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 2aam-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2aam-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2aam-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aam-3.6-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/2aam-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aam-3.6-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 ============================================================ 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/2aam-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aam-3.6-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 3850 and 0 Target number of residues in the AU: 3850 Target solvent content: 0.6263 Target number of residues exceeds 1700, conditional restraints are disabled Checking the provided sequence file Detected sequence length: 309 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1854 Adjusted target solvent content: 0.82 Input MTZ file: 2aam-3.6-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: 4 Cell parameters: 195.000 84.610 194.910 90.000 119.891 90.000 Input sequence file: 2aam-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 14832 target number of atoms Had to go as low as 1.50 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 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. 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: 169.060 3.600 Wilson plot Bfac: 64.60 63881 reflections ( 98.93 % complete ) and 0 restraints for refining 16479 atoms. Observations/parameters ratio is 0.97 ------------------------------------------------------ Starting model: R = 0.3435 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2911 (Rfree = 0.000) for 16479 atoms. Found 105 (105 requested) and removed 81 (52 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.38 2.04 Search for helices and strands: 0 residues in 0 chains, 16858 seeds are put forward NCS extension: 0 residues added, 16858 seeds are put forward Round 1: 1238 peptides, 146 chains. Longest chain 32 peptides. Score 0.419 Round 2: 1262 peptides, 145 chains. Longest chain 30 peptides. Score 0.428 Round 3: 1256 peptides, 143 chains. Longest chain 25 peptides. Score 0.429 Round 4: 1262 peptides, 135 chains. Longest chain 27 peptides. Score 0.443 Round 5: 1269 peptides, 140 chains. Longest chain 34 peptides. Score 0.438 Taking the results from Round 4 Chains 137, Residues 1127, Estimated correctness of the model 0.0 % 5 chains (88 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 63881 reflections ( 98.93 % complete ) and 4777 restraints for refining 15230 atoms. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2449 (Rfree = 0.000) for 15230 atoms. Found 97 (97 requested) and removed 56 (48 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2358 (Rfree = 0.000) for 15271 atoms. Found 97 (97 requested) and removed 63 (48 requested) atoms. Cycle 3: After refmac, R = 0.2241 (Rfree = 0.000) for 15305 atoms. Found 98 (98 requested) and removed 59 (49 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2170 (Rfree = 0.000) for 15344 atoms. Found 98 (98 requested) and removed 64 (49 requested) atoms. Cycle 5: After refmac, R = 0.2108 (Rfree = 0.000) for 15378 atoms. Found 98 (98 requested) and removed 67 (49 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 2.01 Search for helices and strands: 0 residues in 0 chains, 15943 seeds are put forward NCS extension: 21 residues added (5 deleted due to clashes), 15964 seeds are put forward Round 1: 1306 peptides, 135 chains. Longest chain 51 peptides. Score 0.456 Round 2: 1342 peptides, 126 chains. Longest chain 42 peptides. Score 0.479 Round 3: 1301 peptides, 155 chains. Longest chain 32 peptides. Score 0.425 Round 4: 1277 peptides, 133 chains. Longest chain 34 peptides. Score 0.450 Round 5: 1357 peptides, 135 chains. Longest chain 47 peptides. Score 0.470 Taking the results from Round 2 Chains 135, Residues 1216, Estimated correctness of the model 0.0 % 9 chains (148 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 63881 reflections ( 98.93 % complete ) and 5400 restraints for refining 14992 atoms. Observations/parameters ratio is 1.07 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2265 (Rfree = 0.000) for 14992 atoms. Found 96 (96 requested) and removed 57 (48 requested) atoms. Cycle 7: After refmac, R = 0.2145 (Rfree = 0.000) for 