null Mon 24 Dec 07:34:29 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2p97-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2p97-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2p97-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p97-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2p97-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p97-3.6-parrot-noncs ############### 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 07:34:33 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/noncs/ArpWArp/wArpResults/WorkingDir/2p97-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p97-3.6-parrot-noncs/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 347 and 0 Target number of residues in the AU: 347 Target solvent content: 0.6324 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: 2p97-3.6-parrot-noncs.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: 2p97-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 3216 target number of atoms Had to go as low as 0.80 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 3.600 Wilson plot Bfac: 67.66 6389 reflections ( 99.72 % complete ) and 0 restraints for refining 3580 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3352 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3144 (Rfree = 0.000) for 3580 atoms. Found 22 (22 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.38 3.08 Search for helices and strands: 0 residues in 0 chains, 3642 seeds are put forward NCS extension: 0 residues added, 3642 seeds are put forward Round 1: 206 peptides, 34 chains. Longest chain 13 peptides. Score 0.414 Round 2: 273 peptides, 33 chains. Longest chain 32 peptides. Score 0.608 Round 3: 275 peptides, 32 chains. Longest chain 30 peptides. Score 0.623 Round 4: 288 peptides, 28 chains. Longest chain 39 peptides. Score 0.688 Round 5: 281 peptides, 26 chains. Longest chain 43 peptides. Score 0.693 Taking the results from Round 5 Chains 28, Residues 255, Estimated correctness of the model 47.4 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 6389 reflections ( 99.72 % complete ) and 6151 restraints for refining 2915 atoms. 5083 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2734 (Rfree = 0.000) for 2915 atoms. Found 18 (18 requested) and removed 22 (9 requested) atoms. Cycle 2: After refmac, R = 0.2477 (Rfree = 0.000) for 2882 atoms. Found 6 (18 requested) and removed 16 (9 requested) atoms. Cycle 3: After refmac, R = 0.2415 (Rfree = 0.000) for 2864 atoms. Found 7 (18 requested) and removed 14 (9 requested) atoms. Cycle 4: After refmac, R = 0.2392 (Rfree = 0.000) for 2854 atoms. Found 3 (18 requested) and removed 10 (9 requested) atoms. Cycle 5: After refmac, R = 0.2406 (Rfree = 0.000) for 2845 atoms. Found 2 (18 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 3.07 Search for helices and strands: 0 residues in 0 chains, 2910 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 2937 seeds are put forward Round 1: 236 peptides, 34 chains. Longest chain 22 peptides. Score 0.502 Round 2: 280 peptides, 31 chains. Longest chain 22 peptides. Score 0.644 Round 3: 267 peptides, 34 chains. Longest chain 24 peptides. Score 0.583 Round 4: 274 peptides, 25 chains. Longest chain 39 peptides. Score 0.689 Round 5: 286 peptides, 32 chains. Longest chain 25 peptides. Score 0.647 Taking the results from Round 4 Chains 25, Residues 249, Estimated correctness of the model 46.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6389 reflections ( 99.72 % complete ) and 6425 restraints for refining 2916 atoms. 