Sun 23 Dec 22:22:43 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1o6a-1.9-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1o6a-1.9-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1o6a-1.9-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1o6a-1.9-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1o6a-1.9-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1o6a-1.9-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:22:52 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/hancs/ArpWArp/wArpResults/WorkingDir/1o6a-1.9-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1o6a-1.9-parrot-hancs/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-hancs.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-hancs.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 1707 atoms. Observations/parameters ratio is 2.62 ------------------------------------------------------ Starting model: R = 0.3733 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3292 (Rfree = 0.000) for 1707 atoms. Found 30 (67 requested) and removed 43 (33 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.95 1.90 NCS extension: 0 residues added, 1694 seeds are put forward Round 1: 137 peptides, 13 chains. Longest chain 28 peptides. Score 0.731 Round 2: 153 peptides, 9 chains. Longest chain 51 peptides. Score 0.844 Round 3: 159 peptides, 4 chains. Longest chain 75 peptides. Score 0.911 Round 4: 161 peptides, 4 chains. Longest chain 77 peptides. Score 0.914 Round 5: 161 peptides, 3 chains. Longest chain 83 peptides. Score 0.923 Taking the results from Round 5 Chains 3, Residues 158, Estimated correctness of the model 99.4 % 3 chains (158 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 67 B and 70 B 2 chains (160 residues) following loop building 2 chains (160 residues) in sequence following loop building ------------------------------------------------------ 17921 reflections ( 99.98 % complete ) and 1489 restraints for refining 1503 atoms. 224 conditional restraints added. Observations/parameters ratio is 2.98 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3391 (Rfree = 0.000) for 1503 atoms. Found 29 (59 requested) and removed 32 (29 requested) atoms. Cycle 2: After refmac, R = 0.3026 (Rfree = 0.000) for 1493 atoms. Found 22 (58 requested) and removed 29 (29 requested) atoms. Cycle 3: After refmac, R = 0.2890 (Rfree = 0.000) for 1481 atoms. Found 18 (56 requested) and removed 28 (29 requested) atoms. Cycle 4: After refmac, R = 0.2843 (Rfree = 0.000) for 1470 atoms. Found 20 (55 requested) and removed 10 (29 requested) atoms. Cycle 5: After refmac, R = 0.2802 (Rfree = 0.000) for 1478 atoms. Found 10 (55 requested) and removed 8 (29 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.93 1.88 NCS extension: 5 residues added (0 deleted due to clashes), 1485 seeds are put forward Round 1: 160 peptides, 4 chains. Longest chain 83 peptides. Score 0.912 Round 2: 161 peptides, 2 chains. Longest chain 81 peptides. Score 0.932 Round 3: 162 peptides, 4 chains. Longest chain 83 peptides. Score 0.915 Round 4: 163 peptides, 2 chains. Longest chain 83 peptides. Score 0.934 Round 5: 162 peptides, 4 chains. Longest chain 64 peptides. Score 0.915 Taking the results from Round 4 Chains 2, Residues 161, Estimated correctness of the model 99.6 % 2 chains (161 residues) have been docked in sequence Building loops using Loopy2018 2 chains (161 residues) following loop building 2 chains (161 residues) in sequence following loop building ------------------------------------------------------ 17921 reflections ( 99.98 % complete ) and 1467 restraints for refining 1503 atoms. 194 conditional restraints added. Observations/parameters ratio is 2.98 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2860 (Rfree = 0.000) for 1503 atoms. Found 45 (54 requested) and removed 30 (29 requested) atoms. Cycle 7: After refmac, R = 0.2849 (Rfree = 0.000) for 1517 atoms. Found 21 (54 requested) and removed 19 (30 requested) atoms. Cycle 8: After refmac, R = 0.2766 (Rfree = 0.000) for 1517 atoms. Found 22 (53 requested) and removed 11 (30 requested) atoms. Cycle 9: After refmac, R = 0.2747 (Rfree = 0.000) for 1525 atoms. Found 11 (53 requested) and removed 7 (30 requested) atoms. Cycle 10: After refmac, R = 0.2709 (Rfree = 0.000) for 1527 atoms. Found 11 (52 requested) and removed 4 (30 