null 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 2hag-2.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hag-2.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hag-2.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hag-2.8-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/2hag-2.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hag-2.8-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 19:28:04 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/2hag-2.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hag-2.8-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 419 and 0 Target number of residues in the AU: 419 Target solvent content: 0.5568 Checking the provided sequence file Detected sequence length: 312 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 312 Adjusted target solvent content: 0.67 Input MTZ file: 2hag-2.8-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: 96 Cell parameters: 94.680 94.680 114.160 90.000 90.000 90.000 Input sequence file: 2hag-2.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2496 target number of atoms Had to go as low as 1.05 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 Loops will be built when appropriate and at the last cycle Resolution range: 29.659 2.750 Wilson plot Bfac: 37.45 13981 reflections ( 99.48 % complete ) and 0 restraints for refining 2756 atoms. Observations/parameters ratio is 1.27 ------------------------------------------------------ Starting model: R = 0.3504 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2686 (Rfree = 0.000) for 2756 atoms. Found 24 (38 requested) and removed 24 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.88 2.27 Search for helices and strands: 0 residues in 0 chains, 2816 seeds are put forward Round 1: 209 peptides, 32 chains. Longest chain 17 peptides. Score 0.450 Round 2: 249 peptides, 29 chains. Longest chain 23 peptides. Score 0.594 Round 3: 252 peptides, 26 chains. Longest chain 26 peptides. Score 0.633 Round 4: 269 peptides, 26 chains. Longest chain 31 peptides. Score 0.669 Round 5: 264 peptides, 24 chains. Longest chain 31 peptides. Score 0.678 Taking the results from Round 5 Chains 26, Residues 240, Estimated correctness of the model 75.4 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 13981 reflections ( 99.48 % complete ) and 4396 restraints for refining 2312 atoms. 3424 conditional restraints added. Observations/parameters ratio is 1.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2879 (Rfree = 0.000) for 2312 atoms. Found 31 (31 requested) and removed 17 (15 requested) atoms. Cycle 2: After refmac, R = 0.2682 (Rfree = 0.000) for 2317 atoms. Found 23 (32 requested) and removed 19 (16 requested) atoms. Cycle 3: After refmac, R = 0.2536 (Rfree = 0.000) for 2317 atoms. Found 10 (32 requested) and removed 18 (16 requested) atoms. Cycle 4: After refmac, R = 0.2501 (Rfree = 0.000) for 2301 atoms. Found 20 (31 requested) and removed 16 (15 requested) atoms. Cycle 5: After refmac, R = 0.2485 (Rfree = 0.000) for 2302 atoms. Found 20 (31 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.67 2.11 Search for helices and strands: 0 residues in 0 chains, 2377 seeds are put forward Round 1: 250 peptides, 26 chains. Longest chain 20 peptides. Score 0.628 Round 2: 255 peptides, 16 chains. Longest chain 57 peptides. Score 0.735 Round 3: 261 peptides, 22 chains. Longest chain 38 peptides. Score 0.691 Round 4: 253 peptides, 18 chains. Longest chain 38 peptides. Score 0.713 Round 5: 265 peptides, 22 chains. Longest chain 38 peptides. Score 0.699 Taking the results from Round 2 Chains 16, Residues 239, Estimated correctness of the model 82.8 % 2 chains (85 residues) have been docked in sequence Building loops using Loopy2018 16 chains (239 residues) following loop building 2 chains (85 residues) in sequence following loop building ------------------------------------------------------ 13981 reflections ( 99.48 % complete ) and 3837 restraints for refining 2392 atoms. 2518 conditional restraints added. Observations/parameters ratio is 1.