null Sun 23 Dec 22:23:08 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 1o6a-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1o6a-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1o6a-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1o6a-3.8-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/1o6a-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1o6a-3.8-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 22:23:18 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/1o6a-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1o6a-3.8-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 135 and 0 Target number of residues in the AU: 135 Target solvent content: 0.6607 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: 0.52 Input MTZ file: 1o6a-3.8-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: 92 Cell parameters: 61.652 61.652 113.295 90.000 90.000 90.000 Input sequence file: 1o6a-3.8-parrot-hancs.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: 41.713 3.801 Wilson plot Bfac: 84.88 2409 reflections ( 99.83 % complete ) and 0 restraints for refining 1700 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.4414 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4340 (Rfree = 0.000) for 1700 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.65 3.55 Search for helices and strands: 0 residues in 0 chains, 1717 seeds are put forward NCS extension: 0 residues added, 1717 seeds are put forward Round 1: 56 peptides, 11 chains. Longest chain 6 peptides. Score 0.282 Round 2: 83 peptides, 15 chains. Longest chain 10 peptides. Score 0.364 Round 3: 75 peptides, 11 chains. Longest chain 14 peptides. Score 0.436 Round 4: 74 peptides, 12 chains. Longest chain 10 peptides. Score 0.395 Round 5: 85 peptides, 14 chains. Longest chain 10 peptides. Score 0.412 Taking the results from Round 3 Chains 11, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2409 reflections ( 99.83 % complete ) and 3355 restraints for refining 1388 atoms. 3110 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3766 (Rfree = 0.000) for 1388 atoms. Found 3 (7 requested) and removed 19 (3 requested) atoms. Cycle 2: After refmac, R = 0.3380 (Rfree = 0.000) for 1350 atoms. Found 3 (7 requested) and removed 16 (3 requested) atoms. Cycle 3: After refmac, R = 0.3260 (Rfree = 0.000) for 1328 atoms. Found 5 (7 requested) and removed 13 (3 requested) atoms. Cycle 4: After refmac, R = 0.3611 (Rfree = 0.000) for 1310 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 5: After refmac, R = 0.3362 (Rfree = 0.000) for 1298 atoms. Found 3 (7 requested) and removed 13 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.56 3.47 Search for helices and strands: 0 residues in 0 chains, 1325 seeds are put forward NCS extension: 0 residues added, 1325 seeds are put forward Round 1: 77 peptides, 15 chains. Longest chain 9 peptides. Score 0.316 Round 2: 88 peptides, 15 chains. Longest chain 9 peptides. Score 0.402 Round 3: 90 peptides, 12 chains. Longest chain 12 peptides. Score 0.509 Round 4: 94 peptides, 15 chains. Longest chain 11 peptides. Score 0.445 Round 5: 95 peptides, 12 chains. Longest chain 17 peptides. Score 0.541 Taking the results from Round 5 Chains 12, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2409 reflections ( 99.83 % complete ) and 2935 restraints for refining 1317 atoms. 2615 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3528 (Rfree = 0.000) for 1317 atoms. Found 7 (7 requested) and removed 37 (3 requested) atoms. Cycle 7: After refmac, R = 0.3220 (Rfree = 0.000) for 1267 atoms. Found 7 (7 requested) and removed 29 (3 requested) atoms. Cycle 8: After refmac, R = 0.3221 (Rfree = 0.000) for 1233 atoms. Found 6 (6 requested) and removed 22 (3 requested) atoms. Cycle 9: After refmac, R = 0.3140 (Rfree = 0.000) for 1214 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 10: After refmac, R = 0.3206 (Rfree = 0.000) for 1202 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.62 3.52 Search for helices and strands: 0 residues in 0 chains, 1261 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 1280 seeds are put forward Round 1: 57 peptides, 13 chains. Longest chain 6 peptides. Score 0.215 Round 2: 80 peptides, 14 chains. Longest chain 14 peptides. Score 0.374 Round 3: 88 peptides, 16 chains. Longest chain 9 peptides. Score 0.369 Round 4: 92 peptides, 14 chains. Longest chain 14 peptides. Score 0.462 Round 5: 91 peptides, 12 chains. Longest chain 15 peptides. Score 0.516 Taking the results from Round 5 Chains 12, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2409 reflections ( 99.83 % complete ) and 2784 restraints for refining 1246 atoms. 