Mon 24 Dec 07:54:19 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2f4p-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2f4p-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2f4p-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4p-3.2-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2f4p-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4p-3.2-parrot-noncs ############### 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 07:54:23 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/noncs/ArpWArp/wArpResults/WorkingDir/2f4p-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4p-3.2-parrot-noncs/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 411 and 0 Target number of residues in the AU: 411 Target solvent content: 0.6032 Checking the provided sequence file Detected sequence length: 147 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 588 Adjusted target solvent content: 0.43 Input MTZ file: 2f4p-3.2-parrot-noncs.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: 170 Cell parameters: 71.746 71.746 188.600 90.000 90.000 120.000 Input sequence file: 2f4p-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 4704 target number of atoms Had to go as low as 0.60 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: 21.543 3.200 Wilson plot Bfac: 53.61 9033 reflections ( 99.64 % complete ) and 0 restraints for refining 5206 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3427 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3117 (Rfree = 0.000) for 5206 atoms. Found 46 (46 requested) and removed 59 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.07 3.37 Search for helices and strands: 0 residues in 0 chains, 5257 seeds are put forward NCS extension: 0 residues added, 5257 seeds are put forward Round 1: 192 peptides, 42 chains. Longest chain 8 peptides. Score 0.249 Round 2: 258 peptides, 47 chains. Longest chain 11 peptides. Score 0.387 Round 3: 280 peptides, 46 chains. Longest chain 14 peptides. Score 0.459 Round 4: 308 peptides, 49 chains. Longest chain 15 peptides. Score 0.497 Round 5: 293 peptides, 47 chains. Longest chain 11 peptides. Score 0.481 Taking the results from Round 4 Chains 49, Residues 259, Estimated correctness of the model 10.4 % 4 chains (17 residues) have been docked in sequence ------------------------------------------------------ 9033 reflections ( 99.64 % complete ) and 9600 restraints for refining 4294 atoms. 8574 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2701 (Rfree = 0.000) for 4294 atoms. Found 36 (38 requested) and removed 37 (19 requested) atoms. Cycle 2: After refmac, R = 0.2439 (Rfree = 0.000) for 4208 atoms. Found 14 (38 requested) and removed 36 (19 requested) atoms. Cycle 3: After refmac, R = 0.2301 (Rfree = 0.000) for 4151 atoms. Found 13 (37 requested) and removed 28 (18 requested) atoms. Cycle 4: After refmac, R = 0.2259 (Rfree = 0.000) for 4107 atoms. Found 18 (37 requested) and removed 25 (18 requested) atoms. Cycle 5: After refmac, R = 0.2559 (Rfree = 0.000) for 4085 atoms. Found 34 (36 requested) and removed 34 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.99 3.28 Search for helices and strands: 0 residues in 0 chains, 4184 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 4208 seeds are put forward Round 1: 269 peptides, 50 chains. Longest chain 14 peptides. Score 0.382 Round 2: 317 peptides, 50 chains. Longest chain 18 peptides. Score 0.509 Round 3: 316 peptides, 49 chains. Longest chain 14 peptides. Score 0.517 Round 4: 312 peptides, 44 chains. Longest chain 19 peptides. Score 0.559 Round 5: 308 peptides, 45 chains. Longest chain 14 peptides. Score 0.539 Taking the results from Round 4 Chains 44, Residues 268, Estimated correctness of the model 29.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9033 reflections ( 99.64 % complete ) and 8931 restraints for refining 4091 atoms. 