null Mon 24 Dec 07:35:56 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2owp-2.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2owp-2.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2owp-2.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2owp-2.0-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2owp-2.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2owp-2.0-parrot-noncs ############### 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 07:36:01 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/noncs/ArpWArp/wArpResults/WorkingDir/2owp-2.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2owp-2.0-parrot-noncs/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-noncs.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-noncs.fasta_lf Building free atoms model in initial map for 2064 target number of atoms Had to go as low as 0.90 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 2293 atoms. Observations/parameters ratio is 3.23 ------------------------------------------------------ Starting model: R = 0.3736 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3373 (Rfree = 0.000) for 2293 atoms. Found 65 (78 requested) and removed 39 (39 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.26 1.76 NCS extension: 0 residues added, 2319 seeds are put forward Round 1: 194 peptides, 22 chains. Longest chain 19 peptides. Score 0.578 Round 2: 228 peptides, 17 chains. Longest chain 42 peptides. Score 0.723 Round 3: 239 peptides, 11 chains. Longest chain 64 peptides. Score 0.800 Round 4: 246 peptides, 8 chains. Longest chain 102 peptides. Score 0.835 Round 5: 246 peptides, 7 chains. Longest chain 103 peptides. Score 0.842 Taking the results from Round 5 Chains 7, Residues 239, Estimated correctness of the model 97.6 % 4 chains (221 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 22 A and 26 A Built loop between residues 37 B and 40 B 5 chains (243 residues) following loop building 2 chains (226 residues) in sequence following loop building ------------------------------------------------------ 29616 reflections ( 98.51 % complete ) and 2575 restraints for refining 2406 atoms. 685 conditional restraints added. Observations/parameters ratio is 3.08 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3340 (Rfree = 0.000) for 2406 atoms. Found 82 (82 requested) and removed 46 (41 requested) atoms. Cycle 2: After refmac, R = 0.3105 (Rfree = 0.000) for 2417 atoms. Found 81 (81 requested) and removed 41 (41 requested) atoms. Cycle 3: After refmac, R = 0.2913 (Rfree = 0.000) for 2438 atoms. Found 74 (81 requested) and removed 30 (42 requested) atoms. Cycle 4: After refmac, R = 0.2763 (Rfree = 0.000) for 2460 atoms. Found 46 (82 requested) and removed 19 (42 requested) atoms. Cycle 5: After refmac, R = 0.2670 (Rfree = 0.000) for 2461 atoms. Found 49 (82 requested) and removed 16 (42 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.08 1.62 NCS extension: 0 residues added (8 deleted due to clashes), 2501 seeds are put forward Round 1: 247 peptides, 5 chains. Longest chain 103 peptides. Score 0.858 Round 2: 253 peptides, 3 chains. Longest chain 128 peptides. Score 0.879 Round 3: 251 peptides, 4 chains. Longest chain 120 peptides. Score 0.870 Round 4: 255 peptides, 4 chains. Longest chain 122 peptides. Score 0.875 Round 5: 253 peptides, 4 chains. Longest chain 128 peptides. Score 0.872 Taking the results from Round 2 Chains 3, Residues 250, 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 2319 restraints for refining 2403 atoms. 279 conditional restraints added. Observations/parameters ratio is 3.08 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2676 (Rfree = 0.000) for 2403 atoms. Found 66 (79 requested) and removed 21 (41 requested) atoms. Cycle 7: After refmac, R = 0.2471 (Rfree = 0.000) for 2447 atoms. Found 37 (80 requested) and removed 16 (41 requested) atoms. Cycle 8: After refmac, R = 0.2369 (Rfree = 0.000) for 2463 atoms. Found 30 (81 requested) and removed 15 (42 requested) atoms. Cycle 9: After refmac, R = 0.2303 (Rfree = 0.000) for 2471 atoms. Found 27 (81 requested) and removed 12 (42 requested) atoms. Cycle 10: After refmac, R = 0.2243 (Rfree = 0.000) for 2476 atoms. Found 34 (82 requested) and removed 16 (42 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.07 1.61 NCS extension: 0 residues added, 2494 seeds are put forward Round 1: 254 peptides, 2 chains. Longest chain 127 peptides. Score 0.887 Round 2: 255 peptides, 2 chains. Longest chain 128 peptides. Score 0.888 Round 3: 252 peptides, 4 chains. Longest chain 71 peptides. Score 0.871 Round 4: 254 peptides, 3 chains. Longest chain 128 peptides. Score 0.880 Round 5: 251 peptides, 5 chains. Longest chain 69 peptides. Score 0.863 Taking the results from Round 2 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 2311 restraints for refining 2412 atoms. 