null Sun 23 Dec 23:59:04 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 2aam-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2aam-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2aam-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aam-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/2aam-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aam-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 ============================================================ Sun 23 Dec 23:59:08 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-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aam-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 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-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-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 14832 target number of atoms Had to go as low as 1.40 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 16592 atoms. Observations/parameters ratio is 1.37 ------------------------------------------------------ Starting model: R = 0.3323 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2600 (Rfree = 0.000) for 16592 atoms. Found 148 (148 requested) and removed 124 (74 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.03 1.83 Search for helices and strands: 0 residues in 0 chains, 17005 seeds are put forward NCS extension: 0 residues added, 17005 seeds are put forward Round 1: 1403 peptides, 162 chains. Longest chain 25 peptides. Score 0.445 Round 2: 1431 peptides, 157 chains. Longest chain 30 peptides. Score 0.460 Round 3: 1417 peptides, 149 chains. Longest chain 27 peptides. Score 0.467 Round 4: 1437 peptides, 166 chains. Longest chain 32 peptides. Score 0.449 Round 5: 1439 peptides, 152 chains. Longest chain 30 peptides. Score 0.470 Taking the results from Round 5 Chains 161, Residues 1287, Estimated correctness of the model 1.4 % 16 chains (232 residues) have been docked in sequence ------------------------------------------------------ 90855 reflections ( 99.15 % complete ) and 6027 restraints for refining 15405 atoms. Observations/parameters ratio is 1.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2577 (Rfree = 0.000) for 15405 atoms. Found 138 (138 requested) and removed 83 (69 requested) atoms. Cycle 2: After refmac, R = 0.2401 (Rfree = 0.000) for 15460 atoms. Found 138 (138 requested) and removed 71 (69 requested) atoms. Cycle 3: After refmac, R = 0.2317 (Rfree = 0.000) for 15527 atoms. Found 92 (139 requested) and removed 71 (69 requested) atoms. Cycle 4: After refmac, R = 0.2270 (Rfree = 0.000) for 15548 atoms. Found 54 (139 requested) and removed 74 (69 requested) atoms. Cycle 5: After refmac, R = 0.2259 (Rfree = 0.000) for 15528 atoms. Found 66 (139 requested) and removed 73 (69 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.06 1.85 Search for helices and strands: 0 residues in 0 chains, 15973 seeds are put forward NCS extension: 12 residues added (18 deleted due to clashes), 15985 seeds are put forward Round 1: 1446 peptides, 131 chains. Longest chain 38 peptides. Score 0.500 Round 2: 1433 peptides, 141 chains. Longest chain 35 peptides. Score 0.483 Round 3: 1452 peptides, 145 chains. Longest chain 37 peptides. Score 0.483 Round 4: 1464 peptides, 139 chains. Longest chain 38 peptides. Score 0.494 Round 5: 1457 peptides, 141 chains. Longest chain 35 peptides. Score 0.490 Taking the results from Round 1 Chains 147, Residues 1315, Estimated correctness of the model 11.3 % 25 chains (456 residues) have been docked in sequence ------------------------------------------------------ 90855 reflections ( 99.15 % complete ) and 7108 restraints for refining 15609 atoms. Observations/parameters ratio is 1.