null Sun 23 Dec 22:22:46 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 2hx1-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hx1-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hx1-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hx1-3.4-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/2hx1-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hx1-3.4-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 22:22:56 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/2hx1-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hx1-3.4-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 868 and 0 Target number of residues in the AU: 868 Target solvent content: 0.6039 Checking the provided sequence file Detected sequence length: 284 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1136 Adjusted target solvent content: 0.48 Input MTZ file: 2hx1-3.4-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: 19 Cell parameters: 65.624 119.462 151.274 90.000 90.000 90.000 Input sequence file: 2hx1-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 9088 target number of atoms Had to go as low as 0.75 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 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: 93.753 3.400 Wilson plot Bfac: 54.11 16942 reflections ( 99.75 % complete ) and 0 restraints for refining 10074 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3172 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2913 (Rfree = 0.000) for 10074 atoms. Found 76 (76 requested) and removed 85 (38 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.14 3.22 Search for helices and strands: 0 residues in 0 chains, 10268 seeds are put forward NCS extension: 0 residues added, 10268 seeds are put forward Round 1: 560 peptides, 107 chains. Longest chain 13 peptides. Score 0.363 Round 2: 690 peptides, 104 chains. Longest chain 23 peptides. Score 0.539 Round 3: 747 peptides, 101 chains. Longest chain 19 peptides. Score 0.612 Round 4: 730 peptides, 92 chains. Longest chain 26 peptides. Score 0.633 Round 5: 767 peptides, 97 chains. Longest chain 23 peptides. Score 0.646 Taking the results from Round 5 Chains 104, Residues 670, Estimated correctness of the model 43.0 % 8 chains (74 residues) have been docked in sequence ------------------------------------------------------ 16942 reflections ( 99.75 % complete ) and 17164 restraints for refining 8261 atoms. 14329 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2670 (Rfree = 0.000) for 8261 atoms. Found 53 (62 requested) and removed 67 (31 requested) atoms. Cycle 2: After refmac, R = 0.2503 (Rfree = 0.000) for 8130 atoms. Found 47 (62 requested) and removed 47 (31 requested) atoms. Cycle 3: After refmac, R = 0.2430 (Rfree = 0.000) for 8078 atoms. Found 37 (61 requested) and removed 42 (30 requested) atoms. Cycle 4: After refmac, R = 0.2351 (Rfree = 0.000) for 8048 atoms. Found 22 (60 requested) and removed 35 (30 requested) atoms. Cycle 5: After refmac, R = 0.2316 (Rfree = 0.000) for 8020 atoms. Found 29 (60 requested) and removed 37 (30 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 3.29 Search for helices and strands: 0 residues in 0 chains, 8272 seeds are put forward NCS extension: 7 residues added (10 deleted due to clashes), 8279 seeds are put forward Round 1: 705 peptides, 98 chains. Longest chain 25 peptides. Score 0.583 Round 2: 759 peptides, 88 chains. Longest chain 36 peptides. Score 0.675 Round 3: 796 peptides, 85 chains. Longest chain 38 peptides. Score 0.715 Round 4: 763 peptides, 89 chains. Longest chain 28 peptides. Score 0.674 Round 5: 801 peptides, 85 chains. Longest chain 30 peptides. Score 0.718 Taking the results from Round 5 Chains 87, Residues 716, Estimated correctness of the model 62.4 % 5 chains (71 residues) have been docked in sequence Building loops using Loopy2018 87 chains (716 residues) following loop building 5 chains (71 residues) in sequence following loop building ------------------------------------------------------ 16942 reflections ( 99.75 % complete ) and 17225 restraints for refining 8262 atoms. 