null Mon 24 Dec 08:01:02 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2o08-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2o08-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2o08-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o08-3.8-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2o08-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o08-3.8-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 08:01:07 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/noncs/ArpWArp/wArpResults/WorkingDir/2o08-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o08-3.8-parrot-noncs/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-noncs.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-noncs.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 3351 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3426 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3044 (Rfree = 0.000) for 3351 atoms. Found 18 (18 requested) and removed 133 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.54 2.97 Search for helices and strands: 0 residues in 0 chains, 3259 seeds are put forward NCS extension: 0 residues added, 3259 seeds are put forward Round 1: 137 peptides, 30 chains. Longest chain 7 peptides. Score 0.232 Round 2: 182 peptides, 35 chains. Longest chain 10 peptides. Score 0.315 Round 3: 181 peptides, 34 chains. Longest chain 11 peptides. Score 0.325 Round 4: 199 peptides, 33 chains. Longest chain 14 peptides. Score 0.395 Round 5: 186 peptides, 31 chains. Longest chain 13 peptides. Score 0.382 Taking the results from Round 4 Chains 34, Residues 166, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5512 reflections ( 97.49 % complete ) and 6095 restraints for refining 2721 atoms. 5430 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2711 (Rfree = 0.000) for 2721 atoms. Found 14 (14 requested) and removed 61 (7 requested) atoms. Cycle 2: After refmac, R = 0.2486 (Rfree = 0.000) for 2651 atoms. Found 14 (14 requested) and removed 48 (7 requested) atoms. Cycle 3: After refmac, R = 0.2472 (Rfree = 0.000) for 2607 atoms. Found 14 (14 requested) and removed 24 (7 requested) atoms. Cycle 4: After refmac, R = 0.2318 (Rfree = 0.000) for 2590 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 5: After refmac, R = 0.2402 (Rfree = 0.000) for 2586 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.50 2.93 Search for helices and strands: 0 residues in 0 chains, 2737 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2757 seeds are put forward Round 1: 194 peptides, 36 chains. Longest chain 9 peptides. Score 0.339 Round 2: 249 peptides, 42 chains. Longest chain 11 peptides. Score 0.427 Round 3: 240 peptides, 35 chains. Longest chain 17 peptides. Score 0.486 Round 4: 230 peptides, 31 chains. Longest chain 20 peptides. Score 0.507 Round 5: 232 peptides, 32 chains. Longest chain 17 peptides. Score 0.501 Taking the results from Round 4 Chains 32, Residues 199, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5512 reflections ( 97.49 % complete ) and 5856 restraints for refining 2720 atoms. 5061 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2919 (Rfree = 0.000) for 2720 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. Cycle 7: After refmac, R = 0.2825 (Rfree = 0.000) for 2692 atoms. Found 10 (14 requested) and removed 11 (7 requested) atoms. Cycle 8: After refmac, R = 0.2889 (Rfree = 0.000) for 2684 atoms. Found 5 (14 requested) and removed 19 (7 requested) atoms. Cycle 9: After refmac, R = 0.3009 (Rfree = 0.000) for 2666 atoms. Found 2 (14 requested) and removed 12 (7 requested) atoms. Cycle 10: After refmac, R = 0.2981 (Rfree = 0.000) for 2656 atoms. Found 1 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.61 3.02 Search for helices and strands: 0 residues in 0 chains, 2798 seeds are put forward NCS extension: 32 residues added (3 deleted due to clashes), 2830 seeds are put forward Round 1: 219 peptides, 36 chains. Longest chain 13 peptides. Score 0.415 Round 2: 216 peptides, 28 chains. Longest chain 17 peptides. Score 0.506 Round 3: 229 peptides, 30 chains. Longest chain 20 peptides. Score 0.516 Round 4: 244 peptides, 35 chains. Longest chain 23 peptides. Score 0.497 Round 5: 231 peptides, 31 chains. Longest chain 23 peptides. Score 0.510 Taking the results from Round 3 Chains 32, Residues 199, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5512 reflections ( 97.49 % complete ) and 5991 restraints for refining 2720 atoms. 