Mon 24 Dec 00:45:10 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-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2obp-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2obp-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obp-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/2obp-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obp-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 ============================================================ Mon 24 Dec 00:45:15 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-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obp-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 162 and 0 Target number of residues in the AU: 162 Target solvent content: 0.6260 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-3.2-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: 182 Cell parameters: 76.690 76.690 138.090 90.000 90.000 120.000 Input sequence file: 2obp-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1536 target number of atoms Had to go as low as 0.70 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 3.200 Wilson plot Bfac: 63.74 4340 reflections ( 99.47 % complete ) and 0 restraints for refining 1695 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Starting model: R = 0.3573 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3305 (Rfree = 0.000) for 1695 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.26 3.01 Search for helices and strands: 0 residues in 0 chains, 1723 seeds are put forward NCS extension: 0 residues added, 1723 seeds are put forward Round 1: 90 peptides, 16 chains. Longest chain 12 peptides. Score 0.371 Round 2: 108 peptides, 16 chains. Longest chain 11 peptides. Score 0.490 Round 3: 103 peptides, 13 chains. Longest chain 25 peptides. Score 0.540 Round 4: 111 peptides, 15 chains. Longest chain 15 peptides. Score 0.534 Round 5: 106 peptides, 13 chains. Longest chain 24 peptides. Score 0.557 Taking the results from Round 5 Chains 13, Residues 93, Estimated correctness of the model 28.9 % 4 chains (15 residues) have been docked in sequence ------------------------------------------------------ 4340 reflections ( 99.47 % complete ) and 3108 restraints for refining 1399 atoms. 2718 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2900 (Rfree = 0.000) for 1399 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 2: After refmac, R = 0.2883 (Rfree = 0.000) for 1372 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 3: After refmac, R = 0.2855 (Rfree = 0.000) for 1349 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 4: After refmac, R = 0.2767 (Rfree = 0.000) for 1330 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 5: After refmac, R = 0.2696 (Rfree = 0.000) for 1320 atoms. Found 8 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.19 2.94 Search for helices and strands: 0 residues in 0 chains, 1375 seeds are put forward NCS extension: 35 residues added (2 deleted due to clashes), 1410 seeds are put forward Round 1: 99 peptides, 15 chains. Longest chain 15 peptides. Score 0.461 Round 2: 121 peptides, 16 chains. Longest chain 11 peptides. Score 0.565 Round 3: 125 peptides, 15 chains. Longest chain 15 peptides. Score 0.610 Round 4: 116 peptides, 14 chains. Longest chain 15 peptides. Score 0.587 Round 5: 118 peptides, 14 chains. Longest chain 18 peptides. Score 0.597 Taking the results from Round 3 Chains 15, Residues 110, Estimated correctness of the model 43.7 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 4340 reflections ( 99.47 % complete ) and 2553 restraints for refining 1310 atoms. 2048 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2957 (Rfree = 0.000) for 1310 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 7: After refmac, R = 0.2784 (Rfree = 0.000) for 1298 atoms. Found 10 (11 requested) and removed 9 (5 requested) atoms. Cycle 8: After refmac, R = 0.2834 (Rfree = 0.000) for 1289 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 9: After refmac, R = 0.2814 (Rfree = 0.000) for 1285 atoms. Found 10 (11 requested) and removed 9 (5 requested) atoms. Cycle 10: After refmac, R = 0.2572 (Rfree = 0.000) for 1278 atoms. Found 8 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.21 2.96 Search for helices and strands: 0 residues in 0 chains, 1336 seeds are put forward NCS extension: 8 residues added (3 deleted due to clashes), 1344 seeds are put forward Round 1: 111 peptides, 16 chains. Longest chain 14 peptides. Score 0.508 Round 2: 126 peptides, 12 chains. Longest chain 25 peptides. Score 0.679 Round 3: 120 peptides, 12 chains. Longest chain 23 peptides. Score 0.652 Round 4: 126 peptides, 15 chains. Longest chain 16 peptides. Score 0.615 Round 5: 118 peptides, 14 chains. Longest chain 17 peptides. Score 0.597 Taking the results from Round 2 Chains 12, Residues 114, Estimated correctness of the model 60.6 % 4 chains (41 residues) have been docked in sequence ------------------------------------------------------ 4340 reflections ( 99.47 % complete ) and 2385 restraints for refining 1312 atoms. 