null Mon 24 Dec 00:17:26 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 1vkn-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkn-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkn-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.4-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/1vkn-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.4-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 ============================================================ Mon 24 Dec 00:17:30 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/1vkn-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.4-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 1002 and 0 Target number of residues in the AU: 1002 Target solvent content: 0.6305 Checking the provided sequence file Detected sequence length: 351 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1404 Adjusted target solvent content: 0.48 Input MTZ file: 1vkn-3.4-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: 4 Cell parameters: 85.135 92.128 101.299 90.000 112.538 90.000 Input sequence file: 1vkn-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 11232 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 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: 93.562 3.400 Wilson plot Bfac: 66.71 19863 reflections ( 98.93 % complete ) and 0 restraints for refining 12441 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.2999 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2445 (Rfree = 0.000) for 12441 atoms. Found 93 (93 requested) and removed 83 (46 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.29 3.38 Search for helices and strands: 0 residues in 0 chains, 12696 seeds are put forward NCS extension: 0 residues added, 12696 seeds are put forward Round 1: 689 peptides, 118 chains. Longest chain 17 peptides. Score 0.424 Round 2: 791 peptides, 103 chains. Longest chain 31 peptides. Score 0.583 Round 3: 839 peptides, 112 chains. Longest chain 22 peptides. Score 0.589 Round 4: 899 peptides, 101 chains. Longest chain 34 peptides. Score 0.672 Round 5: 890 peptides, 100 chains. Longest chain 25 peptides. Score 0.669 Taking the results from Round 4 Chains 110, Residues 798, Estimated correctness of the model 50.4 % 12 chains (182 residues) have been docked in sequence ------------------------------------------------------ 19863 reflections ( 98.93 % complete ) and 20412 restraints for refining 10208 atoms. 16614 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2184 (Rfree = 0.000) for 10208 atoms. Found 77 (77 requested) and removed 82 (38 requested) atoms. Cycle 2: After refmac, R = 0.1981 (Rfree = 0.000) for 10027 atoms. Found 50 (77 requested) and removed 50 (38 requested) atoms. Cycle 3: After refmac, R = 0.1940 (Rfree = 0.000) for 9976 atoms. Found 25 (75 requested) and removed 51 (37 requested) atoms. Cycle 4: After refmac, R = 0.1891 (Rfree = 0.000) for 9915 atoms. Found 29 (75 requested) and removed 48 (37 requested) atoms. Cycle 5: After refmac, R = 0.1846 (Rfree = 0.000) for 9867 atoms. Found 21 (74 requested) and removed 47 (37 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.28 3.37 Search for helices and strands: 0 residues in 0 chains, 10192 seeds are put forward NCS extension: 15 residues added (15 deleted due to clashes), 10207 seeds are put forward Round 1: 772 peptides, 115 chains. Longest chain 33 peptides. Score 0.519 Round 2: 864 peptides, 111 chains. Longest chain 29 peptides. Score 0.613 Round 3: 869 peptides, 103 chains. Longest chain 29 peptides. Score 0.644 Round 4: 896 peptides, 102 chains. Longest chain 37 peptides. Score 0.667 Round 5: 903 peptides, 95 chains. Longest chain 34 peptides. Score 0.693 Taking the results from Round 5 Chains 103, Residues 808, Estimated correctness of the model 56.1 % 9 chains (127 residues) have been docked in sequence ------------------------------------------------------ 19863 reflections ( 98.93 % complete ) and 21353 restraints for refining 10213 atoms. 