Mon 24 Dec 00:24:13 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 2owp-2.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2owp-2.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2owp-2.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2owp-2.0-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/2owp-2.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2owp-2.0-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 00:24:18 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/2owp-2.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2owp-2.0-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 410 and 0 Target number of residues in the AU: 410 Target solvent content: 0.4901 Checking the provided sequence file Detected sequence length: 129 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 258 Adjusted target solvent content: 0.68 Input MTZ file: 2owp-2.0-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: 152 Cell parameters: 80.518 80.518 116.256 90.000 90.000 120.000 Input sequence file: 2owp-2.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2064 target number of atoms Had to go as low as 0.85 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 1 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: 29.899 2.000 Wilson plot Bfac: 21.44 29616 reflections ( 98.51 % complete ) and 0 restraints for refining 2288 atoms. Observations/parameters ratio is 3.24 ------------------------------------------------------ Starting model: R = 0.3426 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2998 (Rfree = 0.000) for 2288 atoms. Found 78 (78 requested) and removed 20 (39 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.13 1.66 NCS extension: 0 residues added, 2346 seeds are put forward Round 1: 203 peptides, 21 chains. Longest chain 24 peptides. Score 0.616 Round 2: 230 peptides, 12 chains. Longest chain 64 peptides. Score 0.776 Round 3: 247 peptides, 6 chains. Longest chain 107 peptides. Score 0.851 Round 4: 249 peptides, 4 chains. Longest chain 96 peptides. Score 0.868 Round 5: 252 peptides, 3 chains. Longest chain 128 peptides. Score 0.878 Taking the results from Round 5 Chains 3, Residues 249, Estimated correctness of the model 98.5 % 3 chains (249 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 55 B and 58 B 2 chains (251 residues) following loop building 2 chains (251 residues) in sequence following loop building ------------------------------------------------------ 29616 reflections ( 98.51 % complete ) and 2271 restraints for refining 2301 atoms. 239 conditional restraints added. Observations/parameters ratio is 3.22 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2802 (Rfree = 0.000) for 2301 atoms. Found 78 (78 requested) and removed 41 (39 requested) atoms. Cycle 2: After refmac, R = 0.2535 (Rfree = 0.000) for 2325 atoms. Found 59 (78 requested) and removed 14 (40 requested) atoms. Cycle 3: After refmac, R = 0.2368 (Rfree = 0.000) for 2349 atoms. Found 30 (79 requested) and removed 9 (40 requested) atoms. Cycle 4: After refmac, R = 0.2277 (Rfree = 0.000) for 2356 atoms. Found 25 (79 requested) and removed 5 (40 requested) atoms. Cycle 5: After refmac, R = 0.2228 (Rfree = 0.000) for 2370 atoms. Found 21 (79 requested) and removed 4 (40 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.08 1.62 NCS extension: 1 residues added (2 deleted due to clashes), 2388 seeds are put forward Round 1: 254 peptides, 2 chains. Longest chain 127 peptides. Score 0.887 Round 2: 254 peptides, 2 chains. Longest chain 127 peptides. Score 0.887 Round 3: 254 peptides, 2 chains. Longest chain 127 peptides. Score 0.887 Round 4: 255 peptides, 2 chains. Longest chain 128 peptides. Score 0.888 Round 5: 252 peptides, 4 chains. Longest chain 119 peptides. Score 0.871 Taking the results from Round 4 Chains 2, Residues 253, Estimated correctness of the model 98.7 % 2 chains (253 residues) have been docked in sequence Building loops using Loopy2018 2 chains (253 residues) following loop building 2 chains (253 residues) in sequence following loop building ------------------------------------------------------ 29616 reflections ( 98.51 % complete ) and 2301 restraints for refining 2371 atoms. 