null Mon 24 Dec 08:01:01 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 2p97-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2p97-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2p97-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p97-3.4-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/2p97-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p97-3.4-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 08:01:05 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/2p97-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p97-3.4-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 354 and 0 Target number of residues in the AU: 354 Target solvent content: 0.6250 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: 2p97-3.4-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: 2p97-3.4-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 3.400 Wilson plot Bfac: 63.69 7539 reflections ( 99.76 % complete ) and 0 restraints for refining 3590 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3274 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3125 (Rfree = 0.000) for 3590 atoms. Found 27 (27 requested) and removed 26 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 2.99 Search for helices and strands: 0 residues in 0 chains, 3658 seeds are put forward NCS extension: 0 residues added, 3658 seeds are put forward Round 1: 223 peptides, 37 chains. Longest chain 13 peptides. Score 0.427 Round 2: 259 peptides, 30 chains. Longest chain 22 peptides. Score 0.607 Round 3: 291 peptides, 34 chains. Longest chain 41 peptides. Score 0.638 Round 4: 296 peptides, 32 chains. Longest chain 19 peptides. Score 0.667 Round 5: 309 peptides, 29 chains. Longest chain 33 peptides. Score 0.718 Taking the results from Round 5 Chains 30, Residues 280, Estimated correctness of the model 62.4 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7539 reflections ( 99.76 % complete ) and 6015 restraints for refining 2925 atoms. 4896 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2701 (Rfree = 0.000) for 2925 atoms. Found 22 (22 requested) and removed 16 (11 requested) atoms. Cycle 2: After refmac, R = 0.2557 (Rfree = 0.000) for 2898 atoms. Found 10 (22 requested) and removed 18 (11 requested) atoms. Cycle 3: After refmac, R = 0.2601 (Rfree = 0.000) for 2879 atoms. Found 14 (20 requested) and removed 14 (10 requested) atoms. Cycle 4: After refmac, R = 0.2475 (Rfree = 0.000) for 2870 atoms. Found 7 (20 requested) and removed 11 (10 requested) atoms. Cycle 5: After refmac, R = 0.2391 (Rfree = 0.000) for 2857 atoms. Found 9 (19 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.23 2.94 Search for helices and strands: 0 residues in 0 chains, 2959 seeds are put forward NCS extension: 37 residues added (7 deleted due to clashes), 2996 seeds are put forward Round 1: 269 peptides, 31 chains. Longest chain 20 peptides. Score 0.619 Round 2: 285 peptides, 30 chains. Longest chain 38 peptides. Score 0.664 Round 3: 290 peptides, 25 chains. Longest chain 37 peptides. Score 0.719 Round 4: 284 peptides, 27 chains. Longest chain 38 peptides. Score 0.690 Round 5: 287 peptides, 25 chains. Longest chain 41 peptides. Score 0.713 Taking the results from Round 3 Chains 28, Residues 265, Estimated correctness of the model 62.6 % 3 chains (37 residues) have been docked in sequence Building loops using Loopy2018 28 chains (265 residues) following loop building 3 chains (37 residues) in sequence following loop building ------------------------------------------------------ 7539 reflections ( 99.76 % complete ) and 5851 restraints for refining 2925 atoms. 