null Sun 23 Dec 22:23:10 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 2pv4-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pv4-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pv4-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pv4-3.8-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/2pv4-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pv4-3.8-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 22:23:18 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/2pv4-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pv4-3.8-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 103 and 0 Target number of residues in the AU: 103 Target solvent content: 0.6678 Checking the provided sequence file Detected sequence length: 145 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 145 Adjusted target solvent content: 0.53 Input MTZ file: 2pv4-3.8-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: 19 Cell parameters: 35.957 47.283 98.695 90.000 90.000 90.000 Input sequence file: 2pv4-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1160 target number of atoms Had to go as low as 0.75 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: 49.347 3.800 Wilson plot Bfac: 90.57 1854 reflections ( 99.25 % complete ) and 0 restraints for refining 1286 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3567 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4120 (Rfree = 0.000) for 1286 atoms. Found 4 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.09 3.93 Search for helices and strands: 0 residues in 0 chains, 1314 seeds are put forward Round 1: 40 peptides, 8 chains. Longest chain 8 peptides. Score 0.268 Round 2: 58 peptides, 9 chains. Longest chain 10 peptides. Score 0.413 Round 3: 59 peptides, 11 chains. Longest chain 8 peptides. Score 0.336 Round 4: 61 peptides, 7 chains. Longest chain 20 peptides. Score 0.523 Round 5: 61 peptides, 9 chains. Longest chain 9 peptides. Score 0.442 Taking the results from Round 4 Chains 9, Residues 54, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 1854 reflections ( 99.25 % complete ) and 2089 restraints for refining 979 atoms. 1837 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3289 (Rfree = 0.000) for 979 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 2: After refmac, R = 0.3173 (Rfree = 0.000) for 962 atoms. Found 4 (5 requested) and removed 3 (2 requested) atoms. Cycle 3: After refmac, R = 0.2962 (Rfree = 0.000) for 952 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. Cycle 4: After refmac, R = 0.2977 (Rfree = 0.000) for 939 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 5: After refmac, R = 0.2954 (Rfree = 0.000) for 939 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 4.00 3.84 Search for helices and strands: 0 residues in 0 chains, 1002 seeds are put forward Round 1: 48 peptides, 10 chains. Longest chain 5 peptides. Score 0.263 Round 2: 57 peptides, 10 chains. Longest chain 8 peptides. Score 0.359 Round 3: 71 peptides, 11 chains. Longest chain 10 peptides. Score 0.452 Round 4: 77 peptides, 11 chains. Longest chain 13 peptides. Score 0.504 Round 5: 70 peptides, 9 chains. Longest chain 16 peptides. Score 0.521 Taking the results from Round 5 Chains 9, Residues 61, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 1854 reflections ( 99.25 % complete ) and 1841 restraints for refining 919 atoms. 1537 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3065 (Rfree = 0.000) for 919 atoms. Found 5 (5 requested) and removed 15 (2 requested) atoms. Cycle 7: After refmac, R = 0.2883 (Rfree = 0.000) for 895 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Cycle 8: After refmac, R = 0.2829 (Rfree = 0.000) for 886 atoms. Found 3 (4 requested) and removed 5 (2 requested) atoms. Cycle 9: After refmac, R = 0.2728 (Rfree = 0.000) for 880 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 10: After refmac, R = 0.2718 (Rfree = 0.000) for 875 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 4.02 3.86 Search for helices and strands: 0 residues in 0 chains, 942 seeds are put forward Round 1: 53 peptides, 8 chains. Longest chain 10 peptides. Score 0.408 Round 2: 54 peptides, 8 chains. Longest chain 10 peptides. Score 0.418 Round 3: 55 peptides, 8 chains. Longest chain 11 peptides. Score 0.427 Round 4: 69 peptides, 10 chains. Longest chain 18 peptides. Score 0.474 Round 5: 66 peptides, 9 chains. Longest chain 15 peptides. Score 0.487 Taking the results from Round 5 Chains 9, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1854 reflections ( 99.25 % complete ) and 2097 restraints for refining 911 atoms. 