Sun 23 Dec 22:22:43 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 2pv4-1.9-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pv4-1.9-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pv4-1.9-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pv4-1.9-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/2pv4-1.9-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pv4-1.9-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 ============================================================ Sun 23 Dec 22:22:52 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/2pv4-1.9-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pv4-1.9-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 142 and 0 Target number of residues in the AU: 142 Target solvent content: 0.5420 Checking the provided sequence file Detected sequence length: 145 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 145 Adjusted target solvent content: 0.53 Input MTZ file: 2pv4-1.9-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: 19 Cell parameters: 35.957 47.283 98.695 90.000 90.000 90.000 Input sequence file: 2pv4-1.9-parrot-hancs.fasta_lf Building free atoms model in initial map for 1160 target number of atoms Had to go as low as 0.50 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 1 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: 49.347 1.950 Wilson plot Bfac: 32.94 12845 reflections ( 99.89 % complete ) and 0 restraints for refining 1290 atoms. Observations/parameters ratio is 2.49 ------------------------------------------------------ Starting model: R = 0.3351 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2752 (Rfree = 0.000) for 1290 atoms. Found 47 (47 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.23 2.14 Round 1: 100 peptides, 10 chains. Longest chain 17 peptides. Score 0.698 Round 2: 117 peptides, 8 chains. Longest chain 26 peptides. Score 0.819 Round 3: 129 peptides, 7 chains. Longest chain 28 peptides. Score 0.871 Round 4: 132 peptides, 4 chains. Longest chain 45 peptides. Score 0.915 Round 5: 129 peptides, 4 chains. Longest chain 43 peptides. Score 0.910 Taking the results from Round 4 Chains 5, Residues 128, Estimated correctness of the model 99.3 % 3 chains (119 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 47 A and 52 A 3 chains (130 residues) following loop building 2 chains (123 residues) in sequence following loop building ------------------------------------------------------ 12845 reflections ( 99.89 % complete ) and 1256 restraints for refining 1207 atoms. 232 conditional restraints added. Observations/parameters ratio is 2.66 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2886 (Rfree = 0.000) for 1207 atoms. Found 44 (44 requested) and removed 25 (22 requested) atoms. Cycle 2: After refmac, R = 0.2651 (Rfree = 0.000) for 1215 atoms. Found 31 (44 requested) and removed 22 (22 requested) atoms. Cycle 3: After refmac, R = 0.2504 (Rfree = 0.000) for 1218 atoms. Found 25 (43 requested) and removed 22 (22 requested) atoms. Cycle 4: After refmac, R = 0.2443 (Rfree = 0.000) for 1213 atoms. Found 33 (41 requested) and removed 22 (22 requested) atoms. Cycle 5: After refmac, R = 0.2409 (Rfree = 0.000) for 1218 atoms. Found 32 (41 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.18 2.09 Round 1: 134 peptides, 3 chains. Longest chain 46 peptides. Score 0.929 Round 2: 137 peptides, 2 chains. Longest chain 90 peptides. Score 0.943 Round 3: 132 peptides, 5 chains. Longest chain 47 peptides. Score 0.903 Round 4: 137 peptides, 2 chains. Longest chain 90 peptides. Score 0.943 Round 5: 129 peptides, 7 chains. Longest chain 30 peptides. Score 0.871 Taking the results from Round 4 Chains 3, Residues 135, Estimated correctness of the model 99.7 % 2 chains (134 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 91 A and 100 A 2 chains (143 residues) following loop building 2 chains (143 residues) in sequence following loop building ------------------------------------------------------ 12845 reflections ( 99.89 % complete ) and 1215 restraints for refining 1262 atoms. 68 conditional restraints added. Observations/parameters ratio is 2.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2706 (Rfree = 0.000) for 1262 atoms. Found 36 (41 requested) and removed 28 (23 requested) atoms. Cycle 7: After refmac, R = 0.2537 (Rfree = 0.000) for 1267 atoms. Found 23 (40 requested) and removed 23 (23 requested) atoms. Cycle 8: After refmac, R = 0.2423 (Rfree = 0.000) for 1265 atoms. Found 20 (40 requested) and removed 23 (23 requested) atoms. Cycle 9: After refmac, R = 0.2323 (Rfree = 0.000) for 1261 atoms. Found 22 (39 requested) and removed 15 (23 requested) atoms. Cycle 10: After refmac, R = 0.2267 (Rfree = 0.000) for 1262 atoms. Found 23 (38 requested) and removed 18 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.21 2.12 Round 1: 138 peptides, 2 chains. Longest chain 91 peptides. Score 0.944 Round 2: 139 peptides, 3 chains. Longest chain 57 peptides. Score 0.936 Round 3: 136 peptides, 3 chains. Longest chain 91 peptides. Score 0.932 Round 4: 137 peptides, 3 chains. Longest chain 61 peptides. Score 0.933 Round 5: 137 peptides, 3 chains. Longest chain 47 peptides. Score 0.933 Taking the results from Round 1 Chains 3, Residues 136, Estimated correctness of the model 99.7 % 2 chains (135 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 92 A and 100 A 2 chains (143 residues) following loop building 2 chains (143 residues) in sequence following loop building ------------------------------------------------------ 12845 reflections ( 99.89 % complete ) and 1226 restraints for refining 1274 atoms. 79 conditional restraints added. Observations/parameters ratio is 2.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2661 (Rfree = 0.000) for 1274 atoms. Found 33 (37 requested) and removed 28 (23 requested) atoms. Cycle 12: After refmac, R = 0.2441 (Rfree = 0.000) for 1274 atoms. Found 28 (37 requested) and removed 23 (23 requested) atoms. Cycle 13: After refmac, R = 0.2352 (Rfree = 0.000) for 1277 atoms. Found 27 (36 requested) and removed 23 (23 requested) atoms. Cycle 14: After refmac, R = 0.2262 (Rfree = 0.000) for 1279 atoms. Found 30 (35 requested) and removed 23 (23 requested) atoms. Cycle 15: After refmac, R = 0.2230 (Rfree = 0.000) for 1285 atoms. Found 31 (34 requested) and removed 20 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.19 2.10 Round 1: 136 peptides, 3 chains. Longest chain 61 peptides. Score 0.932 Round 2: 137 peptides, 2 chains. Longest chain 90 peptides. Score 0.943 Round 3: 136 peptides, 3 chains. Longest chain 90 peptides. Score 0.932 Round 4: 134 peptides, 4 chains. Longest chain 61 peptides. Score 0.918 Round 5: 126 peptides, 7 chains. Longest chain 37 peptides. Score 0.863 Taking the results from Round 2 Chains 4, Residues 135, Estimated correctness of the model 99.7 % 3 chains (134 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 92 A and 100 A 3 chains (142 residues) following loop building 2 chains (141 residues) in sequence following loop building ------------------------------------------------------ 12845 reflections ( 99.89 % complete ) and 1234 restraints for refining 1284 atoms. 97 conditional restraints added. Observations/parameters ratio is 2.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2656 (Rfree = 0.000) for 1284 atoms. Found 33 (33 requested) and removed 26 (23 requested) atoms. Cycle 17: After refmac, R = 0.2440 (Rfree = 0.000) for 1288 atoms. Found 18 (32 requested) and removed 22 (23 requested) atoms. Cycle 18: After refmac, R = 0.2302 (Rfree = 0.000) for 1280 atoms. Found 27 (31 requested) and removed 16 (23 requested) atoms. Cycle 19: After refmac, R = 0.2244 (Rfree = 0.000) for 1287 atoms. Found 24 (30 requested) and removed 14 (23 requested) atoms. Cycle 20: After refmac, R = 0.2202 (Rfree = 0.000) for 1294 atoms. Found 26 (29 requested) and removed 18 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.19 2.10 Round 1: 139 peptides, 4 chains. Longest chain 59 peptides. Score 0.926 Round 2: 137 peptides, 2 chains. Longest chain 90 peptides. Score 0.943 Round 3: 136 peptides, 3 chains. Longest chain 47 peptides. Score 0.932 Round 4: 137 peptides, 3 chains. Longest chain 91 peptides. Score 0.933 Round 5: 137 peptides, 3 chains. Longest chain 54 peptides. Score 0.933 Taking the results from Round 2 Chains 4, Residues 135, Estimated correctness of the model 99.7 % 3 chains (134 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 92 A and 100 A 3 chains (142 residues) following loop building 2 chains (141 residues) in sequence following loop building ------------------------------------------------------ 12845 reflections ( 99.89 % complete ) and 1223 restraints for refining 1291 atoms. 