null Tue 25 Dec 19:27:57 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 2oyo-1.5-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2oyo-1.5-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2oyo-1.5-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oyo-1.5-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/2oyo-1.5-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oyo-1.5-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 ============================================================ Tue 25 Dec 19:28:07 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/2oyo-1.5-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oyo-1.5-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 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-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: 155 Cell parameters: 135.664 135.664 118.109 90.000 90.000 120.000 Input sequence file: 2oyo-1.5-parrot-hancs.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 3477 atoms. Observations/parameters ratio is 4.64 ------------------------------------------------------ Starting model: R = 0.3093 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2727 (Rfree = 0.000) for 3477 atoms. Found 261 (265 requested) and removed 145 (132 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.53 1.55 NCS extension: 0 residues added, 3593 seeds are put forward Round 1: 328 peptides, 13 chains. Longest chain 73 peptides. Score 0.900 Round 2: 349 peptides, 8 chains. Longest chain 93 peptides. Score 0.935 Round 3: 363 peptides, 4 chains. Longest chain 123 peptides. Score 0.956 Round 4: 363 peptides, 6 chains. Longest chain 102 peptides. Score 0.949 Round 5: 366 peptides, 4 chains. Longest chain 184 peptides. Score 0.957 Taking the results from Round 5 Chains 4, Residues 362, Estimated correctness of the model 99.9 % 4 chains (362 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 33 B and 36 B Built loop between residues 69 B and 72 B 2 chains (366 residues) following loop building 2 chains (366 residues) in sequence following loop building ------------------------------------------------------ 64556 reflections ( 98.98 % complete ) and 3295 restraints for refining 3321 atoms. 359 conditional restraints added. Observations/parameters ratio is 4.86 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2654 (Rfree = 0.000) for 3321 atoms. Found 174 (253 requested) and removed 38 (126 requested) atoms. Cycle 2: After refmac, R = 0.2468 (Rfree = 0.000) for 3456 atoms. Found 113 (263 requested) and removed 25 (131 requested) atoms. Cycle 3: After refmac, R = 0.2214 (Rfree = 0.000) for 3538 atoms. Found 138 (270 requested) and removed 25 (135 requested) atoms. Cycle 4: After refmac, R = 0.2120 (Rfree = 0.000) for 3648 atoms. Found 145 (278 requested) and removed 39 (139 requested) atoms. Cycle 5: After refmac, R = 0.2066 (Rfree = 0.000) for 3749 atoms. Found 133 (286 requested) and removed 41 (143 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.40 1.42 NCS extension: 0 residues added, 3841 seeds are put forward Round 1: 368 peptides, 3 chains. Longest chain 185 peptides. Score 0.961 Round 2: 369 peptides, 2 chains. Longest chain 185 peptides. Score 0.965 Round 3: 365 peptides, 6 chains. Longest chain 103 peptides. Score 0.950 Round 4: 365 peptides, 5 chains. Longest chain 185 peptides. Score 0.954 Round 5: 366 peptides, 5 chains. Longest chain 161 peptides. Score 0.954 Taking the results from Round 2 Chains 2, Residues 367, Estimated correctness of the model 99.9 % 2 chains (367 residues) have been docked in sequence Building loops using Loopy2018 2 chains (367 residues) following loop building 2 chains (367 residues) in sequence following loop building ------------------------------------------------------ 64556 reflections ( 98.98 % complete ) and 3500 restraints for refining 3581 atoms. 553 conditional restraints added. Observations/parameters ratio is 4.