Sun 23 Dec 23:52:18 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-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ich-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ich-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ich-3.6-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-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ich-3.6-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 ============================================================ Sun 23 Dec 23:52:23 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-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ich-3.6-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 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-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-3.6-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 3.600 Wilson plot Bfac: 59.53 8970 reflections ( 99.62 % complete ) and 0 restraints for refining 5898 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3066 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3078 (Rfree = 0.000) for 5898 atoms. Found 37 (37 requested) and removed 51 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.31 3.27 Search for helices and strands: 0 residues in 0 chains, 5951 seeds are put forward NCS extension: 0 residues added, 5951 seeds are put forward Round 1: 307 peptides, 55 chains. Longest chain 10 peptides. Score 0.380 Round 2: 384 peptides, 59 chains. Longest chain 13 peptides. Score 0.502 Round 3: 422 peptides, 59 chains. Longest chain 28 peptides. Score 0.570 Round 4: 415 peptides, 56 chains. Longest chain 19 peptides. Score 0.581 Round 5: 396 peptides, 53 chains. Longest chain 19 peptides. Score 0.571 Taking the results from Round 4 Chains 62, Residues 359, Estimated correctness of the model 7.1 % 4 chains (38 residues) have been docked in sequence ------------------------------------------------------ 8970 reflections ( 99.62 % complete ) and 10367 restraints for refining 4857 atoms. 8854 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2592 (Rfree = 0.000) for 4857 atoms. Found 31 (31 requested) and removed 44 (15 requested) atoms. Cycle 2: After refmac, R = 0.2509 (Rfree = 0.000) for 4777 atoms. Found 31 (31 requested) and removed 33 (15 requested) atoms. Cycle 3: After refmac, R = 0.2264 (Rfree = 0.000) for 4751 atoms. Found 15 (30 requested) and removed 23 (15 requested) atoms. Cycle 4: After refmac, R = 0.2235 (Rfree = 0.000) for 4719 atoms. Found 19 (30 requested) and removed 24 (15 requested) atoms. Cycle 5: After refmac, R = 0.2188 (Rfree = 0.000) for 4699 atoms. Found 14 (30 requested) and removed 26 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 3.22 Search for helices and strands: 0 residues in 0 chains, 4783 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 4802 seeds are put forward Round 1: 394 peptides, 65 chains. Longest chain 15 peptides. Score 0.472 Round 2: 413 peptides, 56 chains. Longest chain 22 peptides. Score 0.578 Round 3: 431 peptides, 58 chains. Longest chain 22 peptides. Score 0.593 Round 4: 430 peptides, 53 chains. Longest chain 24 peptides. Score 0.626 Round 5: 447 peptides, 48 chains. Longest chain 33 peptides. Score 0.683 Taking the results from Round 5 Chains 56, Residues 399, Estimated correctness of the model 44.2 % 9 chains (118 residues) have been docked in sequence ------------------------------------------------------ 8970 reflections ( 99.62 % complete ) and 9416 restraints for refining 4858 atoms. 