null Mon 24 Dec 00:57:50 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 1o6a-1.9-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1o6a-1.9-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1o6a-1.9-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1o6a-1.9-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/1o6a-1.9-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1o6a-1.9-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 00:57:54 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/1o6a-1.9-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1o6a-1.9-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 208 and 0 Target number of residues in the AU: 208 Target solvent content: 0.4772 Checking the provided sequence file Detected sequence length: 96 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 192 Adjusted target solvent content: 0.52 Input MTZ file: 1o6a-1.9-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: 92 Cell parameters: 61.652 61.652 113.295 90.000 90.000 90.000 Input sequence file: 1o6a-1.9-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1536 target number of atoms Had to go as low as 0.45 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 1 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: 41.713 1.900 Wilson plot Bfac: 18.79 17921 reflections ( 99.98 % complete ) and 0 restraints for refining 1699 atoms. Observations/parameters ratio is 2.64 ------------------------------------------------------ Starting model: R = 0.3759 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3228 (Rfree = 0.000) for 1699 atoms. Found 49 (67 requested) and removed 37 (33 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.96 1.91 NCS extension: 0 residues added, 1711 seeds are put forward Round 1: 137 peptides, 10 chains. Longest chain 37 peptides. Score 0.784 Round 2: 148 peptides, 5 chains. Longest chain 51 peptides. Score 0.882 Round 3: 154 peptides, 5 chains. Longest chain 80 peptides. Score 0.893 Round 4: 158 peptides, 2 chains. Longest chain 80 peptides. Score 0.928 Round 5: 155 peptides, 5 chains. Longest chain 51 peptides. Score 0.895 Taking the results from Round 4 Chains 2, Residues 156, Estimated correctness of the model 99.5 % 2 chains (156 residues) have been docked in sequence Building loops using Loopy2018 2 chains (156 residues) following loop building 2 chains (156 residues) in sequence following loop building ------------------------------------------------------ 17921 reflections ( 99.98 % complete ) and 1500 restraints for refining 1503 atoms. 268 conditional restraints added. Observations/parameters ratio is 2.98 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3457 (Rfree = 0.000) for 1503 atoms. Found 41 (59 requested) and removed 36 (29 requested) atoms. Cycle 2: After refmac, R = 0.3176 (Rfree = 0.000) for 1505 atoms. Found 18 (58 requested) and removed 29 (29 requested) atoms. Cycle 3: After refmac, R = 0.3009 (Rfree = 0.000) for 1491 atoms. Found 25 (57 requested) and removed 10 (29 requested) atoms. Cycle 4: After refmac, R = 0.2906 (Rfree = 0.000) for 1502 atoms. Found 14 (57 requested) and removed 11 (29 requested) atoms. Cycle 5: After refmac, R = 0.2851 (Rfree = 0.000) for 1504 atoms. Found 15 (55 requested) and removed 13 (29 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.93 1.88 NCS extension: 0 residues added, 1507 seeds are put forward Round 1: 157 peptides, 3 chains. Longest chain 79 peptides. Score 0.918 Round 2: 159 peptides, 3 chains. Longest chain 79 peptides. Score 0.920 Round 3: 157 peptides, 3 chains. Longest chain 79 peptides. Score 0.918 Round 4: 158 peptides, 3 chains. Longest chain 80 peptides. Score 0.919 Round 5: 157 peptides, 3 chains. Longest chain 79 peptides. Score 0.918 Taking the results from Round 2 Chains 4, Residues 156, Estimated correctness of the model 99.4 % 3 chains (155 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 34 B and 37 B 3 chains (158 residues) following loop building 2 chains (157 residues) in sequence following loop building ------------------------------------------------------ 17921 reflections ( 99.98 % complete ) and 1464 restraints for refining 1503 atoms. 