Sun 23 Dec 22:22:46 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 2pn2-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pn2-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pn2-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn2-3.4-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/2pn2-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn2-3.4-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 22:22:57 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/2pn2-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn2-3.4-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 90 and 0 Target number of residues in the AU: 90 Target solvent content: 0.6539 Checking the provided sequence file Detected sequence length: 155 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 155 Adjusted target solvent content: 0.40 Input MTZ file: 2pn2-3.4-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: 20 Cell parameters: 47.282 57.586 103.372 90.000 90.000 90.000 Input sequence file: 2pn2-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1240 target number of atoms Had to go as low as 0.50 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: 51.686 3.400 Wilson plot Bfac: 79.16 2072 reflections ( 99.04 % complete ) and 0 restraints for refining 1370 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3332 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3303 (Rfree = 0.000) for 1370 atoms. Found 9 (10 requested) and removed 26 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.43 3.93 Search for helices and strands: 0 residues in 0 chains, 1371 seeds are put forward Round 1: 54 peptides, 10 chains. Longest chain 11 peptides. Score 0.350 Round 2: 69 peptides, 9 chains. Longest chain 15 peptides. Score 0.556 Round 3: 74 peptides, 11 chains. Longest chain 13 peptides. Score 0.520 Round 4: 75 peptides, 10 chains. Longest chain 14 peptides. Score 0.570 Round 5: 83 peptides, 12 chains. Longest chain 16 peptides. Score 0.563 Taking the results from Round 4 Chains 10, Residues 65, Estimated correctness of the model 18.6 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2072 reflections ( 99.04 % complete ) and 2644 restraints for refining 1125 atoms. 2381 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2791 (Rfree = 0.000) for 1125 atoms. Found 6 (8 requested) and removed 11 (4 requested) atoms. Cycle 2: After refmac, R = 0.2818 (Rfree = 0.000) for 1093 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 3: After refmac, R = 0.2513 (Rfree = 0.000) for 1081 atoms. Found 5 (8 requested) and removed 9 (4 requested) atoms. Cycle 4: After refmac, R = 0.2572 (Rfree = 0.000) for 1073 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 5: After refmac, R = 0.2596 (Rfree = 0.000) for 1071 atoms. Found 5 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 3.89 Search for helices and strands: 0 residues in 0 chains, 1103 seeds are put forward Round 1: 56 peptides, 11 chains. Longest chain 8 peptides. Score 0.323 Round 2: 60 peptides, 10 chains. Longest chain 13 peptides. Score 0.420 Round 3: 57 peptides, 8 chains. Longest chain 15 peptides. Score 0.483 Round 4: 56 peptides, 7 chains. Longest chain 15 peptides. Score 0.519 Round 5: 67 peptides, 7 chains. Longest chain 18 peptides. Score 0.620 Taking the results from Round 5 Chains 7, Residues 60, Estimated correctness of the model 35.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2072 reflections ( 99.04 % complete ) and 2301 restraints for refining 994 atoms. 2068 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2471 (Rfree = 0.000) for 994 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 7: After refmac, R = 0.2341 (Rfree = 0.000) for 987 atoms. Found 6 (7 requested) and removed 3 (3 requested) atoms. Cycle 8: After refmac, R = 0.2120 (Rfree = 0.000) for 979 atoms. Found 5 (7 requested) and removed 3 (3 requested) atoms. Cycle 9: After refmac, R = 0.2081 (Rfree = 0.000) for 979 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 10: After refmac, R = 0.2144 (Rfree = 0.000) for 972 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.45 3.95 Search for helices and strands: 0 residues in 0 chains, 1007 seeds are put forward Round 1: 61 peptides, 12 chains. Longest chain 9 peptides. Score 0.333 Round 2: 74 peptides, 11 chains. Longest chain 12 peptides. Score 0.520 Round 3: 80 peptides, 13 chains. Longest chain 14 peptides. Score 0.494 Round 4: 76 peptides, 12 chains. Longest chain 13 peptides. Score 0.497 Round 5: 77 peptides, 12 chains. Longest chain 12 peptides. Score 0.507 Taking the results from Round 2 Chains 11, Residues 63, Estimated correctness of the model 0.