Sun 23 Dec 22:23:10 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 2aam-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2aam-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2aam-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aam-3.2-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/2aam-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aam-3.2-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 22:23:18 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/2aam-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aam-3.2-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 4070 and 0 Target number of residues in the AU: 4070 Target solvent content: 0.6050 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-3.2-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: 4 Cell parameters: 195.000 84.610 194.910 90.000 119.891 90.000 Input sequence file: 2aam-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 14832 target number of atoms Had to go as low as 1.45 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 3.200 Wilson plot Bfac: 54.68 90855 reflections ( 99.15 % complete ) and 0 restraints for refining 16318 atoms. Observations/parameters ratio is 1.39 ------------------------------------------------------ Starting model: R = 0.3407 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2584 (Rfree = 0.000) for 16318 atoms. Found 146 (146 requested) and removed 124 (73 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.06 1.85 Search for helices and strands: 0 residues in 0 chains, 16730 seeds are put forward NCS extension: 0 residues added, 16730 seeds are put forward Round 1: 1424 peptides, 155 chains. Longest chain 31 peptides. Score 0.461 Round 2: 1408 peptides, 154 chains. Longest chain 27 peptides. Score 0.458 Round 3: 1406 peptides, 152 chains. Longest chain 31 peptides. Score 0.460 Round 4: 1441 peptides, 161 chains. Longest chain 27 peptides. Score 0.458 Round 5: 1410 peptides, 145 chains. Longest chain 34 peptides. Score 0.471 Taking the results from Round 5 Chains 155, Residues 1265, Estimated correctness of the model 1.7 % 15 chains (234 residues) have been docked in sequence ------------------------------------------------------ 90855 reflections ( 99.15 % complete ) and 5986 restraints for refining 15414 atoms. Observations/parameters ratio is 1.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2604 (Rfree = 0.000) for 15414 atoms. Found 138 (138 requested) and removed 82 (69 requested) atoms. Cycle 2: After refmac, R = 0.2425 (Rfree = 0.000) for 15470 atoms. Found 138 (138 requested) and removed 71 (69 requested) atoms. Cycle 3: After refmac, R = 0.2337 (Rfree = 0.000) for 15537 atoms. Found 80 (139 requested) and removed 76 (69 requested) atoms. Cycle 4: After refmac, R = 0.2295 (Rfree = 0.000) for 15541 atoms. Found 60 (139 requested) and removed 72 (69 requested) atoms. Cycle 5: After refmac, R = 0.2276 (Rfree = 0.000) for 15529 atoms. Found 65 (139 requested) and removed 73 (69 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.05 1.84 Search for helices and strands: 0 residues in 0 chains, 16027 seeds are put forward NCS extension: 15 residues added (14 deleted due to clashes), 16042 seeds are put forward Round 1: 1382 peptides, 141 chains. Longest chain 38 peptides. Score 0.469 Round 2: 1399 peptides, 141 chains. Longest chain 42 peptides. Score 0.474 Round 3: 1405 peptides, 148 chains. Longest chain 32 peptides. Score 0.466 Round 4: 1415 peptides, 145 chains. Longest chain 40 peptides. Score 0.473 Round 5: 1419 peptides, 150 chains. Longest chain 41 peptides. Score 0.467 Taking the results from Round 2 Chains 153, Residues 1258, Estimated correctness of the model 2.7 % 17 chains (262 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 90855 reflections ( 99.15 % complete ) and 6047 restraints for refining 15350 atoms. Observations/parameters ratio is 1.