# Date 2008-01-16 Time 05:44:11 PST -0800 (1200491051.73 s)
#phil __OFF__

Command line arguments: "../861.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26816
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 861

-------------------------------------------------------------------------------
  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: (70.9525, 45.9914, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 45.9914, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0608 1.96275
Completeness in resolution range: 0.951338
Completeness with d_max=infinity: 0.948528

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0608
                             d_min =   1.9628

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: (70.9525, 45.9914, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0608 1.96275
Completeness in resolution range: 0.951338
Completeness with d_max=infinity: 0.948528

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0613 -  4.2009 [2160/2186]  1946   214   9.9%
  bin  2:  4.2009 -  3.3464 [2077/2097]  1868   209  10.1%
  bin  3:  3.3464 -  2.9269 [2057/2076]  1852   205  10.0%
  bin  4:  2.9269 -  2.6609 [2030/2060]  1825   205  10.1%
  bin  5:  2.6609 -  2.4711 [2019/2038]  1824   195   9.7%
  bin  6:  2.4711 -  2.3260 [2011/2036]  1798   213  10.6%
  bin  7:  2.3260 -  2.2098 [2007/2035]  1812   195   9.7%
  bin  8:  2.2098 -  2.1139 [1976/2012]  1778   198  10.0%
  bin  9:  2.1139 -  2.0327 [1992/2034]  1795   197   9.9%
  bin 10:  2.0327 -  1.9628 [1260/2017]  1132   128  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_861/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: 0.15 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:
        1.74 -     2.37: 33
        2.37 -     3.00: 1981
        3.00 -     3.64: 4686
        3.64 -     4.27: 9224
        4.27 -     4.90: 12636
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.741 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.858 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  ... (remaining 28555 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_861/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_861/model_refine_001.geo

CPU time processing inputs: 9.61


============================ 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 = 70.9525 45.9914 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4261   r_free= 0.4258   ksol= 0.00   Bsol= 0.00   scale= 0.924    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.233996                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0613 -  4.6860 0.99   1402  159 0.3481 0.3521      6.5016      6.5107|
|  2:  4.6860 -  3.7381 0.99   1351  147 0.3572 0.3496      6.7288      6.6544|
|  3:  3.7381 -  3.2711 0.99   1328  143 0.3849 0.3610      6.6012       6.683|
|  4:  3.2711 -  2.9746 0.99   1322  155 0.4055 0.4348      6.4743      6.4505|
|  5:  2.9746 -  2.7628 0.99   1302  146 0.4541 0.4372      6.3167      6.3348|
|  6:  2.7628 -  2.6007 0.99   1311  142 0.4540 0.4656      6.2425       6.204|
|  7:  2.6007 -  2.4711 0.99   1299  136 0.4594 0.4614      6.2013      6.1722|
|  8:  2.4711 -  2.3639 0.98   1267  146 0.4732 0.4121      6.1371      6.1007|
|  9:  2.3639 -  2.2733 0.98   1282  153 0.4643 0.5067      6.0914      6.1346|
| 10:  2.2733 -  2.1951 1.00   1312  142 0.4737 0.4911      6.0599      6.0775|
| 11:  2.1951 -  2.1266 0.98   1286  136 0.4739 0.4832      6.0054      6.0249|
| 12:  2.1266 -  2.0660 0.98   1261  144 0.4809 0.5011      5.9406      6.0042|
| 13:  2.0660 -  2.0117 0.98   1273  139 0.4840 0.4767      5.8551       5.773|
| 14:  2.0117 -  1.9628 0.49    634   71 0.5194 0.4746      5.8474      5.8325|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0613 -  4.6860  1402   159  0.73  31.68   0.84     0.78      62867.73|
|  2:  4.6860 -  3.7381  1351   147  0.75  30.98   0.93     0.86      86775.39|
|  3:  3.7381 -  3.2711  1328   143  0.66  38.80   0.95     0.85      93415.99|
|  4:  3.2711 -  2.9746  1322   155  0.58  45.42   0.96     0.78      87491.33|
|  5:  2.9746 -  2.7628  1302   146  0.49  52.37   0.91     0.70      71023.92|
|  6:  2.7628 -  2.6007  1311   142  0.49  52.93   0.92     0.67      61937.66|
|  7:  2.6007 -  2.4711  1299   136  0.48  53.50   0.95     0.66      54062.20|
|  8:  2.4711 -  2.3639  1267   146  0.47  54.51   0.93     0.67      49680.16|
|  9:  2.3639 -  2.2733  1282   153  0.48  53.92   0.96     0.67      44555.67|
| 10:  2.2733 -  2.1951  1312   142  0.47  54.59   0.96     0.68      41572.80|
| 11:  2.1951 -  2.1266  1286   136  0.45  56.26   1.01     0.68      40529.83|
| 12:  2.1266 -  2.0660  1261   144  0.43  57.83   0.98     0.66      37208.49|
| 13:  2.0660 -  2.0117  1273   139  0.41  59.12   0.97     0.65      31975.70|
| 14:  2.0117 -  1.9628   634    71  0.47  55.07   0.96     0.67      25079.62|
|alpha:            min =        0.65 max =            0.86 mean =         0.72|
|beta:             min =    25079.62 max =        93415.99 mean =     57813.37|
|figures of merit: min =        0.00 max =            1.00 mean =         0.53|
|phase err.(work): min =        0.00 max =           89.98 mean =        49.36|
|phase err.(test): min =        0.00 max =           89.91 mean =        49.77|
|-----------------------------------------------------------------------------|

