Sun 23 Dec 22:22:55 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 2fg9-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fg9-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fg9-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg9-3.2-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/2fg9-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg9-3.2-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 22:23:04 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/2fg9-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg9-3.2-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 133 and 0 Target number of residues in the AU: 133 Target solvent content: 0.6410 Checking the provided sequence file Detected sequence length: 178 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 178 Adjusted target solvent content: 0.52 Input MTZ file: 2fg9-3.2-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: 211 Cell parameters: 134.000 134.000 134.000 90.000 90.000 90.000 Input sequence file: 2fg9-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1424 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: 94.752 3.201 Wilson plot Bfac: 71.38 3624 reflections ( 99.67 % complete ) and 0 restraints for refining 1570 atoms. Observations/parameters ratio is 0.58 ------------------------------------------------------ Starting model: R = 0.3388 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3049 (Rfree = 0.000) for 1570 atoms. Found 2 (14 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.26 3.17 Search for helices and strands: 0 residues in 0 chains, 1591 seeds are put forward Round 1: 97 peptides, 17 chains. Longest chain 13 peptides. Score 0.418 Round 2: 114 peptides, 16 chains. Longest chain 15 peptides. Score 0.567 Round 3: 132 peptides, 17 chains. Longest chain 15 peptides. Score 0.645 Round 4: 133 peptides, 16 chains. Longest chain 17 peptides. Score 0.673 Round 5: 132 peptides, 16 chains. Longest chain 24 peptides. Score 0.668 Taking the results from Round 4 Chains 17, Residues 117, Estimated correctness of the model 59.2 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3624 reflections ( 99.67 % complete ) and 2660 restraints for refining 1299 atoms. 2174 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2840 (Rfree = 0.000) for 1299 atoms. Found 8 (11 requested) and removed 10 (5 requested) atoms. Cycle 2: After refmac, R = 0.2674 (Rfree = 0.000) for 1271 atoms. Found 8 (11 requested) and removed 7 (5 requested) atoms. Cycle 3: After refmac, R = 0.2536 (Rfree = 0.000) for 1261 atoms. Found 5 (11 requested) and removed 5 (5 requested) atoms. Cycle 4: After refmac, R = 0.2474 (Rfree = 0.000) for 1254 atoms. Found 1 (11 requested) and removed 7 (5 requested) atoms. Cycle 5: After refmac, R = 0.2728 (Rfree = 0.000) for 1245 atoms. Found 4 (11 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.25 3.16 Search for helices and strands: 0 residues in 0 chains, 1286 seeds are put forward Round 1: 111 peptides, 16 chains. Longest chain 13 peptides. Score 0.548 Round 2: 128 peptides, 14 chains. Longest chain 17 peptides. Score 0.693 Round 3: 139 peptides, 15 chains. Longest chain 26 peptides. Score 0.722 Round 4: 137 peptides, 14 chains. Longest chain 22 peptides. Score 0.733 Round 5: 130 peptides, 13 chains. Longest chain 27 peptides. Score 0.723 Taking the results from Round 4 Chains 14, Residues 123, Estimated correctness of the model 71.8 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 3624 reflections ( 99.67 % complete ) and 2516 restraints for refining 1300 atoms. 1943 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2823 (Rfree = 0.000) for 1300 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Cycle 7: After refmac, R = 0.2551 (Rfree = 0.000) for 1291 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 8: After refmac, R = 0.2514 (Rfree = 0.000) for 1284 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. Cycle 9: After refmac, R = 0.2512 (Rfree = 0.000) for 1277 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. Cycle 10: After refmac, R = 0.2533 (Rfree = 0.000) for 1272 atoms. Found 1 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.34 3.25 Search for helices and strands: 0 residues in 0 chains, 1307 seeds are put forward Round 1: 123 peptides, 15 chains. Longest chain 19 peptides. Score 0.645 Round 2: 132 peptides, 13 chains. Longest chain 26 peptides. Score 0.732 Round 3: 128 peptides, 13 chains. Longest chain 22 peptides. Score 0.715 Round 4: 134 peptides, 15 chains. Longest chain 26 peptides. Score 0.700 Round 5: 126 peptides, 13 chains. Longest chain 23 peptides. Score 0.706 Taking the results from Round 2 Chains 15, Residues 119, Estimated correctness of the model 71.6 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 3624 reflections ( 99.67 % complete ) and 2553 restraints for refining 1300 atoms. 