Mon 24 Dec 08:00:56 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 2ouw-1.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ouw-1.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ouw-1.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ouw-1.8-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/2ouw-1.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ouw-1.8-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 08:01:01 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/2ouw-1.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ouw-1.8-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 236 and 0 Target number of residues in the AU: 236 Target solvent content: 0.4804 Checking the provided sequence file Detected sequence length: 138 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 276 Adjusted target solvent content: 0.39 Input MTZ file: 2ouw-1.8-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: 182 Cell parameters: 62.683 62.683 216.710 90.000 90.000 120.000 Input sequence file: 2ouw-1.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 2208 target number of atoms Had to go as low as 0.40 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 1 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: 108.355 1.800 Wilson plot Bfac: 19.42 24440 reflections ( 99.91 % complete ) and 0 restraints for refining 2433 atoms. Observations/parameters ratio is 2.51 ------------------------------------------------------ Starting model: R = 0.3269 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2816 (Rfree = 0.000) for 2433 atoms. Found 84 (112 requested) and removed 57 (56 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.13 2.47 NCS extension: 0 residues added, 2460 seeds are put forward Round 1: 203 peptides, 20 chains. Longest chain 33 peptides. Score 0.795 Round 2: 240 peptides, 9 chains. Longest chain 61 peptides. Score 0.938 Round 3: 250 peptides, 7 chains. Longest chain 71 peptides. Score 0.954 Round 4: 241 peptides, 9 chains. Longest chain 59 peptides. Score 0.939 Round 5: 248 peptides, 8 chains. Longest chain 60 peptides. Score 0.949 Taking the results from Round 3 Chains 8, Residues 243, Estimated correctness of the model 99.8 % 5 chains (218 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 60 A and 65 A Built loop between residues 100 A and 110 A Built loop between residues 71 B and 74 B 4 chains (251 residues) following loop building 2 chains (233 residues) in sequence following loop building ------------------------------------------------------ 24440 reflections ( 99.91 % complete ) and 2379 restraints for refining 2179 atoms. 531 conditional restraints added. Observations/parameters ratio is 2.80 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2895 (Rfree = 0.000) for 2179 atoms. Found 52 (100 requested) and removed 57 (50 requested) atoms. Cycle 2: After refmac, R = 0.2704 (Rfree = 0.000) for 2169 atoms. Found 52 (98 requested) and removed 19 (50 requested) atoms. Cycle 3: After refmac, R = 0.2611 (Rfree = 0.000) for 2191 atoms. Found 45 (99 requested) and removed 6 (50 requested) atoms. Cycle 4: After refmac, R = 0.2562 (Rfree = 0.000) for 2227 atoms. Found 39 (101 requested) and removed 10 (51 requested) atoms. Cycle 5: After refmac, R = 0.2516 (Rfree = 0.000) for 2250 atoms. Found 33 (102 requested) and removed 11 (52 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.00 2.32 NCS extension: 16 residues added (116 deleted due to clashes), 2291 seeds are put forward Round 1: 256 peptides, 5 chains. Longest chain 70 peptides. Score 0.966 Round 2: 257 peptides, 7 chains. Longest chain 71 peptides. Score 0.958 Round 3: 260 peptides, 6 chains. Longest chain 111 peptides. Score 0.963 Round 4: 263 peptides, 4 chains. Longest chain 116 peptides. Score 0.972 Round 5: 263 peptides, 4 chains. Longest chain 134 peptides. Score 0.972 Taking the results from Round 5 Chains 7, Residues 259, Estimated correctness of the model 99.9 % 4 chains (252 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 56 A and 67 A Built loop between residues 106 A and 110 A 2 chains (265 residues) following loop building 2 chains (265 residues) in sequence following loop building ------------------------------------------------------ 24440 reflections ( 99.91 % complete ) and 2232 restraints for refining 2279 atoms. 