============================== 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 = 6.585746              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.162   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.849871              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.862   (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 |  1.741 -  2.057:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.057 -  2.373:       27 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.373 -  2.689:      118 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.689 -  3.004:     1863 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.004 -  3.320:     1928 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.320 -  3.636:     2758 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.636 -  3.952:     4750 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.952 -  4.268:     4474 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.268 -  4.584:     5732 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.584 -  4.900:     6904 |
|-----------------------------------------------------------------------------|
|-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 |        0.173 |
| 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  1.741 |       0.344 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.665)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4261   r_free= 0.4258   ksol= 0.00   Bsol= 0.00   scale= 0.924    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.233996                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4156   r_free= 0.4182   ksol= 0.34   Bsol= 38.46   scale= 0.950   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.78,2.86,-0.94,0.00,-0.00,-0.00); trace/3= 0.05                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.223546                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.638853              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.201   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.939807              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.662   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4156      final r-factor (work) = 0.3131          |
| start r-factor (free) = 0.4182      final r-factor (free) = 0.3451          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.7159 = 5.64 * 0.50 * 6.2223 + 1.00 * 0.1725                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.2699 = 5.64 * 0.50 * 6.0894 + 1.00 * 0.1012                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3131      final r-factor (work) = 0.2853          |
| start r-factor (free) = 0.3451      final r-factor (free) = 0.3574          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7290 = 0.94 * 1.00 * 6.0894 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6238 = 0.94 * 1.00 * 5.9668 + 1.00 * 0.0161                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.665)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.27   18.24    None  None   None       |
|    all(noH): 2823   0      0.00    99.27   18.24    None  None   None       |
|    Sol.    : 438    0      1.78    99.27   37.55    None  None   None       |
|    Mac.    : 2385   0      0.00    75.41   14.69    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 -   9.927:  898   |   5:    49.637 -  59.564:   69        |
|      1:     9.927 -  19.855:  977   |   6:    59.564 -  69.491:   36        |
|      2:    19.855 -  29.782:  456   |   7:    69.491 -  79.419:   14        |
|      3:    29.782 -  39.709:  233   |   8:    79.419 -  89.346:    0        |
|      4:    39.709 -  49.637:  139   |   9:    89.346 -  99.273:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2853 r_free = 0.3574             target_work(ml) = 5.973         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2851 r_free = 0.3577             target_work(ml) = 5.972         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2851   r_free= 0.3577   ksol= 0.34   Bsol= 38.46   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.78,2.86,-0.94,0.00,-0.00,-0.00); trace/3= 0.05                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.972487                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2848   r_free= 0.3545   ksol= 0.34   Bsol= 52.16   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.59,0.13,-0.92,0.00,-0.00,-0.00); trace/3= -0.79                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.971352                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.105403              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.791   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.395320              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.533  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2848      final r-factor (work) = 0.2042          |
| start r-factor (free) = 0.3545      final r-factor (free) = 0.2626          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.2833 = 8.11 * 0.50 * 5.9669 + 1.00 * 0.1012                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.7522 = 8.11 * 0.50 * 5.8394 + 1.00 * 0.0870                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2042      final r-factor (work) = 0.1790          |
| start r-factor (free) = 0.2626      final r-factor (free) = 0.2356          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3244 = 0.40 * 1.00 * 5.8394 + 1.00 * 0.0160                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2270 = 0.40 * 1.00 * 5.6087 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.665)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.84   17.59    None  None   None       |
|    all(noH): 2823   0      0.00    93.84   17.59    None  None   None       |
|    Sol.    : 438    0      5.03    93.84   40.61    None  None   None       |
|    Mac.    : 2385   0      0.00    83.06   13.37    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 -   9.384:  878   |   5:    46.920 -  56.303:  109        |
|      1:     9.384 -  18.768: 1156   |   6:    56.303 -  65.687:   61        |
|      2:    18.768 -  28.152:  310   |   7:    65.687 -  75.071:   19        |
|      3:    28.152 -  37.536:  159   |   8:    75.071 -  84.455:    2        |
|      4:    37.536 -  46.920:  128   |   9:    84.455 -  93.839:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1790 r_free = 0.2356             target_work(ml) = 5.554         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1789 r_free = 0.2351             target_work(ml) = 5.553         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1789   r_free= 0.2351   ksol= 0.34   Bsol= 52.16   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.59,0.13,-0.92,0.00,-0.00,-0.00); trace/3= -0.79                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.553341                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1781   r_free= 0.2330   ksol= 0.33   Bsol= 52.16   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.73,-1.57,-1.00,-0.00,-0.00,-0.00); trace/3= -1.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.546507                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.800613              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.782   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.148073              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.033  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1781      final r-factor (work) = 0.1410          |
| start r-factor (free) = 0.2330      final r-factor (free) = 0.1926          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9406 = 2.80 * 0.50 * 5.6085 + 1.00 * 0.0870                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6837 = 2.80 * 0.50 * 5.4494 + 1.00 * 0.0528                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1410      final r-factor (work) = 0.1353          |
| start r-factor (free) = 0.1926      final r-factor (free) = 0.1825          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8166 = 0.15 * 1.00 * 5.4494 + 1.00 * 0.0097                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7961 = 0.15 * 1.00 * 5.3287 + 1.00 * 0.0071                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.665)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.72   16.83    None  None   None       |
|    all(noH): 2823   0      0.00    81.72   16.83    None  None   None       |
|    Sol.    : 438    0      5.78    81.72   38.70    None  None   None       |
|    Mac.    : 2385   0      0.00    81.70   12.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.172:  592   |   5:    40.859 -  49.031:  105        |
|      1:     8.172 -  16.344: 1372   |   6:    49.031 -  57.203:   79        |
|      2:    16.344 -  24.516:  354   |   7:    57.203 -  65.375:   42        |
|      3:    24.516 -  32.688:  139   |   8:    65.375 -  73.547:    8        |
|      4:    32.688 -  40.859:  128   |   9:    73.547 -  81.719:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1353 r_free = 0.1825             target_work(ml) = 5.301         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1351 r_free = 0.1823             target_work(ml) = 5.300         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1351   r_free= 0.1823   ksol= 0.33   Bsol= 52.16   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.73,-1.57,-1.00,-0.00,-0.00,-0.00); trace/3= -1.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.300167                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1352   r_free= 0.1819   ksol= 0.33   Bsol= 52.16   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-2.43,-1.41,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.300119                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.914186              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.795  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.183282              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.762  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1352      final r-factor (work) = 0.1162          |
| start r-factor (free) = 0.1819      final r-factor (free) = 0.1621          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4873 = 3.91 * 0.50 * 5.3316 + 1.00 * 0.0528                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.3174 = 3.91 * 0.50 * 5.2370 + 1.00 * 0.0682                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1162      final r-factor (work) = 0.1131          |
