# Date 2008-01-16 Time 05:02:30 PST -0800 (1200488550.03 s)
#phil __OFF__

Command line arguments: "../572.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 5337
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 572

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 47.6339, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.31, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.6339, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8572 1.95149
Completeness in resolution range: 0.930903
Completeness with d_max=infinity: 0.928125

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8572
                             d_min =   1.9515

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.6339, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8572 1.95149
Completeness in resolution range: 0.930903
Completeness with d_max=infinity: 0.928125

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8576 -  4.1762 [2213/2242]  1991   222  10.0%
  bin  2:  4.1762 -  3.3270 [2109/2132]  1900   209   9.9%
  bin  3:  3.3270 -  2.9100 [2087/2112]  1876   211  10.1%
  bin  4:  2.9100 -  2.6456 [2074/2091]  1869   205   9.9%
  bin  5:  2.6456 -  2.4569 [2075/2118]  1866   209  10.1%
  bin  6:  2.4569 -  2.3126 [2046/2074]  1849   197   9.6%
  bin  7:  2.3126 -  2.1971 [2025/2061]  1820   205  10.1%
  bin  8:  2.1971 -  2.1018 [2030/2072]  1822   208  10.2%
  bin  9:  2.1018 -  2.0211 [2010/2068]  1806   204  10.1%
  bin 10:  2.0211 -  1.9515 [ 920/2073]   831    89   9.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_572/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.48 -     2.17: 26
        2.17 -     2.85: 1131
        2.85 -     3.53: 4436
        3.53 -     4.22: 9337
        4.22 -     4.90: 13639
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.483 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.498 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.606 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.678 3.040 -x+1/2,-y+1,z+1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.728 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28564 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_572/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_572/model_refine_001.geo

CPU time processing inputs: 9.76


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 47.63395 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4404   r_free= 0.4353   ksol= 0.00   Bsol= 0.00   scale= 0.916    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.250970                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8576 -  4.6581 0.99   1435  163 0.3494 0.3569      6.5117      6.5266|
|  2:  4.6581 -  3.7163 0.99   1376  147 0.3705 0.3662      6.7448      6.7101|
|  3:  3.7163 -  3.2522 0.99   1350  153 0.3982 0.3881      6.6063      6.6937|
|  4:  3.2522 -  2.9574 0.99   1343  147 0.4201 0.4028      6.4584      6.4372|
|  5:  2.9574 -  2.7468 0.99   1341  149 0.4536 0.4168       6.321      6.2697|
|  6:  2.7468 -  2.5858 0.99   1324  150 0.4654 0.4405      6.2409      6.1541|
|  7:  2.5858 -  2.4569 0.98   1333  147 0.4709 0.4275      6.2181      6.1653|
|  8:  2.4569 -  2.3504 0.98   1310  143 0.4888 0.5429      6.1421      6.1815|
|  9:  2.3504 -  2.2602 0.99   1316  143 0.5105 0.5071      6.1235      6.1238|
| 10:  2.2602 -  2.1825 0.98   1312  148 0.4953 0.5206      6.0798      6.1331|
| 11:  2.1825 -  2.1144 0.97   1288  143 0.5121 0.5457      6.0286      6.0123|
| 12:  2.1144 -  2.0541 0.98   1302  150 0.4979 0.5326      5.9385      5.9901|
| 13:  2.0541 -  2.0002 0.91   1197  134 0.5093 0.4701      5.8755      5.8358|
| 14:  2.0002 -  1.9515 0.30    403   42 0.5566 0.4905      5.8261      5.7135|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8576 -  4.6581  1435   163  0.71  33.28   0.84     0.74      65776.30|
|  2:  4.6581 -  3.7163  1376   147  0.74  32.09   0.93     0.83      88731.31|
|  3:  3.7163 -  3.2522  1350   153  0.66  38.96   0.94     0.84      92213.59|
|  4:  3.2522 -  2.9574  1343   147  0.59  44.75   0.94     0.81      81152.50|
|  5:  2.9574 -  2.7468  1341   149  0.55  48.19   0.90     0.76      63630.23|
|  6:  2.7468 -  2.5858  1324   150  0.52  50.79   0.93     0.72      55930.66|
|  7:  2.5858 -  2.4569  1333   147  0.50  52.13   0.94     0.67      52454.59|
|  8:  2.4569 -  2.3504  1310   143  0.41  58.83   0.91     0.61      54034.41|
|  9:  2.3504 -  2.2602  1316   143  0.36  62.72   0.94     0.53      51952.89|
| 10:  2.2602 -  2.1825  1312   148  0.30  67.78   0.98     0.44      53321.96|
| 11:  2.1825 -  2.1144  1288   143  0.24  72.00   0.95     0.37      51111.34|
| 12:  2.1144 -  2.0541  1302   150  0.21  74.57   0.95     0.34      48896.27|
| 13:  2.0541 -  2.0002  1197   134  0.25  71.61   0.96     0.40      39643.49|
| 14:  2.0002 -  1.9515   403    42  0.33  65.31   0.89     0.52      30833.56|
|alpha:            min =        0.34 max =            0.84 mean =         0.62|
|beta:             min =    30833.56 max =        92213.59 mean =     61131.52|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           90.00 mean =        54.25|
|phase err.(test): min =        0.00 max =           89.98 mean =        54.35|
|-----------------------------------------------------------------------------|

