Sun 23 Dec 22:22:46 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 2owp-2.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2owp-2.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2owp-2.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2owp-2.0-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/2owp-2.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2owp-2.0-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 22:22:56 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/2owp-2.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2owp-2.0-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 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-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: 152 Cell parameters: 80.518 80.518 116.256 90.000 90.000 120.000 Input sequence file: 2owp-2.0-parrot-hancs.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 2292 atoms. Observations/parameters ratio is 3.23 ------------------------------------------------------ Starting model: R = 0.3451 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3006 (Rfree = 0.000) for 2292 atoms. Found 78 (78 requested) and removed 21 (39 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.12 1.65 NCS extension: 0 residues added, 2349 seeds are put forward Round 1: 223 peptides, 21 chains. Longest chain 36 peptides. Score 0.668 Round 2: 234 peptides, 8 chains. Longest chain 100 peptides. Score 0.818 Round 3: 246 peptides, 7 chains. Longest chain 106 peptides. Score 0.842 Round 4: 245 peptides, 7 chains. Longest chain 74 peptides. Score 0.841 Round 5: 247 peptides, 6 chains. Longest chain 111 peptides. Score 0.851 Taking the results from Round 5 Chains 6, Residues 241, Estimated correctness of the model 97.8 % 3 chains (218 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 66 B and 69 B 5 chains (243 residues) following loop building 2 chains (220 residues) in sequence following loop building ------------------------------------------------------ 29616 reflections ( 98.51 % complete ) and 2511 restraints for refining 2287 atoms. 624 conditional restraints added. Observations/parameters ratio is 3.24 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2925 (Rfree = 0.000) for 2287 atoms. Found 78 (78 requested) and removed 43 (39 requested) atoms. Cycle 2: After refmac, R = 0.2679 (Rfree = 0.000) for 2294 atoms. Found 53 (77 requested) and removed 9 (39 requested) atoms. Cycle 3: After refmac, R = 0.2519 (Rfree = 0.000) for 2322 atoms. Found 56 (78 requested) and removed 8 (40 requested) atoms. Cycle 4: After refmac, R = 0.2401 (Rfree = 0.000) for 2360 atoms. Found 35 (79 requested) and removed 9 (40 requested) atoms. Cycle 5: After refmac, R = 0.2326 (Rfree = 0.000) for 2377 atoms. Found 26 (79 requested) and removed 8 (40 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.09 1.63 NCS extension: 0 residues added (8 deleted due to clashes), 2397 seeds are put forward Round 1: 249 peptides, 3 chains. Longest chain 124 peptides. Score 0.875 Round 2: 250 peptides, 3 chains. Longest chain 125 peptides. Score 0.876 Round 3: 253 peptides, 3 chains. Longest chain 127 peptides. Score 0.879 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 5 Chains 3, Residues 251, Estimated correctness of the model 98.5 % 2 chains (247 residues) have been docked in sequence Building loops using Loopy2018 3 chains (251 residues) following loop building 2 chains (247 residues) in sequence following loop building ------------------------------------------------------ 29616 reflections ( 98.51 % complete ) and 2294 restraints for refining 2350 atoms. 280 conditional restraints added. Observations/parameters ratio is 3.15 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2348 (Rfree = 0.000) for 2350 atoms. Found 39 (78 requested) and removed 17 (40 requested) atoms. Cycle 7: After refmac, R = 0.2258 (Rfree = 0.000) for 2364 atoms. Found 28 (79 requested) and removed 7 (40 requested) atoms. Cycle 8: After refmac, R = 0.2207 (Rfree = 0.000) for 2381 atoms. Found 23 (79 requested) and removed 5 (40 requested) atoms. Cycle 9: After refmac, R = 0.2165 (Rfree = 0.000) for 2396 atoms. Found 16 (80 requested) and removed 8 (41 requested) atoms. Cycle 10: After refmac, R = 0.2148 (Rfree = 0.000) for 2403 atoms. Found 10 (80 requested) and