| start r-factor (free) = 0.1621      final r-factor (free) = 0.1589          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9669 = 0.18 * 1.00 * 5.2370 + 1.00 * 0.0071                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9533 = 0.18 * 1.00 * 5.1625 + 1.00 * 0.0071                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.665)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.29    83.59   16.67    None  None   None       |
|    all(noH): 2823   0      1.29    83.59   16.67    None  None   None       |
|    Sol.    : 438    0      5.97    79.69   38.39    None  None   None       |
|    Mac.    : 2385   0      1.29    83.59   12.68    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.287 -   9.517:  910   |   5:    42.436 -  50.666:   99        |
|      1:     9.517 -  17.746: 1176   |   6:    50.666 -  58.896:   73        |
|      2:    17.746 -  25.976:  272   |   7:    58.896 -  67.126:   31        |
|      3:    25.976 -  34.206:  137   |   8:    67.126 -  75.356:    8        |
|      4:    34.206 -  42.436:  113   |   9:    75.356 -  83.586:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1131 r_free = 0.1589             target_work(ml) = 5.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1130 r_free = 0.1588             target_work(ml) = 5.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1588   ksol= 0.33   Bsol= 52.16   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-2.43,-1.41,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.151699                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1588   ksol= 0.33   Bsol= 52.16   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-2.57,-1.43,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.151473                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.917073              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 147.499  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.186493              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 163.955  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1130      final r-factor (work) = 0.1104          |
| start r-factor (free) = 0.1588      final r-factor (free) = 0.1555          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5975 = 2.92 * 0.50 * 5.1622 + 1.00 * 0.0682                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5633 = 2.92 * 0.50 * 5.1420 + 1.00 * 0.0635                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1104      final r-factor (work) = 0.1098          |
| start r-factor (free) = 0.1555      final r-factor (free) = 0.1547          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9660 = 0.19 * 1.00 * 5.1420 + 1.00 * 0.0071                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9635 = 0.19 * 1.00 * 5.1284 + 1.00 * 0.0071                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.665)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.29    84.97   16.51    None  None   None       |
|    all(noH): 2823   0      1.29    84.97   16.51    None  None   None       |
|    Sol.    : 438    0      6.51    77.89   37.91    None  None   None       |
|    Mac.    : 2385   0      1.29    84.97   12.58    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.288 -   9.657:  964   |   5:    43.129 -  51.497:   97        |
|      1:     9.657 -  18.025: 1149   |   6:    51.497 -  59.865:   58        |
|      2:    18.025 -  26.393:  252   |   7:    59.865 -  68.233:   23        |
|      3:    26.393 -  34.761:  142   |   8:    68.233 -  76.601:    8        |
|      4:    34.761 -  43.129:  125   |   9:    76.601 -  84.970:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1098 r_free = 0.1547             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1097 r_free = 0.1546             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1097   r_free= 0.1546   ksol= 0.33   Bsol= 52.16   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-2.57,-1.43,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.126973                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0613 -  4.6860 0.99   1402  159 0.0977 0.1284      5.3675      5.5694|
|  2:  4.6860 -  3.7381 0.99   1351  147 0.0859 0.1148      5.4524      5.6356|
|  3:  3.7381 -  3.2711 0.99   1328  143 0.1097 0.1537      5.4892      5.8659|
|  4:  3.2711 -  2.9746 0.99   1322  155 0.1213 0.1597       5.448      5.5833|
|  5:  2.9746 -  2.7628 0.99   1302  146 0.1324 0.1708      5.3031      5.5418|
|  6:  2.7628 -  2.6007 0.99   1311  142 0.1160 0.1636      5.1743      5.3867|
|  7:  2.6007 -  2.4711 0.99   1299  136 0.1236 0.1564      5.1464      5.3319|
|  8:  2.4711 -  2.3639 0.98   1267  146 0.1109 0.1803      5.0231      5.3737|
|  9:  2.3639 -  2.2733 0.98   1282  153 0.1128 0.1736      5.0047      5.2879|
| 10:  2.2733 -  2.1951 1.00   1312  142 0.1077 0.1639      4.9164      5.1607|
| 11:  2.1951 -  2.1266 0.98   1286  136 0.1091 0.1826      4.9205      5.2926|
| 12:  2.1266 -  2.0660 0.98   1261  144 0.1062 0.1490      4.8418      5.0358|
| 13:  2.0660 -  2.0117 0.98   1273  139 0.1102 0.1750      4.7491        5.04|
| 14:  2.0117 -  1.9628 0.49    634   71 0.0962 0.1470      4.6092      4.8516|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0613 -  4.6860  1402   159  0.94   8.68   0.98     0.96       6786.81|
|  2:  4.6860 -  3.7381  1351   147  0.95   8.04   1.02     1.01       9296.62|
|  3:  3.7381 -  3.2711  1328   143  0.93  11.49   1.02     1.02      10507.39|
|  4:  3.2711 -  2.9746  1322   155  0.92  13.60   1.01     0.98      10121.45|
|  5:  2.9746 -  2.7628  1302   146  0.90  15.47   0.99     0.97       7710.95|
|  6:  2.7628 -  2.6007  1311   142  0.90  15.57   0.99     0.97       6661.43|
|  7:  2.6007 -  2.4711  1299   136  0.91  15.10   1.00     0.97       5947.09|
|  8:  2.4711 -  2.3639  1267   146  0.91  15.08   0.99     0.97       4936.60|
|  9:  2.3639 -  2.2733  1282   153  0.91  14.83   1.00     0.98       4722.72|
| 10:  2.2733 -  2.1951  1312   142  0.91  15.08   1.00     0.97       4099.13|
| 11:  2.1951 -  2.1266  1286   136  0.90  15.63   1.00     0.95       4153.81|
| 12:  2.1266 -  2.0660  1261   144  0.91  15.04   1.01     1.01       3787.59|
| 13:  2.0660 -  2.0117  1273   139  0.91  15.48   1.00     0.99       3081.67|
| 14:  2.0117 -  1.9628   634    71  0.92  13.69   0.99     0.96       2353.98|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2353.98 max =        10507.39 mean =      6189.90|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.71|
|phase err.(test): min =        0.00 max =           89.44 mean =        13.18|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1098   r_free= 0.1541   ksol= 0.33   Bsol= 52.11   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,-2.53,-1.34,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.125741                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1098   r_free= 0.1541   ksol= 0.33   Bsol= 52.11   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,-2.53,-1.34,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.125741                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0613 -  4.6860 0.99   1402  159 0.0971 0.1263       5.353      5.5494|
|  2:  4.6860 -  3.7381 0.99   1351  147 0.0866 0.1136       5.452      5.6357|
|  3:  3.7381 -  3.2711 0.99   1328  143 0.1098 0.1516      5.4883      5.8549|
|  4:  3.2711 -  2.9746 0.99   1322  155 0.1213 0.1593       5.448       5.584|
|  5:  2.9746 -  2.7628 0.99   1302  146 0.1322 0.1707      5.3031      5.5419|
|  6:  2.7628 -  2.6007 0.99   1311  142 0.1163 0.1648      5.1763      5.3898|
|  7:  2.6007 -  2.4711 0.99   1299  136 0.1237 0.1565      5.1473      5.3331|
|  8:  2.4711 -  2.3639 0.98   1267  146 0.1104 0.1808      5.0234      5.3738|
|  9:  2.3639 -  2.2733 0.98   1282  153 0.1129 0.1735      5.0052      5.2884|
| 10:  2.2733 -  2.1951 1.00   1312  142 0.1076 0.1641      4.9162      5.1615|
| 11:  2.1951 -  2.1266 0.98   1286  136 0.1091 0.1822      4.9199      5.2919|
| 12:  2.1266 -  2.0660 0.98   1261  144 0.1061 0.1487      4.8406      5.0352|
| 13:  2.0660 -  2.0117 0.98   1273  139 0.1100 0.1747      4.7482      5.0397|
| 14:  2.0117 -  1.9628 0.49    634   71 0.0960 0.1468      4.6083      4.8512|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0613 -  4.6860  1402   159  0.94   8.50   0.98     0.96       6463.13|
|  2:  4.6860 -  3.7381  1351   147  0.95   7.89   1.02     1.02       9032.50|
|  3:  3.7381 -  3.2711  1328   143  0.93  11.41   1.03     1.02      10421.76|
|  4:  3.2711 -  2.9746  1322   155  0.92  13.59   1.01     0.98      10118.30|
|  5:  2.9746 -  2.7628  1302   146  0.90  15.50   0.99     0.97       7729.20|
|  6:  2.7628 -  2.6007  1311   142  0.90  15.61   0.99     0.97       6683.11|
|  7:  2.6007 -  2.4711  1299   136  0.91  15.11   1.00     0.97       5961.37|
|  8:  2.4711 -  2.3639  1267   146  0.91  15.11   0.99     0.97       4958.43|
|  9:  2.3639 -  2.2733  1282   153  0.91  14.85   1.01     0.98       4733.83|
| 10:  2.2733 -  2.1951  1312   142  0.91  15.10   1.00     0.97       4104.08|
| 11:  2.1951 -  2.1266  1286   136  0.90  15.64   1.00     0.95       4151.91|
| 12:  2.1266 -  2.0660  1261   144  0.91  15.03   1.02     1.02       3781.02|
| 13:  2.0660 -  2.0117  1273   139  0.91  15.48   1.01     0.99       3078.55|
| 14:  2.0117 -  1.9628   634    71  0.92  13.68   0.99     0.96       2349.77|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2349.77 max =        10421.76 mean =      6143.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.69|
|phase err.(test): min =        0.00 max =           89.78 mean =        13.17|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.665)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.24    84.92   16.47    None  None   None       |
|    all(noH): 2823   0      1.24    84.92   16.47    None  None   None       |
|    Sol.    : 438    0      6.46    77.85   37.86    None  None   None       |
|    Mac.    : 2385   0      1.24    84.92   12.54    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.243 -   9.611:  964   |   5:    43.084 -  51.452:   97        |
|      1:     9.611 -  17.979: 1149   |   6:    51.452 -  59.820:   58        |
|      2:    17.979 -  26.347:  252   |   7:    59.820 -  68.188:   23        |
|      3:    26.347 -  34.716:  142   |   8:    68.188 -  76.556:    8        |
|      4:    34.716 -  43.084:  125   |   9:    76.556 -  84.924:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 315         
Filter by distance & map next to the model:
   mapped sites are within: 0.655 - 4.571
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 313 from: 315
   mapped sites are within: 0.738 - 4.571