2480 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3001 (Rfree = 0.000) for 1246 atoms. Found 4 (6 requested) and removed 14 (3 requested) atoms. Cycle 12: After refmac, R = 0.2768 (Rfree = 0.000) for 1221 atoms. Found 2 (6 requested) and removed 9 (3 requested) atoms. Cycle 13: After refmac, R = 0.2664 (Rfree = 0.000) for 1208 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. Cycle 14: After refmac, R = 0.2672 (Rfree = 0.000) for 1203 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.2695 (Rfree = 0.000) for 1197 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.66 3.56 Search for helices and strands: 0 residues in 0 chains, 1239 seeds are put forward NCS extension: 0 residues added, 1239 seeds are put forward Round 1: 87 peptides, 16 chains. Longest chain 10 peptides. Score 0.361 Round 2: 92 peptides, 14 chains. Longest chain 16 peptides. Score 0.462 Round 3: 98 peptides, 15 chains. Longest chain 13 peptides. Score 0.473 Round 4: 87 peptides, 11 chains. Longest chain 15 peptides. Score 0.519 Round 5: 94 peptides, 13 chains. Longest chain 13 peptides. Score 0.506 Taking the results from Round 4 Chains 11, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2409 reflections ( 99.83 % complete ) and 2910 restraints for refining 1290 atoms. 2617 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3156 (Rfree = 0.000) for 1290 atoms. Found 2 (7 requested) and removed 24 (3 requested) atoms. Cycle 17: After refmac, R = 0.2817 (Rfree = 0.000) for 1264 atoms. Found 2 (6 requested) and removed 7 (3 requested) atoms. Cycle 18: After refmac, R = 0.2800 (Rfree = 0.000) for 1257 atoms. Found 2 (6 requested) and removed 7 (3 requested) atoms. Cycle 19: After refmac, R = 0.2825 (Rfree = 0.000) for 1247 atoms. Found 0 (6 requested) and removed 5 (3 requested) atoms. Cycle 20: After refmac, R = 0.3249 (Rfree = 0.000) for 1240 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.69 3.59 Search for helices and strands: 0 residues in 0 chains, 1273 seeds are put forward NCS extension: 0 residues added, 1273 seeds are put forward Round 1: 68 peptides, 13 chains. Longest chain 13 peptides. Score 0.312 Round 2: 73 peptides, 13 chains. Longest chain 11 peptides. Score 0.353 Round 3: 73 peptides, 15 chains. Longest chain 8 peptides. Score 0.283 Round 4: 76 peptides, 15 chains. Longest chain 11 peptides. Score 0.307 Round 5: 88 peptides, 15 chains. Longest chain 13 peptides. Score 0.402 Taking the results from Round 5 Chains 15, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2409 reflections ( 99.83 % complete ) and 2848 restraints for refining 1270 atoms. 2571 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3052 (Rfree = 0.000) for 1270 atoms. Found 3 (6 requested) and removed 11 (3 requested) atoms. Cycle 22: After refmac, R = 0.2851 (Rfree = 0.000) for 1250 atoms. Found 2 (6 requested) and removed 7 (3 requested) atoms. Cycle 23: After refmac, R = 0.2784 (Rfree = 0.000) for 1243 atoms. Found 2 (6 requested) and removed 8 (3 requested) atoms. Cycle 24: After refmac, R = 0.2780 (Rfree = 0.000) for 1236 atoms. Found 1 (6 requested) and removed 14 (3 requested) atoms. Cycle 25: After refmac, R = 0.2737 (Rfree = 0.000) for 1222 atoms. Found 1 (6 requested) and removed 12 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.63 3.53 Search for helices and strands: 0 residues in 0 chains, 1238 seeds are put forward NCS extension: 0 residues added, 1238 seeds are put forward Round 1: 61 peptides, 12 chains. Longest chain 10 peptides. Score 0.288 Round 2: 66 peptides, 11 chains. Longest chain 10 peptides. Score 0.367 Round 3: 68 peptides, 12 chains. Longest chain 11 peptides. Score 0.347 Round 4: 73 peptides, 12 chains. Longest chain 12 peptides. Score 0.387 Round 5: 77 peptides, 11 chains. Longest chain 13 peptides. Score 0.450 Taking the results from Round 5 Chains 11, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2409 reflections ( 99.83 % complete ) and 2893 restraints for refining 1278 atoms. 2640 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2982 (Rfree = 0.000) for 1278 atoms. Found 6 (7 requested) and removed 7 (3 requested) atoms. Cycle 27: After refmac, R = 0.2720 (Rfree = 0.000) for 1271 atoms. Found 2 (7 requested) and removed 6 (3 requested) atoms. Cycle 28: After refmac, R = 0.2639 (Rfree = 0.000) for 1266 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. Cycle 29: After refmac, R = 0.2590 (Rfree = 0.000) for 1261 atoms. Found 0 (6 requested) and removed 5 (3 requested) atoms. Cycle 30: After refmac, R = 0.2541 (Rfree = 0.000) for 1255 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.60 3.51 Search for helices and strands: 0 residues in 0 chains, 1286 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 1289 seeds are put forward Round 1: 72 peptides, 16 chains. Longest chain 6 peptides. Score 0.238 Round 2: 79 peptides, 14 chains. Longest chain 13 peptides. Score 0.366 Round 3: 75 peptides, 13 chains. Longest chain 11 peptides. Score 0.368 Round 4: 86 peptides, 13 chains. Longest chain 14 peptides. Score 0.451 Round 5: 76 peptides, 13 chains. Longest chain 9 peptides. Score 0.376 Taking the results from Round 4 Chains 13, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2409 reflections ( 99.83 % complete ) and 2933 restraints for refining 1305 atoms. 