Mon 24 Dec 07:35:56 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-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkn-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkn-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.8-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-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.8-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 07:36:01 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-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.8-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 943 and 0 Target number of residues in the AU: 943 Target solvent content: 0.6523 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-3.8-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-3.8-parrot-noncs.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 3.800 Wilson plot Bfac: 79.66 14292 reflections ( 98.94 % complete ) and 0 restraints for refining 12520 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3165 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2979 (Rfree = 0.000) for 12520 atoms. Found 68 (68 requested) and removed 70 (34 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.65 3.75 Search for helices and strands: 0 residues in 0 chains, 12735 seeds are put forward NCS extension: 0 residues added, 12735 seeds are put forward Round 1: 531 peptides, 104 chains. Longest chain 14 peptides. Score 0.314 Round 2: 651 peptides, 102 chains. Longest chain 17 peptides. Score 0.457 Round 3: 684 peptides, 101 chains. Longest chain 22 peptides. Score 0.494 Round 4: 780 peptides, 99 chains. Longest chain 39 peptides. Score 0.589 Round 5: 775 peptides, 100 chains. Longest chain 22 peptides. Score 0.581 Taking the results from Round 4 Chains 100, Residues 681, Estimated correctness of the model 0.0 % 8 chains (69 residues) have been docked in sequence ------------------------------------------------------ 14292 reflections ( 98.94 % complete ) and 22838 restraints for refining 10159 atoms. 19988 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2356 (Rfree = 0.000) for 10159 atoms. Found 50 (55 requested) and removed 77 (27 requested) atoms. Cycle 2: After refmac, R = 0.2208 (Rfree = 0.000) for 9947 atoms. Found 44 (55 requested) and removed 61 (27 requested) atoms. Cycle 3: After refmac, R = 0.2140 (Rfree = 0.000) for 9822 atoms. Found 54 (54 requested) and removed 71 (27 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.1968 (Rfree = 0.000) for 9736 atoms. Found 52 (53 requested) and removed 41 (26 requested) atoms. Cycle 5: After refmac, R = 0.1957 (Rfree = 0.000) for 9704 atoms. Found 50 (53 requested) and removed 52 (26 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 10012 seeds are put forward NCS extension: 39 residues added (2 deleted due to clashes), 10051 seeds are put forward Round 1: 644 peptides, 111 chains. Longest chain 16 peptides. Score 0.408 Round 2: 727 peptides, 111 chains. Longest chain 18 peptides. Score 0.493 Round 3: 710 peptides, 101 chains. Longest chain 23 peptides. Score 0.519 Round 4: 716 peptides, 104 chains. Longest chain 17 peptides. Score 0.512 Round 5: 713 peptides, 90 chains. Longest chain 39 peptides. Score 0.566 Taking the results from Round 5 Chains 93, Residues 623, Estimated correctness of the model 0.0 % 4 chains (36 residues) have been docked in sequence ------------------------------------------------------ 14292 reflections ( 98.94 % complete ) and 23480 restraints for refining 10157 atoms. 