null Sun 23 Dec 22:22:42 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 2a6a-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a6a-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a6a-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6a-4.0-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/2a6a-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6a-4.0-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 22:22:57 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/2a6a-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6a-4.0-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 310 and 0 Target number of residues in the AU: 310 Target solvent content: 0.6814 Checking the provided sequence file Detected sequence length: 218 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 436 Adjusted target solvent content: 0.55 Input MTZ file: 2a6a-4.0-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: 21 Cell parameters: 93.313 217.176 51.977 90.000 90.000 90.000 Input sequence file: 2a6a-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3488 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: 108.588 4.000 Wilson plot Bfac: 102.25 4693 reflections ( 98.41 % complete ) and 0 restraints for refining 3857 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3636 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3446 (Rfree = 0.000) for 3857 atoms. Found 18 (18 requested) and removed 42 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.93 3.68 Search for helices and strands: 0 residues in 0 chains, 3896 seeds are put forward NCS extension: 0 residues added, 3896 seeds are put forward Round 1: 128 peptides, 26 chains. Longest chain 7 peptides. Score 0.263 Round 2: 160 peptides, 26 chains. Longest chain 15 peptides. Score 0.375 Round 3: 175 peptides, 28 chains. Longest chain 15 peptides. Score 0.394 Round 4: 186 peptides, 29 chains. Longest chain 13 peptides. Score 0.415 Round 5: 195 peptides, 33 chains. Longest chain 13 peptides. Score 0.388 Taking the results from Round 4 Chains 29, Residues 157, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4693 reflections ( 98.41 % complete ) and 7682 restraints for refining 3150 atoms. 7043 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2689 (Rfree = 0.000) for 3150 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. Cycle 2: After refmac, R = 0.2643 (Rfree = 0.000) for 3051 atoms. Found 14 (14 requested) and removed 29 (7 requested) atoms. Cycle 3: After refmac, R = 0.2586 (Rfree = 0.000) for 2996 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 4: After refmac, R = 0.2550 (Rfree = 0.000) for 2950 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 5: After refmac, R = 0.2492 (Rfree = 0.000) for 2913 atoms. Found 13 (13 requested) and removed 28 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.89 3.64 Search for helices and strands: 0 residues in 0 chains, 2995 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 3005 seeds are put forward Round 1: 168 peptides, 32 chains. Longest chain 9 peptides. Score 0.314 Round 2: 208 peptides, 31 chains. Longest chain 17 peptides. Score 0.454 Round 3: 204 peptides, 31 chains. Longest chain 13 peptides. Score 0.442 Round 4: 223 peptides, 32 chains. Longest chain 17 peptides. Score 0.484 Round 5: 203 peptides, 30 chains. Longest chain 16 peptides. Score 0.452 Taking the results from Round 4 Chains 34, Residues 191, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 4693 reflections ( 98.41 % complete ) and 6363 restraints for refining 2920 atoms. 5597 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2448 (Rfree = 0.000) for 2920 atoms. Found 13 (13 requested) and removed 41 (6 requested) atoms. Cycle 7: After refmac, R = 0.2254 (Rfree = 0.000) for 2859 atoms. Found 13 (13 requested) and removed 26 (6 requested) atoms. Cycle 8: After refmac, R = 0.2304 (Rfree = 0.000) for 2835 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 9: After refmac, R = 0.2193 (Rfree = 0.000) for 2808 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 10: After refmac, R = 0.2293 (Rfree = 0.000) for 2781 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.94 3.69 Search for helices and strands: 0 residues in 0 chains, 2901 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 2920 seeds are put forward Round 1: 173 peptides, 33 chains. Longest chain 10 peptides. Score 0.317 Round 2: 204 peptides, 28 chains. Longest chain 20 peptides. Score 0.481 Round 3: 198 peptides, 30 chains. Longest chain 16 peptides. Score 0.438 Round 4: 197 peptides, 27 chains. Longest chain 14 peptides. Score 0.474 Round 5: 215 peptides, 31 chains. Longest chain 17 peptides. Score 0.474 Taking the results from Round 2 Chains 29, Residues 176, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4693 reflections ( 98.41 % complete ) and 6169 restraints for refining 2875 atoms. 