Mon 24 Dec 00:33:56 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 2obp-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2obp-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2obp-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obp-3.6-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/2obp-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obp-3.6-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 00:34:01 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/2obp-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obp-3.6-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 148 and 0 Target number of residues in the AU: 148 Target solvent content: 0.6584 Checking the provided sequence file Detected sequence length: 96 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 192 Adjusted target solvent content: 0.56 Input MTZ file: 2obp-3.6-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: 182 Cell parameters: 76.690 76.690 138.090 90.000 90.000 120.000 Input sequence file: 2obp-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1536 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 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: 29.462 3.600 Wilson plot Bfac: 82.30 3103 reflections ( 99.30 % complete ) and 0 restraints for refining 1707 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3594 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3422 (Rfree = 0.000) for 1707 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.57 3.29 Search for helices and strands: 0 residues in 0 chains, 1732 seeds are put forward NCS extension: 0 residues added, 1732 seeds are put forward Round 1: 91 peptides, 16 chains. Longest chain 13 peptides. Score 0.378 Round 2: 112 peptides, 13 chains. Longest chain 15 peptides. Score 0.590 Round 3: 117 peptides, 15 chains. Longest chain 14 peptides. Score 0.568 Round 4: 114 peptides, 16 chains. Longest chain 15 peptides. Score 0.526 Round 5: 105 peptides, 12 chains. Longest chain 14 peptides. Score 0.577 Taking the results from Round 2 Chains 13, Residues 99, Estimated correctness of the model 10.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3103 reflections ( 99.30 % complete ) and 3081 restraints for refining 1347 atoms. 2698 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3162 (Rfree = 0.000) for 1347 atoms. Found 8 (8 requested) and removed 33 (4 requested) atoms. Cycle 2: After refmac, R = 0.3670 (Rfree = 0.000) for 1290 atoms. Found 8 (8 requested) and removed 30 (4 requested) atoms. Cycle 3: After refmac, R = 0.3095 (Rfree = 0.000) for 1244 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 4: After refmac, R = 0.3068 (Rfree = 0.000) for 1225 atoms. Found 7 (7 requested) and removed 18 (3 requested) atoms. Cycle 5: After refmac, R = 0.2854 (Rfree = 0.000) for 1207 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.38 3.12 Search for helices and strands: 0 residues in 0 chains, 1290 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 1315 seeds are put forward Round 1: 105 peptides, 16 chains. Longest chain 11 peptides. Score 0.471 Round 2: 113 peptides, 15 chains. Longest chain 12 peptides. Score 0.546 Round 3: 121 peptides, 15 chains. Longest chain 14 peptides. Score 0.589 Round 4: 121 peptides, 14 chains. Longest chain 14 peptides. Score 0.612 Round 5: 116 peptides, 16 chains. Longest chain 13 peptides. Score 0.537 Taking the results from Round 4 Chains 14, Residues 107, Estimated correctness of the model 19.3 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 3103 reflections ( 99.30 % complete ) and 2742 restraints for refining 1340 atoms. 2279 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3225 (Rfree = 0.000) for 1340 atoms. Found 8 (8 requested) and removed 22 (4 requested) atoms. Cycle 7: After refmac, R = 0.3067 (Rfree = 0.000) for 1303 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 8: After refmac, R = 0.3170 (Rfree = 0.000) for 1276 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 9: After refmac, R = 0.3064 (Rfree = 0.000) for 1254 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 10: After refmac, R = 0.2976 (Rfree = 0.000) for 1237 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.11 Search for helices and strands: 0 residues in 0 chains, 1307 seeds are put forward NCS extension: 0 residues added, 1307 seeds are put forward Round 1: 96 peptides, 14 chains. Longest chain 13 peptides. Score 0.470 Round 2: 116 peptides, 15 chains. Longest chain 17 peptides. Score 0.562 Round 3: 117 peptides, 15 chains. Longest chain 16 peptides. Score 0.568 Round 4: 123 peptides, 12 chains. Longest chain 28 peptides. Score 0.666 Round 5: 118 peptides, 15 chains. Longest chain 14 peptides. Score 0.573 Taking the results from Round 4 Chains 13, Residues 111, Estimated correctness of the model 38.6 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3103 reflections ( 99.30 % complete ) and 2796 restraints for refining 1361 atoms. 