Sun 23 Dec 22:22:49 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 2od5-1.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2od5-1.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2od5-1.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od5-1.8-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/2od5-1.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od5-1.8-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 22:22:59 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/2od5-1.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od5-1.8-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 149 and 0 Target number of residues in the AU: 149 Target solvent content: 0.4951 Checking the provided sequence file Detected sequence length: 116 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 116 Adjusted target solvent content: 0.61 Input MTZ file: 2od5-1.8-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: 180 Cell parameters: 64.428 64.428 133.292 90.000 90.000 120.000 Input sequence file: 2od5-1.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 928 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 1 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: 55.796 1.790 Wilson plot Bfac: 22.18 16128 reflections ( 99.95 % complete ) and 0 restraints for refining 1045 atoms. Observations/parameters ratio is 3.86 ------------------------------------------------------ Starting model: R = 0.3638 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3076 (Rfree = 0.000) for 1045 atoms. Found 49 (49 requested) and removed 26 (24 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.01 1.73 Round 1: 84 peptides, 6 chains. Longest chain 42 peptides. Score 0.730 Round 2: 86 peptides, 4 chains. Longest chain 53 peptides. Score 0.792 Round 3: 80 peptides, 2 chains. Longest chain 61 peptides. Score 0.815 Round 4: 88 peptides, 3 chains. Longest chain 55 peptides. Score 0.824 Round 5: 88 peptides, 1 chains. Longest chain 88 peptides. Score 0.866 Taking the results from Round 5 Chains 1, Residues 87, Estimated correctness of the model 98.7 % 1 chains (87 residues) have been docked in sequence ------------------------------------------------------ 16128 reflections ( 99.95 % complete ) and 850 restraints for refining 916 atoms. 134 conditional restraints added. Observations/parameters ratio is 4.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3091 (Rfree = 0.000) for 916 atoms. Found 43 (43 requested) and removed 22 (21 requested) atoms. Cycle 2: After refmac, R = 0.2726 (Rfree = 0.000) for 933 atoms. Found 42 (42 requested) and removed 21 (21 requested) atoms. Cycle 3: After refmac, R = 0.2567 (Rfree = 0.000) for 941 atoms. Found 43 (43 requested) and removed 22 (22 requested) atoms. Cycle 4: After refmac, R = 0.2497 (Rfree = 0.000) for 939 atoms. Found 43 (43 requested) and removed 22 (22 requested) atoms. Cycle 5: After refmac, R = 0.2459 (Rfree = 0.000) for 939 atoms. Found 42 (42 requested) and removed 18 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.92 1.65 Round 1: 89 peptides, 2 chains. Longest chain 75 peptides. Score 0.849 Round 2: 88 peptides, 2 chains. Longest chain 58 peptides. Score 0.845 Round 3: 89 peptides, 1 chains. Longest chain 89 peptides. Score 0.869 Round 4: 87 peptides, 2 chains. Longest chain 50 peptides. Score 0.842 Round 5: 86 peptides, 3 chains. Longest chain 71 peptides. Score 0.816 Taking the results from Round 3 Chains 1, Residues 88, Estimated correctness of the model 98.8 % 1 chains (88 residues) have been docked in sequence ------------------------------------------------------ 16128 reflections ( 99.95 % complete ) and 898 restraints for refining 917 atoms. 175 conditional restraints added. Observations/parameters ratio is 4.