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 2inb-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2inb-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2inb-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2inb-3.4-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/2inb-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2inb-3.4-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 22:23:19 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/2inb-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2inb-3.4-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 99 and 0 Target number of residues in the AU: 99 Target solvent content: 0.6338 Checking the provided sequence file Detected sequence length: 140 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 140 Adjusted target solvent content: 0.48 Input MTZ file: 2inb-3.4-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: 152 Cell parameters: 59.524 59.524 71.521 90.000 90.000 120.000 Input sequence file: 2inb-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1120 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: 29.762 3.401 Wilson plot Bfac: 67.87 2190 reflections ( 99.82 % complete ) and 0 restraints for refining 1247 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3396 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2863 (Rfree = 0.000) for 1247 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 1270 seeds are put forward Round 1: 48 peptides, 8 chains. Longest chain 14 peptides. Score 0.376 Round 2: 65 peptides, 10 chains. Longest chain 11 peptides. Score 0.465 Round 3: 69 peptides, 10 chains. Longest chain 12 peptides. Score 0.505 Round 4: 68 peptides, 11 chains. Longest chain 9 peptides. Score 0.452 Round 5: 71 peptides, 10 chains. Longest chain 12 peptides. Score 0.524 Taking the results from Round 5 Chains 10, Residues 61, Estimated correctness of the model 1.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2190 reflections ( 99.82 % complete ) and 2435 restraints for refining 1018 atoms. 2201 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2496 (Rfree = 0.000) for 1018 atoms. Found 5 (7 requested) and removed 7 (3 requested) atoms. Cycle 2: After refmac, R = 0.2252 (Rfree = 0.000) for 1012 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 3: After refmac, R = 0.2166 (Rfree = 0.000) for 1004 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 4: After refmac, R = 0.2116 (Rfree = 0.000) for 998 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 5: After refmac, R = 0.2038 (Rfree = 0.000) for 991 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 3.35 Search for helices and strands: 0 residues in 0 chains, 1022 seeds are put forward Round 1: 85 peptides, 17 chains. Longest chain 8 peptides. Score 0.363 Round 2: 83 peptides, 15 chains. Longest chain 11 peptides. Score 0.430 Round 3: 90 peptides, 13 chains. Longest chain 20 peptides. Score 0.575 Round 4: 85 peptides, 14 chains. Longest chain 17 peptides. Score 0.492 Round 5: 88 peptides, 14 chains. Longest chain 17 peptides. Score 0.520 Taking the results from Round 3 Chains 14, Residues 77, Estimated correctness of the model 20.2 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 2190 reflections ( 99.82 % complete ) and 2170 restraints for refining 1018 atoms. 1824 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2482 (Rfree = 0.000) for 1018 atoms. Found 5 (7 requested) and removed 11 (3 requested) atoms. Cycle 7: After refmac, R = 0.2359 (Rfree = 0.000) for 1005 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 8: After refmac, R = 0.2354 (Rfree = 0.000) for 1000 atoms. Found 2 (7 requested) and removed 5 (3 requested) atoms. Cycle 9: After refmac, R = 0.2258 (Rfree = 0.000) for 993 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. Cycle 10: After refmac, R = 0.2409 (Rfree = 0.000) for 989 atoms. Found 3 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.24 3.33 Search for helices and strands: 0 residues in 0 chains, 1021 seeds are put forward Round 1: 61 peptides, 12 chains. Longest chain 8 peptides. Score 0.328 Round 2: 73 peptides, 11 chains. Longest chain 16 peptides. Score 0.501 Round 3: 73 peptides, 11 chains. Longest chain 15 peptides. Score 0.501 Round 4: 76 peptides, 10 chains. Longest chain 17 peptides. Score 0.569 Round 5: 75 peptides, 9 chains. Longest chain 18 peptides. Score 0.599 Taking the results from Round 5 Chains 9, Residues 66, Estimated correctness of the model 28.3 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 2190 reflections ( 99.82 % complete ) and 2160 restraints for refining 1018 atoms. 