# Date 2008-01-16 Time 04:07:47 PST -0800 (1200485267.47 s)
#phil __OFF__

Command line arguments: "../183.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1483
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 183

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.845, 46.93, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.32, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 46.93, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8121 1.9608
Completeness in resolution range: 0.939475
Completeness with d_max=infinity: 0.936601

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 46.93, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8121 1.9608
Completeness in resolution range: 0.939475
Completeness with d_max=infinity: 0.936601

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8125 -  4.1954 [2195/2223]  1974   221  10.1%
  bin  2:  4.1954 -  3.3426 [2096/2115]  1883   213  10.2%
  bin  3:  3.3426 -  2.9238 [2074/2095]  1873   201   9.7%
  bin  4:  2.9238 -  2.6581 [2058/2082]  1851   207  10.1%
  bin  5:  2.6581 -  2.4685 [2028/2048]  1824   204  10.1%
  bin  6:  2.4685 -  2.3236 [2040/2087]  1834   206  10.1%
  bin  7:  2.3236 -  2.2076 [2021/2054]  1822   199   9.8%
  bin  8:  2.2076 -  2.1118 [2023/2057]  1813   210  10.4%
  bin  9:  2.1118 -  2.0307 [2011/2041]  1814   197   9.8%
  bin 10:  2.0307 -  1.9608 [1043/2049]   942   101   9.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_183/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: 0.12 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:
        1.51 -     2.19: 14
        2.19 -     2.86: 1200
        2.86 -     3.54: 4470
        3.54 -     4.22: 9280
        4.22 -     4.90: 13538
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.506 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.586 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.626 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.669 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.726 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28497 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_183/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_183/model_refine_001.geo

CPU time processing inputs: 8.93


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 46.93 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3364   r_free= 0.3334   ksol= 0.00   Bsol= 0.00   scale= 0.969    |
|                                                                             |
| 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:   0.39 A                  |
| x-ray target function (ml) for work reflections: 6.078489                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8125 -  4.6792 0.99   1421  158 0.2793 0.2837      6.3585      6.3713|
|  2:  4.6792 -  3.7336 0.99   1379  152 0.2584 0.2413      6.4324       6.442|
|  3:  3.7336 -  3.2675 0.99   1331  150 0.2969 0.2854      6.3788      6.4143|
|  4:  3.2675 -  2.9713 0.99   1345  142 0.3101 0.3524      6.2547      6.3484|
|  5:  2.9713 -  2.7598 0.99   1301  153 0.3445 0.3321      6.1285      6.1187|
|  6:  2.7598 -  2.5980 0.98   1332  145 0.3525 0.3820      6.0565      6.0076|
|  7:  2.5980 -  2.4685 0.99   1296  146 0.3546 0.2998      6.0278      5.9044|
|  8:  2.4685 -  2.3615 0.98   1319  143 0.3755 0.3527      6.0068       6.006|
|  9:  2.3615 -  2.2710 0.98   1309  145 0.3947 0.3875      5.9755      5.9827|
| 10:  2.2710 -  2.1928 0.98   1296  143 0.3792 0.3601      5.9401      5.8571|
| 11:  2.1928 -  2.1245 0.99   1296  153 0.3947 0.3980      5.8761      5.9309|
| 12:  2.1245 -  2.0639 0.98   1298  139 0.4045 0.4023      5.8452      5.8707|
| 13:  2.0639 -  2.0097 0.95   1266  132 0.4023 0.4171      5.7581      5.7036|
| 14:  2.0097 -  1.9608 0.34    441   58 0.4319 0.4339       5.821      5.6318|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8125 -  4.6792  1421   158  0.79  26.46   0.87     0.80      43620.79|
|  2:  4.6792 -  3.7336  1379   152  0.83  23.27   0.98     0.91      50995.70|
|  3:  3.7336 -  3.2675  1331   150  0.78  28.13   0.99     0.93      51218.63|
|  4:  3.2675 -  2.9713  1345   142  0.74  31.84   0.99     0.90      45997.92|
|  5:  2.9713 -  2.7598  1301   153  0.68  36.92   0.99     0.87      38487.38|
|  6:  2.7598 -  2.5980  1332   145  0.68  37.19   0.97     0.87      32765.38|
|  7:  2.5980 -  2.4685  1296   146  0.70  35.99   1.01     0.89      28225.92|
|  8:  2.4685 -  2.3615  1319   143  0.70  35.97   1.01     0.90      25220.41|
|  9:  2.3615 -  2.2710  1309   145  0.69  36.23   1.00     0.93      23692.41|
| 10:  2.2710 -  2.1928  1296   143  0.68  37.29   1.04     0.91      22960.08|
| 11:  2.1928 -  2.1245  1296   153  0.65  40.22   1.01     0.93      23793.55|
| 12:  2.1245 -  2.0639  1298   139  0.62  42.79   1.04     0.92      23612.35|
| 13:  2.0639 -  2.0097  1266   132  0.59  44.98   1.03     0.88      21392.17|
| 14:  2.0097 -  1.9608   441    58  0.63  41.89   1.02     0.79      16958.07|
|alpha:            min =        0.79 max =            0.93 mean =         0.89|
|beta:             min =    16958.07 max =        51218.63 mean =     33053.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.70|
|phase err.(work): min =        0.00 max =           89.96 mean =        35.19|
|phase err.(test): min =        0.00 max =           89.96 mean =        35.09|
|-----------------------------------------------------------------------------|

