null Mon 24 Dec 07:42:48 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vrb-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vrb-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vrb-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vrb-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vrb-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vrb-3.6-parrot-noncs ############### 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 07:42:52 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/noncs/ArpWArp/wArpResults/WorkingDir/1vrb-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vrb-3.6-parrot-noncs/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 896 and 0 Target number of residues in the AU: 896 Target solvent content: 0.6580 Checking the provided sequence file Detected sequence length: 342 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1368 Adjusted target solvent content: 0.48 Input MTZ file: 1vrb-3.6-parrot-noncs.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: 47.576 104.273 285.843 90.000 90.000 90.000 Input sequence file: 1vrb-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 10944 target number of atoms Had to go as low as 0.65 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: 48.979 3.600 Wilson plot Bfac: 83.52 17139 reflections ( 98.80 % complete ) and 0 restraints for refining 12177 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3582 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3277 (Rfree = 0.000) for 12177 atoms. Found 78 (78 requested) and removed 198 (39 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.55 3.65 Search for helices and strands: 0 residues in 0 chains, 12285 seeds are put forward NCS extension: 0 residues added, 12285 seeds are put forward Round 1: 402 peptides, 84 chains. Longest chain 10 peptides. Score 0.261 Round 2: 522 peptides, 98 chains. Longest chain 12 peptides. Score 0.338 Round 3: 546 peptides, 95 chains. Longest chain 18 peptides. Score 0.382 Round 4: 606 peptides, 98 chains. Longest chain 15 peptides. Score 0.435 Round 5: 604 peptides, 98 chains. Longest chain 17 peptides. Score 0.432 Taking the results from Round 4 Chains 98, Residues 508, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 17139 reflections ( 98.80 % complete ) and 23436 restraints for refining 9919 atoms. 21446 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2652 (Rfree = 0.000) for 9919 atoms. Found 54 (63 requested) and removed 81 (31 requested) atoms. Cycle 2: After refmac, R = 0.2468 (Rfree = 0.000) for 9736 atoms. Found 44 (63 requested) and removed 69 (31 requested) atoms. Cycle 3: After refmac, R = 0.2355 (Rfree = 0.000) for 9638 atoms. Found 47 (62 requested) and removed 70 (31 requested) atoms. Cycle 4: After refmac, R = 0.2310 (Rfree = 0.000) for 9577 atoms. Found 39 (61 requested) and removed 51 (30 requested) atoms. Cycle 5: After refmac, R = 0.2311 (Rfree = 0.000) for 9528 atoms. Found 50 (61 requested) and removed 57 (30 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.54 Search for helices and strands: 0 residues in 0 chains, 9900 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 9920 seeds are put forward Round 1: 504 peptides, 100 chains. Longest chain 12 peptides. Score 0.305 Round 2: 583 peptides, 106 chains. Longest chain 13 peptides. Score 0.370 Round 3: 578 peptides, 97 chains. Longest chain 17 peptides. Score 0.408 Round 4: 584 peptides, 96 chains. Longest chain 17 peptides. Score 0.420 Round 5: 612 peptides, 99 chains. Longest chain 17 peptides. Score 0.436 Taking the results from Round 5 Chains 99, Residues 513, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ 17139 reflections ( 98.80 % complete ) and 22543 restraints for refining 9670 atoms. 