null Mon 24 Dec 00:01:16 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2gvh-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2gvh-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2gvh-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gvh-3.2-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2gvh-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gvh-3.2-parrot-mrncs ############### 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 00:01:21 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/mrncs/ArpWArp/wArpResults/WorkingDir/2gvh-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gvh-3.2-parrot-mrncs/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 765 and 0 Target number of residues in the AU: 765 Target solvent content: 0.6556 Checking the provided sequence file Detected sequence length: 288 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 864 Adjusted target solvent content: 0.61 Input MTZ file: 2gvh-3.2-parrot-mrncs.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: 78 Cell parameters: 121.211 121.211 81.834 90.000 90.000 90.000 Input sequence file: 2gvh-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 6912 target number of atoms Had to go as low as 0.85 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: 121.211 3.200 Wilson plot Bfac: 81.85 19717 reflections ( 99.66 % complete ) and 0 restraints for refining 7742 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Starting model: R = 0.3409 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3139 (Rfree = 0.000) for 7742 atoms. Found 63 (69 requested) and removed 144 (34 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.42 2.95 Search for helices and strands: 0 residues in 0 chains, 7779 seeds are put forward NCS extension: 0 residues added, 7779 seeds are put forward Round 1: 465 peptides, 67 chains. Longest chain 18 peptides. Score 0.463 Round 2: 525 peptides, 64 chains. Longest chain 22 peptides. Score 0.550 Round 3: 538 peptides, 62 chains. Longest chain 24 peptides. Score 0.574 Round 4: 548 peptides, 60 chains. Longest chain 41 peptides. Score 0.595 Round 5: 540 peptides, 58 chains. Longest chain 27 peptides. Score 0.596 Taking the results from Round 5 Chains 65, Residues 482, Estimated correctness of the model 40.0 % 8 chains (88 residues) have been docked in sequence ------------------------------------------------------ 19717 reflections ( 99.66 % complete ) and 13096 restraints for refining 6308 atoms. 10925 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2743 (Rfree = 0.000) for 6308 atoms. Found 53 (56 requested) and removed 82 (28 requested) atoms. Cycle 2: After refmac, R = 0.2522 (Rfree = 0.000) for 6191 atoms. Found 46 (56 requested) and removed 57 (28 requested) atoms. Cycle 3: After refmac, R = 0.2759 (Rfree = 0.000) for 6137 atoms. Found 55 (55 requested) and removed 56 (27 requested) atoms. Cycle 4: After refmac, R = 0.2740 (Rfree = 0.000) for 6095 atoms. Found 55 (55 requested) and removed 55 (27 requested) atoms. Cycle 5: After refmac, R = 0.2724 (Rfree = 0.000) for 6067 atoms. Found 51 (54 requested) and removed 58 (27 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 2.93 Search for helices and strands: 0 residues in 0 chains, 6192 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 6215 seeds are put forward Round 1: 547 peptides, 65 chains. Longest chain 30 peptides. Score 0.569 Round 2: 567 peptides, 65 chains. Longest chain 31 peptides. Score 0.590 Round 3: 550 peptides, 54 chains. Longest chain 35 peptides. Score 0.625 Round 4: 517 peptides, 56 chains. Longest chain 29 peptides. Score 0.582 Round 5: 535 peptides, 59 chains. Longest chain 30 peptides. Score 0.586 Taking the results from Round 3 Chains 68, Residues 496, Estimated correctness of the model 47.6 % 12 chains (123 residues) have been docked in sequence ------------------------------------------------------ 19717 reflections ( 99.66 % complete ) and 12406 restraints for refining 6308 atoms. 