null Sun 23 Dec 22:23:07 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 2p97-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p97-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p97-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p97-3.8-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/2p97-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p97-3.8-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 22:23:17 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/2p97-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p97-3.8-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 334 and 0 Target number of residues in the AU: 334 Target solvent content: 0.6462 Checking the provided sequence file Detected sequence length: 201 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 402 Adjusted target solvent content: 0.57 Input MTZ file: 2p97-3.8-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: 103.080 103.080 96.168 90.000 90.000 90.000 Input sequence file: 2p97-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 3216 target number of atoms Had to go as low as 0.85 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: 72.889 3.800 Wilson plot Bfac: 75.43 5456 reflections ( 99.67 % complete ) and 0 restraints for refining 3570 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3425 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3257 (Rfree = 0.000) for 3570 atoms. Found 19 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.55 3.23 Search for helices and strands: 0 residues in 0 chains, 3633 seeds are put forward NCS extension: 0 residues added, 3633 seeds are put forward Round 1: 198 peptides, 39 chains. Longest chain 9 peptides. Score 0.319 Round 2: 249 peptides, 32 chains. Longest chain 21 peptides. Score 0.561 Round 3: 263 peptides, 32 chains. Longest chain 21 peptides. Score 0.595 Round 4: 276 peptides, 30 chains. Longest chain 21 peptides. Score 0.645 Round 5: 262 peptides, 28 chains. Longest chain 21 peptides. Score 0.635 Taking the results from Round 4 Chains 33, Residues 246, Estimated correctness of the model 18.7 % 3 chains (37 residues) have been docked in sequence ------------------------------------------------------ 5456 reflections ( 99.67 % complete ) and 6001 restraints for refining 2908 atoms. 4908 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2974 (Rfree = 0.000) for 2908 atoms. Found 15 (15 requested) and removed 20 (7 requested) atoms. Cycle 2: After refmac, R = 0.2632 (Rfree = 0.000) for 2874 atoms. Found 14 (15 requested) and removed 18 (7 requested) atoms. Cycle 3: After refmac, R = 0.2575 (Rfree = 0.000) for 2863 atoms. Found 8 (15 requested) and removed 15 (7 requested) atoms. Cycle 4: After refmac, R = 0.2512 (Rfree = 0.000) for 2848 atoms. Found 5 (15 requested) and removed 14 (7 requested) atoms. Cycle 5: After refmac, R = 0.2407 (Rfree = 0.000) for 2838 atoms. Found 7 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.52 3.20 Search for helices and strands: 0 residues in 0 chains, 2937 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 2961 seeds are put forward Round 1: 226 peptides, 34 chains. Longest chain 16 peptides. Score 0.474 Round 2: 245 peptides, 29 chains. Longest chain 16 peptides. Score 0.585 Round 3: 256 peptides, 31 chains. Longest chain 18 peptides. Score 0.589 Round 4: 265 peptides, 26 chains. Longest chain 25 peptides. Score 0.661 Round 5: 243 peptides, 29 chains. Longest chain 26 peptides. Score 0.580 Taking the results from Round 4 Chains 26, Residues 239, Estimated correctness of the model 25.3 % 1 chains (24 residues) have been docked in sequence ------------------------------------------------------ 5456 reflections ( 99.67 % complete ) and 5963 restraints for refining 2909 atoms. 4944 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2663 (Rfree = 0.000) for 2909 atoms. Found 13 (15 requested) and removed 10 (7 requested) atoms. Cycle 7: After refmac, R = 0.2506 (Rfree = 0.000) for 2889 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 8: After refmac, R = 0.2423 (Rfree = 0.000) for 2874 atoms. Found 12 (15 requested) and removed 15 (7 requested) atoms. Cycle 9: After refmac, R = 0.2245 (Rfree = 0.000) for 2860 atoms. Found 7 (15 requested) and removed 16 (7 requested) atoms. Cycle 10: After refmac, R = 0.2061 (Rfree = 0.000) for 2840 atoms. Found 7 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 3.20 Search for helices and strands: 0 residues in 0 chains, 2941 seeds are put forward NCS extension: 18 residues added (4 deleted due to clashes), 2959 seeds are put forward Round 1: 238 peptides, 38 chains. Longest chain 15 peptides. Score 0.458 Round 2: 256 peptides, 33 chains. Longest chain 20 peptides. Score 0.567 Round 3: 257 peptides, 30 chains. Longest chain 24 peptides. Score 0.602 Round 4: 254 peptides, 33 chains. Longest chain 24 peptides. Score 0.562 Round 5: 266 peptides, 30 chains. Longest chain 33 peptides. Score 0.623 Taking the results from Round 5 Chains 30, Residues 236, Estimated correctness of the model 9.