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2522 (Rfree = 0.000) for 917 atoms. Found 40 (40 requested) and removed 21 (21 requested) atoms. Cycle 7: After refmac, R = 0.2402 (Rfree = 0.000) for 932 atoms. Found 40 (40 requested) and removed 19 (21 requested) atoms. Cycle 8: After refmac, R = 0.2324 (Rfree = 0.000) for 947 atoms. Found 31 (40 requested) and removed 13 (22 requested) atoms. Cycle 9: After refmac, R = 0.2273 (Rfree = 0.000) for 949 atoms. Found 33 (41 requested) and removed 10 (22 requested) atoms. Cycle 10: After refmac, R = 0.2245 (Rfree = 0.000) for 962 atoms. Found 36 (41 requested) and removed 12 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.93 1.66 Round 1: 86 peptides, 3 chains. Longest chain 61 peptides. Score 0.816 Round 2: 89 peptides, 1 chains. Longest chain 89 peptides. Score 0.869 Round 3: 90 peptides, 1 chains. Longest chain 90 peptides. Score 0.872 Round 4: 90 peptides, 1 chains. Longest chain 90 peptides. Score 0.872 Round 5: 89 peptides, 3 chains. Longest chain 43 peptides. Score 0.828 Taking the results from Round 4 Chains 1, Residues 89, Estimated correctness of the model 98.8 % 1 chains (89 residues) have been docked in sequence ------------------------------------------------------ 16128 reflections ( 99.95 % complete ) and 881 restraints for refining 917 atoms. 151 conditional restraints added. Observations/parameters ratio is 4.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2544 (Rfree = 0.000) for 917 atoms. Found 40 (40 requested) and removed 21 (21 requested) atoms. Cycle 12: After refmac, R = 0.2355 (Rfree = 0.000) for 934 atoms. Found 39 (39 requested) and removed 13 (21 requested) atoms. Cycle 13: After refmac, R = 0.2331 (Rfree = 0.000) for 953 atoms. Found 40 (40 requested) and removed 17 (22 requested) atoms. Cycle 14: After refmac, R = 0.2282 (Rfree = 0.000) for 973 atoms. Found 31 (40 requested) and removed 15 (22 requested) atoms. Cycle 15: After refmac, R = 0.2256 (Rfree = 0.000) for 979 atoms. Found 41 (41 requested) and removed 18 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.91 1.65 Round 1: 85 peptides, 2 chains. Longest chain 58 peptides. Score 0.834 Round 2: 87 peptides, 1 chains. Longest chain 87 peptides. Score 0.863 Round 3: 87 peptides, 1 chains. Longest chain 87 peptides. Score 0.863 Round 4: 87 peptides, 1 chains. Longest chain 87 peptides. Score 0.863 Round 5: 86 peptides, 3 chains. Longest chain 49 peptides. Score 0.816 Taking the results from Round 4 Chains 1, Residues 86, Estimated correctness of the model 98.7 % 1 chains (86 residues) have been docked in sequence ------------------------------------------------------ 16128 reflections ( 99.95 % complete ) and 921 restraints for refining 917 atoms. 223 conditional restraints added. Observations/parameters ratio is 4.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2356 (Rfree = 0.000) for 917 atoms. Found 39 (39 requested) and removed 21 (21 requested) atoms. Cycle 17: After refmac, R = 0.2311 (Rfree = 0.000) for 928 atoms. Found 38 (38 requested) and removed 17 (21 requested) atoms. Cycle 18: After refmac, R = 0.2280 (Rfree = 0.000) for 947 atoms. Found 39 (39 requested) and removed 18 (22 requested) atoms. Cycle 19: After refmac, R = 0.2279 (Rfree = 0.000) for 964 atoms. Found 40 (40 requested) and removed 20 (22 requested) atoms. Cycle 20: After refmac, R = 0.2277 (Rfree = 0.000) for 972 atoms. Found 40 (40 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.92 1.65 Round 1: 88 peptides, 2 chains. Longest chain 58 peptides. Score 0.845 Round 2: 89 peptides, 1 chains. Longest chain 89 peptides. Score 0.869 Round 3: 89 peptides, 1 chains. Longest chain 89 peptides. Score 0.869 Round 4: 88 peptides, 2 chains. Longest chain 47 peptides. Score 0.845 Round 5: 89 peptides, 1 chains. Longest chain 89 peptides. Score 0.869 Taking the results from Round 5 Chains 1, Residues 88, Estimated correctness of the model 98.8 % 1 chains (88 residues) have been docked in sequence ------------------------------------------------------ 16128 reflections ( 99.95 % complete ) and 888 restraints for refining 917 atoms. 