Sun 23 Dec 22:22:46 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 2b8m-1.7-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2b8m-1.7-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2b8m-1.7-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2b8m-1.7-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/2b8m-1.7-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2b8m-1.7-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 ============================================================ Sun 23 Dec 22:22:55 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/2b8m-1.7-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2b8m-1.7-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 130 and 0 Target number of residues in the AU: 130 Target solvent content: 0.3834 Checking the provided sequence file Detected sequence length: 117 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 117 Adjusted target solvent content: 0.45 Input MTZ file: 2b8m-1.7-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: 152 Cell parameters: 50.280 50.280 78.170 90.000 90.000 120.000 Input sequence file: 2b8m-1.7-parrot-hancs.fasta_lf Building free atoms model in initial map for 936 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 Loops will be built when appropriate and at the last cycle Resolution range: 29.086 1.700 Wilson plot Bfac: 6.25 12899 reflections ( 98.70 % complete ) and 0 restraints for refining 1037 atoms. Observations/parameters ratio is 3.11 ------------------------------------------------------ Starting model: R = 0.3130 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2775 (Rfree = 0.000) for 1037 atoms. Found 51 (56 requested) and removed 32 (28 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.49 1.59 Round 1: 95 peptides, 4 chains. Longest chain 66 peptides. Score 0.908 Round 2: 99 peptides, 2 chains. Longest chain 62 peptides. Score 0.945 Round 3: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Round 4: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Round 5: 95 peptides, 2 chains. Longest chain 91 peptides. Score 0.938 Taking the results from Round 4 Chains 1, Residues 99, Estimated correctness of the model 99.9 % 1 chains (99 residues) have been docked in sequence ------------------------------------------------------ 12899 reflections ( 98.70 % complete ) and 1011 restraints for refining 978 atoms. 171 conditional restraints added. Observations/parameters ratio is 3.30 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2763 (Rfree = 0.000) for 978 atoms. Found 37 (53 requested) and removed 20 (26 requested) atoms. Cycle 2: After refmac, R = 0.2558 (Rfree = 0.000) for 994 atoms. Found 27 (53 requested) and removed 5 (27 requested) atoms. Cycle 3: After refmac, R = 0.2441 (Rfree = 0.000) for 1015 atoms. Found 21 (54 requested) and removed 3 (27 requested) atoms. Cycle 4: After refmac, R = 0.2343 (Rfree = 0.000) for 1031 atoms. Found 19 (55 requested) and removed 4 (28 requested) atoms. Cycle 5: After refmac, R = 0.2197 (Rfree = 0.000) for 1045 atoms. Found 23 (55 requested) and removed 3 (28 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.40 1.50 Round 1: 101 peptides, 1 chains. Longest chain 101 peptides. Score 0.960 Round 2: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Round 3: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Round 4: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Round 5: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Taking the results from Round 1 Chains 1, Residues 100, Estimated correctness of the model 99.9 % 1 chains (100 residues) have been docked in sequence ------------------------------------------------------ 12899 reflections ( 98.70 % complete ) and 1023 restraints for refining 1027 atoms. 178 conditional restraints added. Observations/parameters ratio is 3.14 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2225 (Rfree = 0.000) for 1027 atoms. Found 33 (54 requested) and removed 10 (27 requested) atoms. Cycle 7: After refmac, R = 0.2202 (Rfree = 0.000) for 1048 atoms. Found 24 (56 requested) and removed 5 (28 requested) atoms. Cycle 8: After refmac, R = 0.2075 (Rfree = 0.000) for 1067 atoms. Found 31 (57 requested) and removed 4 (29 requested) atoms. Cycle 9: After refmac, R = 0.2023 (Rfree = 0.000) for 1093 atoms. Found 34 (58 requested) and removed 4 (29 requested) atoms. Cycle 10: After refmac, R = 0.1996 (Rfree = 0.000) for 1119 atoms. Found 24 (60 requested) and removed 6 (30 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.38 1.48 Round 1: 101 peptides, 1 chains. Longest chain 101 peptides. Score 0.960 Round 2: 101 peptides, 1 chains. Longest chain 101 peptides. Score 0.960 Round 3: 101 peptides, 1 chains. Longest chain 101 peptides. Score 0.960 Round 4: 101 peptides, 1 chains. Longest chain 101 peptides. Score 0.960 Round 5: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Taking the results from Round 4 Chains 1, Residues 100, Estimated correctness of the model 99.9 % 1 chains (100 residues) have been docked in sequence ------------------------------------------------------ 12899 reflections ( 98.70 % complete ) and 1092 restraints for refining 1086 atoms. 