221 conditional restraints added. Observations/parameters ratio is 2.98 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2934 (Rfree = 0.000) for 1503 atoms. Found 37 (54 requested) and removed 31 (29 requested) atoms. Cycle 7: After refmac, R = 0.2880 (Rfree = 0.000) for 1506 atoms. Found 18 (53 requested) and removed 17 (29 requested) atoms. Cycle 8: After refmac, R = 0.2830 (Rfree = 0.000) for 1507 atoms. Found 19 (52 requested) and removed 9 (29 requested) atoms. Cycle 9: After refmac, R = 0.2804 (Rfree = 0.000) for 1516 atoms. Found 9 (53 requested) and removed 12 (30 requested) atoms. Cycle 10: After refmac, R = 0.2758 (Rfree = 0.000) for 1512 atoms. Found 11 (51 requested) and removed 6 (29 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.93 1.88 NCS extension: 0 residues added, 1517 seeds are put forward Round 1: 157 peptides, 4 chains. Longest chain 57 peptides. Score 0.908 Round 2: 159 peptides, 3 chains. Longest chain 81 peptides. Score 0.920 Round 3: 157 peptides, 5 chains. Longest chain 57 peptides. Score 0.898 Round 4: 158 peptides, 2 chains. Longest chain 81 peptides. Score 0.928 Round 5: 158 peptides, 3 chains. Longest chain 79 peptides. Score 0.919 Taking the results from Round 4 Chains 3, Residues 156, Estimated correctness of the model 99.5 % 2 chains (155 residues) have been docked in sequence Building loops using Loopy2018 3 chains (156 residues) following loop building 2 chains (155 residues) in sequence following loop building ------------------------------------------------------ 17921 reflections ( 99.98 % complete ) and 1480 restraints for refining 1503 atoms. 253 conditional restraints added. Observations/parameters ratio is 2.98 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2825 (Rfree = 0.000) for 1503 atoms. Found 36 (50 requested) and removed 31 (29 requested) atoms. Cycle 12: After refmac, R = 0.2835 (Rfree = 0.000) for 1506 atoms. Found 10 (48 requested) and removed 12 (29 requested) atoms. Cycle 13: After refmac, R = 0.2761 (Rfree = 0.000) for 1503 atoms. Found 15 (47 requested) and removed 6 (29 requested) atoms. Cycle 14: After refmac, R = 0.2748 (Rfree = 0.000) for 1510 atoms. Found 11 (47 requested) and removed 13 (29 requested) atoms. Cycle 15: After refmac, R = 0.2726 (Rfree = 0.000) for 1507 atoms. Found 14 (46 requested) and removed 7 (29 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.92 1.87 NCS extension: 1 residues added (2 deleted due to clashes), 1515 seeds are put forward Round 1: 157 peptides, 3 chains. Longest chain 79 peptides. Score 0.918 Round 2: 160 peptides, 2 chains. Longest chain 81 peptides. Score 0.931 Round 3: 156 peptides, 3 chains. Longest chain 78 peptides. Score 0.916 Round 4: 159 peptides, 2 chains. Longest chain 80 peptides. Score 0.930 Round 5: 157 peptides, 3 chains. Longest chain 79 peptides. Score 0.918 Taking the results from Round 2 Chains 3, Residues 158, Estimated correctness of the model 99.5 % 2 chains (157 residues) have been docked in sequence Building loops using Loopy2018 3 chains (158 residues) following loop building 2 chains (157 residues) in sequence following loop building ------------------------------------------------------ 17921 reflections ( 99.98 % complete ) and 1440 restraints for refining 1503 atoms. 197 conditional restraints added. Observations/parameters ratio is 2.98 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2800 (Rfree = 0.000) for 1503 atoms. Found 32 (46 requested) and removed 29 (29 requested) atoms. Cycle 17: After refmac, R = 0.2780 (Rfree = 0.000) for 1504 atoms. Found 20 (45 requested) and removed 22 (29 requested) atoms. Cycle 18: After refmac, R = 0.2742 (Rfree = 0.000) for 1502 atoms. Found 21 (44 requested) and removed 13 (29 requested) atoms. Cycle 19: After refmac, R = 0.2741 (Rfree = 0.000) for 1510 atoms. Found 22 (42 requested) and removed 12 (29 requested) atoms. Cycle 20: After refmac, R = 0.2736 (Rfree = 0.000) for 1518 atoms. Found 14 (42 requested) and removed 15 (30 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.93 1.88 NCS extension: 0 residues added, 1517 seeds are put forward Round 1: 157 peptides, 3 chains. Longest chain 79 peptides. Score 0.918 Round 2: 159 peptides, 2 chains. Longest chain 80 peptides. Score 0.930 Round 3: 157 peptides, 4 chains. Longest chain 79 peptides. Score 0.908 Round 4: 157 peptides, 2 chains. Longest chain 80 peptides. Score 0.927 Round 5: 157 peptides, 3 chains. Longest chain 79 peptides. Score 0.918 Taking the results from Round 2 Chains 2, Residues 157, Estimated correctness of the model 99.5 % 2 chains (157 residues) have been docked in sequence Building loops using Loopy2018 2 chains (157 residues) following loop building 2 chains (157 residues) in sequence following loop building ------------------------------------------------------ 17921 reflections ( 99.98 % complete ) and 1446 restraints for refining 1506 atoms. 