1826 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2942 (Rfree = 0.000) for 1312 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 12: After refmac, R = 0.3170 (Rfree = 0.000) for 1291 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 13: After refmac, R = 0.2780 (Rfree = 0.000) for 1270 atoms. Found 10 (11 requested) and removed 15 (5 requested) atoms. Cycle 14: After refmac, R = 0.2726 (Rfree = 0.000) for 1256 atoms. Found 7 (11 requested) and removed 9 (5 requested) atoms. Cycle 15: After refmac, R = 0.2685 (Rfree = 0.000) for 1250 atoms. Found 8 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.14 2.90 Search for helices and strands: 0 residues in 0 chains, 1303 seeds are put forward NCS extension: 11 residues added (0 deleted due to clashes), 1314 seeds are put forward Round 1: 116 peptides, 14 chains. Longest chain 19 peptides. Score 0.587 Round 2: 117 peptides, 14 chains. Longest chain 23 peptides. Score 0.592 Round 3: 125 peptides, 14 chains. Longest chain 20 peptides. Score 0.632 Round 4: 120 peptides, 11 chains. Longest chain 23 peptides. Score 0.674 Round 5: 122 peptides, 14 chains. Longest chain 20 peptides. Score 0.618 Taking the results from Round 4 Chains 13, Residues 109, Estimated correctness of the model 59.5 % 3 chains (46 residues) have been docked in sequence ------------------------------------------------------ 4340 reflections ( 99.47 % complete ) and 2473 restraints for refining 1353 atoms. 1919 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3102 (Rfree = 0.000) for 1353 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 17: After refmac, R = 0.2957 (Rfree = 0.000) for 1332 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 18: After refmac, R = 0.2849 (Rfree = 0.000) for 1325 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 19: After refmac, R = 0.2827 (Rfree = 0.000) for 1323 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 20: After refmac, R = 0.2725 (Rfree = 0.000) for 1315 atoms. Found 11 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.61 3.33 Search for helices and strands: 0 residues in 0 chains, 1365 seeds are put forward NCS extension: 8 residues added (2 deleted due to clashes), 1373 seeds are put forward Round 1: 122 peptides, 14 chains. Longest chain 15 peptides. Score 0.618 Round 2: 116 peptides, 14 chains. Longest chain 18 peptides. Score 0.587 Round 3: 122 peptides, 11 chains. Longest chain 26 peptides. Score 0.683 Round 4: 125 peptides, 11 chains. Longest chain 26 peptides. Score 0.695 Round 5: 127 peptides, 13 chains. Longest chain 18 peptides. Score 0.663 Taking the results from Round 4 Chains 11, Residues 114, Estimated correctness of the model 64.1 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 4340 reflections ( 99.47 % complete ) and 2511 restraints for refining 1304 atoms. 1991 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2933 (Rfree = 0.000) for 1304 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 22: After refmac, R = 0.2841 (Rfree = 0.000) for 1291 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 23: After refmac, R = 0.2704 (Rfree = 0.000) for 1286 atoms. Found 8 (11 requested) and removed 9 (5 requested) atoms. Cycle 24: After refmac, R = 0.2732 (Rfree = 0.000) for 1282 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 25: After refmac, R = 0.2748 (Rfree = 0.000) for 1280 atoms. Found 10 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.11 2.87 Search for helices and strands: 0 residues in 0 chains, 1325 seeds are put forward NCS extension: 8 residues added (1 deleted due to clashes), 1333 seeds are put forward Round 1: 117 peptides, 15 chains. Longest chain 23 peptides. Score 0.568 Round 2: 131 peptides, 13 chains. Longest chain 28 peptides. Score 0.680 Round 3: 123 peptides, 13 chains. Longest chain 23 peptides. Score 0.645 Round 4: 128 peptides, 12 chains. Longest chain 28 peptides. Score 0.688 Round 5: 137 peptides, 12 chains. Longest chain 28 peptides. Score 0.724 Taking the results from Round 5 Chains 14, Residues 125, Estimated correctness of the model 70.1 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4340 reflections ( 99.47 % complete ) and 2698 restraints for refining 1352 atoms. 2177 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3271 (Rfree = 0.000) for 1352 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 27: After refmac, R = 0.3293 (Rfree = 0.000) for 1333 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 28: After refmac, R = 0.3166 (Rfree = 0.000) for 1315 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 29: After refmac, R = 0.2972 (Rfree = 0.000) for 1311 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 30: After refmac, R = 0.3196 (Rfree = 0.000) for 1300 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.13 2.89 Search for helices and strands: 0 residues in 0 chains, 1344 seeds are put forward NCS extension: 0 residues added, 1344 seeds are put forward Round 1: 124 peptides, 16 chains. Longest chain 18 peptides. Score 0.581 Round 2: 129 peptides, 12 chains. Longest chain 27 peptides. Score 0.692 Round 3: 136 peptides, 14 chains. Longest chain 22 peptides. Score 0.682 Round 4: 134 peptides, 15 chains. Longest chain 17 peptides. Score 0.653 Round 5: 136 peptides, 14 chains. Longest chain 28 peptides. Score 0.682 Taking the results from Round 2 Chains 14, Residues 117, Estimated correctness of the model 63.5 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 4340 reflections ( 99.47 % complete ) and 2666 restraints for refining 1339 atoms. 