null Mon 24 Dec 00:05:31 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 2aam-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2aam-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2aam-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aam-4.0-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/2aam-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aam-4.0-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 00:05:35 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/2aam-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aam-4.0-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 3639 and 0 Target number of residues in the AU: 3639 Target solvent content: 0.6468 Target number of residues exceeds 1700, conditional restraints are disabled Checking the provided sequence file Detected sequence length: 309 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1854 Adjusted target solvent content: 0.82 Input MTZ file: 2aam-4.0-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: 4 Cell parameters: 195.000 84.610 194.910 90.000 119.891 90.000 Input sequence file: 2aam-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 14832 target number of atoms Had to go as low as 1.50 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: 169.060 4.000 Wilson plot Bfac: 76.13 46619 reflections ( 98.70 % complete ) and 0 restraints for refining 20435 atoms. Observations/parameters ratio is 0.57 ------------------------------------------------------ Starting model: R = 0.3275 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3026 (Rfree = 0.000) for 20435 atoms. Found 97 (97 requested) and removed 93 (48 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.71 2.24 Search for helices and strands: 0 residues in 0 chains, 20719 seeds are put forward NCS extension: 0 residues added, 20719 seeds are put forward Round 1: 1133 peptides, 147 chains. Longest chain 35 peptides. Score 0.385 Round 2: 1202 peptides, 132 chains. Longest chain 25 peptides. Score 0.430 Round 3: 1210 peptides, 125 chains. Longest chain 33 peptides. Score 0.443 Round 4: 1226 peptides, 114 chains. Longest chain 39 peptides. Score 0.464 Round 5: 1158 peptides, 116 chains. Longest chain 27 peptides. Score 0.441 Taking the results from Round 4 Chains 120, Residues 1112, Estimated correctness of the model 0.0 % 7 chains (103 residues) have been docked in sequence ------------------------------------------------------ 46619 reflections ( 98.70 % complete ) and 4771 restraints for refining 16273 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2477 (Rfree = 0.000) for 16273 atoms. Found 77 (77 requested) and removed 53 (38 requested) atoms. Cycle 2: After refmac, R = 0.2347 (Rfree = 0.000) for 16297 atoms. Found 77 (77 requested) and removed 53 (38 requested) atoms. Cycle 3: After refmac, R = 0.2283 (Rfree = 0.000) for 16321 atoms. Found 77 (77 requested) and removed 75 (38 requested) atoms. Cycle 4: After refmac, R = 0.1897 (Rfree = 0.000) for 16323 atoms. Found 35 (77 requested) and removed 61 (38 requested) atoms. Cycle 5: After refmac, R = 0.1830 (Rfree = 0.000) for 16297 atoms. Found 22 (77 requested) and removed 64 (38 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.61 2.18 Search for helices and strands: 0 residues in 0 chains, 16729 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 16749 seeds are put forward Round 1: 1193 peptides, 126 chains. Longest chain 31 peptides. Score 0.436 Round 2: 1246 peptides, 121 chains. Longest chain 40 peptides. Score 0.459 Round 3: 1256 peptides, 119 chains. Longest chain 37 peptides. Score 0.465 Round 4: 1204 peptides, 106 chains. Longest chain 45 peptides. Score 0.469 Round 5: 1226 peptides, 108 chains. Longest chain 36 peptides. Score 0.473 Taking the results from Round 5 Chains 116, Residues 1118, Estimated correctness of the model 0.0 % 8 chains (146 residues) have been docked in sequence ------------------------------------------------------ 46619 reflections ( 98.70 % complete ) and 5065 restraints for refining 15865 atoms. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2368 (Rfree = 0.000) for 15865 atoms. Found 75 (75 requested) and removed 54 (37 requested) atoms. Cycle 7: After refmac, R = 0.2273 (Rfree = 0.000) for 15886 atoms. Found 75 (75 requested) and removed 48 (37 requested) atoms. Cycle 8: After refmac, R = 0.2263 (Rfree = 0.000) for 15913 atoms. Found 75 (75 requested) and removed 56 (37 requested) atoms. Cycle 9: After refmac, R = 0.2289 (Rfree = 0.000) for 15932 atoms. Found 75 (75 requested) and removed 74 (37 requested) atoms. Cycle 10: After refmac, R = 0.1959 (Rfree = 0.000) for 15933 atoms. Found 45 (75 requested) and removed 67 (37 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 2.13 Search for helices and strands: 0 residues in 0 chains, 16415 seeds are put forward NCS extension: 46 residues added (1 deleted due to clashes), 16461 seeds are put forward Round 1: 1178 peptides, 142 chains. Longest chain 26 peptides. Score 0.407 Round 2: 1230 peptides, 118 chains. Longest chain 36 peptides. Score 0.459 Round 3: 1225 peptides, 119 chains. Longest chain 38 peptides. Score 0.456 Round 4: 1248 peptides, 123 chains. Longest chain 38 peptides. Score 0.457 Round 5: 1219 peptides, 126 chains. Longest chain 36 peptides. Score 0.444 Taking the results from Round 2 Chains 125, Residues 1112, Estimated correctness of the model 0.0 % 8 chains (133 residues) have been docked in sequence ------------------------------------------------------ 46619 reflections ( 98.70 % complete ) and 4936 restraints for refining 15230 atoms. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2499 (Rfree = 0.000) for 15230 atoms. Found 72 (72 requested) and removed 49 (36 requested) atoms. Cycle 12: After refmac, R = 0.2408 (Rfree = 0.000) for 15253 atoms. Found 72 (72 requested) and removed 50 (36 requested) atoms. Cycle 13: After refmac, R = 0.2410 (Rfree = 0.000) for 15275 atoms. Found 72 (72 requested) and removed 59 (36 requested) atoms. Cycle 14: After refmac, R = 0.2424 (Rfree = 0.000) for 15288 atoms. Found 72 (72 requested) and removed 68 (36 requested) atoms. Cycle 15: After refmac, R = 0.2447 (Rfree = 0.000) for 15292 atoms. Found 72 (72 requested) and removed 71 (36 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 2.08 Search for helices and strands: 0 residues in 0 chains, 15839 seeds are put forward NCS extension: 47 residues added (4 deleted due to clashes), 15886 seeds are put forward Round 1: 1163 peptides, 147 chains. Longest chain 25 peptides. Score 0.395 Round 2: 1250 peptides, 140 chains. Longest chain 32 peptides. Score 0.432 Round 3: 1258 peptides, 128 chains. Longest chain 34 peptides. Score 0.452 Round 4: 1259 peptides, 134 chains. Longest chain 34 peptides. Score 0.444 Round 5: 1256 peptides, 133 chains. Longest chain 43 peptides. Score 0.444 Taking the results from Round 3 Chains 137, Residues 1130, Estimated correctness of the model 0.0 % 8 chains (88 residues) have been docked in sequence ------------------------------------------------------ 46619 reflections ( 98.70 % complete ) and 4714 restraints for refining 15137 atoms. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2530 (Rfree = 0.000) for 15137 atoms. Found 71 (71 requested) and removed 47 (35 requested) atoms. Cycle 17: After refmac, R = 0.2485 (Rfree = 0.000) for 15161 atoms. Found 72 (72 requested) and removed 57 (36 requested) atoms. Cycle 18: After refmac, R = 0.2130 (Rfree = 0.000) for 15176 atoms. Found 57 (72 requested) and removed 61 (36 requested) atoms. Cycle 19: After refmac, R = 0.2132 (Rfree = 0.000) for 15172 atoms. Found 35 (72 requested) and removed 62 (36 requested) atoms. Cycle 20: After refmac, R = 0.2093 (Rfree = 0.000) for 15145 atoms. Found 24 (71 requested) and removed 47 (35 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 2.06 Search for helices and strands: 0 residues in 0 chains, 15707 seeds are put forward NCS extension: 33 residues added (3 deleted due to clashes), 15740 seeds are put forward Round 1: 1156 peptides, 151 chains. Longest chain 29 peptides. Score 0.386 Round 2: 1228 peptides, 141 chains. Longest chain 27 peptides. Score 0.424 Round 3: 1263 peptides, 141 chains. Longest chain 33 peptides. Score 0.434 Round 4: 1246 peptides, 142 chains. Longest chain 25 peptides. Score 0.428 Round 5: 1220 peptides, 137 chains. Longest chain 30 peptides. Score 0.427 Taking the results from Round 3 Chains 150, Residues 1122, Estimated correctness of the model 0.0 % 9 chains (118 residues) have been docked in sequence ------------------------------------------------------ 46619 reflections ( 98.70 % complete ) and 4890 restraints for refining 15314 atoms. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2607 (Rfree = 0.000) for 15314 atoms. Found 72 (72 requested) and removed 47 (36 requested) atoms. Cycle 22: After refmac, R = 0.2585 (Rfree = 0.000) for 15339 atoms. Found 72 (72 requested) and removed 49 (36 requested) atoms. Cycle 23: After refmac, R = 0.2533 (Rfree = 0.000) for 15362 atoms. Found 72 (72 requested) and removed 48 (36 requested) atoms. Cycle 24: After refmac, R = 0.2482 (Rfree = 0.000) for 15386 atoms. Found 73 (73 requested) and removed 58 (36 requested) atoms. Cycle 25: After refmac, R = 0.2548 (Rfree = 0.000) for 15401 atoms. Found 73 (73 requested) and removed 62 (36 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 2.08 Search for helices and strands: 0 residues in 0 chains, 16005 seeds are put forward NCS extension: 42 residues added (0 deleted due to clashes), 16047 seeds are put forward Round 1: 1133 peptides, 157 chains. Longest chain 23 peptides. Score 0.369 Round 2: 1244 peptides, 144 chains. Longest chain 31 peptides. Score 0.424 Round 3: 1212 peptides, 135 chains. Longest chain 28 peptides. Score 0.428 Round 4: 1247 peptides, 155 chains. Longest chain 28 peptides. Score 0.409 Round 5: 1227 peptides, 139 chains. Longest chain 29 peptides. Score 0.427 Taking the results from Round 3 Chains 139, Residues 1077, Estimated correctness of the model 0.0 % 5 chains (58 residues) have been docked in sequence ------------------------------------------------------ 46619 reflections ( 98.70 % complete ) and 4465 restraints for refining 15298 atoms. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2539 (Rfree = 0.000) for 15298 atoms. Found 72 (72 requested) and removed 42 (36 requested) atoms. Cycle 27: After refmac, R = 0.2598 (Rfree = 0.000) for 15328 atoms. Found 72 (72 requested) and removed 49 (36 requested) atoms. Cycle 28: After refmac, R = 0.2507 (Rfree = 0.000) for 15351 atoms. Found 72 (72 requested) and removed 55 (36 requested) atoms. Cycle 29: After refmac, R = 0.2586 (Rfree = 0.000) for 15368 atoms. Found 73 (73 requested) and removed 75 (36 requested) atoms. Cycle 30: After refmac, R = 0.2486 (Rfree = 0.000) for 15366 atoms. Found 73 (73 requested) and removed 54 (36 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.50 2.11 Search for helices and strands: 0 residues in 0 chains, 16007 seeds are put forward NCS extension: 32 residues added (2 deleted due to clashes), 16039 seeds are put forward Round 1: 1072 peptides, 151 chains. Longest chain 25 peptides. Score 0.359 Round 2: 1157 peptides, 139 chains. Longest chain 30 peptides. Score 0.405 Round 3: 1201 peptides, 142 chains. Longest chain 25 peptides. Score 0.414 Round 4: 1166 peptides, 135 chains. Longest chain 34 peptides. Score 0.414 Round 5: 1179 peptides, 140 chains. Longest chain 35 peptides. Score 0.410 Taking the results from Round 4 Chains 137, Residues 1031, Estimated correctness of the model 0.0 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 46619 reflections ( 98.70 % complete ) and 4117 restraints for refining 15299 atoms. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2583 (Rfree = 0.000) for 15299 atoms. Found 72 (72 requested) and removed 45 (36 requested) atoms. Cycle 32: After refmac, R = 0.2530 (Rfree = 0.000) for 15326 atoms. Found 72 (72 requested) and removed 65 (36 requested) atoms. Cycle 33: After refmac, R = 0.2482 (Rfree = 0.000) for 15333 atoms. Found 72 (72 requested) and removed 51 (36 requested) atoms. Cycle 34: After refmac, R = 0.2455 (Rfree = 0.000) for 15354 atoms. Found 72 (72 requested) and removed 61 (36 requested) atoms. Cycle 35: After refmac, R = 0.2068 (Rfree = 0.000) for 15365 atoms. Found 38 (73 requested) and removed 48 (36 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.46 2.09 Search for helices and strands: 0 residues in 0 chains, 15849 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 15872 seeds are put forward Round 1: 1099 peptides, 163 chains. Longest chain 21 peptides. Score 0.348 Round 2: 1180 peptides, 154 chains. Longest chain 28 peptides. Score 0.389 Round 3: 1180 peptides, 152 chains. Longest chain 30 peptides. Score 0.392 Round 4: 1168 peptides, 143 chains. Longest chain 29 peptides. Score 0.402 Round 5: 1197 peptides, 139 chains. Longest chain 32 peptides. Score 0.417 Taking the results from Round 5 Chains 142, Residues 1058, Estimated correctness of the model 0.0 % 4 chains (79 residues) have been docked in sequence ------------------------------------------------------ 46619 reflections ( 98.70 % complete ) and 4460 restraints for refining 15399 atoms. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2716 (Rfree = 0.000) for 15399 atoms. Found 73 (73 requested) and removed 54 (36 requested) atoms. Cycle 37: After refmac, R = 0.2567 (Rfree = 0.000) for 15418 atoms. Found 73 (73 requested) and removed 50 (36 requested) atoms. Cycle 38: After refmac, R = 0.2643 (Rfree = 0.000) for 15441 atoms. Found 73 (73 requested) and removed 70 (36 requested) atoms. Cycle 39: After refmac, R = 0.2521 (Rfree = 0.000) for 15444 atoms. Found 73 (73 requested) and removed 50 (36 requested) atoms. Cycle 40: After refmac, R = 0.2200 (Rfree = 0.000) for 15467 atoms. Found 43 (73 requested) and removed 54 (36 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.47 2.09 Search for helices and strands: 0 residues in 0 chains, 15971 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 15994 seeds are put forward Round 1: 1066 peptides, 163 chains. Longest chain 22 peptides. Score 0.337 Round 2: 1127 peptides, 148 chains. Longest chain 30 peptides. Score 0.381 Round 3: 1170 peptides, 147 chains. Longest chain 32 peptides. Score 0.397 Round 4: 1171 peptides, 141 chains. Longest chain 29 peptides. Score 0.406 Round 5: 1159 peptides, 138 chains. Longest chain 30 peptides. Score 0.407 Taking the results from Round 5 Chains 142, Residues 1021, Estimated correctness of the model 0.0 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 46619 reflections ( 98.70 % complete ) and 4119 restraints for refining 15326 atoms. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2712 (Rfree = 0.000) for 15326 atoms. Found 72 (72 requested) and removed 44 (36 requested) atoms. Cycle 42: After refmac, R = 0.2565 (Rfree = 0.000) for 15354 atoms. Found 72 (72 requested) and removed 44 (36 requested) atoms. Cycle 43: After refmac, R = 0.2539 (Rfree = 0.000) for 15382 atoms. Found 73 (73 requested) and removed 53 (36 requested) atoms. Cycle 44: After refmac, R = 0.2498 (Rfree = 0.000) for 15402 atoms. Found 73 (73 requested) and removed 55 (36 requested) atoms. Cycle 45: After refmac, R = 0.2507 (Rfree = 0.000) for 15420 atoms. Found 73 (73 requested) and removed 75 (36 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.50 2.11 Search for helices and strands: 0 residues in 0 chains, 15986 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 16001 seeds are put forward Round 1: 999 peptides, 157 chains. Longest chain 16 peptides. Score 0.323 Round 2: 1110 peptides, 146 chains. Longest chain 24 peptides. Score 0.379 Round 3: 1117 peptides, 148 chains. Longest chain 26 peptides. Score 0.378 Round 4: 1134 peptides, 145 chains. Longest chain 30 peptides. Score 0.388 Round 5: 1136 peptides, 145 chains. Longest chain 25 peptides. Score 0.389 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 145, Residues 991, 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 2aam-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 46619 reflections ( 98.70 % complete ) and 3819 restraints for refining 14686 atoms. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2658 (Rfree = 0.000) for 14686 atoms. Found 0 (69 requested) and removed 34 (34 requested) atoms. Cycle 47: After refmac, R = 0.2484 (Rfree = 0.000) for 14652 atoms. Found 0 (69 requested) and removed 34 (34 requested) atoms. Cycle 48: After refmac, R = 0.2510 (Rfree = 0.000) for 14618 atoms. Found 0 (69 requested) and removed 34 (34 requested) atoms. Cycle 49: After refmac, R = 0.2429 (Rfree = 0.000) for 14584 atoms. Found 0 (69 requested) and removed 34 (34 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 03:21:39 GMT 2018 Job finished. TimeTaking 196.13 Used memory is bytes: 19392776