5454 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2568 (Rfree = 0.000) for 2916 atoms. Found 16 (18 requested) and removed 12 (9 requested) atoms. Cycle 7: After refmac, R = 0.2397 (Rfree = 0.000) for 2907 atoms. Found 6 (18 requested) and removed 13 (9 requested) atoms. Cycle 8: After refmac, R = 0.2381 (Rfree = 0.000) for 2892 atoms. Found 13 (18 requested) and removed 12 (9 requested) atoms. Cycle 9: After refmac, R = 0.2333 (Rfree = 0.000) for 2890 atoms. Found 6 (18 requested) and removed 10 (9 requested) atoms. Cycle 10: After refmac, R = 0.2218 (Rfree = 0.000) for 2881 atoms. Found 5 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.06 Search for helices and strands: 0 residues in 0 chains, 2949 seeds are put forward NCS extension: 14 residues added (4 deleted due to clashes), 2963 seeds are put forward Round 1: 242 peptides, 33 chains. Longest chain 22 peptides. Score 0.531 Round 2: 249 peptides, 26 chains. Longest chain 27 peptides. Score 0.627 Round 3: 260 peptides, 25 chains. Longest chain 39 peptides. Score 0.661 Round 4: 247 peptides, 28 chains. Longest chain 24 peptides. Score 0.601 Round 5: 268 peptides, 29 chains. Longest chain 28 peptides. Score 0.638 Taking the results from Round 3 Chains 26, Residues 235, Estimated correctness of the model 37.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6389 reflections ( 99.72 % complete ) and 6272 restraints for refining 2916 atoms. 5309 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2533 (Rfree = 0.000) for 2916 atoms. Found 16 (18 requested) and removed 10 (9 requested) atoms. Cycle 12: After refmac, R = 0.2417 (Rfree = 0.000) for 2910 atoms. Found 11 (18 requested) and removed 10 (9 requested) atoms. Cycle 13: After refmac, R = 0.2308 (Rfree = 0.000) for 2906 atoms. Found 6 (18 requested) and removed 9 (9 requested) atoms. Cycle 14: After refmac, R = 0.2293 (Rfree = 0.000) for 2896 atoms. Found 11 (18 requested) and removed 13 (9 requested) atoms. Cycle 15: After refmac, R = 0.1936 (Rfree = 0.000) for 2891 atoms. Found 3 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 3.05 Search for helices and strands: 0 residues in 0 chains, 2950 seeds are put forward NCS extension: 22 residues added (16 deleted due to clashes), 2972 seeds are put forward Round 1: 228 peptides, 32 chains. Longest chain 18 peptides. Score 0.505 Round 2: 249 peptides, 31 chains. Longest chain 21 peptides. Score 0.572 Round 3: 251 peptides, 32 chains. Longest chain 20 peptides. Score 0.566 Round 4: 260 peptides, 31 chains. Longest chain 21 peptides. Score 0.599 Round 5: 257 peptides, 26 chains. Longest chain 21 peptides. Score 0.644 Taking the results from Round 5 Chains 26, Residues 231, Estimated correctness of the model 31.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6389 reflections ( 99.72 % complete ) and 6426 restraints for refining 2916 atoms. 5528 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2411 (Rfree = 0.000) for 2916 atoms. Found 12 (18 requested) and removed 12 (9 requested) atoms. Cycle 17: After refmac, R = 0.2250 (Rfree = 0.000) for 2907 atoms. Found 13 (18 requested) and removed 10 (9 requested) atoms. Cycle 18: After refmac, R = 0.2147 (Rfree = 0.000) for 2903 atoms. Found 6 (18 requested) and removed 9 (9 requested) atoms. Cycle 19: After refmac, R = 0.2122 (Rfree = 0.000) for 2893 atoms. Found 13 (18 requested) and removed 11 (9 requested) atoms. Cycle 20: After refmac, R = 0.2020 (Rfree = 0.000) for 2887 atoms. Found 10 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.31 3.01 Search for helices and strands: 0 residues in 0 chains, 2973 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 2991 seeds are put forward Round 1: 225 peptides, 32 chains. Longest chain 20 peptides. Score 0.497 Round 2: 257 peptides, 32 chains. Longest chain 20 peptides. Score 0.581 Round 3: 250 peptides, 33 chains. Longest chain 22 peptides. Score 0.552 Round 4: 276 peptides, 34 chains. Longest chain 29 peptides. Score 0.604 Round 5: 260 peptides, 33 chains. Longest chain 21 peptides. Score 0.577 Taking the results from Round 4 Chains 34, Residues 242, Estimated correctness of the model 16.2 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 6389 reflections ( 99.72 % complete ) and 6094 restraints for refining 2916 atoms. 