Sun 23 Dec 22:22:52 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 2pim-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pim-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pim-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pim-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/2pim-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pim-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 22:23:00 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/2pim-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pim-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 115 and 0 Target number of residues in the AU: 115 Target solvent content: 0.6282 Checking the provided sequence file Detected sequence length: 141 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 141 Adjusted target solvent content: 0.54 Input MTZ file: 2pim-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: 177 Cell parameters: 111.771 111.771 46.411 90.000 90.000 120.000 Input sequence file: 2pim-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1128 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: 96.797 3.400 Wilson plot Bfac: 65.24 2594 reflections ( 99.35 % complete ) and 0 restraints for refining 1253 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.3245 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3004 (Rfree = 0.000) for 1253 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.20 3.03 Search for helices and strands: 0 residues in 0 chains, 1268 seeds are put forward Round 1: 81 peptides, 10 chains. Longest chain 14 peptides. Score 0.572 Round 2: 101 peptides, 10 chains. Longest chain 29 peptides. Score 0.703 Round 3: 105 peptides, 12 chains. Longest chain 16 peptides. Score 0.673 Round 4: 103 peptides, 10 chains. Longest chain 34 peptides. Score 0.714 Round 5: 105 peptides, 7 chains. Longest chain 44 peptides. Score 0.793 Taking the results from Round 5 Chains 11, Residues 98, Estimated correctness of the model 78.6 % 3 chains (35 residues) have been docked in sequence Building loops using Loopy2018 11 chains (98 residues) following loop building 3 chains (35 residues) in sequence following loop building ------------------------------------------------------ 2594 reflections ( 99.35 % complete ) and 1751 restraints for refining 1026 atoms. 1250 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2748 (Rfree = 0.000) for 1026 atoms. Found 7 (7 requested) and removed 34 (3 requested) atoms. Cycle 2: After refmac, R = 0.2512 (Rfree = 0.000) for 979 atoms. Found 1 (7 requested) and removed 11 (3 requested) atoms. Cycle 3: After refmac, R = 0.2515 (Rfree = 0.000) for 958 atoms. Found 0 (7 requested) and removed 11 (3 requested) atoms. Cycle 4: After refmac, R = 0.2623 (Rfree = 0.000) for 943 atoms. Found 3 (7 requested) and removed 11 (3 requested) atoms. Cycle 5: After refmac, R = 0.2453 (Rfree = 0.000) for 926 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.18 3.01 Search for helices and strands: 0 residues in 0 chains, 958 seeds are put forward Round 1: 90 peptides, 14 chains. Longest chain 17 peptides. Score 0.503 Round 2: 98 peptides, 8 chains. Longest chain 31 peptides. Score 0.738 Round 3: 101 peptides, 9 chains. Longest chain 38 peptides. Score 0.729 Round 4: 97 peptides, 9 chains. Longest chain 30 peptides. Score 0.707 Round 5: 106 peptides, 8 chains. Longest chain 43 peptides. Score 0.776 Taking the results from Round 5 Chains 9, Residues 98, Estimated correctness of the model 75.3 % 1 chains (40 residues) have been docked in sequence ------------------------------------------------------ 2594 reflections ( 99.35 % complete ) and 1697 restraints for refining 1009 atoms. 