Sun 23 Dec 22:23:05 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-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hag-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hag-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hag-3.2-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-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hag-3.2-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 22:23:15 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-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hag-3.2-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 345 and 0 Target number of residues in the AU: 345 Target solvent content: 0.6351 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-3.2-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-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2496 target number of atoms Had to go as low as 0.95 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 3.201 Wilson plot Bfac: 69.00 9001 reflections ( 99.68 % complete ) and 0 restraints for refining 2779 atoms. Observations/parameters ratio is 0.81 ------------------------------------------------------ Starting model: R = 0.3210 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2755 (Rfree = 0.000) for 2779 atoms. Found 24 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.32 2.62 Search for helices and strands: 0 residues in 0 chains, 2848 seeds are put forward Round 1: 206 peptides, 30 chains. Longest chain 15 peptides. Score 0.467 Round 2: 217 peptides, 25 chains. Longest chain 20 peptides. Score 0.560 Round 3: 228 peptides, 22 chains. Longest chain 21 peptides. Score 0.621 Round 4: 231 peptides, 25 chains. Longest chain 24 peptides. Score 0.595 Round 5: 235 peptides, 22 chains. Longest chain 23 peptides. Score 0.637 Taking the results from Round 5 Chains 23, Residues 213, Estimated correctness of the model 50.6 % 2 chains (32 residues) have been docked in sequence ------------------------------------------------------ 9001 reflections ( 99.68 % complete ) and 4317 restraints for refining 2278 atoms. 3349 conditional restraints added. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2733 (Rfree = 0.000) for 2278 atoms. Found 20 (20 requested) and removed 21 (10 requested) atoms. Cycle 2: After refmac, R = 0.2595 (Rfree = 0.000) for 2244 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 3: After refmac, R = 0.2439 (Rfree = 0.000) for 2239 atoms. Found 9 (20 requested) and removed 11 (10 requested) atoms. Cycle 4: After refmac, R = 0.2378 (Rfree = 0.000) for 2228 atoms. Found 5 (20 requested) and removed 11 (10 requested) atoms. Cycle 5: After refmac, R = 0.2318 (Rfree = 0.000) for 2216 atoms. Found 4 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.24 2.56 Search for helices and strands: 0 residues in 0 chains, 2296 seeds are put forward Round 1: 223 peptides, 22 chains. Longest chain 22 peptides. Score 0.610 Round 2: 249 peptides, 17 chains. Longest chain 35 peptides. Score 0.715 Round 3: 251 peptides, 24 chains. Longest chain 24 peptides. Score 0.651 Round 4: 244 peptides, 23 chains. Longest chain 20 peptides. Score 0.646 Round 5: 241 peptides, 21 chains. Longest chain 29 peptides. Score 0.661 Taking the results from Round 2 Chains 19, Residues 232, Estimated correctness of the model 68.3 % 4 chains (102 residues) have been docked in sequence Building loops using Loopy2018 19 chains (232 residues) following loop building 4 chains (102 residues) in sequence following loop building ------------------------------------------------------ 9001 reflections ( 99.68 % complete ) and 3629 restraints for refining 2312 atoms. 2271 conditional restraints added. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2889 (Rfree = 0.000) for 2312 atoms. Found 20 (20 requested) and removed 27 (10 requested) atoms. Cycle 7: After refmac, R = 0.2711 (Rfree = 0.000) for 2288 atoms. Found 14 (20 requested) and removed 15 (10 requested) atoms. Cycle 8: After refmac, R = 0.2596 (Rfree = 0.000) for 2273 atoms. Found 8 (19 requested) and removed 10 (10 requested) atoms. Cycle 9: After refmac, R = 0.2499 (Rfree = 0.000) for 2259 atoms. Found 5 (19 requested) and removed 10 (10 requested) atoms. Cycle 10: After refmac, R = 0.2469 (Rfree = 0.000) for 2242 atoms. Found 12 (18 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.30 2.61 Search for helices and strands: 0 residues in 0 chains, 2308 seeds are put forward Round 1: 239 peptides, 21 chains. Longest chain 27 peptides. Score 0.656 Round 2: 235 peptides, 18 chains. Longest chain 33 peptides. Score 0.679 Round 3: 255 peptides, 21 chains. Longest chain 27 peptides. Score 0.689 Round 4: 255 peptides, 22 chains. Longest chain 32 peptides. Score 0.679 Round 5: 254 peptides, 19 chains. Longest chain 28 peptides. Score 0.706 Taking the results from Round 5 Chains 22, Residues 235, Estimated correctness of the model 66.4 % 3 chains (45 residues) have been docked in sequence Building loops using Loopy2018 22 chains (235 residues) following loop building 3 chains (45 residues) in sequence following loop building ------------------------------------------------------ 9001 reflections ( 99.68 % complete ) and 4213 restraints for refining 2278 atoms. 3091 conditional restraints added. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2790 (Rfree = 0.000) for 2278 atoms. Found 18 (18 requested) and removed 23 (10 requested) atoms. Cycle 12: After refmac, R = 0.2655 (Rfree = 0.000) for 2268 atoms. Found 11 (18 requested) and removed 14 (10 requested) atoms. Cycle 13: After refmac, R = 0.2528 (Rfree = 0.000) for 2256 atoms. Found 9 (17 requested) and removed 17 (10 requested) atoms. Cycle 14: After refmac, R = 0.2463 (Rfree = 0.000) for 2239 atoms. Found 8 (17 requested) and removed 14 (10 requested) atoms. Cycle 15: After refmac, R = 0.2386 (Rfree = 0.000) for 2226 atoms. Found 8 (16 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.27 2.58 Search for helices and strands: 0 residues in 0 chains, 2310 seeds are put forward Round 1: 231 peptides, 28 chains. Longest chain 19 peptides. Score 0.561 Round 2: 214 peptides, 18 chains. Longest chain 28 peptides. Score 0.634 Round 3: 231 peptides, 21 chains. Longest chain 27 peptides. Score 0.639 Round 4: 245 peptides, 21 chains. Longest chain 25 peptides. Score 0.669 Round 5: 230 peptides, 21 chains. Longest chain 21 peptides. Score 0.637 Taking the results from Round 4 Chains 25, Residues 224, Estimated correctness of the model 58.3 % 4 chains (59 residues) have been docked in sequence ------------------------------------------------------ 9001 reflections ( 99.68 % complete ) and 4094 restraints for refining 2278 atoms. 2981 conditional restraints added. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2828 (Rfree = 0.000) for 2278 atoms. Found 16 (16 requested) and removed 16 (10 requested) atoms. Cycle 17: After refmac, R = 0.2566 (Rfree = 0.000) for 2264 atoms. Found 16 (16 requested) and removed 16 (10 requested) atoms. Cycle 18: After refmac, R = 0.2565 (Rfree = 0.000) for 2253 atoms. Found 16 (16 requested) and removed 15 (10 requested) atoms. Cycle 19: After refmac, R = 0.2676 (Rfree = 0.000) for 2247 atoms. Found 16 (16 requested) and removed 18 (10 requested) atoms. Cycle 20: After refmac, R = 0.2554 (Rfree = 0.000) for 2238 atoms. Found 16 (16 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.25 2.57 Search for helices and strands: 0 residues in 0 chains, 2305 seeds are put forward Round 1: 209 peptides, 24 chains. Longest chain 22 peptides. Score 0.551 Round 2: 239 peptides, 24 chains. Longest chain 22 peptides. Score 0.625 Round 3: 244 peptides, 23 chains. Longest chain 35 peptides. Score 0.646 Round 4: 250 peptides, 22 chains. Longest chain 30 peptides. Score 0.669 Round 5: 238 peptides, 21 chains. Longest chain 39 peptides. Score 0.654 Taking the results from Round 4 Chains 23, Residues 228, Estimated correctness of the model 58.3 % 3 chains (49 residues) have been docked in sequence ------------------------------------------------------ 9001 reflections ( 99.68 % complete ) and 4164 restraints for refining 2278 atoms. 3063 conditional restraints added. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2756 (Rfree = 0.000) for 2278 atoms. Found 16 (16 requested) and removed 18 (10 requested) atoms. Cycle 22: After refmac, R = 0.2560 (Rfree = 0.000) for 2260 atoms. Found 10 (16 requested) and removed 15 (10 requested) atoms. Cycle 23: After refmac, R = 0.2438 (Rfree = 0.000) for 2244 atoms. Found 7 (16 requested) and removed 16 (10 requested) atoms. Cycle 24: After refmac, R = 0.2390 (Rfree = 0.000) for 2228 atoms. Found 6 (16 requested) and removed 14 (10 requested) atoms. Cycle 25: After refmac, R = 0.2365 (Rfree = 0.000) for 2214 atoms. Found 8 (15 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.24 2.56 Search for helices and strands: 0 residues in 0 chains, 2275 seeds are put forward Round 1: 239 peptides, 26 chains. Longest chain 20 peptides. Score 0.603 Round 2: 245 peptides, 19 chains. Longest chain 25 peptides. Score 0.689 Round 3: 249 peptides, 21 chains. Longest chain 35 peptides. Score 0.677 Round 4: 247 peptides, 21 chains. Longest chain 31 peptides. Score 0.673 Round 5: 263 peptides, 18 chains. Longest chain 33 peptides. Score 0.731 Taking the results from Round 5 Chains 22, Residues 245, Estimated correctness of the model 71.5 % 4 chains (80 residues) have been docked in sequence Building loops using Loopy2018 22 chains (245 residues) following loop building 4 chains (80 residues) in sequence following loop building ------------------------------------------------------ 9001 reflections ( 99.68 % complete ) and 3715 restraints for refining 2278 atoms. 2408 conditional restraints added. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2704 (Rfree = 0.000) for 2278 atoms. Found 16 (16 requested) and removed 13 (10 requested) atoms. Cycle 27: After refmac, R = 0.2532 (Rfree = 0.000) for 2269 atoms. Found 14 (16 requested) and removed 15 (10 requested) atoms. Cycle 28: After refmac, R = 0.2398 (Rfree = 0.000) for 2257 atoms. Found 12 (15 requested) and removed 11 (10 requested) atoms. Cycle 29: After refmac, R = 0.2317 (Rfree = 0.000) for 2250 atoms. Found 10 (15 requested) and removed 16 (10 requested) atoms. Cycle 30: After refmac, R = 0.2252 (Rfree = 0.000) for 2242 atoms. Found 10 (14 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.24 2.56 Search for helices and strands: 0 residues in 0 chains, 2309 seeds are put forward Round 1: 239 peptides, 27 chains. Longest chain 26 peptides. Score 0.592 Round 2: 250 peptides, 22 chains. Longest chain 29 peptides. Score 0.669 Round 3: 257 peptides, 19 chains. Longest chain 37 peptides. Score 0.712 Round 4: 244 peptides, 24 chains. Longest chain 29 peptides. Score 0.636 Round 5: 251 peptides, 24 chains. Longest chain 25 peptides. Score 0.651 Taking the results from Round 3 Chains 23, Residues 238, Estimated correctness of the model 67.7 % 4 chains (93 residues) have been docked in sequence Building loops using Loopy2018 23 chains (238 residues) following loop building 4 chains (93 residues) in sequence following loop building ------------------------------------------------------ 9001 reflections ( 99.68 % complete ) and 3586 restraints for refining 2287 atoms. 2239 conditional restraints added. Observations/parameters ratio is 0.98 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2867 (Rfree = 0.000) for 2287 atoms. Found 14 (14 requested) and removed 19 (10 requested) atoms. Cycle 32: After refmac, R = 0.2553 (Rfree = 0.000) for 2270 atoms. Found 14 (14 requested) and removed 19 (10 requested) atoms. Cycle 33: After refmac, R = 0.2620 (Rfree = 0.000) for 2253 atoms. Found 13 (13 requested) and removed 17 (10 requested) atoms. Cycle 34: After refmac, R = 0.2520 (Rfree = 0.000) for 2243 atoms. Found 13 (13 requested) and removed 14 (10 requested) atoms. Cycle 35: After refmac, R = 0.2487 (Rfree = 0.000) for 2239 atoms. Found 11 (12 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.20 2.53 Search for helices and strands: 0 residues in 0 chains, 2279 seeds are put forward Round 1: 237 peptides, 26 chains. Longest chain 22 peptides. Score 0.598 Round 2: 254 peptides, 22 chains. Longest chain 33 peptides. Score 0.677 Round 3: 263 peptides, 21 chains. Longest chain 38 peptides. Score 0.704 Round 4: 261 peptides, 21 chains. Longest chain 43 peptides. Score 0.701 Round 5: 260 peptides, 18 chains. Longest chain 39 peptides. Score 0.726 Taking the results from Round 5 Chains 22, Residues 242, Estimated correctness of the model 70.5 % 5 chains (95 residues) have been docked in sequence Building loops using Loopy2018 22 chains (242 residues) following loop building 5 chains (95 residues) in sequence following loop building ------------------------------------------------------ 9001 reflections ( 99.68 % complete ) and 3700 restraints for refining 2278 atoms. 