null Tue 25 Dec 19:27:57 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-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2opl-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2opl-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opl-3.2-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-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opl-3.2-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 19:28:07 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-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opl-3.2-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 266 and 0 Target number of residues in the AU: 266 Target solvent content: 0.6145 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-3.2-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-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2992 target number of atoms Had to go as low as 0.70 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 3.200 Wilson plot Bfac: 58.42 6543 reflections ( 99.53 % complete ) and 0 restraints for refining 3308 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3134 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2702 (Rfree = 0.000) for 3308 atoms. Found 26 (29 requested) and removed 28 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.07 3.24 Search for helices and strands: 0 residues in 0 chains, 3394 seeds are put forward NCS extension: 0 residues added, 3394 seeds are put forward Round 1: 205 peptides, 35 chains. Longest chain 17 peptides. Score 0.458 Round 2: 254 peptides, 30 chains. Longest chain 24 peptides. Score 0.687 Round 3: 270 peptides, 30 chains. Longest chain 22 peptides. Score 0.725 Round 4: 258 peptides, 31 chains. Longest chain 21 peptides. Score 0.685 Round 5: 272 peptides, 31 chains. Longest chain 21 peptides. Score 0.719 Taking the results from Round 3 Chains 32, Residues 240, Estimated correctness of the model 70.3 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6543 reflections ( 99.53 % complete ) and 5702 restraints for refining 2732 atoms. 4731 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2352 (Rfree = 0.000) for 2732 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. Cycle 2: After refmac, R = 0.2252 (Rfree = 0.000) for 2715 atoms. Found 6 (24 requested) and removed 16 (12 requested) atoms. Cycle 3: After refmac, R = 0.2213 (Rfree = 0.000) for 2690 atoms. Found 8 (23 requested) and removed 12 (12 requested) atoms. Cycle 4: After refmac, R = 0.2306 (Rfree = 0.000) for 2675 atoms. Found 9 (23 requested) and removed 12 (12 requested) atoms. Cycle 5: After refmac, R = 0.2222 (Rfree = 0.000) for 2668 atoms. Found 17 (21 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.10 3.27 Search for helices and strands: 0 residues in 0 chains, 2782 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 2799 seeds are put forward Round 1: 247 peptides, 30 chains. Longest chain 23 peptides. Score 0.669 Round 2: 270 peptides, 27 chains. Longest chain 28 peptides. Score 0.755 Round 3: 281 peptides, 25 chains. Longest chain 34 peptides. Score 0.793 Round 4: 285 peptides, 27 chains. Longest chain 30 peptides. Score 0.783 Round 5: 277 peptides, 28 chains. Longest chain 31 peptides. Score 0.759 Taking the results from Round 3 Chains 28, Residues 256, Estimated correctness of the model 82.3 % 5 chains (77 residues) have been docked in sequence Building loops using Loopy2018 28 chains (256 residues) following loop building 5 chains (77 residues) in sequence following loop building ------------------------------------------------------ 6543 reflections ( 99.53 % complete ) and 5048 restraints for refining 2732 atoms. 