20976 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2023 (Rfree = 0.000) for 10157 atoms. Found 48 (55 requested) and removed 63 (27 requested) atoms. Cycle 7: After refmac, R = 0.1863 (Rfree = 0.000) for 10068 atoms. Found 29 (55 requested) and removed 40 (27 requested) atoms. Cycle 8: After refmac, R = 0.1563 (Rfree = 0.000) for 10015 atoms. Found 8 (55 requested) and removed 43 (27 requested) atoms. Cycle 9: After refmac, R = 0.1603 (Rfree = 0.000) for 9949 atoms. Found 11 (54 requested) and removed 35 (27 requested) atoms. Cycle 10: After refmac, R = 0.1719 (Rfree = 0.000) for 9905 atoms. Found 54 (54 requested) and removed 43 (27 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 10184 seeds are put forward NCS extension: 44 residues added (3 deleted due to clashes), 10228 seeds are put forward Round 1: 629 peptides, 121 chains. Longest chain 11 peptides. Score 0.345 Round 2: 693 peptides, 110 chains. Longest chain 14 peptides. Score 0.464 Round 3: 686 peptides, 104 chains. Longest chain 22 peptides. Score 0.483 Round 4: 696 peptides, 104 chains. Longest chain 22 peptides. Score 0.493 Round 5: 705 peptides, 100 chains. Longest chain 22 peptides. Score 0.518 Taking the results from Round 5 Chains 103, Residues 605, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 14292 reflections ( 98.94 % complete ) and 23479 restraints for refining 10159 atoms. 21075 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1963 (Rfree = 0.000) for 10159 atoms. Found 48 (55 requested) and removed 65 (27 requested) atoms. Cycle 12: After refmac, R = 0.1818 (Rfree = 0.000) for 10059 atoms. Found 53 (55 requested) and removed 43 (27 requested) atoms. Cycle 13: After refmac, R = 0.1725 (Rfree = 0.000) for 10032 atoms. Found 48 (55 requested) and removed 40 (27 requested) atoms. Cycle 14: After refmac, R = 0.1767 (Rfree = 0.000) for 10007 atoms. Found 47 (55 requested) and removed 52 (27 requested) atoms. Cycle 15: After refmac, R = 0.1742 (Rfree = 0.000) for 9981 atoms. Found 55 (55 requested) and removed 45 (27 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.60 3.70 Search for helices and strands: 0 residues in 0 chains, 10300 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 10316 seeds are put forward Round 1: 601 peptides, 112 chains. Longest chain 12 peptides. Score 0.356 Round 2: 670 peptides, 106 chains. Longest chain 24 peptides. Score 0.458 Round 3: 686 peptides, 106 chains. Longest chain 15 peptides. Score 0.474 Round 4: 662 peptides, 99 chains. Longest chain 16 peptides. Score 0.481 Round 5: 673 peptides, 99 chains. Longest chain 17 peptides. Score 0.492 Taking the results from Round 5 Chains 99, Residues 574, Estimated correctness of the model 0.0 % 6 chains (23 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 14292 reflections ( 98.94 % complete ) and 23759 restraints for refining 10158 atoms. 21512 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1954 (Rfree = 0.000) for 10158 atoms. Found 55 (55 requested) and removed 53 (27 requested) atoms. Cycle 17: After refmac, R = 0.1746 (Rfree = 0.000) for 10088 atoms. Found 55 (55 requested) and removed 49 (27 requested) atoms. Cycle 18: After refmac, R = 0.1667 (Rfree = 0.000) for 10053 atoms. Found 48 (55 requested) and removed 43 (27 requested) atoms. Cycle 19: After refmac, R = 0.1677 (Rfree = 0.000) for 10028 atoms. Found 55 (55 requested) and removed 45 (27 requested) atoms. Cycle 20: After refmac, R = 0.1346 (Rfree = 0.000) for 10018 atoms. Found 16 (55 requested) and removed 33 (27 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.65 3.75 Search for helices and strands: 0 residues in 0 chains, 10278 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 10292 seeds are put forward Round 1: 556 peptides, 114 chains. Longest chain 10 peptides. Score 0.294 Round 2: 666 peptides, 109 chains. Longest chain 16 peptides. Score 0.441 Round 3: 683 peptides, 106 chains. Longest chain 15 peptides. Score 0.471 Round 4: 659 peptides, 101 chains. Longest chain 24 peptides. Score 0.469 Round 5: 682 peptides, 101 chains. Longest chain 16 peptides. Score 0.492 Taking the results from Round 5 Chains 102, Residues 581, Estimated correctness of the model 0.0 % 6 chains (35 residues) have been docked in sequence ------------------------------------------------------ 14292 reflections ( 98.94 % complete ) and 23471 restraints for refining 10157 atoms. 