165 conditional restraints added. Observations/parameters ratio is 4.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2325 (Rfree = 0.000) for 917 atoms. Found 37 (37 requested) and removed 22 (21 requested) atoms. Cycle 22: After refmac, R = 0.2235 (Rfree = 0.000) for 928 atoms. Found 36 (36 requested) and removed 11 (21 requested) atoms. Cycle 23: After refmac, R = 0.2235 (Rfree = 0.000) for 948 atoms. Found 37 (37 requested) and removed 19 (22 requested) atoms. Cycle 24: After refmac, R = 0.2207 (Rfree = 0.000) for 964 atoms. Found 37 (37 requested) and removed 14 (22 requested) atoms. Cycle 25: After refmac, R = 0.2207 (Rfree = 0.000) for 977 atoms. Found 37 (38 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.92 1.65 Round 1: 85 peptides, 2 chains. Longest chain 58 peptides. Score 0.834 Round 2: 88 peptides, 2 chains. Longest chain 59 peptides. Score 0.845 Round 3: 89 peptides, 3 chains. Longest chain 62 peptides. Score 0.828 Round 4: 86 peptides, 3 chains. Longest chain 47 peptides. Score 0.816 Round 5: 87 peptides, 3 chains. Longest chain 67 peptides. Score 0.820 Taking the results from Round 2 Chains 2, Residues 86, Estimated correctness of the model 98.4 % 2 chains (86 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 65 A and 68 A 1 chains (88 residues) following loop building 1 chains (88 residues) in sequence following loop building ------------------------------------------------------ 16128 reflections ( 99.95 % complete ) and 868 restraints for refining 917 atoms. 145 conditional restraints added. Observations/parameters ratio is 4.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2390 (Rfree = 0.000) for 917 atoms. Found 34 (34 requested) and removed 21 (21 requested) atoms. Cycle 27: After refmac, R = 0.2297 (Rfree = 0.000) for 924 atoms. Found 34 (34 requested) and removed 18 (21 requested) atoms. Cycle 28: After refmac, R = 0.2262 (Rfree = 0.000) for 935 atoms. Found 33 (33 requested) and removed 18 (22 requested) atoms. Cycle 29: After refmac, R = 0.2227 (Rfree = 0.000) for 945 atoms. Found 32 (33 requested) and removed 13 (22 requested) atoms. Cycle 30: After refmac, R = 0.2234 (Rfree = 0.000) for 955 atoms. Found 33 (33 requested) and removed 19 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.92 1.65 Round 1: 89 peptides, 1 chains. Longest chain 89 peptides. Score 0.869 Round 2: 89 peptides, 1 chains. Longest chain 89 peptides. Score 0.869 Round 3: 88 peptides, 2 chains. Longest chain 47 peptides. Score 0.845 Round 4: 83 peptides, 2 chains. Longest chain 67 peptides. Score 0.827 Round 5: 86 peptides, 3 chains. Longest chain 47 peptides. Score 0.816 Taking the results from Round 2 Chains 2, Residues 88, Estimated correctness of the model 98.8 % 1 chains (84 residues) have been docked in sequence ------------------------------------------------------ 16128 reflections ( 99.95 % complete ) and 873 restraints for refining 917 atoms. 165 conditional restraints added. Observations/parameters ratio is 4.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2343 (Rfree = 0.000) for 917 atoms. Found 31 (31 requested) and removed 21 (21 requested) atoms. Cycle 32: After refmac, R = 0.2287 (Rfree = 0.000) for 922 atoms. Found 30 (30 requested) and removed 22 (21 requested) atoms. Cycle 33: After refmac, R = 0.2249 (Rfree = 0.000) for 927 atoms. Found 29 (29 requested) and removed 16 (21 requested) atoms. Cycle 34: After refmac, R = 0.2220 (Rfree = 0.000) for 930 atoms. Found 29 (29 requested) and removed 10 (22 requested) atoms. Cycle 35: After refmac, R = 0.2257 (Rfree = 0.000) for 942 atoms. Found 29 (29 requested) and removed 8 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.92 1.65 Round 1: 86 peptides, 3 chains. Longest chain 58 peptides. Score 0.816 Round 2: 84 peptides, 3 chains. Longest chain 54 peptides. Score 0.808 Round 3: 86 peptides, 1 chains. Longest chain 86 peptides. Score 0.859 Round 4: 87 peptides, 2 chains. Longest chain 71 peptides. Score 0.842 Round 5: 89 peptides, 1 chains. Longest chain 89 peptides. Score 0.869 Taking the results from Round 5 Chains 1, Residues 88, Estimated correctness of the model 98.8 % 1 chains (88 residues) have been docked in sequence ------------------------------------------------------ 16128 reflections ( 99.95 % complete ) and 887 restraints for refining 917 atoms. 