14191 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2718 (Rfree = 0.000) for 8262 atoms. Found 62 (62 requested) and removed 53 (31 requested) atoms. Cycle 7: After refmac, R = 0.2564 (Rfree = 0.000) for 8218 atoms. Found 50 (61 requested) and removed 45 (31 requested) atoms. Cycle 8: After refmac, R = 0.2427 (Rfree = 0.000) for 8184 atoms. Found 43 (60 requested) and removed 40 (31 requested) atoms. Cycle 9: After refmac, R = 0.2375 (Rfree = 0.000) for 8158 atoms. Found 48 (57 requested) and removed 38 (30 requested) atoms. Cycle 10: After refmac, R = 0.2200 (Rfree = 0.000) for 8148 atoms. Found 20 (56 requested) and removed 35 (30 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 3.29 Search for helices and strands: 0 residues in 0 chains, 8372 seeds are put forward NCS extension: 16 residues added (18 deleted due to clashes), 8388 seeds are put forward Round 1: 739 peptides, 105 chains. Longest chain 21 peptides. Score 0.586 Round 2: 794 peptides, 92 chains. Longest chain 32 peptides. Score 0.688 Round 3: 813 peptides, 89 chains. Longest chain 24 peptides. Score 0.714 Round 4: 825 peptides, 90 chains. Longest chain 44 peptides. Score 0.719 Round 5: 837 peptides, 91 chains. Longest chain 27 peptides. Score 0.724 Taking the results from Round 5 Chains 92, Residues 746, Estimated correctness of the model 63.8 % 3 chains (48 residues) have been docked in sequence Building loops using Loopy2018 92 chains (746 residues) following loop building 3 chains (48 residues) in sequence following loop building ------------------------------------------------------ 16942 reflections ( 99.75 % complete ) and 17439 restraints for refining 8262 atoms. 14372 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2622 (Rfree = 0.000) for 8262 atoms. Found 56 (56 requested) and removed 49 (31 requested) atoms. Cycle 12: After refmac, R = 0.2474 (Rfree = 0.000) for 8219 atoms. Found 32 (55 requested) and removed 46 (31 requested) atoms. Cycle 13: After refmac, R = 0.2414 (Rfree = 0.000) for 8170 atoms. Found 39 (52 requested) and removed 36 (30 requested) atoms. Cycle 14: After refmac, R = 0.2364 (Rfree = 0.000) for 8159 atoms. Found 44 (51 requested) and removed 38 (30 requested) atoms. Cycle 15: After refmac, R = 0.2343 (Rfree = 0.000) for 8145 atoms. Found 43 (50 requested) and removed 36 (30 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 8387 seeds are put forward NCS extension: 7 residues added (9 deleted due to clashes), 8394 seeds are put forward Round 1: 703 peptides, 92 chains. Longest chain 28 peptides. Score 0.608 Round 2: 787 peptides, 86 chains. Longest chain 24 peptides. Score 0.704 Round 3: 769 peptides, 86 chains. Longest chain 26 peptides. Score 0.690 Round 4: 765 peptides, 84 chains. Longest chain 38 peptides. Score 0.694 Round 5: 732 peptides, 80 chains. Longest chain 19 peptides. Score 0.683 Taking the results from Round 2 Chains 89, Residues 701, Estimated correctness of the model 58.9 % 7 chains (103 residues) have been docked in sequence Building loops using Loopy2018 89 chains (701 residues) following loop building 7 chains (103 residues) in sequence following loop building ------------------------------------------------------ 16942 reflections ( 99.75 % complete ) and 17061 restraints for refining 8263 atoms. 13982 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2528 (Rfree = 0.000) for 8263 atoms. Found 47 (50 requested) and removed 62 (31 requested) atoms. Cycle 17: After refmac, R = 0.2419 (Rfree = 0.000) for 8221 atoms. Found 30 (48 requested) and removed 39 (31 requested) atoms. Cycle 18: After refmac, R = 0.2354 (Rfree = 0.000) for 8193 atoms. Found 28 (47 requested) and removed 35 (31 requested) atoms. Cycle 19: After refmac, R = 0.2317 (Rfree = 0.000) for 8179 atoms. Found 34 (45 requested) and removed 31 (30 requested) atoms. Cycle 20: After refmac, R = 0.2299 (Rfree = 0.000) for 8173 atoms. Found 29 (44 requested) and removed 31 (30 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.14 3.22 Search for helices and strands: 0 residues in 0 chains, 8423 seeds are put forward NCS extension: 10 residues added (9 deleted due to clashes), 8433 seeds are put forward Round 1: 711 peptides, 98 chains. Longest chain 24 peptides. Score 0.589 Round 2: 765 peptides, 82 chains. Longest chain 26 peptides. Score 0.702 Round 3: 775 peptides, 87 chains. Longest chain 25 peptides. Score 0.691 Round 4: 763 peptides, 82 chains. Longest chain 23 peptides. Score 0.700 Round 5: 755 peptides, 82 chains. Longest chain 28 peptides. Score 0.694 Taking the results from Round 2 Chains 83, Residues 683, Estimated correctness of the model 58.4 % 5 chains (69 residues) have been docked in sequence Building loops using Loopy2018 83 chains (683 residues) following loop building 5 chains (69 residues) in sequence following loop building ------------------------------------------------------ 16942 reflections ( 99.75 % complete ) and 17286 restraints for refining 8263 atoms. 