Sun 23 Dec 23:41:31 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 2pbl-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pbl-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pbl-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pbl-4.0-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/2pbl-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pbl-4.0-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 ============================================================ Sun 23 Dec 23:41:36 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/2pbl-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pbl-4.0-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 635 and 0 Target number of residues in the AU: 635 Target solvent content: 0.6597 Checking the provided sequence file Detected sequence length: 262 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1048 Adjusted target solvent content: 0.44 Input MTZ file: 2pbl-4.0-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: 77.197 74.438 95.727 90.000 113.394 90.000 Input sequence file: 2pbl-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 8384 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: 87.858 4.000 Wilson plot Bfac: 84.56 8486 reflections ( 98.79 % complete ) and 0 restraints for refining 9224 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3695 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4253 (Rfree = 0.000) for 9224 atoms. Found 43 (43 requested) and removed 119 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.64 3.94 Search for helices and strands: 0 residues in 0 chains, 9310 seeds are put forward NCS extension: 0 residues added, 9310 seeds are put forward Round 1: 265 peptides, 60 chains. Longest chain 8 peptides. Score 0.218 Round 2: 324 peptides, 63 chains. Longest chain 9 peptides. Score 0.305 Round 3: 369 peptides, 69 chains. Longest chain 17 peptides. Score 0.339 Round 4: 374 peptides, 66 chains. Longest chain 17 peptides. Score 0.369 Round 5: 375 peptides, 68 chains. Longest chain 15 peptides. Score 0.356 Taking the results from Round 4 Chains 67, Residues 308, Estimated correctness of the model 0.0 % 9 chains (50 residues) have been docked in sequence ------------------------------------------------------ 8486 reflections ( 98.79 % complete ) and 18171 restraints for refining 7566 atoms. 16870 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3672 (Rfree = 0.000) for 7566 atoms. Found 35 (35 requested) and removed 71 (17 requested) atoms. Cycle 2: After refmac, R = 0.3646 (Rfree = 0.000) for 7296 atoms. Found 35 (35 requested) and removed 54 (17 requested) atoms. Cycle 3: After refmac, R = 0.3714 (Rfree = 0.000) for 7167 atoms. Found 34 (34 requested) and removed 50 (17 requested) atoms. Cycle 4: After refmac, R = 0.2924 (Rfree = 0.000) for 7051 atoms. Found 33 (33 requested) and removed 31 (16 requested) atoms. Cycle 5: After refmac, R = 0.3485 (Rfree = 0.000) for 6999 atoms. Found 33 (33 requested) and removed 43 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.62 3.92 Search for helices and strands: 0 residues in 0 chains, 7227 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 7257 seeds are put forward Round 1: 354 peptides, 76 chains. Longest chain 9 peptides. Score 0.261 Round 2: 416 peptides, 78 chains. Longest chain 10 peptides. Score 0.354 Round 3: 413 peptides, 72 chains. Longest chain 13 peptides. Score 0.391 Round 4: 449 peptides, 80 chains. Longest chain 18 peptides. Score 0.393 Round 5: 462 peptides, 73 chains. Longest chain 17 peptides. Score 0.459 Taking the results from Round 5 Chains 74, Residues 389, Estimated correctness of the model 0.0 % 8 chains (46 residues) have been docked in sequence ------------------------------------------------------ 8486 reflections ( 98.79 % complete ) and 15615 restraints for refining 6888 atoms. 13994 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3285 (Rfree = 0.000) for 6888 atoms. Found 32 (32 requested) and removed 103 (16 requested) atoms. Cycle 7: After refmac, R = 0.3182 (Rfree = 0.000) for 6695 atoms. Found 32 (32 requested) and removed 52 (16 requested) atoms. Cycle 8: After refmac, R = 0.3130 (Rfree = 0.000) for 6606 atoms. Found 31 (31 requested) and removed 32 (15 requested) atoms. Cycle 9: After refmac, R = 0.2384 (Rfree = 0.000) for 6534 atoms. Found 31 (31 requested) and removed 25 (15 requested) atoms. Cycle 10: After refmac, R = 0.2221 (Rfree = 0.000) for 6506 atoms. Found 31 (31 requested) and removed 24 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.75 4.06 Search for helices and strands: 0 residues in 0 chains, 6746 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 6767 seeds are put forward Round 1: 360 peptides, 69 chains. Longest chain 14 peptides. Score 0.324 Round 2: 438 peptides, 74 chains. Longest chain 12 peptides. Score 0.416 Round 3: 453 peptides, 76 chains. Longest chain 15 peptides. Score 0.426 Round 4: 447 peptides, 68 chains. Longest chain 17 peptides. Score 0.470 Round 5: 445 peptides, 69 chains. Longest chain 19 peptides. Score 0.460 Taking the results from Round 4 Chains 69, Residues 379, Estimated correctness of the model 0.0 % 7 chains (58 residues) have been docked in sequence ------------------------------------------------------ 8486 reflections ( 98.79 % complete ) and 15378 restraints for refining 6868 atoms. 