============================== 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 = 4.903755              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.135   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.639993              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.953   (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 |  1.506 -  1.846:        8 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.846 -  2.185:        6 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.185 -  2.525:       38 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.525 -  2.864:     1162 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.864 -  3.203:     1941 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.203 -  3.543:     2529 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.543 -  3.882:     4644 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.882 -  4.221:     4636 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.221 -  4.561:     6184 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.561 -  4.900:     7354 |
|-----------------------------------------------------------------------------|
|-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 |        0.184 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.506 |       0.502 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.696)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3364   r_free= 0.3334   ksol= 0.00   Bsol= 0.00   scale= 0.969    |
|                                                                             |
| 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:   0.39 A                  |
| x-ray target function (ml) for work reflections: 6.078489                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3238   r_free= 0.3229   ksol= 0.33   Bsol= 36.96   scale= 0.981   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.44,-2.86,0.43,-0.00,0.00,0.00); trace/3= -0.66                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 6.055862                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.360633              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.781   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.363334              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.640   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3238      final r-factor (work) = 0.1886          |
| start r-factor (free) = 0.3229      final r-factor (free) = 0.2172          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.4109 = 4.36 * 0.50 * 6.0667 + 1.00 * 0.1836                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.6720 = 4.36 * 0.50 * 5.7790 + 1.00 * 0.0719                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1886      final r-factor (work) = 0.1734          |
| start r-factor (free) = 0.2172      final r-factor (free) = 0.2220          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1061 = 0.36 * 1.00 * 5.7790 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0502 = 0.36 * 1.00 * 5.5034 + 1.00 * 0.0506                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.696)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.34   16.81    None  None   None       |
|    all(noH): 2823   0      0.00    80.34   16.81    None  None   None       |
|    Sol.    : 438    0      6.18    62.65   37.81    None  None   None       |
|    Mac.    : 2385   0      0.00    80.34   12.96    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.034:  531   |   5:    40.168 -  48.202:  126        |
|      1:     8.034 -  16.067: 1317   |   6:    48.202 -  56.236:   81        |
|      2:    16.067 -  24.101:  455   |   7:    56.236 -  64.269:   24        |
|      3:    24.101 -  32.135:  164   |   8:    64.269 -  72.303:    0        |
|      4:    32.135 -  40.168:  124   |   9:    72.303 -  80.336:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1734 r_free = 0.2220             target_work(ml) = 5.517         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1731 r_free = 0.2220             target_work(ml) = 5.516         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1731   r_free= 0.2220   ksol= 0.33   Bsol= 36.96   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.44,-2.86,0.43,-0.00,0.00,0.00); trace/3= -0.66                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.516377                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1688   r_free= 0.2171   ksol= 0.33   Bsol= 48.28   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.61,-2.90,-1.00,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.502587                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.127677              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.433  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.324353              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.099   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1688      final r-factor (work) = 0.1281          |
| start r-factor (free) = 0.2171      final r-factor (free) = 0.1648          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6973 = 3.13 * 0.50 * 5.5155 + 1.00 * 0.0719                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4915 = 3.13 * 0.50 * 5.3925 + 1.00 * 0.0584                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1281      final r-factor (work) = 0.1213          |
| start r-factor (free) = 0.1648      final r-factor (free) = 0.1604          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6104 = 0.32 * 1.00 * 5.3925 + 1.00 * 0.8613                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6988 = 0.32 * 1.00 * 5.2132 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.696)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.65    64.97   16.91    None  None   None       |
|    all(noH): 2823   0      0.65    64.97   16.91    None  None   None       |
|    Sol.    : 438    0      6.39    64.97   38.42    None  None   None       |
|    Mac.    : 2385   0      0.65    62.07   12.96    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.655 -   7.086:  316   |   5:    32.811 -  39.242:  101        |
|      1:     7.086 -  13.517: 1348   |   6:    39.242 -  45.674:   96        |
|      2:    13.517 -  19.949:  509   |   7:    45.674 -  52.105:   95        |
|      3:    19.949 -  26.380:  170   |   8:    52.105 -  58.536:   62        |
|      4:    26.380 -  32.811:  107   |   9:    58.536 -  64.967:   19        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1213 r_free = 0.1604             target_work(ml) = 5.197         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1212 r_free = 0.1603             target_work(ml) = 5.196         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1212   r_free= 0.1603   ksol= 0.33   Bsol= 48.28   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.61,-2.90,-1.00,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.196352                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1212   r_free= 0.1600   ksol= 0.33   Bsol= 48.28   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.05,-2.58,-1.04,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.193886                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.368684              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.623  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 5.350141              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.392  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1212      final r-factor (work) = 0.1125          |
| start r-factor (free) = 0.1600      final r-factor (free) = 0.1540          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2319 = 2.37 * 0.50 * 5.2126 + 1.00 * 0.0584                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1736 = 2.37 * 0.50 * 5.1607 + 1.00 * 0.0616                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1125      final r-factor (work) = 0.1101          |
| start r-factor (free) = 0.1540      final r-factor (free) = 0.1552          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 27.6183 = 5.35 * 1.00 * 5.1607 + 1.00 * 0.0078                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 27.4577 = 5.35 * 1.00 * 5.1303 + 1.00 * 0.0101                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.696)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.49    88.90   17.44    None  None   None       |
|    all(noH): 2823   0      0.49    88.90   17.44    None  None   None       |
|    Sol.    : 438    0      1.79    84.60   41.06    None  None   None       |
|    Mac.    : 2385   0      0.49    88.90   13.10    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:     0.486 -   9.327:  859   |   5:    44.692 -  53.533:   96        |
|      1:     9.327 -  18.168: 1223   |   6:    53.533 -  62.375:   71        |
|      2:    18.168 -  27.010:  266   |   7:    62.375 -  71.216:   40        |
|      3:    27.010 -  35.851:  120   |   8:    71.216 -  80.057:   18        |
|      4:    35.851 -  44.692:  124   |   9:    80.057 -  88.898:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1101 r_free = 0.1552             target_work(ml) = 5.134         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1100 r_free = 0.1553             target_work(ml) = 5.134         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1100   r_free= 0.1553   ksol= 0.33   Bsol= 48.28   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.05,-2.58,-1.04,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.134395                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1098   r_free= 0.1551   ksol= 0.32   Bsol= 49.68   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-2.27,-0.85,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.134098                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.800296              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 153.856  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.082148              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.221  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1098      final r-factor (work) = 0.1099          |
| start r-factor (free) = 0.1551      final r-factor (free) = 0.1557          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6801 = 1.80 * 0.50 * 5.1308 + 1.00 * 0.0616                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6766 = 1.80 * 0.50 * 5.1353 + 1.00 * 0.0541                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1099      final r-factor (work) = 0.1101          |
| start r-factor (free) = 0.1557      final r-factor (free) = 0.1544          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.4326 = 0.08 * 1.00 * 5.1353 + 1.00 * 0.0107                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5631 = 0.08 * 1.00 * 5.1394 + 1.00 * 0.1409                               |
