null Mon 24 Dec 07:40:25 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 2pnk-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2pnk-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2pnk-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pnk-3.8-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/2pnk-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pnk-3.8-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 07:40:30 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/2pnk-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pnk-3.8-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 4485 and 0 Target number of residues in the AU: 4485 Target solvent content: 0.6566 Target number of residues exceeds 1700, conditional restraints are disabled Checking the provided sequence file Detected sequence length: 428 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 12 Adjusted target number of residues: 5136 Adjusted target solvent content: 0.61 Input MTZ file: 2pnk-3.8-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: 5 Cell parameters: 273.720 158.560 181.240 90.000 116.029 90.000 Input sequence file: 2pnk-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 41088 target number of atoms Had to go as low as 0.95 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. 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: 162.857 3.800 Wilson plot Bfac: 82.54 63786 reflections ( 92.90 % complete ) and 0 restraints for refining 45608 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3187 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2831 (Rfree = 0.000) for 45608 atoms. Found 250 (250 requested) and removed 254 (125 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.67 3.16 Search for helices and strands: 0 residues in 0 chains, 46613 seeds are put forward NCS extension: 0 residues added, 46613 seeds are put forward Round 1: 2457 peptides, 439 chains. Longest chain 19 peptides. Score 0.354 Round 2: 2953 peptides, 414 chains. Longest chain 29 peptides. Score 0.490 Round 3: 3118 peptides, 395 chains. Longest chain 28 peptides. Score 0.540 Round 4: 3154 peptides, 384 chains. Longest chain 32 peptides. Score 0.556 Round 5: 3205 peptides, 381 chains. Longest chain 27 peptides. Score 0.568 Taking the results from Round 5 Chains 390, Residues 2824, Estimated correctness of the model 0.0 % 18 chains (150 residues) have been docked in sequence ------------------------------------------------------ 63786 reflections ( 92.90 % complete ) and 11437 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2237 (Rfree = 0.000) for 37165 atoms. Found 165 (204 requested) and removed 209 (102 requested) atoms. Cycle 2: After refmac, R = 0.2044 (Rfree = 0.000) for 37121 atoms. Found 167 (204 requested) and removed 155 (102 requested) atoms. Cycle 3: After refmac, R = 0.1899 (Rfree = 0.000) for 37133 atoms. Found 136 (204 requested) and removed 163 (102 requested) atoms. Cycle 4: After refmac, R = 0.1842 (Rfree = 0.000) for 37106 atoms. Found 146 (204 requested) and removed 153 (102 requested) atoms. Cycle 5: After refmac, R = 0.1458 (Rfree = 0.000) for 37099 atoms. Found 24 (204 requested) and removed 146 (102 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.63 3.13 Search for helices and strands: 0 residues in 0 chains, 38437 seeds are put forward NCS extension: 0 residues added, 38437 seeds are put forward Round 1: 2782 peptides, 442 chains. Longest chain 22 peptides. Score 0.427 Round 2: 3151 peptides, 416 chains. Longest chain 26 peptides. Score 0.528 Round 3: 3142 peptides, 395 chains. Longest chain 31 peptides. Score 0.544 Round 4: 3163 peptides, 384 chains. Longest chain 30 peptides. Score 0.558 Round 5: 3182 peptides, 395 chains. Longest chain 29 peptides. Score 0.552 Taking the results from Round 4 Chains 410, Residues 2779, Estimated correctness of the model 0.0 % 25 chains (272 residues) have been docked in sequence ------------------------------------------------------ 63786 reflections ( 92.90 % complete ) and 11842 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2010 (Rfree = 0.000) for 37165 atoms. Found 204 (204 requested) and removed 172 (102 requested) atoms. Cycle 7: After refmac, R = 0.1896 (Rfree = 0.000) for 