5192 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2683 (Rfree = 0.000) for 2720 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 12: After refmac, R = 0.2615 (Rfree = 0.000) for 2701 atoms. Found 7 (14 requested) and removed 48 (7 requested) atoms. Cycle 13: After refmac, R = 0.2490 (Rfree = 0.000) for 2654 atoms. Found 11 (14 requested) and removed 11 (7 requested) atoms. Cycle 14: After refmac, R = 0.2427 (Rfree = 0.000) for 2647 atoms. Found 7 (14 requested) and removed 8 (7 requested) atoms. Cycle 15: After refmac, R = 0.2353 (Rfree = 0.000) for 2643 atoms. Found 7 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 3.01 Search for helices and strands: 0 residues in 0 chains, 2753 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 2774 seeds are put forward Round 1: 186 peptides, 32 chains. Longest chain 12 peptides. Score 0.369 Round 2: 205 peptides, 29 chains. Longest chain 14 peptides. Score 0.464 Round 3: 225 peptides, 29 chains. Longest chain 29 peptides. Score 0.518 Round 4: 218 peptides, 31 chains. Longest chain 19 peptides. Score 0.475 Round 5: 221 peptides, 28 chains. Longest chain 27 peptides. Score 0.519 Taking the results from Round 5 Chains 28, Residues 193, Estimated correctness of the model 0.0 % 2 chains (36 residues) have been docked in sequence ------------------------------------------------------ 5512 reflections ( 97.49 % complete ) and 5649 restraints for refining 2721 atoms. 4763 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2777 (Rfree = 0.000) for 2721 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 17: After refmac, R = 0.2542 (Rfree = 0.000) for 2698 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 18: After refmac, R = 0.2412 (Rfree = 0.000) for 2683 atoms. Found 14 (14 requested) and removed 82 (7 requested) atoms. Cycle 19: After refmac, R = 0.2404 (Rfree = 0.000) for 2613 atoms. Found 14 (14 requested) and removed 46 (7 requested) atoms. Cycle 20: After refmac, R = 0.2330 (Rfree = 0.000) for 2575 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.64 3.05 Search for helices and strands: 0 residues in 0 chains, 2687 seeds are put forward NCS extension: 26 residues added (5 deleted due to clashes), 2713 seeds are put forward Round 1: 197 peptides, 34 chains. Longest chain 16 peptides. Score 0.376 Round 2: 210 peptides, 32 chains. Longest chain 19 peptides. Score 0.440 Round 3: 229 peptides, 32 chains. Longest chain 16 peptides. Score 0.493 Round 4: 221 peptides, 32 chains. Longest chain 27 peptides. Score 0.471 Round 5: 215 peptides, 33 chains. Longest chain 18 peptides. Score 0.442 Taking the results from Round 3 Chains 32, Residues 197, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5512 reflections ( 97.49 % complete ) and 5999 restraints for refining 2719 atoms. 5243 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2504 (Rfree = 0.000) for 2719 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 22: After refmac, R = 0.2272 (Rfree = 0.000) for 2696 atoms. Found 12 (14 requested) and removed 13 (7 requested) atoms. Cycle 23: After refmac, R = 0.2208 (Rfree = 0.000) for 2686 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 24: After refmac, R = 0.2143 (Rfree = 0.000) for 2679 atoms. Found 12 (14 requested) and removed 10 (7 requested) atoms. Cycle 25: After refmac, R = 0.2021 (Rfree = 0.000) for 2676 atoms. Found 10 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.58 3.00 Search for helices and strands: 0 residues in 0 chains, 2810 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 2825 seeds are put forward Round 1: 186 peptides, 34 chains. Longest chain 11 peptides. Score 0.341 Round 2: 218 peptides, 32 chains. Longest chain 13 peptides. Score 0.463 Round 3: 212 peptides, 31 chains. Longest chain 17 peptides. Score 0.458 Round 4: 225 peptides, 33 chains. Longest chain 14 peptides. Score 0.470 Round 5: 214 peptides, 30 chains. Longest chain 16 peptides. Score 0.476 Taking the results from Round 5 Chains 31, Residues 184, Estimated correctness of the model 0.0 % 3 chains (35 residues) have been docked in sequence ------------------------------------------------------ 5512 reflections ( 97.49 % complete ) and 5671 restraints for refining 2721 atoms. 4835 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2738 (Rfree = 0.000) for 2721 atoms. Found 11 (14 requested) and removed 24 (7 requested) atoms. Cycle 27: After refmac, R = 0.2330 (Rfree = 0.000) for 2687 atoms. Found 8 (14 requested) and removed 13 (7 requested) atoms. Cycle 28: After refmac, R = 0.2325 (Rfree = 0.000) for 2665 atoms. Found 9 (14 requested) and removed 13 (7 requested) atoms. Cycle 29: After refmac, R = 0.2365 (Rfree = 0.000) for 2649 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 30: After refmac, R = 0.2277 (Rfree = 0.000) for 2647 atoms. Found 11 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.58 3.00 Search for helices and strands: 0 residues in 0 chains, 2794 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 2814 seeds are put forward Round 1: 181 peptides, 37 chains. Longest chain 9 peptides. Score 0.283 Round 2: 181 peptides, 31 chains. Longest chain 11 peptides. Score 0.367 Round 3: 202 peptides, 32 chains. Longest chain 11 peptides. Score 0.417 Round 4: 196 peptides, 30 chains. Longest chain 13 peptides. Score 0.425 Round 5: 194 peptides, 30 chains. Longest chain 15 peptides. Score 0.419 Taking the results from Round 4 Chains 30, Residues 166, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5512 reflections ( 97.49 % complete ) and 6171 restraints for refining 2721 atoms. 