null Sun 23 Dec 22:23:02 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 2huj-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2huj-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2huj-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2huj-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/2huj-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2huj-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 22:23:11 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/2huj-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2huj-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 135 and 0 Target number of residues in the AU: 135 Target solvent content: 0.6206 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: 0.61 Input MTZ file: 2huj-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: 182 Cell parameters: 100.110 100.110 66.570 90.000 90.000 120.000 Input sequence file: 2huj-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1120 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 Loops will be built when appropriate and at the last cycle Resolution range: 86.698 3.400 Wilson plot Bfac: 60.86 2974 reflections ( 99.70 % complete ) and 0 restraints for refining 1244 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Starting model: R = 0.3447 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3735 (Rfree = 0.000) for 1244 atoms. Found 9 (9 requested) and removed 43 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 2.87 Search for helices and strands: 0 residues in 0 chains, 1263 seeds are put forward Round 1: 64 peptides, 12 chains. Longest chain 12 peptides. Score 0.326 Round 2: 74 peptides, 11 chains. Longest chain 13 peptides. Score 0.450 Round 3: 75 peptides, 8 chains. Longest chain 16 peptides. Score 0.560 Round 4: 73 peptides, 9 chains. Longest chain 14 peptides. Score 0.512 Round 5: 73 peptides, 8 chains. Longest chain 17 peptides. Score 0.546 Taking the results from Round 3 Chains 8, Residues 67, Estimated correctness of the model 15.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2974 reflections ( 99.70 % complete ) and 2156 restraints for refining 956 atoms. 1896 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3780 (Rfree = 0.000) for 956 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 2: After refmac, R = 0.3258 (Rfree = 0.000) for 917 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 3: After refmac, R = 0.4028 (Rfree = 0.000) for 906 atoms. Found 6 (6 requested) and removed 28 (3 requested) atoms. Cycle 4: After refmac, R = 0.3384 (Rfree = 0.000) for 869 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 5: After refmac, R = 0.3489 (Rfree = 0.000) for 860 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.28 2.83 Search for helices and strands: 0 residues in 0 chains, 938 seeds are put forward Round 1: 67 peptides, 11 chains. Longest chain 10 peptides. Score 0.392 Round 2: 77 peptides, 10 chains. Longest chain 17 peptides. Score 0.508 Round 3: 73 peptides, 8 chains. Longest chain 15 peptides. Score 0.546 Round 4: 67 peptides, 8 chains. Longest chain 14 peptides. Score 0.502 Round 5: 70 peptides, 9 chains. Longest chain 12 peptides. Score 0.489 Taking the results from Round 3 Chains 8, Residues 65, Estimated correctness of the model 10.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2974 reflections ( 99.70 % complete ) and 1860 restraints for refining 876 atoms. 1608 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3983 (Rfree = 0.000) for 876 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 7: After refmac, R = 0.3649 (Rfree = 0.000) for 854 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 8: After refmac, R = 0.3766 (Rfree = 0.000) for 837 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 9: After refmac, R = 0.3145 (Rfree = 0.000) for 824 atoms. Found 4 (6 requested) and removed 5 (3 requested) atoms. Cycle 10: After refmac, R = 0.3288 (Rfree = 0.000) for 817 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 2.95 Search for helices and strands: 0 residues in 0 chains, 914 seeds are put forward Round 1: 66 peptides, 12 chains. Longest chain 9 peptides. Score 0.344 Round 2: 74 peptides, 10 chains. Longest chain 13 peptides. Score 0.485 Round 3: 68 peptides, 7 chains. Longest chain 16 peptides. Score 0.544 Round 4: 69 peptides, 9 chains. Longest chain 17 peptides. Score 0.482 Round 5: 69 peptides, 9 chains. Longest chain 15 peptides. Score 0.482 Taking the results from Round 3 Chains 7, Residues 61, Estimated correctness of the model 9.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2974 reflections ( 99.70 % complete ) and 1963 restraints for refining 907 atoms. 