Tue 25 Dec 19:27:55 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 2opl-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2opl-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2opl-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opl-3.6-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/2opl-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opl-3.6-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 ============================================================ Tue 25 Dec 19:28:05 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/2opl-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opl-3.6-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 245 and 0 Target number of residues in the AU: 245 Target solvent content: 0.6449 Checking the provided sequence file Detected sequence length: 187 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 374 Adjusted target solvent content: 0.46 Input MTZ file: 2opl-3.6-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: 19 Cell parameters: 47.200 82.950 95.370 90.000 90.000 90.000 Input sequence file: 2opl-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2992 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: 62.588 3.600 Wilson plot Bfac: 74.47 4639 reflections ( 99.40 % complete ) and 0 restraints for refining 3301 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3295 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3156 (Rfree = 0.000) for 3301 atoms. Found 21 (21 requested) and removed 23 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.48 3.67 Search for helices and strands: 0 residues in 0 chains, 3356 seeds are put forward NCS extension: 0 residues added, 3356 seeds are put forward Round 1: 154 peptides, 30 chains. Longest chain 9 peptides. Score 0.332 Round 2: 186 peptides, 29 chains. Longest chain 12 peptides. Score 0.485 Round 3: 204 peptides, 29 chains. Longest chain 13 peptides. Score 0.550 Round 4: 238 peptides, 29 chains. Longest chain 21 peptides. Score 0.656 Round 5: 231 peptides, 27 chains. Longest chain 26 peptides. Score 0.662 Taking the results from Round 5 Chains 28, Residues 204, Estimated correctness of the model 37.3 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 4639 reflections ( 99.40 % complete ) and 6000 restraints for refining 2711 atoms. 5168 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2478 (Rfree = 0.000) for 2711 atoms. Found 12 (17 requested) and removed 23 (8 requested) atoms. Cycle 2: After refmac, R = 0.2135 (Rfree = 0.000) for 2664 atoms. Found 10 (17 requested) and removed 11 (8 requested) atoms. Cycle 3: After refmac, R = 0.2042 (Rfree = 0.000) for 2654 atoms. Found 5 (17 requested) and removed 10 (8 requested) atoms. Cycle 4: After refmac, R = 0.2076 (Rfree = 0.000) for 2648 atoms. Found 6 (16 requested) and removed 14 (8 requested) atoms. Cycle 5: After refmac, R = 0.1953 (Rfree = 0.000) for 2639 atoms. Found 9 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.42 3.61 Search for helices and strands: 0 residues in 0 chains, 2713 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 2728 seeds are put forward Round 1: 198 peptides, 30 chains. Longest chain 16 peptides. Score 0.513 Round 2: 210 peptides, 27 chains. Longest chain 20 peptides. Score 0.600 Round 3: 211 peptides, 27 chains. Longest chain 26 peptides. Score 0.603 Round 4: 218 peptides, 25 chains. Longest chain 27 peptides. Score 0.651 Round 5: 219 peptides, 28 chains. Longest chain 25 peptides. Score 0.614 Taking the results from Round 4 Chains 25, Residues 193, Estimated correctness of the model 33.5 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 4639 reflections ( 99.40 % complete ) and 6005 restraints for refining 2712 atoms. 5203 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2343 (Rfree = 0.000) for 2712 atoms. Found 13 (17 requested) and removed 15 (8 requested) atoms. Cycle 7: After refmac, R = 0.2188 (Rfree = 0.000) for 2690 atoms. Found 11 (17 requested) and removed 15 (8 requested) atoms. Cycle 8: After refmac, R = 0.2151 (Rfree = 0.000) for 2672 atoms. Found 9 (17 requested) and removed 11 (8 requested) atoms. Cycle 9: After refmac, R = 0.1862 (Rfree = 0.000) for 2659 atoms. Found 4 (17 requested) and removed 13 (8 requested) atoms. Cycle 10: After refmac, R = 0.2046 (Rfree = 0.000) for 2644 atoms. Found 10 (17 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.41 3.60 Search for helices and strands: 0 residues in 0 chains, 2748 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 2770 seeds are put forward Round 1: 208 peptides, 34 chains. Longest chain 24 peptides. Score 0.486 Round 2: 232 peptides, 34 chains. Longest chain 26 peptides. Score 0.571 Round 3: 222 peptides, 30 chains. Longest chain 27 peptides. Score 0.596 Round 4: 225 peptides, 31 chains. Longest chain 27 peptides. Score 0.591 Round 5: 213 peptides, 31 chains. Longest chain 19 peptides. Score 0.551 Taking the results from Round 3 Chains 33, Residues 192, Estimated correctness of the model 13.1 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4639 reflections ( 99.40 % complete ) and 5914 restraints for refining 2712 atoms. 