============================== 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 = 12.478590             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.917   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.340316              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.981   (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 |  1.483 -  1.825:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.825 -  2.167:       17 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.167 -  2.508:       32 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.508 -  2.850:     1099 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.850 -  3.192:     1963 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.192 -  3.533:     2473 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.533 -  3.875:     4672 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.875 -  4.217:     4665 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.217 -  4.558:     6182 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.558 -  4.900:     7457 |
|-----------------------------------------------------------------------------|
|-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 |        0.192 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.483 |       0.627 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4404   r_free= 0.4353   ksol= 0.00   Bsol= 0.00   scale= 0.916    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.250970                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4293   r_free= 0.4243   ksol= 0.31   Bsol= 23.02   scale= 0.950   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.29,2.14,2.44,0.00,0.00,0.00); trace/3= 0.43                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.241369                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.389674             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.710   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.039033              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.745   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4293      final r-factor (work) = 0.2974          |
| start r-factor (free) = 0.4243      final r-factor (free) = 0.3247          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.6119 = 10.39 * 0.50 * 6.2408 + 1.00 * 0.1917                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.6939 = 10.39 * 0.50 * 6.0754 + 1.00 * 0.1332                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2974      final r-factor (work) = 0.2736          |
| start r-factor (free) = 0.3247      final r-factor (free) = 0.3341          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3198 = 1.04 * 1.00 * 6.0754 + 1.00 * 0.0072                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1930 = 1.04 * 1.00 * 5.8937 + 1.00 * 0.0692                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    140.74  17.31    None  None   None       |
|    all(noH): 2823   0      0.00    140.74  17.31    None  None   None       |
|    Sol.    : 438    0      3.35    65.62   38.47    None  None   None       |
|    Mac.    : 2385   0      0.00    140.74  13.42    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 -  14.074: 1445   |   5:    70.371 -  84.445:    0        |
|      1:    14.074 -  28.148:  890   |   6:    84.445 -  98.519:    0        |
|      2:    28.148 -  42.223:  275   |   7:    98.519 - 112.593:    0        |
|      3:    42.223 -  56.297:  181   |   8:   112.593 - 126.668:    0        |
|      4:    56.297 -  70.371:   31   |   9:   126.668 - 140.742:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2736 r_free = 0.3341             target_work(ml) = 5.901         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2730 r_free = 0.3348             target_work(ml) = 5.900         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2730   r_free= 0.3348   ksol= 0.31   Bsol= 23.02   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.29,2.14,2.44,0.00,0.00,0.00); trace/3= 0.43                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.899516                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2693   r_free= 0.3307   ksol= 0.33   Bsol= 50.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.72,-0.07,-0.14,-0.00,-0.00,-0.00); trace/3= -0.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.894004                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.595141              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.905   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.009425              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.338   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2693      final r-factor (work) = 0.1945          |
| start r-factor (free) = 0.3307      final r-factor (free) = 0.2431          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.6733 = 4.60 * 0.50 * 5.8932 + 1.00 * 0.1333                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.3291 = 4.60 * 0.50 * 5.7703 + 1.00 * 0.0714                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1945      final r-factor (work) = 0.1732          |
| start r-factor (free) = 0.2431      final r-factor (free) = 0.2278          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8693 = 1.01 * 1.00 * 5.7703 + 1.00 * 0.0446                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6220 = 1.01 * 1.00 * 5.5568 + 1.00 * 0.0129                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.61   18.20    None  None   None       |
|    all(noH): 2823   0      0.00    92.61   18.20    None  None   None       |
|    Sol.    : 438    0      5.82    85.29   43.57    None  None   None       |
|    Mac.    : 2385   0      0.00    92.61   13.54    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:     0.000 -   9.261:  925   |   5:    46.305 -  55.567:  109        |
|      1:     9.261 -  18.522: 1076   |   6:    55.567 -  64.828:   81        |
|      2:    18.522 -  27.783:  311   |   7:    64.828 -  74.089:   43        |
|      3:    27.783 -  37.044:  142   |   8:    74.089 -  83.350:   14        |
|      4:    37.044 -  46.305:  114   |   9:    83.350 -  92.611:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1732 r_free = 0.2278             target_work(ml) = 5.526         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1730 r_free = 0.2280             target_work(ml) = 5.526         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1730   r_free= 0.2280   ksol= 0.33   Bsol= 50.00   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.72,-0.07,-0.14,-0.00,-0.00,-0.00); trace/3= -0.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.525977                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1734   r_free= 0.2271   ksol= 0.32   Bsol= 50.64   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.42,-0.76,-1.01,-0.00,-0.00,-0.00); trace/3= -1.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.523235                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.242193              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.838   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.873523              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.474  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1734      final r-factor (work) = 0.1419          |
| start r-factor (free) = 0.2271      final r-factor (free) = 0.1916          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3011 = 2.24 * 0.50 * 5.5568 + 1.00 * 0.0714                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1536 = 2.24 * 0.50 * 5.4387 + 1.00 * 0.0564                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1419      final r-factor (work) = 0.1339          |
| start r-factor (free) = 0.1916      final r-factor (free) = 0.1811          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7634 = 0.87 * 1.00 * 5.4387 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6623 = 0.87 * 1.00 * 5.3242 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.52  17.95    None  None   None       |
|    all(noH): 2823   0      0.00    106.52  17.95    None  None   None       |
|    Sol.    : 438    0      2.55    88.50   44.07    None  None   None       |
|    Mac.    : 2385   0      0.00    106.52  13.15    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.652: 1199   |   5:    53.258 -  63.910:  104        |
|      1:    10.652 -  21.303:  997   |   6:    63.910 -  74.561:   45        |
|      2:    21.303 -  31.955:  210   |   7:    74.561 -  85.213:   26        |
|      3:    31.955 -  42.606:  116   |   8:    85.213 -  95.864:    8        |
|      4:    42.606 -  53.258:  115   |   9:    95.864 - 106.516:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1339 r_free = 0.1811             target_work(ml) = 5.297         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1338 r_free = 0.1811             target_work(ml) = 5.296         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1338   r_free= 0.1811   ksol= 0.32   Bsol= 50.64   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.42,-0.76,-1.01,-0.00,-0.00,-0.00); trace/3= -1.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.296466                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1341   r_free= 0.1816   ksol= 0.32   Bsol= 50.64   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-1.19,-1.45,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.299339                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.016961              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.654  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.185119              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.088  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1341      final r-factor (work) = 0.1215          |
| start r-factor (free) = 0.1816      final r-factor (free) = 0.1691          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4277 = 2.02 * 0.50 * 5.3262 + 1.00 * 0.0564                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3586 = 2.02 * 0.50 * 5.2581 + 1.00 * 0.0560                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1215      final r-factor (work) = 0.1202          |
