null Sun 23 Dec 22:23:01 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 2ilb-1.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ilb-1.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ilb-1.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ilb-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/2ilb-1.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ilb-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 22:23:11 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/2ilb-1.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ilb-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 117 and 0 Target number of residues in the AU: 117 Target solvent content: 0.4126 Checking the provided sequence file Detected sequence length: 114 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 114 Adjusted target solvent content: 0.43 Input MTZ file: 2ilb-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: 5 Cell parameters: 48.900 72.000 32.740 90.000 110.754 90.000 Input sequence file: 2ilb-1.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 912 target number of atoms Had to go as low as 0.50 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: 38.600 1.600 Wilson plot Bfac: 9.33 13886 reflections ( 98.97 % complete ) and 0 restraints for refining 1005 atoms. Observations/parameters ratio is 3.45 ------------------------------------------------------ Starting model: R = 0.3469 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3021 (Rfree = 0.000) for 1005 atoms. Found 64 (64 requested) and removed 35 (32 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.62 1.78 Round 1: 88 peptides, 9 chains. Longest chain 21 peptides. Score 0.784 Round 2: 96 peptides, 5 chains. Longest chain 60 peptides. Score 0.904 Round 3: 100 peptides, 5 chains. Longest chain 64 peptides. Score 0.914 Round 4: 98 peptides, 4 chains. Longest chain 75 peptides. Score 0.924 Round 5: 101 peptides, 4 chains. Longest chain 65 peptides. Score 0.931 Taking the results from Round 5 Chains 4, Residues 97, Estimated correctness of the model 99.7 % 2 chains (79 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 30 A and 34 A 3 chains (100 residues) following loop building 1 chains (82 residues) in sequence following loop building ------------------------------------------------------ 13886 reflections ( 98.97 % complete ) and 1149 restraints for refining 976 atoms. 444 conditional restraints added. Observations/parameters ratio is 3.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2992 (Rfree = 0.000) for 976 atoms. Found 57 (63 requested) and removed 25 (31 requested) atoms. Cycle 2: After refmac, R = 0.2840 (Rfree = 0.000) for 1008 atoms. Found 36 (65 requested) and removed 7 (32 requested) atoms. Cycle 3: After refmac, R = 0.2670 (Rfree = 0.000) for 1037 atoms. Found 37 (66 requested) and removed 2 (33 requested) atoms. Cycle 4: After refmac, R = 0.2442 (Rfree = 0.000) for 1071 atoms. Found 41 (69 requested) and removed 8 (34 requested) atoms. Cycle 5: After refmac, R = 0.2330 (Rfree = 0.000) for 1102 atoms. Found 34 (71 requested) and removed 7 (35 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.46 1.60 Round 1: 107 peptides, 5 chains. Longest chain 42 peptides. Score 0.929 Round 2: 111 peptides, 2 chains. Longest chain 96 peptides. Score 0.967 Round 3: 111 peptides, 3 chains. Longest chain 54 peptides. Score 0.957 Round 4: 112 peptides, 2 chains. Longest chain 97 peptides. Score 0.968 Round 5: 110 peptides, 4 chains. Longest chain 57 peptides. Score 0.945 Taking the results from Round 4 Chains 2, Residues 110, Estimated correctness of the model 99.9 % 2 chains (110 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 97 A and 100 A 1 chains (112 residues) following loop building 1 chains (112 residues) in sequence following loop building ------------------------------------------------------ 13886 reflections ( 98.97 % complete ) and 1098 restraints for refining 1105 atoms. 