Tue 25 Dec 19:27:55 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2o08-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o08-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o08-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o08-3.8-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o08-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o08-3.8-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Tue 25 Dec 19:28:05 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o08-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o08-3.8-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 352 and 0 Target number of residues in the AU: 352 Target solvent content: 0.6503 Checking the provided sequence file Detected sequence length: 188 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 376 Adjusted target solvent content: 0.63 Input MTZ file: 2o08-3.8-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 20 Cell parameters: 87.690 166.470 74.630 90.000 90.000 90.000 Input sequence file: 2o08-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 3008 target number of atoms Had to go as low as 0.90 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 83.235 3.800 Wilson plot Bfac: 78.33 5512 reflections ( 97.49 % complete ) and 0 restraints for refining 3332 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3352 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3295 (Rfree = 0.000) for 3332 atoms. Found 18 (18 requested) and removed 28 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 2.94 Search for helices and strands: 0 residues in 0 chains, 3423 seeds are put forward NCS extension: 0 residues added, 3423 seeds are put forward Round 1: 182 peptides, 37 chains. Longest chain 9 peptides. Score 0.287 Round 2: 203 peptides, 32 chains. Longest chain 12 peptides. Score 0.420 Round 3: 217 peptides, 30 chains. Longest chain 15 peptides. Score 0.484 Round 4: 213 peptides, 30 chains. Longest chain 17 peptides. Score 0.474 Round 5: 232 peptides, 31 chains. Longest chain 18 peptides. Score 0.512 Taking the results from Round 5 Chains 31, Residues 201, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5512 reflections ( 97.49 % complete ) and 6065 restraints for refining 2720 atoms. 5292 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2826 (Rfree = 0.000) for 2720 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 2: After refmac, R = 0.2590 (Rfree = 0.000) for 2672 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 3: After refmac, R = 0.2347 (Rfree = 0.000) for 2645 atoms. Found 12 (14 requested) and removed 11 (7 requested) atoms. Cycle 4: After refmac, R = 0.2377 (Rfree = 0.000) for 2624 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 5: After refmac, R = 0.2056 (Rfree = 0.000) for 2613 atoms. Found 10 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.60 3.02 Search for helices and strands: 0 residues in 0 chains, 2776 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2789 seeds are put forward Round 1: 212 peptides, 34 chains. Longest chain 12 peptides. Score 0.420 Round 2: 220 peptides, 30 chains. Longest chain 16 peptides. Score 0.493 Round 3: 222 peptides, 29 chains. Longest chain 15 peptides. Score 0.510 Round 4: 223 peptides, 31 chains. Longest chain 16 peptides. Score 0.489 Round 5: 216 peptides, 27 chains. Longest chain 16 peptides. Score 0.518 Taking the results from Round 5 Chains 27, Residues 189, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5512 reflections ( 97.49 % complete ) and 5976 restraints for refining 2721 atoms. 5247 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2593 (Rfree = 0.000) for 2721 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2334 (Rfree = 0.000) for 2687 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2303 (Rfree = 0.000) for 2664 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 9: After refmac, R = 0.2212 (Rfree = 0.000) for 2657 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 10: After refmac, R = 0.1979 (Rfree = 0.000) for 2651 atoms. Found 5 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.60 3.02 Search for helices and strands: 0 residues in 0 chains, 2799 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2816 seeds are put forward Round 1: 201 peptides, 35 chains. Longest chain 11 peptides. Score 0.375 Round 2: 215 peptides, 29 chains. Longest chain 18 peptides. Score 0.491 Round 3: 237 peptides, 27 chains. Longest chain 20 peptides. Score 0.570 Round 4: 236 peptides, 31 chains. Longest chain 16 peptides. Score 0.522 Round 5: 234 peptides, 27 chains. Longest chain 17 peptides. Score 0.563 Taking the results from Round 3 Chains 27, Residues 210, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5512 reflections ( 97.49 % complete ) and 5938 restraints for refining 2721 atoms. 