Mon 24 Dec 00:45:34 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2aam-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2aam-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2aam-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aam-3.8-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2aam-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aam-3.8-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:45:38 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/mrncs/ArpWArp/wArpResults/WorkingDir/2aam-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aam-3.8-parrot-mrncs/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 3732 and 0 Target number of residues in the AU: 3732 Target solvent content: 0.6378 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-3.8-parrot-mrncs.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-3.8-parrot-mrncs.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 3.800 Wilson plot Bfac: 70.79 54333 reflections ( 98.81 % complete ) and 0 restraints for refining 18548 atoms. Observations/parameters ratio is 0.73 ------------------------------------------------------ Starting model: R = 0.3311 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2975 (Rfree = 0.000) for 18548 atoms. Found 102 (102 requested) and removed 96 (51 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 2.12 Search for helices and strands: 0 residues in 0 chains, 18914 seeds are put forward NCS extension: 0 residues added, 18914 seeds are put forward Round 1: 1198 peptides, 132 chains. Longest chain 33 peptides. Score 0.428 Round 2: 1223 peptides, 128 chains. Longest chain 23 peptides. Score 0.442 Round 3: 1222 peptides, 124 chains. Longest chain 27 peptides. Score 0.448 Round 4: 1233 peptides, 130 chains. Longest chain 33 peptides. Score 0.442 Round 5: 1211 peptides, 133 chains. Longest chain 36 peptides. Score 0.431 Taking the results from Round 3 Chains 135, Residues 1098, Estimated correctness of the model 0.0 % 8 chains (112 residues) have been docked in sequence ------------------------------------------------------ 54333 reflections ( 98.81 % complete ) and 4785 restraints for refining 16080 atoms. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2377 (Rfree = 0.000) for 16080 atoms. Found 88 (88 requested) and removed 62 (44 requested) atoms. Cycle 2: After refmac, R = 0.2227 (Rfree = 0.000) for 16106 atoms. Found 88 (88 requested) and removed 73 (44 requested) atoms. Cycle 3: After refmac, R = 0.2203 (Rfree = 0.000) for 16121 atoms. Found 88 (88 requested) and removed 66 (44 requested) atoms. Cycle 4: After refmac, R = 0.2174 (Rfree = 0.000) for 16143 atoms. Found 88 (88 requested) and removed 85 (44 requested) atoms. Cycle 5: After refmac, R = 0.1876 (Rfree = 0.000) for 16146 atoms. Found 31 (88 requested) and removed 79 (44 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 2.09 Search for helices and strands: 0 residues in 0 chains, 16568 seeds are put forward NCS extension: 15 residues added (7 deleted due to clashes), 16583 seeds are put forward Round 1: 1264 peptides, 136 chains. Longest chain 26 peptides. Score 0.442 Round 2: 1291 peptides, 127 chains. Longest chain 39 peptides. Score 0.463 Round 3: 1280 peptides, 126 chains. Longest chain 39 peptides. Score 0.461 Round 4: 1228 peptides, 132 chains. Longest chain 35 peptides. Score 0.437 Round 5: 1225 peptides, 134 chains. Longest chain 33 peptides. Score 0.433 Taking the results from Round 2 Chains 133, Residues 1164, Estimated correctness of the model 0.0 % 5 chains (81 residues) have been docked in sequence ------------------------------------------------------ 54333 reflections ( 98.81 % complete ) and 4893 restraints for refining 15103 atoms. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2231 (Rfree = 0.000) for 15103 atoms. Found 83 (83 requested) and removed 48 (41 requested) atoms. Cycle 7: After refmac, R = 0.2178 (Rfree = 0.000) for 15138 atoms. Found 83 (83 requested) and removed 55 (41 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2144 (Rfree = 0.000) for 15166 atoms. Found 83 (83 requested) and removed 52 (41 requested) atoms. Cycle 9: After refmac, R = 0.2117 (Rfree = 0.000) for 15197 atoms. Found 83 (83 requested) and removed 59 (41 requested) atoms. Cycle 10: After refmac, R = 0.1897 (Rfree = 0.000) for 15221 atoms. Found 33 (83 requested) and removed 61 (41 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.40 2.05 Search for helices and strands: 0 residues in 0 chains, 15690 seeds are put forward NCS extension: 44 residues added (3 deleted due to clashes), 15734 seeds are put forward Round 1: 1233 peptides, 135 chains. Longest chain 31 peptides. Score 0.434 Round 2: 1289 peptides, 126 chains. Longest chain 39 peptides. Score 0.464 Round 3: 1323 peptides, 135 chains. Longest chain 46 peptides. Score 0.461 Round 4: 1287 peptides, 129 chains. Longest chain 33 peptides. Score 0.459 Round 5: 1298 peptides, 134 chains. Longest chain 41 peptides. Score 0.455 Taking the results from Round 2 Chains 136, Residues 1163, Estimated correctness of the model 0.0 % 11 chains (170 residues) have been docked in sequence ------------------------------------------------------ 54333 reflections ( 98.81 % complete ) and 5331 restraints for refining 15126 atoms. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2286 (Rfree = 0.000) for 15126 atoms. Found 83 (83 requested) and removed 61 (41 requested) atoms. Cycle 12: After refmac, R = 0.2230 (Rfree = 0.000) for 15148 atoms. Found 83 (83 requested) and removed 56 (41 requested) atoms. Cycle 13: After refmac, R = 0.2197 (Rfree = 0.000) for 15175 atoms. Found 83 (83 requested) and removed 62 (41 requested) atoms. Cycle 14: After refmac, R = 0.2190 (Rfree = 0.000) for 15196 atoms. Found 83 (83 requested) and removed 59 (41 requested) atoms. Cycle 15: After refmac, R = 0.2208 (Rfree = 0.000) for 15220 atoms. Found 83 (83 requested) and removed 79 (41 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.29 1.99 Search for helices and strands: 0 residues in 0 chains, 15786 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 15817 seeds are put forward Round 1: 1255 peptides, 155 chains. Longest chain 32 peptides. Score 0.411 Round 2: 1267 peptides, 143 chains. Longest chain 32 peptides. Score 0.433 Round 3: 1280 peptides, 140 chains. Longest chain 36 peptides. Score 0.441 Round 4: 1296 peptides, 131 chains. Longest chain 44 peptides. Score 0.459 Round 5: 1302 peptides, 149 chains. Longest chain 37 peptides. Score 0.434 Taking the results from Round 4 Chains 138, Residues 1165, Estimated correctness of the model 0.0 % 7 chains (96 residues) have been docked in sequence ------------------------------------------------------ 54333 reflections ( 98.81 % complete ) and 4967 restraints for refining 15450 atoms. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2427 (Rfree = 0.000) for 15450 atoms. Found 84 (84 requested) and removed 69 (42 requested) atoms. Cycle 17: After refmac, R = 0.2428 (Rfree = 0.000) for 15465 atoms. Found 85 (85 requested) and removed 70 (42 requested) atoms. Cycle 18: After refmac, R = 0.2462 (Rfree = 0.000) for 15480 atoms. Found 85 (85 requested) and removed 67 (42 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2475 (Rfree = 0.000) for 15498 atoms. Found 85 (85 requested) and removed 62 (42 requested) atoms. Cycle 20: After refmac, R = 0.2107 (Rfree = 0.000) for 15521 atoms. Found 50 (85 requested) and removed 64 (42 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.25 1.96 Search for helices and strands: 0 residues in 0 chains, 15994 seeds are put forward NCS extension: 46 residues added (6 deleted due to clashes), 16040 seeds are put forward Round 1: 1239 peptides, 175 chains. Longest chain 32 peptides. Score 0.376 Round 2: 1327 peptides, 165 chains. Longest chain 29 peptides. Score 0.418 Round 3: 1323 peptides, 159 chains. Longest chain 26 peptides. Score 0.426 Round 4: 1335 peptides, 164 chains. Longest chain 30 peptides. Score 0.422 Round 5: 1344 peptides, 161 chains. Longest chain 28 peptides. Score 0.429 Taking the results from Round 5 Chains 164, Residues 1183, Estimated correctness of the model 0.0 % 6 chains (67 residues) have been docked in sequence ------------------------------------------------------ 54333 reflections ( 98.81 % complete ) and 4834 restraints for refining 15347 atoms. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2595 (Rfree = 0.000) for 15347 atoms. Found 84 (84 requested) and removed 59 (42 requested) atoms. Cycle 22: After refmac, R = 0.2575 (Rfree = 0.000) for 15372 atoms. Found 84 (84 requested) and removed 71 (42 requested) atoms. Cycle 23: After refmac, R = 0.2551 (Rfree = 0.000) for 15385 atoms. Found 84 (84 requested) and removed 64 (42 requested) atoms. Cycle 24: After refmac, R = 0.2519 (Rfree = 0.000) for 15405 atoms. Found 84 (84 requested) and removed 60 (42 requested) atoms. Cycle 25: After refmac, R = 0.2532 (Rfree = 0.000) for 15429 atoms. Found 84 (84 requested) and removed 65 (42 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 1.99 Search for helices and strands: 0 residues in 0 chains, 16020 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 16042 seeds are put forward Round 1: 1249 peptides, 178 chains. Longest chain 24 peptides. Score 0.374 Round 2: 1286 peptides, 162 chains. Longest chain 25 peptides. Score 0.410 Round 3: 1281 peptides, 157 chains. Longest chain 35 peptides. Score 0.416 Round 4: 1275 peptides, 149 chains. Longest chain 34 peptides. Score 0.426 Round 5: 1270 peptides, 148 chains. Longest chain 29 peptides. Score 0.426 Taking the results from Round 5 Chains 153, Residues 1122, Estimated correctness of the model 0.0 % 6 chains (55 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 54333 reflections ( 98.81 % complete ) and 4603 restraints for refining 15523 atoms. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2514 (Rfree = 0.000) for 15523 atoms. Found 85 (85 requested) and removed 49 (42 requested) atoms. Cycle 27: After refmac, R = 0.2566 (Rfree = 0.000) for 15559 atoms. Found 85 (85 requested) and removed 62 (42 requested) atoms. Cycle 28: After refmac, R = 0.2559 (Rfree = 0.000) for 15582 atoms. Found 85 (85 requested) and removed 58 (42 requested) atoms. Cycle 29: After refmac, R = 0.2572 (Rfree = 0.000) for 15609 atoms. Found 85 (85 requested) and removed 74 (42 requested) atoms. Cycle 30: After refmac, R = 0.2215 (Rfree = 0.000) for 15620 atoms. Found 70 (85 requested) and removed 63 (42 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.26 1.97 Search for helices and strands: 0 residues in 0 chains, 16225 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 16253 seeds are put forward Round 1: 1170 peptides, 180 chains. Longest chain 25 peptides. Score 0.345 Round 2: 1281 peptides, 162 chains. Longest chain 30 peptides. Score 0.409 Round 3: 1295 peptides, 168 chains. Longest chain 32 peptides. Score 0.404 Round 4: 1290 peptides, 154 chains. Longest chain 33 peptides. Score 0.423 Round 5: 1296 peptides, 159 chains. Longest chain 29 peptides. Score 0.418 Taking the results from Round 4 Chains 159, Residues 1136, Estimated correctness of the model 0.0 % 8 chains (99 residues) have been docked in sequence ------------------------------------------------------ 54333 reflections ( 98.81 % complete ) and 4826 restraints for refining 15433 atoms. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2583 (Rfree = 0.000) for 15433 atoms. Found 84 (84 requested) and removed 52 (42 requested) atoms. Cycle 32: After refmac, R = 0.2600 (Rfree = 0.000) for 15465 atoms. Found 85 (85 requested) and removed 51 (42 requested) atoms. Cycle 33: After refmac, R = 0.2536 (Rfree = 0.000) for 15499 atoms. Found 85 (85 requested) and removed 53 (42 requested) atoms. Cycle 34: After refmac, R = 0.2530 (Rfree = 0.000) for 15531 atoms. Found 85 (85 requested) and removed 63 (42 requested) atoms. Cycle 35: After refmac, R = 0.2496 (Rfree = 0.000) for 15553 atoms. Found 85 (85 requested) and removed 65 (42 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.26 1.97 Search for helices and strands: 0 residues in 0 chains, 16126 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 16144 seeds are put forward Round 1: 1161 peptides, 181 chains. Longest chain 27 peptides. Score 0.341 Round 2: 1273 peptides, 162 chains. Longest chain 27 peptides. Score 0.406 Round 3: 1252 peptides, 157 chains. Longest chain 37 peptides. Score 0.407 Round 4: 1278 peptides, 154 chains. Longest chain 34 peptides. Score 0.420 Round 5: 1268 peptides, 157 chains. Longest chain 30 peptides. Score 0.412 Taking the results from Round 4 Chains 157, Residues 1124, Estimated correctness of the model 0.0 % 5 chains (52 residues) have been docked in sequence ------------------------------------------------------ 54333 reflections ( 98.81 % complete ) and 4572 restraints for refining 15444 atoms. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2609 (Rfree = 0.000) for 15444 atoms. Found 84 (84 requested) and removed 54 (42 requested) atoms. Cycle 37: After refmac, R = 0.2546 (Rfree = 0.000) for 15474 atoms. Found 85 (85 requested) and removed 50 (42 requested) atoms. Cycle 38: After refmac, R = 0.2565 (Rfree = 0.000) for 15509 atoms. Found 85 (85 requested) and removed 52 (42 requested) atoms. Cycle 39: After refmac, R = 0.2529 (Rfree = 0.000) for 15542 atoms. Found 85 (85 requested) and removed 56 (42 requested) atoms. Cycle 40: After refmac, R = 0.2117 (Rfree = 0.000) for 15571 atoms. Found 48 (85 requested) and removed 46 (42 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.26 1.97 Search for helices and strands: 0 residues in 0 chains, 16146 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 16177 seeds are put forward Round 1: 1155 peptides, 196 chains. Longest chain 16 peptides. Score 0.315 Round 2: 1288 peptides, 186 chains. Longest chain 24 peptides. Score 0.375 Round 3: 1240 peptides, 171 chains. Longest chain 29 peptides. Score 0.382 Round 4: 1255 peptides, 169 chains. Longest chain 28 peptides. Score 0.390 Round 5: 1232 peptides, 166 chains. Longest chain 18 peptides. Score 0.387 Taking the results from Round 4 Chains 170, Residues 1086, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 54333 reflections ( 98.81 % complete ) and 4236 restraints for refining 15485 atoms. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2545 (Rfree = 0.000) for 15485 atoms. Found 85 (85 requested) and removed 47 (42 requested) atoms. Cycle 42: After refmac, R = 0.2596 (Rfree = 0.000) for 15523 atoms. Found 85 (85 requested) and removed 49 (42 requested) atoms. Cycle 43: After refmac, R = 0.2561 (Rfree = 0.000) for 15559 atoms. Found 85 (85 requested) and removed 57 (42 requested) atoms. Cycle 44: After refmac, R = 0.2550 (Rfree = 0.000) for 15587 atoms. Found 85 (85 requested) and removed 57 (42 requested) atoms. Cycle 45: After refmac, R = 0.2156 (Rfree = 0.000) for 15615 atoms. Found 41 (85 requested) and removed 52 (42 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.23 1.95 Search for helices and strands: 0 residues in 0 chains, 16171 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 16187 seeds are put forward Round 1: 1084 peptides, 189 chains. Longest chain 18 peptides. Score 0.301 Round 2: 1243 peptides, 173 chains. Longest chain 24 peptides. Score 0.380 Round 3: 1283 peptides, 182 chains. Longest chain 23 peptides. Score 0.379 Round 4: 1291 peptides, 186 chains. Longest chain 24 peptides. Score 0.376 Round 5: 1271 peptides, 169 chains. Longest chain 22 peptides. Score 0.395 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 175, Residues 1102, Estimated correctness of the model 0.0 % 6 chains (69 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2aam-3_warpNtrace.pdb as input Building loops using Loopy2018 175 chains (1102 residues) following loop building 6 chains (69 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. Failed to save intermediate PDB 54333 reflections ( 98.81 % complete ) and 4540 restraints for refining 15447 atoms. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2617 (Rfree = 0.000) for 15447 atoms. Found 0 (84 requested) and removed 42 (42 requested) atoms. Cycle 47: After refmac, R = 0.2704 (Rfree = 0.000) for 15405 atoms. Found 0 (84 requested) and removed 42 (42 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2597 (Rfree = 0.000) for 15363 atoms. Found 0 (84 requested) and removed 42 (42 requested) atoms. Cycle 49: After refmac, R = 0.2652 (Rfree = 0.000) for 15321 atoms. Found 0 (84 requested) and removed 42 (42 requested) atoms. Writing output files ... TimeTaking 191.47