null Tue 25 Dec 19:27:56 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 1vp8-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vp8-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vp8-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp8-3.8-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/1vp8-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp8-3.8-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 ============================================================ Tue 25 Dec 19:28:11 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/1vp8-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp8-3.8-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 176 and 0 Target number of residues in the AU: 176 Target solvent content: 0.6421 Checking the provided sequence file Detected sequence length: 201 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 201 Adjusted target solvent content: 0.59 Input MTZ file: 1vp8-3.8-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: 182 Cell parameters: 109.749 109.749 76.534 90.000 90.000 120.000 Input sequence file: 1vp8-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1608 target number of atoms Had to go as low as 0.75 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 Loops will be built when appropriate and at the last cycle Resolution range: 18.945 3.800 Wilson plot Bfac: 72.39 2914 reflections ( 98.75 % complete ) and 0 restraints for refining 1777 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3276 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2347 (Rfree = 0.000) for 1777 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.75 3.32 Search for helices and strands: 0 residues in 0 chains, 1808 seeds are put forward Round 1: 114 peptides, 18 chains. Longest chain 20 peptides. Score 0.446 Round 2: 129 peptides, 16 chains. Longest chain 26 peptides. Score 0.571 Round 3: 145 peptides, 15 chains. Longest chain 24 peptides. Score 0.661 Round 4: 145 peptides, 13 chains. Longest chain 22 peptides. Score 0.697 Round 5: 140 peptides, 12 chains. Longest chain 26 peptides. Score 0.696 Taking the results from Round 4 Chains 14, Residues 132, Estimated correctness of the model 39.2 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2914 reflections ( 98.75 % complete ) and 3043 restraints for refining 1454 atoms. 2492 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2952 (Rfree = 0.000) for 1454 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 2: After refmac, R = 0.2798 (Rfree = 0.000) for 1436 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 3: After refmac, R = 0.2637 (Rfree = 0.000) for 1416 atoms. Found 4 (7 requested) and removed 5 (3 requested) atoms. Cycle 4: After refmac, R = 0.2576 (Rfree = 0.000) for 1406 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. Cycle 5: After refmac, R = 0.2483 (Rfree = 0.000) for 1398 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.67 3.25 Search for helices and strands: 0 residues in 0 chains, 1438 seeds are put forward Round 1: 117 peptides, 17 chains. Longest chain 14 peptides. Score 0.487 Round 2: 128 peptides, 18 chains. Longest chain 16 peptides. Score 0.522 Round 3: 138 peptides, 13 chains. Longest chain 25 peptides. Score 0.671 Round 4: 142 peptides, 13 chains. Longest chain 24 peptides. Score 0.686 Round 5: 132 peptides, 15 chains. Longest chain 21 peptides. Score 0.606 Taking the results from Round 4 Chains 13, Residues 129, Estimated correctness of the model 35.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2914 reflections ( 98.75 % complete ) and 3010 restraints for refining 1405 atoms. 2507 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2706 (Rfree = 0.000) for 1405 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 7: After refmac, R = 0.2608 (Rfree = 0.000) for 1378 atoms. Found 4 (7 requested) and removed 9 (3 requested) atoms. Cycle 8: After refmac, R = 0.2444 (Rfree = 0.000) for 1367 atoms. Found 5 (7 requested) and removed 4 (3 requested) atoms. Cycle 9: After refmac, R = 0.2363 (Rfree = 0.000) for 1364 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 10: After refmac, R = 0.2253 (Rfree = 0.000) for 1360 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.56 3.15 Search for helices and strands: 0 residues in 0 chains, 1402 seeds are put forward Round 1: 115 peptides, 17 chains. Longest chain 13 peptides. Score 0.476 Round 2: 135 peptides, 12 chains. Longest chain 24 peptides. Score 0.678 Round 3: 139 peptides, 16 chains. Longest chain 16 peptides. Score 0.617 Round 4: 135 peptides, 15 chains. Longest chain 16 peptides. Score 0.620 Round 5: 138 peptides, 14 chains. Longest chain 23 peptides. Score 0.652 Taking the results from Round 2 Chains 14, Residues 123, Estimated correctness of the model 32.