null Sun 23 Dec 22:23:05 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 2p4o-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p4o-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p4o-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4o-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/2p4o-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4o-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 22:23:13 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/2p4o-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4o-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 206 and 0 Target number of residues in the AU: 206 Target solvent content: 0.6447 Checking the provided sequence file Detected sequence length: 306 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 306 Adjusted target solvent content: 0.47 Input MTZ file: 2p4o-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: 94 Cell parameters: 91.400 91.400 75.131 90.000 90.000 90.000 Input sequence file: 2p4o-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2448 target number of atoms Had to go as low as 0.65 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: 29.686 3.200 Wilson plot Bfac: 74.60 5601 reflections ( 99.80 % complete ) and 0 restraints for refining 2719 atoms. Observations/parameters ratio is 0.51 ------------------------------------------------------ Starting model: R = 0.3399 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3141 (Rfree = 0.000) for 2719 atoms. Found 24 (24 requested) and removed 25 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.32 3.46 Search for helices and strands: 0 residues in 0 chains, 2746 seeds are put forward Round 1: 144 peptides, 26 chains. Longest chain 13 peptides. Score 0.391 Round 2: 177 peptides, 24 chains. Longest chain 18 peptides. Score 0.579 Round 3: 181 peptides, 24 chains. Longest chain 17 peptides. Score 0.594 Round 4: 203 peptides, 26 chains. Longest chain 16 peptides. Score 0.641 Round 5: 199 peptides, 24 chains. Longest chain 17 peptides. Score 0.658 Taking the results from Round 5 Chains 24, Residues 175, Estimated correctness of the model 55.7 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5601 reflections ( 99.80 % complete ) and 4864 restraints for refining 2235 atoms. 4161 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3075 (Rfree = 0.000) for 2235 atoms. Found 20 (20 requested) and removed 23 (10 requested) atoms. Cycle 2: After refmac, R = 0.2908 (Rfree = 0.000) for 2197 atoms. Found 13 (20 requested) and removed 17 (10 requested) atoms. Cycle 3: After refmac, R = 0.2825 (Rfree = 0.000) for 2181 atoms. Found 15 (19 requested) and removed 14 (9 requested) atoms. Cycle 4: After refmac, R = 0.2543 (Rfree = 0.000) for 2171 atoms. Found 10 (19 requested) and removed 13 (9 requested) atoms. Cycle 5: After refmac, R = 0.2344 (Rfree = 0.000) for 2163 atoms. Found 3 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 3.48 Search for helices and strands: 0 residues in 0 chains, 2248 seeds are put forward Round 1: 159 peptides, 26 chains. Longest chain 12 peptides. Score 0.464 Round 2: 180 peptides, 26 chains. Longest chain 15 peptides. Score 0.556 Round 3: 193 peptides, 24 chains. Longest chain 33 peptides. Score 0.638 Round 4: 193 peptides, 24 chains. Longest chain 27 peptides. Score 0.638 Round 5: 198 peptides, 23 chains. Longest chain 27 peptides. Score 0.670 Taking the results from Round 5 Chains 26, Residues 175, Estimated correctness of the model 58.5 % 3 chains (38 residues) have been docked in sequence ------------------------------------------------------ 5601 reflections ( 99.80 % complete ) and 4632 restraints for refining 2235 atoms. 3822 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2912 (Rfree = 0.000) for 2235 atoms. Found 14 (20 requested) and removed 33 (10 requested) atoms. Cycle 7: After refmac, R = 0.2794 (Rfree = 0.000) for 2204 atoms. Found 8 (19 requested) and removed 18 (9 requested) atoms. Cycle 8: After refmac, R = 0.2753 (Rfree = 0.000) for 2175 atoms. Found 9 (19 requested) and removed 14 (9 requested) atoms. Cycle 9: After refmac, R = 0.2626 (Rfree = 0.000) for 2156 atoms. Found 17 (19 requested) and removed 12 (9 requested) atoms. Cycle 10: After refmac, R = 0.2416 (Rfree = 0.000) for 2150 atoms. Found 2 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.29 3.42 Search for helices and strands: 0 residues in 0 chains, 2193 seeds are put forward Round 1: 167 peptides, 25 chains. Longest chain 16 peptides. Score 0.520 Round 2: 188 peptides, 22 chains. Longest chain 25 peptides. Score 0.652 Round 3: 187 peptides, 23 chains. Longest chain 27 peptides. Score 0.633 Round 4: 187 peptides, 21 chains. Longest chain 25 peptides. Score 0.664 Round 5: 183 peptides, 20 chains. Longest chain 29 peptides. Score 0.666 Taking the results from Round 5 Chains 20, Residues 163, Estimated correctness of the model 57.6 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 5601 reflections ( 99.80 % complete ) and 4830 restraints for refining 2235 atoms. 