263 conditional restraints added. Observations/parameters ratio is 3.07 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2332 (Rfree = 0.000) for 2412 atoms. Found 47 (79 requested) and removed 20 (41 requested) atoms. Cycle 12: After refmac, R = 0.2248 (Rfree = 0.000) for 2435 atoms. Found 28 (80 requested) and removed 17 (41 requested) atoms. Cycle 13: After refmac, R = 0.2196 (Rfree = 0.000) for 2444 atoms. Found 21 (78 requested) and removed 6 (41 requested) atoms. Cycle 14: After refmac, R = 0.2175 (Rfree = 0.000) for 2458 atoms. Found 10 (79 requested) and removed 17 (42 requested) atoms. Cycle 15: After refmac, R = 0.2149 (Rfree = 0.000) for 2449 atoms. Found 17 (76 requested) and removed 9 (41 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.08 1.62 NCS extension: 0 residues added, 2457 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: 252 peptides, 4 chains. Longest chain 71 peptides. Score 0.871 Round 4: 254 peptides, 3 chains. Longest chain 127 peptides. Score 0.880 Round 5: 252 peptides, 4 chains. Longest chain 120 peptides. Score 0.871 Taking the results from Round 4 Chains 3, Residues 251, Estimated correctness of the model 98.5 % 2 chains (244 residues) have been docked in sequence Building loops using Loopy2018 3 chains (251 residues) following loop building 2 chains (244 residues) in sequence following loop building ------------------------------------------------------ 29616 reflections ( 98.51 % complete ) and 2376 restraints for refining 2392 atoms. 373 conditional restraints added. Observations/parameters ratio is 3.10 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2290 (Rfree = 0.000) for 2392 atoms. Found 42 (73 requested) and removed 14 (40 requested) atoms. Cycle 17: After refmac, R = 0.2212 (Rfree = 0.000) for 2419 atoms. Found 22 (74 requested) and removed 11 (41 requested) atoms. Cycle 18: After refmac, R = 0.2175 (Rfree = 0.000) for 2425 atoms. Found 18 (75 requested) and removed 9 (41 requested) atoms. Cycle 19: After refmac, R = 0.2145 (Rfree = 0.000) for 2433 atoms. Found 19 (75 requested) and removed 6 (41 requested) atoms. Cycle 20: After refmac, R = 0.2124 (Rfree = 0.000) for 2444 atoms. Found 10 (75 requested) and removed 9 (41 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.08 1.62 NCS extension: 0 residues added (8 deleted due to clashes), 2445 seeds are put forward Round 1: 254 peptides, 2 chains. Longest chain 127 peptides. Score 0.887 Round 2: 254 peptides, 3 chains. Longest chain 127 peptides. Score 0.880 Round 3: 254 peptides, 3 chains. Longest chain 127 peptides. Score 0.880 Round 4: 253 peptides, 4 chains. Longest chain 120 peptides. Score 0.872 Round 5: 255 peptides, 2 chains. Longest chain 128 peptides. Score 0.888 Taking the results from Round 5 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 2299 restraints for refining 2399 atoms. 251 conditional restraints added. Observations/parameters ratio is 3.09 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2246 (Rfree = 0.000) for 2399 atoms. Found 39 (72 requested) and removed 18 (41 requested) atoms. Cycle 22: After refmac, R = 0.2175 (Rfree = 0.000) for 2419 atoms. Found 12 (72 requested) and removed 8 (41 requested) atoms. Cycle 23: After refmac, R = 0.2135 (Rfree = 0.000) for 2423 atoms. Found 12 (71 requested) and removed 5 (41 requested) atoms. Cycle 24: After refmac, R = 0.2107 (Rfree = 0.000) for 2428 atoms. Found 17 (71 requested) and removed 7 (41 requested) atoms. Cycle 25: After refmac, R = 0.2094 (Rfree = 0.000) for 2437 atoms. Found 13 (71 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: 253 peptides, 3 chains. Longest chain 127 peptides. Score 0.879 Round 2: 254 peptides, 3 chains. Longest chain 127 peptides. Score 0.880 Round 3: 254 peptides, 3 chains. Longest chain 127 peptides. Score 0.880 Round 4: 255 peptides, 2 chains. Longest chain 128 peptides. Score 0.888 Round 5: 254 peptides, 3 chains. Longest chain 127 peptides. Score 0.880 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 2294 restraints for refining 2407 atoms. 246 conditional restraints added. Observations/parameters ratio is 3.08 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2227 (Rfree = 0.000) for 2407 atoms. Found 42 (71 requested) and removed 20 (41 requested) atoms. Cycle 27: After refmac, R = 0.2164 (Rfree = 0.000) for 2427 atoms. Found 18 (71 requested) and removed 6 (41 requested) atoms. Cycle 28: After refmac, R = 0.2126 (Rfree = 0.000) for 2437 atoms. Found 19 (71 requested) and removed 7 (41 requested) atoms. Cycle 29: After refmac, R = 0.2099 (Rfree = 0.000) for 2448 atoms. Found 12 (71 requested) and removed 11 (41 requested) atoms. Cycle 30: After refmac, R = 0.2079 (Rfree = 0.000) for 2447 atoms. Found 12 (70 requested) and removed 8 (41 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.08 1.62 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, 3 chains. Longest chain 127 peptides. Score 0.880 Round 3: 254 peptides, 3 chains. Longest chain 127 peptides. Score 0.880 Round 4: 255 peptides, 2 chains. Longest chain 128 peptides. Score 0.888 Round 5: 254 peptides, 3 chains. Longest chain 127 peptides. Score 0.880 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 2413 atoms. 