2334 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3123 (Rfree = 0.000) for 1361 atoms. Found 8 (8 requested) and removed 26 (4 requested) atoms. Cycle 12: After refmac, R = 0.2917 (Rfree = 0.000) for 1328 atoms. Found 3 (8 requested) and removed 14 (4 requested) atoms. Cycle 13: After refmac, R = 0.2782 (Rfree = 0.000) for 1306 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 14: After refmac, R = 0.2707 (Rfree = 0.000) for 1299 atoms. Found 5 (8 requested) and removed 7 (4 requested) atoms. Cycle 15: After refmac, R = 0.2706 (Rfree = 0.000) for 1292 atoms. Found 7 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.41 3.15 Search for helices and strands: 0 residues in 0 chains, 1349 seeds are put forward NCS extension: 0 residues added, 1349 seeds are put forward Round 1: 109 peptides, 18 chains. Longest chain 12 peptides. Score 0.441 Round 2: 108 peptides, 15 chains. Longest chain 16 peptides. Score 0.517 Round 3: 105 peptides, 13 chains. Longest chain 19 peptides. Score 0.552 Round 4: 117 peptides, 13 chains. Longest chain 17 peptides. Score 0.616 Round 5: 117 peptides, 15 chains. Longest chain 18 peptides. Score 0.568 Taking the results from Round 4 Chains 14, Residues 104, Estimated correctness of the model 20.8 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 3103 reflections ( 99.30 % complete ) and 2711 restraints for refining 1331 atoms. 2256 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3159 (Rfree = 0.000) for 1331 atoms. Found 8 (8 requested) and removed 20 (4 requested) atoms. Cycle 17: After refmac, R = 0.2964 (Rfree = 0.000) for 1297 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 18: After refmac, R = 0.2870 (Rfree = 0.000) for 1278 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 19: After refmac, R = 0.2776 (Rfree = 0.000) for 1269 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 20: After refmac, R = 0.2860 (Rfree = 0.000) for 1262 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 3.17 Search for helices and strands: 0 residues in 0 chains, 1338 seeds are put forward NCS extension: 11 residues added (0 deleted due to clashes), 1349 seeds are put forward Round 1: 94 peptides, 14 chains. Longest chain 15 peptides. Score 0.458 Round 2: 104 peptides, 14 chains. Longest chain 17 peptides. Score 0.520 Round 3: 102 peptides, 12 chains. Longest chain 14 peptides. Score 0.561 Round 4: 111 peptides, 12 chains. Longest chain 14 peptides. Score 0.609 Round 5: 103 peptides, 13 chains. Longest chain 15 peptides. Score 0.540 Taking the results from Round 4 Chains 12, Residues 99, Estimated correctness of the model 18.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3103 reflections ( 99.30 % complete ) and 2829 restraints for refining 1289 atoms. 2445 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2901 (Rfree = 0.000) for 1289 atoms. Found 5 (8 requested) and removed 12 (4 requested) atoms. Cycle 22: After refmac, R = 0.2942 (Rfree = 0.000) for 1273 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 23: After refmac, R = 0.2979 (Rfree = 0.000) for 1272 atoms. Found 7 (8 requested) and removed 8 (4 requested) atoms. Cycle 24: After refmac, R = 0.2875 (Rfree = 0.000) for 1270 atoms. Found 5 (8 requested) and removed 11 (4 requested) atoms. Cycle 25: After refmac, R = 0.2847 (Rfree = 0.000) for 1261 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 3.18 Search for helices and strands: 0 residues in 0 chains, 1334 seeds are put forward NCS extension: 0 residues added, 1334 seeds are put forward Round 1: 99 peptides, 18 chains. Longest chain 13 peptides. Score 0.374 Round 2: 102 peptides, 16 chains. Longest chain 9 peptides. Score 0.452 Round 3: 110 peptides, 14 chains. Longest chain 17 peptides. Score 0.554 Round 4: 112 peptides, 13 chains. Longest chain 15 peptides. Score 0.590 Round 5: 117 peptides, 16 chains. Longest chain 14 peptides. Score 0.543 Taking the results from Round 4 Chains 13, Residues 99, Estimated correctness of the model 10.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3103 reflections ( 99.30 % complete ) and 2846 restraints for refining 1317 atoms. 2463 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2975 (Rfree = 0.000) for 1317 atoms. Found 6 (8 requested) and removed 11 (4 requested) atoms. Cycle 27: After refmac, R = 0.2991 (Rfree = 0.000) for 1307 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 28: After refmac, R = 0.2804 (Rfree = 0.000) for 1298 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 29: After refmac, R = 0.2913 (Rfree = 0.000) for 1293 atoms. Found 4 (8 requested) and removed 10 (4 requested) atoms. Cycle 30: After refmac, R = 0.2829 (Rfree = 0.000) for 1285 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.45 3.18 Search for helices and strands: 0 residues in 0 chains, 1344 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 1356 seeds are put forward Round 1: 97 peptides, 18 chains. Longest chain 12 peptides. Score 0.360 Round 2: 109 peptides, 15 chains. Longest chain 14 peptides. Score 0.523 Round 3: 120 peptides, 14 chains. Longest chain 15 peptides. Score 0.607 Round 4: 118 peptides, 13 chains. Longest chain 22 peptides. Score 0.621 Round 5: 120 peptides, 14 chains. Longest chain 17 peptides. Score 0.607 Taking the results from Round 4 Chains 13, Residues 105, Estimated correctness of the model 22.7 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3103 reflections ( 99.30 % complete ) and 2707 restraints for refining 1302 atoms. 