null Mon 24 Dec 08:06:55 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vkn-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkn-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkn-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.4-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.4-parrot-noncs ############### 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 08:07:00 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/noncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.4-parrot-noncs/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-noncs.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-noncs.fasta_lf Building free atoms model in initial map for 11232 target number of atoms Had to go as low as 0.70 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 12385 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3044 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2563 (Rfree = 0.000) for 12385 atoms. Found 93 (93 requested) and removed 82 (46 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 12630 seeds are put forward NCS extension: 0 residues added, 12630 seeds are put forward Round 1: 640 peptides, 113 chains. Longest chain 16 peptides. Score 0.395 Round 2: 829 peptides, 113 chains. Longest chain 28 peptides. Score 0.577 Round 3: 838 peptides, 95 chains. Longest chain 29 peptides. Score 0.648 Round 4: 869 peptides, 96 chains. Longest chain 35 peptides. Score 0.667 Round 5: 881 peptides, 93 chains. Longest chain 27 peptides. Score 0.685 Taking the results from Round 5 Chains 99, Residues 788, Estimated correctness of the model 53.9 % 12 chains (124 residues) have been docked in sequence ------------------------------------------------------ 19863 reflections ( 98.93 % complete ) and 21307 restraints for refining 10206 atoms. 17787 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2207 (Rfree = 0.000) for 10206 atoms. Found 70 (77 requested) and removed 64 (38 requested) atoms. Cycle 2: After refmac, R = 0.2006 (Rfree = 0.000) for 10109 atoms. Found 37 (77 requested) and removed 51 (38 requested) atoms. Cycle 3: After refmac, R = 0.1995 (Rfree = 0.000) for 10042 atoms. Found 27 (76 requested) and removed 47 (38 requested) atoms. Cycle 4: After refmac, R = 0.1934 (Rfree = 0.000) for 9983 atoms. Found 37 (75 requested) and removed 46 (37 requested) atoms. Cycle 5: After refmac, R = 0.1852 (Rfree = 0.000) for 9956 atoms. Found 25 (75 requested) and removed 42 (37 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 10248 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 10265 seeds are put forward Round 1: 764 peptides, 114 chains. Longest chain 16 peptides. Score 0.516 Round 2: 854 peptides, 98 chains. Longest chain 25 peptides. Score 0.650 Round 3: 889 peptides, 107 chains. Longest chain 46 peptides. Score 0.646 Round 4: 884 peptides, 99 chains. Longest chain 33 peptides. Score 0.668 Round 5: 882 peptides, 94 chains. Longest chain 42 peptides. Score 0.682 Taking the results from Round 5 Chains 99, Residues 788, Estimated correctness of the model 53.1 % 12 chains (166 residues) have been docked in sequence ------------------------------------------------------ 19863 reflections ( 98.93 % complete ) and 21091 restraints for refining 10212 atoms. 17431 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2222 (Rfree = 0.000) for 10212 atoms. Found 77 (77 requested) and removed 75 (38 requested) atoms. Cycle 7: After refmac, R = 0.2022 (Rfree = 0.000) for 10127 atoms. Found 38 (77 requested) and removed 51 (38 requested) atoms. Cycle 8: After refmac, R = 0.1969 (Rfree = 0.000) for 10071 atoms. Found 32 (76 requested) and removed 48 (38 requested) atoms. Cycle 9: After refmac, R = 0.1893 (Rfree = 0.000) for 10034 atoms. Found 38 (75 requested) and removed 49 (37 requested) atoms. Cycle 10: After refmac, R = 0.1830 (Rfree = 0.000) for 10008 atoms. Found 26 (75 requested) and removed 44 (37 