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 2914 reflections ( 98.75 % complete ) and 2713 restraints for refining 1355 atoms. 2196 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2718 (Rfree = 0.000) for 1355 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 12: After refmac, R = 0.2608 (Rfree = 0.000) for 1340 atoms. Found 4 (7 requested) and removed 6 (3 requested) atoms. Cycle 13: After refmac, R = 0.2412 (Rfree = 0.000) for 1330 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 14: After refmac, R = 0.2352 (Rfree = 0.000) for 1325 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.2437 (Rfree = 0.000) for 1320 atoms. Found 5 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.71 3.29 Search for helices and strands: 0 residues in 0 chains, 1376 seeds are put forward Round 1: 127 peptides, 16 chains. Longest chain 18 peptides. Score 0.562 Round 2: 139 peptides, 14 chains. Longest chain 18 peptides. Score 0.656 Round 3: 149 peptides, 15 chains. Longest chain 17 peptides. Score 0.677 Round 4: 136 peptides, 15 chains. Longest chain 24 peptides. Score 0.624 Round 5: 131 peptides, 16 chains. Longest chain 15 peptides. Score 0.581 Taking the results from Round 3 Chains 15, Residues 134, Estimated correctness of the model 31.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2914 reflections ( 98.75 % complete ) and 2854 restraints for refining 1401 atoms. 2333 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2875 (Rfree = 0.000) for 1401 atoms. Found 7 (7 requested) and removed 32 (3 requested) atoms. Cycle 17: After refmac, R = 0.2317 (Rfree = 0.000) for 1366 atoms. Found 2 (7 requested) and removed 14 (3 requested) atoms. Cycle 18: After refmac, R = 0.2182 (Rfree = 0.000) for 1351 atoms. Found 5 (7 requested) and removed 6 (3 requested) atoms. Cycle 19: After refmac, R = 0.2154 (Rfree = 0.000) for 1348 atoms. Found 4 (7 requested) and removed 6 (3 requested) atoms. Cycle 20: After refmac, R = 0.2104 (Rfree = 0.000) for 1344 atoms. Found 3 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.53 3.13 Search for helices and strands: 0 residues in 0 chains, 1419 seeds are put forward Round 1: 132 peptides, 21 chains. Longest chain 15 peptides. Score 0.473 Round 2: 119 peptides, 16 chains. Longest chain 18 peptides. Score 0.521 Round 3: 127 peptides, 15 chains. Longest chain 23 peptides. Score 0.583 Round 4: 132 peptides, 17 chains. Longest chain 21 peptides. Score 0.564 Round 5: 122 peptides, 17 chains. Longest chain 20 peptides. Score 0.514 Taking the results from Round 3 Chains 16, Residues 112, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 2914 reflections ( 98.75 % complete ) and 2842 restraints for refining 1454 atoms. 2318 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2574 (Rfree = 0.000) for 1454 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 22: After refmac, R = 0.2201 (Rfree = 0.000) for 1429 atoms. Found 5 (7 requested) and removed 6 (3 requested) atoms. Cycle 23: After refmac, R = 0.2174 (Rfree = 0.000) for 1421 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 24: After refmac, R = 0.2192 (Rfree = 0.000) for 1417 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 25: After refmac, R = 0.2082 (Rfree = 0.000) for 1414 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 3.12 Search for helices and strands: 0 residues in 0 chains, 1472 seeds are put forward Round 1: 120 peptides, 20 chains. Longest chain 11 peptides. Score 0.430 Round 2: 125 peptides, 16 chains. Longest chain 20 peptides. Score 0.552 Round 3: 125 peptides, 14 chains. Longest chain 15 peptides. Score 0.596 Round 4: 135 peptides, 16 chains. Longest chain 20 peptides. Score 0.599 Round 5: 122 peptides, 15 chains. Longest chain 17 peptides. Score 0.559 Taking the results from Round 4 Chains 16, Residues 119, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2914 reflections ( 98.75 % complete ) and 3169 restraints for refining 1455 atoms. 2709 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2514 (Rfree = 0.000) for 1455 atoms. Found 8 (8 requested) and removed 38 (4 requested) atoms. Cycle 27: After refmac, R = 0.2383 (Rfree = 0.000) for 1416 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 28: After refmac, R = 0.2221 (Rfree = 0.000) for 1411 atoms. Found 3 (7 requested) and removed 11 (3 requested) atoms. Cycle 29: After refmac, R = 0.2362 (Rfree = 0.000) for 1399 atoms. Found 6 (7 requested) and removed 7 (3 requested) atoms. Cycle 30: After refmac, R = 0.2327 (Rfree = 0.000) for 1396 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.53 3.13 Search for helices and strands: 0 residues in 0 chains, 1463 seeds are put forward Round 1: 92 peptides, 16 chains. Longest chain 13 peptides. Score 0.365 Round 2: 98 peptides, 15 chains. Longest chain 13 peptides. Score 0.429 Round 3: 105 peptides, 17 chains. Longest chain 15 peptides. Score 0.419 Round 4: 106 peptides, 17 chains. Longest chain 18 peptides. Score 0.425 Round 5: 117 peptides, 15 chains. Longest chain 17 peptides. Score 0.534 Taking the results from Round 5 Chains 15, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2914 reflections ( 98.75 % complete ) and 3293 restraints for refining 1455 atoms. 