7903 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2448 (Rfree = 0.000) for 4091 atoms. Found 33 (36 requested) and removed 31 (18 requested) atoms. Cycle 7: After refmac, R = 0.2439 (Rfree = 0.000) for 4073 atoms. Found 20 (36 requested) and removed 31 (18 requested) atoms. Cycle 8: After refmac, R = 0.2238 (Rfree = 0.000) for 4047 atoms. Found 22 (36 requested) and removed 24 (18 requested) atoms. Cycle 9: After refmac, R = 0.1960 (Rfree = 0.000) for 4037 atoms. Found 11 (36 requested) and removed 21 (18 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1980 (Rfree = 0.000) for 4025 atoms. Found 3 (36 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.00 3.30 Search for helices and strands: 0 residues in 0 chains, 4107 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 4134 seeds are put forward Round 1: 301 peptides, 52 chains. Longest chain 16 peptides. Score 0.447 Round 2: 321 peptides, 48 chains. Longest chain 21 peptides. Score 0.539 Round 3: 318 peptides, 49 chains. Longest chain 14 peptides. Score 0.522 Round 4: 318 peptides, 47 chains. Longest chain 18 peptides. Score 0.542 Round 5: 311 peptides, 47 chains. Longest chain 15 peptides. Score 0.526 Taking the results from Round 4 Chains 47, Residues 271, Estimated correctness of the model 24.5 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 9033 reflections ( 99.64 % complete ) and 9036 restraints for refining 4138 atoms. 7975 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2240 (Rfree = 0.000) for 4138 atoms. Found 23 (37 requested) and removed 32 (18 requested) atoms. Cycle 12: After refmac, R = 0.2111 (Rfree = 0.000) for 4118 atoms. Found 13 (37 requested) and removed 28 (18 requested) atoms. Cycle 13: After refmac, R = 0.1989 (Rfree = 0.000) for 4100 atoms. Found 16 (36 requested) and removed 31 (18 requested) atoms. Cycle 14: After refmac, R = 0.1923 (Rfree = 0.000) for 4078 atoms. Found 12 (36 requested) and removed 27 (18 requested) atoms. Cycle 15: After refmac, R = 0.1839 (Rfree = 0.000) for 4058 atoms. Found 11 (36 requested) and removed 25 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.01 3.31 Search for helices and strands: 0 residues in 0 chains, 4163 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4181 seeds are put forward Round 1: 260 peptides, 47 chains. Longest chain 16 peptides. Score 0.393 Round 2: 286 peptides, 45 chains. Longest chain 19 peptides. Score 0.486 Round 3: 308 peptides, 48 chains. Longest chain 16 peptides. Score 0.508 Round 4: 298 peptides, 47 chains. Longest chain 15 peptides. Score 0.494 Round 5: 281 peptides, 42 chains. Longest chain 21 peptides. Score 0.506 Taking the results from Round 3 Chains 48, Residues 260, Estimated correctness of the model 13.9 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 9033 reflections ( 99.64 % complete ) and 9238 restraints for refining 4225 atoms. 8229 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2174 (Rfree = 0.000) for 4225 atoms. Found 35 (37 requested) and removed 33 (18 requested) atoms. Cycle 17: After refmac, R = 0.2102 (Rfree = 0.000) for 4213 atoms. Found 13 (37 requested) and removed 27 (18 requested) atoms. Cycle 18: After refmac, R = 0.2327 (Rfree = 0.000) for 4193 atoms. Found 24 (37 requested) and removed 30 (18 requested) atoms. Cycle 19: After refmac, R = 0.1943 (Rfree = 0.000) for 4176 atoms. Found 14 (37 requested) and removed 28 (18 requested) atoms. Cycle 20: After refmac, R = 0.1816 (Rfree = 0.000) for 4145 atoms. Found 19 (37 requested) and removed 22 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.02 3.32 Search for helices and strands: 0 residues in 0 chains, 4243 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 4256 seeds are put forward Round 1: 258 peptides, 51 chains. Longest chain 10 peptides. Score 0.338 Round 2: 309 peptides, 51 chains. Longest chain 14 peptides. Score 0.478 Round 3: 304 peptides, 49 chains. Longest chain 16 peptides. Score 0.487 Round 4: 311 peptides, 49 chains. Longest chain 15 peptides. Score 0.505 Round 5: 298 peptides, 45 chains. Longest chain 17 peptides. Score 0.516 Taking the results from Round 5 Chains 45, Residues 253, Estimated correctness of the model 16.5 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 9033 reflections ( 99.64 % complete ) and 9476 restraints for refining 4294 atoms. 