null Mon 24 Dec 07:57:26 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 2oc6-1.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2oc6-1.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2oc6-1.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oc6-1.8-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/2oc6-1.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oc6-1.8-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 07:57:31 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/2oc6-1.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oc6-1.8-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 250 and 0 Target number of residues in the AU: 250 Target solvent content: 0.5124 Checking the provided sequence file Detected sequence length: 124 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 248 Adjusted target solvent content: 0.52 Input MTZ file: 2oc6-1.8-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: 3 Cell parameters: 48.794 46.883 64.576 90.000 110.073 90.000 Input sequence file: 2oc6-1.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 1984 target number of atoms Had to go as low as 0.60 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: 60.653 1.751 Wilson plot Bfac: 25.86 21417 reflections ( 85.37 % complete ) and 0 restraints for refining 2205 atoms. Observations/parameters ratio is 2.43 ------------------------------------------------------ Starting model: R = 0.3633 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3165 (Rfree = 0.000) for 2205 atoms. Found 58 (110 requested) and removed 60 (55 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.09 2.04 NCS extension: 0 residues added, 2203 seeds are put forward Round 1: 159 peptides, 28 chains. Longest chain 11 peptides. Score 0.449 Round 2: 185 peptides, 18 chains. Longest chain 27 peptides. Score 0.738 Round 3: 198 peptides, 12 chains. Longest chain 37 peptides. Score 0.841 Round 4: 202 peptides, 11 chains. Longest chain 41 peptides. Score 0.858 Round 5: 206 peptides, 10 chains. Longest chain 46 peptides. Score 0.873 Taking the results from Round 5 Chains 14, Residues 196, Estimated correctness of the model 98.9 % 6 chains (148 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 101 A and 105 A Built loop between residues 48 B and 56 B Built loop between residues 69 B and 74 B 9 chains (205 residues) following loop building 3 chains (162 residues) in sequence following loop building ------------------------------------------------------ 21417 reflections ( 85.37 % complete ) and 2654 restraints for refining 2132 atoms. 1121 conditional restraints added. Observations/parameters ratio is 2.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3221 (Rfree = 0.000) for 2132 atoms. Found 84 (106 requested) and removed 58 (53 requested) atoms. Cycle 2: After refmac, R = 0.2936 (Rfree = 0.000) for 2147 atoms. Found 48 (105 requested) and removed 36 (53 requested) atoms. Cycle 3: After refmac, R = 0.2811 (Rfree = 0.000) for 2143 atoms. Found 47 (103 requested) and removed 18 (53 requested) atoms. Cycle 4: After refmac, R = 0.2664 (Rfree = 0.000) for 2165 atoms. Found 38 (104 requested) and removed 21 (54 requested) atoms. Cycle 5: After refmac, R = 0.2570 (Rfree = 0.000) for 2179 atoms. Found 32 (102 requested) and removed 7 (54 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.03 1.98 NCS extension: 11 residues added (115 deleted due to clashes), 2218 seeds are put forward Round 1: 222 peptides, 5 chains. Longest chain 115 peptides. Score 0.929 Round 2: 227 peptides, 4 chains. Longest chain 121 peptides. Score 0.940 Round 3: 232 peptides, 5 chains. Longest chain 80 peptides. Score 0.938 Round 4: 232 peptides, 6 chains. Longest chain 104 peptides. Score 0.932 Round 5: 230 peptides, 4 chains. Longest chain 75 peptides. Score 0.942 Taking the results from Round 5 Chains 5, Residues 226, Estimated correctness of the model 99.7 % 4 chains (223 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 A and 75 A Built loop between residues 40 B and 50 B 2 chains (234 residues) following loop building 2 chains (234 residues) in sequence following loop building ------------------------------------------------------ 21417 reflections ( 85.37 % complete ) and 2241 restraints for refining 2240 atoms. 245 conditional restraints added. Observations/parameters ratio is 2.