17755 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2091 (Rfree = 0.000) for 10213 atoms. Found 70 (77 requested) and removed 80 (38 requested) atoms. Cycle 7: After refmac, R = 0.1902 (Rfree = 0.000) for 10134 atoms. Found 33 (77 requested) and removed 57 (38 requested) atoms. Cycle 8: After refmac, R = 0.1898 (Rfree = 0.000) for 10077 atoms. Found 37 (76 requested) and removed 49 (38 requested) atoms. Cycle 9: After refmac, R = 0.1853 (Rfree = 0.000) for 10045 atoms. Found 32 (75 requested) and removed 47 (37 requested) atoms. Cycle 10: After refmac, R = 0.1769 (Rfree = 0.000) for 10017 atoms. Found 29 (75 requested) and removed 43 (37 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 3.42 Search for helices and strands: 0 residues in 0 chains, 10329 seeds are put forward NCS extension: 36 residues added (6 deleted due to clashes), 10365 seeds are put forward Round 1: 772 peptides, 115 chains. Longest chain 24 peptides. Score 0.519 Round 2: 847 peptides, 102 chains. Longest chain 31 peptides. Score 0.631 Round 3: 860 peptides, 106 chains. Longest chain 30 peptides. Score 0.627 Round 4: 862 peptides, 100 chains. Longest chain 29 peptides. Score 0.649 Round 5: 879 peptides, 99 chains. Longest chain 31 peptides. Score 0.664 Taking the results from Round 5 Chains 104, Residues 780, Estimated correctness of the model 48.2 % 9 chains (115 residues) have been docked in sequence ------------------------------------------------------ 19863 reflections ( 98.93 % complete ) and 21619 restraints for refining 10213 atoms. 18139 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2079 (Rfree = 0.000) for 10213 atoms. Found 62 (77 requested) and removed 75 (38 requested) atoms. Cycle 12: After refmac, R = 0.1934 (Rfree = 0.000) for 10147 atoms. Found 33 (77 requested) and removed 52 (38 requested) atoms. Cycle 13: After refmac, R = 0.1833 (Rfree = 0.000) for 10108 atoms. Found 25 (76 requested) and removed 52 (38 requested) atoms. Cycle 14: After refmac, R = 0.1739 (Rfree = 0.000) for 10060 atoms. Found 9 (76 requested) and removed 40 (38 requested) atoms. Cycle 15: After refmac, R = 0.1691 (Rfree = 0.000) for 10014 atoms. Found 11 (75 requested) and removed 38 (37 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.33 3.42 Search for helices and strands: 0 residues in 0 chains, 10306 seeds are put forward NCS extension: 13 residues added (8 deleted due to clashes), 10319 seeds are put forward Round 1: 764 peptides, 111 chains. Longest chain 27 peptides. Score 0.528 Round 2: 809 peptides, 98 chains. Longest chain 37 peptides. Score 0.616 Round 3: 829 peptides, 102 chains. Longest chain 45 peptides. Score 0.617 Round 4: 845 peptides, 99 chains. Longest chain 27 peptides. Score 0.640 Round 5: 847 peptides, 106 chains. Longest chain 26 peptides. Score 0.617 Taking the results from Round 4 Chains 104, Residues 746, Estimated correctness of the model 41.2 % 12 chains (117 residues) have been docked in sequence ------------------------------------------------------ 19863 reflections ( 98.93 % complete ) and 21929 restraints for refining 10213 atoms. 18627 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2037 (Rfree = 0.000) for 10213 atoms. Found 74 (77 requested) and removed 64 (38 requested) atoms. Cycle 17: After refmac, R = 0.1866 (Rfree = 0.000) for 10184 atoms. Found 27 (77 requested) and removed 45 (38 requested) atoms. Cycle 18: After refmac, R = 0.1825 (Rfree = 0.000) for 10146 atoms. Found 23 (76 requested) and removed 40 (38 requested) atoms. Cycle 19: After refmac, R = 0.1751 (Rfree = 0.000) for 10118 atoms. Found 15 (76 requested) and removed 38 (38 requested) atoms. Cycle 20: After refmac, R = 0.1707 (Rfree = 0.000) for 10079 atoms. Found 17 (76 requested) and removed 38 (38 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 3.41 Search for helices and strands: 0 residues in 0 chains, 10352 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 10368 seeds are put forward Round 1: 738 peptides, 121 chains. Longest chain 18 peptides. Score 0.461 Round 2: 810 peptides, 110 chains. Longest chain 20 peptides. Score 0.573 Round 3: 825 peptides, 112 chains. Longest chain 20 peptides. Score 0.578 Round 4: 813 peptides, 105 chains. Longest chain 18 peptides. Score 0.594 Round 5: 821 peptides, 104 chains. Longest chain 26 peptides. Score 0.604 Taking the results from Round 5 Chains 107, Residues 717, Estimated correctness of the model 30.0 % 7 chains (78 residues) have been docked in sequence ------------------------------------------------------ 19863 reflections ( 98.93 % complete ) and 22315 restraints for refining 10211 atoms. 