null Sun 23 Dec 22:23:05 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 2pv4-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pv4-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pv4-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pv4-4.0-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/2pv4-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pv4-4.0-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 22:23:15 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/2pv4-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pv4-4.0-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 98 and 0 Target number of residues in the AU: 98 Target solvent content: 0.6839 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: 2pv4-4.0-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: 2pv4-4.0-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 4.002 Wilson plot Bfac: 102.72 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 1588 reflections ( 99.13 % complete ) and 0 restraints for refining 1284 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3666 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4087 (Rfree = 0.000) for 1284 atoms. Found 4 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.07 3.91 Search for helices and strands: 0 residues in 0 chains, 1317 seeds are put forward Round 1: 34 peptides, 7 chains. Longest chain 7 peptides. Score 0.247 Round 2: 43 peptides, 6 chains. Longest chain 11 peptides. Score 0.400 Round 3: 49 peptides, 4 chains. Longest chain 16 peptides. Score 0.545 Round 4: 52 peptides, 6 chains. Longest chain 15 peptides. Score 0.486 Round 5: 65 peptides, 6 chains. Longest chain 19 peptides. Score 0.593 Taking the results from Round 5 Chains 6, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1588 reflections ( 99.13 % complete ) and 1801 restraints for refining 835 atoms. 1571 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3874 (Rfree = 0.000) for 835 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. Cycle 2: After refmac, R = 0.3485 (Rfree = 0.000) for 812 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. Cycle 3: After refmac, R = 0.3416 (Rfree = 0.000) for 799 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. Cycle 4: After refmac, R = 0.3471 (Rfree = 0.000) for 780 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. Cycle 5: After refmac, R = 0.3117 (Rfree = 0.000) for 773 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.95 3.80 Search for helices and strands: 0 residues in 0 chains, 836 seeds are put forward Round 1: 61 peptides, 9 chains. Longest chain 16 peptides. Score 0.442 Round 2: 60 peptides, 8 chains. Longest chain 16 peptides. Score 0.474 Round 3: 69 peptides, 9 chains. Longest chain 16 peptides. Score 0.513 Round 4: 68 peptides, 8 chains. Longest chain 18 peptides. Score 0.542 Round 5: 72 peptides, 9 chains. Longest chain 16 peptides. Score 0.538 Taking the results from Round 4 Chains 8, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1588 reflections ( 99.13 % complete ) and 1884 restraints for refining 874 atoms. 1652 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3371 (Rfree = 0.000) for 874 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 7: After refmac, R = 0.3227 (Rfree = 0.000) for 856 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 8: After refmac, R = 0.3282 (Rfree = 0.000) for 833 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 9: After refmac, R = 0.3216 (Rfree = 0.000) for 823 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. Cycle 10: After refmac, R = 0.3057 (Rfree = 0.000) for 814 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.85 3.70 Search for helices and strands: 0 residues in 0 chains, 850 seeds are put forward Round 1: 52 peptides, 9 chains. Longest chain 10 peptides. Score 0.353 Round 2: 65 peptides, 8 chains. Longest chain 21 peptides. Score 0.518 Round 3: 64 peptides, 9 chains. Longest chain 15 peptides. Score 0.469 Round 4: 67 peptides, 10 chains. Longest chain 12 peptides. Score 0.456 Round 5: 69 peptides, 11 chains. Longest chain 11 peptides. Score 0.434 Taking the results from Round 2 Chains 8, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1588 reflections ( 99.13 % complete ) and 1703 restraints for refining 824 atoms. 