Sun 23 Dec 22:22:42 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 2ia7-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ia7-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ia7-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ia7-3.2-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/2ia7-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ia7-3.2-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 22:22:52 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/2ia7-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ia7-3.2-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 81 and 0 Target number of residues in the AU: 81 Target solvent content: 0.6113 Checking the provided sequence file Detected sequence length: 134 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 134 Adjusted target solvent content: 0.36 Input MTZ file: 2ia7-3.2-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: 40.240 43.350 64.660 90.000 90.000 90.000 Input sequence file: 2ia7-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1072 target number of atoms Had to go as low as 0.55 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 Loops will be built when appropriate and at the last cycle Resolution range: 26.833 3.200 Wilson plot Bfac: 57.26 2030 reflections ( 98.16 % complete ) and 0 restraints for refining 1194 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3511 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3366 (Rfree = 0.000) for 1194 atoms. Found 10 (10 requested) and removed 22 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.17 3.84 Search for helices and strands: 0 residues in 0 chains, 1201 seeds are put forward Round 1: 37 peptides, 9 chains. Longest chain 5 peptides. Score 0.184 Round 2: 45 peptides, 10 chains. Longest chain 6 peptides. Score 0.249 Round 3: 54 peptides, 9 chains. Longest chain 15 peptides. Score 0.442 Round 4: 52 peptides, 9 chains. Longest chain 12 peptides. Score 0.415 Round 5: 54 peptides, 10 chains. Longest chain 9 peptides. Score 0.384 Taking the results from Round 3 Chains 9, Residues 45, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2030 reflections ( 98.16 % complete ) and 2213 restraints for refining 979 atoms. 2042 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2982 (Rfree = 0.000) for 979 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 2: After refmac, R = 0.2983 (Rfree = 0.000) for 963 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 3: After refmac, R = 0.2694 (Rfree = 0.000) for 958 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 4: After refmac, R = 0.2570 (Rfree = 0.000) for 958 atoms. Found 7 (8 requested) and removed 6 (4 requested) atoms. Cycle 5: After refmac, R = 0.2412 (Rfree = 0.000) for 956 atoms. Found 7 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.11 3.77 Search for helices and strands: 0 residues in 0 chains, 999 seeds are put forward Round 1: 57 peptides, 12 chains. Longest chain 10 peptides. Score 0.306 Round 2: 70 peptides, 12 chains. Longest chain 11 peptides. Score 0.483 Round 3: 66 peptides, 11 chains. Longest chain 17 peptides. Score 0.486 Round 4: 58 peptides, 11 chains. Longest chain 9 peptides. Score 0.381 Round 5: 71 peptides, 11 chains. Longest chain 19 peptides. Score 0.546 Taking the results from Round 5 Chains 13, Residues 60, Estimated correctness of the model 25.7 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2030 reflections ( 98.16 % complete ) and 2179 restraints for refining 973 atoms. 1929 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2745 (Rfree = 0.000) for 973 atoms. Found 5 (8 requested) and removed 11 (4 requested) atoms. Cycle 7: After refmac, R = 0.2416 (Rfree = 0.000) for 953 atoms. Found 0 (8 requested) and removed 8 (4 requested) atoms. Cycle 8: After refmac, R = 0.2413 (Rfree = 0.000) for 937 atoms. Found 6 (8 requested) and removed 6 (4 requested) atoms. Cycle 9: After refmac, R = 0.2213 (Rfree = 0.000) for 935 atoms. Found 5 (8 requested) and removed 5 (4 requested) atoms. Cycle 10: After refmac, R = 0.2187 (Rfree = 0.000) for 934 atoms. Found 6 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.12 3.78 Search for helices and strands: 0 residues in 0 chains, 966 seeds are put forward Round 1: 52 peptides, 11 chains. Longest chain 8 peptides. Score 0.293 Round 2: 60 peptides, 11 chains. Longest chain 12 peptides. Score 0.408 Round 3: 57 peptides, 10 chains. Longest chain 13 peptides. Score 0.425 Round 4: 61 peptides, 11 chains. Longest chain 10 peptides. Score 0.422 Round 5: 60 peptides, 11 chains. Longest chain 11 peptides. Score 0.408 Taking the results from Round 3 Chains 10, Residues 47, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2030 reflections ( 98.16 % complete ) and 2158 restraints for refining 949 atoms. 