null Sun 23 Dec 22:22:50 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 2gfg-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gfg-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gfg-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gfg-3.2-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/2gfg-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gfg-3.2-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 22:22:59 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/2gfg-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gfg-3.2-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 429 and 0 Target number of residues in the AU: 429 Target solvent content: 0.6160 Checking the provided sequence file Detected sequence length: 193 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 579 Adjusted target solvent content: 0.48 Input MTZ file: 2gfg-3.2-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: 19 Cell parameters: 43.030 74.690 188.130 90.000 90.000 90.000 Input sequence file: 2gfg-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 4632 target number of atoms Had to go as low as 0.65 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. 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 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: 94.065 3.200 Wilson plot Bfac: 59.54 10582 reflections ( 99.61 % complete ) and 0 restraints for refining 5171 atoms. Observations/parameters ratio is 0.51 ------------------------------------------------------ Starting model: R = 0.3595 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3388 (Rfree = 0.000) for 5171 atoms. Found 46 (46 requested) and removed 72 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.14 3.22 Search for helices and strands: 0 residues in 0 chains, 5230 seeds are put forward NCS extension: 0 residues added, 5230 seeds are put forward Round 1: 233 peptides, 49 chains. Longest chain 8 peptides. Score 0.280 Round 2: 306 peptides, 53 chains. Longest chain 12 peptides. Score 0.433 Round 3: 307 peptides, 48 chains. Longest chain 13 peptides. Score 0.488 Round 4: 313 peptides, 52 chains. Longest chain 13 peptides. Score 0.461 Round 5: 295 peptides, 42 chains. Longest chain 15 peptides. Score 0.521 Taking the results from Round 5 Chains 42, Residues 253, Estimated correctness of the model 18.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10582 reflections ( 99.61 % complete ) and 9714 restraints for refining 4229 atoms. 8744 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2925 (Rfree = 0.000) for 4229 atoms. Found 28 (37 requested) and removed 33 (18 requested) atoms. Cycle 2: After refmac, R = 0.2852 (Rfree = 0.000) for 4174 atoms. Found 34 (37 requested) and removed 20 (18 requested) atoms. Cycle 3: After refmac, R = 0.2646 (Rfree = 0.000) for 4150 atoms. Found 23 (37 requested) and removed 24 (18 requested) atoms. Cycle 4: After refmac, R = 0.2345 (Rfree = 0.000) for 4122 atoms. Found 13 (37 requested) and removed 20 (18 requested) atoms. Cycle 5: After refmac, R = 0.2277 (Rfree = 0.000) for 4104 atoms. Found 14 (36 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.12 3.20 Search for helices and strands: 0 residues in 0 chains, 4242 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 4261 seeds are put forward Round 1: 252 peptides, 50 chains. Longest chain 9 peptides. Score 0.323 Round 2: 296 peptides, 45 chains. Longest chain 13 peptides. Score 0.493 Round 3: 276 peptides, 44 chains. Longest chain 16 peptides. Score 0.455 Round 4: 287 peptides, 42 chains. Longest chain 11 peptides. Score 0.502 Round 5: 296 peptides, 45 chains. Longest chain 14 peptides. Score 0.493 Taking the results from Round 4 Chains 42, Residues 245, Estimated correctness of the model 12.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10582 reflections ( 99.61 % complete ) and 9593 restraints for refining 4187 atoms. 