1483 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3125 (Rfree = 0.000) for 824 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. Cycle 12: After refmac, R = 0.2837 (Rfree = 0.000) for 811 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. Cycle 13: After refmac, R = 0.2718 (Rfree = 0.000) for 808 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. Cycle 14: After refmac, R = 0.2708 (Rfree = 0.000) for 807 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. Cycle 15: After refmac, R = 0.2527 (Rfree = 0.000) for 806 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.95 3.80 Search for helices and strands: 0 residues in 0 chains, 855 seeds are put forward Round 1: 51 peptides, 10 chains. Longest chain 8 peptides. Score 0.296 Round 2: 58 peptides, 8 chains. Longest chain 16 peptides. Score 0.456 Round 3: 65 peptides, 10 chains. Longest chain 12 peptides. Score 0.437 Round 4: 72 peptides, 10 chains. Longest chain 11 peptides. Score 0.500 Round 5: 70 peptides, 10 chains. Longest chain 11 peptides. Score 0.483 Taking the results from Round 4 Chains 10, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1588 reflections ( 99.13 % complete ) and 1811 restraints for refining 849 atoms. 1573 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2846 (Rfree = 0.000) for 849 atoms. Found 2 (4 requested) and removed 10 (2 requested) atoms. Cycle 17: After refmac, R = 0.2663 (Rfree = 0.000) for 830 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 18: After refmac, R = 0.2741 (Rfree = 0.000) for 821 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. Cycle 19: After refmac, R = 0.2791 (Rfree = 0.000) for 821 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 20: After refmac, R = 0.2594 (Rfree = 0.000) for 817 atoms. Found 2 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 4.00 3.84 Search for helices and strands: 0 residues in 0 chains, 876 seeds are put forward Round 1: 58 peptides, 11 chains. Longest chain 10 peptides. Score 0.325 Round 2: 61 peptides, 10 chains. Longest chain 12 peptides. Score 0.399 Round 3: 66 peptides, 9 chains. Longest chain 12 peptides. Score 0.487 Round 4: 65 peptides, 11 chains. Longest chain 12 peptides. Score 0.396 Round 5: 61 peptides, 9 chains. Longest chain 12 peptides. Score 0.442 Taking the results from Round 3 Chains 9, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1588 reflections ( 99.13 % complete ) and 1784 restraints for refining 845 atoms. 1565 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3059 (Rfree = 0.000) for 845 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 22: After refmac, R = 0.2437 (Rfree = 0.000) for 836 atoms. Found 2 (4 requested) and removed 3 (2 requested) atoms. Cycle 23: After refmac, R = 0.2736 (Rfree = 0.000) for 829 atoms. Found 3 (3 requested) and removed 15 (1 requested) atoms. Cycle 24: After refmac, R = 0.2418 (Rfree = 0.000) for 808 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 25: After refmac, R = 0.2259 (Rfree = 0.000) for 804 atoms. Found 3 (3 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.93 3.78 Search for helices and strands: 0 residues in 0 chains, 841 seeds are put forward Round 1: 58 peptides, 11 chains. Longest chain 10 peptides. Score 0.325 Round 2: 63 peptides, 11 chains. Longest chain 10 peptides. Score 0.376 Round 3: 64 peptides, 11 chains. Longest chain 10 peptides. Score 0.386 Round 4: 65 peptides, 11 chains. Longest chain 10 peptides. Score 0.396 Round 5: 62 peptides, 11 chains. Longest chain 13 peptides. Score 0.366 Taking the results from Round 4 Chains 11, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1588 reflections ( 99.13 % complete ) and 1845 restraints for refining 862 atoms. 1640 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2414 (Rfree = 0.000) for 862 atoms. Found 3 (4 requested) and removed 4 (2 requested) atoms. Cycle 27: After refmac, R = 0.2171 (Rfree = 0.000) for 849 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 28: After refmac, R = 0.2038 (Rfree = 0.000) for 847 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 29: After refmac, R = 0.1961 (Rfree = 0.000) for 843 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 30: After refmac, R = 0.2198 (Rfree = 0.000) for 840 atoms. Found 3 (3 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.99 3.83 Search for helices and strands: 0 residues in 0 chains, 884 seeds are put forward Round 1: 48 peptides, 11 chains. Longest chain 6 peptides. Score 0.215 Round 2: 59 peptides, 10 chains. Longest chain 11 peptides. Score 0.380 Round 3: 54 peptides, 10 chains. Longest chain 9 peptides. Score 0.328 Round 4: 64 peptides, 10 chains. Longest chain 10 peptides. Score 0.428 Round 5: 61 peptides, 10 chains. Longest chain 10 peptides. Score 0.399 Taking the results from Round 4 Chains 10, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1588 reflections ( 99.13 % complete ) and 1880 restraints for refining 881 atoms. 