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2418 (Rfree = 0.000) for 15350 atoms. Found 137 (137 requested) and removed 78 (68 requested) atoms. Cycle 7: After refmac, R = 0.2292 (Rfree = 0.000) for 15409 atoms. Found 117 (138 requested) and removed 73 (69 requested) atoms. Cycle 8: After refmac, R = 0.2240 (Rfree = 0.000) for 15453 atoms. Found 70 (138 requested) and removed 74 (69 requested) atoms. Cycle 9: After refmac, R = 0.2211 (Rfree = 0.000) for 15449 atoms. Found 69 (138 requested) and removed 71 (69 requested) atoms. Cycle 10: After refmac, R = 0.2170 (Rfree = 0.000) for 15447 atoms. Found 67 (138 requested) and removed 73 (69 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.03 1.83 Search for helices and strands: 0 residues in 0 chains, 15822 seeds are put forward NCS extension: 18 residues added (8 deleted due to clashes), 15840 seeds are put forward Round 1: 1433 peptides, 144 chains. Longest chain 51 peptides. Score 0.479 Round 2: 1416 peptides, 151 chains. Longest chain 39 peptides. Score 0.464 Round 3: 1403 peptides, 148 chains. Longest chain 32 peptides. Score 0.465 Round 4: 1437 peptides, 146 chains. Longest chain 35 peptides. Score 0.477 Round 5: 1404 peptides, 153 chains. Longest chain 34 peptides. Score 0.458 Taking the results from Round 1 Chains 154, Residues 1289, Estimated correctness of the model 4.4 % 19 chains (324 residues) have been docked in sequence ------------------------------------------------------ 90855 reflections ( 99.15 % complete ) and 6628 restraints for refining 15674 atoms. Observations/parameters ratio is 1.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2318 (Rfree = 0.000) for 15674 atoms. Found 140 (140 requested) and removed 93 (70 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2191 (Rfree = 0.000) for 15721 atoms. Found 96 (141 requested) and removed 75 (70 requested) atoms. Cycle 13: After refmac, R = 0.2139 (Rfree = 0.000) for 15742 atoms. Found 61 (141 requested) and removed 74 (70 requested) atoms. Cycle 14: After refmac, R = 0.2118 (Rfree = 0.000) for 15729 atoms. Found 52 (141 requested) and removed 71 (70 requested) atoms. Cycle 15: After refmac, R = 0.2110 (Rfree = 0.000) for 15710 atoms. Found 67 (140 requested) and removed 77 (70 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.04 1.83 Search for helices and strands: 0 residues in 0 chains, 16160 seeds are put forward NCS extension: 16 residues added (13 deleted due to clashes), 16176 seeds are put forward Round 1: 1412 peptides, 156 chains. Longest chain 46 peptides. Score 0.456 Round 2: 1450 peptides, 157 chains. Longest chain 34 peptides. Score 0.466 Round 3: 1430 peptides, 146 chains. Longest chain 36 peptides. Score 0.475 Round 4: 1454 peptides, 154 chains. Longest chain 33 peptides. Score 0.471 Round 5: 1436 peptides, 150 chains. Longest chain 27 peptides. Score 0.471 Taking the results from Round 3 Chains 153, Residues 1284, Estimated correctness of the model 3.1 % 15 chains (221 residues) have been docked in sequence ------------------------------------------------------ 90855 reflections ( 99.15 % complete ) and 5975 restraints for refining 15952 atoms. Observations/parameters ratio is 1.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2346 (Rfree = 0.000) for 15952 atoms. Found 143 (143 requested) and removed 78 (71 requested) atoms. Cycle 17: After refmac, R = 0.2184 (Rfree = 0.000) for 16017 atoms. Found 133 (143 requested) and removed 73 (71 requested) atoms. Cycle 18: After refmac, R = 0.2142 (Rfree = 0.000) for 16077 atoms. Found 82 (144 requested) and removed 81 (72 requested) atoms. Cycle 19: After refmac, R = 0.2116 (Rfree = 0.000) for 16078 atoms. Found 77 (144 requested) and removed 76 (72 requested) atoms. Cycle 20: After refmac, R = 0.2099 (Rfree = 0.000) for 16079 atoms. Found 63 (144 requested) and removed 85 (72 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.03 1.83 Search for helices and strands: 0 residues in 0 chains, 16523 seeds are put forward NCS extension: 19 residues added (14 deleted due to clashes), 16542 seeds are put forward Round 1: 1424 peptides, 146 chains. Longest chain 39 peptides. Score 0.474 Round 2: 1447 peptides, 131 chains. Longest chain 40 peptides. Score 0.501 Round 3: 1435 peptides, 130 chains. Longest chain 42 peptides. Score 0.499 Round 4: 1435 peptides, 136 chains. Longest chain 42 peptides. Score 0.491 Round 5: 1404 peptides, 139 chains. Longest chain 51 peptides. Score 0.478 Taking the results from Round 2 Chains 148, Residues 1316, Estimated correctness of the model 11.7 % 15 chains (299 residues) have been docked in sequence ------------------------------------------------------ 90855 reflections ( 99.15 % complete ) and 6453 restraints for refining 16065 atoms. Observations/parameters ratio is 1.