5082 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2319 (Rfree = 0.000) for 2712 atoms. Found 11 (17 requested) and removed 22 (8 requested) atoms. Cycle 12: After refmac, R = 0.2103 (Rfree = 0.000) for 2685 atoms. Found 10 (17 requested) and removed 11 (8 requested) atoms. Cycle 13: After refmac, R = 0.1961 (Rfree = 0.000) for 2678 atoms. Found 10 (17 requested) and removed 9 (8 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.1898 (Rfree = 0.000) for 2671 atoms. Found 7 (17 requested) and removed 9 (8 requested) atoms. Cycle 15: After refmac, R = 0.1855 (Rfree = 0.000) for 2658 atoms. Found 6 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.41 3.60 Search for helices and strands: 0 residues in 0 chains, 2763 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 2781 seeds are put forward Round 1: 159 peptides, 26 chains. Longest chain 18 peptides. Score 0.429 Round 2: 207 peptides, 31 chains. Longest chain 27 peptides. Score 0.530 Round 3: 195 peptides, 30 chains. Longest chain 19 peptides. Score 0.502 Round 4: 182 peptides, 26 chains. Longest chain 19 peptides. Score 0.519 Round 5: 192 peptides, 27 chains. Longest chain 18 peptides. Score 0.539 Taking the results from Round 5 Chains 27, Residues 165, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4639 reflections ( 99.40 % complete ) and 6250 restraints for refining 2712 atoms. 5579 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2084 (Rfree = 0.000) for 2712 atoms. Found 12 (17 requested) and removed 12 (8 requested) atoms. Cycle 17: After refmac, R = 0.1881 (Rfree = 0.000) for 2697 atoms. Found 3 (17 requested) and removed 9 (8 requested) atoms. Cycle 18: After refmac, R = 0.1916 (Rfree = 0.000) for 2687 atoms. Found 3 (17 requested) and removed 9 (8 requested) atoms. Cycle 19: After refmac, R = 0.1894 (Rfree = 0.000) for 2679 atoms. Found 5 (17 requested) and removed 9 (8 requested) atoms. Cycle 20: After refmac, R = 0.2250 (Rfree = 0.000) for 2672 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 3.66 Search for helices and strands: 0 residues in 0 chains, 2778 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 2802 seeds are put forward Round 1: 189 peptides, 36 chains. Longest chain 14 peptides. Score 0.375 Round 2: 197 peptides, 30 chains. Longest chain 14 peptides. Score 0.510 Round 3: 204 peptides, 29 chains. Longest chain 15 peptides. Score 0.550 Round 4: 215 peptides, 31 chains. Longest chain 15 peptides. Score 0.558 Round 5: 201 peptides, 30 chains. Longest chain 15 peptides. Score 0.524 Taking the results from Round 4 Chains 31, Residues 184, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4639 reflections ( 99.40 % complete ) and 6098 restraints for refining 2711 atoms. 5346 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2193 (Rfree = 0.000) for 2711 atoms. Found 10 (17 requested) and removed 9 (8 requested) atoms. Cycle 22: After refmac, R = 0.2077 (Rfree = 0.000) for 2699 atoms. Found 11 (17 requested) and removed 10 (8 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2031 (Rfree = 0.000) for 2690 atoms. Found 12 (17 requested) and removed 9 (8 requested) atoms. Cycle 24: After refmac, R = 0.1749 (Rfree = 0.000) for 2684 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. Cycle 25: After refmac, R = 0.1749 (Rfree = 0.000) for 2675 atoms. Found 4 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.63 Search for helices and strands: 0 residues in 0 chains, 2764 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 2783 seeds are put forward Round 1: 157 peptides, 34 chains. Longest chain 12 peptides. Score 0.269 Round 2: 170 peptides, 33 chains. Longest chain 12 peptides. Score 0.348 Round 3: 176 peptides, 31 chains. Longest chain 14 peptides. Score 0.410 Round 4: 166 peptides, 29 chains. Longest chain 10 peptides. Score 0.404 Round 5: 190 peptides, 34 chains. Longest chain 13 peptides. Score 0.415 Taking the results from Round 5 Chains 34, Residues 156, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4639 reflections ( 99.40 % complete ) and 6387 restraints for refining 2711 atoms. 5797 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2219 (Rfree = 0.000) for 2711 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 27: After refmac, R = 0.2309 (Rfree = 0.000) for 2696 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 28: After refmac, R = 0.2271 (Rfree = 0.000) for 2683 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2149 (Rfree = 0.000) for 2681 atoms. Found 16 (17 requested) and removed 10 (8 requested) atoms. Cycle 30: After refmac, R = 0.1681 (Rfree = 0.000) for 2679 atoms. Found 1 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.44 3.63 Search for helices and strands: 0 residues in 0 chains, 2783 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 2796 seeds are put forward Round 1: 131 peptides, 28 chains. Longest chain 10 peptides. Score 0.264 Round 2: 138 peptides, 24 chains. Longest chain 10 peptides. Score 0.376 Round 3: 156 peptides, 27 chains. Longest chain 8 peptides. Score 0.398 Round 4: 157 peptides, 26 chains. Longest chain 13 peptides. Score 0.420 Round 5: 153 peptides, 26 chains. Longest chain 12 peptides. Score 0.403 Taking the results from Round 4 Chains 26, Residues 131, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4639 reflections ( 99.40 % complete ) and 6368 restraints for refining 2688 atoms. 