5453 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2242 (Rfree = 0.000) for 2875 atoms. Found 12 (13 requested) and removed 37 (6 requested) atoms. Cycle 12: After refmac, R = 0.2204 (Rfree = 0.000) for 2835 atoms. Found 13 (13 requested) and removed 24 (6 requested) atoms. Cycle 13: After refmac, R = 0.2034 (Rfree = 0.000) for 2815 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 14: After refmac, R = 0.1974 (Rfree = 0.000) for 2802 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 15: After refmac, R = 0.1856 (Rfree = 0.000) for 2788 atoms. Found 13 (13 requested) and removed 21 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.95 3.69 Search for helices and strands: 0 residues in 0 chains, 2900 seeds are put forward NCS extension: 0 residues added, 2900 seeds are put forward Round 1: 172 peptides, 30 chains. Longest chain 12 peptides. Score 0.356 Round 2: 193 peptides, 26 chains. Longest chain 17 peptides. Score 0.476 Round 3: 197 peptides, 25 chains. Longest chain 16 peptides. Score 0.500 Round 4: 194 peptides, 25 chains. Longest chain 20 peptides. Score 0.491 Round 5: 200 peptides, 27 chains. Longest chain 15 peptides. Score 0.483 Taking the results from Round 3 Chains 25, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4693 reflections ( 98.41 % complete ) and 6477 restraints for refining 2904 atoms. 5814 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2177 (Rfree = 0.000) for 2904 atoms. Found 13 (13 requested) and removed 43 (6 requested) atoms. Cycle 17: After refmac, R = 0.2291 (Rfree = 0.000) for 2856 atoms. Found 13 (13 requested) and removed 34 (6 requested) atoms. Cycle 18: After refmac, R = 0.2111 (Rfree = 0.000) for 2829 atoms. Found 13 (13 requested) and removed 29 (6 requested) atoms. Cycle 19: After refmac, R = 0.2365 (Rfree = 0.000) for 2801 atoms. Found 13 (13 requested) and removed 25 (6 requested) atoms. Cycle 20: After refmac, R = 0.2133 (Rfree = 0.000) for 2771 atoms. Found 13 (13 requested) and removed 21 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.95 3.69 Search for helices and strands: 0 residues in 0 chains, 2905 seeds are put forward NCS extension: 0 residues added, 2905 seeds are put forward Round 1: 174 peptides, 32 chains. Longest chain 9 peptides. Score 0.334 Round 2: 197 peptides, 32 chains. Longest chain 11 peptides. Score 0.408 Round 3: 199 peptides, 34 chains. Longest chain 11 peptides. Score 0.387 Round 4: 197 peptides, 30 chains. Longest chain 16 peptides. Score 0.435 Round 5: 219 peptides, 34 chains. Longest chain 11 peptides. Score 0.447 Taking the results from Round 5 Chains 34, Residues 185, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4693 reflections ( 98.41 % complete ) and 6782 restraints for refining 3033 atoms. 6076 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2366 (Rfree = 0.000) for 3033 atoms. Found 14 (14 requested) and removed 63 (7 requested) atoms. Cycle 22: After refmac, R = 0.2189 (Rfree = 0.000) for 2954 atoms. Found 14 (14 requested) and removed 33 (7 requested) atoms. Cycle 23: After refmac, R = 0.2213 (Rfree = 0.000) for 2908 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. Cycle 24: After refmac, R = 0.2004 (Rfree = 0.000) for 2881 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 25: After refmac, R = 0.2221 (Rfree = 0.000) for 2859 atoms. Found 13 (13 requested) and removed 25 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.90 3.65 Search for helices and strands: 0 residues in 0 chains, 3023 seeds are put forward NCS extension: 0 residues added, 3023 seeds are put forward Round 1: 154 peptides, 30 chains. Longest chain 10 peptides. Score 0.295 Round 2: 177 peptides, 27 chains. Longest chain 17 peptides. Score 0.415 Round 3: 195 peptides, 30 chains. Longest chain 17 peptides. Score 0.429 Round 4: 195 peptides, 29 chains. Longest chain 17 peptides. Score 0.442 Round 5: 199 peptides, 28 chains. Longest chain 17 peptides. Score 0.467 Taking the results from Round 5 Chains 29, Residues 171, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4693 reflections ( 98.41 % complete ) and 6949 restraints for refining 3072 atoms. 6264 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2387 (Rfree = 0.000) for 3072 atoms. Found 14 (14 requested) and removed 56 (7 requested) atoms. Cycle 27: After refmac, R = 0.2361 (Rfree = 0.000) for 3011 atoms. Found 14 (14 requested) and removed 49 (7 requested) atoms. Cycle 28: After refmac, R = 0.2135 (Rfree = 0.000) for 2950 atoms. Found 14 (14 requested) and removed 49 (7 requested) atoms. Cycle 29: After refmac, R = 0.1581 (Rfree = 0.000) for 2891 atoms. Found 8 (13 requested) and removed 11 (6 requested) atoms. Cycle 30: After refmac, R = 0.1390 (Rfree = 0.000) for 2881 atoms. Found 4 (13 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.90 3.65 Search for helices and strands: 0 residues in 0 chains, 2985 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3004 seeds are put forward Round 1: 151 peptides, 32 chains. Longest chain 8 peptides. Score 0.254 Round 2: 177 peptides, 31 chains. Longest chain 12 peptides. Score 0.359 Round 3: 178 peptides, 28 chains. Longest chain 14 peptides. Score 0.404 Round 4: 174 peptides, 26 chains. Longest chain 15 peptides. Score 0.419 Round 5: 180 peptides, 28 chains. Longest chain 19 peptides. Score 0.410 Taking the results from Round 4 Chains 26, Residues 148, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4693 reflections ( 98.41 % complete ) and 6937 restraints for refining 3000 atoms. 