null Mon 24 Dec 00:30:20 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 2oyo-1.5-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2oyo-1.5-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2oyo-1.5-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oyo-1.5-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/2oyo-1.5-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oyo-1.5-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 00:30:24 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/2oyo-1.5-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oyo-1.5-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 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-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: 155 Cell parameters: 135.664 135.664 118.109 90.000 90.000 120.000 Input sequence file: 2oyo-1.5-parrot-mrncs.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 3454 atoms. Observations/parameters ratio is 4.67 ------------------------------------------------------ Starting model: R = 0.3100 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2724 (Rfree = 0.000) for 3454 atoms. Found 263 (263 requested) and removed 138 (131 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.52 1.54 NCS extension: 0 residues added, 3579 seeds are put forward Round 1: 346 peptides, 16 chains. Longest chain 48 peptides. Score 0.900 Round 2: 362 peptides, 7 chains. Longest chain 94 peptides. Score 0.945 Round 3: 365 peptides, 5 chains. Longest chain 142 peptides. Score 0.954 Round 4: 367 peptides, 2 chains. Longest chain 184 peptides. Score 0.964 Round 5: 363 peptides, 6 chains. Longest chain 140 peptides. Score 0.949 Taking the results from Round 4 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 3271 restraints for refining 3316 atoms. 340 conditional restraints added. Observations/parameters ratio is 4.87 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2662 (Rfree = 0.000) for 3316 atoms. Found 154 (253 requested) and removed 36 (126 requested) atoms. Cycle 2: After refmac, R = 0.2511 (Rfree = 0.000) for 3433 atoms. Found 141 (261 requested) and removed 17 (130 requested) atoms. Cycle 3: After refmac, R = 0.2253 (Rfree = 0.000) for 3550 atoms. Found 146 (271 requested) and removed 25 (135 requested) atoms. Cycle 4: After refmac, R = 0.2134 (Rfree = 0.000) for 3666 atoms. Found 127 (280 requested) and removed 36 (140 requested) atoms. Cycle 5: After refmac, R = 0.2062 (Rfree = 0.000) for 3748 atoms. Found 114 (286 requested) and removed 46 (143 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.41 1.43 NCS extension: 0 residues added, 3816 seeds are put forward Round 1: 367 peptides, 2 chains. Longest chain 184 peptides. Score 0.964 Round 2: 366 peptides, 3 chains. Longest chain 183 peptides. Score 0.960 Round 3: 362 peptides, 6 chains. Longest chain 132 peptides. Score 0.949 Round 4: 366 peptides, 3 chains. Longest chain 183 peptides. Score 0.960 Round 5: 365 peptides, 4 chains. Longest chain 160 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 3492 restraints for refining 3568 atoms. 561 conditional restraints added. Observations/parameters ratio is 4.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2115 (Rfree = 0.000) for 3568 atoms. Found 208 (272 requested) and removed 41 (136 requested) atoms. Cycle 7: After refmac, R = 0.2079 (Rfree = 0.000) for 3730 atoms. Found 129 (284 requested) and removed 78 (142 requested) atoms. Cycle 8: After refmac, R = 0.2011 (Rfree = 0.000) for 3778 atoms. Found 149 (282 requested) and removed 56 (144 requested) atoms. Cycle 9: After refmac, R = 0.2003 (Rfree = 0.000) for 3869 atoms. Found 145 (289 requested) and removed 81 (147 requested) atoms. Cycle 10: After refmac, R = 0.1986 (Rfree = 0.000) for 3922 atoms. Found 165 (287 requested) and removed 82 (149 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.39 1.41 NCS extension: 0 residues added, 4005 seeds are put forward Round 1: 366 peptides, 3 chains. Longest