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2332 (Rfree = 0.000) for 16065 atoms. Found 144 (144 requested) and removed 84 (72 requested) atoms. Cycle 22: After refmac, R = 0.2210 (Rfree = 0.000) for 16125 atoms. Found 101 (144 requested) and removed 74 (72 requested) atoms. Cycle 23: After refmac, R = 0.2168 (Rfree = 0.000) for 16152 atoms. Found 65 (144 requested) and removed 74 (72 requested) atoms. Cycle 24: After refmac, R = 0.2154 (Rfree = 0.000) for 16143 atoms. Found 76 (144 requested) and removed 75 (72 requested) atoms. Cycle 25: After refmac, R = 0.2147 (Rfree = 0.000) for 16144 atoms. Found 66 (144 requested) and removed 79 (72 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.03 1.83 Search for helices and strands: 0 residues in 0 chains, 16586 seeds are put forward NCS extension: 21 residues added (16 deleted due to clashes), 16607 seeds are put forward Round 1: 1422 peptides, 132 chains. Longest chain 43 peptides. Score 0.493 Round 2: 1473 peptides, 137 chains. Longest chain 48 peptides. Score 0.500 Round 3: 1482 peptides, 135 chains. Longest chain 45 peptides. Score 0.505 Round 4: 1451 peptides, 127 chains. Longest chain 54 peptides. Score 0.507 Round 5: 1449 peptides, 127 chains. Longest chain 51 peptides. Score 0.507 Taking the results from Round 5 Chains 138, Residues 1322, Estimated correctness of the model 13.6 % 15 chains (293 residues) have been docked in sequence ------------------------------------------------------ 90855 reflections ( 99.15 % complete ) and 6470 restraints for refining 16221 atoms. Observations/parameters ratio is 1.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2377 (Rfree = 0.000) for 16221 atoms. Found 145 (145 requested) and removed 82 (72 requested) atoms. Cycle 27: After refmac, R = 0.2248 (Rfree = 0.000) for 16284 atoms. Found 101 (146 requested) and removed 75 (73 requested) atoms. Cycle 28: After refmac, R = 0.2189 (Rfree = 0.000) for 16310 atoms. Found 37 (146 requested) and removed 76 (73 requested) atoms. Cycle 29: After refmac, R = 0.2171 (Rfree = 0.000) for 16271 atoms. Found 28 (146 requested) and removed 76 (73 requested) atoms. Cycle 30: After refmac, R = 0.2165 (Rfree = 0.000) for 16223 atoms. Found 42 (145 requested) and removed 75 (72 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.02 1.82 Search for helices and strands: 0 residues in 0 chains, 16688 seeds are put forward NCS extension: 31 residues added (5 deleted due to clashes), 16719 seeds are put forward Round 1: 1432 peptides, 153 chains. Longest chain 33 peptides. Score 0.466 Round 2: 1447 peptides, 137 chains. Longest chain 38 peptides. Score 0.492 Round 3: 1463 peptides, 147 chains. Longest chain 51 peptides. Score 0.483 Round 4: 1470 peptides, 144 chains. Longest chain 45 peptides. Score 0.489 Round 5: 1447 peptides, 150 chains. Longest chain 42 peptides. Score 0.475 Taking the results from Round 2 Chains 148, Residues 1310, Estimated correctness of the model 8.7 % 22 chains (370 residues) have been docked in sequence ------------------------------------------------------ 90855 reflections ( 99.15 % complete ) and 6852 restraints for refining 16351 atoms. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2403 (Rfree = 0.000) for 16351 atoms. Found 146 (146 requested) and removed 98 (73 requested) atoms. Cycle 32: After refmac, R = 0.2273 (Rfree = 0.000) for 16399 atoms. Found 110 (147 requested) and removed 80 (73 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2220 (Rfree = 0.000) for 16429 atoms. Found 45 (147 requested) and removed 77 (73 requested) atoms. Cycle 34: After refmac, R = 0.2199 (Rfree = 0.000) for 16397 atoms. Found 48 (147 requested) and removed 74 (73 requested) atoms. Cycle 35: After refmac, R = 0.2178 (Rfree = 0.000) for 16371 atoms. Found 39 (146 requested) and removed 77 (73 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.01 1.82 Search for helices and strands: 0 residues in 0 chains, 16756 seeds are put forward NCS extension: 25 residues added (13 deleted due to clashes), 16781 seeds are put forward Round 1: 1388 peptides, 151 chains. Longest chain 33 peptides. Score 0.456 Round 2: 1457 peptides, 131 chains. Longest chain 51 peptides. Score 0.503 Round 3: 1437 peptides, 132 chains. Longest chain 38 peptides. Score 0.497 Round 4: 1423 peptides, 140 chains. Longest chain 33 peptides. Score 0.482 Round 5: 1437 peptides, 133 chains. Longest chain 50 peptides. Score 0.495 Taking the results from Round 2 Chains 149, Residues 1326, Estimated correctness of the model 12.3 % 19 chains (380 residues) have been docked in sequence ------------------------------------------------------ 90855 reflections ( 99.15 % complete ) and 6938 restraints for refining 16441 atoms. Observations/parameters ratio is 1.