2005 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2707 (Rfree = 0.000) for 1300 atoms. Found 8 (10 requested) and removed 11 (5 requested) atoms. Cycle 12: After refmac, R = 0.2326 (Rfree = 0.000) for 1293 atoms. Found 5 (10 requested) and removed 6 (5 requested) atoms. Cycle 13: After refmac, R = 0.2479 (Rfree = 0.000) for 1287 atoms. Found 9 (9 requested) and removed 8 (5 requested) atoms. Cycle 14: After refmac, R = 0.2201 (Rfree = 0.000) for 1286 atoms. Found 1 (9 requested) and removed 8 (5 requested) atoms. Cycle 15: After refmac, R = 0.2312 (Rfree = 0.000) for 1276 atoms. Found 5 (9 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.22 3.14 Search for helices and strands: 0 residues in 0 chains, 1323 seeds are put forward Round 1: 119 peptides, 15 chains. Longest chain 25 peptides. Score 0.623 Round 2: 124 peptides, 10 chains. Longest chain 31 peptides. Score 0.758 Round 3: 121 peptides, 11 chains. Longest chain 29 peptides. Score 0.726 Round 4: 128 peptides, 14 chains. Longest chain 19 peptides. Score 0.693 Round 5: 125 peptides, 11 chains. Longest chain 23 peptides. Score 0.743 Taking the results from Round 2 Chains 11, Residues 114, Estimated correctness of the model 76.5 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 3624 reflections ( 99.67 % complete ) and 2484 restraints for refining 1300 atoms. 1934 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2535 (Rfree = 0.000) for 1300 atoms. Found 7 (9 requested) and removed 9 (5 requested) atoms. Cycle 17: After refmac, R = 0.2295 (Rfree = 0.000) for 1294 atoms. Found 1 (9 requested) and removed 6 (5 requested) atoms. Cycle 18: After refmac, R = 0.2507 (Rfree = 0.000) for 1285 atoms. Found 8 (8 requested) and removed 7 (5 requested) atoms. Cycle 19: After refmac, R = 0.2221 (Rfree = 0.000) for 1283 atoms. Found 3 (8 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.2231 (Rfree = 0.000) for 1279 atoms. Found 2 (8 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.33 3.24 Search for helices and strands: 0 residues in 0 chains, 1310 seeds are put forward Round 1: 138 peptides, 15 chains. Longest chain 29 peptides. Score 0.718 Round 2: 133 peptides, 16 chains. Longest chain 20 peptides. Score 0.673 Round 3: 134 peptides, 15 chains. Longest chain 19 peptides. Score 0.700 Round 4: 138 peptides, 12 chains. Longest chain 22 peptides. Score 0.774 Round 5: 140 peptides, 15 chains. Longest chain 20 peptides. Score 0.726 Taking the results from Round 4 Chains 13, Residues 126, Estimated correctness of the model 79.2 % 2 chains (23 residues) have been docked in sequence Building loops using Loopy2018 13 chains (126 residues) following loop building 2 chains (23 residues) in sequence following loop building ------------------------------------------------------ 3624 reflections ( 99.67 % complete ) and 2374 restraints for refining 1300 atoms. 1783 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2637 (Rfree = 0.000) for 1300 atoms. Found 8 (8 requested) and removed 8 (5 requested) atoms. Cycle 22: After refmac, R = 0.2429 (Rfree = 0.000) for 1294 atoms. Found 4 (7 requested) and removed 7 (5 requested) atoms. Cycle 23: After refmac, R = 0.2758 (Rfree = 0.000) for 1287 atoms. Found 7 (7 requested) and removed 6 (5 requested) atoms. Cycle 24: After refmac, R = 0.2311 (Rfree = 0.000) for 1286 atoms. Found 2 (7 requested) and removed 6 (5 requested) atoms. Cycle 25: After refmac, R = 0.2807 (Rfree = 0.000) for 1279 atoms. Found 7 (7 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 3.23 Search for helices and strands: 0 residues in 0 chains, 1313 seeds are put forward Round 1: 116 peptides, 15 chains. Longest chain 15 peptides. Score 0.606 Round 2: 127 peptides, 11 chains. Longest chain 22 peptides. Score 0.751 Round 3: 126 peptides, 12 chains. Longest chain 21 peptides. Score 0.727 Round 4: 131 peptides, 13 chains. Longest chain 22 peptides. Score 0.728 Round 5: 125 peptides, 10 chains. Longest chain 22 peptides. Score 0.762 Taking the results from Round 5 Chains 12, Residues 115, Estimated correctness of the model 77.2 % 3 chains (39 residues) have been docked in sequence Building loops using Loopy2018 12 chains (115 residues) following loop building 3 chains (39 residues) in sequence following loop building ------------------------------------------------------ 3624 reflections ( 99.67 % complete ) and 2368 restraints for refining 1300 atoms. 1749 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2783 (Rfree = 0.000) for 1300 atoms. Found 5 (7 requested) and removed 47 (5 requested) atoms. Cycle 27: After refmac, R = 0.2522 (Rfree = 0.000) for 1255 atoms. Found 6 (6 requested) and removed 6 (5 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2381 (Rfree = 0.000) for 1252 atoms. Found 6 (6 requested) and removed 7 (5 requested) atoms. Cycle 29: After refmac, R = 0.2303 (Rfree = 0.000) for 1247 atoms. Found 6 (6 requested) and removed 8 (5 requested) atoms. Cycle 30: After refmac, R = 0.2551 (Rfree = 0.000) for 1242 atoms. Found 6 (6 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.39 3.30 Search for helices and strands: 0 residues in 0 chains, 1262 seeds are put forward Round 1: 120 peptides, 15 chains. Longest chain 22 peptides. Score 0.629 Round 2: 122 peptides, 10 chains. Longest chain 31 peptides. Score 0.750 Round 3: 128 peptides, 12 chains. Longest chain 27 peptides. Score 0.735 Round 4: 123 peptides, 12 chains. Longest chain 23 peptides. Score 0.713 Round 5: 119 peptides, 12 chains. Longest chain 24 peptides. Score 0.695 Taking the results from Round 2 Chains 11, Residues 112, Estimated correctness of the model 75.