null Sun 23 Dec 23:49:05 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 2p97-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2p97-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2p97-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p97-3.8-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/2p97-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p97-3.8-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 23:49:09 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/2p97-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p97-3.8-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 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-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: 94 Cell parameters: 103.080 103.080 96.168 90.000 90.000 90.000 Input sequence file: 2p97-3.8-parrot-mrncs.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 3556 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3426 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3219 (Rfree = 0.000) for 3556 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, 3618 seeds are put forward NCS extension: 0 residues added, 3618 seeds are put forward Round 1: 184 peptides, 36 chains. Longest chain 8 peptides. Score 0.314 Round 2: 227 peptides, 32 chains. Longest chain 14 peptides. Score 0.502 Round 3: 261 peptides, 33 chains. Longest chain 18 peptides. Score 0.579 Round 4: 266 peptides, 30 chains. Longest chain 23 peptides. Score 0.623 Round 5: 274 peptides, 28 chains. Longest chain 31 peptides. Score 0.660 Taking the results from Round 5 Chains 29, Residues 246, Estimated correctness of the model 24.9 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 5456 reflections ( 99.67 % complete ) and 6022 restraints for refining 2909 atoms. 4954 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2776 (Rfree = 0.000) for 2909 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 2: After refmac, R = 0.2535 (Rfree = 0.000) for 2859 atoms. Found 6 (15 requested) and removed 13 (7 requested) atoms. Cycle 3: After refmac, R = 0.2520 (Rfree = 0.000) for 2836 atoms. Found 13 (15 requested) and removed 10 (7 requested) atoms. Cycle 4: After refmac, R = 0.2375 (Rfree = 0.000) for 2831 atoms. Found 6 (15 requested) and removed 13 (7 requested) atoms. Cycle 5: After refmac, R = 0.2365 (Rfree = 0.000) for 2809 atoms. Found 8 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.53 3.21 Search for helices and strands: 0 residues in 0 chains, 2889 seeds are put forward NCS extension: 33 residues added (2 deleted due to clashes), 2922 seeds are put forward Round 1: 244 peptides, 33 chains. Longest chain 17 peptides. Score 0.536 Round 2: 259 peptides, 32 chains. Longest chain 22 peptides. Score 0.585 Round 3: 268 peptides, 31 chains. Longest chain 30 peptides. Score 0.617 Round 4: 266 peptides, 26 chains. Longest chain 32 peptides. Score 0.663 Round 5: 273 peptides, 30 chains. Longest chain 28 peptides. Score 0.639 Taking the results from Round 4 Chains 31, Residues 240, Estimated correctness of the model 26.1 % 3 chains (44 residues) have been docked in sequence ------------------------------------------------------ 5456 reflections ( 99.67 % complete ) and 5930 restraints for refining 2909 atoms. 4836 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2551 (Rfree = 0.000) for 2909 atoms. Found 12 (15 requested) and removed 20 (7 requested) atoms. Cycle 7: After refmac, R = 0.2405 (Rfree = 0.000) for 2871 atoms. Found 10 (15 requested) and removed 14 (7 requested) atoms. Cycle 8: After refmac, R = 0.2335 (Rfree = 0.000) for 2849 atoms. Found 12 (15 requested) and removed 10 (7 requested) atoms. Cycle 9: After refmac, R = 0.2229 (Rfree = 0.000) for 2837 atoms. Found 8 (15 requested) and removed 12 (7 requested) atoms. Cycle 10: After refmac, R = 0.2178 (Rfree = 0.000) for 2827 atoms. Found 5 (15 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.45 3.14 Search for helices and strands: 0 residues in 0 chains, 2909 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 2920 seeds are put forward Round 1: 241 peptides, 39 chains. Longest chain 16 peptides. Score 0.454 Round 2: 252 peptides, 35 chains. Longest chain 19 peptides. Score 0.534 Round 3: 236 peptides, 29 chains. Longest chain 18 peptides. Score 0.562 Round 4: 247 peptides, 29 chains. Longest chain 18 peptides. Score 0.590 Round 5: 267 peptides, 30 chains. Longest chain 25 peptides. Score 0.625 Taking the results from Round 5 Chains 32, Residues 237, Estimated correctness of the model 10.2 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 5456 reflections ( 99.67 % complete ) and 6071 restraints for refining 2908 atoms. 