null 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 2p4o-1.9-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p4o-1.9-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p4o-1.9-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4o-1.9-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/2p4o-1.9-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4o-1.9-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/2p4o-1.9-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4o-1.9-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 269 and 0 Target number of residues in the AU: 269 Target solvent content: 0.5361 Checking the provided sequence file Detected sequence length: 306 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 306 Adjusted target solvent content: 0.47 Input MTZ file: 2p4o-1.9-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: 94 Cell parameters: 91.400 91.400 75.131 90.000 90.000 90.000 Input sequence file: 2p4o-1.9-parrot-hancs.fasta_lf Building free atoms model in initial map for 2448 target number of atoms Had to go as low as 0.45 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 Loops will be built when appropriate and at the last cycle Resolution range: 29.686 1.900 Wilson plot Bfac: 31.59 25670 reflections ( 99.96 % complete ) and 0 restraints for refining 2714 atoms. Observations/parameters ratio is 2.36 ------------------------------------------------------ Starting model: R = 0.3580 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3202 (Rfree = 0.000) for 2714 atoms. Found 65 (107 requested) and removed 63 (53 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.20 2.29 Round 1: 214 peptides, 29 chains. Longest chain 20 peptides. Score 0.634 Round 2: 234 peptides, 19 chains. Longest chain 35 peptides. Score 0.809 Round 3: 251 peptides, 12 chains. Longest chain 64 peptides. Score 0.890 Round 4: 267 peptides, 12 chains. Longest chain 59 peptides. Score 0.907 Round 5: 269 peptides, 10 chains. Longest chain 83 peptides. Score 0.920 Taking the results from Round 5 Chains 11, Residues 259, Estimated correctness of the model 99.4 % 8 chains (249 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 58 A and 69 A Built loop between residues 79 A and 84 A Built loop between residues 97 A and 104 A Built loop between residues 146 A and 150 A Built loop between residues 172 A and 174 A 4 chains (277 residues) following loop building 3 chains (273 residues) in sequence following loop building ------------------------------------------------------ 25670 reflections ( 99.96 % complete ) and 2661 restraints for refining 2485 atoms. 526 conditional restraints added. Observations/parameters ratio is 2.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3294 (Rfree = 0.000) for 2485 atoms. Found 85 (98 requested) and removed 56 (49 requested) atoms. Cycle 2: After refmac, R = 0.2994 (Rfree = 0.000) for 2501 atoms. Found 69 (97 requested) and removed 49 (49 requested) atoms. Cycle 3: After refmac, R = 0.2860 (Rfree = 0.000) for 2514 atoms. Found 58 (95 requested) and removed 45 (49 requested) atoms. Cycle 4: After refmac, R = 0.2769 (Rfree = 0.000) for 2521 atoms. Found 49 (94 requested) and removed 33 (50 requested) atoms. Cycle 5: After refmac, R = 0.2699 (Rfree = 0.000) for 2535 atoms. Found 50 (92 requested) and removed 22 (50 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.16 2.25 Round 1: 277 peptides, 10 chains. Longest chain 44 peptides. Score 0.926 Round 2: 281 peptides, 9 chains. Longest chain 90 peptides. Score 0.934 Round 3: 280 peptides, 9 chains. Longest chain 65 peptides. Score 0.933 Round 4: 280 peptides, 9 chains. Longest chain 65 peptides. Score 0.933 Round 5: 281 peptides, 9 chains. Longest chain 94 peptides. Score 0.934 Taking the results from Round 5 Chains 10, Residues 272, Estimated correctness of the model 99.6 % 8 chains (267 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 17 A and 20 A Built loop between residues 36 A and 44 A Built loop between residues 80 A and 83 A Built loop between residues 146 A and 149 A Built loop between residues 161 A and 171 A Built loop between residues 263 A and 266 A Built loop between residues 284 A and 292 A 1 chains (298 residues) following loop building 1 chains (298 residues) in sequence following loop building ------------------------------------------------------ 25670 reflections ( 99.96 % complete ) and 2452 restraints for refining 2564 atoms. 160 conditional restraints added. Observations/parameters ratio is 2.