|-----------------------------------------------------------------------------|
| number of iterations = 4       |    number of function evaluations = 4      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.696)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.68   17.42    None  None   None       |
|    all(noH): 2823   0      0.00    88.68   17.42    None  None   None       |
|    Sol.    : 438    0      3.31    83.62   40.76    None  None   None       |
|    Mac.    : 2385   0      0.00    88.68   13.14    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.868:  741   |   5:    44.339 -  53.207:   95        |
|      1:     8.868 -  17.736: 1333   |   6:    53.207 -  62.075:   71        |
|      2:    17.736 -  26.604:  272   |   7:    62.075 -  70.943:   40        |
|      3:    26.604 -  35.472:  121   |   8:    70.943 -  79.811:   18        |
|      4:    35.472 -  44.339:  126   |   9:    79.811 -  88.679:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1101 r_free = 0.1544             target_work(ml) = 5.134         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1100 r_free = 0.1544             target_work(ml) = 5.134         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1100   r_free= 0.1544   ksol= 0.32   Bsol= 49.68   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-2.27,-0.85,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.133678                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1100   r_free= 0.1544   ksol= 0.31   Bsol= 49.68   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-2.27,-0.85,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.133527                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.368469              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 165.196  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.248187              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.922   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1100      final r-factor (work) = 0.1074          |
| start r-factor (free) = 0.1544      final r-factor (free) = 0.1534          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1401 = 2.37 * 0.50 * 5.1392 + 1.00 * 0.0541                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1291 = 2.37 * 0.50 * 5.1230 + 1.00 * 0.0624                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1074      final r-factor (work) = 0.1072          |
| start r-factor (free) = 0.1534      final r-factor (free) = 0.1542          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4096 = 1.25 * 1.00 * 5.1230 + 1.00 * 0.0152                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3959 = 1.25 * 1.00 * 5.1164 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.696)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.73    90.63   17.26    None  None   None       |
|    all(noH): 2823   0      0.73    90.63   17.26    None  None   None       |
|    Sol.    : 438    0      4.55    84.15   40.59    None  None   None       |
|    Mac.    : 2385   0      0.73    90.63   12.97    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.727 -   9.718:  979   |   5:    45.680 -  54.670:   97        |
|      1:     9.718 -  18.708: 1143   |   6:    54.670 -  63.660:   66        |
|      2:    18.708 -  27.699:  239   |   7:    63.660 -  72.651:   33        |
|      3:    27.699 -  36.689:  121   |   8:    72.651 -  81.641:   11        |
|      4:    36.689 -  45.680:  128   |   9:    81.641 -  90.632:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1072 r_free = 0.1542             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1072 r_free = 0.1542             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1072   r_free= 0.1542   ksol= 0.31   Bsol= 49.68   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-2.27,-0.85,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.120290                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8125 -  4.6792 0.99   1421  158 0.0975 0.1288       5.389      5.5517|
|  2:  4.6792 -  3.7336 0.99   1379  152 0.0818 0.1068      5.4064      5.5901|
|  3:  3.7336 -  3.2675 0.99   1331  150 0.1022 0.1515      5.4332      5.8257|
|  4:  3.2675 -  2.9713 0.99   1345  142 0.1150 0.1520      5.4045      5.5689|
|  5:  2.9713 -  2.7598 0.99   1301  153 0.1226 0.1534      5.2638      5.4726|
|  6:  2.7598 -  2.5980 0.98   1332  145 0.1180 0.1983      5.1735      5.4688|
|  7:  2.5980 -  2.4685 0.99   1296  146 0.1205 0.1596       5.136      5.2985|
|  8:  2.4685 -  2.3615 0.98   1319  143 0.1080 0.1562      5.0411      5.2742|
|  9:  2.3615 -  2.2710 0.98   1309  145 0.1143 0.1941      4.9982      5.3589|
| 10:  2.2710 -  2.1928 0.98   1296  143 0.1061 0.1643      4.9159      5.1237|
| 11:  2.1928 -  2.1245 0.99   1296  153 0.1096 0.1782      4.8959       5.272|
| 12:  2.1245 -  2.0639 0.98   1298  139 0.1085 0.1656        4.85      5.1052|
| 13:  2.0639 -  2.0097 0.95   1266  132 0.1059 0.1626      4.7513      4.9698|
| 14:  2.0097 -  1.9608 0.34    441   58 0.0946 0.1792      4.6326      4.9299|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8125 -  4.6792  1421   158  0.94   9.29   0.98     0.95       7325.57|
|  2:  4.6792 -  3.7336  1379   152  0.95   7.71   1.02     1.00       8720.38|
|  3:  3.7336 -  3.2675  1331   150  0.94  10.96   1.03     1.03       9602.21|
|  4:  3.2675 -  2.9713  1345   142  0.93  13.00   1.01     1.01       9573.08|
|  5:  2.9713 -  2.7598  1301   153  0.91  15.18   1.00     0.98       7594.67|
|  6:  2.7598 -  2.5980  1332   145  0.90  16.07   0.98     0.96       6677.51|
|  7:  2.5980 -  2.4685  1296   146  0.91  15.12   0.99     0.96       5897.69|
|  8:  2.4685 -  2.3615  1319   143  0.91  14.83   1.00     0.97       5253.64|
|  9:  2.3615 -  2.2710  1309   145  0.91  15.41   1.00     0.96       4714.95|
| 10:  2.2710 -  2.1928  1296   143  0.91  15.23   0.99     0.95       4164.84|
| 11:  2.1928 -  2.1245  1296   153  0.90  15.82   0.99     0.96       4106.59|
| 12:  2.1245 -  2.0639  1298   139  0.91  15.45   1.01     1.00       3811.67|
| 13:  2.0639 -  2.0097  1266   132  0.90  15.83   1.00     0.98       3200.03|
| 14:  2.0097 -  1.9608   441    58  0.93  13.23   0.97     0.93       2378.96|
|alpha:            min =        0.93 max =            1.03 mean =         0.98|
|beta:             min =     2378.96 max =         9602.21 mean =      6147.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.76|
|phase err.(test): min =        0.00 max =           88.73 mean =        13.35|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1071   r_free= 0.1542   ksol= 0.31   Bsol= 49.66   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,-2.09,-0.72,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.120316                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1071   r_free= 0.1542   ksol= 0.31   Bsol= 49.66   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,-2.09,-0.72,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.120316                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8125 -  4.6792 0.99   1421  158 0.0975 0.1289      5.3895      5.5522|
|  2:  4.6792 -  3.7336 0.99   1379  152 0.0819 0.1068      5.4066      5.5898|
|  3:  3.7336 -  3.2675 0.99   1331  150 0.1021 0.1514      5.4329       5.825|
|  4:  3.2675 -  2.9713 0.99   1345  142 0.1150 0.1520      5.4043      5.5688|
|  5:  2.9713 -  2.7598 0.99   1301  153 0.1226 0.1535      5.2638      5.4726|
|  6:  2.7598 -  2.5980 0.98   1332  145 0.1181 0.1984      5.1737      5.4689|
|  7:  2.5980 -  2.4685 0.99   1296  146 0.1205 0.1594       5.136      5.2981|
|  8:  2.4685 -  2.3615 0.98   1319  143 0.1080 0.1561      5.0411       5.274|
|  9:  2.3615 -  2.2710 0.98   1309  145 0.1144 0.1942      4.9982      5.3589|
| 10:  2.2710 -  2.1928 0.98   1296  143 0.1061 0.1641      4.9158      5.1227|
| 11:  2.1928 -  2.1245 0.99   1296  153 0.1096 0.1783       4.896      5.2726|
| 12:  2.1245 -  2.0639 0.98   1298  139 0.1085 0.1657      4.8499       5.105|
| 13:  2.0639 -  2.0097 0.95   1266  132 0.1059 0.1626      4.7514      4.9697|
| 14:  2.0097 -  1.9608 0.34    441   58 0.0947 0.1793      4.6326      4.9302|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8125 -  4.6792  1421   158  0.94   9.29   0.98     0.95       7323.75|
|  2:  4.6792 -  3.7336  1379   152  0.95   7.71   1.02     1.01       8718.69|
|  3:  3.7336 -  3.2675  1331   150  0.94  10.96   1.03     1.03       9594.10|
|  4:  3.2675 -  2.9713  1345   142  0.93  13.00   1.02     1.01       9568.06|
|  5:  2.9713 -  2.7598  1301   153  0.91  15.19   1.00     0.98       7596.58|
|  6:  2.7598 -  2.5980  1332   145  0.90  16.08   0.99     0.96       6679.28|
|  7:  2.5980 -  2.4685  1296   146  0.91  15.12   0.99     0.96       5897.32|
|  8:  2.4685 -  2.3615  1319   143  0.91  14.83   1.00     0.97       5253.08|
|  9:  2.3615 -  2.2710  1309   145  0.91  15.41   1.00     0.97       4711.15|
| 10:  2.2710 -  2.1928  1296   143  0.91  15.23   1.00     0.96       4163.60|
| 11:  2.1928 -  2.1245  1296   153  0.90  15.82   1.00     0.97       4105.36|
| 12:  2.1245 -  2.0639  1298   139  0.91  15.46   1.01     1.01       3812.16|
| 13:  2.0639 -  2.0097  1266   132  0.90  15.84   1.00     0.99       3202.95|
| 14:  2.0097 -  1.9608   441    58  0.93  13.24   0.98     0.94       2382.98|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2382.98 max =         9594.10 mean =      6146.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.76|
|phase err.(test): min =        0.00 max =           88.86 mean =        13.34|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.696)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.70    90.61   17.23    None  None   None       |
|    all(noH): 2823   0      0.70    90.61   17.23    None  None   None       |
|    Sol.    : 438    0      4.53    84.13   40.56    None  None   None       |
|    Mac.    : 2385   0      0.70    90.61   12.95    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:     0.703 -   9.693:  979   |   5:    45.655 -  54.646:   97        |
|      1:     9.693 -  18.684: 1143   |   6:    54.646 -  63.636:   66        |
|      2:    18.684 -  27.674:  239   |   7:    63.636 -  72.627:   33        |
|      3:    27.674 -  36.665:  121   |   8:    72.627 -  81.617:   11        |
|      4:    36.665 -  45.655:  128   |   9:    81.617 -  90.608:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 282         
Filter by distance & map next to the model:
   mapped sites are within: 0.168 - 5.470
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 275 from: 282
   mapped sites are within: 0.747 - 5.470