6371 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2282 (Rfree = 0.000) for 3000 atoms. Found 14 (14 requested) and removed 34 (7 requested) atoms. Cycle 32: After refmac, R = 0.2302 (Rfree = 0.000) for 2959 atoms. Found 14 (14 requested) and removed 24 (7 requested) atoms. Cycle 33: After refmac, R = 0.2216 (Rfree = 0.000) for 2933 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 34: After refmac, R = 0.2221 (Rfree = 0.000) for 2913 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 35: After refmac, R = 0.2113 (Rfree = 0.000) for 2894 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.90 3.65 Search for helices and strands: 0 residues in 0 chains, 3013 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 3043 seeds are put forward Round 1: 129 peptides, 26 chains. Longest chain 9 peptides. Score 0.267 Round 2: 165 peptides, 29 chains. Longest chain 13 peptides. Score 0.348 Round 3: 163 peptides, 26 chains. Longest chain 16 peptides. Score 0.385 Round 4: 162 peptides, 28 chains. Longest chain 15 peptides. Score 0.352 Round 5: 164 peptides, 28 chains. Longest chain 16 peptides. Score 0.359 Taking the results from Round 3 Chains 26, Residues 137, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4693 reflections ( 98.41 % complete ) and 6482 restraints for refining 2870 atoms. 5960 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2179 (Rfree = 0.000) for 2870 atoms. Found 13 (13 requested) and removed 69 (6 requested) atoms. Cycle 37: After refmac, R = 0.1940 (Rfree = 0.000) for 2801 atoms. Found 13 (13 requested) and removed 32 (6 requested) atoms. Cycle 38: After refmac, R = 0.2112 (Rfree = 0.000) for 2775 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 39: After refmac, R = 0.2103 (Rfree = 0.000) for 2766 atoms. Found 13 (13 requested) and removed 28 (6 requested) atoms. Cycle 40: After refmac, R = 0.2157 (Rfree = 0.000) for 2743 atoms. Found 13 (13 requested) and removed 24 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.81 3.56 Search for helices and strands: 0 residues in 0 chains, 2854 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 2885 seeds are put forward Round 1: 143 peptides, 26 chains. Longest chain 13 peptides. Score 0.317 Round 2: 157 peptides, 27 chains. Longest chain 11 peptides. Score 0.350 Round 3: 144 peptides, 23 chains. Longest chain 14 peptides. Score 0.366 Round 4: 150 peptides, 24 chains. Longest chain 14 peptides. Score 0.371 Round 5: 142 peptides, 24 chains. Longest chain 12 peptides. Score 0.344 Taking the results from Round 4 Chains 24, Residues 126, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4693 reflections ( 98.41 % complete ) and 6591 restraints for refining 2856 atoms. 6111 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2301 (Rfree = 0.000) for 2856 atoms. Found 13 (13 requested) and removed 23 (6 requested) atoms. Cycle 42: After refmac, R = 0.2186 (Rfree = 0.000) for 2829 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 43: After refmac, R = 0.2312 (Rfree = 0.000) for 2814 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 44: After refmac, R = 0.2312 (Rfree = 0.000) for 2802 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 45: After refmac, R = 0.2297 (Rfree = 0.000) for 2788 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.90 3.65 Search for helices and strands: 0 residues in 0 chains, 2896 seeds are put forward NCS extension: 0 residues added, 2896 seeds are put forward Round 1: 110 peptides, 25 chains. Longest chain 7 peptides. Score 0.209 Round 2: 135 peptides, 25 chains. Longest chain 11 peptides. Score 0.304 Round 3: 138 peptides, 23 chains. Longest chain 11 peptides. Score 0.346 Round 4: 143 peptides, 23 chains. Longest chain 11 peptides. Score 0.363 Round 5: 142 peptides, 22 chains. Longest chain 13 peptides. Score 0.375 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 120, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2a6a-4_warpNtrace.pdb as input Building loops using Loopy2018 22 chains (120 residues) following loop building 2 chains (13 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4693 reflections ( 98.41 % complete ) and 6573 restraints for refining 2887 atoms. 6086 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2191 (Rfree = 0.000) for 2887 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2180 (Rfree = 0.000) for 2863 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2025 (Rfree = 0.000) for 2845 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1953 (Rfree = 0.000) for 2829 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:55:34 GMT 2018 Job finished. TimeTaking 92.87 Used memory is bytes: 15287640