247 conditional restraints added. Observations/parameters ratio is 2.97 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2111 (Rfree = 0.000) for 1086 atoms. Found 39 (58 requested) and removed 14 (29 requested) atoms. Cycle 12: After refmac, R = 0.2008 (Rfree = 0.000) for 1111 atoms. Found 31 (59 requested) and removed 6 (30 requested) atoms. Cycle 13: After refmac, R = 0.1949 (Rfree = 0.000) for 1136 atoms. Found 28 (60 requested) and removed 7 (30 requested) atoms. Cycle 14: After refmac, R = 0.1936 (Rfree = 0.000) for 1154 atoms. Found 23 (61 requested) and removed 8 (31 requested) atoms. Cycle 15: After refmac, R = 0.1905 (Rfree = 0.000) for 1169 atoms. Found 31 (62 requested) and removed 9 (31 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.36 1.45 Round 1: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Round 2: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Round 3: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Round 4: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Round 5: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Taking the results from Round 5 Chains 1, Residues 99, Estimated correctness of the model 99.9 % 1 chains (99 residues) have been docked in sequence ------------------------------------------------------ 12899 reflections ( 98.70 % complete ) and 1146 restraints for refining 1114 atoms. 306 conditional restraints added. Observations/parameters ratio is 2.89 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2058 (Rfree = 0.000) for 1114 atoms. Found 55 (59 requested) and removed 12 (30 requested) atoms. Cycle 17: After refmac, R = 0.1993 (Rfree = 0.000) for 1156 atoms. Found 24 (61 requested) and removed 4 (31 requested) atoms. Cycle 18: After refmac, R = 0.1934 (Rfree = 0.000) for 1176 atoms. Found 29 (62 requested) and removed 6 (31 requested) atoms. Cycle 19: After refmac, R = 0.1908 (Rfree = 0.000) for 1198 atoms. Found 23 (64 requested) and removed 10 (32 requested) atoms. Cycle 20: After refmac, R = 0.1891 (Rfree = 0.000) for 1209 atoms. Found 23 (64 requested) and removed 11 (32 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.36 1.45 Round 1: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Round 2: 101 peptides, 1 chains. Longest chain 101 peptides. Score 0.960 Round 3: 101 peptides, 1 chains. Longest chain 101 peptides. Score 0.960 Round 4: 101 peptides, 1 chains. Longest chain 101 peptides. Score 0.960 Round 5: 101 peptides, 1 chains. Longest chain 101 peptides. Score 0.960 Taking the results from Round 5 Chains 1, Residues 100, Estimated correctness of the model 99.9 % 1 chains (100 residues) have been docked in sequence ------------------------------------------------------ 12899 reflections ( 98.70 % complete ) and 1165 restraints for refining 1138 atoms. 320 conditional restraints added. Observations/parameters ratio is 2.83 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2062 (Rfree = 0.000) for 1138 atoms. Found 53 (60 requested) and removed 16 (30 requested) atoms. Cycle 22: After refmac, R = 0.1986 (Rfree = 0.000) for 1174 atoms. Found 35 (62 requested) and removed 5 (31 requested) atoms. Cycle 23: After refmac, R = 0.1932 (Rfree = 0.000) for 1203 atoms. Found 20 (64 requested) and removed 4 (32 requested) atoms. Cycle 24: After refmac, R = 0.1863 (Rfree = 0.000) for 1219 atoms. Found 20 (65 requested) and removed 4 (33 requested) atoms. Cycle 25: After refmac, R = 0.1845 (Rfree = 0.000) for 1233 atoms. Found 19 (66 requested) and removed 5 (33 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.35 1.44 Round 1: 101 peptides, 1 chains. Longest chain 101 peptides. Score 0.960 Round 2: 101 peptides, 1 chains. Longest chain 101 peptides. Score 0.960 Round 3: 101 peptides, 1 chains. Longest chain 101 peptides. Score 0.960 Round 4: 101 peptides, 1 chains. Longest chain 101 peptides. Score 0.960 Round 5: 101 peptides, 1 chains. Longest chain 101 peptides. Score 0.960 Taking the results from Round 5 Chains 1, Residues 100, Estimated correctness of the model 99.9 % 1 chains (100 residues) have been docked in sequence ------------------------------------------------------ 12899 reflections ( 98.70 % complete ) and 1191 restraints for refining 1165 atoms. 346 conditional restraints added. Observations/parameters ratio is 2.77 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2015 (Rfree = 0.000) for 1165 atoms. Found 62 (62 requested) and removed 8 (31 requested) atoms. Cycle 27: After refmac, R = 0.1974 (Rfree = 0.000) for 1216 atoms. Found 27 (65 requested) and removed 10 (33 requested) atoms. Cycle 28: After refmac, R = 0.1904 (Rfree = 0.000) for 1232 atoms. Found 28 (66 requested) and removed 2 (33 requested) atoms. Cycle 29: After refmac, R = 0.1877 (Rfree = 0.000) for 1254 atoms. Found 18 (67 requested) and removed 9 (34 requested) atoms. Cycle 30: After refmac, R = 0.1844 (Rfree = 0.000) for 1261 atoms. Found 21 (67 requested) and removed 5 (34 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.36 1.45 Round 1: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Round 2: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Round 3: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Round 4: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Round 5: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Taking the results from Round 5 Chains 1, Residues 99, Estimated correctness of the model 99.9 % 1 chains (99 residues) have been docked in sequence ------------------------------------------------------ 12899 reflections ( 98.70 % complete ) and 1293 restraints for refining 1188 atoms. 