null Sun 23 Dec 22:22:59 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 2inb-1.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2inb-1.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2inb-1.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2inb-1.6-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/2inb-1.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2inb-1.6-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 22:23:08 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/2inb-1.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2inb-1.6-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 146 and 0 Target number of residues in the AU: 146 Target solvent content: 0.4599 Checking the provided sequence file Detected sequence length: 140 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 140 Adjusted target solvent content: 0.48 Input MTZ file: 2inb-1.6-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: 59.524 59.524 71.521 90.000 90.000 120.000 Input sequence file: 2inb-1.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1120 target number of atoms Had to go as low as 0.35 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: 29.762 1.600 Wilson plot Bfac: 15.61 19818 reflections ( 99.98 % complete ) and 0 restraints for refining 1233 atoms. Observations/parameters ratio is 4.02 ------------------------------------------------------ Starting model: R = 0.3248 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2686 (Rfree = 0.000) for 1233 atoms. Found 79 (79 requested) and removed 42 (39 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.65 1.69 Round 1: 107 peptides, 8 chains. Longest chain 41 peptides. Score 0.818 Round 2: 116 peptides, 5 chains. Longest chain 64 peptides. Score 0.897 Round 3: 119 peptides, 4 chains. Longest chain 74 peptides. Score 0.916 Round 4: 120 peptides, 4 chains. Longest chain 75 peptides. Score 0.918 Round 5: 121 peptides, 5 chains. Longest chain 65 peptides. Score 0.907 Taking the results from Round 4 Chains 4, Residues 116, Estimated correctness of the model 99.6 % 3 chains (109 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 63 A and 67 A 3 chains (119 residues) following loop building 2 chains (112 residues) in sequence following loop building ------------------------------------------------------ 19818 reflections ( 99.98 % complete ) and 1217 restraints for refining 1150 atoms. 243 conditional restraints added. Observations/parameters ratio is 4.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2746 (Rfree = 0.000) for 1150 atoms. Found 46 (74 requested) and removed 26 (37 requested) atoms. Cycle 2: After refmac, R = 0.2518 (Rfree = 0.000) for 1168 atoms. Found 46 (73 requested) and removed 8 (37 requested) atoms. Cycle 3: After refmac, R = 0.2244 (Rfree = 0.000) for 1203 atoms. Found 50 (76 requested) and removed 10 (39 requested) atoms. Cycle 4: After refmac, R = 0.2133 (Rfree = 0.000) for 1241 atoms. Found 41 (78 requested) and removed 14 (40 requested) atoms. Cycle 5: After refmac, R = 0.2057 (Rfree = 0.000) for 1266 atoms. Found 43 (79 requested) and removed 9 (40 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.64 1.68 Round 1: 116 peptides, 5 chains. Longest chain 62 peptides. Score 0.897 Round 2: 118 peptides, 4 chains. Longest chain 71 peptides. Score 0.914 Round 3: 120 peptides, 5 chains. Longest chain 62 peptides. Score 0.905 Round 4: 120 peptides, 4 chains. Longest chain 71 peptides. Score 0.918 Round 5: 121 peptides, 4 chains. Longest chain 40 peptides. Score 0.920 Taking the results from Round 5 Chains 5, Residues 117, Estimated correctness of the model 99.7 % 4 chains (115 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 36 A and 46 A Built loop between residues 63 A and 71 A Built loop between residues 107 A and 110 A 1 chains (133 residues) following loop building 1 chains (133 residues) in sequence following loop building ------------------------------------------------------ 19818 reflections ( 99.98 % complete ) and 1262 restraints for refining 1280 atoms. 