Mon 24 Dec 07:48:43 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ich-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ich-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ich-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ich-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2ich-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ich-3.6-parrot-noncs ############### 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 07:48:48 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/noncs/ArpWArp/wArpResults/WorkingDir/2ich-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ich-3.6-parrot-noncs/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 522 and 0 Target number of residues in the AU: 522 Target solvent content: 0.6163 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-3.6-parrot-noncs.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-3.6-parrot-noncs.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 3.600 Wilson plot Bfac: 59.53 8970 reflections ( 99.62 % complete ) and 0 restraints for refining 5908 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3164 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3204 (Rfree = 0.000) for 5908 atoms. Found 37 (37 requested) and removed 79 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.31 3.27 Search for helices and strands: 0 residues in 0 chains, 5936 seeds are put forward NCS extension: 0 residues added, 5936 seeds are put forward Round 1: 271 peptides, 50 chains. Longest chain 10 peptides. Score 0.347 Round 2: 350 peptides, 56 chains. Longest chain 18 peptides. Score 0.461 Round 3: 384 peptides, 53 chains. Longest chain 19 peptides. Score 0.551 Round 4: 416 peptides, 55 chains. Longest chain 24 peptides. Score 0.590 Round 5: 401 peptides, 52 chains. Longest chain 19 peptides. Score 0.587 Taking the results from Round 4 Chains 58, Residues 361, Estimated correctness of the model 10.7 % 6 chains (43 residues) have been docked in sequence ------------------------------------------------------ 8970 reflections ( 99.62 % complete ) and 10260 restraints for refining 4859 atoms. 8717 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2755 (Rfree = 0.000) for 4859 atoms. Found 31 (31 requested) and removed 43 (15 requested) atoms. Cycle 2: After refmac, R = 0.2617 (Rfree = 0.000) for 4764 atoms. Found 21 (31 requested) and removed 39 (15 requested) atoms. Cycle 3: After refmac, R = 0.2424 (Rfree = 0.000) for 4719 atoms. Found 18 (30 requested) and removed 28 (15 requested) atoms. Cycle 4: After refmac, R = 0.2387 (Rfree = 0.000) for 4682 atoms. Found 18 (30 requested) and removed 27 (15 requested) atoms. Cycle 5: After refmac, R = 0.2423 (Rfree = 0.000) for 4657 atoms. Found 25 (29 requested) and removed 30 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 3.22 Search for helices and strands: 0 residues in 0 chains, 4753 seeds are put forward NCS extension: 27 residues added (7 deleted due to clashes), 4780 seeds are put forward Round 1: 363 peptides, 60 chains. Longest chain 22 peptides. Score 0.453 Round 2: 403 peptides, 56 chains. Longest chain 18 peptides. Score 0.560 Round 3: 407 peptides, 59 chains. Longest chain 24 peptides. Score 0.544 Round 4: 399 peptides, 49 chains. Longest chain 23 peptides. Score 0.606 Round 5: 398 peptides, 49 chains. Longest chain 25 peptides. Score 0.604 Taking the results from Round 4 Chains 53, Residues 350, Estimated correctness of the model 17.0 % 9 chains (77 residues) have been docked in sequence ------------------------------------------------------ 8970 reflections ( 99.62 % complete ) and 10117 restraints for refining 4859 atoms. 