453 conditional restraints added. Observations/parameters ratio is 2.71 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2038 (Rfree = 0.000) for 1188 atoms. Found 55 (63 requested) and removed 12 (32 requested) atoms. Cycle 32: After refmac, R = 0.1971 (Rfree = 0.000) for 1229 atoms. Found 27 (66 requested) and removed 4 (33 requested) atoms. Cycle 33: After refmac, R = 0.1891 (Rfree = 0.000) for 1252 atoms. Found 17 (67 requested) and removed 4 (34 requested) atoms. Cycle 34: After refmac, R = 0.1860 (Rfree = 0.000) for 1262 atoms. Found 21 (67 requested) and removed 4 (34 requested) atoms. Cycle 35: After refmac, R = 0.1838 (Rfree = 0.000) for 1278 atoms. Found 17 (68 requested) and removed 12 (34 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.35 1.44 Round 1: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Round 2: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Round 3: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Round 4: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Round 5: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Taking the results from Round 5 Chains 1, Residues 99, Estimated correctness of the model 99.9 % 1 chains (99 residues) have been docked in sequence ------------------------------------------------------ 12899 reflections ( 98.70 % complete ) and 1279 restraints for refining 1197 atoms. 439 conditional restraints added. Observations/parameters ratio is 2.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2049 (Rfree = 0.000) for 1197 atoms. Found 57 (62 requested) and removed 12 (32 requested) atoms. Cycle 37: After refmac, R = 0.1971 (Rfree = 0.000) for 1240 atoms. Found 36 (64 requested) and removed 3 (33 requested) atoms. Cycle 38: After refmac, R = 0.1915 (Rfree = 0.000) for 1272 atoms. Found 24 (66 requested) and removed 4 (34 requested) atoms. Cycle 39: After refmac, R = 0.1887 (Rfree = 0.000) for 1288 atoms. Found 24 (67 requested) and removed 4 (35 requested) atoms. Cycle 40: After refmac, R = 0.1858 (Rfree = 0.000) for 1303 atoms. Found 19 (68 requested) and removed 7 (35 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.39 1.49 Round 1: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Round 2: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Round 3: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Round 4: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Round 5: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Taking the results from Round 5 Chains 1, Residues 99, Estimated correctness of the model 99.9 % 1 chains (99 residues) have been docked in sequence ------------------------------------------------------ 12899 reflections ( 98.70 % complete ) and 1315 restraints for refining 1208 atoms. 475 conditional restraints added. Observations/parameters ratio is 2.67 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2055 (Rfree = 0.000) for 1208 atoms. Found 59 (62 requested) and removed 10 (32 requested) atoms. Cycle 42: After refmac, R = 0.1963 (Rfree = 0.000) for 1255 atoms. Found 28 (65 requested) and removed 4 (34 requested) atoms. Cycle 43: After refmac, R = 0.1926 (Rfree = 0.000) for 1276 atoms. Found 19 (66 requested) and removed 3 (34 requested) atoms. Cycle 44: After refmac, R = 0.1896 (Rfree = 0.000) for 1285 atoms. Found 18 (67 requested) and removed 2 (35 requested) atoms. Cycle 45: After refmac, R = 0.1845 (Rfree = 0.000) for 1299 atoms. Found 9 (67 requested) and removed 3 (35 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.35 1.44 Round 1: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Round 2: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Round 3: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Round 4: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Round 5: 100 peptides, 1 chains. Longest chain 100 peptides. Score 0.959 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 1, Residues 99, Estimated correctness of the model 99.9 % 1 chains (99 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 12899 reflections ( 98.70 % complete ) and 840 restraints for refining 823 atoms. Observations/parameters ratio is 3.92 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2823 (Rfree = 0.000) for 823 atoms. Found 37 (42 requested) and removed 0 (42 requested) atoms. Cycle 47: After refmac, R = 0.2476 (Rfree = 0.000) for 823 atoms. Found 18 (44 requested) and removed 0 (23 requested) atoms. Cycle 48: After refmac, R = 0.2322 (Rfree = 0.000) for 823 atoms. Found 15 (45 requested) and removed 4 (23 requested) atoms. Cycle 49: After refmac, R = 0.2226 (Rfree = 0.000) for 823 atoms. TimeTaking 27.27