3758 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2455 (Rfree = 0.000) for 2732 atoms. Found 18 (22 requested) and removed 22 (12 requested) atoms. Cycle 7: After refmac, R = 0.2344 (Rfree = 0.000) for 2711 atoms. Found 8 (21 requested) and removed 15 (12 requested) atoms. Cycle 8: After refmac, R = 0.2201 (Rfree = 0.000) for 2694 atoms. Found 10 (21 requested) and removed 14 (12 requested) atoms. Cycle 9: After refmac, R = 0.2142 (Rfree = 0.000) for 2686 atoms. Found 6 (20 requested) and removed 13 (12 requested) atoms. Cycle 10: After refmac, R = 0.2119 (Rfree = 0.000) for 2675 atoms. Found 8 (20 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.12 3.29 Search for helices and strands: 0 residues in 0 chains, 2743 seeds are put forward NCS extension: 21 residues added (7 deleted due to clashes), 2764 seeds are put forward Round 1: 245 peptides, 30 chains. Longest chain 22 peptides. Score 0.663 Round 2: 251 peptides, 26 chains. Longest chain 30 peptides. Score 0.724 Round 3: 245 peptides, 24 chains. Longest chain 26 peptides. Score 0.732 Round 4: 258 peptides, 27 chains. Longest chain 26 peptides. Score 0.729 Round 5: 262 peptides, 25 chains. Longest chain 23 peptides. Score 0.758 Taking the results from Round 5 Chains 28, Residues 237, Estimated correctness of the model 76.5 % 5 chains (73 residues) have been docked in sequence Building loops using Loopy2018 28 chains (237 residues) following loop building 5 chains (73 residues) in sequence following loop building ------------------------------------------------------ 6543 reflections ( 99.53 % complete ) and 5244 restraints for refining 2732 atoms. 4016 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2386 (Rfree = 0.000) for 2732 atoms. Found 18 (19 requested) and removed 18 (12 requested) atoms. Cycle 12: After refmac, R = 0.2131 (Rfree = 0.000) for 2726 atoms. Found 14 (19 requested) and removed 15 (12 requested) atoms. Cycle 13: After refmac, R = 0.2305 (Rfree = 0.000) for 2718 atoms. Found 18 (18 requested) and removed 18 (12 requested) atoms. Cycle 14: After refmac, R = 0.1973 (Rfree = 0.000) for 2708 atoms. Found 9 (18 requested) and removed 13 (12 requested) atoms. Cycle 15: After refmac, R = 0.1883 (Rfree = 0.000) for 2701 atoms. Found 9 (17 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.04 3.21 Search for helices and strands: 0 residues in 0 chains, 2789 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2809 seeds are put forward Round 1: 242 peptides, 29 chains. Longest chain 22 peptides. Score 0.667 Round 2: 257 peptides, 23 chains. Longest chain 38 peptides. Score 0.767 Round 3: 255 peptides, 25 chains. Longest chain 34 peptides. Score 0.743 Round 4: 268 peptides, 23 chains. Longest chain 36 peptides. Score 0.788 Round 5: 257 peptides, 26 chains. Longest chain 26 peptides. Score 0.737 Taking the results from Round 4 Chains 24, Residues 245, Estimated correctness of the model 81.6 % 3 chains (73 residues) have been docked in sequence Building loops using Loopy2018 24 chains (245 residues) following loop building 3 chains (73 residues) in sequence following loop building ------------------------------------------------------ 6543 reflections ( 99.53 % complete ) and 5258 restraints for refining 2732 atoms. 4014 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2291 (Rfree = 0.000) for 2732 atoms. Found 17 (17 requested) and removed 28 (12 requested) atoms. Cycle 17: After refmac, R = 0.2041 (Rfree = 0.000) for 2712 atoms. Found 11 (16 requested) and removed 13 (12 requested) atoms. Cycle 18: After refmac, R = 0.1973 (Rfree = 0.000) for 2706 atoms. Found 7 (16 requested) and removed 12 (12 requested) atoms. Cycle 19: After refmac, R = 0.1920 (Rfree = 0.000) for 2699 atoms. Found 8 (15 requested) and removed 12 (12 requested) atoms. Cycle 20: After refmac, R = 0.1782 (Rfree = 0.000) for 2689 atoms. Found 4 (15 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.10 3.27 Search for helices and strands: 0 residues in 0 chains, 2753 seeds are put forward NCS extension: 30 residues added (5 deleted due to clashes), 2783 seeds are put forward Round 1: 256 peptides, 27 chains. Longest chain 25 peptides. Score 0.725 Round 2: 261 peptides, 25 chains. Longest chain 26 peptides. Score 0.756 Round 3: 259 peptides, 26 chains. Longest chain 26 peptides. Score 0.742 Round 4: 258 peptides, 24 chains. Longest chain 27 peptides. Score 0.760 Round 5: 269 peptides, 26 chains. Longest chain 25 peptides. Score 0.762 Taking the results from Round 5 Chains 28, Residues 243, Estimated correctness of the model 77.2 % 4 chains (61 residues) have been docked in sequence Building loops using Loopy2018 28 chains (243 residues) following loop building 4 chains (61 residues) in sequence following loop building ------------------------------------------------------ 6543 reflections ( 99.53 % complete ) and 5316 restraints for refining 2731 atoms. 