null Mon 24 Dec 08:08:41 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 2op5-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2op5-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2op5-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2op5-3.8-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/2op5-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2op5-3.8-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 08:08:46 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/2op5-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2op5-3.8-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 467 and 0 Target number of residues in the AU: 467 Target solvent content: 0.6358 Checking the provided sequence file Detected sequence length: 117 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 702 Adjusted target solvent content: 0.45 Input MTZ file: 2op5-3.8-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: 19 Cell parameters: 56.562 84.634 144.950 90.000 90.000 90.000 Input sequence file: 2op5-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 5616 target number of atoms Had to go as low as 0.75 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: 73.087 3.800 Wilson plot Bfac: 69.37 7266 reflections ( 99.77 % complete ) and 0 restraints for refining 6249 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3427 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3191 (Rfree = 0.000) for 6249 atoms. Found 28 (34 requested) and removed 70 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.47 3.71 Search for helices and strands: 0 residues in 0 chains, 6289 seeds are put forward NCS extension: 0 residues added, 6289 seeds are put forward Round 1: 184 peptides, 39 chains. Longest chain 8 peptides. Score 0.250 Round 2: 265 peptides, 54 chains. Longest chain 10 peptides. Score 0.298 Round 3: 291 peptides, 53 chains. Longest chain 11 peptides. Score 0.372 Round 4: 325 peptides, 56 chains. Longest chain 12 peptides. Score 0.421 Round 5: 318 peptides, 54 chains. Longest chain 12 peptides. Score 0.424 Taking the results from Round 5 Chains 54, Residues 264, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7266 reflections ( 99.77 % complete ) and 12268 restraints for refining 5076 atoms. 11266 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3011 (Rfree = 0.000) for 5076 atoms. Found 23 (27 requested) and removed 54 (13 requested) atoms. Cycle 2: After refmac, R = 0.2812 (Rfree = 0.000) for 4954 atoms. Found 15 (27 requested) and removed 51 (13 requested) atoms. Cycle 3: After refmac, R = 0.2438 (Rfree = 0.000) for 4866 atoms. Found 15 (27 requested) and removed 28 (13 requested) atoms. Cycle 4: After refmac, R = 0.2761 (Rfree = 0.000) for 4816 atoms. Found 24 (26 requested) and removed 33 (13 requested) atoms. Cycle 5: After refmac, R = 0.2810 (Rfree = 0.000) for 4774 atoms. Found 19 (26 requested) and removed 42 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.48 3.72 Search for helices and strands: 0 residues in 0 chains, 4955 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4971 seeds are put forward Round 1: 240 peptides, 51 chains. Longest chain 9 peptides. Score 0.266 Round 2: 260 peptides, 50 chains. Longest chain 14 peptides. Score 0.328 Round 3: 270 peptides, 51 chains. Longest chain 13 peptides. Score 0.342 Round 4: 280 peptides, 49 chains. Longest chain 15 peptides. Score 0.386 Round 5: 275 peptides, 47 chains. Longest chain 13 peptides. Score 0.395 Taking the results from Round 5 Chains 47, Residues 228, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7266 reflections ( 99.77 % complete ) and 11541 restraints for refining 4850 atoms. 10676 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2580 (Rfree = 0.000) for 4850 atoms. Found 21 (26 requested) and removed 38 (13 requested) atoms. Cycle 7: After refmac, R = 0.2223 (Rfree = 0.000) for 4773 atoms. Found 14 (26 requested) and removed 40 (13 requested) atoms. Cycle 8: After refmac, R = 0.2172 (Rfree = 0.000) for 4713 atoms. Found 9 (26 requested) and removed 23 (13 requested) atoms. Cycle 9: After refmac, R = 0.2140 (Rfree = 0.000) for 4675 atoms. Found 5 (25 requested) and removed 21 (12 requested) atoms. Cycle 10: After refmac, R = 0.2077 (Rfree = 0.000) for 4638 atoms. Found 7 (25 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.44 3.68 Search for helices and strands: 0 residues in 0 chains, 4756 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 4767 seeds are put forward Round 1: 223 peptides, 47 chains. Longest chain 7 peptides. Score 0.265 Round 2: 292 peptides, 52 chains. Longest chain 14 peptides. Score 0.384 Round 3: 299 peptides, 53 chains. Longest chain 14 peptides. Score 0.391 Round 4: 306 peptides, 54 chains. Longest chain 10 peptides. Score 0.397 Round 5: 296 peptides, 45 chains. Longest chain 26 peptides. Score 0.462 Taking the results from Round 5 Chains 45, Residues 251, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7266 reflections ( 99.77 % complete ) and 11049 restraints for refining 4782 atoms. 