null Sun 23 Dec 22:22:50 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 2etd-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2etd-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2etd-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etd-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/2etd-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etd-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 22:22:59 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/2etd-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etd-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 108 and 0 Target number of residues in the AU: 108 Target solvent content: 0.6805 Checking the provided sequence file Detected sequence length: 171 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 171 Adjusted target solvent content: 0.49 Input MTZ file: 2etd-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: 21 Cell parameters: 80.417 85.225 53.388 90.000 90.000 90.000 Input sequence file: 2etd-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1368 target number of atoms Had to go as low as 0.60 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: 58.489 4.000 Wilson plot Bfac: 99.65 1671 reflections ( 98.24 % complete ) and 0 restraints for refining 1511 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3910 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3620 (Rfree = 0.000) for 1511 atoms. Found 2 (7 requested) and removed 17 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.05 4.10 Search for helices and strands: 0 residues in 0 chains, 1527 seeds are put forward Round 1: 26 peptides, 6 chains. Longest chain 5 peptides. Score 0.195 Round 2: 41 peptides, 8 chains. Longest chain 7 peptides. Score 0.274 Round 3: 45 peptides, 9 chains. Longest chain 7 peptides. Score 0.270 Round 4: 44 peptides, 8 chains. Longest chain 7 peptides. Score 0.306 Round 5: 54 peptides, 11 chains. Longest chain 7 peptides. Score 0.276 Taking the results from Round 4 Chains 8, Residues 36, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 1671 reflections ( 98.24 % complete ) and 3073 restraints for refining 1201 atoms. 2922 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3183 (Rfree = 0.000) for 1201 atoms. Found 5 (5 requested) and removed 24 (2 requested) atoms. Cycle 2: After refmac, R = 0.2626 (Rfree = 0.000) for 1159 atoms. Found 2 (5 requested) and removed 14 (2 requested) atoms. Cycle 3: After refmac, R = 0.2470 (Rfree = 0.000) for 1139 atoms. Found 4 (5 requested) and removed 7 (2 requested) atoms. Cycle 4: After refmac, R = 0.2389 (Rfree = 0.000) for 1133 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. Cycle 5: After refmac, R = 0.2250 (Rfree = 0.000) for 1128 atoms. Found 0 (5 requested) and removed 8 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.81 3.86 Search for helices and strands: 0 residues in 0 chains, 1160 seeds are put forward Round 1: 53 peptides, 12 chains. Longest chain 6 peptides. Score 0.222 Round 2: 61 peptides, 12 chains. Longest chain 8 peptides. Score 0.303 Round 3: 71 peptides, 14 chains. Longest chain 9 peptides. Score 0.318 Round 4: 73 peptides, 14 chains. Longest chain 10 peptides. Score 0.337 Round 5: 66 peptides, 12 chains. Longest chain 12 peptides. Score 0.351 Taking the results from Round 5 Chains 12, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1671 reflections ( 98.24 % complete ) and 2550 restraints for refining 1103 atoms. 2346 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2503 (Rfree = 0.000) for 1103 atoms. Found 1 (5 requested) and removed 10 (2 requested) atoms. Cycle 7: After refmac, R = 0.2311 (Rfree = 0.000) for 1082 atoms. Found 0 (5 requested) and removed 5 (2 requested) atoms. Cycle 8: After refmac, R = 0.2223 (Rfree = 0.000) for 1076 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. Cycle 9: After refmac, R = 0.2175 (Rfree = 0.000) for 1069 atoms. Found 0 (5 requested) and removed 6 (2 requested) atoms. Cycle 10: After refmac, R = 0.2118 (Rfree = 0.000) for 1060 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.77 3.82 Search for helices and strands: 0 residues in 0 chains, 1101 seeds are put forward Round 1: 58 peptides, 12 chains. Longest chain 9 peptides. Score 0.273 Round 2: 76 peptides, 14 chains. Longest chain 11 peptides. Score 0.365 Round 3: 79 peptides, 14 chains. Longest chain 9 peptides. Score 0.391 Round 4: 71 peptides, 12 chains. Longest chain 9 peptides. Score 0.397 Round 5: 78 peptides, 15 chains. Longest chain 11 peptides. Score 0.344 Taking the results from Round 4 Chains 12, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1671 reflections ( 98.24 % complete ) and 2465 restraints for refining 1109 atoms. 