20555 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2369 (Rfree = 0.000) for 9670 atoms. Found 53 (62 requested) and removed 78 (31 requested) atoms. Cycle 7: After refmac, R = 0.2289 (Rfree = 0.000) for 9567 atoms. Found 58 (61 requested) and removed 66 (30 requested) atoms. Cycle 8: After refmac, R = 0.2238 (Rfree = 0.000) for 9507 atoms. Found 57 (61 requested) and removed 54 (30 requested) atoms. Cycle 9: After refmac, R = 0.2148 (Rfree = 0.000) for 9458 atoms. Found 56 (61 requested) and removed 47 (30 requested) atoms. Cycle 10: After refmac, R = 0.1898 (Rfree = 0.000) for 9439 atoms. Found 20 (60 requested) and removed 38 (30 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.44 3.53 Search for helices and strands: 0 residues in 0 chains, 9749 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 9762 seeds are put forward Round 1: 499 peptides, 105 chains. Longest chain 12 peptides. Score 0.273 Round 2: 556 peptides, 99 chains. Longest chain 15 peptides. Score 0.373 Round 3: 614 peptides, 103 chains. Longest chain 17 peptides. Score 0.420 Round 4: 608 peptides, 99 chains. Longest chain 19 peptides. Score 0.432 Round 5: 652 peptides, 105 chains. Longest chain 19 peptides. Score 0.451 Taking the results from Round 5 Chains 107, Residues 547, Estimated correctness of the model 0.0 % 10 chains (50 residues) have been docked in sequence ------------------------------------------------------ 17139 reflections ( 98.80 % complete ) and 21962 restraints for refining 9826 atoms. 19712 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2255 (Rfree = 0.000) for 9826 atoms. Found 57 (63 requested) and removed 97 (31 requested) atoms. Cycle 12: After refmac, R = 0.2096 (Rfree = 0.000) for 9705 atoms. Found 39 (62 requested) and removed 66 (31 requested) atoms. Cycle 13: After refmac, R = 0.2049 (Rfree = 0.000) for 9623 atoms. Found 41 (62 requested) and removed 60 (31 requested) atoms. Cycle 14: After refmac, R = 0.2010 (Rfree = 0.000) for 9578 atoms. Found 44 (61 requested) and removed 55 (30 requested) atoms. Cycle 15: After refmac, R = 0.1981 (Rfree = 0.000) for 9547 atoms. Found 37 (61 requested) and removed 53 (30 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 3.54 Search for helices and strands: 0 residues in 0 chains, 9830 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 9850 seeds are put forward Round 1: 502 peptides, 101 chains. Longest chain 18 peptides. Score 0.298 Round 2: 564 peptides, 98 chains. Longest chain 18 peptides. Score 0.388 Round 3: 577 peptides, 91 chains. Longest chain 20 peptides. Score 0.436 Round 4: 573 peptides, 87 chains. Longest chain 23 peptides. Score 0.451 Round 5: 591 peptides, 94 chains. Longest chain 20 peptides. Score 0.437 Taking the results from Round 4 Chains 88, Residues 486, Estimated correctness of the model 0.0 % 9 chains (55 residues) have been docked in sequence ------------------------------------------------------ 17139 reflections ( 98.80 % complete ) and 22788 restraints for refining 9920 atoms. 20759 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2238 (Rfree = 0.000) for 9920 atoms. Found 55 (63 requested) and removed 85 (31 requested) atoms. Cycle 17: After refmac, R = 0.2137 (Rfree = 0.000) for 9834 atoms. Found 49 (63 requested) and removed 52 (31 requested) atoms. Cycle 18: After refmac, R = 0.2131 (Rfree = 0.000) for 9799 atoms. Found 36 (63 requested) and removed 57 (31 requested) atoms. Cycle 19: After refmac, R = 0.2102 (Rfree = 0.000) for 9743 atoms. Found 49 (62 requested) and removed 42 (31 requested) atoms. Cycle 20: After refmac, R = 0.2118 (Rfree = 0.000) for 9722 atoms. Found 54 (62 requested) and removed 48 (31 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.51 Search for helices and strands: 0 residues in 0 chains, 10000 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 10023 seeds are put forward Round 1: 486 peptides, 98 chains. Longest chain 13 peptides. Score 0.293 Round 2: 539 peptides, 96 chains. Longest chain 12 peptides. Score 0.368 Round 3: 551 peptides, 100 chains. Longest chain 10 peptides. Score 0.362 Round 4: 533 peptides, 85 chains. Longest chain 14 peptides. Score 0.417 Round 5: 548 peptides, 93 chains. Longest chain 14 peptides. Score 0.394 Taking the results from Round 4 Chains 85, Residues 448, Estimated correctness of the model 0.0 % 4 chains (21 residues) have been docked in sequence ------------------------------------------------------ 17139 reflections ( 98.80 % complete ) and 23058 restraints for refining 9921 atoms. 