253 conditional restraints added. Observations/parameters ratio is 3.07 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2220 (Rfree = 0.000) for 2413 atoms. Found 43 (67 requested) and removed 15 (41 requested) atoms. Cycle 32: After refmac, R = 0.2148 (Rfree = 0.000) for 2440 atoms. Found 18 (68 requested) and removed 5 (41 requested) atoms. Cycle 33: After refmac, R = 0.2112 (Rfree = 0.000) for 2452 atoms. Found 10 (69 requested) and removed 5 (42 requested) atoms. Cycle 34: After refmac, R = 0.2093 (Rfree = 0.000) for 2452 atoms. Found 14 (69 requested) and removed 4 (42 requested) atoms. Cycle 35: After refmac, R = 0.2070 (Rfree = 0.000) for 2460 atoms. Found 10 (69 requested) and removed 4 (42 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.08 1.62 NCS extension: 0 residues added, 2467 seeds are put forward Round 1: 253 peptides, 3 chains. Longest chain 127 peptides. Score 0.879 Round 2: 254 peptides, 3 chains. Longest chain 127 peptides. Score 0.880 Round 3: 254 peptides, 3 chains. Longest chain 127 peptides. Score 0.880 Round 4: 255 peptides, 2 chains. Longest chain 128 peptides. Score 0.888 Round 5: 254 peptides, 3 chains. Longest chain 127 peptides. Score 0.880 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 2306 restraints for refining 2419 atoms. 258 conditional restraints added. Observations/parameters ratio is 3.06 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2210 (Rfree = 0.000) for 2419 atoms. Found 39 (67 requested) and removed 18 (41 requested) atoms. Cycle 37: After refmac, R = 0.2148 (Rfree = 0.000) for 2437 atoms. Found 16 (68 requested) and removed 6 (41 requested) atoms. Cycle 38: After refmac, R = 0.2105 (Rfree = 0.000) for 2443 atoms. Found 7 (68 requested) and removed 4 (41 requested) atoms. Cycle 39: After refmac, R = 0.2078 (Rfree = 0.000) for 2444 atoms. Found 13 (66 requested) and removed 4 (41 requested) atoms. Cycle 40: After refmac, R = 0.2061 (Rfree = 0.000) for 2452 atoms. Found 7 (67 requested) and removed 4 (42 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.08 1.62 NCS extension: 0 residues added, 2456 seeds are put forward Round 1: 254 peptides, 2 chains. Longest chain 127 peptides. Score 0.887 Round 2: 255 peptides, 2 chains. Longest chain 128 peptides. Score 0.888 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: 253 peptides, 4 chains. Longest chain 119 peptides. Score 0.872 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 2294 restraints for refining 2413 atoms. 246 conditional restraints added. Observations/parameters ratio is 3.07 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2203 (Rfree = 0.000) for 2413 atoms. Found 43 (64 requested) and removed 16 (41 requested) atoms. Cycle 42: After refmac, R = 0.2136 (Rfree = 0.000) for 2438 atoms. Found 17 (65 requested) and removed 6 (41 requested) atoms. Cycle 43: After refmac, R = 0.2101 (Rfree = 0.000) for 2444 atoms. Found 8 (65 requested) and removed 3 (41 requested) atoms. Cycle 44: After refmac, R = 0.2069 (Rfree = 0.000) for 2447 atoms. Found 9 (65 requested) and removed 4 (41 requested) atoms. Cycle 45: After refmac, R = 0.2057 (Rfree = 0.000) for 2443 atoms. Found 14 (66 requested) and removed 6 (42 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.08 1.62 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, 3 chains. Longest chain 127 peptides. Score 0.880 Round 3: 254 peptides, 3 chains. Longest chain 127 peptides. Score 0.880 Round 4: 254 peptides, 3 chains. Longest chain 128 peptides. Score 0.880 Round 5: 254 peptides, 3 chains. Longest chain 127 peptides. Score 0.880 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 251, Estimated correctness of the model 98.5 % 2 chains (244 residues) have been docked in sequence Sequence coverage is 96 % All DUM atoms will be removed Building loops using Loopy2018 3 chains (251 residues) following loop building 2 chains (244 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 29616 reflections ( 98.51 % complete ) and 2003 restraints for refining 1957 atoms. Observations/parameters ratio is 3.78 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2846 (Rfree = 0.000) for 1957 atoms. Found 42 (52 requested) and removed 0 (52 requested) atoms. Cycle 47: After refmac, R = 0.2690 (Rfree = 0.000) for 1957 atoms. Found 29 (53 requested) and removed 0 (34 requested) atoms. Cycle 48: After refmac, R = 0.2578 (Rfree = 0.000) for 1957 atoms. Found 19 (54 requested) and removed 2 (34 requested) atoms. Cycle 49: After refmac, R = 0.2519 (Rfree = 0.000) for 1957 atoms. Found 8 (55 requested) and removed 2 (35 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:16:55 GMT 2018 Job finished. TimeTaking 40.98 Used memory is bytes: 12153360