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 2inb-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2inb-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2inb-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2inb-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/2inb-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2inb-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 22:22:55 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/2inb-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2inb-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 101 and 0 Target number of residues in the AU: 101 Target solvent content: 0.6264 Checking the provided sequence file Detected sequence length: 140 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 140 Adjusted target solvent content: 0.48 Input MTZ file: 2inb-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: 152 Cell parameters: 59.524 59.524 71.521 90.000 90.000 120.000 Input sequence file: 2inb-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1120 target number of atoms Had to go as low as 0.70 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: 29.762 3.201 Wilson plot Bfac: 63.91 2608 reflections ( 99.85 % complete ) and 0 restraints for refining 1249 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.3512 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3247 (Rfree = 0.000) for 1249 atoms. Found 9 (11 requested) and removed 17 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.23 3.32 Search for helices and strands: 0 residues in 0 chains, 1267 seeds are put forward Round 1: 56 peptides, 10 chains. Longest chain 14 peptides. Score 0.368 Round 2: 80 peptides, 12 chains. Longest chain 14 peptides. Score 0.526 Round 3: 74 peptides, 9 chains. Longest chain 14 peptides. Score 0.590 Round 4: 78 peptides, 9 chains. Longest chain 15 peptides. Score 0.623 Round 5: 81 peptides, 10 chains. Longest chain 15 peptides. Score 0.610 Taking the results from Round 4 Chains 9, Residues 69, Estimated correctness of the model 47.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2608 reflections ( 99.85 % complete ) and 2299 restraints for refining 1023 atoms. 2032 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3258 (Rfree = 0.000) for 1023 atoms. Found 9 (9 requested) and removed 22 (4 requested) atoms. Cycle 2: After refmac, R = 0.2985 (Rfree = 0.000) for 989 atoms. Found 4 (9 requested) and removed 11 (4 requested) atoms. Cycle 3: After refmac, R = 0.2751 (Rfree = 0.000) for 972 atoms. Found 5 (8 requested) and removed 9 (4 requested) atoms. Cycle 4: After refmac, R = 0.2529 (Rfree = 0.000) for 962 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 5: After refmac, R = 0.2651 (Rfree = 0.000) for 959 atoms. Found 4 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.17 3.26 Search for helices and strands: 0 residues in 0 chains, 998 seeds are put forward Round 1: 66 peptides, 10 chains. Longest chain 17 peptides. Score 0.475 Round 2: 75 peptides, 7 chains. Longest chain 18 peptides. Score 0.670 Round 3: 71 peptides, 7 chains. Longest chain 22 peptides. Score 0.641 Round 4: 71 peptides, 8 chains. Longest chain 17 peptides. Score 0.603 Round 5: 74 peptides, 6 chains. Longest chain 22 peptides. Score 0.697 Taking the results from Round 5 Chains 8, Residues 68, Estimated correctness of the model 64.5 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 2608 reflections ( 99.85 % complete ) and 1856 restraints for refining 967 atoms. 1515 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2960 (Rfree = 0.000) for 967 atoms. Found 6 (8 requested) and removed 10 (4 requested) atoms. Cycle 7: After refmac, R = 0.2803 (Rfree = 0.000) for 962 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 8: After refmac, R = 0.2779 (Rfree = 0.000) for 955 atoms. Found 3 (8 requested) and removed 7 (4 requested) atoms. Cycle 9: After refmac, R = 0.2776 (Rfree = 0.000) for 949 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. Cycle 10: After refmac, R = 0.2829 (Rfree = 0.000) for 941 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.23 3.32 Search for helices and strands: 0 residues in 0 chains, 952 seeds are put forward Round 1: 75 peptides, 12 chains. Longest chain 12 peptides. Score 0.478 Round 2: 87 peptides, 11 chains. Longest chain 16 peptides. Score 0.622 Round 3: 82 peptides, 11 chains. Longest chain 17 peptides. Score 0.582 Round 4: 74 peptides, 11 chains. Longest chain 10 peptides. Score 0.511 Round 5: 80 peptides, 11 chains. Longest chain 11 peptides. Score 0.565 Taking the results from Round 2 Chains 11, Residues 76, Estimated correctness of the model 46.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2608 reflections ( 99.85 % complete ) and 2022 restraints for refining 951 atoms. 