Mon 24 Dec 07:34:25 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 1z82-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1z82-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1z82-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1z82-3.6-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/1z82-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1z82-3.6-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 07:34:30 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/1z82-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1z82-3.6-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 400 and 0 Target number of residues in the AU: 400 Target solvent content: 0.6446 Checking the provided sequence file Detected sequence length: 335 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 670 Adjusted target solvent content: 0.40 Input MTZ file: 1z82-3.6-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: 4 Cell parameters: 65.170 67.461 75.617 90.000 113.643 90.000 Input sequence file: 1z82-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 5360 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: 29.850 3.600 Wilson plot Bfac: 74.45 7073 reflections ( 99.58 % complete ) and 0 restraints for refining 5914 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3231 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3129 (Rfree = 0.000) for 5914 atoms. Found 37 (37 requested) and removed 47 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.54 4.05 Search for helices and strands: 0 residues in 0 chains, 6023 seeds are put forward NCS extension: 0 residues added, 6023 seeds are put forward Round 1: 167 peptides, 39 chains. Longest chain 7 peptides. Score 0.204 Round 2: 223 peptides, 42 chains. Longest chain 14 peptides. Score 0.336 Round 3: 256 peptides, 42 chains. Longest chain 14 peptides. Score 0.425 Round 4: 258 peptides, 43 chains. Longest chain 14 peptides. Score 0.419 Round 5: 274 peptides, 44 chains. Longest chain 14 peptides. Score 0.448 Taking the results from Round 5 Chains 44, Residues 230, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7073 reflections ( 99.58 % complete ) and 11397 restraints for refining 4857 atoms. 10508 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2624 (Rfree = 0.000) for 4857 atoms. Found 31 (31 requested) and removed 31 (15 requested) atoms. Cycle 2: After refmac, R = 0.2449 (Rfree = 0.000) for 4770 atoms. Found 31 (31 requested) and removed 27 (15 requested) atoms. Cycle 3: After refmac, R = 0.2355 (Rfree = 0.000) for 4739 atoms. Found 30 (30 requested) and removed 31 (15 requested) atoms. Cycle 4: After refmac, R = 0.2097 (Rfree = 0.000) for 4700 atoms. Found 28 (30 requested) and removed 24 (15 requested) atoms. Cycle 5: After refmac, R = 0.2092 (Rfree = 0.000) for 4680 atoms. Found 25 (30 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 3.96 Search for helices and strands: 0 residues in 0 chains, 4880 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 4902 seeds are put forward Round 1: 193 peptides, 40 chains. Longest chain 9 peptides. Score 0.273 Round 2: 243 peptides, 46 chains. Longest chain 10 peptides. Score 0.344 Round 3: 256 peptides, 46 chains. Longest chain 10 peptides. Score 0.380 Round 4: 263 peptides, 45 chains. Longest chain 13 peptides. Score 0.409 Round 5: 260 peptides, 47 chains. Longest chain 15 peptides. Score 0.379 Taking the results from Round 4 Chains 45, Residues 218, Estimated correctness of the model 0.0 % 6 chains (28 residues) have been docked in sequence ------------------------------------------------------ 7073 reflections ( 99.58 % complete ) and 9906 restraints for refining 4326 atoms. 