Sun 23 Dec 22:23:08 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-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vll-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vll-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vll-3.2-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-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vll-3.2-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 22:23:18 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-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vll-3.2-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 437 and 0 Target number of residues in the AU: 437 Target solvent content: 0.6678 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-3.2-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-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 5344 target number of atoms Had to go as low as 0.70 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 3.200 Wilson plot Bfac: 90.38 12307 reflections ( 99.98 % complete ) and 0 restraints for refining 5892 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.3490 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2948 (Rfree = 0.000) for 5892 atoms. Found 27 (52 requested) and removed 55 (26 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 3.56 Search for helices and strands: 0 residues in 0 chains, 5993 seeds are put forward NCS extension: 0 residues added, 5993 seeds are put forward Round 1: 355 peptides, 57 chains. Longest chain 16 peptides. Score 0.470 Round 2: 391 peptides, 51 chains. Longest chain 24 peptides. Score 0.587 Round 3: 404 peptides, 45 chains. Longest chain 28 peptides. Score 0.652 Round 4: 408 peptides, 49 chains. Longest chain 24 peptides. Score 0.630 Round 5: 397 peptides, 46 chains. Longest chain 29 peptides. Score 0.634 Taking the results from Round 3 Chains 47, Residues 359, Estimated correctness of the model 54.3 % 6 chains (93 residues) have been docked in sequence ------------------------------------------------------ 12307 reflections ( 99.98 % complete ) and 10067 restraints for refining 4869 atoms. 8352 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2759 (Rfree = 0.000) for 4869 atoms. Found 14 (43 requested) and removed 61 (21 requested) atoms. Cycle 2: After refmac, R = 0.2629 (Rfree = 0.000) for 4764 atoms. Found 11 (43 requested) and removed 32 (21 requested) atoms. Cycle 3: After refmac, R = 0.2594 (Rfree = 0.000) for 4726 atoms. Found 7 (42 requested) and removed 25 (21 requested) atoms. Cycle 4: After refmac, R = 0.2605 (Rfree = 0.000) for 4695 atoms. Found 4 (42 requested) and removed 24 (21 requested) atoms. Cycle 5: After refmac, R = 0.2554 (Rfree = 0.000) for 4666 atoms. Found 7 (41 requested) and removed 25 (20 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.49 3.54 Search for helices and strands: 0 residues in 0 chains, 4843 seeds are put forward NCS extension: 28 residues added (5 deleted due to clashes), 4871 seeds are put forward Round 1: 346 peptides, 54 chains. Longest chain 22 peptides. Score 0.478 Round 2: 384 peptides, 51 chains. Longest chain 23 peptides. Score 0.575 Round 3: 385 peptides, 48 chains. Longest chain 25 peptides. Score 0.600 Round 4: 395 peptides, 47 chains. Longest chain 27 peptides. Score 0.624 Round 5: 401 peptides, 48 chains. Longest chain 25 peptides. Score 0.626 Taking the results from Round 5 Chains 54, Residues 353, Estimated correctness of the model 47.9 % 8 chains (93 residues) have been docked in sequence ------------------------------------------------------ 12307 reflections ( 99.98 % complete ) and 10324 restraints for refining 4878 atoms. 