null Mon 24 Dec 00:34:04 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 2i51-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2i51-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2i51-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i51-3.2-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/2i51-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i51-3.2-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 00:34:09 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/2i51-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i51-3.2-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 349 and 0 Target number of residues in the AU: 349 Target solvent content: 0.6114 Checking the provided sequence file Detected sequence length: 195 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 390 Adjusted target solvent content: 0.57 Input MTZ file: 2i51-3.2-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: 19 Cell parameters: 65.591 65.955 112.360 90.000 90.000 90.000 Input sequence file: 2i51-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3120 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: 56.880 3.200 Wilson plot Bfac: 57.27 7279 reflections ( 85.94 % complete ) and 0 restraints for refining 3509 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.3185 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2501 (Rfree = 0.000) for 3509 atoms. Found 21 (31 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.05 2.78 Search for helices and strands: 0 residues in 0 chains, 3551 seeds are put forward NCS extension: 0 residues added, 3551 seeds are put forward Round 1: 218 peptides, 34 chains. Longest chain 19 peptides. Score 0.461 Round 2: 250 peptides, 33 chains. Longest chain 20 peptides. Score 0.565 Round 3: 269 peptides, 36 chains. Longest chain 26 peptides. Score 0.579 Round 4: 268 peptides, 31 chains. Longest chain 30 peptides. Score 0.632 Round 5: 261 peptides, 30 chains. Longest chain 23 peptides. Score 0.626 Taking the results from Round 4 Chains 34, Residues 237, Estimated correctness of the model 49.4 % 5 chains (75 residues) have been docked in sequence ------------------------------------------------------ 7279 reflections ( 85.94 % complete ) and 5559 restraints for refining 2959 atoms. 4325 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2568 (Rfree = 0.000) for 2959 atoms. Found 26 (26 requested) and removed 29 (13 requested) atoms. Cycle 2: After refmac, R = 0.2466 (Rfree = 0.000) for 2934 atoms. Found 17 (26 requested) and removed 17 (13 requested) atoms. Cycle 3: After refmac, R = 0.2416 (Rfree = 0.000) for 2927 atoms. Found 11 (26 requested) and removed 13 (13 requested) atoms. Cycle 4: After refmac, R = 0.2357 (Rfree = 0.000) for 2919 atoms. Found 7 (26 requested) and removed 15 (13 requested) atoms. Cycle 5: After refmac, R = 0.2327 (Rfree = 0.000) for 2910 atoms. Found 6 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.06 2.79 Search for helices and strands: 0 residues in 0 chains, 2974 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 2995 seeds are put forward Round 1: 212 peptides, 30 chains. Longest chain 30 peptides. Score 0.496 Round 2: 246 peptides, 28 chains. Longest chain 39 peptides. Score 0.612 Round 3: 253 peptides, 31 chains. Longest chain 20 peptides. Score 0.596 Round 4: 251 peptides, 28 chains. Longest chain 37 peptides. Score 0.624 Round 5: 266 peptides, 29 chains. Longest chain 23 peptides. Score 0.648 Taking the results from Round 5 Chains 34, Residues 237, Estimated correctness of the model 53.4 % 5 chains (61 residues) have been docked in sequence ------------------------------------------------------ 7279 reflections ( 85.94 % complete ) and 5417 restraints for refining 2848 atoms. 