10090 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3027 (Rfree = 0.000) for 4782 atoms. Found 26 (26 requested) and removed 60 (13 requested) atoms. Cycle 12: After refmac, R = 0.2419 (Rfree = 0.000) for 4686 atoms. Found 15 (26 requested) and removed 34 (13 requested) atoms. Cycle 13: After refmac, R = 0.2840 (Rfree = 0.000) for 4637 atoms. Found 25 (25 requested) and removed 37 (12 requested) atoms. Cycle 14: After refmac, R = 0.2964 (Rfree = 0.000) for 4594 atoms. Found 25 (25 requested) and removed 32 (12 requested) atoms. Cycle 15: After refmac, R = 0.2766 (Rfree = 0.000) for 4543 atoms. Found 25 (25 requested) and removed 27 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 3.67 Search for helices and strands: 0 residues in 0 chains, 4687 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 4714 seeds are put forward Round 1: 203 peptides, 45 chains. Longest chain 9 peptides. Score 0.233 Round 2: 254 peptides, 48 chains. Longest chain 11 peptides. Score 0.334 Round 3: 261 peptides, 47 chains. Longest chain 13 peptides. Score 0.362 Round 4: 274 peptides, 48 chains. Longest chain 16 peptides. Score 0.382 Round 5: 275 peptides, 47 chains. Longest chain 12 peptides. Score 0.395 Taking the results from Round 5 Chains 47, Residues 228, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7266 reflections ( 99.77 % complete ) and 10767 restraints for refining 4673 atoms. 9902 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3098 (Rfree = 0.000) for 4673 atoms. Found 25 (25 requested) and removed 61 (12 requested) atoms. Cycle 17: After refmac, R = 0.2903 (Rfree = 0.000) for 4586 atoms. Found 25 (25 requested) and removed 30 (12 requested) atoms. Cycle 18: After refmac, R = 0.2895 (Rfree = 0.000) for 4549 atoms. Found 25 (25 requested) and removed 23 (12 requested) atoms. Cycle 19: After refmac, R = 0.2886 (Rfree = 0.000) for 4520 atoms. Found 25 (25 requested) and removed 29 (12 requested) atoms. Cycle 20: After refmac, R = 0.2808 (Rfree = 0.000) for 4496 atoms. Found 22 (24 requested) and removed 25 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 3.69 Search for helices and strands: 0 residues in 0 chains, 4635 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4649 seeds are put forward Round 1: 172 peptides, 38 chains. Longest chain 8 peptides. Score 0.227 Round 2: 222 peptides, 41 chains. Longest chain 13 peptides. Score 0.329 Round 3: 240 peptides, 44 chains. Longest chain 12 peptides. Score 0.342 Round 4: 244 peptides, 42 chains. Longest chain 15 peptides. Score 0.373 Round 5: 251 peptides, 45 chains. Longest chain 12 peptides. Score 0.358 Taking the results from Round 4 Chains 42, Residues 202, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7266 reflections ( 99.77 % complete ) and 9647 restraints for refining 4306 atoms. 8881 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3074 (Rfree = 0.000) for 4306 atoms. Found 23 (23 requested) and removed 39 (11 requested) atoms. Cycle 22: After refmac, R = 0.2942 (Rfree = 0.000) for 4254 atoms. Found 23 (23 requested) and removed 30 (11 requested) atoms. Cycle 23: After refmac, R = 0.2778 (Rfree = 0.000) for 4227 atoms. Found 23 (23 requested) and removed 32 (11 requested) atoms. Cycle 24: After refmac, R = 0.2746 (Rfree = 0.000) for 4208 atoms. Found 23 (23 requested) and removed 29 (11 requested) atoms. Cycle 25: After refmac, R = 0.2685 (Rfree = 0.000) for 4192 atoms. Found 23 (23 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.47 3.71 Search for helices and strands: 0 residues in 0 chains, 4287 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 4307 seeds are put forward Round 1: 209 peptides, 46 chains. Longest chain 7 peptides. Score 0.238 Round 2: 260 peptides, 52 chains. Longest chain 9 peptides. Score 0.307 Round 3: 253 peptides, 45 chains. Longest chain 13 peptides. Score 0.363 Round 4: 256 peptides, 46 chains. Longest chain 11 peptides. Score 0.360 Round 5: 237 peptides, 44 chains. Longest chain 12 peptides. Score 0.334 Taking the results from Round 3 Chains 45, Residues 208, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7266 reflections ( 99.77 % complete ) and 9110 restraints for refining 4149 atoms. 8323 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3013 (Rfree = 0.000) for 4149 atoms. Found 22 (22 requested) and removed 31 (11 requested) atoms. Cycle 27: After refmac, R = 0.2461 (Rfree = 0.000) for 4109 atoms. Found 22 (22 requested) and removed 18 (11 requested) atoms. Cycle 28: After refmac, R = 0.2844 (Rfree = 0.000) for 4093 atoms. Found 22 (22 requested) and removed 21 (11 requested) atoms. Cycle 29: After refmac, R = 0.2351 (Rfree = 0.000) for 4078 atoms. Found 16 (22 requested) and removed 15 (11 requested) atoms. Cycle 30: After refmac, R = 0.2774 (Rfree = 0.000) for 4068 atoms. Found 22 (22 requested) and removed 22 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.52 3.76 Search for helices and strands: 0 residues in 0 chains, 4164 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 4177 seeds are put forward Round 1: 225 peptides, 51 chains. Longest chain 8 peptides. Score 0.226 Round 2: 254 peptides, 49 chains. Longest chain 10 peptides. Score 0.323 Round 3: 262 peptides, 48 chains. Longest chain 12 peptides. Score 0.354 Round 4: 256 peptides, 44 chains. Longest chain 12 peptides. Score 0.381 Round 5: 271 peptides, 52 chains. Longest chain 10 peptides. Score 0.334 Taking the results from Round 4 Chains 44, Residues 212, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7266 reflections ( 99.77 % complete ) and 9306 restraints for refining 4220 atoms. 