Sun 23 Dec 23:42:56 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2p10-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2p10-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2p10-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p10-3.6-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2p10-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p10-3.6-parrot-mrncs ############### 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 23:43:00 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/mrncs/ArpWArp/wArpResults/WorkingDir/2p10-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p10-3.6-parrot-mrncs/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 1517 and 0 Target number of residues in the AU: 1517 Target solvent content: 0.6462 Checking the provided sequence file Detected sequence length: 286 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1716 Adjusted target solvent content: 0.60 Input MTZ file: 2p10-3.6-parrot-mrncs.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: 146 Cell parameters: 180.269 180.269 185.514 90.000 90.000 120.000 Input sequence file: 2p10-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 13728 target number of atoms Had to go as low as 0.85 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 119.449 3.600 Wilson plot Bfac: 75.71 25300 reflections ( 97.09 % complete ) and 0 restraints for refining 15195 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3066 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2739 (Rfree = 0.000) for 15195 atoms. Found 97 (97 requested) and removed 70 (48 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.49 3.05 Search for helices and strands: 0 residues in 0 chains, 15556 seeds are put forward NCS extension: 0 residues added, 15556 seeds are put forward Round 1: 854 peptides, 142 chains. Longest chain 17 peptides. Score 0.395 Round 2: 974 peptides, 131 chains. Longest chain 23 peptides. Score 0.507 Round 3: 1028 peptides, 122 chains. Longest chain 28 peptides. Score 0.563 Round 4: 1044 peptides, 122 chains. Longest chain 28 peptides. Score 0.572 Round 5: 1061 peptides, 118 chains. Longest chain 26 peptides. Score 0.591 Taking the results from Round 5 Chains 130, Residues 943, Estimated correctness of the model 11.1 % 24 chains (250 residues) have been docked in sequence ------------------------------------------------------ 25300 reflections ( 97.09 % complete ) and 26080 restraints for refining 12435 atoms. 21671 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2218 (Rfree = 0.000) for 12435 atoms. Found 79 (79 requested) and removed 88 (39 requested) atoms. Cycle 2: After refmac, R = 0.2027 (Rfree = 0.000) for 12241 atoms. Found 27 (79 requested) and removed 69 (39 requested) atoms. Cycle 3: After refmac, R = 0.1958 (Rfree = 0.000) for 12122 atoms. Found 26 (78 requested) and removed 56 (39 requested) atoms. Cycle 4: After refmac, R = 0.1908 (Rfree = 0.000) for 12047 atoms. Found 22 (77 requested) and removed 57 (38 requested) atoms. Cycle 5: After refmac, R = 0.1858 (Rfree = 0.000) for 11978 atoms. Found 15 (77 requested) and removed 52 (38 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.48 3.04 Search for helices and strands: 0 residues in 0 chains, 12430 seeds are put forward NCS extension: 22 residues added (5 deleted due to clashes), 12452 seeds are put forward Round 1: 944 peptides, 135 chains. Longest chain 36 peptides. Score 0.477 Round 2: 1000 peptides, 114 chains. Longest chain 31 peptides. Score 0.568 Round 3: 1025 peptides, 111 chains. Longest chain 32 peptides. Score 0.589 Round 4: 1018 peptides, 112 chains. Longest chain 33 peptides. Score 0.583 Round 5: 1040 peptides, 116 chains. Longest chain 28 peptides. Score 0.585 Taking the results from Round 3 Chains 128, Residues 914, Estimated correctness of the model 10.3 % 16 chains (201 residues) have been docked in sequence ------------------------------------------------------ 25300 reflections ( 97.09 % complete ) and 26343 restraints for refining 12437 atoms. 