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2762 (Rfree = 0.000) for 2392 atoms. Found 33 (33 requested) and removed 22 (16 requested) atoms. Cycle 7: After refmac, R = 0.2558 (Rfree = 0.000) for 2395 atoms. Found 15 (32 requested) and removed 17 (16 requested) atoms. Cycle 8: After refmac, R = 0.2527 (Rfree = 0.000) for 2388 atoms. Found 13 (32 requested) and removed 18 (16 requested) atoms. Cycle 9: After refmac, R = 0.2406 (Rfree = 0.000) for 2379 atoms. Found 6 (30 requested) and removed 16 (16 requested) atoms. Cycle 10: After refmac, R = 0.2377 (Rfree = 0.000) for 2368 atoms. Found 7 (29 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.02 2.39 Search for helices and strands: 0 residues in 0 chains, 2435 seeds are put forward Round 1: 246 peptides, 25 chains. Longest chain 35 peptides. Score 0.630 Round 2: 247 peptides, 20 chains. Longest chain 30 peptides. Score 0.683 Round 3: 251 peptides, 21 chains. Longest chain 38 peptides. Score 0.681 Round 4: 242 peptides, 23 chains. Longest chain 32 peptides. Score 0.642 Round 5: 245 peptides, 25 chains. Longest chain 27 peptides. Score 0.628 Taking the results from Round 2 Chains 21, Residues 227, Estimated correctness of the model 76.1 % 3 chains (71 residues) have been docked in sequence ------------------------------------------------------ 13981 reflections ( 99.48 % complete ) and 3952 restraints for refining 2312 atoms. 2739 conditional restraints added. Observations/parameters ratio is 1.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2850 (Rfree = 0.000) for 2312 atoms. Found 28 (28 requested) and removed 21 (15 requested) atoms. Cycle 12: After refmac, R = 0.2618 (Rfree = 0.000) for 2313 atoms. Found 22 (29 requested) and removed 20 (16 requested) atoms. Cycle 13: After refmac, R = 0.2490 (Rfree = 0.000) for 2312 atoms. Found 17 (28 requested) and removed 16 (15 requested) atoms. Cycle 14: After refmac, R = 0.2392 (Rfree = 0.000) for 2309 atoms. Found 12 (28 requested) and removed 16 (15 requested) atoms. Cycle 15: After refmac, R = 0.2371 (Rfree = 0.000) for 2302 atoms. Found 11 (28 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.85 2.25 Search for helices and strands: 0 residues in 0 chains, 2370 seeds are put forward Round 1: 235 peptides, 24 chains. Longest chain 23 peptides. Score 0.616 Round 2: 247 peptides, 19 chains. Longest chain 40 peptides. Score 0.693 Round 3: 234 peptides, 20 chains. Longest chain 29 peptides. Score 0.656 Round 4: 243 peptides, 17 chains. Longest chain 30 peptides. Score 0.704 Round 5: 254 peptides, 20 chains. Longest chain 35 peptides. Score 0.697 Taking the results from Round 4 Chains 18, Residues 226, Estimated correctness of the model 78.9 % 6 chains (128 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 117 A and 126 A 16 chains (233 residues) following loop building 5 chains (136 residues) in sequence following loop building ------------------------------------------------------ 13981 reflections ( 99.48 % complete ) and 3628 restraints for refining 2416 atoms. 2128 conditional restraints added. Observations/parameters ratio is 1.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2858 (Rfree = 0.000) for 2416 atoms. Found 30 (30 requested) and removed 27 (16 requested) atoms. Cycle 17: After refmac, R = 0.2844 (Rfree = 0.000) for 2411 atoms. Found 29 (29 requested) and removed 24 (16 requested) atoms. Cycle 18: After refmac, R = 0.2569 (Rfree = 0.000) for 2402 atoms. Found 10 (28 requested) and removed 20 (16 requested) atoms. Cycle 19: After refmac, R = 0.2626 (Rfree = 0.000) for 2383 atoms. Found 27 (28 requested) and removed 16 (16 requested) atoms. Cycle 20: After refmac, R = 0.2527 (Rfree = 0.000) for 2390 atoms. Found 12 (27 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.09 2.44 Search for helices and strands: 0 residues in 0 chains, 2436 seeds are put forward Round 1: 254 peptides, 24 chains. Longest chain 29 peptides. Score 0.658 Round 2: 241 peptides, 22 chains. Longest chain 37 peptides. Score 0.650 Round 3: 246 peptides, 22 chains. Longest chain 30 peptides. Score 0.661 Round 4: 249 peptides, 18 chains. Longest chain 31 peptides. Score 0.706 Round 5: 245 peptides, 17 chains. Longest chain 31 peptides. Score 0.708 Taking the results from Round 5 Chains 17, Residues 228, Estimated correctness of the model 79.5 % 6 chains (123 residues) have been docked in sequence Building loops using Loopy2018 17 chains (228 residues) following loop building 6 chains (123 residues) in sequence following loop building ------------------------------------------------------ 13981 reflections ( 99.48 % complete ) and 3609 restraints for refining 2336 atoms. 2186 conditional restraints added. Observations/parameters ratio is 1.