253 conditional restraints added. Observations/parameters ratio is 3.12 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2393 (Rfree = 0.000) for 2371 atoms. Found 39 (79 requested) and removed 13 (40 requested) atoms. Cycle 7: After refmac, R = 0.2247 (Rfree = 0.000) for 2396 atoms. Found 24 (80 requested) and removed 9 (41 requested) atoms. Cycle 8: After refmac, R = 0.2182 (Rfree = 0.000) for 2407 atoms. Found 14 (80 requested) and removed 9 (41 requested) atoms. Cycle 9: After refmac, R = 0.2138 (Rfree = 0.000) for 2411 atoms. Found 15 (79 requested) and removed 10 (41 requested) atoms. Cycle 10: After refmac, R = 0.2117 (Rfree = 0.000) for 2410 atoms. Found 12 (77 requested) and removed 9 (41 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.08 1.62 NCS extension: 0 residues added, 2413 seeds are put forward Round 1: 255 peptides, 2 chains. Longest chain 128 peptides. Score 0.888 Round 2: 256 peptides, 2 chains. Longest chain 128 peptides. Score 0.889 Round 3: 255 peptides, 3 chains. Longest chain 128 peptides. Score 0.881 Round 4: 256 peptides, 2 chains. Longest chain 128 peptides. Score 0.889 Round 5: 254 peptides, 3 chains. Longest chain 128 peptides. Score 0.880 Taking the results from Round 4 Chains 2, Residues 254, Estimated correctness of the model 98.7 % 2 chains (254 residues) have been docked in sequence Building loops using Loopy2018 2 chains (254 residues) following loop building 2 chains (254 residues) in sequence following loop building ------------------------------------------------------ 29616 reflections ( 98.51 % complete ) and 2287 restraints for refining 2385 atoms. 231 conditional restraints added. Observations/parameters ratio is 3.10 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2255 (Rfree = 0.000) for 2385 atoms. Found 37 (75 requested) and removed 17 (40 requested) atoms. Cycle 12: After refmac, R = 0.2175 (Rfree = 0.000) for 2400 atoms. Found 13 (75 requested) and removed 7 (41 requested) atoms. Cycle 13: After refmac, R = 0.2134 (Rfree = 0.000) for 2404 atoms. Found 15 (74 requested) and removed 6 (41 requested) atoms. Cycle 14: After refmac, R = 0.2120 (Rfree = 0.000) for 2412 atoms. Found 14 (74 requested) and removed 6 (41 requested) atoms. Cycle 15: After refmac, R = 0.2096 (Rfree = 0.000) for 2418 atoms. Found 12 (74 requested) and removed 8 (41 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.08 1.62 NCS extension: 0 residues added, 2422 seeds are put forward Round 1: 255 peptides, 2 chains. Longest chain 128 peptides. Score 0.888 Round 2: 255 peptides, 3 chains. Longest chain 128 peptides. Score 0.881 Round 3: 256 peptides, 2 chains. Longest chain 128 peptides. Score 0.889 Round 4: 256 peptides, 2 chains. Longest chain 128 peptides. Score 0.889 Round 5: 254 peptides, 3 chains. Longest chain 128 peptides. Score 0.880 Taking the results from Round 4 Chains 2, Residues 254, Estimated correctness of the model 98.7 % 2 chains (254 residues) have been docked in sequence Building loops using Loopy2018 2 chains (254 residues) following loop building 2 chains (254 residues) in sequence following loop building ------------------------------------------------------ 29616 reflections ( 98.51 % complete ) and 2309 restraints for refining 2392 atoms. 253 conditional restraints added. Observations/parameters ratio is 3.10 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2239 (Rfree = 0.000) for 2392 atoms. Found 34 (71 requested) and removed 17 (40 requested) atoms. Cycle 17: After refmac, R = 0.2161 (Rfree = 0.000) for 2407 atoms. Found 18 (72 requested) and removed 6 (41 requested) atoms. Cycle 18: After refmac, R = 0.2131 (Rfree = 0.000) for 2415 atoms. Found 12 (72 requested) and removed 9 (41 requested) atoms. Cycle 19: After refmac, R = 0.2104 (Rfree = 0.000) for 2417 atoms. Found 14 (71 requested) and removed 5 (41 requested) atoms. Cycle 20: After refmac, R = 0.2089 (Rfree = 0.000) for 2423 atoms. Found 11 (71 requested) and removed 11 (41 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.08 1.62 NCS extension: 0 residues added, 2423 seeds are put forward Round 1: 255 peptides, 2 chains. Longest chain 128 peptides. Score 0.888 Round 2: 256 peptides, 2 chains. Longest chain 128 peptides. Score 0.889 Round 3: 256 peptides, 2 chains. Longest chain 128 peptides. Score 0.889 Round 4: 257 peptides, 2 chains. Longest chain 129 peptides. Score 0.890 Round 5: 253 peptides, 4 chains. Longest chain 119 peptides. Score 0.872 Taking the results from Round 4 Chains 3, Residues 255, Estimated correctness of the model 98.8 % 2 chains (251 residues) have been docked in sequence Building loops using Loopy2018 3 chains (255 residues) following loop building 2 chains (251 residues) in sequence following loop building ------------------------------------------------------ 29616 reflections ( 98.51 % complete ) and 2299 restraints for refining 2388 atoms. 