peak=    5.696 closest distance to " NH2 ARG A  56 " =    2.197
peak=    5.606 closest distance to " CB  ARG A 275 " =    0.943
peak=    5.296 closest distance to " NE2 GLN A  11 " =    1.085
peak=    5.218 closest distance to " CG  PRO A  54 " =    1.246
peak=    5.047 closest distance to " O   HOH Z 142 " =    1.623
peak=    5.009 closest distance to " O   HOH Z 126 " =    1.807
peak=    4.778 closest distance to " O   HOH Z 232 " =    2.428
peak=    4.738 closest distance to " CB  GLN A 223 " =    1.451
peak=    4.729 closest distance to " CB  GLN A 183 " =    1.282
peak=    4.702 closest distance to " O   HOH Z 369 " =    2.370
peak=    4.643 closest distance to " CB  ARG A  79 " =    1.375
peak=    4.595 closest distance to " CA  TYR A  30 " =    0.908
peak=    4.544 closest distance to " CB  SER A  63 " =    1.150
peak=    4.534 closest distance to " CG  PRO A 213 " =    1.222
peak=    4.534 closest distance to " O   HOH Z  15 " =    2.273
peak=    4.501 closest distance to " CB  GLU A 152 " =    1.184
peak=    4.500 closest distance to " O   HOH Z  78 " =    1.779
peak=    4.475 closest distance to " O   HOH Z 427 " =    2.952
peak=    4.474 closest distance to " CD2 TRP A 179 " =    1.317
peak=    4.412 closest distance to " O   HOH Z 402 " =    1.410
peak=    4.400 closest distance to " C   PRO A 198 " =    1.480
peak=    4.395 closest distance to " O   HOH Z 287 " =    1.948
peak=    4.366 closest distance to " O   HOH Z 298 " =    1.778
peak=    4.336 closest distance to " O   SER A  87 " =    2.236
peak=    4.334 closest distance to " O   HOH Z 250 " =    1.474
peak=    4.277 closest distance to " CB  ARG A 190 " =    1.720
peak=    4.234 closest distance to " O   HOH Z 346 " =    1.643
peak=    4.230 closest distance to " CB  PRO A  54 " =    0.959
peak=    4.224 closest distance to " OG ASER A 258 " =    2.997
peak=    4.208 closest distance to " CB  ASN A 148 " =    1.453
peak=    4.205 closest distance to " ND2 ASN A 187 " =    1.399
peak=    4.182 closest distance to " NZ  LYS A 117 " =    3.083
peak=    4.175 closest distance to " O   HOH Z 303 " =    2.093
peak=    4.148 closest distance to " O   HOH Z 406 " =    1.580
peak=    4.134 closest distance to " O   HOH Z 209 " =    2.259
peak=    4.117 closest distance to " O   HOH Z 158 " =    3.042
peak=    4.065 closest distance to " O   HOH Z  44 " =    1.883
peak=    4.062 closest distance to " O   HOH Z 392 " =    2.829
peak=    4.051 closest distance to " CG  PRO A  90 " =    1.151
peak=    4.031 closest distance to " O   HOH Z  97 " =    2.340
peak=    4.029 closest distance to " O   HOH Z 128 " =    1.940
peak=    4.027 closest distance to " O   HOH Z 132 " =    2.805
peak=    4.026 closest distance to " O   HOH Z  43 " =    1.895
peak=    4.016 closest distance to " O   HOH Z 403 " =    1.714
peak=    4.013 closest distance to " CB  VAL A 265 " =    1.240
peak=    4.010 closest distance to " CB  VAL A 202 " =    1.576
peak=    3.990 closest distance to " CG  PRO A 198 " =    1.223
peak=    3.988 closest distance to " O   HOH Z 272 " =    1.838
peak=    3.965 closest distance to " O   HOH Z 327 " =    1.524
peak=    3.941 closest distance to " CG  ARG A  66 " =    2.512
peak=    3.922 closest distance to " O   HOH Z  61 " =    1.653
peak=    3.920 closest distance to " CZ  PHE A 218 " =    1.090
peak=    3.908 closest distance to " CG2 VAL A 257 " =    0.837
peak=    3.908 closest distance to " O   HOH Z 189 " =    2.688
peak=    3.908 closest distance to " O   HOH Z 423 " =    1.978
peak=    3.901 closest distance to " O   HOH Z 234 " =    3.588
peak=    3.892 closest distance to " O   HOH Z  97 " =    1.995
peak=    3.890 closest distance to " O   HOH Z 313 " =    1.993
peak=    3.880 closest distance to " O   HOH Z 365 " =    2.746
peak=    3.878 closest distance to " O   HOH Z  40 " =    1.852
peak=    3.868 closest distance to " O   HOH Z 193 " =    1.824
peak=    3.858 closest distance to " O   HOH Z 128 " =    2.235
peak=    3.842 closest distance to " O  BHOH Z 338 " =    2.315
peak=    3.832 closest distance to " O   HOH Z  19 " =    2.256
peak=    3.828 closest distance to " CA  ARG A  36 " =    1.016
peak=    3.827 closest distance to " OG BSER A 164 " =    2.293
peak=    3.809 closest distance to " O   HOH Z 353 " =    2.662
peak=    3.806 closest distance to " CB  THR A  31 " =    1.597
peak=    3.802 closest distance to " CB  GLU A 277 " =    3.565
peak=    3.796 closest distance to " O   HOH Z  59 " =    1.949
peak=    3.782 closest distance to " O   HOH Z 291 " =    1.528
peak=    3.780 closest distance to " CB  ASN A 110 " =    1.069
peak=    3.774 closest distance to " CG  PRO A 243 " =    1.033
peak=    3.767 closest distance to " O   HOH Z 203 " =    1.694
peak=    3.764 closest distance to " NH2BARG A 145 " =    2.084
peak=    3.763 closest distance to " O   HOH Z 180 " =    2.240
peak=    3.760 closest distance to " O   HOH Z 389 " =    1.749
peak=    3.756 closest distance to " CB  TRP A 266 " =    1.015
peak=    3.724 closest distance to " O   HOH Z 173 " =    1.953
peak=    3.724 closest distance to " CG1 ILE A  33 " =    1.181
peak=    3.722 closest distance to " CG2 ILE A 120 " =    1.213
peak=    3.718 closest distance to " O   HOH Z  54 " =    1.659
peak=    3.718 closest distance to " CD  ARG A 269 " =    1.016
peak=    3.703 closest distance to " CA  ARG A 195 " =    1.254
peak=    3.691 closest distance to " O   HOH Z 368 " =    3.676
peak=    3.684 closest distance to " O   ASN A  74 " =    1.466
peak=    3.680 closest distance to " O   HOH Z 214 " =    2.253
peak=    3.670 closest distance to " CA  ASN A 215 " =    1.019
peak=    3.646 closest distance to " CD2 LEU A 297 " =    0.951
peak=    3.646 closest distance to " O   HOH Z  61 " =    1.471
peak=    3.634 closest distance to " N   TYR A 116 " =    1.546
peak=    3.630 closest distance to " O   HOH Z 411 " =    3.871
peak=    3.617 closest distance to " O   HOH Z 368 " =    2.119
peak=    3.597 closest distance to " O   HOH Z 193 " =    2.004
peak=    3.595 closest distance to " CB  GLU A  46 " =    1.026
peak=    3.587 closest distance to " O   HOH Z   1 " =    1.886
peak=    3.578 closest distance to " O   HOH Z  21 " =    1.844
peak=    3.577 closest distance to " CB  TYR A 169 " =    0.865
peak=    3.577 closest distance to " O   HOH Z 305 " =    3.549
peak=    3.570 closest distance to " OD1 ASN A  69 " =    2.557
peak=    3.567 closest distance to " ND2 ASN A 249 " =    0.901
peak=    3.565 closest distance to " O   HOH Z 371 " =    3.062
peak=    3.557 closest distance to " CB  ASP A 140 " =    1.133
peak=    3.554 closest distance to " O   HOH Z 132 " =    2.362
peak=    3.551 closest distance to " CG  MET A 185 " =    1.110
peak=    3.535 closest distance to " CB  ASN A  39 " =    0.842
peak=    3.531 closest distance to " O  BHOH Z  74 " =    1.279
peak=    3.529 closest distance to " O   HOH Z  88 " =    2.526
peak=    3.528 closest distance to " CB  GLU A 128 " =    1.038
peak=    3.527 closest distance to " O   HOH Z  66 " =    2.194
peak=    3.527 closest distance to " O   HOH Z 325 " =    2.346
peak=    3.527 closest distance to " O   HOH Z 172 " =    3.667
peak=    3.524 closest distance to " O   HOH Z 280 " =    2.996
peak=    3.520 closest distance to " O   HOH Z 417 " =    3.573
peak=    3.520 closest distance to " O   HOH Z 126 " =    1.567
peak=    3.517 closest distance to " CB  SER A  26 " =    1.718
peak=    3.511 closest distance to " O   HOH Z  88 " =    2.973
peak=    3.510 closest distance to " O   HOH Z 265 " =    2.241
peak=    3.506 closest distance to " O   HOH Z 407 " =    2.646
peak=    3.505 closest distance to " O   HOH Z 425 " =    1.964
peak=    3.502 closest distance to " O   HOH Z 185 " =    1.822
peak=    3.502 closest distance to " CD  LYS A  76 " =    1.828
peak=    3.500 closest distance to " O   HOH Z 245 " =    1.323
peak=    3.497 closest distance to " O   HOH Z 371 " =    1.544
peak=    3.483 closest distance to " CG  LEU A 167 " =    1.284
peak=    3.479 closest distance to " CB  LEU A 228 " =    1.095
peak=    3.475 closest distance to " CA  ALA A  84 " =    1.190
peak=    3.475 closest distance to " O   HOH Z 344 " =    3.082
peak=    3.469 closest distance to " N   ASN A  39 " =    1.275
peak=    3.464 closest distance to " O   HOH Z 345 " =    3.139
peak=    3.459 closest distance to " CB  GLN A  88 " =    1.175
peak=    3.457 closest distance to " O   HOH Z 248 " =    1.534
peak=    3.446 closest distance to " CE  LYS A  76 " =    0.866
peak=    3.445 closest distance to " O   HOH Z 337 " =    3.581
peak=    3.443 closest distance to " NH1AARG A 145 " =    1.273
peak=    3.436 closest distance to " N   PHE A 130 " =    1.282
peak=    3.436 closest distance to " O   HOH Z  10 " =    1.772
peak=    3.433 closest distance to " O   HOH Z 359 " =    1.452