1878 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2893 (Rfree = 0.000) for 911 atoms. Found 2 (5 requested) and removed 8 (2 requested) atoms. Cycle 12: After refmac, R = 0.2797 (Rfree = 0.000) for 892 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. Cycle 13: After refmac, R = 0.2614 (Rfree = 0.000) for 892 atoms. Found 2 (4 requested) and removed 3 (2 requested) atoms. Cycle 14: After refmac, R = 0.2598 (Rfree = 0.000) for 889 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 15: After refmac, R = 0.2598 (Rfree = 0.000) for 887 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 4.10 3.94 Search for helices and strands: 0 residues in 0 chains, 949 seeds are put forward Round 1: 53 peptides, 10 chains. Longest chain 9 peptides. Score 0.318 Round 2: 71 peptides, 12 chains. Longest chain 9 peptides. Score 0.412 Round 3: 63 peptides, 10 chains. Longest chain 9 peptides. Score 0.419 Round 4: 64 peptides, 9 chains. Longest chain 11 peptides. Score 0.469 Round 5: 64 peptides, 10 chains. Longest chain 9 peptides. Score 0.428 Taking the results from Round 4 Chains 9, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1854 reflections ( 99.25 % complete ) and 1989 restraints for refining 883 atoms. 1778 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2823 (Rfree = 0.000) for 883 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 17: After refmac, R = 0.2673 (Rfree = 0.000) for 883 atoms. Found 3 (4 requested) and removed 5 (2 requested) atoms. Cycle 18: After refmac, R = 0.2651 (Rfree = 0.000) for 878 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 19: After refmac, R = 0.2582 (Rfree = 0.000) for 877 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 20: After refmac, R = 0.2552 (Rfree = 0.000) for 876 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 4.01 3.85 Search for helices and strands: 0 residues in 0 chains, 926 seeds are put forward Round 1: 57 peptides, 10 chains. Longest chain 8 peptides. Score 0.359 Round 2: 58 peptides, 9 chains. Longest chain 9 peptides. Score 0.413 Round 3: 63 peptides, 10 chains. Longest chain 9 peptides. Score 0.419 Round 4: 64 peptides, 10 chains. Longest chain 9 peptides. Score 0.428 Round 5: 69 peptides, 10 chains. Longest chain 12 peptides. Score 0.474 Taking the results from Round 5 Chains 10, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1854 reflections ( 99.25 % complete ) and 2028 restraints for refining 904 atoms. 1802 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3038 (Rfree = 0.000) for 904 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 22: After refmac, R = 0.2828 (Rfree = 0.000) for 901 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 23: After refmac, R = 0.2688 (Rfree = 0.000) for 897 atoms. Found 3 (4 requested) and removed 3 (2 requested) atoms. Cycle 24: After refmac, R = 0.2587 (Rfree = 0.000) for 897 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 25: After refmac, R = 0.2547 (Rfree = 0.000) for 895 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.81 3.66 Search for helices and strands: 0 residues in 0 chains, 931 seeds are put forward Round 1: 54 peptides, 11 chains. Longest chain 8 peptides. Score 0.283 Round 2: 65 peptides, 12 chains. Longest chain 8 peptides. Score 0.353 Round 3: 64 peptides, 12 chains. Longest chain 9 peptides. Score 0.343 Round 4: 69 peptides, 12 chains. Longest chain 9 peptides. Score 0.393 Round 5: 62 peptides, 9 chains. Longest chain 12 peptides. Score 0.451 Taking the results from Round 5 Chains 9, Residues 53, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1854 reflections ( 99.25 % complete ) and 2251 restraints for refining 970 atoms. 2048 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2898 (Rfree = 0.000) for 970 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 27: After refmac, R = 0.2802 (Rfree = 0.000) for 956 atoms. Found 4 (5 requested) and removed 3 (2 requested) atoms. Cycle 28: After refmac, R = 0.2425 (Rfree = 0.000) for 956 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 29: After refmac, R = 0.2362 (Rfree = 0.000) for 950 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 30: After refmac, R = 0.2311 (Rfree = 0.000) for 948 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 4.01 3.85 Search for helices and strands: 0 residues in 0 chains, 978 seeds are put forward Round 1: 45 peptides, 10 chains. Longest chain 6 peptides. Score 0.228 Round 2: 60 peptides, 12 chains. Longest chain 7 peptides. Score 0.302 Round 3: 61 peptides, 11 chains. Longest chain 10 peptides. Score 0.356 Round 4: 52 peptides, 10 chains. Longest chain 7 peptides. Score 0.307 Round 5: 57 peptides, 10 chains. Longest chain 7 peptides. Score 0.359 Taking the results from Round 5 Chains 10, Residues 47, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1854 reflections ( 99.25 % complete ) and 2134 restraints for refining 931 atoms. 