null Mon 24 Dec 00:55:18 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 2p97-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2p97-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2p97-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p97-4.0-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/2p97-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p97-4.0-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 ============================================================ Mon 24 Dec 00:55:22 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/2p97-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p97-4.0-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 327 and 0 Target number of residues in the AU: 327 Target solvent content: 0.6536 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: 2p97-4.0-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: 2p97-4.0-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 4.001 Wilson plot Bfac: 80.39 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 4698 reflections ( 99.62 % complete ) and 0 restraints for refining 3577 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3389 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3359 (Rfree = 0.000) for 3577 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.70 3.37 Search for helices and strands: 0 residues in 0 chains, 3627 seeds are put forward NCS extension: 0 residues added, 3627 seeds are put forward Round 1: 154 peptides, 30 chains. Longest chain 8 peptides. Score 0.298 Round 2: 205 peptides, 31 chains. Longest chain 14 peptides. Score 0.451 Round 3: 211 peptides, 29 chains. Longest chain 19 peptides. Score 0.495 Round 4: 221 peptides, 28 chains. Longest chain 26 peptides. Score 0.535 Round 5: 224 peptides, 30 chains. Longest chain 17 peptides. Score 0.519 Taking the results from Round 4 Chains 30, Residues 193, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 4698 reflections ( 99.62 % complete ) and 6524 restraints for refining 2904 atoms. 5692 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2819 (Rfree = 0.000) for 2904 atoms. Found 11 (13 requested) and removed 12 (6 requested) atoms. Cycle 2: After refmac, R = 0.2643 (Rfree = 0.000) for 2864 atoms. Found 7 (13 requested) and removed 8 (6 requested) atoms. Cycle 3: After refmac, R = 0.2497 (Rfree = 0.000) for 2842 atoms. Found 3 (13 requested) and removed 9 (6 requested) atoms. Cycle 4: After refmac, R = 0.2437 (Rfree = 0.000) for 2815 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. Cycle 5: After refmac, R = 0.2383 (Rfree = 0.000) for 2801 atoms. Found 5 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.72 3.39 Search for helices and strands: 0 residues in 0 chains, 2874 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2893 seeds are put forward Round 1: 220 peptides, 34 chains. Longest chain 16 peptides. Score 0.457 Round 2: 239 peptides, 28 chains. Longest chain 24 peptides. Score 0.581 Round 3: 252 peptides, 31 chains. Longest chain 27 peptides. Score 0.579 Round 4: 262 peptides, 33 chains. Longest chain 25 peptides. Score 0.582 Round 5: 245 peptides, 30 chains. Longest chain 21 peptides. Score 0.573 Taking the results from Round 4 Chains 33, Residues 229, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4698 reflections ( 99.62 % complete ) and 6575 restraints for refining 2869 atoms. 5692 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2604 (Rfree = 0.000) for 2869 atoms. Found 11 (13 requested) and removed 12 (6 requested) atoms. Cycle 7: After refmac, R = 0.2379 (Rfree = 0.000) for 2847 atoms. Found 4 (13 requested) and removed 9 (6 requested) atoms. Cycle 8: After refmac, R = 0.2318 (Rfree = 0.000) for 2825 atoms. Found 6 (13 requested) and removed 11 (6 requested) atoms. Cycle 9: After refmac, R = 0.2240 (Rfree = 0.000) for 2811 atoms. Found 4 (13 requested) and removed 9 (6 requested) atoms. Cycle 10: After refmac, R = 0.2209 (Rfree = 0.000) for 2802 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.74 3.40 Search for helices and strands: 0 residues in 0 chains, 2879 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 2906 seeds are put forward Round 1: 221 peptides, 33 chains. Longest chain 22 peptides. Score 0.473 Round 2: 246 peptides, 30 chains. Longest chain 23 peptides. Score 0.576 Round 3: 258 peptides, 29 chains. Longest chain 29 peptides. Score 0.615 Round 4: 256 peptides, 27 chains. Longest chain 27 peptides. Score 0.632 Round 5: 251 peptides, 32 chains. Longest chain 19 peptides. Score 0.566 Taking the results from Round 4 Chains 27, Residues 229, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4698 reflections ( 99.62 % complete ) and 6614 restraints for refining 2903 atoms. 