removed 7 (41 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.09 1.63 NCS extension: 0 residues added (5 deleted due to clashes), 2407 seeds are put forward Round 1: 254 peptides, 3 chains. Longest chain 127 peptides. Score 0.880 Round 2: 253 peptides, 3 chains. Longest chain 127 peptides. Score 0.879 Round 3: 254 peptides, 3 chains. Longest chain 127 peptides. Score 0.880 Round 4: 254 peptides, 3 chains. Longest chain 127 peptides. Score 0.880 Round 5: 254 peptides, 3 chains. Longest chain 127 peptides. Score 0.880 Taking the results from Round 5 Chains 3, Residues 251, Estimated correctness of the model 98.5 % 2 chains (245 residues) have been docked in sequence Building loops using Loopy2018 3 chains (251 residues) following loop building 2 chains (245 residues) in sequence following loop building ------------------------------------------------------ 29616 reflections ( 98.51 % complete ) and 2339 restraints for refining 2366 atoms. 333 conditional restraints added. Observations/parameters ratio is 3.13 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2283 (Rfree = 0.000) for 2366 atoms. Found 40 (78 requested) and removed 17 (40 requested) atoms. Cycle 12: After refmac, R = 0.2206 (Rfree = 0.000) for 2388 atoms. Found 19 (78 requested) and removed 6 (40 requested) atoms. Cycle 13: After refmac, R = 0.2166 (Rfree = 0.000) for 2397 atoms. Found 18 (79 requested) and removed 4 (41 requested) atoms. Cycle 14: After refmac, R = 0.2130 (Rfree = 0.000) for 2410 atoms. Found 12 (79 requested) and removed 4 (41 requested) atoms. Cycle 15: After refmac, R = 0.2113 (Rfree = 0.000) for 2415 atoms. Found 10 (79 requested) and removed 4 (41 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.09 1.63 NCS extension: 0 residues added (7 deleted due to clashes), 2422 seeds are put forward Round 1: 254 peptides, 2 chains. Longest chain 128 peptides. Score 0.887 Round 2: 254 peptides, 2 chains. Longest chain 128 peptides. Score 0.887 Round 3: 254 peptides, 2 chains. Longest chain 128 peptides. Score 0.887 Round 4: 254 peptides, 2 chains. Longest chain 128 peptides. Score 0.887 Round 5: 253 peptides, 4 chains. Longest chain 119 peptides. Score 0.872 Taking the results from Round 4 Chains 2, Residues 252, Estimated correctness of the model 98.7 % 2 chains (252 residues) have been docked in sequence Building loops using Loopy2018 2 chains (252 residues) following loop building 2 chains (252 residues) in sequence following loop building ------------------------------------------------------ 29616 reflections ( 98.51 % complete ) and 2307 restraints for refining 2382 atoms. 268 conditional restraints added. Observations/parameters ratio is 3.11 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2257 (Rfree = 0.000) for 2382 atoms. Found 48 (78 requested) and removed 18 (40 requested) atoms. Cycle 17: After refmac, R = 0.2177 (Rfree = 0.000) for 2411 atoms. Found 18 (79 requested) and removed 8 (41 requested) atoms. Cycle 18: After refmac, R = 0.2125 (Rfree = 0.000) for 2419 atoms. Found 16 (79 requested) and removed 1 (41 requested) atoms. Cycle 19: After refmac, R = 0.2106 (Rfree = 0.000) for 2432 atoms. Found 9 (80 requested) and removed 11 (41 requested) atoms. Cycle 20: After refmac, R = 0.2089 (Rfree = 0.000) for 2425 atoms. Found 20 (78 requested) and removed 2 (41 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.09 1.63 NCS extension: 0 residues added, 2443 seeds are put forward Round 1: 254 peptides, 2 chains. Longest chain 128 peptides. Score 0.887 Round 2: 253 peptides, 3 chains. Longest chain 126 peptides. Score 0.879 Round 3: 254 peptides, 2 chains. Longest chain 128 peptides. Score 0.887 Round 4: 253 peptides, 4 chains. Longest chain 119 peptides. Score 0.872 Round 5: 253 peptides, 3 chains. Longest chain 126 peptides. Score 0.879 Taking the results from Round 3 Chains 2, Residues 252, Estimated correctness of the model 98.7 % 2 chains (252 residues) have been docked in sequence Building loops using Loopy2018 2 chains (252 residues) following loop building 2 chains (252 residues) in sequence following loop building ------------------------------------------------------ 29616 reflections ( 98.51 % complete ) and 2314 restraints for refining 2390 atoms. 