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2845 (Rfree = 0.000) for 2564 atoms. Found 93 (93 requested) and removed 54 (50 requested) atoms. Cycle 7: After refmac, R = 0.2672 (Rfree = 0.000) for 2599 atoms. Found 59 (93 requested) and removed 51 (51 requested) atoms. Cycle 8: After refmac, R = 0.2582 (Rfree = 0.000) for 2602 atoms. Found 51 (91 requested) and removed 33 (51 requested) atoms. Cycle 9: After refmac, R = 0.2528 (Rfree = 0.000) for 2615 atoms. Found 45 (89 requested) and removed 24 (51 requested) atoms. Cycle 10: After refmac, R = 0.2475 (Rfree = 0.000) for 2633 atoms. Found 52 (87 requested) and removed 25 (52 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.18 2.27 Round 1: 282 peptides, 10 chains. Longest chain 80 peptides. Score 0.930 Round 2: 288 peptides, 6 chains. Longest chain 115 peptides. Score 0.951 Round 3: 290 peptides, 7 chains. Longest chain 91 peptides. Score 0.948 Round 4: 291 peptides, 4 chains. Longest chain 155 peptides. Score 0.961 Round 5: 288 peptides, 8 chains. Longest chain 90 peptides. Score 0.943 Taking the results from Round 4 Chains 4, Residues 287, Estimated correctness of the model 99.8 % 4 chains (287 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 39 A and 44 A Built loop between residues 90 A and 93 A Built loop between residues 146 A and 151 A 1 chains (297 residues) following loop building 1 chains (297 residues) in sequence following loop building ------------------------------------------------------ 25670 reflections ( 99.96 % complete ) and 2435 restraints for refining 2583 atoms. 147 conditional restraints added. Observations/parameters ratio is 2.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2616 (Rfree = 0.000) for 2583 atoms. Found 86 (86 requested) and removed 55 (51 requested) atoms. Cycle 12: After refmac, R = 0.2476 (Rfree = 0.000) for 2611 atoms. Found 57 (84 requested) and removed 30 (51 requested) atoms. Cycle 13: After refmac, R = 0.2431 (Rfree = 0.000) for 2634 atoms. Found 52 (83 requested) and removed 24 (52 requested) atoms. Cycle 14: After refmac, R = 0.2431 (Rfree = 0.000) for 2661 atoms. Found 43 (84 requested) and removed 25 (52 requested) atoms. Cycle 15: After refmac, R = 0.2392 (Rfree = 0.000) for 2678 atoms. Found 46 (83 requested) and removed 20 (53 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.18 2.27 Round 1: 284 peptides, 12 chains. Longest chain 65 peptides. Score 0.921 Round 2: 291 peptides, 6 chains. Longest chain 84 peptides. Score 0.953 Round 3: 290 peptides, 8 chains. Longest chain 92 peptides. Score 0.944 Round 4: 287 peptides, 9 chains. Longest chain 86 peptides. Score 0.938 Round 5: 290 peptides, 7 chains. Longest chain 91 peptides. Score 0.948 Taking the results from Round 2 Chains 6, Residues 285, Estimated correctness of the model 99.8 % 6 chains (285 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 41 A and 44 A Built loop between residues 80 A and 84 A Built loop between residues 103 A and 107 A Built loop between residues 146 A and 149 A Built loop between residues 231 A and 234 A 1 chains (297 residues) following loop building 1 chains (297 residues) in sequence following loop building ------------------------------------------------------ 25670 reflections ( 99.96 % complete ) and 2479 restraints for refining 2627 atoms. 191 conditional restraints added. Observations/parameters ratio is 2.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2605 (Rfree = 0.000) for 2627 atoms. Found 81 (81 requested) and removed 56 (52 requested) atoms. Cycle 17: After refmac, R = 0.2487 (Rfree = 0.000) for 2651 atoms. Found 49 (80 requested) and removed 35 (52 requested) atoms. Cycle 18: After refmac, R = 0.2444 (Rfree = 0.000) for 2665 atoms. Found 47 (78 requested) and removed 21 (52 requested) atoms. Cycle 19: After refmac, R = 0.2420 (Rfree = 0.000) for 2690 atoms. Found 44 (78 requested) and removed 27 (53 requested) atoms. Cycle 20: After refmac, R = 0.2398 (Rfree = 0.000) for 2703 atoms. Found 45 (77 requested) and removed 29 (53 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.17 2.26 Round 1: 286 peptides, 8 chains. Longest chain 133 peptides. Score 0.942 Round 2: 291 peptides, 5 chains. Longest chain 110 peptides. Score 0.957 Round 3: 292 peptides, 5 chains. Longest chain 131 peptides. Score 0.957 Round 4: 294 peptides, 5 chains. Longest chain 136 peptides. Score 0.958 Round 5: 294 peptides, 3 chains. Longest chain 197 peptides. Score 0.966 Taking the results from Round 5 Chains 4, Residues 291, Estimated correctness of the model 99.9 % 3 chains (290 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 40 A and 44 A Built loop between residues 107 A and 110 A 1 chains (295 residues) following loop building 1 chains (295 residues) in sequence following loop building ------------------------------------------------------ 25670 reflections ( 99.96 % complete ) and 2508 restraints for refining 2624 atoms. 