8660 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2952 (Rfree = 0.000) for 4878 atoms. Found 14 (43 requested) and removed 62 (21 requested) atoms. Cycle 7: After refmac, R = 0.2632 (Rfree = 0.000) for 4798 atoms. Found 16 (43 requested) and removed 39 (21 requested) atoms. Cycle 8: After refmac, R = 0.2588 (Rfree = 0.000) for 4752 atoms. Found 12 (42 requested) and removed 42 (21 requested) atoms. Cycle 9: After refmac, R = 0.2773 (Rfree = 0.000) for 4712 atoms. Found 40 (42 requested) and removed 44 (21 requested) atoms. Cycle 10: After refmac, R = 0.2400 (Rfree = 0.000) for 4692 atoms. Found 10 (42 requested) and removed 37 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.47 3.52 Search for helices and strands: 0 residues in 0 chains, 4840 seeds are put forward NCS extension: 14 residues added (8 deleted due to clashes), 4854 seeds are put forward Round 1: 337 peptides, 49 chains. Longest chain 26 peptides. Score 0.504 Round 2: 375 peptides, 48 chains. Longest chain 26 peptides. Score 0.583 Round 3: 377 peptides, 45 chains. Longest chain 37 peptides. Score 0.610 Round 4: 385 peptides, 48 chains. Longest chain 27 peptides. Score 0.600 Round 5: 372 peptides, 45 chains. Longest chain 26 peptides. Score 0.601 Taking the results from Round 3 Chains 48, Residues 332, Estimated correctness of the model 43.7 % 7 chains (51 residues) have been docked in sequence ------------------------------------------------------ 12307 reflections ( 99.98 % complete ) and 10575 restraints for refining 4878 atoms. 9150 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2547 (Rfree = 0.000) for 4878 atoms. Found 10 (43 requested) and removed 54 (21 requested) atoms. Cycle 12: After refmac, R = 0.2324 (Rfree = 0.000) for 4789 atoms. Found 6 (43 requested) and removed 28 (21 requested) atoms. Cycle 13: After refmac, R = 0.2295 (Rfree = 0.000) for 4748 atoms. Found 4 (42 requested) and removed 28 (21 requested) atoms. Cycle 14: After refmac, R = 0.2221 (Rfree = 0.000) for 4717 atoms. Found 3 (42 requested) and removed 25 (21 requested) atoms. Cycle 15: After refmac, R = 0.2264 (Rfree = 0.000) for 4692 atoms. Found 2 (42 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.50 3.55 Search for helices and strands: 0 residues in 0 chains, 4862 seeds are put forward NCS extension: 45 residues added (9 deleted due to clashes), 4907 seeds are put forward Round 1: 327 peptides, 53 chains. Longest chain 24 peptides. Score 0.448 Round 2: 364 peptides, 50 chains. Longest chain 25 peptides. Score 0.547 Round 3: 364 peptides, 46 chains. Longest chain 27 peptides. Score 0.580 Round 4: 381 peptides, 46 chains. Longest chain 36 peptides. Score 0.609 Round 5: 381 peptides, 46 chains. Longest chain 27 peptides. Score 0.609 Taking the results from Round 5 Chains 47, Residues 335, Estimated correctness of the model 43.5 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 12307 reflections ( 99.98 % complete ) and 10724 restraints for refining 4878 atoms. 9343 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2509 (Rfree = 0.000) for 4878 atoms. Found 18 (43 requested) and removed 33 (21 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2547 (Rfree = 0.000) for 4845 atoms. Found 24 (43 requested) and removed 31 (21 requested) atoms. Cycle 18: After refmac, R = 0.2451 (Rfree = 0.000) for 4827 atoms. Found 13 (43 requested) and removed 29 (21 requested) atoms. Cycle 19: After refmac, R = 0.2729 (Rfree = 0.000) for 4802 atoms. Found 32 (43 requested) and removed 39 (21 requested) atoms. Cycle 20: After refmac, R = 0.2659 (Rfree = 0.000) for 4775 atoms. Found 26 (43 requested) and removed 36 (21 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.51 Search for helices and strands: 0 residues in 0 chains, 4952 seeds are put forward NCS extension: 27 residues added (4 deleted due to clashes), 4979 seeds are put forward Round 1: 324 peptides, 56 chains. Longest chain 19 peptides. Score 0.414 Round 2: 335 peptides, 46 chains. Longest chain 19 peptides. Score 0.526 Round 3: 350 peptides, 49 chains. Longest chain 26 peptides. Score 0.530 Round 4: 348 peptides, 44 chains. Longest chain 27 peptides. Score 0.567 Round 5: 333 peptides, 47 chains. Longest chain 21 peptides. Score 0.514 Taking the results from Round 4 Chains 45, Residues 304, Estimated correctness of the model 31.9 % 5 chains (32 residues) have been docked in sequence ------------------------------------------------------ 12307 reflections ( 99.98 % complete ) and 10749 restraints for refining 4876 atoms. 