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 10300 seeds are put forward NCS extension: 8 residues added (8 deleted due to clashes), 10308 seeds are put forward Round 1: 756 peptides, 115 chains. Longest chain 41 peptides. Score 0.504 Round 2: 833 peptides, 106 chains. Longest chain 28 peptides. Score 0.606 Round 3: 856 peptides, 102 chains. Longest chain 30 peptides. Score 0.638 Round 4: 854 peptides, 108 chains. Longest chain 31 peptides. Score 0.616 Round 5: 848 peptides, 103 chains. Longest chain 27 peptides. Score 0.628 Taking the results from Round 3 Chains 105, Residues 754, Estimated correctness of the model 40.6 % 9 chains (120 residues) have been docked in sequence ------------------------------------------------------ 19863 reflections ( 98.93 % complete ) and 21832 restraints for refining 10211 atoms. 18476 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2033 (Rfree = 0.000) for 10211 atoms. Found 70 (77 requested) and removed 67 (38 requested) atoms. Cycle 12: After refmac, R = 0.1884 (Rfree = 0.000) for 10157 atoms. Found 41 (77 requested) and removed 49 (38 requested) atoms. Cycle 13: After refmac, R = 0.1819 (Rfree = 0.000) for 10123 atoms. Found 45 (76 requested) and removed 60 (38 requested) atoms. Cycle 14: After refmac, R = 0.1714 (Rfree = 0.000) for 10086 atoms. Found 32 (76 requested) and removed 54 (38 requested) atoms. Cycle 15: After refmac, R = 0.1678 (Rfree = 0.000) for 10053 atoms. Found 18 (75 requested) and removed 47 (37 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 10344 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 10374 seeds are put forward Round 1: 719 peptides, 111 chains. Longest chain 20 peptides. Score 0.485 Round 2: 828 peptides, 103 chains. Longest chain 28 peptides. Score 0.613 Round 3: 808 peptides, 109 chains. Longest chain 28 peptides. Score 0.575 Round 4: 821 peptides, 99 chains. Longest chain 19 peptides. Score 0.622 Round 5: 804 peptides, 108 chains. Longest chain 19 peptides. Score 0.575 Taking the results from Round 4 Chains 99, Residues 722, Estimated correctness of the model 35.7 % 5 chains (33 residues) have been docked in sequence ------------------------------------------------------ 19863 reflections ( 98.93 % complete ) and 22947 restraints for refining 10211 atoms. 20059 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2000 (Rfree = 0.000) for 10211 atoms. Found 57 (77 requested) and removed 53 (38 requested) atoms. Cycle 17: After refmac, R = 0.1832 (Rfree = 0.000) for 10186 atoms. Found 35 (77 requested) and removed 47 (38 requested) atoms. Cycle 18: After refmac, R = 0.1731 (Rfree = 0.000) for 10156 atoms. Found 43 (76 requested) and removed 40 (38 requested) atoms. Cycle 19: After refmac, R = 0.1712 (Rfree = 0.000) for 10143 atoms. Found 37 (76 requested) and removed 39 (38 requested) atoms. Cycle 20: After refmac, R = 0.1644 (Rfree = 0.000) for 10130 atoms. Found 25 (76 requested) and removed 40 (38 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 10469 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 10483 seeds are put forward Round 1: 711 peptides, 115 chains. Longest chain 28 peptides. Score 0.460 Round 2: 813 peptides, 105 chains. Longest chain 30 peptides. Score 0.594 Round 3: 810 peptides, 106 chains. Longest chain 20 peptides. Score 0.588 Round 4: 806 peptides, 97 chains. Longest chain 28 peptides. Score 0.617 Round 5: 803 peptides, 99 chains. Longest chain 23 peptides. Score 0.607 Taking the results from Round 4 Chains 99, Residues 709, Estimated correctness of the model 34.1 % 7 chains (61 residues) have been docked in sequence ------------------------------------------------------ 19863 reflections ( 98.93 % complete ) and 22601 restraints for refining 10212 atoms. 