5093 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2613 (Rfree = 0.000) for 2908 atoms. Found 8 (15 requested) and removed 16 (7 requested) atoms. Cycle 12: After refmac, R = 0.2409 (Rfree = 0.000) for 2877 atoms. Found 12 (15 requested) and removed 14 (7 requested) atoms. Cycle 13: After refmac, R = 0.2206 (Rfree = 0.000) for 2862 atoms. Found 8 (15 requested) and removed 13 (7 requested) atoms. Cycle 14: After refmac, R = 0.2165 (Rfree = 0.000) for 2850 atoms. Found 10 (15 requested) and removed 13 (7 requested) atoms. Cycle 15: After refmac, R = 0.2105 (Rfree = 0.000) for 2842 atoms. Found 10 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.51 3.20 Search for helices and strands: 0 residues in 0 chains, 2948 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 2982 seeds are put forward Round 1: 217 peptides, 36 chains. Longest chain 15 peptides. Score 0.421 Round 2: 237 peptides, 29 chains. Longest chain 25 peptides. Score 0.565 Round 3: 251 peptides, 32 chains. Longest chain 17 peptides. Score 0.566 Round 4: 250 peptides, 30 chains. Longest chain 18 peptides. Score 0.586 Round 5: 267 peptides, 36 chains. Longest chain 16 peptides. Score 0.561 Taking the results from Round 4 Chains 32, Residues 220, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 5456 reflections ( 99.67 % complete ) and 6248 restraints for refining 2909 atoms. 5317 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2484 (Rfree = 0.000) for 2909 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 17: After refmac, R = 0.2382 (Rfree = 0.000) for 2890 atoms. Found 13 (16 requested) and removed 12 (8 requested) atoms. Cycle 18: After refmac, R = 0.2418 (Rfree = 0.000) for 2879 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 19: After refmac, R = 0.2337 (Rfree = 0.000) for 2877 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 20: After refmac, R = 0.2334 (Rfree = 0.000) for 2874 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.53 3.21 Search for helices and strands: 0 residues in 0 chains, 2985 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3001 seeds are put forward Round 1: 225 peptides, 38 chains. Longest chain 16 peptides. Score 0.419 Round 2: 241 peptides, 36 chains. Longest chain 18 peptides. Score 0.492 Round 3: 238 peptides, 34 chains. Longest chain 17 peptides. Score 0.508 Round 4: 244 peptides, 32 chains. Longest chain 21 peptides. Score 0.548 Round 5: 244 peptides, 36 chains. Longest chain 17 peptides. Score 0.500 Taking the results from Round 4 Chains 35, Residues 212, Estimated correctness of the model 0.0 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ 5456 reflections ( 99.67 % complete ) and 6161 restraints for refining 2909 atoms. 5228 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2942 (Rfree = 0.000) for 2909 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 22: After refmac, R = 0.2594 (Rfree = 0.000) for 2884 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. Cycle 23: After refmac, R = 0.2481 (Rfree = 0.000) for 2881 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 24: After refmac, R = 0.2342 (Rfree = 0.000) for 2872 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 25: After refmac, R = 0.2242 (Rfree = 0.000) for 2866 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.53 3.21 Search for helices and strands: 0 residues in 0 chains, 2955 seeds are put forward NCS extension: 11 residues added (3 deleted due to clashes), 2966 seeds are put forward Round 1: 199 peptides, 34 chains. Longest chain 12 peptides. Score 0.392 Round 2: 228 peptides, 33 chains. Longest chain 16 peptides. Score 0.492 Round 3: 238 peptides, 28 chains. Longest chain 18 peptides. Score 0.579 Round 4: 232 peptides, 30 chains. Longest chain 16 peptides. Score 0.540 Round 5: 248 peptides, 27 chains. Longest chain 25 peptides. Score 0.614 Taking the results from Round 5 Chains 27, Residues 221, Estimated correctness of the model 5.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5456 reflections ( 99.67 % complete ) and 6482 restraints for refining 2908 atoms. 5625 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2470 (Rfree = 0.000) for 2908 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 27: After refmac, R = 0.2295 (Rfree = 0.000) for 2887 atoms. Found 13 (16 requested) and removed 9 (8 requested) atoms. Cycle 28: After refmac, R = 0.2227 (Rfree = 0.000) for 2879 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 29: After refmac, R = 0.2274 (Rfree = 0.000) for 2873 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 30: After refmac, R = 0.2250 (Rfree = 0.000) for 2864 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.57 3.25 Search for helices and strands: 0 residues in 0 chains, 2958 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 2979 seeds are put forward Round 1: 211 peptides, 37 chains. Longest chain 18 peptides. Score 0.389 Round 2: 237 peptides, 36 chains. Longest chain 13 peptides. Score 0.481 Round 3: 234 peptides, 36 chains. Longest chain 18 peptides. Score 0.472 Round 4: 243 peptides, 35 chains. Longest chain 18 peptides. Score 0.510 Round 5: 240 peptides, 33 chains. Longest chain 17 peptides. Score 0.526 Taking the results from Round 5 Chains 35, Residues 207, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5456 reflections ( 99.67 % complete ) and 6487 restraints for refining 2906 atoms. 