10040 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2702 (Rfree = 0.000) for 6308 atoms. Found 50 (56 requested) and removed 59 (28 requested) atoms. Cycle 7: After refmac, R = 0.2430 (Rfree = 0.000) for 6261 atoms. Found 23 (56 requested) and removed 39 (28 requested) atoms. Cycle 8: After refmac, R = 0.2250 (Rfree = 0.000) for 6211 atoms. Found 21 (56 requested) and removed 53 (28 requested) atoms. Cycle 9: After refmac, R = 0.2217 (Rfree = 0.000) for 6162 atoms. Found 19 (55 requested) and removed 37 (27 requested) atoms. Cycle 10: After refmac, R = 0.2190 (Rfree = 0.000) for 6133 atoms. Found 11 (55 requested) and removed 36 (27 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 2.96 Search for helices and strands: 0 residues in 0 chains, 6226 seeds are put forward NCS extension: 33 residues added (5 deleted due to clashes), 6259 seeds are put forward Round 1: 534 peptides, 66 chains. Longest chain 20 peptides. Score 0.550 Round 2: 558 peptides, 55 chains. Longest chain 35 peptides. Score 0.628 Round 3: 580 peptides, 56 chains. Longest chain 44 peptides. Score 0.644 Round 4: 554 peptides, 56 chains. Longest chain 31 peptides. Score 0.619 Round 5: 558 peptides, 55 chains. Longest chain 28 peptides. Score 0.628 Taking the results from Round 3 Chains 61, Residues 524, Estimated correctness of the model 52.4 % 11 chains (151 residues) have been docked in sequence ------------------------------------------------------ 19717 reflections ( 99.66 % complete ) and 11783 restraints for refining 6309 atoms. 9165 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2906 (Rfree = 0.000) for 6309 atoms. Found 56 (56 requested) and removed 120 (28 requested) atoms. Cycle 12: After refmac, R = 0.2641 (Rfree = 0.000) for 6201 atoms. Found 56 (56 requested) and removed 65 (28 requested) atoms. Cycle 13: After refmac, R = 0.2223 (Rfree = 0.000) for 6175 atoms. Found 23 (55 requested) and removed 45 (27 requested) atoms. Cycle 14: After refmac, R = 0.2075 (Rfree = 0.000) for 6140 atoms. Found 16 (55 requested) and removed 40 (27 requested) atoms. Cycle 15: After refmac, R = 0.1983 (Rfree = 0.000) for 6105 atoms. Found 13 (54 requested) and removed 44 (27 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 2.96 Search for helices and strands: 0 residues in 0 chains, 6219 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 6235 seeds are put forward Round 1: 526 peptides, 61 chains. Longest chain 22 peptides. Score 0.566 Round 2: 556 peptides, 57 chains. Longest chain 25 peptides. Score 0.617 Round 3: 565 peptides, 51 chains. Longest chain 40 peptides. Score 0.652 Round 4: 555 peptides, 53 chains. Longest chain 38 peptides. Score 0.634 Round 5: 574 peptides, 58 chains. Longest chain 29 peptides. Score 0.630 Taking the results from Round 3 Chains 58, Residues 514, Estimated correctness of the model 54.3 % 9 chains (135 residues) have been docked in sequence ------------------------------------------------------ 19717 reflections ( 99.66 % complete ) and 12091 restraints for refining 6309 atoms. 9580 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2637 (Rfree = 0.000) for 6309 atoms. Found 49 (56 requested) and removed 62 (28 requested) atoms. Cycle 17: After refmac, R = 0.2491 (Rfree = 0.000) for 6249 atoms. Found 56 (56 requested) and removed 42 (28 requested) atoms. Cycle 18: After refmac, R = 0.2405 (Rfree = 0.000) for 6239 atoms. Found 56 (56 requested) and removed 34 (28 requested) atoms. Cycle 19: After refmac, R = 0.2398 (Rfree = 0.000) for 6243 atoms. Found 56 (56 requested) and removed 39 (28 requested) atoms. Cycle 20: After refmac, R = 0.2366 (Rfree = 0.000) for 6240 atoms. Found 56 (56 requested) and removed 44 (28 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 2.96 Search for helices and strands: 0 residues in 0 chains, 6424 seeds are put forward NCS extension: 22 residues added (7 deleted due to clashes), 6446 seeds are put forward Round 1: 510 peptides, 59 chains. Longest chain 38 peptides. Score 0.559 Round 2: 565 peptides, 53 chains. Longest chain 47 peptides. Score 0.644 Round 3: 563 peptides, 47 chains. Longest chain 49 peptides. Score 0.668 Round 4: 576 peptides, 50 chains. Longest chain 56 peptides. Score 0.667 Round 5: 573 peptides, 51 chains. Longest chain 57 peptides. Score 0.660 Taking the results from Round 3 Chains 52, Residues 516, Estimated correctness of the model 58.1 % 11 chains (211 residues) have been docked in sequence ------------------------------------------------------ 19717 reflections ( 99.66 % complete ) and 11361 restraints for refining 6309 atoms. 