null Mon 24 Dec 07:39:26 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 2oyo-1.5-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2oyo-1.5-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2oyo-1.5-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oyo-1.5-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/2oyo-1.5-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oyo-1.5-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 07:39:31 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/2oyo-1.5-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oyo-1.5-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 466 and 0 Target number of residues in the AU: 466 Target solvent content: 0.3971 Checking the provided sequence file Detected sequence length: 196 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 392 Adjusted target solvent content: 0.49 Input MTZ file: 2oyo-1.5-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: 155 Cell parameters: 135.664 135.664 118.109 90.000 90.000 120.000 Input sequence file: 2oyo-1.5-parrot-noncs.fasta_lf Building free atoms model in initial map for 3136 target number of atoms Had to go as low as 0.30 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: 83.295 1.510 Wilson plot Bfac: 7.61 64556 reflections ( 98.98 % complete ) and 0 restraints for refining 3483 atoms. Observations/parameters ratio is 4.63 ------------------------------------------------------ Starting model: R = 0.3158 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2790 (Rfree = 0.000) for 3483 atoms. Found 265 (265 requested) and removed 142 (132 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.55 1.57 NCS extension: 0 residues added, 3606 seeds are put forward Round 1: 328 peptides, 20 chains. Longest chain 51 peptides. Score 0.863 Round 2: 350 peptides, 9 chains. Longest chain 129 peptides. Score 0.932 Round 3: 357 peptides, 5 chains. Longest chain 167 peptides. Score 0.950 Round 4: 361 peptides, 6 chains. Longest chain 164 peptides. Score 0.949 Round 5: 360 peptides, 7 chains. Longest chain 151 peptides. Score 0.945 Taking the results from Round 3 Chains 6, Residues 352, Estimated correctness of the model 99.9 % 4 chains (344 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 179 A and 182 A Built loop between residues 103 B and 109 B 4 chains (359 residues) following loop building 2 chains (351 residues) in sequence following loop building ------------------------------------------------------ 64556 reflections ( 98.98 % complete ) and 3403 restraints for refining 3293 atoms. 575 conditional restraints added. Observations/parameters ratio is 4.90 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2741 (Rfree = 0.000) for 3293 atoms. Found 201 (251 requested) and removed 43 (125 requested) atoms. Cycle 2: After refmac, R = 0.2549 (Rfree = 0.000) for 3447 atoms. Found 149 (263 requested) and removed 28 (131 requested) atoms. Cycle 3: After refmac, R = 0.2298 (Rfree = 0.000) for 3556 atoms. Found 135 (272 requested) and removed 23 (136 requested) atoms. Cycle 4: After refmac, R = 0.2187 (Rfree = 0.000) for 3651 atoms. Found 134 (279 requested) and removed 36 (139 requested) atoms. Cycle 5: After refmac, R = 0.2116 (Rfree = 0.000) for 3741 atoms. Found 129 (286 requested) and removed 47 (143 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.42 1.44 NCS extension: 0 residues added (7 deleted due to clashes), 3823 seeds are put forward Round 1: 364 peptides, 4 chains. Longest chain 160 peptides. Score 0.956 Round 2: 366 peptides, 3 chains. Longest chain 183 peptides. Score 0.960 Round 3: 366 peptides, 3 chains. Longest chain 183 peptides. Score 0.960 Round 4: 365 peptides, 5 chains. Longest chain 155 peptides. Score 0.954 Round 5: 365 peptides, 4 chains. Longest chain 160 peptides. Score 0.957 Taking the results from Round 3 Chains 3, Residues 363, Estimated correctness of the model 99.9 % 3 chains (363 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 33 A and 36 A 2 chains (365 residues) following loop building 2 chains (365 residues) in sequence following loop building ------------------------------------------------------ 64556 reflections ( 98.98 % complete ) and 3423 restraints for refining 3539 atoms. 490 conditional restraints added. Observations/parameters ratio is 4.