8496 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2305 (Rfree = 0.000) for 4294 atoms. Found 29 (38 requested) and removed 29 (19 requested) atoms. Cycle 22: After refmac, R = 0.2169 (Rfree = 0.000) for 4283 atoms. Found 17 (38 requested) and removed 33 (19 requested) atoms. Cycle 23: After refmac, R = 0.2068 (Rfree = 0.000) for 4264 atoms. Found 10 (38 requested) and removed 25 (19 requested) atoms. Cycle 24: After refmac, R = 0.1983 (Rfree = 0.000) for 4248 atoms. Found 10 (38 requested) and removed 20 (19 requested) atoms. Cycle 25: After refmac, R = 0.2319 (Rfree = 0.000) for 4238 atoms. Found 27 (38 requested) and removed 29 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.95 3.24 Search for helices and strands: 0 residues in 0 chains, 4321 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4337 seeds are put forward Round 1: 258 peptides, 49 chains. Longest chain 12 peptides. Score 0.362 Round 2: 286 peptides, 47 chains. Longest chain 17 peptides. Score 0.463 Round 3: 272 peptides, 44 chains. Longest chain 15 peptides. Score 0.461 Round 4: 270 peptides, 40 chains. Longest chain 17 peptides. Score 0.500 Round 5: 280 peptides, 42 chains. Longest chain 15 peptides. Score 0.504 Taking the results from Round 5 Chains 42, Residues 238, Estimated correctness of the model 12.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9033 reflections ( 99.64 % complete ) and 9600 restraints for refining 4294 atoms. 8690 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2161 (Rfree = 0.000) for 4294 atoms. Found 24 (38 requested) and removed 34 (19 requested) atoms. Cycle 27: After refmac, R = 0.2042 (Rfree = 0.000) for 4280 atoms. Found 17 (38 requested) and removed 26 (19 requested) atoms. Cycle 28: After refmac, R = 0.1941 (Rfree = 0.000) for 4267 atoms. Found 21 (38 requested) and removed 26 (19 requested) atoms. Cycle 29: After refmac, R = 0.1811 (Rfree = 0.000) for 4259 atoms. Found 16 (38 requested) and removed 33 (19 requested) atoms. Cycle 30: After refmac, R = 0.1788 (Rfree = 0.000) for 4237 atoms. Found 10 (38 requested) and removed 23 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.02 3.32 Search for helices and strands: 0 residues in 0 chains, 4334 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 4348 seeds are put forward Round 1: 213 peptides, 43 chains. Longest chain 8 peptides. Score 0.303 Round 2: 251 peptides, 39 chains. Longest chain 14 peptides. Score 0.463 Round 3: 263 peptides, 38 chains. Longest chain 27 peptides. Score 0.505 Round 4: 284 peptides, 43 chains. Longest chain 29 peptides. Score 0.503 Round 5: 258 peptides, 40 chains. Longest chain 13 peptides. Score 0.470 Taking the results from Round 3 Chains 40, Residues 225, Estimated correctness of the model 12.9 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 9033 reflections ( 99.64 % complete ) and 9372 restraints for refining 4294 atoms. 8449 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2012 (Rfree = 0.000) for 4294 atoms. Found 34 (38 requested) and removed 25 (19 requested) atoms. Cycle 32: After refmac, R = 0.1848 (Rfree = 0.000) for 4299 atoms. Found 15 (38 requested) and removed 22 (19 requested) atoms. Cycle 33: After refmac, R = 0.2106 (Rfree = 0.000) for 4287 atoms. Found 38 (38 requested) and removed 23 (19 requested) atoms. Cycle 34: After refmac, R = 0.1788 (Rfree = 0.000) for 4299 atoms. Found 22 (38 requested) and removed 26 (19 requested) atoms. Cycle 35: After refmac, R = 0.2097 (Rfree = 0.000) for 4292 atoms. Found 38 (38 requested) and removed 23 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.99 3.28 Search for helices and strands: 0 residues in 0 chains, 4400 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 4419 seeds are put forward Round 1: 196 peptides, 36 chains. Longest chain 12 peptides. Score 0.342 Round 2: 246 peptides, 45 chains. Longest chain 12 peptides. Score 0.377 Round 3: 226 peptides, 40 chains. Longest chain 10 peptides. Score 0.381 Round 4: 241 peptides, 37 chains. Longest chain 14 peptides. Score 0.459 Round 5: 240 peptides, 41 chains. Longest chain 10 peptides. Score 0.409 Taking the results from Round 4 Chains 38, Residues 204, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 9033 reflections ( 99.64 % complete ) and 9680 restraints for refining 4293 atoms. 