21302 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2301 (Rfree = 0.000) for 9921 atoms. Found 61 (63 requested) and removed 88 (31 requested) atoms. Cycle 22: After refmac, R = 0.2171 (Rfree = 0.000) for 9846 atoms. Found 56 (63 requested) and removed 49 (31 requested) atoms. Cycle 23: After refmac, R = 0.1896 (Rfree = 0.000) for 9820 atoms. Found 21 (63 requested) and removed 41 (31 requested) atoms. Cycle 24: After refmac, R = 0.1798 (Rfree = 0.000) for 9776 atoms. Found 18 (62 requested) and removed 39 (31 requested) atoms. Cycle 25: After refmac, R = 0.1763 (Rfree = 0.000) for 9741 atoms. Found 13 (62 requested) and removed 35 (31 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.40 3.49 Search for helices and strands: 0 residues in 0 chains, 10013 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 10027 seeds are put forward Round 1: 419 peptides, 90 chains. Longest chain 11 peptides. Score 0.250 Round 2: 461 peptides, 86 chains. Longest chain 10 peptides. Score 0.326 Round 3: 473 peptides, 85 chains. Longest chain 11 peptides. Score 0.346 Round 4: 490 peptides, 86 chains. Longest chain 13 peptides. Score 0.362 Round 5: 483 peptides, 81 chains. Longest chain 16 peptides. Score 0.379 Taking the results from Round 5 Chains 82, Residues 402, Estimated correctness of the model 0.0 % 8 chains (42 residues) have been docked in sequence ------------------------------------------------------ 17139 reflections ( 98.80 % complete ) and 23146 restraints for refining 9917 atoms. 21511 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2193 (Rfree = 0.000) for 9917 atoms. Found 55 (63 requested) and removed 79 (31 requested) atoms. Cycle 27: After refmac, R = 0.2062 (Rfree = 0.000) for 9857 atoms. Found 61 (63 requested) and removed 50 (31 requested) atoms. Cycle 28: After refmac, R = 0.2077 (Rfree = 0.000) for 9844 atoms. Found 55 (63 requested) and removed 52 (31 requested) atoms. Cycle 29: After refmac, R = 0.2029 (Rfree = 0.000) for 9820 atoms. Found 51 (63 requested) and removed 47 (31 requested) atoms. Cycle 30: After refmac, R = 0.2015 (Rfree = 0.000) for 9805 atoms. Found 49 (63 requested) and removed 47 (31 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.49 Search for helices and strands: 0 residues in 0 chains, 10003 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 10016 seeds are put forward Round 1: 399 peptides, 85 chains. Longest chain 10 peptides. Score 0.251 Round 2: 469 peptides, 87 chains. Longest chain 11 peptides. Score 0.331 Round 3: 442 peptides, 77 chains. Longest chain 13 peptides. Score 0.351 Round 4: 488 peptides, 87 chains. Longest chain 13 peptides. Score 0.354 Round 5: 480 peptides, 83 chains. Longest chain 16 peptides. Score 0.365 Taking the results from Round 5 Chains 83, Residues 397, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 17139 reflections ( 98.80 % complete ) and 22924 restraints for refining 9872 atoms. 21342 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2247 (Rfree = 0.000) for 9872 atoms. Found 60 (63 requested) and removed 80 (31 requested) atoms. Cycle 32: After refmac, R = 0.2112 (Rfree = 0.000) for 9814 atoms. Found 62 (63 requested) and removed 47 (31 requested) atoms. Cycle 33: After refmac, R = 0.1840 (Rfree = 0.000) for 9803 atoms. Found 22 (63 requested) and removed 45 (31 requested) atoms. Cycle 34: After refmac, R = 0.1759 (Rfree = 0.000) for 9756 atoms. Found 13 (62 requested) and removed 37 (31 requested) atoms. Cycle 35: After refmac, R = 0.1746 (Rfree = 0.000) for 9721 atoms. Found 10 (62 requested) and removed 39 (31 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 3.47 Search for helices and strands: 0 residues in 0 chains, 9949 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 9964 seeds are put forward Round 1: 396 peptides, 87 chains. Longest chain 9 peptides. Score 0.235 Round 2: 448 peptides, 84 chains. Longest chain 11 peptides. Score 0.320 Round 3: 461 peptides, 85 chains. Longest chain 11 peptides. Score 0.331 Round 4: 452 peptides, 78 chains. Longest chain 14 peptides. Score 0.358 Round 5: 464 peptides, 85 chains. Longest chain 16 peptides. Score 0.335 Taking the results from Round 4 Chains 78, Residues 374, Estimated correctness of the model 0.0 % 8 chains (39 residues) have been docked in sequence ------------------------------------------------------ 17139 reflections ( 98.80 % complete ) and 22912 restraints for refining 9852 atoms. 