null Sun 23 Dec 22:22:59 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 2p10-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p10-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p10-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p10-3.6-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/2p10-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p10-3.6-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 22:23:08 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/2p10-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p10-3.6-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 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-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: 146 Cell parameters: 180.269 180.269 185.514 90.000 90.000 120.000 Input sequence file: 2p10-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 13728 target number of atoms Had to go as low as 0.90 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 15201 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3048 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2704 (Rfree = 0.000) for 15201 atoms. Found 97 (97 requested) and removed 66 (48 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.47 3.03 Search for helices and strands: 0 residues in 0 chains, 15550 seeds are put forward NCS extension: 0 residues added, 15550 seeds are put forward Round 1: 825 peptides, 134 chains. Longest chain 15 peptides. Score 0.399 Round 2: 1011 peptides, 136 chains. Longest chain 23 peptides. Score 0.515 Round 3: 1050 peptides, 118 chains. Longest chain 30 peptides. Score 0.585 Round 4: 1083 peptides, 122 chains. Longest chain 32 peptides. Score 0.593 Round 5: 1022 peptides, 109 chains. Longest chain 35 peptides. Score 0.592 Taking the results from Round 4 Chains 137, Residues 961, Estimated correctness of the model 11.9 % 27 chains (297 residues) have been docked in sequence ------------------------------------------------------ 25300 reflections ( 97.09 % complete ) and 24992 restraints for refining 12440 atoms. 20342 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2231 (Rfree = 0.000) for 12440 atoms. Found 75 (79 requested) and removed 115 (39 requested) atoms. Cycle 2: After refmac, R = 0.2079 (Rfree = 0.000) for 12194 atoms. Found 54 (79 requested) and removed 64 (39 requested) atoms. Cycle 3: After refmac, R = 0.2012 (Rfree = 0.000) for 12114 atoms. Found 44 (78 requested) and removed 57 (39 requested) atoms. Cycle 4: After refmac, R = 0.1970 (Rfree = 0.000) for 12057 atoms. Found 28 (77 requested) and removed 53 (38 requested) atoms. Cycle 5: After refmac, R = 0.1928 (Rfree = 0.000) for 11986 atoms. Found 31 (77 requested) and removed 46 (38 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 3.02 Search for helices and strands: 0 residues in 0 chains, 12429 seeds are put forward NCS extension: 16 residues added (8 deleted due to clashes), 12445 seeds are put forward Round 1: 949 peptides, 127 chains. Longest chain 28 peptides. Score 0.502 Round 2: 1034 peptides, 117 chains. Longest chain 32 peptides. Score 0.579 Round 3: 1037 peptides, 114 chains. Longest chain 36 peptides. Score 0.588 Round 4: 1059 peptides, 116 chains. Longest chain 26 peptides. Score 0.595 Round 5: 1054 peptides, 116 chains. Longest chain 34 peptides. Score 0.592 Taking the results from Round 4 Chains 133, Residues 943, Estimated correctness of the model 12.7 % 19 chains (194 residues) have been docked in sequence ------------------------------------------------------ 25300 reflections ( 97.09 % complete ) and 26380 restraints for refining 12441 atoms. 