peak=    3.429 closest distance to " CA  ASN A 176 " =    1.220
peak=    3.423 closest distance to " O   HOH Z 261 " =    1.873
peak=    3.423 closest distance to " CB  TRP A 179 " =    1.268
peak=    3.422 closest distance to " OG  SER A  22 " =    2.628
peak=    3.419 closest distance to " OH  TYR A 116 " =    1.082
peak=    3.411 closest distance to " CB  GLN A  89 " =    1.345
peak=    3.410 closest distance to " CG2 ILE A  20 " =    1.461
peak=    3.408 closest distance to " CA  MET A 105 " =    0.989
peak=    3.408 closest distance to " O   HOH Z 422 " =    2.595
peak=    3.404 closest distance to " O   HOH Z 357 " =    1.968
peak=    3.404 closest distance to " O   HOH Z 421 " =    2.062
peak=    3.399 closest distance to " OG  SER A  62 " =    2.764
peak=    3.390 closest distance to " O   HOH Z 290 " =    0.941
peak=    3.382 closest distance to " CD  LYS A 166 " =    1.260
peak=    3.382 closest distance to " OE1 GLU A   2 " =    2.298
peak=    3.377 closest distance to " O   HOH Z 187 " =    2.202
peak=    3.376 closest distance to " O   HOH Z 298 " =    2.708
peak=    3.375 closest distance to " N   ASP A 162 " =    1.123
peak=    3.372 closest distance to " O   HOH Z 299 " =    4.306
peak=    3.372 closest distance to " O   HOH Z 394 " =    3.783
peak=    3.371 closest distance to " N   HIS A 108 " =    1.820
peak=    3.370 closest distance to " NE2 GLN A  73 " =    3.883
peak=    3.364 closest distance to " CA  ASN A 217 " =    1.213
peak=    3.361 closest distance to " O   HOH Z 329 " =    4.063
peak=    3.360 closest distance to " O   HOH Z 380 " =    1.974
peak=    3.355 closest distance to " CB  ASN A 215 " =    1.143
peak=    3.344 closest distance to " O   HOH Z  80 " =    1.647
peak=    3.340 closest distance to " CD1 ILE A 106 " =    0.884
peak=    3.339 closest distance to " O   HOH Z 258 " =    2.231
peak=    3.338 closest distance to " CG AARG A 275 " =    1.018
peak=    3.337 closest distance to " O   HOH Z 148 " =    3.390
peak=    3.335 closest distance to " O   THR A 220 " =    1.265
peak=    3.330 closest distance to " CB  ARG A 139 " =    1.036
peak=    3.326 closest distance to " CA  VAL A 125 " =    1.135
peak=    3.320 closest distance to " O   HOH Z 361 " =    2.522
peak=    3.319 closest distance to " CA  ALA A 158 " =    1.306
peak=    3.319 closest distance to " O   HOH Z 285 " =    2.525
peak=    3.311 closest distance to " CB  TYR A 169 " =    0.981
peak=    3.307 closest distance to " O   HOH Z 273 " =    2.853
peak=    3.300 closest distance to " OD2 ASP A 286 " =    2.775
peak=    3.298 closest distance to " O   HOH Z 227 " =    2.128
peak=    3.294 closest distance to " NE2 HIS A 207 " =    1.281
peak=    3.292 closest distance to " O   HOH Z 419 " =    2.091
peak=    3.290 closest distance to " CA  MET A  40 " =    1.138
peak=    3.289 closest distance to " CG1BVAL A  72 " =    1.579
peak=    3.286 closest distance to " CD  ARG A  66 " =    2.639
peak=    3.282 closest distance to " CA  ALA A  51 " =    0.919
peak=    3.279 closest distance to " CG  GLU A  37 " =    0.912
peak=    3.277 closest distance to " CB  ASN A 142 " =    1.073
peak=    3.276 closest distance to " CG1 ILE A  49 " =    1.454
peak=    3.274 closest distance to " O   HOH Z 147 " =    1.772
peak=    3.274 closest distance to " CB  SER A 212 " =    1.073
peak=    3.268 closest distance to " CA  ALA A  21 " =    1.122
peak=    3.265 closest distance to " CE  LYS A 119 " =    1.150
peak=    3.263 closest distance to " CG2 VAL A 197 " =    1.048
peak=    3.256 closest distance to " CB  SER A   3 " =    1.273
peak=    3.256 closest distance to " CA  TYR A 116 " =    1.302
peak=    3.254 closest distance to " N   ARG A 156 " =    1.331
peak=    3.252 closest distance to " CB  ALA A 114 " =    1.213
peak=    3.251 closest distance to " CB  ALA A 242 " =    1.022
peak=    3.249 closest distance to " CB  SER A  62 " =    1.405
peak=    3.245 closest distance to " O   HOH Z  66 " =    2.124
peak=    3.243 closest distance to " CG2 THR A 221 " =    1.123
peak=    3.239 closest distance to " CB  PRO A  90 " =    1.079
peak=    3.229 closest distance to " O   HOH Z 425 " =    1.266
peak=    3.227 closest distance to " O   ALA A 165 " =    1.478
peak=    3.227 closest distance to " CA  SER A  32 " =    1.623
peak=    3.224 closest distance to " O   ALA A   1 " =    1.642
peak=    3.221 closest distance to " CB  ALA A 291 " =    1.279
peak=    3.217 closest distance to " CB  HIS A 108 " =    0.856
peak=    3.216 closest distance to " O   HOH Z 261 " =    1.930
peak=    3.215 closest distance to " O   HOH Z 380 " =    1.881
peak=    3.213 closest distance to " CB  VAL A 126 " =    1.235
peak=    3.213 closest distance to " O   HOH Z 336 " =    1.678
peak=    3.212 closest distance to " O   HOH Z 233 " =    1.940
peak=    3.212 closest distance to " CB  ALA A 227 " =    1.184
peak=    3.211 closest distance to " CD1AILE A 234 " =    0.921
peak=    3.210 closest distance to " O   HOH Z   1 " =    1.489
peak=    3.209 closest distance to " CB  ILE A 120 " =    1.308
peak=    3.208 closest distance to " CA  THR A 221 " =    1.014
peak=    3.207 closest distance to " CG  GLN A  77 " =    2.383
peak=    3.207 closest distance to " CA  THR A 264 " =    0.881
peak=    3.197 closest distance to " CA  ARG A 159 " =    1.258
peak=    3.194 closest distance to " CB  SER A  62 " =    0.861
peak=    3.193 closest distance to " CA  ILE A 234 " =    1.006
peak=    3.186 closest distance to " CG1 ILE A 120 " =    1.093
peak=    3.185 closest distance to " ND1 HIS A  81 " =    1.645
peak=    3.180 closest distance to " CA  ASP A 162 " =    1.091
peak=    3.179 closest distance to " O   LEU A 228 " =    1.792
peak=    3.176 closest distance to " O   HOH Z 130 " =    2.274
peak=    3.175 closest distance to " O   HOH Z  44 " =    3.012
peak=    3.175 closest distance to " CA  ALA A 291 " =    0.756
peak=    3.173 closest distance to " CA  LYS A 117 " =    1.259
peak=    3.172 closest distance to " CB  ALA A   9 " =    1.559
peak=    3.171 closest distance to " O   HOH Z  85 " =    1.795
peak=    3.170 closest distance to " O   HOH Z 433 " =    1.846
peak=    3.161 closest distance to " O   HOH Z  85 " =    1.298
peak=    3.160 closest distance to " N   GLU A   2 " =    1.568
peak=    3.159 closest distance to " CB  THR A 279 " =    1.645
peak=    3.158 closest distance to " CB  LEU A 300 " =    0.930
peak=    3.157 closest distance to " CA  ALA A 233 " =    1.317
peak=    3.157 closest distance to " C   PHE A  59 " =    0.920
peak=    3.153 closest distance to " CB  TYR A 116 " =    0.747
peak=    3.150 closest distance to " CZ3 TRP A 266 " =    1.072
peak=    3.150 closest distance to " OG BSER A  99 " =    2.428
peak=    3.148 closest distance to " O   THR A 182 " =    1.448
peak=    3.146 closest distance to " CZ  PHE A  38 " =    1.183
peak=    3.142 closest distance to " CG  LYS A  76 " =    0.906
peak=    3.141 closest distance to " CB  ALA A 114 " =    1.104
peak=    3.140 closest distance to " NE AARG A 190 " =    2.016
peak=    3.139 closest distance to " O   HOH Z 156 " =    3.376
peak=    3.138 closest distance to " O   HOH Z 332 " =    1.510
peak=    3.136 closest distance to " OG1 THR A 221 " =    1.240
peak=    3.135 closest distance to " O   HOH Z 251 " =    1.516
peak=    3.134 closest distance to " CD1 ILE A 199 " =    1.140
peak=    3.130 closest distance to " O   HOH Z  28 " =    1.748
peak=    3.130 closest distance to " O   HOH Z  62 " =    2.347
peak=    3.125 closest distance to " CB  THR A 294 " =    1.659
peak=    3.123 closest distance to " CB  ALA A   1 " =    4.774
peak=    3.121 closest distance to " O   HOH Z 302 " =    1.895
peak=    3.120 closest distance to " CG  GLN A  11 " =    1.878
peak=    3.118 closest distance to " CB  GLU A 236 " =    1.087
peak=    3.107 closest distance to " O   HOH Z 234 " =    2.213
peak=    3.106 closest distance to " CA  SER A 146 " =    1.772
peak=    3.095 closest distance to " NE  ARG A  79 " =    0.963
peak=    3.089 closest distance to " CG  MET A 113 " =    1.052
peak=    3.088 closest distance to " OG1 THR A 264 " =    0.775
peak=    3.084 closest distance to " CB  LYS A 290 " =    1.323
peak=    3.083 closest distance to " O   HOH Z 430 " =    5.470
peak=    3.082 closest distance to " O   HOH Z  88 " =    3.173
peak=    3.066 closest distance to " OE2 GLU A  53 " =    2.031
peak=    3.049 closest distance to " CA  ASP A 140 " =    1.195
peak=    3.045 closest distance to " CD  LYS A 119 " =    1.299
peak=    3.040 closest distance to " CA  ALA A 248 " =    1.183
peak=    3.039 closest distance to " CE AMET A  47 " =    1.471
peak=    3.031 closest distance to " CA  ALA A 299 " =    0.864
peak=    3.030 closest distance to " CA  ARG A 102 " =    1.039