225 conditional restraints added. Observations/parameters ratio is 3.14 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2649 (Rfree = 0.000) for 1105 atoms. Found 39 (71 requested) and removed 22 (35 requested) atoms. Cycle 7: After refmac, R = 0.2389 (Rfree = 0.000) for 1121 atoms. Found 48 (71 requested) and removed 7 (36 requested) atoms. Cycle 8: After refmac, R = 0.2278 (Rfree = 0.000) for 1162 atoms. Found 23 (73 requested) and removed 7 (37 requested) atoms. Cycle 9: After refmac, R = 0.2223 (Rfree = 0.000) for 1176 atoms. Found 24 (73 requested) and removed 8 (37 requested) atoms. Cycle 10: After refmac, R = 0.2170 (Rfree = 0.000) for 1189 atoms. Found 33 (74 requested) and removed 10 (38 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.44 1.58 Round 1: 111 peptides, 3 chains. Longest chain 82 peptides. Score 0.957 Round 2: 110 peptides, 3 chains. Longest chain 54 peptides. Score 0.956 Round 3: 112 peptides, 2 chains. Longest chain 97 peptides. Score 0.968 Round 4: 110 peptides, 3 chains. Longest chain 54 peptides. Score 0.956 Round 5: 112 peptides, 2 chains. Longest chain 97 peptides. Score 0.968 Taking the results from Round 5 Chains 2, Residues 110, Estimated correctness of the model 99.9 % 2 chains (110 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 97 A and 100 A 1 chains (112 residues) following loop building 1 chains (112 residues) in sequence following loop building ------------------------------------------------------ 13886 reflections ( 98.97 % complete ) and 1137 restraints for refining 1144 atoms. 264 conditional restraints added. Observations/parameters ratio is 3.03 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2304 (Rfree = 0.000) for 1144 atoms. Found 54 (73 requested) and removed 13 (37 requested) atoms. Cycle 12: After refmac, R = 0.2207 (Rfree = 0.000) for 1184 atoms. Found 29 (74 requested) and removed 5 (38 requested) atoms. Cycle 13: After refmac, R = 0.2150 (Rfree = 0.000) for 1208 atoms. Found 23 (75 requested) and removed 1 (38 requested) atoms. Cycle 14: After refmac, R = 0.2063 (Rfree = 0.000) for 1227 atoms. Found 24 (77 requested) and removed 5 (39 requested) atoms. Cycle 15: After refmac, R = 0.2042 (Rfree = 0.000) for 1244 atoms. Found 24 (78 requested) and removed 12 (40 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.45 1.59 Round 1: 109 peptides, 5 chains. Longest chain 42 peptides. Score 0.933 Round 2: 111 peptides, 3 chains. Longest chain 97 peptides. Score 0.957 Round 3: 111 peptides, 3 chains. Longest chain 97 peptides. Score 0.957 Round 4: 109 peptides, 5 chains. Longest chain 42 peptides. Score 0.933 Round 5: 111 peptides, 3 chains. Longest chain 97 peptides. Score 0.957 Taking the results from Round 5 Chains 3, Residues 108, Estimated correctness of the model 99.9 % 1 chains (96 residues) have been docked in sequence ------------------------------------------------------ 13886 reflections ( 98.97 % complete ) and 1353 restraints for refining 1167 atoms. 556 conditional restraints added. Observations/parameters ratio is 2.97 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2444 (Rfree = 0.000) for 1167 atoms. Found 46 (73 requested) and removed 13 (37 requested) atoms. Cycle 17: After refmac, R = 0.2207 (Rfree = 0.000) for 1200 atoms. Found 32 (75 requested) and removed 3 (38 requested) atoms. Cycle 18: After refmac, R = 0.2085 (Rfree = 0.000) for 1227 atoms. Found 24 (77 requested) and removed 6 (39 requested) atoms. Cycle 19: After refmac, R = 0.2058 (Rfree = 0.000) for 1244 atoms. Found 28 (78 requested) and removed 10 (40 requested) atoms. Cycle 20: After refmac, R = 0.2027 (Rfree = 0.000) for 1260 atoms. Found 35 (79 requested) and removed 6 (40 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.44 1.58 Round 1: 110 peptides, 3 chains. Longest chain 54 peptides. Score 0.956 Round 2: 112 peptides, 2 chains. Longest chain 97 peptides. Score 0.968 Round 3: 110 peptides, 3 chains. Longest chain 54 peptides. Score 0.956 Round 4: 112 peptides, 2 chains. Longest chain 97 peptides. Score 0.968 Round 5: 111 peptides, 2 chains. Longest chain 97 peptides. Score 0.967 Taking the results from Round 4 Chains 2, Residues 110, Estimated correctness of the model 99.9 % 2 chains (110 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 97 A and 100 A 1 chains (112 residues) following loop building 1 chains (112 residues) in sequence following loop building ------------------------------------------------------ 13886 reflections ( 98.97 % complete ) and 1293 restraints for refining 1220 atoms. 