9013 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1998 (Rfree = 0.000) for 4326 atoms. Found 19 (27 requested) and removed 33 (13 requested) atoms. Cycle 7: After refmac, R = 0.1812 (Rfree = 0.000) for 4294 atoms. Found 14 (27 requested) and removed 23 (13 requested) atoms. Cycle 8: After refmac, R = 0.1781 (Rfree = 0.000) for 4275 atoms. Found 18 (27 requested) and removed 14 (13 requested) atoms. Cycle 9: After refmac, R = 0.1737 (Rfree = 0.000) for 4268 atoms. Found 14 (27 requested) and removed 16 (13 requested) atoms. Cycle 10: After refmac, R = 0.1685 (Rfree = 0.000) for 4263 atoms. Found 9 (27 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.49 3.99 Search for helices and strands: 0 residues in 0 chains, 4470 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4485 seeds are put forward Round 1: 240 peptides, 47 chains. Longest chain 12 peptides. Score 0.324 Round 2: 294 peptides, 52 chains. Longest chain 12 peptides. Score 0.412 Round 3: 310 peptides, 50 chains. Longest chain 16 peptides. Score 0.473 Round 4: 298 peptides, 47 chains. Longest chain 20 peptides. Score 0.475 Round 5: 310 peptides, 49 chains. Longest chain 16 peptides. Score 0.483 Taking the results from Round 5 Chains 49, Residues 261, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7073 reflections ( 99.58 % complete ) and 10407 restraints for refining 4524 atoms. 9399 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1889 (Rfree = 0.000) for 4524 atoms. Found 20 (29 requested) and removed 32 (14 requested) atoms. Cycle 12: After refmac, R = 0.1622 (Rfree = 0.000) for 4472 atoms. Found 19 (28 requested) and removed 30 (14 requested) atoms. Cycle 13: After refmac, R = 0.1536 (Rfree = 0.000) for 4446 atoms. Found 10 (28 requested) and removed 17 (14 requested) atoms. Cycle 14: After refmac, R = 0.1505 (Rfree = 0.000) for 4434 atoms. Found 14 (28 requested) and removed 18 (14 requested) atoms. Cycle 15: After refmac, R = 0.1613 (Rfree = 0.000) for 4425 atoms. Found 27 (28 requested) and removed 20 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 3.93 Search for helices and strands: 0 residues in 0 chains, 4640 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4658 seeds are put forward Round 1: 216 peptides, 42 chains. Longest chain 10 peptides. Score 0.316 Round 2: 270 peptides, 48 chains. Longest chain 11 peptides. Score 0.394 Round 3: 266 peptides, 46 chains. Longest chain 13 peptides. Score 0.406 Round 4: 290 peptides, 46 chains. Longest chain 17 peptides. Score 0.466 Round 5: 293 peptides, 52 chains. Longest chain 14 peptides. Score 0.409 Taking the results from Round 4 Chains 47, Residues 244, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 7073 reflections ( 99.58 % complete ) and 10636 restraints for refining 4608 atoms. 9670 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1812 (Rfree = 0.000) for 4608 atoms. Found 25 (29 requested) and removed 38 (14 requested) atoms. Cycle 17: After refmac, R = 0.1736 (Rfree = 0.000) for 4567 atoms. Found 29 (29 requested) and removed 24 (14 requested) atoms. Cycle 18: After refmac, R = 0.1634 (Rfree = 0.000) for 4562 atoms. Found 17 (29 requested) and removed 20 (14 requested) atoms. Cycle 19: After refmac, R = 0.1580 (Rfree = 0.000) for 4550 atoms. Found 29 (29 requested) and removed 17 (14 requested) atoms. Cycle 20: After refmac, R = 0.1689 (Rfree = 0.000) for 4555 atoms. Found 29 (29 requested) and removed 24 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 3.95 Search for helices and strands: 0 residues in 0 chains, 4786 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 4809 seeds are put forward Round 1: 177 peptides, 38 chains. Longest chain 8 peptides. Score 0.249 Round 2: 235 peptides, 43 chains. Longest chain 19 peptides. Score 0.357 Round 3: 229 peptides, 36 chains. Longest chain 23 peptides. Score 0.423 Round 4: 225 peptides, 40 chains. Longest chain 15 peptides. Score 0.365 Round 5: 251 peptides, 42 chains. Longest chain 18 peptides. Score 0.412 Taking the results from Round 3 Chains 38, Residues 193, Estimated correctness of the model 0.0 % 6 chains (31 residues) have been docked in sequence ------------------------------------------------------ 7073 reflections ( 99.58 % complete ) and 10747 restraints for refining 4584 atoms. 