1726 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3348 (Rfree = 0.000) for 907 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 12: After refmac, R = 0.3407 (Rfree = 0.000) for 896 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 13: After refmac, R = 0.3461 (Rfree = 0.000) for 887 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 14: After refmac, R = 0.3448 (Rfree = 0.000) for 880 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 15: After refmac, R = 0.3369 (Rfree = 0.000) for 869 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 2.85 Search for helices and strands: 0 residues in 0 chains, 937 seeds are put forward Round 1: 67 peptides, 12 chains. Longest chain 11 peptides. Score 0.353 Round 2: 73 peptides, 11 chains. Longest chain 14 peptides. Score 0.442 Round 3: 75 peptides, 11 chains. Longest chain 13 peptides. Score 0.458 Round 4: 81 peptides, 11 chains. Longest chain 13 peptides. Score 0.504 Round 5: 77 peptides, 11 chains. Longest chain 13 peptides. Score 0.473 Taking the results from Round 4 Chains 11, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2974 reflections ( 99.70 % complete ) and 1967 restraints for refining 927 atoms. 1698 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3438 (Rfree = 0.000) for 927 atoms. Found 6 (6 requested) and removed 16 (3 requested) atoms. Cycle 17: After refmac, R = 0.3267 (Rfree = 0.000) for 906 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 18: After refmac, R = 0.3247 (Rfree = 0.000) for 895 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 19: After refmac, R = 0.3090 (Rfree = 0.000) for 889 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 20: After refmac, R = 0.3030 (Rfree = 0.000) for 883 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.21 2.77 Search for helices and strands: 0 residues in 0 chains, 965 seeds are put forward Round 1: 61 peptides, 12 chains. Longest chain 11 peptides. Score 0.298 Round 2: 77 peptides, 13 chains. Longest chain 13 peptides. Score 0.402 Round 3: 79 peptides, 11 chains. Longest chain 14 peptides. Score 0.489 Round 4: 78 peptides, 12 chains. Longest chain 11 peptides. Score 0.446 Round 5: 71 peptides, 10 chains. Longest chain 22 peptides. Score 0.462 Taking the results from Round 3 Chains 11, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2974 reflections ( 99.70 % complete ) and 1835 restraints for refining 907 atoms. 1574 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3236 (Rfree = 0.000) for 907 atoms. Found 6 (6 requested) and removed 31 (3 requested) atoms. Cycle 22: After refmac, R = 0.3351 (Rfree = 0.000) for 869 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 23: After refmac, R = 0.3365 (Rfree = 0.000) for 857 atoms. Found 6 (6 requested) and removed 17 (3 requested) atoms. Cycle 24: After refmac, R = 0.3469 (Rfree = 0.000) for 842 atoms. Found 6 (6 requested) and removed 18 (3 requested) atoms. Cycle 25: After refmac, R = 0.3049 (Rfree = 0.000) for 822 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.24 2.79 Search for helices and strands: 0 residues in 0 chains, 889 seeds are put forward Round 1: 60 peptides, 11 chains. Longest chain 11 peptides. Score 0.329 Round 2: 56 peptides, 10 chains. Longest chain 8 peptides. Score 0.332 Round 3: 74 peptides, 13 chains. Longest chain 10 peptides. Score 0.377 Round 4: 68 peptides, 11 chains. Longest chain 11 peptides. Score 0.400 Round 5: 85 peptides, 15 chains. Longest chain 12 peptides. Score 0.397 Taking the results from Round 4 Chains 11, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2974 reflections ( 99.70 % complete ) and 1944 restraints for refining 878 atoms. 1727 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3579 (Rfree = 0.000) for 878 atoms. Found 6 (6 requested) and removed 16 (3 requested) atoms. Cycle 27: After refmac, R = 0.3144 (Rfree = 0.000) for 861 atoms. Found 6 (6 requested) and removed 17 (3 requested) atoms. Cycle 28: After refmac, R = 0.3009 (Rfree = 0.000) for 847 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 29: After refmac, R = 0.2899 (Rfree = 0.000) for 842 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 30: After refmac, R = 0.2838 (Rfree = 0.000) for 840 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 2.74 Search for helices and strands: 0 residues in 0 chains, 911 seeds are put forward Round 1: 65 peptides, 14 chains. Longest chain 7 peptides. Score 0.257 Round 2: 64 peptides, 13 chains. Longest chain 8 peptides. Score 0.287 Round 3: 63 peptides, 12 chains. Longest chain 9 peptides. Score 0.317 Round 4: 63 peptides, 11 chains. Longest chain 10 peptides. Score 0.356 Round 5: 63 peptides, 10 chains. Longest chain 12 peptides. Score 0.395 Taking the results from Round 5 Chains 10, Residues 53, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2974 reflections ( 99.70 % complete ) and 2131 restraints for refining 936 atoms. 