peak=    6.619 closest distance to " NE2 GLN A  11 " =    1.318
peak=    5.784 closest distance to " NH2 ARG A  56 " =    2.107
peak=    5.639 closest distance to " O   HOH Z 126 " =    2.059
peak=    5.404 closest distance to " O   HOH Z   7 " =    1.462
peak=    5.303 closest distance to " O   HOH Z  63 " =    1.777
peak=    5.151 closest distance to " CB  SER A  63 " =    1.254
peak=    5.113 closest distance to " CG  PRO A  54 " =    1.235
peak=    5.057 closest distance to " CB  GLN A 223 " =    1.502
peak=    5.013 closest distance to " O   HOH Z 423 " =    1.790
peak=    4.954 closest distance to " O   HOH Z 232 " =    2.339
peak=    4.914 closest distance to " O   HOH Z 369 " =    2.134
peak=    4.912 closest distance to " O   HOH Z 298 " =    1.937
peak=    4.850 closest distance to " O   HOH Z 417 " =    1.492
peak=    4.830 closest distance to " O   HOH Z 144 " =    1.629
peak=    4.751 closest distance to " ND2 ASN A 187 " =    1.530
peak=    4.729 closest distance to " O   HOH Z 419 " =    2.238
peak=    4.719 closest distance to " O   HOH Z 427 " =    2.477
peak=    4.704 closest distance to " CG  PRO A 213 " =    1.257
peak=    4.659 closest distance to " C   PRO A 198 " =    1.484
peak=    4.637 closest distance to " O   HOH Z 236 " =    1.509
peak=    4.605 closest distance to " O   HOH Z 287 " =    2.041
peak=    4.547 closest distance to " O   HOH Z 425 " =    1.403
peak=    4.517 closest distance to " CB  ASN A 148 " =    1.430
peak=    4.498 closest distance to " O   HOH Z 380 " =    1.761
peak=    4.469 closest distance to " CB  ASN A 187 " =    1.088
peak=    4.457 closest distance to " CG  TRP A 179 " =    2.277
peak=    4.441 closest distance to " O   HOH Z 193 " =    1.926
peak=    4.428 closest distance to " O   HOH Z  78 " =    1.747
peak=    4.415 closest distance to " O   HOH Z   2 " =    1.670
peak=    4.401 closest distance to " CB  GLU A 152 " =    1.297
peak=    4.383 closest distance to " O   HOH Z   1 " =    1.748
peak=    4.370 closest distance to " CB  PRO A  54 " =    0.914
peak=    4.358 closest distance to " O   HOH Z 217 " =    2.713
peak=    4.345 closest distance to " O   HOH Z  10 " =    1.803
peak=    4.304 closest distance to " CB  GLU A 128 " =    0.952
peak=    4.298 closest distance to " CB  GLN A 183 " =    1.178
peak=    4.275 closest distance to " CB  ARG A 275 " =    0.913
peak=    4.219 closest distance to " CA  TYR A  30 " =    0.981
peak=    4.198 closest distance to " O   HOH Z 261 " =    1.785
peak=    4.193 closest distance to " CB  ARG A 139 " =    1.024
peak=    4.180 closest distance to " O   SER A  87 " =    2.174
peak=    4.171 closest distance to " CB  SER A   3 " =    1.494
peak=    4.170 closest distance to " O   HOH Z   9 " =    2.096
peak=    4.092 closest distance to " O   HOH Z 368 " =    3.649
peak=    4.080 closest distance to " CB  LEU A 228 " =    1.071
peak=    4.033 closest distance to " O   HOH Z 327 " =    1.749
peak=    4.014 closest distance to " O   HOH Z 272 " =    1.802
peak=    4.012 closest distance to " O   HOH Z 193 " =    1.673
peak=    4.008 closest distance to " CG  PRO A 198 " =    1.231
peak=    4.002 closest distance to " O   HOH Z 234 " =    3.781
peak=    3.984 closest distance to " CB  SER A 216 " =    0.764
peak=    3.982 closest distance to " O   HOH Z  44 " =    1.707
peak=    3.966 closest distance to " CD  ARG A  66 " =    2.272
peak=    3.964 closest distance to " CB  ARG A  79 " =    1.303
peak=    3.954 closest distance to " O   HOH Z 405 " =    1.408
peak=    3.953 closest distance to " O   HOH Z 108 " =    1.601
peak=    3.945 closest distance to " O   HOH Z  78 " =    2.302
peak=    3.939 closest distance to " CB  ARG A 190 " =    1.649
peak=    3.925 closest distance to " O   HOH Z 437 " =    1.973
peak=    3.919 closest distance to " N   PHE A 130 " =    1.247
peak=    3.905 closest distance to " OD1 ASN A  69 " =    2.741
peak=    3.891 closest distance to " CA  ALA A 233 " =    1.101
peak=    3.885 closest distance to " OG ASER A 258 " =    3.038
peak=    3.858 closest distance to " O   HOH Z  61 " =    1.597
peak=    3.843 closest distance to " O   HOH Z 146 " =    1.850
peak=    3.839 closest distance to " O   HOH Z 394 " =    1.632
peak=    3.837 closest distance to " CG2 VAL A 257 " =    0.968
peak=    3.832 closest distance to " CD  ARG A 159 " =    0.774
peak=    3.825 closest distance to " O   HOH Z 217 " =    1.738
peak=    3.823 closest distance to " O   HOH Z 175 " =    2.143
peak=    3.817 closest distance to " O   HOH Z 132 " =    2.397
peak=    3.812 closest distance to " O   HOH Z 313 " =    1.704
peak=    3.804 closest distance to " O   HOH Z  40 " =    2.168
peak=    3.791 closest distance to " O   HOH Z   1 " =    1.752
peak=    3.789 closest distance to " O   HOH Z 147 " =    1.755
peak=    3.788 closest distance to " CB  VAL A 265 " =    1.284
peak=    3.787 closest distance to " CG  LEU A 167 " =    1.274
peak=    3.783 closest distance to " O   HOH Z  61 " =    1.532
peak=    3.782 closest distance to " ND1 HIS A  86 " =    1.750
peak=    3.774 closest distance to " N   ALA A   1 " =    2.231
peak=    3.769 closest distance to " OD2 ASP A 286 " =    2.741
peak=    3.766 closest distance to " O   HOH Z 257 " =    2.259
peak=    3.765 closest distance to " O   HOH Z 392 " =    1.323
peak=    3.754 closest distance to " CG1 ILE A  33 " =    1.239
peak=    3.751 closest distance to " O   HOH Z  21 " =    1.707
peak=    3.746 closest distance to " O   HOH Z 368 " =    1.839
peak=    3.739 closest distance to " O   HOH Z 209 " =    2.307
peak=    3.736 closest distance to " OD1BASN A 224 " =    2.261
peak=    3.733 closest distance to " CG  GLN A  11 " =    2.037
peak=    3.732 closest distance to " CA  GLY A 241 " =    3.684
peak=    3.729 closest distance to " CB  ASN A  39 " =    0.822
peak=    3.722 closest distance to " O   HOH Z 352 " =    1.872
peak=    3.721 closest distance to " O   HOH Z 128 " =    2.155
peak=    3.718 closest distance to " CB  TYR A 169 " =    0.863
peak=    3.714 closest distance to " O   HOH Z 371 " =    1.834
peak=    3.712 closest distance to " O   HOH Z 403 " =    1.384
peak=    3.709 closest distance to " CA  THR A 264 " =    0.855
peak=    3.685 closest distance to " O   HOH Z 371 " =    2.736
peak=    3.684 closest distance to " O   HOH Z  68 " =    2.038
peak=    3.683 closest distance to " O   HOH Z  59 " =    1.998
peak=    3.681 closest distance to " NE AARG A 275 " =    1.451
peak=    3.678 closest distance to " O   HOH Z 183 " =    1.437
peak=    3.673 closest distance to " CD2 LEU A 255 " =    1.619
peak=    3.672 closest distance to " O   HOH Z  64 " =    2.034
peak=    3.670 closest distance to " CE  LYS A  76 " =    0.846
peak=    3.658 closest distance to " O   HOH Z 365 " =    2.737
peak=    3.646 closest distance to " O   HOH Z 344 " =    3.097
peak=    3.643 closest distance to " O   HOH Z 128 " =    2.090
peak=    3.639 closest distance to " O   HOH Z 119 " =    1.606
peak=    3.636 closest distance to " O   HOH Z  30 " =    1.734
peak=    3.633 closest distance to " O   HOH Z 144 " =    2.325
peak=    3.628 closest distance to " CB  THR A 157 " =    1.113
peak=    3.627 closest distance to " O   HOH Z 362 " =    2.127
peak=    3.623 closest distance to " CA  ALA A  21 " =    1.250
peak=    3.616 closest distance to " O   HOH Z 214 " =    1.310
peak=    3.615 closest distance to " CB  TRP A 266 " =    1.029
peak=    3.613 closest distance to " O   HOH Z 158 " =    2.865
peak=    3.611 closest distance to " CA  ASN A 215 " =    1.074
peak=    3.604 closest distance to " O   HOH Z 250 " =    1.513
peak=    3.603 closest distance to " O   HOH Z 188 " =    2.053
peak=    3.594 closest distance to " CD  PRO A 243 " =    1.597
peak=    3.587 closest distance to " CG2 THR A 221 " =    1.026
peak=    3.571 closest distance to " CE1 TYR A 186 " =    1.362
peak=    3.571 closest distance to " O   HOH Z  88 " =    3.006
peak=    3.567 closest distance to " CG  PRO A 243 " =    1.078
peak=    3.564 closest distance to " CG  PRO A  90 " =    1.148
peak=    3.562 closest distance to " O   HOH Z 389 " =    1.946
peak=    3.560 closest distance to " CB  GLU A 277 " =    3.497
peak=    3.558 closest distance to " CA  ILE A 234 " =    1.005
peak=    3.558 closest distance to " O   HOH Z 135 " =    1.695
peak=    3.549 closest distance to " O   ASN A 209 " =    1.256
peak=    3.542 closest distance to " O   HOH Z 133 " =    2.435
peak=    3.540 closest distance to " CA  SER A  87 " =    0.971
peak=    3.535 closest distance to " CB  LEU A 143 " =    1.113
peak=    3.533 closest distance to " CB  ALA A  34 " =    1.198
peak=    3.516 closest distance to " O   HOH Z  44 " =    2.992
peak=    3.515 closest distance to " CA  ALA A 299 " =    0.835
peak=    3.514 closest distance to " O   HOH Z 374 " =    2.645
peak=    3.506 closest distance to " NH1BARG A 145 " =    1.309
peak=    3.503 closest distance to " CB  TRP A 179 " =    1.441
peak=    3.491 closest distance to " O   HOH Z 281 " =    1.793
peak=    3.490 closest distance to " O   HOH Z 386 " =    3.106
peak=    3.472 closest distance to " NH1AARG A 145 " =    1.130
peak=    3.472 closest distance to " O   HOH Z 426 " =    1.851
peak=    3.470 closest distance to " O   HOH Z 435 " =    1.937
peak=    3.467 closest distance to " NH2BARG A 145 " =    2.080
peak=    3.465 closest distance to " CA  TYR A  30 " =    1.047
peak=    3.463 closest distance to " O   HOH Z 302 " =    1.714
peak=    3.460 closest distance to " O   HOH Z  49 " =    1.408
peak=    3.458 closest distance to " O   HOH Z 139 " =    1.249
peak=    3.457 closest distance to " OG  SER A  62 " =    3.086
peak=    3.454 closest distance to " O   HOH Z 116 " =    2.854
peak=    3.453 closest distance to " CD  ARG A 138 " =    0.757
peak=    3.453 closest distance to " CB  ASN A 142 " =    0.930
peak=    3.443 closest distance to " CZ  PHE A 218 " =    1.029
peak=    3.442 closest distance to " NE2 GLN A 278 " =    3.603
peak=    3.440 closest distance to " O   GLY A 302 " =    1.591
