Sun 23 Dec 22:22:43 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 2ouw-1.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ouw-1.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ouw-1.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ouw-1.8-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/2ouw-1.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ouw-1.8-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 ============================================================ Sun 23 Dec 22:22:53 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/2ouw-1.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ouw-1.8-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 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-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: 182 Cell parameters: 62.683 62.683 216.710 90.000 90.000 120.000 Input sequence file: 2ouw-1.8-parrot-hancs.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 2448 atoms. Observations/parameters ratio is 2.50 ------------------------------------------------------ Starting model: R = 0.3251 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2780 (Rfree = 0.000) for 2448 atoms. Found 58 (113 requested) and removed 59 (56 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.11 2.45 NCS extension: 0 residues added, 2447 seeds are put forward Round 1: 204 peptides, 20 chains. Longest chain 34 peptides. Score 0.797 Round 2: 235 peptides, 9 chains. Longest chain 67 peptides. Score 0.934 Round 3: 244 peptides, 6 chains. Longest chain 68 peptides. Score 0.956 Round 4: 249 peptides, 8 chains. Longest chain 70 peptides. Score 0.949 Round 5: 249 peptides, 7 chains. Longest chain 100 peptides. Score 0.954 Taking the results from Round 3 Chains 6, Residues 238, Estimated correctness of the model 99.8 % 4 chains (220 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 61 A and 65 A Built loop between residues 61 B and 65 B 4 chains (244 residues) following loop building 2 chains (226 residues) in sequence following loop building ------------------------------------------------------ 24440 reflections ( 99.91 % complete ) and 2436 restraints for refining 2179 atoms. 641 conditional restraints added. Observations/parameters ratio is 2.80 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3031 (Rfree = 0.000) for 2179 atoms. Found 65 (100 requested) and removed 56 (50 requested) atoms. Cycle 2: After refmac, R = 0.2769 (Rfree = 0.000) for 2184 atoms. Found 47 (99 requested) and removed 13 (50 requested) atoms. Cycle 3: After refmac, R = 0.2638 (Rfree = 0.000) for 2209 atoms. Found 40 (100 requested) and removed 15 (51 requested) atoms. Cycle 4: After refmac, R = 0.2533 (Rfree = 0.000) for 2229 atoms. Found 33 (101 requested) and removed 9 (51 requested) atoms. Cycle 5: After refmac, R = 0.2490 (Rfree = 0.000) for 2249 atoms. Found 29 (102 requested) and removed 11 (52 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.05 2.38 NCS extension: 19 residues added (111 deleted due to clashes), 2288 seeds are put forward Round 1: 251 peptides, 6 chains. Longest chain 99 peptides. Score 0.959 Round 2: 254 peptides, 7 chains. Longest chain 100 peptides. Score 0.956 Round 3: 256 peptides, 7 chains. Longest chain 101 peptides. Score 0.957 Round 4: 261 peptides, 5 chains. Longest chain 133 peptides. Score 0.968 Round 5: 261 peptides, 6 chains. Longest chain 102 peptides. Score 0.964 Taking the results from Round 4 Chains 5, Residues 256, Estimated correctness of the model 99.9 % 4 chains (249 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 24 B and 27 B Built loop between residues 60 B and 65 B 3 chains (262 residues) following loop building 2 chains (255 residues) in sequence following loop building ------------------------------------------------------ 24440 reflections ( 99.91 % complete ) and 2302 restraints for refining 2259 atoms. 327 conditional restraints added. Observations/parameters ratio is 2.