8535 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2672 (Rfree = 0.000) for 6309 atoms. Found 51 (56 requested) and removed 48 (28 requested) atoms. Cycle 22: After refmac, R = 0.2565 (Rfree = 0.000) for 6265 atoms. Found 56 (56 requested) and removed 43 (28 requested) atoms. Cycle 23: After refmac, R = 0.2525 (Rfree = 0.000) for 6234 atoms. Found 56 (56 requested) and removed 47 (28 requested) atoms. Cycle 24: After refmac, R = 0.2406 (Rfree = 0.000) for 6224 atoms. Found 52 (56 requested) and removed 38 (28 requested) atoms. Cycle 25: After refmac, R = 0.2392 (Rfree = 0.000) for 6208 atoms. Found 54 (55 requested) and removed 41 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 2.96 Search for helices and strands: 0 residues in 0 chains, 6359 seeds are put forward NCS extension: 35 residues added (19 deleted due to clashes), 6394 seeds are put forward Round 1: 528 peptides, 61 chains. Longest chain 48 peptides. Score 0.569 Round 2: 553 peptides, 53 chains. Longest chain 51 peptides. Score 0.632 Round 3: 567 peptides, 54 chains. Longest chain 54 peptides. Score 0.641 Round 4: 570 peptides, 54 chains. Longest chain 35 peptides. Score 0.644 Round 5: 541 peptides, 53 chains. Longest chain 35 peptides. Score 0.621 Taking the results from Round 4 Chains 59, Residues 516, Estimated correctness of the model 52.4 % 8 chains (141 residues) have been docked in sequence ------------------------------------------------------ 19717 reflections ( 99.66 % complete ) and 12134 restraints for refining 6309 atoms. 9578 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2615 (Rfree = 0.000) for 6309 atoms. Found 56 (56 requested) and removed 58 (28 requested) atoms. Cycle 27: After refmac, R = 0.2471 (Rfree = 0.000) for 6272 atoms. Found 37 (56 requested) and removed 52 (28 requested) atoms. Cycle 28: After refmac, R = 0.2464 (Rfree = 0.000) for 6241 atoms. Found 52 (56 requested) and removed 45 (28 requested) atoms. Cycle 29: After refmac, R = 0.2395 (Rfree = 0.000) for 6229 atoms. Found 56 (56 requested) and removed 42 (28 requested) atoms. Cycle 30: After refmac, R = 0.2329 (Rfree = 0.000) for 6232 atoms. Found 56 (56 requested) and removed 39 (28 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.42 2.95 Search for helices and strands: 0 residues in 0 chains, 6386 seeds are put forward NCS extension: 26 residues added (13 deleted due to clashes), 6412 seeds are put forward Round 1: 502 peptides, 58 chains. Longest chain 33 peptides. Score 0.555 Round 2: 550 peptides, 54 chains. Longest chain 50 peptides. Score 0.625 Round 3: 541 peptides, 53 chains. Longest chain 48 peptides. Score 0.621 Round 4: 548 peptides, 50 chains. Longest chain 52 peptides. Score 0.641 Round 5: 565 peptides, 54 chains. Longest chain 48 peptides. Score 0.639 Taking the results from Round 4 Chains 53, Residues 498, Estimated correctness of the model 51.6 % 8 chains (161 residues) have been docked in sequence ------------------------------------------------------ 19717 reflections ( 99.66 % complete ) and 11986 restraints for refining 6310 atoms. 9424 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2332 (Rfree = 0.000) for 6310 atoms. Found 51 (56 requested) and removed 47 (28 requested) atoms. Cycle 32: After refmac, R = 0.2202 (Rfree = 0.000) for 6285 atoms. Found 31 (56 requested) and removed 42 (28 requested) atoms. Cycle 33: After refmac, R = 0.2007 (Rfree = 0.000) for 6246 atoms. Found 20 (56 requested) and removed 37 (28 requested) atoms. Cycle 34: After refmac, R = 0.2026 (Rfree = 0.000) for 6223 atoms. Found 8 (55 requested) and removed 32 (27 requested) atoms. Cycle 35: After refmac, R = 0.1950 (Rfree = 0.000) for 6196 atoms. Found 16 (55 requested) and removed 34 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.45 2.97 Search for helices and strands: 0 residues in 0 chains, 6290 seeds are put forward NCS extension: 19 residues added (40 deleted due to clashes), 6309 seeds are put forward Round 1: 500 peptides, 60 chains. Longest chain 26 peptides. Score 0.543 Round 2: 529 peptides, 55 chains. Longest chain 35 peptides. Score 0.599 Round 3: 562 peptides, 56 chains. Longest chain 36 peptides. Score 0.627 Round 4: 550 peptides, 62 chains. Longest chain 34 peptides. Score 0.587 Round 5: 545 peptides, 52 chains. Longest chain 55 peptides. Score 0.629 Taking the results from Round 5 Chains 54, Residues 493, Estimated correctness of the model 48.6 % 10 chains (229 residues) have been docked in sequence ------------------------------------------------------ 19717 reflections ( 99.66 % complete ) and 11439 restraints for refining 6310 atoms. 