1162 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2735 (Rfree = 0.000) for 1009 atoms. Found 6 (6 requested) and removed 25 (3 requested) atoms. Cycle 7: After refmac, R = 0.2542 (Rfree = 0.000) for 976 atoms. Found 4 (6 requested) and removed 12 (3 requested) atoms. Cycle 8: After refmac, R = 0.2461 (Rfree = 0.000) for 962 atoms. Found 0 (6 requested) and removed 10 (3 requested) atoms. Cycle 9: After refmac, R = 0.2410 (Rfree = 0.000) for 942 atoms. Found 3 (6 requested) and removed 10 (3 requested) atoms. Cycle 10: After refmac, R = 0.2317 (Rfree = 0.000) for 929 atoms. Found 5 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.15 2.99 Search for helices and strands: 0 residues in 0 chains, 961 seeds are put forward Round 1: 91 peptides, 10 chains. Longest chain 30 peptides. Score 0.643 Round 2: 99 peptides, 9 chains. Longest chain 30 peptides. Score 0.718 Round 3: 110 peptides, 9 chains. Longest chain 50 peptides. Score 0.772 Round 4: 100 peptides, 8 chains. Longest chain 30 peptides. Score 0.748 Round 5: 107 peptides, 9 chains. Longest chain 25 peptides. Score 0.758 Taking the results from Round 3 Chains 9, Residues 101, Estimated correctness of the model 74.5 % 2 chains (62 residues) have been docked in sequence Building loops using Loopy2018 9 chains (101 residues) following loop building 2 chains (62 residues) in sequence following loop building ------------------------------------------------------ 2594 reflections ( 99.35 % complete ) and 1464 restraints for refining 997 atoms. 847 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2687 (Rfree = 0.000) for 997 atoms. Found 6 (6 requested) and removed 25 (3 requested) atoms. Cycle 12: After refmac, R = 0.2515 (Rfree = 0.000) for 963 atoms. Found 4 (5 requested) and removed 11 (3 requested) atoms. Cycle 13: After refmac, R = 0.2558 (Rfree = 0.000) for 952 atoms. Found 2 (5 requested) and removed 9 (3 requested) atoms. Cycle 14: After refmac, R = 0.2301 (Rfree = 0.000) for 939 atoms. Found 2 (5 requested) and removed 9 (3 requested) atoms. Cycle 15: After refmac, R = 0.2288 (Rfree = 0.000) for 931 atoms. Found 1 (5 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.16 3.00 Search for helices and strands: 0 residues in 0 chains, 963 seeds are put forward Round 1: 87 peptides, 9 chains. Longest chain 27 peptides. Score 0.647 Round 2: 100 peptides, 7 chains. Longest chain 56 peptides. Score 0.772 Round 3: 105 peptides, 11 chains. Longest chain 30 peptides. Score 0.699 Round 4: 102 peptides, 8 chains. Longest chain 50 peptides. Score 0.758 Round 5: 106 peptides, 8 chains. Longest chain 45 peptides. Score 0.776 Taking the results from Round 5 Chains 8, Residues 98, Estimated correctness of the model 75.3 % 1 chains (44 residues) have been docked in sequence ------------------------------------------------------ 2594 reflections ( 99.35 % complete ) and 1707 restraints for refining 1026 atoms. 1166 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2723 (Rfree = 0.000) for 1026 atoms. Found 5 (5 requested) and removed 56 (3 requested) atoms. Cycle 17: After refmac, R = 0.2444 (Rfree = 0.000) for 963 atoms. Found 3 (5 requested) and removed 15 (3 requested) atoms. Cycle 18: After refmac, R = 0.2350 (Rfree = 0.000) for 948 atoms. Found 4 (5 requested) and removed 12 (3 requested) atoms. Cycle 19: After refmac, R = 0.2273 (Rfree = 0.000) for 938 atoms. Found 4 (4 requested) and removed 13 (3 requested) atoms. Cycle 20: After refmac, R = 0.2048 (Rfree = 0.000) for 928 atoms. Found 4 (4 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 3.12 Search for helices and strands: 0 residues in 0 chains, 955 seeds are put forward Round 1: 86 peptides, 11 chains. Longest chain 13 peptides. Score 0.576 Round 2: 96 peptides, 11 chains. Longest chain 30 peptides. Score 0.645 Round 3: 98 peptides, 12 chains. Longest chain 19 peptides. Score 0.629 Round 4: 98 peptides, 9 chains. Longest chain 24 peptides. Score 0.713 Round 5: 103 peptides, 6 chains. Longest chain 56 peptides. Score 0.806 Taking the results from Round 5 Chains 9, Residues 97, Estimated correctness of the model 81.0 % 3 chains (60 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 120 A and 127 A 6 chains (99 residues) following loop building 2 chains (66 residues) in sequence following loop building ------------------------------------------------------ 2594 reflections ( 99.35 % complete ) and 1503 restraints for refining 1026 atoms. 