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5456 reflections ( 99.67 % complete ) and 6457 restraints for refining 2908 atoms. 5543 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2605 (Rfree = 0.000) for 2908 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 12: After refmac, R = 0.2449 (Rfree = 0.000) for 2890 atoms. Found 14 (16 requested) and removed 11 (8 requested) atoms. Cycle 13: After refmac, R = 0.2273 (Rfree = 0.000) for 2879 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 14: After refmac, R = 0.2372 (Rfree = 0.000) for 2877 atoms. Found 13 (15 requested) and removed 12 (7 requested) atoms. Cycle 15: After refmac, R = 0.2242 (Rfree = 0.000) for 2869 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 3.25 Search for helices and strands: 0 residues in 0 chains, 2995 seeds are put forward NCS extension: 33 residues added (7 deleted due to clashes), 3028 seeds are put forward Round 1: 209 peptides, 33 chains. Longest chain 21 peptides. Score 0.437 Round 2: 243 peptides, 33 chains. Longest chain 36 peptides. Score 0.534 Round 3: 232 peptides, 31 chains. Longest chain 21 peptides. Score 0.528 Round 4: 243 peptides, 31 chains. Longest chain 21 peptides. Score 0.557 Round 5: 241 peptides, 31 chains. Longest chain 29 peptides. Score 0.552 Taking the results from Round 4 Chains 31, Residues 212, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5456 reflections ( 99.67 % complete ) and 6606 restraints for refining 2909 atoms. 5789 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2471 (Rfree = 0.000) for 2909 atoms. Found 9 (15 requested) and removed 10 (7 requested) atoms. Cycle 17: After refmac, R = 0.2393 (Rfree = 0.000) for 2900 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 18: After refmac, R = 0.2211 (Rfree = 0.000) for 2897 atoms. Found 13 (15 requested) and removed 16 (7 requested) atoms. Cycle 19: After refmac, R = 0.2174 (Rfree = 0.000) for 2892 atoms. Found 10 (15 requested) and removed 15 (7 requested) atoms. Cycle 20: After refmac, R = 0.2076 (Rfree = 0.000) for 2884 atoms. Found 11 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.48 3.17 Search for helices and strands: 0 residues in 0 chains, 2985 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3002 seeds are put forward Round 1: 209 peptides, 35 chains. Longest chain 15 peptides. Score 0.410 Round 2: 216 peptides, 28 chains. Longest chain 17 peptides. Score 0.521 Round 3: 219 peptides, 29 chains. Longest chain 17 peptides. Score 0.517 Round 4: 228 peptides, 29 chains. Longest chain 16 peptides. Score 0.542 Round 5: 227 peptides, 27 chains. Longest chain 21 peptides. Score 0.563 Taking the results from Round 5 Chains 27, Residues 200, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5456 reflections ( 99.67 % complete ) and 6637 restraints for refining 2908 atoms. 5864 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2460 (Rfree = 0.000) for 2908 atoms. Found 9 (15 requested) and removed 9 (7 requested) atoms. Cycle 22: After refmac, R = 0.2445 (Rfree = 0.000) for 2899 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 23: After refmac, R = 0.2222 (Rfree = 0.000) for 2887 atoms. Found 14 (15 requested) and removed 9 (7 requested) atoms. Cycle 24: After refmac, R = 0.2014 (Rfree = 0.000) for 2884 atoms. Found 5 (15 requested) and removed 9 (7 requested) atoms. Cycle 25: After refmac, R = 0.2143 (Rfree = 0.000) for 2875 atoms. Found 13 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.55 3.23 Search for helices and strands: 0 residues in 0 chains, 2981 seeds are put forward NCS extension: 32 residues added (2 deleted due to clashes), 3013 seeds are put forward Round 1: 196 peptides, 35 chains. Longest chain 10 peptides. Score 0.369 Round 2: 228 peptides, 31 chains. Longest chain 16 peptides. Score 0.517 Round 3: 234 peptides, 30 chains. Longest chain 22 peptides. Score 0.545 Round 4: 252 peptides, 31 chains. Longest chain 17 peptides. Score 0.579 Round 5: 250 peptides, 27 chains. Longest chain 23 peptides. Score 0.618 Taking the results from Round 5 Chains 28, Residues 223, Estimated correctness of the model 7.1 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5456 reflections ( 99.67 % complete ) and 6356 restraints for refining 2909 atoms. 5452 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2685 (Rfree = 0.000) for 2909 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 27: After refmac, R = 0.2442 (Rfree = 0.000) for 2894 atoms. Found 12 (16 requested) and removed 12 (8 requested) atoms. Cycle 28: After refmac, R = 0.2288 (Rfree = 0.000) for 2886 atoms. Found 12 (15 requested) and removed 11 (7 requested) atoms. Cycle 29: After refmac, R = 0.2231 (Rfree = 0.000) for 2876 atoms. Found 12 (15 requested) and removed 12 (7 requested) atoms. Cycle 30: After refmac, R = 0.2031 (Rfree = 0.000) for 2870 atoms. Found 5 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 3.17 Search for helices and strands: 0 residues in 0 chains, 2950 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2965 seeds are put forward Round 1: 199 peptides, 30 chains. Longest chain 16 peptides. Score 0.447 Round 2: 204 peptides, 27 chains. Longest chain 22 peptides. Score 0.501 Round 3: 211 peptides, 26 chains. Longest chain 31 peptides. Score 0.533 Round 4: 216 peptides, 26 chains. Longest chain 19 peptides. Score 0.546 Round 5: 220 peptides, 27 chains. Longest chain 22 peptides. Score 0.544 Taking the results from Round 4 Chains 27, Residues 190, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5456 reflections ( 99.67 % complete ) and 6520 restraints for refining 2908 atoms. 