null Sun 23 Dec 22:22:53 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 2p4g-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p4g-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p4g-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4g-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/2p4g-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4g-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 22:23:03 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/2p4g-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4g-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 283 and 0 Target number of residues in the AU: 283 Target solvent content: 0.6516 Checking the provided sequence file Detected sequence length: 270 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 270 Adjusted target solvent content: 0.67 Input MTZ file: 2p4g-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: 172 Cell parameters: 115.650 115.650 56.930 90.000 90.000 120.000 Input sequence file: 2p4g-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2160 target number of atoms Had to go as low as 1.10 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: 28.913 3.200 Wilson plot Bfac: 78.61 7307 reflections ( 99.73 % complete ) and 0 restraints for refining 2414 atoms. Observations/parameters ratio is 0.76 ------------------------------------------------------ Starting model: R = 0.3528 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3434 (Rfree = 0.000) for 2414 atoms. Found 21 (21 requested) and removed 24 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.57 2.82 Search for helices and strands: 0 residues in 0 chains, 2461 seeds are put forward Round 1: 133 peptides, 23 chains. Longest chain 13 peptides. Score 0.350 Round 2: 149 peptides, 21 chains. Longest chain 16 peptides. Score 0.444 Round 3: 151 peptides, 19 chains. Longest chain 23 peptides. Score 0.483 Round 4: 160 peptides, 19 chains. Longest chain 26 peptides. Score 0.514 Round 5: 163 peptides, 18 chains. Longest chain 24 peptides. Score 0.538 Taking the results from Round 5 Chains 18, Residues 145, Estimated correctness of the model 23.3 % 1 chains (23 residues) have been docked in sequence ------------------------------------------------------ 7307 reflections ( 99.73 % complete ) and 4118 restraints for refining 1971 atoms. 3461 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2860 (Rfree = 0.000) for 1971 atoms. Found 17 (17 requested) and removed 24 (8 requested) atoms. Cycle 2: After refmac, R = 0.2762 (Rfree = 0.000) for 1935 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 3: After refmac, R = 0.2499 (Rfree = 0.000) for 1911 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 4: After refmac, R = 0.2305 (Rfree = 0.000) for 1901 atoms. Found 10 (17 requested) and removed 13 (8 requested) atoms. Cycle 5: After refmac, R = 0.2369 (Rfree = 0.000) for 1893 atoms. Found 13 (17 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.32 2.62 Search for helices and strands: 0 residues in 0 chains, 1964 seeds are put forward Round 1: 166 peptides, 23 chains. Longest chain 17 peptides. Score 0.472 Round 2: 181 peptides, 18 chains. Longest chain 28 peptides. Score 0.592 Round 3: 175 peptides, 19 chains. Longest chain 29 peptides. Score 0.561 Round 4: 180 peptides, 20 chains. Longest chain 30 peptides. Score 0.562 Round 5: 181 peptides, 18 chains. Longest chain 27 peptides. Score 0.592 Taking the results from Round 5 Chains 18, Residues 163, Estimated correctness of the model 38.9 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7307 reflections ( 99.73 % complete ) and 4182 restraints for refining 1972 atoms. 3535 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2590 (Rfree = 0.000) for 1972 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 7: After refmac, R = 0.2284 (Rfree = 0.000) for 1966 atoms. Found 11 (17 requested) and removed 10 (8 requested) atoms. Cycle 8: After refmac, R = 0.2157 (Rfree = 0.000) for 1962 atoms. Found 6 (17 requested) and removed 13 (8 requested) atoms. Cycle 9: After refmac, R = 0.2197 (Rfree = 0.000) for 1954 atoms. Found 12 (17 requested) and removed 13 (8 requested) atoms. Cycle 10: After refmac, R = 0.2010 (Rfree = 0.000) for 1947 atoms. Found 11 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.35 2.65 Search for helices and strands: 0 residues in 0 chains, 2027 seeds are put forward Round 1: 170 peptides, 21 chains. Longest chain 20 peptides. Score 0.516 Round 2: 173 peptides, 21 chains. Longest chain 21 peptides. Score 0.526 Round 3: 185 peptides, 22 chains. Longest chain 22 peptides. Score 0.549 Round 4: 183 peptides, 19 chains. Longest chain 30 peptides. Score 0.584 Round 5: 177 peptides, 17 chains. Longest chain 20 peptides. Score 0.594 Taking the results from Round 5 Chains 18, Residues 160, Estimated correctness of the model 39.4 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 7307 reflections ( 99.73 % complete ) and 4073 restraints for refining 1972 atoms. 