peak=    3.436 closest distance to " O   HOH Z 291 " =    1.444
peak=    3.431 closest distance to " CD1 ILE A 263 " =    1.376
peak=    3.431 closest distance to " CB  ALA A  10 " =    0.792
peak=    3.420 closest distance to " O   HOH Z 108 " =    1.912
peak=    3.418 closest distance to " O   HOH Z  58 " =    1.509
peak=    3.418 closest distance to " O   HOH Z  43 " =    2.288
peak=    3.416 closest distance to " O   HOH Z 263 " =    2.336
peak=    3.415 closest distance to " O   HOH Z 425 " =    1.974
peak=    3.413 closest distance to " OG BSER A  99 " =    2.222
peak=    3.409 closest distance to " O   HOH Z 195 " =    1.385
peak=    3.409 closest distance to " O   HOH Z 180 " =    2.111
peak=    3.407 closest distance to " N   ASN A 127 " =    1.300
peak=    3.405 closest distance to " O   HOH Z 283 " =    2.384
peak=    3.402 closest distance to " CG  GLN A  89 " =    1.423
peak=    3.402 closest distance to " CG1 ILE A 151 " =    1.012
peak=    3.400 closest distance to " O   HOH Z 113 " =    1.891
peak=    3.394 closest distance to " O   HOH Z 207 " =    1.688
peak=    3.393 closest distance to " N   TYR A  15 " =    0.863
peak=    3.393 closest distance to " CG2AVAL A 121 " =    2.422
peak=    3.382 closest distance to " CA  GLY A 267 " =    1.237
peak=    3.379 closest distance to " O   HOH Z 189 " =    2.165
peak=    3.379 closest distance to " O   ALA A   1 " =    1.585
peak=    3.373 closest distance to " NE2 GLN A  73 " =    3.653
peak=    3.372 closest distance to " CB  LYS A 117 " =    1.215
peak=    3.371 closest distance to " O   HOH Z 171 " =    2.806
peak=    3.370 closest distance to " O   HOH Z 281 " =    4.571
peak=    3.367 closest distance to " O   HOH Z 289 " =    1.731
peak=    3.365 closest distance to " N   CYS A 260 " =    0.738
peak=    3.361 closest distance to " O   HOH Z 151 " =    1.979
peak=    3.360 closest distance to " O   HOH Z  88 " =    2.633
peak=    3.357 closest distance to " CB  ILE A 120 " =    1.193
peak=    3.357 closest distance to " O   HOH Z 266 " =    3.196
peak=    3.353 closest distance to " OG  SER A  62 " =    3.025
peak=    3.346 closest distance to " O   HOH Z 248 " =    1.599
peak=    3.343 closest distance to " O   HOH Z 388 " =    2.076
peak=    3.343 closest distance to " O   HOH Z 133 " =    1.549
peak=    3.341 closest distance to " CA  TYR A 116 " =    1.331
peak=    3.339 closest distance to " N   SER A  97 " =    0.848
peak=    3.336 closest distance to " O   HOH Z 255 " =    1.702
peak=    3.336 closest distance to " O   HOH Z 145 " =    2.223
peak=    3.326 closest distance to " CB  SER A  62 " =    1.198
peak=    3.324 closest distance to " N   SER A 134 " =    1.306
peak=    3.321 closest distance to " O   HOH Z 193 " =    2.008
peak=    3.320 closest distance to " OG  SER A  22 " =    2.790
peak=    3.317 closest distance to " CD BLYS A 290 " =    1.183
peak=    3.316 closest distance to " O   HOH Z 244 " =    1.642
peak=    3.312 closest distance to " O   HOH Z 145 " =    1.466
peak=    3.309 closest distance to " O   HOH Z  97 " =    1.886
peak=    3.307 closest distance to " O   ALA A 165 " =    1.323
peak=    3.304 closest distance to " CD2 TRP A 179 " =    1.244
peak=    3.304 closest distance to " O   HOH Z 184 " =    1.874
peak=    3.304 closest distance to " O   HOH Z 352 " =    1.506
peak=    3.302 closest distance to " O   HOH Z 263 " =    1.794
peak=    3.295 closest distance to " CA  ASP A 162 " =    1.067
peak=    3.289 closest distance to " OG BSER A 164 " =    2.295
peak=    3.288 closest distance to " NH2BARG A 190 " =    1.525
peak=    3.288 closest distance to " O   HOH Z 334 " =    2.994
peak=    3.285 closest distance to " CB  SER A 212 " =    1.155
peak=    3.276 closest distance to " CA  SER A  32 " =    1.641
peak=    3.274 closest distance to " O   HOH Z 128 " =    2.067
peak=    3.268 closest distance to " O   HOH Z 334 " =    1.451
peak=    3.265 closest distance to " CA  MET A  40 " =    1.097
peak=    3.262 closest distance to " NH2 ARG A 219 " =    1.838
peak=    3.261 closest distance to " O   HOH Z  88 " =    3.901
peak=    3.260 closest distance to " CD2 TYR A 186 " =    0.986
peak=    3.260 closest distance to " CB  VAL A 202 " =    1.641
peak=    3.260 closest distance to " O   HOH Z 126 " =    1.458
peak=    3.258 closest distance to " O   HOH Z 273 " =    2.820
peak=    3.257 closest distance to " O   HOH Z 329 " =    3.767
peak=    3.256 closest distance to " O   HOH Z  50 " =    1.747
peak=    3.252 closest distance to " CB  ALA A 180 " =    1.291
peak=    3.251 closest distance to " O   HOH Z  17 " =    1.946
peak=    3.250 closest distance to " O   HOH Z 407 " =    2.129
peak=    3.246 closest distance to " O   HOH Z 207 " =    2.039
peak=    3.245 closest distance to " O   HOH Z 271 " =    2.360
peak=    3.238 closest distance to " CE BLYS A 290 " =    1.279
peak=    3.237 closest distance to " O   HOH Z 393 " =    1.273
peak=    3.227 closest distance to " N   GLN A 278 " =    1.105
peak=    3.227 closest distance to " CA  ALA A  51 " =    1.025
peak=    3.226 closest distance to " O   HOH Z   9 " =    1.196
peak=    3.226 closest distance to " O   TYR A 116 " =    1.374
peak=    3.223 closest distance to " O   HOH Z 110 " =    1.573
peak=    3.220 closest distance to " CB  ALA A 114 " =    1.460
peak=    3.209 closest distance to " O   HOH Z 409 " =    2.277
peak=    3.206 closest distance to " CH2 TRP A  92 " =    2.120
peak=    3.205 closest distance to " O   HOH Z 148 " =    3.334
peak=    3.204 closest distance to " O   MET A 105 " =    1.773
peak=    3.203 closest distance to " CD  LYS A 166 " =    1.321
peak=    3.202 closest distance to " CB  ARG A 138 " =    0.989
peak=    3.199 closest distance to " O   HOH Z 305 " =    3.613
peak=    3.198 closest distance to " CA  ALA A 291 " =    0.969
peak=    3.198 closest distance to " O   HOH Z  73 " =    1.969
peak=    3.197 closest distance to " NE2 GLN A  58 " =    3.633
peak=    3.191 closest distance to " CB  TYR A 116 " =    0.877
peak=    3.189 closest distance to " CA  ARG A 195 " =    1.315
peak=    3.188 closest distance to " CB  MET A  40 " =    0.911
peak=    3.187 closest distance to " CD1 LEU A 300 " =    1.241
peak=    3.187 closest distance to " CB  ALA A 114 " =    1.171
peak=    3.186 closest distance to " O   HOH Z 172 " =    2.732
peak=    3.184 closest distance to " O   HOH Z 154 " =    1.952
peak=    3.184 closest distance to " O   HOH Z 213 " =    1.966
peak=    3.183 closest distance to " CG  GLN A 144 " =    0.939
peak=    3.181 closest distance to " O   HOH Z 345 " =    1.825
peak=    3.179 closest distance to " CD  ARG A 219 " =    1.109
peak=    3.177 closest distance to " O   HOH Z 155 " =    1.479
peak=    3.177 closest distance to " CB  ALA A   7 " =    1.196
peak=    3.176 closest distance to " O   HOH Z 295 " =    1.545
peak=    3.176 closest distance to " CA  GLY A 136 " =    0.971
peak=    3.173 closest distance to " N   GLU A   2 " =    1.325
peak=    3.173 closest distance to " O   GLY A 147 " =    1.408
peak=    3.172 closest distance to " O   HOH Z 422 " =    2.745
peak=    3.171 closest distance to " CB  GLN A  88 " =    1.294
peak=    3.171 closest distance to " CA  LEU A 101 " =    1.641
peak=    3.171 closest distance to " O   HOH Z 359 " =    1.443
peak=    3.167 closest distance to " CB  SER A 276 " =    1.248
peak=    3.167 closest distance to " CA  ALA A 154 " =    0.908
peak=    3.166 closest distance to " O   HOH Z 140 " =    2.395
peak=    3.162 closest distance to " CG  MET A 113 " =    1.323
peak=    3.161 closest distance to " NE  ARG A  66 " =    3.792
peak=    3.161 closest distance to " CB  ASP A 140 " =    0.792
peak=    3.155 closest distance to " O   HOH Z 303 " =    1.762
peak=    3.154 closest distance to " CB  ASN A 224 " =    0.978
peak=    3.154 closest distance to " O   HOH Z 403 " =    1.543
peak=    3.152 closest distance to " NH2AARG A 190 " =    1.557
peak=    3.149 closest distance to " O   HOH Z 415 " =    3.651
peak=    3.148 closest distance to " OG BSER A 134 " =    3.118
peak=    3.147 closest distance to " N   GLY A 241 " =    1.476
peak=    3.143 closest distance to " O   HOH Z 211 " =    2.462
peak=    3.141 closest distance to " O   HOH Z 115 " =    1.751
peak=    3.138 closest distance to " O   HOH Z 173 " =    1.801
peak=    3.133 closest distance to " CG  PRO A 280 " =    0.750
peak=    3.132 closest distance to " CB  LEU A 255 " =    1.415
peak=    3.132 closest distance to " N   ARG A 156 " =    1.300
peak=    3.131 closest distance to " CG  ARG A 159 " =    0.753
peak=    3.129 closest distance to " O   HOH Z 282 " =    1.408
peak=    3.126 closest distance to " O   HOH Z 151 " =    2.487
peak=    3.126 closest distance to " CG  GLU A 277 " =    2.059
peak=    3.123 closest distance to " CB  LEU A 300 " =    0.938
peak=    3.120 closest distance to " O   HOH Z 227 " =    1.989
peak=    3.116 closest distance to " O   HOH Z 286 " =    2.500
peak=    3.108 closest distance to " CD1 ILE A  33 " =    1.620
peak=    3.106 closest distance to " CG1BVAL A  72 " =    1.387
peak=    3.104 closest distance to " CB  PRO A 243 " =    1.159
peak=    3.102 closest distance to " O   HOH Z 332 " =    1.525
peak=    3.096 closest distance to " CG  GLN A 278 " =    1.294
peak=    3.082 closest distance to " O   GLY A 302 " =    2.107
peak=    3.062 closest distance to " CB  GLU A 152 " =    1.341
peak=    3.056 closest distance to " CA  ASP A 140 " =    1.233
peak=    3.055 closest distance to " CB  TRP A 150 " =    1.368
peak=    3.052 closest distance to " CA  SER A  95 " =    1.091
peak=    3.050 closest distance to " CD2 HIS A  81 " =    1.185
peak=    3.048 closest distance to " CE  MET A  93 " =    1.489
peak=    3.042 closest distance to " O   HOH Z  29 " =    2.298
peak=    3.036 closest distance to " CG BARG A 102 " =    1.827
peak=    3.019 closest distance to " O   HOH Z 130 " =    2.098
peak=    3.007 closest distance to " CB  VAL A 265 " =    2.090

