Mon 24 Dec 00:05:29 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ich-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ich-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ich-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ich-3.8-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2ich-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ich-3.8-parrot-mrncs ############### 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 00:05:33 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/mrncs/ArpWArp/wArpResults/WorkingDir/2ich-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ich-3.8-parrot-mrncs/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 509 and 0 Target number of residues in the AU: 509 Target solvent content: 0.6258 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-3.8-parrot-mrncs.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-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5360 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: 29.160 3.800 Wilson plot Bfac: 64.14 7662 reflections ( 99.64 % complete ) and 0 restraints for refining 5907 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3170 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3206 (Rfree = 0.000) for 5907 atoms. Found 32 (32 requested) and removed 50 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 3.40 Search for helices and strands: 0 residues in 0 chains, 5965 seeds are put forward NCS extension: 0 residues added, 5965 seeds are put forward Round 1: 294 peptides, 55 chains. Longest chain 16 peptides. Score 0.350 Round 2: 350 peptides, 53 chains. Longest chain 19 peptides. Score 0.487 Round 3: 364 peptides, 56 chains. Longest chain 13 peptides. Score 0.489 Round 4: 376 peptides, 54 chains. Longest chain 14 peptides. Score 0.528 Round 5: 394 peptides, 56 chains. Longest chain 15 peptides. Score 0.545 Taking the results from Round 5 Chains 57, Residues 338, Estimated correctness of the model 0.0 % 6 chains (36 residues) have been docked in sequence ------------------------------------------------------ 7662 reflections ( 99.64 % complete ) and 10735 restraints for refining 4848 atoms. 9319 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2712 (Rfree = 0.000) for 4848 atoms. Found 26 (26 requested) and removed 54 (13 requested) atoms. Cycle 2: After refmac, R = 0.2507 (Rfree = 0.000) for 4766 atoms. Found 26 (26 requested) and removed 46 (13 requested) atoms. Cycle 3: After refmac, R = 0.2406 (Rfree = 0.000) for 4721 atoms. Found 26 (26 requested) and removed 70 (13 requested) atoms. Cycle 4: After refmac, R = 0.1915 (Rfree = 0.000) for 4667 atoms. Found 15 (25 requested) and removed 21 (12 requested) atoms. Cycle 5: After refmac, R = 0.1851 (Rfree = 0.000) for 4651 atoms. Found 11 (25 requested) and removed 31 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 4754 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 4769 seeds are put forward Round 1: 370 peptides, 65 chains. Longest chain 14 peptides. Score 0.423 Round 2: 400 peptides, 58 chains. Longest chain 14 peptides. Score 0.540 Round 3: 394 peptides, 54 chains. Longest chain 21 peptides. Score 0.560 Round 4: 401 peptides, 55 chains. Longest chain 20 peptides. Score 0.565 Round 5: 419 peptides, 56 chains. Longest chain 17 peptides. Score 0.588 Taking the results from Round 5 Chains 58, Residues 363, Estimated correctness of the model 0.0 % 5 chains (42 residues) have been docked in sequence ------------------------------------------------------ 7662 reflections ( 99.64 % complete ) and 10445 restraints for refining 4847 atoms. 