1968 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2419 (Rfree = 0.000) for 949 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 12: After refmac, R = 0.2408 (Rfree = 0.000) for 949 atoms. Found 3 (8 requested) and removed 8 (4 requested) atoms. Cycle 13: After refmac, R = 0.2317 (Rfree = 0.000) for 941 atoms. Found 7 (8 requested) and removed 6 (4 requested) atoms. Cycle 14: After refmac, R = 0.2425 (Rfree = 0.000) for 940 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 15: After refmac, R = 0.2345 (Rfree = 0.000) for 939 atoms. Found 5 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.08 3.73 Search for helices and strands: 0 residues in 0 chains, 968 seeds are put forward Round 1: 46 peptides, 10 chains. Longest chain 6 peptides. Score 0.264 Round 2: 43 peptides, 9 chains. Longest chain 6 peptides. Score 0.282 Round 3: 44 peptides, 9 chains. Longest chain 7 peptides. Score 0.298 Round 4: 48 peptides, 9 chains. Longest chain 7 peptides. Score 0.358 Round 5: 52 peptides, 10 chains. Longest chain 8 peptides. Score 0.355 Taking the results from Round 4 Chains 9, Residues 39, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2030 reflections ( 98.16 % complete ) and 2201 restraints for refining 943 atoms. 2054 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2262 (Rfree = 0.000) for 943 atoms. Found 6 (8 requested) and removed 7 (4 requested) atoms. Cycle 17: After refmac, R = 0.2036 (Rfree = 0.000) for 937 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. Cycle 18: After refmac, R = 0.1960 (Rfree = 0.000) for 931 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 19: After refmac, R = 0.1877 (Rfree = 0.000) for 929 atoms. Found 1 (8 requested) and removed 6 (4 requested) atoms. Cycle 20: After refmac, R = 0.1828 (Rfree = 0.000) for 924 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.15 3.82 Search for helices and strands: 0 residues in 0 chains, 950 seeds are put forward Round 1: 40 peptides, 9 chains. Longest chain 6 peptides. Score 0.234 Round 2: 50 peptides, 10 chains. Longest chain 6 peptides. Score 0.325 Round 3: 53 peptides, 10 chains. Longest chain 8 peptides. Score 0.369 Round 4: 57 peptides, 12 chains. Longest chain 6 peptides. Score 0.306 Round 5: 52 peptides, 10 chains. Longest chain 7 peptides. Score 0.355 Taking the results from Round 3 Chains 10, Residues 43, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2030 reflections ( 98.16 % complete ) and 2178 restraints for refining 948 atoms. 2003 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2126 (Rfree = 0.000) for 948 atoms. Found 5 (8 requested) and removed 10 (4 requested) atoms. Cycle 22: After refmac, R = 0.2098 (Rfree = 0.000) for 940 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2840 (Rfree = 0.000) for 935 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 24: After refmac, R = 0.1983 (Rfree = 0.000) for 932 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.1958 (Rfree = 0.000) for 929 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.13 3.79 Search for helices and strands: 0 residues in 0 chains, 953 seeds are put forward Round 1: 32 peptides, 7 chains. Longest chain 6 peptides. Score 0.238 Round 2: 35 peptides, 7 chains. Longest chain 7 peptides. Score 0.288 Round 3: 41 peptides, 8 chains. Longest chain 7 peptides. Score 0.316 Round 4: 39 peptides, 7 chains. Longest chain 9 peptides. Score 0.351 Round 5: 41 peptides, 8 chains. Longest chain 7 peptides. Score 0.316 Taking the results from Round 4 Chains 7, Residues 32, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2030 reflections ( 98.16 % complete ) and 2327 restraints for refining 976 atoms. 2206 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2028 (Rfree = 0.000) for 976 atoms. Found 5 (8 requested) and removed 6 (4 requested) atoms. Cycle 27: After refmac, R = 0.1906 (Rfree = 0.000) for 975 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 28: After refmac, R = 0.1859 (Rfree = 0.000) for 971 atoms. Found 0 (8 requested) and removed 6 (4 requested) atoms. Cycle 29: After refmac, R = 0.1833 (Rfree = 0.000) for 965 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.1781 (Rfree = 0.000) for 963 atoms. Found 0 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.13 3.79 Search for helices and strands: 0 residues in 0 chains, 980 seeds are put forward Round 1: 40 peptides, 9 chains. Longest chain 5 peptides. Score 0.234 Round 2: 53 peptides, 10 chains. Longest chain 8 peptides. Score 0.369 Round 3: 53 peptides, 9 chains. Longest chain 11 peptides. Score 0.429 Round 4: 56 peptides, 10 chains. Longest chain 10 peptides. Score 0.411 Round 5: 48 peptides, 9 chains. Longest chain 7 peptides. Score 0.358 Taking the results from Round 3 Chains 9, Residues 44, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2030 reflections ( 98.16 % complete ) and 2280 restraints for refining 966 atoms. 