null Mon 24 Dec 07:25:52 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-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vrb-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vrb-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vrb-3.4-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-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vrb-3.4-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 07:25:56 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/noncs/ArpWArp/wArpResults/WorkingDir/1vrb-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vrb-3.4-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 927 and 0 Target number of residues in the AU: 927 Target solvent content: 0.6462 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-3.4-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-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 10944 target number of atoms Had to go as low as 0.60 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 3.400 Wilson plot Bfac: 75.79 20098 reflections ( 98.18 % complete ) and 0 restraints for refining 12186 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3528 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3044 (Rfree = 0.000) for 12186 atoms. Found 81 (92 requested) and removed 184 (46 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.34 3.43 Search for helices and strands: 0 residues in 0 chains, 12326 seeds are put forward NCS extension: 0 residues added, 12326 seeds are put forward Round 1: 446 peptides, 94 chains. Longest chain 13 peptides. Score 0.263 Round 2: 563 peptides, 99 chains. Longest chain 19 peptides. Score 0.381 Round 3: 619 peptides, 102 chains. Longest chain 28 peptides. Score 0.430 Round 4: 633 peptides, 102 chains. Longest chain 15 peptides. Score 0.445 Round 5: 640 peptides, 104 chains. Longest chain 13 peptides. Score 0.443 Taking the results from Round 4 Chains 102, Residues 531, Estimated correctness of the model 0.0 % 7 chains (41 residues) have been docked in sequence ------------------------------------------------------ 20098 reflections ( 98.18 % complete ) and 23446 restraints for refining 9948 atoms. 21317 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2707 (Rfree = 0.000) for 9948 atoms. Found 39 (75 requested) and removed 82 (37 requested) atoms. Cycle 2: After refmac, R = 0.2631 (Rfree = 0.000) for 9737 atoms. Found 51 (74 requested) and removed 71 (37 requested) atoms. Cycle 3: After refmac, R = 0.2483 (Rfree = 0.000) for 9654 atoms. Found 31 (73 requested) and removed 56 (36 requested) atoms. Cycle 4: After refmac, R = 0.2406 (Rfree = 0.000) for 9590 atoms. Found 45 (72 requested) and removed 52 (36 requested) atoms. Cycle 5: After refmac, R = 0.2362 (Rfree = 0.000) for 9553 atoms. Found 38 (72 requested) and removed 51 (36 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 9873 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 9888 seeds are put forward Round 1: 534 peptides, 108 chains. Longest chain 14 peptides. Score 0.301 Round 2: 634 peptides, 114 chains. Longest chain 16 peptides. Score 0.389 Round 3: 636 peptides, 102 chains. Longest chain 19 peptides. Score 0.448 Round 4: 626 peptides, 99 chains. Longest chain 25 peptides. Score 0.451 Round 5: 636 peptides, 102 chains. Longest chain 20 peptides. Score 0.448 Taking the results from Round 4 Chains 102, Residues 527, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 20098 reflections ( 98.18 % complete ) and 22344 restraints for refining 9668 atoms. 