| start r-factor (free) = 0.1691      final r-factor (free) = 0.1643          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9848 = 0.19 * 1.00 * 5.2581 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9738 = 0.19 * 1.00 * 5.2156 + 1.00 * 0.0083                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.70    99.17   17.03    None  None   None       |
|    all(noH): 2823   0      1.70    99.17   17.03    None  None   None       |
|    Sol.    : 438    0      4.25    86.35   40.28    None  None   None       |
|    Mac.    : 2385   0      1.70    99.17   12.76    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:     1.701 -  11.448: 1400   |   5:    50.437 -  60.184:   76        |
|      1:    11.448 -  21.196:  847   |   6:    60.184 -  69.931:   36        |
|      2:    21.196 -  30.943:  183   |   7:    69.931 -  79.678:   17        |
|      3:    30.943 -  40.690:  126   |   8:    79.678 -  89.425:    8        |
|      4:    40.690 -  50.437:  127   |   9:    89.425 -  99.172:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1202 r_free = 0.1643             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1201 r_free = 0.1642             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1201   r_free= 0.1642   ksol= 0.32   Bsol= 50.64   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-1.19,-1.45,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.199651                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1201   r_free= 0.1642   ksol= 0.33   Bsol= 50.64   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-1.42,-1.62,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.199597                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.583354              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.178  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.212145              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.907  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1201      final r-factor (work) = 0.1162          |
| start r-factor (free) = 0.1642      final r-factor (free) = 0.1607          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1848 = 1.58 * 0.50 * 5.2153 + 1.00 * 0.0560                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1582 = 1.58 * 0.50 * 5.1874 + 1.00 * 0.0514                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1162      final r-factor (work) = 0.1157          |
| start r-factor (free) = 0.1607      final r-factor (free) = 0.1605          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1087 = 0.21 * 1.00 * 5.1874 + 1.00 * 0.0082                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1051 = 0.21 * 1.00 * 5.1714 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.60    97.91   16.83    None  None   None       |
|    all(noH): 2823   0      1.60    97.91   16.83    None  None   None       |
|    Sol.    : 438    0      5.27    86.78   39.67    None  None   None       |
|    Mac.    : 2385   0      1.60    97.91   12.63    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:     1.602 -  11.232: 1367   |   5:    49.754 -  59.384:   79        |
|      1:    11.232 -  20.863:  878   |   6:    59.384 -  69.014:   34        |
|      2:    20.863 -  30.493:  185   |   7:    69.014 -  78.645:   16        |
|      3:    30.493 -  40.123:  124   |   8:    78.645 -  88.275:   10        |
|      4:    40.123 -  49.754:  127   |   9:    88.275 -  97.906:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1157 r_free = 0.1605             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1157 r_free = 0.1605             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1157   r_free= 0.1605   ksol= 0.33   Bsol= 50.64   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-1.42,-1.62,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.170633                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8576 -  4.6581 0.99   1435  163 0.0990 0.1246      5.3703       5.522|
|  2:  4.6581 -  3.7163 0.99   1376  147 0.0859 0.1087      5.4288      5.6232|
|  3:  3.7163 -  3.2522 0.99   1350  153 0.1081 0.1619        5.48      5.8822|
|  4:  3.2522 -  2.9574 0.99   1343  147 0.1320 0.1550      5.4965      5.6181|
|  5:  2.9574 -  2.7468 0.99   1341  149 0.1366 0.1798      5.3431      5.4987|
|  6:  2.7468 -  2.5858 0.99   1324  150 0.1302 0.1968      5.2422      5.4755|
|  7:  2.5858 -  2.4569 0.98   1333  147 0.1281 0.1706      5.1797      5.3736|
|  8:  2.4569 -  2.3504 0.98   1310  143 0.1247 0.1691       5.096       5.278|
|  9:  2.3504 -  2.2602 0.99   1316  143 0.1238 0.1907      5.0456      5.3083|
| 10:  2.2602 -  2.1825 0.98   1312  148 0.1169 0.1745      4.9821      5.2475|
| 11:  2.1825 -  2.1144 0.97   1288  143 0.1156 0.1854      4.9341      5.2407|
| 12:  2.1144 -  2.0541 0.98   1302  150 0.1160 0.1695       4.865      5.0813|
| 13:  2.0541 -  2.0002 0.91   1197  134 0.1151 0.1848      4.7986      5.0517|
| 14:  2.0002 -  1.9515 0.30    403   42 0.1208 0.1683        4.73      4.9506|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8576 -  4.6581  1435   163  0.94   8.67   0.98     0.96       6691.88|
|  2:  4.6581 -  3.7163  1376   147  0.96   7.67   1.02     1.00       8544.33|
|  3:  3.7163 -  3.2522  1350   153  0.93  11.46   1.03     1.02      10311.37|
|  4:  3.2522 -  2.9574  1343   147  0.91  14.37   1.01     0.98      10742.91|
|  5:  2.9574 -  2.7468  1341   149  0.90  16.37   1.00     0.97       8449.16|
|  6:  2.7468 -  2.5858  1324   150  0.90  16.18   0.98     0.96       7212.67|
|  7:  2.5858 -  2.4569  1333   147  0.90  15.64   0.99     0.97       6269.00|
|  8:  2.4569 -  2.3504  1310   143  0.90  16.01   1.00     0.97       5657.56|
|  9:  2.3504 -  2.2602  1316   143  0.90  16.31   1.00     0.97       5040.12|
| 10:  2.2602 -  2.1825  1312   148  0.91  15.23   1.00     0.96       4499.95|
| 11:  2.1825 -  2.1144  1288   143  0.90  16.22   1.00     0.97       4294.89|
| 12:  2.1144 -  2.0541  1302   150  0.91  15.14   1.00     1.00       3767.88|
| 13:  2.0541 -  2.0002  1197   134  0.90  16.60   1.00     0.99       3404.95|
| 14:  2.0002 -  1.9515   403    42  0.89  17.03   0.98     0.94       2908.44|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2908.44 max =        10742.91 mean =      6499.03|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.28|
|phase err.(test): min =        0.00 max =           89.66 mean =        13.89|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1157   r_free= 0.1605   ksol= 0.33   Bsol= 50.58   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-1.37,-1.56,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.170633                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1157   r_free= 0.1605   ksol= 0.33   Bsol= 50.58   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-1.37,-1.56,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.170633                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8576 -  4.6581 0.99   1435  163 0.0990 0.1246      5.3703       5.522|
|  2:  4.6581 -  3.7163 0.99   1376  147 0.0859 0.1087      5.4288      5.6232|
|  3:  3.7163 -  3.2522 0.99   1350  153 0.1081 0.1619        5.48      5.8822|
|  4:  3.2522 -  2.9574 0.99   1343  147 0.1320 0.1550      5.4965      5.6181|
|  5:  2.9574 -  2.7468 0.99   1341  149 0.1366 0.1798      5.3431      5.4987|
|  6:  2.7468 -  2.5858 0.99   1324  150 0.1302 0.1968      5.2422      5.4755|
|  7:  2.5858 -  2.4569 0.98   1333  147 0.1281 0.1706      5.1797      5.3736|
|  8:  2.4569 -  2.3504 0.98   1310  143 0.1247 0.1691       5.096       5.278|
|  9:  2.3504 -  2.2602 0.99   1316  143 0.1238 0.1907      5.0456      5.3083|
| 10:  2.2602 -  2.1825 0.98   1312  148 0.1169 0.1745      4.9821      5.2475|
| 11:  2.1825 -  2.1144 0.97   1288  143 0.1156 0.1854      4.9341      5.2407|
| 12:  2.1144 -  2.0541 0.98   1302  150 0.1160 0.1695       4.865      5.0813|
| 13:  2.0541 -  2.0002 0.91   1197  134 0.1151 0.1848      4.7986      5.0517|
| 14:  2.0002 -  1.9515 0.30    403   42 0.1208 0.1683        4.73      4.9506|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8576 -  4.6581  1435   163  0.94   8.67   0.98     0.96       6691.88|
|  2:  4.6581 -  3.7163  1376   147  0.96   7.67   1.02     1.00       8544.33|
|  3:  3.7163 -  3.2522  1350   153  0.93  11.46   1.03     1.02      10311.37|
|  4:  3.2522 -  2.9574  1343   147  0.91  14.37   1.01     0.98      10742.91|
|  5:  2.9574 -  2.7468  1341   149  0.90  16.37   1.00     0.97       8449.16|
|  6:  2.7468 -  2.5858  1324   150  0.90  16.18   0.98     0.96       7212.67|
|  7:  2.5858 -  2.4569  1333   147  0.90  15.64   0.99     0.97       6269.00|
|  8:  2.4569 -  2.3504  1310   143  0.90  16.01   1.00     0.97       5657.56|
|  9:  2.3504 -  2.2602  1316   143  0.90  16.31   1.00     0.97       5040.12|
| 10:  2.2602 -  2.1825  1312   148  0.91  15.23   1.00     0.96       4499.95|
| 11:  2.1825 -  2.1144  1288   143  0.90  16.22   1.00     0.97       4294.89|
| 12:  2.1144 -  2.0541  1302   150  0.91  15.14   1.00     1.00       3767.88|
| 13:  2.0541 -  2.0002  1197   134  0.90  16.60   1.00     0.99       3404.95|
| 14:  2.0002 -  1.9515   403    42  0.89  17.03   0.98     0.94       2908.44|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2908.44 max =        10742.91 mean =      6499.03|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.28|
|phase err.(test): min =        0.00 max =           89.66 mean =        13.89|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.686)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.54    97.85   16.77    None  None   None       |
|    all(noH): 2823   0      1.54    97.85   16.77    None  None   None       |
|    Sol.    : 438    0      5.22    86.72   39.61    None  None   None       |
|    Mac.    : 2385   0      1.54    97.85   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:     1.545 -  11.175: 1367   |   5:    49.697 -  59.327:   79        |
|      1:    11.175 -  20.805:  878   |   6:    59.327 -  68.957:   34        |
|      2:    20.805 -  30.436:  185   |   7:    68.957 -  78.588:   16        |
|      3:    30.436 -  40.066:  124   |   8:    78.588 -  88.218:   10        |
|      4:    40.066 -  49.697:  127   |   9:    88.218 -  97.848:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 329         
Filter by distance & map next to the model:
   mapped sites are within: 0.438 - 5.880
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 327 from: 329
   mapped sites are within: 0.707 - 5.880