8894 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2412 (Rfree = 0.000) for 4847 atoms. Found 24 (26 requested) and removed 47 (13 requested) atoms. Cycle 7: After refmac, R = 0.2219 (Rfree = 0.000) for 4763 atoms. Found 21 (26 requested) and removed 48 (13 requested) atoms. Cycle 8: After refmac, R = 0.2108 (Rfree = 0.000) for 4710 atoms. Found 26 (26 requested) and removed 32 (13 requested) atoms. Cycle 9: After refmac, R = 0.2113 (Rfree = 0.000) for 4690 atoms. Found 25 (25 requested) and removed 29 (12 requested) atoms. Cycle 10: After refmac, R = 0.1931 (Rfree = 0.000) for 4663 atoms. Found 25 (25 requested) and removed 27 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 4773 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 4790 seeds are put forward Round 1: 361 peptides, 61 chains. Longest chain 13 peptides. Score 0.440 Round 2: 375 peptides, 57 chains. Longest chain 13 peptides. Score 0.502 Round 3: 389 peptides, 57 chains. Longest chain 16 peptides. Score 0.528 Round 4: 390 peptides, 54 chains. Longest chain 16 peptides. Score 0.553 Round 5: 371 peptides, 49 chains. Longest chain 18 peptides. Score 0.559 Taking the results from Round 5 Chains 49, Residues 322, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 7662 reflections ( 99.64 % complete ) and 10966 restraints for refining 4847 atoms. 9674 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2307 (Rfree = 0.000) for 4847 atoms. Found 22 (26 requested) and removed 49 (13 requested) atoms. Cycle 12: After refmac, R = 0.2111 (Rfree = 0.000) for 4790 atoms. Found 24 (26 requested) and removed 34 (13 requested) atoms. Cycle 13: After refmac, R = 0.1975 (Rfree = 0.000) for 4766 atoms. Found 23 (26 requested) and removed 23 (13 requested) atoms. Cycle 14: After refmac, R = 0.1864 (Rfree = 0.000) for 4757 atoms. Found 16 (26 requested) and removed 24 (13 requested) atoms. Cycle 15: After refmac, R = 0.1601 (Rfree = 0.000) for 4737 atoms. Found 8 (26 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 4797 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 4820 seeds are put forward Round 1: 307 peptides, 57 chains. Longest chain 17 peptides. Score 0.361 Round 2: 359 peptides, 54 chains. Longest chain 17 peptides. Score 0.496 Round 3: 365 peptides, 48 chains. Longest chain 18 peptides. Score 0.556 Round 4: 394 peptides, 50 chains. Longest chain 27 peptides. Score 0.591 Round 5: 378 peptides, 54 chains. Longest chain 18 peptides. Score 0.532 Taking the results from Round 4 Chains 52, Residues 344, Estimated correctness of the model 0.0 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 7662 reflections ( 99.64 % complete ) and 10313 restraints for refining 4847 atoms. 8856 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2167 (Rfree = 0.000) for 4847 atoms. Found 22 (26 requested) and removed 47 (13 requested) atoms. Cycle 17: After refmac, R = 0.1907 (Rfree = 0.000) for 4792 atoms. Found 16 (26 requested) and removed 28 (13 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1786 (Rfree = 0.000) for 4772 atoms. Found 10 (26 requested) and removed 27 (13 requested) atoms. Cycle 19: After refmac, R = 0.1756 (Rfree = 0.000) for 4745 atoms. Found 12 (26 requested) and removed 34 (13 requested) atoms. Cycle 20: After refmac, R = 0.1645 (Rfree = 0.000) for 4718 atoms. Found 9 (25 requested) and removed 22 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 4801 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 4820 seeds are put forward Round 1: 315 peptides, 55 chains. Longest chain 10 peptides. Score 0.397 Round 2: 355 peptides, 49 chains. Longest chain 16 peptides. Score 0.530 Round 3: 379 peptides, 51 chains. Longest chain 18 peptides. Score 0.557 Round 4: 383 peptides, 53 chains. Longest chain 20 peptides. Score 0.549 Round 5: 383 peptides, 47 chains. Longest chain 22 peptides. Score 0.595 Taking the results from Round 5 Chains 49, Residues 336, Estimated correctness of the model 0.0 % 8 chains (61 residues) have been docked in sequence ------------------------------------------------------ 7662 reflections ( 99.64 % complete ) and 10164 restraints for refining 4847 atoms. 