null Sun 23 Dec 22:22:40 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 2ich-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ich-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ich-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ich-4.0-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/2ich-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ich-4.0-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 22:22:50 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/2ich-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ich-4.0-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 510 and 0 Target number of residues in the AU: 510 Target solvent content: 0.6251 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: 0.51 Input MTZ file: 2ich-4.0-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: 63.275 95.573 121.745 90.000 90.000 90.000 Input sequence file: 2ich-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 5360 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: 29.160 4.000 Wilson plot Bfac: 63.72 6601 reflections ( 99.58 % complete ) and 0 restraints for refining 5930 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3168 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3065 (Rfree = 0.000) for 5930 atoms. Found 28 (28 requested) and removed 53 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 3.47 Search for helices and strands: 0 residues in 0 chains, 5966 seeds are put forward NCS extension: 0 residues added, 5966 seeds are put forward Round 1: 292 peptides, 59 chains. Longest chain 12 peptides. Score 0.307 Round 2: 377 peptides, 60 chains. Longest chain 14 peptides. Score 0.480 Round 3: 391 peptides, 59 chains. Longest chain 14 peptides. Score 0.515 Round 4: 378 peptides, 55 chains. Longest chain 17 peptides. Score 0.524 Round 5: 408 peptides, 52 chains. Longest chain 19 peptides. Score 0.599 Taking the results from Round 5 Chains 55, Residues 356, Estimated correctness of the model 0.0 % 7 chains (68 residues) have been docked in sequence ------------------------------------------------------ 6601 reflections ( 99.58 % complete ) and 10258 restraints for refining 4839 atoms. 8624 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2575 (Rfree = 0.000) for 4839 atoms. Found 23 (23 requested) and removed 35 (11 requested) atoms. Cycle 2: After refmac, R = 0.2467 (Rfree = 0.000) for 4766 atoms. Found 15 (22 requested) and removed 41 (11 requested) atoms. Cycle 3: After refmac, R = 0.2256 (Rfree = 0.000) for 4705 atoms. Found 22 (22 requested) and removed 37 (11 requested) atoms. Cycle 4: After refmac, R = 0.2295 (Rfree = 0.000) for 4657 atoms. Found 22 (22 requested) and removed 45 (11 requested) atoms. Cycle 5: After refmac, R = 0.2182 (Rfree = 0.000) for 4620 atoms. Found 16 (22 requested) and removed 37 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.50 3.45 Search for helices and strands: 0 residues in 0 chains, 4694 seeds are put forward NCS extension: 17 residues added (7 deleted due to clashes), 4711 seeds are put forward Round 1: 330 peptides, 60 chains. Longest chain 10 peptides. Score 0.383 Round 2: 359 peptides, 54 chains. Longest chain 14 peptides. Score 0.496 Round 3: 380 peptides, 54 chains. Longest chain 17 peptides. Score 0.535 Round 4: 374 peptides, 54 chains. Longest chain 19 peptides. Score 0.525 Round 5: 370 peptides, 53 chains. Longest chain 15 peptides. Score 0.525 Taking the results from Round 3 Chains 56, Residues 326, Estimated correctness of the model 0.0 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 6601 reflections ( 99.58 % complete ) and 10901 restraints for refining 4841 atoms. 