5055 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2434 (Rfree = 0.000) for 2916 atoms. Found 13 (18 requested) and removed 16 (9 requested) atoms. Cycle 22: After refmac, R = 0.2375 (Rfree = 0.000) for 2886 atoms. Found 7 (18 requested) and removed 11 (9 requested) atoms. Cycle 23: After refmac, R = 0.2360 (Rfree = 0.000) for 2863 atoms. Found 11 (18 requested) and removed 13 (9 requested) atoms. Cycle 24: After refmac, R = 0.2282 (Rfree = 0.000) for 2852 atoms. Found 6 (18 requested) and removed 13 (9 requested) atoms. Cycle 25: After refmac, R = 0.2249 (Rfree = 0.000) for 2837 atoms. Found 7 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.36 3.06 Search for helices and strands: 0 residues in 0 chains, 2910 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 2935 seeds are put forward Round 1: 224 peptides, 39 chains. Longest chain 13 peptides. Score 0.403 Round 2: 241 peptides, 34 chains. Longest chain 18 peptides. Score 0.516 Round 3: 260 peptides, 34 chains. Longest chain 19 peptides. Score 0.566 Round 4: 256 peptides, 34 chains. Longest chain 16 peptides. Score 0.556 Round 5: 265 peptides, 32 chains. Longest chain 21 peptides. Score 0.600 Taking the results from Round 5 Chains 32, Residues 233, Estimated correctness of the model 14.7 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6389 reflections ( 99.72 % complete ) and 6416 restraints for refining 2916 atoms. 5504 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2553 (Rfree = 0.000) for 2916 atoms. Found 16 (18 requested) and removed 13 (9 requested) atoms. Cycle 27: After refmac, R = 0.2243 (Rfree = 0.000) for 2901 atoms. Found 7 (18 requested) and removed 10 (9 requested) atoms. Cycle 28: After refmac, R = 0.2183 (Rfree = 0.000) for 2891 atoms. Found 6 (18 requested) and removed 13 (9 requested) atoms. Cycle 29: After refmac, R = 0.2043 (Rfree = 0.000) for 2876 atoms. Found 4 (18 requested) and removed 9 (9 requested) atoms. Cycle 30: After refmac, R = 0.1997 (Rfree = 0.000) for 2866 atoms. Found 6 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.34 3.04 Search for helices and strands: 0 residues in 0 chains, 2984 seeds are put forward NCS extension: 23 residues added (5 deleted due to clashes), 3007 seeds are put forward Round 1: 213 peptides, 31 chains. Longest chain 27 peptides. Score 0.475 Round 2: 240 peptides, 34 chains. Longest chain 24 peptides. Score 0.513 Round 3: 246 peptides, 29 chains. Longest chain 18 peptides. Score 0.587 Round 4: 252 peptides, 33 chains. Longest chain 22 peptides. Score 0.557 Round 5: 250 peptides, 27 chains. Longest chain 21 peptides. Score 0.618 Taking the results from Round 5 Chains 27, Residues 223, Estimated correctness of the model 21.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6389 reflections ( 99.72 % complete ) and 6370 restraints for refining 2915 atoms. 5505 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2196 (Rfree = 0.000) for 2915 atoms. Found 11 (18 requested) and removed 9 (9 requested) atoms. Cycle 32: After refmac, R = 0.2076 (Rfree = 0.000) for 2903 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. Cycle 33: After refmac, R = 0.2133 (Rfree = 0.000) for 2893 atoms. Found 8 (18 requested) and removed 9 (9 requested) atoms. Cycle 34: After refmac, R = 0.2074 (Rfree = 0.000) for 2889 atoms. Found 9 (18 requested) and removed 10 (9 requested) atoms. Cycle 35: After refmac, R = 0.2004 (Rfree = 0.000) for 2886 atoms. Found 5 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 3.07 Search for helices and strands: 0 residues in 0 chains, 2973 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 2992 seeds are put forward Round 1: 193 peptides, 28 chains. Longest chain 22 peptides. Score 0.456 Round 2: 216 peptides, 29 chains. Longest chain 31 peptides. Score 0.509 Round 3: 233 peptides, 28 chains. Longest chain 32 peptides. Score 0.566 Round 4: 232 peptides, 30 chains. Longest chain 22 peptides. Score 0.540 Round 5: 224 peptides, 30 chains. Longest chain 22 peptides. Score 0.519 Taking the results from Round 3 Chains 28, Residues 205, Estimated correctness of the model 0.