22127 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2145 (Rfree = 0.000) for 12441 atoms. Found 57 (79 requested) and removed 103 (39 requested) atoms. Cycle 7: After refmac, R = 0.2003 (Rfree = 0.000) for 12326 atoms. Found 29 (79 requested) and removed 73 (39 requested) atoms. Cycle 8: After refmac, R = 0.1976 (Rfree = 0.000) for 12248 atoms. Found 21 (78 requested) and removed 72 (39 requested) atoms. Cycle 9: After refmac, R = 0.1931 (Rfree = 0.000) for 12172 atoms. Found 33 (78 requested) and removed 55 (39 requested) atoms. Cycle 10: After refmac, R = 0.1892 (Rfree = 0.000) for 12122 atoms. Found 34 (77 requested) and removed 47 (38 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.45 3.01 Search for helices and strands: 0 residues in 0 chains, 12603 seeds are put forward NCS extension: 15 residues added (7 deleted due to clashes), 12618 seeds are put forward Round 1: 951 peptides, 134 chains. Longest chain 32 peptides. Score 0.484 Round 2: 1000 peptides, 114 chains. Longest chain 41 peptides. Score 0.568 Round 3: 1006 peptides, 122 chains. Longest chain 33 peptides. Score 0.550 Round 4: 980 peptides, 118 chains. Longest chain 28 peptides. Score 0.546 Round 5: 993 peptides, 118 chains. Longest chain 25 peptides. Score 0.553 Taking the results from Round 2 Chains 127, Residues 886, Estimated correctness of the model 1.7 % 19 chains (219 residues) have been docked in sequence ------------------------------------------------------ 25300 reflections ( 97.09 % complete ) and 26261 restraints for refining 12444 atoms. 22110 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2102 (Rfree = 0.000) for 12444 atoms. Found 79 (79 requested) and removed 91 (39 requested) atoms. Cycle 12: After refmac, R = 0.1956 (Rfree = 0.000) for 12361 atoms. Found 22 (79 requested) and removed 61 (39 requested) atoms. Cycle 13: After refmac, R = 0.1930 (Rfree = 0.000) for 12284 atoms. Found 34 (79 requested) and removed 64 (39 requested) atoms. Cycle 14: After refmac, R = 0.1861 (Rfree = 0.000) for 12231 atoms. Found 22 (78 requested) and removed 47 (39 requested) atoms. Cycle 15: After refmac, R = 0.1812 (Rfree = 0.000) for 12191 atoms. Found 12 (78 requested) and removed 47 (39 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.47 3.03 Search for helices and strands: 0 residues in 0 chains, 12599 seeds are put forward NCS extension: 12 residues added (9 deleted due to clashes), 12611 seeds are put forward Round 1: 921 peptides, 141 chains. Longest chain 18 peptides. Score 0.444 Round 2: 998 peptides, 121 chains. Longest chain 32 peptides. Score 0.548 Round 3: 1022 peptides, 125 chains. Longest chain 23 peptides. Score 0.551 Round 4: 990 peptides, 121 chains. Longest chain 27 peptides. Score 0.543 Round 5: 1016 peptides, 120 chains. Longest chain 35 peptides. Score 0.561 Taking the results from Round 5 Chains 131, Residues 896, Estimated correctness of the model 0.0 % 16 chains (138 residues) have been docked in sequence ------------------------------------------------------ 25300 reflections ( 97.09 % complete ) and 27337 restraints for refining 12444 atoms. 23478 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2166 (Rfree = 0.000) for 12444 atoms. Found 57 (79 requested) and removed 82 (39 requested) atoms. Cycle 17: After refmac, R = 0.1973 (Rfree = 0.000) for 12318 atoms. Found 32 (79 requested) and removed 58 (39 requested) atoms. Cycle 18: After refmac, R = 0.1902 (Rfree = 0.000) for 12249 atoms. Found 16 (78 requested) and removed 60 (39 requested) atoms. Cycle 19: After refmac, R = 0.1869 (Rfree = 0.000) for 12179 atoms. Found 24 (78 requested) and removed 50 (39 requested) atoms. Cycle 20: After refmac, R = 0.1865 (Rfree = 0.000) for 12135 atoms. Found 22 (77 requested) and removed 52 (38 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.02 Search for helices and strands: 0 residues in 0 chains, 12544 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 12562 seeds are put forward Round 1: 890 peptides, 140 chains. Longest chain 25 peptides. Score 0.426 Round 2: 963 peptides, 125 chains. Longest chain 26 peptides. Score 0.517 Round 3: 969 peptides, 126 chains. Longest chain 33 peptides. Score 0.517 Round 4: 967 peptides, 121 chains. Longest chain 31 peptides. Score 0.530 Round 5: 965 peptides, 122 chains. Longest chain 38 peptides. Score 0.526 Taking the results from Round 4 Chains 131, Residues 846, Estimated correctness of the model 0.0 % 15 chains (158 residues) have been docked in sequence ------------------------------------------------------ 25300 reflections ( 97.09 % complete ) and 26839 restraints for refining 12444 atoms. 