null Sun 23 Dec 22:22:59 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vll-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vll-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vll-3.6-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-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vll-3.6-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 22:23:08 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vll-3.6-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 416 and 0 Target number of residues in the AU: 416 Target solvent content: 0.6837 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-3.6-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-3.6-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 3.600 Wilson plot Bfac: 104.31 8728 reflections ( 99.97 % complete ) and 0 restraints for refining 5904 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3697 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3134 (Rfree = 0.000) for 5904 atoms. Found 36 (37 requested) and removed 33 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.90 3.95 Search for helices and strands: 0 residues in 0 chains, 6035 seeds are put forward NCS extension: 0 residues added, 6035 seeds are put forward Round 1: 287 peptides, 53 chains. Longest chain 18 peptides. Score 0.359 Round 2: 338 peptides, 53 chains. Longest chain 16 peptides. Score 0.471 Round 3: 366 peptides, 50 chains. Longest chain 22 peptides. Score 0.551 Round 4: 352 peptides, 48 chains. Longest chain 22 peptides. Score 0.542 Round 5: 377 peptides, 44 chains. Longest chain 29 peptides. Score 0.617 Taking the results from Round 5 Chains 48, Residues 333, Estimated correctness of the model 21.2 % 4 chains (44 residues) have been docked in sequence ------------------------------------------------------ 8728 reflections ( 99.97 % complete ) and 10997 restraints for refining 4840 atoms. 9579 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2824 (Rfree = 0.000) for 4840 atoms. Found 7 (31 requested) and removed 40 (15 requested) atoms. Cycle 2: After refmac, R = 0.2644 (Rfree = 0.000) for 4735 atoms. Found 10 (30 requested) and removed 27 (15 requested) atoms. Cycle 3: After refmac, R = 0.2449 (Rfree = 0.000) for 4688 atoms. Found 5 (30 requested) and removed 30 (15 requested) atoms. Cycle 4: After refmac, R = 0.2390 (Rfree = 0.000) for 4643 atoms. Found 4 (29 requested) and removed 24 (14 requested) atoms. Cycle 5: After refmac, R = 0.2384 (Rfree = 0.000) for 4606 atoms. Found 9 (29 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.76 3.81 Search for helices and strands: 0 residues in 0 chains, 4778 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 4797 seeds are put forward Round 1: 316 peptides, 57 chains. Longest chain 13 peptides. Score 0.386 Round 2: 332 peptides, 52 chains. Longest chain 13 peptides. Score 0.468 Round 3: 358 peptides, 53 chains. Longest chain 14 peptides. Score 0.511 Round 4: 352 peptides, 51 chains. Longest chain 17 peptides. Score 0.516 Round 5: 359 peptides, 48 chains. Longest chain 18 peptides. Score 0.555 Taking the results from Round 5 Chains 51, Residues 311, Estimated correctness of the model 0.0 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 8728 reflections ( 99.97 % complete ) and 10963 restraints for refining 4765 atoms. 