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2129 (Rfree = 0.000) for 3581 atoms. Found 196 (273 requested) and removed 35 (136 requested) atoms. Cycle 7: After refmac, R = 0.2085 (Rfree = 0.000) for 3735 atoms. Found 125 (285 requested) and removed 65 (142 requested) atoms. Cycle 8: After refmac, R = 0.2034 (Rfree = 0.000) for 3793 atoms. Found 158 (283 requested) and removed 50 (144 requested) atoms. Cycle 9: After refmac, R = 0.2017 (Rfree = 0.000) for 3898 atoms. Found 116 (291 requested) and removed 94 (148 requested) atoms. Cycle 10: After refmac, R = 0.1992 (Rfree = 0.000) for 3918 atoms. Found 148 (287 requested) and removed 81 (149 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.39 1.41 NCS extension: 0 residues added, 3985 seeds are put forward Round 1: 369 peptides, 2 chains. Longest chain 185 peptides. Score 0.965 Round 2: 367 peptides, 4 chains. Longest chain 185 peptides. Score 0.958 Round 3: 369 peptides, 2 chains. Longest chain 185 peptides. Score 0.965 Round 4: 367 peptides, 4 chains. Longest chain 160 peptides. Score 0.958 Round 5: 368 peptides, 3 chains. Longest chain 185 peptides. Score 0.961 Taking the results from Round 3 Chains 2, Residues 367, Estimated correctness of the model 99.9 % 2 chains (367 residues) have been docked in sequence Building loops using Loopy2018 2 chains (367 residues) following loop building 2 chains (367 residues) in sequence following loop building ------------------------------------------------------ 64556 reflections ( 98.98 % complete ) and 3599 restraints for refining 3647 atoms. 652 conditional restraints added. Observations/parameters ratio is 4.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2062 (Rfree = 0.000) for 3647 atoms. Found 228 (261 requested) and removed 39 (139 requested) atoms. Cycle 12: After refmac, R = 0.2053 (Rfree = 0.000) for 3830 atoms. Found 141 (274 requested) and removed 92 (146 requested) atoms. Cycle 13: After refmac, R = 0.2011 (Rfree = 0.000) for 3875 atoms. Found 157 (271 requested) and removed 77 (147 requested) atoms. Cycle 14: After refmac, R = 0.1998 (Rfree = 0.000) for 3948 atoms. Found 147 (277 requested) and removed 89 (150 requested) atoms. Cycle 15: After refmac, R = 0.1962 (Rfree = 0.000) for 4000 atoms. Found 147 (274 requested) and removed 81 (152 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.39 1.41 NCS extension: 0 residues added, 4067 seeds are put forward Round 1: 369 peptides, 2 chains. Longest chain 185 peptides. Score 0.965 Round 2: 367 peptides, 4 chains. Longest chain 185 peptides. Score 0.958 Round 3: 368 peptides, 3 chains. Longest chain 184 peptides. Score 0.961 Round 4: 365 peptides, 5 chains. Longest chain 160 peptides. Score 0.954 Round 5: 366 peptides, 5 chains. Longest chain 185 peptides. Score 0.954 Taking the results from Round 1 Chains 2, Residues 367, Estimated correctness of the model 99.9 % 2 chains (367 residues) have been docked in sequence Building loops using Loopy2018 2 chains (367 residues) following loop building 2 chains (367 residues) in sequence following loop building ------------------------------------------------------ 64556 reflections ( 98.98 % complete ) and 3622 restraints for refining 3699 atoms. 675 conditional restraints added. Observations/parameters ratio is 4.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2046 (Rfree = 0.000) for 3699 atoms. Found 242 (248 requested) and removed 55 (141 requested) atoms. Cycle 17: After refmac, R = 0.2059 (Rfree = 0.000) for 3877 atoms. Found 136 (260 requested) and removed 91 (148 requested) atoms. Cycle 18: After refmac, R = 0.1993 (Rfree = 0.000) for 3917 atoms. Found 150 (257 requested) and removed 54 (149 requested) atoms. Cycle 19: After refmac, R = 0.1967 (Rfree = 0.000) for 4007 atoms. Found 127 (263 requested) and removed 77 (153 requested) atoms. Cycle 20: After refmac, R = 0.1954 (Rfree = 0.000) for 4049 atoms. Found 132 (260 requested) and removed 73 (154 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.39 1.41 NCS extension: 0 residues added, 4109 seeds are put forward Round 1: 368 peptides, 3 chains. Longest chain 185 peptides. Score 0.961 Round 2: 367 peptides, 4 chains. Longest chain 185 peptides. Score 0.958 Round 3: 368 peptides, 3 chains. Longest chain 184 peptides. Score 0.961 Round 4: 368 peptides, 3 chains. Longest chain 184 peptides. Score 0.961 Round 5: 365 peptides, 5 chains. Longest chain 145 peptides. Score 0.954 Taking the results from Round 4 Chains 3, Residues 365, Estimated correctness of the model 99.9 % 3 chains (365 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 49 B and 52 B 2 chains (367 residues) following loop building 2 chains (367 residues) in sequence following loop building ------------------------------------------------------ 64556 reflections ( 98.98 % complete ) and 3661 restraints for refining 3711 atoms. 