Sun 23 Dec 22:22:40 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 2p97-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p97-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p97-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p97-4.0-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/2p97-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p97-4.0-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 22:22:49 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/2p97-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p97-4.0-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 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-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: 2p97-4.0-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 4.001 Wilson plot Bfac: 80.39 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** Failed to save intermediate PDB 4698 reflections ( 99.62 % complete ) and 0 restraints for refining 3583 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3431 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3171 (Rfree = 0.000) for 3583 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.69 3.36 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: 171 peptides, 33 chains. Longest chain 8 peptides. Score 0.313 Round 2: 231 peptides, 32 chains. Longest chain 20 peptides. Score 0.513 Round 3: 247 peptides, 28 chains. Longest chain 27 peptides. Score 0.601 Round 4: 251 peptides, 30 chains. Longest chain 19 peptides. Score 0.588 Round 5: 267 peptides, 25 chains. Longest chain 33 peptides. Score 0.675 Taking the results from Round 5 Chains 25, Residues 242, Estimated correctness of the model 18.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4698 reflections ( 99.62 % complete ) and 6491 restraints for refining 2904 atoms. 5548 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2668 (Rfree = 0.000) for 2904 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 2: After refmac, R = 0.2392 (Rfree = 0.000) for 2830 atoms. Found 12 (13 requested) and removed 9 (6 requested) atoms. Cycle 3: After refmac, R = 0.2310 (Rfree = 0.000) for 2799 atoms. Found 5 (13 requested) and removed 9 (6 requested) atoms. Cycle 4: After refmac, R = 0.2246 (Rfree = 0.000) for 2790 atoms. Found 0 (13 requested) and removed 9 (6 requested) atoms. Cycle 5: After refmac, R = 0.2229 (Rfree = 0.000) for 2774 atoms. Found 1 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.73 3.40 Search for helices and strands: 0 residues in 0 chains, 2848 seeds are put forward NCS extension: 39 residues added (2 deleted due to clashes), 2887 seeds are put forward Round 1: 233 peptides, 34 chains. Longest chain 19 peptides. Score 0.494 Round 2: 234 peptides, 32 chains. Longest chain 21 peptides. Score 0.521 Round 3: 243 peptides, 32 chains. Longest chain 20 peptides. Score 0.545 Round 4: 252 peptides, 29 chains. Longest chain 19 peptides. Score 0.601 Round 5: 252 peptides, 29 chains. Longest chain 18 peptides. Score 0.601 Taking the results from Round 5 Chains 29, Residues 223, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4698 reflections ( 99.62 % complete ) and 6547 restraints for refining 2904 atoms. 5684 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2858 (Rfree = 0.000) for 2904 atoms. Found 12 (13 requested) and removed 10 (6 requested) atoms. Cycle 7: After refmac, R = 0.2681 (Rfree = 0.000) for 2891 atoms. Found 4 (13 requested) and removed 6 (6 requested) atoms. Cycle 8: After refmac, R = 0.2625 (Rfree = 0.000) for 2882 atoms. Found 1 (13 requested) and removed 8 (6 requested) atoms. Cycle 9: After refmac, R = 0.2590 (Rfree = 0.000) for 2871 atoms. Found 1 (13 requested) and removed 9 (6 requested) atoms. Cycle 10: After refmac, R = 0.2546 (Rfree = 0.000) for 2861 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.69 3.36 Search for helices and strands: 0 residues in 0 chains, 2936 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 2951 seeds are put forward Round 1: 211 peptides, 32 chains. Longest chain 14 peptides. Score 0.456 Round 2: 234 peptides, 32 chains. Longest chain 20 peptides. Score 0.521 Round 3: 238 peptides, 29 chains. Longest chain 22 peptides. Score 0.567 Round 4: 238 peptides, 29 chains. Longest chain 22 peptides. Score 0.567 Round 5: 230 peptides, 33 chains. Longest chain 18 peptides. Score 0.498 Taking the results from Round 4 Chains 30, Residues 209, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4698 reflections ( 99.62 % complete ) and 6481 restraints for refining 2902 atoms. 