19654 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1916 (Rfree = 0.000) for 10212 atoms. Found 39 (77 requested) and removed 51 (38 requested) atoms. Cycle 22: After refmac, R = 0.1840 (Rfree = 0.000) for 10167 atoms. Found 30 (77 requested) and removed 47 (38 requested) atoms. Cycle 23: After refmac, R = 0.1756 (Rfree = 0.000) for 10137 atoms. Found 28 (76 requested) and removed 45 (38 requested) atoms. Cycle 24: After refmac, R = 0.1747 (Rfree = 0.000) for 10103 atoms. Found 33 (76 requested) and removed 45 (38 requested) atoms. Cycle 25: After refmac, R = 0.1712 (Rfree = 0.000) for 10077 atoms. Found 43 (76 requested) and removed 43 (38 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 10399 seeds are put forward NCS extension: 17 residues added (7 deleted due to clashes), 10416 seeds are put forward Round 1: 686 peptides, 115 chains. Longest chain 13 peptides. Score 0.435 Round 2: 761 peptides, 100 chains. Longest chain 23 peptides. Score 0.569 Round 3: 782 peptides, 98 chains. Longest chain 25 peptides. Score 0.594 Round 4: 784 peptides, 100 chains. Longest chain 32 peptides. Score 0.588 Round 5: 762 peptides, 103 chains. Longest chain 26 peptides. Score 0.558 Taking the results from Round 3 Chains 103, Residues 684, Estimated correctness of the model 26.7 % 8 chains (84 residues) have been docked in sequence ------------------------------------------------------ 19863 reflections ( 98.93 % complete ) and 22420 restraints for refining 10211 atoms. 19477 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1900 (Rfree = 0.000) for 10211 atoms. Found 50 (77 requested) and removed 59 (38 requested) atoms. Cycle 27: After refmac, R = 0.1925 (Rfree = 0.000) for 10174 atoms. Found 48 (77 requested) and removed 45 (38 requested) atoms. Cycle 28: After refmac, R = 0.1758 (Rfree = 0.000) for 10145 atoms. Found 42 (76 requested) and removed 46 (38 requested) atoms. Cycle 29: After refmac, R = 0.1711 (Rfree = 0.000) for 10127 atoms. Found 37 (76 requested) and removed 39 (38 requested) atoms. Cycle 30: After refmac, R = 0.1659 (Rfree = 0.000) for 10118 atoms. Found 28 (76 requested) and removed 43 (38 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 10421 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 10435 seeds are put forward Round 1: 672 peptides, 111 chains. Longest chain 21 peptides. Score 0.438 Round 2: 722 peptides, 99 chains. Longest chain 28 peptides. Score 0.538 Round 3: 740 peptides, 98 chains. Longest chain 19 peptides. Score 0.558 Round 4: 726 peptides, 95 chains. Longest chain 28 peptides. Score 0.558 Round 5: 726 peptides, 94 chains. Longest chain 23 peptides. Score 0.562 Taking the results from Round 5 Chains 97, Residues 632, Estimated correctness of the model 15.8 % 9 chains (78 residues) have been docked in sequence ------------------------------------------------------ 19863 reflections ( 98.93 % complete ) and 22766 restraints for refining 10213 atoms. 20059 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1922 (Rfree = 0.000) for 10213 atoms. Found 70 (77 requested) and removed 48 (38 requested) atoms. Cycle 32: After refmac, R = 0.1773 (Rfree = 0.000) for 10210 atoms. Found 36 (77 requested) and removed 38 (38 requested) atoms. Cycle 33: After refmac, R = 0.1717 (Rfree = 0.000) for 10183 atoms. Found 57 (77 requested) and removed 43 (38 requested) atoms. Cycle 34: After refmac, R = 0.1649 (Rfree = 0.000) for 10186 atoms. Found 38 (76 requested) and removed 46 (38 requested) atoms. Cycle 35: After refmac, R = 0.1581 (Rfree = 0.000) for 10164 atoms. Found 31 (76 requested) and removed 45 (38 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.32 3.41 Search for helices and strands: 0 residues in 0 chains, 10456 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 10477 seeds are put forward Round 1: 584 peptides, 102 chains. Longest chain 16 peptides. Score 0.385 Round 2: 646 peptides, 92 chains. Longest chain 19 peptides. Score 0.496 Round 3: 666 peptides, 92 chains. Longest chain 22 peptides. Score 0.515 Round 4: 667 peptides, 93 chains. Longest chain 18 peptides. Score 0.512 Round 5: 700 peptides, 95 chains. Longest chain 25 peptides. Score 0.534 Taking the results from Round 5 Chains 97, Residues 605, Estimated correctness of the model 5.7 % 8 chains (57 residues) have been docked in sequence ------------------------------------------------------ 19863 reflections ( 98.93 % complete ) and 23206 restraints for refining 10211 atoms. 