22180 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2096 (Rfree = 0.000) for 12437 atoms. Found 67 (79 requested) and removed 99 (39 requested) atoms. Cycle 7: After refmac, R = 0.1914 (Rfree = 0.000) for 12316 atoms. Found 37 (79 requested) and removed 70 (39 requested) atoms. Cycle 8: After refmac, R = 0.1847 (Rfree = 0.000) for 12239 atoms. Found 28 (78 requested) and removed 57 (39 requested) atoms. Cycle 9: After refmac, R = 0.1810 (Rfree = 0.000) for 12176 atoms. Found 27 (78 requested) and removed 61 (39 requested) atoms. Cycle 10: After refmac, R = 0.1776 (Rfree = 0.000) for 12121 atoms. Found 18 (77 requested) and removed 55 (38 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 3.02 Search for helices and strands: 0 residues in 0 chains, 12531 seeds are put forward NCS extension: 9 residues added (7 deleted due to clashes), 12540 seeds are put forward Round 1: 937 peptides, 144 chains. Longest chain 23 peptides. Score 0.446 Round 2: 1004 peptides, 125 chains. Longest chain 28 peptides. Score 0.541 Round 3: 1019 peptides, 125 chains. Longest chain 25 peptides. Score 0.550 Round 4: 1045 peptides, 126 chains. Longest chain 22 peptides. Score 0.562 Round 5: 1046 peptides, 118 chains. Longest chain 31 peptides. Score 0.583 Taking the results from Round 5 Chains 126, Residues 928, Estimated correctness of the model 7.9 % 15 chains (159 residues) have been docked in sequence ------------------------------------------------------ 25300 reflections ( 97.09 % complete ) and 26507 restraints for refining 12445 atoms. 22400 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2211 (Rfree = 0.000) for 12445 atoms. Found 55 (79 requested) and removed 70 (39 requested) atoms. Cycle 12: After refmac, R = 0.1990 (Rfree = 0.000) for 12350 atoms. Found 27 (79 requested) and removed 55 (39 requested) atoms. Cycle 13: After refmac, R = 0.1925 (Rfree = 0.000) for 12289 atoms. Found 25 (79 requested) and removed 59 (39 requested) atoms. Cycle 14: After refmac, R = 0.1834 (Rfree = 0.000) for 12230 atoms. Found 19 (78 requested) and removed 52 (39 requested) atoms. Cycle 15: After refmac, R = 0.1768 (Rfree = 0.000) for 12174 atoms. Found 13 (78 requested) and removed 49 (39 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 3.01 Search for helices and strands: 0 residues in 0 chains, 12556 seeds are put forward NCS extension: 13 residues added (6 deleted due to clashes), 12569 seeds are put forward Round 1: 918 peptides, 136 chains. Longest chain 23 peptides. Score 0.457 Round 2: 998 peptides, 122 chains. Longest chain 28 peptides. Score 0.545 Round 3: 982 peptides, 121 chains. Longest chain 31 peptides. Score 0.539 Round 4: 986 peptides, 120 chains. Longest chain 30 peptides. Score 0.544 Round 5: 998 peptides, 114 chains. Longest chain 31 peptides. Score 0.566 Taking the results from Round 5 Chains 118, Residues 884, Estimated correctness of the model 0.9 % 12 chains (124 residues) have been docked in sequence ------------------------------------------------------ 25300 reflections ( 97.09 % complete ) and 27291 restraints for refining 12444 atoms. 23475 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2076 (Rfree = 0.000) for 12444 atoms. Found 56 (79 requested) and removed 58 (39 requested) atoms. Cycle 17: After refmac, R = 0.1898 (Rfree = 0.000) for 12379 atoms. Found 24 (79 requested) and removed 50 (39 requested) atoms. Cycle 18: After refmac, R = 0.1876 (Rfree = 0.000) for 12326 atoms. Found 19 (79 requested) and removed 49 (39 requested) atoms. Cycle 19: After refmac, R = 0.1840 (Rfree = 0.000) for 12280 atoms. Found 37 (78 requested) and removed 45 (39 requested) atoms. Cycle 20: After refmac, R = 0.1791 (Rfree = 0.000) for 12250 atoms. Found 29 (78 requested) and removed 49 (39 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 3.03 Search for helices and strands: 0 residues in 0 chains, 12672 seeds are put forward NCS extension: 27 residues added (16 deleted due to clashes), 12699 seeds are put forward Round 1: 902 peptides, 133 chains. Longest chain 20 peptides. Score 0.455 Round 2: 955 peptides, 117 chains. Longest chain 26 peptides. Score 0.534 Round 3: 973 peptides, 120 chains. Longest chain 21 peptides. Score 0.536 Round 4: 987 peptides, 111 chains. Longest chain 32 peptides. Score 0.568 Round 5: 979 peptides, 115 chains. Longest chain 38 peptides. Score 0.553 Taking the results from Round 4 Chains 119, Residues 876, Estimated correctness of the model 1.7 % 13 chains (167 residues) have been docked in sequence ------------------------------------------------------ 25300 reflections ( 97.09 % complete ) and 26531 restraints for refining 12445 atoms. 