4111 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2889 (Rfree = 0.000) for 2235 atoms. Found 17 (20 requested) and removed 52 (10 requested) atoms. Cycle 12: After refmac, R = 0.2765 (Rfree = 0.000) for 2179 atoms. Found 15 (19 requested) and removed 12 (9 requested) atoms. Cycle 13: After refmac, R = 0.2529 (Rfree = 0.000) for 2167 atoms. Found 16 (19 requested) and removed 15 (9 requested) atoms. Cycle 14: After refmac, R = 0.2739 (Rfree = 0.000) for 2161 atoms. Found 16 (19 requested) and removed 19 (9 requested) atoms. Cycle 15: After refmac, R = 0.2504 (Rfree = 0.000) for 2150 atoms. Found 15 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 3.45 Search for helices and strands: 0 residues in 0 chains, 2228 seeds are put forward Round 1: 132 peptides, 19 chains. Longest chain 15 peptides. Score 0.481 Round 2: 152 peptides, 22 chains. Longest chain 25 peptides. Score 0.512 Round 3: 163 peptides, 19 chains. Longest chain 16 peptides. Score 0.612 Round 4: 151 peptides, 14 chains. Longest chain 42 peptides. Score 0.653 Round 5: 161 peptides, 20 chains. Longest chain 19 peptides. Score 0.587 Taking the results from Round 4 Chains 14, Residues 137, Estimated correctness of the model 54.6 % 1 chains (23 residues) have been docked in sequence ------------------------------------------------------ 5601 reflections ( 99.80 % complete ) and 4776 restraints for refining 2214 atoms. 4150 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2535 (Rfree = 0.000) for 2214 atoms. Found 15 (19 requested) and removed 25 (9 requested) atoms. Cycle 17: After refmac, R = 0.2243 (Rfree = 0.000) for 2198 atoms. Found 11 (19 requested) and removed 18 (9 requested) atoms. Cycle 18: After refmac, R = 0.2120 (Rfree = 0.000) for 2185 atoms. Found 5 (19 requested) and removed 13 (9 requested) atoms. Cycle 19: After refmac, R = 0.2397 (Rfree = 0.000) for 2175 atoms. Found 16 (19 requested) and removed 11 (9 requested) atoms. Cycle 20: After refmac, R = 0.2781 (Rfree = 0.000) for 2178 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.28 3.41 Search for helices and strands: 0 residues in 0 chains, 2199 seeds are put forward Round 1: 147 peptides, 24 chains. Longest chain 15 peptides. Score 0.448 Round 2: 181 peptides, 21 chains. Longest chain 20 peptides. Score 0.644 Round 3: 171 peptides, 20 chains. Longest chain 19 peptides. Score 0.624 Round 4: 180 peptides, 23 chains. Longest chain 14 peptides. Score 0.607 Round 5: 174 peptides, 20 chains. Longest chain 19 peptides. Score 0.635 Taking the results from Round 2 Chains 21, Residues 160, Estimated correctness of the model 52.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5601 reflections ( 99.80 % complete ) and 4917 restraints for refining 2208 atoms. 4298 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2263 (Rfree = 0.000) for 2208 atoms. Found 15 (19 requested) and removed 14 (9 requested) atoms. Cycle 22: After refmac, R = 0.2037 (Rfree = 0.000) for 2197 atoms. Found 5 (19 requested) and removed 11 (9 requested) atoms. Cycle 23: After refmac, R = 0.2110 (Rfree = 0.000) for 2184 atoms. Found 8 (19 requested) and removed 13 (9 requested) atoms. Cycle 24: After refmac, R = 0.2425 (Rfree = 0.000) for 2177 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. Cycle 25: After refmac, R = 0.2079 (Rfree = 0.000) for 2178 atoms. Found 9 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.23 3.36 Search for helices and strands: 0 residues in 0 chains, 2225 seeds are put forward Round 1: 124 peptides, 21 chains. Longest chain 14 peptides. Score 0.399 Round 2: 144 peptides, 21 chains. Longest chain 17 peptides. Score 0.496 Round 3: 143 peptides, 20 chains. Longest chain 18 peptides. Score 0.511 Round 4: 153 peptides, 23 chains. Longest chain 18 peptides. Score 0.496 Round 5: 151 peptides, 22 chains. Longest chain 20 peptides. Score 0.507 Taking the results from Round 3 Chains 20, Residues 123, Estimated correctness of the model 14.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5601 reflections ( 99.80 % complete ) and 5257 restraints for refining 2225 atoms. 4785 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2185 (Rfree = 0.000) for 2225 atoms. Found 18 (19 requested) and removed 15 (9 requested) atoms. Cycle 27: After refmac, R = 0.1938 (Rfree = 0.000) for 2222 atoms. Found 9 (19 requested) and removed 12 (9 requested) atoms. Cycle 28: After refmac, R = 0.1849 (Rfree = 0.000) for 2214 atoms. Found 10 (19 requested) and removed 9 (9 requested) atoms. Cycle 29: After refmac, R = 0.1732 (Rfree = 0.000) for 2215 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 30: After refmac, R = 0.1798 (Rfree = 0.000) for 2206 atoms. Found 1 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 3.45 Search for helices and strands: 0 residues in 0 chains, 2244 seeds are put forward Round 1: 145 peptides, 24 chains. Longest chain 17 peptides. Score 0.439 Round 2: 145 peptides, 21 chains. Longest chain 16 peptides. Score 0.500 Round 3: 149 peptides, 22 chains. Longest chain 19 peptides. Score 0.498 Round 4: 146 peptides, 18 chains. Longest chain 18 peptides. Score 0.563 Round 5: 150 peptides, 20 chains. Longest chain 20 peptides. Score 0.542 Taking the results from Round 4 Chains 18, Residues 128, Estimated correctness of the model 30.