19295 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2029 (Rfree = 0.000) for 10211 atoms. Found 77 (77 requested) and removed 58 (38 requested) atoms. Cycle 22: After refmac, R = 0.1923 (Rfree = 0.000) for 10189 atoms. Found 35 (77 requested) and removed 43 (38 requested) atoms. Cycle 23: After refmac, R = 0.1835 (Rfree = 0.000) for 10151 atoms. Found 36 (76 requested) and removed 42 (38 requested) atoms. Cycle 24: After refmac, R = 0.1792 (Rfree = 0.000) for 10125 atoms. Found 33 (76 requested) and removed 41 (38 requested) atoms. Cycle 25: After refmac, R = 0.1783 (Rfree = 0.000) for 10099 atoms. Found 49 (76 requested) and removed 45 (38 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 3.42 Search for helices and strands: 0 residues in 0 chains, 10425 seeds are put forward NCS extension: 24 residues added (8 deleted due to clashes), 10449 seeds are put forward Round 1: 722 peptides, 116 chains. Longest chain 16 peptides. Score 0.467 Round 2: 789 peptides, 113 chains. Longest chain 26 peptides. Score 0.543 Round 3: 798 peptides, 105 chains. Longest chain 19 peptides. Score 0.581 Round 4: 807 peptides, 108 chains. Longest chain 27 peptides. Score 0.578 Round 5: 825 peptides, 106 chains. Longest chain 22 peptides. Score 0.600 Taking the results from Round 5 Chains 109, Residues 719, Estimated correctness of the model 28.7 % 6 chains (57 residues) have been docked in sequence ------------------------------------------------------ 19863 reflections ( 98.93 % complete ) and 22784 restraints for refining 10211 atoms. 19837 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2014 (Rfree = 0.000) for 10211 atoms. Found 73 (77 requested) and removed 48 (38 requested) atoms. Cycle 27: After refmac, R = 0.1920 (Rfree = 0.000) for 10207 atoms. Found 36 (77 requested) and removed 45 (38 requested) atoms. Cycle 28: After refmac, R = 0.1847 (Rfree = 0.000) for 10172 atoms. Found 52 (77 requested) and removed 44 (38 requested) atoms. Cycle 29: After refmac, R = 0.1766 (Rfree = 0.000) for 10161 atoms. Found 37 (76 requested) and removed 43 (38 requested) atoms. Cycle 30: After refmac, R = 0.1723 (Rfree = 0.000) for 10139 atoms. Found 47 (76 requested) and removed 44 (38 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.32 3.41 Search for helices and strands: 0 residues in 0 chains, 10444 seeds are put forward NCS extension: 29 residues added (4 deleted due to clashes), 10473 seeds are put forward Round 1: 660 peptides, 113 chains. Longest chain 17 peptides. Score 0.416 Round 2: 741 peptides, 100 chains. Longest chain 28 peptides. Score 0.551 Round 3: 761 peptides, 108 chains. Longest chain 19 peptides. Score 0.537 Round 4: 727 peptides, 101 chains. Longest chain 20 peptides. Score 0.535 Round 5: 725 peptides, 98 chains. Longest chain 27 peptides. Score 0.545 Taking the results from Round 2 Chains 102, Residues 641, Estimated correctness of the model 11.9 % 6 chains (61 residues) have been docked in sequence ------------------------------------------------------ 19863 reflections ( 98.93 % complete ) and 22909 restraints for refining 10212 atoms. 20216 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1862 (Rfree = 0.000) for 10212 atoms. Found 57 (77 requested) and removed 47 (38 requested) atoms. Cycle 32: After refmac, R = 0.1794 (Rfree = 0.000) for 10199 atoms. Found 33 (77 requested) and removed 41 (38 requested) atoms. Cycle 33: After refmac, R = 0.1728 (Rfree = 0.000) for 10177 atoms. Found 38 (76 requested) and removed 43 (38 requested) atoms. Cycle 34: After refmac, R = 0.1699 (Rfree = 0.000) for 10153 atoms. Found 36 (76 requested) and removed 39 (38 requested) atoms. Cycle 35: After refmac, R = 0.1646 (Rfree = 0.000) for 10139 atoms. Found 38 (76 requested) and removed 39 (38 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 10414 seeds are put forward NCS extension: 35 residues added (2 deleted due to clashes), 10449 seeds are put forward Round 1: 598 peptides, 104 chains. Longest chain 13 peptides. Score 0.391 Round 2: 687 peptides, 98 chains. Longest chain 18 peptides. Score 0.510 Round 3: 699 peptides, 97 chains. Longest chain 17 peptides. Score 0.525 Round 4: 705 peptides, 92 chains. Longest chain 21 peptides. Score 0.551 Round 5: 714 peptides, 102 chains. Longest chain 20 peptides. Score 0.518 Taking the results from Round 4 Chains 92, Residues 613, Estimated correctness of the model 11.9 % 5 chains (21 residues) have been docked in sequence ------------------------------------------------------ 19863 reflections ( 98.93 % complete ) and 23533 restraints for refining 10213 atoms. 