4244 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2501 (Rfree = 0.000) for 2848 atoms. Found 25 (25 requested) and removed 21 (12 requested) atoms. Cycle 7: After refmac, R = 0.2371 (Rfree = 0.000) for 2844 atoms. Found 9 (25 requested) and removed 12 (12 requested) atoms. Cycle 8: After refmac, R = 0.2362 (Rfree = 0.000) for 2835 atoms. Found 11 (25 requested) and removed 13 (12 requested) atoms. Cycle 9: After refmac, R = 0.2183 (Rfree = 0.000) for 2830 atoms. Found 5 (25 requested) and removed 14 (12 requested) atoms. Cycle 10: After refmac, R = 0.2083 (Rfree = 0.000) for 2811 atoms. Found 8 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.02 2.75 Search for helices and strands: 0 residues in 0 chains, 2884 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 2912 seeds are put forward Round 1: 247 peptides, 32 chains. Longest chain 26 peptides. Score 0.569 Round 2: 254 peptides, 28 chains. Longest chain 30 peptides. Score 0.631 Round 3: 266 peptides, 25 chains. Longest chain 30 peptides. Score 0.688 Round 4: 262 peptides, 31 chains. Longest chain 17 peptides. Score 0.618 Round 5: 266 peptides, 29 chains. Longest chain 30 peptides. Score 0.648 Taking the results from Round 3 Chains 28, Residues 241, Estimated correctness of the model 62.6 % 4 chains (51 residues) have been docked in sequence ------------------------------------------------------ 7279 reflections ( 85.94 % complete ) and 5391 restraints for refining 2848 atoms. 4214 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2500 (Rfree = 0.000) for 2848 atoms. Found 25 (25 requested) and removed 17 (12 requested) atoms. Cycle 12: After refmac, R = 0.2276 (Rfree = 0.000) for 2849 atoms. Found 9 (25 requested) and removed 14 (12 requested) atoms. Cycle 13: After refmac, R = 0.2169 (Rfree = 0.000) for 2839 atoms. Found 5 (25 requested) and removed 12 (12 requested) atoms. Cycle 14: After refmac, R = 0.2103 (Rfree = 0.000) for 2824 atoms. Found 6 (25 requested) and removed 12 (12 requested) atoms. Cycle 15: After refmac, R = 0.2097 (Rfree = 0.000) for 2814 atoms. Found 15 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.06 2.79 Search for helices and strands: 0 residues in 0 chains, 2879 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2897 seeds are put forward Round 1: 262 peptides, 31 chains. Longest chain 29 peptides. Score 0.618 Round 2: 259 peptides, 28 chains. Longest chain 24 peptides. Score 0.643 Round 3: 279 peptides, 29 chains. Longest chain 29 peptides. Score 0.676 Round 4: 282 peptides, 31 chains. Longest chain 28 peptides. Score 0.663 Round 5: 266 peptides, 30 chains. Longest chain 29 peptides. Score 0.637 Taking the results from Round 3 Chains 29, Residues 250, Estimated correctness of the model 59.9 % 4 chains (50 residues) have been docked in sequence ------------------------------------------------------ 7279 reflections ( 85.94 % complete ) and 5555 restraints for refining 2848 atoms. 4376 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2542 (Rfree = 0.000) for 2848 atoms. Found 25 (25 requested) and removed 18 (12 requested) atoms. Cycle 17: After refmac, R = 0.2277 (Rfree = 0.000) for 2853 atoms. Found 18 (25 requested) and removed 14 (12 requested) atoms. Cycle 18: After refmac, R = 0.2186 (Rfree = 0.000) for 2853 atoms. Found 4 (25 requested) and removed 12 (12 requested) atoms. Cycle 19: After refmac, R = 0.2154 (Rfree = 0.000) for 2840 atoms. Found 8 (25 requested) and removed 12 (12 requested) atoms. Cycle 20: After refmac, R = 0.2277 (Rfree = 0.000) for 2829 atoms. Found 19 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.06 2.79 Search for helices and strands: 0 residues in 0 chains, 2898 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 2924 seeds are put forward Round 1: 225 peptides, 32 chains. Longest chain 29 peptides. Score 0.508 Round 2: 251 peptides, 34 chains. Longest chain 27 peptides. Score 0.556 Round 3: 266 peptides, 34 chains. Longest chain 28 peptides. Score 0.594 Round 4: 258 peptides, 31 chains. Longest chain 22 peptides. Score 0.608 Round 5: 275 peptides, 36 chains. Longest chain 30 peptides. Score 0.594 Taking the results from Round 4 Chains 31, Residues 227, Estimated correctness of the model 43.