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2135 (Rfree = 0.000) for 3539 atoms. Found 217 (270 requested) and removed 46 (135 requested) atoms. Cycle 7: After refmac, R = 0.2093 (Rfree = 0.000) for 3708 atoms. Found 135 (282 requested) and removed 79 (141 requested) atoms. Cycle 8: After refmac, R = 0.2029 (Rfree = 0.000) for 3757 atoms. Found 151 (281 requested) and removed 46 (143 requested) atoms. Cycle 9: After refmac, R = 0.2014 (Rfree = 0.000) for 3859 atoms. Found 118 (288 requested) and removed 76 (147 requested) atoms. Cycle 10: After refmac, R = 0.1988 (Rfree = 0.000) for 3896 atoms. Found 153 (285 requested) and removed 73 (148 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.40 1.42 NCS extension: 0 residues added, 3976 seeds are put forward Round 1: 367 peptides, 2 chains. Longest chain 184 peptides. Score 0.964 Round 2: 367 peptides, 3 chains. Longest chain 183 peptides. Score 0.961 Round 3: 366 peptides, 3 chains. Longest chain 183 peptides. Score 0.960 Round 4: 367 peptides, 3 chains. Longest chain 183 peptides. Score 0.961 Round 5: 365 peptides, 4 chains. Longest chain 183 peptides. Score 0.957 Taking the results from Round 1 Chains 2, Residues 365, Estimated correctness of the model 99.9 % 2 chains (365 residues) have been docked in sequence Building loops using Loopy2018 2 chains (365 residues) following loop building 2 chains (365 residues) in sequence following loop building ------------------------------------------------------ 64556 reflections ( 98.98 % complete ) and 3514 restraints for refining 3614 atoms. 581 conditional restraints added. Observations/parameters ratio is 4.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2292 (Rfree = 0.000) for 3614 atoms. Found 179 (264 requested) and removed 47 (137 requested) atoms. Cycle 12: After refmac, R = 0.2100 (Rfree = 0.000) for 3743 atoms. Found 155 (274 requested) and removed 48 (142 requested) atoms. Cycle 13: After refmac, R = 0.2048 (Rfree = 0.000) for 3843 atoms. Found 154 (281 requested) and removed 69 (146 requested) atoms. Cycle 14: After refmac, R = 0.2019 (Rfree = 0.000) for 3923 atoms. Found 141 (287 requested) and removed 79 (149 requested) atoms. Cycle 15: After refmac, R = 0.1981 (Rfree = 0.000) for 3980 atoms. Found 145 (285 requested) and removed 67 (151 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.39 1.41 NCS extension: 0 residues added, 4058 seeds are put forward Round 1: 367 peptides, 2 chains. Longest chain 184 peptides. Score 0.964 Round 2: 365 peptides, 4 chains. Longest chain 183 peptides. Score 0.957 Round 3: 366 peptides, 3 chains. Longest chain 183 peptides. Score 0.960 Round 4: 362 peptides, 6 chains. Longest chain 101 peptides. Score 0.949 Round 5: 365 peptides, 3 chains. Longest chain 183 peptides. Score 0.960 Taking the results from Round 1 Chains 2, Residues 365, Estimated correctness of the model 99.9 % 2 chains (365 residues) have been docked in sequence Building loops using Loopy2018 2 chains (365 residues) following loop building 2 chains (365 residues) in sequence following loop building ------------------------------------------------------ 64556 reflections ( 98.98 % complete ) and 3615 restraints for refining 3715 atoms. 682 conditional restraints added. Observations/parameters ratio is 4.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2284 (Rfree = 0.000) for 3715 atoms. Found 217 (266 requested) and removed 30 (141 requested) atoms. Cycle 17: After refmac, R = 0.2134 (Rfree = 0.000) for 3898 atoms. Found 137 (279 requested) and removed 57 (148 requested) atoms. Cycle 18: After refmac, R = 0.2045 (Rfree = 0.000) for 3967 atoms. Found 137 (285 requested) and removed 47 (151 requested) atoms. Cycle 19: After refmac, R = 0.1990 (Rfree = 0.000) for 4055 atoms. Found 122 (290 requested) and removed 56 (154 requested) atoms. Cycle 20: After refmac, R = 0.1965 (Rfree = 0.000) for 4114 atoms. Found 136 (295 requested) and removed 68 (157 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.39 1.41 NCS extension: 0 residues added, 4182 seeds are put forward Round 1: 366 peptides, 3 chains. Longest chain 183 peptides. Score 0.960 Round 2: 365 peptides, 4 chains. Longest chain 183 peptides. Score 0.957 Round 3: 364 peptides, 5 chains. Longest chain 160 peptides. Score 0.953 Round 4: 361 peptides, 7 chains. Longest chain 159 peptides. Score 0.945 Round 5: 365 peptides, 2 chains. Longest chain 183 peptides. Score 0.963 Taking the results from Round 5 Chains 2, Residues 363, Estimated correctness of the model 99.9 % 2 chains (363 residues) have been docked in sequence Building loops using Loopy2018 2 chains (363 residues) following loop building 2 chains (363 residues) in sequence following loop building ------------------------------------------------------ 64556 reflections ( 98.98 % complete ) and 3790 restraints for refining 3793 atoms. 