9951 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1750 (Rfree = 0.000) for 4584 atoms. Found 26 (29 requested) and removed 33 (14 requested) atoms. Cycle 22: After refmac, R = 0.1787 (Rfree = 0.000) for 4565 atoms. Found 29 (29 requested) and removed 27 (14 requested) atoms. Cycle 23: After refmac, R = 0.1800 (Rfree = 0.000) for 4555 atoms. Found 29 (29 requested) and removed 21 (14 requested) atoms. Cycle 24: After refmac, R = 0.1719 (Rfree = 0.000) for 4558 atoms. Found 29 (29 requested) and removed 19 (14 requested) atoms. Cycle 25: After refmac, R = 0.1300 (Rfree = 0.000) for 4561 atoms. Found 3 (29 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.46 3.96 Search for helices and strands: 0 residues in 0 chains, 4735 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 4752 seeds are put forward Round 1: 188 peptides, 39 chains. Longest chain 9 peptides. Score 0.270 Round 2: 209 peptides, 39 chains. Longest chain 11 peptides. Score 0.332 Round 3: 226 peptides, 42 chains. Longest chain 11 peptides. Score 0.344 Round 4: 230 peptides, 43 chains. Longest chain 11 peptides. Score 0.343 Round 5: 242 peptides, 40 chains. Longest chain 15 peptides. Score 0.411 Taking the results from Round 5 Chains 40, Residues 202, Estimated correctness of the model 0.0 % 4 chains (18 residues) have been docked in sequence ------------------------------------------------------ 7073 reflections ( 99.58 % complete ) and 10752 restraints for refining 4574 atoms. 9941 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1728 (Rfree = 0.000) for 4574 atoms. Found 24 (29 requested) and removed 29 (14 requested) atoms. Cycle 27: After refmac, R = 0.1692 (Rfree = 0.000) for 4552 atoms. Found 29 (29 requested) and removed 22 (14 requested) atoms. Cycle 28: After refmac, R = 0.1843 (Rfree = 0.000) for 4546 atoms. Found 29 (29 requested) and removed 25 (14 requested) atoms. Cycle 29: After refmac, R = 0.1378 (Rfree = 0.000) for 4545 atoms. Found 9 (29 requested) and removed 18 (14 requested) atoms. Cycle 30: After refmac, R = 0.1317 (Rfree = 0.000) for 4526 atoms. Found 13 (29 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.45 3.95 Search for helices and strands: 0 residues in 0 chains, 4703 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 4717 seeds are put forward Round 1: 195 peptides, 42 chains. Longest chain 10 peptides. Score 0.253 Round 2: 229 peptides, 40 chains. Longest chain 13 peptides. Score 0.376 Round 3: 245 peptides, 47 chains. Longest chain 10 peptides. Score 0.338 Round 4: 229 peptides, 41 chains. Longest chain 10 peptides. Score 0.364 Round 5: 243 peptides, 44 chains. Longest chain 11 peptides. Score 0.368 Taking the results from Round 2 Chains 40, Residues 189, Estimated correctness of the model 0.0 % 5 chains (23 residues) have been docked in sequence ------------------------------------------------------ 7073 reflections ( 99.58 % complete ) and 10474 restraints for refining 4546 atoms. 9704 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1601 (Rfree = 0.000) for 4546 atoms. Found 14 (29 requested) and removed 29 (14 requested) atoms. Cycle 32: After refmac, R = 0.1612 (Rfree = 0.000) for 4524 atoms. Found 29 (29 requested) and removed 24 (14 requested) atoms. Cycle 33: After refmac, R = 0.1720 (Rfree = 0.000) for 4522 atoms. Found 29 (29 requested) and removed 21 (14 requested) atoms. Cycle 34: After refmac, R = 0.1359 (Rfree = 0.000) for 4522 atoms. Found 8 (29 requested) and removed 18 (14 requested) atoms. Cycle 35: After refmac, R = 0.1302 (Rfree = 0.000) for 4502 atoms. Found 9 (28 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.45 3.95 Search for helices and strands: 0 residues in 0 chains, 4686 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4702 seeds are put forward Round 1: 184 peptides, 38 