23067 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2125 (Rfree = 0.000) for 12444 atoms. Found 67 (79 requested) and removed 73 (39 requested) atoms. Cycle 22: After refmac, R = 0.2010 (Rfree = 0.000) for 12376 atoms. Found 27 (79 requested) and removed 57 (39 requested) atoms. Cycle 23: After refmac, R = 0.1991 (Rfree = 0.000) for 12326 atoms. Found 28 (79 requested) and removed 50 (39 requested) atoms. Cycle 24: After refmac, R = 0.1964 (Rfree = 0.000) for 12287 atoms. Found 32 (78 requested) and removed 51 (39 requested) atoms. Cycle 25: After refmac, R = 0.1908 (Rfree = 0.000) for 12248 atoms. Found 30 (78 requested) and removed 45 (39 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.47 3.03 Search for helices and strands: 0 residues in 0 chains, 12718 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 12735 seeds are put forward Round 1: 870 peptides, 140 chains. Longest chain 20 peptides. Score 0.413 Round 2: 924 peptides, 125 chains. Longest chain 23 peptides. Score 0.492 Round 3: 929 peptides, 124 chains. Longest chain 22 peptides. Score 0.498 Round 4: 954 peptides, 115 chains. Longest chain 29 peptides. Score 0.538 Round 5: 926 peptides, 121 chains. Longest chain 21 peptides. Score 0.505 Taking the results from Round 4 Chains 119, Residues 839, Estimated correctness of the model 0.0 % 13 chains (102 residues) have been docked in sequence ------------------------------------------------------ 25300 reflections ( 97.09 % complete ) and 28064 restraints for refining 12444 atoms. 24512 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2118 (Rfree = 0.000) for 12444 atoms. Found 67 (79 requested) and removed 56 (39 requested) atoms. Cycle 27: After refmac, R = 0.1968 (Rfree = 0.000) for 12391 atoms. Found 23 (79 requested) and removed 58 (39 requested) atoms. Cycle 28: After refmac, R = 0.1926 (Rfree = 0.000) for 12324 atoms. Found 34 (79 requested) and removed 48 (39 requested) atoms. Cycle 29: After refmac, R = 0.1855 (Rfree = 0.000) for 12283 atoms. Found 18 (78 requested) and removed 53 (39 requested) atoms. Cycle 30: After refmac, R = 0.1836 (Rfree = 0.000) for 12230 atoms. Found 26 (78 requested) and removed 46 (39 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 3.04 Search for helices and strands: 0 residues in 0 chains, 12686 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 12705 seeds are put forward Round 1: 836 peptides, 135 chains. Longest chain 21 peptides. Score 0.404 Round 2: 947 peptides, 122 chains. Longest chain 31 peptides. Score 0.515 Round 3: 958 peptides, 120 chains. Longest chain 32 peptides. Score 0.527 Round 4: 940 peptides, 120 chains. Longest chain 33 peptides. Score 0.516 Round 5: 938 peptides, 118 chains. Longest chain 33 peptides. Score 0.521 Taking the results from Round 3 Chains 130, Residues 838, Estimated correctness of the model 0.0 % 17 chains (148 residues) have been docked in sequence ------------------------------------------------------ 25300 reflections ( 97.09 % complete ) and 27426 restraints for refining 12445 atoms. 23765 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2054 (Rfree = 0.000) for 12445 atoms. Found 65 (79 requested) and removed 60 (39 requested) atoms. Cycle 32: After refmac, R = 0.1918 (Rfree = 0.000) for 12396 atoms. Found 26 (79 requested) and removed 51 (39 requested) atoms. Cycle 33: After refmac, R = 0.1917 (Rfree = 0.000) for 12341 atoms. Found 26 (79 requested) and removed 50 (39 requested) atoms. Cycle 34: After refmac, R = 0.1917 (Rfree = 0.000) for 12297 atoms. Found 26 (79 requested) and removed 48 (39 requested) atoms. Cycle 35: After refmac, R = 0.1907 (Rfree = 0.000) for 12253 atoms. Found 38 (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, 12638 seeds are put forward NCS extension: 21 residues added (9 deleted due to clashes), 12659 seeds are put forward Round 1: 816 peptides, 143 chains. Longest chain 17 peptides. Score 0.365 Round 2: 910 peptides, 128 chains. Longest chain 20 peptides. Score 0.475 Round 3: 920 peptides, 120 chains. Longest chain 22 peptides. Score 0.504 Round 4: 896 peptides, 120 chains. Longest chain 20 peptides. Score 0.489 Round 5: 916 peptides, 115 chains. Longest chain 33 peptides. Score 0.516 Taking the results from Round 5 Chains 127, Residues 801, Estimated correctness of the model 0.0 % 15 chains (135 residues) have been docked in sequence ------------------------------------------------------ 25300 reflections ( 97.09 % complete ) and 27637 restraints for refining 12445 atoms. 