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.93 1.88 NCS extension: 4 residues added (0 deleted due to clashes), 1538 seeds are put forward Round 1: 162 peptides, 3 chains. Longest chain 83 peptides. Score 0.924 Round 2: 160 peptides, 3 chains. Longest chain 82 peptides. Score 0.922 Round 3: 163 peptides, 2 chains. Longest chain 83 peptides. Score 0.934 Round 4: 161 peptides, 4 chains. Longest chain 83 peptides. Score 0.914 Round 5: 163 peptides, 2 chains. Longest chain 83 peptides. Score 0.934 Taking the results from Round 5 Chains 2, Residues 161, Estimated correctness of the model 99.6 % 2 chains (161 residues) have been docked in sequence Building loops using Loopy2018 2 chains (161 residues) following loop building 2 chains (161 residues) in sequence following loop building ------------------------------------------------------ 17921 reflections ( 99.98 % complete ) and 1454 restraints for refining 1508 atoms. 181 conditional restraints added. Observations/parameters ratio is 2.97 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2775 (Rfree = 0.000) for 1508 atoms. Found 39 (51 requested) and removed 31 (29 requested) atoms. Cycle 12: After refmac, R = 0.2765 (Rfree = 0.000) for 1515 atoms. Found 17 (50 requested) and removed 18 (30 requested) atoms. Cycle 13: After refmac, R = 0.2708 (Rfree = 0.000) for 1514 atoms. Found 22 (48 requested) and removed 5 (29 requested) atoms. Cycle 14: After refmac, R = 0.2678 (Rfree = 0.000) for 1531 atoms. Found 17 (49 requested) and removed 11 (30 requested) atoms. Cycle 15: After refmac, R = 0.2664 (Rfree = 0.000) for 1537 atoms. Found 15 (48 requested) and removed 9 (30 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.93 1.88 NCS extension: 4 residues added (0 deleted due to clashes), 1547 seeds are put forward Round 1: 162 peptides, 3 chains. Longest chain 83 peptides. Score 0.924 Round 2: 160 peptides, 3 chains. Longest chain 82 peptides. Score 0.922 Round 3: 163 peptides, 2 chains. Longest chain 83 peptides. Score 0.934 Round 4: 161 peptides, 4 chains. Longest chain 83 peptides. Score 0.914 Round 5: 163 peptides, 2 chains. Longest chain 83 peptides. Score 0.934 Taking the results from Round 5 Chains 2, Residues 161, Estimated correctness of the model 99.6 % 2 chains (161 residues) have been docked in sequence Building loops using Loopy2018 2 chains (161 residues) following loop building 2 chains (161 residues) in sequence following loop building ------------------------------------------------------ 17921 reflections ( 99.98 % complete ) and 1434 restraints for refining 1512 atoms. 161 conditional restraints added. Observations/parameters ratio is 2.96 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2784 (Rfree = 0.000) for 1512 atoms. Found 46 (46 requested) and removed 30 (29 requested) atoms. Cycle 17: After refmac, R = 0.2786 (Rfree = 0.000) for 1526 atoms. Found 24 (46 requested) and removed 9 (30 requested) atoms. Cycle 18: After refmac, R = 0.2713 (Rfree = 0.000) for 1539 atoms. Found 20 (46 requested) and removed 11 (30 requested) atoms. Cycle 19: After refmac, R = 0.2697 (Rfree = 0.000) for 1547 atoms. Found 14 (45 requested) and removed 16 (30 requested) atoms. Cycle 20: After refmac, R = 0.2671 (Rfree = 0.000) for 1545 atoms. Found 17 (44 requested) and removed 9 (30 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.92 1.87 NCS extension: 4 residues added (0 deleted due to clashes), 1557 seeds are put forward Round 1: 161 peptides, 4 chains. Longest chain 83 peptides. Score 0.914 Round 2: 162 peptides, 3 chains. Longest chain 82 peptides. Score 0.924 Round 3: 163 peptides, 3 chains. Longest chain 83 peptides. Score 0.926 Round 4: 162 peptides, 3 chains. Longest chain 83 peptides. Score 0.924 Round 5: 165 peptides, 2 chains. Longest chain 84 peptides. Score 0.937 Taking the results from Round 5 Chains 3, Residues 163, Estimated correctness of the model 99.6 % 2 chains (162 residues) have been docked in sequence Building loops using Loopy2018 3 chains (163 residues) following loop building 2 chains (162 residues) in sequence following loop building ------------------------------------------------------ 17921 reflections ( 99.98 % complete ) and 1430 restraints for refining 1536 atoms. 