714 conditional restraints added. Observations/parameters ratio is 4.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2299 (Rfree = 0.000) for 3711 atoms. Found 187 (232 requested) and removed 48 (141 requested) atoms. Cycle 22: After refmac, R = 0.2115 (Rfree = 0.000) for 3846 atoms. Found 152 (240 requested) and removed 45 (146 requested) atoms. Cycle 23: After refmac, R = 0.2046 (Rfree = 0.000) for 3940 atoms. Found 127 (247 requested) and removed 52 (150 requested) atoms. Cycle 24: After refmac, R = 0.2001 (Rfree = 0.000) for 4008 atoms. Found 138 (251 requested) and removed 60 (153 requested) atoms. Cycle 25: After refmac, R = 0.1982 (Rfree = 0.000) for 4083 atoms. Found 143 (255 requested) and removed 84 (155 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.39 1.41 NCS extension: 0 residues added, 4143 seeds are put forward Round 1: 368 peptides, 3 chains. Longest chain 185 peptides. Score 0.961 Round 2: 367 peptides, 4 chains. Longest chain 185 peptides. Score 0.958 Round 3: 366 peptides, 5 chains. Longest chain 102 peptides. Score 0.954 Round 4: 367 peptides, 4 chains. Longest chain 160 peptides. Score 0.958 Round 5: 364 peptides, 7 chains. Longest chain 95 peptides. Score 0.946 Taking the results from Round 1 Chains 3, Residues 365, Estimated correctness of the model 99.9 % 3 chains (365 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 69 B and 72 B 2 chains (367 residues) following loop building 2 chains (367 residues) in sequence following loop building ------------------------------------------------------ 64556 reflections ( 98.98 % complete ) and 3743 restraints for refining 3772 atoms. 796 conditional restraints added. Observations/parameters ratio is 4.28 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2310 (Rfree = 0.000) for 3772 atoms. Found 207 (230 requested) and removed 44 (143 requested) atoms. Cycle 27: After refmac, R = 0.2139 (Rfree = 0.000) for 3928 atoms. Found 155 (240 requested) and removed 47 (150 requested) atoms. Cycle 28: After refmac, R = 0.2053 (Rfree = 0.000) for 4024 atoms. Found 125 (246 requested) and removed 43 (153 requested) atoms. Cycle 29: After refmac, R = 0.2004 (Rfree = 0.000) for 4100 atoms. Found 119 (250 requested) and removed 56 (156 requested) atoms. Cycle 30: After refmac, R = 0.1960 (Rfree = 0.000) for 4159 atoms. Found 125 (254 requested) and removed 64 (158 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.39 1.41 NCS extension: 0 residues added, 4220 seeds are put forward Round 1: 368 peptides, 3 chains. Longest chain 185 peptides. Score 0.961 Round 2: 365 peptides, 6 chains. Longest chain 131 peptides. Score 0.950 Round 3: 369 peptides, 2 chains. Longest chain 185 peptides. Score 0.965 Round 4: 363 peptides, 8 chains. Longest chain 103 peptides. Score 0.942 Round 5: 366 peptides, 5 chains. Longest chain 185 peptides. Score 0.954 Taking the results from Round 3 Chains 2, Residues 367, Estimated correctness of the model 99.9 % 2 chains (367 residues) have been docked in sequence Building loops using Loopy2018 2 chains (367 residues) following loop building 2 chains (367 residues) in sequence following loop building ------------------------------------------------------ 64556 reflections ( 98.98 % complete ) and 3823 restraints for refining 3828 atoms. 876 conditional restraints added. Observations/parameters ratio is 4.22 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2313 (Rfree = 0.000) for 3828 atoms. Found 205 (228 requested) and removed 34 (146 requested) atoms. Cycle 32: After refmac, R = 0.2140 (Rfree = 0.000) for 3993 atoms. Found 160 (237 requested) and removed 44 (152 requested) atoms. Cycle 33: After refmac, R = 0.2065 (Rfree = 0.000) for 4097 atoms. Found 131 (244 requested) and removed 54 (156 requested) atoms. Cycle 34: After refmac, R = 0.2016 (Rfree = 0.000) for 4171 atoms. Found 123 (248 requested) and removed 64 (159 requested) atoms. Cycle 35: After refmac, R = 0.1974 (Rfree = 0.000) for 4226 atoms. Found 125 (245 requested) and removed 69 (161 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.39 1.41 NCS extension: 0 residues added, 4282 seeds are put forward Round 1: 366 peptides, 4 chains. Longest chain 161 peptides. Score 0.957 Round 2: 365 peptides, 5 chains. Longest chain 131 peptides. Score 0.954 Round 3: 366 peptides, 4 chains. Longest chain 184 peptides. Score 0.957 Round 4: 364 peptides, 6 chains. Longest chain 93 peptides. Score 0.950 Round 5: 363 peptides, 6 chains. Longest chain 145 peptides. Score 0.949 Taking the results from Round 3 Chains 4, Residues 362, Estimated correctness of the model 99.9 % 4 chains (362 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 33 B and 36 B Built loop between residues 91 B and 94 B 2 chains (366 residues) following loop building 2 chains (366 residues) in sequence following loop building ------------------------------------------------------ 64556 reflections ( 98.98 % complete ) and 3972 restraints for refining 3877 atoms. 