Hi Yuri, Could you send me (off-list) the full log files of runs with the 650 release and the newest release? Ralf

________________________________ From: Yuri To: phenix forum Sent: Saturday, May 21, 2011 7:55 PM Subject: [phenixbb] Weird R-free discrepancy.

I was working on a model for  at 1.9 A using the previous phenix release (650). I was almost finished r-free was 0.197. I installed the newest release and refined again and my r-free went up to 0.228!!. The values for bsol and ksol look significantly different. I do not understand where the biggest difference is coming from... Below I pasted part of the .log files. Old and new, respectively.

=============================== refinement start ==============================

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

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

|--(resolution: 1.90 - 28.74 A; n_refl. = 32203)------------------------------| |                                                                            | | r_work= 0.1747  r_free= 0.1967  ksol= 0.40  Bsol= 39.70  scale= 0.064  | |                                                                            | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (-1.65,-1.65,3.31,-0.00,0.00,0.00); trace/3= -0.00                        | |                                                                            | | maximum likelihood estimate for coordinate error:  0.21 A                | | x-ray target function (ml) for work reflections: 2.567485                  |

=============================== refinement start ==============================

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

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

|--(resolution: 1.90 - 28.74 A; n_refl. = 34277)------------------------------| |                                                                            | | r_work= 0.1911  r_free= 0.2279  ksol= 0.40  Bsol= 59.62  scale= 0.063  | |                                                                            | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (-1.73,-1.73,3.47,0.00,0.00,-0.00); trace/3= 0.00                          | |                                                                            | | maximum likelihood estimate for coordinate error:  0.55 A                | | x-ray target function (ml) for work reflections: 2.591014                  | |-----------------------------------------------------------------------------|

-- Yuri Pompeu _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb