null Mon 24 Dec 00:29:55 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 2o3l-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2o3l-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2o3l-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o3l-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/2o3l-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o3l-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 00:29:59 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/2o3l-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o3l-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 149 and 0 Target number of residues in the AU: 149 Target solvent content: 0.6325 Checking the provided sequence file Detected sequence length: 85 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 170 Adjusted target solvent content: 0.58 Input MTZ file: 2o3l-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: 154 Cell parameters: 61.138 61.138 101.686 90.000 90.000 120.000 Input sequence file: 2o3l-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1360 target number of atoms Had to go as low as 0.85 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: 52.947 3.201 Wilson plot Bfac: 67.07 3896 reflections ( 99.82 % complete ) and 0 restraints for refining 1529 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Starting model: R = 0.3388 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2793 (Rfree = 0.000) for 1529 atoms. Found 10 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.17 2.85 Search for helices and strands: 0 residues in 0 chains, 1571 seeds are put forward NCS extension: 0 residues added, 1571 seeds are put forward Round 1: 92 peptides, 17 chains. Longest chain 10 peptides. Score 0.364 Round 2: 117 peptides, 17 chains. Longest chain 12 peptides. Score 0.534 Round 3: 117 peptides, 14 chains. Longest chain 18 peptides. Score 0.611 Round 4: 120 peptides, 14 chains. Longest chain 20 peptides. Score 0.626 Round 5: 127 peptides, 13 chains. Longest chain 18 peptides. Score 0.683 Taking the results from Round 5 Chains 14, Residues 114, Estimated correctness of the model 61.5 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 3896 reflections ( 99.82 % complete ) and 2329 restraints for refining 1242 atoms. 1778 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3054 (Rfree = 0.000) for 1242 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 2: After refmac, R = 0.2891 (Rfree = 0.000) for 1231 atoms. Found 7 (11 requested) and removed 10 (5 requested) atoms. Cycle 3: After refmac, R = 0.2880 (Rfree = 0.000) for 1210 atoms. Found 5 (11 requested) and removed 8 (5 requested) atoms. Cycle 4: After refmac, R = 0.2854 (Rfree = 0.000) for 1202 atoms. Found 5 (10 requested) and removed 12 (5 requested) atoms. Cycle 5: After refmac, R = 0.2625 (Rfree = 0.000) for 1185 atoms. Found 3 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.16 2.84 Search for helices and strands: 0 residues in 0 chains, 1260 seeds are put forward NCS extension: 10 residues added (3 deleted due to clashes), 1270 seeds are put forward Round 1: 110 peptides, 16 chains. Longest chain 14 peptides. Score 0.518 Round 2: 112 peptides, 12 chains. Longest chain 22 peptides. Score 0.633 Round 3: 122 peptides, 12 chains. Longest chain 20 peptides. Score 0.681 Round 4: 116 peptides, 12 chains. Longest chain 21 peptides. Score 0.653 Round 5: 112 peptides, 12 chains. Longest chain 17 peptides. Score 0.633 Taking the results from Round 3 Chains 14, Residues 110, Estimated correctness of the model 61.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 3896 reflections ( 99.82 % complete ) and 2438 restraints for refining 1216 atoms. 1945 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2731 (Rfree = 0.000) for 1216 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 7: After refmac, R = 0.2505 (Rfree = 0.000) for 1213 atoms. Found 8 (10 requested) and removed 9 (5 requested) atoms. Cycle 8: After refmac, R = 0.2750 (Rfree = 0.000) for 1206 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 9: After refmac, R = 0.2325 (Rfree = 0.000) for 1191 atoms. Found 9 (10 requested) and removed 8 (5 requested) atoms. Cycle 10: After refmac, R = 0.2364 (Rfree = 0.000) for 1189 atoms. Found 5 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 2.87 Search for helices and strands: 0 residues in 0 chains, 1257 seeds are put forward NCS extension: 0 residues added, 1257 seeds are put forward Round 1: 121 peptides, 14 chains. Longest chain 20 peptides. Score 0.632 Round 2: 125 peptides, 12 chains. Longest chain 32 peptides. Score 0.695 Round 3: 125 peptides, 15 chains. Longest chain 22 peptides. Score 0.629 Round 4: 129 peptides, 15 chains. Longest chain 20 peptides. Score 0.649 Round 5: 134 peptides, 13 chains. Longest chain 20 peptides. Score 0.713 Taking the results from Round 5 Chains 14, Residues 121, Estimated correctness of the model 67.9 % 2 chains (28 residues) have been docked in sequence Building loops using Loopy2018 14 chains (121 residues) following loop building 2 chains (28 residues) in sequence following loop building ------------------------------------------------------ 3896 reflections ( 99.82 % complete ) and 2394 restraints for refining 1242 atoms. 1836 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2653 (Rfree = 0.000) for 1242 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 12: After refmac, R = 0.2386 (Rfree = 0.000) for 1234 atoms. Found 8 (11 requested) and removed 8 (5 requested) atoms. Cycle 13: After refmac, R = 0.2208 (Rfree = 0.000) for 1233 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 14: After refmac, R = 0.2136 (Rfree = 0.000) for 1228 atoms. Found 3 (10 requested) and removed 8 (5 requested) atoms. Cycle 15: After refmac, R = 0.2116 (Rfree = 0.000) for 1221 atoms. Found 2 (9 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.21 2.88 Search for helices and strands: 0 residues in 0 chains, 1262 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 1287 seeds are put forward Round 1: 116 peptides, 14 chains. Longest chain 20 peptides. Score 0.605 Round 2: 127 peptides, 13 chains. Longest chain 17 peptides. Score 0.683 Round 3: 122 peptides, 11 chains. Longest chain 31 peptides. Score 0.702 Round 4: 115 peptides, 16 chains. Longest chain 15 peptides. Score 0.549 Round 5: 124 peptides, 14 chains. Longest chain 16 peptides. Score 0.647 Taking the results from Round 3 Chains 13, Residues 111, Estimated correctness of the model 65.6 % 3 chains (51 residues) have been docked in sequence Building loops using Loopy2018 13 chains (111 residues) following loop building 3 chains (51 residues) in sequence following loop building ------------------------------------------------------ 3896 reflections ( 99.82 % complete ) and 2176 restraints for refining 1241 atoms. 1558 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2644 (Rfree = 0.000) for 1241 atoms. Found 9 (10 requested) and removed 9 (5 requested) atoms. Cycle 17: After refmac, R = 0.2334 (Rfree = 0.000) for 1236 atoms. Found 5 (10 requested) and removed 6 (5 requested) atoms. Cycle 18: After refmac, R = 0.2187 (Rfree = 0.000) for 1229 atoms. Found 9 (9 requested) and removed 6 (5 requested) atoms. Cycle 19: After refmac, R = 0.2127 (Rfree = 0.000) for 1230 atoms. Found 2 (9 requested) and removed 7 (5 requested) atoms. Cycle 20: After refmac, R = 0.2050 (Rfree = 0.000) for 1222 atoms. Found 2 (8 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.23 2.90 Search for helices and strands: 0 residues in 0 chains, 1281 seeds are put forward NCS extension: 50 residues added (3 deleted due to clashes), 1331 seeds are put forward Round 1: 109 peptides, 13 chains. Longest chain 21 peptides. Score 0.592 Round 2: 108 peptides, 11 chains. Longest chain 27 peptides. Score 0.636 Round 3: 113 peptides, 14 chains. Longest chain 16 peptides. Score 0.589 Round 4: 115 peptides, 10 chains. Longest chain 26 peptides. Score 0.693 Round 5: 121 peptides, 13 chains. Longest chain 31 peptides. Score 0.654 Taking the results from Round 4 Chains 10, Residues 105, Estimated correctness of the model 63.6 % 3 chains (56 residues) have been docked in sequence ------------------------------------------------------ 3896 reflections ( 99.82 % complete ) and 2209 restraints for refining 1242 atoms. 