peak=    5.848 closest distance to " O   HOH Z 142 " =    1.619
peak=    5.565 closest distance to " O   HOH Z 113 " =    2.229
peak=    5.513 closest distance to " CB  GLN A 223 " =    1.431
peak=    5.501 closest distance to " CG  PRO A  54 " =    1.273
peak=    5.220 closest distance to " O   HOH Z 124 " =    1.541
peak=    5.197 closest distance to " CB  SER A  63 " =    1.162
peak=    5.045 closest distance to " CG  PRO A  90 " =    1.188
peak=    5.021 closest distance to " O   HOH Z 132 " =    1.377
peak=    4.964 closest distance to " CG  PRO A 213 " =    1.257
peak=    4.951 closest distance to " O   HOH Z 234 " =    3.792
peak=    4.863 closest distance to " CB  ARG A 275 " =    0.905
peak=    4.793 closest distance to " O   HOH Z  11 " =    1.355
peak=    4.792 closest distance to " CG  PRO A 198 " =    1.243
peak=    4.783 closest distance to " O   HOH Z 138 " =    1.076
peak=    4.755 closest distance to " O   HOH Z 108 " =    1.465
peak=    4.697 closest distance to " C   PRO A 198 " =    1.556
peak=    4.641 closest distance to " O   HOH Z 316 " =    2.852
peak=    4.584 closest distance to " CB  GLU A 128 " =    1.189
peak=    4.579 closest distance to " CA  TYR A  30 " =    1.015
peak=    4.568 closest distance to " CB  SER A   3 " =    1.324
peak=    4.551 closest distance to " O   HOH Z  15 " =    2.057
peak=    4.542 closest distance to " CB  GLN A 183 " =    1.321
peak=    4.534 closest distance to " O   HOH Z 298 " =    1.941
peak=    4.505 closest distance to " CA  ALA A  21 " =    1.271
peak=    4.486 closest distance to " O   HOH Z 403 " =    1.747
peak=    4.433 closest distance to " O   HOH Z 247 " =    1.396
peak=    4.425 closest distance to " O   HOH Z  97 " =    1.895
peak=    4.418 closest distance to " CB  GLU A 152 " =    1.144
peak=    4.407 closest distance to " O   HOH Z 368 " =    2.028
peak=    4.390 closest distance to " O   SER A  87 " =    2.151
peak=    4.386 closest distance to " O   HOH Z 193 " =    1.786
peak=    4.359 closest distance to " O   HOH Z 126 " =    1.862
peak=    4.345 closest distance to " O   HOH Z 389 " =    1.940
peak=    4.320 closest distance to " NH2 ARG A 156 " =    1.199
peak=    4.282 closest distance to " O   HOH Z 133 " =    1.605
peak=    4.281 closest distance to " O   HOH Z 278 " =    1.055
peak=    4.268 closest distance to " CB  GLU A 277 " =    3.562
peak=    4.263 closest distance to " O   HOH Z 232 " =    2.258
peak=    4.260 closest distance to " O   HOH Z  78 " =    1.957
peak=    4.244 closest distance to " O   HOH Z 272 " =    1.893
peak=    4.236 closest distance to " CB  TYR A 169 " =    0.841
peak=    4.236 closest distance to " O   HOH Z 134 " =    1.648
peak=    4.235 closest distance to " CG1 ILE A  33 " =    1.244
peak=    4.234 closest distance to " O   HOH Z 426 " =    1.451
peak=    4.229 closest distance to " O   HOH Z 154 " =    1.422
peak=    4.227 closest distance to " O   HOH Z  59 " =    2.369
peak=    4.222 closest distance to " O   HOH Z 313 " =    1.818
peak=    4.214 closest distance to " O   HOH Z 357 " =    1.985
peak=    4.206 closest distance to " O   HOH Z  80 " =    1.717
peak=    4.199 closest distance to " NZ  LYS A 117 " =    3.186
peak=    4.174 closest distance to " O   HOH Z 199 " =    0.959
peak=    4.169 closest distance to " O   HOH Z 145 " =    2.137
peak=    4.169 closest distance to " O   HOH Z 326 " =    1.597
peak=    4.165 closest distance to " CB  SER A 141 " =    1.052
peak=    4.157 closest distance to " N   ASN A  39 " =    1.323
peak=    4.153 closest distance to " CB  PRO A  54 " =    0.797
peak=    4.146 closest distance to " O   HOH Z 236 " =    1.970
peak=    4.136 closest distance to " NH2BARG A 145 " =    2.039
peak=    4.120 closest distance to " CB  LEU A 228 " =    1.204
peak=    4.107 closest distance to " CB  PRO A 198 " =    1.105
peak=    4.106 closest distance to " O   HOH Z 128 " =    2.045
peak=    4.104 closest distance to " O   HOH Z 411 " =    3.456
peak=    4.096 closest distance to " O   HOH Z 402 " =    1.456
peak=    4.074 closest distance to " O   HOH Z 279 " =    2.057
peak=    4.042 closest distance to " O   HOH Z 344 " =    2.888
peak=    4.038 closest distance to " O   HOH Z 369 " =    2.116
peak=    4.019 closest distance to " O   HOH Z  44 " =    2.013
peak=    4.018 closest distance to " O   HOH Z  40 " =    1.738
peak=    4.016 closest distance to " O   HOH Z 260 " =    1.410
peak=    4.012 closest distance to " O   HOH Z 374 " =    2.473
peak=    4.007 closest distance to " CG2 THR A 221 " =    1.122
peak=    4.004 closest distance to " O   HOH Z  97 " =    2.484
peak=    4.003 closest distance to " O   HOH Z 427 " =    2.759
peak=    3.998 closest distance to " CG1BVAL A  72 " =    1.653
peak=    3.997 closest distance to " O   HOH Z 132 " =    2.671
peak=    3.989 closest distance to " O   HOH Z 156 " =    3.291
peak=    3.984 closest distance to " CB  ARG A 190 " =    1.712
peak=    3.950 closest distance to " CA  THR A 221 " =    0.943
peak=    3.937 closest distance to " O   HOH Z  63 " =    2.074
peak=    3.931 closest distance to " CB  ARG A  79 " =    1.373
peak=    3.929 closest distance to " CB  ASN A 148 " =    1.524
peak=    3.928 closest distance to " CG  ARG A  66 " =    2.681
peak=    3.925 closest distance to " O   HOH Z 416 " =    2.885
peak=    3.925 closest distance to " OD2 ASP A 286 " =    2.749
peak=    3.910 closest distance to " O   HOH Z  20 " =    1.603
peak=    3.901 closest distance to " CD  ARG A 269 " =    1.001
peak=    3.900 closest distance to " O   HOH Z   6 " =    2.209
peak=    3.882 closest distance to " O   HOH Z 346 " =    1.554
peak=    3.881 closest distance to " CB  VAL A 202 " =    1.543
peak=    3.874 closest distance to " CG AARG A 275 " =    0.947
peak=    3.870 closest distance to " O   HOH Z 334 " =    1.501
peak=    3.864 closest distance to " NZ  LYS A 119 " =    1.775
peak=    3.863 closest distance to " O   HOH Z 189 " =    1.785
peak=    3.854 closest distance to " O   HOH Z 207 " =    1.781
peak=    3.852 closest distance to " NZ  LYS A  76 " =    1.316
peak=    3.843 closest distance to " NE2 GLN A  11 " =    1.042
peak=    3.840 closest distance to " O   HOH Z 203 " =    1.727
peak=    3.812 closest distance to " O   HOH Z  67 " =    1.894
peak=    3.807 closest distance to " O   HOH Z  61 " =    1.474
peak=    3.803 closest distance to " CG  PRO A 243 " =    1.161
peak=    3.803 closest distance to " CG2BVAL A  41 " =    0.944
peak=    3.793 closest distance to " CA  ASP A 191 " =    0.832
peak=    3.774 closest distance to " OE1 GLN A  11 " =    1.899
peak=    3.774 closest distance to " O   HOH Z 133 " =    1.928
peak=    3.758 closest distance to " CA  ASP A 140 " =    1.146
peak=    3.753 closest distance to " O   HOH Z 214 " =    0.962
peak=    3.749 closest distance to " O   HOH Z 147 " =    1.739
peak=    3.745 closest distance to " CB  ALA A 291 " =    1.172
peak=    3.734 closest distance to " O   HOH Z  43 " =    1.504