164 conditional restraints added. Observations/parameters ratio is 4.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2397 (Rfree = 0.000) for 917 atoms. Found 28 (28 requested) and removed 23 (21 requested) atoms. Cycle 37: After refmac, R = 0.2273 (Rfree = 0.000) for 917 atoms. Found 28 (28 requested) and removed 15 (21 requested) atoms. Cycle 38: After refmac, R = 0.2244 (Rfree = 0.000) for 927 atoms. Found 27 (27 requested) and removed 16 (21 requested) atoms. Cycle 39: After refmac, R = 0.2230 (Rfree = 0.000) for 930 atoms. Found 26 (26 requested) and removed 11 (21 requested) atoms. Cycle 40: After refmac, R = 0.2198 (Rfree = 0.000) for 934 atoms. Found 26 (26 requested) and removed 13 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.93 1.66 Round 1: 85 peptides, 1 chains. Longest chain 85 peptides. Score 0.856 Round 2: 85 peptides, 1 chains. Longest chain 85 peptides. Score 0.856 Round 3: 85 peptides, 1 chains. Longest chain 85 peptides. Score 0.856 Round 4: 89 peptides, 1 chains. Longest chain 89 peptides. Score 0.869 Round 5: 88 peptides, 3 chains. Longest chain 43 peptides. Score 0.824 Taking the results from Round 4 Chains 1, Residues 88, Estimated correctness of the model 98.8 % 1 chains (88 residues) have been docked in sequence ------------------------------------------------------ 16128 reflections ( 99.95 % complete ) and 877 restraints for refining 917 atoms. 154 conditional restraints added. Observations/parameters ratio is 4.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2378 (Rfree = 0.000) for 917 atoms. Found 26 (26 requested) and removed 22 (21 requested) atoms. Cycle 42: After refmac, R = 0.2263 (Rfree = 0.000) for 915 atoms. Found 25 (25 requested) and removed 19 (21 requested) atoms. Cycle 43: After refmac, R = 0.2232 (Rfree = 0.000) for 917 atoms. Found 24 (24 requested) and removed 12 (21 requested) atoms. Cycle 44: After refmac, R = 0.2213 (Rfree = 0.000) for 921 atoms. Found 24 (24 requested) and removed 11 (21 requested) atoms. Cycle 45: After refmac, R = 0.2220 (Rfree = 0.000) for 931 atoms. Found 24 (24 requested) and removed 6 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.92 1.65 Round 1: 87 peptides, 1 chains. Longest chain 87 peptides. Score 0.863 Round 2: 88 peptides, 1 chains. Longest chain 88 peptides. Score 0.866 Round 3: 89 peptides, 1 chains. Longest chain 89 peptides. Score 0.869 Round 4: 87 peptides, 3 chains. Longest chain 42 peptides. Score 0.820 Round 5: 85 peptides, 3 chains. Longest chain 65 peptides. Score 0.812 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 1, Residues 88, Estimated correctness of the model 98.8 % 1 chains (88 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 16128 reflections ( 99.95 % complete ) and 723 restraints for refining 710 atoms. Observations/parameters ratio is 5.68 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2804 (Rfree = 0.000) for 710 atoms. Found 18 (18 requested) and removed 0 (18 requested) atoms. Cycle 47: After refmac, R = 0.2537 (Rfree = 0.000) for 710 atoms. Found 19 (19 requested) and removed 0 (17 requested) atoms. Cycle 48: After refmac, R = 0.2354 (Rfree = 0.000) for 710 atoms. Found 7 (20 requested) and removed 0 (17 requested) atoms. Cycle 49: After refmac, R = 0.2270 (Rfree = 0.000) for 710 atoms. TimeTaking 29.57