20693 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1848 (Rfree = 0.000) for 10211 atoms. Found 74 (77 requested) and removed 47 (38 requested) atoms. Cycle 37: After refmac, R = 0.1727 (Rfree = 0.000) for 10211 atoms. Found 37 (77 requested) and removed 45 (38 requested) atoms. Cycle 38: After refmac, R = 0.1659 (Rfree = 0.000) for 10190 atoms. Found 43 (77 requested) and removed 44 (38 requested) atoms. Cycle 39: After refmac, R = 0.1614 (Rfree = 0.000) for 10174 atoms. Found 30 (76 requested) and removed 40 (38 requested) atoms. Cycle 40: After refmac, R = 0.1521 (Rfree = 0.000) for 10150 atoms. Found 34 (76 requested) and removed 42 (38 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 10428 seeds are put forward NCS extension: 13 residues added (6 deleted due to clashes), 10441 seeds are put forward Round 1: 585 peptides, 109 chains. Longest chain 17 peptides. Score 0.352 Round 2: 659 peptides, 95 chains. Longest chain 19 peptides. Score 0.495 Round 3: 655 peptides, 98 chains. Longest chain 24 peptides. Score 0.478 Round 4: 672 peptides, 96 chains. Longest chain 18 peptides. Score 0.504 Round 5: 659 peptides, 93 chains. Longest chain 24 peptides. Score 0.504 Taking the results from Round 5 Chains 95, Residues 566, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 19863 reflections ( 98.93 % complete ) and 23681 restraints for refining 10212 atoms. 21459 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1794 (Rfree = 0.000) for 10212 atoms. Found 56 (77 requested) and removed 43 (38 requested) atoms. Cycle 42: After refmac, R = 0.1733 (Rfree = 0.000) for 10209 atoms. Found 39 (77 requested) and removed 39 (38 requested) atoms. Cycle 43: After refmac, R = 0.1710 (Rfree = 0.000) for 10187 atoms. Found 57 (77 requested) and removed 41 (38 requested) atoms. Cycle 44: After refmac, R = 0.1636 (Rfree = 0.000) for 10191 atoms. Found 37 (77 requested) and removed 41 (38 requested) atoms. Cycle 45: After refmac, R = 0.1613 (Rfree = 0.000) for 10179 atoms. Found 42 (76 requested) and removed 40 (38 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 10443 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 10461 seeds are put forward Round 1: 503 peptides, 97 chains. Longest chain 11 peptides. Score 0.316 Round 2: 580 peptides, 86 chains. Longest chain 20 peptides. Score 0.456 Round 3: 584 peptides, 89 chains. Longest chain 24 peptides. Score 0.447 Round 4: 604 peptides, 89 chains. Longest chain 22 peptides. Score 0.467 Round 5: 606 peptides, 102 chains. Longest chain 18 peptides. Score 0.409 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 91, Residues 515, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vkn-3_warpNtrace.pdb as input Building loops using Loopy2018 91 chains (515 residues) following loop building 2 chains (18 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 19863 reflections ( 98.93 % complete ) and 24160 restraints for refining 10213 atoms. 22143 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1683 (Rfree = 0.000) for 10213 atoms. Found 0 (77 requested) and removed 38 (38 requested) atoms. Cycle 47: After refmac, R = 0.1683 (Rfree = 0.000) for 10153 atoms. Found 0 (76 requested) and removed 38 (38 requested) atoms. Cycle 48: After refmac, R = 0.1671 (Rfree = 0.000) for 10108 atoms. Found 0 (76 requested) and removed 38 (38 requested) atoms. Cycle 49: After refmac, R = 0.1633 (Rfree = 0.000) for 10059 atoms. Found 0 (76 requested) and removed 38 (38 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:56:12 GMT 2018 Job finished. TimeTaking 109.28 Used memory is bytes: 19923600