Mon 24 Dec 00:30:32 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 2opl-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2opl-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2opl-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opl-3.6-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/2opl-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opl-3.6-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 00:30:37 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/2opl-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opl-3.6-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 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-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: 19 Cell parameters: 47.200 82.950 95.370 90.000 90.000 90.000 Input sequence file: 2opl-3.6-parrot-mrncs.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 3326 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3251 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3107 (Rfree = 0.000) for 3326 atoms. Found 21 (21 requested) and removed 25 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.53 3.72 Search for helices and strands: 0 residues in 0 chains, 3373 seeds are put forward NCS extension: 0 residues added, 3373 seeds are put forward Round 1: 158 peptides, 32 chains. Longest chain 9 peptides. Score 0.312 Round 2: 194 peptides, 32 chains. Longest chain 15 peptides. Score 0.465 Round 3: 204 peptides, 30 chains. Longest chain 13 peptides. Score 0.535 Round 4: 188 peptides, 26 chains. Longest chain 14 peptides. Score 0.541 Round 5: 213 peptides, 33 chains. Longest chain 16 peptides. Score 0.521 Taking the results from Round 4 Chains 26, Residues 162, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 4639 reflections ( 99.40 % complete ) and 6145 restraints for refining 2712 atoms. 5464 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2594 (Rfree = 0.000) for 2712 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 2: After refmac, R = 0.2561 (Rfree = 0.000) for 2685 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 3: After refmac, R = 0.2544 (Rfree = 0.000) for 2679 atoms. Found 13 (17 requested) and removed 19 (8 requested) atoms. Cycle 4: After refmac, R = 0.2368 (Rfree = 0.000) for 2656 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 5: After refmac, R = 0.2304 (Rfree = 0.000) for 2648 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.47 3.66 Search for helices and strands: 0 residues in 0 chains, 2749 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2764 seeds are put forward Round 1: 169 peptides, 32 chains. Longest chain 9 peptides. Score 0.362 Round 2: 199 peptides, 31 chains. Longest chain 14 peptides. Score 0.501 Round 3: 214 peptides, 30 chains. Longest chain 17 peptides. Score 0.569 Round 4: 219 peptides, 31 chains. Longest chain 17 peptides. Score 0.571 Round 5: 215 peptides, 32 chains. Longest chain 18 peptides. Score 0.543 Taking the results from Round 4 Chains 31, Residues 188, Estimated correctness of the model 3.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4639 reflections ( 99.40 % complete ) and 6126 restraints for refining 2712 atoms. 5405 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2362 (Rfree = 0.000) for 2712 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2150 (Rfree = 0.000) for 2691 atoms. Found 16 (17 requested) and removed 18 (8 requested) atoms. Cycle 8: After refmac, R = 0.2029 (Rfree = 0.000) for 2679 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 9: After refmac, R = 0.1931 (Rfree = 0.000) for 2680 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 10: After refmac, R = 0.1948 (Rfree = 0.000) for 2683 atoms. Found 15 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.38 3.57 Search for helices and strands: 0 residues in 0 chains, 2807 seeds are put forward NCS extension: 23 residues added (6 deleted due to clashes), 2830 seeds are put forward Round 1: 168 peptides, 30 chains. Longest chain 10 peptides. Score 0.394 Round 2: 180 peptides, 25 chains. Longest chain 19 peptides. Score 0.528 Round 3: 196 peptides, 28 chains. Longest chain 20 peptides. Score 0.538 Round 4: 202 peptides, 26 chains. Longest chain 21 peptides. Score 0.589 Round 5: 201 peptides, 26 chains. Longest chain 27 peptides. Score 0.585 Taking the results from Round 4 Chains 26, Residues 176, Estimated correctness of the model 10.3 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4639 reflections ( 99.40 % complete ) and 6180 restraints for refining 2712 atoms. 