14371 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2520 (Rfree = 0.000) for 8263 atoms. Found 43 (43 requested) and removed 56 (31 requested) atoms. Cycle 22: After refmac, R = 0.2479 (Rfree = 0.000) for 8220 atoms. Found 41 (42 requested) and removed 41 (31 requested) atoms. Cycle 23: After refmac, R = 0.2429 (Rfree = 0.000) for 8199 atoms. Found 34 (41 requested) and removed 38 (31 requested) atoms. Cycle 24: After refmac, R = 0.2385 (Rfree = 0.000) for 8185 atoms. Found 27 (39 requested) and removed 37 (30 requested) atoms. Cycle 25: After refmac, R = 0.2329 (Rfree = 0.000) for 8165 atoms. Found 20 (38 requested) and removed 39 (30 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.14 3.22 Search for helices and strands: 0 residues in 0 chains, 8389 seeds are put forward NCS extension: 16 residues added (9 deleted due to clashes), 8405 seeds are put forward Round 1: 690 peptides, 94 chains. Longest chain 18 peptides. Score 0.586 Round 2: 730 peptides, 85 chains. Longest chain 29 peptides. Score 0.662 Round 3: 715 peptides, 79 chains. Longest chain 26 peptides. Score 0.672 Round 4: 714 peptides, 81 chains. Longest chain 26 peptides. Score 0.664 Round 5: 719 peptides, 84 chains. Longest chain 28 peptides. Score 0.656 Taking the results from Round 3 Chains 81, Residues 636, Estimated correctness of the model 50.4 % 5 chains (57 residues) have been docked in sequence ------------------------------------------------------ 16942 reflections ( 99.75 % complete ) and 17717 restraints for refining 8262 atoms. 15066 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2474 (Rfree = 0.000) for 8262 atoms. Found 37 (37 requested) and removed 44 (31 requested) atoms. Cycle 27: After refmac, R = 0.2495 (Rfree = 0.000) for 8235 atoms. Found 37 (37 requested) and removed 39 (31 requested) atoms. Cycle 28: After refmac, R = 0.2280 (Rfree = 0.000) for 8220 atoms. Found 13 (37 requested) and removed 32 (31 requested) atoms. Cycle 29: After refmac, R = 0.2349 (Rfree = 0.000) for 8189 atoms. Found 37 (37 requested) and removed 34 (30 requested) atoms. Cycle 30: After refmac, R = 0.2424 (Rfree = 0.000) for 8188 atoms. Found 37 (37 requested) and removed 30 (30 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 3.26 Search for helices and strands: 0 residues in 0 chains, 8466 seeds are put forward NCS extension: 11 residues added (7 deleted due to clashes), 8477 seeds are put forward Round 1: 641 peptides, 95 chains. Longest chain 18 peptides. Score 0.528 Round 2: 693 peptides, 87 chains. Longest chain 29 peptides. Score 0.620 Round 3: 708 peptides, 89 chains. Longest chain 24 peptides. Score 0.625 Round 4: 714 peptides, 94 chains. Longest chain 20 peptides. Score 0.610 Round 5: 694 peptides, 88 chains. Longest chain 23 peptides. Score 0.616 Taking the results from Round 3 Chains 89, Residues 619, Estimated correctness of the model 36.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 16942 reflections ( 99.75 % complete ) and 18433 restraints for refining 8258 atoms. 16046 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2491 (Rfree = 0.000) for 8258 atoms. Found 37 (37 requested) and removed 43 (31 requested) atoms. Cycle 32: After refmac, R = 0.2343 (Rfree = 0.000) for 8228 atoms. Found 37 (37 requested) and removed 35 (31 requested) atoms. Cycle 33: After refmac, R = 0.2233 (Rfree = 0.000) for 8220 atoms. Found 37 (37 requested) and removed 36 (31 requested) atoms. Cycle 34: After refmac, R = 0.2213 (Rfree = 0.000) for 8211 atoms. Found 37 (37 requested) and removed 35 (31 requested) atoms. Cycle 35: After refmac, R = 0.2120 (Rfree = 0.000) for 8204 atoms. Found 37 (37 requested) and removed 35 (31 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 3.26 Search for helices and strands: 0 residues in 0 chains, 8417 seeds are put forward NCS extension: 8 residues added (6 deleted due to clashes), 8425 seeds are put forward Round 1: 632 peptides, 98 chains. Longest chain 18 peptides. Score 0.503 Round 2: 689 peptides, 90 chains. Longest chain 19 peptides. Score 0.603 Round 3: 704 peptides, 91 chains. Longest chain 20 peptides. Score 0.613 Round 4: 723 peptides, 92 chains. Longest chain 27 peptides. Score 0.627 Round 5: 726 peptides, 94 chains. Longest chain 18 peptides. Score 0.621 Taking the results from Round 4 Chains 93, Residues 631, Estimated correctness of the model 37.2 % 5 chains (58 residues) have been docked in sequence ------------------------------------------------------ 16942 reflections ( 99.75 % complete ) and 17759 restraints for refining 8263 atoms. 