4127 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2319 (Rfree = 0.000) for 2731 atoms. Found 14 (14 requested) and removed 18 (12 requested) atoms. Cycle 22: After refmac, R = 0.2101 (Rfree = 0.000) for 2721 atoms. Found 8 (14 requested) and removed 13 (12 requested) atoms. Cycle 23: After refmac, R = 0.1953 (Rfree = 0.000) for 2712 atoms. Found 2 (13 requested) and removed 12 (12 requested) atoms. Cycle 24: After refmac, R = 0.1939 (Rfree = 0.000) for 2696 atoms. Found 6 (13 requested) and removed 12 (12 requested) atoms. Cycle 25: After refmac, R = 0.1923 (Rfree = 0.000) for 2690 atoms. Found 8 (12 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.11 3.28 Search for helices and strands: 0 residues in 0 chains, 2770 seeds are put forward NCS extension: 17 residues added (6 deleted due to clashes), 2787 seeds are put forward Round 1: 247 peptides, 32 chains. Longest chain 17 peptides. Score 0.644 Round 2: 259 peptides, 31 chains. Longest chain 27 peptides. Score 0.688 Round 3: 255 peptides, 30 chains. Longest chain 25 peptides. Score 0.689 Round 4: 254 peptides, 29 chains. Longest chain 28 peptides. Score 0.698 Round 5: 256 peptides, 30 chains. Longest chain 25 peptides. Score 0.692 Taking the results from Round 4 Chains 29, Residues 225, Estimated correctness of the model 64.8 % 2 chains (32 residues) have been docked in sequence ------------------------------------------------------ 6543 reflections ( 99.53 % complete ) and 5720 restraints for refining 2731 atoms. 4707 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2271 (Rfree = 0.000) for 2731 atoms. Found 12 (12 requested) and removed 16 (12 requested) atoms. Cycle 27: After refmac, R = 0.2395 (Rfree = 0.000) for 2721 atoms. Found 8 (12 requested) and removed 12 (12 requested) atoms. Cycle 28: After refmac, R = 0.2110 (Rfree = 0.000) for 2712 atoms. Found 6 (12 requested) and removed 12 (12 requested) atoms. Cycle 29: After refmac, R = 0.2028 (Rfree = 0.000) for 2704 atoms. Found 1 (12 requested) and removed 12 (12 requested) atoms. Cycle 30: After refmac, R = 0.2033 (Rfree = 0.000) for 2691 atoms. Found 4 (12 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.13 3.30 Search for helices and strands: 0 residues in 0 chains, 2757 seeds are put forward NCS extension: 37 residues added (4 deleted due to clashes), 2794 seeds are put forward Round 1: 222 peptides, 34 chains. Longest chain 18 peptides. Score 0.537 Round 2: 240 peptides, 26 chains. Longest chain 21 peptides. Score 0.698 Round 3: 239 peptides, 27 chains. Longest chain 30 peptides. Score 0.683 Round 4: 237 peptides, 27 chains. Longest chain 23 peptides. Score 0.678 Round 5: 242 peptides, 32 chains. Longest chain 20 peptides. Score 0.629 Taking the results from Round 2 Chains 30, Residues 214, Estimated correctness of the model 64.8 % 3 chains (44 residues) have been docked in sequence ------------------------------------------------------ 6543 reflections ( 99.53 % complete ) and 5699 restraints for refining 2732 atoms. 4679 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2276 (Rfree = 0.000) for 2732 atoms. Found 12 (12 requested) and removed 15 (12 requested) atoms. Cycle 32: After refmac, R = 0.2132 (Rfree = 0.000) for 2723 atoms. Found 7 (12 requested) and removed 13 (12 requested) atoms. Cycle 33: After refmac, R = 0.2128 (Rfree = 0.000) for 2711 atoms. Found 4 (12 requested) and removed 12 (12 requested) atoms. Cycle 34: After refmac, R = 0.2140 (Rfree = 0.000) for 2702 atoms. Found 6 (12 requested) and removed 12 (12 requested) atoms. Cycle 35: After refmac, R = 0.2104 (Rfree = 0.000) for 2694 atoms. Found 1 (12 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.10 3.27 Search for helices and strands: 0 residues in 0 chains, 2768 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2787 seeds are put forward Round 1: 217 peptides, 26 chains. Longest chain 22 peptides. Score 0.635 Round 2: 228 peptides, 27 chains. Longest chain 24 peptides. Score 0.654 Round 3: 244 peptides, 30 chains. Longest chain 19 peptides. Score 0.660 Round 4: 234 peptides, 28 chains. Longest chain 22 peptides. Score 0.658 Round 5: 238 peptides, 29 chains. Longest chain 23 peptides. Score 0.656 Taking the results from Round 3 Chains 31, Residues 214, Estimated correctness of the model 56.2 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 6543 reflections ( 99.53 % complete ) and 5842 restraints for refining 2732 atoms. 