163 conditional restraints added. Observations/parameters ratio is 3.87 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2322 (Rfree = 0.000) for 1280 atoms. Found 62 (80 requested) and removed 42 (41 requested) atoms. Cycle 7: After refmac, R = 0.2154 (Rfree = 0.000) for 1298 atoms. Found 34 (81 requested) and removed 25 (42 requested) atoms. Cycle 8: After refmac, R = 0.2063 (Rfree = 0.000) for 1304 atoms. Found 32 (79 requested) and removed 14 (42 requested) atoms. Cycle 9: After refmac, R = 0.2001 (Rfree = 0.000) for 1318 atoms. Found 34 (80 requested) and removed 11 (42 requested) atoms. Cycle 10: After refmac, R = 0.1968 (Rfree = 0.000) for 1337 atoms. Found 46 (81 requested) and removed 17 (43 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.64 1.68 Round 1: 120 peptides, 4 chains. Longest chain 71 peptides. Score 0.918 Round 2: 120 peptides, 4 chains. Longest chain 71 peptides. Score 0.918 Round 3: 120 peptides, 5 chains. Longest chain 62 peptides. Score 0.905 Round 4: 120 peptides, 4 chains. Longest chain 71 peptides. Score 0.918 Round 5: 122 peptides, 3 chains. Longest chain 71 peptides. Score 0.933 Taking the results from Round 5 Chains 3, Residues 119, Estimated correctness of the model 99.8 % 3 chains (119 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 A and 46 A Built loop between residues 63 A and 70 A 1 chains (133 residues) following loop building 1 chains (133 residues) in sequence following loop building ------------------------------------------------------ 19818 reflections ( 99.98 % complete ) and 1314 restraints for refining 1317 atoms. 215 conditional restraints added. Observations/parameters ratio is 3.76 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2280 (Rfree = 0.000) for 1317 atoms. Found 45 (80 requested) and removed 48 (42 requested) atoms. Cycle 12: After refmac, R = 0.2084 (Rfree = 0.000) for 1310 atoms. Found 34 (78 requested) and removed 8 (42 requested) atoms. Cycle 13: After refmac, R = 0.2008 (Rfree = 0.000) for 1335 atoms. Found 24 (79 requested) and removed 16 (43 requested) atoms. Cycle 14: After refmac, R = 0.1941 (Rfree = 0.000) for 1337 atoms. Found 26 (77 requested) and removed 16 (43 requested) atoms. Cycle 15: After refmac, R = 0.1912 (Rfree = 0.000) for 1347 atoms. Found 20 (77 requested) and removed 12 (43 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.64 1.68 Round 1: 123 peptides, 4 chains. Longest chain 71 peptides. Score 0.923 Round 2: 125 peptides, 3 chains. Longest chain 71 peptides. Score 0.938 Round 3: 125 peptides, 4 chains. Longest chain 40 peptides. Score 0.927 Round 4: 125 peptides, 3 chains. Longest chain 71 peptides. Score 0.938 Round 5: 123 peptides, 5 chains. Longest chain 62 peptides. Score 0.911 Taking the results from Round 4 Chains 3, Residues 122, Estimated correctness of the model 99.8 % 3 chains (122 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 A and 46 A Built loop between residues 65 A and 70 A 1 chains (133 residues) following loop building 1 chains (133 residues) in sequence following loop building ------------------------------------------------------ 19818 reflections ( 99.98 % complete ) and 1308 restraints for refining 1316 atoms. 209 conditional restraints added. Observations/parameters ratio is 3.76 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2154 (Rfree = 0.000) for 1316 atoms. Found 40 (73 requested) and removed 45 (42 requested) atoms. Cycle 17: After refmac, R = 0.2016 (Rfree = 0.000) for 1306 atoms. Found 30 (71 requested) and removed 12 (42 requested) atoms. Cycle 18: After refmac, R = 0.1930 (Rfree = 0.000) for 1324 atoms. Found 29 (71 requested) and removed 13 (42 requested) atoms. Cycle 19: After refmac, R = 0.1900 (Rfree = 0.000) for 1340 atoms. Found 28 (72 requested) and removed 13 (43 requested) atoms. Cycle 20: After refmac, R = 0.1865 (Rfree = 0.000) for 1352 atoms. Found 32 (73 requested) and removed 25 (43 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.64 1.68 Round 1: 123 peptides, 4 chains. Longest chain 71 peptides. Score 0.923 Round 2: 124 peptides, 4 chains. Longest chain 40 peptides. Score 0.925 Round 3: 123 peptides, 4 chains. Longest chain 71 peptides. Score 0.923 Round 4: 124 peptides, 4 chains. Longest chain 40 peptides. Score 0.925 Round 5: 123 peptides, 4 chains. Longest chain 71 peptides. Score 0.923 Taking the results from Round 4 Chains 4, Residues 120, Estimated correctness of the model 99.7 % 4 chains (120 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 A and 46 A Built loop between residues 65 A and 69 A Built loop between residues 107 A and 110 A 1 chains (133 residues) following loop building 1 chains (133 residues) in sequence following loop building ------------------------------------------------------ 19818 reflections ( 99.98 % complete ) and 1288 restraints for refining 1305 atoms. 