2151 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3225 (Rfree = 0.000) for 1339 atoms. Found 10 (11 requested) and removed 21 (6 requested) atoms. Cycle 32: After refmac, R = 0.3115 (Rfree = 0.000) for 1311 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 33: After refmac, R = 0.2982 (Rfree = 0.000) for 1303 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 34: After refmac, R = 0.3090 (Rfree = 0.000) for 1295 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 35: After refmac, R = 0.2951 (Rfree = 0.000) for 1290 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.13 2.89 Search for helices and strands: 0 residues in 0 chains, 1343 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 1360 seeds are put forward Round 1: 114 peptides, 16 chains. Longest chain 19 peptides. Score 0.526 Round 2: 133 peptides, 14 chains. Longest chain 26 peptides. Score 0.669 Round 3: 122 peptides, 14 chains. Longest chain 19 peptides. Score 0.618 Round 4: 122 peptides, 13 chains. Longest chain 24 peptides. Score 0.640 Round 5: 129 peptides, 10 chains. Longest chain 38 peptides. Score 0.730 Taking the results from Round 5 Chains 10, Residues 119, Estimated correctness of the model 71.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4340 reflections ( 99.47 % complete ) and 2693 restraints for refining 1291 atoms. 2227 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3141 (Rfree = 0.000) for 1291 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 37: After refmac, R = 0.3014 (Rfree = 0.000) for 1286 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 38: After refmac, R = 0.2934 (Rfree = 0.000) for 1281 atoms. Found 9 (9 requested) and removed 7 (5 requested) atoms. Cycle 39: After refmac, R = 0.2890 (Rfree = 0.000) for 1279 atoms. Found 9 (9 requested) and removed 5 (5 requested) atoms. Cycle 40: After refmac, R = 0.2693 (Rfree = 0.000) for 1281 atoms. Found 8 (9 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.10 2.86 Search for helices and strands: 0 residues in 0 chains, 1327 seeds are put forward NCS extension: 33 residues added (6 deleted due to clashes), 1360 seeds are put forward Round 1: 116 peptides, 16 chains. Longest chain 18 peptides. Score 0.537 Round 2: 124 peptides, 14 chains. Longest chain 21 peptides. Score 0.627 Round 3: 123 peptides, 13 chains. Longest chain 21 peptides. Score 0.645 Round 4: 120 peptides, 13 chains. Longest chain 25 peptides. Score 0.630 Round 5: 119 peptides, 14 chains. Longest chain 23 peptides. Score 0.602 Taking the results from Round 3 Chains 13, Residues 110, Estimated correctness of the model 52.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4340 reflections ( 99.47 % complete ) and 2754 restraints for refining 1297 atoms. 2327 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2984 (Rfree = 0.000) for 1297 atoms. Found 9 (9 requested) and removed 11 (5 requested) atoms. Cycle 42: After refmac, R = 0.2889 (Rfree = 0.000) for 1290 atoms. Found 9 (9 requested) and removed 9 (5 requested) atoms. Cycle 43: After refmac, R = 0.2964 (Rfree = 0.000) for 1288 atoms. Found 9 (9 requested) and removed 10 (5 requested) atoms. Cycle 44: After refmac, R = 0.2835 (Rfree = 0.000) for 1284 atoms. Found 9 (9 requested) and removed 6 (5 requested) atoms. Cycle 45: After refmac, R = 0.2924 (Rfree = 0.000) for 1285 atoms. Found 9 (9 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.22 2.97 Search for helices and strands: 0 residues in 0 chains, 1327 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 1348 seeds are put forward Round 1: 101 peptides, 16 chains. Longest chain 15 peptides. Score 0.446 Round 2: 112 peptides, 15 chains. Longest chain 15 peptides. Score 0.540 Round 3: 114 peptides, 15 chains. Longest chain 15 peptides. Score 0.551 Round 4: 109 peptides, 17 chains. Longest chain 16 peptides. Score 0.469 Round 5: 109 peptides, 14 chains. Longest chain 15 peptides. Score 0.548 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 99, Estimated correctness of the model 27.2 % 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. 4340 reflections ( 99.47 % complete ) and 2871 restraints for refining 1303 atoms. 2490 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3026 (Rfree = 0.000) for 1303 atoms. Found 0 (9 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.3044 (Rfree = 0.000) for 1293 atoms. Found 0 (9 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.3011 (Rfree = 0.000) for 1286 atoms. Found 0 (9 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2966 (Rfree = 0.000) for 1276 atoms. TimeTaking 26.68