7415 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2550 (Rfree = 0.000) for 4858 atoms. Found 30 (31 requested) and removed 40 (15 requested) atoms. Cycle 7: After refmac, R = 0.2361 (Rfree = 0.000) for 4791 atoms. Found 23 (31 requested) and removed 36 (15 requested) atoms. Cycle 8: After refmac, R = 0.2224 (Rfree = 0.000) for 4761 atoms. Found 15 (30 requested) and removed 23 (15 requested) atoms. Cycle 9: After refmac, R = 0.2155 (Rfree = 0.000) for 4738 atoms. Found 11 (30 requested) and removed 21 (15 requested) atoms. Cycle 10: After refmac, R = 0.2135 (Rfree = 0.000) for 4716 atoms. Found 6 (30 requested) and removed 24 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.27 3.23 Search for helices and strands: 0 residues in 0 chains, 4796 seeds are put forward NCS extension: 41 residues added (5 deleted due to clashes), 4837 seeds are put forward Round 1: 343 peptides, 53 chains. Longest chain 31 peptides. Score 0.474 Round 2: 401 peptides, 50 chains. Longest chain 38 peptides. Score 0.602 Round 3: 417 peptides, 53 chains. Longest chain 36 peptides. Score 0.606 Round 4: 434 peptides, 52 chains. Longest chain 38 peptides. Score 0.639 Round 5: 418 peptides, 49 chains. Longest chain 27 peptides. Score 0.635 Taking the results from Round 4 Chains 54, Residues 382, Estimated correctness of the model 29.3 % 4 chains (75 residues) have been docked in sequence ------------------------------------------------------ 8970 reflections ( 99.62 % complete ) and 9832 restraints for refining 4859 atoms. 8042 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2408 (Rfree = 0.000) for 4859 atoms. Found 24 (31 requested) and removed 30 (15 requested) atoms. Cycle 12: After refmac, R = 0.2289 (Rfree = 0.000) for 4815 atoms. Found 21 (31 requested) and removed 26 (15 requested) atoms. Cycle 13: After refmac, R = 0.2173 (Rfree = 0.000) for 4793 atoms. Found 13 (30 requested) and removed 26 (15 requested) atoms. Cycle 14: After refmac, R = 0.2113 (Rfree = 0.000) for 4771 atoms. Found 4 (30 requested) and removed 25 (15 requested) atoms. Cycle 15: After refmac, R = 0.2081 (Rfree = 0.000) for 4746 atoms. Found 7 (30 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.28 3.24 Search for helices and strands: 0 residues in 0 chains, 4814 seeds are put forward NCS extension: 43 residues added (3 deleted due to clashes), 4857 seeds are put forward Round 1: 355 peptides, 51 chains. Longest chain 18 peptides. Score 0.514 Round 2: 407 peptides, 49 chains. Longest chain 30 peptides. Score 0.619 Round 3: 397 peptides, 43 chains. Longest chain 30 peptides. Score 0.645 Round 4: 408 peptides, 45 chains. Longest chain 31 peptides. Score 0.648 Round 5: 408 peptides, 49 chains. Longest chain 18 peptides. Score 0.620 Taking the results from Round 4 Chains 46, Residues 363, Estimated correctness of the model 32.5 % 4 chains (53 residues) have been docked in sequence ------------------------------------------------------ 8970 reflections ( 99.62 % complete ) and 10215 restraints for refining 4858 atoms. 8605 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2358 (Rfree = 0.000) for 4858 atoms. Found 21 (31 requested) and removed 27 (15 requested) atoms. Cycle 17: After refmac, R = 0.2228 (Rfree = 0.000) for 4830 atoms. Found 21 (31 requested) and removed 30 (15 requested) atoms. Cycle 18: After refmac, R = 0.2153 (Rfree = 0.000) for 4811 atoms. Found 10 (30 requested) and removed 23 (15 requested) atoms. Cycle 19: After refmac, R = 0.2051 (Rfree = 0.000) for 4792 atoms. Found 11 (30 requested) and removed 23 (15 requested) atoms. Cycle 20: After refmac, R = 0.2013 (Rfree = 0.000) for 4777 atoms. Found 6 (30 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.31 3.27 Search for helices and strands: 0 residues in 0 chains, 4863 seeds are put forward NCS extension: 40 residues added (2 deleted due to clashes), 4903 seeds are put forward Round 1: 358 peptides, 57 chains. Longest chain 16 peptides. Score 0.469 Round 2: 384 peptides, 50 chains. Longest chain 23 peptides. Score 0.574 Round 3: 383 peptides, 45 chains. Longest chain 20 peptides. Score 0.610 Round 4: 392 peptides, 50 chains. Longest chain 23 peptides. Score 0.587 Round 5: 375 peptides, 49 chains. Longest chain 23 peptides. Score 0.566 Taking the results from Round 3 Chains 49, Residues 338, Estimated correctness of the model 18.5 % 6 chains (59 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 8970 reflections ( 99.62 % complete ) and 10230 restraints for refining 4856 atoms. 