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2543 (Rfree = 0.000) for 2240 atoms. Found 80 (105 requested) and removed 60 (56 requested) atoms. Cycle 7: After refmac, R = 0.2342 (Rfree = 0.000) for 2253 atoms. Found 68 (103 requested) and removed 32 (56 requested) atoms. Cycle 8: After refmac, R = 0.2205 (Rfree = 0.000) for 2284 atoms. Found 43 (105 requested) and removed 21 (57 requested) atoms. Cycle 9: After refmac, R = 0.2105 (Rfree = 0.000) for 2304 atoms. Found 51 (106 requested) and removed 18 (57 requested) atoms. Cycle 10: After refmac, R = 0.2027 (Rfree = 0.000) for 2335 atoms. Found 43 (107 requested) and removed 18 (58 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.03 1.98 NCS extension: 5 residues added (3 deleted due to clashes), 2367 seeds are put forward Round 1: 239 peptides, 3 chains. Longest chain 122 peptides. Score 0.953 Round 2: 245 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 3: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 4: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 5: 243 peptides, 5 chains. Longest chain 109 peptides. Score 0.946 Taking the results from Round 4 Chains 2, Residues 244, Estimated correctness of the model 99.9 % 2 chains (244 residues) have been docked in sequence Building loops using Loopy2018 2 chains (244 residues) following loop building 2 chains (244 residues) in sequence following loop building ------------------------------------------------------ 21417 reflections ( 85.37 % complete ) and 2220 restraints for refining 2295 atoms. 140 conditional restraints added. Observations/parameters ratio is 2.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2177 (Rfree = 0.000) for 2295 atoms. Found 83 (105 requested) and removed 55 (57 requested) atoms. Cycle 12: After refmac, R = 0.2055 (Rfree = 0.000) for 2321 atoms. Found 52 (104 requested) and removed 30 (58 requested) atoms. Cycle 13: After refmac, R = 0.1967 (Rfree = 0.000) for 2341 atoms. Found 47 (103 requested) and removed 12 (58 requested) atoms. Cycle 14: After refmac, R = 0.1922 (Rfree = 0.000) for 2375 atoms. Found 31 (104 requested) and removed 36 (59 requested) atoms. Cycle 15: After refmac, R = 0.1881 (Rfree = 0.000) for 2366 atoms. Found 58 (101 requested) and removed 26 (59 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.03 1.98 NCS extension: 0 residues added, 2398 seeds are put forward Round 1: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 2: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 3: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 4: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 5: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Taking the results from Round 5 Chains 2, Residues 244, Estimated correctness of the model 99.9 % 2 chains (244 residues) have been docked in sequence Building loops using Loopy2018 2 chains (244 residues) following loop building 2 chains (244 residues) in sequence following loop building ------------------------------------------------------ 21417 reflections ( 85.37 % complete ) and 2221 restraints for refining 2302 atoms. 141 conditional restraints added. Observations/parameters ratio is 2.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2027 (Rfree = 0.000) for 2302 atoms. Found 77 (99 requested) and removed 34 (57 requested) atoms. Cycle 17: After refmac, R = 0.1937 (Rfree = 0.000) for 2342 atoms. Found 49 (101 requested) and removed 28 (58 requested) atoms. Cycle 18: After refmac, R = 0.1848 (Rfree = 0.000) for 2360 atoms. Found 45 (99 requested) and removed 15 (59 requested) atoms. Cycle 19: After refmac, R = 0.1801 (Rfree = 0.000) for 2388 atoms. Found 42 (100 requested) and removed 19 (59 requested) atoms. Cycle 20: After refmac, R = 0.1753 (Rfree = 0.000) for 2410 atoms. Found 33 (101 requested) and removed 27 (60 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.04 1.99 NCS extension: 0 residues added, 2416 seeds are put forward Round 1: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 2: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 3: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 4: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 5: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Taking the results from Round 5 Chains 2, Residues 244, Estimated correctness of the model 99.9 % 2 chains (244 residues) have been docked in sequence Building loops using Loopy2018 2 chains (244 residues) following loop building 2 chains (244 residues) in sequence following loop building ------------------------------------------------------ 21417 reflections ( 85.37 % complete ) and 2259 restraints for refining 2331 atoms. 