189 conditional restraints added. Observations/parameters ratio is 3.80 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2187 (Rfree = 0.000) for 1305 atoms. Found 58 (69 requested) and removed 45 (42 requested) atoms. Cycle 22: After refmac, R = 0.2044 (Rfree = 0.000) for 1312 atoms. Found 35 (68 requested) and removed 21 (42 requested) atoms. Cycle 23: After refmac, R = 0.1954 (Rfree = 0.000) for 1325 atoms. Found 40 (66 requested) and removed 13 (42 requested) atoms. Cycle 24: After refmac, R = 0.1918 (Rfree = 0.000) for 1350 atoms. Found 35 (68 requested) and removed 26 (43 requested) atoms. Cycle 25: After refmac, R = 0.1883 (Rfree = 0.000) for 1357 atoms. Found 45 (66 requested) and removed 25 (43 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.64 1.68 Round 1: 123 peptides, 5 chains. Longest chain 39 peptides. Score 0.911 Round 2: 123 peptides, 4 chains. Longest chain 71 peptides. Score 0.923 Round 3: 123 peptides, 4 chains. Longest chain 71 peptides. Score 0.923 Round 4: 123 peptides, 5 chains. Longest chain 40 peptides. Score 0.911 Round 5: 123 peptides, 4 chains. Longest chain 71 peptides. Score 0.923 Taking the results from Round 5 Chains 5, Residues 119, Estimated correctness of the model 99.7 % 4 chains (118 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 25 A and 29 A Built loop between residues 37 A and 46 A Built loop between residues 65 A and 70 A 1 chains (133 residues) following loop building 1 chains (133 residues) in sequence following loop building ------------------------------------------------------ 19818 reflections ( 99.98 % complete ) and 1296 restraints for refining 1309 atoms. 197 conditional restraints added. Observations/parameters ratio is 3.78 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2183 (Rfree = 0.000) for 1309 atoms. Found 53 (62 requested) and removed 43 (42 requested) atoms. Cycle 27: After refmac, R = 0.2020 (Rfree = 0.000) for 1313 atoms. Found 40 (61 requested) and removed 23 (42 requested) atoms. Cycle 28: After refmac, R = 0.1944 (Rfree = 0.000) for 1329 atoms. Found 36 (59 requested) and removed 17 (42 requested) atoms. Cycle 29: After refmac, R = 0.1896 (Rfree = 0.000) for 1347 atoms. Found 33 (61 requested) and removed 13 (43 requested) atoms. Cycle 30: After refmac, R = 0.1879 (Rfree = 0.000) for 1366 atoms. Found 33 (62 requested) and removed 15 (44 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.65 1.69 Round 1: 122 peptides, 4 chains. Longest chain 71 peptides. Score 0.922 Round 2: 124 peptides, 4 chains. Longest chain 41 peptides. Score 0.925 Round 3: 124 peptides, 4 chains. Longest chain 73 peptides. Score 0.925 Round 4: 125 peptides, 3 chains. Longest chain 73 peptides. Score 0.938 Round 5: 122 peptides, 5 chains. Longest chain 40 peptides. Score 0.909 Taking the results from Round 4 Chains 3, Residues 122, Estimated correctness of the model 99.8 % 3 chains (122 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 A and 46 A Built loop between residues 64 A and 68 A 1 chains (133 residues) following loop building 1 chains (133 residues) in sequence following loop building ------------------------------------------------------ 19818 reflections ( 99.98 % complete ) and 1307 restraints for refining 1320 atoms. 208 conditional restraints added. Observations/parameters ratio is 3.75 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2176 (Rfree = 0.000) for 1320 atoms. Found 59 (59 requested) and removed 43 (42 requested) atoms. Cycle 32: After refmac, R = 0.2049 (Rfree = 0.000) for 1330 atoms. Found 34 (58 requested) and removed 24 (43 requested) atoms. Cycle 33: After refmac, R = 0.1959 (Rfree = 0.000) for 1338 atoms. Found 34 (57 requested) and removed 13 (43 requested) atoms. Cycle 34: After refmac, R = 0.1900 (Rfree = 0.000) for 1355 atoms. Found 23 (57 requested) and removed 21 (43 requested) atoms. Cycle 35: After refmac, R = 0.1878 (Rfree = 0.000) for 1349 atoms. Found 43 (56 requested) and removed 16 (43 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.64 1.68 Round 1: 123 peptides, 4 chains. Longest chain 71 peptides. Score 0.923 Round 2: 123 peptides, 5 chains. Longest chain 40 peptides. Score 0.911 Round 3: 123 peptides, 4 chains. Longest chain 71 peptides. Score 0.923 Round 4: 123 peptides, 5 chains. Longest chain 39 peptides. Score 0.911 Round 5: 123 peptides, 4 chains. Longest chain 72 peptides. Score 0.923 Taking the results from Round 5 Chains 4, Residues 119, Estimated correctness of the model 99.7 % 4 chains (119 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 25 A and 29 A Built loop between residues 37 A and 46 A Built loop between residues 65 A and 69 A 1 chains (133 residues) following loop building 1 chains (133 residues) in sequence following loop building ------------------------------------------------------ 19818 reflections ( 99.98 % complete ) and 1312 restraints for refining 1317 atoms. 