1729 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2914 (Rfree = 0.000) for 951 atoms. Found 5 (8 requested) and removed 8 (4 requested) atoms. Cycle 12: After refmac, R = 0.2953 (Rfree = 0.000) for 946 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. Cycle 13: After refmac, R = 0.2743 (Rfree = 0.000) for 938 atoms. Found 6 (8 requested) and removed 7 (4 requested) atoms. Cycle 14: After refmac, R = 0.2638 (Rfree = 0.000) for 935 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. Cycle 15: After refmac, R = 0.2583 (Rfree = 0.000) for 929 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.22 3.31 Search for helices and strands: 0 residues in 0 chains, 958 seeds are put forward Round 1: 62 peptides, 11 chains. Longest chain 10 peptides. Score 0.388 Round 2: 75 peptides, 10 chains. Longest chain 17 peptides. Score 0.560 Round 3: 74 peptides, 10 chains. Longest chain 18 peptides. Score 0.551 Round 4: 76 peptides, 10 chains. Longest chain 16 peptides. Score 0.569 Round 5: 67 peptides, 10 chains. Longest chain 16 peptides. Score 0.485 Taking the results from Round 4 Chains 10, Residues 66, Estimated correctness of the model 32.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2608 reflections ( 99.85 % complete ) and 2034 restraints for refining 938 atoms. 1780 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2838 (Rfree = 0.000) for 938 atoms. Found 5 (8 requested) and removed 5 (4 requested) atoms. Cycle 17: After refmac, R = 0.2727 (Rfree = 0.000) for 936 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. Cycle 18: After refmac, R = 0.2965 (Rfree = 0.000) for 930 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 19: After refmac, R = 0.2471 (Rfree = 0.000) for 929 atoms. Found 6 (8 requested) and removed 4 (4 requested) atoms. Cycle 20: After refmac, R = 0.2432 (Rfree = 0.000) for 929 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.19 3.28 Search for helices and strands: 0 residues in 0 chains, 966 seeds are put forward Round 1: 65 peptides, 12 chains. Longest chain 13 peptides. Score 0.374 Round 2: 73 peptides, 14 chains. Longest chain 10 peptides. Score 0.369 Round 3: 80 peptides, 12 chains. Longest chain 13 peptides. Score 0.526 Round 4: 73 peptides, 11 chains. Longest chain 11 peptides. Score 0.501 Round 5: 65 peptides, 11 chains. Longest chain 13 peptides. Score 0.420 Taking the results from Round 3 Chains 12, Residues 68, Estimated correctness of the model 19.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2608 reflections ( 99.85 % complete ) and 2041 restraints for refining 957 atoms. 1781 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2745 (Rfree = 0.000) for 957 atoms. Found 6 (8 requested) and removed 5 (4 requested) atoms. Cycle 22: After refmac, R = 0.2640 (Rfree = 0.000) for 955 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. Cycle 23: After refmac, R = 0.2653 (Rfree = 0.000) for 950 atoms. Found 5 (8 requested) and removed 6 (4 requested) atoms. Cycle 24: After refmac, R = 0.2678 (Rfree = 0.000) for 947 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. Cycle 25: After refmac, R = 0.2666 (Rfree = 0.000) for 940 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.15 3.24 Search for helices and strands: 0 residues in 0 chains, 973 seeds are put forward Round 1: 55 peptides, 10 chains. Longest chain 13 peptides. Score 0.357 Round 2: 69 peptides, 12 chains. Longest chain 14 peptides. Score 0.417 Round 3: 63 peptides, 11 chains. Longest chain 12 peptides. Score 0.399 Round 4: 67 peptides, 11 chains. Longest chain 12 peptides. Score 0.441 Round 5: 67 peptides, 12 chains. Longest chain 11 peptides. Score 0.396 Taking the results from Round 4 Chains 11, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2608 reflections ( 99.85 % complete ) and 2195 restraints for refining 983 atoms. 1982 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2737 (Rfree = 0.000) for 983 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 27: After refmac, R = 0.2619 (Rfree = 0.000) for 981 atoms. Found 7 (8 requested) and removed 5 (4 requested) atoms. Cycle 28: After refmac, R = 0.2599 (Rfree = 0.000) for 979 atoms. Found 5 (8 requested) and removed 4 (4 requested) atoms. Cycle 29: After refmac, R = 0.2507 (Rfree = 0.000) for 979 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. Cycle 30: After refmac, R = 0.2290 (Rfree = 0.000) for 976 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.19 3.28 Search for helices and strands: 0 residues in 0 chains, 1004 seeds are put forward Round 1: 66 peptides, 14 chains. Longest chain 10 peptides. Score 0.289 Round 2: 68 peptides, 12 chains. Longest chain 14 peptides. Score 0.406 Round 3: 82 peptides, 15 chains. Longest chain 9 peptides. Score 0.420 Round 4: 75 peptides, 10 chains. Longest chain 15 peptides. Score 0.560 Round 5: 75 peptides, 11 chains. Longest chain 16 peptides. Score 0.520 Taking the results from Round 4 Chains 11, Residues 65, Estimated correctness of the model 29.8 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2608 reflections ( 99.85 % complete ) and 2103 restraints for refining 1023 atoms. 