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7279 reflections ( 85.94 % complete ) and 6163 restraints for refining 2848 atoms. 5286 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2384 (Rfree = 0.000) for 2848 atoms. Found 25 (25 requested) and removed 13 (12 requested) atoms. Cycle 22: After refmac, R = 0.2256 (Rfree = 0.000) for 2852 atoms. Found 12 (25 requested) and removed 12 (12 requested) atoms. Cycle 23: After refmac, R = 0.2210 (Rfree = 0.000) for 2848 atoms. Found 14 (25 requested) and removed 12 (12 requested) atoms. Cycle 24: After refmac, R = 0.2477 (Rfree = 0.000) for 2846 atoms. Found 25 (25 requested) and removed 13 (12 requested) atoms. Cycle 25: After refmac, R = 0.2135 (Rfree = 0.000) for 2855 atoms. Found 13 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.06 2.79 Search for helices and strands: 0 residues in 0 chains, 2915 seeds are put forward NCS extension: 22 residues added (7 deleted due to clashes), 2937 seeds are put forward Round 1: 231 peptides, 31 chains. Longest chain 30 peptides. Score 0.538 Round 2: 236 peptides, 29 chains. Longest chain 26 peptides. Score 0.575 Round 3: 250 peptides, 33 chains. Longest chain 19 peptides. Score 0.565 Round 4: 252 peptides, 26 chains. Longest chain 30 peptides. Score 0.648 Round 5: 252 peptides, 28 chains. Longest chain 19 peptides. Score 0.626 Taking the results from Round 4 Chains 27, Residues 226, Estimated correctness of the model 53.4 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 7279 reflections ( 85.94 % complete ) and 5931 restraints for refining 2848 atoms. 4941 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2422 (Rfree = 0.000) for 2848 atoms. Found 15 (25 requested) and removed 20 (12 requested) atoms. Cycle 27: After refmac, R = 0.2240 (Rfree = 0.000) for 2840 atoms. Found 10 (25 requested) and removed 13 (12 requested) atoms. Cycle 28: After refmac, R = 0.2194 (Rfree = 0.000) for 2833 atoms. Found 11 (25 requested) and removed 12 (12 requested) atoms. Cycle 29: After refmac, R = 0.2116 (Rfree = 0.000) for 2830 atoms. Found 20 (25 requested) and removed 13 (12 requested) atoms. Cycle 30: After refmac, R = 0.2087 (Rfree = 0.000) for 2834 atoms. Found 16 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.05 2.78 Search for helices and strands: 0 residues in 0 chains, 2892 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 2922 seeds are put forward Round 1: 228 peptides, 33 chains. Longest chain 24 peptides. Score 0.504 Round 2: 248 peptides, 30 chains. Longest chain 20 peptides. Score 0.595 Round 3: 251 peptides, 26 chains. Longest chain 23 peptides. Score 0.646 Round 4: 239 peptides, 29 chains. Longest chain 21 peptides. Score 0.583 Round 5: 249 peptides, 26 chains. Longest chain 24 peptides. Score 0.641 Taking the results from Round 3 Chains 26, Residues 225, Estimated correctness of the model 52.9 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 7279 reflections ( 85.94 % complete ) and 6076 restraints for refining 2848 atoms. 5185 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2344 (Rfree = 0.000) for 2848 atoms. Found 22 (25 requested) and removed 14 (12 requested) atoms. Cycle 32: After refmac, R = 0.2171 (Rfree = 0.000) for 2852 atoms. Found 8 (25 requested) and removed 12 (12 requested) atoms. Cycle 33: After refmac, R = 0.2307 (Rfree = 0.000) for 2845 atoms. Found 21 (25 requested) and removed 12 (12 requested) atoms. Cycle 34: After refmac, R = 0.2126 (Rfree = 0.000) for 2852 atoms. Found 8 (25 requested) and removed 13 (12 requested) atoms. Cycle 35: After refmac, R = 0.2084 (Rfree = 0.000) for 2845 atoms. Found 6 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.06 2.79 Search for helices and strands: 0 residues in 0 chains, 2898 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2918 seeds are put forward Round 1: 229 peptides, 37 chains. Longest chain 17 peptides. Score 0.455 Round 2: 245 peptides, 33 chains. Longest chain 24 peptides. Score 0.552 Round 3: 260 peptides, 32 chains. Longest chain 20 peptides. Score 0.602 Round 4: 251 peptides, 33 chains. Longest chain 21 peptides. Score 0.568 Round 5: 253 peptides, 33 chains. Longest chain 21 peptides. Score 0.573 Taking the results from Round 3 Chains 32, Residues 228, Estimated correctness of the model 41.