9540 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2221 (Rfree = 0.000) for 4841 atoms. Found 9 (23 requested) and removed 48 (11 requested) atoms. Cycle 7: After refmac, R = 0.2060 (Rfree = 0.000) for 4759 atoms. Found 17 (22 requested) and removed 48 (11 requested) atoms. Cycle 8: After refmac, R = 0.1875 (Rfree = 0.000) for 4717 atoms. Found 8 (22 requested) and removed 38 (11 requested) atoms. Cycle 9: After refmac, R = 0.1870 (Rfree = 0.000) for 4676 atoms. Found 13 (22 requested) and removed 39 (11 requested) atoms. Cycle 10: After refmac, R = 0.1548 (Rfree = 0.000) for 4642 atoms. Found 4 (22 requested) and removed 31 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 3.46 Search for helices and strands: 0 residues in 0 chains, 4719 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4735 seeds are put forward Round 1: 321 peptides, 57 chains. Longest chain 15 peptides. Score 0.392 Round 2: 358 peptides, 53 chains. Longest chain 20 peptides. Score 0.503 Round 3: 367 peptides, 54 chains. Longest chain 17 peptides. Score 0.511 Round 4: 388 peptides, 53 chains. Longest chain 19 peptides. Score 0.558 Round 5: 381 peptides, 52 chains. Longest chain 18 peptides. Score 0.553 Taking the results from Round 4 Chains 57, Residues 335, Estimated correctness of the model 0.0 % 5 chains (50 residues) have been docked in sequence ------------------------------------------------------ 6601 reflections ( 99.58 % complete ) and 10606 restraints for refining 4841 atoms. 9164 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2267 (Rfree = 0.000) for 4841 atoms. Found 19 (23 requested) and removed 40 (11 requested) atoms. Cycle 12: After refmac, R = 0.2126 (Rfree = 0.000) for 4791 atoms. Found 18 (22 requested) and removed 40 (11 requested) atoms. Cycle 13: After refmac, R = 0.2035 (Rfree = 0.000) for 4755 atoms. Found 22 (22 requested) and removed 37 (11 requested) atoms. Cycle 14: After refmac, R = 0.1918 (Rfree = 0.000) for 4731 atoms. Found 20 (22 requested) and removed 34 (11 requested) atoms. Cycle 15: After refmac, R = 0.1572 (Rfree = 0.000) for 4708 atoms. Found 5 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.53 3.48 Search for helices and strands: 0 residues in 0 chains, 4795 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 4816 seeds are put forward Round 1: 320 peptides, 60 chains. Longest chain 12 peptides. Score 0.361 Round 2: 354 peptides, 54 chains. Longest chain 12 peptides. Score 0.487 Round 3: 335 peptides, 48 chains. Longest chain 15 peptides. Score 0.501 Round 4: 348 peptides, 52 chains. Longest chain 13 peptides. Score 0.492 Round 5: 333 peptides, 50 chains. Longest chain 18 peptides. Score 0.480 Taking the results from Round 3 Chains 50, Residues 287, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 6601 reflections ( 99.58 % complete ) and 11092 restraints for refining 4841 atoms. 9910 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2233 (Rfree = 0.000) for 4841 atoms. Found 16 (23 requested) and removed 34 (11 requested) atoms. Cycle 17: After refmac, R = 0.2071 (Rfree = 0.000) for 4795 atoms. Found 22 (22 requested) and removed 32 (11 requested) atoms. Cycle 18: After refmac, R = 0.2028 (Rfree = 0.000) for 4765 atoms. Found 22 (22 requested) and removed 28 (11 requested) atoms. Cycle 19: After refmac, R = 0.1904 (Rfree = 0.000) for 4745 atoms. Found 21 (22 requested) and removed 26 (11 requested) atoms. Cycle 20: After refmac, R = 0.1890 (Rfree = 0.000) for 4730 atoms. Found 16 (22 requested) and removed 25 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.57 3.52 Search for helices and strands: 0 residues in 0 chains, 4814 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 4839 seeds are put forward Round 1: 316 peptides, 59 chains. Longest chain 11 peptides. Score 0.362 Round 2: 339 peptides, 56 chains. Longest chain 13 peptides. Score 0.439 Round 3: 325 peptides, 53 chains. Longest chain 11 peptides. Score 0.437 Round 4: 329 peptides, 50 chains. Longest chain 16 peptides. Score 0.472 Round 5: 344 peptides, 51 chains. Longest chain 16 peptides. Score 0.493 Taking the results from Round 5 Chains 52, Residues 293, Estimated correctness of the model 0.0 % 6 chains (30 residues) have been docked in sequence ------------------------------------------------------ 6601 reflections ( 99.58 % complete ) and 11031 restraints for refining 4840 atoms. 