1814 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2656 (Rfree = 0.000) for 1023 atoms. Found 3 (9 requested) and removed 7 (4 requested) atoms. Cycle 32: After refmac, R = 0.2624 (Rfree = 0.000) for 1013 atoms. Found 7 (9 requested) and removed 5 (4 requested) atoms. Cycle 33: After refmac, R = 0.2561 (Rfree = 0.000) for 1012 atoms. Found 5 (9 requested) and removed 7 (4 requested) atoms. Cycle 34: After refmac, R = 0.2310 (Rfree = 0.000) for 1005 atoms. Found 4 (9 requested) and removed 4 (4 requested) atoms. Cycle 35: After refmac, R = 0.2753 (Rfree = 0.000) for 1002 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.19 3.28 Search for helices and strands: 0 residues in 0 chains, 1039 seeds are put forward Round 1: 55 peptides, 11 chains. Longest chain 9 peptides. Score 0.307 Round 2: 69 peptides, 13 chains. Longest chain 9 peptides. Score 0.371 Round 3: 69 peptides, 12 chains. Longest chain 10 peptides. Score 0.417 Round 4: 68 peptides, 11 chains. Longest chain 10 peptides. Score 0.452 Round 5: 72 peptides, 11 chains. Longest chain 10 peptides. Score 0.491 Taking the results from Round 5 Chains 11, Residues 61, Estimated correctness of the model 8.3 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 2608 reflections ( 99.85 % complete ) and 2138 restraints for refining 1023 atoms. 1860 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2725 (Rfree = 0.000) for 1023 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 37: After refmac, R = 0.2631 (Rfree = 0.000) for 1016 atoms. Found 6 (9 requested) and removed 6 (4 requested) atoms. Cycle 38: After refmac, R = 0.2541 (Rfree = 0.000) for 1014 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. Cycle 39: After refmac, R = 0.2406 (Rfree = 0.000) for 1008 atoms. Found 6 (9 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.2183 (Rfree = 0.000) for 1009 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.13 3.21 Search for helices and strands: 0 residues in 0 chains, 1039 seeds are put forward Round 1: 46 peptides, 10 chains. Longest chain 6 peptides. Score 0.247 Round 2: 61 peptides, 11 chains. Longest chain 11 peptides. Score 0.376 Round 3: 62 peptides, 11 chains. Longest chain 11 peptides. Score 0.388 Round 4: 61 peptides, 9 chains. Longest chain 11 peptides. Score 0.470 Round 5: 54 peptides, 8 chains. Longest chain 12 peptides. Score 0.443 Taking the results from Round 4 Chains 9, Residues 52, Estimated correctness of the model 1.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2608 reflections ( 99.85 % complete ) and 2229 restraints for refining 1019 atoms. 2030 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2441 (Rfree = 0.000) for 1019 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 42: After refmac, R = 0.2302 (Rfree = 0.000) for 1016 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. Cycle 43: After refmac, R = 0.2259 (Rfree = 0.000) for 1019 atoms. Found 8 (9 requested) and removed 4 (4 requested) atoms. Cycle 44: After refmac, R = 0.2141 (Rfree = 0.000) for 1022 atoms. Found 4 (9 requested) and removed 6 (4 requested) atoms. Cycle 45: After refmac, R = 0.2108 (Rfree = 0.000) for 1020 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.14 3.22 Search for helices and strands: 0 residues in 0 chains, 1052 seeds are put forward Round 1: 59 peptides, 12 chains. Longest chain 8 peptides. Score 0.305 Round 2: 65 peptides, 12 chains. Longest chain 10 peptides. Score 0.374 Round 3: 62 peptides, 11 chains. Longest chain 11 peptides. Score 0.388 Round 4: 59 peptides, 10 chains. Longest chain 10 peptides. Score 0.402 Round 5: 59 peptides, 11 chains. Longest chain 9 peptides. Score 0.354 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 49, 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 2inb-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2608 reflections ( 99.85 % complete ) and 2225 restraints for refining 1023 atoms. 2039 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2280 (Rfree = 0.000) for 1023 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2316 (Rfree = 0.000) for 1016 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2370 (Rfree = 0.000) for 1009 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2057 (Rfree = 0.000) for 1004 atoms. TimeTaking 24.73