206 conditional restraints added. Observations/parameters ratio is 2.97 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2780 (Rfree = 0.000) for 1506 atoms. Found 39 (40 requested) and removed 31 (29 requested) atoms. Cycle 22: After refmac, R = 0.2773 (Rfree = 0.000) for 1513 atoms. Found 15 (39 requested) and removed 16 (29 requested) atoms. Cycle 23: After refmac, R = 0.2719 (Rfree = 0.000) for 1512 atoms. Found 19 (38 requested) and removed 12 (29 requested) atoms. Cycle 24: After refmac, R = 0.2724 (Rfree = 0.000) for 1519 atoms. Found 14 (37 requested) and removed 12 (30 requested) atoms. Cycle 25: After refmac, R = 0.2699 (Rfree = 0.000) for 1521 atoms. Found 15 (36 requested) and removed 15 (30 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.93 1.88 NCS extension: 0 residues added, 1522 seeds are put forward Round 1: 157 peptides, 3 chains. Longest chain 79 peptides. Score 0.918 Round 2: 157 peptides, 2 chains. Longest chain 80 peptides. Score 0.927 Round 3: 157 peptides, 3 chains. Longest chain 79 peptides. Score 0.918 Round 4: 156 peptides, 3 chains. Longest chain 77 peptides. Score 0.916 Round 5: 157 peptides, 3 chains. Longest chain 79 peptides. Score 0.918 Taking the results from Round 2 Chains 2, Residues 155, Estimated correctness of the model 99.5 % 2 chains (155 residues) have been docked in sequence Building loops using Loopy2018 2 chains (155 residues) following loop building 2 chains (155 residues) in sequence following loop building ------------------------------------------------------ 17921 reflections ( 99.98 % complete ) and 1467 restraints for refining 1503 atoms. 243 conditional restraints added. Observations/parameters ratio is 2.98 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2785 (Rfree = 0.000) for 1503 atoms. Found 32 (34 requested) and removed 32 (29 requested) atoms. Cycle 27: After refmac, R = 0.2756 (Rfree = 0.000) for 1502 atoms. Found 12 (33 requested) and removed 14 (29 requested) atoms. Cycle 28: After refmac, R = 0.2709 (Rfree = 0.000) for 1500 atoms. Found 15 (32 requested) and removed 6 (29 requested) atoms. Cycle 29: After refmac, R = 0.2692 (Rfree = 0.000) for 1509 atoms. Found 7 (32 requested) and removed 15 (29 requested) atoms. Cycle 30: After refmac, R = 0.2696 (Rfree = 0.000) for 1498 atoms. Found 16 (31 requested) and removed 8 (29 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.93 1.88 NCS extension: 0 residues added (3 deleted due to clashes), 1507 seeds are put forward Round 1: 157 peptides, 3 chains. Longest chain 79 peptides. Score 0.918 Round 2: 159 peptides, 2 chains. Longest chain 80 peptides. Score 0.930 Round 3: 156 peptides, 3 chains. Longest chain 78 peptides. Score 0.916 Round 4: 159 peptides, 3 chains. Longest chain 79 peptides. Score 0.920 Round 5: 156 peptides, 4 chains. Longest chain 57 peptides. Score 0.906 Taking the results from Round 2 Chains 2, Residues 157, Estimated correctness of the model 99.5 % 2 chains (157 residues) have been docked in sequence Building loops using Loopy2018 2 chains (157 residues) following loop building 2 chains (157 residues) in sequence following loop building ------------------------------------------------------ 17921 reflections ( 99.98 % complete ) and 1439 restraints for refining 1504 atoms. 199 conditional restraints added. Observations/parameters ratio is 2.98 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2761 (Rfree = 0.000) for 1504 atoms. Found 31 (31 requested) and removed 31 (29 requested) atoms. Cycle 32: After refmac, R = 0.2751 (Rfree = 0.000) for 1504 atoms. Found 10 (29 requested) and removed 13 (29 requested) atoms. Cycle 33: After refmac, R = 0.2701 (Rfree = 0.000) for 1501 atoms. Found 13 (29 requested) and removed 6 (29 requested) atoms. Cycle 34: After refmac, R = 0.2685 (Rfree = 0.000) for 1507 atoms. Found 10 (29 requested) and removed 6 (29 requested) atoms. Cycle 35: After refmac, R = 0.2677 (Rfree = 0.000) for 1509 atoms. Found 10 (29 requested) and removed 6 (29 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.92 1.87 NCS extension: 0 residues added, 1514 seeds are put forward Round 1: 160 peptides, 2 chains. Longest chain 81 peptides. Score 0.931 Round 2: 156 peptides, 3 chains. Longest chain 78 peptides. Score 0.916 Round 3: 159 peptides, 2 chains. Longest chain 80 peptides. Score 0.930 Round 4: 155 peptides, 4 chains. Longest chain 77 peptides. Score 0.905 Round 5: 158 peptides, 2 chains. Longest chain 80 peptides. Score 0.928 Taking the results from Round 1 Chains 3, Residues 158, Estimated correctness of the model 99.5 % 2 chains (157 residues) have been docked in sequence Building loops using Loopy2018 3 chains (158 residues) following loop building 2 chains (157 residues) in sequence following loop building ------------------------------------------------------ 17921 reflections ( 99.98 % complete ) and 1445 restraints for refining 1503 atoms. 