null Sun 23 Dec 22:23:08 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 2pn2-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pn2-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pn2-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn2-3.2-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/2pn2-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn2-3.2-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 22:23:18 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/2pn2-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn2-3.2-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 92 and 0 Target number of residues in the AU: 92 Target solvent content: 0.6462 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: 2pn2-3.2-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: 2pn2-3.2-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 3.201 Wilson plot Bfac: 73.62 2481 reflections ( 99.16 % complete ) and 0 restraints for refining 1375 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3342 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2650 (Rfree = 0.000) for 1375 atoms. Found 7 (12 requested) and removed 20 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 3.75 Search for helices and strands: 0 residues in 0 chains, 1374 seeds are put forward Round 1: 58 peptides, 9 chains. Longest chain 13 peptides. Score 0.446 Round 2: 80 peptides, 10 chains. Longest chain 21 peptides. Score 0.613 Round 3: 87 peptides, 10 chains. Longest chain 16 peptides. Score 0.667 Round 4: 89 peptides, 9 chains. Longest chain 18 peptides. Score 0.712 Round 5: 85 peptides, 10 chains. Longest chain 21 peptides. Score 0.652 Taking the results from Round 4 Chains 13, Residues 80, Estimated correctness of the model 67.7 % 2 chains (24 residues) have been docked in sequence Building loops using Loopy2018 13 chains (80 residues) following loop building 2 chains (24 residues) in sequence following loop building ------------------------------------------------------ 2481 reflections ( 99.16 % complete ) and 2373 restraints for refining 1132 atoms. 1990 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2811 (Rfree = 0.000) for 1132 atoms. Found 5 (10 requested) and removed 20 (5 requested) atoms. Cycle 2: After refmac, R = 0.2497 (Rfree = 0.000) for 1101 atoms. Found 5 (10 requested) and removed 9 (5 requested) atoms. Cycle 3: After refmac, R = 0.2486 (Rfree = 0.000) for 1086 atoms. Found 3 (9 requested) and removed 8 (4 requested) atoms. Cycle 4: After refmac, R = 0.2402 (Rfree = 0.000) for 1078 atoms. Found 1 (8 requested) and removed 6 (4 requested) atoms. Cycle 5: After refmac, R = 0.2408 (Rfree = 0.000) for 1071 atoms. Found 1 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 3.86 Search for helices and strands: 0 residues in 0 chains, 1087 seeds are put forward Round 1: 73 peptides, 9 chains. Longest chain 15 peptides. Score 0.592 Round 2: 86 peptides, 9 chains. Longest chain 20 peptides. Score 0.692 Round 3: 75 peptides, 9 chains. Longest chain 16 peptides. Score 0.609 Round 4: 73 peptides, 8 chains. Longest chain 14 peptides. Score 0.630 Round 5: 77 peptides, 8 chains. Longest chain 15 peptides. Score 0.661 Taking the results from Round 2 Chains 9, Residues 77, Estimated correctness of the model 63.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2481 reflections ( 99.16 % complete ) and 2508 restraints for refining 1054 atoms. 2209 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2741 (Rfree = 0.000) for 1054 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 7: After refmac, R = 0.2548 (Rfree = 0.000) for 1048 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 8: After refmac, R = 0.2375 (Rfree = 0.000) for 1040 atoms. Found 0 (8 requested) and removed 10 (4 requested) atoms. Cycle 9: After refmac, R = 0.2350 (Rfree = 0.000) for 1029 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 10: After refmac, R = 0.2298 (Rfree = 0.000) for 1028 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.86 Search for helices and strands: 0 residues in 0 chains, 1052 seeds are put forward Round 1: 66 peptides, 9 chains. Longest chain 15 peptides. Score 0.528 Round 2: 75 peptides, 7 chains. Longest chain 16 peptides. Score 0.681 Round 3: 73 peptides, 8 chains. Longest chain 16 peptides. Score 0.630 Round 4: 81 peptides, 10 chains. Longest chain 17 peptides. Score 0.621 Round 5: 80 peptides, 9 chains. Longest chain 18 peptides. Score 0.649 Taking the results from Round 2 Chains 7, Residues 68, Estimated correctness of the model 61.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 2481 reflections ( 99.16 % complete ) and 2331 restraints for refining 1062 atoms. 