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.966 - 5.830
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 200 from: 200
   mapped sites are within: 0.966 - 5.830

peak=   -4.660 closest distance to " OG BSER A 134 " =    1.283
peak=   -4.650 closest distance to " C   HIS A 108 " =    1.103
peak=   -4.648 closest distance to " CD  ARG A  14 " =    3.348
peak=   -4.636 closest distance to " O   HOH Z 266 " =    5.261
peak=   -4.454 closest distance to " CG  GLN A  58 " =    1.116
peak=   -4.337 closest distance to " CG  GLN A 223 " =    2.081
peak=   -4.332 closest distance to " CD  ARG A 156 " =    2.098
peak=   -4.284 closest distance to " O   HOH Z 377 " =    2.118
peak=   -4.277 closest distance to " CB  PRO A 243 " =    2.641
peak=   -4.158 closest distance to " O   HOH Z 372 " =    2.298
peak=   -4.127 closest distance to " O   HOH Z 198 " =    1.694
peak=   -4.094 closest distance to " O   PRO A 198 " =    1.265
peak=   -4.083 closest distance to " O   HOH Z 231 " =    2.373
peak=   -4.073 closest distance to " CG1 VAL A 112 " =    2.798
peak=   -4.041 closest distance to " CA  VAL A  67 " =    2.882
peak=   -4.040 closest distance to " O   VAL A  67 " =    2.671
peak=   -4.032 closest distance to " CB  PHE A 192 " =    2.032
peak=   -3.962 closest distance to " O   HOH Z 407 " =    2.731
peak=   -3.942 closest distance to " N   ALA A  43 " =    2.629
peak=   -3.938 closest distance to " CE  MET A 105 " =    2.360
peak=   -3.893 closest distance to " OXT GLY A 302 " =    2.818
peak=   -3.879 closest distance to " CZ  TYR A 169 " =    1.903
peak=   -3.821 closest distance to " O   SER A 210 " =    1.942
peak=   -3.796 closest distance to " OG  SER A  97 " =    2.171
peak=   -3.775 closest distance to " O   HOH Z 290 " =    1.245
peak=   -3.769 closest distance to " N   ALA A 248 " =    1.554
peak=   -3.767 closest distance to " CG2 ILE A 263 " =    2.191
peak=   -3.731 closest distance to " O   PRO A 163 " =    2.068
peak=   -3.726 closest distance to " O   HOH Z 165 " =    2.000
peak=   -3.720 closest distance to " CB  ASN A  39 " =    2.341
peak=   -3.713 closest distance to " OD2 ASP A 171 " =    2.362
peak=   -3.711 closest distance to " O   PHE A 218 " =    1.545
peak=   -3.706 closest distance to " CG  PHE A 283 " =    2.644
peak=   -3.704 closest distance to " ND2 ASN A 249 " =    2.178
peak=   -3.702 closest distance to " O   HOH Z 243 " =    1.961
peak=   -3.697 closest distance to " NE  ARG A 156 " =    1.926
peak=   -3.693 closest distance to " CB  ASP A 132 " =    2.307
peak=   -3.692 closest distance to " CE2 TYR A  30 " =    2.725
peak=   -3.659 closest distance to " O   HOH Z  13 " =    1.713
peak=   -3.658 closest distance to " O   VAL A 174 " =    2.201
peak=   -3.656 closest distance to " CB  ALA A 248 " =    2.216
peak=   -3.651 closest distance to " ND2 ASN A 187 " =    1.415
peak=   -3.621 closest distance to " CB  ALA A 161 " =    2.469
peak=   -3.609 closest distance to " O   HOH Z   6 " =    2.125
peak=   -3.608 closest distance to " OE1 GLN A 183 " =    1.474
peak=   -3.608 closest distance to " CB  ALA A 291 " =    2.207
peak=   -3.597 closest distance to " CA  ASP A 298 " =    1.045
peak=   -3.595 closest distance to " O   HOH Z 351 " =    1.437
peak=   -3.594 closest distance to " CB  TYR A  15 " =    2.191
peak=   -3.589 closest distance to " CD2 TYR A 247 " =    2.420
peak=   -3.582 closest distance to " O   HOH Z 102 " =    1.591
peak=   -3.577 closest distance to " OD2 ASP A 191 " =    1.410
peak=   -3.570 closest distance to " CD  ARG A 139 " =    1.628
peak=   -3.566 closest distance to " CD1 LEU A 101 " =    2.357
peak=   -3.565 closest distance to " NH2AARG A 275 " =    5.051
peak=   -3.564 closest distance to " O   HOH Z 348 " =    2.207
peak=   -3.563 closest distance to " NE2 GLN A  88 " =    1.810
peak=   -3.552 closest distance to " O   HOH Z 166 " =    1.994
peak=   -3.548 closest distance to " CB  ALA A  43 " =    2.469
peak=   -3.544 closest distance to " ND2 ASN A  45 " =    1.111
peak=   -3.526 closest distance to " O   HOH Z 394 " =    1.487
peak=   -3.525 closest distance to " CD1 LEU A 255 " =    2.714
peak=   -3.525 closest distance to " O   PRO A 198 " =    1.288
peak=   -3.516 closest distance to " O   HOH Z 211 " =    1.478
peak=   -3.511 closest distance to " O   HOH Z  88 " =    4.455
peak=   -3.509 closest distance to " ND2 ASN A  45 " =    1.776
peak=   -3.505 closest distance to " N   GLN A  58 " =    1.539
peak=   -3.503 closest distance to " CZ3 TRP A 179 " =    1.226
peak=   -3.502 closest distance to " O   HOH Z  38 " =    1.742
peak=   -3.502 closest distance to " OD1 ASP A 171 " =    1.596
peak=   -3.496 closest distance to " O   HOH Z 353 " =    2.250
peak=   -3.490 closest distance to " O   HOH Z 283 " =    2.386
peak=   -3.479 closest distance to " OD1 ASN A 148 " =    1.505
peak=   -3.472 closest distance to " CE BMET A  47 " =    1.376
peak=   -3.467 closest distance to " O   HOH Z 313 " =    1.873
peak=   -3.466 closest distance to " O   HOH Z  15 " =    1.508
peak=   -3.465 closest distance to " O   HOH Z  63 " =    1.614
peak=   -3.464 closest distance to " O   HOH Z  11 " =    1.722
peak=   -3.463 closest distance to " NH2 ARG A  66 " =    1.210
peak=   -3.462 closest distance to " O   HOH Z 123 " =    2.281
peak=   -3.456 closest distance to " C   GLN A 205 " =    1.767
peak=   -3.456 closest distance to " N   MET A 188 " =    1.958
peak=   -3.446 closest distance to " CA  GLY A 203 " =    2.398
peak=   -3.438 closest distance to " O   HOH Z 114 " =    3.164
peak=   -3.433 closest distance to " CB  ASP A 286 " =    1.815
peak=   -3.431 closest distance to " CG  ARG A  66 " =    2.399
peak=   -3.424 closest distance to " O   HOH Z 185 " =    2.245
peak=   -3.424 closest distance to " O   ALA A 292 " =    2.184
peak=   -3.424 closest distance to " OE2 GLU A 152 " =    1.301
peak=   -3.421 closest distance to " O   HOH Z 421 " =    3.254
peak=   -3.419 closest distance to " ND2 ASN A  60 " =    1.308
peak=   -3.412 closest distance to " CB  PRO A 163 " =    2.450
peak=   -3.408 closest distance to " O   ALA A 161 " =    1.684
peak=   -3.406 closest distance to " CG  ARG A 269 " =    2.254
peak=   -3.405 closest distance to " CD1 PHE A  59 " =    2.032
peak=   -3.403 closest distance to " CD2 TYR A 293 " =    1.970
peak=   -3.397 closest distance to " OD1 ASN A 301 " =    1.943
peak=   -3.393 closest distance to " N   THR A  52 " =    1.738
peak=   -3.391 closest distance to " NE2 GLN A 194 " =    1.884