21117 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1869 (Rfree = 0.000) for 10213 atoms. Found 63 (77 requested) and removed 43 (38 requested) atoms. Cycle 37: After refmac, R = 0.1806 (Rfree = 0.000) for 10217 atoms. Found 46 (77 requested) and removed 41 (38 requested) atoms. Cycle 38: After refmac, R = 0.1709 (Rfree = 0.000) for 10212 atoms. Found 39 (77 requested) and removed 41 (38 requested) atoms. Cycle 39: After refmac, R = 0.1684 (Rfree = 0.000) for 10200 atoms. Found 42 (77 requested) and removed 43 (38 requested) atoms. Cycle 40: After refmac, R = 0.1617 (Rfree = 0.000) for 10195 atoms. Found 38 (77 requested) and removed 41 (38 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.32 3.41 Search for helices and strands: 0 residues in 0 chains, 10474 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 10492 seeds are put forward Round 1: 556 peptides, 98 chains. Longest chain 15 peptides. Score 0.373 Round 2: 636 peptides, 91 chains. Longest chain 21 peptides. Score 0.490 Round 3: 611 peptides, 91 chains. Longest chain 23 peptides. Score 0.465 Round 4: 617 peptides, 80 chains. Longest chain 26 peptides. Score 0.520 Round 5: 631 peptides, 82 chains. Longest chain 23 peptides. Score 0.525 Taking the results from Round 5 Chains 83, Residues 549, Estimated correctness of the model 2.3 % 4 chains (38 residues) have been docked in sequence ------------------------------------------------------ 19863 reflections ( 98.93 % complete ) and 23776 restraints for refining 10212 atoms. 21525 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1864 (Rfree = 0.000) for 10212 atoms. Found 64 (77 requested) and removed 44 (38 requested) atoms. Cycle 42: After refmac, R = 0.1817 (Rfree = 0.000) for 10206 atoms. Found 56 (77 requested) and removed 41 (38 requested) atoms. Cycle 43: After refmac, R = 0.1771 (Rfree = 0.000) for 10195 atoms. Found 70 (77 requested) and removed 39 (38 requested) atoms. Cycle 44: After refmac, R = 0.1708 (Rfree = 0.000) for 10213 atoms. Found 43 (77 requested) and removed 41 (38 requested) atoms. Cycle 45: After refmac, R = 0.1656 (Rfree = 0.000) for 10208 atoms. Found 44 (77 requested) and removed 40 (38 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 3.42 Search for helices and strands: 0 residues in 0 chains, 10470 seeds are put forward NCS extension: 35 residues added (1 deleted due to clashes), 10505 seeds are put forward Round 1: 556 peptides, 103 chains. Longest chain 14 peptides. Score 0.348 Round 2: 611 peptides, 96 chains. Longest chain 19 peptides. Score 0.443 Round 3: 645 peptides, 92 chains. Longest chain 26 peptides. Score 0.495 Round 4: 638 peptides, 92 chains. Longest chain 20 peptides. Score 0.488 Round 5: 644 peptides, 95 chains. Longest chain 17 peptides. Score 0.481 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 97, Residues 553, Estimated correctness of the model 0.0 % 5 chains (63 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 1vkn-3_warpNtrace.pdb as input Building loops using Loopy2018 97 chains (553 residues) following loop building 5 chains (63 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 19863 reflections ( 98.93 % complete ) and 23370 restraints for refining 10213 atoms. 20988 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1817 (Rfree = 0.000) for 10213 atoms. Found 0 (77 requested) and removed 38 (38 requested) atoms. Cycle 47: After refmac, R = 0.1833 (Rfree = 0.000) for 10151 atoms. Found 0 (76 requested) and removed 38 (38 requested) atoms. Cycle 48: After refmac, R = 0.1813 (Rfree = 0.000) for 10108 atoms. Found 0 (76 requested) and removed 38 (38 requested) atoms. Cycle 49: After refmac, R = 0.1765 (Rfree = 0.000) for 10055 atoms. Found 0 (76 requested) and removed 38 (38 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:56:42 GMT 2018 Job finished. TimeTaking 99.27 Used memory is bytes: 7082856