chain 183 peptides. Score 0.960 Round 2: 366 peptides, 3 chains. Longest chain 183 peptides. Score 0.960 Round 3: 365 peptides, 4 chains. Longest chain 160 peptides. Score 0.957 Round 4: 364 peptides, 4 chains. Longest chain 183 peptides. Score 0.956 Round 5: 364 peptides, 5 chains. Longest chain 131 peptides. Score 0.953 Taking the results from Round 2 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 165 B and 168 B 2 chains (365 residues) following loop building 2 chains (365 residues) in sequence following loop building ------------------------------------------------------ 64556 reflections ( 98.98 % complete ) and 3541 restraints for refining 3625 atoms. 610 conditional restraints added. Observations/parameters ratio is 4.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2046 (Rfree = 0.000) for 3625 atoms. Found 232 (265 requested) and removed 49 (138 requested) atoms. Cycle 12: After refmac, R = 0.2046 (Rfree = 0.000) for 3801 atoms. Found 135 (278 requested) and removed 89 (145 requested) atoms. Cycle 13: After refmac, R = 0.1982 (Rfree = 0.000) for 3844 atoms. Found 149 (275 requested) and removed 52 (146 requested) atoms. Cycle 14: After refmac, R = 0.1970 (Rfree = 0.000) for 3937 atoms. Found 121 (282 requested) and removed 84 (150 requested) atoms. Cycle 15: After refmac, R = 0.1962 (Rfree = 0.000) for 3968 atoms. Found 154 (278 requested) and removed 75 (151 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.39 1.41 NCS extension: 0 residues added, 4047 seeds are put forward Round 1: 367 peptides, 2 chains. Longest chain 184 peptides. Score 0.964 Round 2: 364 peptides, 5 chains. Longest chain 183 peptides. Score 0.953 Round 3: 365 peptides, 4 chains. Longest chain 102 peptides. Score 0.957 Round 4: 363 peptides, 5 chains. Longest chain 183 peptides. Score 0.953 Round 5: 363 peptides, 6 chains. Longest chain 102 peptides. Score 0.949 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 3661 restraints for refining 3663 atoms. 730 conditional restraints added. Observations/parameters ratio is 4.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2275 (Rfree = 0.000) for 3663 atoms. Found 201 (257 requested) and removed 36 (139 requested) atoms. Cycle 17: After refmac, R = 0.2118 (Rfree = 0.000) for 3824 atoms. Found 137 (268 requested) and removed 50 (145 requested) atoms. Cycle 18: After refmac, R = 0.2043 (Rfree = 0.000) for 3900 atoms. Found 133 (274 requested) and removed 48 (149 requested) atoms. Cycle 19: After refmac, R = 0.2002 (Rfree = 0.000) for 3981 atoms. Found 128 (279 requested) and removed 71 (151 requested) atoms. Cycle 20: After refmac, R = 0.1976 (Rfree = 0.000) for 4030 atoms. Found 147 (276 requested) and removed 91 (153 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.39 1.41 NCS extension: 0 residues added, 4086 seeds are put forward Round 1: 365 peptides, 3 chains. Longest chain 183 peptides. Score 0.960 Round 2: 362 peptides, 5 chains. Longest chain 102 peptides. Score 0.952 Round 3: 366 peptides, 2 chains. Longest chain 183 peptides. Score 0.964 Round 4: 362 peptides, 6 chains. Longest chain 102 peptides. Score 0.949 Round 5: 364 peptides, 4 chains. Longest chain 144 peptides. Score 0.956 Taking the results from Round 3 Chains 2, Residues 364, Estimated correctness of the model 99.9 % 2 chains (364 residues) have been docked in sequence Building loops using Loopy2018 2 chains (364 residues) following loop building 2 chains (364 residues) in sequence following loop building ------------------------------------------------------ 64556 reflections ( 98.98 % complete ) and 3732 restraints for refining 3732 atoms. 812 conditional restraints added. Observations/parameters ratio is 4.