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2072 reflections ( 99.04 % complete ) and 2194 restraints for refining 966 atoms. 1953 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2197 (Rfree = 0.000) for 966 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 12: After refmac, R = 0.1805 (Rfree = 0.000) for 961 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 13: After refmac, R = 0.1838 (Rfree = 0.000) for 959 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. Cycle 14: After refmac, R = 0.1612 (Rfree = 0.000) for 956 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. Cycle 15: After refmac, R = 0.1532 (Rfree = 0.000) for 955 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 3.94 Search for helices and strands: 0 residues in 0 chains, 987 seeds are put forward Round 1: 69 peptides, 14 chains. Longest chain 7 peptides. Score 0.329 Round 2: 80 peptides, 13 chains. Longest chain 11 peptides. Score 0.494 Round 3: 84 peptides, 14 chains. Longest chain 11 peptides. Score 0.491 Round 4: 85 peptides, 13 chains. Longest chain 12 peptides. Score 0.541 Round 5: 84 peptides, 12 chains. Longest chain 16 peptides. Score 0.572 Taking the results from Round 5 Chains 12, Residues 72, Estimated correctness of the model 19.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2072 reflections ( 99.04 % complete ) and 2416 restraints for refining 1067 atoms. 2140 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2218 (Rfree = 0.000) for 1067 atoms. Found 4 (8 requested) and removed 8 (4 requested) atoms. Cycle 17: After refmac, R = 0.2057 (Rfree = 0.000) for 1061 atoms. Found 0 (8 requested) and removed 5 (4 requested) atoms. Cycle 18: After refmac, R = 0.2030 (Rfree = 0.000) for 1053 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. Cycle 19: After refmac, R = 0.2022 (Rfree = 0.000) for 1052 atoms. Found 2 (7 requested) and removed 6 (3 requested) atoms. Cycle 20: After refmac, R = 0.1942 (Rfree = 0.000) for 1047 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.48 3.98 Search for helices and strands: 0 residues in 0 chains, 1059 seeds are put forward Round 1: 66 peptides, 12 chains. Longest chain 12 peptides. Score 0.391 Round 2: 64 peptides, 11 chains. Longest chain 9 peptides. Score 0.416 Round 3: 77 peptides, 12 chains. Longest chain 10 peptides. Score 0.507 Round 4: 74 peptides, 11 chains. Longest chain 12 peptides. Score 0.520 Round 5: 67 peptides, 10 chains. Longest chain 13 peptides. Score 0.494 Taking the results from Round 4 Chains 11, Residues 63, Estimated correctness of the model 0.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2072 reflections ( 99.04 % complete ) and 2500 restraints for refining 1064 atoms. 2259 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2327 (Rfree = 0.000) for 1064 atoms. Found 3 (8 requested) and removed 8 (4 requested) atoms. Cycle 22: After refmac, R = 0.2045 (Rfree = 0.000) for 1056 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 23: After refmac, R = 0.2152 (Rfree = 0.000) for 1050 atoms. Found 6 (7 requested) and removed 4 (3 requested) atoms. Cycle 24: After refmac, R = 0.2094 (Rfree = 0.000) for 1049 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 25: After refmac, R = 0.2220 (Rfree = 0.000) for 1046 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 3.95 Search for helices and strands: 0 residues in 0 chains, 1080 seeds are put forward Round 1: 46 peptides, 9 chains. Longest chain 9 peptides. Score 0.304 Round 2: 55 peptides, 8 chains. Longest chain 12 peptides. Score 0.461 Round 3: 60 peptides, 9 chains. Longest chain 10 peptides. Score 0.467 Round 4: 69 peptides, 10 chains. Longest chain 11 peptides. Score 0.514 Round 5: 66 peptides, 8 chains. Longest chain 13 peptides. Score 0.571 Taking the results from Round 5 Chains 8, Residues 58, Estimated correctness of the model 18.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2072 reflections ( 99.04 % complete ) and 2416 restraints for refining 1046 atoms. 2192 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2463 (Rfree = 0.000) for 1046 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 27: After refmac, R = 0.2216 (Rfree = 0.000) for 1040 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 28: After refmac, R = 0.2367 (Rfree = 0.000) for 1039 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 29: After refmac, R = 0.2062 (Rfree = 0.000) for 1037 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 30: After refmac, R = 0.2237 (Rfree = 0.000) for 1032 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.47 3.97 Search for helices and strands: 0 residues in 0 chains, 1073 seeds are put forward Round 1: 58 peptides, 10 chains. Longest chain 9 peptides. Score 0.397 Round 2: 61 peptides, 10 chains. Longest chain 12 peptides. Score 0.431 Round 3: 69 peptides, 11 chains. Longest chain 14 peptides. Score 0.470 Round 4: 64 peptides, 9 chains. Longest chain 11 peptides. Score 0.508 Round 5: 64 peptides, 9 chains. Longest chain 15 peptides. Score 0.508 Taking the results from Round 5 Chains 9, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2072 reflections ( 99.04 % complete ) and 2442 restraints for refining 1037 atoms. 