8655 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2524 (Rfree = 0.000) for 4187 atoms. Found 24 (37 requested) and removed 33 (18 requested) atoms. Cycle 7: After refmac, R = 0.2469 (Rfree = 0.000) for 4156 atoms. Found 22 (37 requested) and removed 26 (18 requested) atoms. Cycle 8: After refmac, R = 0.2383 (Rfree = 0.000) for 4141 atoms. Found 18 (37 requested) and removed 21 (18 requested) atoms. Cycle 9: After refmac, R = 0.2231 (Rfree = 0.000) for 4135 atoms. Found 14 (37 requested) and removed 24 (18 requested) atoms. Cycle 10: After refmac, R = 0.2229 (Rfree = 0.000) for 4123 atoms. Found 16 (37 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.09 3.17 Search for helices and strands: 0 residues in 0 chains, 4225 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 4237 seeds are put forward Round 1: 275 peptides, 49 chains. Longest chain 12 peptides. Score 0.397 Round 2: 299 peptides, 50 chains. Longest chain 13 peptides. Score 0.447 Round 3: 325 peptides, 51 chains. Longest chain 13 peptides. Score 0.499 Round 4: 314 peptides, 48 chains. Longest chain 14 peptides. Score 0.504 Round 5: 314 peptides, 48 chains. Longest chain 19 peptides. Score 0.504 Taking the results from Round 5 Chains 48, Residues 266, Estimated correctness of the model 12.6 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 10582 reflections ( 99.61 % complete ) and 9618 restraints for refining 4229 atoms. 8581 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2560 (Rfree = 0.000) for 4229 atoms. Found 25 (37 requested) and removed 26 (18 requested) atoms. Cycle 12: After refmac, R = 0.2400 (Rfree = 0.000) for 4213 atoms. Found 9 (37 requested) and removed 19 (18 requested) atoms. Cycle 13: After refmac, R = 0.2413 (Rfree = 0.000) for 4198 atoms. Found 14 (37 requested) and removed 23 (18 requested) atoms. Cycle 14: After refmac, R = 0.2369 (Rfree = 0.000) for 4184 atoms. Found 10 (37 requested) and removed 22 (18 requested) atoms. Cycle 15: After refmac, R = 0.2308 (Rfree = 0.000) for 4169 atoms. Found 12 (37 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.12 3.20 Search for helices and strands: 0 residues in 0 chains, 4283 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 4308 seeds are put forward Round 1: 281 peptides, 52 chains. Longest chain 11 peptides. Score 0.379 Round 2: 314 peptides, 49 chains. Longest chain 17 peptides. Score 0.494 Round 3: 307 peptides, 49 chains. Longest chain 18 peptides. Score 0.477 Round 4: 308 peptides, 47 chains. Longest chain 18 peptides. Score 0.500 Round 5: 327 peptides, 49 chains. Longest chain 17 peptides. Score 0.523 Taking the results from Round 5 Chains 49, Residues 278, Estimated correctness of the model 18.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10582 reflections ( 99.61 % complete ) and 9490 restraints for refining 4227 atoms. 8427 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3329 (Rfree = 0.000) for 4227 atoms. Found 37 (37 requested) and removed 42 (18 requested) atoms. Cycle 17: After refmac, R = 0.2440 (Rfree = 0.000) for 4189 atoms. Found 23 (37 requested) and removed 24 (18 requested) atoms. Cycle 18: After refmac, R = 0.2363 (Rfree = 0.000) for 4174 atoms. Found 21 (37 requested) and removed 22 (18 requested) atoms. Cycle 19: After refmac, R = 0.2165 (Rfree = 0.000) for 4167 atoms. Found 5 (37 requested) and removed 20 (18 requested) atoms. Cycle 20: After refmac, R = 0.2189 (Rfree = 0.000) for 4140 atoms. Found 8 (37 requested) and removed 19 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.14 3.22 Search for helices and strands: 0 residues in 0 chains, 4260 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 4286 seeds are put forward Round 1: 282 peptides, 56 chains. Longest chain 9 peptides. Score 0.337 Round 2: 292 peptides, 48 chains. Longest chain 14 peptides. Score 0.451 Round 3: 292 peptides, 47 chains. Longest chain 17 peptides. Score 0.462 Round 4: 295 peptides, 44 chains. Longest chain 16 peptides. Score 0.501 Round 5: 294 peptides, 47 chains. Longest chain 13 peptides. Score 0.467 Taking the results from Round 4 Chains 44, Residues 251, Estimated correctness of the model 11.7 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 10582 reflections ( 99.61 % complete ) and 9415 restraints for refining 4229 atoms. 