15031 atoms. Found 96 (96 requested) and removed 56 (48 requested) atoms. Cycle 8: After refmac, R = 0.2119 (Rfree = 0.000) for 15071 atoms. Found 96 (96 requested) and removed 58 (48 requested) atoms. Cycle 9: After refmac, R = 0.2053 (Rfree = 0.000) for 15109 atoms. Found 96 (96 requested) and removed 64 (48 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2015 (Rfree = 0.000) for 15141 atoms. Found 73 (97 requested) and removed 57 (48 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.34 2.02 Search for helices and strands: 0 residues in 0 chains, 15685 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 15710 seeds are put forward Round 1: 1334 peptides, 148 chains. Longest chain 33 peptides. Score 0.445 Round 2: 1376 peptides, 136 chains. Longest chain 45 peptides. Score 0.474 Round 3: 1346 peptides, 138 chains. Longest chain 34 peptides. Score 0.463 Round 4: 1302 peptides, 150 chains. Longest chain 37 peptides. Score 0.433 Round 5: 1288 peptides, 151 chains. Longest chain 29 peptides. Score 0.427 Taking the results from Round 2 Chains 140, Residues 1240, Estimated correctness of the model 0.0 % 6 chains (118 residues) have been docked in sequence ------------------------------------------------------ 63881 reflections ( 98.93 % complete ) and 5342 restraints for refining 15255 atoms. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2205 (Rfree = 0.000) for 15255 atoms. Found 97 (97 requested) and removed 60 (48 requested) atoms. Cycle 12: After refmac, R = 0.2083 (Rfree = 0.000) for 15292 atoms. Found 98 (98 requested) and removed 61 (49 requested) atoms. Cycle 13: After refmac, R = 0.2019 (Rfree = 0.000) for 15329 atoms. Found 68 (98 requested) and removed 55 (49 requested) atoms. Cycle 14: After refmac, R = 0.1983 (Rfree = 0.000) for 15342 atoms. Found 85 (98 requested) and removed 55 (49 requested) atoms. Cycle 15: After refmac, R = 0.1963 (Rfree = 0.000) for 15372 atoms. Found 85 (98 requested) and removed 61 (49 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.37 2.03 Search for helices and strands: 0 residues in 0 chains, 15929 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 15949 seeds are put forward Round 1: 1284 peptides, 134 chains. Longest chain 37 peptides. Score 0.451 Round 2: 1300 peptides, 131 chains. Longest chain 38 peptides. Score 0.460 Round 3: 1347 peptides, 140 chains. Longest chain 38 peptides. Score 0.460 Round 4: 1311 peptides, 143 chains. Longest chain 29 peptides. Score 0.446 Round 5: 1307 peptides, 156 chains. Longest chain 40 peptides. Score 0.425 Taking the results from Round 3 Chains 156, Residues 1207, Estimated correctness of the model 0.0 % 14 chains (193 residues) have been docked in sequence ------------------------------------------------------ 63881 reflections ( 98.93 % complete ) and 5550 restraints for refining 15734 atoms. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2226 (Rfree = 0.000) for 15734 atoms. Found 100 (100 requested) and removed 63 (50 requested) atoms. Cycle 17: After refmac, R = 0.2155 (Rfree = 0.000) for 15771 atoms. Found 101 (101 requested) and removed 69 (50 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2057 (Rfree = 0.000) for 15803 atoms. Found 101 (101 requested) and removed 68 (50 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2022 (Rfree = 0.000) for 15836 atoms. Found 100 (101 requested) and removed 71 (50 requested) atoms. Cycle 20: After refmac, R = 0.1977 (Rfree = 0.000) for 15865 atoms. Found 98 (101 requested) and removed 67 (50 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.35 2.02 Search for helices and strands: 0 residues in 0 chains, 16446 seeds are put forward NCS extension: 25 residues added (5 deleted due to clashes), 16471 seeds are put forward Round 1: 1308 peptides, 144 chains. Longest chain 32 peptides. Score 0.443 Round 2: 1362 peptides, 139 chains. Longest chain 48 peptides. Score 0.466 Round 3: 1356 peptides, 129 chains. Longest chain 45 peptides. Score 0.479 Round 4: 1304 peptides, 136 chains. Longest chain 40 peptides. Score 0.454 Round 5: 1272 peptides, 134 chains. Longest chain 35 peptides. Score 0.447 Taking the results from Round 3 Chains 141, Residues 1227, Estimated correctness of the model 0.0 % 8 chains (145 residues) have been docked in sequence ------------------------------------------------------ 63881 reflections ( 98.93 % complete ) and 5528 restraints for refining 16058 atoms. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2190 (Rfree = 0.000) for 16058 atoms. Found 103 (103 requested) and removed 63 (51 requested) atoms. Cycle 22: After refmac, R = 0.2097 (Rfree = 0.000) for 16098 atoms. Found 103 (103 requested) and removed 64 (51 requested) atoms. Cycle 23: After refmac, R = 0.2036 (Rfree = 0.000) for 16137 atoms. Found 103 (103 requested) and removed 65 (51 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2005 (Rfree = 0.000) for 16175 atoms. Found 103 (103 requested) and removed 63 (51 requested) atoms. Cycle 25: After refmac, R = 0.1964 (Rfree = 0.000) for 16215 atoms. Found 104 (104 requested) and removed 72 (52 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 2.01 Search for helices and strands: 0 residues in 0 chains, 16753 seeds are put forward NCS extension: 27 residues added (4 deleted due to clashes), 16780 seeds are put forward Round 1: 1297 peptides, 154 chains. Longest chain 27 peptides. Score 0.425 Round 2: 1345 peptides, 145 chains. Longest chain 43 peptides. Score 0.453 Round 3: 1315 peptides, 151 chains. Longest chain 37 peptides. Score 0.435 Round 4: 1341 peptides, 142 chains. Longest chain 39 peptides. Score 0.456 Round 5: 1308 peptides, 134 chains. Longest chain 39 peptides. Score 0.458 Taking the results from Round 5 Chains 141, Residues 1174, Estimated correctness of the model 0.0 % 8 chains (127 residues) have been docked in sequence ------------------------------------------------------ 63881 reflections ( 98.93 % complete ) and 5142 restraints for refining 16188 atoms. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2202 (Rfree = 0.000) for 16188 atoms. Found 103 (103 requested) and removed 59 (51 requested) atoms. Cycle 27: After refmac, R = 0.2154 (Rfree = 0.000) for 16232 atoms. Found 104 (104 requested) and removed 64 (52 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2079 (Rfree = 0.000) for 16272 atoms. Found 104 (104 requested) and removed 55 (52 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 29: After refmac, R = 0.2031 (Rfree = 0.000) for 16321 atoms. Found 104 (104 requested) and removed 74 (52 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1983 (Rfree = 0.000) for 16351 atoms. Found 104 (104 requested) and removed 77 (52 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 2.02 Search for helices and strands: 0 residues in 0 chains, 16882 seeds are put forward NCS extension: 30 residues added (10 deleted due to clashes), 16912 seeds are put forward Round 1: 1256 peptides, 159 chains. Longest chain 29 peptides. Score 0.405 Round 2: 1278 peptides, 145 chains. Longest chain 29 peptides. Score 0.433 Round 3: 1288 peptides, 139 chains. Longest chain 35 peptides. Score 0.445 Round 4: 1279 peptides, 136 chains. Longest chain 30 peptides. Score 0.447 Round 5: 1284 peptides, 139 chains. Longest chain 38 peptides. Score 0.444 Taking the results from Round 4 Chains 142, Residues 1143, Estimated correctness of the model 0.0 % 8 chains (132 residues) have been docked in sequence ------------------------------------------------------ 63881 reflections ( 98.93 % complete ) and 5051 restraints for refining 16131 atoms. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2185 (Rfree = 0.000) for 16131 atoms. Found 103 (103 requested) and removed 67 (51 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2097 (Rfree = 0.000) for 16167 atoms. Found 103 (103 requested) and removed 69 (51 requested) atoms. Cycle 33: After refmac, R = 0.1884 (Rfree = 0.000) for 16201 atoms. Found 50 (103 requested) and removed 62 (51 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1887 (Rfree = 0.000) for 16189 atoms. Found 63 (103 requested) and removed 62 (51 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 35: After refmac, R = 0.1813 (Rfree = 0.000) for 16190 atoms. Found 20 (103 requested) and removed 56 (51 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.35 2.02 Search for helices and strands: 0 residues in 0 chains, 16663 seeds are put forward NCS extension: 29 residues added (3 deleted due to clashes), 16692 seeds are put forward Round 1: 1235 peptides, 159 chains. Longest chain 22 peptides. Score 0.399 Round 2: 1309 peptides, 140 chains. Longest chain 29 peptides. Score 0.449 Round 3: 1297 peptides, 144 chains. Longest chain 38 peptides. Score 0.440 Round 4: 