5654 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2837 (Rfree = 0.000) for 2906 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 32: After refmac, R = 0.2524 (Rfree = 0.000) for 2897 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 33: After refmac, R = 0.2422 (Rfree = 0.000) for 2886 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 34: After refmac, R = 0.2267 (Rfree = 0.000) for 2871 atoms. Found 13 (15 requested) and removed 10 (7 requested) atoms. Cycle 35: After refmac, R = 0.1948 (Rfree = 0.000) for 2866 atoms. Found 6 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.53 3.21 Search for helices and strands: 0 residues in 0 chains, 2915 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2927 seeds are put forward Round 1: 205 peptides, 36 chains. Longest chain 14 peptides. Score 0.384 Round 2: 216 peptides, 35 chains. Longest chain 14 peptides. Score 0.432 Round 3: 216 peptides, 33 chains. Longest chain 14 peptides. Score 0.458 Round 4: 216 peptides, 31 chains. Longest chain 18 peptides. Score 0.484 Round 5: 239 peptides, 33 chains. Longest chain 21 peptides. Score 0.523 Taking the results from Round 5 Chains 33, Residues 206, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5456 reflections ( 99.67 % complete ) and 6509 restraints for refining 2909 atoms. 5680 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2533 (Rfree = 0.000) for 2909 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 37: After refmac, R = 0.2416 (Rfree = 0.000) for 2893 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 38: After refmac, R = 0.2300 (Rfree = 0.000) for 2881 atoms. Found 13 (15 requested) and removed 8 (7 requested) atoms. Cycle 39: After refmac, R = 0.2359 (Rfree = 0.000) for 2872 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 40: After refmac, R = 0.2156 (Rfree = 0.000) for 2868 atoms. Found 14 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 3.28 Search for helices and strands: 0 residues in 0 chains, 2959 seeds are put forward NCS extension: 38 residues added (1 deleted due to clashes), 2997 seeds are put forward Round 1: 164 peptides, 33 chains. Longest chain 13 peptides. Score 0.288 Round 2: 203 peptides, 36 chains. Longest chain 13 peptides. Score 0.377 Round 3: 201 peptides, 33 chains. Longest chain 16 peptides. Score 0.412 Round 4: 196 peptides, 33 chains. Longest chain 15 peptides. Score 0.397 Round 5: 202 peptides, 32 chains. Longest chain 15 peptides. Score 0.429 Taking the results from Round 5 Chains 32, Residues 170, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5456 reflections ( 99.67 % complete ) and 6782 restraints for refining 2909 atoms. 6121 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2361 (Rfree = 0.000) for 2909 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 42: After refmac, R = 0.2207 (Rfree = 0.000) for 2896 atoms. Found 16 (16 requested) and removed 8 (8 requested) atoms. Cycle 43: After refmac, R = 0.2310 (Rfree = 0.000) for 2891 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 44: After refmac, R = 0.2226 (Rfree = 0.000) for 2885 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 45: After refmac, R = 0.2196 (Rfree = 0.000) for 2875 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.57 3.25 Search for helices and strands: 0 residues in 0 chains, 2947 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2964 seeds are put forward Round 1: 151 peptides, 29 chains. Longest chain 10 peptides. Score 0.303 Round 2: 174 peptides, 29 chains. Longest chain 12 peptides. Score 0.382 Round 3: 172 peptides, 27 chains. Longest chain 13 peptides. Score 0.404 Round 4: 175 peptides, 28 chains. Longest chain 17 peptides. Score 0.399 Round 5: 177 peptides, 28 chains. Longest chain 14 peptides. Score 0.406 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 149, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 4 % 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 6559 restraints for refining 2909 atoms. 5977 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2563 (Rfree = 0.000) for 2909 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2251 (Rfree = 0.000) for 2878 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2174 (Rfree = 0.000) for 2854 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2265 (Rfree = 0.000) for 2838 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:23:56 GMT 2018 Job finished. TimeTaking 34.84 Used memory is bytes: 20379888