5870 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2433 (Rfree = 0.000) for 2688 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 32: After refmac, R = 0.2319 (Rfree = 0.000) for 2679 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 33: After refmac, R = 0.1901 (Rfree = 0.000) for 2672 atoms. Found 11 (17 requested) and removed 8 (8 requested) atoms. Cycle 34: After refmac, R = 0.1641 (Rfree = 0.000) for 2666 atoms. Found 5 (17 requested) and removed 9 (8 requested) atoms. Cycle 35: After refmac, R = 0.2263 (Rfree = 0.000) for 2658 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.49 3.68 Search for helices and strands: 0 residues in 0 chains, 2754 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2773 seeds are put forward Round 1: 115 peptides, 25 chains. Longest chain 7 peptides. Score 0.246 Round 2: 129 peptides, 23 chains. Longest chain 12 peptides. Score 0.355 Round 3: 141 peptides, 24 chains. Longest chain 10 peptides. Score 0.389 Round 4: 133 peptides, 23 chains. Longest chain 8 peptides. Score 0.373 Round 5: 134 peptides, 23 chains. Longest chain 10 peptides. Score 0.377 Taking the results from Round 3 Chains 24, Residues 117, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4639 reflections ( 99.40 % complete ) and 6245 restraints for refining 2655 atoms. 5784 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2056 (Rfree = 0.000) for 2655 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.1895 (Rfree = 0.000) for 2650 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1796 (Rfree = 0.000) for 2648 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1766 (Rfree = 0.000) for 2647 atoms. Found 15 (17 requested) and removed 12 (8 requested) atoms. Cycle 40: After refmac, R = 0.1455 (Rfree = 0.000) for 2646 atoms. Found 3 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.42 3.61 Search for helices and strands: 0 residues in 0 chains, 2738 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 2744 seeds are put forward Round 1: 111 peptides, 24 chains. Longest chain 8 peptides. Score 0.247 Round 2: 138 peptides, 24 chains. Longest chain 17 peptides. Score 0.376 Round 3: 124 peptides, 20 chains. Longest chain 13 peptides. Score 0.391 Round 4: 125 peptides, 19 chains. Longest chain 14 peptides. Score 0.415 Round 5: 129 peptides, 19 chains. Longest chain 13 peptides. Score 0.433 Taking the results from Round 5 Chains 19, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4639 reflections ( 99.40 % complete ) and 6476 restraints for refining 2712 atoms. 6055 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2308 (Rfree = 0.000) for 2712 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 42: After refmac, R = 0.2062 (Rfree = 0.000) for 2703 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1685 (Rfree = 0.000) for 2699 atoms. Found 5 (17 requested) and removed 9 (8 requested) atoms. Cycle 44: After refmac, R = 0.1624 (Rfree = 0.000) for 2692 atoms. Found 4 (17 requested) and removed 9 (8 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1654 (Rfree = 0.000) for 2686 atoms. Found 4 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 3.66 Search for helices and strands: 0 residues in 0 chains, 2758 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2774 seeds are put forward Round 1: 115 peptides, 25 chains. Longest chain 7 peptides. Score 0.246 Round 2: 130 peptides, 26 chains. Longest chain 10 peptides. Score 0.299 Round 3: 126 peptides, 23 chains. Longest chain 10 peptides. Score 0.341 Round 4: 138 peptides, 27 chains. Longest chain 8 peptides. Score 0.317 Round 5: 140 peptides, 28 chains. Longest chain 9 peptides. Score 0.307 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 103, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2opl-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4639 reflections ( 99.40 % complete ) and 6366 restraints for refining 2681 atoms. 5960 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2063 (Rfree = 0.000) for 2681 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.1951 (Rfree = 0.000) for 2668 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1932 (Rfree = 0.000) for 2656 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1669 (Rfree = 0.000) for 2645 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 50.71