2013 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2507 (Rfree = 0.000) for 1062 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 12: After refmac, R = 0.2339 (Rfree = 0.000) for 1056 atoms. Found 7 (8 requested) and removed 9 (4 requested) atoms. Cycle 13: After refmac, R = 0.2262 (Rfree = 0.000) for 1050 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. Cycle 14: After refmac, R = 0.2240 (Rfree = 0.000) for 1044 atoms. Found 4 (8 requested) and removed 5 (4 requested) atoms. Cycle 15: After refmac, R = 0.2203 (Rfree = 0.000) for 1038 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.37 3.86 Search for helices and strands: 0 residues in 0 chains, 1062 seeds are put forward Round 1: 58 peptides, 8 chains. Longest chain 14 peptides. Score 0.493 Round 2: 61 peptides, 8 chains. Longest chain 12 peptides. Score 0.523 Round 3: 79 peptides, 8 chains. Longest chain 21 peptides. Score 0.676 Round 4: 81 peptides, 10 chains. Longest chain 16 peptides. Score 0.621 Round 5: 88 peptides, 11 chains. Longest chain 19 peptides. Score 0.641 Taking the results from Round 3 Chains 9, Residues 71, Estimated correctness of the model 59.9 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 2481 reflections ( 99.16 % complete ) and 2179 restraints for refining 1036 atoms. 1855 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2497 (Rfree = 0.000) for 1036 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 17: After refmac, R = 0.2666 (Rfree = 0.000) for 1029 atoms. Found 4 (8 requested) and removed 13 (4 requested) atoms. Cycle 18: After refmac, R = 0.2357 (Rfree = 0.000) for 1011 atoms. Found 3 (8 requested) and removed 7 (4 requested) atoms. Cycle 19: After refmac, R = 0.2257 (Rfree = 0.000) for 997 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 20: After refmac, R = 0.2228 (Rfree = 0.000) for 992 atoms. Found 1 (7 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 3.87 Search for helices and strands: 0 residues in 0 chains, 1028 seeds are put forward Round 1: 52 peptides, 7 chains. Longest chain 13 peptides. Score 0.477 Round 2: 70 peptides, 9 chains. Longest chain 15 peptides. Score 0.566 Round 3: 67 peptides, 9 chains. Longest chain 15 peptides. Score 0.538 Round 4: 72 peptides, 9 chains. Longest chain 15 peptides. Score 0.583 Round 5: 69 peptides, 9 chains. Longest chain 15 peptides. Score 0.556 Taking the results from Round 4 Chains 9, Residues 63, Estimated correctness of the model 36.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2481 reflections ( 99.16 % complete ) and 2330 restraints for refining 1008 atoms. 2087 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2503 (Rfree = 0.000) for 1008 atoms. Found 5 (8 requested) and removed 4 (4 requested) atoms. Cycle 22: After refmac, R = 0.2464 (Rfree = 0.000) for 1009 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. Cycle 23: After refmac, R = 0.2318 (Rfree = 0.000) for 1006 atoms. Found 3 (8 requested) and removed 14 (4 requested) atoms. Cycle 24: After refmac, R = 0.2232 (Rfree = 0.000) for 990 atoms. Found 4 (7 requested) and removed 7 (4 requested) atoms. Cycle 25: After refmac, R = 0.2310 (Rfree = 0.000) for 983 atoms. Found 6 (7 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 3.87 Search for helices and strands: 0 residues in 0 chains, 1015 seeds are put forward Round 1: 71 peptides, 11 chains. Longest chain 12 peptides. Score 0.490 Round 2: 71 peptides, 10 chains. Longest chain 17 peptides. Score 0.533 Round 3: 78 peptides, 9 chains. Longest chain 20 peptides. Score 0.634 Round 4: 72 peptides, 11 chains. Longest chain 17 peptides. Score 0.500 Round 5: 73 peptides, 8 chains. Longest chain 17 peptides. Score 0.630 Taking the results from Round 3 Chains 9, Residues 69, Estimated correctness of the model 49.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2481 reflections ( 99.16 % complete ) and 2119 restraints for refining 968 atoms. 1852 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2358 (Rfree = 0.000) for 968 atoms. Found 5 (7 requested) and removed 6 (4 requested) atoms. Cycle 27: After refmac, R = 0.2296 (Rfree = 0.000) for 966 atoms. Found 7 (7 requested) and removed 7 (4 requested) atoms. Cycle 28: After refmac, R = 0.2198 (Rfree = 0.000) for 964 atoms. Found 5 (7 requested) and removed 5 (4 requested) atoms. Cycle 29: After refmac, R = 0.2092 (Rfree = 0.000) for 963 atoms. Found 0 (7 requested) and removed 6 (4 requested) atoms. Cycle 30: After refmac, R = 0.2027 (Rfree = 0.000) for 955 atoms. Found 1 (7 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 3.83 Search for helices and strands: 0 residues in 0 chains, 982 seeds are put forward Round 1: 57 peptides, 7 chains. Longest chain 18 peptides. Score 0.529 Round 2: 54 peptides, 8 chains. Longest chain 12 peptides. Score 0.450 Round 3: 61 peptides, 8 chains. Longest chain 15 peptides. Score 0.523 Round 4: 62 peptides, 8 chains. Longest chain 13 peptides. Score 0.533 Round 5: 71 peptides, 7 chains. Longest chain 18 peptides. Score 0.652 Taking the results from Round 5 Chains 7, Residues 64, Estimated correctness of the model 54.