8720 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2300 (Rfree = 0.000) for 4856 atoms. Found 27 (31 requested) and removed 34 (15 requested) atoms. Cycle 22: After refmac, R = 0.2176 (Rfree = 0.000) for 4835 atoms. Found 8 (31 requested) and removed 17 (15 requested) atoms. Cycle 23: After refmac, R = 0.2136 (Rfree = 0.000) for 4822 atoms. Found 7 (30 requested) and removed 17 (15 requested) atoms. Cycle 24: After refmac, R = 0.2106 (Rfree = 0.000) for 4810 atoms. Found 6 (30 requested) and removed 15 (15 requested) atoms. Cycle 25: After refmac, R = 0.2087 (Rfree = 0.000) for 4801 atoms. Found 3 (30 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.31 3.27 Search for helices and strands: 0 residues in 0 chains, 4883 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 4904 seeds are put forward Round 1: 336 peptides, 54 chains. Longest chain 18 peptides. Score 0.451 Round 2: 378 peptides, 49 chains. Longest chain 20 peptides. Score 0.571 Round 3: 367 peptides, 52 chains. Longest chain 20 peptides. Score 0.528 Round 4: 392 peptides, 50 chains. Longest chain 22 peptides. Score 0.587 Round 5: 378 peptides, 45 chains. Longest chain 20 peptides. Score 0.602 Taking the results from Round 5 Chains 46, Residues 333, Estimated correctness of the model 15.4 % 4 chains (36 residues) have been docked in sequence ------------------------------------------------------ 8970 reflections ( 99.62 % complete ) and 10617 restraints for refining 4859 atoms. 9205 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2382 (Rfree = 0.000) for 4859 atoms. Found 29 (31 requested) and removed 26 (15 requested) atoms. Cycle 27: After refmac, R = 0.2206 (Rfree = 0.000) for 4848 atoms. Found 15 (31 requested) and removed 19 (15 requested) atoms. Cycle 28: After refmac, R = 0.2149 (Rfree = 0.000) for 4840 atoms. Found 7 (31 requested) and removed 19 (15 requested) atoms. Cycle 29: After refmac, R = 0.2125 (Rfree = 0.000) for 4827 atoms. Found 3 (30 requested) and removed 15 (15 requested) atoms. Cycle 30: After refmac, R = 0.2107 (Rfree = 0.000) for 4813 atoms. Found 3 (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, 4872 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 4890 seeds are put forward Round 1: 328 peptides, 52 chains. Longest chain 18 peptides. Score 0.452 Round 2: 377 peptides, 51 chains. Longest chain 23 peptides. Score 0.554 Round 3: 378 peptides, 51 chains. Longest chain 17 peptides. Score 0.556 Round 4: 378 peptides, 49 chains. Longest chain 18 peptides. Score 0.571 Round 5: 369 peptides, 47 chains. Longest chain 22 peptides. Score 0.571 Taking the results from Round 5 Chains 51, Residues 322, Estimated correctness of the model 3.0 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 8970 reflections ( 99.62 % complete ) and 10624 restraints for refining 4859 atoms. 9296 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2415 (Rfree = 0.000) for 4859 atoms. Found 28 (31 requested) and removed 30 (15 requested) atoms. Cycle 32: After refmac, R = 0.2188 (Rfree = 0.000) for 4841 atoms. Found 11 (31 requested) and removed 22 (15 requested) atoms. Cycle 33: After refmac, R = 0.2133 (Rfree = 0.000) for 4820 atoms. Found 16 (30 requested) and removed 17 (15 requested) atoms. Cycle 34: After refmac, R = 0.2069 (Rfree = 0.000) for 4817 atoms. Found 4 (30 requested) and removed 17 (15 requested) atoms. Cycle 35: After refmac, R = 0.2036 (Rfree = 0.000) for 4797 atoms. Found 11 (30 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 3.25 Search for helices and strands: 0 residues in 0 chains, 4893 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4910 seeds are put forward Round 1: 300 peptides, 50 chains. Longest chain 19 peptides. Score 0.411 Round 2: 363 peptides, 51 chains. Longest chain 22 peptides. Score 0.529 Round 3: 357 peptides, 49 chains. Longest chain 20 peptides. Score 0.534 Round 4: 364 peptides, 47 chains. Longest chain 20 peptides. Score 0.563 Round 5: 378 peptides, 50 chains. Longest chain 20 peptides. Score 0.563 Taking the results from Round 5 Chains 51, Residues 328, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 8970 reflections ( 99.62 % complete ) and 10711 restraints for refining 4857 atoms. 