8634 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2553 (Rfree = 0.000) for 6310 atoms. Found 56 (56 requested) and removed 63 (28 requested) atoms. Cycle 37: After refmac, R = 0.2416 (Rfree = 0.000) for 6255 atoms. Found 54 (56 requested) and removed 44 (28 requested) atoms. Cycle 38: After refmac, R = 0.2391 (Rfree = 0.000) for 6233 atoms. Found 56 (56 requested) and removed 41 (28 requested) atoms. Cycle 39: After refmac, R = 0.2024 (Rfree = 0.000) for 6221 atoms. Found 22 (56 requested) and removed 36 (28 requested) atoms. Cycle 40: After refmac, R = 0.1928 (Rfree = 0.000) for 6199 atoms. Found 10 (55 requested) and removed 32 (27 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.44 2.96 Search for helices and strands: 0 residues in 0 chains, 6339 seeds are put forward NCS extension: 34 residues added (17 deleted due to clashes), 6373 seeds are put forward Round 1: 478 peptides, 56 chains. Longest chain 47 peptides. Score 0.539 Round 2: 503 peptides, 50 chains. Longest chain 49 peptides. Score 0.597 Round 3: 504 peptides, 56 chains. Longest chain 36 peptides. Score 0.568 Round 4: 511 peptides, 54 chains. Longest chain 48 peptides. Score 0.585 Round 5: 508 peptides, 49 chains. Longest chain 38 peptides. Score 0.607 Taking the results from Round 5 Chains 57, Residues 459, Estimated correctness of the model 42.9 % 8 chains (138 residues) have been docked in sequence ------------------------------------------------------ 19717 reflections ( 99.66 % complete ) and 12352 restraints for refining 6309 atoms. 10031 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2580 (Rfree = 0.000) for 6309 atoms. Found 56 (56 requested) and removed 46 (28 requested) atoms. Cycle 42: After refmac, R = 0.2506 (Rfree = 0.000) for 6297 atoms. Found 56 (56 requested) and removed 41 (28 requested) atoms. Cycle 43: After refmac, R = 0.2486 (Rfree = 0.000) for 6286 atoms. Found 56 (56 requested) and removed 37 (28 requested) atoms. Cycle 44: After refmac, R = 0.2469 (Rfree = 0.000) for 6279 atoms. Found 56 (56 requested) and removed 37 (28 requested) atoms. Cycle 45: After refmac, R = 0.2456 (Rfree = 0.000) for 6274 atoms. Found 56 (56 requested) and removed 34 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.43 2.96 Search for helices and strands: 0 residues in 0 chains, 6457 seeds are put forward NCS extension: 35 residues added (12 deleted due to clashes), 6492 seeds are put forward Round 1: 483 peptides, 62 chains. Longest chain 29 peptides. Score 0.513 Round 2: 512 peptides, 59 chains. Longest chain 26 peptides. Score 0.561 Round 3: 512 peptides, 51 chains. Longest chain 43 peptides. Score 0.601 Round 4: 523 peptides, 49 chains. Longest chain 35 peptides. Score 0.622 Round 5: 527 peptides, 52 chains. Longest chain 41 peptides. Score 0.611 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 53, Residues 474, Estimated correctness of the model 46.9 % 9 chains (178 residues) have been docked in sequence Sequence coverage is 37 % Consider running further cycles of model building using 2gvh-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 114 A and 119 A Built loop between residues 247 C and 258 C 49 chains (480 residues) following loop building 7 chains (192 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 19717 reflections ( 99.66 % complete ) and 11711 restraints for refining 6309 atoms. 9137 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2366 (Rfree = 0.000) for 6309 atoms. Found 0 (56 requested) and removed 28 (28 requested) atoms. Cycle 47: After refmac, R = 0.2207 (Rfree = 0.000) for 6247 atoms. Found 0 (56 requested) and removed 28 (28 requested) atoms. Cycle 48: After refmac, R = 0.2208 (Rfree = 0.000) for 6209 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 49: After refmac, R = 0.2204 (Rfree = 0.000) for 6177 atoms. Found 0 (55 requested) and removed 24 (27 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:13:05 GMT 2018 Job finished. TimeTaking 71.82 Used memory is bytes: 17337896