275 conditional restraints added. Observations/parameters ratio is 3.10 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2224 (Rfree = 0.000) for 2390 atoms. Found 40 (76 requested) and removed 13 (40 requested) atoms. Cycle 22: After refmac, R = 0.2156 (Rfree = 0.000) for 2414 atoms. Found 20 (77 requested) and removed 4 (41 requested) atoms. Cycle 23: After refmac, R = 0.2122 (Rfree = 0.000) for 2428 atoms. Found 10 (78 requested) and removed 5 (41 requested) atoms. Cycle 24: After refmac, R = 0.2093 (Rfree = 0.000) for 2432 atoms. Found 14 (78 requested) and removed 3 (41 requested) atoms. Cycle 25: After refmac, R = 0.2071 (Rfree = 0.000) for 2440 atoms. Found 11 (78 requested) and removed 5 (41 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.08 1.62 NCS extension: 0 residues added, 2446 seeds are put forward Round 1: 252 peptides, 3 chains. Longest chain 126 peptides. Score 0.878 Round 2: 252 peptides, 3 chains. Longest chain 126 peptides. Score 0.878 Round 3: 253 peptides, 3 chains. Longest chain 126 peptides. Score 0.879 Round 4: 252 peptides, 4 chains. Longest chain 119 peptides. Score 0.871 Round 5: 253 peptides, 3 chains. Longest chain 126 peptides. Score 0.879 Taking the results from Round 5 Chains 3, Residues 250, Estimated correctness of the model 98.5 % 2 chains (244 residues) have been docked in sequence Building loops using Loopy2018 3 chains (250 residues) following loop building 2 chains (244 residues) in sequence following loop building ------------------------------------------------------ 29616 reflections ( 98.51 % complete ) and 2384 restraints for refining 2399 atoms. 387 conditional restraints added. Observations/parameters ratio is 3.09 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2219 (Rfree = 0.000) for 2399 atoms. Found 42 (77 requested) and removed 13 (41 requested) atoms. Cycle 27: After refmac, R = 0.2154 (Rfree = 0.000) for 2426 atoms. Found 17 (78 requested) and removed 7 (41 requested) atoms. Cycle 28: After refmac, R = 0.2113 (Rfree = 0.000) for 2431 atoms. Found 13 (78 requested) and removed 4 (41 requested) atoms. Cycle 29: After refmac, R = 0.2103 (Rfree = 0.000) for 2436 atoms. Found 13 (78 requested) and removed 7 (41 requested) atoms. Cycle 30: After refmac, R = 0.2086 (Rfree = 0.000) for 2441 atoms. Found 11 (76 requested) and removed 4 (41 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.08 1.62 NCS extension: 0 residues added (6 deleted due to clashes), 2448 seeds are put forward Round 1: 253 peptides, 2 chains. Longest chain 127 peptides. Score 0.886 Round 2: 254 peptides, 2 chains. Longest chain 128 peptides. Score 0.887 Round 3: 254 peptides, 2 chains. Longest chain 128 peptides. Score 0.887 Round 4: 253 peptides, 3 chains. Longest chain 128 peptides. Score 0.879 Round 5: 252 peptides, 3 chains. Longest chain 126 peptides. Score 0.878 Taking the results from Round 3 Chains 2, Residues 252, Estimated correctness of the model 98.7 % 2 chains (252 residues) have been docked in sequence Building loops using Loopy2018 2 chains (252 residues) following loop building 2 chains (252 residues) in sequence following loop building ------------------------------------------------------ 29616 reflections ( 98.51 % complete ) and 2328 restraints for refining 2406 atoms. 289 conditional restraints added. Observations/parameters ratio is 3.08 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2204 (Rfree = 0.000) for 2406 atoms. Found 37 (75 requested) and removed 15 (41 requested) atoms. Cycle 32: After refmac, R = 0.2137 (Rfree = 0.000) for 2425 atoms. Found 23 (76 requested) and removed 8 (41 requested) atoms. Cycle 33: After refmac, R = 0.2098 (Rfree = 0.000) for 2437 atoms. Found 14 (76 requested) and removed 4 (41 requested) atoms. Cycle 34: After refmac, R = 0.2057 (Rfree = 0.000) for 2445 atoms. Found 16 (76 requested) and removed 6 (41 requested) atoms. Cycle 35: After refmac, R = 0.2042 (Rfree = 0.000) for 2448 atoms. Found 18 (77 requested) and removed 6 (42 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.08 1.62 NCS extension: 0 residues added, 2460 seeds are put forward Round 1: 253 peptides, 2 chains. Longest chain 127 peptides. Score 0.886 Round 2: 254 peptides, 2 chains. Longest chain 128 peptides. Score 0.887 Round 3: 252 peptides, 3 chains. Longest chain 127 peptides. Score 0.878 Round 4: 253 peptides, 2 chains. Longest chain 127 peptides. Score 0.886 Round 5: 253 peptides, 2 chains. Longest chain 127 peptides. Score 0.886 Taking the results from Round 2 Chains 2, Residues 252, Estimated correctness of the model 98.7 % 2 chains (252 residues) have been docked in sequence Building loops using Loopy2018 2 chains (252 residues) following loop building 2 chains (252 residues) in sequence following loop building ------------------------------------------------------ 29616 reflections ( 98.51 % complete ) and 2326 restraints for refining 2400 atoms. 