9672 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2471 (Rfree = 0.000) for 4765 atoms. Found 12 (30 requested) and removed 58 (15 requested) atoms. Cycle 7: After refmac, R = 0.2320 (Rfree = 0.000) for 4693 atoms. Found 7 (30 requested) and removed 31 (15 requested) atoms. Cycle 8: After refmac, R = 0.2215 (Rfree = 0.000) for 4654 atoms. Found 3 (29 requested) and removed 29 (14 requested) atoms. Cycle 9: After refmac, R = 0.2228 (Rfree = 0.000) for 4621 atoms. Found 7 (29 requested) and removed 26 (14 requested) atoms. Cycle 10: After refmac, R = 0.2150 (Rfree = 0.000) for 4594 atoms. Found 3 (29 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.84 3.89 Search for helices and strands: 0 residues in 0 chains, 4805 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 4819 seeds are put forward Round 1: 300 peptides, 56 chains. Longest chain 11 peptides. Score 0.359 Round 2: 340 peptides, 48 chains. Longest chain 19 peptides. Score 0.519 Round 3: 343 peptides, 47 chains. Longest chain 24 peptides. Score 0.533 Round 4: 345 peptides, 47 chains. Longest chain 24 peptides. Score 0.537 Round 5: 340 peptides, 44 chains. Longest chain 22 peptides. Score 0.553 Taking the results from Round 5 Chains 45, Residues 296, Estimated correctness of the model 0.0 % 3 chains (38 residues) have been docked in sequence ------------------------------------------------------ 8728 reflections ( 99.97 % complete ) and 10922 restraints for refining 4844 atoms. 9651 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2526 (Rfree = 0.000) for 4844 atoms. Found 9 (31 requested) and removed 47 (15 requested) atoms. Cycle 12: After refmac, R = 0.2339 (Rfree = 0.000) for 4767 atoms. Found 6 (30 requested) and removed 31 (15 requested) atoms. Cycle 13: After refmac, R = 0.2198 (Rfree = 0.000) for 4715 atoms. Found 3 (30 requested) and removed 34 (15 requested) atoms. Cycle 14: After refmac, R = 0.2110 (Rfree = 0.000) for 4668 atoms. Found 1 (30 requested) and removed 25 (15 requested) atoms. Cycle 15: After refmac, R = 0.2023 (Rfree = 0.000) for 4635 atoms. Found 4 (29 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.75 3.80 Search for helices and strands: 0 residues in 0 chains, 4775 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 4804 seeds are put forward Round 1: 290 peptides, 57 chains. Longest chain 11 peptides. Score 0.326 Round 2: 298 peptides, 50 chains. Longest chain 12 peptides. Score 0.413 Round 3: 285 peptides, 43 chains. Longest chain 13 peptides. Score 0.452 Round 4: 304 peptides, 48 chains. Longest chain 11 peptides. Score 0.445 Round 5: 316 peptides, 46 chains. Longest chain 14 peptides. Score 0.489 Taking the results from Round 5 Chains 47, Residues 270, Estimated correctness of the model 0.0 % 4 chains (31 residues) have been docked in sequence ------------------------------------------------------ 8728 reflections ( 99.97 % complete ) and 11395 restraints for refining 4842 atoms. 10272 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2303 (Rfree = 0.000) for 4842 atoms. Found 7 (31 requested) and removed 52 (15 requested) atoms. Cycle 17: After refmac, R = 0.2209 (Rfree = 0.000) for 4778 atoms. Found 11 (30 requested) and removed 22 (15 requested) atoms. Cycle 18: After refmac, R = 0.2062 (Rfree = 0.000) for 4753 atoms. Found 6 (30 requested) and removed 28 (15 requested) atoms. Cycle 19: After refmac, R = 0.1994 (Rfree = 0.000) for 4718 atoms. Found 7 (30 requested) and removed 21 (15 requested) atoms. Cycle 20: After refmac, R = 0.1966 (Rfree = 0.000) for 4695 atoms. Found 7 (30 requested) and removed 23 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.78 3.83 Search for helices and strands: 0 residues in 0 chains, 4830 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 4849 seeds are put forward Round 1: 254 peptides, 49 chains. Longest chain 9 peptides. Score 0.320 Round 2: 300 peptides, 45 chains. Longest chain 18 peptides. Score 0.465 Round 3: 294 peptides, 45 chains. Longest chain 18 peptides. Score 0.452 Round 4: 291 peptides, 41 chains. Longest chain 15 peptides. Score 0.483 Round 5: 293 peptides, 42 chains. Longest chain 15 peptides. Score 0.478 Taking the results from Round 4 Chains 43, Residues 250, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 8728 reflections ( 99.97 % complete ) and 11315 restraints for refining 4843 atoms. 