5725 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2464 (Rfree = 0.000) for 2903 atoms. Found 11 (13 requested) and removed 15 (6 requested) atoms. Cycle 12: After refmac, R = 0.2351 (Rfree = 0.000) for 2877 atoms. Found 6 (13 requested) and removed 7 (6 requested) atoms. Cycle 13: After refmac, R = 0.2300 (Rfree = 0.000) for 2866 atoms. Found 4 (13 requested) and removed 10 (6 requested) atoms. Cycle 14: After refmac, R = 0.2256 (Rfree = 0.000) for 2856 atoms. Found 4 (13 requested) and removed 8 (6 requested) atoms. Cycle 15: After refmac, R = 0.2244 (Rfree = 0.000) for 2847 atoms. Found 2 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.70 3.37 Search for helices and strands: 0 residues in 0 chains, 2932 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 2959 seeds are put forward Round 1: 210 peptides, 34 chains. Longest chain 17 peptides. Score 0.427 Round 2: 234 peptides, 27 chains. Longest chain 30 peptides. Score 0.580 Round 3: 246 peptides, 33 chains. Longest chain 21 peptides. Score 0.541 Round 4: 246 peptides, 28 chains. Longest chain 25 peptides. Score 0.598 Round 5: 246 peptides, 29 chains. Longest chain 22 peptides. Score 0.587 Taking the results from Round 4 Chains 28, Residues 218, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4698 reflections ( 99.62 % complete ) and 6561 restraints for refining 2902 atoms. 5678 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2386 (Rfree = 0.000) for 2902 atoms. Found 11 (13 requested) and removed 8 (6 requested) atoms. Cycle 17: After refmac, R = 0.2226 (Rfree = 0.000) for 2898 atoms. Found 4 (13 requested) and removed 10 (6 requested) atoms. Cycle 18: After refmac, R = 0.2109 (Rfree = 0.000) for 2887 atoms. Found 3 (13 requested) and removed 8 (6 requested) atoms. Cycle 19: After refmac, R = 0.2111 (Rfree = 0.000) for 2879 atoms. Found 0 (13 requested) and removed 9 (6 requested) atoms. Cycle 20: After refmac, R = 0.2354 (Rfree = 0.000) for 2867 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.72 3.39 Search for helices and strands: 0 residues in 0 chains, 2946 seeds are put forward NCS extension: 43 residues added (6 deleted due to clashes), 2989 seeds are put forward Round 1: 189 peptides, 32 chains. Longest chain 20 peptides. Score 0.388 Round 2: 202 peptides, 27 chains. Longest chain 15 peptides. Score 0.495 Round 3: 202 peptides, 28 chains. Longest chain 17 peptides. Score 0.482 Round 4: 190 peptides, 28 chains. Longest chain 15 peptides. Score 0.447 Round 5: 216 peptides, 29 chains. Longest chain 17 peptides. Score 0.509 Taking the results from Round 5 Chains 29, Residues 187, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4698 reflections ( 99.62 % complete ) and 6730 restraints for refining 2904 atoms. 6011 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2334 (Rfree = 0.000) for 2904 atoms. Found 9 (13 requested) and removed 7 (6 requested) atoms. Cycle 22: After refmac, R = 0.2174 (Rfree = 0.000) for 2890 atoms. Found 5 (13 requested) and removed 8 (6 requested) atoms. Cycle 23: After refmac, R = 0.2213 (Rfree = 0.000) for 2882 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. Cycle 24: After refmac, R = 0.2106 (Rfree = 0.000) for 2875 atoms. Found 0 (13 requested) and removed 8 (6 requested) atoms. Cycle 25: After refmac, R = 0.2085 (Rfree = 0.000) for 2866 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.71 3.38 Search for helices and strands: 0 residues in 0 chains, 2952 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 2964 seeds are put forward Round 1: 180 peptides, 32 chains. Longest chain 11 peptides. Score 0.358 Round 2: 204 peptides, 31 chains. Longest chain 14 peptides. Score 0.448 Round 3: 211 peptides, 30 chains. Longest chain 18 peptides. Score 0.482 Round 4: 213 peptides, 29 chains. Longest chain 19 peptides. Score 0.501 Round 5: 213 peptides, 31 chains. Longest chain 19 peptides. Score 0.475 Taking the results from Round 4 Chains 29, Residues 184, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4698 reflections ( 99.62 % complete ) and 6747 restraints for refining 2904 atoms. 6040 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2414 (Rfree = 0.000) for 2904 atoms. Found 9 (13 requested) and removed 7 (6 requested) atoms. Cycle 27: After refmac, R = 0.2184 (Rfree = 0.000) for 2889 atoms. Found 8 (13 requested) and removed 9 (6 requested) atoms. Cycle 28: After refmac, R = 0.2156 (Rfree = 0.000) for 2882 atoms. Found 5 (13 requested) and removed 9 (6 requested) atoms. Cycle 29: After refmac, R = 0.2106 (Rfree = 0.000) for 2875 atoms. Found 2 (13 requested) and removed 8 (6 requested) atoms. Cycle 30: After refmac, R = 0.2164 (Rfree = 0.000) for 2866 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 3.39 Search for helices and strands: 0 residues in 0 chains, 2945 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 2976 seeds are put forward Round 1: 193 peptides, 36 chains. Longest chain 10 peptides. Score 0.345 Round 2: 198 peptides, 32 chains. Longest chain 12 peptides. Score 0.417 Round 3: 212 peptides, 33 chains. Longest chain 17 peptides. Score 0.446 Round 4: 204 peptides, 30 chains. Longest chain 20 peptides. Score 0.462 Round 5: 220 peptides, 27 chains. Longest chain 22 peptides. Score 0.544 Taking the results from Round 5 Chains 27, Residues 193, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4698 reflections ( 99.62 % complete ) and 6795 restraints for refining 2903 atoms. 