252 conditional restraints added. Observations/parameters ratio is 3.10 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2237 (Rfree = 0.000) for 2388 atoms. Found 40 (68 requested) and removed 19 (40 requested) atoms. Cycle 22: After refmac, R = 0.2159 (Rfree = 0.000) for 2408 atoms. Found 17 (69 requested) and removed 4 (41 requested) atoms. Cycle 23: After refmac, R = 0.2125 (Rfree = 0.000) for 2420 atoms. Found 13 (69 requested) and removed 3 (41 requested) atoms. Cycle 24: After refmac, R = 0.2108 (Rfree = 0.000) for 2428 atoms. Found 7 (70 requested) and removed 9 (41 requested) atoms. Cycle 25: After refmac, R = 0.2101 (Rfree = 0.000) for 2426 atoms. Found 6 (68 requested) and removed 4 (41 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.09 1.63 NCS extension: 0 residues added (3 deleted due to clashes), 2428 seeds are put forward Round 1: 255 peptides, 2 chains. Longest chain 128 peptides. Score 0.888 Round 2: 254 peptides, 3 chains. Longest chain 128 peptides. Score 0.880 Round 3: 253 peptides, 3 chains. Longest chain 128 peptides. Score 0.879 Round 4: 252 peptides, 4 chains. Longest chain 128 peptides. Score 0.871 Round 5: 251 peptides, 4 chains. Longest chain 121 peptides. Score 0.870 Taking the results from Round 1 Chains 2, Residues 253, Estimated correctness of the model 98.7 % 2 chains (253 residues) have been docked in sequence Building loops using Loopy2018 2 chains (253 residues) following loop building 2 chains (253 residues) in sequence following loop building ------------------------------------------------------ 29616 reflections ( 98.51 % complete ) and 2315 restraints for refining 2403 atoms. 267 conditional restraints added. Observations/parameters ratio is 3.08 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2226 (Rfree = 0.000) for 2403 atoms. Found 37 (66 requested) and removed 17 (41 requested) atoms. Cycle 27: After refmac, R = 0.2164 (Rfree = 0.000) for 2420 atoms. Found 16 (66 requested) and removed 11 (41 requested) atoms. Cycle 28: After refmac, R = 0.2131 (Rfree = 0.000) for 2424 atoms. Found 19 (65 requested) and removed 5 (41 requested) atoms. Cycle 29: After refmac, R = 0.2107 (Rfree = 0.000) for 2436 atoms. Found 12 (65 requested) and removed 7 (41 requested) atoms. Cycle 30: After refmac, R = 0.2098 (Rfree = 0.000) for 2437 atoms. Found 9 (63 requested) and removed 8 (41 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.08 1.62 NCS extension: 0 residues added, 2438 seeds are put forward Round 1: 253 peptides, 3 chains. Longest chain 127 peptides. Score 0.879 Round 2: 252 peptides, 3 chains. Longest chain 127 peptides. Score 0.878 Round 3: 255 peptides, 3 chains. Longest chain 127 peptides. Score 0.881 Round 4: 253 peptides, 3 chains. Longest chain 127 peptides. Score 0.879 Round 5: 253 peptides, 3 chains. Longest chain 127 peptides. Score 0.879 Taking the results from Round 3 Chains 4, Residues 252, Estimated correctness of the model 98.6 % 3 chains (250 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 55 B and 59 B 2 chains (253 residues) following loop building 2 chains (253 residues) in sequence following loop building ------------------------------------------------------ 29616 reflections ( 98.51 % complete ) and 2312 restraints for refining 2402 atoms. 264 conditional restraints added. Observations/parameters ratio is 3.08 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2229 (Rfree = 0.000) for 2402 atoms. Found 44 (61 requested) and removed 22 (41 requested) atoms. Cycle 32: After refmac, R = 0.2167 (Rfree = 0.000) for 2423 atoms. Found 14 (61 requested) and removed 7 (41 requested) atoms. Cycle 33: After refmac, R = 0.2135 (Rfree = 0.000) for 2427 atoms. Found 15 (61 requested) and removed 4 (41 requested) atoms. Cycle 34: After refmac, R = 0.2107 (Rfree = 0.000) for 2438 atoms. Found 8 (61 requested) and removed 8 (41 requested) atoms. Cycle 35: After refmac, R = 0.2093 (Rfree = 0.000) for 2438 atoms. Found 7 (60 requested) and removed 9 (41 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.09 1.63 NCS extension: 0 residues added, 2436 seeds are put forward Round 1: 253 peptides, 3 chains. Longest chain 127 peptides. Score 0.879 Round 2: 252 