236 conditional restraints added. Observations/parameters ratio is 2.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2625 (Rfree = 0.000) for 2624 atoms. Found 73 (73 requested) and removed 57 (52 requested) atoms. Cycle 22: After refmac, R = 0.2485 (Rfree = 0.000) for 2638 atoms. Found 64 (71 requested) and removed 26 (52 requested) atoms. Cycle 23: After refmac, R = 0.2401 (Rfree = 0.000) for 2672 atoms. Found 57 (72 requested) and removed 34 (53 requested) atoms. Cycle 24: After refmac, R = 0.2397 (Rfree = 0.000) for 2694 atoms. Found 51 (70 requested) and removed 40 (53 requested) atoms. Cycle 25: After refmac, R = 0.2397 (Rfree = 0.000) for 2701 atoms. Found 52 (68 requested) and removed 38 (53 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.16 2.25 Round 1: 290 peptides, 8 chains. Longest chain 98 peptides. Score 0.944 Round 2: 292 peptides, 7 chains. Longest chain 91 peptides. Score 0.949 Round 3: 296 peptides, 2 chains. Longest chain 248 peptides. Score 0.970 Round 4: 289 peptides, 8 chains. Longest chain 75 peptides. Score 0.943 Round 5: 296 peptides, 5 chains. Longest chain 89 peptides. Score 0.959 Taking the results from Round 3 Chains 2, Residues 294, Estimated correctness of the model 99.9 % 2 chains (294 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 55 A and 58 A 1 chains (296 residues) following loop building 1 chains (296 residues) in sequence following loop building ------------------------------------------------------ 25670 reflections ( 99.96 % complete ) and 2484 restraints for refining 2623 atoms. 204 conditional restraints added. Observations/parameters ratio is 2.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2532 (Rfree = 0.000) for 2623 atoms. Found 64 (64 requested) and removed 51 (52 requested) atoms. Cycle 27: After refmac, R = 0.2456 (Rfree = 0.000) for 2632 atoms. Found 62 (62 requested) and removed 24 (52 requested) atoms. Cycle 28: After refmac, R = 0.2404 (Rfree = 0.000) for 2665 atoms. Found 52 (63 requested) and removed 28 (52 requested) atoms. Cycle 29: After refmac, R = 0.2402 (Rfree = 0.000) for 2688 atoms. Found 59 (61 requested) and removed 41 (53 requested) atoms. Cycle 30: After refmac, R = 0.2393 (Rfree = 0.000) for 2703 atoms. Found 53 (60 requested) and removed 43 (53 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.17 2.26 Round 1: 291 peptides, 8 chains. Longest chain 134 peptides. Score 0.944 Round 2: 292 peptides, 6 chains. Longest chain 121 peptides. Score 0.953 Round 3: 293 peptides, 5 chains. Longest chain 135 peptides. Score 0.958 Round 4: 295 peptides, 3 chains. Longest chain 156 peptides. Score 0.966 Round 5: 294 peptides, 6 chains. Longest chain 135 peptides. Score 0.954 Taking the results from Round 4 Chains 3, Residues 292, Estimated correctness of the model 99.9 % 3 chains (292 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 163 A and 166 A Built loop between residues 239 A and 242 A 1 chains (296 residues) following loop building 1 chains (296 residues) in sequence following loop building ------------------------------------------------------ 25670 reflections ( 99.96 % complete ) and 2480 restraints for refining 2606 atoms. 200 conditional restraints added. Observations/parameters ratio is 2.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2534 (Rfree = 0.000) for 2606 atoms. Found 56 (56 requested) and removed 53 (51 requested) atoms. Cycle 32: After refmac, R = 0.2441 (Rfree = 0.000) for 2609 atoms. Found 54 (54 requested) and removed 21 (51 requested) atoms. Cycle 33: After refmac, R = 0.2382 (Rfree = 0.000) for 2640 atoms. Found 51 (54 requested) and removed 26 (52 requested) atoms. Cycle 34: After refmac, R = 0.2347 (Rfree = 0.000) for 2662 atoms. Found 51 (52 requested) and removed 30 (52 requested) atoms. Cycle 35: After refmac, R = 0.2351 (Rfree = 0.000) for 2682 atoms. Found 53 (53 requested) and removed 25 (53 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.16 2.25 Round 1: 290 peptides, 9 chains. Longest chain 134 peptides. Score 0.939 Round 2: 294 peptides, 3 chains. Longest chain 156 peptides. Score 0.966 Round 3: 286 peptides, 7 chains. Longest chain 115 peptides. Score 0.946 Round 4: 294 peptides, 4 chains. Longest chain 92 peptides. Score 0.962 Round 5: 292 peptides, 6 chains. Longest chain 103 peptides. Score 0.953 Taking the results from Round 2 Chains 3, Residues 291, Estimated correctness of the model 99.9 % 3 chains (291 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 58 A and 61 A Built loop between residues 146 A and 149 A 1 chains (295 residues) following loop building 1 chains (295 residues) in sequence following loop building ------------------------------------------------------ 25670 reflections ( 99.96 % complete ) and 2519 restraints for refining 2614 atoms. 