2241 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2466 (Rfree = 0.000) for 1109 atoms. Found 3 (5 requested) and removed 17 (2 requested) atoms. Cycle 12: After refmac, R = 0.2169 (Rfree = 0.000) for 1089 atoms. Found 0 (5 requested) and removed 10 (2 requested) atoms. Cycle 13: After refmac, R = 0.2476 (Rfree = 0.000) for 1079 atoms. Found 3 (5 requested) and removed 9 (2 requested) atoms. Cycle 14: After refmac, R = 0.2727 (Rfree = 0.000) for 1068 atoms. Found 4 (5 requested) and removed 16 (2 requested) atoms. Cycle 15: After refmac, R = 0.2169 (Rfree = 0.000) for 1053 atoms. Found 3 (5 requested) and removed 12 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.76 3.81 Search for helices and strands: 0 residues in 0 chains, 1111 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 6 peptides. Score 0.232 Round 2: 63 peptides, 11 chains. Longest chain 11 peptides. Score 0.364 Round 3: 53 peptides, 10 chains. Longest chain 8 peptides. Score 0.309 Round 4: 57 peptides, 10 chains. Longest chain 9 peptides. Score 0.348 Round 5: 57 peptides, 10 chains. Longest chain 8 peptides. Score 0.348 Taking the results from Round 2 Chains 11, Residues 52, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 1671 reflections ( 98.24 % complete ) and 2343 restraints for refining 1097 atoms. 2108 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2161 (Rfree = 0.000) for 1097 atoms. Found 2 (5 requested) and removed 15 (2 requested) atoms. Cycle 17: After refmac, R = 0.2502 (Rfree = 0.000) for 1072 atoms. Found 5 (5 requested) and removed 21 (2 requested) atoms. Cycle 18: After refmac, R = 0.2174 (Rfree = 0.000) for 1049 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 19: After refmac, R = 0.2739 (Rfree = 0.000) for 1039 atoms. Found 4 (4 requested) and removed 17 (2 requested) atoms. Cycle 20: After refmac, R = 0.2108 (Rfree = 0.000) for 1023 atoms. Found 3 (4 requested) and removed 27 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.88 3.93 Search for helices and strands: 0 residues in 0 chains, 1065 seeds are put forward Round 1: 52 peptides, 11 chains. Longest chain 8 peptides. Score 0.255 Round 2: 56 peptides, 11 chains. Longest chain 8 peptides. Score 0.296 Round 3: 63 peptides, 11 chains. Longest chain 10 peptides. Score 0.364 Round 4: 57 peptides, 11 chains. Longest chain 9 peptides. Score 0.306 Round 5: 61 peptides, 11 chains. Longest chain 9 peptides. Score 0.345 Taking the results from Round 3 Chains 11, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1671 reflections ( 98.24 % complete ) and 2242 restraints for refining 1013 atoms. 2045 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2593 (Rfree = 0.000) for 1013 atoms. Found 4 (4 requested) and removed 36 (2 requested) atoms. Cycle 22: After refmac, R = 0.2717 (Rfree = 0.000) for 967 atoms. Found 4 (4 requested) and removed 25 (2 requested) atoms. Cycle 23: After refmac, R = 0.2778 (Rfree = 0.000) for 941 atoms. Found 4 (4 requested) and removed 9 (2 requested) atoms. Cycle 24: After refmac, R = 0.2502 (Rfree = 0.000) for 932 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 25: After refmac, R = 0.2921 (Rfree = 0.000) for 923 atoms. Found 4 (4 requested) and removed 22 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.82 3.87 Search for helices and strands: 0 residues in 0 chains, 973 seeds are put forward Round 1: 50 peptides, 11 chains. Longest chain 6 peptides. Score 0.234 Round 2: 57 peptides, 10 chains. Longest chain 8 peptides. Score 0.348 Round 3: 53 peptides, 10 chains. Longest chain 11 peptides. Score 0.309 Round 4: 53 peptides, 9 chains. Longest chain 10 peptides. Score 0.352 Round 5: 61 peptides, 10 chains. Longest chain 11 peptides. Score 0.386 Taking the results from Round 5 Chains 10, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1671 reflections ( 98.24 % complete ) and 2210 restraints for refining 1005 atoms. 2016 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2254 (Rfree = 0.000) for 1005 atoms. Found 4 (4 requested) and removed 26 (2 requested) atoms. Cycle 27: After refmac, R = 0.1809 (Rfree = 0.000) for 974 atoms. Found 3 (4 requested) and removed 3 (2 requested) atoms. Cycle 28: After refmac, R = 0.1714 (Rfree = 0.000) for 974 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 29: After refmac, R = 0.1863 (Rfree = 0.000) for 971 atoms. Found 3 (4 requested) and removed 7 (2 requested) atoms. Cycle 30: After refmac, R = 0.1899 (Rfree = 0.000) for 967 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.94 3.99 Search for helices and strands: 0 residues in 0 chains, 1017 seeds are put forward Round 1: 50 peptides, 10 chains. Longest chain 9 peptides. Score 0.278 Round 2: 54 peptides, 9 chains. Longest chain 11 peptides. Score 0.361 Round 3: 54 peptides, 8 chains. Longest chain 13 peptides. Score 0.403 Round 4: 53 peptides, 8 chains. Longest chain 12 peptides. Score 0.394 Round 5: 57 peptides, 10 chains. Longest chain 10 peptides. Score 0.348 Taking the results from Round 3 Chains 8, Residues 46, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 1671 reflections ( 98.24 % complete ) and 2196 restraints for refining 1028 atoms. 