8662 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2175 (Rfree = 0.000) for 4847 atoms. Found 16 (26 requested) and removed 41 (13 requested) atoms. Cycle 22: After refmac, R = 0.2062 (Rfree = 0.000) for 4804 atoms. Found 25 (26 requested) and removed 34 (13 requested) atoms. Cycle 23: After refmac, R = 0.1949 (Rfree = 0.000) for 4782 atoms. Found 24 (26 requested) and removed 32 (13 requested) atoms. Cycle 24: After refmac, R = 0.1924 (Rfree = 0.000) for 4753 atoms. Found 24 (26 requested) and removed 34 (13 requested) atoms. Cycle 25: After refmac, R = 0.1881 (Rfree = 0.000) for 4737 atoms. Found 21 (26 requested) and removed 24 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 3.34 Search for helices and strands: 0 residues in 0 chains, 4824 seeds are put forward NCS extension: 31 residues added (2 deleted due to clashes), 4855 seeds are put forward Round 1: 301 peptides, 61 chains. Longest chain 12 peptides. Score 0.308 Round 2: 334 peptides, 51 chains. Longest chain 17 peptides. Score 0.473 Round 3: 362 peptides, 53 chains. Longest chain 20 peptides. Score 0.510 Round 4: 350 peptides, 52 chains. Longest chain 20 peptides. Score 0.496 Round 5: 367 peptides, 55 chains. Longest chain 15 peptides. Score 0.503 Taking the results from Round 3 Chains 55, Residues 309, Estimated correctness of the model 0.0 % 8 chains (53 residues) have been docked in sequence ------------------------------------------------------ 7662 reflections ( 99.64 % complete ) and 10387 restraints for refining 4848 atoms. 9044 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2278 (Rfree = 0.000) for 4848 atoms. Found 26 (26 requested) and removed 46 (13 requested) atoms. Cycle 27: After refmac, R = 0.2214 (Rfree = 0.000) for 4796 atoms. Found 26 (26 requested) and removed 27 (13 requested) atoms. Cycle 28: After refmac, R = 0.2128 (Rfree = 0.000) for 4773 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. Cycle 29: After refmac, R = 0.1985 (Rfree = 0.000) for 4759 atoms. Found 26 (26 requested) and removed 18 (13 requested) atoms. Cycle 30: After refmac, R = 0.1708 (Rfree = 0.000) for 4755 atoms. Found 7 (26 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 3.38 Search for helices and strands: 0 residues in 0 chains, 4833 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4853 seeds are put forward Round 1: 290 peptides, 61 chains. Longest chain 8 peptides. Score 0.282 Round 2: 321 peptides, 52 chains. Longest chain 15 peptides. Score 0.438 Round 3: 329 peptides, 47 chains. Longest chain 16 peptides. Score 0.498 Round 4: 326 peptides, 47 chains. Longest chain 17 peptides. Score 0.492 Round 5: 339 peptides, 47 chains. Longest chain 21 peptides. Score 0.517 Taking the results from Round 5 Chains 48, Residues 292, Estimated correctness of the model 0.0 % 9 chains (46 residues) have been docked in sequence ------------------------------------------------------ 7662 reflections ( 99.64 % complete ) and 10684 restraints for refining 4848 atoms. 9413 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2272 (Rfree = 0.000) for 4848 atoms. Found 26 (26 requested) and removed 33 (13 requested) atoms. Cycle 32: After refmac, R = 0.2206 (Rfree = 0.000) for 4811 atoms. Found 26 (26 requested) and removed 24 (13 requested) atoms. Cycle 33: After refmac, R = 0.2088 (Rfree = 0.000) for 4796 atoms. Found 26 (26 requested) and removed 23 (13 requested) atoms. Cycle 34: After refmac, R = 0.1732 (Rfree = 0.000) for 4785 atoms. Found 9 (26 requested) and removed 18 (13 requested) atoms. Cycle 35: After refmac, R = 0.1908 (Rfree = 0.000) for 4771 atoms. Found 26 (26 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 3.33 Search for helices and strands: 0 residues in 0 chains, 4877 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 4903 seeds are put forward Round 1: 308 peptides, 63 chains. Longest chain 10 peptides. Score 0.305 Round 2: 323 peptides, 56 chains. Longest chain 13 peptides. Score 0.405 Round 3: 327 peptides, 59 chains. Longest chain 10 peptides. Score 0.386 Round 4: 336 peptides, 56 chains. Longest chain 15 peptides. Score 0.433 Round 5: 336 peptides, 51 chains. Longest chain 16 peptides. Score 0.477 Taking the results from Round 5 Chains 51, Residues 285, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 7662 reflections ( 99.64 % complete ) and 11047 restraints for refining 4847 atoms. 