37197 atoms. Found 204 (204 requested) and removed 156 (102 requested) atoms. Cycle 8: After refmac, R = 0.1796 (Rfree = 0.000) for 37245 atoms. Found 195 (204 requested) and removed 159 (102 requested) atoms. Cycle 9: After refmac, R = 0.1449 (Rfree = 0.000) for 37281 atoms. Found 12 (205 requested) and removed 125 (102 requested) atoms. Cycle 10: After refmac, R = 0.1356 (Rfree = 0.000) for 37168 atoms. Found 16 (204 requested) and removed 131 (102 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.65 3.14 Search for helices and strands: 0 residues in 0 chains, 38323 seeds are put forward NCS extension: 0 residues added, 38323 seeds are put forward Round 1: 2833 peptides, 443 chains. Longest chain 19 peptides. Score 0.437 Round 2: 3130 peptides, 397 chains. Longest chain 29 peptides. Score 0.540 Round 3: 3172 peptides, 399 chains. Longest chain 29 peptides. Score 0.547 Round 4: 3134 peptides, 383 chains. Longest chain 46 peptides. Score 0.553 Round 5: 3095 peptides, 392 chains. Longest chain 22 peptides. Score 0.538 Taking the results from Round 4 Chains 399, Residues 2751, Estimated correctness of the model 0.0 % 19 chains (237 residues) have been docked in sequence ------------------------------------------------------ 63786 reflections ( 92.90 % complete ) and 11568 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1958 (Rfree = 0.000) for 37165 atoms. Found 204 (204 requested) and removed 223 (102 requested) atoms. Cycle 12: After refmac, R = 0.1835 (Rfree = 0.000) for 37146 atoms. Found 204 (204 requested) and removed 145 (102 requested) atoms. Cycle 13: After refmac, R = 0.1750 (Rfree = 0.000) for 37205 atoms. Found 200 (204 requested) and removed 151 (102 requested) atoms. Cycle 14: After refmac, R = 0.1728 (Rfree = 0.000) for 37254 atoms. Found 204 (204 requested) and removed 160 (102 requested) atoms. Cycle 15: After refmac, R = 0.1305 (Rfree = 0.000) for 37298 atoms. Found 27 (205 requested) and removed 145 (102 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.64 3.14 Search for helices and strands: 0 residues in 0 chains, 38431 seeds are put forward NCS extension: 45 residues added (18 deleted due to clashes), 38476 seeds are put forward Round 1: 2744 peptides, 448 chains. Longest chain 28 peptides. Score 0.412 Round 2: 3047 peptides, 415 chains. Longest chain 26 peptides. Score 0.508 Round 3: 3096 peptides, 398 chains. Longest chain 34 peptides. Score 0.533 Round 4: 3114 peptides, 398 chains. Longest chain 27 peptides. Score 0.537 Round 5: 3075 peptides, 389 chains. Longest chain 21 peptides. Score 0.537 Taking the results from Round 5 Chains 398, Residues 2686, Estimated correctness of the model 0.0 % 14 chains (137 residues) have been docked in sequence ------------------------------------------------------ 63786 reflections ( 92.90 % complete ) and 10864 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1918 (Rfree = 0.000) for 37165 atoms. Found 204 (204 requested) and removed 153 (102 requested) atoms. Cycle 17: After refmac, R = 0.1809 (Rfree = 0.000) for 37216 atoms. Found 199 (204 requested) and removed 150 (102 requested) atoms. Cycle 18: After refmac, R = 0.1392 (Rfree = 0.000) for 37265 atoms. Found 28 (204 requested) and removed 136 (102 requested) atoms. Cycle 19: After refmac, R = 0.1287 (Rfree = 0.000) for 37157 atoms. Found 15 (204 requested) and removed 130 (102 requested) atoms. Cycle 20: After refmac, R = 0.1274 (Rfree = 0.000) for 37042 atoms. Found 29 (203 requested) and removed 113 (101 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.63 3.13 Search for helices and strands: 0 residues in 0 chains, 38271 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 38285 seeds are put forward Round 1: 2603 peptides, 435 chains. Longest chain 19 peptides. Score 0.393 Round 2: 2936 peptides, 394 chains. Longest chain 25 peptides. Score 0.505 Round 3: 2990 peptides, 398 chains. Longest chain 33 peptides. Score 0.512 Round 4: 2993 peptides, 385 chains. Longest chain 29 peptides. Score 0.524 Round 5: 3045 peptides, 394 chains. Longest chain 29 peptides. Score 0.527 Taking the results from Round 5 Chains 403, Residues 2651, Estimated correctness of the model 0.0 % 12 chains (144 residues) have been docked in