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 199         
Filter by distance & map next to the model:
   mapped sites are within: 0.472 - 5.738
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 199
   mapped sites are within: 0.722 - 5.738

peak=   -4.493 closest distance to " CB  PRO A 243 " =    2.504
peak=   -4.349 closest distance to " O   HOH Z 377 " =    1.961
peak=   -4.303 closest distance to " CD  ARG A  14 " =    3.295
peak=   -4.300 closest distance to " O   PRO A 198 " =    1.315
peak=   -4.295 closest distance to " O   HOH Z 266 " =    4.616
peak=   -4.196 closest distance to " O   HOH Z 290 " =    1.168
peak=   -4.109 closest distance to " O   HOH Z 435 " =    2.946
peak=   -4.070 closest distance to " O   HOH Z 407 " =    3.220
peak=   -4.066 closest distance to " CZ3 TRP A 179 " =    1.143
peak=   -4.065 closest distance to " CA  GLY A  98 " =    1.827
peak=   -4.006 closest distance to " C   HIS A 108 " =    1.168
peak=   -4.001 closest distance to " O   HOH Z 185 " =    2.091
peak=   -3.995 closest distance to " CD  ARG A 156 " =    1.977
peak=   -3.934 closest distance to " O   HOH Z 313 " =    1.943
peak=   -3.901 closest distance to " CG1 VAL A 112 " =    2.836
peak=   -3.896 closest distance to " O   HOH Z  13 " =    1.420
peak=   -3.874 closest distance to " O   HOH Z  65 " =    1.017
peak=   -3.863 closest distance to " O   VAL A 153 " =    2.358
peak=   -3.837 closest distance to " CB  ALA A 248 " =    1.962
peak=   -3.832 closest distance to " O   HOH Z 231 " =    1.964
peak=   -3.822 closest distance to " OG BSER A 134 " =    1.587
peak=   -3.821 closest distance to " OG BSER A 134 " =    1.381
peak=   -3.804 closest distance to " CD1 LEU A 101 " =    2.287
peak=   -3.787 closest distance to " O   SER A 135 " =    1.455
peak=   -3.785 closest distance to " O   HOH Z 438 " =    1.008
peak=   -3.785 closest distance to " CG  ASP A 231 " =    0.752
peak=   -3.783 closest distance to " CA  GLY A  23 " =    2.639
peak=   -3.781 closest distance to " O   HOH Z 351 " =    1.532
peak=   -3.769 closest distance to " OG  SER A   3 " =    1.612
peak=   -3.764 closest distance to " O   VAL A  67 " =    2.509
peak=   -3.745 closest distance to " O   ARG A 145 " =    1.476
peak=   -3.743 closest distance to " O   HOH Z 152 " =    4.768
peak=   -3.742 closest distance to " O   HOH Z  43 " =    1.725
peak=   -3.731 closest distance to " O   PRO A 243 " =    2.458
peak=   -3.708 closest distance to " N   GLN A  58 " =    1.703
peak=   -3.694 closest distance to " O   PRO A 198 " =    1.234
peak=   -3.680 closest distance to " CG  MET A 105 " =    0.942
peak=   -3.672 closest distance to " ND2 ASN A  45 " =    1.118
peak=   -3.660 closest distance to " O   HOH Z 389 " =    1.887
peak=   -3.660 closest distance to " C   ALA A 158 " =    1.512
peak=   -3.650 closest distance to " O   HOH Z 231 " =    0.954
peak=   -3.648 closest distance to " O   HOH Z 385 " =    1.992
peak=   -3.646 closest distance to " O   HOH Z 316 " =    1.911
peak=   -3.638 closest distance to " OG  SER A  87 " =    1.314
peak=   -3.622 closest distance to " CA  GLY A 203 " =    2.220
peak=   -3.618 closest distance to " OG  SER A  97 " =    2.151
peak=   -3.606 closest distance to " O   VAL A 189 " =    2.470
peak=   -3.601 closest distance to " CE3 TRP A 123 " =    1.317
peak=   -3.590 closest distance to " N   THR A 157 " =    1.547
peak=   -3.584 closest distance to " CG  GLN A 223 " =    1.695
peak=   -3.583 closest distance to " CZ  PHE A  59 " =    1.514
peak=   -3.583 closest distance to " CG1 VAL A 197 " =    2.161
peak=   -3.572 closest distance to " CD  GLN A  58 " =    1.278
peak=   -3.569 closest distance to " O   HOH Z   1 " =    1.378
peak=   -3.568 closest distance to " NH2AARG A 275 " =    5.393
peak=   -3.568 closest distance to " O   HOH Z  51 " =    1.026
peak=   -3.565 closest distance to " O   HOH Z 298 " =    1.216
peak=   -3.556 closest distance to " CB  PHE A 192 " =    1.756
peak=   -3.555 closest distance to " CB  ALA A 291 " =    2.166
peak=   -3.546 closest distance to " N   GLN A 122 " =    1.421
peak=   -3.543 closest distance to " O   VAL A  67 " =    2.772
peak=   -3.540 closest distance to " CD2 LEU A 237 " =    2.843
peak=   -3.532 closest distance to " C   ASN A 285 " =    2.323
peak=   -3.528 closest distance to " O   HOH Z 317 " =    1.464
peak=   -3.528 closest distance to " CB  PRO A 163 " =    2.478
peak=   -3.527 closest distance to " OD1 ASN A 148 " =    1.679
peak=   -3.521 closest distance to " CB  ASP A  27 " =    2.360
peak=   -3.516 closest distance to " CA  GLY A 133 " =    2.067
peak=   -3.514 closest distance to " O   HOH Z 359 " =    3.296
peak=   -3.512 closest distance to " CD  GLN A  58 " =    0.985
peak=   -3.512 closest distance to " CB  ASN A  39 " =    2.238
peak=   -3.506 closest distance to " CB  CYS A 254 " =    2.181
peak=   -3.505 closest distance to " CG  PHE A 283 " =    2.578
peak=   -3.491 closest distance to " N   ALA A  43 " =    2.425
peak=   -3.483 closest distance to " CD  GLN A  88 " =    0.809
peak=   -3.483 closest distance to " CD  ARG A 139 " =    1.591
peak=   -3.480 closest distance to " O   HOH Z  38 " =    1.556
peak=   -3.477 closest distance to " CE2 PHE A 218 " =    2.457
peak=   -3.472 closest distance to " O   HOH Z  68 " =    2.329
peak=   -3.470 closest distance to " CG  LYS A 193 " =    2.275
peak=   -3.468 closest distance to " O   HOH Z  60 " =    2.161
peak=   -3.466 closest distance to " ND2 ASN A  45 " =    1.913
peak=   -3.462 closest distance to " O   HOH Z 282 " =    0.827
peak=   -3.462 closest distance to " O   HOH Z 250 " =    1.432
peak=   -3.456 closest distance to " O   HOH Z 131 " =    4.114
peak=   -3.453 closest distance to " CE  LYS A  76 " =    2.895
peak=   -3.431 closest distance to " CA  GLY A 241 " =    2.213
peak=   -3.430 closest distance to " NH2 ARG A  79 " =    1.885
peak=   -3.429 closest distance to " C   LEU A 222 " =    0.778
peak=   -3.422 closest distance to " OD2 ASP A 191 " =    1.490
peak=   -3.416 closest distance to " O   HOH Z 290 " =    0.918
peak=   -3.416 closest distance to " C   LEU A 143 " =    1.239
peak=   -3.410 closest distance to " CE  MET A  93 " =    1.101
peak=   -3.408 closest distance to " O   HOH Z 345 " =    2.160
peak=   -3.407 closest distance to " O   ILE A 109 " =    2.537
peak=   -3.392 closest distance to " CB  TRP A  85 " =    2.405
peak=   -3.390 closest distance to " CB  ASP A 132 " =    2.310
