null Mon 24 Dec 07:38:42 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-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkn-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkn-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.6-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-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.6-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 07:38:47 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-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.6-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 974 and 0 Target number of residues in the AU: 974 Target solvent content: 0.6408 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-3.6-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-3.6-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 3.600 Wilson plot Bfac: 72.40 16761 reflections ( 98.94 % complete ) and 0 restraints for refining 12448 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3109 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2694 (Rfree = 0.000) for 12448 atoms. Found 79 (79 requested) and removed 80 (39 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 3.54 Search for helices and strands: 0 residues in 0 chains, 12692 seeds are put forward NCS extension: 0 residues added, 12692 seeds are put forward Round 1: 610 peptides, 111 chains. Longest chain 11 peptides. Score 0.371 Round 2: 758 peptides, 114 chains. Longest chain 20 peptides. Score 0.510 Round 3: 783 peptides, 104 chains. Longest chain 25 peptides. Score 0.572 Round 4: 809 peptides, 96 chains. Longest chain 41 peptides. Score 0.623 Round 5: 806 peptides, 94 chains. Longest chain 32 peptides. Score 0.628 Taking the results from Round 5 Chains 96, Residues 712, Estimated correctness of the model 25.3 % 5 chains (54 residues) have been docked in sequence ------------------------------------------------------ 16761 reflections ( 98.94 % complete ) and 22734 restraints for refining 10177 atoms. 19803 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2164 (Rfree = 0.000) for 10177 atoms. Found 49 (65 requested) and removed 61 (32 requested) atoms. Cycle 2: After refmac, R = 0.2003 (Rfree = 0.000) for 9962 atoms. Found 44 (65 requested) and removed 46 (32 requested) atoms. Cycle 3: After refmac, R = 0.1928 (Rfree = 0.000) for 9889 atoms. Found 34 (63 requested) and removed 43 (31 requested) atoms. Cycle 4: After refmac, R = 0.1825 (Rfree = 0.000) for 9840 atoms. Found 41 (63 requested) and removed 40 (31 requested) atoms. Cycle 5: After refmac, R = 0.1788 (Rfree = 0.000) for 9814 atoms. Found 37 (63 requested) and removed 44 (31 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 3.55 Search for helices and strands: 0 residues in 0 chains, 10098 seeds are put forward NCS extension: 19 residues added (16 deleted due to clashes), 10117 seeds are put forward Round 1: 711 peptides, 118 chains. Longest chain 18 peptides. Score 0.447 Round 2: 789 peptides, 106 chains. Longest chain 26 peptides. Score 0.570 Round 3: 784 peptides, 100 chains. Longest chain 38 peptides. Score 0.588 Round 4: 801 peptides, 97 chains. Longest chain 23 peptides. Score 0.613 Round 5: 766 peptides, 99 chains. Longest chain 26 peptides. Score 0.577 Taking the results from Round 4 Chains 98, Residues 704, Estimated correctness of the model 19.7 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 16761 reflections ( 98.94 % complete ) and 22969 restraints for refining 10036 atoms. 