877 conditional restraints added. Observations/parameters ratio is 4.25 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2312 (Rfree = 0.000) for 3793 atoms. Found 204 (272 requested) and removed 43 (144 requested) atoms. Cycle 22: After refmac, R = 0.2125 (Rfree = 0.000) for 3951 atoms. Found 129 (283 requested) and removed 46 (150 requested) atoms. Cycle 23: After refmac, R = 0.2039 (Rfree = 0.000) for 4018 atoms. Found 136 (289 requested) and removed 49 (153 requested) atoms. Cycle 24: After refmac, R = 0.1988 (Rfree = 0.000) for 4098 atoms. Found 132 (294 requested) and removed 57 (156 requested) atoms. Cycle 25: After refmac, R = 0.1951 (Rfree = 0.000) for 4167 atoms. Found 127 (299 requested) and removed 65 (159 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.39 1.41 NCS extension: 0 residues added, 4230 seeds are put forward Round 1: 365 peptides, 2 chains. Longest chain 183 peptides. Score 0.963 Round 2: 360 peptides, 7 chains. Longest chain 101 peptides. Score 0.945 Round 3: 361 peptides, 4 chains. Longest chain 159 peptides. Score 0.955 Round 4: 362 peptides, 5 chains. Longest chain 183 peptides. Score 0.952 Round 5: 360 peptides, 7 chains. Longest chain 101 peptides. Score 0.945 Taking the results from Round 1 Chains 2, Residues 363, Estimated correctness of the model 99.9 % 2 chains (363 residues) have been docked in sequence Building loops using Loopy2018 2 chains (363 residues) following loop building 2 chains (363 residues) in sequence following loop building ------------------------------------------------------ 64556 reflections ( 98.98 % complete ) and 3897 restraints for refining 3850 atoms. 984 conditional restraints added. Observations/parameters ratio is 4.19 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2287 (Rfree = 0.000) for 3850 atoms. Found 222 (270 requested) and removed 40 (146 requested) atoms. Cycle 27: After refmac, R = 0.2120 (Rfree = 0.000) for 4023 atoms. Found 158 (282 requested) and removed 48 (153 requested) atoms. Cycle 28: After refmac, R = 0.2043 (Rfree = 0.000) for 4124 atoms. Found 131 (290 requested) and removed 39 (157 requested) atoms. Cycle 29: After refmac, R = 0.2000 (Rfree = 0.000) for 4205 atoms. Found 129 (295 requested) and removed 68 (160 requested) atoms. Cycle 30: After refmac, R = 0.1970 (Rfree = 0.000) for 4261 atoms. Found 146 (292 requested) and removed 69 (162 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.39 1.41 NCS extension: 0 residues added, 4338 seeds are put forward Round 1: 361 peptides, 5 chains. Longest chain 94 peptides. Score 0.952 Round 2: 359 peptides, 7 chains. Longest chain 94 peptides. Score 0.944 Round 3: 362 peptides, 5 chains. Longest chain 123 peptides. Score 0.952 Round 4: 365 peptides, 3 chains. Longest chain 183 peptides. Score 0.960 Round 5: 361 peptides, 5 chains. Longest chain 123 peptides. Score 0.952 Taking the results from Round 4 Chains 3, Residues 362, Estimated correctness of the model 99.9 % 3 chains (362 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 165 B and 168 B 2 chains (364 residues) following loop building 2 chains (364 residues) in sequence following loop building ------------------------------------------------------ 64556 reflections ( 98.98 % complete ) and 3867 restraints for refining 3909 atoms. 943 conditional restraints added. Observations/parameters ratio is 4.13 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2308 (Rfree = 0.000) for 3909 atoms. Found 232 (268 requested) and removed 43 (149 requested) atoms. Cycle 32: After refmac, R = 0.2121 (Rfree = 0.000) for 4095 atoms. Found 160 (281 requested) and removed 40 (156 requested) atoms. Cycle 33: After refmac, R = 0.2055 (Rfree = 0.000) for 4200 atoms. Found 160 (289 requested) and removed 54 (160 requested) atoms. Cycle 34: After refmac, R = 0.2025 (Rfree = 0.000) for 4304 atoms. Found 129 (295 requested) and removed 71 (164 requested) atoms. Cycle 35: After refmac, R = 0.1984 (Rfree = 0.000) for 4350 atoms. Found 151 (292 requested) and removed 78 (166 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.39 1.41 NCS extension: 0 residues added, 4424 seeds are put forward Round 1: 364 peptides, 4 chains. Longest chain 95 peptides. Score 0.956 Round 2: 360 peptides, 8 chains. Longest chain 86 peptides. Score 0.941 Round 3: 360 peptides, 7 chains. Longest chain 91 peptides. Score 0.945 Round 4: 363 peptides, 5 chains. Longest chain 95 peptides. Score 0.953 Round 5: 363 peptides, 4 chains. Longest chain 183 peptides. Score 0.956 Taking the results from Round 5 Chains 4, Residues 359, Estimated correctness of the model 99.9 % 4 chains (359 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 47 B and 51 B Built loop between residues 106 B and 109 B 2 chains (364 residues) following loop building 2 chains (364 residues) in sequence following loop building ------------------------------------------------------ 64556 reflections ( 98.98 % complete ) and 4020 restraints for refining 3973 atoms. 1096 conditional restraints added. Observations/parameters ratio is 4.06 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2307 (Rfree = 0.000) for 3973 atoms. Found 244 (261 requested) and removed 31 (151 requested) atoms. Cycle 37: After refmac, R = 0.2166 (Rfree = 0.000) for 4178 atoms. Found 145 (274 requested) and removed 50 (159 requested) atoms. Cycle 38: After refmac, R = 0.2080 (Rfree = 0.000) for 4264 atoms. Found 140 (279 requested) and removed 40 (162 requested) atoms. Cycle 39: After refmac, R = 0.2036 (Rfree = 0.000) for 4358 atoms. Found 131 (286 requested) and removed 83 (166 requested) atoms. Cycle 40: After refmac, R = 0.1993 (Rfree = 0.000) for 4399 atoms. Found 153 (281 requested) and removed 72 (167 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.39 1.41 NCS extension: 0 residues added, 4480 seeds are put forward Round 1: 363 peptides, 4 chains. Longest chain 95 peptides. Score 0.956 Round 2: 361 peptides, 7 chains. Longest chain 101 peptides. Score 0.945 Round 3: 361 peptides, 5 chains. Longest chain 103 peptides. Score 0.952 Round 4: 362 peptides, 6 chains. Longest chain 143 peptides. Score 0.949 Round 5: 362 peptides, 4 chains. Longest chain 159 peptides. Score 0.956 Taking the results from Round 5 Chains 4, Residues 358, Estimated correctness of the model 99.9 % 4 chains (358 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 33 A and 36 A Built loop between residues 104 B and 109 B 2 chains (364 residues) following loop building 2 chains (364 residues) in sequence following loop building ------------------------------------------------------ 64556 reflections ( 98.98 % complete ) and 4012 restraints for refining 4006 atoms. 1088 conditional restraints added. Observations/parameters ratio is 4.03 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2322 (Rfree = 0.000) for 4006 atoms. Found 228 (256 requested) and removed 46 (152 requested) atoms. Cycle 42: After refmac, R = 0.2155 (Rfree = 0.000) for 4181 atoms. Found 143 (268 requested) and removed 41 (159 requested) atoms. Cycle 43: After refmac, R = 0.2070 (Rfree = 0.000) for 4274 atoms. Found 148 (274 requested) and removed 30 (163 requested) atoms. Cycle 44: After refmac, R = 0.2049 (Rfree = 0.000) for 4386 atoms. Found 138 (281 requested) and removed 75 (167 requested) atoms. Cycle 45: After refmac, R = 0.2021 (Rfree = 0.000) for 4442 atoms. Found 143 (278 requested) and removed 96 (169 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.39 1.41 NCS extension: 0 residues added, 4490 seeds are put forward Round 1: 362 peptides, 4 chains. Longest chain 95 peptides. Score 0.956 Round 2: 363 peptides, 5 chains. Longest chain 159 peptides. Score 0.953 Round 3: 363 peptides, 4 chains. Longest chain 131 peptides. Score 0.956 Round 4: 355 peptides, 7 chains. Longest chain 86 peptides. Score 0.942 Round 5: 363 peptides, 5 chains. Longest chain 101 peptides. Score 0.953 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 359, Estimated correctness of the model 99.9 % 4 chains (359 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 91 A and 94 A Built loop between residues 61 B and 64 B 2 chains (363 residues) following loop building 2 chains (363 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 64556 reflections ( 98.98 % complete ) and 2913 restraints for refining 2847 atoms. Observations/parameters ratio is 5.67 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2526 (Rfree = 0.000) for 2847 atoms. Found 143 (174 requested) and removed 0 (174 requested) atoms. Cycle 47: After refmac, R = 0.2265 (Rfree = 0.000) for 2847 atoms. Found 68 (182 requested) and removed 0 (114 requested) atoms. Cycle 48: After refmac, R = 0.2114 (Rfree = 0.000) for 2847 atoms. Found 51 (186 requested) and removed 5 (116 requested) atoms. Cycle 49: After refmac, R = 0.2029 (Rfree = 0.000) for 2847 atoms. Found 30 (189 requested) and removed 8 (118 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:00:50 GMT 2018 Job finished. TimeTaking 81.4 Used memory is bytes: 8736920