2231 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2457 (Rfree = 0.000) for 1037 atoms. Found 5 (7 requested) and removed 13 (3 requested) atoms. Cycle 32: After refmac, R = 0.1993 (Rfree = 0.000) for 1028 atoms. Found 5 (7 requested) and removed 10 (3 requested) atoms. Cycle 33: After refmac, R = 0.1999 (Rfree = 0.000) for 1022 atoms. Found 5 (7 requested) and removed 3 (3 requested) atoms. Cycle 34: After refmac, R = 0.1983 (Rfree = 0.000) for 1023 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 35: After refmac, R = 0.1915 (Rfree = 0.000) for 1024 atoms. Found 6 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.46 3.96 Search for helices and strands: 0 residues in 0 chains, 1044 seeds are put forward Round 1: 54 peptides, 9 chains. Longest chain 17 peptides. Score 0.401 Round 2: 64 peptides, 10 chains. Longest chain 16 peptides. Score 0.463 Round 3: 64 peptides, 10 chains. Longest chain 17 peptides. Score 0.463 Round 4: 59 peptides, 8 chains. Longest chain 17 peptides. Score 0.503 Round 5: 57 peptides, 8 chains. Longest chain 16 peptides. Score 0.483 Taking the results from Round 4 Chains 8, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2072 reflections ( 99.04 % complete ) and 2351 restraints for refining 1016 atoms. 2155 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2079 (Rfree = 0.000) for 1016 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 37: After refmac, R = 0.2073 (Rfree = 0.000) for 1015 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 38: After refmac, R = 0.1918 (Rfree = 0.000) for 1017 atoms. Found 5 (7 requested) and removed 4 (3 requested) atoms. Cycle 39: After refmac, R = 0.2082 (Rfree = 0.000) for 1017 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 40: After refmac, R = 0.1840 (Rfree = 0.000) for 1020 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.41 3.90 Search for helices and strands: 0 residues in 0 chains, 1053 seeds are put forward Round 1: 54 peptides, 11 chains. Longest chain 8 peptides. Score 0.299 Round 2: 58 peptides, 9 chains. Longest chain 11 peptides. Score 0.446 Round 3: 62 peptides, 9 chains. Longest chain 13 peptides. Score 0.488 Round 4: 53 peptides, 9 chains. Longest chain 9 peptides. Score 0.389 Round 5: 63 peptides, 9 chains. Longest chain 14 peptides. Score 0.498 Taking the results from Round 5 Chains 9, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2072 reflections ( 99.04 % complete ) and 2407 restraints for refining 1023 atoms. 2200 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2195 (Rfree = 0.000) for 1023 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 42: After refmac, R = 0.1858 (Rfree = 0.000) for 1022 atoms. Found 7 (7 requested) and removed 16 (3 requested) atoms. Cycle 43: After refmac, R = 0.1895 (Rfree = 0.000) for 1012 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 44: After refmac, R = 0.1471 (Rfree = 0.000) for 1007 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 45: After refmac, R = 0.1986 (Rfree = 0.000) for 1004 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.46 3.96 Search for helices and strands: 0 residues in 0 chains, 1036 seeds are put forward Round 1: 46 peptides, 11 chains. Longest chain 5 peptides. Score 0.194 Round 2: 41 peptides, 8 chains. Longest chain 11 peptides. Score 0.294 Round 3: 49 peptides, 10 chains. Longest chain 7 peptides. Score 0.288 Round 4: 46 peptides, 9 chains. Longest chain 8 peptides. Score 0.304 Round 5: 44 peptides, 8 chains. Longest chain 11 peptides. Score 0.333 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 8, 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 2pn2-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2072 reflections ( 99.04 % complete ) and 2385 restraints for refining 1008 atoms. 2249 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1897 (Rfree = 0.000) for 1008 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1879 (Rfree = 0.000) for 1005 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1775 (Rfree = 0.000) for 1000 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1798 (Rfree = 0.000) for 993 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 24.79