2279 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2743 (Rfree = 0.000) for 1302 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 32: After refmac, R = 0.2737 (Rfree = 0.000) for 1299 atoms. Found 1 (8 requested) and removed 17 (4 requested) atoms. Cycle 33: After refmac, R = 0.2832 (Rfree = 0.000) for 1280 atoms. Found 6 (8 requested) and removed 7 (4 requested) atoms. Cycle 34: After refmac, R = 0.2802 (Rfree = 0.000) for 1270 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 35: After refmac, R = 0.2679 (Rfree = 0.000) for 1265 atoms. Found 5 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.45 3.18 Search for helices and strands: 0 residues in 0 chains, 1325 seeds are put forward NCS extension: 6 residues added (1 deleted due to clashes), 1331 seeds are put forward Round 1: 90 peptides, 15 chains. Longest chain 13 peptides. Score 0.401 Round 2: 113 peptides, 15 chains. Longest chain 19 peptides. Score 0.546 Round 3: 118 peptides, 15 chains. Longest chain 16 peptides. Score 0.573 Round 4: 127 peptides, 13 chains. Longest chain 20 peptides. Score 0.663 Round 5: 116 peptides, 16 chains. Longest chain 17 peptides. Score 0.537 Taking the results from Round 4 Chains 13, Residues 114, Estimated correctness of the model 37.6 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 3103 reflections ( 99.30 % complete ) and 2832 restraints for refining 1392 atoms. 2307 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2968 (Rfree = 0.000) for 1392 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 37: After refmac, R = 0.2799 (Rfree = 0.000) for 1371 atoms. Found 5 (8 requested) and removed 9 (4 requested) atoms. Cycle 38: After refmac, R = 0.2683 (Rfree = 0.000) for 1363 atoms. Found 6 (8 requested) and removed 8 (4 requested) atoms. Cycle 39: After refmac, R = 0.2676 (Rfree = 0.000) for 1358 atoms. Found 4 (8 requested) and removed 10 (4 requested) atoms. Cycle 40: After refmac, R = 0.2576 (Rfree = 0.000) for 1351 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 3.21 Search for helices and strands: 0 residues in 0 chains, 1393 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 1412 seeds are put forward Round 1: 81 peptides, 13 chains. Longest chain 12 peptides. Score 0.400 Round 2: 108 peptides, 13 chains. Longest chain 26 peptides. Score 0.568 Round 3: 114 peptides, 14 chains. Longest chain 18 peptides. Score 0.576 Round 4: 113 peptides, 14 chains. Longest chain 21 peptides. Score 0.571 Round 5: 112 peptides, 15 chains. Longest chain 21 peptides. Score 0.540 Taking the results from Round 3 Chains 14, Residues 100, Estimated correctness of the model 5.1 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 3103 reflections ( 99.30 % complete ) and 2960 restraints for refining 1385 atoms. 2557 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2895 (Rfree = 0.000) for 1385 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 42: After refmac, R = 0.2760 (Rfree = 0.000) for 1367 atoms. Found 5 (8 requested) and removed 11 (4 requested) atoms. Cycle 43: After refmac, R = 0.2611 (Rfree = 0.000) for 1358 atoms. Found 6 (8 requested) and removed 7 (4 requested) atoms. Cycle 44: After refmac, R = 0.2621 (Rfree = 0.000) for 1350 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 45: After refmac, R = 0.2605 (Rfree = 0.000) for 1346 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 3.16 Search for helices and strands: 0 residues in 0 chains, 1403 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 1419 seeds are put forward Round 1: 96 peptides, 17 chains. Longest chain 18 peptides. Score 0.383 Round 2: 103 peptides, 16 chains. Longest chain 15 peptides. Score 0.459 Round 3: 105 peptides, 16 chains. Longest chain 15 peptides. Score 0.471 Round 4: 110 peptides, 14 chains. Longest chain 15 peptides. Score 0.554 Round 5: 101 peptides, 12 chains. Longest chain 17 peptides. Score 0.555 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 89, 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 2obp-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3103 reflections ( 99.30 % complete ) and 3171 restraints for refining 1393 atoms. 2827 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2627 (Rfree = 0.000) for 1393 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2691 (Rfree = 0.000) for 1385 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2751 (Rfree = 0.000) for 1377 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2765 (Rfree = 0.000) for 1365 atoms. TimeTaking 31.32