null Sun 23 Dec 22:23:10 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 2isb-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2isb-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2isb-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2isb-4.0-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/2isb-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2isb-4.0-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 22:23:20 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/2isb-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2isb-4.0-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: 0.6581 Checking the provided sequence file Detected sequence length: 192 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 192 Adjusted target solvent content: 0.51 Input MTZ file: 2isb-4.0-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: 96 Cell parameters: 51.664 51.664 157.756 90.000 90.000 90.000 Input sequence file: 2isb-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1536 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: 49.098 4.000 Wilson plot Bfac: 81.91 2048 reflections ( 98.89 % complete ) and 0 restraints for refining 1706 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3485 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3347 (Rfree = 0.000) for 1706 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.71 3.66 Search for helices and strands: 0 residues in 0 chains, 1745 seeds are put forward Round 1: 83 peptides, 16 chains. Longest chain 8 peptides. Score 0.333 Round 2: 100 peptides, 15 chains. Longest chain 11 peptides. Score 0.491 Round 3: 105 peptides, 13 chains. Longest chain 12 peptides. Score 0.580 Round 4: 111 peptides, 13 chains. Longest chain 12 peptides. Score 0.614 Round 5: 113 peptides, 12 chains. Longest chain 20 peptides. Score 0.650 Taking the results from Round 5 Chains 12, Residues 101, Estimated correctness of the model 7.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2048 reflections ( 98.89 % complete ) and 3192 restraints for refining 1386 atoms. 2800 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2635 (Rfree = 0.000) for 1386 atoms. Found 5 (6 requested) and removed 8 (3 requested) atoms. Cycle 2: After refmac, R = 0.2495 (Rfree = 0.000) for 1355 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 3: After refmac, R = 0.2401 (Rfree = 0.000) for 1332 atoms. Found 5 (6 requested) and removed 6 (3 requested) atoms. Cycle 4: After refmac, R = 0.2440 (Rfree = 0.000) for 1311 atoms. Found 5 (6 requested) and removed 5 (3 requested) atoms. Cycle 5: After refmac, R = 0.2332 (Rfree = 0.000) for 1303 atoms. Found 4 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.72 3.67 Search for helices and strands: 0 residues in 0 chains, 1381 seeds are put forward Round 1: 65 peptides, 12 chains. Longest chain 8 peptides. Score 0.325 Round 2: 91 peptides, 13 chains. Longest chain 14 peptides. Score 0.490 Round 3: 90 peptides, 13 chains. Longest chain 13 peptides. Score 0.483 Round 4: 103 peptides, 12 chains. Longest chain 18 peptides. Score 0.595 Round 5: 96 peptides, 12 chains. Longest chain 17 peptides. Score 0.553 Taking the results from Round 4 Chains 12, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2048 reflections ( 98.89 % complete ) and 2882 restraints for refining 1289 atoms. 2530 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2635 (Rfree = 0.000) for 1289 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 7: After refmac, R = 0.2247 (Rfree = 0.000) for 1264 atoms. Found 5 (6 requested) and removed 6 (3 requested) atoms. Cycle 8: After refmac, R = 0.2332 (Rfree = 0.000) for 1251 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 9: After refmac, R = 0.2370 (Rfree = 0.000) for 1238 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 10: After refmac, R = 0.2335 (Rfree = 0.000) for 1232 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.66 3.61 Search for helices and strands: 0 residues in 0 chains, 1300 seeds are put forward Round 1: 81 peptides, 14 chains. Longest chain 11 peptides. Score 0.385 Round 2: 89 peptides, 15 chains. Longest chain 10 peptides. Score 0.413 Round 3: 94 peptides, 12 chains. Longest chain 22 peptides. Score 0.540 Round 4: 90 peptides, 12 chains. Longest chain 14 peptides. Score 0.514 Round 5: 97 peptides, 13 chains. Longest chain 14 peptides. Score 0.530 Taking the results from Round 3 Chains 14, Residues 82, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2048 reflections ( 98.89 % complete ) and 2688 restraints for refining 1249 atoms. 