146 conditional restraints added. Observations/parameters ratio is 2.92 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2794 (Rfree = 0.000) for 1536 atoms. Found 41 (42 requested) and removed 33 (30 requested) atoms. Cycle 22: After refmac, R = 0.2765 (Rfree = 0.000) for 1544 atoms. Found 15 (41 requested) and removed 18 (30 requested) atoms. Cycle 23: After refmac, R = 0.2711 (Rfree = 0.000) for 1541 atoms. Found 10 (40 requested) and removed 10 (30 requested) atoms. Cycle 24: After refmac, R = 0.2672 (Rfree = 0.000) for 1539 atoms. Found 11 (39 requested) and removed 5 (30 requested) atoms. Cycle 25: After refmac, R = 0.2668 (Rfree = 0.000) for 1545 atoms. Found 5 (39 requested) and removed 10 (30 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.93 1.88 NCS extension: 4 residues added (0 deleted due to clashes), 1544 seeds are put forward Round 1: 160 peptides, 4 chains. Longest chain 83 peptides. Score 0.912 Round 2: 163 peptides, 3 chains. Longest chain 83 peptides. Score 0.926 Round 3: 160 peptides, 5 chains. Longest chain 83 peptides. Score 0.903 Round 4: 163 peptides, 2 chains. Longest chain 83 peptides. Score 0.934 Round 5: 162 peptides, 3 chains. Longest chain 84 peptides. Score 0.924 Taking the results from Round 4 Chains 2, Residues 161, Estimated correctness of the model 99.6 % 2 chains (161 residues) have been docked in sequence Building loops using Loopy2018 2 chains (161 residues) following loop building 2 chains (161 residues) in sequence following loop building ------------------------------------------------------ 17921 reflections ( 99.98 % complete ) and 1449 restraints for refining 1519 atoms. 176 conditional restraints added. Observations/parameters ratio is 2.95 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2747 (Rfree = 0.000) for 1519 atoms. Found 37 (37 requested) and removed 33 (30 requested) atoms. Cycle 27: After refmac, R = 0.2728 (Rfree = 0.000) for 1522 atoms. Found 18 (36 requested) and removed 13 (30 requested) atoms. Cycle 28: After refmac, R = 0.2693 (Rfree = 0.000) for 1527 atoms. Found 20 (35 requested) and removed 6 (30 requested) atoms. Cycle 29: After refmac, R = 0.2670 (Rfree = 0.000) for 1541 atoms. Found 6 (35 requested) and removed 11 (30 requested) atoms. Cycle 30: After refmac, R = 0.2647 (Rfree = 0.000) for 1536 atoms. Found 11 (34 requested) and removed 1 (30 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.93 1.88 NCS extension: 4 residues added (0 deleted due to clashes), 1550 seeds are put forward Round 1: 161 peptides, 4 chains. Longest chain 83 peptides. Score 0.914 Round 2: 164 peptides, 2 chains. Longest chain 83 peptides. Score 0.935 Round 3: 162 peptides, 3 chains. Longest chain 83 peptides. Score 0.924 Round 4: 163 peptides, 3 chains. Longest chain 83 peptides. Score 0.926 Round 5: 162 peptides, 3 chains. Longest chain 83 peptides. Score 0.924 Taking the results from Round 2 Chains 3, Residues 162, Estimated correctness of the model 99.6 % 2 chains (161 residues) have been docked in sequence Building loops using Loopy2018 3 chains (162 residues) following loop building 2 chains (161 residues) in sequence following loop building ------------------------------------------------------ 17921 reflections ( 99.98 % complete ) and 1457 restraints for refining 1532 atoms. 181 conditional restraints added. Observations/parameters ratio is 2.92 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2736 (Rfree = 0.000) for 1532 atoms. Found 34 (34 requested) and removed 33 (30 requested) atoms. Cycle 32: After refmac, R = 0.2740 (Rfree = 0.000) for 1531 atoms. Found 19 (32 requested) and removed 7 (30 requested) atoms. Cycle 33: After refmac, R = 0.2698 (Rfree = 0.000) for 1542 atoms. Found 9 (33 requested) and removed 13 (30 requested) atoms. Cycle 34: After refmac, R = 0.2679 (Rfree = 0.000) for 1538 atoms. Found 14 (31 requested) and removed 6 (30 requested) atoms. Cycle 35: After refmac, R = 0.2659 (Rfree = 0.000) for 1545 atoms. Found 9 (32 requested) and removed 12 (30 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.92 1.87 NCS extension: 3 residues added (1 deleted due to clashes), 1545 seeds are put forward Round 1: 161 peptides, 4 chains. Longest chain 51 peptides. Score 0.914 Round 2: 164 peptides, 2 chains. Longest chain 83 peptides. Score 0.935 Round 3: 163 peptides, 4 chains. Longest chain 83 peptides. Score 0.917 Round 4: 164 peptides, 2 chains. Longest chain 83 peptides. Score 0.935 Round 5: 162 peptides, 3 chains. Longest chain 83 peptides. Score 0.924 Taking the results from Round 4 Chains 3, Residues 162, Estimated correctness of the model 99.6 % 2 chains (161 residues) have been docked in sequence Building loops using Loopy2018 3 chains (162 residues) following loop building 2 chains (161 residues) in sequence following loop building ------------------------------------------------------ 17921 reflections ( 99.98 % complete ) and 1452 restraints for refining 1524 atoms. 