9819 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2282 (Rfree = 0.000) for 4840 atoms. Found 23 (23 requested) and removed 45 (11 requested) atoms. Cycle 22: After refmac, R = 0.2212 (Rfree = 0.000) for 4779 atoms. Found 22 (22 requested) and removed 32 (11 requested) atoms. Cycle 23: After refmac, R = 0.2020 (Rfree = 0.000) for 4751 atoms. Found 22 (22 requested) and removed 31 (11 requested) atoms. Cycle 24: After refmac, R = 0.2042 (Rfree = 0.000) for 4721 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 25: After refmac, R = 0.1935 (Rfree = 0.000) for 4711 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.55 3.50 Search for helices and strands: 0 residues in 0 chains, 4810 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 4832 seeds are put forward Round 1: 283 peptides, 51 chains. Longest chain 11 peptides. Score 0.364 Round 2: 308 peptides, 47 chains. Longest chain 13 peptides. Score 0.456 Round 3: 298 peptides, 46 chains. Longest chain 13 peptides. Score 0.444 Round 4: 301 peptides, 46 chains. Longest chain 14 peptides. Score 0.451 Round 5: 313 peptides, 44 chains. Longest chain 15 peptides. Score 0.493 Taking the results from Round 5 Chains 44, Residues 269, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6601 reflections ( 99.58 % complete ) and 11390 restraints for refining 4841 atoms. 10344 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2178 (Rfree = 0.000) for 4841 atoms. Found 23 (23 requested) and removed 32 (11 requested) atoms. Cycle 27: After refmac, R = 0.2113 (Rfree = 0.000) for 4811 atoms. Found 22 (22 requested) and removed 29 (11 requested) atoms. Cycle 28: After refmac, R = 0.2045 (Rfree = 0.000) for 4795 atoms. Found 22 (22 requested) and removed 33 (11 requested) atoms. Cycle 29: After refmac, R = 0.1566 (Rfree = 0.000) for 4775 atoms. Found 14 (22 requested) and removed 20 (11 requested) atoms. Cycle 30: After refmac, R = 0.1483 (Rfree = 0.000) for 4764 atoms. Found 3 (22 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 3.50 Search for helices and strands: 0 residues in 0 chains, 4856 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4876 seeds are put forward Round 1: 261 peptides, 51 chains. Longest chain 9 peptides. Score 0.313 Round 2: 298 peptides, 51 chains. Longest chain 12 peptides. Score 0.398 Round 3: 304 peptides, 50 chains. Longest chain 14 peptides. Score 0.420 Round 4: 303 peptides, 50 chains. Longest chain 17 peptides. Score 0.418 Round 5: 320 peptides, 53 chains. Longest chain 14 peptides. Score 0.426 Taking the results from Round 5 Chains 53, Residues 267, Estimated correctness of the model 0.0 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 6601 reflections ( 99.58 % complete ) and 11268 restraints for refining 4840 atoms. 10155 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2200 (Rfree = 0.000) for 4840 atoms. Found 19 (23 requested) and removed 41 (11 requested) atoms. Cycle 32: After refmac, R = 0.2082 (Rfree = 0.000) for 4789 atoms. Found 22 (22 requested) and removed 29 (11 requested) atoms. Cycle 33: After refmac, R = 0.1644 (Rfree = 0.000) for 4759 atoms. Found 6 (22 requested) and removed 26 (11 requested) atoms. Cycle 34: After refmac, R = 0.1557 (Rfree = 0.000) for 4729 atoms. Found 5 (22 requested) and removed 19 (11 requested) atoms. Cycle 35: After refmac, R = 0.1586 (Rfree = 0.000) for 4712 atoms. Found 4 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.51 3.46 Search for helices and strands: 0 residues in 0 chains, 4811 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 4832 seeds are put forward Round 1: 259 peptides, 52 chains. Longest chain 9 peptides. Score 0.298 Round 2: 267 peptides, 44 chains. Longest chain 13 peptides. Score 0.397 Round 3: 283 peptides, 46 chains. Longest chain 12 peptides. Score 0.413 Round 4: 291 peptides, 45 chains. Longest chain 20 peptides. Score 0.439 Round 5: 276 peptides, 44 chains. Longest chain 15 peptides. Score 0.416 Taking the results from Round 4 Chains 46, Residues 246, Estimated correctness of the model 0.0 % 5 chains (36 residues) have been docked in sequence ------------------------------------------------------ 6601 reflections ( 99.58 % complete ) and 11114 restraints for refining 4841 atoms. 