203 conditional restraints added. Observations/parameters ratio is 2.68 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2668 (Rfree = 0.000) for 2279 atoms. Found 70 (103 requested) and removed 57 (52 requested) atoms. Cycle 7: After refmac, R = 0.2545 (Rfree = 0.000) for 2289 atoms. Found 59 (102 requested) and removed 23 (53 requested) atoms. Cycle 8: After refmac, R = 0.2493 (Rfree = 0.000) for 2323 atoms. Found 49 (103 requested) and removed 19 (53 requested) atoms. Cycle 9: After refmac, R = 0.2444 (Rfree = 0.000) for 2353 atoms. Found 46 (104 requested) and removed 13 (54 requested) atoms. Cycle 10: After refmac, R = 0.2401 (Rfree = 0.000) for 2382 atoms. Found 38 (106 requested) and removed 24 (55 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.00 2.32 NCS extension: 0 residues added, 2397 seeds are put forward Round 1: 262 peptides, 5 chains. Longest chain 74 peptides. Score 0.968 Round 2: 266 peptides, 5 chains. Longest chain 134 peptides. Score 0.970 Round 3: 255 peptides, 4 chains. Longest chain 73 peptides. Score 0.969 Round 4: 262 peptides, 5 chains. Longest chain 73 peptides. Score 0.968 Round 5: 257 peptides, 7 chains. Longest chain 73 peptides. Score 0.958 Taking the results from Round 2 Chains 5, Residues 261, Estimated correctness of the model 99.9 % 3 chains (254 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 62 B and 70 B 4 chains (267 residues) following loop building 2 chains (261 residues) in sequence following loop building ------------------------------------------------------ 24440 reflections ( 99.91 % complete ) and 2341 restraints for refining 2353 atoms. 320 conditional restraints added. Observations/parameters ratio is 2.60 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2586 (Rfree = 0.000) for 2353 atoms. Found 72 (102 requested) and removed 61 (54 requested) atoms. Cycle 12: After refmac, R = 0.2500 (Rfree = 0.000) for 2358 atoms. Found 59 (100 requested) and removed 32 (54 requested) atoms. Cycle 13: After refmac, R = 0.2404 (Rfree = 0.000) for 2382 atoms. Found 47 (99 requested) and removed 19 (55 requested) atoms. Cycle 14: After refmac, R = 0.2348 (Rfree = 0.000) for 2409 atoms. Found 39 (100 requested) and removed 16 (55 requested) atoms. Cycle 15: After refmac, R = 0.2300 (Rfree = 0.000) for 2429 atoms. Found 45 (101 requested) and removed 21 (56 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.98 2.30 NCS extension: 19 residues added (119 deleted due to clashes), 2474 seeds are put forward Round 1: 254 peptides, 6 chains. Longest chain 73 peptides. Score 0.961 Round 2: 265 peptides, 3 chains. Longest chain 134 peptides. Score 0.977 Round 3: 262 peptides, 5 chains. Longest chain 104 peptides. Score 0.968 Round 4: 264 peptides, 4 chains. Longest chain 129 peptides. Score 0.973 Round 5: 263 peptides, 4 chains. Longest chain 104 peptides. Score 0.972 Taking the results from Round 2 Chains 3, Residues 262, Estimated correctness of the model 99.9 % 3 chains (262 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 61 B and 66 B 2 chains (266 residues) following loop building 2 chains (266 residues) in sequence following loop building ------------------------------------------------------ 24440 reflections ( 99.91 % complete ) and 2278 restraints for refining 2363 atoms. 241 conditional restraints added. Observations/parameters ratio is 2.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2479 (Rfree = 0.000) for 2363 atoms. Found 75 (98 requested) and removed 52 (54 requested) atoms. Cycle 17: After refmac, R = 0.2432 (Rfree = 0.000) for 2378 atoms. Found 59 (97 requested) and removed 33 (55 requested) atoms. Cycle 18: After refmac, R = 0.2369 (Rfree = 0.000) for 2403 atoms. Found 47 (95 requested) and removed 22 (55 requested) atoms. Cycle 19: After refmac, R = 0.2340 (Rfree = 0.000) for 2424 atoms. Found 48 (96 requested) and removed 29 (56 requested) atoms. Cycle 20: After refmac, R = 0.2296 (Rfree = 0.000) for 2439 atoms. Found 53 (95 requested) and removed 20 (56 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.00 2.32 NCS extension: 0 residues added, 2472 seeds are put forward Round 1: 261 peptides, 5 chains. Longest chain 71 peptides. Score 0.968 Round 2: 262 peptides, 3 chains. Longest chain 134 peptides. Score 0.976 Round 3: 260 peptides, 5 chains. Longest chain 67 peptides. Score 0.967 Round 4: 264 peptides, 5 chains. Longest chain 94 peptides. Score 0.969 Round 5: 261 peptides, 7 chains. Longest chain 89 peptides. Score 0.960 Taking the results from Round 2 Chains 3, Residues 259, Estimated correctness of the model 99.9 % 3 chains (259 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 61 B and 65 B 2 chains (262 residues) following loop building 2 chains (262 residues) in sequence following loop building ------------------------------------------------------ 24440 reflections ( 99.91 % complete ) and 2293 restraints for refining 2362 atoms. 