5125 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2310 (Rfree = 0.000) for 2721 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 12: After refmac, R = 0.2066 (Rfree = 0.000) for 2713 atoms. Found 13 (14 requested) and removed 12 (7 requested) atoms. Cycle 13: After refmac, R = 0.2109 (Rfree = 0.000) for 2704 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 14: After refmac, R = 0.2052 (Rfree = 0.000) for 2696 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1943 (Rfree = 0.000) for 2686 atoms. Found 7 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 2.99 Search for helices and strands: 0 residues in 0 chains, 2830 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 2856 seeds are put forward Round 1: 183 peptides, 29 chains. Longest chain 13 peptides. Score 0.400 Round 2: 207 peptides, 29 chains. Longest chain 14 peptides. Score 0.469 Round 3: 213 peptides, 25 chains. Longest chain 28 peptides. Score 0.534 Round 4: 217 peptides, 29 chains. Longest chain 15 peptides. Score 0.497 Round 5: 226 peptides, 30 chains. Longest chain 18 peptides. Score 0.508 Taking the results from Round 3 Chains 25, Residues 188, Estimated correctness of the model 0.0 % 1 chains (27 residues) have been docked in sequence ------------------------------------------------------ 5512 reflections ( 97.49 % complete ) and 5709 restraints for refining 2721 atoms. 4854 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2531 (Rfree = 0.000) for 2721 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 17: After refmac, R = 0.2376 (Rfree = 0.000) for 2698 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 18: After refmac, R = 0.2338 (Rfree = 0.000) for 2683 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 19: After refmac, R = 0.2243 (Rfree = 0.000) for 2671 atoms. Found 14 (14 requested) and removed 8 (7 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2197 (Rfree = 0.000) for 2664 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 2.97 Search for helices and strands: 0 residues in 0 chains, 2783 seeds are put forward NCS extension: 22 residues added (5 deleted due to clashes), 2805 seeds are put forward Round 1: 194 peptides, 33 chains. Longest chain 14 peptides. Score 0.380 Round 2: 211 peptides, 35 chains. Longest chain 13 peptides. Score 0.405 Round 3: 202 peptides, 34 chains. Longest chain 14 peptides. Score 0.391 Round 4: 218 peptides, 32 chains. Longest chain 12 peptides. Score 0.463 Round 5: 213 peptides, 30 chains. Longest chain 14 peptides. Score 0.474 Taking the results from Round 5 Chains 30, Residues 183, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5512 reflections ( 97.49 % complete ) and 6096 restraints for refining 2721 atoms. 5394 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2572 (Rfree = 0.000) for 2721 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2345 (Rfree = 0.000) for 2694 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 23: After refmac, R = 0.2348 (Rfree = 0.000) for 2688 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 24: After refmac, R = 0.2164 (Rfree = 0.000) for 2683 atoms. Found 13 (14 requested) and removed 10 (7 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2168 (Rfree = 0.000) for 2681 atoms. Found 14 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.51 2.94 Search for helices and strands: 0 residues in 0 chains, 2841 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2858 seeds are put forward Round 1: 163 peptides, 31 chains. Longest chain 10 peptides. Score 0.308 Round 2: 207 peptides, 33 chains. Longest chain 13 peptides. Score 0.419 Round 3: 204 peptides, 31 chains. Longest chain 11 peptides. Score 0.436 Round 4: 204 peptides, 28 chains. Longest chain 20 peptides. Score 0.474 Round 5: 211 peptides, 32 chains. Longest chain 14 peptides. Score 0.443 Taking the results from Round 4 Chains 29, Residues 176, Estimated correctness of the model 0.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 5512 reflections ( 97.49 % complete ) and 5859 restraints for refining 2719 atoms. 5079 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2310 (Rfree = 0.000) for 2719 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 27: After refmac, R = 0.2241 (Rfree = 0.000) for 2701 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 28: After refmac, R = 0.2067 (Rfree = 0.000) for 2695 atoms. Found 8 (14 requested) and removed 10 (7 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2018 (Rfree = 0.000) for 2681 atoms. Found 10 (14 requested) and removed 11 (7 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2063 (Rfree = 0.000) for 2671 atoms. Found 11 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.57 2.99 Search for helices and strands: 0 residues in 0 chains, 2793 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 2813 seeds are put forward Round 1: 172 peptides, 31 chains. Longest chain 15 peptides. Score 0.338 Round 2: 212 peptides, 34 chains. Longest chain 16 peptides. Score 0.420 Round 3: 191 peptides, 29 chains. Longest chain 23 peptides. Score 0.424 Round 4: 210 peptides, 30 chains. Longest chain 22 peptides. Score 0.465 Round 5: 203 peptides, 30 chains. Longest chain 24 peptides. Score 0.446 Taking the results from Round 4 Chains 30, Residues 180, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5512 reflections ( 97.49 % complete ) and 6312 restraints for refining 2721 atoms. 