Sun 23 Dec 22:22:55 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 1vll-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vll-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vll-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vll-3.8-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/1vll-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vll-3.8-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 22:23:04 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/1vll-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vll-3.8-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 405 and 0 Target number of residues in the AU: 405 Target solvent content: 0.6921 Checking the provided sequence file Detected sequence length: 334 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 668 Adjusted target solvent content: 0.49 Input MTZ file: 1vll-3.8-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: 57.294 93.405 133.015 90.000 90.000 90.000 Input sequence file: 1vll-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 5344 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: 76.441 3.800 Wilson plot Bfac: 112.68 7455 reflections ( 99.96 % complete ) and 0 restraints for refining 5947 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3772 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3380 (Rfree = 0.000) for 5947 atoms. Found 32 (32 requested) and removed 47 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.97 4.02 Search for helices and strands: 0 residues in 0 chains, 6056 seeds are put forward NCS extension: 0 residues added, 6056 seeds are put forward Round 1: 220 peptides, 42 chains. Longest chain 12 peptides. Score 0.310 Round 2: 287 peptides, 50 chains. Longest chain 13 peptides. Score 0.388 Round 3: 302 peptides, 48 chains. Longest chain 16 peptides. Score 0.441 Round 4: 325 peptides, 48 chains. Longest chain 16 peptides. Score 0.489 Round 5: 329 peptides, 42 chains. Longest chain 17 peptides. Score 0.549 Taking the results from Round 5 Chains 42, Residues 287, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7455 reflections ( 99.96 % complete ) and 11625 restraints for refining 4832 atoms. 10499 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2792 (Rfree = 0.000) for 4832 atoms. Found 7 (26 requested) and removed 35 (13 requested) atoms. Cycle 2: After refmac, R = 0.2505 (Rfree = 0.000) for 4737 atoms. Found 4 (26 requested) and removed 30 (13 requested) atoms. Cycle 3: After refmac, R = 0.2427 (Rfree = 0.000) for 4685 atoms. Found 6 (25 requested) and removed 27 (12 requested) atoms. Cycle 4: After refmac, R = 0.2283 (Rfree = 0.000) for 4650 atoms. Found 10 (25 requested) and removed 26 (12 requested) atoms. Cycle 5: After refmac, R = 0.2294 (Rfree = 0.000) for 4620 atoms. Found 5 (25 requested) and removed 21 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.92 3.97 Search for helices and strands: 0 residues in 0 chains, 4799 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 4817 seeds are put forward Round 1: 285 peptides, 53 chains. Longest chain 13 peptides. Score 0.354 Round 2: 319 peptides, 46 chains. Longest chain 16 peptides. Score 0.495 Round 3: 312 peptides, 44 chains. Longest chain 16 peptides. Score 0.499 Round 4: 325 peptides, 43 chains. Longest chain 21 peptides. Score 0.533 Round 5: 334 peptides, 44 chains. Longest chain 23 peptides. Score 0.542 Taking the results from Round 5 Chains 47, Residues 290, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 7455 reflections ( 99.96 % complete ) and 11238 restraints for refining 4820 atoms. 10081 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2478 (Rfree = 0.000) for 4820 atoms. Found 9 (26 requested) and removed 53 (13 requested) atoms. Cycle 7: After refmac, R = 0.2463 (Rfree = 0.000) for 4741 atoms. Found 8 (26 requested) and removed 41 (13 requested) atoms. Cycle 8: After refmac, R = 0.2261 (Rfree = 0.000) for 4683 atoms. Found 4 (25 requested) and removed 29 (12 requested) atoms. Cycle 9: After refmac, R = 0.1940 (Rfree = 0.000) for 4642 atoms. Found 1 (25 requested) and removed 18 (12 requested) atoms. Cycle 10: After refmac, R = 0.1990 (Rfree = 0.000) for 4619 atoms. Found 2 (25 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.96 4.01 Search for helices and strands: 0 residues in 0 chains, 4790 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4805 seeds are put forward Round 1: 272 peptides, 46 chains. Longest chain 12 peptides. Score 0.394 Round 2: 299 peptides, 44 chains. Longest chain 16 peptides. Score 0.472 Round 3: 308 peptides, 43 chains. Longest chain 21 peptides. Score 0.500 Round 4: 305 peptides, 43 chains. Longest chain 17 peptides. Score 0.494 Round 5: 301 peptides, 38 chains. Longest chain 18 peptides. Score 0.530 Taking the results from Round 5 Chains 39, Residues 263, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 7455 reflections ( 99.96 % complete ) and 11496 restraints for refining 4831 atoms. 