420 conditional restraints added. Observations/parameters ratio is 2.85 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2221 (Rfree = 0.000) for 1220 atoms. Found 41 (76 requested) and removed 17 (39 requested) atoms. Cycle 22: After refmac, R = 0.2162 (Rfree = 0.000) for 1240 atoms. Found 26 (78 requested) and removed 6 (40 requested) atoms. Cycle 23: After refmac, R = 0.2120 (Rfree = 0.000) for 1259 atoms. Found 24 (79 requested) and removed 5 (40 requested) atoms. Cycle 24: After refmac, R = 0.2030 (Rfree = 0.000) for 1277 atoms. Found 19 (80 requested) and removed 8 (41 requested) atoms. Cycle 25: After refmac, R = 0.1989 (Rfree = 0.000) for 1287 atoms. Found 32 (81 requested) and removed 5 (41 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.44 1.58 Round 1: 109 peptides, 3 chains. Longest chain 54 peptides. Score 0.955 Round 2: 111 peptides, 2 chains. Longest chain 97 peptides. Score 0.967 Round 3: 109 peptides, 3 chains. Longest chain 54 peptides. Score 0.955 Round 4: 112 peptides, 2 chains. Longest chain 98 peptides. Score 0.968 Round 5: 110 peptides, 3 chains. Longest chain 54 peptides. Score 0.956 Taking the results from Round 4 Chains 2, Residues 110, Estimated correctness of the model 99.9 % 2 chains (110 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 14 A and 17 A 1 chains (112 residues) following loop building 1 chains (112 residues) in sequence following loop building ------------------------------------------------------ 13886 reflections ( 98.97 % complete ) and 1278 restraints for refining 1249 atoms. 405 conditional restraints added. Observations/parameters ratio is 2.78 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2386 (Rfree = 0.000) for 1249 atoms. Found 42 (78 requested) and removed 19 (40 requested) atoms. Cycle 27: After refmac, R = 0.2168 (Rfree = 0.000) for 1270 atoms. Found 30 (80 requested) and removed 5 (41 requested) atoms. Cycle 28: After refmac, R = 0.2101 (Rfree = 0.000) for 1291 atoms. Found 30 (81 requested) and removed 6 (41 requested) atoms. Cycle 29: After refmac, R = 0.2035 (Rfree = 0.000) for 1313 atoms. Found 36 (82 requested) and removed 6 (42 requested) atoms. Cycle 30: After refmac, R = 0.1963 (Rfree = 0.000) for 1340 atoms. Found 22 (84 requested) and removed 5 (43 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.44 1.58 Round 1: 110 peptides, 4 chains. Longest chain 61 peptides. Score 0.945 Round 2: 112 peptides, 2 chains. Longest chain 97 peptides. Score 0.968 Round 3: 110 peptides, 3 chains. Longest chain 54 peptides. Score 0.956 Round 4: 112 peptides, 2 chains. Longest chain 97 peptides. Score 0.968 Round 5: 112 peptides, 2 chains. Longest chain 97 peptides. Score 0.968 Taking the results from Round 5 Chains 2, Residues 110, Estimated correctness of the model 99.9 % 2 chains (110 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 97 A and 100 A 1 chains (112 residues) following loop building 1 chains (112 residues) in sequence following loop building ------------------------------------------------------ 13886 reflections ( 98.97 % complete ) and 1343 restraints for refining 1283 atoms. 470 conditional restraints added. Observations/parameters ratio is 2.71 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2340 (Rfree = 0.000) for 1283 atoms. Found 59 (81 requested) and removed 17 (41 requested) atoms. Cycle 32: After refmac, R = 0.2139 (Rfree = 0.000) for 1323 atoms. Found 26 (83 requested) and removed 4 (42 requested) atoms. Cycle 33: After refmac, R = 0.2026 (Rfree = 0.000) for 1341 atoms. Found 37 (84 requested) and removed 5 (43 requested) atoms. Cycle 34: After refmac, R = 0.1966 (Rfree = 0.000) for 1372 atoms. Found 25 (86 requested) and removed 12 (44 requested) atoms. Cycle 35: After refmac, R = 0.1918 (Rfree = 0.000) for 1384 atoms. Found 27 (87 requested) and removed 6 (44 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.44 1.58 Round 1: 110 peptides, 3 chains. Longest chain 54 peptides. Score 0.956 Round 2: 112 peptides, 2 chains. Longest chain 97 peptides. Score 0.968 Round 3: 112 peptides, 2 chains. Longest chain 97 peptides. Score 0.968 Round 4: 111 peptides, 2 chains. Longest chain 97 peptides. Score 0.967 Round 5: 111 peptides, 2 chains. Longest chain 96 peptides. Score 0.967 Taking the results from Round 3 Chains 2, Residues 110, Estimated correctness of the model 99.9 % 2 chains (110 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 97 A and 100 A 1 chains (112 residues) following loop building 1 chains (112 residues) in sequence following loop building ------------------------------------------------------ 13886 reflections ( 98.97 % complete ) and 1429 restraints for refining 1321 atoms. 