24157 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2002 (Rfree = 0.000) for 12445 atoms. Found 71 (79 requested) and removed 69 (39 requested) atoms. Cycle 37: After refmac, R = 0.1897 (Rfree = 0.000) for 12385 atoms. Found 28 (79 requested) and removed 56 (39 requested) atoms. Cycle 38: After refmac, R = 0.1858 (Rfree = 0.000) for 12325 atoms. Found 31 (79 requested) and removed 55 (39 requested) atoms. Cycle 39: After refmac, R = 0.1850 (Rfree = 0.000) for 12285 atoms. Found 29 (78 requested) and removed 45 (39 requested) atoms. Cycle 40: After refmac, R = 0.1831 (Rfree = 0.000) for 12241 atoms. Found 32 (78 requested) and removed 49 (39 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.47 3.03 Search for helices and strands: 0 residues in 0 chains, 12619 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 12635 seeds are put forward Round 1: 790 peptides, 143 chains. Longest chain 15 peptides. Score 0.346 Round 2: 843 peptides, 124 chains. Longest chain 19 peptides. Score 0.443 Round 3: 868 peptides, 125 chains. Longest chain 20 peptides. Score 0.456 Round 4: 901 peptides, 123 chains. Longest chain 21 peptides. Score 0.484 Round 5: 911 peptides, 126 chains. Longest chain 21 peptides. Score 0.481 Taking the results from Round 4 Chains 128, Residues 778, Estimated correctness of the model 0.0 % 14 chains (128 residues) have been docked in sequence ------------------------------------------------------ 25300 reflections ( 97.09 % complete ) and 27900 restraints for refining 12441 atoms. 24525 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2012 (Rfree = 0.000) for 12441 atoms. Found 65 (79 requested) and removed 71 (39 requested) atoms. Cycle 42: After refmac, R = 0.1919 (Rfree = 0.000) for 12385 atoms. Found 47 (79 requested) and removed 48 (39 requested) atoms. Cycle 43: After refmac, R = 0.1832 (Rfree = 0.000) for 12348 atoms. Found 43 (79 requested) and removed 47 (39 requested) atoms. Cycle 44: After refmac, R = 0.1760 (Rfree = 0.000) for 12328 atoms. Found 21 (79 requested) and removed 49 (39 requested) atoms. Cycle 45: After refmac, R = 0.1726 (Rfree = 0.000) for 12284 atoms. Found 38 (78 requested) and removed 42 (39 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 3.03 Search for helices and strands: 0 residues in 0 chains, 12691 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 12711 seeds are put forward Round 1: 717 peptides, 133 chains. Longest chain 18 peptides. Score 0.323 Round 2: 810 peptides, 126 chains. Longest chain 24 peptides. Score 0.414 Round 3: 832 peptides, 117 chains. Longest chain 24 peptides. Score 0.456 Round 4: 856 peptides, 119 chains. Longest chain 22 peptides. Score 0.466 Round 5: 821 peptides, 114 chains. Longest chain 22 peptides. Score 0.458 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 126, Residues 737, Estimated correctness of the model 0.0 % 19 chains (139 residues) have been docked in sequence Sequence coverage is 18 % Consider running further cycles of model building using 2p10-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 186 A and 197 A Built loop between residues 186 D and 199 D 123 chains (752 residues) following loop building 17 chains (161 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 25300 reflections ( 97.09 % complete ) and 27787 restraints for refining 12443 atoms. 24532 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1995 (Rfree = 0.000) for 12443 atoms. Found 0 (79 requested) and removed 39 (39 requested) atoms. Cycle 47: After refmac, R = 0.1934 (Rfree = 0.000) for 12332 atoms. Found 0 (79 requested) and removed 39 (39 requested) atoms. Cycle 48: After refmac, R = 0.1913 (Rfree = 0.000) for 12263 atoms. Found 0 (78 requested) and removed 39 (39 requested) atoms. Cycle 49: After refmac, R = 0.1836 (Rfree = 0.000) for 12212 atoms. Found 0 (78 requested) and removed 39 (39 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:07:30 GMT 2018 Job finished. TimeTaking 164.52 Used memory is bytes: 7239320