8425 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2439 (Rfree = 0.000) for 4229 atoms. Found 24 (37 requested) and removed 24 (18 requested) atoms. Cycle 22: After refmac, R = 0.2354 (Rfree = 0.000) for 4205 atoms. Found 18 (37 requested) and removed 21 (18 requested) atoms. Cycle 23: After refmac, R = 0.2383 (Rfree = 0.000) for 4186 atoms. Found 21 (37 requested) and removed 22 (18 requested) atoms. Cycle 24: After refmac, R = 0.2364 (Rfree = 0.000) for 4171 atoms. Found 24 (37 requested) and removed 22 (18 requested) atoms. Cycle 25: After refmac, R = 0.2120 (Rfree = 0.000) for 4164 atoms. Found 7 (37 requested) and removed 19 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.12 3.20 Search for helices and strands: 0 residues in 0 chains, 4300 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 4323 seeds are put forward Round 1: 233 peptides, 49 chains. Longest chain 11 peptides. Score 0.280 Round 2: 268 peptides, 48 chains. Longest chain 12 peptides. Score 0.390 Round 3: 269 peptides, 45 chains. Longest chain 13 peptides. Score 0.426 Round 4: 281 peptides, 44 chains. Longest chain 15 peptides. Score 0.467 Round 5: 287 peptides, 49 chains. Longest chain 13 peptides. Score 0.428 Taking the results from Round 4 Chains 44, Residues 237, Estimated correctness of the model 0.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10582 reflections ( 99.61 % complete ) and 9565 restraints for refining 4228 atoms. 8661 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2501 (Rfree = 0.000) for 4228 atoms. Found 16 (37 requested) and removed 21 (18 requested) atoms. Cycle 27: After refmac, R = 0.2271 (Rfree = 0.000) for 4204 atoms. Found 27 (37 requested) and removed 18 (18 requested) atoms. Cycle 28: After refmac, R = 0.2153 (Rfree = 0.000) for 4201 atoms. Found 20 (37 requested) and removed 20 (18 requested) atoms. Cycle 29: After refmac, R = 0.2107 (Rfree = 0.000) for 4192 atoms. Found 11 (37 requested) and removed 20 (18 requested) atoms. Cycle 30: After refmac, R = 0.2055 (Rfree = 0.000) for 4179 atoms. Found 20 (37 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.13 3.21 Search for helices and strands: 0 residues in 0 chains, 4315 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4332 seeds are put forward Round 1: 230 peptides, 46 chains. Longest chain 12 peptides. Score 0.308 Round 2: 264 peptides, 45 chains. Longest chain 12 peptides. Score 0.413 Round 3: 261 peptides, 43 chains. Longest chain 12 peptides. Score 0.428 Round 4: 250 peptides, 44 chains. Longest chain 13 peptides. Score 0.388 Round 5: 255 peptides, 41 chains. Longest chain 15 peptides. Score 0.435 Taking the results from Round 5 Chains 41, Residues 214, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10582 reflections ( 99.61 % complete ) and 9642 restraints for refining 4228 atoms. 8827 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2302 (Rfree = 0.000) for 4228 atoms. Found 24 (37 requested) and removed 20 (18 requested) atoms. Cycle 32: After refmac, R = 0.2189 (Rfree = 0.000) for 4214 atoms. Found 19 (37 requested) and removed 19 (18 requested) atoms. Cycle 33: After refmac, R = 0.2141 (Rfree = 0.000) for 4202 atoms. Found 10 (37 requested) and removed 19 (18 requested) atoms. Cycle 34: After refmac, R = 0.2123 (Rfree = 0.000) for 4184 atoms. Found 13 (37 requested) and removed 18 (18 requested) atoms. Cycle 35: After refmac, R = 0.2081 (Rfree = 0.000) for 4169 atoms. Found 23 (37 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.12 3.20 Search for helices and strands: 0 residues in 0 chains, 4287 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4302 seeds are put forward Round 1: 216 peptides, 44 chains. Longest chain 9 peptides. Score 0.292 Round 2: 241 peptides, 43 chains. Longest chain 13 peptides. Score 0.375 Round 3: 249 peptides, 43 chains. Longest chain 15 peptides. Score 0.396 Round 4: 258 peptides, 41 chains. Longest chain 16 peptides. Score 0.442 Round 5: 250 peptides, 39 chains. Longest chain 16 peptides. Score 0.444 Taking the results from Round 5 Chains 39, Residues 211, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 10582 reflections ( 99.61 % complete ) and 9610 restraints for refining 4228 atoms. 