5747 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2520 (Rfree = 0.000) for 2908 atoms. Found 12 (15 requested) and removed 20 (7 requested) atoms. Cycle 32: After refmac, R = 0.2347 (Rfree = 0.000) for 2878 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 33: After refmac, R = 0.2252 (Rfree = 0.000) for 2871 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 34: After refmac, R = 0.1917 (Rfree = 0.000) for 2863 atoms. Found 2 (15 requested) and removed 9 (7 requested) atoms. Cycle 35: After refmac, R = 0.1842 (Rfree = 0.000) for 2852 atoms. Found 2 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 3.22 Search for helices and strands: 0 residues in 0 chains, 2922 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 2940 seeds are put forward Round 1: 206 peptides, 36 chains. Longest chain 13 peptides. Score 0.387 Round 2: 226 peptides, 32 chains. Longest chain 22 peptides. Score 0.499 Round 3: 237 peptides, 32 chains. Longest chain 19 peptides. Score 0.529 Round 4: 252 peptides, 32 chains. Longest chain 31 peptides. Score 0.568 Round 5: 237 peptides, 28 chains. Longest chain 32 peptides. Score 0.576 Taking the results from Round 5 Chains 30, Residues 209, Estimated correctness of the model 0.0 % 2 chains (30 residues) have been docked in sequence ------------------------------------------------------ 5456 reflections ( 99.67 % complete ) and 6268 restraints for refining 2908 atoms. 5331 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2556 (Rfree = 0.000) for 2908 atoms. Found 14 (15 requested) and removed 14 (7 requested) atoms. Cycle 37: After refmac, R = 0.2542 (Rfree = 0.000) for 2881 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 38: After refmac, R = 0.2324 (Rfree = 0.000) for 2867 atoms. Found 11 (15 requested) and removed 8 (7 requested) atoms. Cycle 39: After refmac, R = 0.2419 (Rfree = 0.000) for 2859 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 40: After refmac, R = 0.2223 (Rfree = 0.000) for 2858 atoms. Found 13 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.57 3.25 Search for helices and strands: 0 residues in 0 chains, 2943 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 2967 seeds are put forward Round 1: 180 peptides, 30 chains. Longest chain 14 peptides. Score 0.387 Round 2: 207 peptides, 31 chains. Longest chain 13 peptides. Score 0.457 Round 3: 192 peptides, 30 chains. Longest chain 15 peptides. Score 0.425 Round 4: 197 peptides, 28 chains. Longest chain 17 peptides. Score 0.467 Round 5: 196 peptides, 27 chains. Longest chain 17 peptides. Score 0.478 Taking the results from Round 5 Chains 28, Residues 169, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5456 reflections ( 99.67 % complete ) and 6614 restraints for refining 2909 atoms. 5930 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2626 (Rfree = 0.000) for 2909 atoms. Found 15 (15 requested) and removed 23 (7 requested) atoms. Cycle 42: After refmac, R = 0.2411 (Rfree = 0.000) for 2879 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 43: After refmac, R = 0.2237 (Rfree = 0.000) for 2874 atoms. Found 12 (15 requested) and removed 12 (7 requested) atoms. Cycle 44: After refmac, R = 0.2188 (Rfree = 0.000) for 2871 atoms. Found 14 (15 requested) and removed 9 (7 requested) atoms. Cycle 45: After refmac, R = 0.2171 (Rfree = 0.000) for 2869 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 3.22 Search for helices and strands: 0 residues in 0 chains, 2946 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2964 seeds are put forward Round 1: 180 peptides, 32 chains. Longest chain 10 peptides. Score 0.358 Round 2: 193 peptides, 31 chains. Longest chain 14 peptides. Score 0.415 Round 3: 198 peptides, 31 chains. Longest chain 19 peptides. Score 0.430 Round 4: 196 peptides, 27 chains. Longest chain 27 peptides. Score 0.478 Round 5: 205 peptides, 33 chains. Longest chain 19 peptides. Score 0.425 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 169, 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 2p97-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5456 reflections ( 99.67 % complete ) and 6798 restraints for refining 2908 atoms. 6149 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2292 (Rfree = 0.000) for 2908 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2396 (Rfree = 0.000) for 2887 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2408 (Rfree = 0.000) for 2868 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2279 (Rfree = 0.000) for 2846 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:16:27 GMT 2018 Job finished. TimeTaking 53.33 Used memory is bytes: 7290296