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2064 (Rfree = 0.000) for 3732 atoms. Found 247 (250 requested) and removed 45 (142 requested) atoms. Cycle 22: After refmac, R = 0.2041 (Rfree = 0.000) for 3926 atoms. Found 151 (264 requested) and removed 80 (150 requested) atoms. Cycle 23: After refmac, R = 0.2005 (Rfree = 0.000) for 3991 atoms. Found 156 (261 requested) and removed 70 (152 requested) atoms. Cycle 24: After refmac, R = 0.2000 (Rfree = 0.000) for 4073 atoms. Found 130 (267 requested) and removed 105 (155 requested) atoms. Cycle 25: After refmac, R = 0.1961 (Rfree = 0.000) for 4093 atoms. Found 166 (262 requested) and removed 80 (156 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.39 1.41 NCS extension: 0 residues added, 4179 seeds are put forward Round 1: 365 peptides, 3 chains. Longest chain 183 peptides. Score 0.960 Round 2: 364 peptides, 4 chains. Longest chain 183 peptides. Score 0.956 Round 3: 365 peptides, 3 chains. Longest chain 183 peptides. Score 0.960 Round 4: 363 peptides, 5 chains. Longest chain 102 peptides. Score 0.953 Round 5: 366 peptides, 3 chains. Longest chain 183 peptides. Score 0.960 Taking the results from Round 5 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 166 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 3737 restraints for refining 3737 atoms. 817 conditional restraints added. Observations/parameters ratio is 4.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2051 (Rfree = 0.000) for 3737 atoms. Found 239 (239 requested) and removed 54 (142 requested) atoms. Cycle 27: After refmac, R = 0.2045 (Rfree = 0.000) for 3919 atoms. Found 145 (251 requested) and removed 81 (149 requested) atoms. Cycle 28: After refmac, R = 0.1998 (Rfree = 0.000) for 3975 atoms. Found 159 (248 requested) and removed 67 (151 requested) atoms. Cycle 29: After refmac, R = 0.1993 (Rfree = 0.000) for 4063 atoms. Found 148 (254 requested) and removed 103 (155 requested) atoms. Cycle 30: After refmac, R = 0.1977 (Rfree = 0.000) for 4100 atoms. Found 151 (250 requested) and removed 98 (156 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.39 1.41 NCS extension: 0 residues added, 4153 seeds are put forward Round 1: 364 peptides, 4 chains. Longest chain 183 peptides. Score 0.956 Round 2: 365 peptides, 3 chains. Longest chain 183 peptides. Score 0.960 Round 3: 366 peptides, 2 chains. Longest chain 183 peptides. Score 0.964 Round 4: 363 peptides, 5 chains. Longest chain 144 peptides. Score 0.953 Round 5: 363 peptides, 5 chains. Longest chain 154 peptides. Score 0.953 Taking the results from Round 3 Chains 2, Residues 364, Estimated correctness of the model 99.9 % 2 chains (364 residues) have been docked in sequence Building loops using Loopy2018 2 chains (364 residues) following loop building 2 chains (364 residues) in sequence following loop building ------------------------------------------------------ 64556 reflections ( 98.98 % complete ) and 3745 restraints for refining 3739 atoms. 825 conditional restraints added. Observations/parameters ratio is 4.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2306 (Rfree = 0.000) for 3739 atoms. Found 222 (222 requested) and removed 35 (142 requested) atoms. Cycle 32: After refmac, R = 0.2143 (Rfree = 0.000) for 3920 atoms. Found 160 (233 requested) and removed 60 (149 requested) atoms. Cycle 33: After refmac, R = 0.2054 (Rfree = 0.000) for 4010 atoms. Found 146 (239 requested) and removed 56 (153 requested) atoms. Cycle 34: After refmac, R = 0.2021 (Rfree = 0.000) for 4093 atoms. Found 145 (243 requested) and removed 76 (156 requested) atoms. Cycle 35: After refmac, R = 0.2004 (Rfree = 0.000) for 4157 atoms. Found 131 (241 requested) and removed 81 (158 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.39 1.41 NCS extension: 0 residues added, 4207 seeds are put forward Round 1: 363 peptides, 4 chains. Longest chain 183 peptides. Score 0.956 Round 2: 364 peptides, 4 chains. Longest chain 183 peptides. Score 0.956 Round 3: 365 peptides, 3 chains. Longest chain 183 peptides. Score 0.960 Round 4: 362 peptides, 6 chains. Longest chain 144 peptides. Score 0.949 Round 5: 364 peptides, 4 chains. Longest chain 183 peptides. Score 0.956 Taking the results from Round 3 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 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 3791 restraints for refining 3796 atoms. 