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2481 reflections ( 99.16 % complete ) and 2137 restraints for refining 973 atoms. 1888 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2446 (Rfree = 0.000) for 973 atoms. Found 7 (7 requested) and removed 7 (4 requested) atoms. Cycle 32: After refmac, R = 0.2246 (Rfree = 0.000) for 972 atoms. Found 1 (7 requested) and removed 4 (4 requested) atoms. Cycle 33: After refmac, R = 0.2145 (Rfree = 0.000) for 968 atoms. Found 1 (7 requested) and removed 8 (4 requested) atoms. Cycle 34: After refmac, R = 0.2087 (Rfree = 0.000) for 961 atoms. Found 1 (7 requested) and removed 5 (4 requested) atoms. Cycle 35: After refmac, R = 0.1968 (Rfree = 0.000) for 957 atoms. Found 0 (7 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 3.75 Search for helices and strands: 0 residues in 0 chains, 979 seeds are put forward Round 1: 54 peptides, 8 chains. Longest chain 12 peptides. Score 0.450 Round 2: 67 peptides, 11 chains. Longest chain 13 peptides. Score 0.449 Round 3: 64 peptides, 7 chains. Longest chain 20 peptides. Score 0.594 Round 4: 69 peptides, 9 chains. Longest chain 14 peptides. Score 0.556 Round 5: 71 peptides, 10 chains. Longest chain 17 peptides. Score 0.533 Taking the results from Round 3 Chains 7, Residues 57, Estimated correctness of the model 39.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2481 reflections ( 99.16 % complete ) and 2193 restraints for refining 974 atoms. 1972 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2975 (Rfree = 0.000) for 974 atoms. Found 7 (7 requested) and removed 12 (4 requested) atoms. Cycle 37: After refmac, R = 0.2401 (Rfree = 0.000) for 963 atoms. Found 7 (7 requested) and removed 6 (4 requested) atoms. Cycle 38: After refmac, R = 0.2549 (Rfree = 0.000) for 964 atoms. Found 7 (7 requested) and removed 8 (4 requested) atoms. Cycle 39: After refmac, R = 0.2365 (Rfree = 0.000) for 962 atoms. Found 7 (7 requested) and removed 5 (4 requested) atoms. Cycle 40: After refmac, R = 0.2805 (Rfree = 0.000) for 963 atoms. Found 7 (7 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 3.86 Search for helices and strands: 0 residues in 0 chains, 1008 seeds are put forward Round 1: 55 peptides, 8 chains. Longest chain 10 peptides. Score 0.461 Round 2: 56 peptides, 8 chains. Longest chain 12 peptides. Score 0.472 Round 3: 66 peptides, 8 chains. Longest chain 15 peptides. Score 0.571 Round 4: 70 peptides, 7 chains. Longest chain 18 peptides. Score 0.644 Round 5: 57 peptides, 7 chains. Longest chain 15 peptides. Score 0.529 Taking the results from Round 4 Chains 9, Residues 63, Estimated correctness of the model 52.3 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2481 reflections ( 99.16 % complete ) and 1993 restraints for refining 975 atoms. 1721 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2473 (Rfree = 0.000) for 975 atoms. Found 5 (7 requested) and removed 15 (4 requested) atoms. Cycle 42: After refmac, R = 0.2331 (Rfree = 0.000) for 965 atoms. Found 7 (7 requested) and removed 4 (4 requested) atoms. Cycle 43: After refmac, R = 0.2540 (Rfree = 0.000) for 966 atoms. Found 7 (7 requested) and removed 11 (4 requested) atoms. Cycle 44: After refmac, R = 0.2588 (Rfree = 0.000) for 955 atoms. Found 2 (7 requested) and removed 22 (4 requested) atoms. Cycle 45: After refmac, R = 0.2457 (Rfree = 0.000) for 934 atoms. Found 7 (7 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.24 3.71 Search for helices and strands: 0 residues in 0 chains, 971 seeds are put forward Round 1: 55 peptides, 10 chains. Longest chain 11 peptides. Score 0.362 Round 2: 62 peptides, 9 chains. Longest chain 11 peptides. Score 0.488 Round 3: 68 peptides, 9 chains. Longest chain 13 peptides. Score 0.547 Round 4: 76 peptides, 10 chains. Longest chain 14 peptides. Score 0.579 Round 5: 72 peptides, 12 chains. Longest chain 13 peptides. Score 0.456 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 66, Estimated correctness of the model 35.2 % 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. 2481 reflections ( 99.16 % complete ) and 2119 restraints for refining 976 atoms. 1865 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2140 (Rfree = 0.000) for 976 atoms. Found 0 (7 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2022 (Rfree = 0.000) for 972 atoms. Found 0 (7 requested) and removed 3 (4 requested) atoms. Cycle 48: After refmac, R = 0.1985 (Rfree = 0.000) for 969 atoms. Found 0 (7 requested) and removed 2 (4 requested) atoms. Cycle 49: After refmac, R = 0.1984 (Rfree = 0.000) for 967 atoms. Found 0 (7 requested) and removed 0 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:48:32 GMT 2018 Job finished. TimeTaking 25.4 Used memory is bytes: 16846544