9379 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2193 (Rfree = 0.000) for 4857 atoms. Found 31 (31 requested) and removed 23 (15 requested) atoms. Cycle 37: After refmac, R = 0.2023 (Rfree = 0.000) for 4856 atoms. Found 13 (31 requested) and removed 16 (15 requested) atoms. Cycle 38: After refmac, R = 0.1981 (Rfree = 0.000) for 4853 atoms. Found 11 (31 requested) and removed 16 (15 requested) atoms. Cycle 39: After refmac, R = 0.1949 (Rfree = 0.000) for 4846 atoms. Found 6 (31 requested) and removed 15 (15 requested) atoms. Cycle 40: After refmac, R = 0.1932 (Rfree = 0.000) for 4837 atoms. Found 4 (31 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 3.25 Search for helices and strands: 0 residues in 0 chains, 4919 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 4949 seeds are put forward Round 1: 287 peptides, 53 chains. Longest chain 16 peptides. Score 0.354 Round 2: 347 peptides, 54 chains. Longest chain 20 peptides. Score 0.473 Round 3: 357 peptides, 54 chains. Longest chain 15 peptides. Score 0.492 Round 4: 345 peptides, 56 chains. Longest chain 20 peptides. Score 0.451 Round 5: 351 peptides, 52 chains. Longest chain 17 peptides. Score 0.498 Taking the results from Round 5 Chains 54, Residues 299, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 8970 reflections ( 99.62 % complete ) and 10861 restraints for refining 4859 atoms. 9634 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2123 (Rfree = 0.000) for 4859 atoms. Found 22 (31 requested) and removed 26 (15 requested) atoms. Cycle 42: After refmac, R = 0.2022 (Rfree = 0.000) for 4840 atoms. Found 9 (31 requested) and removed 15 (15 requested) atoms. Cycle 43: After refmac, R = 0.1987 (Rfree = 0.000) for 4830 atoms. Found 7 (31 requested) and removed 16 (15 requested) atoms. Cycle 44: After refmac, R = 0.1973 (Rfree = 0.000) for 4819 atoms. Found 7 (30 requested) and removed 15 (15 requested) atoms. Cycle 45: After refmac, R = 0.1956 (Rfree = 0.000) for 4810 atoms. Found 4 (30 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.31 3.27 Search for helices and strands: 0 residues in 0 chains, 4858 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4875 seeds are put forward Round 1: 298 peptides, 57 chains. Longest chain 11 peptides. Score 0.340 Round 2: 328 peptides, 48 chains. Longest chain 18 peptides. Score 0.487 Round 3: 318 peptides, 49 chains. Longest chain 16 peptides. Score 0.459 Round 4: 308 peptides, 47 chains. Longest chain 17 peptides. Score 0.456 Round 5: 328 peptides, 52 chains. Longest chain 18 peptides. Score 0.452 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 48, Residues 280, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2ich-3_warpNtrace.pdb as input Building loops using Loopy2018 48 chains (280 residues) following loop building 3 chains (20 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8970 reflections ( 99.62 % complete ) and 10912 restraints for refining 4859 atoms. 9763 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2061 (Rfree = 0.000) for 4859 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2020 (Rfree = 0.000) for 4839 atoms. Found 0 (31 requested) and removed 6 (15 requested) atoms. Cycle 48: After refmac, R = 0.2018 (Rfree = 0.000) for 4832 atoms. Found 0 (31 requested) and removed 1 (15 requested) atoms. Cycle 49: After refmac, R = 0.2014 (Rfree = 0.000) for 4831 atoms. TimeTaking 50.82