1839 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2604 (Rfree = 0.000) for 1018 atoms. Found 1 (7 requested) and removed 11 (3 requested) atoms. Cycle 12: After refmac, R = 0.2580 (Rfree = 0.000) for 997 atoms. Found 6 (7 requested) and removed 3 (3 requested) atoms. Cycle 13: After refmac, R = 0.2308 (Rfree = 0.000) for 999 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. Cycle 14: After refmac, R = 0.2041 (Rfree = 0.000) for 996 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.2067 (Rfree = 0.000) for 993 atoms. Found 0 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.29 3.38 Search for helices and strands: 0 residues in 0 chains, 1016 seeds are put forward Round 1: 55 peptides, 11 chains. Longest chain 8 peptides. Score 0.307 Round 2: 68 peptides, 11 chains. Longest chain 16 peptides. Score 0.452 Round 3: 76 peptides, 11 chains. Longest chain 16 peptides. Score 0.529 Round 4: 75 peptides, 12 chains. Longest chain 16 peptides. Score 0.478 Round 5: 74 peptides, 11 chains. Longest chain 16 peptides. Score 0.511 Taking the results from Round 3 Chains 11, Residues 65, Estimated correctness of the model 3.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2190 reflections ( 99.82 % complete ) and 2311 restraints for refining 1013 atoms. 2062 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2285 (Rfree = 0.000) for 1013 atoms. Found 3 (7 requested) and removed 8 (3 requested) atoms. Cycle 17: After refmac, R = 0.2175 (Rfree = 0.000) for 1003 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 18: After refmac, R = 0.2314 (Rfree = 0.000) for 1001 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. Cycle 19: After refmac, R = 0.2237 (Rfree = 0.000) for 995 atoms. Found 3 (7 requested) and removed 6 (3 requested) atoms. Cycle 20: After refmac, R = 0.2445 (Rfree = 0.000) for 991 atoms. Found 6 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 1040 seeds are put forward Round 1: 45 peptides, 8 chains. Longest chain 9 peptides. Score 0.341 Round 2: 61 peptides, 10 chains. Longest chain 15 peptides. Score 0.424 Round 3: 66 peptides, 10 chains. Longest chain 17 peptides. Score 0.475 Round 4: 67 peptides, 9 chains. Longest chain 22 peptides. Score 0.528 Round 5: 63 peptides, 8 chains. Longest chain 22 peptides. Score 0.533 Taking the results from Round 5 Chains 8, Residues 55, Estimated correctness of the model 5.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2190 reflections ( 99.82 % complete ) and 2211 restraints for refining 989 atoms. 1999 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2238 (Rfree = 0.000) for 989 atoms. Found 4 (7 requested) and removed 6 (3 requested) atoms. Cycle 22: After refmac, R = 0.1942 (Rfree = 0.000) for 983 atoms. Found 4 (7 requested) and removed 3 (3 requested) atoms. Cycle 23: After refmac, R = 0.1907 (Rfree = 0.000) for 984 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. Cycle 24: After refmac, R = 0.1889 (Rfree = 0.000) for 982 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 25: After refmac, R = 0.1875 (Rfree = 0.000) for 980 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.25 3.34 Search for helices and strands: 0 residues in 0 chains, 1015 seeds are put forward Round 1: 65 peptides, 12 chains. Longest chain 9 peptides. Score 0.374 Round 2: 59 peptides, 10 chains. Longest chain 9 peptides. Score 0.402 Round 3: 62 peptides, 9 chains. Longest chain 11 peptides. Score 0.480 Round 4: 53 peptides, 8 chains. Longest chain 14 peptides. Score 0.432 Round 5: 55 peptides, 10 chains. Longest chain 9 peptides. Score 0.357 Taking the results from Round 3 Chains 9, Residues 53, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2190 reflections ( 99.82 % complete ) and 2324 restraints for refining 1014 atoms. 2121 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2021 (Rfree = 0.000) for 1014 atoms. Found 4 (7 requested) and removed 5 (3 requested) atoms. Cycle 27: After refmac, R = 0.1900 (Rfree = 0.000) for 1011 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. Cycle 28: After refmac, R = 0.1840 (Rfree = 0.000) for 1010 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. Cycle 29: After refmac, R = 0.1820 (Rfree = 0.000) for 1006 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 30: After refmac, R = 0.1821 (Rfree = 0.000) for 1003 atoms. Found 1 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 3.36 Search for helices and strands: 0 residues in 0 chains, 1037 seeds are put forward Round 1: 55 peptides, 10 chains. Longest chain 9 peptides. Score 0.357 Round 2: 61 peptides, 10 chains. Longest chain 12 peptides. Score 0.424 Round 3: 62 peptides, 10 chains. Longest chain 16 peptides. Score 0.434 Round 4: 65 peptides, 11 chains. Longest chain 8 peptides. Score 0.420 Round 5: 67 peptides, 11 chains. Longest chain 15 peptides. Score 0.441 Taking the results from Round 5 Chains 11, Residues 56, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 2190 reflections ( 99.82 % complete ) and 2166 restraints for refining 1018 atoms. 