4679 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2635 (Rfree = 0.000) for 2925 atoms. Found 20 (20 requested) and removed 19 (11 requested) atoms. Cycle 7: After refmac, R = 0.2416 (Rfree = 0.000) for 2916 atoms. Found 11 (19 requested) and removed 15 (11 requested) atoms. Cycle 8: After refmac, R = 0.2381 (Rfree = 0.000) for 2899 atoms. Found 7 (18 requested) and removed 11 (10 requested) atoms. Cycle 9: After refmac, R = 0.2342 (Rfree = 0.000) for 2891 atoms. Found 5 (18 requested) and removed 11 (10 requested) atoms. Cycle 10: After refmac, R = 0.2351 (Rfree = 0.000) for 2883 atoms. Found 0 (17 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.26 2.97 Search for helices and strands: 0 residues in 0 chains, 2981 seeds are put forward NCS extension: 42 residues added (7 deleted due to clashes), 3023 seeds are put forward Round 1: 277 peptides, 32 chains. Longest chain 23 peptides. Score 0.627 Round 2: 281 peptides, 31 chains. Longest chain 21 peptides. Score 0.646 Round 3: 283 peptides, 30 chains. Longest chain 24 peptides. Score 0.660 Round 4: 289 peptides, 27 chains. Longest chain 49 peptides. Score 0.699 Round 5: 293 peptides, 27 chains. Longest chain 39 peptides. Score 0.707 Taking the results from Round 5 Chains 29, Residues 266, Estimated correctness of the model 59.7 % 5 chains (93 residues) have been docked in sequence Building loops using Loopy2018 29 chains (266 residues) following loop building 5 chains (93 residues) in sequence following loop building ------------------------------------------------------ 7539 reflections ( 99.76 % complete ) and 5275 restraints for refining 2925 atoms. 3878 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2718 (Rfree = 0.000) for 2925 atoms. Found 17 (18 requested) and removed 20 (11 requested) atoms. Cycle 12: After refmac, R = 0.2582 (Rfree = 0.000) for 2900 atoms. Found 10 (17 requested) and removed 13 (11 requested) atoms. Cycle 13: After refmac, R = 0.2497 (Rfree = 0.000) for 2885 atoms. Found 7 (16 requested) and removed 14 (10 requested) atoms. Cycle 14: After refmac, R = 0.2393 (Rfree = 0.000) for 2870 atoms. Found 10 (16 requested) and removed 12 (10 requested) atoms. Cycle 15: After refmac, R = 0.2314 (Rfree = 0.000) for 2865 atoms. Found 3 (15 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 2.94 Search for helices and strands: 0 residues in 0 chains, 2946 seeds are put forward NCS extension: 24 residues added (25 deleted due to clashes), 2970 seeds are put forward Round 1: 274 peptides, 35 chains. Longest chain 18 peptides. Score 0.589 Round 2: 291 peptides, 27 chains. Longest chain 32 peptides. Score 0.703 Round 3: 293 peptides, 26 chains. Longest chain 26 peptides. Score 0.715 Round 4: 292 peptides, 27 chains. Longest chain 32 peptides. Score 0.705 Round 5: 292 peptides, 28 chains. Longest chain 36 peptides. Score 0.696 Taking the results from Round 3 Chains 26, Residues 267, Estimated correctness of the model 61.6 % 2 chains (43 residues) have been docked in sequence Building loops using Loopy2018 26 chains (267 residues) following loop building 2 chains (43 residues) in sequence following loop building ------------------------------------------------------ 7539 reflections ( 99.76 % complete ) and 5786 restraints for refining 2925 atoms. 4595 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2524 (Rfree = 0.000) for 2925 atoms. Found 15 (15 requested) and removed 14 (11 requested) atoms. Cycle 17: After refmac, R = 0.2412 (Rfree = 0.000) for 2921 atoms. Found 9 (15 requested) and removed 16 (11 requested) atoms. Cycle 18: After refmac, R = 0.2362 (Rfree = 0.000) for 2910 atoms. Found 4 (14 requested) and removed 10 (10 requested) atoms. Cycle 19: After refmac, R = 0.2343 (Rfree = 0.000) for 2901 atoms. Found 8 (13 requested) and removed 11 (10 requested) atoms. Cycle 20: After refmac, R = 0.2256 (Rfree = 0.000) for 2892 atoms. Found 7 (13 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.26 2.97 Search for helices and strands: 0 residues in 0 chains, 2965 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 2989 seeds are put forward Round 1: 261 peptides, 32 chains. Longest chain 24 peptides. Score 0.590 Round 2: 284 peptides, 28 chains. Longest chain 21 peptides. Score 0.681 Round 3: 278 peptides, 28 chains. Longest chain 20 peptides. Score 0.669 Round 4: 268 peptides, 30 chains. Longest chain 16 peptides. Score 0.628 Round 5: 281 peptides, 27 chains. Longest chain 25 peptides. Score 0.684 Taking the results from Round 5 Chains 28, Residues 254, Estimated correctness of the model 53.7 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 7539 reflections ( 99.76 % complete ) and 6081 restraints for refining 2925 atoms. 