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2771 (Rfree = 0.000) for 2336 atoms. Found 26 (26 requested) and removed 18 (16 requested) atoms. Cycle 22: After refmac, R = 0.2792 (Rfree = 0.000) for 2328 atoms. Found 25 (25 requested) and removed 25 (16 requested) atoms. Cycle 23: After refmac, R = 0.2763 (Rfree = 0.000) for 2323 atoms. Found 24 (24 requested) and removed 21 (16 requested) atoms. Cycle 24: After refmac, R = 0.2540 (Rfree = 0.000) for 2319 atoms. Found 18 (24 requested) and removed 17 (16 requested) atoms. Cycle 25: After refmac, R = 0.2497 (Rfree = 0.000) for 2318 atoms. Found 11 (23 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.99 2.36 Search for helices and strands: 0 residues in 0 chains, 2372 seeds are put forward Round 1: 236 peptides, 23 chains. Longest chain 21 peptides. Score 0.629 Round 2: 234 peptides, 16 chains. Longest chain 32 peptides. Score 0.697 Round 3: 252 peptides, 20 chains. Longest chain 36 peptides. Score 0.693 Round 4: 246 peptides, 20 chains. Longest chain 33 peptides. Score 0.681 Round 5: 242 peptides, 18 chains. Longest chain 55 peptides. Score 0.693 Taking the results from Round 2 Chains 16, Residues 218, Estimated correctness of the model 78.0 % 5 chains (133 residues) have been docked in sequence ------------------------------------------------------ 13981 reflections ( 99.48 % complete ) and 3482 restraints for refining 2312 atoms. 2047 conditional restraints added. Observations/parameters ratio is 1.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2713 (Rfree = 0.000) for 2312 atoms. Found 22 (22 requested) and removed 23 (15 requested) atoms. Cycle 27: After refmac, R = 0.2650 (Rfree = 0.000) for 2296 atoms. Found 22 (22 requested) and removed 16 (15 requested) atoms. Cycle 28: After refmac, R = 0.2428 (Rfree = 0.000) for 2298 atoms. Found 16 (22 requested) and removed 15 (15 requested) atoms. Cycle 29: After refmac, R = 0.2375 (Rfree = 0.000) for 2294 atoms. Found 14 (22 requested) and removed 15 (15 requested) atoms. Cycle 30: After refmac, R = 0.2325 (Rfree = 0.000) for 2289 atoms. Found 12 (22 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.96 2.34 Search for helices and strands: 0 residues in 0 chains, 2347 seeds are put forward Round 1: 237 peptides, 24 chains. Longest chain 27 peptides. Score 0.620 Round 2: 245 peptides, 20 chains. Longest chain 56 peptides. Score 0.679 Round 3: 256 peptides, 20 chains. Longest chain 28 peptides. Score 0.700 Round 4: 252 peptides, 18 chains. Longest chain 62 peptides. Score 0.712 Round 5: 241 peptides, 19 chains. Longest chain 54 peptides. Score 0.681 Taking the results from Round 4 Chains 19, Residues 234, Estimated correctness of the model 80.0 % 5 chains (131 residues) have been docked in sequence Building loops using Loopy2018 19 chains (234 residues) following loop building 5 chains (131 residues) in sequence following loop building ------------------------------------------------------ 13981 reflections ( 99.48 % complete ) and 3432 restraints for refining 2331 atoms. 1946 conditional restraints added. Observations/parameters ratio is 1.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2767 (Rfree = 0.000) for 2331 atoms. Found 22 (22 requested) and removed 19 (16 requested) atoms. Cycle 32: After refmac, R = 0.2799 (Rfree = 0.000) for 2326 atoms. Found 22 (22 requested) and removed 21 (16 requested) atoms. Cycle 33: After refmac, R = 0.2768 (Rfree = 0.000) for 2324 atoms. Found 21 (21 requested) and removed 23 (16 requested) atoms. Cycle 34: After refmac, R = 0.2563 (Rfree = 0.000) for 2319 atoms. Found 20 (20 requested) and removed 16 (16 requested) atoms. Cycle 35: After refmac, R = 0.2498 (Rfree = 0.000) for 2323 atoms. Found 20 (20 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.00 2.37 Search for helices and strands: 0 residues in 0 chains, 2397 seeds are put forward Round 1: 252 peptides, 23 chains. Longest chain 34 peptides. Score 0.663 Round 2: 261 peptides, 18 chains. Longest chain 29 peptides. Score 0.728 Round 3: 252 peptides, 18 chains. Longest chain 39 peptides. Score 0.712 Round 4: 265 peptides, 17 chains. Longest chain 39 peptides. Score 0.743 Round 5: 256 peptides, 20 chains. Longest chain 51 peptides. Score 0.700 Taking the results from Round 4 Chains 20, Residues 248, Estimated correctness of the model 83.7 % 6 chains (140 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 111 A and 114 A 19 chains (250 residues) following loop building 5 chains (142 residues) in sequence following loop building ------------------------------------------------------ 13981 reflections ( 99.48 % complete ) and 3374 restraints for refining 2376 atoms. 