20247 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2545 (Rfree = 0.000) for 9668 atoms. Found 57 (73 requested) and removed 92 (36 requested) atoms. Cycle 7: After refmac, R = 0.2345 (Rfree = 0.000) for 9568 atoms. Found 24 (72 requested) and removed 62 (36 requested) atoms. Cycle 8: After refmac, R = 0.2215 (Rfree = 0.000) for 9493 atoms. Found 23 (71 requested) and removed 43 (35 requested) atoms. Cycle 9: After refmac, R = 0.2184 (Rfree = 0.000) for 9453 atoms. Found 9 (71 requested) and removed 42 (35 requested) atoms. Cycle 10: After refmac, R = 0.2173 (Rfree = 0.000) for 9406 atoms. Found 11 (71 requested) and removed 41 (35 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 9703 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 9719 seeds are put forward Round 1: 545 peptides, 107 chains. Longest chain 12 peptides. Score 0.319 Round 2: 627 peptides, 107 chains. Longest chain 17 peptides. Score 0.415 Round 3: 645 peptides, 107 chains. Longest chain 17 peptides. Score 0.435 Round 4: 642 peptides, 108 chains. Longest chain 17 peptides. Score 0.427 Round 5: 643 peptides, 100 chains. Longest chain 17 peptides. Score 0.465 Taking the results from Round 5 Chains 103, Residues 543, Estimated correctness of the model 0.0 % 7 chains (52 residues) have been docked in sequence ------------------------------------------------------ 20098 reflections ( 98.18 % complete ) and 22368 restraints for refining 9910 atoms. 20125 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2541 (Rfree = 0.000) for 9910 atoms. Found 61 (74 requested) and removed 88 (37 requested) atoms. Cycle 12: After refmac, R = 0.2430 (Rfree = 0.000) for 9790 atoms. Found 62 (74 requested) and removed 64 (37 requested) atoms. Cycle 13: After refmac, R = 0.2352 (Rfree = 0.000) for 9739 atoms. Found 51 (73 requested) and removed 59 (36 requested) atoms. Cycle 14: After refmac, R = 0.2086 (Rfree = 0.000) for 9690 atoms. Found 19 (73 requested) and removed 48 (36 requested) atoms. Cycle 15: After refmac, R = 0.2036 (Rfree = 0.000) for 9629 atoms. Found 22 (72 requested) and removed 45 (36 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.33 3.42 Search for helices and strands: 0 residues in 0 chains, 9932 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 9950 seeds are put forward Round 1: 510 peptides, 105 chains. Longest chain 10 peptides. Score 0.286 Round 2: 609 peptides, 107 chains. Longest chain 13 peptides. Score 0.395 Round 3: 620 peptides, 103 chains. Longest chain 23 peptides. Score 0.426 Round 4: 634 peptides, 102 chains. Longest chain 24 peptides. Score 0.446 Round 5: 626 peptides, 96 chains. Longest chain 23 peptides. Score 0.465 Taking the results from Round 5 Chains 97, Residues 530, Estimated correctness of the model 0.0 % 8 chains (67 residues) have been docked in sequence ------------------------------------------------------ 20098 reflections ( 98.18 % complete ) and 22280 restraints for refining 9949 atoms. 20047 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2476 (Rfree = 0.000) for 9949 atoms. Found 54 (75 requested) and removed 84 (37 requested) atoms. Cycle 17: After refmac, R = 0.2366 (Rfree = 0.000) for 9861 atoms. Found 39 (74 requested) and removed 62 (37 requested) atoms. Cycle 18: After refmac, R = 0.2331 (Rfree = 0.000) for 9807 atoms. Found 39 (74 requested) and removed 54 (37 requested) atoms. Cycle 19: After refmac, R = 0.2335 (Rfree = 0.000) for 9758 atoms. Found 43 (73 requested) and removed 51 (36 requested) atoms. Cycle 20: After refmac, R = 0.2272 (Rfree = 0.000) for 9718 atoms. Found 39 (73 requested) and removed 49 (36 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.33 3.42 Search for helices and strands: 0 residues in 0 chains, 9969 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 9991 seeds are put forward Round 1: 492 peptides, 98 chains. Longest chain 16 peptides. Score 0.301 Round 2: 565 peptides, 93 chains. Longest chain 21 peptides. Score 0.413 Round 3: 561 peptides, 92 chains. Longest chain 25 peptides. Score 0.414 Round 4: 568 peptides, 92 chains. Longest chain 15 peptides. Score 0.422 Round 5: 565 peptides, 91 chains. Longest chain 20 peptides. Score 0.423 Taking the results from Round 5 Chains 91, Residues 474, Estimated correctness of the model 0.0 % 8 chains (39 residues) have been docked in sequence ------------------------------------------------------ 20098 reflections ( 98.18 % complete ) and 22933 restraints for refining 9950 atoms. 