1583 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2700 (Rfree = 0.000) for 1242 atoms. Found 9 (9 requested) and removed 12 (5 requested) atoms. Cycle 22: After refmac, R = 0.2827 (Rfree = 0.000) for 1233 atoms. Found 9 (9 requested) and removed 8 (5 requested) atoms. Cycle 23: After refmac, R = 0.2878 (Rfree = 0.000) for 1224 atoms. Found 9 (9 requested) and removed 11 (5 requested) atoms. Cycle 24: After refmac, R = 0.2269 (Rfree = 0.000) for 1215 atoms. Found 6 (8 requested) and removed 10 (5 requested) atoms. Cycle 25: After refmac, R = 0.2508 (Rfree = 0.000) for 1209 atoms. Found 6 (8 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.18 2.86 Search for helices and strands: 0 residues in 0 chains, 1266 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 1284 seeds are put forward Round 1: 109 peptides, 14 chains. Longest chain 17 peptides. Score 0.566 Round 2: 119 peptides, 11 chains. Longest chain 28 peptides. Score 0.689 Round 3: 129 peptides, 9 chains. Longest chain 36 peptides. Score 0.768 Round 4: 130 peptides, 9 chains. Longest chain 34 peptides. Score 0.772 Round 5: 117 peptides, 9 chains. Longest chain 34 peptides. Score 0.723 Taking the results from Round 4 Chains 12, Residues 121, Estimated correctness of the model 78.9 % 4 chains (71 residues) have been docked in sequence Building loops using Loopy2018 12 chains (121 residues) following loop building 4 chains (71 residues) in sequence following loop building ------------------------------------------------------ 3896 reflections ( 99.82 % complete ) and 1911 restraints for refining 1242 atoms. 1153 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2716 (Rfree = 0.000) for 1242 atoms. Found 9 (9 requested) and removed 16 (5 requested) atoms. Cycle 27: After refmac, R = 0.2549 (Rfree = 0.000) for 1230 atoms. Found 9 (9 requested) and removed 10 (5 requested) atoms. Cycle 28: After refmac, R = 0.2542 (Rfree = 0.000) for 1225 atoms. Found 8 (8 requested) and removed 14 (5 requested) atoms. Cycle 29: After refmac, R = 0.2481 (Rfree = 0.000) for 1214 atoms. Found 7 (7 requested) and removed 9 (5 requested) atoms. Cycle 30: After refmac, R = 0.2404 (Rfree = 0.000) for 1210 atoms. Found 7 (7 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.19 2.86 Search for helices and strands: 0 residues in 0 chains, 1270 seeds are put forward NCS extension: 36 residues added (6 deleted due to clashes), 1306 seeds are put forward Round 1: 109 peptides, 13 chains. Longest chain 19 peptides. Score 0.592 Round 2: 129 peptides, 10 chains. Longest chain 27 peptides. Score 0.750 Round 3: 124 peptides, 7 chains. Longest chain 35 peptides. Score 0.786 Round 4: 113 peptides, 9 chains. Longest chain 21 peptides. Score 0.706 Round 5: 116 peptides, 11 chains. Longest chain 28 peptides. Score 0.675 Taking the results from Round 3 Chains 8, Residues 117, Estimated correctness of the model 81.2 % 3 chains (81 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 36 A and 47 A 6 chains (124 residues) following loop building 2 chains (91 residues) in sequence following loop building ------------------------------------------------------ 3896 reflections ( 99.82 % complete ) and 1674 restraints for refining 1242 atoms. 800 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3216 (Rfree = 0.000) for 1242 atoms. Found 8 (8 requested) and removed 17 (5 requested) atoms. Cycle 32: After refmac, R = 0.2713 (Rfree = 0.000) for 1213 atoms. Found 6 (7 requested) and removed 7 (5 requested) atoms. Cycle 33: After refmac, R = 0.2750 (Rfree = 0.000) for 1205 atoms. Found 7 (7 requested) and removed 11 (5 requested) atoms. Cycle 34: After refmac, R = 0.2348 (Rfree = 0.000) for 1196 atoms. Found 6 (6 requested) and removed 6 (5 requested) atoms. Cycle 35: After refmac, R = 0.2233 (Rfree = 0.000) for 1190 atoms. Found 1 (6 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.18 2.86 Search for helices and strands: 0 residues in 0 chains, 1245 seeds are put forward NCS extension: 25 residues added (12 deleted due to clashes), 1270 seeds are put forward Round 1: 115 peptides, 9 chains. Longest chain 30 peptides. Score 0.714 Round 2: 111 peptides, 11 chains. Longest chain 22 peptides. Score 0.651 Round 3: 114 peptides, 9 chains. Longest chain 30 peptides. Score 0.710 Round 4: 113 peptides, 10 chains. Longest chain 24 peptides. Score 0.684 Round 5: 110 peptides, 9 chains. Longest chain 23 peptides. Score 0.692 Taking the results from Round 1 Chains 10, Residues 106, Estimated correctness of the model 68.1 % 3 chains (65 residues) have been docked in sequence Building loops using Loopy2018 10 chains (106 residues) following loop building 3 chains (65 residues) in sequence following loop building ------------------------------------------------------ 3896 reflections ( 99.82 % complete ) and 2021 restraints for refining 1221 atoms. 