2339 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2342 (Rfree = 0.000) for 1249 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 12: After refmac, R = 0.2019 (Rfree = 0.000) for 1236 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 13: After refmac, R = 0.1976 (Rfree = 0.000) for 1225 atoms. Found 0 (5 requested) and removed 6 (2 requested) atoms. Cycle 14: After refmac, R = 0.2139 (Rfree = 0.000) for 1216 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 15: After refmac, R = 0.2079 (Rfree = 0.000) for 1209 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.71 3.66 Search for helices and strands: 0 residues in 0 chains, 1265 seeds are put forward Round 1: 90 peptides, 16 chains. Longest chain 10 peptides. Score 0.388 Round 2: 92 peptides, 14 chains. Longest chain 13 peptides. Score 0.466 Round 3: 98 peptides, 14 chains. Longest chain 13 peptides. Score 0.507 Round 4: 97 peptides, 13 chains. Longest chain 18 peptides. Score 0.530 Round 5: 101 peptides, 14 chains. Longest chain 15 peptides. Score 0.527 Taking the results from Round 4 Chains 13, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2048 reflections ( 98.89 % complete ) and 3122 restraints for refining 1325 atoms. 2799 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2521 (Rfree = 0.000) for 1325 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 17: After refmac, R = 0.3582 (Rfree = 0.000) for 1304 atoms. Found 6 (6 requested) and removed 91 (3 requested) atoms. Cycle 18: After refmac, R = 0.2489 (Rfree = 0.000) for 1203 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 19: After refmac, R = 0.2276 (Rfree = 0.000) for 1181 atoms. Found 4 (5 requested) and removed 5 (2 requested) atoms. Cycle 20: After refmac, R = 0.2112 (Rfree = 0.000) for 1177 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.69 3.64 Search for helices and strands: 0 residues in 0 chains, 1243 seeds are put forward Round 1: 80 peptides, 15 chains. Longest chain 10 peptides. Score 0.343 Round 2: 85 peptides, 15 chains. Longest chain 9 peptides. Score 0.382 Round 3: 93 peptides, 14 chains. Longest chain 14 peptides. Score 0.473 Round 4: 97 peptides, 13 chains. Longest chain 16 peptides. Score 0.530 Round 5: 96 peptides, 13 chains. Longest chain 13 peptides. Score 0.524 Taking the results from Round 4 Chains 13, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2048 reflections ( 98.89 % complete ) and 2911 restraints for refining 1291 atoms. 2588 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2387 (Rfree = 0.000) for 1291 atoms. Found 2 (6 requested) and removed 9 (3 requested) atoms. Cycle 22: After refmac, R = 0.2248 (Rfree = 0.000) for 1257 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 23: After refmac, R = 0.2211 (Rfree = 0.000) for 1248 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. Cycle 24: After refmac, R = 0.2146 (Rfree = 0.000) for 1241 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. Cycle 25: After refmac, R = 0.2064 (Rfree = 0.000) for 1230 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.57 3.52 Search for helices and strands: 0 residues in 0 chains, 1286 seeds are put forward Round 1: 54 peptides, 11 chains. Longest chain 8 peptides. Score 0.265 Round 2: 97 peptides, 18 chains. Longest chain 9 peptides. Score 0.376 Round 3: 92 peptides, 15 chains. Longest chain 9 peptides. Score 0.435 Round 4: 104 peptides, 16 chains. Longest chain 16 peptides. Score 0.489 Round 5: 105 peptides, 18 chains. Longest chain 12 peptides. Score 0.435 Taking the results from Round 4 Chains 17, Residues 88, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 2048 reflections ( 98.89 % complete ) and 2767 restraints for refining 1274 atoms. 2388 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2670 (Rfree = 0.000) for 1274 atoms. Found 4 (6 requested) and removed 17 (3 requested) atoms. Cycle 27: After refmac, R = 0.2845 (Rfree = 0.000) for 1250 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. Cycle 28: After refmac, R = 0.2124 (Rfree = 0.000) for 1230 atoms. Found 2 (5 requested) and removed 10 (2 requested) atoms. Cycle 29: After refmac, R = 0.2225 (Rfree = 0.000) for 1212 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 30: After refmac, R = 0.2216 (Rfree = 0.000) for 1209 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.62 3.57 Search for helices and strands: 0 residues in 0 chains, 1251 seeds are put forward Round 1: 65 peptides, 15 chains. Longest chain 6 peptides. Score 0.213 Round 2: 88 peptides, 15 chains. Longest chain 10 peptides. Score 0.405 Round 3: 87 peptides, 15 chains. Longest chain 11 peptides. Score 0.398 Round 4: 86 peptides, 12 chains. Longest chain 11 peptides. Score 0.487 Round 5: 82 peptides, 11 chains. Longest chain 13 peptides. Score 0.490 Taking the results from Round 5 Chains 11, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2048 reflections ( 98.89 % complete ) and 2931 restraints for refining 1290 atoms. 