10423 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2482 (Rfree = 0.000) for 4831 atoms. Found 7 (26 requested) and removed 39 (13 requested) atoms. Cycle 12: After refmac, R = 0.2449 (Rfree = 0.000) for 4762 atoms. Found 8 (26 requested) and removed 30 (13 requested) atoms. Cycle 13: After refmac, R = 0.2341 (Rfree = 0.000) for 4721 atoms. Found 6 (26 requested) and removed 27 (13 requested) atoms. Cycle 14: After refmac, R = 0.1957 (Rfree = 0.000) for 4689 atoms. Found 4 (25 requested) and removed 16 (12 requested) atoms. Cycle 15: After refmac, R = 0.1916 (Rfree = 0.000) for 4671 atoms. Found 0 (25 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.94 3.99 Search for helices and strands: 0 residues in 0 chains, 4818 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4834 seeds are put forward Round 1: 250 peptides, 48 chains. Longest chain 10 peptides. Score 0.321 Round 2: 293 peptides, 48 chains. Longest chain 20 peptides. Score 0.421 Round 3: 283 peptides, 42 chains. Longest chain 18 peptides. Score 0.457 Round 4: 317 peptides, 43 chains. Longest chain 20 peptides. Score 0.518 Round 5: 301 peptides, 45 chains. Longest chain 16 peptides. Score 0.467 Taking the results from Round 4 Chains 46, Residues 274, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 7455 reflections ( 99.96 % complete ) and 11210 restraints for refining 4832 atoms. 10083 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2610 (Rfree = 0.000) for 4832 atoms. Found 6 (26 requested) and removed 35 (13 requested) atoms. Cycle 17: After refmac, R = 0.2310 (Rfree = 0.000) for 4768 atoms. Found 8 (26 requested) and removed 30 (13 requested) atoms. Cycle 18: After refmac, R = 0.2315 (Rfree = 0.000) for 4729 atoms. Found 6 (26 requested) and removed 24 (13 requested) atoms. Cycle 19: After refmac, R = 0.2208 (Rfree = 0.000) for 4697 atoms. Found 15 (25 requested) and removed 18 (12 requested) atoms. Cycle 20: After refmac, R = 0.2106 (Rfree = 0.000) for 4682 atoms. Found 11 (25 requested) and removed 22 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.90 3.95 Search for helices and strands: 0 residues in 0 chains, 4879 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 4893 seeds are put forward Round 1: 223 peptides, 44 chains. Longest chain 13 peptides. Score 0.296 Round 2: 258 peptides, 43 chains. Longest chain 17 peptides. Score 0.392 Round 3: 280 peptides, 43 chains. Longest chain 18 peptides. Score 0.441 Round 4: 279 peptides, 43 chains. Longest chain 19 peptides. Score 0.439 Round 5: 267 peptides, 39 chains. Longest chain 17 peptides. Score 0.451 Taking the results from Round 5 Chains 40, Residues 228, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 7455 reflections ( 99.96 % complete ) and 11669 restraints for refining 4833 atoms. 10760 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2450 (Rfree = 0.000) for 4833 atoms. Found 12 (26 requested) and removed 20 (13 requested) atoms. Cycle 22: After refmac, R = 0.2259 (Rfree = 0.000) for 4800 atoms. Found 22 (26 requested) and removed 22 (13 requested) atoms. Cycle 23: After refmac, R = 0.2237 (Rfree = 0.000) for 4779 atoms. Found 26 (26 requested) and removed 19 (13 requested) atoms. Cycle 24: After refmac, R = 0.1956 (Rfree = 0.000) for 4772 atoms. Found 4 (26 requested) and removed 15 (13 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1937 (Rfree = 0.000) for 4755 atoms. Found 2 (26 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.97 4.02 Search for helices and strands: 0 residues in 0 chains, 4900 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 4926 seeds are put forward Round 1: 224 peptides, 45 chains. Longest chain 12 peptides. Score 0.288 Round 2: 254 peptides, 42 chains. Longest chain 13 peptides. Score 0.393 Round 3: 252 peptides, 38 chains. Longest chain 19 peptides. Score 0.428 Round 4: 255 peptides, 38 chains. Longest chain 13 peptides. Score 0.435 Round 5: 263 peptides, 37 chains. Longest chain 23 peptides. Score 0.462 Taking the results from Round 5 Chains 39, Residues 226, Estimated correctness of the model 0.0 % 3 chains (33 residues) have been docked in sequence ------------------------------------------------------ 7455 reflections ( 99.96 % complete ) and 11172 restraints for refining 4833 atoms. 10191 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2176 (Rfree = 0.000) for 4833 atoms. Found 26 (26 requested) and removed 32 (13 requested) atoms. Cycle 27: After refmac, R = 0.2188 (Rfree = 0.000) for 4808 atoms. Found 24 (26 requested) and removed 70 (13 requested) atoms. Cycle 28: After refmac, R = 0.2140 (Rfree = 0.000) for 4745 atoms. Found 26 (26 requested) and removed 28 (13 requested) atoms. Cycle 29: After refmac, R = 0.2033 (Rfree = 0.000) for 4729 atoms. Found 26 (26 requested) and removed 41 (13 requested) atoms. Cycle 30: After refmac, R = 0.1652 (Rfree = 0.000) for 4703 atoms. Found 4 (25 requested) and removed 22 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.93 3.98 Search for helices and strands: 0 residues in 0 chains, 4822 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 4835 seeds are put forward Round 1: 222 peptides, 47 chains. Longest chain 8 peptides. Score 0.260 Round 2: 229 peptides, 36 chains. Longest chain 14 peptides. Score 0.396 Round 3: 246 peptides, 36 chains. Longest chain 14 peptides. Score 0.435 Round 4: 244 peptides, 40 chains. Longest chain 14 peptides. Score 0.390 Round 5: 242 peptides, 35 chains. Longest chain 14 peptides. Score 0.436 Taking the results from Round 5 Chains 35, Residues 207, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 7455 reflections ( 99.96 % complete ) and 11533 restraints for refining 4832 atoms. 