20174 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1970 (Rfree = 0.000) for 10036 atoms. Found 39 (64 requested) and removed 64 (32 requested) atoms. Cycle 7: After refmac, R = 0.1893 (Rfree = 0.000) for 9944 atoms. Found 52 (64 requested) and removed 59 (32 requested) atoms. Cycle 8: After refmac, R = 0.1747 (Rfree = 0.000) for 9904 atoms. Found 34 (63 requested) and removed 45 (31 requested) atoms. Cycle 9: After refmac, R = 0.1679 (Rfree = 0.000) for 9868 atoms. Found 40 (63 requested) and removed 41 (31 requested) atoms. Cycle 10: After refmac, R = 0.1647 (Rfree = 0.000) for 9844 atoms. Found 33 (63 requested) and removed 39 (31 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.44 3.53 Search for helices and strands: 0 residues in 0 chains, 10196 seeds are put forward NCS extension: 36 residues added (3 deleted due to clashes), 10232 seeds are put forward Round 1: 706 peptides, 119 chains. Longest chain 25 peptides. Score 0.438 Round 2: 760 peptides, 99 chains. Longest chain 26 peptides. Score 0.572 Round 3: 789 peptides, 104 chains. Longest chain 19 peptides. Score 0.577 Round 4: 790 peptides, 104 chains. Longest chain 34 peptides. Score 0.578 Round 5: 808 peptides, 100 chains. Longest chain 34 peptides. Score 0.608 Taking the results from Round 5 Chains 104, Residues 708, Estimated correctness of the model 17.8 % 6 chains (73 residues) have been docked in sequence ------------------------------------------------------ 16761 reflections ( 98.94 % complete ) and 22435 restraints for refining 10181 atoms. 19461 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1903 (Rfree = 0.000) for 10181 atoms. Found 45 (65 requested) and removed 97 (32 requested) atoms. Cycle 12: After refmac, R = 0.1702 (Rfree = 0.000) for 10058 atoms. Found 25 (64 requested) and removed 41 (32 requested) atoms. Cycle 13: After refmac, R = 0.1679 (Rfree = 0.000) for 10022 atoms. Found 25 (64 requested) and removed 43 (32 requested) atoms. Cycle 14: After refmac, R = 0.1669 (Rfree = 0.000) for 9987 atoms. Found 26 (64 requested) and removed 41 (32 requested) atoms. Cycle 15: After refmac, R = 0.1642 (Rfree = 0.000) for 9958 atoms. Found 21 (63 requested) and removed 41 (31 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 10263 seeds are put forward NCS extension: 23 residues added (9 deleted due to clashes), 10286 seeds are put forward Round 1: 675 peptides, 118 chains. Longest chain 15 peptides. Score 0.409 Round 2: 748 peptides, 105 chains. Longest chain 24 peptides. Score 0.538 Round 3: 740 peptides, 93 chains. Longest chain 28 peptides. Score 0.578 Round 4: 756 peptides, 98 chains. Longest chain 17 peptides. Score 0.572 Round 5: 792 peptides, 103 chains. Longest chain 24 peptides. Score 0.584 Taking the results from Round 5 Chains 105, Residues 689, Estimated correctness of the model 8.3 % 8 chains (60 residues) have been docked in sequence ------------------------------------------------------ 16761 reflections ( 98.94 % complete ) and 22954 restraints for refining 10180 atoms. 20124 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1932 (Rfree = 0.000) for 10180 atoms. Found 50 (65 requested) and removed 57 (32 requested) atoms. Cycle 17: After refmac, R = 0.1761 (Rfree = 0.000) for 10105 atoms. Found 32 (65 requested) and removed 45 (32 requested) atoms. Cycle 18: After refmac, R = 0.1646 (Rfree = 0.000) for 10067 atoms. Found 22 (64 requested) and removed 42 (32 requested) atoms. Cycle 19: After refmac, R = 0.1596 (Rfree = 0.000) for 10025 atoms. Found 27 (64 requested) and removed 42 (32 requested) atoms. Cycle 20: After refmac, R = 0.1566 (Rfree = 0.000) for 9991 atoms. Found 33 (64 requested) and removed 35 (32 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 10298 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 10323 seeds are put forward Round 1: 637 peptides, 108 chains. Longest chain 17 peptides. Score 0.415 Round 2: 697 peptides, 98 chains. Longest chain 19 peptides. Score 0.519 Round 3: 706 peptides, 103 chains. Longest chain 25 peptides. Score 0.507 Round 4: 694 peptides, 91 chains. Longest chain 21 peptides. Score 0.545 Round 5: 716 peptides, 98 chains. Longest chain 20 peptides. Score 0.537 Taking the results from Round 4 Chains 93, Residues 603, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 16761 reflections ( 98.94 % complete ) and 23864 restraints for refining 10179 atoms. 