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2629 (Rfree = 0.000) for 2259 atoms. Found 57 (102 requested) and removed 51 (52 requested) atoms. Cycle 7: After refmac, R = 0.2483 (Rfree = 0.000) for 2261 atoms. Found 56 (100 requested) and removed 15 (52 requested) atoms. Cycle 8: After refmac, R = 0.2427 (Rfree = 0.000) for 2299 atoms. Found 49 (102 requested) and removed 16 (53 requested) atoms. Cycle 9: After refmac, R = 0.2400 (Rfree = 0.000) for 2330 atoms. Found 56 (103 requested) and removed 23 (53 requested) atoms. Cycle 10: After refmac, R = 0.2383 (Rfree = 0.000) for 2362 atoms. Found 51 (105 requested) and removed 24 (54 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.00 2.32 NCS extension: 24 residues added (110 deleted due to clashes), 2414 seeds are put forward Round 1: 256 peptides, 7 chains. Longest chain 71 peptides. Score 0.957 Round 2: 259 peptides, 6 chains. Longest chain 71 peptides. Score 0.963 Round 3: 258 peptides, 6 chains. Longest chain 72 peptides. Score 0.963 Round 4: 260 peptides, 3 chains. Longest chain 129 peptides. Score 0.975 Round 5: 261 peptides, 4 chains. Longest chain 116 peptides. Score 0.972 Taking the results from Round 4 Chains 4, Residues 257, Estimated correctness of the model 99.9 % 2 chains (242 residues) have been docked in sequence Building loops using Loopy2018 4 chains (257 residues) following loop building 2 chains (242 residues) in sequence following loop building ------------------------------------------------------ 24440 reflections ( 99.91 % complete ) and 2368 restraints for refining 2257 atoms. 455 conditional restraints added. Observations/parameters ratio is 2.71 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2518 (Rfree = 0.000) for 2257 atoms. Found 75 (100 requested) and removed 45 (52 requested) atoms. Cycle 12: After refmac, R = 0.2389 (Rfree = 0.000) for 2286 atoms. Found 53 (99 requested) and removed 16 (52 requested) atoms. Cycle 13: After refmac, R = 0.2323 (Rfree = 0.000) for 2319 atoms. Found 49 (101 requested) and removed 14 (53 requested) atoms. Cycle 14: After refmac, R = 0.2262 (Rfree = 0.000) for 2353 atoms. Found 48 (102 requested) and removed 20 (54 requested) atoms. Cycle 15: After refmac, R = 0.2221 (Rfree = 0.000) for 2379 atoms. Found 46 (103 requested) and removed 23 (55 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.98 2.30 NCS extension: 15 residues added (116 deleted due to clashes), 2420 seeds are put forward Round 1: 257 peptides, 7 chains. Longest chain 72 peptides. Score 0.958 Round 2: 261 peptides, 4 chains. Longest chain 117 peptides. Score 0.972 Round 3: 257 peptides, 6 chains. Longest chain 101 peptides. Score 0.962 Round 4: 259 peptides, 4 chains. Longest chain 117 peptides. Score 0.971 Round 5: 259 peptides, 6 chains. Longest chain 117 peptides. Score 0.963 Taking the results from Round 2 Chains 4, Residues 257, Estimated correctness of the model 99.9 % 4 chains (257 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 15 A and 19 A Built loop between residues 60 B and 65 B 2 chains (264 residues) following loop building 2 chains (264 residues) in sequence following loop building ------------------------------------------------------ 24440 reflections ( 99.91 % complete ) and 2267 restraints for refining 2339 atoms. 242 conditional restraints added. Observations/parameters ratio is 2.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2448 (Rfree = 0.000) for 2339 atoms. Found 63 (102 requested) and removed 47 (54 requested) atoms. Cycle 17: After refmac, R = 0.2359 (Rfree = 0.000) for 2350 atoms. Found 49 (99 requested) and removed 22 (54 requested) atoms. Cycle 18: After refmac, R = 0.2287 (Rfree = 0.000) for 2376 atoms. Found 46 (100 requested) and removed 22 (54 requested) atoms. Cycle 19: After refmac, R = 0.2232 (Rfree = 0.000) for 2400 atoms. Found 43 (102 requested) and removed 15 (55 requested) atoms. Cycle 20: After refmac, R = 0.2194 (Rfree = 0.000) for 2426 atoms. Found 47 (103 requested) and removed 21 (56 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.97 2.29 NCS extension: 18 residues added (114 deleted due to clashes), 2474 seeds are put forward Round 1: 258 peptides, 6 chains. Longest chain 70 peptides. Score 0.963 Round 2: 260 peptides, 6 chains. Longest chain 71 peptides. Score 0.963 Round 3: 255 peptides, 6 chains. Longest chain 71 peptides. Score 0.961 Round 4: 260 peptides, 7 chains. Longest chain 60 peptides. Score 0.959 Round 5: 258 peptides, 8 chains. Longest chain 71 peptides. Score 0.954 Taking the results from Round 2 Chains 6, Residues 254, Estimated correctness of the model 99.9 % 5 chains (248 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 15 A and 19 A Built loop between residues 61 A and 65 A 4 chains (260 residues) following loop building 3 chains (254 residues) in sequence following loop building ------------------------------------------------------ 24440 reflections ( 99.91 % complete ) and 2360 restraints for refining 2344 atoms. 