8857 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1956 (Rfree = 0.000) for 4293 atoms. Found 38 (38 requested) and removed 24 (19 requested) atoms. Cycle 37: After refmac, R = 0.2031 (Rfree = 0.000) for 4301 atoms. Found 36 (38 requested) and removed 23 (19 requested) atoms. Cycle 38: After refmac, R = 0.1681 (Rfree = 0.000) for 4311 atoms. Found 26 (38 requested) and removed 21 (19 requested) atoms. Cycle 39: After refmac, R = 0.1661 (Rfree = 0.000) for 4312 atoms. Found 21 (38 requested) and removed 23 (19 requested) atoms. Cycle 40: After refmac, R = 0.1663 (Rfree = 0.000) for 4309 atoms. Found 16 (38 requested) and removed 21 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.04 3.34 Search for helices and strands: 0 residues in 0 chains, 4401 seeds are put forward NCS extension: 0 residues added, 4401 seeds are put forward Round 1: 214 peptides, 42 chains. Longest chain 10 peptides. Score 0.319 Round 2: 222 peptides, 39 chains. Longest chain 9 peptides. Score 0.382 Round 3: 245 peptides, 43 chains. Longest chain 11 peptides. Score 0.398 Round 4: 234 peptides, 41 chains. Longest chain 10 peptides. Score 0.391 Round 5: 219 peptides, 38 chains. Longest chain 16 peptides. Score 0.385 Taking the results from Round 3 Chains 43, Residues 202, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 9033 reflections ( 99.64 % complete ) and 9604 restraints for refining 4293 atoms. 8795 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1862 (Rfree = 0.000) for 4293 atoms. Found 35 (38 requested) and removed 21 (19 requested) atoms. Cycle 42: After refmac, R = 0.1769 (Rfree = 0.000) for 4299 atoms. Found 15 (38 requested) and removed 20 (19 requested) atoms. Cycle 43: After refmac, R = 0.1663 (Rfree = 0.000) for 4288 atoms. Found 23 (38 requested) and removed 20 (19 requested) atoms. Cycle 44: After refmac, R = 0.1605 (Rfree = 0.000) for 4281 atoms. Found 14 (38 requested) and removed 20 (19 requested) atoms. Cycle 45: After refmac, R = 0.1550 (Rfree = 0.000) for 4271 atoms. Found 14 (38 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.03 3.33 Search for helices and strands: 0 residues in 0 chains, 4375 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 4388 seeds are put forward Round 1: 220 peptides, 43 chains. Longest chain 9 peptides. Score 0.325 Round 2: 250 peptides, 43 chains. Longest chain 14 peptides. Score 0.413 Round 3: 253 peptides, 43 chains. Longest chain 15 peptides. Score 0.421 Round 4: 224 peptides, 38 chains. Longest chain 17 peptides. Score 0.400 Round 5: 242 peptides, 39 chains. Longest chain 12 peptides. Score 0.438 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 39, Residues 203, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2f4p-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9033 reflections ( 99.64 % complete ) and 9586 restraints for refining 4294 atoms. 8787 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1778 (Rfree = 0.000) for 4294 atoms. Found 0 (38 requested) and removed 12 (19 requested) atoms. Cycle 47: After refmac, R = 0.1694 (Rfree = 0.000) for 4277 atoms. Found 0 (38 requested) and removed 7 (19 requested) atoms. Cycle 48: After refmac, R = 0.1598 (Rfree = 0.000) for 4268 atoms. Found 0 (38 requested) and removed 5 (19 requested) atoms. Cycle 49: After refmac, R = 0.1665 (Rfree = 0.000) for 4262 atoms. Found 0 (38 requested) and removed 17 (19 requested) atoms. Writing output files ... TimeTaking 47.28