21023 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2465 (Rfree = 0.000) for 9950 atoms. Found 75 (75 requested) and removed 67 (37 requested) atoms. Cycle 22: After refmac, R = 0.2337 (Rfree = 0.000) for 9922 atoms. Found 66 (75 requested) and removed 56 (37 requested) atoms. Cycle 23: After refmac, R = 0.2297 (Rfree = 0.000) for 9898 atoms. Found 58 (74 requested) and removed 52 (37 requested) atoms. Cycle 24: After refmac, R = 0.2268 (Rfree = 0.000) for 9886 atoms. Found 64 (74 requested) and removed 54 (37 requested) atoms. Cycle 25: After refmac, R = 0.2265 (Rfree = 0.000) for 9871 atoms. Found 54 (74 requested) and removed 54 (37 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.36 3.45 Search for helices and strands: 0 residues in 0 chains, 10190 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 10208 seeds are put forward Round 1: 487 peptides, 99 chains. Longest chain 12 peptides. Score 0.289 Round 2: 543 peptides, 98 chains. Longest chain 17 peptides. Score 0.363 Round 3: 563 peptides, 95 chains. Longest chain 17 peptides. Score 0.401 Round 4: 582 peptides, 94 chains. Longest chain 15 peptides. Score 0.427 Round 5: 567 peptides, 100 chains. Longest chain 14 peptides. Score 0.381 Taking the results from Round 4 Chains 94, Residues 488, Estimated correctness of the model 0.0 % 7 chains (32 residues) have been docked in sequence ------------------------------------------------------ 20098 reflections ( 98.18 % complete ) and 22810 restraints for refining 9951 atoms. 20883 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2458 (Rfree = 0.000) for 9951 atoms. Found 65 (75 requested) and removed 71 (37 requested) atoms. Cycle 27: After refmac, R = 0.2288 (Rfree = 0.000) for 9906 atoms. Found 61 (75 requested) and removed 48 (37 requested) atoms. Cycle 28: After refmac, R = 0.2228 (Rfree = 0.000) for 9902 atoms. Found 40 (74 requested) and removed 56 (37 requested) atoms. Cycle 29: After refmac, R = 0.2214 (Rfree = 0.000) for 9868 atoms. Found 61 (74 requested) and removed 47 (37 requested) atoms. Cycle 30: After refmac, R = 0.1958 (Rfree = 0.000) for 9865 atoms. Found 20 (74 requested) and removed 43 (37 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 10134 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 10152 seeds are put forward Round 1: 472 peptides, 97 chains. Longest chain 23 peptides. Score 0.281 Round 2: 528 peptides, 92 chains. Longest chain 17 peptides. Score 0.376 Round 3: 533 peptides, 87 chains. Longest chain 16 peptides. Score 0.407 Round 4: 540 peptides, 90 chains. Longest chain 15 peptides. Score 0.400 Round 5: 536 peptides, 86 chains. Longest chain 17 peptides. Score 0.415 Taking the results from Round 5 Chains 87, Residues 450, Estimated correctness of the model 0.0 % 6 chains (36 residues) have been docked in sequence ------------------------------------------------------ 20098 reflections ( 98.18 % complete ) and 23131 restraints for refining 9950 atoms. 21278 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2420 (Rfree = 0.000) for 9950 atoms. Found 68 (75 requested) and removed 58 (37 requested) atoms. Cycle 32: After refmac, R = 0.2361 (Rfree = 0.000) for 9933 atoms. Found 75 (75 requested) and removed 58 (37 requested) atoms. Cycle 33: After refmac, R = 0.2299 (Rfree = 0.000) for 9924 atoms. Found 68 (75 requested) and removed 47 (37 requested) atoms. Cycle 34: After refmac, R = 0.2251 (Rfree = 0.000) for 9922 atoms. Found 69 (75 requested) and removed 49 (37 requested) atoms. Cycle 35: After refmac, R = 0.2222 (Rfree = 0.000) for 9925 atoms. Found 68 (75 requested) and removed 57 (37 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 10166 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 10183 seeds are put forward Round 1: 411 peptides, 87 chains. Longest chain 11 peptides. Score 0.256 Round 2: 505 peptides, 93 chains. Longest chain 14 peptides. Score 0.343 Round 3: 517 peptides, 92 chains. Longest chain 14 peptides. Score 0.363 Round 4: 492 peptides, 89 chains. Longest chain 16 peptides. Score 0.348 Round 5: 504 peptides, 91 chains. Longest chain 15 peptides. Score 0.352 Taking the results from Round 3 Chains 94, Residues 425, Estimated correctness of the model 0.0 % 4 chains (23 residues) have been docked in sequence ------------------------------------------------------ 20098 reflections ( 98.18 % complete ) and 22916 restraints for refining 9950 atoms. 