5622 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2301 (Rfree = 0.000) for 2721 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2177 (Rfree = 0.000) for 2712 atoms. Found 13 (14 requested) and removed 21 (7 requested) atoms. Cycle 33: After refmac, R = 0.2195 (Rfree = 0.000) for 2697 atoms. Found 11 (14 requested) and removed 9 (7 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.2149 (Rfree = 0.000) for 2691 atoms. Found 11 (14 requested) and removed 13 (7 requested) atoms. Cycle 35: After refmac, R = 0.2154 (Rfree = 0.000) for 2685 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 2.97 Search for helices and strands: 0 residues in 0 chains, 2817 seeds are put forward NCS extension: 36 residues added (2 deleted due to clashes), 2853 seeds are put forward Round 1: 149 peptides, 26 chains. Longest chain 10 peptides. Score 0.334 Round 2: 179 peptides, 28 chains. Longest chain 11 peptides. Score 0.401 Round 3: 166 peptides, 25 chains. Longest chain 13 peptides. Score 0.403 Round 4: 173 peptides, 25 chains. Longest chain 13 peptides. Score 0.424 Round 5: 183 peptides, 27 chains. Longest chain 13 peptides. Score 0.427 Taking the results from Round 5 Chains 28, Residues 156, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5512 reflections ( 97.49 % complete ) and 6192 restraints for refining 2718 atoms. 5566 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2404 (Rfree = 0.000) for 2718 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 37: After refmac, R = 0.2284 (Rfree = 0.000) for 2698 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 38: After refmac, R = 0.2147 (Rfree = 0.000) for 2698 atoms. Found 12 (14 requested) and removed 11 (7 requested) atoms. Cycle 39: After refmac, R = 0.2077 (Rfree = 0.000) for 2694 atoms. Found 13 (14 requested) and removed 16 (7 requested) atoms. Cycle 40: After refmac, R = 0.2347 (Rfree = 0.000) for 2686 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.53 2.96 Search for helices and strands: 0 residues in 0 chains, 2797 seeds are put forward NCS extension: 0 residues added, 2797 seeds are put forward Round 1: 167 peptides, 29 chains. Longest chain 11 peptides. Score 0.350 Round 2: 188 peptides, 29 chains. Longest chain 13 peptides. Score 0.415 Round 3: 187 peptides, 27 chains. Longest chain 16 peptides. Score 0.438 Round 4: 187 peptides, 25 chains. Longest chain 18 peptides. Score 0.464 Round 5: 178 peptides, 26 chains. Longest chain 14 peptides. Score 0.425 Taking the results from Round 4 Chains 25, Residues 162, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5512 reflections ( 97.49 % complete ) and 6239 restraints for refining 2721 atoms. 5571 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2393 (Rfree = 0.000) for 2721 atoms. Found 13 (14 requested) and removed 11 (7 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2413 (Rfree = 0.000) for 2698 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 43: After refmac, R = 0.2355 (Rfree = 0.000) for 2684 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 44: After refmac, R = 0.2429 (Rfree = 0.000) for 2669 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 45: After refmac, R = 0.2248 (Rfree = 0.000) for 2659 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.56 2.98 Search for helices and strands: 0 residues in 0 chains, 2788 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 2810 seeds are put forward Round 1: 147 peptides, 29 chains. Longest chain 10 peptides. Score 0.283 Round 2: 166 peptides, 30 chains. Longest chain 10 peptides. Score 0.333 Round 3: 179 peptides, 28 chains. Longest chain 16 peptides. Score 0.401 Round 4: 172 peptides, 27 chains. Longest chain 12 peptides. Score 0.393 Round 5: 171 peptides, 26 chains. Longest chain 18 peptides. Score 0.404 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 145, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2o08-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5512 reflections ( 97.49 % complete ) and 6192 restraints for refining 2713 atoms. 5638 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2296 (Rfree = 0.000) for 2713 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2276 (Rfree = 0.000) for 2689 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2177 (Rfree = 0.000) for 2670 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2163 (Rfree = 0.000) for 2659 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 52.87