2900 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2714 (Rfree = 0.000) for 1455 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 32: After refmac, R = 0.2309 (Rfree = 0.000) for 1446 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 33: After refmac, R = 0.2367 (Rfree = 0.000) for 1442 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 34: After refmac, R = 0.2243 (Rfree = 0.000) for 1436 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 35: After refmac, R = 0.2229 (Rfree = 0.000) for 1435 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.57 3.16 Search for helices and strands: 0 residues in 0 chains, 1491 seeds are put forward Round 1: 90 peptides, 14 chains. Longest chain 14 peptides. Score 0.408 Round 2: 94 peptides, 14 chains. Longest chain 11 peptides. Score 0.432 Round 3: 104 peptides, 12 chains. Longest chain 16 peptides. Score 0.539 Round 4: 97 peptides, 11 chains. Longest chain 15 peptides. Score 0.527 Round 5: 101 peptides, 12 chains. Longest chain 13 peptides. Score 0.523 Taking the results from Round 3 Chains 12, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2914 reflections ( 98.75 % complete ) and 3246 restraints for refining 1453 atoms. 2890 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2692 (Rfree = 0.000) for 1453 atoms. Found 7 (8 requested) and removed 10 (4 requested) atoms. Cycle 37: After refmac, R = 0.1985 (Rfree = 0.000) for 1445 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 38: After refmac, R = 0.2220 (Rfree = 0.000) for 1446 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 39: After refmac, R = 0.2175 (Rfree = 0.000) for 1442 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 40: After refmac, R = 0.2175 (Rfree = 0.000) for 1431 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.53 3.13 Search for helices and strands: 0 residues in 0 chains, 1490 seeds are put forward Round 1: 84 peptides, 15 chains. Longest chain 9 peptides. Score 0.342 Round 2: 91 peptides, 13 chains. Longest chain 13 peptides. Score 0.441 Round 3: 95 peptides, 15 chains. Longest chain 12 peptides. Score 0.411 Round 4: 100 peptides, 13 chains. Longest chain 15 peptides. Score 0.493 Round 5: 100 peptides, 16 chains. Longest chain 12 peptides. Score 0.415 Taking the results from Round 4 Chains 14, Residues 87, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2914 reflections ( 98.75 % complete ) and 3245 restraints for refining 1455 atoms. 2880 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2399 (Rfree = 0.000) for 1455 atoms. Found 8 (8 requested) and removed 41 (4 requested) atoms. Cycle 42: After refmac, R = 0.2481 (Rfree = 0.000) for 1408 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 43: After refmac, R = 0.2161 (Rfree = 0.000) for 1403 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 44: After refmac, R = 0.2224 (Rfree = 0.000) for 1396 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 45: After refmac, R = 0.1914 (Rfree = 0.000) for 1390 atoms. Found 3 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.51 3.11 Search for helices and strands: 0 residues in 0 chains, 1445 seeds are put forward Round 1: 79 peptides, 17 chains. Longest chain 7 peptides. Score 0.249 Round 2: 99 peptides, 16 chains. Longest chain 12 peptides. Score 0.409 Round 3: 93 peptides, 16 chains. Longest chain 14 peptides. Score 0.372 Round 4: 92 peptides, 15 chains. Longest chain 13 peptides. Score 0.393 Round 5: 96 peptides, 15 chains. Longest chain 11 peptides. Score 0.417 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 81, 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 1vp8-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2914 reflections ( 98.75 % complete ) and 3439 restraints for refining 1455 atoms. 3130 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2114 (Rfree = 0.000) for 1455 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1921 (Rfree = 0.000) for 1446 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1883 (Rfree = 0.000) for 1440 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1839 (Rfree = 0.000) for 1437 atoms. Found 0 (7 requested) and removed 2 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:20:13 GMT 2018 Job finished. TimeTaking 52.28 Used memory is bytes: 2819024