sequence ------------------------------------------------------ 63786 reflections ( 92.90 % complete ) and 10865 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1912 (Rfree = 0.000) for 37165 atoms. Found 204 (204 requested) and removed 152 (102 requested) atoms. Cycle 22: After refmac, R = 0.1809 (Rfree = 0.000) for 37217 atoms. Found 203 (204 requested) and removed 138 (102 requested) atoms. Cycle 23: After refmac, R = 0.1760 (Rfree = 0.000) for 37282 atoms. Found 194 (205 requested) and removed 144 (102 requested) atoms. Cycle 24: After refmac, R = 0.1350 (Rfree = 0.000) for 37332 atoms. Found 22 (205 requested) and removed 125 (102 requested) atoms. Cycle 25: After refmac, R = 0.1236 (Rfree = 0.000) for 37229 atoms. Found 21 (204 requested) and removed 124 (102 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.65 3.14 Search for helices and strands: 0 residues in 0 chains, 38446 seeds are put forward NCS extension: 0 residues added, 38446 seeds are put forward Round 1: 2513 peptides, 435 chains. Longest chain 20 peptides. Score 0.372 Round 2: 2827 peptides, 418 chains. Longest chain 29 peptides. Score 0.460 Round 3: 2910 peptides, 413 chains. Longest chain 28 peptides. Score 0.482 Round 4: 2887 peptides, 407 chains. Longest chain 24 peptides. Score 0.483 Round 5: 2936 peptides, 412 chains. Longest chain 25 peptides. Score 0.488 Taking the results from Round 5 Chains 422, Residues 2524, Estimated correctness of the model 0.0 % 15 chains (159 residues) have been docked in sequence ------------------------------------------------------ 63786 reflections ( 92.90 % complete ) and 10304 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1940 (Rfree = 0.000) for 37165 atoms. Found 204 (204 requested) and removed 140 (102 requested) atoms. Cycle 27: After refmac, R = 0.1853 (Rfree = 0.000) for 37229 atoms. Found 204 (204 requested) and removed 138 (102 requested) atoms. Cycle 28: After refmac, R = 0.1396 (Rfree = 0.000) for 37295 atoms. Found 31 (205 requested) and removed 127 (102 requested) atoms. Cycle 29: After refmac, R = 0.1285 (Rfree = 0.000) for 37199 atoms. Found 26 (204 requested) and removed 125 (102 requested) atoms. Cycle 30: After refmac, R = 0.1284 (Rfree = 0.000) for 37100 atoms. Found 25 (204 requested) and removed 124 (102 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.64 3.14 Search for helices and strands: 0 residues in 0 chains, 38291 seeds are put forward NCS extension: 0 residues added, 38291 seeds are put forward Round 1: 2463 peptides, 445 chains. Longest chain 16 peptides. Score 0.349 Round 2: 2716 peptides, 397 chains. Longest chain 21 peptides. Score 0.456 Round 3: 2805 peptides, 400 chains. Longest chain 28 peptides. Score 0.472 Round 4: 2798 peptides, 393 chains. Longest chain 25 peptides. Score 0.477 Round 5: 2826 peptides, 388 chains. Longest chain 27 peptides. Score 0.488 Taking the results from Round 5 Chains 393, Residues 2438, Estimated correctness of the model 0.0 % 12 chains (126 residues) have been docked in sequence ------------------------------------------------------ 63786 reflections ( 92.90 % complete ) and 9839 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1844 (Rfree = 0.000) for 37165 atoms. Found 177 (204 requested) and removed 135 (102 requested) atoms. Cycle 32: After refmac, R = 0.1819 (Rfree = 0.000) for 37207 atoms. Found 204 (204 requested) and removed 131 (102 requested) atoms. Cycle 33: After refmac, R = 0.1350 (Rfree = 0.000) for 37280 atoms. Found 44 (205 requested) and removed 130 (102 requested) atoms. Cycle 34: After refmac, R = 0.1250 (Rfree = 0.000) for 37194 atoms. Found 25 (204 requested) and removed 120 (102 requested) atoms. Cycle 35: After refmac, R = 0.1219 (Rfree = 0.000) for 37099 atoms. Found 22 (204 requested) and removed 123 (102 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.63 3.13 Search for helices and strands: 0 residues in 0 chains, 38246 seeds are put forward NCS extension: 0 residues added, 38246 seeds are put forward Round 1: 2308 peptides, 413 chains. Longest chain 14 peptides. Score 0.345 Round 2: 2586 peptides, 405 chains. Longest chain 29 peptides. Score 0.419 Round 3: 2691 peptides, 393 chains. Longest chain 21 peptides. Score 0.455 Round 