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2389 (Rfree = 0.000) for 16441 atoms. Found 147 (147 requested) and removed 102 (73 requested) atoms. Cycle 37: After refmac, R = 0.2245 (Rfree = 0.000) for 16486 atoms. Found 116 (147 requested) and removed 82 (73 requested) atoms. Cycle 38: After refmac, R = 0.2197 (Rfree = 0.000) for 16520 atoms. Found 59 (148 requested) and removed 77 (74 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2165 (Rfree = 0.000) for 16502 atoms. Found 52 (148 requested) and removed 77 (74 requested) atoms. Cycle 40: After refmac, R = 0.2168 (Rfree = 0.000) for 16477 atoms. Found 55 (147 requested) and removed 76 (73 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.01 1.82 Search for helices and strands: 0 residues in 0 chains, 16877 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 16897 seeds are put forward Round 1: 1377 peptides, 148 chains. Longest chain 46 peptides. Score 0.458 Round 2: 1449 peptides, 144 chains. Longest chain 37 peptides. Score 0.483 Round 3: 1448 peptides, 139 chains. Longest chain 49 peptides. Score 0.490 Round 4: 1446 peptides, 136 chains. Longest chain 35 peptides. Score 0.494 Round 5: 1424 peptides, 142 chains. Longest chain 46 peptides. Score 0.479 Taking the results from Round 4 Chains 149, Residues 1310, Estimated correctness of the model 9.4 % 17 chains (318 residues) have been docked in sequence ------------------------------------------------------ 90855 reflections ( 99.15 % complete ) and 6538 restraints for refining 16334 atoms. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2398 (Rfree = 0.000) for 16334 atoms. Found 146 (146 requested) and removed 93 (73 requested) atoms. Cycle 42: After refmac, R = 0.2243 (Rfree = 0.000) for 16387 atoms. Found 147 (147 requested) and removed 74 (73 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2176 (Rfree = 0.000) for 16460 atoms. Found 62 (147 requested) and removed 77 (73 requested) atoms. Cycle 44: After refmac, R = 0.2163 (Rfree = 0.000) for 16445 atoms. Found 59 (147 requested) and removed 74 (73 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.2138 (Rfree = 0.000) for 16430 atoms. Found 56 (147 requested) and removed 79 (73 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.00 1.81 Search for helices and strands: 0 residues in 0 chains, 16822 seeds are put forward NCS extension: 26 residues added (8 deleted due to clashes), 16848 seeds are put forward Round 1: 1320 peptides, 147 chains. Longest chain 36 peptides. Score 0.442 Round 2: 1391 peptides, 137 chains. Longest chain 36 peptides. Score 0.477 Round 3: 1433 peptides, 141 chains. Longest chain 58 peptides. Score 0.483 Round 4: 1439 peptides, 131 chains. Longest chain 44 peptides. Score 0.499 Round 5: 1397 peptides, 135 chains. Longest chain 41 peptides. Score 0.482 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 148, Residues 1308, Estimated correctness of the model 11.0 % 25 chains (479 residues) have been docked in sequence Sequence coverage is 36 % Consider running further cycles of model building using 2aam-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 145 A and 156 A Built loop between residues 186 F and 191 F 144 chains (1307 residues) following loop building 23 chains (493 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 90855 reflections ( 99.15 % complete ) and 7215 restraints for refining 16385 atoms. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2432 (Rfree = 0.000) for 16385 atoms. Found 0 (147 requested) and removed 37 (73 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2310 (Rfree = 0.000) for 16348 atoms. Found 0 (146 requested) and removed 30 (73 requested) atoms. Cycle 48: After refmac, R = 0.2275 (Rfree = 0.000) for 16318 atoms. Found 0 (146 requested) and removed 14 (73 requested) atoms. Cycle 49: After refmac, R = 0.2249 (Rfree = 0.000) for 16304 atoms. TimeTaking 236.83