peak=    3.728 closest distance to " O   HOH Z  21 " =    1.809
peak=    3.727 closest distance to " CA  ARG A  36 " =    1.067
peak=    3.722 closest distance to " CB  TRP A 179 " =    1.208
peak=    3.712 closest distance to " CD2 LEU A 297 " =    0.918
peak=    3.708 closest distance to " O   TRP A 274 " =    1.770
peak=    3.695 closest distance to " OG BSER A 164 " =    2.526
peak=    3.695 closest distance to " O   HOH Z 209 " =    2.264
peak=    3.689 closest distance to " O   HOH Z 227 " =    1.676
peak=    3.689 closest distance to " O   HOH Z  10 " =    1.762
peak=    3.687 closest distance to " NH2AARG A 190 " =    1.291
peak=    3.686 closest distance to " O   HOH Z  88 " =    3.284
peak=    3.683 closest distance to " OD1 ASN A  69 " =    2.614
peak=    3.681 closest distance to " CB  ARG A 139 " =    0.943
peak=    3.668 closest distance to " CG2 VAL A  78 " =    1.001
peak=    3.660 closest distance to " O   HOH Z  85 " =    1.717
peak=    3.651 closest distance to " O   HOH Z 279 " =    1.099
peak=    3.642 closest distance to " C   GLY A  80 " =    1.159
peak=    3.638 closest distance to " O   HOH Z 193 " =    2.275
peak=    3.637 closest distance to " CD  PRO A  54 " =    1.133
peak=    3.628 closest distance to " OD1 ASP A 238 " =    0.856
peak=    3.627 closest distance to " CB  SER A 273 " =    0.842
peak=    3.624 closest distance to " O   HOH Z 408 " =    1.544
peak=    3.624 closest distance to " O   HOH Z 227 " =    1.715
peak=    3.613 closest distance to " O   HOH Z 284 " =    2.867
peak=    3.613 closest distance to " O   GLY A  23 " =    2.331
peak=    3.593 closest distance to " CG2 VAL A 197 " =    1.099
peak=    3.591 closest distance to " O   SER A  26 " =    1.692
peak=    3.588 closest distance to " CG2AVAL A 121 " =    2.158
peak=    3.584 closest distance to " O   HOH Z 358 " =    2.124
peak=    3.581 closest distance to " NH2AARG A 145 " =    2.226
peak=    3.579 closest distance to " O   HOH Z 194 " =    1.970
peak=    3.576 closest distance to " O   HOH Z  54 " =    1.644
peak=    3.566 closest distance to " O   HOH Z 128 " =    2.176
peak=    3.561 closest distance to " O   HOH Z 215 " =    1.645
peak=    3.555 closest distance to " CD  LYS A 166 " =    1.342
peak=    3.554 closest distance to " CG  GLN A  58 " =    2.386
peak=    3.550 closest distance to " O   HOH Z 423 " =    1.966
peak=    3.543 closest distance to " O   HOH Z 336 " =    1.674
peak=    3.539 closest distance to " CG1 VAL A 153 " =    1.087
peak=    3.538 closest distance to " ND2 ASN A 187 " =    1.615
peak=    3.526 closest distance to " O   HOH Z 173 " =    2.122
peak=    3.524 closest distance to " CB  GLN A 103 " =    0.943
peak=    3.509 closest distance to " O   HOH Z 250 " =    1.393
peak=    3.508 closest distance to " CA  VAL A  41 " =    0.854
peak=    3.505 closest distance to " NH1AARG A 145 " =    1.129
peak=    3.504 closest distance to " CG2 ILE A 120 " =    1.220
peak=    3.503 closest distance to " O   HOH Z 295 " =    1.472
peak=    3.499 closest distance to " O   HOH Z 106 " =    2.206
peak=    3.499 closest distance to " O   HOH Z 434 " =    1.482
peak=    3.493 closest distance to " O   HOH Z 214 " =    2.391
peak=    3.491 closest distance to " O   HOH Z 291 " =    1.610
peak=    3.490 closest distance to " O   HOH Z 303 " =    1.987
peak=    3.485 closest distance to " O   HOH Z 102 " =    1.257
peak=    3.474 closest distance to " CA  ASN A 176 " =    1.162
peak=    3.473 closest distance to " CB  ALA A 100 " =    1.275
peak=    3.471 closest distance to " CG  ARG A  66 " =    1.057
peak=    3.470 closest distance to " CA  GLN A 223 " =    0.856
peak=    3.468 closest distance to " O   HOH Z 368 " =    3.499
peak=    3.467 closest distance to " O   HOH Z 276 " =    1.347
peak=    3.465 closest distance to " CD1 LEU A  96 " =    0.784
peak=    3.460 closest distance to " O   HOH Z 135 " =    1.843
peak=    3.458 closest distance to " O   HOH Z 345 " =    1.721
peak=    3.457 closest distance to " CG1 ILE A 120 " =    1.042
peak=    3.456 closest distance to " O   HOH Z 245 " =    1.330
peak=    3.449 closest distance to " CB  ILE A 199 " =    1.012
peak=    3.447 closest distance to " CB  ALA A 256 " =    1.050
peak=    3.446 closest distance to " O   ALA A 165 " =    1.364
peak=    3.445 closest distance to " O   HOH Z 108 " =    2.078
peak=    3.444 closest distance to " O   HOH Z 163 " =    1.482
peak=    3.435 closest distance to " O   HOH Z 419 " =    1.481
peak=    3.434 closest distance to " OG  SER A  62 " =    3.001
peak=    3.428 closest distance to " O   HOH Z 118 " =    1.152
peak=    3.425 closest distance to " O   HOH Z  30 " =    1.293
peak=    3.424 closest distance to " CA  LYS A 117 " =    1.227
peak=    3.420 closest distance to " O   HOH Z 263 " =    2.166
peak=    3.418 closest distance to " O   HOH Z 261 " =    2.090
peak=    3.413 closest distance to " O   HOH Z 313 " =    2.277
peak=    3.410 closest distance to " O   HOH Z 427 " =    2.966
peak=    3.408 closest distance to " CD  LYS A 119 " =    1.270
peak=    3.394 closest distance to " O   HOH Z 280 " =    2.384
peak=    3.391 closest distance to " O   HOH Z 207 " =    2.227
peak=    3.390 closest distance to " CB  SER A 216 " =    0.735
peak=    3.380 closest distance to " C   SER A  32 " =    1.020
peak=    3.374 closest distance to " O   SER A 164 " =    1.475
peak=    3.374 closest distance to " CA  ALA A 248 " =    1.212
peak=    3.372 closest distance to " OH  TYR A  30 " =    1.131
peak=    3.371 closest distance to " CB  SER A  62 " =    0.809
peak=    3.370 closest distance to " O   HOH Z 365 " =    2.883
peak=    3.364 closest distance to " O   HOH Z 255 " =    1.591
peak=    3.363 closest distance to " O   HOH Z 126 " =    1.628
peak=    3.362 closest distance to " O   HOH Z 183 " =    1.471
peak=    3.357 closest distance to " O  BHOH Z  74 " =    1.469
peak=    3.353 closest distance to " CB  ALA A 242 " =    0.936
peak=    3.352 closest distance to " O   HOH Z 215 " =    1.493
peak=    3.348 closest distance to " NH1 ARG A 269 " =    0.741
peak=    3.341 closest distance to " O   HOH Z  19 " =    1.744
peak=    3.339 closest distance to " O   HOH Z  71 " =    1.205
peak=    3.339 closest distance to " O   HOH Z 106 " =    1.619
peak=    3.335 closest distance to " O   HOH Z 197 " =    2.508
peak=    3.335 closest distance to " OE1 GLN A  58 " =    5.880
peak=    3.334 closest distance to " NE AARG A 275 " =    1.242
peak=    3.327 closest distance to " CA  ASP A 124 " =    0.707
peak=    3.324 closest distance to " O   HOH Z 287 " =    1.725
peak=    3.324 closest distance to " O   THR A 251 " =    1.273
peak=    3.324 closest distance to " CD2 TRP A 179 " =    1.350
peak=    3.323 closest distance to " O   HOH Z 185 " =    1.643
peak=    3.322 closest distance to " CA  ARG A  66 " =    1.084
peak=    3.319 closest distance to " O   HOH Z 438 " =    2.256
peak=    3.316 closest distance to " CA  LEU A 282 " =    1.150