8497 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2612 (Rfree = 0.000) for 4859 atoms. Found 29 (31 requested) and removed 48 (15 requested) atoms. Cycle 7: After refmac, R = 0.2307 (Rfree = 0.000) for 4789 atoms. Found 19 (31 requested) and removed 36 (15 requested) atoms. Cycle 8: After refmac, R = 0.2188 (Rfree = 0.000) for 4749 atoms. Found 13 (30 requested) and removed 29 (15 requested) atoms. Cycle 9: After refmac, R = 0.2125 (Rfree = 0.000) for 4719 atoms. Found 12 (30 requested) and removed 22 (15 requested) atoms. Cycle 10: After refmac, R = 0.2049 (Rfree = 0.000) for 4699 atoms. Found 12 (30 requested) and removed 23 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.29 3.25 Search for helices and strands: 0 residues in 0 chains, 4807 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 4832 seeds are put forward Round 1: 377 peptides, 64 chains. Longest chain 15 peptides. Score 0.446 Round 2: 415 peptides, 61 chains. Longest chain 16 peptides. Score 0.543 Round 3: 427 peptides, 54 chains. Longest chain 27 peptides. Score 0.615 Round 4: 435 peptides, 55 chains. Longest chain 29 peptides. Score 0.620 Round 5: 416 peptides, 55 chains. Longest chain 26 peptides. Score 0.590 Taking the results from Round 4 Chains 56, Residues 380, Estimated correctness of the model 22.3 % 6 chains (71 residues) have been docked in sequence ------------------------------------------------------ 8970 reflections ( 99.62 % complete ) and 10058 restraints for refining 4858 atoms. 8313 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2389 (Rfree = 0.000) for 4858 atoms. Found 29 (31 requested) and removed 31 (15 requested) atoms. Cycle 12: After refmac, R = 0.2229 (Rfree = 0.000) for 4828 atoms. Found 13 (31 requested) and removed 26 (15 requested) atoms. Cycle 13: After refmac, R = 0.2134 (Rfree = 0.000) for 4797 atoms. Found 11 (30 requested) and removed 23 (15 requested) atoms. Cycle 14: After refmac, R = 0.2075 (Rfree = 0.000) for 4774 atoms. Found 8 (30 requested) and removed 17 (15 requested) atoms. Cycle 15: After refmac, R = 0.2063 (Rfree = 0.000) for 4763 atoms. Found 3 (30 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.32 3.28 Search for helices and strands: 0 residues in 0 chains, 4860 seeds are put forward NCS extension: 31 residues added (3 deleted due to clashes), 4891 seeds are put forward Round 1: 371 peptides, 61 chains. Longest chain 14 peptides. Score 0.460 Round 2: 385 peptides, 51 chains. Longest chain 18 peptides. Score 0.568 Round 3: 397 peptides, 51 chains. Longest chain 17 peptides. Score 0.588 Round 4: 401 peptides, 54 chains. Longest chain 20 peptides. Score 0.572 Round 5: 414 peptides, 58 chains. Longest chain 21 peptides. Score 0.564 Taking the results from Round 3 Chains 56, Residues 346, Estimated correctness of the model 9.9 % 6 chains (53 residues) have been docked in sequence ------------------------------------------------------ 8970 reflections ( 99.62 % complete ) and 10297 restraints for refining 4859 atoms. 8783 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2361 (Rfree = 0.000) for 4859 atoms. Found 15 (31 requested) and removed 41 (15 requested) atoms. Cycle 17: After refmac, R = 0.2217 (Rfree = 0.000) for 4815 atoms. Found 11 (31 requested) and removed 34 (15 requested) atoms. Cycle 18: After refmac, R = 0.2130 (Rfree = 0.000) for 4779 atoms. Found 7 (30 requested) and removed 21 (15 requested) atoms. Cycle 19: After refmac, R = 0.2113 (Rfree = 0.000) for 4757 atoms. Found 2 (30 requested) and removed 16 (15 requested) atoms. Cycle 20: After refmac, R = 0.2053 (Rfree = 0.000) for 4740 atoms. Found 3 (30 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.30 3.26 Search for helices and strands: 0 residues in 0 chains, 4836 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 4854 seeds are put forward Round 1: 343 peptides, 63 chains. Longest chain 11 peptides. Score 0.384 Round 2: 379 peptides, 53 chains. Longest chain 18 peptides. Score 0.542 Round 3: 371 peptides, 55 chains. Longest chain 18 peptides. Score 0.511 Round 4: 393 peptides, 54 chains. Longest chain 19 peptides. Score 0.559 Round 5: 394 peptides, 51 chains. Longest chain 20 peptides. Score 0.583 Taking the results from Round 5 Chains 53, Residues 343, Estimated correctness of the model 7.9 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 8970 reflections ( 99.62 % complete ) and 10592 restraints for refining 4858 atoms. 