Mon 24 Dec 01:11:21 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 1vk8-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vk8-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vk8-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vk8-4.0-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/1vk8-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vk8-4.0-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 01:11:25 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/1vk8-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vk8-4.0-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 253 and 0 Target number of residues in the AU: 253 Target solvent content: 0.6385 Checking the provided sequence file Detected sequence length: 106 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 424 Adjusted target solvent content: 0.39 Input MTZ file: 1vk8-4.0-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: 1 Cell parameters: 47.646 47.650 49.609 73.804 62.898 73.615 Input sequence file: 1vk8-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3392 target number of atoms Had to go as low as 0.55 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: 41.711 4.001 Wilson plot Bfac: 70.82 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2973 reflections ( 96.18 % complete ) and 0 restraints for refining 3733 atoms. Observations/parameters ratio is 0.20 ------------------------------------------------------ Starting model: R = 0.3075 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2990 (Rfree = 0.000) for 3733 atoms. Found 17 (17 requested) and removed 70 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 4.09 Search for helices and strands: 0 residues in 0 chains, 3770 seeds are put forward NCS extension: 0 residues added, 3770 seeds are put forward Round 1: 121 peptides, 29 chains. Longest chain 6 peptides. Score 0.193 Round 2: 156 peptides, 30 chains. Longest chain 10 peptides. Score 0.340 Round 3: 171 peptides, 30 chains. Longest chain 11 peptides. Score 0.404 Round 4: 155 peptides, 27 chains. Longest chain 10 peptides. Score 0.391 Round 5: 160 peptides, 27 chains. Longest chain 11 peptides. Score 0.412 Taking the results from Round 5 Chains 27, Residues 133, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2973 reflections ( 96.18 % complete ) and 7606 restraints for refining 3063 atoms. 7101 conditional restraints added. Observations/parameters ratio is 0.24 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2711 (Rfree = 0.000) for 3063 atoms. Found 14 (14 requested) and removed 41 (7 requested) atoms. Cycle 2: After refmac, R = 0.2489 (Rfree = 0.000) for 2971 atoms. Found 14 (14 requested) and removed 28 (7 requested) atoms. Cycle 3: After refmac, R = 0.2311 (Rfree = 0.000) for 2922 atoms. Found 14 (14 requested) and removed 32 (7 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2103 (Rfree = 0.000) for 2874 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 5: After refmac, R = 0.2064 (Rfree = 0.000) for 2850 atoms. Found 13 (13 requested) and removed 24 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.51 4.07 Search for helices and strands: 0 residues in 0 chains, 2967 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2980 seeds are put forward Round 1: 106 peptides, 24 chains. Longest chain 6 peptides. Score 0.220 Round 2: 152 peptides, 27 chains. Longest chain 10 peptides. Score 0.378 Round 3: 165 peptides, 30 chains. Longest chain 11 peptides. Score 0.379 Round 4: 163 peptides, 30 chains. Longest chain 10 peptides. Score 0.370 Round 5: 169 peptides, 28 chains. Longest chain 11 peptides. Score 0.432 Taking the results from Round 5 Chains 28, Residues 141, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2973 reflections ( 96.18 % complete ) and 6384 restraints for refining 2711 atoms. 5848 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1951 (Rfree = 0.000) for 2711 atoms. Found 12 (12 requested) and removed 37 (6 requested) atoms. Cycle 7: After refmac, R = 0.1979 (Rfree = 0.000) for 2669 atoms. Found 12 (12 requested) and removed 34 (6 requested) atoms. Cycle 8: After refmac, R = 0.1892 (Rfree = 0.000) for 2625 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 9: After refmac, R = 0.1679 (Rfree = 0.000) for 2600 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 10: After refmac, R = 0.1802 (Rfree = 0.000) for 2588 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.47 4.03 Search for helices and strands: 0 residues in 0 chains, 2693 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 2704 seeds are put forward Round 1: 137 peptides, 28 chains. Longest chain 12 peptides. Score 0.291 Round 2: 159 peptides, 30 chains. Longest chain 13 peptides. Score 0.353 Round 3: 176 peptides, 32 chains. Longest chain 11 peptides. Score 0.390 Round 4: 168 peptides, 28 chains. Longest chain 16 peptides. Score 0.427 Round 5: 169 peptides, 27 chains. Longest chain 16 peptides. Score 0.449 Taking the results from Round 5 Chains 27, Residues 142, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2973 reflections ( 96.18 % complete ) and 6298 restraints for refining 2702 atoms. 