4914 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2251 (Rfree = 0.000) for 2732 atoms. Found 12 (12 requested) and removed 15 (12 requested) atoms. Cycle 37: After refmac, R = 0.2116 (Rfree = 0.000) for 2720 atoms. Found 6 (12 requested) and removed 12 (12 requested) atoms. Cycle 38: After refmac, R = 0.2238 (Rfree = 0.000) for 2711 atoms. Found 8 (12 requested) and removed 15 (12 requested) atoms. Cycle 39: After refmac, R = 0.2258 (Rfree = 0.000) for 2703 atoms. Found 6 (12 requested) and removed 14 (12 requested) atoms. Cycle 40: After refmac, R = 0.2049 (Rfree = 0.000) for 2694 atoms. Found 5 (12 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.12 3.29 Search for helices and strands: 0 residues in 0 chains, 2762 seeds are put forward NCS extension: 11 residues added (8 deleted due to clashes), 2773 seeds are put forward Round 1: 195 peptides, 28 chains. Longest chain 21 peptides. Score 0.534 Round 2: 210 peptides, 29 chains. Longest chain 21 peptides. Score 0.571 Round 3: 208 peptides, 26 chains. Longest chain 18 peptides. Score 0.608 Round 4: 218 peptides, 25 chains. Longest chain 19 peptides. Score 0.651 Round 5: 229 peptides, 28 chains. Longest chain 25 peptides. Score 0.644 Taking the results from Round 4 Chains 25, Residues 193, Estimated correctness of the model 54.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6543 reflections ( 99.53 % complete ) and 6251 restraints for refining 2732 atoms. 5504 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2250 (Rfree = 0.000) for 2732 atoms. Found 9 (12 requested) and removed 12 (12 requested) atoms. Cycle 42: After refmac, R = 0.2517 (Rfree = 0.000) for 2726 atoms. Found 12 (12 requested) and removed 13 (12 requested) atoms. Cycle 43: After refmac, R = 0.2347 (Rfree = 0.000) for 2723 atoms. Found 12 (12 requested) and removed 12 (12 requested) atoms. Cycle 44: After refmac, R = 0.2301 (Rfree = 0.000) for 2723 atoms. Found 12 (12 requested) and removed 12 (12 requested) atoms. Cycle 45: After refmac, R = 0.2340 (Rfree = 0.000) for 2722 atoms. Found 12 (12 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.10 3.27 Search for helices and strands: 0 residues in 0 chains, 2810 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 2836 seeds are put forward Round 1: 169 peptides, 28 chains. Longest chain 12 peptides. Score 0.434 Round 2: 209 peptides, 25 chains. Longest chain 20 peptides. Score 0.625 Round 3: 207 peptides, 29 chains. Longest chain 21 peptides. Score 0.561 Round 4: 209 peptides, 27 chains. Longest chain 19 peptides. Score 0.597 Round 5: 206 peptides, 29 chains. Longest chain 19 peptides. Score 0.557 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 184, Estimated correctness of the model 47.6 % 2 chains (19 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2opl-3_warpNtrace.pdb as input Building loops using Loopy2018 26 chains (184 residues) following loop building 2 chains (19 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6543 reflections ( 99.53 % complete ) and 6124 restraints for refining 2731 atoms. 5343 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2366 (Rfree = 0.000) for 2731 atoms. Found 0 (12 requested) and removed 10 (12 requested) atoms. Cycle 47: After refmac, R = 0.2258 (Rfree = 0.000) for 2721 atoms. Found 0 (12 requested) and removed 4 (12 requested) atoms. Cycle 48: After refmac, R = 0.2503 (Rfree = 0.000) for 2714 atoms. Found 0 (12 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.2232 (Rfree = 0.000) for 2700 atoms. Found 0 (12 requested) and removed 9 (12 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:22:19 GMT 2018 Job finished. TimeTaking 54.37 Used memory is bytes: 12880992