null Sun 23 Dec 22:23:05 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-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2aam-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2aam-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aam-4.0-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-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aam-4.0-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 22:23:15 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-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aam-4.0-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 3639 and 0 Target number of residues in the AU: 3639 Target solvent content: 0.6468 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-4.0-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-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 14832 target number of atoms Had to go as low as 1.55 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 4.000 Wilson plot Bfac: 76.13 46619 reflections ( 98.70 % complete ) and 0 restraints for refining 20134 atoms. Observations/parameters ratio is 0.58 ------------------------------------------------------ Starting model: R = 0.3407 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3026 (Rfree = 0.000) for 20134 atoms. Found 95 (95 requested) and removed 99 (47 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.69 2.23 Search for helices and strands: 0 residues in 0 chains, 20429 seeds are put forward NCS extension: 0 residues added, 20429 seeds are put forward Round 1: 1101 peptides, 144 chains. Longest chain 26 peptides. Score 0.379 Round 2: 1164 peptides, 129 chains. Longest chain 29 peptides. Score 0.423 Round 3: 1198 peptides, 131 chains. Longest chain 24 peptides. Score 0.430 Round 4: 1207 peptides, 135 chains. Longest chain 36 peptides. Score 0.427 Round 5: 1181 peptides, 119 chains. Longest chain 30 peptides. Score 0.443 Taking the results from Round 5 Chains 124, Residues 1062, Estimated correctness of the model 0.0 % 4 chains (60 residues) have been docked in sequence ------------------------------------------------------ 46619 reflections ( 98.70 % complete ) and 4415 restraints for refining 16063 atoms. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2603 (Rfree = 0.000) for 16063 atoms. Found 76 (76 requested) and removed 54 (38 requested) atoms. Cycle 2: After refmac, R = 0.2418 (Rfree = 0.000) for 16085 atoms. Found 76 (76 requested) and removed 63 (38 requested) atoms. Cycle 3: After refmac, R = 0.2025 (Rfree = 0.000) for 16098 atoms. Found 47 (76 requested) and removed 56 (38 requested) atoms. Cycle 4: After refmac, R = 0.1959 (Rfree = 0.000) for 16089 atoms. Found 28 (76 requested) and removed 61 (38 requested) atoms. Cycle 5: After refmac, R = 0.1883 (Rfree = 0.000) for 16056 atoms. Found 12 (76 requested) and removed 51 (38 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.66 2.21 Search for helices and strands: 0 residues in 0 chains, 16555 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 16573 seeds are put forward Round 1: 1189 peptides, 120 chains. Longest chain 29 peptides. Score 0.444 Round 2: 1230 peptides, 116 chains. Longest chain 37 peptides. Score 0.462 Round 3: 1188 peptides, 124 chains. Longest chain 28 peptides. Score 0.438 Round 4: 1216 peptides, 109 chains. Longest chain 38 peptides. Score 0.468 Round 5: 1183 peptides, 107 chains. Longest chain 37 peptides. Score 0.462 Taking the results from Round 4 Chains 116, Residues 1107, Estimated correctness of the model 0.0 % 5 chains (71 residues) have been docked in sequence ------------------------------------------------------ 46619 reflections ( 98.70 % complete ) and 4674 restraints for refining 15828 atoms. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2390 (Rfree = 0.000) for 15828 atoms. Found 75 (75 requested) and removed 45 (37 requested) atoms. Cycle 7: After refmac, R = 0.2268 (Rfree = 0.000) for 15858 atoms. Found 75 (75 requested) and removed 50 (37 requested) atoms. Cycle 8: After refmac, R = 0.2196 (Rfree = 0.000) for 15883 atoms. Found 75 (75 requested) and removed 65 (37 requested) atoms. Cycle 9: After refmac, R = 0.2264 (Rfree = 0.000) for 15893 atoms. Found 75 (75 requested) and removed 69 (37 requested) atoms. Cycle 10: After refmac, R = 0.2274 (Rfree = 0.000) for 15899 atoms. Found 75 (75 requested) and removed 71 (37 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.65 2.20 Search for helices and strands: 0 residues in 0 chains, 16447 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 16463 seeds are put forward Round 1: 1204 peptides, 135 chains. Longest chain 39 peptides. Score 0.426 Round 2: 1243 peptides, 124 chains. Longest chain 43 peptides. Score 0.454 Round 3: 1221 peptides, 117 chains. Longest chain 29 peptides. Score 0.458 Round 4: 1235 peptides, 124 chains. Longest chain 41 peptides. Score 0.451 Round 5: 1215 peptides, 125 chains. Longest chain 43 peptides. Score 0.444 Taking the results from Round 3 Chains 120, Residues 1104, Estimated correctness of the model 0.0 % 4 chains (71 residues) have been docked in sequence ------------------------------------------------------ 46619 reflections ( 98.70 % complete ) and 4662 restraints for refining 15460 atoms. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2282 (Rfree = 0.000) for 15460 atoms. Found 73 (73 requested) and removed 50 (36 requested) atoms. Cycle 12: After refmac, R = 0.2167 (Rfree = 0.000) for 15483 atoms. Found 73 (73 requested) and removed 45 (36 requested) atoms. Cycle 13: After refmac, R = 0.2136 (Rfree = 0.000) for 15511 atoms. Found 73 (73 requested) and removed 59 (36 requested) atoms. Cycle 14: After refmac, R = 0.2114 (Rfree = 0.000) for 15525 atoms. Found 73 (73 requested) and removed 60 (36 requested) atoms. Cycle 15: After refmac, R = 0.2101 (Rfree = 0.000) for 15538 atoms. Found 73 (73 requested) and removed 80 (36 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.56 2.15 Search for helices and strands: 0 residues in 0 chains, 16046 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 16070 seeds are put forward Round 1: 1156 peptides, 139 chains. Longest chain 29 peptides. Score 0.405 Round 2: 1212 peptides, 125 chains. Longest chain 39 peptides. Score 0.443 Round 3: 1214 peptides, 129 chains. Longest chain 29 peptides. Score 0.438 Round 4: 1214 peptides, 121 chains. Longest chain 37 peptides. Score 0.450 Round 5: 1243 peptides, 128 chains. Longest chain 51 peptides. Score 0.448 Taking the results from Round 4 Chains 126, Residues 1093, Estimated correctness of the model 0.0 % 3 chains (50 residues) have been docked in sequence ------------------------------------------------------ 46619 reflections ( 98.70 % complete ) and 4460 restraints for refining 15580 atoms. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2328 (Rfree = 0.000) for 15580 atoms. Found 74 (74 requested) and removed 58 (37 requested) atoms. Cycle 17: After refmac, R = 0.2255 (Rfree = 0.000) for 15596 atoms. Found 74 (74 requested) and removed 66 (37 requested) atoms. Cycle 18: After refmac, R = 0.2288 (Rfree = 0.000) for 15604 atoms. Found 74 (74 requested) and removed 82 (37 requested) atoms. Cycle 19: After refmac, R = 0.2264 (Rfree = 0.000) for 15596 atoms. Found 74 (74 requested) and removed 71 (37 requested) atoms. Cycle 20: After refmac, R = 0.2381 (Rfree = 0.000) for 15599 atoms. Found 74 (74 requested) and removed 94 (37 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 2.06 Search for helices and strands: 0 residues in 0 chains, 16071 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 16101 seeds are put forward Round 1: 1138 peptides, 150 chains. Longest chain 33 peptides. Score 0.382 Round 2: 1230 peptides, 142 chains. Longest chain 29 peptides. Score 0.423 Round 3: 1237 peptides, 140 chains. Longest chain 31 peptides. Score 0.428 Round 4: 1233 peptides, 140 chains. Longest chain 36 peptides. Score 0.427 Round 5: 1245 peptides, 146 chains. Longest chain 33 peptides. Score 0.421 Taking the results from Round 3 Chains 148, Residues 1097, Estimated correctness of the model 0.0 % 7 chains (98 residues) have been docked in sequence ------------------------------------------------------ 46619 reflections ( 98.70 % complete ) and 4711 restraints for refining 15292 atoms. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2523 (Rfree = 0.000) for 15292 atoms. Found 72 (72 requested) and removed 51 (36 requested) atoms. Cycle 22: After refmac, R = 0.2412 (Rfree = 0.000) for 15313 atoms. Found 72 (72 requested) and removed 58 (36 requested) atoms. Cycle 23: After refmac, R = 0.2448 (Rfree = 0.000) for 15327 atoms. Found 72 (72 requested) and removed 63 (36 requested) atoms. Cycle 24: After refmac, R = 0.2390 (Rfree = 0.000) for 15336 atoms. Found 72 (72 requested) and removed 72 (36 requested) atoms. Cycle 25: After refmac, R = 0.2414 (Rfree = 0.000) for 15336 atoms. Found 72 (72 requested) and removed 90 (36 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.47 2.09 Search for helices and strands: 0 residues in 0 chains, 15884 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 15904 seeds are put forward Round 1: 1168 peptides, 166 chains. Longest chain 28 peptides. Score 0.367 Round 2: 1226 peptides, 149 chains. Longest chain 30 peptides. Score 0.411 Round 3: 1254 peptides, 152 chains. Longest chain 25 peptides. Score 0.415 Round 4: 1239 peptides, 146 chains. Longest chain 33 peptides. Score 0.420 Round 5: 1245 peptides, 144 chains. Longest chain 26 peptides. Score 0.425 Taking the results from Round 5 Chains 152, Residues 1101, Estimated correctness of the model 0.0 % 6 chains (64 residues) have been docked in sequence ------------------------------------------------------ 46619 reflections ( 98.70 % complete ) and 4519 restraints for refining 15554 atoms. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2527 (Rfree = 0.000) for 15554 atoms. Found 73 (73 requested) and removed 54 (36 requested) atoms. Cycle 27: After refmac, R = 0.2463 (Rfree = 0.000) for 15573 atoms. Found 73 (73 requested) and removed 52 (36 requested) atoms. Cycle 28: After refmac, R = 0.2453 (Rfree = 0.000) for 15594 atoms. Found 74 (74 requested) and removed 78 (37 requested) atoms. Cycle 29: After refmac, R = 0.2413 (Rfree = 0.000) for 15590 atoms. Found 74 (74 requested) and removed 57 (37 requested) atoms. Cycle 30: After refmac, R = 0.2437 (Rfree = 0.000) for 15607 atoms. Found 74 (74 requested) and removed 64 (37 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.42 2.06 Search for helices and strands: 0 residues in 0 chains, 16169 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 16185 seeds are put forward Round 1: 1133 peptides, 164 chains. Longest chain 22 peptides. Score 0.358 Round 2: 1244 peptides, 159 chains. Longest chain 24 peptides. Score 0.402 Round 3: 1239 peptides, 157 chains. Longest chain 22 peptides. Score 0.403 Round 4: 1232 peptides, 154 chains. Longest chain 28 peptides. Score 0.405 Round 5: 1216 peptides, 154 chains. Longest chain 25 peptides. Score 0.400 Taking the results from Round 4 Chains 158, Residues 1078, Estimated correctness of the model 0.0 % 4 chains (67 residues) have been docked in sequence ------------------------------------------------------ 46619 reflections ( 98.70 % complete ) and 4460 restraints for refining 15559 atoms. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2506 (Rfree = 0.000) for 15559 atoms. Found 73 (73 requested) and removed 54 (36 requested) atoms. Cycle 32: After refmac, R = 0.2415 (Rfree = 0.000) for 15578 atoms. Found 74 (74 requested) and removed 53 (37 requested) atoms. Cycle 33: After refmac, R = 0.2049 (Rfree = 0.000) for 15599 atoms. Found 53 (74 requested) and removed 53 (37 requested) atoms. Cycle 34: After refmac, R = 0.2005 (Rfree = 0.000) for 15599 atoms. Found 35 (74 requested) and removed 56 (37 requested) atoms. Cycle 35: After refmac, R = 0.1976 (Rfree = 0.000) for 15578 atoms. Found 22 (74 requested) and removed 69 (37 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 2.03 Search for helices and strands: 0 residues in 0 chains, 16128 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 16145 seeds are put forward Round 1: 1100 peptides, 177 chains. Longest chain 19 peptides. Score 0.326 Round 2: 1226 peptides, 163 chains. Longest chain 22 peptides. Score 0.390 Round 3: 1236 peptides, 160 chains. Longest chain 27 peptides. Score 0.398 Round 4: 1229 peptides, 164 chains. Longest chain 27 peptides. Score 0.389 Round 5: 1213 peptides, 158 chains. Longest chain 29 peptides. Score 0.393 Taking the results from Round 3 Chains 163, Residues 1076, Estimated correctness of the model 0.0 % 4 chains (40 residues) have been docked in sequence ------------------------------------------------------ 46619 reflections ( 98.70 % complete ) and 4325 restraints for refining 15230 atoms. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2594 (Rfree = 0.000) for 15230 atoms. Found 72 (72 requested) and removed 54 (36 requested) atoms. Cycle 37: After refmac, R = 0.2503 (Rfree = 0.000) for 15248 atoms. Found 72 (72 requested) and removed 49 (36 requested) atoms. Cycle 38: After refmac, R = 0.2552 (Rfree = 0.000) for 15271 atoms. Found 72 (72 requested) and removed 59 (36 requested) atoms. Cycle 39: After refmac, R = 0.2493 (Rfree = 0.000) for 15284 atoms. Found 72 (72 requested) and removed 60 (36 requested) atoms. Cycle 40: After refmac, R = 0.2491 (Rfree = 0.000) for 15296 atoms. Found 72 (72 requested) and removed 53 (36 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 2.12 Search for helices and strands: 0 residues in 0 chains, 15905 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 15925 seeds are put forward Round 1: 1048 peptides, 158 chains. Longest chain 26 peptides. Score 0.339 Round 2: 1196 peptides, 159 chains. Longest chain 21 peptides. Score 0.387 Round 3: 1186 peptides, 147 chains. Longest chain 32 peptides. Score 0.402 Round 4: 1167 peptides, 150 chains. Longest chain 23 peptides. Score 0.391 Round 5: 1155 peptides, 146 chains. Longest chain 24 peptides. Score 0.394 Taking the results from Round 3 Chains 147, Residues 1039, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 46619 reflections ( 98.70 % complete ) and 4009 restraints for refining 14886 atoms. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2565 (Rfree = 0.000) for 14886 atoms. Found 70 (70 requested) and removed 39 (35 requested) atoms. Cycle 42: After refmac, R = 0.2622 (Rfree = 0.000) for 14917 atoms. Found 70 (70 requested) and removed 41 (35 requested) atoms. Cycle 43: After refmac, R = 0.2643 (Rfree = 0.000) for 14946 atoms. Found 71 (71 requested) and removed 57 (35 requested) atoms. Cycle 44: After refmac, R = 0.2556 (Rfree = 0.000) for 14960 atoms. Found 71 (71 requested) and removed 54 (35 requested) atoms. Cycle 45: After refmac, R = 0.2542 (Rfree = 0.000) for 14977 atoms. Found 71 (71 requested) and removed 57 (35 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.48 2.10 Search for helices and strands: 0 residues in 0 chains, 15639 seeds are put forward NCS extension: 44 residues added (2 deleted due to clashes), 15683 seeds are put forward Round 1: 1025 peptides, 181 chains. Longest chain 16 peptides. Score 0.293 Round 2: 1125 peptides, 155 chains. Longest chain 24 peptides. Score 0.370 Round 3: 1198 peptides, 157 chains. Longest chain 23 peptides. Score 0.390 Round 4: 1157 peptides, 158 chains. Longest chain 24 peptides. Score 0.375 Round 5: 1181 peptides, 156 chains. Longest chain 19 peptides. Score 0.386 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 159, Residues 1041, Estimated correctness of the model 0.0 % 4 chains (28 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2aam-4_warpNtrace.pdb as input Building loops using Loopy2018 159 chains (1041 residues) following loop building 4 chains (28 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 46619 reflections ( 98.70 % complete ) and 4096 restraints for refining 14639 atoms. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2514 (Rfree = 0.000) for 14639 atoms. Found 0 (69 requested) and removed 34 (34 requested) atoms. Cycle 47: After refmac, R = 0.2463 (Rfree = 0.000) for 14605 atoms. Found 0 (69 requested) and removed 34 (34 requested) atoms. Cycle 48: After refmac, R = 0.2477 (Rfree = 0.000) for 14571 atoms. Found 0 (69 requested) and removed 34 (34 requested) atoms. Cycle 49: After refmac, R = 0.2427 (Rfree = 0.000) for 14537 atoms. Found 0 (69 requested) and removed 34 (34 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:50:18 GMT 2018 Job finished. TimeTaking 207.22 Used memory is bytes: 20320984