5487 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2142 (Rfree = 0.000) for 2712 atoms. Found 12 (17 requested) and removed 15 (8 requested) atoms. Cycle 12: After refmac, R = 0.2139 (Rfree = 0.000) for 2696 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 13: After refmac, R = 0.1973 (Rfree = 0.000) for 2691 atoms. Found 16 (17 requested) and removed 11 (8 requested) atoms. Cycle 14: After refmac, R = 0.1915 (Rfree = 0.000) for 2688 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 15: After refmac, R = 0.1798 (Rfree = 0.000) for 2692 atoms. Found 16 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.58 Search for helices and strands: 0 residues in 0 chains, 2766 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 2786 seeds are put forward Round 1: 180 peptides, 32 chains. Longest chain 13 peptides. Score 0.409 Round 2: 185 peptides, 27 chains. Longest chain 14 peptides. Score 0.514 Round 3: 206 peptides, 28 chains. Longest chain 20 peptides. Score 0.572 Round 4: 201 peptides, 28 chains. Longest chain 15 peptides. Score 0.555 Round 5: 197 peptides, 30 chains. Longest chain 12 peptides. Score 0.510 Taking the results from Round 3 Chains 30, Residues 178, Estimated correctness of the model 3.4 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4639 reflections ( 99.40 % complete ) and 6097 restraints for refining 2711 atoms. 5382 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2045 (Rfree = 0.000) for 2711 atoms. Found 7 (17 requested) and removed 15 (8 requested) atoms. Cycle 17: After refmac, R = 0.2171 (Rfree = 0.000) for 2690 atoms. Found 11 (17 requested) and removed 11 (8 requested) atoms. Cycle 18: After refmac, R = 0.2108 (Rfree = 0.000) for 2683 atoms. Found 12 (17 requested) and removed 13 (8 requested) atoms. Cycle 19: After refmac, R = 0.1916 (Rfree = 0.000) for 2676 atoms. Found 9 (17 requested) and removed 10 (8 requested) atoms. Cycle 20: After refmac, R = 0.2004 (Rfree = 0.000) for 2671 atoms. Found 11 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 3.62 Search for helices and strands: 0 residues in 0 chains, 2750 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 2768 seeds are put forward Round 1: 168 peptides, 29 chains. Longest chain 11 peptides. Score 0.412 Round 2: 188 peptides, 27 chains. Longest chain 15 peptides. Score 0.525 Round 3: 193 peptides, 25 chains. Longest chain 22 peptides. Score 0.574 Round 4: 189 peptides, 24 chains. Longest chain 16 peptides. Score 0.575 Round 5: 198 peptides, 24 chains. Longest chain 15 peptides. Score 0.605 Taking the results from Round 5 Chains 24, Residues 174, Estimated correctness of the model 16.6 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 4639 reflections ( 99.40 % complete ) and 5895 restraints for refining 2711 atoms. 5147 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1960 (Rfree = 0.000) for 2711 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 22: After refmac, R = 0.1789 (Rfree = 0.000) for 2700 atoms. Found 10 (17 requested) and removed 9 (8 requested) atoms. Cycle 23: After refmac, R = 0.1746 (Rfree = 0.000) for 2697 atoms. Found 7 (17 requested) and removed 12 (8 requested) atoms. Cycle 24: After refmac, R = 0.1949 (Rfree = 0.000) for 2691 atoms. Found 15 (17 requested) and removed 13 (8 requested) atoms. Cycle 25: After refmac, R = 0.1643 (Rfree = 0.000) for 2683 atoms. Found 4 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 3.62 Search for helices and strands: 0 residues in 0 chains, 2748 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 2770 seeds are put forward Round 1: 162 peptides, 30 chains. Longest chain 12 peptides. Score 0.368 Round 2: 171 peptides, 27 chains. Longest chain 14 peptides. Score 0.460 Round 3: 180 peptides, 26 chains. Longest chain 17 peptides. Score 0.512 Round 4: 176 peptides, 25 chains. Longest chain 17 peptides. Score 0.513 Round 5: 184 peptides, 27 chains. Longest chain 15 peptides. Score 0.510 Taking the results from Round 4 Chains 27, Residues 151, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4639 reflections ( 99.40 % complete ) and 6169 restraints for refining 2712 atoms. 5550 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1911 (Rfree = 0.000) for 2712 atoms. Found 15 (17 requested) and removed 11 (8 requested) atoms. Cycle 27: After refmac, R = 0.1809 (Rfree = 0.000) for 2706 atoms. Found 10 (17 requested) and removed 8 (8 requested) atoms. Cycle 28: After refmac, R = 0.1850 (Rfree = 0.000) for 2705 atoms. Found 15 (17 requested) and removed 9 (8 requested) atoms. Cycle 29: After refmac, R = 0.1789 (Rfree = 0.000) for 2708 atoms. Found 8 (17 requested) and removed 9 (8 requested) atoms. Cycle 30: After refmac, R = 0.1557 (Rfree = 0.000) for 2700 atoms. Found 1 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.42 3.61 Search for helices and strands: 0 residues in 0 chains, 2777 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2791 seeds are put forward Round 1: 122 peptides, 26 chains. Longest chain 8 peptides. Score 0.260 Round 2: 164 peptides, 30 chains. Longest chain 11 peptides. Score 0.377 Round 3: 165 peptides, 28 chains. Longest chain 18 peptides. Score 0.418 Round 4: 166 peptides, 26 chains. Longest chain 15 peptides. Score 0.458 Round 5: 164 peptides, 27 chains. Longest chain 13 peptides. Score 0.432 Taking the results from Round 4 Chains 26, Residues 140, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4639 reflections ( 99.40 % complete ) and 6286 restraints for refining 2712 atoms. 