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5601 reflections ( 99.80 % complete ) and 5258 restraints for refining 2235 atoms. 4764 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2084 (Rfree = 0.000) for 2235 atoms. Found 16 (20 requested) and removed 11 (10 requested) atoms. Cycle 32: After refmac, R = 0.1909 (Rfree = 0.000) for 2234 atoms. Found 1 (20 requested) and removed 11 (10 requested) atoms. Cycle 33: After refmac, R = 0.1858 (Rfree = 0.000) for 2222 atoms. Found 4 (19 requested) and removed 9 (9 requested) atoms. Cycle 34: After refmac, R = 0.1812 (Rfree = 0.000) for 2214 atoms. Found 5 (19 requested) and removed 9 (9 requested) atoms. Cycle 35: After refmac, R = 0.1767 (Rfree = 0.000) for 2209 atoms. Found 1 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 3.42 Search for helices and strands: 0 residues in 0 chains, 2243 seeds are put forward Round 1: 130 peptides, 22 chains. Longest chain 16 peptides. Score 0.407 Round 2: 146 peptides, 21 chains. Longest chain 18 peptides. Score 0.505 Round 3: 142 peptides, 25 chains. Longest chain 13 peptides. Score 0.403 Round 4: 144 peptides, 21 chains. Longest chain 16 peptides. Score 0.496 Round 5: 152 peptides, 22 chains. Longest chain 13 peptides. Score 0.512 Taking the results from Round 5 Chains 22, Residues 130, Estimated correctness of the model 15.2 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 5601 reflections ( 99.80 % complete ) and 5184 restraints for refining 2234 atoms. 4667 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2452 (Rfree = 0.000) for 2234 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 37: After refmac, R = 0.2603 (Rfree = 0.000) for 2231 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 38: After refmac, R = 0.2354 (Rfree = 0.000) for 2225 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. Cycle 39: After refmac, R = 0.2552 (Rfree = 0.000) for 2223 atoms. Found 18 (20 requested) and removed 16 (10 requested) atoms. Cycle 40: After refmac, R = 0.2009 (Rfree = 0.000) for 2218 atoms. Found 8 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 3.42 Search for helices and strands: 0 residues in 0 chains, 2250 seeds are put forward Round 1: 131 peptides, 25 chains. Longest chain 10 peptides. Score 0.346 Round 2: 137 peptides, 23 chains. Longest chain 15 peptides. Score 0.421 Round 3: 143 peptides, 25 chains. Longest chain 11 peptides. Score 0.408 Round 4: 147 peptides, 22 chains. Longest chain 15 peptides. Score 0.489 Round 5: 153 peptides, 24 chains. Longest chain 13 peptides. Score 0.477 Taking the results from Round 4 Chains 22, Residues 125, Estimated correctness of the model 7.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5601 reflections ( 99.80 % complete ) and 5019 restraints for refining 2235 atoms. 4541 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2850 (Rfree = 0.000) for 2235 atoms. Found 20 (20 requested) and removed 19 (10 requested) atoms. Cycle 42: After refmac, R = 0.2931 (Rfree = 0.000) for 2233 atoms. Found 20 (20 requested) and removed 28 (10 requested) atoms. Cycle 43: After refmac, R = 0.2256 (Rfree = 0.000) for 2217 atoms. Found 14 (19 requested) and removed 10 (9 requested) atoms. Cycle 44: After refmac, R = 0.2651 (Rfree = 0.000) for 2217 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 45: After refmac, R = 0.2338 (Rfree = 0.000) for 2217 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.51 Search for helices and strands: 0 residues in 0 chains, 2263 seeds are put forward Round 1: 99 peptides, 21 chains. Longest chain 8 peptides. Score 0.260 Round 2: 118 peptides, 21 chains. Longest chain 15 peptides. Score 0.367 Round 3: 111 peptides, 18 chains. Longest chain 13 peptides. Score 0.399 Round 4: 109 peptides, 16 chains. Longest chain 13 peptides. Score 0.435 Round 5: 109 peptides, 17 chains. Longest chain 15 peptides. Score 0.412 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 93, 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 2p4o-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5601 reflections ( 99.80 % complete ) and 5225 restraints for refining 2200 atoms. 4869 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3186 (Rfree = 0.000) for 2200 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2901 (Rfree = 0.000) for 2187 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2824 (Rfree = 0.000) for 2175 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2740 (Rfree = 0.000) for 2164 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:09:20 GMT 2018 Job finished. TimeTaking 46.27 Used memory is bytes: 6883080