peak=   -3.385 closest distance to " O   HOH Z 191 " =    5.369
peak=   -3.382 closest distance to " O   HOH Z  63 " =    2.351
peak=   -3.380 closest distance to " O   HOH Z 409 " =    5.738
peak=   -3.376 closest distance to " O   VAL A 174 " =    2.256
peak=   -3.363 closest distance to " CG  PRO A 163 " =    2.447
peak=   -3.359 closest distance to " O   HOH Z 211 " =    1.526
peak=   -3.351 closest distance to " O   HOH Z 111 " =    1.084
peak=   -3.349 closest distance to " O   SER A  95 " =    1.430
peak=   -3.346 closest distance to " O   HOH Z  11 " =    1.878
peak=   -3.345 closest distance to " O   HOH Z 298 " =    2.553
peak=   -3.341 closest distance to " O   HOH Z 377 " =    0.782
peak=   -3.341 closest distance to " CD  GLN A 223 " =    1.056
peak=   -3.341 closest distance to " O   HOH Z 166 " =    1.295
peak=   -3.338 closest distance to " ND2 ASN A  60 " =    1.890
peak=   -3.333 closest distance to " O   HOH Z  88 " =    1.727
peak=   -3.332 closest distance to " O   HOH Z 393 " =    3.267
peak=   -3.328 closest distance to " NH1AARG A 275 " =    1.790
peak=   -3.320 closest distance to " OE1 GLN A  88 " =    1.157
peak=   -3.318 closest distance to " O   HOH Z 281 " =    3.091
peak=   -3.313 closest distance to " O   SER A   3 " =    1.125
peak=   -3.312 closest distance to " O   HOH Z 282 " =    4.556
peak=   -3.310 closest distance to " CE3 TRP A 274 " =    0.966
peak=   -3.305 closest distance to " O   PRO A 163 " =    1.896
peak=   -3.304 closest distance to " O   HOH Z 417 " =    2.245
peak=   -3.301 closest distance to " O   LEU A 101 " =    2.288
peak=   -3.291 closest distance to " OD2 ASP A 171 " =    1.989
peak=   -3.285 closest distance to " O   PHE A 218 " =    1.435
peak=   -3.282 closest distance to " CA  GLY A  57 " =    2.094
peak=   -3.282 closest distance to " CZ  ARG A  66 " =    0.741
peak=   -3.282 closest distance to " OD2 ASP A  27 " =    1.634
peak=   -3.273 closest distance to " OD1 ASP A 171 " =    1.594
peak=   -3.266 closest distance to " O   HOH Z  60 " =    2.373
peak=   -3.265 closest distance to " ND2 ASN A 249 " =    2.298
peak=   -3.264 closest distance to " CE  LYS A  76 " =    2.788
peak=   -3.263 closest distance to " CD2 TYR A 293 " =    1.947
peak=   -3.261 closest distance to " O   HOH Z 281 " =    2.896
peak=   -3.257 closest distance to " CB  ALA A  43 " =    2.310
peak=   -3.255 closest distance to " O   GLY A  80 " =    2.362
peak=   -3.251 closest distance to " CB  CYS A 201 " =    2.476
peak=   -3.243 closest distance to " OG  SER A 245 " =    1.107
peak=   -3.242 closest distance to " C   LYS A  76 " =    1.656
peak=   -3.240 closest distance to " O   HOH Z 384 " =    2.810
peak=   -3.237 closest distance to " CE  MET A 105 " =    2.326
peak=   -3.234 closest distance to " CE2 TYR A  30 " =    2.641
peak=   -3.233 closest distance to " O   HOH Z 234 " =    4.012
peak=   -3.233 closest distance to " O   HOH Z 198 " =    1.532
peak=   -3.232 closest distance to " O   GLY A  17 " =    1.154
peak=   -3.231 closest distance to " O   HOH Z 102 " =    1.607
peak=   -3.230 closest distance to " O   HOH Z 348 " =    1.798
peak=   -3.227 closest distance to " NE2 GLN A  58 " =    2.972
peak=   -3.226 closest distance to " O   LYS A 289 " =    3.218
peak=   -3.224 closest distance to " CE3 TRP A 274 " =    2.438
peak=   -3.222 closest distance to " O   HOH Z  90 " =    2.665
peak=   -3.220 closest distance to " OG1 THR A 178 " =    1.186
peak=   -3.219 closest distance to " O   ALA A 161 " =    1.574
peak=   -3.218 closest distance to " O   HOH Z  52 " =    1.353
peak=   -3.218 closest distance to " O   HOH Z  24 " =    1.199
peak=   -3.218 closest distance to " CD1 PHE A  59 " =    1.959
peak=   -3.217 closest distance to " OXT GLY A 302 " =    3.003
peak=   -3.217 closest distance to " O   HOH Z 210 " =    0.722
peak=   -3.216 closest distance to " O   HOH Z 390 " =    2.415
peak=   -3.211 closest distance to " OG  SER A  26 " =    1.074
peak=   -3.207 closest distance to " CE1 TYR A 169 " =    2.484
peak=   -3.206 closest distance to " O   HOH Z 175 " =    2.502
peak=   -3.204 closest distance to " O   HOH Z 292 " =    1.361
peak=   -3.203 closest distance to " O   HOH Z 256 " =    1.490
peak=   -3.201 closest distance to " CZ BARG A 275 " =    1.567
peak=   -3.201 closest distance to " CG2 THR A  18 " =    2.735
peak=   -3.191 closest distance to " CB  PRO A  54 " =    2.350
peak=   -3.187 closest distance to " ND2 ASN A 285 " =    2.058
peak=   -3.187 closest distance to " OD1 ASN A 301 " =    1.625
peak=   -3.185 closest distance to " CG  GLU A 152 " =    1.156
peak=   -3.183 closest distance to " O   HOH Z 243 " =    1.971
peak=   -3.178 closest distance to " CB  ALA A 291 " =    2.359
peak=   -3.178 closest distance to " CD2 LEU A 237 " =    2.696
peak=   -3.175 closest distance to " CD  GLU A 277 " =    0.972
peak=   -3.169 closest distance to " CZ  TYR A 169 " =    1.491
peak=   -3.165 closest distance to " O   HOH Z 114 " =    2.838
peak=   -3.152 closest distance to " O   HOH Z 388 " =    2.104
peak=   -3.149 closest distance to " SD  MET A 188 " =    2.374
peak=   -3.146 closest distance to " O   HOH Z 168 " =    1.757
peak=   -3.142 closest distance to " CZ3 TRP A 123 " =    1.640
peak=   -3.142 closest distance to " CB  ALA A   7 " =    1.991
peak=   -3.139 closest distance to " CB  ASP A 132 " =    2.179
peak=   -3.138 closest distance to " ND2 ASN A  69 " =    1.659
peak=   -3.134 closest distance to " O   ASP A 162 " =    2.207
peak=   -3.131 closest distance to " ND2BASN A 224 " =    1.657
peak=   -3.128 closest distance to " C   MET A 188 " =    1.548
peak=   -3.126 closest distance to " CA  SER A 146 " =    2.375
peak=   -3.123 closest distance to " NE  ARG A  36 " =    1.954
peak=   -3.113 closest distance to " O   HOH Z 198 " =    1.905
peak=   -3.113 closest distance to " O   ALA A   1 " =    1.751
peak=   -3.106 closest distance to " C   ALA A 114 " =    2.299
peak=   -3.104 closest distance to " CG1 VAL A 230 " =    1.889
peak=   -3.103 closest distance to " CB  ALA A 248 " =    2.418
peak=   -3.100 closest distance to " N   ASP A 270 " =    1.389
peak=   -3.069 closest distance to " N   ASP A 171 " =    2.440
peak=   -3.069 closest distance to " O   HOH Z 351 " =    1.707
peak=   -3.026 closest distance to " CD  GLN A 223 " =    1.358
peak=   -3.020 closest distance to " NH1BARG A 145 " =    3.958