5037 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2398 (Rfree = 0.000) for 2925 atoms. Found 13 (13 requested) and removed 13 (11 requested) atoms. Cycle 22: After refmac, R = 0.2222 (Rfree = 0.000) for 2918 atoms. Found 8 (13 requested) and removed 14 (11 requested) atoms. Cycle 23: After refmac, R = 0.2106 (Rfree = 0.000) for 2907 atoms. Found 2 (13 requested) and removed 12 (10 requested) atoms. Cycle 24: After refmac, R = 0.2065 (Rfree = 0.000) for 2893 atoms. Found 3 (13 requested) and removed 11 (10 requested) atoms. Cycle 25: After refmac, R = 0.2010 (Rfree = 0.000) for 2882 atoms. Found 3 (13 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 2.92 Search for helices and strands: 0 residues in 0 chains, 2957 seeds are put forward NCS extension: 14 residues added (4 deleted due to clashes), 2971 seeds are put forward Round 1: 253 peptides, 34 chains. Longest chain 21 peptides. Score 0.548 Round 2: 282 peptides, 32 chains. Longest chain 17 peptides. Score 0.638 Round 3: 282 peptides, 31 chains. Longest chain 21 peptides. Score 0.648 Round 4: 283 peptides, 26 chains. Longest chain 29 peptides. Score 0.697 Round 5: 285 peptides, 29 chains. Longest chain 32 peptides. Score 0.673 Taking the results from Round 4 Chains 26, Residues 257, Estimated correctness of the model 57.1 % 1 chains (28 residues) have been docked in sequence ------------------------------------------------------ 7539 reflections ( 99.76 % complete ) and 5899 restraints for refining 2925 atoms. 4768 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2514 (Rfree = 0.000) for 2925 atoms. Found 13 (13 requested) and removed 14 (11 requested) atoms. Cycle 27: After refmac, R = 0.2349 (Rfree = 0.000) for 2916 atoms. Found 11 (13 requested) and removed 11 (11 requested) atoms. Cycle 28: After refmac, R = 0.2275 (Rfree = 0.000) for 2912 atoms. Found 7 (13 requested) and removed 14 (11 requested) atoms. Cycle 29: After refmac, R = 0.2192 (Rfree = 0.000) for 2902 atoms. Found 10 (13 requested) and removed 11 (10 requested) atoms. Cycle 30: After refmac, R = 0.2133 (Rfree = 0.000) for 2898 atoms. Found 3 (13 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.25 2.96 Search for helices and strands: 0 residues in 0 chains, 2966 seeds are put forward NCS extension: 38 residues added (3 deleted due to clashes), 3004 seeds are put forward Round 1: 270 peptides, 34 chains. Longest chain 23 peptides. Score 0.590 Round 2: 281 peptides, 30 chains. Longest chain 24 peptides. Score 0.656 Round 3: 280 peptides, 30 chains. Longest chain 30 peptides. Score 0.654 Round 4: 279 peptides, 28 chains. Longest chain 27 peptides. Score 0.671 Round 5: 288 peptides, 29 chains. Longest chain 24 peptides. Score 0.679 Taking the results from Round 5 Chains 29, Residues 259, Estimated correctness of the model 52.3 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 7539 reflections ( 99.76 % complete ) and 6004 restraints for refining 2925 atoms. 4895 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2544 (Rfree = 0.000) for 2925 atoms. Found 13 (13 requested) and removed 15 (11 requested) atoms. Cycle 32: After refmac, R = 0.2334 (Rfree = 0.000) for 2915 atoms. Found 12 (13 requested) and removed 12 (11 requested) atoms. Cycle 33: After refmac, R = 0.2231 (Rfree = 0.000) for 2912 atoms. Found 3 (13 requested) and removed 11 (11 requested) atoms. Cycle 34: After refmac, R = 0.2197 (Rfree = 0.000) for 2903 atoms. Found 6 (13 requested) and removed 10 (10 requested) atoms. Cycle 35: After refmac, R = 0.2183 (Rfree = 0.000) for 2898 atoms. Found 3 (13 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 2.99 Search for helices and strands: 0 residues in 0 chains, 2955 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 2974 seeds are put forward Round 1: 244 peptides, 33 chains. Longest chain 16 peptides. Score 0.536 Round 2: 275 peptides, 27 chains. Longest chain 27 peptides. Score 0.672 Round 3: 278 peptides, 31 chains. Longest chain 20 peptides. Score 0.639 Round 4: 269 peptides, 28 chains. Longest chain 30 peptides. Score 0.650 Round 5: 277 peptides, 32 chains. Longest chain 20 peptides. Score 0.627 Taking the results from Round 2 Chains 30, Residues 248, Estimated correctness of the model 50.4 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 7539 reflections ( 99.76 % complete ) and 5972 restraints for refining 2925 atoms. 