213 conditional restraints added. Observations/parameters ratio is 3.76 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2131 (Rfree = 0.000) for 1317 atoms. Found 46 (54 requested) and removed 45 (42 requested) atoms. Cycle 37: After refmac, R = 0.1997 (Rfree = 0.000) for 1312 atoms. Found 42 (53 requested) and removed 17 (42 requested) atoms. Cycle 38: After refmac, R = 0.1953 (Rfree = 0.000) for 1334 atoms. Found 32 (53 requested) and removed 19 (43 requested) atoms. Cycle 39: After refmac, R = 0.1897 (Rfree = 0.000) for 1346 atoms. Found 26 (52 requested) and removed 12 (43 requested) atoms. Cycle 40: After refmac, R = 0.1866 (Rfree = 0.000) for 1354 atoms. Found 36 (53 requested) and removed 21 (44 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.64 1.68 Round 1: 120 peptides, 4 chains. Longest chain 71 peptides. Score 0.918 Round 2: 124 peptides, 4 chains. Longest chain 40 peptides. Score 0.925 Round 3: 118 peptides, 5 chains. Longest chain 71 peptides. Score 0.901 Round 4: 124 peptides, 4 chains. Longest chain 39 peptides. Score 0.925 Round 5: 123 peptides, 4 chains. Longest chain 71 peptides. Score 0.923 Taking the results from Round 4 Chains 4, Residues 120, Estimated correctness of the model 99.7 % 4 chains (120 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 A and 46 A Built loop between residues 65 A and 69 A Built loop between residues 106 A and 109 A 1 chains (133 residues) following loop building 1 chains (133 residues) in sequence following loop building ------------------------------------------------------ 19818 reflections ( 99.98 % complete ) and 1326 restraints for refining 1313 atoms. 227 conditional restraints added. Observations/parameters ratio is 3.77 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2176 (Rfree = 0.000) for 1313 atoms. Found 49 (49 requested) and removed 42 (42 requested) atoms. Cycle 42: After refmac, R = 0.2025 (Rfree = 0.000) for 1316 atoms. Found 41 (48 requested) and removed 18 (42 requested) atoms. Cycle 43: After refmac, R = 0.1956 (Rfree = 0.000) for 1336 atoms. Found 37 (48 requested) and removed 21 (43 requested) atoms. Cycle 44: After refmac, R = 0.1906 (Rfree = 0.000) for 1351 atoms. Found 34 (47 requested) and removed 21 (43 requested) atoms. Cycle 45: After refmac, R = 0.1868 (Rfree = 0.000) for 1360 atoms. Found 38 (46 requested) and removed 26 (44 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.64 1.68 Round 1: 122 peptides, 4 chains. Longest chain 71 peptides. Score 0.922 Round 2: 122 peptides, 4 chains. Longest chain 71 peptides. Score 0.922 Round 3: 124 peptides, 5 chains. Longest chain 40 peptides. Score 0.913 Round 4: 121 peptides, 6 chains. Longest chain 62 peptides. Score 0.894 Round 5: 124 peptides, 4 chains. Longest chain 71 peptides. Score 0.925 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 120, Estimated correctness of the model 99.7 % 4 chains (119 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 25 A and 29 A Built loop between residues 38 A and 46 A Built loop between residues 65 A and 70 A 1 chains (133 residues) following loop building 1 chains (133 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 19818 reflections ( 99.98 % complete ) and 1099 restraints for refining 1078 atoms. Observations/parameters ratio is 4.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2792 (Rfree = 0.000) for 1078 atoms. Found 34 (34 requested) and removed 0 (34 requested) atoms. Cycle 47: After refmac, R = 0.2425 (Rfree = 0.000) for 1078 atoms. Found 22 (35 requested) and removed 0 (35 requested) atoms. Cycle 48: After refmac, R = 0.2217 (Rfree = 0.000) for 1078 atoms. Found 12 (36 requested) and removed 0 (36 requested) atoms. Cycle 49: After refmac, R = 0.2102 (Rfree = 0.000) for 1078 atoms. Found 8 (37 requested) and removed 2 (37 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:06:15 GMT 2018 Job finished. TimeTaking 43.27 Used memory is bytes: 12637904