5537 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2622 (Rfree = 0.000) for 2721 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 32: After refmac, R = 0.2443 (Rfree = 0.000) for 2707 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 33: After refmac, R = 0.2461 (Rfree = 0.000) for 2692 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 34: After refmac, R = 0.2351 (Rfree = 0.000) for 2687 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 35: After refmac, R = 0.2557 (Rfree = 0.000) for 2677 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 3.02 Search for helices and strands: 0 residues in 0 chains, 2829 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 2848 seeds are put forward Round 1: 181 peptides, 34 chains. Longest chain 9 peptides. Score 0.325 Round 2: 200 peptides, 33 chains. Longest chain 16 peptides. Score 0.398 Round 3: 210 peptides, 31 chains. Longest chain 14 peptides. Score 0.453 Round 4: 197 peptides, 33 chains. Longest chain 14 peptides. Score 0.389 Round 5: 196 peptides, 32 chains. Longest chain 14 peptides. Score 0.399 Taking the results from Round 3 Chains 32, Residues 179, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5512 reflections ( 97.49 % complete ) and 5917 restraints for refining 2721 atoms. 5183 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2490 (Rfree = 0.000) for 2721 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 37: After refmac, R = 0.2369 (Rfree = 0.000) for 2707 atoms. Found 14 (14 requested) and removed 8 (7 requested) atoms. Cycle 38: After refmac, R = 0.2403 (Rfree = 0.000) for 2703 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 39: After refmac, R = 0.2245 (Rfree = 0.000) for 2697 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 40: After refmac, R = 0.2217 (Rfree = 0.000) for 2692 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.53 2.96 Search for helices and strands: 0 residues in 0 chains, 2833 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2846 seeds are put forward Round 1: 164 peptides, 32 chains. Longest chain 9 peptides. Score 0.297 Round 2: 195 peptides, 35 chains. Longest chain 13 peptides. Score 0.356 Round 3: 192 peptides, 32 chains. Longest chain 10 peptides. Score 0.387 Round 4: 197 peptides, 31 chains. Longest chain 13 peptides. Score 0.415 Round 5: 209 peptides, 33 chains. Longest chain 14 peptides. Score 0.425 Taking the results from Round 5 Chains 33, Residues 176, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5512 reflections ( 97.49 % complete ) and 6141 restraints for refining 2721 atoms. 5470 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2500 (Rfree = 0.000) for 2721 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 42: After refmac, R = 0.2385 (Rfree = 0.000) for 2695 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 43: After refmac, R = 0.2240 (Rfree = 0.000) for 2686 atoms. Found 4 (14 requested) and removed 12 (7 requested) atoms. Cycle 44: After refmac, R = 0.2226 (Rfree = 0.000) for 2672 atoms. Found 3 (14 requested) and removed 11 (7 requested) atoms. Cycle 45: After refmac, R = 0.2200 (Rfree = 0.000) for 2660 atoms. Found 2 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.56 2.98 Search for helices and strands: 0 residues in 0 chains, 2751 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 2763 seeds are put forward Round 1: 151 peptides, 32 chains. Longest chain 8 peptides. Score 0.252 Round 2: 169 peptides, 29 chains. Longest chain 13 peptides. Score 0.356 Round 3: 167 peptides, 27 chains. Longest chain 15 peptides. Score 0.378 Round 4: 161 peptides, 27 chains. Longest chain 11 peptides. Score 0.359 Round 5: 172 peptides, 29 chains. Longest chain 16 peptides. Score 0.366 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 140, 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 6302 restraints for refining 2721 atoms. 5769 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2472 (Rfree = 0.000) for 2721 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2402 (Rfree = 0.000) for 2701 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2137 (Rfree = 0.000) for 2685 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2505 (Rfree = 0.000) for 2674 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:36:44 GMT 2018 Job finished. TimeTaking 35.71 Used memory is bytes: 12046696