5621 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2820 (Rfree = 0.000) for 2902 atoms. Found 12 (13 requested) and removed 7 (6 requested) atoms. Cycle 12: After refmac, R = 0.2601 (Rfree = 0.000) for 2896 atoms. Found 4 (13 requested) and removed 8 (6 requested) atoms. Cycle 13: After refmac, R = 0.2480 (Rfree = 0.000) for 2887 atoms. Found 3 (13 requested) and removed 8 (6 requested) atoms. Cycle 14: After refmac, R = 0.2396 (Rfree = 0.000) for 2880 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 15: After refmac, R = 0.2326 (Rfree = 0.000) for 2870 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.66 3.33 Search for helices and strands: 0 residues in 0 chains, 2952 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 2975 seeds are put forward Round 1: 215 peptides, 36 chains. Longest chain 12 peptides. Score 0.415 Round 2: 235 peptides, 31 chains. Longest chain 20 peptides. Score 0.536 Round 3: 227 peptides, 28 chains. Longest chain 20 peptides. Score 0.551 Round 4: 234 peptides, 30 chains. Longest chain 20 peptides. Score 0.545 Round 5: 244 peptides, 29 chains. Longest chain 14 peptides. Score 0.582 Taking the results from Round 5 Chains 30, Residues 215, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4698 reflections ( 99.62 % complete ) and 6553 restraints for refining 2904 atoms. 5686 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2649 (Rfree = 0.000) for 2904 atoms. Found 10 (13 requested) and removed 10 (6 requested) atoms. Cycle 17: After refmac, R = 0.2539 (Rfree = 0.000) for 2890 atoms. Found 5 (13 requested) and removed 8 (6 requested) atoms. Cycle 18: After refmac, R = 0.2458 (Rfree = 0.000) for 2882 atoms. Found 4 (13 requested) and removed 6 (6 requested) atoms. Cycle 19: After refmac, R = 0.2410 (Rfree = 0.000) for 2876 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. Cycle 20: After refmac, R = 0.2367 (Rfree = 0.000) for 2867 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.66 3.33 Search for helices and strands: 0 residues in 0 chains, 2927 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2945 seeds are put forward Round 1: 195 peptides, 32 chains. Longest chain 13 peptides. Score 0.407 Round 2: 236 peptides, 35 chains. Longest chain 15 peptides. Score 0.490 Round 3: 249 peptides, 30 chains. Longest chain 24 peptides. Score 0.583 Round 4: 233 peptides, 28 chains. Longest chain 24 peptides. Score 0.566 Round 5: 232 peptides, 29 chains. Longest chain 16 peptides. Score 0.552 Taking the results from Round 3 Chains 30, Residues 219, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4698 reflections ( 99.62 % complete ) and 6599 restraints for refining 2903 atoms. 5730 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2548 (Rfree = 0.000) for 2903 atoms. Found 4 (13 requested) and removed 11 (6 requested) atoms. Cycle 22: After refmac, R = 0.2331 (Rfree = 0.000) for 2881 atoms. Found 6 (13 requested) and removed 7 (6 requested) atoms. Cycle 23: After refmac, R = 0.2258 (Rfree = 0.000) for 2875 atoms. Found 2 (13 requested) and removed 8 (6 requested) atoms. Cycle 24: After refmac, R = 0.2238 (Rfree = 0.000) for 2867 atoms. Found 2 (13 requested) and removed 9 (6 requested) atoms. Cycle 25: After refmac, R = 0.2245 (Rfree = 0.000) for 2856 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.73 3.40 Search for helices and strands: 0 residues in 0 chains, 2919 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 2947 seeds are put forward Round 1: 190 peptides, 34 chains. Longest chain 16 peptides. Score 0.363 Round 2: 200 peptides, 24 chains. Longest chain 23 peptides. Score 0.528 Round 3: 208 peptides, 28 chains. Longest chain 13 peptides. Score 0.499 Round 4: 214 peptides, 26 chains. Longest chain 23 peptides. Score 0.541 Round 5: 207 peptides, 28 chains. Longest chain 16 peptides. Score 0.496 Taking the results from Round 4 Chains 26, Residues 188, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4698 reflections ( 99.62 % complete ) and 6745 restraints for refining 2904 atoms. 6019 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2572 (Rfree = 0.000) for 2904 atoms. Found 10 (13 requested) and removed 7 (6 requested) atoms. Cycle 27: After refmac, R = 0.2418 (Rfree = 0.000) for 2901 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. Cycle 28: After refmac, R = 0.2344 (Rfree = 0.000) for 2892 atoms. Found 1 (13 requested) and removed 7 (6 requested) atoms. Cycle 29: After refmac, R = 0.2333 (Rfree = 0.000) for 2886 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 30: After refmac, R = 0.2290 (Rfree = 0.000) for 2881 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.70 3.37 Search for helices and strands: 0 residues in 0 chains, 2927 seeds are put forward NCS extension: 32 residues added (3 deleted due to clashes), 2959 seeds are put forward Round 1: 194 peptides, 32 chains. Longest chain 13 peptides. Score 0.404 Round 2: 204 peptides, 30 chains. Longest chain 14 peptides. Score 0.462 Round 3: 209 peptides, 30 chains. Longest chain 19 peptides. Score 0.476 Round 4: 212 peptides, 31 chains. Longest chain 13 peptides. Score 0.472 Round 5: 213 peptides, 29 chains. Longest chain 15 peptides. Score 0.501 Taking the results from Round 5 Chains 29, Residues 184, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4698 reflections ( 99.62 % complete ) and 6669 restraints for refining 2903 atoms. 