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3624 reflections ( 99.67 % complete ) and 2518 restraints for refining 1300 atoms. 2002 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2491 (Rfree = 0.000) for 1300 atoms. Found 5 (5 requested) and removed 11 (5 requested) atoms. Cycle 32: After refmac, R = 0.2265 (Rfree = 0.000) for 1290 atoms. Found 4 (5 requested) and removed 7 (5 requested) atoms. Cycle 33: After refmac, R = 0.2199 (Rfree = 0.000) for 1287 atoms. Found 3 (5 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.2261 (Rfree = 0.000) for 1285 atoms. Found 5 (5 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.2268 (Rfree = 0.000) for 1285 atoms. Found 3 (5 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.23 3.15 Search for helices and strands: 0 residues in 0 chains, 1321 seeds are put forward Round 1: 109 peptides, 17 chains. Longest chain 16 peptides. Score 0.506 Round 2: 109 peptides, 15 chains. Longest chain 15 peptides. Score 0.564 Round 3: 113 peptides, 15 chains. Longest chain 15 peptides. Score 0.588 Round 4: 118 peptides, 16 chains. Longest chain 17 peptides. Score 0.592 Round 5: 113 peptides, 14 chains. Longest chain 15 peptides. Score 0.615 Taking the results from Round 5 Chains 14, Residues 99, Estimated correctness of the model 45.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3624 reflections ( 99.67 % complete ) and 2828 restraints for refining 1300 atoms. 2446 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2434 (Rfree = 0.000) for 1300 atoms. Found 5 (5 requested) and removed 6 (5 requested) atoms. Cycle 37: After refmac, R = 0.2373 (Rfree = 0.000) for 1297 atoms. Found 4 (5 requested) and removed 5 (5 requested) atoms. Cycle 38: After refmac, R = 0.2372 (Rfree = 0.000) for 1293 atoms. Found 3 (5 requested) and removed 7 (5 requested) atoms. Cycle 39: After refmac, R = 0.2177 (Rfree = 0.000) for 1288 atoms. Found 1 (5 requested) and removed 5 (5 requested) atoms. Cycle 40: After refmac, R = 0.2214 (Rfree = 0.000) for 1283 atoms. Found 1 (5 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.34 3.25 Search for helices and strands: 0 residues in 0 chains, 1316 seeds are put forward Round 1: 87 peptides, 14 chains. Longest chain 14 peptides. Score 0.440 Round 2: 101 peptides, 14 chains. Longest chain 18 peptides. Score 0.540 Round 3: 116 peptides, 16 chains. Longest chain 16 peptides. Score 0.580 Round 4: 116 peptides, 16 chains. Longest chain 19 peptides. Score 0.580 Round 5: 110 peptides, 17 chains. Longest chain 11 peptides. Score 0.512 Taking the results from Round 4 Chains 16, Residues 100, Estimated correctness of the model 35.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3624 reflections ( 99.67 % complete ) and 2832 restraints for refining 1300 atoms. 2448 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2401 (Rfree = 0.000) for 1300 atoms. Found 5 (5 requested) and removed 5 (5 requested) atoms. Cycle 42: After refmac, R = 0.2422 (Rfree = 0.000) for 1298 atoms. Found 5 (5 requested) and removed 6 (5 requested) atoms. Cycle 43: After refmac, R = 0.2524 (Rfree = 0.000) for 1296 atoms. Found 5 (5 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.2239 (Rfree = 0.000) for 1294 atoms. Found 5 (5 requested) and removed 6 (5 requested) atoms. Cycle 45: After refmac, R = 0.2183 (Rfree = 0.000) for 1293 atoms. Found 4 (5 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.22 3.14 Search for helices and strands: 0 residues in 0 chains, 1339 seeds are put forward Round 1: 76 peptides, 12 chains. Longest chain 14 peptides. Score 0.423 Round 2: 92 peptides, 13 chains. Longest chain 16 peptides. Score 0.509 Round 3: 101 peptides, 13 chains. Longest chain 19 peptides. Score 0.570 Round 4: 89 peptides, 13 chains. Longest chain 20 peptides. Score 0.488 Round 5: 95 peptides, 14 chains. Longest chain 14 peptides. Score 0.499 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 88, Estimated correctness of the model 32.7 % 1 chains (13 residues) have been docked in sequence Sequence coverage is 14 % Consider running further cycles of model building using 2fg9-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3624 reflections ( 99.67 % complete ) and 2662 restraints for refining 1300 atoms. 2280 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2397 (Rfree = 0.000) for 1300 atoms. Found 0 (5 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2683 (Rfree = 0.000) for 1291 atoms. Found 0 (5 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2202 (Rfree = 0.000) for 1285 atoms. Found 0 (5 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2293 (Rfree = 0.000) for 1276 atoms. TimeTaking 52.22