1289 peptides, 140 chains. Longest chain 29 peptides. Score 0.444 Round 5: 1260 peptides, 149 chains. Longest chain 31 peptides. Score 0.422 Taking the results from Round 2 Chains 148, Residues 1169, Estimated correctness of the model 0.0 % 7 chains (88 residues) have been docked in sequence ------------------------------------------------------ 63881 reflections ( 98.93 % complete ) and 4957 restraints for refining 15742 atoms. Observations/parameters ratio is 1.01 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2112 (Rfree = 0.000) for 15742 atoms. Found 100 (100 requested) and removed 61 (50 requested) atoms. Cycle 37: After refmac, R = 0.2077 (Rfree = 0.000) for 15781 atoms. Found 101 (101 requested) and removed 56 (50 requested) atoms. Cycle 38: After refmac, R = 0.2037 (Rfree = 0.000) for 15826 atoms. Found 101 (101 requested) and removed 57 (50 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1998 (Rfree = 0.000) for 15870 atoms. Found 101 (101 requested) and removed 72 (50 requested) atoms. Cycle 40: After refmac, R = 0.1997 (Rfree = 0.000) for 15899 atoms. Found 102 (102 requested) and removed 70 (51 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.34 2.02 Search for helices and strands: 0 residues in 0 chains, 16447 seeds are put forward NCS extension: 8 residues added (13 deleted due to clashes), 16455 seeds are put forward Round 1: 1244 peptides, 161 chains. Longest chain 22 peptides. Score 0.399 Round 2: 1297 peptides, 141 chains. Longest chain 31 peptides. Score 0.444 Round 3: 1295 peptides, 137 chains. Longest chain 30 peptides. Score 0.450 Round 4: 1288 peptides, 135 chains. Longest chain 41 peptides. Score 0.451 Round 5: 1298 peptides, 136 chains. Longest chain 34 peptides. Score 0.452 Taking the results from Round 5 Chains 142, Residues 1162, Estimated correctness of the model 0.0 % 4 chains (77 residues) have been docked in sequence ------------------------------------------------------ 63881 reflections ( 98.93 % complete ) and 4853 restraints for refining 15780 atoms. Observations/parameters ratio is 1.01 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2142 (Rfree = 0.000) for 15780 atoms. Found 101 (101 requested) and removed 58 (50 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2075 (Rfree = 0.000) for 15823 atoms. Found 101 (101 requested) and removed 59 (50 requested) atoms. Cycle 43: After refmac, R = 0.2022 (Rfree = 0.000) for 15865 atoms. Found 101 (101 requested) and removed 59 (50 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1967 (Rfree = 0.000) for 15907 atoms. Found 102 (102 requested) and removed 67 (51 requested) atoms. Cycle 45: After refmac, R = 0.1801 (Rfree = 0.000) for 15942 atoms. Found 20 (102 requested) and removed 60 (51 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.34 2.02 Search for helices and strands: 0 residues in 0 chains, 16429 seeds are put forward NCS extension: 29 residues added (8 deleted due to clashes), 16458 seeds are put forward Round 1: 1236 peptides, 174 chains. Longest chain 27 peptides. Score 0.376 Round 2: 1280 peptides, 144 chains. Longest chain 31 peptides. Score 0.435 Round 3: 1292 peptides, 137 chains. Longest chain 38 peptides. Score 0.449 Round 4: 1265 peptides, 144 chains. Longest chain 33 peptides. Score 0.431 Round 5: 1252 peptides, 141 chains. Longest chain 29 peptides. Score 0.431 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 141, Residues 1155, Estimated correctness of the model 0.0 % 3 chains (42 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2aam-3_warpNtrace.pdb as input Building loops using Loopy2018 141 chains (1155 residues) following loop building 3 chains (42 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 63881 reflections ( 98.93 % complete ) and 4683 restraints for refining 15681 atoms. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2131 (Rfree = 0.000) for 15681 atoms. Found 0 (100 requested) and removed 50 (50 requested) atoms. Cycle 47: After refmac, R = 0.2088 (Rfree = 0.000) for 15631 atoms. Found 0 (100 requested) and removed 50 (50 requested) atoms. Cycle 48: After refmac, R = 0.2050 (Rfree = 0.000) for 15581 atoms. Found 0 (99 requested) and removed 49 (49 requested) atoms. Cycle 49: After refmac, R = 0.2051 (Rfree = 0.000) for 15532 atoms. Found 0 (99 requested) and removed 49 (49 requested) atoms. Writing output files ... TimeTaking 259.8