179 conditional restraints added. Observations/parameters ratio is 2.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1968 (Rfree = 0.000) for 2331 atoms. Found 74 (95 requested) and removed 33 (58 requested) atoms. Cycle 22: After refmac, R = 0.1866 (Rfree = 0.000) for 2372 atoms. Found 44 (97 requested) and removed 25 (59 requested) atoms. Cycle 23: After refmac, R = 0.1797 (Rfree = 0.000) for 2390 atoms. Found 48 (95 requested) and removed 22 (59 requested) atoms. Cycle 24: After refmac, R = 0.1758 (Rfree = 0.000) for 2413 atoms. Found 42 (96 requested) and removed 28 (60 requested) atoms. Cycle 25: After refmac, R = 0.1744 (Rfree = 0.000) for 2426 atoms. Found 38 (94 requested) and removed 27 (60 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.03 1.98 NCS extension: 0 residues added, 2437 seeds are put forward Round 1: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 2: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 3: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 4: 244 peptides, 3 chains. Longest chain 123 peptides. Score 0.956 Round 5: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Taking the results from Round 3 Chains 2, Residues 244, Estimated correctness of the model 99.9 % 2 chains (244 residues) have been docked in sequence Building loops using Loopy2018 2 chains (244 residues) following loop building 2 chains (244 residues) in sequence following loop building ------------------------------------------------------ 21417 reflections ( 85.37 % complete ) and 2254 restraints for refining 2343 atoms. 174 conditional restraints added. Observations/parameters ratio is 2.29 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1962 (Rfree = 0.000) for 2343 atoms. Found 78 (89 requested) and removed 33 (58 requested) atoms. Cycle 27: After refmac, R = 0.1850 (Rfree = 0.000) for 2387 atoms. Found 41 (90 requested) and removed 33 (59 requested) atoms. Cycle 28: After refmac, R = 0.1787 (Rfree = 0.000) for 2394 atoms. Found 45 (88 requested) and removed 18 (59 requested) atoms. Cycle 29: After refmac, R = 0.1758 (Rfree = 0.000) for 2419 atoms. Found 36 (90 requested) and removed 29 (60 requested) atoms. Cycle 30: After refmac, R = 0.1747 (Rfree = 0.000) for 2423 atoms. Found 41 (87 requested) and removed 20 (60 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.03 1.98 NCS extension: 0 residues added, 2444 seeds are put forward Round 1: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 2: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Round 3: 244 peptides, 3 chains. Longest chain 123 peptides. Score 0.956 Round 4: 244 peptides, 4 chains. Longest chain 123 peptides. Score 0.951 Round 5: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Taking the results from Round 5 Chains 2, Residues 244, Estimated correctness of the model 99.9 % 2 chains (244 residues) have been docked in sequence Building loops using Loopy2018 2 chains (244 residues) following loop building 2 chains (244 residues) in sequence following loop building ------------------------------------------------------ 21417 reflections ( 85.37 % complete ) and 2268 restraints for refining 2341 atoms. 188 conditional restraints added. Observations/parameters ratio is 2.29 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1936 (Rfree = 0.000) for 2341 atoms. Found 67 (84 requested) and removed 33 (58 requested) atoms. Cycle 32: After refmac, R = 0.1822 (Rfree = 0.000) for 2375 atoms. Found 43 (85 requested) and removed 28 (59 requested) atoms. Cycle 33: After refmac, R = 0.1782 (Rfree = 0.000) for 2390 atoms. Found 47 (83 requested) and removed 21 (59 requested) atoms. Cycle 34: After refmac, R = 0.1748 (Rfree = 0.000) for 2415 atoms. Found 42 (84 requested) and removed 33 (60 requested) atoms. Cycle 35: After refmac, R = 0.1730 (Rfree = 0.000) for 2424 atoms. Found 41 (82 requested) and removed 22 (60 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.03 1.98 NCS extension: 0 residues added, 2443 seeds are put forward Round 1: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 2: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 3: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 4: 244 peptides, 4 chains. Longest chain 104 peptides. Score 0.951 Round 5: 244 peptides, 3 chains. Longest chain 123 peptides. Score 0.956 Taking the results from Round 3 Chains 2, Residues 244, Estimated correctness of the model 99.9 % 2 chains (244 residues) have been docked in sequence Building loops using Loopy2018 2 chains (244 residues) following loop building 2 chains (244 residues) in sequence following loop building ------------------------------------------------------ 21417 reflections ( 85.37 % complete ) and 2249 restraints for refining 2341 atoms. 