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7279 reflections ( 85.94 % complete ) and 6136 restraints for refining 2848 atoms. 5256 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2311 (Rfree = 0.000) for 2848 atoms. Found 25 (25 requested) and removed 13 (12 requested) atoms. Cycle 37: After refmac, R = 0.2102 (Rfree = 0.000) for 2855 atoms. Found 6 (25 requested) and removed 12 (12 requested) atoms. Cycle 38: After refmac, R = 0.2106 (Rfree = 0.000) for 2846 atoms. Found 9 (25 requested) and removed 14 (12 requested) atoms. Cycle 39: After refmac, R = 0.2430 (Rfree = 0.000) for 2839 atoms. Found 25 (25 requested) and removed 13 (12 requested) atoms. Cycle 40: After refmac, R = 0.2047 (Rfree = 0.000) for 2850 atoms. Found 7 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.06 2.79 Search for helices and strands: 0 residues in 0 chains, 2908 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2927 seeds are put forward Round 1: 216 peptides, 32 chains. Longest chain 20 peptides. Score 0.482 Round 2: 221 peptides, 30 chains. Longest chain 17 peptides. Score 0.522 Round 3: 232 peptides, 27 chains. Longest chain 20 peptides. Score 0.589 Round 4: 224 peptides, 26 chains. Longest chain 20 peptides. Score 0.580 Round 5: 221 peptides, 26 chains. Longest chain 28 peptides. Score 0.572 Taking the results from Round 3 Chains 27, Residues 205, Estimated correctness of the model 38.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7279 reflections ( 85.94 % complete ) and 6311 restraints for refining 2848 atoms. 5518 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2365 (Rfree = 0.000) for 2848 atoms. Found 21 (25 requested) and removed 16 (12 requested) atoms. Cycle 42: After refmac, R = 0.2169 (Rfree = 0.000) for 2845 atoms. Found 19 (25 requested) and removed 12 (12 requested) atoms. Cycle 43: After refmac, R = 0.2540 (Rfree = 0.000) for 2848 atoms. Found 25 (25 requested) and removed 14 (12 requested) atoms. Cycle 44: After refmac, R = 0.2093 (Rfree = 0.000) for 2859 atoms. Found 9 (25 requested) and removed 13 (12 requested) atoms. Cycle 45: After refmac, R = 0.2098 (Rfree = 0.000) for 2855 atoms. Found 16 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.08 2.80 Search for helices and strands: 0 residues in 0 chains, 2907 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2924 seeds are put forward Round 1: 211 peptides, 31 chains. Longest chain 15 peptides. Score 0.480 Round 2: 238 peptides, 27 chains. Longest chain 24 peptides. Score 0.604 Round 3: 247 peptides, 30 chains. Longest chain 22 peptides. Score 0.592 Round 4: 236 peptides, 26 chains. Longest chain 23 peptides. Score 0.610 Round 5: 233 peptides, 27 chains. Longest chain 25 peptides. Score 0.591 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 210, Estimated correctness of the model 43.7 % 1 chains (15 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2i51-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7279 reflections ( 85.94 % complete ) and 6049 restraints for refining 2848 atoms. 5175 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2549 (Rfree = 0.000) for 2848 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2440 (Rfree = 0.000) for 2833 atoms. Found 0 (25 requested) and removed 10 (12 requested) atoms. Cycle 48: After refmac, R = 0.2227 (Rfree = 0.000) for 2820 atoms. Found 0 (25 requested) and removed 5 (12 requested) atoms. Cycle 49: After refmac, R = 0.2160 (Rfree = 0.000) for 2814 atoms. Found 0 (25 requested) and removed 9 (12 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:10:28 GMT 2018 Job finished. TimeTaking 36.4 Used memory is bytes: 8575232