202 conditional restraints added. Observations/parameters ratio is 2.98 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2757 (Rfree = 0.000) for 1503 atoms. Found 29 (29 requested) and removed 32 (29 requested) atoms. Cycle 37: After refmac, R = 0.2728 (Rfree = 0.000) for 1499 atoms. Found 16 (29 requested) and removed 9 (29 requested) atoms. Cycle 38: After refmac, R = 0.2726 (Rfree = 0.000) for 1506 atoms. Found 13 (29 requested) and removed 12 (29 requested) atoms. Cycle 39: After refmac, R = 0.2695 (Rfree = 0.000) for 1506 atoms. Found 14 (29 requested) and removed 7 (29 requested) atoms. Cycle 40: After refmac, R = 0.2696 (Rfree = 0.000) for 1513 atoms. Found 9 (29 requested) and removed 10 (29 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.93 1.88 NCS extension: 0 residues added, 1513 seeds are put forward Round 1: 157 peptides, 3 chains. Longest chain 79 peptides. Score 0.918 Round 2: 157 peptides, 2 chains. Longest chain 80 peptides. Score 0.927 Round 3: 157 peptides, 3 chains. Longest chain 79 peptides. Score 0.918 Round 4: 159 peptides, 3 chains. Longest chain 79 peptides. Score 0.920 Round 5: 157 peptides, 3 chains. Longest chain 79 peptides. Score 0.918 Taking the results from Round 2 Chains 2, Residues 155, Estimated correctness of the model 99.5 % 2 chains (155 residues) have been docked in sequence Building loops using Loopy2018 2 chains (155 residues) following loop building 2 chains (155 residues) in sequence following loop building ------------------------------------------------------ 17921 reflections ( 99.98 % complete ) and 1483 restraints for refining 1503 atoms. 259 conditional restraints added. Observations/parameters ratio is 2.98 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2768 (Rfree = 0.000) for 1503 atoms. Found 29 (29 requested) and removed 32 (29 requested) atoms. Cycle 42: After refmac, R = 0.2761 (Rfree = 0.000) for 1500 atoms. Found 14 (29 requested) and removed 12 (29 requested) atoms. Cycle 43: After refmac, R = 0.2726 (Rfree = 0.000) for 1500 atoms. Found 19 (29 requested) and removed 12 (29 requested) atoms. Cycle 44: After refmac, R = 0.2716 (Rfree = 0.000) for 1507 atoms. Found 10 (29 requested) and removed 11 (29 requested) atoms. Cycle 45: After refmac, R = 0.2696 (Rfree = 0.000) for 1504 atoms. Found 16 (29 requested) and removed 7 (29 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.93 1.88 NCS extension: 0 residues added (3 deleted due to clashes), 1514 seeds are put forward Round 1: 157 peptides, 3 chains. Longest chain 79 peptides. Score 0.918 Round 2: 158 peptides, 2 chains. Longest chain 80 peptides. Score 0.928 Round 3: 156 peptides, 3 chains. Longest chain 78 peptides. Score 0.916 Round 4: 157 peptides, 2 chains. Longest chain 80 peptides. Score 0.927 Round 5: 156 peptides, 3 chains. Longest chain 78 peptides. Score 0.916 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 156, Estimated correctness of the model 99.5 % 2 chains (156 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 2 chains (156 residues) following loop building 2 chains (156 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 17921 reflections ( 99.98 % complete ) and 1232 restraints for refining 1224 atoms. Observations/parameters ratio is 3.66 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3248 (Rfree = 0.000) for 1224 atoms. Found 9 (24 requested) and removed 0 (24 requested) atoms. Cycle 47: After refmac, R = 0.3181 (Rfree = 0.000) for 1224 atoms. Found 1 (24 requested) and removed 0 (24 requested) atoms. Cycle 48: After refmac, R = 0.3124 (Rfree = 0.000) for 1224 atoms. Found 1 (24 requested) and removed 0 (24 requested) atoms. Cycle 49: After refmac, R = 0.3104 (Rfree = 0.000) for 1224 atoms. Found 1 (24 requested) and removed 0 (24 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:25:04 GMT 2018 Job finished. TimeTaking 27.23 Used memory is bytes: 21957768