2658 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2640 (Rfree = 0.000) for 1290 atoms. Found 6 (6 requested) and removed 20 (3 requested) atoms. Cycle 32: After refmac, R = 0.2447 (Rfree = 0.000) for 1261 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 33: After refmac, R = 0.2499 (Rfree = 0.000) for 1245 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 34: After refmac, R = 0.2713 (Rfree = 0.000) for 1236 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 35: After refmac, R = 0.2367 (Rfree = 0.000) for 1230 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.71 3.66 Search for helices and strands: 0 residues in 0 chains, 1283 seeds are put forward Round 1: 62 peptides, 13 chains. Longest chain 8 peptides. Score 0.261 Round 2: 72 peptides, 13 chains. Longest chain 12 peptides. Score 0.347 Round 3: 75 peptides, 11 chains. Longest chain 13 peptides. Score 0.440 Round 4: 78 peptides, 10 chains. Longest chain 17 peptides. Score 0.494 Round 5: 70 peptides, 10 chains. Longest chain 18 peptides. Score 0.436 Taking the results from Round 4 Chains 11, Residues 68, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 2048 reflections ( 98.89 % complete ) and 2532 restraints for refining 1201 atoms. 2228 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2796 (Rfree = 0.000) for 1201 atoms. Found 5 (5 requested) and removed 54 (2 requested) atoms. Cycle 37: After refmac, R = 0.2843 (Rfree = 0.000) for 1144 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 38: After refmac, R = 0.2312 (Rfree = 0.000) for 1132 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 39: After refmac, R = 0.2231 (Rfree = 0.000) for 1126 atoms. Found 5 (5 requested) and removed 37 (2 requested) atoms. Cycle 40: After refmac, R = 0.2669 (Rfree = 0.000) for 1093 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.63 3.58 Search for helices and strands: 0 residues in 0 chains, 1132 seeds are put forward Round 1: 63 peptides, 13 chains. Longest chain 7 peptides. Score 0.270 Round 2: 85 peptides, 14 chains. Longest chain 10 peptides. Score 0.415 Round 3: 78 peptides, 12 chains. Longest chain 12 peptides. Score 0.429 Round 4: 78 peptides, 13 chains. Longest chain 11 peptides. Score 0.395 Round 5: 79 peptides, 13 chains. Longest chain 11 peptides. Score 0.403 Taking the results from Round 3 Chains 12, Residues 66, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2048 reflections ( 98.89 % complete ) and 2664 restraints for refining 1194 atoms. 2399 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2341 (Rfree = 0.000) for 1194 atoms. Found 2 (5 requested) and removed 9 (2 requested) atoms. Cycle 42: After refmac, R = 0.2169 (Rfree = 0.000) for 1182 atoms. Found 4 (5 requested) and removed 5 (2 requested) atoms. Cycle 43: After refmac, R = 0.2069 (Rfree = 0.000) for 1176 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. Cycle 44: After refmac, R = 0.2109 (Rfree = 0.000) for 1173 atoms. Found 2 (5 requested) and removed 5 (2 requested) atoms. Cycle 45: After refmac, R = 0.2008 (Rfree = 0.000) for 1167 atoms. Found 3 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.72 3.67 Search for helices and strands: 0 residues in 0 chains, 1205 seeds are put forward Round 1: 64 peptides, 13 chains. Longest chain 7 peptides. Score 0.279 Round 2: 74 peptides, 14 chains. Longest chain 8 peptides. Score 0.328 Round 3: 78 peptides, 14 chains. Longest chain 8 peptides. Score 0.361 Round 4: 78 peptides, 12 chains. Longest chain 12 peptides. Score 0.429 Round 5: 79 peptides, 11 chains. Longest chain 15 peptides. Score 0.469 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 68, 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 2isb-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2048 reflections ( 98.89 % complete ) and 2906 restraints for refining 1273 atoms. 2645 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2789 (Rfree = 0.000) for 1273 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2356 (Rfree = 0.000) for 1262 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2055 (Rfree = 0.000) for 1257 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2078 (Rfree = 0.000) for 1252 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:50:28 GMT 2018 Job finished. TimeTaking 27.29 Used memory is bytes: 9720000