chains. Longest chain 8 peptides. Score 0.271 Round 2: 213 peptides, 36 chains. Longest chain 11 peptides. Score 0.380 Round 3: 214 peptides, 37 chains. Longest chain 12 peptides. Score 0.371 Round 4: 235 peptides, 35 chains. Longest chain 15 peptides. Score 0.450 Round 5: 237 peptides, 40 chains. Longest chain 13 peptides. Score 0.398 Taking the results from Round 4 Chains 35, Residues 200, Estimated correctness of the model 0.0 % 6 chains (43 residues) have been docked in sequence ------------------------------------------------------ 7073 reflections ( 99.58 % complete ) and 10620 restraints for refining 4623 atoms. 9724 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1763 (Rfree = 0.000) for 4623 atoms. Found 25 (29 requested) and removed 33 (14 requested) atoms. Cycle 37: After refmac, R = 0.1767 (Rfree = 0.000) for 4603 atoms. Found 23 (29 requested) and removed 26 (14 requested) atoms. Cycle 38: After refmac, R = 0.1712 (Rfree = 0.000) for 4588 atoms. Found 16 (29 requested) and removed 22 (14 requested) atoms. Cycle 39: After refmac, R = 0.1744 (Rfree = 0.000) for 4578 atoms. Found 19 (29 requested) and removed 20 (14 requested) atoms. Cycle 40: After refmac, R = 0.1675 (Rfree = 0.000) for 4567 atoms. Found 18 (29 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.41 3.90 Search for helices and strands: 0 residues in 0 chains, 4754 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4771 seeds are put forward Round 1: 160 peptides, 35 chains. Longest chain 8 peptides. Score 0.235 Round 2: 188 peptides, 36 chains. Longest chain 9 peptides. Score 0.308 Round 3: 191 peptides, 34 chains. Longest chain 11 peptides. Score 0.343 Round 4: 204 peptides, 36 chains. Longest chain 11 peptides. Score 0.355 Round 5: 199 peptides, 34 chains. Longest chain 9 peptides. Score 0.365 Taking the results from Round 5 Chains 34, Residues 165, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 7073 reflections ( 99.58 % complete ) and 11126 restraints for refining 4630 atoms. 10486 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1781 (Rfree = 0.000) for 4630 atoms. Found 29 (29 requested) and removed 32 (14 requested) atoms. Cycle 42: After refmac, R = 0.1780 (Rfree = 0.000) for 4618 atoms. Found 23 (29 requested) and removed 22 (14 requested) atoms. Cycle 43: After refmac, R = 0.1844 (Rfree = 0.000) for 4609 atoms. Found 29 (29 requested) and removed 22 (14 requested) atoms. Cycle 44: After refmac, R = 0.1522 (Rfree = 0.000) for 4607 atoms. Found 11 (29 requested) and removed 19 (14 requested) atoms. Cycle 45: After refmac, R = 0.1394 (Rfree = 0.000) for 4590 atoms. Found 13 (29 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.44 3.94 Search for helices and strands: 0 residues in 0 chains, 4776 seeds are put forward NCS extension: 0 residues added, 4776 seeds are put forward Round 1: 122 peptides, 27 chains. Longest chain 7 peptides. Score 0.219 Round 2: 163 peptides, 33 chains. Longest chain 11 peptides. Score 0.271 Round 3: 158 peptides, 32 chains. Longest chain 8 peptides. Score 0.269 Round 4: 156 peptides, 31 chains. Longest chain 10 peptides. Score 0.276 Round 5: 154 peptides, 29 chains. Longest chain 9 peptides. Score 0.297 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 125, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1z82-3_warpNtrace.pdb as input Building loops using Loopy2018 29 chains (125 residues) following loop building 2 chains (6 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7073 reflections ( 99.58 % complete ) and 11122 restraints for refining 4576 atoms. 10638 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2014 (Rfree = 0.000) for 4576 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2072 (Rfree = 0.000) for 4549 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.1912 (Rfree = 0.000) for 4523 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.1461 (Rfree = 0.000) for 4502 atoms. TimeTaking 51.38