871 conditional restraints added. Observations/parameters ratio is 4.25 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2292 (Rfree = 0.000) for 3796 atoms. Found 214 (214 requested) and removed 36 (144 requested) atoms. Cycle 37: After refmac, R = 0.2145 (Rfree = 0.000) for 3970 atoms. Found 148 (224 requested) and removed 54 (151 requested) atoms. Cycle 38: After refmac, R = 0.2051 (Rfree = 0.000) for 4053 atoms. Found 141 (229 requested) and removed 49 (154 requested) atoms. Cycle 39: After refmac, R = 0.2022 (Rfree = 0.000) for 4144 atoms. Found 131 (234 requested) and removed 65 (158 requested) atoms. Cycle 40: After refmac, R = 0.1987 (Rfree = 0.000) for 4204 atoms. Found 131 (238 requested) and removed 72 (160 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.39 1.41 NCS extension: 0 residues added, 4263 seeds are put forward Round 1: 365 peptides, 3 chains. Longest chain 183 peptides. Score 0.960 Round 2: 363 peptides, 5 chains. Longest chain 183 peptides. Score 0.953 Round 3: 364 peptides, 4 chains. Longest chain 102 peptides. Score 0.956 Round 4: 357 peptides, 7 chains. Longest chain 144 peptides. Score 0.943 Round 5: 358 peptides, 5 chains. Longest chain 102 peptides. Score 0.951 Taking the results from Round 1 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 69 A and 72 A 2 chains (364 residues) following loop building 2 chains (364 residues) in sequence following loop building ------------------------------------------------------ 64556 reflections ( 98.98 % complete ) and 3877 restraints for refining 3824 atoms. 957 conditional restraints added. Observations/parameters ratio is 4.22 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2329 (Rfree = 0.000) for 3824 atoms. Found 210 (210 requested) and removed 32 (145 requested) atoms. Cycle 42: After refmac, R = 0.2153 (Rfree = 0.000) for 3997 atoms. Found 149 (220 requested) and removed 40 (152 requested) atoms. Cycle 43: After refmac, R = 0.2070 (Rfree = 0.000) for 4094 atoms. Found 134 (225 requested) and removed 54 (156 requested) atoms. Cycle 44: After refmac, R = 0.2045 (Rfree = 0.000) for 4167 atoms. Found 141 (229 requested) and removed 83 (159 requested) atoms. Cycle 45: After refmac, R = 0.2011 (Rfree = 0.000) for 4221 atoms. Found 134 (225 requested) and removed 86 (161 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.39 1.41 NCS extension: 0 residues added, 4269 seeds are put forward Round 1: 367 peptides, 2 chains. Longest chain 184 peptides. Score 0.964 Round 2: 364 peptides, 5 chains. Longest chain 183 peptides. Score 0.953 Round 3: 366 peptides, 3 chains. Longest chain 184 peptides. Score 0.960 Round 4: 364 peptides, 5 chains. Longest chain 144 peptides. Score 0.953 Round 5: 364 peptides, 5 chains. Longest chain 132 peptides. Score 0.953 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 365, Estimated correctness of the model 99.9 % 2 chains (365 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 2 chains (365 residues) following loop building 2 chains (365 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 64556 reflections ( 98.98 % complete ) and 2925 restraints for refining 2859 atoms. Observations/parameters ratio is 5.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2491 (Rfree = 0.000) for 2859 atoms. Found 148 (148 requested) and removed 0 (148 requested) atoms. Cycle 47: After refmac, R = 0.2229 (Rfree = 0.000) for 2859 atoms. Found 86 (156 requested) and removed 0 (114 requested) atoms. Cycle 48: After refmac, R = 0.2079 (Rfree = 0.000) for 2859 atoms. Found 32 (160 requested) and removed 5 (118 requested) atoms. Cycle 49: After refmac, R = 0.2004 (Rfree = 0.000) for 2859 atoms. Found 21 (162 requested) and removed 7 (119 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:44:59 GMT 2018 Job finished. TimeTaking 74.66 Used memory is bytes: 14164336