4: 2721 peptides, 402 chains. Longest chain 23 peptides. Score 0.452 Round 5: 2670 peptides, 397 chains. Longest chain 20 peptides. Score 0.446 Taking the results from Round 3 Chains 398, Residues 2298, Estimated correctness of the model 0.0 % 7 chains (72 residues) have been docked in sequence ------------------------------------------------------ 63786 reflections ( 92.90 % complete ) and 9052 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1812 (Rfree = 0.000) for 37165 atoms. Found 204 (204 requested) and removed 137 (102 requested) atoms. Cycle 37: After refmac, R = 0.1806 (Rfree = 0.000) for 37232 atoms. Found 204 (204 requested) and removed 146 (102 requested) atoms. Cycle 38: After refmac, R = 0.1743 (Rfree = 0.000) for 37290 atoms. Found 205 (205 requested) and removed 158 (102 requested) atoms. Cycle 39: After refmac, R = 0.1259 (Rfree = 0.000) for 37337 atoms. Found 30 (205 requested) and removed 120 (102 requested) atoms. Cycle 40: After refmac, R = 0.1460 (Rfree = 0.000) for 37247 atoms. Found 181 (204 requested) and removed 135 (102 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.63 3.13 Search for helices and strands: 0 residues in 0 chains, 38521 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 38535 seeds are put forward Round 1: 2171 peptides, 417 chains. Longest chain 21 peptides. Score 0.306 Round 2: 2595 peptides, 422 chains. Longest chain 22 peptides. Score 0.404 Round 3: 2572 peptides, 396 chains. Longest chain 22 peptides. Score 0.425 Round 4: 2592 peptides, 390 chains. Longest chain 22 peptides. Score 0.436 Round 5: 2633 peptides, 391 chains. Longest chain 20 peptides. Score 0.444 Taking the results from Round 5 Chains 393, Residues 2242, Estimated correctness of the model 0.0 % 10 chains (77 residues) have been docked in sequence ------------------------------------------------------ 63786 reflections ( 92.90 % complete ) and 8861 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1838 (Rfree = 0.000) for 37165 atoms. Found 204 (204 requested) and removed 129 (102 requested) atoms. Cycle 42: After refmac, R = 0.1771 (Rfree = 0.000) for 37240 atoms. Found 204 (204 requested) and removed 149 (102 requested) atoms. Cycle 43: After refmac, R = 0.1734 (Rfree = 0.000) for 37295 atoms. Found 205 (205 requested) and removed 150 (102 requested) atoms. Cycle 44: After refmac, R = 0.1655 (Rfree = 0.000) for 37350 atoms. Found 205 (205 requested) and removed 151 (102 requested) atoms. Cycle 45: After refmac, R = 0.1226 (Rfree = 0.000) for 37404 atoms. Found 30 (205 requested) and removed 123 (102 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.64 3.14 Search for helices and strands: 0 residues in 0 chains, 38517 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 38530 seeds are put forward Round 1: 2091 peptides, 403 chains. Longest chain 15 peptides. Score 0.301 Round 2: 2474 peptides, 416 chains. Longest chain 19 peptides. Score 0.382 Round 3: 2479 peptides, 394 chains. Longest chain 19 peptides. Score 0.406 Round 4: 2476 peptides, 390 chains. Longest chain 19 peptides. Score 0.409 Round 5: 2491 peptides, 378 chains. Longest chain 29 peptides. Score 0.425 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 381, Residues 2113, Estimated correctness of the model 0.0 % 6 chains (53 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2pnk-3_warpNtrace.pdb as input Building loops using Loopy2018 381 chains (2113 residues) following loop building 6 chains (53 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 63786 reflections ( 92.90 % complete ) and 8294 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1756 (Rfree = 0.000) for 37165 atoms. Found 0 (204 requested) and removed 102 (102 requested) atoms. Cycle 47: After refmac, R = 0.1724 (Rfree = 0.000) for 37063 atoms. Found 0 (203 requested) and removed 101 (101 requested) atoms. Cycle 48: After refmac, R = 0.1660 (Rfree = 0.000) for 36962 atoms. Found 0 (203 requested) and removed 101 (101 requested) atoms. Cycle 49: After refmac, R = 0.1195 (Rfree = 0.000) for 36861 atoms. Found 0 (202 requested) and removed 101 (101 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 13:53:14 GMT 2018 Job finished. TimeTaking 372.82 Used memory is bytes: 19502256