Sun 23 Dec 22:22:44 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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2etd-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2etd-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etd-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/2etd-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etd-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 22:22:53 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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etd-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 112 and 0 Target number of residues in the AU: 112 Target solvent content: 0.6687 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-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: 21 Cell parameters: 80.417 85.225 53.388 90.000 90.000 90.000 Input sequence file: 2etd-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1368 target number of atoms Had to go as low as 0.55 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 3.800 Wilson plot Bfac: 89.47 1816 reflections ( 92.56 % complete ) and 0 restraints for refining 1507 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3805 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4367 (Rfree = 0.000) for 1507 atoms. Found 2 (8 requested) and removed 29 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.84 3.89 Search for helices and strands: 0 residues in 0 chains, 1508 seeds are put forward Round 1: 29 peptides, 7 chains. Longest chain 5 peptides. Score 0.180 Round 2: 38 peptides, 8 chains. Longest chain 8 peptides. Score 0.240 Round 3: 43 peptides, 9 chains. Longest chain 6 peptides. Score 0.249 Round 4: 52 peptides, 11 chains. Longest chain 7 peptides. Score 0.255 Round 5: 53 peptides, 10 chains. Longest chain 8 peptides. Score 0.309 Taking the results from Round 5 Chains 10, Residues 43, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1816 reflections ( 92.56 % complete ) and 2782 restraints for refining 1122 atoms. 2620 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3747 (Rfree = 0.000) for 1122 atoms. Found 3 (6 requested) and removed 12 (3 requested) atoms. Cycle 2: After refmac, R = 0.3770 (Rfree = 0.000) for 1093 atoms. Found 2 (6 requested) and removed 14 (3 requested) atoms. Cycle 3: After refmac, R = 0.3553 (Rfree = 0.000) for 1066 atoms. Found 4 (5 requested) and removed 8 (2 requested) atoms. Cycle 4: After refmac, R = 0.3569 (Rfree = 0.000) for 1049 atoms. Found 2 (5 requested) and removed 5 (2 requested) atoms. Cycle 5: After refmac, R = 0.3431 (Rfree = 0.000) for 1037 atoms. Found 2 (5 requested) and removed 8 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 1073 seeds are put forward Round 1: 39 peptides, 9 chains. Longest chain 5 peptides. Score 0.203 Round 2: 54 peptides, 11 chains. Longest chain 9 peptides. Score 0.276 Round 3: 57 peptides, 11 chains. Longest chain 8 peptides. Score 0.306 Round 4: 59 peptides, 12 chains. Longest chain 7 peptides. Score 0.284 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 ------------------------------------------------------ 1816 reflections ( 92.56 % complete ) and 2014 restraints for refining 926 atoms. 1820 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3476 (Rfree = 0.000) for 926 atoms. Found 5 (5 requested) and removed 25 (2 requested) atoms. Cycle 7: After refmac, R = 0.3418 (Rfree = 0.000) for 895 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. Cycle 8: After refmac, R = 0.3561 (Rfree = 0.000) for 888 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 9: After refmac, R = 0.3207 (Rfree = 0.000) for 880 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 10: After refmac, R = 0.3058 (Rfree = 0.000) for 872 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.71 3.76 Search for helices and strands: 0 residues in 0 chains, 914 seeds are put forward Round 1: 57 peptides, 13 chains. Longest chain 7 peptides. Score 0.221 Round 2: 79 peptides, 15 chains. Longest chain 9 peptides. Score 0.353 Round 3: 73 peptides, 13 chains. Longest chain 11 peptides. Score 0.376 Round 4: 77 peptides, 14 chains. Longest chain 9 peptides. Score 0.374 Round 5: 83 peptides, 15 chains. Longest chain 10 peptides. Score 0.389 Taking the results from Round 5 Chains 15, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1816 reflections ( 92.56 % complete ) and 1930 restraints for refining 934 atoms. 