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2449 (Rfree = 0.000) for 15609 atoms. Found 140 (140 requested) and removed 112 (70 requested) atoms. Cycle 7: After refmac, R = 0.2293 (Rfree = 0.000) for 15637 atoms. Found 113 (140 requested) and removed 77 (70 requested) atoms. Cycle 8: After refmac, R = 0.2230 (Rfree = 0.000) for 15673 atoms. Found 45 (140 requested) and removed 77 (70 requested) atoms. Cycle 9: After refmac, R = 0.2200 (Rfree = 0.000) for 15641 atoms. Found 38 (140 requested) and removed 70 (70 requested) atoms. Cycle 10: After refmac, R = 0.2187 (Rfree = 0.000) for 15609 atoms. Found 42 (140 requested) and removed 71 (70 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.03 1.83 Search for helices and strands: 0 residues in 0 chains, 16067 seeds are put forward NCS extension: 17 residues added (9 deleted due to clashes), 16084 seeds are put forward Round 1: 1452 peptides, 135 chains. Longest chain 50 peptides. Score 0.497 Round 2: 1458 peptides, 138 chains. Longest chain 43 peptides. Score 0.494 Round 3: 1466 peptides, 138 chains. Longest chain 42 peptides. Score 0.496 Round 4: 1483 peptides, 134 chains. Longest chain 59 peptides. Score 0.506 Round 5: 1475 peptides, 133 chains. Longest chain 40 peptides. Score 0.505 Taking the results from Round 4 Chains 149, Residues 1349, Estimated correctness of the model 13.3 % 26 chains (495 residues) have been docked in sequence ------------------------------------------------------ 90855 reflections ( 99.15 % complete ) and 7541 restraints for refining 16053 atoms. Observations/parameters ratio is 1.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2453 (Rfree = 0.000) for 16053 atoms. Found 144 (144 requested) and removed 88 (72 requested) atoms. Cycle 12: After refmac, R = 0.2258 (Rfree = 0.000) for 16109 atoms. Found 121 (144 requested) and removed 77 (72 requested) atoms. Cycle 13: After refmac, R = 0.2178 (Rfree = 0.000) for 16153 atoms. Found 54 (144 requested) and removed 76 (72 requested) atoms. Cycle 14: After refmac, R = 0.2144 (Rfree = 0.000) for 16131 atoms. Found 42 (144 requested) and removed 74 (72 requested) atoms. Cycle 15: After refmac, R = 0.2131 (Rfree = 0.000) for 16099 atoms. Found 50 (144 requested) and removed 76 (72 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.04 1.83 Search for helices and strands: 0 residues in 0 chains, 16573 seeds are put forward NCS extension: 21 residues added (22 deleted due to clashes), 16594 seeds are put forward Round 1: 1478 peptides, 124 chains. Longest chain 55 peptides. Score 0.518 Round 2: 1491 peptides, 122 chains. Longest chain 54 peptides. Score 0.525 Round 3: 1497 peptides, 138 chains. Longest chain 48 peptides. Score 0.505 Round 4: 1437 peptides, 144 chains. Longest chain 51 peptides. Score 0.480 Round 5: 1518 peptides, 133 chains. Longest chain 50 peptides. Score 0.517 Taking the results from Round 2 Chains 139, Residues 1369, Estimated correctness of the model 19.3 % 26 chains (531 residues) have been docked in sequence ------------------------------------------------------ 90855 reflections ( 99.15 % complete ) and 7756 restraints for refining 16216 atoms. Observations/parameters ratio is 1.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2374 (Rfree = 0.000) for 16216 atoms. Found 145 (145 requested) and removed 101 (72 requested) atoms. Cycle 17: After refmac, R = 0.2226 (Rfree = 0.000) for 16260 atoms. Found 124 (145 requested) and removed 79 (72 requested) atoms. Cycle 18: After refmac, R = 0.2151 (Rfree = 0.000) for 16305 atoms. Found 45 (146 requested) and removed 77 (73 requested) atoms. Cycle 19: After refmac, R = 0.2103 (Rfree = 0.000) for 16273 atoms. Found 37 (146 requested) and removed 75 (73 requested) atoms. Cycle 20: After refmac, R = 0.2074 (Rfree = 0.000) for 16235 atoms. Found 31 (145 requested) and removed 74 (72 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.03 1.83 Search for helices and strands: 0 residues in 0 chains, 16609 seeds are put forward NCS extension: 12 residues added (35 deleted due to clashes), 16621 seeds are put forward Round 1: 1462 peptides, 141 chains. Longest chain 47 peptides. Score 0.491 Round 2: 1501 peptides, 132 chains. Longest chain 59 peptides. Score 0.514 Round 3: 1482 peptides, 131 chains. Longest chain 56 peptides. Score 0.510 Round 4: 1481 peptides, 129 chains. Longest chain 85 peptides. Score 0.513 Round 5: 1479 peptides, 125 chains. Longest chain 51 peptides. Score 0.517 Taking the results from Round 5 Chains 151, Residues 1354, Estimated correctness of the model 16.8 % 27 chains (516 residues) have been docked in sequence ------------------------------------------------------ 90855 reflections ( 99.15 % complete ) and 7705 restraints for refining 16398 atoms. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2443 (Rfree = 0.000) for 16398 atoms. Found 147 (147 requested) and removed 96 (73 requested) atoms. Cycle 22: After refmac, R = 0.2265 (Rfree = 0.000) for 16449 atoms. Found 128 (147 requested) and removed 79 (73 requested) atoms. Cycle 23: After refmac, R = 0.2181 (Rfree = 0.000) for 16498 atoms. Found 58 (148 requested) and removed 75 (74 requested) atoms. Cycle 24: After refmac, R = 0.2152 (Rfree = 0.000) for 16481 atoms. Found 42 (147 requested) and removed 74 (73 requested) atoms. Cycle 25: After refmac, R = 0.2120 (Rfree = 0.000) for 16449 atoms. Found 33 (147 requested) and removed 75 (73 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.02 1.82 Search for helices and strands: 0 residues in 0 chains, 16873 seeds are put forward NCS extension: 44 residues added (13 deleted due to clashes), 16917 seeds are put forward Round 1: 1431 peptides, 136 chains. Longest chain 49 peptides. Score 0.489 Round 2: 1473 peptides, 130 chains. Longest chain 51 peptides. Score 0.509 Round 3: 1485 peptides, 127 chains. Longest chain 68 peptides. Score 0.516 Round 4: 1441 peptides, 122 chains. Longest chain 37 peptides. Score 0.511 Round 5: 1486 peptides, 132 chains. Longest chain 48 peptides. Score 0.510 Taking the results from Round 3 Chains 138, Residues 1358, Estimated correctness of the model 16.5 % 17 chains (435 residues) have been docked in sequence ------------------------------------------------------ 90855 reflections ( 99.15 % complete ) and 7380 restraints for refining 16325 atoms. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2414 (Rfree = 0.000) for 16325 atoms. Found 146 (146 requested) and removed 98 (73 requested) atoms. Cycle 27: After refmac, R = 0.2226 (Rfree = 0.000) for 16373 atoms. Found 104 (146 requested) and removed 80 (73 requested) atoms. Cycle 28: After refmac, R = 0.2149 (Rfree = 0.000) for 16397 atoms. Found 56 (147 requested) and removed 78 (73 requested) atoms. Cycle 29: After refmac, R = 0.2109 (Rfree = 0.000) for 16375 atoms. Found 40 (146 requested) and removed 76 (73 requested) atoms. Cycle 30: After refmac, R = 0.2076 (Rfree = 0.000) for 16339 atoms. Found 29 (146 requested) and removed 75 (73 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.01 1.82 Search for helices and strands: 0 residues in 0 chains, 16716 seeds are put forward NCS extension: 29 residues added (20 deleted due to clashes), 16745 seeds are put forward Round 1: 1427 peptides, 137 chains. Longest chain 59 peptides. Score 0.487 Round 2: 1459 peptides, 118 chains. Longest chain 52 peptides. Score 0.522 Round 3: 1489 peptides, 133 chains. Longest chain 60 peptides. Score 0.509 Round 4: 1465 peptides, 133 chains. Longest chain 46 peptides. Score 0.503 Round 5: 1450 peptides, 130 chains. Longest chain 55 peptides. Score 0.503 Taking the results from Round 2 Chains 132, Residues 1341, Estimated correctness of the model 18.3 % 24 chains (554 residues) have been docked in sequence ------------------------------------------------------ 90855 reflections ( 99.15 % complete ) and 7824 restraints for refining 16509 atoms. Observations/parameters ratio is 1.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2370 (Rfree = 0.000) for 16509 atoms. Found 148 (148 requested) and removed 98 (74 requested) atoms. Cycle 32: After refmac, R = 0.2229 (Rfree = 0.000) for 16559 atoms. Found 104 (148 requested) and removed 80 (74 requested) atoms. Cycle 33: After refmac, R = 0.2165 (Rfree = 0.000) for 16583 atoms. Found 45 (148 requested) and removed 76 (74 requested) atoms. Cycle 34: After refmac, R = 0.2130 (Rfree = 0.000) for 16552 atoms. Found 28 (148 requested) and removed 78 (74 requested) atoms. Cycle 35: After refmac, R = 0.2109 (Rfree = 0.000) for 16502 atoms. Found 38 (148 requested) and removed 77 (74 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.00 1.81 Search for helices and strands: 0 residues in 0 chains, 16842 seeds are put forward NCS extension: 25 residues added (12 deleted due to clashes), 16867 seeds are put forward Round 1: 1440 peptides, 145 chains. Longest chain 56 peptides. Score 0.480 Round 2: 1452 peptides, 118 chains. Longest chain 62 peptides. Score 0.520 Round 3: 1456 peptides, 133 chains. Longest chain 50 peptides. Score 0.500 Round 4: 1459 peptides, 123 chains. Longest chain 57 peptides. Score 0.515 Round 5: 1409 peptides, 124 chains. Longest chain 57 peptides. Score 0.500 Taking the results from Round 2 Chains 134, Residues 1334, Estimated correctness of the model 17.7 % 22 chains (512 residues) have been docked in sequence ------------------------------------------------------ 90855 reflections ( 99.15 % complete ) and 7565 restraints for refining 16429 atoms. Observations/parameters ratio is 1.