22582 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2084 (Rfree = 0.000) for 12445 atoms. Found 55 (79 requested) and removed 65 (39 requested) atoms. Cycle 22: After refmac, R = 0.1986 (Rfree = 0.000) for 12349 atoms. Found 33 (79 requested) and removed 56 (39 requested) atoms. Cycle 23: After refmac, R = 0.1931 (Rfree = 0.000) for 12280 atoms. Found 39 (79 requested) and removed 55 (39 requested) atoms. Cycle 24: After refmac, R = 0.1856 (Rfree = 0.000) for 12228 atoms. Found 24 (78 requested) and removed 49 (39 requested) atoms. Cycle 25: After refmac, R = 0.1804 (Rfree = 0.000) for 12176 atoms. Found 22 (78 requested) and removed 54 (39 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.46 3.02 Search for helices and strands: 0 residues in 0 chains, 12636 seeds are put forward NCS extension: 35 residues added (12 deleted due to clashes), 12671 seeds are put forward Round 1: 888 peptides, 137 chains. Longest chain 30 peptides. Score 0.434 Round 2: 965 peptides, 127 chains. Longest chain 33 peptides. Score 0.512 Round 3: 956 peptides, 126 chains. Longest chain 30 peptides. Score 0.509 Round 4: 969 peptides, 131 chains. Longest chain 25 peptides. Score 0.504 Round 5: 974 peptides, 121 chains. Longest chain 27 peptides. Score 0.534 Taking the results from Round 5 Chains 126, Residues 853, Estimated correctness of the model 0.0 % 17 chains (126 residues) have been docked in sequence ------------------------------------------------------ 25300 reflections ( 97.09 % complete ) and 27405 restraints for refining 12440 atoms. 23726 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2129 (Rfree = 0.000) for 12440 atoms. Found 59 (79 requested) and removed 65 (39 requested) atoms. Cycle 27: After refmac, R = 0.1981 (Rfree = 0.000) for 12366 atoms. Found 27 (79 requested) and removed 47 (39 requested) atoms. Cycle 28: After refmac, R = 0.1960 (Rfree = 0.000) for 12317 atoms. Found 42 (79 requested) and removed 49 (39 requested) atoms. Cycle 29: After refmac, R = 0.1885 (Rfree = 0.000) for 12284 atoms. Found 32 (78 requested) and removed 46 (39 requested) atoms. Cycle 30: After refmac, R = 0.1854 (Rfree = 0.000) for 12242 atoms. Found 31 (78 requested) and removed 50 (39 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.49 3.05 Search for helices and strands: 0 residues in 0 chains, 12678 seeds are put forward NCS extension: 22 residues added (5 deleted due to clashes), 12700 seeds are put forward Round 1: 864 peptides, 140 chains. Longest chain 19 peptides. Score 0.408 Round 2: 920 peptides, 126 chains. Longest chain 19 peptides. Score 0.487 Round 3: 929 peptides, 123 chains. Longest chain 20 peptides. Score 0.501 Round 4: 919 peptides, 119 chains. Longest chain 25 peptides. Score 0.506 Round 5: 943 peptides, 125 chains. Longest chain 29 peptides. Score 0.504 Taking the results from Round 4 Chains 127, Residues 800, Estimated correctness of the model 0.0 % 10 chains (85 residues) have been docked in sequence ------------------------------------------------------ 25300 reflections ( 97.09 % complete ) and 28002 restraints for refining 12444 atoms. 24649 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2082 (Rfree = 0.000) for 12444 atoms. Found 70 (79 requested) and removed 55 (39 requested) atoms. Cycle 32: After refmac, R = 0.1930 (Rfree = 0.000) for 12391 atoms. Found 30 (79 requested) and removed 52 (39 requested) atoms. Cycle 33: After refmac, R = 0.1895 (Rfree = 0.000) for 12334 atoms. Found 38 (79 requested) and removed 45 (39 requested) atoms. Cycle 34: After refmac, R = 0.1864 (Rfree = 0.000) for 12307 atoms. Found 37 (79 requested) and removed 52 (39 requested) atoms. Cycle 35: After refmac, R = 0.1800 (Rfree = 0.000) for 12277 atoms. Found 22 (78 requested) and removed 47 (39 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.46 3.02 Search for helices and strands: 0 residues in 0 chains, 12673 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 12689 seeds are put forward Round 1: 848 peptides, 142 chains. Longest chain 18 peptides. Score 0.391 Round 2: 924 peptides, 133 chains. Longest chain 20 peptides. Score 0.469 Round 3: 900 peptides, 129 chains. Longest chain 24 peptides. Score 0.466 Round 4: 898 peptides, 115 chains. Longest chain 31 peptides. Score 0.505 Round 5: 941 peptides, 126 chains. Longest chain 26 peptides. Score 0.500 Taking the results from Round 4 Chains 118, Residues 783, Estimated correctness of the model 0.0 % 13 chains (83 residues) have been docked in sequence ------------------------------------------------------ 25300 reflections ( 97.09 % complete ) and 28346 restraints for refining 12439 atoms. 