1673 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3261 (Rfree = 0.000) for 934 atoms. Found 4 (5 requested) and removed 14 (2 requested) atoms. Cycle 12: After refmac, R = 0.3308 (Rfree = 0.000) for 907 atoms. Found 4 (5 requested) and removed 9 (2 requested) atoms. Cycle 13: After refmac, R = 0.2919 (Rfree = 0.000) for 896 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 14: After refmac, R = 0.2977 (Rfree = 0.000) for 892 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 15: After refmac, R = 0.3050 (Rfree = 0.000) for 885 atoms. Found 3 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.71 3.76 Search for helices and strands: 0 residues in 0 chains, 956 seeds are put forward Round 1: 52 peptides, 10 chains. Longest chain 8 peptides. Score 0.299 Round 2: 63 peptides, 11 chains. Longest chain 10 peptides. Score 0.364 Round 3: 70 peptides, 10 chains. Longest chain 11 peptides. Score 0.464 Round 4: 68 peptides, 11 chains. Longest chain 10 peptides. Score 0.409 Round 5: 73 peptides, 11 chains. Longest chain 13 peptides. Score 0.452 Taking the results from Round 3 Chains 10, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1816 reflections ( 92.56 % complete ) and 2025 restraints for refining 953 atoms. 1795 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3077 (Rfree = 0.000) for 953 atoms. Found 5 (5 requested) and removed 15 (2 requested) atoms. Cycle 17: After refmac, R = 0.2479 (Rfree = 0.000) for 931 atoms. Found 4 (5 requested) and removed 9 (2 requested) atoms. Cycle 18: After refmac, R = 0.2267 (Rfree = 0.000) for 921 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 19: After refmac, R = 0.1948 (Rfree = 0.000) for 916 atoms. Found 0 (5 requested) and removed 4 (2 requested) atoms. Cycle 20: After refmac, R = 0.2058 (Rfree = 0.000) for 911 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.66 3.71 Search for helices and strands: 0 residues in 0 chains, 964 seeds are put forward Round 1: 64 peptides, 12 chains. Longest chain 8 peptides. Score 0.332 Round 2: 78 peptides, 16 chains. Longest chain 8 peptides. Score 0.305 Round 3: 78 peptides, 16 chains. Longest chain 7 peptides. Score 0.305 Round 4: 77 peptides, 14 chains. Longest chain 11 peptides. Score 0.374 Round 5: 75 peptides, 13 chains. Longest chain 10 peptides. Score 0.394 Taking the results from Round 5 Chains 13, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1816 reflections ( 92.56 % complete ) and 2421 restraints for refining 1072 atoms. 2186 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2816 (Rfree = 0.000) for 1072 atoms. Found 5 (5 requested) and removed 50 (2 requested) atoms. Cycle 22: After refmac, R = 0.2415 (Rfree = 0.000) for 1025 atoms. Found 2 (5 requested) and removed 19 (2 requested) atoms. Cycle 23: After refmac, R = 0.2241 (Rfree = 0.000) for 1007 atoms. Found 3 (5 requested) and removed 7 (2 requested) atoms. Cycle 24: After refmac, R = 0.1998 (Rfree = 0.000) for 1003 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. Cycle 25: After refmac, R = 0.2016 (Rfree = 0.000) for 999 atoms. Found 2 (5 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.69 3.74 Search for helices and strands: 0 residues in 0 chains, 1045 seeds are put forward Round 1: 55 peptides, 12 chains. Longest chain 6 peptides. Score 0.243 Round 2: 62 peptides, 12 chains. Longest chain 7 peptides. Score 0.313 Round 3: 54 peptides, 10 chains. Longest chain 8 peptides. Score 0.319 Round 4: 62 peptides, 10 chains. Longest chain 10 peptides. Score 0.395 Round 5: 62 peptides, 10 chains. Longest chain 12 peptides. Score 0.395 Taking the results from Round 5 Chains 10, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1816 reflections ( 92.56 % complete ) and 2633 restraints for refining 1124 atoms. 2435 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2444 (Rfree = 0.000) for 1124 atoms. Found 6 (6 requested) and removed 21 (3 requested) atoms. Cycle 27: After refmac, R = 0.2108 (Rfree = 0.000) for 1104 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 28: After refmac, R = 0.2022 (Rfree = 0.000) for 1098 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 29: After refmac, R = 0.1944 (Rfree = 0.000) for 1087 atoms. Found 4 (6 requested) and removed 6 (3 requested) atoms. Cycle 30: After refmac, R = 0.1676 (Rfree = 0.000) for 1084 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.61 3.66 Search for helices and strands: 0 residues in 0 chains, 1121 seeds are put forward Round 1: 45 peptides, 10 chains. Longest chain 6 peptides. Score 0.224 Round 2: 44 peptides, 10 chains. Longest chain 5 peptides. Score 0.213 Round 3: 44 peptides, 9 chains. Longest chain 7 peptides. Score 0.260 Round 4: 44 peptides, 9 chains. Longest chain 7 peptides. Score 0.260 Round 5: 44 peptides, 9 chains. Longest chain 8 peptides. Score 0.260 Taking the results from Round 5 Chains 9, Residues 35, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1816 reflections ( 92.56 % complete ) and 2467 restraints for refining 1064 atoms. 