3409 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2388 (Rfree = 0.000) for 1972 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 12: After refmac, R = 0.2135 (Rfree = 0.000) for 1963 atoms. Found 12 (17 requested) and removed 15 (8 requested) atoms. Cycle 13: After refmac, R = 0.1979 (Rfree = 0.000) for 1954 atoms. Found 6 (17 requested) and removed 10 (8 requested) atoms. Cycle 14: After refmac, R = 0.1953 (Rfree = 0.000) for 1946 atoms. Found 4 (17 requested) and removed 8 (8 requested) atoms. Cycle 15: After refmac, R = 0.1900 (Rfree = 0.000) for 1941 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.36 2.65 Search for helices and strands: 0 residues in 0 chains, 2034 seeds are put forward Round 1: 155 peptides, 21 chains. Longest chain 16 peptides. Score 0.466 Round 2: 173 peptides, 22 chains. Longest chain 21 peptides. Score 0.511 Round 3: 181 peptides, 26 chains. Longest chain 17 peptides. Score 0.477 Round 4: 184 peptides, 21 chains. Longest chain 22 peptides. Score 0.559 Round 5: 170 peptides, 18 chains. Longest chain 17 peptides. Score 0.560 Taking the results from Round 5 Chains 18, Residues 152, Estimated correctness of the model 29.8 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7307 reflections ( 99.73 % complete ) and 4126 restraints for refining 1972 atoms. 3496 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2698 (Rfree = 0.000) for 1972 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 17: After refmac, R = 0.2547 (Rfree = 0.000) for 1978 atoms. Found 11 (17 requested) and removed 14 (8 requested) atoms. Cycle 18: After refmac, R = 0.2466 (Rfree = 0.000) for 1975 atoms. Found 11 (17 requested) and removed 9 (8 requested) atoms. Cycle 19: After refmac, R = 0.2375 (Rfree = 0.000) for 1977 atoms. Found 7 (17 requested) and removed 8 (8 requested) atoms. Cycle 20: After refmac, R = 0.2319 (Rfree = 0.000) for 1975 atoms. Found 2 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 2.71 Search for helices and strands: 0 residues in 0 chains, 2029 seeds are put forward Round 1: 161 peptides, 27 chains. Longest chain 17 peptides. Score 0.391 Round 2: 166 peptides, 21 chains. Longest chain 18 peptides. Score 0.503 Round 3: 174 peptides, 22 chains. Longest chain 26 peptides. Score 0.514 Round 4: 178 peptides, 21 chains. Longest chain 14 peptides. Score 0.541 Round 5: 181 peptides, 22 chains. Longest chain 15 peptides. Score 0.536 Taking the results from Round 4 Chains 21, Residues 157, Estimated correctness of the model 24.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7307 reflections ( 99.73 % complete ) and 4138 restraints for refining 1972 atoms. 3531 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2867 (Rfree = 0.000) for 1972 atoms. Found 17 (17 requested) and removed 8 (8 requested) atoms. Cycle 22: After refmac, R = 0.2611 (Rfree = 0.000) for 1981 atoms. Found 16 (17 requested) and removed 8 (8 requested) atoms. Cycle 23: After refmac, R = 0.2498 (Rfree = 0.000) for 1986 atoms. Found 2 (17 requested) and removed 8 (8 requested) atoms. Cycle 24: After refmac, R = 0.2441 (Rfree = 0.000) for 1979 atoms. Found 4 (17 requested) and removed 8 (8 requested) atoms. Cycle 25: After refmac, R = 0.2393 (Rfree = 0.000) for 1975 atoms. Found 2 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 2.72 Search for helices and strands: 0 residues in 0 chains, 2025 seeds are put forward Round 1: 156 peptides, 20 chains. Longest chain 16 peptides. Score 0.485 Round 2: 169 peptides, 20 chains. Longest chain 22 peptides. Score 0.528 Round 3: 172 peptides, 21 chains. Longest chain 20 peptides. Score 0.522 Round 4: 160 peptides, 18 chains. Longest chain 16 peptides. Score 0.529 Round 5: 167 peptides, 19 chains. Longest chain 20 peptides. Score 0.536 Taking the results from Round 5 Chains 19, Residues 148, Estimated correctness of the model 22.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7307 reflections ( 99.73 % complete ) and 4379 restraints for refining 1972 atoms. 3806 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2772 (Rfree = 0.000) for 1972 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 27: After refmac, R = 0.2509 (Rfree = 0.000) for 1977 atoms. Found 9 (17 requested) and removed 8 (8 requested) atoms. Cycle 28: After refmac, R = 0.2450 (Rfree = 0.000) for 1975 atoms. Found 11 (17 requested) and removed 8 (8 requested) atoms. Cycle 29: After refmac, R = 0.2407 (Rfree = 0.000) for 1977 atoms. Found 4 (17 requested) and removed 8 (8 requested) atoms. Cycle 30: After refmac, R = 0.2364 (Rfree = 0.000) for 1972 atoms. Found 4 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 2.71 Search for helices and strands: 0 residues in 0 chains, 2019 seeds are put forward Round 1: 141 peptides, 22 chains. Longest chain 14 peptides. Score 0.398 Round 2: 153 peptides, 20 chains. Longest chain 15 peptides. Score 0.475 Round 3: 160 peptides, 20 chains. Longest chain 16 peptides. Score 0.498 Round 4: 161 peptides, 19 chains. Longest chain 27 peptides. Score 0.517 Round 5: 163 peptides, 18 chains. Longest chain 21 peptides. Score 0.538 Taking the results from Round 5 Chains 18, Residues 145, Estimated correctness of the model 23.