21383 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2166 (Rfree = 0.000) for 9852 atoms. Found 63 (63 requested) and removed 78 (31 requested) atoms. Cycle 37: After refmac, R = 0.2050 (Rfree = 0.000) for 9809 atoms. Found 63 (63 requested) and removed 59 (31 requested) atoms. Cycle 38: After refmac, R = 0.2045 (Rfree = 0.000) for 9786 atoms. Found 62 (62 requested) and removed 47 (31 requested) atoms. Cycle 39: After refmac, R = 0.2020 (Rfree = 0.000) for 9776 atoms. Found 62 (62 requested) and removed 48 (31 requested) atoms. Cycle 40: After refmac, R = 0.1836 (Rfree = 0.000) for 9776 atoms. Found 17 (62 requested) and removed 34 (31 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.38 3.47 Search for helices and strands: 0 residues in 0 chains, 9995 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 10014 seeds are put forward Round 1: 402 peptides, 90 chains. Longest chain 12 peptides. Score 0.226 Round 2: 454 peptides, 89 chains. Longest chain 13 peptides. Score 0.301 Round 3: 451 peptides, 79 chains. Longest chain 15 peptides. Score 0.351 Round 4: 453 peptides, 82 chains. Longest chain 13 peptides. Score 0.338 Round 5: 452 peptides, 84 chains. Longest chain 18 peptides. Score 0.325 Taking the results from Round 3 Chains 79, Residues 372, Estimated correctness of the model 0.0 % 4 chains (18 residues) have been docked in sequence ------------------------------------------------------ 17139 reflections ( 98.80 % complete ) and 23124 restraints for refining 9872 atoms. 21672 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2304 (Rfree = 0.000) for 9872 atoms. Found 63 (63 requested) and removed 68 (31 requested) atoms. Cycle 42: After refmac, R = 0.2250 (Rfree = 0.000) for 9833 atoms. Found 63 (63 requested) and removed 55 (31 requested) atoms. Cycle 43: After refmac, R = 0.2257 (Rfree = 0.000) for 9814 atoms. Found 63 (63 requested) and removed 66 (31 requested) atoms. Cycle 44: After refmac, R = 0.1977 (Rfree = 0.000) for 9785 atoms. Found 21 (62 requested) and removed 41 (31 requested) atoms. Cycle 45: After refmac, R = 0.1914 (Rfree = 0.000) for 9750 atoms. Found 16 (62 requested) and removed 34 (31 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 3.48 Search for helices and strands: 0 residues in 0 chains, 9954 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 9976 seeds are put forward Round 1: 363 peptides, 82 chains. Longest chain 8 peptides. Score 0.218 Round 2: 398 peptides, 78 chains. Longest chain 10 peptides. Score 0.289 Round 3: 401 peptides, 78 chains. Longest chain 10 peptides. Score 0.293 Round 4: 403 peptides, 76 chains. Longest chain 11 peptides. Score 0.307 Round 5: 423 peptides, 76 chains. Longest chain 11 peptides. Score 0.333 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 76, Residues 347, Estimated correctness of the model 0.0 % 8 chains (42 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 1vrb-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 138 A and 148 A 75 chains (356 residues) following loop building 7 chains (51 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17139 reflections ( 98.80 % complete ) and 22934 restraints for refining 9895 atoms. 21433 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2232 (Rfree = 0.000) for 9895 atoms. Found 0 (63 requested) and removed 31 (31 requested) atoms. Cycle 47: After refmac, R = 0.2169 (Rfree = 0.000) for 9817 atoms. Found 0 (63 requested) and removed 31 (31 requested) atoms. Cycle 48: After refmac, R = 0.2182 (Rfree = 0.000) for 9760 atoms. Found 0 (62 requested) and removed 31 (31 requested) atoms. Cycle 49: After refmac, R = 0.2154 (Rfree = 0.000) for 9705 atoms. Found 0 (62 requested) and removed 31 (31 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:17:30 GMT 2018 Job finished. TimeTaking 94.71 Used memory is bytes: 16020112