21497 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1889 (Rfree = 0.000) for 10179 atoms. Found 54 (65 requested) and removed 40 (32 requested) atoms. Cycle 22: After refmac, R = 0.1771 (Rfree = 0.000) for 10149 atoms. Found 39 (65 requested) and removed 40 (32 requested) atoms. Cycle 23: After refmac, R = 0.1747 (Rfree = 0.000) for 10124 atoms. Found 38 (65 requested) and removed 41 (32 requested) atoms. Cycle 24: After refmac, R = 0.1642 (Rfree = 0.000) for 10094 atoms. Found 29 (64 requested) and removed 35 (32 requested) atoms. Cycle 25: After refmac, R = 0.1602 (Rfree = 0.000) for 10073 atoms. Found 33 (64 requested) and removed 33 (32 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 3.54 Search for helices and strands: 0 residues in 0 chains, 10383 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 10398 seeds are put forward Round 1: 634 peptides, 112 chains. Longest chain 18 peptides. Score 0.393 Round 2: 718 peptides, 105 chains. Longest chain 23 peptides. Score 0.510 Round 3: 676 peptides, 97 chains. Longest chain 24 peptides. Score 0.503 Round 4: 714 peptides, 100 chains. Longest chain 20 peptides. Score 0.527 Round 5: 692 peptides, 103 chains. Longest chain 18 peptides. Score 0.493 Taking the results from Round 4 Chains 101, Residues 614, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 16761 reflections ( 98.94 % complete ) and 23834 restraints for refining 10182 atoms. 21439 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1780 (Rfree = 0.000) for 10182 atoms. Found 35 (65 requested) and removed 42 (32 requested) atoms. Cycle 27: After refmac, R = 0.1684 (Rfree = 0.000) for 10139 atoms. Found 29 (65 requested) and removed 35 (32 requested) atoms. Cycle 28: After refmac, R = 0.1610 (Rfree = 0.000) for 10103 atoms. Found 30 (65 requested) and removed 39 (32 requested) atoms. Cycle 29: After refmac, R = 0.1581 (Rfree = 0.000) for 10079 atoms. Found 34 (64 requested) and removed 41 (32 requested) atoms. Cycle 30: After refmac, R = 0.1541 (Rfree = 0.000) for 10068 atoms. Found 26 (64 requested) and removed 39 (32 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.42 3.51 Search for helices and strands: 0 residues in 0 chains, 10333 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 10353 seeds are put forward Round 1: 625 peptides, 109 chains. Longest chain 20 peptides. Score 0.397 Round 2: 676 peptides, 100 chains. Longest chain 19 peptides. Score 0.490 Round 3: 672 peptides, 94 chains. Longest chain 43 peptides. Score 0.512 Round 4: 679 peptides, 103 chains. Longest chain 27 peptides. Score 0.480 Round 5: 693 peptides, 96 chains. Longest chain 26 peptides. Score 0.524 Taking the results from Round 5 Chains 100, Residues 597, Estimated correctness of the model 0.0 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 16761 reflections ( 98.94 % complete ) and 23679 restraints for refining 10181 atoms. 21303 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1806 (Rfree = 0.000) for 10181 atoms. Found 49 (65 requested) and removed 43 (32 requested) atoms. Cycle 32: After refmac, R = 0.1662 (Rfree = 0.000) for 10158 atoms. Found 27 (65 requested) and removed 36 (32 requested) atoms. Cycle 33: After refmac, R = 0.1557 (Rfree = 0.000) for 10122 atoms. Found 28 (65 requested) and removed 34 (32 requested) atoms. Cycle 34: After refmac, R = 0.1497 (Rfree = 0.000) for 10096 atoms. Found 28 (64 requested) and removed 35 (32 requested) atoms. Cycle 35: After refmac, R = 0.1510 (Rfree = 0.000) for 10079 atoms. Found 30 (64 requested) and removed 37 (32 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 10379 seeds are put forward NCS extension: 21 residues added (4 deleted due to clashes), 10400 seeds are put forward Round 1: 570 peptides, 107 chains. Longest chain 13 peptides. Score 0.345 Round 2: 657 peptides, 107 chains. Longest chain 19 peptides. Score 0.440 Round 3: 645 peptides, 107 chains. Longest chain 14 peptides. Score 0.428 Round 4: 655 peptides, 108 chains. Longest chain 16 peptides. Score 0.434 Round 5: 647 peptides, 103 chains. Longest chain 15 peptides. Score 0.448 Taking the results from Round 5 Chains 103, Residues 544, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 16761 reflections ( 98.94 % complete ) and 23908 restraints for refining 10179 atoms. 