9491 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2422 (Rfree = 0.000) for 4876 atoms. Found 15 (43 requested) and removed 33 (21 requested) atoms. Cycle 22: After refmac, R = 0.2360 (Rfree = 0.000) for 4844 atoms. Found 16 (43 requested) and removed 31 (21 requested) atoms. Cycle 23: After refmac, R = 0.2197 (Rfree = 0.000) for 4821 atoms. Found 10 (43 requested) and removed 21 (21 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 24: After refmac, R = 0.2203 (Rfree = 0.000) for 4810 atoms. Found 8 (43 requested) and removed 24 (21 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2119 (Rfree = 0.000) for 4789 atoms. Found 2 (43 requested) and removed 22 (21 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.50 3.55 Search for helices and strands: 0 residues in 0 chains, 4920 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 4945 seeds are put forward Round 1: 292 peptides, 48 chains. Longest chain 17 peptides. Score 0.419 Round 2: 299 peptides, 45 chains. Longest chain 19 peptides. Score 0.463 Round 3: 315 peptides, 49 chains. Longest chain 19 peptides. Score 0.459 Round 4: 319 peptides, 46 chains. Longest chain 20 peptides. Score 0.495 Round 5: 299 peptides, 45 chains. Longest chain 19 peptides. Score 0.463 Taking the results from Round 4 Chains 47, Residues 273, Estimated correctness of the model 9.7 % 5 chains (44 residues) have been docked in sequence ------------------------------------------------------ 12307 reflections ( 99.98 % complete ) and 10826 restraints for refining 4877 atoms. 9624 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2381 (Rfree = 0.000) for 4877 atoms. Found 12 (43 requested) and removed 32 (21 requested) atoms. Cycle 27: After refmac, R = 0.2566 (Rfree = 0.000) for 4838 atoms. Found 28 (43 requested) and removed 29 (21 requested) atoms. Cycle 28: After refmac, R = 0.2249 (Rfree = 0.000) for 4827 atoms. Found 14 (43 requested) and removed 24 (21 requested) atoms. Cycle 29: After refmac, R = 0.2183 (Rfree = 0.000) for 4808 atoms. Found 7 (43 requested) and removed 22 (21 requested) atoms. Cycle 30: After refmac, R = 0.2145 (Rfree = 0.000) for 4791 atoms. Found 2 (43 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 3.53 Search for helices and strands: 0 residues in 0 chains, 4960 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 4984 seeds are put forward Round 1: 240 peptides, 46 chains. Longest chain 11 peptides. Score 0.317 Round 2: 287 peptides, 45 chains. Longest chain 20 peptides. Score 0.437 Round 3: 298 peptides, 45 chains. Longest chain 21 peptides. Score 0.461 Round 4: 289 peptides, 42 chains. Longest chain 28 peptides. Score 0.470 Round 5: 303 peptides, 46 chains. Longest chain 22 peptides. Score 0.462 Taking the results from Round 4 Chains 42, Residues 247, Estimated correctness of the model 1.4 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 12307 reflections ( 99.98 % complete ) and 11387 restraints for refining 4878 atoms. 10416 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2387 (Rfree = 0.000) for 4878 atoms. Found 7 (43 requested) and removed 24 (21 requested) atoms. Cycle 32: After refmac, R = 0.2371 (Rfree = 0.000) for 4851 atoms. Found 8 (43 requested) and removed 25 (21 requested) atoms. Cycle 33: After refmac, R = 0.2329 (Rfree = 0.000) for 4828 atoms. Found 8 (43 requested) and removed 23 (21 requested) atoms. Cycle 34: After refmac, R = 0.2274 (Rfree = 0.000) for 4809 atoms. Found 9 (43 requested) and removed 23 (21 requested) atoms. Cycle 35: After refmac, R = 0.2218 (Rfree = 0.000) for 4790 atoms. Found 6 (43 requested) and removed 26 (21 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 3.52 Search for helices and strands: 0 residues in 0 chains, 4938 seeds are put forward NCS extension: 32 residues added (2 deleted due to clashes), 4970 seeds are put forward Round 1: 257 peptides, 51 chains. Longest chain 11 peptides. Score 0.307 Round 2: 286 peptides, 44 chains. Longest chain 20 peptides. Score 0.444 Round 3: 284 peptides, 43 chains. Longest chain 16 peptides. Score 0.450 Round 4: 302 peptides, 44 chains. Longest chain 19 peptides. Score 0.478 Round 5: 303 peptides, 43 chains. Longest chain 27 peptides. Score 0.490 Taking the results from Round 5 Chains 44, Residues 260, Estimated correctness of the model 8.1 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 12307 reflections ( 99.98 % complete ) and 11083 restraints for refining 4877 atoms. 