923 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2979 (Rfree = 0.000) for 1026 atoms. Found 4 (4 requested) and removed 67 (3 requested) atoms. Cycle 22: After refmac, R = 0.2888 (Rfree = 0.000) for 952 atoms. Found 4 (4 requested) and removed 16 (3 requested) atoms. Cycle 23: After refmac, R = 0.2685 (Rfree = 0.000) for 934 atoms. Found 0 (4 requested) and removed 9 (3 requested) atoms. Cycle 24: After refmac, R = 0.2580 (Rfree = 0.000) for 923 atoms. Found 1 (3 requested) and removed 5 (3 requested) atoms. Cycle 25: After refmac, R = 0.2497 (Rfree = 0.000) for 916 atoms. Found 2 (3 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 3.15 Search for helices and strands: 0 residues in 0 chains, 946 seeds are put forward Round 1: 94 peptides, 14 chains. Longest chain 21 peptides. Score 0.535 Round 2: 86 peptides, 11 chains. Longest chain 17 peptides. Score 0.576 Round 3: 90 peptides, 9 chains. Longest chain 26 peptides. Score 0.666 Round 4: 92 peptides, 10 chains. Longest chain 23 peptides. Score 0.649 Round 5: 84 peptides, 9 chains. Longest chain 17 peptides. Score 0.627 Taking the results from Round 3 Chains 9, Residues 81, Estimated correctness of the model 48.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2594 reflections ( 99.35 % complete ) and 2056 restraints for refining 973 atoms. 1741 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2611 (Rfree = 0.000) for 973 atoms. Found 3 (3 requested) and removed 23 (3 requested) atoms. Cycle 27: After refmac, R = 0.2479 (Rfree = 0.000) for 950 atoms. Found 3 (3 requested) and removed 8 (3 requested) atoms. Cycle 28: After refmac, R = 0.2314 (Rfree = 0.000) for 941 atoms. Found 1 (3 requested) and removed 6 (3 requested) atoms. Cycle 29: After refmac, R = 0.2288 (Rfree = 0.000) for 935 atoms. Found 3 (3 requested) and removed 6 (3 requested) atoms. Cycle 30: After refmac, R = 0.2110 (Rfree = 0.000) for 932 atoms. Found 3 (3 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 3.10 Search for helices and strands: 0 residues in 0 chains, 972 seeds are put forward Round 1: 71 peptides, 9 chains. Longest chain 15 peptides. Score 0.529 Round 2: 92 peptides, 10 chains. Longest chain 26 peptides. Score 0.649 Round 3: 90 peptides, 10 chains. Longest chain 15 peptides. Score 0.636 Round 4: 89 peptides, 10 chains. Longest chain 30 peptides. Score 0.630 Round 5: 89 peptides, 11 chains. Longest chain 17 peptides. Score 0.598 Taking the results from Round 2 Chains 11, Residues 82, Estimated correctness of the model 43.8 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 2594 reflections ( 99.35 % complete ) and 1860 restraints for refining 991 atoms. 1482 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2352 (Rfree = 0.000) for 991 atoms. Found 3 (3 requested) and removed 27 (3 requested) atoms. Cycle 32: After refmac, R = 0.2171 (Rfree = 0.000) for 964 atoms. Found 0 (3 requested) and removed 15 (3 requested) atoms. Cycle 33: After refmac, R = 0.2145 (Rfree = 0.000) for 949 atoms. Found 1 (3 requested) and removed 8 (3 requested) atoms. Cycle 34: After refmac, R = 0.2126 (Rfree = 0.000) for 941 atoms. Found 2 (3 requested) and removed 6 (3 requested) atoms. Cycle 35: After refmac, R = 0.2173 (Rfree = 0.000) for 937 atoms. Found 3 (3 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.19 3.02 Search for helices and strands: 0 residues in 0 chains, 963 seeds are put forward Round 1: 87 peptides, 11 chains. Longest chain 26 peptides. Score 0.583 Round 2: 104 peptides, 11 chains. Longest chain 32 peptides. Score 0.694 Round 3: 96 peptides, 9 chains. Longest chain 26 peptides. Score 0.702 Round 4: 92 peptides, 9 chains. Longest chain 26 peptides. Score 0.678 Round 5: 84 peptides, 10 chains. Longest chain 26 peptides. Score 0.595 Taking the results from Round 3 Chains 10, Residues 87, Estimated correctness of the model 58.4 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2594 reflections ( 99.35 % complete ) and 1982 restraints for refining 983 atoms. 