================= 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    :  0.4261 0.4258   6.233996e+00   6.231251e+00
   1_bss:  0.4156 0.4182   6.223546e+00   6.216143e+00
   1_xyz:  0.3131 0.3451   6.025159e+00   6.084585e+00
   1_adp:  0.2853 0.3574   5.973294e+00   6.100330e+00
   1_occ:  0.2851 0.3577   5.972487e+00   6.100053e+00
   2_bss:  0.2848 0.3545   5.971352e+00   6.097211e+00
   2_xyz:  0.2042 0.2626   5.671815e+00   5.850678e+00
   2_adp:  0.1790 0.2356   5.554466e+00   5.759542e+00
   2_occ:  0.1789 0.2351   5.553341e+00   5.758158e+00
   3_bss:  0.1781 0.2330   5.546507e+00   5.749668e+00
   3_xyz:  0.1410 0.1926   5.342812e+00   5.575351e+00
   3_adp:  0.1353 0.1825   5.301142e+00   5.525781e+00
   3_occ:  0.1351 0.1823   5.300167e+00   5.524573e+00
   4_bss:  0.1352 0.1819   5.300119e+00   5.523614e+00
   4_xyz:  0.1162 0.1621   5.174216e+00   5.417213e+00
   4_adp:  0.1131 0.1589   5.152366e+00   5.399384e+00
   4_occ:  0.1130 0.1588   5.151699e+00   5.398646e+00
   5_bss:  0.1130 0.1588   5.151473e+00   5.398442e+00
   5_xyz:  0.1104 0.1555   5.131318e+00   5.380054e+00
   5_adp:  0.1098 0.1547   5.127373e+00   5.377475e+00
   5_occ:  0.1097 0.1546   5.126973e+00   5.377111e+00
   5_bss:  0.1098 0.1541   5.125741e+00   5.375038e+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:  0.344  38.461  -1.779   2.864  -0.942   0.000  -0.000  -0.000
   1_xyz:  0.344  38.461  -1.779   2.864  -0.942   0.000  -0.000  -0.000
   1_adp:  0.344  38.461  -1.779   2.864  -0.942   0.000  -0.000  -0.000
   1_occ:  0.344  38.461  -1.779   2.864  -0.942   0.000  -0.000  -0.000
   2_bss:  0.340  52.159  -1.593   0.134  -0.917   0.000  -0.000  -0.000
   2_xyz:  0.340  52.159  -1.593   0.134  -0.917   0.000  -0.000  -0.000
   2_adp:  0.340  52.159  -1.593   0.134  -0.917   0.000  -0.000  -0.000
   2_occ:  0.340  52.159  -1.593   0.134  -0.917   0.000  -0.000  -0.000
   3_bss:  0.332  52.159  -1.727  -1.573  -1.002  -0.000  -0.000  -0.000
   3_xyz:  0.332  52.159  -1.727  -1.573  -1.002  -0.000  -0.000  -0.000
   3_adp:  0.332  52.159  -1.727  -1.573  -1.002  -0.000  -0.000  -0.000
   3_occ:  0.332  52.159  -1.727  -1.573  -1.002  -0.000  -0.000  -0.000
   4_bss:  0.334  52.159  -2.178  -2.432  -1.415  -0.000  -0.000  -0.000
   4_xyz:  0.334  52.159  -2.178  -2.432  -1.415  -0.000  -0.000  -0.000
   4_adp:  0.334  52.159  -2.178  -2.432  -1.415  -0.000  -0.000  -0.000
   4_occ:  0.334  52.159  -2.178  -2.432  -1.415  -0.000  -0.000  -0.000
   5_bss:  0.334  52.159  -2.186  -2.567  -1.428  -0.000  -0.000  -0.000
   5_xyz:  0.334  52.159  -2.186  -2.567  -1.428  -0.000  -0.000  -0.000
   5_adp:  0.334  52.159  -2.186  -2.567  -1.428  -0.000  -0.000  -0.000
   5_occ:  0.334  52.159  -2.186  -2.567  -1.428  -0.000  -0.000  -0.000
   5_bss:  0.334  52.113  -2.086  -2.535  -1.336  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.399 0.5295  0.7159    57813.438
   1_bss:  48.534 0.5387  0.7306    54737.570
   1_xyz:  37.074 0.6781  0.8817    34369.588
   1_adp:  38.238 0.6632  0.8672    35725.700
   1_occ:  38.263 0.6629  0.8667    35756.295
   2_bss:  37.833 0.6679  0.8496    35126.789
   2_xyz:  26.566 0.7939  0.9721    17794.965
   2_adp:  23.050 0.8316  0.9903    14223.977
   2_occ:  23.016 0.8319  0.9901    14176.953
   3_bss:  22.710 0.8346  0.9697    13795.504
   3_xyz:  18.212 0.8779  0.9939     9306.803
   3_adp:  16.841 0.8912  0.9964     8483.619
   3_occ:  16.815 0.8914  0.9960     8449.350
   4_bss:  16.780 0.8917  0.9758     8430.958
   4_xyz:  14.615 0.9097  0.9851     6743.748
   4_adp:  14.181 0.9135  0.9839     6522.249
   4_occ:  14.169 0.9136  0.9839     6505.519
   5_bss:  14.163 0.9136  0.9821     6503.224
   5_xyz:  13.745 0.9171  0.9827     6239.204
   5_adp:  13.667 0.9178  0.9794     6198.359
   5_occ:  13.661 0.9178  0.9794     6190.040
   5_bss:  13.641 0.9179  0.9806     6143.155
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.7253e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.7253e-01
   1_xyz:   1.387  0.011  0.093 15.198  0.006  4.105   1.0124e-01
   1_adp:   1.387  0.011  0.093 15.198  0.006  4.105   1.0124e-01
   1_occ:   1.387  0.011  0.093 15.198  0.006  4.105   1.0124e-01
   2_bss:   1.387  0.011  0.093 15.198  0.006  4.105   1.0124e-01
   2_xyz:   1.241  0.010  0.086 15.026  0.004  4.107   8.6980e-02
   2_adp:   1.241  0.010  0.086 15.026  0.004  4.107   8.6980e-02
   2_occ:   1.241  0.010  0.086 15.026  0.004  4.107   8.6980e-02
   3_bss:   1.241  0.010  0.086 15.026  0.004  4.107   8.6980e-02
   3_xyz:   0.925  0.006  0.066 14.341  0.003  4.112   5.2822e-02
   3_adp:   0.925  0.006  0.066 14.341  0.003  4.112   5.2822e-02
   3_occ:   0.925  0.006  0.066 14.341  0.003  4.112   5.2822e-02
   4_bss:   0.925  0.006  0.066 14.341  0.003  4.112   5.2822e-02
   4_xyz:   1.083  0.008  0.078 14.737  0.004  4.109   6.8192e-02
   4_adp:   1.083  0.008  0.078 14.737  0.004  4.109   6.8192e-02
   4_occ:   1.083  0.008  0.078 14.737  0.004  4.109   6.8192e-02
   5_bss:   1.083  0.008  0.078 14.737  0.004  4.109   6.8192e-02
   5_xyz:   1.035  0.008  0.075 14.676  0.004  4.110   6.3542e-02
   5_adp:   1.035  0.008  0.075 14.676  0.004  4.110   6.3542e-02
   5_occ:   1.035  0.008  0.075 14.676  0.004  4.110   6.3542e-02
   5_bss:   1.035  0.008  0.075 14.676  0.004  4.110   6.3542e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.741   2.3946e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.741   2.3946e-01
   1_xyz:   8.985  0.080  0.390 87.682  0.049  2.068   8.4022e-02
   1_adp:   8.985  0.080  0.390 87.682  0.049  2.068   8.4022e-02
   1_occ:   8.985  0.080  0.390 87.682  0.049  2.068   8.4022e-02
   2_bss:   8.985  0.080  0.390 87.682  0.049  2.068   8.4022e-02
   2_xyz:   7.867  0.071  0.255 84.385  0.035  2.067   1.3745e-01
   2_adp:   7.867  0.071  0.255 84.385  0.035  2.067   1.3745e-01
   2_occ:   7.867  0.071  0.255 84.385  0.035  2.067   1.3745e-01
   3_bss:   7.867  0.071  0.255 84.385  0.035  2.067   1.3745e-01
   3_xyz:   7.702  0.029  0.211 82.971  0.022  2.313   4.6235e-02
   3_adp:   7.702  0.029  0.211 82.971  0.022  2.313   4.6235e-02
   3_occ:   7.702  0.029  0.211 82.971  0.022  2.313   4.6235e-02
   4_bss:   7.702  0.029  0.211 82.971  0.022  2.313   4.6235e-02
   4_xyz:   7.254  0.044  0.260 84.737  0.033  2.265   5.7496e-02
   4_adp:   7.254  0.044  0.260 84.737  0.033  2.265   5.7496e-02
   4_occ:   7.254  0.044  0.260 84.737  0.033  2.265   5.7496e-02
   5_bss:   7.254  0.044  0.260 84.737  0.033  2.265   5.7496e-02
   5_xyz:   7.433  0.035  0.232 85.403  0.034  2.276   5.0354e-02
   5_adp:   7.433  0.035  0.232 85.403  0.034  2.276   5.0354e-02
   5_occ:   7.433  0.035  0.232 85.403  0.034  2.276   5.0354e-02
   5_bss:   7.433  0.035  0.232 85.403  0.034  2.276   5.0354e-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:  99.27   0.00  18.24  75.41   0.00  14.69  99.27   1.78  37.55
   1_occ:  99.27   0.00  18.24  75.41   0.00  14.69  99.27   1.78  37.55
   2_bss:  99.27   0.00  18.24  75.41   0.00  14.69  99.27   1.78  37.55
   2_xyz:  99.27   0.00  18.24  75.41   0.00  14.69  99.27   1.78  37.55
   2_adp:  93.84   0.00  17.59  83.06   0.00  13.37  93.84   5.03  40.61
   2_occ:  93.84   0.00  17.59  83.06   0.00  13.37  93.84   5.03  40.61
   3_bss:  93.84   0.00  17.59  83.06   0.00  13.37  93.84   5.03  40.61
   3_xyz:  93.84   0.00  17.59  83.06   0.00  13.37  93.84   5.03  40.61
   3_adp:  81.72   0.00  16.83  81.70   0.00  12.81  81.72   5.78  38.70
   3_occ:  81.72   0.00  16.83  81.70   0.00  12.81  81.72   5.78  38.70
   4_bss:  81.72   0.00  16.83  81.70   0.00  12.81  81.72   5.78  38.70
   4_xyz:  81.72   0.00  16.83  81.70   0.00  12.81  81.72   5.78  38.70
   4_adp:  83.59   1.29  16.67  83.59   1.29  12.68  79.69   5.97  38.39
   4_occ:  83.59   1.29  16.67  83.59   1.29  12.68  79.69   5.97  38.39
   5_bss:  83.59   1.29  16.67  83.59   1.29  12.68  79.69   5.97  38.39
   5_xyz:  83.59   1.29  16.67  83.59   1.29  12.68  79.69   5.97  38.39
   5_adp:  84.97   1.29  16.51  84.97   1.29  12.58  77.89   6.51  37.91
   5_occ:  84.97   1.29  16.51  84.97   1.29  12.58  77.89   6.51  37.91
   5_bss:  84.92   1.24  16.47  84.92   1.24  12.54  77.85   6.46  37.86
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.746    0.026    0.306
   1_adp:    1.746    0.026    0.306
   1_occ:    1.746    0.026    0.306
   2_bss:    1.746    0.026    0.306
   2_xyz:    1.385    0.051    0.558
   2_adp:    1.385    0.051    0.558
   2_occ:    1.385    0.051    0.558
   3_bss:    1.385    0.051    0.558
   3_xyz:    1.304    0.041    0.619
   3_adp:    1.304    0.041    0.619
   3_occ:    1.304    0.041    0.619
   4_bss:    1.304    0.041    0.619
   4_xyz:    1.383    0.088    0.669
   4_adp:    1.383    0.088    0.669
   4_occ:    1.383    0.088    0.669
   5_bss:    1.383    0.088    0.669
   5_xyz:    1.516    0.073    0.677
   5_adp:    1.516    0.073    0.677
   5_occ:    1.516    0.073    0.677
   5_bss:    1.516    0.073    0.677
------------------------------------------------------------------------

CPU time actual refinement: 355.65


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_861/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_861/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_861/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_861/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_861/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 355.51 
  Macro-tasks:
    bulk solvent and scale       = 35.72  
    individual site refinement   = 150.69 
    weights calculation          = 30.27  
    collect and process          = 6.61   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 223.38 
  Micro-tasks:
    mask                            = 2.52   
    f_calc                          = 119.31 
    alpha_beta                      = 8.45   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 127.03 
    fmodel                         = 6.57   
    r_factors                      = 0.22   
    phase_errors                   = 10.43  
    foms                           = 0.33   
    TOTAL for micro-tasks          = 276.02 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.990 micro seconds
Total CPU time: 6.16 minutes
from_scatterers_fft:    667 calls, 118.96 s
gradients_fft:          612 calls, 113.19 s

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

# Date 2008-01-16 Time 05:50:20 PST -0800 (1200491420.70 s)
Start R-work = 0.4261, R-free = 0.4258 (no bulk solvent and anisotropic scale)
Final R-work = 0.1342, R-free = 0.1755 (no bulk solvent and anisotropic scale)

Start R-work = 0.4156, R-free = 0.4182
Final R-work = 0.1098, R-free = 0.1541