peak=    3.313 closest distance to " CG2 VAL A 257 " =    0.836
peak=    3.313 closest distance to " O   HOH Z 394 " =    1.585
peak=    3.312 closest distance to " O   HOH Z 383 " =    1.999
peak=    3.311 closest distance to " CZ  PHE A 218 " =    1.010
peak=    3.310 closest distance to " CA  ARG A 195 " =    1.236
peak=    3.310 closest distance to " O   HOH Z 421 " =    1.615
peak=    3.310 closest distance to " CH2 TRP A 274 " =    2.077
peak=    3.308 closest distance to " O   HOH Z 343 " =    2.358
peak=    3.307 closest distance to " OG1 THR A 294 " =    2.342
peak=    3.307 closest distance to " CB  MET A  47 " =    1.108
peak=    3.302 closest distance to " O   HOH Z  59 " =    1.795
peak=    3.299 closest distance to " O   HOH Z 345 " =    2.837
peak=    3.299 closest distance to " CB  TRP A 266 " =    0.944
peak=    3.295 closest distance to " O   HOH Z 166 " =    3.297
peak=    3.292 closest distance to " O   HOH Z 171 " =    2.690
peak=    3.288 closest distance to " CD1 LEU A 300 " =    1.226
peak=    3.287 closest distance to " NZ  LYS A 117 " =    1.399
peak=    3.285 closest distance to " CB  ASN A  39 " =    0.879
peak=    3.283 closest distance to " O   HOH Z 155 " =    2.885
peak=    3.282 closest distance to " O   HOH Z 166 " =    1.374
peak=    3.277 closest distance to " CB  GLN A  58 " =    0.796
peak=    3.276 closest distance to " CD  GLN A 194 " =    1.582
peak=    3.275 closest distance to " CB  SER A  62 " =    1.181
peak=    3.274 closest distance to " CA  GLU A 152 " =    0.850
peak=    3.273 closest distance to " O   HOH Z 266 " =    1.633
peak=    3.271 closest distance to " CA  ASN A 215 " =    1.173
peak=    3.269 closest distance to " CD2 LEU A 255 " =    1.090
peak=    3.264 closest distance to " CZ AARG A 102 " =    1.806
peak=    3.261 closest distance to " NE1 TRP A 274 " =    0.921
peak=    3.260 closest distance to " CG2 ILE A 106 " =    0.868
peak=    3.259 closest distance to " O   HOH Z  66 " =    2.307
peak=    3.257 closest distance to " O   ALA A 158 " =    1.181
peak=    3.255 closest distance to " CB  ARG A 259 " =    1.915
peak=    3.254 closest distance to " O   MET A 105 " =    1.926
peak=    3.254 closest distance to " CD  ARG A 195 " =    3.485
peak=    3.251 closest distance to " O   HOH Z 292 " =    1.639
peak=    3.249 closest distance to " CD1 TRP A 266 " =    1.254
peak=    3.244 closest distance to " CB  VAL A 265 " =    1.144
peak=    3.242 closest distance to " CA  GLU A  46 " =    0.748
peak=    3.242 closest distance to " CB  GLU A 175 " =    1.301
peak=    3.241 closest distance to " O   HOH Z 273 " =    2.650
peak=    3.241 closest distance to " NH1BARG A 145 " =    1.232
peak=    3.232 closest distance to " N   SER A 135 " =    1.259
peak=    3.232 closest distance to " O   HOH Z 261 " =    1.571
peak=    3.227 closest distance to " CD AARG A 102 " =    2.352
peak=    3.226 closest distance to " OD2 ASP A 298 " =    4.006
peak=    3.226 closest distance to " CG  GLN A  11 " =    1.138
peak=    3.224 closest distance to " CD2 HIS A  81 " =    1.209
peak=    3.223 closest distance to " OG BSER A 210 " =    1.172
peak=    3.223 closest distance to " CG2 THR A 220 " =    0.746
peak=    3.220 closest distance to " CG2 ILE A  20 " =    1.371
peak=    3.219 closest distance to " CB  ALA A 244 " =    0.951
peak=    3.218 closest distance to " CA  ASP A 162 " =    1.179
peak=    3.218 closest distance to " CA  ILE A  33 " =    1.401
peak=    3.216 closest distance to " CA  VAL A 126 " =    0.960
peak=    3.214 closest distance to " O   HOH Z 261 " =    1.960
peak=    3.213 closest distance to " O   HOH Z 387 " =    2.581
peak=    3.211 closest distance to " O   HOH Z 162 " =    1.575
peak=    3.211 closest distance to " CZ  PHE A  38 " =    1.492
peak=    3.210 closest distance to " OG  SER A  22 " =    2.720
peak=    3.205 closest distance to " O   HOH Z  20 " =    1.188
peak=    3.203 closest distance to " O   HOH Z 433 " =    1.447
peak=    3.196 closest distance to " CD BLYS A 290 " =    1.150
peak=    3.187 closest distance to " O   HOH Z 163 " =    1.877
peak=    3.186 closest distance to " O   HOH Z 156 " =    2.794
peak=    3.186 closest distance to " N   ARG A 156 " =    1.374
peak=    3.184 closest distance to " O   HOH Z  35 " =    2.478
peak=    3.184 closest distance to " CD2 PHE A 225 " =    1.071
peak=    3.182 closest distance to " O   HOH Z 355 " =    1.656
peak=    3.176 closest distance to " CZ2 TRP A 274 " =    1.657
peak=    3.175 closest distance to " CA  ALA A 160 " =    0.825
peak=    3.171 closest distance to " O   HOH Z 411 " =    1.638
peak=    3.171 closest distance to " O   HOH Z 148 " =    3.084
peak=    3.171 closest distance to " CG  MET A 185 " =    1.222
peak=    3.170 closest distance to " O   HOH Z 427 " =    3.381
peak=    3.165 closest distance to " O   HOH Z 299 " =    2.193
peak=    3.160 closest distance to " CA  ALA A 233 " =    1.552
peak=    3.160 closest distance to " CE  LYS A 119 " =    1.038
peak=    3.159 closest distance to " CB  TRP A 150 " =    1.667
peak=    3.154 closest distance to " O   HOH Z 197 " =    1.826
peak=    3.154 closest distance to " CB  ARG A 269 " =    0.946
peak=    3.154 closest distance to " CG2 VAL A 112 " =    1.583
peak=    3.153 closest distance to " O   HOH Z 337 " =    3.691
peak=    3.152 closest distance to " O   HOH Z 128 " =    1.729
peak=    3.149 closest distance to " CA  ASN A 217 " =    1.400
peak=    3.143 closest distance to " CB  ALA A   1 " =    1.190
peak=    3.142 closest distance to " CB  GLN A 194 " =    0.854
peak=    3.140 closest distance to " O   HOH Z 267 " =    2.093
peak=    3.131 closest distance to " O   HOH Z 227 " =    2.223
peak=    3.131 closest distance to " CB  ARG A 102 " =    0.780
peak=    3.127 closest distance to " O   HOH Z 248 " =    1.534
peak=    3.118 closest distance to " CA  MET A  40 " =    1.050
peak=    3.114 closest distance to " CA  THR A 264 " =    0.831
peak=    3.109 closest distance to " O   HOH Z 217 " =    1.217
peak=    3.106 closest distance to " O   HOH Z 211 " =    2.455
peak=    3.105 closest distance to " O   HOH Z 368 " =    2.427
peak=    3.101 closest distance to " O   HOH Z  22 " =    2.354
peak=    3.099 closest distance to " O   HOH Z 104 " =    3.002
peak=    3.097 closest distance to " O   HOH Z 125 " =    2.300
peak=    3.096 closest distance to " CG  MET A  93 " =    1.089
peak=    3.091 closest distance to " CB  GLN A 278 " =    0.821
peak=    3.087 closest distance to " O   HOH Z  61 " =    1.545
peak=    3.079 closest distance to " CA  ALA A  84 " =    1.219
peak=    3.078 closest distance to " CB  TYR A 247 " =    1.047
peak=    3.071 closest distance to " CB  TYR A  30 " =    1.456
peak=    3.060 closest distance to " O   HOH Z 123 " =    1.927
peak=    3.060 closest distance to " O   HOH Z 285 " =    2.025
peak=    3.034 closest distance to " CB  ASN A 215 " =    1.076
peak=    3.033 closest distance to " CB  ILE A 120 " =    1.342