247 conditional restraints added. Observations/parameters ratio is 2.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2519 (Rfree = 0.000) for 2614 atoms. Found 51 (51 requested) and removed 53 (51 requested) atoms. Cycle 37: After refmac, R = 0.2422 (Rfree = 0.000) for 2609 atoms. Found 51 (51 requested) and removed 19 (51 requested) atoms. Cycle 38: After refmac, R = 0.2380 (Rfree = 0.000) for 2640 atoms. Found 52 (52 requested) and removed 24 (52 requested) atoms. Cycle 39: After refmac, R = 0.2377 (Rfree = 0.000) for 2668 atoms. Found 52 (52 requested) and removed 35 (52 requested) atoms. Cycle 40: After refmac, R = 0.2350 (Rfree = 0.000) for 2683 atoms. Found 53 (53 requested) and removed 34 (53 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.16 2.25 Round 1: 289 peptides, 8 chains. Longest chain 134 peptides. Score 0.943 Round 2: 293 peptides, 5 chains. Longest chain 148 peptides. Score 0.958 Round 3: 291 peptides, 7 chains. Longest chain 88 peptides. Score 0.949 Round 4: 295 peptides, 3 chains. Longest chain 225 peptides. Score 0.966 Round 5: 290 peptides, 8 chains. Longest chain 120 peptides. Score 0.944 Taking the results from Round 4 Chains 4, Residues 292, Estimated correctness of the model 99.9 % 3 chains (291 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 58 A and 61 A Built loop between residues 284 A and 288 A 1 chains (296 residues) following loop building 1 chains (296 residues) in sequence following loop building ------------------------------------------------------ 25670 reflections ( 99.96 % complete ) and 2498 restraints for refining 2621 atoms. 218 conditional restraints added. Observations/parameters ratio is 2.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2514 (Rfree = 0.000) for 2621 atoms. Found 51 (51 requested) and removed 52 (51 requested) atoms. Cycle 42: After refmac, R = 0.2397 (Rfree = 0.000) for 2618 atoms. Found 51 (51 requested) and removed 17 (51 requested) atoms. Cycle 43: After refmac, R = 0.2345 (Rfree = 0.000) for 2650 atoms. Found 52 (52 requested) and removed 25 (52 requested) atoms. Cycle 44: After refmac, R = 0.2317 (Rfree = 0.000) for 2676 atoms. Found 53 (53 requested) and removed 25 (53 requested) atoms. Cycle 45: After refmac, R = 0.2294 (Rfree = 0.000) for 2701 atoms. Found 47 (53 requested) and removed 28 (53 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.16 2.25 Round 1: 282 peptides, 10 chains. Longest chain 133 peptides. Score 0.930 Round 2: 292 peptides, 5 chains. Longest chain 225 peptides. Score 0.957 Round 3: 290 peptides, 7 chains. Longest chain 135 peptides. Score 0.948 Round 4: 289 peptides, 6 chains. Longest chain 120 peptides. Score 0.952 Round 5: 291 peptides, 6 chains. Longest chain 134 peptides. Score 0.953 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 287, Estimated correctness of the model 99.8 % 4 chains (276 residues) have been docked in sequence Sequence coverage is 95 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 56 A and 61 A Built loop between residues 284 A and 287 A 3 chains (291 residues) following loop building 2 chains (282 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 25670 reflections ( 99.96 % complete ) and 2210 restraints for refining 2162 atoms. Observations/parameters ratio is 2.97 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2915 (Rfree = 0.000) for 2162 atoms. Found 33 (42 requested) and removed 0 (42 requested) atoms. Cycle 47: After refmac, R = 0.2741 (Rfree = 0.000) for 2162 atoms. Found 8 (43 requested) and removed 0 (43 requested) atoms. Cycle 48: After refmac, R = 0.2634 (Rfree = 0.000) for 2162 atoms. Found 6 (43 requested) and removed 1 (43 requested) atoms. Cycle 49: After refmac, R = 0.2574 (Rfree = 0.000) for 2162 atoms. Found 4 (43 requested) and removed 3 (43 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:21:36 GMT 2018 Job finished. TimeTaking 58.52 Used memory is bytes: 13592768