21774 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1757 (Rfree = 0.000) for 10179 atoms. Found 45 (65 requested) and removed 43 (32 requested) atoms. Cycle 37: After refmac, R = 0.1652 (Rfree = 0.000) for 10144 atoms. Found 60 (65 requested) and removed 39 (32 requested) atoms. Cycle 38: After refmac, R = 0.1582 (Rfree = 0.000) for 10141 atoms. Found 38 (65 requested) and removed 35 (32 requested) atoms. Cycle 39: After refmac, R = 0.1527 (Rfree = 0.000) for 10133 atoms. Found 39 (65 requested) and removed 37 (32 requested) atoms. Cycle 40: After refmac, R = 0.1471 (Rfree = 0.000) for 10125 atoms. Found 33 (65 requested) and removed 36 (32 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.41 3.50 Search for helices and strands: 0 residues in 0 chains, 10421 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 10441 seeds are put forward Round 1: 525 peptides, 104 chains. Longest chain 11 peptides. Score 0.307 Round 2: 576 peptides, 95 chains. Longest chain 13 peptides. Score 0.410 Round 3: 592 peptides, 100 chains. Longest chain 13 peptides. Score 0.403 Round 4: 599 peptides, 97 chains. Longest chain 16 peptides. Score 0.425 Round 5: 579 peptides, 91 chains. Longest chain 13 peptides. Score 0.432 Taking the results from Round 5 Chains 91, Residues 488, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 16761 reflections ( 98.94 % complete ) and 24175 restraints for refining 10180 atoms. 22262 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1784 (Rfree = 0.000) for 10180 atoms. Found 52 (65 requested) and removed 43 (32 requested) atoms. Cycle 42: After refmac, R = 0.1677 (Rfree = 0.000) for 10161 atoms. Found 65 (65 requested) and removed 40 (32 requested) atoms. Cycle 43: After refmac, R = 0.1540 (Rfree = 0.000) for 10168 atoms. Found 31 (65 requested) and removed 38 (32 requested) atoms. Cycle 44: After refmac, R = 0.1504 (Rfree = 0.000) for 10138 atoms. Found 35 (65 requested) and removed 35 (32 requested) atoms. Cycle 45: After refmac, R = 0.1434 (Rfree = 0.000) for 10127 atoms. Found 21 (65 requested) and removed 39 (32 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 3.51 Search for helices and strands: 0 residues in 0 chains, 10391 seeds are put forward NCS extension: 14 residues added (4 deleted due to clashes), 10405 seeds are put forward Round 1: 463 peptides, 93 chains. Longest chain 10 peptides. Score 0.288 Round 2: 545 peptides, 96 chains. Longest chain 13 peptides. Score 0.370 Round 3: 554 peptides, 93 chains. Longest chain 18 peptides. Score 0.395 Round 4: 549 peptides, 89 chains. Longest chain 16 peptides. Score 0.409 Round 5: 544 peptides, 87 chains. Longest chain 14 peptides. Score 0.413 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 88, Residues 457, Estimated correctness of the model 0.0 % 6 chains (29 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 Built loop between residues 21 A and 35 A 86 chains (468 residues) following loop building 5 chains (42 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16761 reflections ( 98.94 % complete ) and 23847 restraints for refining 10182 atoms. 21938 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1740 (Rfree = 0.000) for 10182 atoms. Found 0 (65 requested) and removed 32 (32 requested) atoms. Cycle 47: After refmac, R = 0.1642 (Rfree = 0.000) for 10122 atoms. Found 0 (65 requested) and removed 32 (32 requested) atoms. Cycle 48: After refmac, R = 0.1612 (Rfree = 0.000) for 10069 atoms. Found 0 (64 requested) and removed 32 (32 requested) atoms. Cycle 49: After refmac, R = 0.1574 (Rfree = 0.000) for 10024 atoms. Found 0 (64 requested) and removed 32 (32 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:33:41 GMT 2018 Job finished. TimeTaking 114.98 Used memory is bytes: 13714120