10281 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2231 (Rfree = 0.000) for 4843 atoms. Found 7 (31 requested) and removed 32 (15 requested) atoms. Cycle 22: After refmac, R = 0.2128 (Rfree = 0.000) for 4799 atoms. Found 10 (30 requested) and removed 22 (15 requested) atoms. Cycle 23: After refmac, R = 0.2111 (Rfree = 0.000) for 4773 atoms. Found 2 (30 requested) and removed 23 (15 requested) atoms. Cycle 24: After refmac, R = 0.2120 (Rfree = 0.000) for 4745 atoms. Found 6 (30 requested) and removed 23 (15 requested) atoms. Cycle 25: After refmac, R = 0.1987 (Rfree = 0.000) for 4722 atoms. Found 4 (30 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.77 3.82 Search for helices and strands: 0 residues in 0 chains, 4857 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 4871 seeds are put forward Round 1: 255 peptides, 50 chains. Longest chain 10 peptides. Score 0.312 Round 2: 296 peptides, 51 chains. Longest chain 16 peptides. Score 0.399 Round 3: 301 peptides, 51 chains. Longest chain 17 peptides. Score 0.410 Round 4: 298 peptides, 45 chains. Longest chain 16 peptides. Score 0.461 Round 5: 303 peptides, 45 chains. Longest chain 21 peptides. Score 0.471 Taking the results from Round 5 Chains 46, Residues 258, Estimated correctness of the model 0.0 % 5 chains (35 residues) have been docked in sequence ------------------------------------------------------ 8728 reflections ( 99.97 % complete ) and 11173 restraints for refining 4843 atoms. 10090 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2221 (Rfree = 0.000) for 4843 atoms. Found 21 (31 requested) and removed 29 (15 requested) atoms. Cycle 27: After refmac, R = 0.2018 (Rfree = 0.000) for 4807 atoms. Found 11 (31 requested) and removed 21 (15 requested) atoms. Cycle 28: After refmac, R = 0.1979 (Rfree = 0.000) for 4769 atoms. Found 12 (30 requested) and removed 22 (15 requested) atoms. Cycle 29: After refmac, R = 0.1856 (Rfree = 0.000) for 4746 atoms. Found 13 (30 requested) and removed 19 (15 requested) atoms. Cycle 30: After refmac, R = 0.1834 (Rfree = 0.000) for 4732 atoms. Found 12 (30 requested) and removed 23 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.76 3.81 Search for helices and strands: 0 residues in 0 chains, 4894 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 4910 seeds are put forward Round 1: 253 peptides, 51 chains. Longest chain 13 peptides. Score 0.297 Round 2: 286 peptides, 49 chains. Longest chain 16 peptides. Score 0.396 Round 3: 278 peptides, 47 chains. Longest chain 13 peptides. Score 0.398 Round 4: 272 peptides, 48 chains. Longest chain 17 peptides. Score 0.374 Round 5: 275 peptides, 45 chains. Longest chain 13 peptides. Score 0.411 Taking the results from Round 5 Chains 45, Residues 230, Estimated correctness of the model 0.0 % 3 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8728 reflections ( 99.97 % complete ) and 11525 restraints for refining 4844 atoms. 10632 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2051 (Rfree = 0.000) for 4844 atoms. Found 11 (31 requested) and removed 29 (15 requested) atoms. Cycle 32: After refmac, R = 0.1943 (Rfree = 0.000) for 4809 atoms. Found 12 (30 requested) and removed 28 (15 requested) atoms. Cycle 33: After refmac, R = 0.1889 (Rfree = 0.000) for 4780 atoms. Found 9 (30 requested) and removed 21 (15 requested) atoms. Cycle 34: After refmac, R = 0.1811 (Rfree = 0.000) for 4763 atoms. Found 7 (30 requested) and removed 19 (15 requested) atoms. Cycle 35: After refmac, R = 0.1849 (Rfree = 0.000) for 4743 atoms. Found 9 (30 requested) and removed 24 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.79 3.84 Search for helices and strands: 0 residues in 0 chains, 4880 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 4893 seeds are put forward Round 1: 235 peptides, 46 chains. Longest chain 11 peptides. Score 0.305 Round 2: 266 peptides, 45 chains. Longest chain 13 peptides. Score 0.390 Round 3: 262 peptides, 42 chains. Longest chain 20 peptides. Score 0.411 Round 4: 256 peptides, 42 chains. Longest chain 11 peptides. Score 0.397 Round 5: 264 peptides, 43 chains. Longest chain 15 peptides. Score 0.405 Taking the results from Round 3 Chains 42, Residues 220, Estimated correctness of the model 0.