1929 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3629 (Rfree = 0.000) for 936 atoms. Found 7 (7 requested) and removed 20 (3 requested) atoms. Cycle 32: After refmac, R = 0.3347 (Rfree = 0.000) for 911 atoms. Found 6 (6 requested) and removed 22 (3 requested) atoms. Cycle 33: After refmac, R = 0.3612 (Rfree = 0.000) for 890 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 34: After refmac, R = 0.3492 (Rfree = 0.000) for 879 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 35: After refmac, R = 0.3514 (Rfree = 0.000) for 872 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 2.91 Search for helices and strands: 0 residues in 0 chains, 934 seeds are put forward Round 1: 55 peptides, 11 chains. Longest chain 6 peptides. Score 0.282 Round 2: 67 peptides, 10 chains. Longest chain 10 peptides. Score 0.429 Round 3: 69 peptides, 11 chains. Longest chain 11 peptides. Score 0.409 Round 4: 76 peptides, 11 chains. Longest chain 20 peptides. Score 0.466 Round 5: 74 peptides, 9 chains. Longest chain 17 peptides. Score 0.519 Taking the results from Round 5 Chains 9, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2974 reflections ( 99.70 % complete ) and 1967 restraints for refining 937 atoms. 1716 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3473 (Rfree = 0.000) for 937 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 37: After refmac, R = 0.3491 (Rfree = 0.000) for 920 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 38: After refmac, R = 0.3249 (Rfree = 0.000) for 904 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 39: After refmac, R = 0.3078 (Rfree = 0.000) for 888 atoms. Found 6 (6 requested) and removed 17 (3 requested) atoms. Cycle 40: After refmac, R = 0.3110 (Rfree = 0.000) for 876 atoms. Found 6 (6 requested) and removed 16 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.28 2.83 Search for helices and strands: 0 residues in 0 chains, 942 seeds are put forward Round 1: 54 peptides, 11 chains. Longest chain 8 peptides. Score 0.272 Round 2: 63 peptides, 11 chains. Longest chain 8 peptides. Score 0.356 Round 3: 64 peptides, 11 chains. Longest chain 8 peptides. Score 0.365 Round 4: 57 peptides, 10 chains. Longest chain 9 peptides. Score 0.341 Round 5: 62 peptides, 11 chains. Longest chain 8 peptides. Score 0.347 Taking the results from Round 3 Chains 11, Residues 53, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2974 reflections ( 99.70 % complete ) and 1941 restraints for refining 900 atoms. 1740 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3231 (Rfree = 0.000) for 900 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 42: After refmac, R = 0.3215 (Rfree = 0.000) for 885 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 43: After refmac, R = 0.3747 (Rfree = 0.000) for 872 atoms. Found 6 (6 requested) and removed 18 (3 requested) atoms. Cycle 44: After refmac, R = 0.3271 (Rfree = 0.000) for 851 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 45: After refmac, R = 0.3371 (Rfree = 0.000) for 840 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 2.91 Search for helices and strands: 0 residues in 0 chains, 921 seeds are put forward Round 1: 56 peptides, 11 chains. Longest chain 8 peptides. Score 0.291 Round 2: 72 peptides, 13 chains. Longest chain 9 peptides. Score 0.359 Round 3: 64 peptides, 10 chains. Longest chain 12 peptides. Score 0.404 Round 4: 57 peptides, 11 chains. Longest chain 7 peptides. Score 0.301 Round 5: 56 peptides, 10 chains. Longest chain 8 peptides. Score 0.332 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 54, 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 2huj-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2974 reflections ( 99.70 % complete ) and 1731 restraints for refining 852 atoms. 1525 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3498 (Rfree = 0.000) for 852 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3814 (Rfree = 0.000) for 843 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.3643 (Rfree = 0.000) for 829 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.3295 (Rfree = 0.000) for 814 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:51:03 GMT 2018 Job finished. TimeTaking 28.01 Used memory is bytes: 21658216