1956 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3430 (Rfree = 0.000) for 931 atoms. Found 3 (5 requested) and removed 2 (2 requested) atoms. Cycle 32: After refmac, R = 0.3155 (Rfree = 0.000) for 915 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. Cycle 33: After refmac, R = 0.3163 (Rfree = 0.000) for 907 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. Cycle 34: After refmac, R = 0.2877 (Rfree = 0.000) for 902 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. Cycle 35: After refmac, R = 0.2819 (Rfree = 0.000) for 901 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.96 3.80 Search for helices and strands: 0 residues in 0 chains, 940 seeds are put forward Round 1: 44 peptides, 8 chains. Longest chain 10 peptides. Score 0.314 Round 2: 61 peptides, 10 chains. Longest chain 12 peptides. Score 0.399 Round 3: 53 peptides, 10 chains. Longest chain 10 peptides. Score 0.318 Round 4: 53 peptides, 10 chains. Longest chain 9 peptides. Score 0.318 Round 5: 59 peptides, 10 chains. Longest chain 10 peptides. Score 0.380 Taking the results from Round 2 Chains 10, Residues 51, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 1854 reflections ( 99.25 % complete ) and 1804 restraints for refining 878 atoms. 1570 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3037 (Rfree = 0.000) for 878 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Cycle 37: After refmac, R = 0.2888 (Rfree = 0.000) for 873 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 38: After refmac, R = 0.2807 (Rfree = 0.000) for 869 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Cycle 39: After refmac, R = 0.2733 (Rfree = 0.000) for 864 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 40: After refmac, R = 0.2695 (Rfree = 0.000) for 861 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.97 3.81 Search for helices and strands: 0 residues in 0 chains, 890 seeds are put forward Round 1: 35 peptides, 8 chains. Longest chain 5 peptides. Score 0.207 Round 2: 39 peptides, 7 chains. Longest chain 10 peptides. Score 0.307 Round 3: 44 peptides, 9 chains. Longest chain 7 peptides. Score 0.265 Round 4: 44 peptides, 9 chains. Longest chain 7 peptides. Score 0.265 Round 5: 48 peptides, 10 chains. Longest chain 6 peptides. Score 0.263 Taking the results from Round 2 Chains 7, Residues 32, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1854 reflections ( 99.25 % complete ) and 2099 restraints for refining 882 atoms. 1978 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3160 (Rfree = 0.000) for 882 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 42: After refmac, R = 0.2929 (Rfree = 0.000) for 882 atoms. Found 3 (4 requested) and removed 3 (2 requested) atoms. Cycle 43: After refmac, R = 0.2835 (Rfree = 0.000) for 882 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 44: After refmac, R = 0.2810 (Rfree = 0.000) for 882 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 45: After refmac, R = 0.2763 (Rfree = 0.000) for 880 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.94 3.79 Search for helices and strands: 0 residues in 0 chains, 901 seeds are put forward Round 1: 37 peptides, 8 chains. Longest chain 6 peptides. Score 0.232 Round 2: 38 peptides, 6 chains. Longest chain 9 peptides. Score 0.346 Round 3: 40 peptides, 6 chains. Longest chain 13 peptides. Score 0.368 Round 4: 43 peptides, 7 chains. Longest chain 13 peptides. Score 0.351 Round 5: 38 peptides, 7 chains. Longest chain 8 peptides. Score 0.296 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 34, 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 2pv4-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1854 reflections ( 99.25 % complete ) and 2221 restraints for refining 908 atoms. 2091 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2940 (Rfree = 0.000) for 908 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2804 (Rfree = 0.000) for 904 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2792 (Rfree = 0.000) for 900 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2745 (Rfree = 0.000) for 898 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:45:06 GMT 2018 Job finished. TimeTaking 21.94 Used memory is bytes: 4542016