2113 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2164 (Rfree = 0.000) for 966 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 32: After refmac, R = 0.2022 (Rfree = 0.000) for 963 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. Cycle 33: After refmac, R = 0.2273 (Rfree = 0.000) for 959 atoms. Found 5 (8 requested) and removed 7 (4 requested) atoms. Cycle 34: After refmac, R = 0.1888 (Rfree = 0.000) for 957 atoms. Found 4 (8 requested) and removed 5 (4 requested) atoms. Cycle 35: After refmac, R = 0.1467 (Rfree = 0.000) for 956 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.13 3.79 Search for helices and strands: 0 residues in 0 chains, 983 seeds are put forward Round 1: 42 peptides, 9 chains. Longest chain 7 peptides. Score 0.266 Round 2: 36 peptides, 7 chains. Longest chain 7 peptides. Score 0.304 Round 3: 39 peptides, 8 chains. Longest chain 7 peptides. Score 0.285 Round 4: 41 peptides, 8 chains. Longest chain 7 peptides. Score 0.316 Round 5: 38 peptides, 8 chains. Longest chain 6 peptides. Score 0.269 Taking the results from Round 4 Chains 8, Residues 33, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2030 reflections ( 98.16 % complete ) and 2189 restraints for refining 948 atoms. 2058 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2253 (Rfree = 0.000) for 948 atoms. Found 6 (8 requested) and removed 6 (4 requested) atoms. Cycle 37: After refmac, R = 0.2574 (Rfree = 0.000) for 946 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 38: After refmac, R = 0.1635 (Rfree = 0.000) for 946 atoms. Found 5 (8 requested) and removed 6 (4 requested) atoms. Cycle 39: After refmac, R = 0.1620 (Rfree = 0.000) for 944 atoms. Found 6 (8 requested) and removed 5 (4 requested) atoms. Cycle 40: After refmac, R = 0.1508 (Rfree = 0.000) for 944 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.10 3.75 Search for helices and strands: 0 residues in 0 chains, 967 seeds are put forward Round 1: 47 peptides, 11 chains. Longest chain 6 peptides. Score 0.215 Round 2: 48 peptides, 10 chains. Longest chain 7 peptides. Score 0.295 Round 3: 52 peptides, 10 chains. Longest chain 7 peptides. Score 0.355 Round 4: 48 peptides, 10 chains. Longest chain 7 peptides. Score 0.295 Round 5: 43 peptides, 9 chains. Longest chain 8 peptides. Score 0.282 Taking the results from Round 3 Chains 10, Residues 42, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2030 reflections ( 98.16 % complete ) and 2268 restraints for refining 970 atoms. 2110 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1718 (Rfree = 0.000) for 970 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. Cycle 42: After refmac, R = 0.1589 (Rfree = 0.000) for 964 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 43: After refmac, R = 0.1543 (Rfree = 0.000) for 961 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 44: After refmac, R = 0.1355 (Rfree = 0.000) for 959 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.1297 (Rfree = 0.000) for 957 atoms. Found 5 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.15 3.82 Search for helices and strands: 0 residues in 0 chains, 982 seeds are put forward Round 1: 33 peptides, 7 chains. Longest chain 7 peptides. Score 0.255 Round 2: 34 peptides, 7 chains. Longest chain 6 peptides. Score 0.272 Round 3: 35 peptides, 6 chains. Longest chain 7 peptides. Score 0.357 Round 4: 33 peptides, 6 chains. Longest chain 8 peptides. Score 0.325 Round 5: 38 peptides, 6 chains. Longest chain 8 peptides. Score 0.402 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 32, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2ia7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2030 reflections ( 98.16 % complete ) and 2253 restraints for refining 957 atoms. 2131 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1695 (Rfree = 0.000) for 957 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1625 (Rfree = 0.000) for 951 atoms. Found 0 (8 requested) and removed 1 (4 requested) atoms. Cycle 48: After refmac, R = 0.1638 (Rfree = 0.000) for 950 atoms. Found 0 (8 requested) and removed 1 (4 requested) atoms. Cycle 49: After refmac, R = 0.1507 (Rfree = 0.000) for 949 atoms. TimeTaking 22.35