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6389 reflections ( 99.72 % complete ) and 6501 restraints for refining 2916 atoms. 5709 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2226 (Rfree = 0.000) for 2916 atoms. Found 13 (18 requested) and removed 10 (9 requested) atoms. Cycle 37: After refmac, R = 0.2121 (Rfree = 0.000) for 2911 atoms. Found 8 (18 requested) and removed 9 (9 requested) atoms. Cycle 38: After refmac, R = 0.2067 (Rfree = 0.000) for 2904 atoms. Found 11 (18 requested) and removed 9 (9 requested) atoms. Cycle 39: After refmac, R = 0.1976 (Rfree = 0.000) for 2903 atoms. Found 7 (18 requested) and removed 11 (9 requested) atoms. Cycle 40: After refmac, R = 0.1958 (Rfree = 0.000) for 2895 atoms. Found 8 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 3.05 Search for helices and strands: 0 residues in 0 chains, 2985 seeds are put forward NCS extension: 44 residues added (2 deleted due to clashes), 3029 seeds are put forward Round 1: 203 peptides, 33 chains. Longest chain 19 peptides. Score 0.419 Round 2: 243 peptides, 32 chains. Longest chain 22 peptides. Score 0.545 Round 3: 249 peptides, 31 chains. Longest chain 22 peptides. Score 0.572 Round 4: 254 peptides, 30 chains. Longest chain 33 peptides. Score 0.595 Round 5: 244 peptides, 28 chains. Longest chain 37 peptides. Score 0.593 Taking the results from Round 4 Chains 30, Residues 224, Estimated correctness of the model 12.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6389 reflections ( 99.72 % complete ) and 6407 restraints for refining 2916 atoms. 5541 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2156 (Rfree = 0.000) for 2916 atoms. Found 12 (18 requested) and removed 10 (9 requested) atoms. Cycle 42: After refmac, R = 0.2038 (Rfree = 0.000) for 2904 atoms. Found 9 (18 requested) and removed 10 (9 requested) atoms. Cycle 43: After refmac, R = 0.1978 (Rfree = 0.000) for 2900 atoms. Found 9 (18 requested) and removed 10 (9 requested) atoms. Cycle 44: After refmac, R = 0.1942 (Rfree = 0.000) for 2893 atoms. Found 7 (18 requested) and removed 10 (9 requested) atoms. Cycle 45: After refmac, R = 0.1899 (Rfree = 0.000) for 2886 atoms. Found 6 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.32 3.02 Search for helices and strands: 0 residues in 0 chains, 2969 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 2995 seeds are put forward Round 1: 195 peptides, 36 chains. Longest chain 11 peptides. Score 0.351 Round 2: 216 peptides, 33 chains. Longest chain 15 peptides. Score 0.458 Round 3: 229 peptides, 29 chains. Longest chain 28 peptides. Score 0.544 Round 4: 231 peptides, 28 chains. Longest chain 25 peptides. Score 0.561 Round 5: 232 peptides, 28 chains. Longest chain 23 peptides. Score 0.564 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 204, Estimated correctness of the model 0.1 % 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. 6389 reflections ( 99.72 % complete ) and 6635 restraints for refining 2916 atoms. 5847 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2052 (Rfree = 0.000) for 2916 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1986 (Rfree = 0.000) for 2902 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2041 (Rfree = 0.000) for 2892 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1911 (Rfree = 0.000) for 2880 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:12:35 GMT 2018 Job finished. TimeTaking 38.11 Used memory is bytes: 9682808