1036 conditional restraints added. Observations/parameters ratio is 4.16 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2315 (Rfree = 0.000) for 3877 atoms. Found 218 (218 requested) and removed 40 (147 requested) atoms. Cycle 37: After refmac, R = 0.2132 (Rfree = 0.000) for 4052 atoms. Found 146 (229 requested) and removed 48 (154 requested) atoms. Cycle 38: After refmac, R = 0.2061 (Rfree = 0.000) for 4136 atoms. Found 139 (234 requested) and removed 42 (158 requested) atoms. Cycle 39: After refmac, R = 0.2018 (Rfree = 0.000) for 4226 atoms. Found 114 (238 requested) and removed 65 (161 requested) atoms. Cycle 40: After refmac, R = 0.1967 (Rfree = 0.000) for 4265 atoms. Found 127 (235 requested) and removed 48 (163 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.40 1.42 NCS extension: 0 residues added, 4344 seeds are put forward Round 1: 361 peptides, 6 chains. Longest chain 88 peptides. Score 0.949 Round 2: 366 peptides, 3 chains. Longest chain 184 peptides. Score 0.960 Round 3: 362 peptides, 7 chains. Longest chain 160 peptides. Score 0.945 Round 4: 365 peptides, 3 chains. Longest chain 184 peptides. Score 0.960 Round 5: 362 peptides, 7 chains. Longest chain 132 peptides. Score 0.945 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 105 B and 109 B 2 chains (365 residues) following loop building 2 chains (365 residues) in sequence following loop building ------------------------------------------------------ 64556 reflections ( 98.98 % complete ) and 4036 restraints for refining 3894 atoms. 1105 conditional restraints added. Observations/parameters ratio is 4.14 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2323 (Rfree = 0.000) for 3894 atoms. Found 214 (214 requested) and removed 35 (148 requested) atoms. Cycle 42: After refmac, R = 0.2153 (Rfree = 0.000) for 4067 atoms. Found 163 (223 requested) and removed 39 (155 requested) atoms. Cycle 43: After refmac, R = 0.2081 (Rfree = 0.000) for 4182 atoms. Found 119 (230 requested) and removed 49 (159 requested) atoms. Cycle 44: After refmac, R = 0.2016 (Rfree = 0.000) for 4247 atoms. Found 121 (233 requested) and removed 47 (162 requested) atoms. Cycle 45: After refmac, R = 0.1985 (Rfree = 0.000) for 4313 atoms. Found 127 (237 requested) and removed 69 (164 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.40 1.42 NCS extension: 0 residues added, 4371 seeds are put forward Round 1: 361 peptides, 6 chains. Longest chain 124 peptides. Score 0.949 Round 2: 362 peptides, 6 chains. Longest chain 160 peptides. Score 0.949 Round 3: 365 peptides, 4 chains. Longest chain 155 peptides. Score 0.957 Round 4: 366 peptides, 3 chains. Longest chain 184 peptides. Score 0.960 Round 5: 362 peptides, 5 chains. Longest chain 145 peptides. Score 0.952 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 363, Estimated correctness of the model 99.9 % 3 chains (363 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 33 B and 36 B 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 2931 restraints for refining 2865 atoms. Observations/parameters ratio is 5.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2512 (Rfree = 0.000) for 2865 atoms. Found 146 (153 requested) and removed 0 (153 requested) atoms. Cycle 47: After refmac, R = 0.2246 (Rfree = 0.000) for 2865 atoms. Found 66 (160 requested) and removed 0 (114 requested) atoms. Cycle 48: After refmac, R = 0.2095 (Rfree = 0.000) for 2865 atoms. Found 45 (164 requested) and removed 6 (117 requested) atoms. Cycle 49: After refmac, R = 0.2022 (Rfree = 0.000) for 2865 atoms. Found 24 (166 requested) and removed 5 (118 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:11:17 GMT 2018 Job finished. TimeTaking 103.34 Used memory is bytes: 18550736