176 conditional restraints added. Observations/parameters ratio is 2.94 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2747 (Rfree = 0.000) for 1524 atoms. Found 30 (30 requested) and removed 34 (30 requested) atoms. Cycle 37: After refmac, R = 0.2739 (Rfree = 0.000) for 1519 atoms. Found 18 (30 requested) and removed 10 (30 requested) atoms. Cycle 38: After refmac, R = 0.2688 (Rfree = 0.000) for 1527 atoms. Found 15 (30 requested) and removed 11 (30 requested) atoms. Cycle 39: After refmac, R = 0.2680 (Rfree = 0.000) for 1531 atoms. Found 14 (30 requested) and removed 11 (30 requested) atoms. Cycle 40: After refmac, R = 0.2663 (Rfree = 0.000) for 1534 atoms. Found 22 (30 requested) and removed 12 (30 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.92 1.87 NCS extension: 4 residues added (0 deleted due to clashes), 1548 seeds are put forward Round 1: 162 peptides, 4 chains. Longest chain 83 peptides. Score 0.915 Round 2: 162 peptides, 2 chains. Longest chain 81 peptides. Score 0.933 Round 3: 162 peptides, 4 chains. Longest chain 83 peptides. Score 0.915 Round 4: 159 peptides, 2 chains. Longest chain 81 peptides. Score 0.930 Round 5: 162 peptides, 3 chains. Longest chain 83 peptides. Score 0.924 Taking the results from Round 2 Chains 3, Residues 160, Estimated correctness of the model 99.6 % 2 chains (159 residues) have been docked in sequence Building loops using Loopy2018 3 chains (160 residues) following loop building 2 chains (159 residues) in sequence following loop building ------------------------------------------------------ 17921 reflections ( 99.98 % complete ) and 1449 restraints for refining 1515 atoms. 189 conditional restraints added. Observations/parameters ratio is 2.96 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2750 (Rfree = 0.000) for 1515 atoms. Found 30 (30 requested) and removed 31 (30 requested) atoms. Cycle 42: After refmac, R = 0.2744 (Rfree = 0.000) for 1514 atoms. Found 23 (29 requested) and removed 12 (29 requested) atoms. Cycle 43: After refmac, R = 0.2709 (Rfree = 0.000) for 1525 atoms. Found 15 (30 requested) and removed 10 (30 requested) atoms. Cycle 44: After refmac, R = 0.2682 (Rfree = 0.000) for 1529 atoms. Found 13 (30 requested) and removed 10 (30 requested) atoms. Cycle 45: After refmac, R = 0.2676 (Rfree = 0.000) for 1530 atoms. Found 22 (30 requested) and removed 9 (30 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.93 1.88 NCS extension: 4 residues added (3 deleted due to clashes), 1547 seeds are put forward Round 1: 161 peptides, 4 chains. Longest chain 83 peptides. Score 0.914 Round 2: 163 peptides, 3 chains. Longest chain 83 peptides. Score 0.926 Round 3: 160 peptides, 4 chains. Longest chain 81 peptides. Score 0.912 Round 4: 163 peptides, 2 chains. Longest chain 83 peptides. Score 0.934 Round 5: 160 peptides, 3 chains. Longest chain 81 peptides. Score 0.922 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 161, Estimated correctness of the model 99.6 % 2 chains (161 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 2 chains (161 residues) following loop building 2 chains (161 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 17921 reflections ( 99.98 % complete ) and 1273 restraints for refining 1265 atoms. Observations/parameters ratio is 3.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3173 (Rfree = 0.000) for 1265 atoms. Found 10 (25 requested) and removed 0 (25 requested) atoms. Cycle 47: After refmac, R = 0.3084 (Rfree = 0.000) for 1265 atoms. Found 6 (25 requested) and removed 0 (25 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.3024 (Rfree = 0.000) for 1265 atoms. Found 1 (25 requested) and removed 0 (25 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2994 (Rfree = 0.000) for 1265 atoms. Found 0 (25 requested) and removed 0 (25 requested) atoms. Writing output files ... TimeTaking 42.99