388 conditional restraints added. Observations/parameters ratio is 2.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2410 (Rfree = 0.000) for 2344 atoms. Found 68 (99 requested) and removed 41 (54 requested) atoms. Cycle 22: After refmac, R = 0.2327 (Rfree = 0.000) for 2367 atoms. Found 46 (98 requested) and removed 14 (54 requested) atoms. Cycle 23: After refmac, R = 0.2258 (Rfree = 0.000) for 2397 atoms. Found 37 (99 requested) and removed 16 (55 requested) atoms. Cycle 24: After refmac, R = 0.2211 (Rfree = 0.000) for 2416 atoms. Found 46 (100 requested) and removed 23 (55 requested) atoms. Cycle 25: After refmac, R = 0.2187 (Rfree = 0.000) for 2437 atoms. Found 39 (101 requested) and removed 24 (56 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.00 2.32 NCS extension: 24 residues added (121 deleted due to clashes), 2480 seeds are put forward Round 1: 258 peptides, 5 chains. Longest chain 72 peptides. Score 0.967 Round 2: 259 peptides, 6 chains. Longest chain 72 peptides. Score 0.963 Round 3: 254 peptides, 7 chains. Longest chain 72 peptides. Score 0.956 Round 4: 247 peptides, 6 chains. Longest chain 68 peptides. Score 0.957 Round 5: 258 peptides, 8 chains. Longest chain 61 peptides. Score 0.954 Taking the results from Round 1 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 61 A and 65 A Built loop between residues 60 B and 66 B 2 chains (264 residues) following loop building 2 chains (264 residues) in sequence following loop building ------------------------------------------------------ 24440 reflections ( 99.91 % complete ) and 2024 restraints for refining 2374 atoms. 0 conditional restraints added. Observations/parameters ratio is 2.57 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2383 (Rfree = 0.000) for 2374 atoms. Found 68 (96 requested) and removed 38 (54 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2305 (Rfree = 0.000) for 2401 atoms. Found 49 (95 requested) and removed 26 (55 requested) atoms. Cycle 28: After refmac, R = 0.2260 (Rfree = 0.000) for 2421 atoms. Found 40 (94 requested) and removed 19 (56 requested) atoms. Cycle 29: After refmac, R = 0.2211 (Rfree = 0.000) for 2440 atoms. Found 37 (94 requested) and removed 17 (56 requested) atoms. Cycle 30: After refmac, R = 0.2187 (Rfree = 0.000) for 2457 atoms. Found 40 (95 requested) and removed 16 (56 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.99 2.31 NCS extension: 25 residues added (108 deleted due to clashes), 2510 seeds are put forward Round 1: 256 peptides, 6 chains. Longest chain 71 peptides. Score 0.962 Round 2: 259 peptides, 6 chains. Longest chain 104 peptides. Score 0.963 Round 3: 254 peptides, 9 chains. Longest chain 58 peptides. Score 0.947 Round 4: 260 peptides, 6 chains. Longest chain 71 peptides. Score 0.963 Round 5: 253 peptides, 8 chains. Longest chain 63 peptides. Score 0.951 Taking the results from Round 4 Chains 9, Residues 254, Estimated correctness of the model 99.9 % 4 chains (220 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 73 B and 76 B 8 chains (256 residues) following loop building 3 chains (222 residues) in sequence following loop building ------------------------------------------------------ 24440 reflections ( 99.91 % complete ) and 2548 restraints for refining 2331 atoms. 711 conditional restraints added. Observations/parameters ratio is 2.62 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2404 (Rfree = 0.000) for 2331 atoms. Found 81 (90 requested) and removed 27 (53 requested) atoms. Cycle 32: After refmac, R = 0.2326 (Rfree = 0.000) for 2379 atoms. Found 40 (92 requested) and removed 25 (55 requested) atoms. Cycle 33: After refmac, R = 0.2262 (Rfree = 0.000) for 2391 atoms. Found 50 (90 requested) and removed 17 (55 requested) atoms. Cycle 34: After refmac, R = 0.2250 (Rfree = 0.000) for 2422 atoms. Found 29 (92 requested) and removed 28 (56 requested) atoms. Cycle 35: After refmac, R = 0.2222 (Rfree = 0.000) for 2419 atoms. Found 42 (90 requested) and removed 18 (56 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.98 2.30 NCS extension: 12 residues added (24 deleted due to clashes), 2456 seeds are put forward Round 1: 255 peptides, 6 chains. Longest chain 71 peptides. Score 0.961 Round 2: 258 peptides, 7 chains. Longest chain 104 peptides. Score 0.958 Round 3: 258 peptides, 7 chains. Longest chain 71 peptides. Score 0.958 Round 4: 254 peptides, 7 chains. Longest chain 88 peptides. Score 0.956 Round 5: 254 peptides, 7 chains. Longest chain 67 peptides. Score 0.956 Taking the results from Round 1 Chains 6, Residues 249, Estimated correctness of the model 99.9 % 4 chains (227 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 61 A and 65 A Built loop between residues 60 B and 65 B 4 chains (256 residues) following loop building 2 chains (234 residues) in sequence following loop building ------------------------------------------------------ 24440 reflections ( 99.91 % complete ) and 2531 restraints for refining 2347 atoms. 