290 conditional restraints added. Observations/parameters ratio is 2.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2477 (Rfree = 0.000) for 2362 atoms. Found 86 (92 requested) and removed 46 (54 requested) atoms. Cycle 22: After refmac, R = 0.2421 (Rfree = 0.000) for 2395 atoms. Found 40 (91 requested) and removed 35 (55 requested) atoms. Cycle 23: After refmac, R = 0.2357 (Rfree = 0.000) for 2399 atoms. Found 46 (89 requested) and removed 22 (55 requested) atoms. Cycle 24: After refmac, R = 0.2334 (Rfree = 0.000) for 2422 atoms. Found 48 (90 requested) and removed 22 (56 requested) atoms. Cycle 25: After refmac, R = 0.2317 (Rfree = 0.000) for 2444 atoms. Found 42 (90 requested) and removed 25 (56 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.98 2.30 NCS extension: 2 residues added (3 deleted due to clashes), 2463 seeds are put forward Round 1: 258 peptides, 5 chains. Longest chain 110 peptides. Score 0.967 Round 2: 260 peptides, 5 chains. Longest chain 113 peptides. Score 0.967 Round 3: 255 peptides, 6 chains. Longest chain 74 peptides. Score 0.961 Round 4: 259 peptides, 6 chains. Longest chain 88 peptides. Score 0.963 Round 5: 262 peptides, 4 chains. Longest chain 118 peptides. Score 0.972 Taking the results from Round 5 Chains 5, Residues 258, Estimated correctness of the model 99.9 % 3 chains (245 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 60 B and 65 B 4 chains (262 residues) following loop building 2 chains (249 residues) in sequence following loop building ------------------------------------------------------ 24440 reflections ( 99.91 % complete ) and 2362 restraints for refining 2352 atoms. 405 conditional restraints added. Observations/parameters ratio is 2.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2549 (Rfree = 0.000) for 2352 atoms. Found 78 (84 requested) and removed 58 (54 requested) atoms. Cycle 27: After refmac, R = 0.2489 (Rfree = 0.000) for 2367 atoms. Found 52 (83 requested) and removed 14 (54 requested) atoms. Cycle 28: After refmac, R = 0.2401 (Rfree = 0.000) for 2403 atoms. Found 48 (84 requested) and removed 10 (55 requested) atoms. Cycle 29: After refmac, R = 0.2357 (Rfree = 0.000) for 2441 atoms. Found 35 (85 requested) and removed 16 (56 requested) atoms. Cycle 30: After refmac, R = 0.2329 (Rfree = 0.000) for 2456 atoms. Found 39 (86 requested) and removed 20 (56 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.99 2.31 NCS extension: 0 residues added (27 deleted due to clashes), 2476 seeds are put forward Round 1: 256 peptides, 6 chains. Longest chain 70 peptides. Score 0.962 Round 2: 258 peptides, 5 chains. Longest chain 70 peptides. Score 0.967 Round 3: 253 peptides, 6 chains. Longest chain 70 peptides. Score 0.960 Round 4: 251 peptides, 8 chains. Longest chain 60 peptides. Score 0.950 Round 5: 256 peptides, 6 chains. Longest chain 70 peptides. Score 0.962 Taking the results from Round 2 Chains 5, Residues 253, Estimated correctness of the model 99.9 % 5 chains (253 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 15 A and 19 A Built loop between residues 60 A and 66 A Built loop between residues 61 B and 66 B 2 chains (265 residues) following loop building 2 chains (265 residues) in sequence following loop building ------------------------------------------------------ 24440 reflections ( 99.91 % complete ) and 2313 restraints for refining 2402 atoms. 283 conditional restraints added. Observations/parameters ratio is 2.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2524 (Rfree = 0.000) for 2402 atoms. Found 82 (82 requested) and removed 52 (55 requested) atoms. Cycle 32: After refmac, R = 0.2463 (Rfree = 0.000) for 2428 atoms. Found 47 (81 requested) and removed 26 (56 requested) atoms. Cycle 33: After refmac, R = 0.2385 (Rfree = 0.000) for 2445 atoms. Found 39 (79 requested) and removed 23 (56 requested) atoms. Cycle 34: After refmac, R = 0.2336 (Rfree = 0.000) for 2459 atoms. Found 46 (77 requested) and removed 14 (56 requested) atoms. Cycle 35: After refmac, R = 0.2342 (Rfree = 0.000) for 2486 atoms. Found 37 (78 requested) and removed 28 (57 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.00 2.32 NCS extension: 0 residues added, 2495 seeds are put forward Round 1: 257 peptides, 6 chains. Longest chain 72 peptides. Score 0.962 Round 2: 255 peptides, 6 chains. Longest chain 73 peptides. Score 0.961 Round 3: 256 peptides, 6 chains. Longest chain 106 peptides. Score 0.962 Round 4: 259 peptides, 7 chains. Longest chain 67 peptides. Score 0.959 Round 5: 257 peptides, 7 chains. Longest chain 69 peptides. Score 0.958 Taking the results from Round 3 Chains 6, Residues 250, Estimated correctness of the model 99.9 % 5 chains (237 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 107 A and 110 A Built loop between residues 47 B and 50 B Built loop between residues 60 B and 64 B 3 chains (257 residues) following loop building 2 chains (244 residues) in sequence following loop building ------------------------------------------------------ 24440 reflections ( 99.91 % complete ) and 2468 restraints for refining 2379 atoms. 