2336 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2585 (Rfree = 0.000) for 1064 atoms. Found 5 (5 requested) and removed 24 (2 requested) atoms. Cycle 32: After refmac, R = 0.2047 (Rfree = 0.000) for 1042 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 33: After refmac, R = 0.1920 (Rfree = 0.000) for 1036 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. Cycle 34: After refmac, R = 0.1962 (Rfree = 0.000) for 1033 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. Cycle 35: After refmac, R = 0.1896 (Rfree = 0.000) for 1028 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.65 3.70 Search for helices and strands: 0 residues in 0 chains, 1052 seeds are put forward Round 1: 42 peptides, 10 chains. Longest chain 6 peptides. Score 0.190 Round 2: 48 peptides, 11 chains. Longest chain 6 peptides. Score 0.212 Round 3: 45 peptides, 10 chains. Longest chain 6 peptides. Score 0.224 Round 4: 41 peptides, 9 chains. Longest chain 6 peptides. Score 0.226 Round 5: 45 peptides, 10 chains. Longest chain 6 peptides. Score 0.224 Taking the results from Round 4 Chains 9, Residues 32, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1816 reflections ( 92.56 % complete ) and 2346 restraints for refining 1013 atoms. 2227 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2179 (Rfree = 0.000) for 1013 atoms. Found 3 (5 requested) and removed 12 (2 requested) atoms. Cycle 37: After refmac, R = 0.2714 (Rfree = 0.000) for 999 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 38: After refmac, R = 0.2196 (Rfree = 0.000) for 997 atoms. Found 4 (5 requested) and removed 2 (2 requested) atoms. Cycle 39: After refmac, R = 0.1970 (Rfree = 0.000) for 996 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 40: After refmac, R = 0.2250 (Rfree = 0.000) for 994 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.68 3.73 Search for helices and strands: 0 residues in 0 chains, 1041 seeds are put forward Round 1: 32 peptides, 7 chains. Longest chain 6 peptides. Score 0.219 Round 2: 47 peptides, 9 chains. Longest chain 8 peptides. Score 0.291 Round 3: 44 peptides, 9 chains. Longest chain 6 peptides. Score 0.260 Round 4: 47 peptides, 9 chains. Longest chain 8 peptides. Score 0.291 Round 5: 48 peptides, 10 chains. Longest chain 7 peptides. Score 0.257 Taking the results from Round 4 Chains 9, Residues 38, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1816 reflections ( 92.56 % complete ) and 2124 restraints for refining 981 atoms. 1981 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2152 (Rfree = 0.000) for 981 atoms. Found 4 (5 requested) and removed 22 (2 requested) atoms. Cycle 42: After refmac, R = 0.2024 (Rfree = 0.000) for 960 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 43: After refmac, R = 0.1923 (Rfree = 0.000) for 960 atoms. Found 4 (5 requested) and removed 2 (2 requested) atoms. Cycle 44: After refmac, R = 0.1900 (Rfree = 0.000) for 962 atoms. Found 2 (5 requested) and removed 5 (2 requested) atoms. Cycle 45: After refmac, R = 0.1648 (Rfree = 0.000) for 956 atoms. Found 0 (5 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 3.73 Search for helices and strands: 0 residues in 0 chains, 1001 seeds are put forward Round 1: 50 peptides, 12 chains. Longest chain 5 peptides. Score 0.189 Round 2: 55 peptides, 11 chains. Longest chain 7 peptides. Score 0.286 Round 3: 54 peptides, 11 chains. Longest chain 9 peptides. Score 0.276 Round 4: 52 peptides, 10 chains. Longest chain 9 peptides. Score 0.299 Round 5: 43 peptides, 7 chains. Longest chain 10 peptides. Score 0.341 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 36, 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-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1816 reflections ( 92.56 % complete ) and 2285 restraints for refining 1044 atoms. 2148 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2554 (Rfree = 0.000) for 1044 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.1908 (Rfree = 0.000) for 1042 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.1894 (Rfree = 0.000) for 1040 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.1804 (Rfree = 0.000) for 1038 atoms. TimeTaking 24.32