287 conditional restraints added. Observations/parameters ratio is 3.08 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2203 (Rfree = 0.000) for 2400 atoms. Found 48 (75 requested) and removed 13 (41 requested) atoms. Cycle 37: After refmac, R = 0.2123 (Rfree = 0.000) for 2432 atoms. Found 17 (76 requested) and removed 7 (41 requested) atoms. Cycle 38: After refmac, R = 0.2087 (Rfree = 0.000) for 2438 atoms. Found 16 (76 requested) and removed 2 (41 requested) atoms. Cycle 39: After refmac, R = 0.2060 (Rfree = 0.000) for 2450 atoms. Found 7 (77 requested) and removed 5 (42 requested) atoms. Cycle 40: After refmac, R = 0.2043 (Rfree = 0.000) for 2450 atoms. Found 12 (76 requested) and removed 3 (42 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.08 1.62 NCS extension: 0 residues added, 2459 seeds are put forward Round 1: 251 peptides, 3 chains. Longest chain 126 peptides. Score 0.877 Round 2: 251 peptides, 3 chains. Longest chain 126 peptides. Score 0.877 Round 3: 252 peptides, 2 chains. Longest chain 126 peptides. Score 0.885 Round 4: 251 peptides, 3 chains. Longest chain 126 peptides. Score 0.877 Round 5: 249 peptides, 4 chains. Longest chain 73 peptides. Score 0.868 Taking the results from Round 3 Chains 2, Residues 250, Estimated correctness of the model 98.6 % 2 chains (250 residues) have been docked in sequence Building loops using Loopy2018 2 chains (250 residues) following loop building 2 chains (250 residues) in sequence following loop building ------------------------------------------------------ 29616 reflections ( 98.51 % complete ) and 2344 restraints for refining 2399 atoms. 321 conditional restraints added. Observations/parameters ratio is 3.09 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2202 (Rfree = 0.000) for 2399 atoms. Found 45 (74 requested) and removed 13 (41 requested) atoms. Cycle 42: After refmac, R = 0.2135 (Rfree = 0.000) for 2427 atoms. Found 22 (75 requested) and removed 8 (41 requested) atoms. Cycle 43: After refmac, R = 0.2096 (Rfree = 0.000) for 2438 atoms. Found 15 (75 requested) and removed 1 (41 requested) atoms. Cycle 44: After refmac, R = 0.2073 (Rfree = 0.000) for 2448 atoms. Found 11 (76 requested) and removed 5 (42 requested) atoms. Cycle 45: After refmac, R = 0.2055 (Rfree = 0.000) for 2451 atoms. Found 11 (76 requested) and removed 7 (42 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.08 1.62 NCS extension: 0 residues added, 2455 seeds are put forward Round 1: 253 peptides, 2 chains. Longest chain 127 peptides. Score 0.886 Round 2: 253 peptides, 3 chains. Longest chain 126 peptides. Score 0.879 Round 3: 253 peptides, 3 chains. Longest chain 126 peptides. Score 0.879 Round 4: 252 peptides, 3 chains. Longest chain 126 peptides. Score 0.878 Round 5: 253 peptides, 3 chains. Longest chain 126 peptides. Score 0.879 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 251, Estimated correctness of the model 98.7 % 2 chains (251 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 2 chains (251 residues) following loop building 2 chains (251 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 29616 reflections ( 98.51 % complete ) and 2031 restraints for refining 1983 atoms. Observations/parameters ratio is 3.73 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2767 (Rfree = 0.000) for 1983 atoms. Found 56 (59 requested) and removed 0 (59 requested) atoms. Cycle 47: After refmac, R = 0.2583 (Rfree = 0.000) for 1983 atoms. Found 29 (61 requested) and removed 0 (34 requested) atoms. Cycle 48: After refmac, R = 0.2467 (Rfree = 0.000) for 1983 atoms. Found 29 (62 requested) and removed 1 (35 requested) atoms. Cycle 49: After refmac, R = 0.2385 (Rfree = 0.000) for 1983 atoms. TimeTaking 53.77