21141 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1892 (Rfree = 0.000) for 10157 atoms. Found 52 (55 requested) and removed 50 (27 requested) atoms. Cycle 22: After refmac, R = 0.1782 (Rfree = 0.000) for 10084 atoms. Found 50 (55 requested) and removed 43 (27 requested) atoms. Cycle 23: After refmac, R = 0.1707 (Rfree = 0.000) for 10049 atoms. Found 38 (55 requested) and removed 42 (27 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1653 (Rfree = 0.000) for 10016 atoms. Found 44 (55 requested) and removed 39 (27 requested) atoms. Cycle 25: After refmac, R = 0.1595 (Rfree = 0.000) for 10007 atoms. Found 37 (55 requested) and removed 35 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.61 3.71 Search for helices and strands: 0 residues in 0 chains, 10296 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 10315 seeds are put forward Round 1: 577 peptides, 116 chains. Longest chain 13 peptides. Score 0.309 Round 2: 635 peptides, 108 chains. Longest chain 16 peptides. Score 0.413 Round 3: 628 peptides, 101 chains. Longest chain 16 peptides. Score 0.437 Round 4: 630 peptides, 99 chains. Longest chain 22 peptides. Score 0.449 Round 5: 640 peptides, 106 chains. Longest chain 16 peptides. Score 0.427 Taking the results from Round 4 Chains 100, Residues 531, Estimated correctness of the model 0.0 % 4 chains (31 residues) have been docked in sequence ------------------------------------------------------ 14292 reflections ( 98.94 % complete ) and 23694 restraints for refining 10160 atoms. 21571 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1982 (Rfree = 0.000) for 10160 atoms. Found 55 (55 requested) and removed 54 (27 requested) atoms. Cycle 27: After refmac, R = 0.1796 (Rfree = 0.000) for 10103 atoms. Found 55 (55 requested) and removed 43 (27 requested) atoms. Cycle 28: After refmac, R = 0.1702 (Rfree = 0.000) for 10076 atoms. Found 55 (55 requested) and removed 38 (27 requested) atoms. Cycle 29: After refmac, R = 0.1330 (Rfree = 0.000) for 10068 atoms. Found 13 (55 requested) and removed 30 (27 requested) atoms. Cycle 30: After refmac, R = 0.1263 (Rfree = 0.000) for 10037 atoms. Found 18 (55 requested) and removed 33 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.66 3.76 Search for helices and strands: 0 residues in 0 chains, 10271 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 10291 seeds are put forward Round 1: 560 peptides, 118 chains. Longest chain 10 peptides. Score 0.278 Round 2: 616 peptides, 108 chains. Longest chain 15 peptides. Score 0.392 Round 3: 598 peptides, 105 chains. Longest chain 16 peptides. Score 0.386 Round 4: 602 peptides, 102 chains. Longest chain 18 peptides. Score 0.405 Round 5: 591 peptides, 103 chains. Longest chain 12 peptides. Score 0.388 Taking the results from Round 4 Chains 103, Residues 500, Estimated correctness of the model 0.0 % 5 chains (29 residues) have been docked in sequence ------------------------------------------------------ 14292 reflections ( 98.94 % complete ) and 23970 restraints for refining 10159 atoms. 21993 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1859 (Rfree = 0.000) for 10159 atoms. Found 52 (55 requested) and removed 51 (27 requested) atoms. Cycle 32: After refmac, R = 0.1856 (Rfree = 0.000) for 10109 atoms. Found 55 (55 requested) and removed 45 (27 requested) atoms. Cycle 33: After refmac, R = 0.1700 (Rfree = 0.000) for 10085 atoms. Found 54 (55 requested) and removed 40 (27 requested) atoms. Cycle 34: After refmac, R = 0.1636 (Rfree = 0.000) for 10063 atoms. Found 55 (55 requested) and removed 36 (27 requested) atoms. Cycle 35: After refmac, R = 0.1569 (Rfree = 0.000) for 10071 atoms. Found 55 (55 requested) and removed 39 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.63 3.73 Search for helices and strands: 0 residues in 0 chains, 10378 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 10398 seeds are put forward Round 1: 449 peptides, 98 chains. Longest chain 12 peptides. Score 0.243 Round 2: 520 peptides, 98 chains. Longest chain 12 peptides. Score 0.331 Round 3: 533 peptides, 95 chains. Longest chain 17 peptides. Score 0.361 Round 4: 515 peptides, 94 chains. Longest chain 13 peptides. Score 0.346 Round 5: 563 peptides, 90 chains. Longest chain 21 peptides. Score 0.419 Taking the results from Round 5 Chains 91, Residues 473, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 14292 reflections ( 98.94 % complete ) and 24206 restraints for refining 10159 atoms. 