8502 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3220 (Rfree = 0.000) for 4220 atoms. Found 23 (23 requested) and removed 37 (11 requested) atoms. Cycle 32: After refmac, R = 0.2943 (Rfree = 0.000) for 4183 atoms. Found 23 (23 requested) and removed 28 (11 requested) atoms. Cycle 33: After refmac, R = 0.2891 (Rfree = 0.000) for 4154 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 34: After refmac, R = 0.2807 (Rfree = 0.000) for 4138 atoms. Found 22 (22 requested) and removed 21 (11 requested) atoms. Cycle 35: After refmac, R = 0.2793 (Rfree = 0.000) for 4125 atoms. Found 16 (22 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.49 3.73 Search for helices and strands: 0 residues in 0 chains, 4206 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4223 seeds are put forward Round 1: 166 peptides, 37 chains. Longest chain 6 peptides. Score 0.222 Round 2: 220 peptides, 41 chains. Longest chain 12 peptides. Score 0.324 Round 3: 216 peptides, 40 chains. Longest chain 14 peptides. Score 0.324 Round 4: 216 peptides, 39 chains. Longest chain 9 peptides. Score 0.336 Round 5: 217 peptides, 39 chains. Longest chain 14 peptides. Score 0.338 Taking the results from Round 5 Chains 39, Residues 178, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7266 reflections ( 99.77 % complete ) and 9219 restraints for refining 4177 atoms. 8546 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3166 (Rfree = 0.000) for 4177 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. Cycle 37: After refmac, R = 0.2776 (Rfree = 0.000) for 4149 atoms. Found 22 (22 requested) and removed 35 (11 requested) atoms. Cycle 38: After refmac, R = 0.2504 (Rfree = 0.000) for 4121 atoms. Found 12 (22 requested) and removed 16 (11 requested) atoms. Cycle 39: After refmac, R = 0.2394 (Rfree = 0.000) for 4107 atoms. Found 7 (22 requested) and removed 14 (11 requested) atoms. Cycle 40: After refmac, R = 0.2903 (Rfree = 0.000) for 4097 atoms. Found 22 (22 requested) and removed 22 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.50 3.74 Search for helices and strands: 0 residues in 0 chains, 4181 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4201 seeds are put forward Round 1: 193 peptides, 42 chains. Longest chain 11 peptides. Score 0.240 Round 2: 201 peptides, 38 chains. Longest chain 15 peptides. Score 0.308 Round 3: 216 peptides, 39 chains. Longest chain 19 peptides. Score 0.336 Round 4: 226 peptides, 39 chains. Longest chain 11 peptides. Score 0.361 Round 5: 232 peptides, 44 chains. Longest chain 10 peptides. Score 0.322 Taking the results from Round 4 Chains 39, Residues 187, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7266 reflections ( 99.77 % complete ) and 9362 restraints for refining 4248 atoms. 8653 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2902 (Rfree = 0.000) for 4248 atoms. Found 23 (23 requested) and removed 37 (11 requested) atoms. Cycle 42: After refmac, R = 0.2675 (Rfree = 0.000) for 4212 atoms. Found 23 (23 requested) and removed 23 (11 requested) atoms. Cycle 43: After refmac, R = 0.2589 (Rfree = 0.000) for 4205 atoms. Found 23 (23 requested) and removed 24 (11 requested) atoms. Cycle 44: After refmac, R = 0.2567 (Rfree = 0.000) for 4190 atoms. Found 23 (23 requested) and removed 18 (11 requested) atoms. Cycle 45: After refmac, R = 0.2613 (Rfree = 0.000) for 4184 atoms. Found 23 (23 requested) and removed 23 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.52 3.76 Search for helices and strands: 0 residues in 0 chains, 4250 seeds are put forward NCS extension: 0 residues added, 4250 seeds are put forward Round 1: 183 peptides, 41 chains. Longest chain 7 peptides. Score 0.223 Round 2: 205 peptides, 38 chains. Longest chain 14 peptides. Score 0.318 Round 3: 195 peptides, 38 chains. Longest chain 10 peptides. Score 0.292 Round 4: 207 peptides, 37 chains. Longest chain 11 peptides. Score 0.335 Round 5: 198 peptides, 34 chains. Longest chain 12 peptides. Score 0.345 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 164, 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 2op5-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7266 reflections ( 99.77 % complete ) and 9750 restraints for refining 4318 atoms. 9128 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2870 (Rfree = 0.000) for 4318 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2632 (Rfree = 0.000) for 4292 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2717 (Rfree = 0.000) for 4263 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2577 (Rfree = 0.000) for 4246 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:51:26 GMT 2018 Job finished. TimeTaking 42.75 Used memory is bytes: 136208