10662 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2141 (Rfree = 0.000) for 4832 atoms. Found 24 (26 requested) and removed 43 (13 requested) atoms. Cycle 32: After refmac, R = 0.2117 (Rfree = 0.000) for 4789 atoms. Found 26 (26 requested) and removed 40 (13 requested) atoms. Cycle 33: After refmac, R = 0.2026 (Rfree = 0.000) for 4758 atoms. Found 26 (26 requested) and removed 29 (13 requested) atoms. Cycle 34: After refmac, R = 0.1605 (Rfree = 0.000) for 4743 atoms. Found 1 (26 requested) and removed 20 (13 requested) atoms. Cycle 35: After refmac, R = 0.1670 (Rfree = 0.000) for 4715 atoms. Found 5 (25 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.98 4.03 Search for helices and strands: 0 residues in 0 chains, 4862 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 4882 seeds are put forward Round 1: 211 peptides, 46 chains. Longest chain 8 peptides. Score 0.242 Round 2: 248 peptides, 46 chains. Longest chain 10 peptides. Score 0.337 Round 3: 235 peptides, 41 chains. Longest chain 12 peptides. Score 0.358 Round 4: 241 peptides, 41 chains. Longest chain 14 peptides. Score 0.372 Round 5: 234 peptides, 41 chains. Longest chain 15 peptides. Score 0.355 Taking the results from Round 4 Chains 41, Residues 200, Estimated correctness of the model 0.0 % 4 chains (20 residues) have been docked in sequence ------------------------------------------------------ 7455 reflections ( 99.96 % complete ) and 11597 restraints for refining 4832 atoms. 10777 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2277 (Rfree = 0.000) for 4832 atoms. Found 20 (26 requested) and removed 26 (13 requested) atoms. Cycle 37: After refmac, R = 0.2232 (Rfree = 0.000) for 4810 atoms. Found 26 (26 requested) and removed 26 (13 requested) atoms. Cycle 38: After refmac, R = 0.2197 (Rfree = 0.000) for 4797 atoms. Found 26 (26 requested) and removed 28 (13 requested) atoms. Cycle 39: After refmac, R = 0.2113 (Rfree = 0.000) for 4784 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. Cycle 40: After refmac, R = 0.2144 (Rfree = 0.000) for 4783 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.93 3.98 Search for helices and strands: 0 residues in 0 chains, 4957 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 4979 seeds are put forward Round 1: 196 peptides, 40 chains. Longest chain 11 peptides. Score 0.269 Round 2: 219 peptides, 37 chains. Longest chain 10 peptides. Score 0.362 Round 3: 212 peptides, 36 chains. Longest chain 11 peptides. Score 0.355 Round 4: 220 peptides, 34 chains. Longest chain 13 peptides. Score 0.396 Round 5: 223 peptides, 34 chains. Longest chain 13 peptides. Score 0.403 Taking the results from Round 5 Chains 34, Residues 189, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 7455 reflections ( 99.96 % complete ) and 11798 restraints for refining 4832 atoms. 11041 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2191 (Rfree = 0.000) for 4832 atoms. Found 12 (26 requested) and removed 29 (13 requested) atoms. Cycle 42: After refmac, R = 0.2129 (Rfree = 0.000) for 4793 atoms. Found 26 (26 requested) and removed 20 (13 requested) atoms. Cycle 43: After refmac, R = 0.2227 (Rfree = 0.000) for 4791 atoms. Found 26 (26 requested) and removed 21 (13 requested) atoms. Cycle 44: After refmac, R = 0.2139 (Rfree = 0.000) for 4784 atoms. Found 26 (26 requested) and removed 29 (13 requested) atoms. Cycle 45: After refmac, R = 0.2134 (Rfree = 0.000) for 4770 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.97 4.02 Search for helices and strands: 0 residues in 0 chains, 4923 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 4937 seeds are put forward Round 1: 170 peptides, 36 chains. Longest chain 9 peptides. Score 0.244 Round 2: 186 peptides, 35 chains. Longest chain 14 peptides. Score 0.300 Round 3: 189 peptides, 37 chains. Longest chain 10 peptides. Score 0.285 Round 4: 190 peptides, 34 chains. Longest chain 15 peptides. Score 0.322 Round 5: 183 peptides, 33 chains. Longest chain 15 peptides. Score 0.315 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 156, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vll-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7455 reflections ( 99.96 % complete ) and 11882 restraints for refining 4799 atoms. 11292 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2469 (Rfree = 0.000) for 4799 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2310 (Rfree = 0.000) for 4768 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2362 (Rfree = 0.000) for 4742 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2479 (Rfree = 0.000) for 4715 atoms. TimeTaking 68.42