2379 conditional restraints added. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2704 (Rfree = 0.000) for 2278 atoms. Found 12 (12 requested) and removed 23 (10 requested) atoms. Cycle 37: After refmac, R = 0.2469 (Rfree = 0.000) for 2259 atoms. Found 12 (12 requested) and removed 14 (10 requested) atoms. Cycle 38: After refmac, R = 0.2531 (Rfree = 0.000) for 2253 atoms. Found 11 (11 requested) and removed 19 (10 requested) atoms. Cycle 39: After refmac, R = 0.2578 (Rfree = 0.000) for 2238 atoms. Found 11 (11 requested) and removed 12 (10 requested) atoms. Cycle 40: After refmac, R = 0.2550 (Rfree = 0.000) for 2235 atoms. Found 10 (10 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.24 2.56 Search for helices and strands: 0 residues in 0 chains, 2305 seeds are put forward Round 1: 231 peptides, 22 chains. Longest chain 24 peptides. Score 0.628 Round 2: 249 peptides, 20 chains. Longest chain 26 peptides. Score 0.687 Round 3: 251 peptides, 21 chains. Longest chain 34 peptides. Score 0.681 Round 4: 259 peptides, 20 chains. Longest chain 40 peptides. Score 0.706 Round 5: 237 peptides, 20 chains. Longest chain 44 peptides. Score 0.662 Taking the results from Round 4 Chains 21, Residues 239, Estimated correctness of the model 66.4 % 3 chains (64 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 275 A and 286 A 19 chains (240 residues) following loop building 2 chains (74 residues) in sequence following loop building ------------------------------------------------------ 9001 reflections ( 99.68 % complete ) and 3762 restraints for refining 2278 atoms. 2514 conditional restraints added. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2756 (Rfree = 0.000) for 2278 atoms. Found 10 (10 requested) and removed 21 (10 requested) atoms. Cycle 42: After refmac, R = 0.2580 (Rfree = 0.000) for 2260 atoms. Found 10 (10 requested) and removed 14 (10 requested) atoms. Cycle 43: After refmac, R = 0.2523 (Rfree = 0.000) for 2254 atoms. Found 10 (10 requested) and removed 10 (10 requested) atoms. Cycle 44: After refmac, R = 0.2442 (Rfree = 0.000) for 2252 atoms. Found 8 (10 requested) and removed 10 (10 requested) atoms. Cycle 45: After refmac, R = 0.2388 (Rfree = 0.000) for 2248 atoms. Found 7 (10 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.25 2.57 Search for helices and strands: 0 residues in 0 chains, 2294 seeds are put forward Round 1: 229 peptides, 22 chains. Longest chain 23 peptides. Score 0.624 Round 2: 239 peptides, 18 chains. Longest chain 32 peptides. Score 0.687 Round 3: 245 peptides, 22 chains. Longest chain 30 peptides. Score 0.659 Round 4: 241 peptides, 23 chains. Longest chain 36 peptides. Score 0.640 Round 5: 242 peptides, 22 chains. Longest chain 27 peptides. Score 0.653 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 221, Estimated correctness of the model 62.3 % 2 chains (43 residues) have been docked in sequence Sequence coverage is 19 % Consider running further cycles of model building using 2hag-3_warpNtrace.pdb as input Building loops using Loopy2018 19 chains (221 residues) following loop building 2 chains (43 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9001 reflections ( 99.68 % complete ) and 4229 restraints for refining 2277 atoms. 3162 conditional restraints added. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2627 (Rfree = 0.000) for 2277 atoms. Found 0 (10 requested) and removed 8 (10 requested) atoms. Cycle 47: After refmac, R = 0.2449 (Rfree = 0.000) for 2263 atoms. Found 0 (10 requested) and removed 6 (10 requested) atoms. Cycle 48: After refmac, R = 0.2313 (Rfree = 0.000) for 2254 atoms. Found 0 (10 requested) and removed 4 (10 requested) atoms. Cycle 49: After refmac, R = 0.2281 (Rfree = 0.000) for 2249 atoms. TimeTaking 52.5