22339 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1762 (Rfree = 0.000) for 10159 atoms. Found 52 (55 requested) and removed 49 (27 requested) atoms. Cycle 37: After refmac, R = 0.1674 (Rfree = 0.000) for 10096 atoms. Found 55 (55 requested) and removed 41 (27 requested) atoms. Cycle 38: After refmac, R = 0.1700 (Rfree = 0.000) for 10086 atoms. Found 55 (55 requested) and removed 40 (27 requested) atoms. Cycle 39: After refmac, R = 0.1656 (Rfree = 0.000) for 10082 atoms. Found 55 (55 requested) and removed 36 (27 requested) atoms. Cycle 40: After refmac, R = 0.1664 (Rfree = 0.000) for 10075 atoms. Found 55 (55 requested) and removed 36 (27 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.62 3.72 Search for helices and strands: 0 residues in 0 chains, 10387 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 10408 seeds are put forward Round 1: 434 peptides, 95 chains. Longest chain 8 peptides. Score 0.240 Round 2: 528 peptides, 98 chains. Longest chain 19 peptides. Score 0.341 Round 3: 482 peptides, 89 chains. Longest chain 13 peptides. Score 0.332 Round 4: 511 peptides, 92 chains. Longest chain 15 peptides. Score 0.351 Round 5: 500 peptides, 88 chains. Longest chain 13 peptides. Score 0.358 Taking the results from Round 5 Chains 90, Residues 412, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 14292 reflections ( 98.94 % complete ) and 24473 restraints for refining 10160 atoms. 22827 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1808 (Rfree = 0.000) for 10160 atoms. Found 55 (55 requested) and removed 42 (27 requested) atoms. Cycle 42: After refmac, R = 0.1735 (Rfree = 0.000) for 10132 atoms. Found 55 (55 requested) and removed 39 (27 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1698 (Rfree = 0.000) for 10128 atoms. Found 55 (55 requested) and removed 37 (27 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1284 (Rfree = 0.000) for 10133 atoms. Found 13 (55 requested) and removed 30 (27 requested) atoms. Cycle 45: After refmac, R = 0.1236 (Rfree = 0.000) for 10110 atoms. Found 15 (55 requested) and removed 30 (27 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.63 3.73 Search for helices and strands: 0 residues in 0 chains, 10337 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 10356 seeds are put forward Round 1: 393 peptides, 82 chains. Longest chain 8 peptides. Score 0.258 Round 2: 403 peptides, 78 chains. Longest chain 16 peptides. Score 0.293 Round 3: 432 peptides, 76 chains. Longest chain 13 peptides. Score 0.340 Round 4: 430 peptides, 74 chains. Longest chain 16 peptides. Score 0.348 Round 5: 423 peptides, 76 chains. Longest chain 16 peptides. Score 0.329 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 74, Residues 356, Estimated correctness of the model 0.0 % 6 chains (24 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 1vkn-3_warpNtrace.pdb as input Building loops using Loopy2018 74 chains (356 residues) following loop building 6 chains (24 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14292 reflections ( 98.94 % complete ) and 24886 restraints for refining 10159 atoms. 23465 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1663 (Rfree = 0.000) for 10159 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 47: After refmac, R = 0.1775 (Rfree = 0.000) for 10098 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 48: After refmac, R = 0.1655 (Rfree = 0.000) for 10057 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 49: After refmac, R = 0.1684 (Rfree = 0.000) for 10016 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Writing output files ... TimeTaking 107.92