9141 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2614 (Rfree = 0.000) for 4858 atoms. Found 29 (31 requested) and removed 34 (15 requested) atoms. Cycle 22: After refmac, R = 0.2384 (Rfree = 0.000) for 4825 atoms. Found 26 (31 requested) and removed 36 (15 requested) atoms. Cycle 23: After refmac, R = 0.2200 (Rfree = 0.000) for 4801 atoms. Found 14 (30 requested) and removed 34 (15 requested) atoms. Cycle 24: After refmac, R = 0.2048 (Rfree = 0.000) for 4771 atoms. Found 14 (30 requested) and removed 23 (15 requested) atoms. Cycle 25: After refmac, R = 0.1977 (Rfree = 0.000) for 4758 atoms. Found 8 (30 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 3.28 Search for helices and strands: 0 residues in 0 chains, 4851 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 4870 seeds are put forward Round 1: 348 peptides, 65 chains. Longest chain 11 peptides. Score 0.376 Round 2: 372 peptides, 57 chains. Longest chain 15 peptides. Score 0.496 Round 3: 367 peptides, 51 chains. Longest chain 26 peptides. Score 0.536 Round 4: 372 peptides, 56 chains. Longest chain 15 peptides. Score 0.504 Round 5: 365 peptides, 54 chains. Longest chain 13 peptides. Score 0.508 Taking the results from Round 3 Chains 52, Residues 316, Estimated correctness of the model 0.0 % 4 chains (29 residues) have been docked in sequence ------------------------------------------------------ 8970 reflections ( 99.62 % complete ) and 10829 restraints for refining 4859 atoms. 9501 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2292 (Rfree = 0.000) for 4859 atoms. Found 22 (31 requested) and removed 25 (15 requested) atoms. Cycle 27: After refmac, R = 0.2025 (Rfree = 0.000) for 4842 atoms. Found 6 (31 requested) and removed 20 (15 requested) atoms. Cycle 28: After refmac, R = 0.1986 (Rfree = 0.000) for 4821 atoms. Found 12 (30 requested) and removed 21 (15 requested) atoms. Cycle 29: After refmac, R = 0.1961 (Rfree = 0.000) for 4810 atoms. Found 6 (30 requested) and removed 16 (15 requested) atoms. Cycle 30: After refmac, R = 0.1953 (Rfree = 0.000) for 4800 atoms. Found 6 (30 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 3.25 Search for helices and strands: 0 residues in 0 chains, 4892 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 4923 seeds are put forward Round 1: 341 peptides, 63 chains. Longest chain 12 peptides. Score 0.380 Round 2: 347 peptides, 55 chains. Longest chain 14 peptides. Score 0.464 Round 3: 375 peptides, 52 chains. Longest chain 21 peptides. Score 0.542 Round 4: 372 peptides, 53 chains. Longest chain 15 peptides. Score 0.529 Round 5: 386 peptides, 52 chains. Longest chain 23 peptides. Score 0.562 Taking the results from Round 5 Chains 53, Residues 334, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 8970 reflections ( 99.62 % complete ) and 10958 restraints for refining 4859 atoms. 9620 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2365 (Rfree = 0.000) for 4859 atoms. Found 28 (31 requested) and removed 24 (15 requested) atoms. Cycle 32: After refmac, R = 0.2288 (Rfree = 0.000) for 4845 atoms. Found 20 (31 requested) and removed 34 (15 requested) atoms. Cycle 33: After refmac, R = 0.2124 (Rfree = 0.000) for 4825 atoms. Found 14 (30 requested) and removed 27 (15 requested) atoms. Cycle 34: After refmac, R = 0.2059 (Rfree = 0.000) for 4808 atoms. Found 23 (30 requested) and removed 27 (15 requested) atoms. Cycle 35: After refmac, R = 0.2007 (Rfree = 0.000) for 4794 atoms. Found 15 (30 requested) and removed 26 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 3.23 Search for helices and strands: 0 residues in 0 chains, 4890 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 4912 seeds are put forward Round 1: 332 peptides, 60 chains. Longest chain 14 peptides. Score 0.388 Round 2: 362 peptides, 52 chains. Longest chain 22 peptides. Score 0.519 Round 3: 357 peptides, 52 chains. Longest chain 15 peptides. Score 0.509 Round 4: 360 peptides, 50 chains. Longest chain 21 peptides. Score 0.531 Round 5: 350 peptides, 49 chains. Longest chain 15 peptides. Score 0.521 Taking the results from Round 4 Chains 52, Residues 310, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 8970 reflections ( 99.62 % complete ) and 10805 restraints for refining 4859 atoms. 