15166 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2379 (Rfree = 0.000) for 8263 atoms. Found 37 (37 requested) and removed 40 (31 requested) atoms. Cycle 37: After refmac, R = 0.2320 (Rfree = 0.000) for 8243 atoms. Found 37 (37 requested) and removed 39 (31 requested) atoms. Cycle 38: After refmac, R = 0.2226 (Rfree = 0.000) for 8232 atoms. Found 34 (37 requested) and removed 35 (31 requested) atoms. Cycle 39: After refmac, R = 0.2198 (Rfree = 0.000) for 8223 atoms. Found 37 (37 requested) and removed 35 (31 requested) atoms. Cycle 40: After refmac, R = 0.2132 (Rfree = 0.000) for 8218 atoms. Found 31 (37 requested) and removed 35 (31 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.13 3.21 Search for helices and strands: 0 residues in 0 chains, 8432 seeds are put forward NCS extension: 15 residues added (10 deleted due to clashes), 8447 seeds are put forward Round 1: 592 peptides, 92 chains. Longest chain 17 peptides. Score 0.487 Round 2: 651 peptides, 96 chains. Longest chain 21 peptides. Score 0.535 Round 3: 666 peptides, 86 chains. Longest chain 23 peptides. Score 0.598 Round 4: 671 peptides, 80 chains. Longest chain 27 peptides. Score 0.629 Round 5: 657 peptides, 89 chains. Longest chain 21 peptides. Score 0.575 Taking the results from Round 4 Chains 81, Residues 591, Estimated correctness of the model 37.9 % 3 chains (61 residues) have been docked in sequence ------------------------------------------------------ 16942 reflections ( 99.75 % complete ) and 17858 restraints for refining 8261 atoms. 15347 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2359 (Rfree = 0.000) for 8261 atoms. Found 37 (37 requested) and removed 42 (31 requested) atoms. Cycle 42: After refmac, R = 0.2281 (Rfree = 0.000) for 8220 atoms. Found 37 (37 requested) and removed 33 (31 requested) atoms. Cycle 43: After refmac, R = 0.2227 (Rfree = 0.000) for 8215 atoms. Found 37 (37 requested) and removed 35 (31 requested) atoms. Cycle 44: After refmac, R = 0.2183 (Rfree = 0.000) for 8207 atoms. Found 37 (37 requested) and removed 35 (31 requested) atoms. Cycle 45: After refmac, R = 0.2164 (Rfree = 0.000) for 8201 atoms. Found 37 (37 requested) and removed 31 (30 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.17 3.26 Search for helices and strands: 0 residues in 0 chains, 8422 seeds are put forward NCS extension: 17 residues added (5 deleted due to clashes), 8439 seeds are put forward Round 1: 591 peptides, 94 chains. Longest chain 20 peptides. Score 0.475 Round 2: 645 peptides, 90 chains. Longest chain 28 peptides. Score 0.557 Round 3: 665 peptides, 86 chains. Longest chain 20 peptides. Score 0.597 Round 4: 646 peptides, 84 chains. Longest chain 22 peptides. Score 0.586 Round 5: 631 peptides, 83 chains. Longest chain 22 peptides. Score 0.575 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 86, Residues 579, Estimated correctness of the model 27.7 % 1 chains (11 residues) have been docked in sequence Sequence coverage is 1 % Consider running further cycles of model building using 2hx1-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16942 reflections ( 99.75 % complete ) and 18277 restraints for refining 8263 atoms. 15993 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2353 (Rfree = 0.000) for 8263 atoms. Found 0 (37 requested) and removed 31 (31 requested) atoms. Cycle 47: After refmac, R = 0.2293 (Rfree = 0.000) for 8219 atoms. Found 0 (37 requested) and removed 31 (31 requested) atoms. Cycle 48: After refmac, R = 0.2253 (Rfree = 0.000) for 8184 atoms. Found 0 (37 requested) and removed 30 (30 requested) atoms. Cycle 49: After refmac, R = 0.2149 (Rfree = 0.000) for 8150 atoms. Found 0 (37 requested) and removed 30 (30 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:05:28 GMT 2018 Job finished. TimeTaking 102.7 Used memory is bytes: 10199992