peptides, 3 chains. Longest chain 127 peptides. Score 0.878 Round 3: 254 peptides, 3 chains. Longest chain 127 peptides. Score 0.880 Round 4: 251 peptides, 3 chains. Longest chain 127 peptides. Score 0.877 Round 5: 251 peptides, 3 chains. Longest chain 127 peptides. Score 0.877 Taking the results from Round 3 Chains 4, Residues 251, Estimated correctness of the model 98.5 % 3 chains (250 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 56 B and 59 B 2 chains (252 residues) following loop building 2 chains (252 residues) in sequence following loop building ------------------------------------------------------ 29616 reflections ( 98.51 % complete ) and 2335 restraints for refining 2401 atoms. 295 conditional restraints added. Observations/parameters ratio is 3.08 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2226 (Rfree = 0.000) for 2401 atoms. Found 42 (57 requested) and removed 21 (41 requested) atoms. Cycle 37: After refmac, R = 0.2154 (Rfree = 0.000) for 2421 atoms. Found 21 (57 requested) and removed 11 (41 requested) atoms. Cycle 38: After refmac, R = 0.2130 (Rfree = 0.000) for 2429 atoms. Found 13 (56 requested) and removed 1 (41 requested) atoms. Cycle 39: After refmac, R = 0.2097 (Rfree = 0.000) for 2437 atoms. Found 6 (56 requested) and removed 4 (41 requested) atoms. Cycle 40: After refmac, R = 0.2086 (Rfree = 0.000) for 2433 atoms. Found 12 (55 requested) and removed 10 (41 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.09 1.63 NCS extension: 0 residues added, 2435 seeds are put forward Round 1: 253 peptides, 3 chains. Longest chain 127 peptides. Score 0.879 Round 2: 252 peptides, 3 chains. Longest chain 127 peptides. Score 0.878 Round 3: 255 peptides, 3 chains. Longest chain 127 peptides. Score 0.881 Round 4: 253 peptides, 3 chains. Longest chain 127 peptides. Score 0.879 Round 5: 254 peptides, 3 chains. Longest chain 127 peptides. Score 0.880 Taking the results from Round 3 Chains 4, Residues 252, Estimated correctness of the model 98.6 % 3 chains (250 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 55 A and 59 A 2 chains (253 residues) following loop building 2 chains (253 residues) in sequence following loop building ------------------------------------------------------ 29616 reflections ( 98.51 % complete ) and 2294 restraints for refining 2413 atoms. 246 conditional restraints added. Observations/parameters ratio is 3.07 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2233 (Rfree = 0.000) for 2413 atoms. Found 39 (52 requested) and removed 21 (41 requested) atoms. Cycle 42: After refmac, R = 0.2159 (Rfree = 0.000) for 2429 atoms. Found 18 (51 requested) and removed 7 (41 requested) atoms. Cycle 43: After refmac, R = 0.2120 (Rfree = 0.000) for 2437 atoms. Found 15 (51 requested) and removed 5 (41 requested) atoms. Cycle 44: After refmac, R = 0.2096 (Rfree = 0.000) for 2444 atoms. Found 17 (51 requested) and removed 6 (41 requested) atoms. Cycle 45: After refmac, R = 0.2076 (Rfree = 0.000) for 2452 atoms. Found 10 (52 requested) and removed 11 (42 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.09 1.63 NCS extension: 0 residues added, 2452 seeds are put forward Round 1: 253 peptides, 3 chains. Longest chain 127 peptides. Score 0.879 Round 2: 254 peptides, 2 chains. Longest chain 127 peptides. Score 0.887 Round 3: 255 peptides, 2 chains. Longest chain 128 peptides. Score 0.888 Round 4: 255 peptides, 2 chains. Longest chain 128 peptides. Score 0.888 Round 5: 252 peptides, 4 chains. Longest chain 122 peptides. Score 0.871 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 253, Estimated correctness of the model 98.7 % 2 chains (253 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 2 chains (253 residues) following loop building 2 chains (253 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 29616 reflections ( 98.51 % complete ) and 2048 restraints for refining 2000 atoms. Observations/parameters ratio is 3.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2778 (Rfree = 0.000) for 2000 atoms. Found 41 (41 requested) and removed 0 (41 requested) atoms. Cycle 47: After refmac, R = 0.2619 (Rfree = 0.000) for 2000 atoms. Found 33 (41 requested) and removed 1 (34 requested) atoms. Cycle 48: After refmac, R = 0.2498 (Rfree = 0.000) for 2000 atoms. Found 21 (43 requested) and removed 0 (35 requested) atoms. Cycle 49: After refmac, R = 0.2420 (Rfree = 0.000) for 2000 atoms. TimeTaking 37.13