4878 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2385 (Rfree = 0.000) for 2925 atoms. Found 13 (13 requested) and removed 18 (11 requested) atoms. Cycle 37: After refmac, R = 0.2262 (Rfree = 0.000) for 2912 atoms. Found 6 (13 requested) and removed 11 (11 requested) atoms. Cycle 38: After refmac, R = 0.2212 (Rfree = 0.000) for 2906 atoms. Found 5 (13 requested) and removed 10 (10 requested) atoms. Cycle 39: After refmac, R = 0.2210 (Rfree = 0.000) for 2898 atoms. Found 4 (13 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.2202 (Rfree = 0.000) for 2891 atoms. Found 0 (13 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 3.03 Search for helices and strands: 0 residues in 0 chains, 2939 seeds are put forward NCS extension: 22 residues added (5 deleted due to clashes), 2961 seeds are put forward Round 1: 225 peptides, 33 chains. Longest chain 16 peptides. Score 0.484 Round 2: 245 peptides, 28 chains. Longest chain 30 peptides. Score 0.596 Round 3: 247 peptides, 29 chains. Longest chain 23 peptides. Score 0.590 Round 4: 247 peptides, 28 chains. Longest chain 29 peptides. Score 0.601 Round 5: 247 peptides, 29 chains. Longest chain 27 peptides. Score 0.590 Taking the results from Round 4 Chains 30, Residues 219, Estimated correctness of the model 29.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 7539 reflections ( 99.76 % complete ) and 6289 restraints for refining 2925 atoms. 5356 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2507 (Rfree = 0.000) for 2925 atoms. Found 13 (13 requested) and removed 15 (11 requested) atoms. Cycle 42: After refmac, R = 0.2405 (Rfree = 0.000) for 2920 atoms. Found 6 (13 requested) and removed 11 (11 requested) atoms. Cycle 43: After refmac, R = 0.2378 (Rfree = 0.000) for 2910 atoms. Found 7 (13 requested) and removed 11 (11 requested) atoms. Cycle 44: After refmac, R = 0.2378 (Rfree = 0.000) for 2905 atoms. Found 6 (13 requested) and removed 10 (10 requested) atoms. Cycle 45: After refmac, R = 0.2370 (Rfree = 0.000) for 2901 atoms. Found 5 (13 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.32 3.02 Search for helices and strands: 0 residues in 0 chains, 2962 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 2986 seeds are put forward Round 1: 210 peptides, 31 chains. Longest chain 20 peptides. Score 0.466 Round 2: 246 peptides, 31 chains. Longest chain 18 peptides. Score 0.565 Round 3: 242 peptides, 28 chains. Longest chain 22 peptides. Score 0.589 Round 4: 241 peptides, 26 chains. Longest chain 30 peptides. Score 0.608 Round 5: 246 peptides, 28 chains. Longest chain 27 peptides. Score 0.598 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 215, Estimated correctness of the model 31.3 % 2 chains (35 residues) have been docked in sequence Sequence coverage is 16 % Consider running further cycles of model building using 2p97-3_warpNtrace.pdb as input Building loops using Loopy2018 26 chains (215 residues) following loop building 2 chains (35 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7539 reflections ( 99.76 % complete ) and 6189 restraints for refining 2925 atoms. 5198 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2562 (Rfree = 0.000) for 2925 atoms. Found 0 (13 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2454 (Rfree = 0.000) for 2909 atoms. Found 0 (13 requested) and removed 6 (11 requested) atoms. Cycle 48: After refmac, R = 0.2416 (Rfree = 0.000) for 2900 atoms. Found 0 (13 requested) and removed 4 (10 requested) atoms. Cycle 49: After refmac, R = 0.2379 (Rfree = 0.000) for 2892 atoms. Found 0 (13 requested) and removed 2 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:40:21 GMT 2018 Job finished. TimeTaking 39.34 Used memory is bytes: 8943496