10040 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2391 (Rfree = 0.000) for 4877 atoms. Found 17 (43 requested) and removed 26 (21 requested) atoms. Cycle 37: After refmac, R = 0.2279 (Rfree = 0.000) for 4861 atoms. Found 5 (43 requested) and removed 22 (21 requested) atoms. Cycle 38: After refmac, R = 0.2225 (Rfree = 0.000) for 4841 atoms. Found 8 (43 requested) and removed 21 (21 requested) atoms. Cycle 39: After refmac, R = 0.2167 (Rfree = 0.000) for 4825 atoms. Found 3 (43 requested) and removed 22 (21 requested) atoms. Cycle 40: After refmac, R = 0.2556 (Rfree = 0.000) for 4804 atoms. Found 43 (43 requested) and removed 22 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 3.51 Search for helices and strands: 0 residues in 0 chains, 4981 seeds are put forward NCS extension: 33 residues added (0 deleted due to clashes), 5014 seeds are put forward Round 1: 239 peptides, 46 chains. Longest chain 15 peptides. Score 0.315 Round 2: 259 peptides, 42 chains. Longest chain 15 peptides. Score 0.404 Round 3: 265 peptides, 44 chains. Longest chain 19 peptides. Score 0.398 Round 4: 266 peptides, 38 chains. Longest chain 20 peptides. Score 0.459 Round 5: 259 peptides, 42 chains. Longest chain 19 peptides. Score 0.404 Taking the results from Round 4 Chains 40, Residues 228, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 12307 reflections ( 99.98 % complete ) and 11134 restraints for refining 4877 atoms. 10166 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2345 (Rfree = 0.000) for 4877 atoms. Found 9 (43 requested) and removed 26 (21 requested) atoms. Cycle 42: After refmac, R = 0.2242 (Rfree = 0.000) for 4846 atoms. Found 6 (43 requested) and removed 21 (21 requested) atoms. Cycle 43: After refmac, R = 0.2257 (Rfree = 0.000) for 4826 atoms. Found 6 (43 requested) and removed 21 (21 requested) atoms. Cycle 44: After refmac, R = 0.2155 (Rfree = 0.000) for 4808 atoms. Found 7 (43 requested) and removed 21 (21 requested) atoms. Cycle 45: After refmac, R = 0.2097 (Rfree = 0.000) for 4789 atoms. Found 7 (43 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.44 3.49 Search for helices and strands: 0 residues in 0 chains, 4880 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 4896 seeds are put forward Round 1: 218 peptides, 45 chains. Longest chain 10 peptides. Score 0.272 Round 2: 233 peptides, 42 chains. Longest chain 12 peptides. Score 0.342 Round 3: 241 peptides, 43 chains. Longest chain 13 peptides. Score 0.351 Round 4: 236 peptides, 41 chains. Longest chain 13 peptides. Score 0.360 Round 5: 225 peptides, 40 chains. Longest chain 13 peptides. Score 0.344 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 41, Residues 195, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1vll-3_warpNtrace.pdb as input Building loops using Loopy2018 41 chains (195 residues) following loop building 2 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12307 reflections ( 99.98 % complete ) and 11648 restraints for refining 4878 atoms. 10888 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2252 (Rfree = 0.000) for 4878 atoms. Found 0 (43 requested) and removed 17 (21 requested) atoms. Cycle 47: After refmac, R = 0.2179 (Rfree = 0.000) for 4855 atoms. Found 0 (43 requested) and removed 12 (21 requested) atoms. Cycle 48: After refmac, R = 0.2246 (Rfree = 0.000) for 4840 atoms. Found 0 (43 requested) and removed 15 (21 requested) atoms. Cycle 49: After refmac, R = 0.2229 (Rfree = 0.000) for 4819 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Writing output files ... TimeTaking 69.78