1337 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2877 (Rfree = 0.000) for 1221 atoms. Found 6 (6 requested) and removed 15 (5 requested) atoms. Cycle 37: After refmac, R = 0.2658 (Rfree = 0.000) for 1210 atoms. Found 6 (6 requested) and removed 7 (5 requested) atoms. Cycle 38: After refmac, R = 0.2408 (Rfree = 0.000) for 1208 atoms. Found 6 (6 requested) and removed 6 (5 requested) atoms. Cycle 39: After refmac, R = 0.2247 (Rfree = 0.000) for 1207 atoms. Found 4 (5 requested) and removed 5 (5 requested) atoms. Cycle 40: After refmac, R = 0.2039 (Rfree = 0.000) for 1203 atoms. Found 1 (5 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.21 2.88 Search for helices and strands: 0 residues in 0 chains, 1254 seeds are put forward NCS extension: 19 residues added (9 deleted due to clashes), 1273 seeds are put forward Round 1: 97 peptides, 12 chains. Longest chain 20 peptides. Score 0.549 Round 2: 107 peptides, 9 chains. Longest chain 26 peptides. Score 0.679 Round 3: 106 peptides, 9 chains. Longest chain 23 peptides. Score 0.674 Round 4: 108 peptides, 9 chains. Longest chain 30 peptides. Score 0.683 Round 5: 104 peptides, 9 chains. Longest chain 28 peptides. Score 0.664 Taking the results from Round 4 Chains 9, Residues 99, Estimated correctness of the model 61.5 % 2 chains (49 residues) have been docked in sequence ------------------------------------------------------ 3896 reflections ( 99.82 % complete ) and 2155 restraints for refining 1241 atoms. 1554 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2427 (Rfree = 0.000) for 1241 atoms. Found 5 (5 requested) and removed 7 (5 requested) atoms. Cycle 42: After refmac, R = 0.2324 (Rfree = 0.000) for 1233 atoms. Found 2 (5 requested) and removed 9 (5 requested) atoms. Cycle 43: After refmac, R = 0.2239 (Rfree = 0.000) for 1223 atoms. Found 0 (5 requested) and removed 6 (5 requested) atoms. Cycle 44: After refmac, R = 0.2271 (Rfree = 0.000) for 1217 atoms. Found 3 (5 requested) and removed 5 (5 requested) atoms. Cycle 45: After refmac, R = 0.2137 (Rfree = 0.000) for 1213 atoms. Found 0 (5 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.19 2.86 Search for helices and strands: 0 residues in 0 chains, 1275 seeds are put forward NCS extension: 30 residues added (5 deleted due to clashes), 1305 seeds are put forward Round 1: 88 peptides, 9 chains. Longest chain 18 peptides. Score 0.578 Round 2: 104 peptides, 9 chains. Longest chain 22 peptides. Score 0.664 Round 3: 108 peptides, 11 chains. Longest chain 21 peptides. Score 0.636 Round 4: 102 peptides, 10 chains. Longest chain 17 peptides. Score 0.630 Round 5: 93 peptides, 9 chains. Longest chain 17 peptides. Score 0.607 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 95, Estimated correctness of the model 57.1 % 2 chains (36 residues) have been docked in sequence Sequence coverage is 37 % Consider running further cycles of model building using 2o3l-3_warpNtrace.pdb as input Building loops using Loopy2018 10 chains (95 residues) following loop building 2 chains (36 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3896 reflections ( 99.82 % complete ) and 2312 restraints for refining 1233 atoms. 1788 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2320 (Rfree = 0.000) for 1233 atoms. Found 0 (5 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2611 (Rfree = 0.000) for 1227 atoms. Found 0 (5 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2272 (Rfree = 0.000) for 1219 atoms. Found 0 (5 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2163 (Rfree = 0.000) for 1212 atoms. Found 0 (5 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:52:39 GMT 2018 Job finished. TimeTaking 22.75 Used memory is bytes: 9924896