divergence of R and Rfree at the last step of refinement
I'm refining a structure with phenix-dev-1414 version, and R-free decreases until the last step where R-work drops sharply and R-free increases. Am I doing something wrong? 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 : 0.3068 0.3347 4.111964e+00 4.184576e+00 1_bss: 0.2296 0.2735 3.919523e+00 4.036648e+00 1_weight: 0.2296 0.2735 3.919523e+00 4.036648e+00 1_xyzrec: 0.2377 0.2725 3.938818e+00 4.036514e+00 1_adp: 0.2311 0.2707 3.918953e+00 4.031556e+00 1_occ: 0.2311 0.2707 3.918944e+00 4.031541e+00 end: 0.2187 0.2795 3.907777e+00 4.050961e+00 ////////////////////////////////////////////////////////////////// Looking in the log file, it seems that this happens at the stage of correcting the solvent mask: ============================= updating all scales ============================= start: r_work=0.3152 r_free=0.3389 (reset all scales to undefined) bulk-solvent and scaling: r_work=0.2324 r_free=0.2703 remove outliers: r_work=0.2324 r_free=0.2703 *-> correct solvent mask: r_work=0.2187 r_free=0.2795 <--*** final: r_work=0.2187 r_free=0.2795 overall anisotropic scale matrix: V0: 2.5130,-0.3626,1.3424,-0.7174,-0.0625,-2.3276 V1: -0.0348,-0.0556,-0.0105,-0.0091,0.0085,0.0052
Hi Ed, please try latest build - this keeps changing from build to build. If this doesn't fix it then please send me the files off list and I will investigate. Pavel On 7/3/13 1:40 PM, Edward A. Berry wrote:
I'm refining a structure with phenix-dev-1414 version, and R-free decreases until the last step where R-work drops sharply and R-free increases. Am I doing something wrong?
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 : 0.3068 0.3347 4.111964e+00 4.184576e+00 1_bss: 0.2296 0.2735 3.919523e+00 4.036648e+00 1_weight: 0.2296 0.2735 3.919523e+00 4.036648e+00 1_xyzrec: 0.2377 0.2725 3.938818e+00 4.036514e+00 1_adp: 0.2311 0.2707 3.918953e+00 4.031556e+00 1_occ: 0.2311 0.2707 3.918944e+00 4.031541e+00 end: 0.2187 0.2795 3.907777e+00 4.050961e+00 //////////////////////////////////////////////////////////////////
Looking in the log file, it seems that this happens at the stage of correcting the solvent mask: ============================= updating all scales =============================
start: r_work=0.3152 r_free=0.3389 (reset all scales to undefined) bulk-solvent and scaling: r_work=0.2324 r_free=0.2703 remove outliers: r_work=0.2324 r_free=0.2703 *-> correct solvent mask: r_work=0.2187 r_free=0.2795 <--*** final: r_work=0.2187 r_free=0.2795
overall anisotropic scale matrix: V0: 2.5130,-0.3626,1.3424,-0.7174,-0.0625,-2.3276 V1: -0.0348,-0.0556,-0.0105,-0.0091,0.0085,0.0052
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Yes, running dev-1420, using exactly the same .eff file except for serial number, the problem is gone. R-free actually improves in the "end" step, with almost no change on correcting solvent mask. Thanks! start: r_work=0.2315 r_free=0.2704 n_reflections: 87125 start: r_work=0.3154 r_free=0.3389 (reset all scales to undefined) bulk-solvent and scaling: r_work=0.2326 r_free=0.2699 remove outliers: r_work=0.2326 r_free=0.2699 correct solvent mask: r_work=0.2314 r_free=0.2700 final: r_work=0.2314 r_free=0.2700 n_reflections: 87125 Pavel Afonine wrote:
Hi Ed,
please try latest build - this keeps changing from build to build. If this doesn't fix it then please send me the files off list and I will investigate.
Pavel
On 7/3/13 1:40 PM, Edward A. Berry wrote:
I'm refining a structure with phenix-dev-1414 version, and R-free decreases until the last step where R-work drops sharply and R-free increases. Am I doing something wrong?
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 : 0.3068 0.3347 4.111964e+00 4.184576e+00 1_bss: 0.2296 0.2735 3.919523e+00 4.036648e+00 1_weight: 0.2296 0.2735 3.919523e+00 4.036648e+00 1_xyzrec: 0.2377 0.2725 3.938818e+00 4.036514e+00 1_adp: 0.2311 0.2707 3.918953e+00 4.031556e+00 1_occ: 0.2311 0.2707 3.918944e+00 4.031541e+00 end: 0.2187 0.2795 3.907777e+00 4.050961e+00 //////////////////////////////////////////////////////////////////
Looking in the log file, it seems that this happens at the stage of correcting the solvent mask: ============================= updating all scales =============================
start: r_work=0.3152 r_free=0.3389 (reset all scales to undefined) bulk-solvent and scaling: r_work=0.2324 r_free=0.2703 remove outliers: r_work=0.2324 r_free=0.2703 *-> correct solvent mask: r_work=0.2187 r_free=0.2795 <--*** final: r_work=0.2187 r_free=0.2795
overall anisotropic scale matrix: V0: 2.5130,-0.3626,1.3424,-0.7174,-0.0625,-2.3276 V1: -0.0348,-0.0556,-0.0105,-0.0091,0.0085,0.0052
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participants (2)
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Edward A. Berry -
Pavel Afonine