peak=   -3.379 closest distance to " O   HOH Z  37 " =    1.772
peak=   -3.378 closest distance to " O   VAL A 189 " =    1.683
peak=   -3.376 closest distance to " OD1 ASP A 191 " =    1.719
peak=   -3.369 closest distance to " O   HOH Z 134 " =    3.166
peak=   -3.367 closest distance to " CA  GLY A 241 " =    2.352
peak=   -3.362 closest distance to " CG2 ILE A  49 " =    2.700
peak=   -3.358 closest distance to " O   GLN A  89 " =    1.525
peak=   -3.351 closest distance to " CD2 PHE A  61 " =    2.302
peak=   -3.348 closest distance to " CD2 PHE A 225 " =    1.313
peak=   -3.341 closest distance to " CG2 THR A 178 " =    2.310
peak=   -3.334 closest distance to " O   HOH Z 139 " =    5.177
peak=   -3.334 closest distance to " O   VAL A 189 " =    2.686
peak=   -3.325 closest distance to " O   HOH Z 166 " =    1.970
peak=   -3.323 closest distance to " CB  ALA A 291 " =    2.214
peak=   -3.307 closest distance to " O   HOH Z 357 " =    2.096
peak=   -3.303 closest distance to " CG1 VAL A 112 " =    2.622
peak=   -3.300 closest distance to " OG  SER A   3 " =    1.754
peak=   -3.296 closest distance to " O   SER A  95 " =    1.524
peak=   -3.293 closest distance to " O   ALA A  34 " =    2.063
peak=   -3.291 closest distance to " O   HOH Z 389 " =    1.856
peak=   -3.290 closest distance to " O   TRP A  92 " =    1.762
peak=   -3.287 closest distance to " CB  SER A 245 " =    2.144
peak=   -3.284 closest distance to " CB  TRP A  85 " =    2.526
peak=   -3.284 closest distance to " O   HOH Z 385 " =    2.031
peak=   -3.283 closest distance to " O   ILE A 106 " =    1.988
peak=   -3.280 closest distance to " CE2 PHE A 218 " =    2.461
peak=   -3.280 closest distance to " NE2 GLN A 278 " =    1.759
peak=   -3.280 closest distance to " CE3 TRP A 274 " =    2.336
peak=   -3.271 closest distance to " OE1 GLN A 223 " =    2.010
peak=   -3.270 closest distance to " OG BSER A 134 " =    1.735
peak=   -3.269 closest distance to " O   HOH Z 362 " =    5.830
peak=   -3.268 closest distance to " O   HOH Z 183 " =    1.567
peak=   -3.263 closest distance to " O   HOH Z 233 " =    2.394
peak=   -3.260 closest distance to " O   HOH Z 252 " =    3.752
peak=   -3.259 closest distance to " O   HOH Z 281 " =    2.727
peak=   -3.257 closest distance to " CD  GLU A 236 " =    1.064
peak=   -3.256 closest distance to " OE1 GLN A 194 " =    1.742
peak=   -3.251 closest distance to " CE2 PHE A  61 " =    2.616
peak=   -3.248 closest distance to " O   SER A   3 " =    1.019
peak=   -3.242 closest distance to " CA  GLY A 241 " =    3.151
peak=   -3.242 closest distance to " O   HOH Z  60 " =    2.098
peak=   -3.240 closest distance to " CG  GLU A 277 " =    1.364
peak=   -3.228 closest distance to " O   HOH Z 317 " =    1.469
peak=   -3.228 closest distance to " O   HOH Z  10 " =    1.408
peak=   -3.223 closest distance to " N   SER A 276 " =    1.257
peak=   -3.220 closest distance to " CG1 VAL A  67 " =    3.115
peak=   -3.218 closest distance to " CG2 VAL A 189 " =    2.102
peak=   -3.218 closest distance to " NE2 GLN A  11 " =    1.859
peak=   -3.212 closest distance to " O   SER A 135 " =    1.522
peak=   -3.211 closest distance to " O   ASN A 187 " =    1.518
peak=   -3.210 closest distance to " CG1 VAL A 268 " =    2.447
peak=   -3.206 closest distance to " OD2 ASP A  50 " =    1.418
peak=   -3.205 closest distance to " OE1 GLN A  88 " =    1.089
peak=   -3.203 closest distance to " CG  GLU A   2 " =    2.036
peak=   -3.202 closest distance to " O   HOH Z 197 " =    5.113
peak=   -3.197 closest distance to " O   ALA A  10 " =    1.755
peak=   -3.196 closest distance to " O   HOH Z 193 " =    1.536
peak=   -3.192 closest distance to " O   HOH Z 405 " =    2.657
peak=   -3.192 closest distance to " O   LEU A 167 " =    1.473
peak=   -3.191 closest distance to " CG1 VAL A 250 " =    2.606
peak=   -3.187 closest distance to " CD1 LEU A 228 " =    2.005
peak=   -3.187 closest distance to " O   HOH Z 298 " =    1.298
peak=   -3.186 closest distance to " CB  ALA A 248 " =    2.198
peak=   -3.184 closest distance to " O   HOH Z 174 " =    2.360
peak=   -3.178 closest distance to " O   MET A  40 " =    2.835
peak=   -3.170 closest distance to " CA  GLY A 133 " =    2.238
peak=   -3.169 closest distance to " O   HOH Z 166 " =    1.556
peak=   -3.167 closest distance to " CE3 TRP A 150 " =    2.164
peak=   -3.161 closest distance to " O   HOH Z  71 " =    2.116
peak=   -3.160 closest distance to " CG1AVAL A  41 " =    2.666
peak=   -3.159 closest distance to " CZ2 TRP A 274 " =    1.034
peak=   -3.159 closest distance to " CA  GLY A 133 " =    2.021
peak=   -3.158 closest distance to " OH  TYR A 169 " =    0.966
peak=   -3.157 closest distance to " O   TRP A  70 " =    1.467
peak=   -3.156 closest distance to " O   GLN A 240 " =    2.050
peak=   -3.142 closest distance to " ND2 ASN A  39 " =    1.157
peak=   -3.141 closest distance to " NE  ARG A  36 " =    1.951
peak=   -3.141 closest distance to " CA  GLY A  57 " =    2.180
peak=   -3.137 closest distance to " O   ASN A 252 " =    1.361
peak=   -3.136 closest distance to " CD1 ILE A 199 " =    2.395
peak=   -3.135 closest distance to " N   PHE A  59 " =    1.812
peak=   -3.134 closest distance to " CG1 VAL A 125 " =    2.296
peak=   -3.131 closest distance to " CB  SER A 210 " =    1.255
peak=   -3.131 closest distance to " CD2 LEU A 237 " =    2.803
peak=   -3.129 closest distance to " N   ALA A 226 " =    1.928
peak=   -3.127 closest distance to " O   HOH Z 371 " =    1.719
peak=   -3.124 closest distance to " CG  GLU A 152 " =    1.183
peak=   -3.119 closest distance to " CG  TRP A 266 " =    1.970
peak=   -3.117 closest distance to " O   HOH Z 216 " =    1.752
peak=   -3.107 closest distance to " CA  TRP A 274 " =    1.437
peak=   -3.103 closest distance to " O   ASN A  45 " =    1.896
peak=   -3.101 closest distance to " NH1 ARG A 195 " =    2.649
peak=   -3.098 closest distance to " O   HOH Z 250 " =    1.509
peak=   -3.091 closest distance to " CG  PRO A 163 " =    2.782
peak=   -3.088 closest distance to " O   ALA A   1 " =    1.820
peak=   -3.085 closest distance to " O   ALA A  51 " =    1.176
peak=   -3.080 closest distance to " O   HOH Z   6 " =    1.504
peak=   -3.075 closest distance to " CD2 LEU A 237 " =    2.373
peak=   -3.057 closest distance to " C   ALA A 158 " =    1.412
peak=   -3.006 closest distance to " O   LYS A  76 " =    1.970
peak=   -3.000 closest distance to " C   ALA A 114 " =    2.248

================= 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    :  0.3364 0.3334   6.078489e+00   6.067208e+00
   1_bss:  0.3238 0.3229   6.055862e+00   6.044502e+00
   1_xyz:  0.1886 0.2172   5.561035e+00   5.671633e+00
   1_adp:  0.1734 0.2220   5.516893e+00   5.704651e+00
   1_occ:  0.1731 0.2220   5.516377e+00   5.704421e+00
   2_bss:  0.1688 0.2171   5.502587e+00   5.690762e+00
   2_xyz:  0.1281 0.1648   5.240544e+00   5.441966e+00
   2_adp:  0.1213 0.1604   5.197005e+00   5.408067e+00
   2_occ:  0.1212 0.1603   5.196352e+00   5.407592e+00
   3_bss:  0.1212 0.1600   5.193886e+00   5.402004e+00
   3_xyz:  0.1125 0.1540   5.141896e+00   5.368899e+00
   3_adp:  0.1101 0.1552   5.134475e+00   5.373929e+00
   3_occ:  0.1100 0.1553   5.134395e+00   5.374041e+00
   4_bss:  0.1098 0.1551   5.134098e+00   5.373466e+00
   4_xyz:  0.1099 0.1557   5.137355e+00   5.378231e+00
   4_adp:  0.1101 0.1544   5.133851e+00   5.369163e+00
   4_occ:  0.1100 0.1544   5.133678e+00   5.369261e+00
   5_bss:  0.1100 0.1544   5.133527e+00   5.369040e+00
   5_xyz:  0.1074 0.1534   5.118964e+00   5.363002e+00
   5_adp:  0.1072 0.1542   5.120308e+00   5.368658e+00
   5_occ:  0.1072 0.1542   5.120290e+00   5.368808e+00
   5_bss:  0.1071 0.1542   5.120316e+00   5.368708e+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:  0.328  36.965   0.437  -2.857   0.425  -0.000   0.000   0.000
   1_xyz:  0.328  36.965   0.437  -2.857   0.425  -0.000   0.000   0.000
   1_adp:  0.328  36.965   0.437  -2.857   0.425  -0.000   0.000   0.000
   1_occ:  0.328  36.965   0.437  -2.857   0.425  -0.000   0.000   0.000
   2_bss:  0.328  48.279  -2.614  -2.902  -1.003  -0.000  -0.000  -0.000
   2_xyz:  0.328  48.279  -2.614  -2.902  -1.003  -0.000  -0.000  -0.000
   2_adp:  0.328  48.279  -2.614  -2.902  -1.003  -0.000  -0.000  -0.000
   2_occ:  0.328  48.279  -2.614  -2.902  -1.003  -0.000  -0.000  -0.000
   3_bss:  0.326  48.279  -3.045  -2.578  -1.041  -0.000  -0.000  -0.000
   3_xyz:  0.326  48.279  -3.045  -2.578  -1.041  -0.000  -0.000  -0.000
   3_adp:  0.326  48.279  -3.045  -2.578  -1.041  -0.000  -0.000  -0.000
   3_occ:  0.326  48.279  -3.045  -2.578  -1.041  -0.000  -0.000  -0.000
   4_bss:  0.322  49.680  -2.922  -2.266  -0.849  -0.000  -0.000  -0.000
   4_xyz:  0.322  49.680  -2.922  -2.266  -0.849  -0.000  -0.000  -0.000
   4_adp:  0.322  49.680  -2.922  -2.266  -0.849  -0.000  -0.000  -0.000
   4_occ:  0.322  49.680  -2.922  -2.266  -0.849  -0.000  -0.000  -0.000
   5_bss:  0.314  49.680  -2.922  -2.266  -0.849  -0.000  -0.000  -0.000
   5_xyz:  0.314  49.680  -2.922  -2.266  -0.849  -0.000  -0.000  -0.000
   5_adp:  0.314  49.680  -2.922  -2.266  -0.849  -0.000  -0.000  -0.000
   5_occ:  0.314  49.680  -2.922  -2.266  -0.849  -0.000  -0.000  -0.000
   5_bss:  0.312  49.655  -2.840  -2.089  -0.719  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  35.182 0.7024  0.8925    33049.105
   1_bss:  33.976 0.7144  0.8940    29982.455
   1_xyz:  20.664 0.8560  1.0115    11903.461
   1_adp:  21.489 0.8475  1.0090    12648.233
   1_occ:  21.507 0.8474  1.0086    12648.494
   2_bss:  21.069 0.8514  0.9575    12183.759
   2_xyz:  15.374 0.9032  0.9825     7106.060
   2_adp:  14.657 0.9093  0.9797     6701.812
   2_occ:  14.650 0.9094  0.9795     6687.520
   3_bss:  14.561 0.9101  0.9773     6600.258
   3_xyz:  13.819 0.9163  0.9794     6151.486
   3_adp:  13.901 0.9157  0.9725     6186.001
   3_occ:  13.901 0.9157  0.9724     6181.930
   4_bss:  13.896 0.9157  0.9795     6173.527
   4_xyz:  13.908 0.9159  0.9796     6242.785
   4_adp:  13.747 0.9172  0.9818     6151.083
   4_occ:  13.749 0.9171  0.9818     6151.991
   5_bss:  13.743 0.9172  0.9817     6145.863
   5_xyz:  13.632 0.9180  0.9824     6090.423
   5_adp:  13.718 0.9174  0.9761     6146.737
   5_occ:  13.719 0.9174  0.9761     6146.406
   5_bss:  13.719 0.9174  0.9796     6145.223
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.8355e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.8355e-01
   1_xyz:   1.145  0.008  0.074 15.155  0.005  4.109   7.1886e-02
   1_adp:   1.145  0.008  0.074 15.155  0.005  4.109   7.1886e-02
   1_occ:   1.145  0.008  0.074 15.155  0.005  4.109   7.1886e-02
   2_bss:   1.145  0.008  0.074 15.155  0.005  4.109   7.1886e-02
   2_xyz:   1.013  0.007  0.072 14.711  0.004  4.118   5.8445e-02
   2_adp:   1.013  0.007  0.072 14.711  0.004  4.118   5.8445e-02
   2_occ:   1.013  0.007  0.072 14.711  0.004  4.118   5.8445e-02
   3_bss:   1.013  0.007  0.072 14.711  0.004  4.118   5.8445e-02
   3_xyz:   1.026  0.007  0.077 14.814  0.004  4.109   6.1600e-02
   3_adp:   1.026  0.007  0.077 14.814  0.004  4.109   6.1600e-02
   3_occ:   1.026  0.007  0.077 14.814  0.004  4.109   6.1600e-02
   4_bss:   1.026  0.007  0.077 14.814  0.004  4.109   6.1600e-02
   4_xyz:   0.948  0.006  0.073 14.530  0.004  4.109   5.4089e-02
   4_adp:   0.948  0.006  0.073 14.530  0.004  4.109   5.4089e-02
   4_occ:   0.948  0.006  0.073 14.530  0.004  4.109   5.4089e-02
   5_bss:   0.948  0.006  0.073 14.530  0.004  4.109   5.4089e-02
   5_xyz:   1.036  0.008  0.078 14.735  0.004  4.110   6.2357e-02
   5_adp:   1.036  0.008  0.078 14.735  0.004  4.110   6.2357e-02
   5_occ:   1.036  0.008  0.078 14.735  0.004  4.110   6.2357e-02
   5_bss:   1.036  0.008  0.078 14.735  0.004  4.110   6.2357e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.506   2.4066e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.506   2.4066e-01
   1_xyz:   9.184  0.044  0.294 83.726  0.051  2.155   6.0037e-02
   1_adp:   9.184  0.044  0.294 83.726  0.051  2.155   6.0037e-02
   1_occ:   9.184  0.044  0.294 83.726  0.051  2.155   6.0037e-02
   2_bss:   9.184  0.044  0.294 83.726  0.051  2.155   6.0037e-02
   2_xyz:   7.282  0.036  0.247 81.504  0.036  2.300   4.7475e-02
   2_adp:   7.282  0.036  0.247 81.504  0.036  2.300   4.7475e-02
   2_occ:   7.282  0.036  0.247 81.504  0.036  2.300   4.7475e-02
   3_bss:   7.282  0.036  0.247 81.504  0.036  2.300   4.7475e-02
   3_xyz:   7.101  0.048  0.265 83.742  0.037  2.351   4.4214e-02
   3_adp:   7.101  0.048  0.265 83.742  0.037  2.351   4.4214e-02
   3_occ:   7.101  0.048  0.265 83.742  0.037  2.351   4.4214e-02
   4_bss:   7.101  0.048  0.265 83.742  0.037  2.351   4.4214e-02
   4_xyz:   6.404  0.047  0.240 82.423  0.036  2.369   3.6015e-02
   4_adp:   6.404  0.047  0.240 82.423  0.036  2.369   3.6015e-02
   4_occ:   6.404  0.047  0.240 82.423  0.036  2.369   3.6015e-02
   5_bss:   6.404  0.047  0.240 82.423  0.036  2.369   3.6015e-02
   5_xyz:   7.105  0.053  0.269 83.593  0.038  2.314   4.4997e-02
   5_adp:   7.105  0.053  0.269 83.593  0.038  2.314   4.4997e-02
   5_occ:   7.105  0.053  0.269 83.593  0.038  2.314   4.4997e-02
   5_bss:   7.105  0.053  0.269 83.593  0.038  2.314   4.4997e-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:  80.34   0.00  16.81  80.34   0.00  12.96  62.65   6.18  37.81
   1_occ:  80.34   0.00  16.81  80.34   0.00  12.96  62.65   6.18  37.81
   2_bss:  80.34   0.00  16.81  80.34   0.00  12.96  62.65   6.18  37.81
   2_xyz:  80.34   0.00  16.81  80.34   0.00  12.96  62.65   6.18  37.81
   2_adp:  64.97   0.65  16.91  62.07   0.65  12.96  64.97   6.39  38.42
   2_occ:  64.97   0.65  16.91  62.07   0.65  12.96  64.97   6.39  38.42
   3_bss:  64.97   0.65  16.91  62.07   0.65  12.96  64.97   6.39  38.42
   3_xyz:  64.97   0.65  16.91  62.07   0.65  12.96  64.97   6.39  38.42
   3_adp:  88.90   0.49  17.44  88.90   0.49  13.10  84.60   1.79  41.06
   3_occ:  88.90   0.49  17.44  88.90   0.49  13.10  84.60   1.79  41.06
   4_bss:  88.90   0.49  17.44  88.90   0.49  13.10  84.60   1.79  41.06
   4_xyz:  88.90   0.49  17.44  88.90   0.49  13.10  84.60   1.79  41.06
   4_adp:  88.68   0.00  17.42  88.68   0.00  13.14  83.62   3.31  40.76
   4_occ:  88.68   0.00  17.42  88.68   0.00  13.14  83.62   3.31  40.76
   5_bss:  88.68   0.00  17.42  88.68   0.00  13.14  83.62   3.31  40.76
   5_xyz:  88.68   0.00  17.42  88.68   0.00  13.14  83.62   3.31  40.76
   5_adp:  90.63   0.73  17.26  90.63   0.73  12.97  84.15   4.55  40.59
   5_occ:  90.63   0.73  17.26  90.63   0.73  12.97  84.15   4.55  40.59
   5_bss:  90.61   0.70  17.23  90.61   0.70  12.95  84.13   4.53  40.56
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.251    0.012    0.320
   1_adp:    1.251    0.012    0.320
   1_occ:    1.251    0.012    0.320
   2_bss:    1.251    0.012    0.320
   2_xyz:    1.256    0.024    0.376
   2_adp:    1.256    0.024    0.376
   2_occ:    1.256    0.024    0.376
   3_bss:    1.256    0.024    0.376
   3_xyz:    1.150    0.021    0.405
   3_adp:    1.150    0.021    0.405
   3_occ:    1.150    0.021    0.405
   4_bss:    1.150    0.021    0.405
   4_xyz:    1.198    0.033    0.412
   4_adp:    1.198    0.033    0.412
   4_occ:    1.198    0.033    0.412
   5_bss:    1.198    0.033    0.412
   5_xyz:    1.250    0.023    0.416
   5_adp:    1.250    0.023    0.416
   5_occ:    1.250    0.023    0.416
   5_bss:    1.250    0.023    0.416
------------------------------------------------------------------------

CPU time actual refinement: 324.93


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_183/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_183/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_183/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_183/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_183/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 324.79 
  Macro-tasks:
    bulk solvent and scale       = 40.44  
    individual site refinement   = 131.48 
    weights calculation          = 29.47  
    collect and process          = 6.70   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 208.17 
  Micro-tasks:
    mask                            = 1.10   
    f_calc                          = 104.03 
    alpha_beta                      = 8.10   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 107.41 
    fmodel                         = 6.75   
    r_factors                      = 0.21   
    phase_errors                   = 12.15  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 241.20 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.654 micro seconds
Total CPU time: 5.63 minutes
from_scatterers_fft:    628 calls, 103.57 s
gradients_fft:          573 calls,  96.22 s

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

# Date 2008-01-16 Time 04:13:25 PST -0800 (1200485605.50 s)
Start R-work = 0.3364, R-free = 0.3334 (no bulk solvent and anisotropic scale)
Final R-work = 0.1319, R-free = 0.1739 (no bulk solvent and anisotropic scale)

Start R-work = 0.3238, R-free = 0.3229
Final R-work = 0.1071, R-free = 0.1542