1623 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2426 (Rfree = 0.000) for 983 atoms. Found 2 (3 requested) and removed 14 (3 requested) atoms. Cycle 37: After refmac, R = 0.2540 (Rfree = 0.000) for 964 atoms. Found 3 (3 requested) and removed 12 (3 requested) atoms. Cycle 38: After refmac, R = 0.2548 (Rfree = 0.000) for 949 atoms. Found 3 (3 requested) and removed 7 (3 requested) atoms. Cycle 39: After refmac, R = 0.2194 (Rfree = 0.000) for 943 atoms. Found 3 (3 requested) and removed 7 (3 requested) atoms. Cycle 40: After refmac, R = 0.2718 (Rfree = 0.000) for 938 atoms. Found 3 (3 requested) and removed 12 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.18 3.01 Search for helices and strands: 0 residues in 0 chains, 968 seeds are put forward Round 1: 68 peptides, 9 chains. Longest chain 25 peptides. Score 0.504 Round 2: 84 peptides, 9 chains. Longest chain 25 peptides. Score 0.627 Round 3: 86 peptides, 9 chains. Longest chain 25 peptides. Score 0.641 Round 4: 88 peptides, 8 chains. Longest chain 25 peptides. Score 0.683 Round 5: 85 peptides, 7 chains. Longest chain 30 peptides. Score 0.694 Taking the results from Round 5 Chains 9, Residues 78, Estimated correctness of the model 56.3 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 2594 reflections ( 99.35 % complete ) and 1922 restraints for refining 992 atoms. 1558 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2553 (Rfree = 0.000) for 992 atoms. Found 3 (3 requested) and removed 11 (3 requested) atoms. Cycle 42: After refmac, R = 0.2294 (Rfree = 0.000) for 979 atoms. Found 3 (3 requested) and removed 9 (3 requested) atoms. Cycle 43: After refmac, R = 0.2264 (Rfree = 0.000) for 972 atoms. Found 3 (3 requested) and removed 7 (3 requested) atoms. Cycle 44: After refmac, R = 0.2103 (Rfree = 0.000) for 968 atoms. Found 1 (3 requested) and removed 7 (3 requested) atoms. Cycle 45: After refmac, R = 0.2252 (Rfree = 0.000) for 961 atoms. Found 3 (3 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.21 3.04 Search for helices and strands: 0 residues in 0 chains, 992 seeds are put forward Round 1: 71 peptides, 8 chains. Longest chain 22 peptides. Score 0.566 Round 2: 79 peptides, 9 chains. Longest chain 22 peptides. Score 0.592 Round 3: 81 peptides, 8 chains. Longest chain 25 peptides. Score 0.639 Round 4: 77 peptides, 8 chains. Longest chain 25 peptides. Score 0.611 Round 5: 72 peptides, 8 chains. Longest chain 25 peptides. Score 0.574 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 73, Estimated correctness of the model 40.9 % 2 chains (21 residues) have been docked in sequence Sequence coverage is 28 % Consider running further cycles of model building using 2pim-3_warpNtrace.pdb as input Building loops using Loopy2018 10 chains (73 residues) following loop building 2 chains (21 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2594 reflections ( 99.35 % complete ) and 1899 restraints for refining 991 atoms. 1542 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2292 (Rfree = 0.000) for 991 atoms. Found 0 (3 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2777 (Rfree = 0.000) for 987 atoms. Found 0 (3 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2109 (Rfree = 0.000) for 979 atoms. Found 0 (3 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2080 (Rfree = 0.000) for 976 atoms. TimeTaking 31.95