10069 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2155 (Rfree = 0.000) for 4841 atoms. Found 23 (23 requested) and removed 41 (11 requested) atoms. Cycle 37: After refmac, R = 0.2073 (Rfree = 0.000) for 4803 atoms. Found 22 (22 requested) and removed 38 (11 requested) atoms. Cycle 38: After refmac, R = 0.1931 (Rfree = 0.000) for 4773 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 39: After refmac, R = 0.1468 (Rfree = 0.000) for 4756 atoms. Found 5 (22 requested) and removed 21 (11 requested) atoms. Cycle 40: After refmac, R = 0.1390 (Rfree = 0.000) for 4736 atoms. Found 5 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.51 3.46 Search for helices and strands: 0 residues in 0 chains, 4815 seeds are put forward NCS extension: 30 residues added (4 deleted due to clashes), 4845 seeds are put forward Round 1: 220 peptides, 46 chains. Longest chain 8 peptides. Score 0.264 Round 2: 234 peptides, 43 chains. Longest chain 10 peptides. Score 0.330 Round 3: 243 peptides, 44 chains. Longest chain 17 peptides. Score 0.341 Round 4: 253 peptides, 46 chains. Longest chain 14 peptides. Score 0.345 Round 5: 257 peptides, 41 chains. Longest chain 15 peptides. Score 0.404 Taking the results from Round 5 Chains 43, Residues 216, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 6601 reflections ( 99.58 % complete ) and 11315 restraints for refining 4839 atoms. 10421 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2056 (Rfree = 0.000) for 4839 atoms. Found 20 (23 requested) and removed 29 (11 requested) atoms. Cycle 42: After refmac, R = 0.2017 (Rfree = 0.000) for 4806 atoms. Found 22 (22 requested) and removed 28 (11 requested) atoms. Cycle 43: After refmac, R = 0.1861 (Rfree = 0.000) for 4784 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 44: After refmac, R = 0.1847 (Rfree = 0.000) for 4772 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. Cycle 45: After refmac, R = 0.1834 (Rfree = 0.000) for 4756 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 3.42 Search for helices and strands: 0 residues in 0 chains, 4846 seeds are put forward NCS extension: 10 residues added (4 deleted due to clashes), 4856 seeds are put forward Round 1: 221 peptides, 45 chains. Longest chain 9 peptides. Score 0.277 Round 2: 246 peptides, 48 chains. Longest chain 10 peptides. Score 0.308 Round 3: 251 peptides, 42 chains. Longest chain 13 peptides. Score 0.380 Round 4: 262 peptides, 45 chains. Longest chain 11 peptides. Score 0.375 Round 5: 256 peptides, 43 chains. Longest chain 11 peptides. Score 0.382 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 43, Residues 213, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2ich-4_warpNtrace.pdb as input Building loops using Loopy2018 43 chains (213 residues) following loop building 2 chains (11 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6601 reflections ( 99.58 % complete ) and 11511 restraints for refining 4841 atoms. 10659 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2112 (Rfree = 0.000) for 4841 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2083 (Rfree = 0.000) for 4810 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2003 (Rfree = 0.000) for 4786 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1932 (Rfree = 0.000) for 4763 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:31:21 GMT 2018 Job finished. TimeTaking 68.69 Used memory is bytes: 13598912