551 conditional restraints added. Observations/parameters ratio is 2.57 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2541 (Rfree = 0.000) for 2379 atoms. Found 69 (73 requested) and removed 55 (55 requested) atoms. Cycle 37: After refmac, R = 0.2473 (Rfree = 0.000) for 2389 atoms. Found 46 (70 requested) and removed 19 (55 requested) atoms. Cycle 38: After refmac, R = 0.2387 (Rfree = 0.000) for 2412 atoms. Found 46 (71 requested) and removed 11 (55 requested) atoms. Cycle 39: After refmac, R = 0.2339 (Rfree = 0.000) for 2445 atoms. Found 36 (72 requested) and removed 15 (56 requested) atoms. Cycle 40: After refmac, R = 0.2298 (Rfree = 0.000) for 2463 atoms. Found 42 (73 requested) and removed 19 (57 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.99 2.31 NCS extension: 3 residues added (17 deleted due to clashes), 2490 seeds are put forward Round 1: 251 peptides, 7 chains. Longest chain 70 peptides. Score 0.955 Round 2: 261 peptides, 5 chains. Longest chain 72 peptides. Score 0.968 Round 3: 251 peptides, 7 chains. Longest chain 72 peptides. Score 0.955 Round 4: 256 peptides, 6 chains. Longest chain 65 peptides. Score 0.962 Round 5: 256 peptides, 7 chains. Longest chain 72 peptides. Score 0.957 Taking the results from Round 2 Chains 6, Residues 256, Estimated correctness of the model 99.9 % 4 chains (241 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 60 A and 64 A Built loop between residues 71 B and 75 B 4 chains (262 residues) following loop building 2 chains (247 residues) in sequence following loop building ------------------------------------------------------ 24440 reflections ( 99.91 % complete ) and 2383 restraints for refining 2353 atoms. 433 conditional restraints added. Observations/parameters ratio is 2.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2479 (Rfree = 0.000) for 2353 atoms. Found 69 (69 requested) and removed 42 (54 requested) atoms. Cycle 42: After refmac, R = 0.2435 (Rfree = 0.000) for 2374 atoms. Found 56 (68 requested) and removed 15 (55 requested) atoms. Cycle 43: After refmac, R = 0.2355 (Rfree = 0.000) for 2412 atoms. Found 50 (69 requested) and removed 5 (55 requested) atoms. Cycle 44: After refmac, R = 0.2303 (Rfree = 0.000) for 2454 atoms. Found 35 (70 requested) and removed 13 (56 requested) atoms. Cycle 45: After refmac, R = 0.2258 (Rfree = 0.000) for 2474 atoms. Found 34 (71 requested) and removed 18 (57 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.98 2.30 NCS extension: 21 residues added (112 deleted due to clashes), 2512 seeds are put forward Round 1: 247 peptides, 6 chains. Longest chain 70 peptides. Score 0.957 Round 2: 250 peptides, 5 chains. Longest chain 103 peptides. Score 0.963 Round 3: 253 peptides, 6 chains. Longest chain 88 peptides. Score 0.960 Round 4: 261 peptides, 5 chains. Longest chain 116 peptides. Score 0.968 Round 5: 261 peptides, 7 chains. Longest chain 118 peptides. Score 0.960 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 256, Estimated correctness of the model 99.9 % 3 chains (235 residues) have been docked in sequence Sequence coverage is 91 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 56 A and 69 A 3 chains (261 residues) following loop building 2 chains (247 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 24440 reflections ( 99.91 % complete ) and 1946 restraints for refining 1914 atoms. Observations/parameters ratio is 3.19 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2910 (Rfree = 0.000) for 1914 atoms. Found 21 (53 requested) and removed 0 (53 requested) atoms. Cycle 47: After refmac, R = 0.2742 (Rfree = 0.000) for 1914 atoms. Found 9 (53 requested) and removed 0 (44 requested) atoms. Cycle 48: After refmac, R = 0.2646 (Rfree = 0.000) for 1914 atoms. Found 6 (53 requested) and removed 1 (44 requested) atoms. Cycle 49: After refmac, R = 0.2600 (Rfree = 0.000) for 1914 atoms. TimeTaking 53.97