9515 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2237 (Rfree = 0.000) for 4859 atoms. Found 26 (31 requested) and removed 37 (15 requested) atoms. Cycle 37: After refmac, R = 0.2086 (Rfree = 0.000) for 4829 atoms. Found 10 (31 requested) and removed 28 (15 requested) atoms. Cycle 38: After refmac, R = 0.2037 (Rfree = 0.000) for 4803 atoms. Found 16 (30 requested) and removed 23 (15 requested) atoms. Cycle 39: After refmac, R = 0.2005 (Rfree = 0.000) for 4780 atoms. Found 15 (30 requested) and removed 23 (15 requested) atoms. Cycle 40: After refmac, R = 0.1998 (Rfree = 0.000) for 4764 atoms. Found 24 (30 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 3.25 Search for helices and strands: 0 residues in 0 chains, 4881 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 4897 seeds are put forward Round 1: 301 peptides, 53 chains. Longest chain 13 peptides. Score 0.385 Round 2: 332 peptides, 51 chains. Longest chain 14 peptides. Score 0.469 Round 3: 340 peptides, 50 chains. Longest chain 18 peptides. Score 0.494 Round 4: 336 peptides, 48 chains. Longest chain 24 peptides. Score 0.503 Round 5: 350 peptides, 46 chains. Longest chain 25 peptides. Score 0.546 Taking the results from Round 5 Chains 49, Residues 304, Estimated correctness of the model 0.0 % 8 chains (66 residues) have been docked in sequence ------------------------------------------------------ 8970 reflections ( 99.62 % complete ) and 10330 restraints for refining 4858 atoms. 8923 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2319 (Rfree = 0.000) for 4858 atoms. Found 27 (31 requested) and removed 39 (15 requested) atoms. Cycle 42: After refmac, R = 0.2169 (Rfree = 0.000) for 4825 atoms. Found 15 (31 requested) and removed 22 (15 requested) atoms. Cycle 43: After refmac, R = 0.2144 (Rfree = 0.000) for 4811 atoms. Found 10 (30 requested) and removed 25 (15 requested) atoms. Cycle 44: After refmac, R = 0.2129 (Rfree = 0.000) for 4791 atoms. Found 15 (30 requested) and removed 30 (15 requested) atoms. Cycle 45: After refmac, R = 0.2110 (Rfree = 0.000) for 4772 atoms. Found 13 (30 requested) and removed 26 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.27 3.23 Search for helices and strands: 0 residues in 0 chains, 4828 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 4846 seeds are put forward Round 1: 290 peptides, 56 chains. Longest chain 15 peptides. Score 0.332 Round 2: 309 peptides, 49 chains. Longest chain 20 peptides. Score 0.440 Round 3: 304 peptides, 43 chains. Longest chain 13 peptides. Score 0.484 Round 4: 294 peptides, 44 chains. Longest chain 21 peptides. Score 0.455 Round 5: 300 peptides, 42 chains. Longest chain 21 peptides. Score 0.485 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 42, Residues 258, Estimated correctness of the model 0.0 % 3 chains (28 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2ich-3_warpNtrace.pdb as input Building loops using Loopy2018 42 chains (258 residues) following loop building 3 chains (28 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8970 reflections ( 99.62 % complete ) and 10938 restraints for refining 4859 atoms. 9830 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2174 (Rfree = 0.000) for 4859 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2005 (Rfree = 0.000) for 4835 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.1942 (Rfree = 0.000) for 4818 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.1940 (Rfree = 0.000) for 4802 atoms. TimeTaking 50.38