1881 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2149 (Rfree = 0.000) for 1018 atoms. Found 4 (7 requested) and removed 5 (3 requested) atoms. Cycle 32: After refmac, R = 0.2046 (Rfree = 0.000) for 1012 atoms. Found 0 (7 requested) and removed 5 (3 requested) atoms. Cycle 33: After refmac, R = 0.2028 (Rfree = 0.000) for 1007 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 34: After refmac, R = 0.2000 (Rfree = 0.000) for 1003 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. Cycle 35: After refmac, R = 0.1986 (Rfree = 0.000) for 1001 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 3.36 Search for helices and strands: 0 residues in 0 chains, 1031 seeds are put forward Round 1: 57 peptides, 10 chains. Longest chain 10 peptides. Score 0.380 Round 2: 60 peptides, 10 chains. Longest chain 10 peptides. Score 0.413 Round 3: 62 peptides, 11 chains. Longest chain 10 peptides. Score 0.388 Round 4: 63 peptides, 11 chains. Longest chain 11 peptides. Score 0.399 Round 5: 66 peptides, 11 chains. Longest chain 10 peptides. Score 0.431 Taking the results from Round 5 Chains 11, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2190 reflections ( 99.82 % complete ) and 2361 restraints for refining 1018 atoms. 2152 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2283 (Rfree = 0.000) for 1018 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 37: After refmac, R = 0.2208 (Rfree = 0.000) for 1014 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. Cycle 38: After refmac, R = 0.2158 (Rfree = 0.000) for 1011 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 39: After refmac, R = 0.2137 (Rfree = 0.000) for 1007 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. Cycle 40: After refmac, R = 0.2110 (Rfree = 0.000) for 1004 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.32 3.41 Search for helices and strands: 0 residues in 0 chains, 1030 seeds are put forward Round 1: 54 peptides, 10 chains. Longest chain 11 peptides. Score 0.345 Round 2: 67 peptides, 9 chains. Longest chain 17 peptides. Score 0.528 Round 3: 64 peptides, 11 chains. Longest chain 13 peptides. Score 0.409 Round 4: 70 peptides, 12 chains. Longest chain 14 peptides. Score 0.427 Round 5: 63 peptides, 9 chains. Longest chain 17 peptides. Score 0.490 Taking the results from Round 2 Chains 9, Residues 58, Estimated correctness of the model 3.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2190 reflections ( 99.82 % complete ) and 2280 restraints for refining 1011 atoms. 2057 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2262 (Rfree = 0.000) for 1011 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 42: After refmac, R = 0.2166 (Rfree = 0.000) for 1009 atoms. Found 5 (7 requested) and removed 3 (3 requested) atoms. Cycle 43: After refmac, R = 0.2118 (Rfree = 0.000) for 1011 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. Cycle 44: After refmac, R = 0.2012 (Rfree = 0.000) for 1010 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. Cycle 45: After refmac, R = 0.1976 (Rfree = 0.000) for 1008 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.25 3.34 Search for helices and strands: 0 residues in 0 chains, 1039 seeds are put forward Round 1: 54 peptides, 10 chains. Longest chain 9 peptides. Score 0.345 Round 2: 59 peptides, 10 chains. Longest chain 11 peptides. Score 0.402 Round 3: 62 peptides, 10 chains. Longest chain 10 peptides. Score 0.434 Round 4: 60 peptides, 11 chains. Longest chain 8 peptides. Score 0.365 Round 5: 59 peptides, 8 chains. Longest chain 10 peptides. Score 0.495 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 51, 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 2inb-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2190 reflections ( 99.82 % complete ) and 2368 restraints for refining 1018 atoms. 2172 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2290 (Rfree = 0.000) for 1018 atoms. Found 0 (7 requested) and removed 1 (3 requested) atoms. Cycle 47: After refmac, R = 0.2108 (Rfree = 0.000) for 1016 atoms. Found 0 (7 requested) and removed 0 (3 requested) atoms. Cycle 48: After refmac, R = 0.2021 (Rfree = 0.000) for 1016 atoms. Found 0 (7 requested) and removed 0 (3 requested) atoms. Cycle 49: After refmac, R = 0.1983 (Rfree = 0.000) for 1016 atoms. Found 0 (7 requested) and removed 0 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:47:53 GMT 2018 Job finished. TimeTaking 24.72 Used memory is bytes: 14051232