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 195         
Filter by distance & map next to the model:
   mapped sites are within: 0.674 - 5.145
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 195
   mapped sites are within: 0.720 - 5.145

peak=   -4.523 closest distance to " O   HOH Z 266 " =    4.051
peak=   -4.456 closest distance to " OXT GLY A 302 " =    2.901
peak=   -4.295 closest distance to " CD1 LEU A 101 " =    2.544
peak=   -4.185 closest distance to " O   HOH Z 290 " =    0.920
peak=   -4.172 closest distance to " CD  ARG A 156 " =    1.994
peak=   -4.163 closest distance to " O   HOH Z  13 " =    1.410
peak=   -4.154 closest distance to " O   HOH Z 292 " =    4.451
peak=   -4.126 closest distance to " CB  TYR A  15 " =    2.253
peak=   -4.125 closest distance to " OG ASER A 134 " =    1.310
peak=   -4.083 closest distance to " O   HOH Z 234 " =    4.233
peak=   -4.075 closest distance to " C   HIS A 108 " =    1.092
peak=   -4.056 closest distance to " O   VAL A  67 " =    2.726
peak=   -3.999 closest distance to " CA  SER A 164 " =    1.955
peak=   -3.989 closest distance to " CE2 TYR A  30 " =    2.777
peak=   -3.986 closest distance to " ND2 ASN A 187 " =    1.483
peak=   -3.960 closest distance to " O   HOH Z  11 " =    1.645
peak=   -3.957 closest distance to " O   TRP A  92 " =    1.813
peak=   -3.905 closest distance to " CH2 TRP A 179 " =    1.276
peak=   -3.885 closest distance to " ND2 ASN A  45 " =    0.915
peak=   -3.878 closest distance to " O   HOH Z  43 " =    1.580
peak=   -3.854 closest distance to " O   PRO A 198 " =    1.276
peak=   -3.848 closest distance to " O   HOH Z 165 " =    2.147
peak=   -3.838 closest distance to " O   HOH Z 210 " =    0.748
peak=   -3.835 closest distance to " N   GLN A  58 " =    1.745
peak=   -3.823 closest distance to " O   HOH Z  93 " =    1.235
peak=   -3.817 closest distance to " O   HOH Z  10 " =    1.554
peak=   -3.786 closest distance to " O   HOH Z 423 " =    2.341
peak=   -3.785 closest distance to " O   HOH Z 377 " =    1.892
peak=   -3.783 closest distance to " N   ALA A  43 " =    2.524
peak=   -3.780 closest distance to " C   ALA A 158 " =    1.198
peak=   -3.765 closest distance to " NE2 GLN A  58 " =    0.988
peak=   -3.750 closest distance to " O   HOH Z 407 " =    3.259
peak=   -3.744 closest distance to " O   GLY A 196 " =    0.980
peak=   -3.731 closest distance to " CB  ALA A 291 " =    2.351
peak=   -3.729 closest distance to " O   HOH Z  17 " =    1.274
peak=   -3.726 closest distance to " O   ALA A 256 " =    1.390
peak=   -3.721 closest distance to " OG  SER A  97 " =    2.125
peak=   -3.714 closest distance to " CG  GLU A  53 " =    1.392
peak=   -3.713 closest distance to " CG2 THR A   4 " =    1.824
peak=   -3.710 closest distance to " NH2 ARG A  66 " =    1.717
peak=   -3.704 closest distance to " CG  LYS A 193 " =    2.338
peak=   -3.689 closest distance to " CD2 LEU A 300 " =    2.839
peak=   -3.685 closest distance to " CB  ALA A 161 " =    2.604
peak=   -3.676 closest distance to " C   ASN A 285 " =    2.239
peak=   -3.675 closest distance to " O   HOH Z 377 " =    1.160
peak=   -3.667 closest distance to " OG  SER A  62 " =    1.422
peak=   -3.665 closest distance to " CG  ASP A 231 " =    0.817
peak=   -3.664 closest distance to " CZ  TYR A 169 " =    1.888
peak=   -3.663 closest distance to " O   HOH Z 118 " =    3.019
peak=   -3.656 closest distance to " O   HOH Z  52 " =    1.796
peak=   -3.646 closest distance to " CD1 LEU A 228 " =    2.257
peak=   -3.645 closest distance to " CB  CYS A 254 " =    2.612
peak=   -3.643 closest distance to " O   SER A 210 " =    1.822
peak=   -3.634 closest distance to " SG  CYS A 254 " =    3.332
peak=   -3.627 closest distance to " CG  ASP A  50 " =    2.382
peak=   -3.619 closest distance to " CD  PRO A 198 " =    1.243
peak=   -3.618 closest distance to " CE  MET A  93 " =    1.153
peak=   -3.601 closest distance to " NH2 ARG A  79 " =    1.913
peak=   -3.598 closest distance to " O   GLN A 205 " =    1.711
peak=   -3.591 closest distance to " ND2 ASN A  60 " =    1.367
peak=   -3.588 closest distance to " CG  GLN A  58 " =    1.458
peak=   -3.587 closest distance to " O   HOH Z  71 " =    1.220
peak=   -3.585 closest distance to " CD  ARG A 139 " =    1.583
peak=   -3.584 closest distance to " CB  PHE A 208 " =    2.267
peak=   -3.580 closest distance to " O   HOH Z 418 " =    1.336
peak=   -3.560 closest distance to " O   HOH Z 166 " =    2.002
peak=   -3.558 closest distance to " N   MET A 188 " =    1.941
peak=   -3.555 closest distance to " CE  MET A 105 " =    1.783
peak=   -3.550 closest distance to " CB  PRO A 243 " =    2.597
peak=   -3.549 closest distance to " C   THR A 279 " =    1.208
peak=   -3.546 closest distance to " OG  SER A   3 " =    1.711
peak=   -3.537 closest distance to " O   ALA A 161 " =    1.418
peak=   -3.535 closest distance to " CB  ASP A 162 " =    2.678
peak=   -3.532 closest distance to " O   HOH Z 353 " =    2.261
peak=   -3.529 closest distance to " N   SER A 276 " =    1.371
peak=   -3.515 closest distance to " CE3 TRP A 150 " =    2.135
peak=   -3.511 closest distance to " CA  GLY A 133 " =    1.771
peak=   -3.510 closest distance to " CA  TRP A 274 " =    1.652
peak=   -3.503 closest distance to " O   HOH Z  98 " =    1.743
peak=   -3.496 closest distance to " OD2 ASP A 171 " =    2.309
peak=   -3.495 closest distance to " OD1 ASN A 148 " =    1.720
peak=   -3.494 closest distance to " CG  LEU A  83 " =    1.898
peak=   -3.494 closest distance to " O   VAL A  67 " =    2.714
peak=   -3.491 closest distance to " OE2 GLU A   2 " =    1.554
peak=   -3.490 closest distance to " O   HOH Z 313 " =    1.019
peak=   -3.489 closest distance to " O   HOH Z 396 " =    1.698
peak=   -3.487 closest distance to " O   HOH Z 266 " =    4.742
peak=   -3.483 closest distance to " O   HOH Z 150 " =    1.431
peak=   -3.481 closest distance to " N   LEU A 281 " =    1.807
peak=   -3.463 closest distance to " CA  GLY A 241 " =    2.253
peak=   -3.462 closest distance to " CA  ASP A 298 " =    1.090
peak=   -3.462 closest distance to " O   HOH Z  15 " =    1.582
peak=   -3.461 closest distance to " O   HOH Z  92 " =    1.556
peak=   -3.459 closest distance to " O   HOH Z 196 " =    2.061
peak=   -3.451 closest distance to " NH1 ARG A 195 " =    2.528
peak=   -3.440 closest distance to " O   LEU A 167 " =    1.555
peak=   -3.439 closest distance to " OD1 ASP A 200 " =    1.195
peak=   -3.436 closest distance to " NH2 ARG A  66 " =    4.949
peak=   -3.431 closest distance to " CA  GLY A 203 " =    2.189
peak=   -3.428 closest distance to " O   HOH Z  88 " =    2.500
peak=   -3.416 closest distance to " CD  GLN A  88 " =    0.720
peak=   -3.415 closest distance to " O   HOH Z 388 " =    2.119
peak=   -3.398 closest distance to " CD1 LEU A  25 " =    2.467
peak=   -3.390 closest distance to " O   HOH Z 145 " =    1.760
peak=   -3.390 closest distance to " OG BSER A 134 " =    1.763
peak=   -3.389 closest distance to " O   HOH Z 185 " =    2.298
peak=   -3.389 closest distance to " SG ACYS A 201 " =    2.425
peak=   -3.387 closest distance to " CD  ARG A 195 " =    5.145
peak=   -3.385 closest distance to " O   HOH Z 166 " =    1.737
peak=   -3.378 closest distance to " O   HOH Z  63 " =    1.165
peak=   -3.378 closest distance to " CG1AVAL A 121 " =    1.606
peak=   -3.372 closest distance to " CB  PRO A 163 " =    2.814
peak=   -3.364 closest distance to " CG  ASP A 132 " =    2.200
peak=   -3.361 closest distance to " O   HOH Z 222 " =    1.343
peak=   -3.357 closest distance to " CB  LEU A 167 " =    2.141
peak=   -3.352 closest distance to " O   HOH Z  97 " =    1.545
peak=   -3.351 closest distance to " CB  ASN A  39 " =    2.264
peak=   -3.347 closest distance to " O   HOH Z 151 " =    1.344
peak=   -3.346 closest distance to " O   HOH Z 412 " =    4.512
peak=   -3.346 closest distance to " OG  SER A  63 " =    1.398
peak=   -3.334 closest distance to " CD2 LEU A 237 " =    2.248
peak=   -3.332 closest distance to " O   SER A 146 " =    0.889
peak=   -3.331 closest distance to " CD2 LEU A 237 " =    2.724
peak=   -3.331 closest distance to " O   HOH Z 231 " =    2.240
peak=   -3.329 closest distance to " O   HOH Z 417 " =    2.621
peak=   -3.317 closest distance to " O   ALA A  34 " =    2.461
peak=   -3.315 closest distance to " CB  ALA A 248 " =    1.922
peak=   -3.308 closest distance to " O   HOH Z  38 " =    1.513
peak=   -3.302 closest distance to " O   HOH Z 100 " =    0.885
peak=   -3.298 closest distance to " CA  VAL A 197 " =    0.971
peak=   -3.292 closest distance to " O   HOH Z 265 " =    1.889
peak=   -3.289 closest distance to " OD1 ASP A 191 " =    1.704
peak=   -3.288 closest distance to " O   ALA A 160 " =    1.487
peak=   -3.287 closest distance to " N   ALA A 248 " =    1.761
peak=   -3.280 closest distance to " O   SER A 273 " =    1.492
peak=   -3.277 closest distance to " O   HOH Z 360 " =    2.517
peak=   -3.276 closest distance to " CG  LYS A 119 " =    2.936
peak=   -3.269 closest distance to " O   HOH Z 213 " =    1.326
peak=   -3.268 closest distance to " CD  LYS A 289 " =    2.491
peak=   -3.265 closest distance to " O   VAL A 174 " =    1.948
peak=   -3.249 closest distance to " CB  ASP A 286 " =    2.194
peak=   -3.248 closest distance to " CG  GLU A 152 " =    2.456
peak=   -3.245 closest distance to " O   ASN A 187 " =    1.458
peak=   -3.242 closest distance to " O   GLY A 211 " =    1.396
peak=   -3.240 closest distance to " O   HOH Z 297 " =    2.792
peak=   -3.234 closest distance to " O   GLY A 118 " =    2.185
peak=   -3.232 closest distance to " O   ALA A   1 " =    1.892
peak=   -3.230 closest distance to " CD1 TYR A 247 " =    2.286
peak=   -3.228 closest distance to " O   HOH Z 424 " =    2.964
peak=   -3.224 closest distance to " CG  GLU A 277 " =    1.174
peak=   -3.223 closest distance to " CD1 PHE A  59 " =    1.819
peak=   -3.218 closest distance to " O   HOH Z 171 " =    2.204
peak=   -3.215 closest distance to " O   GLN A  11 " =    1.292
peak=   -3.214 closest distance to " O   HOH Z 148 " =    3.615
peak=   -3.207 closest distance to " CE3 TRP A 123 " =    1.300
peak=   -3.206 closest distance to " OG BSER A 134 " =    1.276
peak=   -3.203 closest distance to " CB  PHE A 192 " =    1.923
peak=   -3.203 closest distance to " O   MET A  40 " =    2.590
peak=   -3.201 closest distance to " N   VAL A 189 " =    1.821
peak=   -3.197 closest distance to " CD2 TRP A 274 " =    1.125
peak=   -3.197 closest distance to " CG1 VAL A 112 " =    2.559
peak=   -3.196 closest distance to " O   ASN A  45 " =    1.855
peak=   -3.193 closest distance to " O  BHOH Z 338 " =    1.566
peak=   -3.192 closest distance to " O   HOH Z 283 " =    1.704
peak=   -3.184 closest distance to " CD2 LEU A 167 " =    1.666
peak=   -3.184 closest distance to " O   GLY A  80 " =    2.360
peak=   -3.178 closest distance to " C   LEU A 143 " =    1.302
peak=   -3.175 closest distance to " O   HOH Z 351 " =    1.445
peak=   -3.173 closest distance to " N   ALA A 226 " =    2.064
peak=   -3.172 closest distance to " N   GLN A  77 " =    1.413
peak=   -3.171 closest distance to " NH2 ARG A 159 " =    2.259
peak=   -3.169 closest distance to " O   HOH Z  61 " =    1.562
peak=   -3.169 closest distance to " OG  SER A  32 " =    1.091
peak=   -3.157 closest distance to " OG  SER A 206 " =    1.720
peak=   -3.156 closest distance to " O   HOH Z   6 " =    1.857
peak=   -3.155 closest distance to " O   HOH Z 414 " =    1.399
peak=   -3.155 closest distance to " O   HOH Z 287 " =    2.089
peak=   -3.152 closest distance to " CB  SER A 146 " =    2.178
peak=   -3.150 closest distance to " O   HOH Z 385 " =    1.955
peak=   -3.148 closest distance to " O   HOH Z 385 " =    3.555
peak=   -3.145 closest distance to " O   PHE A 218 " =    1.577
peak=   -3.143 closest distance to " CB  CYS A 201 " =    2.505
peak=   -3.141 closest distance to " O   HOH Z 198 " =    1.998
peak=   -3.135 closest distance to " CD  GLN A  88 " =    2.045
peak=   -3.118 closest distance to " O   HOH Z 140 " =    0.886
peak=   -3.114 closest distance to " O   PRO A 198 " =    1.295
peak=   -3.112 closest distance to " C   ASP A 191 " =    1.362
peak=   -3.110 closest distance to " O   GLY A  23 " =    1.748
peak=   -3.110 closest distance to " O   HOH Z 361 " =    3.360
peak=   -3.099 closest distance to " OG  SER A  26 " =    1.379
peak=   -3.097 closest distance to " CD  GLU A 152 " =    1.111
peak=   -3.064 closest distance to " N   THR A  52 " =    1.679
peak=   -3.063 closest distance to " N   ALA A 248 " =    1.857