1674 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2657 (Rfree = 0.000) for 881 atoms. Found 4 (4 requested) and removed 11 (2 requested) atoms. Cycle 32: After refmac, R = 0.2527 (Rfree = 0.000) for 869 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 33: After refmac, R = 0.2627 (Rfree = 0.000) for 861 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 34: After refmac, R = 0.2135 (Rfree = 0.000) for 852 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. Cycle 35: After refmac, R = 0.2181 (Rfree = 0.000) for 851 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.91 3.76 Search for helices and strands: 0 residues in 0 chains, 889 seeds are put forward Round 1: 52 peptides, 12 chains. Longest chain 6 peptides. Score 0.214 Round 2: 60 peptides, 11 chains. Longest chain 10 peptides. Score 0.346 Round 3: 52 peptides, 10 chains. Longest chain 7 peptides. Score 0.307 Round 4: 58 peptides, 11 chains. Longest chain 8 peptides. Score 0.325 Round 5: 55 peptides, 9 chains. Longest chain 9 peptides. Score 0.384 Taking the results from Round 5 Chains 9, Residues 46, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1588 reflections ( 99.13 % complete ) and 2233 restraints for refining 950 atoms. 2058 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3470 (Rfree = 0.000) for 950 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. Cycle 37: After refmac, R = 0.2899 (Rfree = 0.000) for 933 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 38: After refmac, R = 0.2099 (Rfree = 0.000) for 919 atoms. Found 3 (4 requested) and removed 3 (2 requested) atoms. Cycle 39: After refmac, R = 0.2097 (Rfree = 0.000) for 912 atoms. Found 2 (4 requested) and removed 5 (2 requested) atoms. Cycle 40: After refmac, R = 0.1934 (Rfree = 0.000) for 905 atoms. Found 1 (4 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.92 3.77 Search for helices and strands: 0 residues in 0 chains, 938 seeds are put forward Round 1: 34 peptides, 8 chains. Longest chain 5 peptides. Score 0.194 Round 2: 48 peptides, 8 chains. Longest chain 9 peptides. Score 0.357 Round 3: 45 peptides, 9 chains. Longest chain 9 peptides. Score 0.277 Round 4: 50 peptides, 10 chains. Longest chain 8 peptides. Score 0.285 Round 5: 50 peptides, 10 chains. Longest chain 8 peptides. Score 0.285 Taking the results from Round 2 Chains 8, Residues 40, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1588 reflections ( 99.13 % complete ) and 1913 restraints for refining 859 atoms. 1761 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2351 (Rfree = 0.000) for 859 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 42: After refmac, R = 0.2172 (Rfree = 0.000) for 859 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 43: After refmac, R = 0.1930 (Rfree = 0.000) for 859 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 44: After refmac, R = 0.1848 (Rfree = 0.000) for 858 atoms. Found 0 (4 requested) and removed 7 (2 requested) atoms. Cycle 45: After refmac, R = 0.1776 (Rfree = 0.000) for 849 atoms. Found 1 (4 requested) and removed 13 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.92 3.77 Search for helices and strands: 0 residues in 0 chains, 879 seeds are put forward Round 1: 38 peptides, 8 chains. Longest chain 6 peptides. Score 0.244 Round 2: 40 peptides, 9 chains. Longest chain 6 peptides. Score 0.217 Round 3: 47 peptides, 10 chains. Longest chain 7 peptides. Score 0.251 Round 4: 42 peptides, 8 chains. Longest chain 7 peptides. Score 0.291 Round 5: 43 peptides, 8 chains. Longest chain 7 peptides. Score 0.303 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 35, 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 2pv4-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1588 reflections ( 99.13 % complete ) and 1884 restraints for refining 861 atoms. 1752 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2320 (Rfree = 0.000) for 861 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2160 (Rfree = 0.000) for 853 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2026 (Rfree = 0.000) for 850 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.1951 (Rfree = 0.000) for 847 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:44:52 GMT 2018 Job finished. TimeTaking 21.79 Used memory is bytes: 2926352