8780 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2489 (Rfree = 0.000) for 4228 atoms. Found 37 (37 requested) and removed 23 (18 requested) atoms. Cycle 37: After refmac, R = 0.2076 (Rfree = 0.000) for 4229 atoms. Found 37 (38 requested) and removed 19 (19 requested) atoms. Cycle 38: After refmac, R = 0.1855 (Rfree = 0.000) for 4240 atoms. Found 10 (38 requested) and removed 20 (19 requested) atoms. Cycle 39: After refmac, R = 0.1852 (Rfree = 0.000) for 4224 atoms. Found 10 (37 requested) and removed 18 (18 requested) atoms. Cycle 40: After refmac, R = 0.1695 (Rfree = 0.000) for 4213 atoms. Found 7 (37 requested) and removed 19 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.13 3.21 Search for helices and strands: 0 residues in 0 chains, 4334 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 4348 seeds are put forward Round 1: 223 peptides, 48 chains. Longest chain 10 peptides. Score 0.263 Round 2: 251 peptides, 44 chains. Longest chain 11 peptides. Score 0.390 Round 3: 239 peptides, 38 chains. Longest chain 14 peptides. Score 0.427 Round 4: 255 peptides, 41 chains. Longest chain 13 peptides. Score 0.435 Round 5: 254 peptides, 37 chains. Longest chain 18 peptides. Score 0.476 Taking the results from Round 5 Chains 37, Residues 217, Estimated correctness of the model 3.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10582 reflections ( 99.61 % complete ) and 9521 restraints for refining 4228 atoms. 8690 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2166 (Rfree = 0.000) for 4228 atoms. Found 26 (37 requested) and removed 21 (18 requested) atoms. Cycle 42: After refmac, R = 0.2058 (Rfree = 0.000) for 4225 atoms. Found 17 (37 requested) and removed 21 (18 requested) atoms. Cycle 43: After refmac, R = 0.2015 (Rfree = 0.000) for 4217 atoms. Found 18 (37 requested) and removed 18 (18 requested) atoms. Cycle 44: After refmac, R = 0.1920 (Rfree = 0.000) for 4214 atoms. Found 10 (37 requested) and removed 19 (18 requested) atoms. Cycle 45: After refmac, R = 0.1931 (Rfree = 0.000) for 4204 atoms. Found 16 (37 requested) and removed 19 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.09 3.17 Search for helices and strands: 0 residues in 0 chains, 4308 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4328 seeds are put forward Round 1: 189 peptides, 40 chains. Longest chain 10 peptides. Score 0.261 Round 2: 215 peptides, 35 chains. Longest chain 13 peptides. Score 0.399 Round 3: 224 peptides, 37 chains. Longest chain 14 peptides. Score 0.399 Round 4: 235 peptides, 39 chains. Longest chain 14 peptides. Score 0.405 Round 5: 232 peptides, 38 chains. Longest chain 13 peptides. Score 0.409 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 38, Residues 194, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2gfg-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10582 reflections ( 99.61 % complete ) and 9693 restraints for refining 4229 atoms. 8955 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2156 (Rfree = 0.000) for 4229 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2088 (Rfree = 0.000) for 4202 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.1826 (Rfree = 0.000) for 4177 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.1776 (Rfree = 0.000) for 4156 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:26:01 GMT 2018 Job finished. TimeTaking 63.19 Used memory is bytes: 12001776