25104 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2024 (Rfree = 0.000) for 12439 atoms. Found 64 (79 requested) and removed 52 (39 requested) atoms. Cycle 37: After refmac, R = 0.1921 (Rfree = 0.000) for 12398 atoms. Found 28 (79 requested) and removed 51 (39 requested) atoms. Cycle 38: After refmac, R = 0.1863 (Rfree = 0.000) for 12360 atoms. Found 31 (79 requested) and removed 48 (39 requested) atoms. Cycle 39: After refmac, R = 0.1791 (Rfree = 0.000) for 12322 atoms. Found 24 (79 requested) and removed 48 (39 requested) atoms. Cycle 40: After refmac, R = 0.1768 (Rfree = 0.000) for 12282 atoms. Found 18 (78 requested) and removed 44 (39 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.47 3.03 Search for helices and strands: 0 residues in 0 chains, 12677 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 12702 seeds are put forward Round 1: 788 peptides, 132 chains. Longest chain 14 peptides. Score 0.379 Round 2: 872 peptides, 126 chains. Longest chain 25 peptides. Score 0.456 Round 3: 891 peptides, 126 chains. Longest chain 22 peptides. Score 0.468 Round 4: 883 peptides, 127 chains. Longest chain 20 peptides. Score 0.460 Round 5: 877 peptides, 122 chains. Longest chain 29 peptides. Score 0.471 Taking the results from Round 5 Chains 127, Residues 755, Estimated correctness of the model 0.0 % 13 chains (100 residues) have been docked in sequence ------------------------------------------------------ 25300 reflections ( 97.09 % complete ) and 28212 restraints for refining 12444 atoms. 25044 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2023 (Rfree = 0.000) for 12444 atoms. Found 55 (79 requested) and removed 58 (39 requested) atoms. Cycle 42: After refmac, R = 0.1921 (Rfree = 0.000) for 12390 atoms. Found 47 (79 requested) and removed 52 (39 requested) atoms. Cycle 43: After refmac, R = 0.1858 (Rfree = 0.000) for 12366 atoms. Found 33 (79 requested) and removed 50 (39 requested) atoms. Cycle 44: After refmac, R = 0.1835 (Rfree = 0.000) for 12328 atoms. Found 26 (79 requested) and removed 49 (39 requested) atoms. Cycle 45: After refmac, R = 0.1772 (Rfree = 0.000) for 12296 atoms. Found 35 (78 requested) and removed 51 (39 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.45 3.01 Search for helices and strands: 0 residues in 0 chains, 12655 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 12677 seeds are put forward Round 1: 792 peptides, 142 chains. Longest chain 16 peptides. Score 0.350 Round 2: 848 peptides, 122 chains. Longest chain 22 peptides. Score 0.452 Round 3: 862 peptides, 119 chains. Longest chain 24 peptides. Score 0.470 Round 4: 895 peptides, 127 chains. Longest chain 33 peptides. Score 0.468 Round 5: 864 peptides, 119 chains. Longest chain 24 peptides. Score 0.471 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 121, Residues 745, Estimated correctness of the model 0.0 % 12 chains (115 residues) have been docked in sequence Sequence coverage is 15 % Consider running further cycles of model building using 2p10-3_warpNtrace.pdb as input Building loops using Loopy2018 121 chains (745 residues) following loop building 12 chains (115 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 25300 reflections ( 97.09 % complete ) and 28216 restraints for refining 12442 atoms. 24991 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2021 (Rfree = 0.000) for 12442 atoms. Found 0 (79 requested) and removed 39 (39 requested) atoms. Cycle 47: After refmac, R = 0.1975 (Rfree = 0.000) for 12354 atoms. Found 0 (79 requested) and removed 39 (39 requested) atoms. Cycle 48: After refmac, R = 0.1932 (Rfree = 0.000) for 12295 atoms. Found 0 (79 requested) and removed 39 (39 requested) atoms. Cycle 49: After refmac, R = 0.1881 (Rfree = 0.000) for 12239 atoms. TimeTaking 146.8