6050 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2458 (Rfree = 0.000) for 2903 atoms. Found 11 (13 requested) and removed 8 (6 requested) atoms. Cycle 32: After refmac, R = 0.2259 (Rfree = 0.000) for 2889 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. Cycle 33: After refmac, R = 0.2175 (Rfree = 0.000) for 2879 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. Cycle 34: After refmac, R = 0.2061 (Rfree = 0.000) for 2872 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.2038 (Rfree = 0.000) for 2862 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.66 3.33 Search for helices and strands: 0 residues in 0 chains, 2928 seeds are put forward NCS extension: 37 residues added (1 deleted due to clashes), 2965 seeds are put forward Round 1: 174 peptides, 34 chains. Longest chain 12 peptides. Score 0.309 Round 2: 185 peptides, 31 chains. Longest chain 14 peptides. Score 0.389 Round 3: 195 peptides, 30 chains. Longest chain 14 peptides. Score 0.435 Round 4: 190 peptides, 29 chains. Longest chain 15 peptides. Score 0.433 Round 5: 192 peptides, 31 chains. Longest chain 13 peptides. Score 0.412 Taking the results from Round 3 Chains 30, Residues 165, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4698 reflections ( 99.62 % complete ) and 6858 restraints for refining 2902 atoms. 6200 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2138 (Rfree = 0.000) for 2902 atoms. Found 4 (13 requested) and removed 9 (6 requested) atoms. Cycle 37: After refmac, R = 0.2021 (Rfree = 0.000) for 2867 atoms. Found 8 (13 requested) and removed 7 (6 requested) atoms. Cycle 38: After refmac, R = 0.1946 (Rfree = 0.000) for 2856 atoms. Found 9 (13 requested) and removed 7 (6 requested) atoms. Cycle 39: After refmac, R = 0.1821 (Rfree = 0.000) for 2842 atoms. Found 4 (13 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.1833 (Rfree = 0.000) for 2834 atoms. Found 3 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 3.34 Search for helices and strands: 0 residues in 0 chains, 2904 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2922 seeds are put forward Round 1: 158 peptides, 32 chains. Longest chain 9 peptides. Score 0.282 Round 2: 195 peptides, 31 chains. Longest chain 10 peptides. Score 0.421 Round 3: 201 peptides, 30 chains. Longest chain 22 peptides. Score 0.453 Round 4: 204 peptides, 27 chains. Longest chain 17 peptides. Score 0.501 Round 5: 190 peptides, 27 chains. Longest chain 21 peptides. Score 0.460 Taking the results from Round 4 Chains 27, Residues 177, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4698 reflections ( 99.62 % complete ) and 6964 restraints for refining 2904 atoms. 6283 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2065 (Rfree = 0.000) for 2904 atoms. Found 4 (13 requested) and removed 8 (6 requested) atoms. Cycle 42: After refmac, R = 0.1892 (Rfree = 0.000) for 2890 atoms. Found 1 (13 requested) and removed 7 (6 requested) atoms. Cycle 43: After refmac, R = 0.1877 (Rfree = 0.000) for 2879 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.1860 (Rfree = 0.000) for 2873 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.1854 (Rfree = 0.000) for 2868 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.65 3.32 Search for helices and strands: 0 residues in 0 chains, 2923 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 2947 seeds are put forward Round 1: 160 peptides, 31 chains. Longest chain 10 peptides. Score 0.304 Round 2: 173 peptides, 29 chains. Longest chain 12 peptides. Score 0.379 Round 3: 182 peptides, 29 chains. Longest chain 18 peptides. Score 0.408 Round 4: 186 peptides, 28 chains. Longest chain 14 peptides. Score 0.434 Round 5: 194 peptides, 27 chains. Longest chain 22 peptides. Score 0.472 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 167, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2p97-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4698 reflections ( 99.62 % complete ) and 6846 restraints for refining 2904 atoms. 6192 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2116 (Rfree = 0.000) for 2904 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2035 (Rfree = 0.000) for 2869 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2000 (Rfree = 0.000) for 2853 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1983 (Rfree = 0.000) for 2846 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:29:40 GMT 2018 Job finished. TimeTaking 34.37 Used memory is bytes: 21175880