================= 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    :  0.4404 0.4353   6.250970e+00   6.243922e+00
   1_bss:  0.4293 0.4243   6.241369e+00   6.225008e+00
   1_xyz:  0.2974 0.3247   5.949285e+00   6.023180e+00
   1_adp:  0.2736 0.3341   5.900573e+00   6.041285e+00
   1_occ:  0.2730 0.3348   5.899516e+00   6.040147e+00
   2_bss:  0.2693 0.3307   5.894004e+00   6.036038e+00
   2_xyz:  0.1945 0.2431   5.610730e+00   5.794081e+00
   2_adp:  0.1732 0.2278   5.525922e+00   5.735082e+00
   2_occ:  0.1730 0.2280   5.525977e+00   5.735225e+00
   3_bss:  0.1734 0.2271   5.523235e+00   5.732504e+00
   3_xyz:  0.1419 0.1916   5.347427e+00   5.575902e+00
   3_adp:  0.1339 0.1811   5.296596e+00   5.521187e+00
   3_occ:  0.1338 0.1811   5.296466e+00   5.521336e+00
   4_bss:  0.1341 0.1816   5.299339e+00   5.523515e+00
   4_xyz:  0.1215 0.1691   5.216800e+00   5.448854e+00
   4_adp:  0.1202 0.1643   5.199809e+00   5.420510e+00
   4_occ:  0.1201 0.1642   5.199651e+00   5.421004e+00
   5_bss:  0.1201 0.1642   5.199597e+00   5.420920e+00
   5_xyz:  0.1162 0.1607   5.173581e+00   5.396367e+00
   5_adp:  0.1157 0.1605   5.170723e+00   5.395256e+00
   5_occ:  0.1157 0.1605   5.170633e+00   5.395624e+00
   5_bss:  0.1157 0.1605   5.170633e+00   5.395624e+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:  0.306  23.025  -3.286   2.141   2.436   0.000   0.000   0.000
   1_xyz:  0.306  23.025  -3.286   2.141   2.436   0.000   0.000   0.000
   1_adp:  0.306  23.025  -3.286   2.141   2.436   0.000   0.000   0.000
   1_occ:  0.306  23.025  -3.286   2.141   2.436   0.000   0.000   0.000
   2_bss:  0.327  50.000  -2.719  -0.073  -0.142  -0.000  -0.000  -0.000
   2_xyz:  0.327  50.000  -2.719  -0.073  -0.142  -0.000  -0.000  -0.000
   2_adp:  0.327  50.000  -2.719  -0.073  -0.142  -0.000  -0.000  -0.000
   2_occ:  0.327  50.000  -2.719  -0.073  -0.142  -0.000  -0.000  -0.000
   3_bss:  0.322  50.636  -2.423  -0.762  -1.011  -0.000  -0.000  -0.000
   3_xyz:  0.322  50.636  -2.423  -0.762  -1.011  -0.000  -0.000  -0.000
   3_adp:  0.322  50.636  -2.423  -0.762  -1.011  -0.000  -0.000  -0.000
   3_occ:  0.322  50.636  -2.423  -0.762  -1.011  -0.000  -0.000  -0.000
   4_bss:  0.322  50.636  -2.400  -1.191  -1.446  -0.000  -0.000  -0.000
   4_xyz:  0.322  50.636  -2.400  -1.191  -1.446  -0.000  -0.000  -0.000
   4_adp:  0.322  50.636  -2.400  -1.191  -1.446  -0.000  -0.000  -0.000
   4_occ:  0.322  50.636  -2.400  -1.191  -1.446  -0.000  -0.000  -0.000
   5_bss:  0.328  50.636  -2.440  -1.423  -1.621  -0.000  -0.000  -0.000
   5_xyz:  0.328  50.636  -2.440  -1.423  -1.621  -0.000  -0.000  -0.000
   5_adp:  0.328  50.636  -2.440  -1.423  -1.621  -0.000  -0.000  -0.000
   5_occ:  0.328  50.636  -2.440  -1.423  -1.621  -0.000  -0.000  -0.000
   5_bss:  0.328  50.579  -2.383  -1.366  -1.564  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.257 0.4659  0.6222    61127.758
   1_bss:  52.289 0.4892  0.6635    56541.726
   1_xyz:  34.061 0.7120  0.9285    28102.642
   1_adp:  35.189 0.6981  0.9118    29505.330
   1_occ:  35.155 0.6985  0.9114    29446.860
   2_bss:  34.691 0.7037  0.8767    28870.664
   2_xyz:  24.373 0.8166  0.9735    15205.016
   2_adp:  22.222 0.8393  0.9802    13276.926
   2_occ:  22.250 0.8391  0.9797    13310.227
   3_bss:  22.102 0.8404  0.9664    13145.848
   3_xyz:  18.272 0.8770  0.9886     9273.078
   3_adp:  16.903 0.8902  0.9899     8340.304
   3_occ:  16.906 0.8902  0.9897     8344.524
   4_bss:  16.957 0.8899  0.9796     8422.456
   4_xyz:  15.487 0.9023  0.9854     7234.569
   4_adp:  14.827 0.9082  0.9848     6890.807
   4_occ:  14.836 0.9081  0.9847     6903.907
   5_bss:  14.832 0.9082  0.9797     6904.376
   5_xyz:  14.299 0.9127  0.9811     6505.831
   5_adp:  14.236 0.9133  0.9784     6492.386
   5_occ:  14.240 0.9133  0.9783     6498.418
   5_bss:  14.240 0.9133  0.9783     6498.418
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.9168e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.9168e-01
   1_xyz:   1.549  0.013  0.094 16.274  0.006  4.115   1.3316e-01
   1_adp:   1.549  0.013  0.094 16.274  0.006  4.115   1.3316e-01
   1_occ:   1.549  0.013  0.094 16.274  0.006  4.115   1.3316e-01
   2_bss:   1.549  0.013  0.094 16.274  0.006  4.115   1.3316e-01
   2_xyz:   1.154  0.008  0.077 14.453  0.004  4.121   7.1379e-02
   2_adp:   1.154  0.008  0.077 14.453  0.004  4.121   7.1379e-02
   2_occ:   1.154  0.008  0.077 14.453  0.004  4.121   7.1379e-02
   3_bss:   1.154  0.008  0.077 14.453  0.004  4.121   7.1379e-02
   3_xyz:   0.951  0.006  0.064 14.386  0.004  4.110   5.6377e-02
   3_adp:   0.951  0.006  0.064 14.386  0.004  4.110   5.6377e-02
   3_occ:   0.951  0.006  0.064 14.386  0.004  4.110   5.6377e-02
   4_bss:   0.951  0.006  0.064 14.386  0.004  4.110   5.6377e-02
   4_xyz:   0.990  0.006  0.070 14.457  0.004  4.112   5.5989e-02
   4_adp:   0.990  0.006  0.070 14.457  0.004  4.112   5.5989e-02
   4_occ:   0.990  0.006  0.070 14.457  0.004  4.112   5.5989e-02
   5_bss:   0.990  0.006  0.070 14.457  0.004  4.112   5.5989e-02
   5_xyz:   0.935  0.006  0.066 14.321  0.004  4.113   5.1441e-02
   5_adp:   0.935  0.006  0.066 14.321  0.004  4.113   5.1441e-02
   5_occ:   0.935  0.006  0.066 14.321  0.004  4.113   5.1441e-02
   5_bss:   0.935  0.006  0.066 14.321  0.004  4.113   5.1441e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.483   2.4078e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.483   2.4078e-01
   1_xyz:   9.895  0.093  0.409 88.580  0.031  2.116   1.0138e-01
   1_adp:   9.895  0.093  0.409 88.580  0.031  2.116   1.0138e-01
   1_occ:   9.895  0.093  0.409 88.580  0.031  2.116   1.0138e-01
   2_bss:   9.895  0.093  0.409 88.580  0.031  2.116   1.0138e-01
   2_xyz:   8.696  0.041  0.229 84.795  0.039  2.291   1.0865e-01
   2_adp:   8.696  0.041  0.229 84.795  0.039  2.291   1.0865e-01
   2_occ:   8.696  0.041  0.229 84.795  0.039  2.291   1.0865e-01
   3_bss:   8.696  0.041  0.229 84.795  0.039  2.291   1.0865e-01
   3_xyz:   7.045  0.042  0.246 81.693  0.031  2.380   1.0490e-01
   3_adp:   7.045  0.042  0.246 81.693  0.031  2.380   1.0490e-01
   3_occ:   7.045  0.042  0.246 81.693  0.031  2.380   1.0490e-01
   4_bss:   7.045  0.042  0.246 81.693  0.031  2.380   1.0490e-01
   4_xyz:   6.699  0.032  0.215 82.824  0.029  2.377   5.0032e-02
   4_adp:   6.699  0.032  0.215 82.824  0.029  2.377   5.0032e-02
   4_occ:   6.699  0.032  0.215 82.824  0.029  2.377   5.0032e-02
   5_bss:   6.699  0.032  0.215 82.824  0.029  2.377   5.0032e-02
   5_xyz:   6.718  0.038  0.226 80.762  0.032  2.357   3.5255e-02
   5_adp:   6.718  0.038  0.226 80.762  0.032  2.357   3.5255e-02
   5_occ:   6.718  0.038  0.226 80.762  0.032  2.357   3.5255e-02
   5_bss:   6.718  0.038  0.226 80.762  0.032  2.357   3.5255e-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: 140.74   0.00  17.31 140.74   0.00  13.42  65.62   3.35  38.47
   1_occ: 140.74   0.00  17.31 140.74   0.00  13.42  65.62   3.35  38.47
   2_bss: 140.74   0.00  17.31 140.74   0.00  13.42  65.62   3.35  38.47
   2_xyz: 140.74   0.00  17.31 140.74   0.00  13.42  65.62   3.35  38.47
   2_adp:  92.61   0.00  18.20  92.61   0.00  13.54  85.29   5.82  43.57
   2_occ:  92.61   0.00  18.20  92.61   0.00  13.54  85.29   5.82  43.57
   3_bss:  92.61   0.00  18.20  92.61   0.00  13.54  85.29   5.82  43.57
   3_xyz:  92.61   0.00  18.20  92.61   0.00  13.54  85.29   5.82  43.57
   3_adp: 106.52   0.00  17.95 106.52   0.00  13.15  88.50   2.55  44.07
   3_occ: 106.52   0.00  17.95 106.52   0.00  13.15  88.50   2.55  44.07
   4_bss: 106.52   0.00  17.95 106.52   0.00  13.15  88.50   2.55  44.07
   4_xyz: 106.52   0.00  17.95 106.52   0.00  13.15  88.50   2.55  44.07
   4_adp:  99.17   1.70  17.03  99.17   1.70  12.76  86.35   4.25  40.28
   4_occ:  99.17   1.70  17.03  99.17   1.70  12.76  86.35   4.25  40.28
   5_bss:  99.17   1.70  17.03  99.17   1.70  12.76  86.35   4.25  40.28
   5_xyz:  99.17   1.70  17.03  99.17   1.70  12.76  86.35   4.25  40.28
   5_adp:  97.91   1.60  16.83  97.91   1.60  12.63  86.78   5.27  39.67
   5_occ:  97.91   1.60  16.83  97.91   1.60  12.63  86.78   5.27  39.67
   5_bss:  97.85   1.54  16.77  97.85   1.54  12.58  86.72   5.22  39.61
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    2.023    0.016    0.449
   1_adp:    2.023    0.016    0.449
   1_occ:    2.023    0.016    0.449
   2_bss:    2.023    0.016    0.449
   2_xyz:    1.484    0.053    0.572
   2_adp:    1.484    0.053    0.572
   2_occ:    1.484    0.053    0.572
   3_bss:    1.484    0.053    0.572
   3_xyz:    1.568    0.025    0.646
   3_adp:    1.568    0.025    0.646
   3_occ:    1.568    0.025    0.646
   4_bss:    1.568    0.025    0.646
   4_xyz:    1.664    0.052    0.681
   4_adp:    1.664    0.052    0.681
   4_occ:    1.664    0.052    0.681
   5_bss:    1.664    0.052    0.681
   5_xyz:    1.752    0.075    0.697
   5_adp:    1.752    0.075    0.697
   5_occ:    1.752    0.075    0.697
   5_bss:    1.752    0.075    0.697
------------------------------------------------------------------------

CPU time actual refinement: 340.12


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_572/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_572/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_572/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_572/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_572/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 339.97 
  Macro-tasks:
    bulk solvent and scale       = 43.21  
    individual site refinement   = 141.23 
    weights calculation          = 29.72  
    collect and process          = 6.57   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 220.84 
  Micro-tasks:
    mask                            = 1.84   
    f_calc                          = 107.94 
    alpha_beta                      = 8.19   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 117.12 
    fmodel                         = 7.25   
    r_factors                      = 0.25   
    phase_errors                   = 10.43  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 254.47 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.800 micro seconds
Total CPU time: 5.90 minutes
from_scatterers_fft:    643 calls, 107.65 s
gradients_fft:          588 calls, 103.61 s

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

# Date 2008-01-16 Time 05:08:23 PST -0800 (1200488903.47 s)
Start R-work = 0.4404, R-free = 0.4353 (no bulk solvent and anisotropic scale)
Final R-work = 0.1384, R-free = 0.1814 (no bulk solvent and anisotropic scale)

Start R-work = 0.4293, R-free = 0.4243
Final R-work = 0.1157, R-free = 0.1605