5912 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2352 (Rfree = 0.000) for 2903 atoms. Found 3 (13 requested) and removed 9 (6 requested) atoms. Cycle 32: After refmac, R = 0.2228 (Rfree = 0.000) for 2887 atoms. Found 1 (13 requested) and removed 8 (6 requested) atoms. Cycle 33: After refmac, R = 0.2162 (Rfree = 0.000) for 2873 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. Cycle 34: After refmac, R = 0.2131 (Rfree = 0.000) for 2868 atoms. Found 0 (13 requested) and removed 7 (6 requested) atoms. Cycle 35: After refmac, R = 0.2123 (Rfree = 0.000) for 2860 atoms. Found 0 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.65 3.32 Search for helices and strands: 0 residues in 0 chains, 2929 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2950 seeds are put forward Round 1: 177 peptides, 33 chains. Longest chain 9 peptides. Score 0.334 Round 2: 182 peptides, 26 chains. Longest chain 12 peptides. Score 0.450 Round 3: 200 peptides, 30 chains. Longest chain 17 peptides. Score 0.450 Round 4: 208 peptides, 30 chains. Longest chain 17 peptides. Score 0.474 Round 5: 203 peptides, 28 chains. Longest chain 18 peptides. Score 0.485 Taking the results from Round 5 Chains 28, Residues 175, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4698 reflections ( 99.62 % complete ) and 6951 restraints for refining 2904 atoms. 6279 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2511 (Rfree = 0.000) for 2904 atoms. Found 13 (13 requested) and removed 6 (6 requested) atoms. Cycle 37: After refmac, R = 0.2329 (Rfree = 0.000) for 2906 atoms. Found 5 (13 requested) and removed 6 (6 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.2262 (Rfree = 0.000) for 2900 atoms. Found 5 (13 requested) and removed 6 (6 requested) atoms. Cycle 39: After refmac, R = 0.2215 (Rfree = 0.000) for 2894 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. Cycle 40: After refmac, R = 0.2169 (Rfree = 0.000) for 2887 atoms. Found 1 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.62 3.30 Search for helices and strands: 0 residues in 0 chains, 2949 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 2974 seeds are put forward Round 1: 182 peptides, 36 chains. Longest chain 12 peptides. Score 0.307 Round 2: 195 peptides, 32 chains. Longest chain 15 peptides. Score 0.407 Round 3: 185 peptides, 29 chains. Longest chain 17 peptides. Score 0.417 Round 4: 193 peptides, 29 chains. Longest chain 15 peptides. Score 0.442 Round 5: 182 peptides, 28 chains. Longest chain 14 peptides. Score 0.422 Taking the results from Round 4 Chains 29, Residues 164, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4698 reflections ( 99.62 % complete ) and 6928 restraints for refining 2904 atoms. 6301 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2334 (Rfree = 0.000) for 2904 atoms. Found 12 (13 requested) and removed 7 (6 requested) atoms. Cycle 42: After refmac, R = 0.2131 (Rfree = 0.000) for 2896 atoms. Found 5 (13 requested) and removed 6 (6 requested) atoms. Cycle 43: After refmac, R = 0.2066 (Rfree = 0.000) for 2891 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.2231 (Rfree = 0.000) for 2880 atoms. Found 5 (13 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.1940 (Rfree = 0.000) for 2875 atoms. Found 6 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.62 3.30 Search for helices and strands: 0 residues in 0 chains, 2929 seeds are put forward NCS extension: 20 residues added (4 deleted due to clashes), 2949 seeds are put forward Round 1: 152 peptides, 33 chains. Longest chain 7 peptides. Score 0.245 Round 2: 171 peptides, 29 chains. Longest chain 11 peptides. Score 0.372 Round 3: 183 peptides, 30 chains. Longest chain 14 peptides. Score 0.397 Round 4: 188 peptides, 31 chains. Longest chain 13 peptides. Score 0.399 Round 5: 179 peptides, 28 chains. Longest chain 14 peptides. Score 0.412 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 151, 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 2p97-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4698 reflections ( 99.62 % complete ) and 6983 restraints for refining 2904 atoms. 6407 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2260 (Rfree = 0.000) for 2904 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2188 (Rfree = 0.000) for 2870 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1855 (Rfree = 0.000) for 2852 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1886 (Rfree = 0.000) for 2840 atoms. TimeTaking 51.95