43  99.09   4.84  42.00
   5_bss:  99.10   0.00  17.02  97.64   0.00  12.43  99.10   4.85  42.00
------------------------------------------------------------------------
 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:    2.853    0.025    0.415
   1_adp:    2.853    0.025    0.415
   1_occ:    2.853    0.025    0.415
   2_bss:    2.853    0.025    0.415
   2_xyz:    2.402    0.056    0.696
   2_adp:    2.402    0.056    0.696
   2_occ:    2.402    0.056    0.696
   3_bss:    2.402    0.056    0.696
   3_xyz:    2.149    0.066    0.789
   3_adp:    2.149    0.066    0.789
   3_occ:    2.149    0.066    0.789
   4_bss:    2.149    0.066    0.789
   4_xyz:    1.957    0.064    0.895
   4_adp:    1.957    0.064    0.895
   4_occ:    1.957    0.064    0.895
   5_bss:    1.957    0.064    0.895
   5_xyz:    1.737    0.117    0.920
   5_adp:    1.737    0.117    0.920
   5_occ:    1.737    0.117    0.920
   5_bss:    1.737    0.117    0.920
------------------------------------------------------------------------

CPU time actual refinement: 372.17


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_836/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_836/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_836/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_836/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_836/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 372.02 
  Macro-tasks:
    bulk solvent and scale       = 42.81  
    individual site refinement   = 164.81 
    weights calculation          = 30.97  
    collect and process          = 6.49   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 245.21 
  Micro-tasks:
    mask                            = 2.52   
    f_calc                          = 121.81 
    alpha_beta                      = 8.35   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 131.44 
    fmodel                         = 7.38   
    r_factors                      = 0.24   
    phase_errors                   = 10.35  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 283.54 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.196 micro seconds
Total CPU time: 6.43 minutes
from_scatterers_fft:    641 calls, 121.43 s
gradients_fft:          586 calls, 117.41 s

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

# Date 2008-01-16 Time 05:47:53 PST -0800 (1200491273.32 s)
Start R-work = 0.4791, R-free = 0.4667 (no bulk solvent and anisotropic scale)
Final R-work = 0.1459, R-free = 0.1919 (no bulk solvent and anisotropic scale)

Start R-work = 0.4696, R-free = 0.4555
Final R-work = 0.1256, R-free = 0.1730