2654 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2715 (Rfree = 0.000) for 1305 atoms. Found 0 (7 requested) and removed 11 (3 requested) atoms. Cycle 32: After refmac, R = 0.2572 (Rfree = 0.000) for 1284 atoms. Found 1 (7 requested) and removed 8 (3 requested) atoms. Cycle 33: After refmac, R = 0.2535 (Rfree = 0.000) for 1271 atoms. Found 2 (7 requested) and removed 5 (3 requested) atoms. Cycle 34: After refmac, R = 0.2467 (Rfree = 0.000) for 1267 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 35: After refmac, R = 0.2441 (Rfree = 0.000) for 1263 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.64 3.54 Search for helices and strands: 0 residues in 0 chains, 1283 seeds are put forward NCS extension: 0 residues added, 1283 seeds are put forward Round 1: 66 peptides, 14 chains. Longest chain 7 peptides. Score 0.258 Round 2: 82 peptides, 15 chains. Longest chain 11 peptides. Score 0.356 Round 3: 75 peptides, 13 chains. Longest chain 10 peptides. Score 0.368 Round 4: 74 peptides, 13 chains. Longest chain 10 peptides. Score 0.361 Round 5: 76 peptides, 14 chains. Longest chain 9 peptides. Score 0.342 Taking the results from Round 3 Chains 13, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2409 reflections ( 99.83 % complete ) and 2940 restraints for refining 1311 atoms. 2705 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2837 (Rfree = 0.000) for 1311 atoms. Found 7 (7 requested) and removed 33 (3 requested) atoms. Cycle 37: After refmac, R = 0.2998 (Rfree = 0.000) for 1270 atoms. Found 7 (7 requested) and removed 38 (3 requested) atoms. Cycle 38: After refmac, R = 0.3086 (Rfree = 0.000) for 1232 atoms. Found 6 (6 requested) and removed 25 (3 requested) atoms. Cycle 39: After refmac, R = 0.3186 (Rfree = 0.000) for 1206 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 40: After refmac, R = 0.3072 (Rfree = 0.000) for 1194 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 3.51 Search for helices and strands: 0 residues in 0 chains, 1238 seeds are put forward NCS extension: 0 residues added, 1238 seeds are put forward Round 1: 55 peptides, 12 chains. Longest chain 6 peptides. Score 0.234 Round 2: 64 peptides, 13 chains. Longest chain 7 peptides. Score 0.278 Round 3: 71 peptides, 14 chains. Longest chain 9 peptides. Score 0.301 Round 4: 66 peptides, 13 chains. Longest chain 7 peptides. Score 0.295 Round 5: 70 peptides, 12 chains. Longest chain 9 peptides. Score 0.363 Taking the results from Round 5 Chains 12, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2409 reflections ( 99.83 % complete ) and 2559 restraints for refining 1166 atoms. 2339 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2903 (Rfree = 0.000) for 1166 atoms. Found 6 (6 requested) and removed 23 (3 requested) atoms. Cycle 42: After refmac, R = 0.2720 (Rfree = 0.000) for 1142 atoms. Found 0 (6 requested) and removed 11 (3 requested) atoms. Cycle 43: After refmac, R = 0.2818 (Rfree = 0.000) for 1126 atoms. Found 4 (6 requested) and removed 12 (3 requested) atoms. Cycle 44: After refmac, R = 0.3100 (Rfree = 0.000) for 1115 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 45: After refmac, R = 0.3050 (Rfree = 0.000) for 1109 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.58 3.49 Search for helices and strands: 0 residues in 0 chains, 1142 seeds are put forward NCS extension: 0 residues added, 1142 seeds are put forward Round 1: 59 peptides, 13 chains. Longest chain 7 peptides. Score 0.233 Round 2: 68 peptides, 10 chains. Longest chain 13 peptides. Score 0.417 Round 3: 55 peptides, 9 chains. Longest chain 12 peptides. Score 0.349 Round 4: 63 peptides, 10 chains. Longest chain 12 peptides. Score 0.378 Round 5: 69 peptides, 10 chains. Longest chain 12 peptides. Score 0.425 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 59, 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 1o6a-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2409 reflections ( 99.83 % complete ) and 2485 restraints for refining 1160 atoms. 2259 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3356 (Rfree = 0.000) for 1160 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3095 (Rfree = 0.000) for 1150 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.3288 (Rfree = 0.000) for 1145 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.3250 (Rfree = 0.000) for 1139 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:49:45 GMT 2018 Job finished. TimeTaking 26.62 Used memory is bytes: 18013416