86 conditional restraints added. Observations/parameters ratio is 2.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2625 (Rfree = 0.000) for 1291 atoms. Found 28 (28 requested) and removed 27 (23 requested) atoms. Cycle 22: After refmac, R = 0.2404 (Rfree = 0.000) for 1291 atoms. Found 23 (27 requested) and removed 21 (23 requested) atoms. Cycle 23: After refmac, R = 0.2291 (Rfree = 0.000) for 1290 atoms. Found 20 (26 requested) and removed 10 (23 requested) atoms. Cycle 24: After refmac, R = 0.2231 (Rfree = 0.000) for 1300 atoms. Found 20 (26 requested) and removed 13 (23 requested) atoms. Cycle 25: After refmac, R = 0.2199 (Rfree = 0.000) for 1307 atoms. Found 18 (26 requested) and removed 18 (24 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.19 2.10 Round 1: 133 peptides, 3 chains. Longest chain 58 peptides. Score 0.928 Round 2: 133 peptides, 5 chains. Longest chain 59 peptides. Score 0.905 Round 3: 133 peptides, 4 chains. Longest chain 47 peptides. Score 0.917 Round 4: 139 peptides, 4 chains. Longest chain 54 peptides. Score 0.926 Round 5: 139 peptides, 3 chains. Longest chain 89 peptides. Score 0.936 Taking the results from Round 5 Chains 3, Residues 136, Estimated correctness of the model 99.6 % 2 chains (133 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 92 A and 100 A 1 chains (140 residues) following loop building 1 chains (140 residues) in sequence following loop building ------------------------------------------------------ 12845 reflections ( 99.89 % complete ) and 1259 restraints for refining 1286 atoms. 130 conditional restraints added. Observations/parameters ratio is 2.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2684 (Rfree = 0.000) for 1286 atoms. Found 24 (24 requested) and removed 28 (23 requested) atoms. Cycle 27: After refmac, R = 0.2459 (Rfree = 0.000) for 1278 atoms. Found 23 (23 requested) and removed 23 (23 requested) atoms. Cycle 28: After refmac, R = 0.2337 (Rfree = 0.000) for 1278 atoms. Found 18 (23 requested) and removed 19 (23 requested) atoms. Cycle 29: After refmac, R = 0.2264 (Rfree = 0.000) for 1276 atoms. Found 23 (23 requested) and removed 8 (23 requested) atoms. Cycle 30: After refmac, R = 0.2202 (Rfree = 0.000) for 1289 atoms. Found 20 (23 requested) and removed 11 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.19 2.10 Round 1: 138 peptides, 4 chains. Longest chain 60 peptides. Score 0.925 Round 2: 140 peptides, 2 chains. Longest chain 108 peptides. Score 0.947 Round 3: 139 peptides, 3 chains. Longest chain 60 peptides. Score 0.936 Round 4: 139 peptides, 4 chains. Longest chain 58 peptides. Score 0.926 Round 5: 136 peptides, 3 chains. Longest chain 53 peptides. Score 0.932 Taking the results from Round 2 Chains 4, Residues 138, Estimated correctness of the model 99.7 % 3 chains (135 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 108 A and 114 A 2 chains (140 residues) following loop building 2 chains (140 residues) in sequence following loop building ------------------------------------------------------ 12845 reflections ( 99.89 % complete ) and 1246 restraints for refining 1297 atoms. 115 conditional restraints added. Observations/parameters ratio is 2.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2548 (Rfree = 0.000) for 1297 atoms. Found 23 (23 requested) and removed 28 (23 requested) atoms. Cycle 32: After refmac, R = 0.2398 (Rfree = 0.000) for 1290 atoms. Found 23 (23 requested) and removed 23 (23 requested) atoms. Cycle 33: After refmac, R = 0.2287 (Rfree = 0.000) for 1290 atoms. Found 21 (23 requested) and removed 17 (23 requested) atoms. Cycle 34: After refmac, R = 0.2241 (Rfree = 0.000) for 1294 atoms. Found 16 (23 requested) and removed 14 (23 requested) atoms. Cycle 35: After refmac, R = 0.2193 (Rfree = 0.000) for 1296 atoms. Found 23 (23 requested) and removed 11 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.19 2.10 Round 1: 139 peptides, 3 chains. Longest chain 60 peptides. Score 0.936 Round 2: 142 peptides, 3 chains. Longest chain 90 peptides. Score 0.940 Round 3: 137 peptides, 3 chains. Longest chain 58 