556 conditional restraints added. Observations/parameters ratio is 2.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2319 (Rfree = 0.000) for 1321 atoms. Found 53 (83 requested) and removed 16 (42 requested) atoms. Cycle 37: After refmac, R = 0.2117 (Rfree = 0.000) for 1356 atoms. Found 45 (85 requested) and removed 3 (43 requested) atoms. Cycle 38: After refmac, R = 0.2030 (Rfree = 0.000) for 1396 atoms. Found 20 (88 requested) and removed 7 (45 requested) atoms. Cycle 39: After refmac, R = 0.1946 (Rfree = 0.000) for 1408 atoms. Found 25 (88 requested) and removed 5 (45 requested) atoms. Cycle 40: After refmac, R = 0.1937 (Rfree = 0.000) for 1424 atoms. Found 30 (90 requested) and removed 6 (46 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.44 1.58 Round 1: 110 peptides, 3 chains. Longest chain 97 peptides. Score 0.956 Round 2: 112 peptides, 2 chains. Longest chain 97 peptides. Score 0.968 Round 3: 112 peptides, 2 chains. Longest chain 97 peptides. Score 0.968 Round 4: 112 peptides, 2 chains. Longest chain 97 peptides. Score 0.968 Round 5: 112 peptides, 2 chains. Longest chain 97 peptides. Score 0.968 Taking the results from Round 5 Chains 2, Residues 110, Estimated correctness of the model 99.9 % 1 chains (96 residues) have been docked in sequence ------------------------------------------------------ 13886 reflections ( 98.97 % complete ) and 1645 restraints for refining 1359 atoms. 839 conditional restraints added. Observations/parameters ratio is 2.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2310 (Rfree = 0.000) for 1359 atoms. Found 67 (85 requested) and removed 13 (43 requested) atoms. Cycle 42: After refmac, R = 0.2173 (Rfree = 0.000) for 1410 atoms. Found 33 (89 requested) and removed 9 (45 requested) atoms. Cycle 43: After refmac, R = 0.2035 (Rfree = 0.000) for 1431 atoms. Found 31 (90 requested) and removed 6 (46 requested) atoms. Cycle 44: After refmac, R = 0.1967 (Rfree = 0.000) for 1453 atoms. Found 37 (91 requested) and removed 16 (46 requested) atoms. Cycle 45: After refmac, R = 0.1918 (Rfree = 0.000) for 1473 atoms. Found 32 (92 requested) and removed 15 (47 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.44 1.58 Round 1: 111 peptides, 3 chains. Longest chain 89 peptides. Score 0.957 Round 2: 112 peptides, 2 chains. Longest chain 97 peptides. Score 0.968 Round 3: 110 peptides, 3 chains. Longest chain 89 peptides. Score 0.956 Round 4: 112 peptides, 2 chains. Longest chain 97 peptides. Score 0.968 Round 5: 112 peptides, 2 chains. Longest chain 97 peptides. Score 0.968 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 110, Estimated correctness of the model 99.9 % 2 chains (110 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 97 A and 100 A 1 chains (112 residues) following loop building 1 chains (112 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 13886 reflections ( 98.97 % complete ) and 873 restraints for refining 855 atoms. Observations/parameters ratio is 4.06 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3253 (Rfree = 0.000) for 855 atoms. Found 12 (54 requested) and removed 0 (54 requested) atoms. Cycle 47: After refmac, R = 0.2940 (Rfree = 0.000) for 855 atoms. Found 8 (55 requested) and removed 0 (28 requested) atoms. Cycle 48: After refmac, R = 0.2811 (Rfree = 0.000) for 855 atoms. Found 4 (55 requested) and removed 1 (28 requested) atoms. Cycle 49: After refmac, R = 0.2784 (Rfree = 0.000) for 855 atoms. Found 1 (55 requested) and removed 0 (28 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:51:45 GMT 2018 Job finished. TimeTaking 28.74 Used memory is bytes: 11006904