1755 conditional restraints added. Observations/parameters ratio is 1.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2744 (Rfree = 0.000) for 2376 atoms. Found 19 (19 requested) and removed 19 (16 requested) atoms. Cycle 37: After refmac, R = 0.2585 (Rfree = 0.000) for 2373 atoms. Found 19 (19 requested) and removed 18 (16 requested) atoms. Cycle 38: After refmac, R = 0.2435 (Rfree = 0.000) for 2369 atoms. Found 15 (18 requested) and removed 17 (16 requested) atoms. Cycle 39: After refmac, R = 0.2397 (Rfree = 0.000) for 2366 atoms. Found 9 (17 requested) and removed 17 (16 requested) atoms. Cycle 40: After refmac, R = 0.2417 (Rfree = 0.000) for 2357 atoms. Found 9 (17 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.98 2.35 Search for helices and strands: 0 residues in 0 chains, 2393 seeds are put forward Round 1: 246 peptides, 17 chains. Longest chain 36 peptides. Score 0.710 Round 2: 270 peptides, 16 chains. Longest chain 34 peptides. Score 0.760 Round 3: 266 peptides, 18 chains. Longest chain 34 peptides. Score 0.737 Round 4: 253 peptides, 25 chains. Longest chain 27 peptides. Score 0.645 Round 5: 259 peptides, 18 chains. Longest chain 35 peptides. Score 0.724 Taking the results from Round 2 Chains 17, Residues 254, Estimated correctness of the model 85.7 % 6 chains (147 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 109 A and 120 A 16 chains (259 residues) following loop building 5 chains (157 residues) in sequence following loop building ------------------------------------------------------ 13981 reflections ( 99.48 % complete ) and 3148 restraints for refining 2353 atoms. 1497 conditional restraints added. Observations/parameters ratio is 1.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2795 (Rfree = 0.000) for 2353 atoms. Found 16 (16 requested) and removed 32 (16 requested) atoms. Cycle 42: After refmac, R = 0.2736 (Rfree = 0.000) for 2333 atoms. Found 16 (16 requested) and removed 23 (16 requested) atoms. Cycle 43: After refmac, R = 0.2538 (Rfree = 0.000) for 2321 atoms. Found 16 (16 requested) and removed 18 (16 requested) atoms. Cycle 44: After refmac, R = 0.2506 (Rfree = 0.000) for 2316 atoms. Found 16 (16 requested) and removed 16 (16 requested) atoms. Cycle 45: After refmac, R = 0.2534 (Rfree = 0.000) for 2316 atoms. Found 13 (16 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.00 2.37 Search for helices and strands: 0 residues in 0 chains, 2389 seeds are put forward Round 1: 248 peptides, 21 chains. Longest chain 27 peptides. Score 0.675 Round 2: 253 peptides, 19 chains. Longest chain 29 peptides. Score 0.704 Round 3: 245 peptides, 17 chains. Longest chain 39 peptides. Score 0.708 Round 4: 251 peptides, 19 chains. Longest chain 30 peptides. Score 0.700 Round 5: 241 peptides, 19 chains. Longest chain 31 peptides. Score 0.681 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 228, Estimated correctness of the model 79.5 % 6 chains (145 residues) have been docked in sequence Sequence coverage is 63 % Consider running further cycles of model building using 2hag-2_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 33 A and 39 A Built loop between residues 112 A and 119 A 14 chains (236 residues) following loop building 4 chains (156 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13981 reflections ( 99.48 % complete ) and 3206 restraints for refining 2312 atoms. 1626 conditional restraints added. Observations/parameters ratio is 1.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2839 (Rfree = 0.000) for 2312 atoms. Found 0 (15 requested) and removed 10 (15 requested) atoms. Cycle 47: After refmac, R = 0.2641 (Rfree = 0.000) for 2296 atoms. Found 0 (15 requested) and removed 9 (15 requested) atoms. Cycle 48: After refmac, R = 0.2547 (Rfree = 0.000) for 2281 atoms. Found 0 (15 requested) and removed 2 (15 requested) atoms. Cycle 49: After refmac, R = 0.2506 (Rfree = 0.000) for 2278 atoms. Found 0 (15 requested) and removed 2 (15 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:26:16 GMT 2018 Job finished. TimeTaking 58.34 Used memory is bytes: 437648