peptides. Score 0.933 Round 4: 137 peptides, 3 chains. Longest chain 51 peptides. Score 0.933 Round 5: 130 peptides, 4 chains. Longest chain 54 peptides. Score 0.912 Taking the results from Round 2 Chains 5, Residues 139, Estimated correctness of the model 99.6 % 4 chains (134 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 30 A and 37 A Built loop between residues 91 A and 94 A Built loop between residues 110 A and 113 A 1 chains (144 residues) following loop building 1 chains (144 residues) in sequence following loop building ------------------------------------------------------ 12845 reflections ( 99.89 % complete ) and 1263 restraints for refining 1325 atoms. 103 conditional restraints added. Observations/parameters ratio is 2.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2635 (Rfree = 0.000) for 1325 atoms. Found 23 (24 requested) and removed 31 (24 requested) atoms. Cycle 37: After refmac, R = 0.2399 (Rfree = 0.000) for 1313 atoms. Found 24 (24 requested) and removed 24 (24 requested) atoms. Cycle 38: After refmac, R = 0.2345 (Rfree = 0.000) for 1311 atoms. Found 16 (24 requested) and removed 24 (24 requested) atoms. Cycle 39: After refmac, R = 0.2280 (Rfree = 0.000) for 1302 atoms. Found 21 (23 requested) and removed 19 (23 requested) atoms. Cycle 40: After refmac, R = 0.2248 (Rfree = 0.000) for 1301 atoms. Found 20 (24 requested) and removed 12 (24 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.19 2.10 Round 1: 136 peptides, 3 chains. Longest chain 58 peptides. Score 0.932 Round 2: 142 peptides, 2 chains. Longest chain 110 peptides. Score 0.949 Round 3: 134 peptides, 5 chains. Longest chain 51 peptides. Score 0.907 Round 4: 141 peptides, 3 chains. Longest chain 89 peptides. Score 0.939 Round 5: 142 peptides, 2 chains. Longest chain 106 peptides. Score 0.949 Taking the results from Round 5 Chains 2, Residues 140, Estimated correctness of the model 99.7 % 2 chains (140 residues) have been docked in sequence Building loops using Loopy2018 2 chains (140 residues) following loop building 2 chains (140 residues) in sequence following loop building ------------------------------------------------------ 12845 reflections ( 99.89 % complete ) and 1283 restraints for refining 1299 atoms. 161 conditional restraints added. Observations/parameters ratio is 2.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2625 (Rfree = 0.000) for 1299 atoms. Found 23 (23 requested) and removed 28 (23 requested) atoms. Cycle 42: After refmac, R = 0.2420 (Rfree = 0.000) for 1290 atoms. Found 17 (23 requested) and removed 24 (23 requested) atoms. Cycle 43: After refmac, R = 0.2295 (Rfree = 0.000) for 1282 atoms. Found 23 (23 requested) and removed 18 (23 requested) atoms. Cycle 44: After refmac, R = 0.2237 (Rfree = 0.000) for 1285 atoms. Found 20 (23 requested) and removed 7 (23 requested) atoms. Cycle 45: After refmac, R = 0.2177 (Rfree = 0.000) for 1296 atoms. Found 18 (23 requested) and removed 14 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.21 2.12 Round 1: 136 peptides, 3 chains. Longest chain 51 peptides. Score 0.932 Round 2: 139 peptides, 4 chains. Longest chain 51 peptides. Score 0.926 Round 3: 141 peptides, 2 chains. Longest chain 94 peptides. Score 0.948 Round 4: 137 peptides, 5 chains. Longest chain 36 peptides. Score 0.912 Round 5: 139 peptides, 4 chains. Longest chain 60 peptides. Score 0.926 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 139, Estimated correctness of the model 99.7 % 2 chains (139 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 47 A and 52 A 1 chains (143 residues) following loop building 1 chains (143 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 12845 reflections ( 99.89 % complete ) and 1152 restraints for refining 1136 atoms. Observations/parameters ratio is 2.83 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3147 (Rfree = 0.000) for 1136 atoms. Found 7 (20 requested) and removed 0 (20 requested) atoms. Cycle 47: After refmac, R = 0.2939 (Rfree = 0.000) for 1136 atoms. Found 4 (21 requested) and removed 0 (21 requested) atoms. Cycle 48: After refmac, R = 0.2814 (Rfree = 0.000) for 1136 atoms. Found 2 (21 requested) and removed 1 (21 requested) atoms. Cycle 49: After refmac, R = 0.2734 (Rfree = 0.000) for 1136 atoms. TimeTaking 29.63