5719 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1921 (Rfree = 0.000) for 2712 atoms. Found 12 (17 requested) and removed 10 (8 requested) atoms. Cycle 32: After refmac, R = 0.1814 (Rfree = 0.000) for 2706 atoms. Found 7 (17 requested) and removed 9 (8 requested) atoms. Cycle 33: After refmac, R = 0.1689 (Rfree = 0.000) for 2698 atoms. Found 5 (17 requested) and removed 11 (8 requested) atoms. Cycle 34: After refmac, R = 0.1679 (Rfree = 0.000) for 2689 atoms. Found 1 (17 requested) and removed 8 (8 requested) atoms. Cycle 35: After refmac, R = 0.1633 (Rfree = 0.000) for 2678 atoms. Found 2 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.42 3.61 Search for helices and strands: 0 residues in 0 chains, 2763 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2782 seeds are put forward Round 1: 146 peptides, 26 chains. Longest chain 13 peptides. Score 0.373 Round 2: 161 peptides, 28 chains. Longest chain 11 peptides. Score 0.401 Round 3: 160 peptides, 26 chains. Longest chain 12 peptides. Score 0.433 Round 4: 154 peptides, 26 chains. Longest chain 11 peptides. Score 0.408 Round 5: 158 peptides, 24 chains. Longest chain 12 peptides. Score 0.461 Taking the results from Round 5 Chains 24, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4639 reflections ( 99.40 % complete ) and 6494 restraints for refining 2711 atoms. 5982 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1824 (Rfree = 0.000) for 2711 atoms. Found 11 (17 requested) and removed 10 (8 requested) atoms. Cycle 37: After refmac, R = 0.1756 (Rfree = 0.000) for 2707 atoms. Found 12 (17 requested) and removed 9 (8 requested) atoms. Cycle 38: After refmac, R = 0.1842 (Rfree = 0.000) for 2707 atoms. Found 16 (17 requested) and removed 9 (8 requested) atoms. Cycle 39: After refmac, R = 0.1528 (Rfree = 0.000) for 2710 atoms. Found 2 (17 requested) and removed 10 (8 requested) atoms. Cycle 40: After refmac, R = 0.1701 (Rfree = 0.000) for 2700 atoms. Found 16 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.41 3.60 Search for helices and strands: 0 residues in 0 chains, 2786 seeds are put forward NCS extension: 7 residues added (0 deleted due to clashes), 2793 seeds are put forward Round 1: 117 peptides, 23 chains. Longest chain 11 peptides. Score 0.298 Round 2: 144 peptides, 24 chains. Longest chain 12 peptides. Score 0.402 Round 3: 158 peptides, 25 chains. Longest chain 13 peptides. Score 0.443 Round 4: 152 peptides, 25 chains. Longest chain 12 peptides. Score 0.418 Round 5: 154 peptides, 25 chains. Longest chain 12 peptides. Score 0.426 Taking the results from Round 3 Chains 25, Residues 133, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4639 reflections ( 99.40 % complete ) and 6437 restraints for refining 2712 atoms. 5930 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1832 (Rfree = 0.000) for 2712 atoms. Found 11 (17 requested) and removed 10 (8 requested) atoms. Cycle 42: After refmac, R = 0.1991 (Rfree = 0.000) for 2708 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 43: After refmac, R = 0.1918 (Rfree = 0.000) for 2706 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 44: After refmac, R = 0.1553 (Rfree = 0.000) for 2706 atoms. Found 4 (17 requested) and removed 9 (8 requested) atoms. Cycle 45: After refmac, R = 0.1454 (Rfree = 0.000) for 2699 atoms. Found 3 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.44 3.63 Search for helices and strands: 0 residues in 0 chains, 2761 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2777 seeds are put forward Round 1: 122 peptides, 25 chains. Longest chain 11 peptides. Score 0.281 Round 2: 133 peptides, 23 chains. Longest chain 11 peptides. Score 0.373 Round 3: 136 peptides, 23 chains. Longest chain 11 peptides. Score 0.386 Round 4: 143 peptides, 25 chains. Longest chain 11 peptides. Score 0.379 Round 5: 140 peptides, 25 chains. Longest chain 11 peptides. Score 0.365 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 113, 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 2opl-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4639 reflections ( 99.40 % complete ) and 6517 restraints for refining 2705 atoms. 6088 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2102 (Rfree = 0.000) for 2705 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2052 (Rfree = 0.000) for 2688 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1635 (Rfree = 0.000) for 2674 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1503 (Rfree = 0.000) for 2663 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... TimeTaking 31.15