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2318 (Rfree = 0.000) for 16429 atoms. Found 147 (147 requested) and removed 98 (73 requested) atoms. Cycle 37: After refmac, R = 0.2153 (Rfree = 0.000) for 16478 atoms. Found 90 (147 requested) and removed 77 (73 requested) atoms. Cycle 38: After refmac, R = 0.2091 (Rfree = 0.000) for 16491 atoms. Found 40 (148 requested) and removed 81 (74 requested) atoms. Cycle 39: After refmac, R = 0.2061 (Rfree = 0.000) for 16450 atoms. Found 40 (147 requested) and removed 77 (73 requested) atoms. Cycle 40: After refmac, R = 0.2043 (Rfree = 0.000) for 16413 atoms. Found 47 (147 requested) and removed 79 (73 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.99 1.80 Search for helices and strands: 0 residues in 0 chains, 16813 seeds are put forward NCS extension: 17 residues added (37 deleted due to clashes), 16830 seeds are put forward Round 1: 1405 peptides, 138 chains. Longest chain 45 peptides. Score 0.480 Round 2: 1443 peptides, 118 chains. Longest chain 67 peptides. Score 0.517 Round 3: 1465 peptides, 122 chains. Longest chain 49 peptides. Score 0.518 Round 4: 1438 peptides, 130 chains. Longest chain 67 peptides. Score 0.500 Round 5: 1444 peptides, 131 chains. Longest chain 59 peptides. Score 0.500 Taking the results from Round 3 Chains 129, Residues 1343, Estimated correctness of the model 17.1 % 18 chains (483 residues) have been docked in sequence ------------------------------------------------------ 90855 reflections ( 99.15 % complete ) and 7506 restraints for refining 16496 atoms. Observations/parameters ratio is 1.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2396 (Rfree = 0.000) for 16496 atoms. Found 148 (148 requested) and removed 96 (74 requested) atoms. Cycle 42: After refmac, R = 0.2182 (Rfree = 0.000) for 16548 atoms. Found 100 (148 requested) and removed 79 (74 requested) atoms. Cycle 43: After refmac, R = 0.2111 (Rfree = 0.000) for 16569 atoms. Found 41 (148 requested) and removed 79 (74 requested) atoms. Cycle 44: After refmac, R = 0.2078 (Rfree = 0.000) for 16531 atoms. Found 32 (148 requested) and removed 74 (74 requested) atoms. Cycle 45: After refmac, R = 0.2061 (Rfree = 0.000) for 16489 atoms. Found 27 (147 requested) and removed 78 (73 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.99 1.80 Search for helices and strands: 0 residues in 0 chains, 16820 seeds are put forward NCS extension: 12 residues added (17 deleted due to clashes), 16832 seeds are put forward Round 1: 1377 peptides, 146 chains. Longest chain 48 peptides. Score 0.460 Round 2: 1460 peptides, 135 chains. Longest chain 51 peptides. Score 0.499 Round 3: 1445 peptides, 135 chains. Longest chain 51 peptides. Score 0.495 Round 4: 1452 peptides, 128 chains. Longest chain 48 peptides. Score 0.506 Round 5: 1458 peptides, 125 chains. Longest chain 48 peptides. Score 0.512 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 136, Residues 1333, Estimated correctness of the model 15.2 % 19 chains (374 residues) have been docked in sequence Sequence coverage is 28 % Consider running further cycles of model building using 2aam-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 215 B and 226 B 133 chains (1339 residues) following loop building 18 chains (384 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 90855 reflections ( 99.15 % complete ) and 6989 restraints for refining 16390 atoms. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2351 (Rfree = 0.000) for 16390 atoms. Found 0 (147 requested) and removed 52 (73 requested) atoms. Cycle 47: After refmac, R = 0.2247 (Rfree = 0.000) for 16338 atoms. Found 0 (146 requested) and removed 30 (73 requested) atoms. Cycle 48: After refmac, R = 0.2197 (Rfree = 0.000) for 16308 atoms. Found 0 (146 requested) and removed 43 (73 requested) atoms. Cycle 49: After refmac, R = 0.2165 (Rfree = 0.000) for 16265 atoms. Found 0 (145 requested) and removed 28 (72 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 03:46:28 GMT 2018 Job finished. TimeTaking 227.4 Used memory is bytes: 18747256