169 conditional restraints added. Observations/parameters ratio is 2.29 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1934 (Rfree = 0.000) for 2341 atoms. Found 71 (77 requested) and removed 29 (58 requested) atoms. Cycle 37: After refmac, R = 0.1830 (Rfree = 0.000) for 2383 atoms. Found 47 (79 requested) and removed 18 (59 requested) atoms. Cycle 38: After refmac, R = 0.1781 (Rfree = 0.000) for 2410 atoms. Found 35 (79 requested) and removed 30 (60 requested) atoms. Cycle 39: After refmac, R = 0.1749 (Rfree = 0.000) for 2415 atoms. Found 29 (77 requested) and removed 23 (60 requested) atoms. Cycle 40: After refmac, R = 0.1714 (Rfree = 0.000) for 2419 atoms. Found 35 (75 requested) and removed 21 (60 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.03 1.98 NCS extension: 0 residues added, 2433 seeds are put forward Round 1: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Round 2: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 3: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Round 4: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Round 5: 243 peptides, 5 chains. Longest chain 104 peptides. Score 0.946 Taking the results from Round 2 Chains 2, Residues 244, Estimated correctness of the model 99.9 % 2 chains (244 residues) have been docked in sequence Building loops using Loopy2018 2 chains (244 residues) following loop building 2 chains (244 residues) in sequence following loop building ------------------------------------------------------ 21417 reflections ( 85.37 % complete ) and 2259 restraints for refining 2342 atoms. 179 conditional restraints added. Observations/parameters ratio is 2.29 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1923 (Rfree = 0.000) for 2342 atoms. Found 70 (70 requested) and removed 28 (58 requested) atoms. Cycle 42: After refmac, R = 0.1833 (Rfree = 0.000) for 2381 atoms. Found 50 (71 requested) and removed 28 (59 requested) atoms. Cycle 43: After refmac, R = 0.1766 (Rfree = 0.000) for 2402 atoms. Found 37 (69 requested) and removed 33 (59 requested) atoms. Cycle 44: After refmac, R = 0.1743 (Rfree = 0.000) for 2405 atoms. Found 48 (67 requested) and removed 30 (60 requested) atoms. Cycle 45: After refmac, R = 0.1718 (Rfree = 0.000) for 2422 atoms. Found 45 (65 requested) and removed 34 (60 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.03 1.98 NCS extension: 0 residues added, 2433 seeds are put forward Round 1: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Round 2: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Round 3: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 4: 242 peptides, 5 chains. Longest chain 62 peptides. Score 0.945 Round 5: 246 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 244, Estimated correctness of the model 99.9 % 2 chains (244 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 2 chains (244 residues) following loop building 2 chains (244 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 21417 reflections ( 85.37 % complete ) and 2080 restraints for refining 2020 atoms. Observations/parameters ratio is 2.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2440 (Rfree = 0.000) for 2020 atoms. Found 37 (53 requested) and removed 0 (53 requested) atoms. Cycle 47: After refmac, R = 0.2261 (Rfree = 0.000) for 2020 atoms. Found 18 (53 requested) and removed 0 (51 requested) atoms. Cycle 48: After refmac, R = 0.2145 (Rfree = 0.000) for 2020 atoms. Found 5 (54 requested) and removed 0 (51 requested) atoms. Cycle 49: After refmac, R = 0.2086 (Rfree = 0.000) for 2020 atoms. Found 3 (54 requested) and removed 2 (51 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:34:22 GMT 2018 Job finished. TimeTaking 36.93 Used memory is bytes: 2575408