9925 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2363 (Rfree = 0.000) for 4847 atoms. Found 26 (26 requested) and removed 30 (13 requested) atoms. Cycle 37: After refmac, R = 0.2233 (Rfree = 0.000) for 4814 atoms. Found 26 (26 requested) and removed 36 (13 requested) atoms. Cycle 38: After refmac, R = 0.2105 (Rfree = 0.000) for 4792 atoms. Found 26 (26 requested) and removed 23 (13 requested) atoms. Cycle 39: After refmac, R = 0.1733 (Rfree = 0.000) for 4785 atoms. Found 9 (26 requested) and removed 28 (13 requested) atoms. Cycle 40: After refmac, R = 0.1924 (Rfree = 0.000) for 4757 atoms. Found 26 (26 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.38 3.34 Search for helices and strands: 0 residues in 0 chains, 4869 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 4886 seeds are put forward Round 1: 231 peptides, 49 chains. Longest chain 8 peptides. Score 0.260 Round 2: 263 peptides, 46 chains. Longest chain 10 peptides. Score 0.368 Round 3: 282 peptides, 47 chains. Longest chain 11 peptides. Score 0.401 Round 4: 293 peptides, 49 chains. Longest chain 14 peptides. Score 0.406 Round 5: 319 peptides, 49 chains. Longest chain 17 peptides. Score 0.461 Taking the results from Round 5 Chains 50, Residues 270, Estimated correctness of the model 0.0 % 4 chains (20 residues) have been docked in sequence ------------------------------------------------------ 7662 reflections ( 99.64 % complete ) and 10990 restraints for refining 4846 atoms. 9907 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2425 (Rfree = 0.000) for 4846 atoms. Found 26 (26 requested) and removed 39 (13 requested) atoms. Cycle 42: After refmac, R = 0.2371 (Rfree = 0.000) for 4809 atoms. Found 26 (26 requested) and removed 34 (13 requested) atoms. Cycle 43: After refmac, R = 0.2137 (Rfree = 0.000) for 4790 atoms. Found 26 (26 requested) and removed 27 (13 requested) atoms. Cycle 44: After refmac, R = 0.2118 (Rfree = 0.000) for 4776 atoms. Found 26 (26 requested) and removed 29 (13 requested) atoms. Cycle 45: After refmac, R = 0.1682 (Rfree = 0.000) for 4767 atoms. Found 8 (26 requested) and removed 22 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 3.35 Search for helices and strands: 0 residues in 0 chains, 4832 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 4851 seeds are put forward Round 1: 237 peptides, 50 chains. Longest chain 8 peptides. Score 0.264 Round 2: 271 peptides, 45 chains. Longest chain 12 peptides. Score 0.396 Round 3: 273 peptides, 42 chains. Longest chain 13 peptides. Score 0.429 Round 4: 254 peptides, 40 chains. Longest chain 14 peptides. Score 0.407 Round 5: 262 peptides, 42 chains. Longest chain 13 peptides. Score 0.405 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 43, Residues 231, Estimated correctness of the model 0.0 % 6 chains (33 residues) have been docked in sequence Sequence coverage is 14 % Consider running further cycles of model building using 2ich-3_warpNtrace.pdb as input Building loops using Loopy2018 43 chains (231 residues) following loop building 6 chains (33 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7662 reflections ( 99.64 % complete ) and 10953 restraints for refining 4848 atoms. 9963 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2200 (Rfree = 0.000) for 4848 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2185 (Rfree = 0.000) for 4813 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2095 (Rfree = 0.000) for 4787 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2116 (Rfree = 0.000) for 4769 atoms. TimeTaking 50.43