21250 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2407 (Rfree = 0.000) for 9950 atoms. Found 75 (75 requested) and removed 48 (37 requested) atoms. Cycle 37: After refmac, R = 0.2334 (Rfree = 0.000) for 9954 atoms. Found 75 (75 requested) and removed 48 (37 requested) atoms. Cycle 38: After refmac, R = 0.2236 (Rfree = 0.000) for 9952 atoms. Found 57 (75 requested) and removed 51 (37 requested) atoms. Cycle 39: After refmac, R = 0.2201 (Rfree = 0.000) for 9942 atoms. Found 62 (75 requested) and removed 47 (37 requested) atoms. Cycle 40: After refmac, R = 0.2183 (Rfree = 0.000) for 9942 atoms. Found 75 (75 requested) and removed 48 (37 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 3.42 Search for helices and strands: 0 residues in 0 chains, 10218 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 10231 seeds are put forward Round 1: 392 peptides, 84 chains. Longest chain 10 peptides. Score 0.247 Round 2: 463 peptides, 90 chains. Longest chain 11 peptides. Score 0.307 Round 3: 473 peptides, 86 chains. Longest chain 16 peptides. Score 0.341 Round 4: 457 peptides, 87 chains. Longest chain 9 peptides. Score 0.316 Round 5: 476 peptides, 86 chains. Longest chain 11 peptides. Score 0.345 Taking the results from Round 5 Chains 86, Residues 390, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 20098 reflections ( 98.18 % complete ) and 23519 restraints for refining 9950 atoms. 22001 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2220 (Rfree = 0.000) for 9950 atoms. Found 70 (75 requested) and removed 48 (37 requested) atoms. Cycle 42: After refmac, R = 0.2181 (Rfree = 0.000) for 9942 atoms. Found 75 (75 requested) and removed 46 (37 requested) atoms. Cycle 43: After refmac, R = 0.2108 (Rfree = 0.000) for 9949 atoms. Found 63 (75 requested) and removed 47 (37 requested) atoms. Cycle 44: After refmac, R = 0.2123 (Rfree = 0.000) for 9942 atoms. Found 68 (75 requested) and removed 43 (37 requested) atoms. Cycle 45: After refmac, R = 0.2101 (Rfree = 0.000) for 9952 atoms. Found 75 (75 requested) and removed 44 (37 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 3.42 Search for helices and strands: 0 residues in 0 chains, 10255 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 10269 seeds are put forward Round 1: 358 peptides, 81 chains. Longest chain 9 peptides. Score 0.217 Round 2: 424 peptides, 82 chains. Longest chain 14 peptides. Score 0.301 Round 3: 429 peptides, 76 chains. Longest chain 13 peptides. Score 0.340 Round 4: 425 peptides, 77 chains. Longest chain 13 peptides. Score 0.330 Round 5: 435 peptides, 74 chains. Longest chain 12 peptides. Score 0.358 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 74, Residues 361, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1vrb-3_warpNtrace.pdb as input Building loops using Loopy2018 74 chains (361 residues) following loop building 3 chains (15 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20098 reflections ( 98.18 % complete ) and 23621 restraints for refining 9951 atoms. 22207 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2258 (Rfree = 0.000) for 9951 atoms. Found 0 (75 requested) and removed 37 (37 requested) atoms. Cycle 47: After refmac, R = 0.2171 (Rfree = 0.000) for 9889 atoms. Found 0 (74 requested) and removed 37 (37 requested) atoms. Cycle 48: After refmac, R = 0.2124 (Rfree = 0.000) for 9837 atoms. Found 0 (74 requested) and removed 37 (37 requested) atoms. Cycle 49: After refmac, R = 0.1858 (Rfree = 0.000) for 9787 atoms. Found 0 (73 requested) and removed 36 (36 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:07:25 GMT 2018 Job finished. TimeTaking 101.55 Used memory is bytes: 11616208