653 conditional restraints added. Observations/parameters ratio is 2.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2396 (Rfree = 0.000) for 2347 atoms. Found 81 (86 requested) and removed 34 (54 requested) atoms. Cycle 37: After refmac, R = 0.2319 (Rfree = 0.000) for 2392 atoms. Found 46 (88 requested) and removed 20 (55 requested) atoms. Cycle 38: After refmac, R = 0.2272 (Rfree = 0.000) for 2417 atoms. Found 33 (89 requested) and removed 20 (55 requested) atoms. Cycle 39: After refmac, R = 0.2231 (Rfree = 0.000) for 2426 atoms. Found 35 (87 requested) and removed 12 (56 requested) atoms. Cycle 40: After refmac, R = 0.2221 (Rfree = 0.000) for 2447 atoms. Found 23 (88 requested) and removed 16 (56 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.99 2.31 NCS extension: 2 residues added (28 deleted due to clashes), 2456 seeds are put forward Round 1: 247 peptides, 6 chains. Longest chain 71 peptides. Score 0.957 Round 2: 255 peptides, 8 chains. Longest chain 99 peptides. Score 0.953 Round 3: 256 peptides, 7 chains. Longest chain 87 peptides. Score 0.957 Round 4: 258 peptides, 7 chains. Longest chain 73 peptides. Score 0.958 Round 5: 253 peptides, 9 chains. Longest chain 60 peptides. Score 0.947 Taking the results from Round 4 Chains 8, Residues 251, Estimated correctness of the model 99.8 % 5 chains (179 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 119 A and 122 A Built loop between residues 27 B and 33 B 5 chains (256 residues) following loop building 3 chains (186 residues) in sequence following loop building ------------------------------------------------------ 24440 reflections ( 99.91 % complete ) and 3018 restraints for refining 2340 atoms. 1332 conditional restraints added. Observations/parameters ratio is 2.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2504 (Rfree = 0.000) for 2340 atoms. Found 75 (82 requested) and removed 29 (54 requested) atoms. Cycle 42: After refmac, R = 0.2389 (Rfree = 0.000) for 2382 atoms. Found 39 (84 requested) and removed 15 (55 requested) atoms. Cycle 43: After refmac, R = 0.2302 (Rfree = 0.000) for 2403 atoms. Found 38 (84 requested) and removed 10 (55 requested) atoms. Cycle 44: After refmac, R = 0.2271 (Rfree = 0.000) for 2430 atoms. Found 30 (85 requested) and removed 15 (56 requested) atoms. Cycle 45: After refmac, R = 0.2237 (Rfree = 0.000) for 2443 atoms. Found 28 (86 requested) and removed 15 (56 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.99 2.31 NCS extension: 8 residues added (9 deleted due to clashes), 2465 seeds are put forward Round 1: 251 peptides, 5 chains. Longest chain 71 peptides. Score 0.964 Round 2: 255 peptides, 6 chains. Longest chain 118 peptides. Score 0.961 Round 3: 251 peptides, 6 chains. Longest chain 88 peptides. Score 0.959 Round 4: 248 peptides, 6 chains. Longest chain 74 peptides. Score 0.958 Round 5: 246 peptides, 6 chains. Longest chain 72 peptides. Score 0.957 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 246, Estimated correctness of the model 99.9 % 4 chains (236 residues) have been docked in sequence Sequence coverage is 95 % All DUM atoms will be removed Building loops using Loopy2018 6 chains (246 residues) following loop building 4 chains (236 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 24440 reflections ( 99.91 % complete ) and 1859 restraints for refining 1830 atoms. Observations/parameters ratio is 3.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2918 (Rfree = 0.000) for 1830 atoms. Found 23 (62 requested) and removed 0 (62 requested) atoms. Cycle 47: After refmac, R = 0.2782 (Rfree = 0.000) for 1830 atoms. Found 14 (63 requested) and removed 0 (42 requested) atoms. Cycle 48: After refmac, R = 0.2688 (Rfree = 0.000) for 1830 atoms. Found 8 (64 requested) and removed 2 (43 requested) atoms. Cycle 49: After refmac, R = 0.2643 (Rfree = 0.000) for 1830 atoms. TimeTaking 64.7