5757 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1952 (Rfree = 0.000) for 2702 atoms. Found 12 (12 requested) and removed 37 (6 requested) atoms. Cycle 12: After refmac, R = 0.1926 (Rfree = 0.000) for 2670 atoms. Found 12 (12 requested) and removed 27 (6 requested) atoms. Cycle 13: After refmac, R = 0.1704 (Rfree = 0.000) for 2649 atoms. Found 12 (12 requested) and removed 30 (6 requested) atoms. Cycle 14: After refmac, R = 0.1637 (Rfree = 0.000) for 2627 atoms. Found 12 (12 requested) and removed 22 (6 requested) atoms. Cycle 15: After refmac, R = 0.1595 (Rfree = 0.000) for 2608 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.58 4.16 Search for helices and strands: 0 residues in 0 chains, 2720 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2736 seeds are put forward Round 1: 153 peptides, 28 chains. Longest chain 11 peptides. Score 0.364 Round 2: 169 peptides, 26 chains. Longest chain 14 peptides. Score 0.466 Round 3: 171 peptides, 26 chains. Longest chain 14 peptides. Score 0.474 Round 4: 169 peptides, 24 chains. Longest chain 20 peptides. Score 0.500 Round 5: 173 peptides, 26 chains. Longest chain 16 peptides. Score 0.482 Taking the results from Round 4 Chains 24, Residues 145, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2973 reflections ( 96.18 % complete ) and 6427 restraints for refining 2760 atoms. 5871 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2041 (Rfree = 0.000) for 2760 atoms. Found 13 (13 requested) and removed 36 (6 requested) atoms. Cycle 17: After refmac, R = 0.1909 (Rfree = 0.000) for 2724 atoms. Found 12 (12 requested) and removed 27 (6 requested) atoms. Cycle 18: After refmac, R = 0.1399 (Rfree = 0.000) for 2701 atoms. Found 10 (12 requested) and removed 16 (6 requested) atoms. Cycle 19: After refmac, R = 0.1246 (Rfree = 0.000) for 2691 atoms. Found 2 (12 requested) and removed 17 (6 requested) atoms. Cycle 20: After refmac, R = 0.1322 (Rfree = 0.000) for 2676 atoms. Found 3 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 4.16 Search for helices and strands: 0 residues in 0 chains, 2776 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 2800 seeds are put forward Round 1: 148 peptides, 26 chains. Longest chain 9 peptides. Score 0.379 Round 2: 141 peptides, 21 chains. Longest chain 14 peptides. Score 0.443 Round 3: 135 peptides, 20 chains. Longest chain 15 peptides. Score 0.436 Round 4: 145 peptides, 21 chains. Longest chain 15 peptides. Score 0.459 Round 5: 143 peptides, 21 chains. Longest chain 16 peptides. Score 0.451 Taking the results from Round 4 Chains 21, Residues 124, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2973 reflections ( 96.18 % complete ) and 6667 restraints for refining 2805 atoms. 6192 conditional restraints added. Observations/parameters ratio is 0.26 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2223 (Rfree = 0.000) for 2805 atoms. Found 13 (13 requested) and removed 24 (6 requested) atoms. Cycle 22: After refmac, R = 0.2102 (Rfree = 0.000) for 2776 atoms. Found 13 (13 requested) and removed 26 (6 requested) atoms. Cycle 23: After refmac, R = 0.1928 (Rfree = 0.000) for 2752 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 24: After refmac, R = 0.1906 (Rfree = 0.000) for 2743 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 25: After refmac, R = 0.2002 (Rfree = 0.000) for 2729 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 4.13 Search for helices and strands: 0 residues in 0 chains, 2816 seeds are put forward NCS extension: 0 residues added, 2816 seeds are put forward Round 1: 117 peptides, 26 chains. Longest chain 6 peptides. Score 0.234 Round 2: 149 peptides, 29 chains. Longest chain 9 peptides. Score 0.327 Round 3: 144 peptides, 26 chains. Longest chain 10 peptides. Score 0.362 Round 4: 152 peptides, 28 chains. Longest chain 9 peptides. Score 0.359 Round 5: 151 peptides, 26 chains. Longest chain 12 peptides. Score 0.392 Taking the results from Round 5 Chains 26, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2973 reflections ( 96.18 % complete ) and 6605 restraints for refining 2810 atoms. 