1992 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2496 (Rfree = 0.000) for 1028 atoms. Found 4 (4 requested) and removed 30 (2 requested) atoms. Cycle 32: After refmac, R = 0.2444 (Rfree = 0.000) for 992 atoms. Found 4 (4 requested) and removed 27 (2 requested) atoms. Cycle 33: After refmac, R = 0.2836 (Rfree = 0.000) for 964 atoms. Found 4 (4 requested) and removed 17 (2 requested) atoms. Cycle 34: After refmac, R = 0.1912 (Rfree = 0.000) for 943 atoms. Found 3 (4 requested) and removed 12 (2 requested) atoms. Cycle 35: After refmac, R = 0.1853 (Rfree = 0.000) for 932 atoms. Found 3 (4 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.91 3.96 Search for helices and strands: 0 residues in 0 chains, 972 seeds are put forward Round 1: 50 peptides, 11 chains. Longest chain 6 peptides. Score 0.234 Round 2: 45 peptides, 9 chains. Longest chain 7 peptides. Score 0.270 Round 3: 51 peptides, 9 chains. Longest chain 8 peptides. Score 0.332 Round 4: 47 peptides, 9 chains. Longest chain 7 peptides. Score 0.291 Round 5: 45 peptides, 8 chains. Longest chain 7 peptides. Score 0.316 Taking the results from Round 3 Chains 9, Residues 42, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1671 reflections ( 98.24 % complete ) and 2191 restraints for refining 995 atoms. 2032 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2951 (Rfree = 0.000) for 995 atoms. Found 4 (4 requested) and removed 22 (2 requested) atoms. Cycle 37: After refmac, R = 0.2807 (Rfree = 0.000) for 971 atoms. Found 4 (4 requested) and removed 22 (2 requested) atoms. Cycle 38: After refmac, R = 0.2446 (Rfree = 0.000) for 944 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 39: After refmac, R = 0.2409 (Rfree = 0.000) for 934 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 40: After refmac, R = 0.2987 (Rfree = 0.000) for 928 atoms. Found 4 (4 requested) and removed 11 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.86 3.91 Search for helices and strands: 0 residues in 0 chains, 972 seeds are put forward Round 1: 53 peptides, 12 chains. Longest chain 6 peptides. Score 0.222 Round 2: 58 peptides, 11 chains. Longest chain 8 peptides. Score 0.316 Round 3: 52 peptides, 9 chains. Longest chain 7 peptides. Score 0.342 Round 4: 52 peptides, 9 chains. Longest chain 8 peptides. Score 0.342 Round 5: 53 peptides, 11 chains. Longest chain 8 peptides. Score 0.265 Taking the results from Round 4 Chains 9, Residues 43, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 1671 reflections ( 98.24 % complete ) and 2079 restraints for refining 980 atoms. 1893 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2208 (Rfree = 0.000) for 980 atoms. Found 3 (4 requested) and removed 14 (2 requested) atoms. Cycle 42: After refmac, R = 0.2068 (Rfree = 0.000) for 963 atoms. Found 3 (4 requested) and removed 6 (2 requested) atoms. Cycle 43: After refmac, R = 0.1996 (Rfree = 0.000) for 959 atoms. Found 3 (4 requested) and removed 7 (2 requested) atoms. Cycle 44: After refmac, R = 0.1984 (Rfree = 0.000) for 955 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 45: After refmac, R = 0.2002 (Rfree = 0.000) for 953 atoms. Found 0 (4 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.81 3.86 Search for helices and strands: 0 residues in 0 chains, 991 seeds are put forward Round 1: 47 peptides, 9 chains. Longest chain 8 peptides. Score 0.291 Round 2: 54 peptides, 9 chains. Longest chain 9 peptides. Score 0.361 Round 3: 53 peptides, 9 chains. Longest chain 10 peptides. Score 0.352 Round 4: 55 peptides, 9 chains. Longest chain 10 peptides. Score 0.371 Round 5: 53 peptides, 9 chains. Longest chain 9 peptides. Score 0.352 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 46, 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 2etd-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1671 reflections ( 98.24 % complete ) and 2293 restraints for refining 1050 atoms. 2118 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2470 (Rfree = 0.000) for 1050 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2957 (Rfree = 0.000) for 1040 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2091 (Rfree = 0.000) for 1024 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2168 (Rfree = 0.000) for 1014 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:47:55 GMT 2018 Job finished. TimeTaking 25.09 Used memory is bytes: 6679456