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7307 reflections ( 99.73 % complete ) and 4337 restraints for refining 1971 atoms. 3775 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2778 (Rfree = 0.000) for 1971 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 32: After refmac, R = 0.2568 (Rfree = 0.000) for 1973 atoms. Found 16 (17 requested) and removed 9 (8 requested) atoms. Cycle 33: After refmac, R = 0.2406 (Rfree = 0.000) for 1979 atoms. Found 6 (17 requested) and removed 8 (8 requested) atoms. Cycle 34: After refmac, R = 0.2310 (Rfree = 0.000) for 1975 atoms. Found 4 (17 requested) and removed 9 (8 requested) atoms. Cycle 35: After refmac, R = 0.2268 (Rfree = 0.000) for 1966 atoms. Found 6 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 2.69 Search for helices and strands: 0 residues in 0 chains, 2012 seeds are put forward Round 1: 144 peptides, 23 chains. Longest chain 14 peptides. Score 0.393 Round 2: 160 peptides, 21 chains. Longest chain 15 peptides. Score 0.483 Round 3: 152 peptides, 18 chains. Longest chain 20 peptides. Score 0.503 Round 4: 154 peptides, 19 chains. Longest chain 21 peptides. Score 0.494 Round 5: 158 peptides, 18 chains. Longest chain 22 peptides. Score 0.522 Taking the results from Round 5 Chains 18, Residues 140, Estimated correctness of the model 18.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7307 reflections ( 99.73 % complete ) and 4310 restraints for refining 1972 atoms. 3768 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2483 (Rfree = 0.000) for 1972 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 37: After refmac, R = 0.2262 (Rfree = 0.000) for 1969 atoms. Found 11 (17 requested) and removed 8 (8 requested) atoms. Cycle 38: After refmac, R = 0.2139 (Rfree = 0.000) for 1970 atoms. Found 5 (17 requested) and removed 8 (8 requested) atoms. Cycle 39: After refmac, R = 0.2064 (Rfree = 0.000) for 1963 atoms. Found 3 (17 requested) and removed 11 (8 requested) atoms. Cycle 40: After refmac, R = 0.2027 (Rfree = 0.000) for 1951 atoms. Found 5 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 2.68 Search for helices and strands: 0 residues in 0 chains, 2006 seeds are put forward Round 1: 134 peptides, 22 chains. Longest chain 11 peptides. Score 0.371 Round 2: 147 peptides, 17 chains. Longest chain 17 peptides. Score 0.502 Round 3: 159 peptides, 18 chains. Longest chain 18 peptides. Score 0.526 Round 4: 154 peptides, 20 chains. Longest chain 13 peptides. Score 0.478 Round 5: 164 peptides, 19 chains. Longest chain 16 peptides. Score 0.526 Taking the results from Round 5 Chains 19, Residues 145, Estimated correctness of the model 19.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7307 reflections ( 99.73 % complete ) and 4237 restraints for refining 1970 atoms. 3676 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2339 (Rfree = 0.000) for 1970 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 42: After refmac, R = 0.2137 (Rfree = 0.000) for 1968 atoms. Found 12 (17 requested) and removed 11 (8 requested) atoms. Cycle 43: After refmac, R = 0.2052 (Rfree = 0.000) for 1968 atoms. Found 4 (17 requested) and removed 9 (8 requested) atoms. Cycle 44: After refmac, R = 0.2001 (Rfree = 0.000) for 1960 atoms. Found 2 (17 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.1974 (Rfree = 0.000) for 1953 atoms. Found 6 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 2.67 Search for helices and strands: 0 residues in 0 chains, 2013 seeds are put forward Round 1: 152 peptides, 24 chains. Longest chain 16 peptides. Score 0.406 Round 2: 162 peptides, 20 chains. Longest chain 21 peptides. Score 0.505 Round 3: 161 peptides, 19 chains. Longest chain 16 peptides. Score 0.517 Round 4: 163 peptides, 18 chains. Longest chain 24 peptides. Score 0.538 Round 5: 165 peptides, 19 chains. Longest chain 16 peptides. Score 0.530 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 145, Estimated correctness of the model 23.3 % 2 chains (29 residues) have been docked in sequence Sequence coverage is 19 % Consider running further cycles of model building using 2p4g-3_warpNtrace.pdb as input Building loops using Loopy2018 20 chains (145 residues) following loop building 2 chains (29 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7307 reflections ( 99.73 % complete ) and 3956 restraints for refining 1972 atoms. 3293 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2283 (Rfree = 0.000) for 1972 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2208 (Rfree = 0.000) for 1956 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2335 (Rfree = 0.000) for 1939 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2045 (Rfree = 0.000) for 1923 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:10:33 GMT 2018 Job finished. TimeTaking 47.67 Used memory is bytes: 21275576