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 8728 reflections ( 99.97 % complete ) and 11212 restraints for refining 4844 atoms. 10293 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2063 (Rfree = 0.000) for 4844 atoms. Found 19 (31 requested) and removed 30 (15 requested) atoms. Cycle 37: After refmac, R = 0.1995 (Rfree = 0.000) for 4816 atoms. Found 13 (31 requested) and removed 25 (15 requested) atoms. Cycle 38: After refmac, R = 0.1827 (Rfree = 0.000) for 4790 atoms. Found 8 (30 requested) and removed 22 (15 requested) atoms. Cycle 39: After refmac, R = 0.1888 (Rfree = 0.000) for 4768 atoms. Found 13 (30 requested) and removed 21 (15 requested) atoms. Cycle 40: After refmac, R = 0.1768 (Rfree = 0.000) for 4757 atoms. Found 7 (30 requested) and removed 24 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.79 3.84 Search for helices and strands: 0 residues in 0 chains, 4871 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 4888 seeds are put forward Round 1: 211 peptides, 44 chains. Longest chain 8 peptides. Score 0.265 Round 2: 223 peptides, 40 chains. Longest chain 13 peptides. Score 0.339 Round 3: 227 peptides, 40 chains. Longest chain 13 peptides. Score 0.349 Round 4: 223 peptides, 40 chains. Longest chain 12 peptides. Score 0.339 Round 5: 215 peptides, 39 chains. Longest chain 11 peptides. Score 0.330 Taking the results from Round 3 Chains 40, Residues 187, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 8728 reflections ( 99.97 % complete ) and 11624 restraints for refining 4844 atoms. 10901 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2009 (Rfree = 0.000) for 4844 atoms. Found 15 (31 requested) and removed 30 (15 requested) atoms. Cycle 42: After refmac, R = 0.1934 (Rfree = 0.000) for 4812 atoms. Found 10 (30 requested) and removed 25 (15 requested) atoms. Cycle 43: After refmac, R = 0.1815 (Rfree = 0.000) for 4793 atoms. Found 7 (30 requested) and removed 21 (15 requested) atoms. Cycle 44: After refmac, R = 0.1876 (Rfree = 0.000) for 4771 atoms. Found 6 (30 requested) and removed 24 (15 requested) atoms. Cycle 45: After refmac, R = 0.1710 (Rfree = 0.000) for 4748 atoms. Found 8 (30 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.78 3.83 Search for helices and strands: 0 residues in 0 chains, 4896 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 4911 seeds are put forward Round 1: 174 peptides, 37 chains. Longest chain 8 peptides. Score 0.244 Round 2: 209 peptides, 39 chains. Longest chain 11 peptides. Score 0.315 Round 3: 207 peptides, 36 chains. Longest chain 17 peptides. Score 0.343 Round 4: 200 peptides, 35 chains. Longest chain 14 peptides. Score 0.336 Round 5: 206 peptides, 35 chains. Longest chain 15 peptides. Score 0.351 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 171, Estimated correctness of the model 0.0 % 4 chains (21 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 1vll-3_warpNtrace.pdb as input Building loops using Loopy2018 35 chains (171 residues) following loop building 4 chains (21 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8728 reflections ( 99.97 % complete ) and 11426 restraints for refining 4843 atoms. 10720 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1859 (Rfree = 0.000) for 4843 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.1902 (Rfree = 0.000) for 4812 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.1828 (Rfree = 0.000) for 4788 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.1882 (Rfree = 0.000) for 4766 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:29:26 GMT 2018 Job finished. TimeTaking 66.46 Used memory is bytes: 8164800