6131 conditional restraints added. Observations/parameters ratio is 0.26 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1915 (Rfree = 0.000) for 2810 atoms. Found 13 (13 requested) and removed 29 (6 requested) atoms. Cycle 27: After refmac, R = 0.2043 (Rfree = 0.000) for 2773 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 28: After refmac, R = 0.1977 (Rfree = 0.000) for 2763 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 29: After refmac, R = 0.1989 (Rfree = 0.000) for 2754 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 30: After refmac, R = 0.1873 (Rfree = 0.000) for 2745 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.64 4.22 Search for helices and strands: 0 residues in 0 chains, 2849 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 2864 seeds are put forward Round 1: 83 peptides, 17 chains. Longest chain 8 peptides. Score 0.253 Round 2: 115 peptides, 24 chains. Longest chain 8 peptides. Score 0.266 Round 3: 136 peptides, 26 chains. Longest chain 8 peptides. Score 0.326 Round 4: 134 peptides, 25 chains. Longest chain 10 peptides. Score 0.336 Round 5: 126 peptides, 23 chains. Longest chain 10 peptides. Score 0.339 Taking the results from Round 5 Chains 23, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2973 reflections ( 96.18 % complete ) and 6326 restraints for refining 2654 atoms. 5937 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1999 (Rfree = 0.000) for 2654 atoms. Found 12 (12 requested) and removed 24 (6 requested) atoms. Cycle 32: After refmac, R = 0.1796 (Rfree = 0.000) for 2636 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 33: After refmac, R = 0.1787 (Rfree = 0.000) for 2626 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 34: After refmac, R = 0.1737 (Rfree = 0.000) for 2615 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 35: After refmac, R = 0.1692 (Rfree = 0.000) for 2603 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.62 4.20 Search for helices and strands: 0 residues in 0 chains, 2703 seeds are put forward NCS extension: 0 residues added, 2703 seeds are put forward Round 1: 105 peptides, 23 chains. Longest chain 7 peptides. Score 0.236 Round 2: 114 peptides, 22 chains. Longest chain 10 peptides. Score 0.302 Round 3: 125 peptides, 22 chains. Longest chain 11 peptides. Score 0.354 Round 4: 115 peptides, 21 chains. Longest chain 12 peptides. Score 0.328 Round 5: 137 peptides, 23 chains. Longest chain 12 peptides. Score 0.388 Taking the results from Round 5 Chains 23, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2973 reflections ( 96.18 % complete ) and 5871 restraints for refining 2588 atoms. 5438 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1827 (Rfree = 0.000) for 2588 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 37: After refmac, R = 0.1787 (Rfree = 0.000) for 2571 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 38: After refmac, R = 0.1907 (Rfree = 0.000) for 2559 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 39: After refmac, R = 0.1738 (Rfree = 0.000) for 2548 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 40: After refmac, R = 0.1772 (Rfree = 0.000) for 2541 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.62 4.20 Search for helices and strands: 0 residues in 0 chains, 2641 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2656 seeds are put forward Round 1: 82 peptides, 19 chains. Longest chain 5 peptides. Score 0.202 Round 2: 100 peptides, 20 chains. Longest chain 10 peptides. Score 0.275 Round 3: 99 peptides, 18 chains. Longest chain 13 peptides. Score 0.314 Round 4: 96 peptides, 18 chains. Longest chain 10 peptides. Score 0.299 Round 5: 103 peptides, 19 chains. Longest chain 10 peptides. Score 0.312 Taking the results from Round 3 Chains 18, Residues 81, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2973 reflections ( 96.18 % complete ) and 5576 restraints for refining 2506 atoms. 5270 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1524 (Rfree = 0.000) for 2506 atoms. Found 11 (11 requested) and removed 20 (5 requested) atoms. Cycle 42: After refmac, R = 0.1832 (Rfree = 0.000) for 2485 atoms. Found 11 (11 requested) and removed 19 (5 requested) atoms. Cycle 43: After refmac, R = 0.1790 (Rfree = 0.000) for 2473 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 44: After refmac, R = 0.1565 (Rfree = 0.000) for 2466 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 45: After refmac, R = 0.1707 (Rfree = 0.000) for 2465 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.60 4.18 Search for helices and strands: 0 residues in 0 chains, 2543 seeds are put forward NCS extension: 0 residues added, 2543 seeds are put forward Round 1: 78 peptides, 18 chains. Longest chain 5 peptides. Score 0.202 Round 2: 106 peptides, 22 chains. Longest chain 8 peptides. Score 0.263 Round 3: 93 peptides, 18 chains. Longest chain 8 peptides. Score 0.284 Round 4: 97 peptides, 20 chains. Longest chain 8 peptides. Score 0.260 Round 5: 102 peptides, 19 chains. Longest chain 9 peptides. Score 0.307 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vk8-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2973 reflections ( 96.18 % complete ) and 5238 restraints for refining 2417 atoms. 4925 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1538 (Rfree = 0.000) for 2417 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1642 (Rfree = 0.000) for 2401 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1561 (Rfree = 0.000) for 2387 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1554 (Rfree = 0.000) for 2380 atoms. TimeTaking 33.7