13757 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3006 (Rfree = 0.000) for 6868 atoms. Found 32 (32 requested) and removed 85 (16 requested) atoms. Cycle 12: After refmac, R = 0.2965 (Rfree = 0.000) for 6728 atoms. Found 32 (32 requested) and removed 44 (16 requested) atoms. Cycle 13: After refmac, R = 0.2841 (Rfree = 0.000) for 6660 atoms. Found 31 (31 requested) and removed 39 (15 requested) atoms. Cycle 14: After refmac, R = 0.2842 (Rfree = 0.000) for 6608 atoms. Found 31 (31 requested) and removed 36 (15 requested) atoms. Cycle 15: After refmac, R = 0.2747 (Rfree = 0.000) for 6565 atoms. Found 31 (31 requested) and removed 37 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.68 3.99 Search for helices and strands: 0 residues in 0 chains, 6766 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 6785 seeds are put forward Round 1: 355 peptides, 75 chains. Longest chain 9 peptides. Score 0.270 Round 2: 423 peptides, 73 chains. Longest chain 12 peptides. Score 0.400 Round 3: 431 peptides, 72 chains. Longest chain 15 peptides. Score 0.419 Round 4: 432 peptides, 72 chains. Longest chain 18 peptides. Score 0.420 Round 5: 434 peptides, 69 chains. Longest chain 16 peptides. Score 0.444 Taking the results from Round 5 Chains 70, Residues 365, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 8486 reflections ( 98.79 % complete ) and 15662 restraints for refining 6929 atoms. 14225 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3191 (Rfree = 0.000) for 6929 atoms. Found 32 (32 requested) and removed 66 (16 requested) atoms. Cycle 17: After refmac, R = 0.2978 (Rfree = 0.000) for 6801 atoms. Found 32 (32 requested) and removed 54 (16 requested) atoms. Cycle 18: After refmac, R = 0.2268 (Rfree = 0.000) for 6705 atoms. Found 32 (32 requested) and removed 32 (16 requested) atoms. Cycle 19: After refmac, R = 0.2796 (Rfree = 0.000) for 6672 atoms. Found 31 (31 requested) and removed 36 (15 requested) atoms. Cycle 20: After refmac, R = 0.2886 (Rfree = 0.000) for 6634 atoms. Found 31 (31 requested) and removed 27 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.69 4.00 Search for helices and strands: 0 residues in 0 chains, 6879 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 6904 seeds are put forward Round 1: 340 peptides, 70 chains. Longest chain 8 peptides. Score 0.281 Round 2: 396 peptides, 68 chains. Longest chain 11 peptides. Score 0.391 Round 3: 408 peptides, 68 chains. Longest chain 17 peptides. Score 0.410 Round 4: 414 peptides, 63 chains. Longest chain 19 peptides. Score 0.453 Round 5: 422 peptides, 65 chains. Longest chain 15 peptides. Score 0.452 Taking the results from Round 4 Chains 64, Residues 351, Estimated correctness of the model 0.0 % 5 chains (29 residues) have been docked in sequence ------------------------------------------------------ 8486 reflections ( 98.79 % complete ) and 15445 restraints for refining 6884 atoms. 14026 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3077 (Rfree = 0.000) for 6884 atoms. Found 32 (32 requested) and removed 76 (16 requested) atoms. Cycle 22: After refmac, R = 0.2856 (Rfree = 0.000) for 6739 atoms. Found 32 (32 requested) and removed 49 (16 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2840 (Rfree = 0.000) for 6670 atoms. Found 31 (31 requested) and removed 42 (15 requested) atoms. Cycle 24: After refmac, R = 0.2718 (Rfree = 0.000) for 6624 atoms. Found 31 (31 requested) and removed 25 (15 requested) atoms. Cycle 25: After refmac, R = 0.2726 (Rfree = 0.000) for 6595 atoms. Found 31 (31 requested) and removed 26 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.60 3.90 Search for helices and strands: 0 residues in 0 chains, 6821 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 6834 seeds are put forward Round 1: 328 peptides, 66 chains. Longest chain 14 peptides. Score 0.290 Round 2: 378 peptides, 67 chains. Longest chain 14 peptides. Score 0.369 Round 3: 386 peptides, 65 chains. Longest chain 17 peptides. Score 0.396 Round 4: 385 peptides, 62 chains. Longest chain 15 peptides. Score 0.415 Round 5: 393 peptides, 62 chains. Longest chain 15 peptides. Score 0.428 Taking the results from Round 5 Chains 62, Residues 331, Estimated correctness of the model 0.0 % 7 chains (50 residues) have been docked in sequence ------------------------------------------------------ 8486 reflections ( 98.79 % complete ) and 15456 restraints for refining 6946 atoms. 14032 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2994 (Rfree = 0.000) for 6946 atoms. Found 33 (33 requested) and removed 95 (16 requested) atoms. Cycle 27: After refmac, R = 0.2741 (Rfree = 0.000) for 6807 atoms. Found 32 (32 requested) and removed 56 (16 requested) atoms. Cycle 28: After refmac, R = 0.2711 (Rfree = 0.000) for 6732 atoms. Found 32 (32 requested) and removed 45 (16 requested) atoms. Cycle 29: After refmac, R = 0.2589 (Rfree = 0.000) for 6683 atoms. Found 31 (31 requested) and removed 33 (15 requested) atoms. Cycle 30: After refmac, R = 0.2650 (Rfree = 0.000) for 6657 atoms. Found 31 (31 requested) and removed 23 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.62 3.92 Search for helices and strands: 0 residues in 0 chains, 6887 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 6907 seeds are put forward Round 1: 297 peptides, 67 chains. Longest chain 7 peptides. Score 0.224 Round 2: 365 peptides, 68 chains. Longest chain 9 peptides. Score 0.339 Round 3: 360 peptides, 63 chains. Longest chain 14 peptides. Score 0.367 Round 4: 351 peptides, 63 chains. Longest chain 12 peptides. Score 0.352 Round 5: 369 peptides, 64 chains. Longest chain 15 peptides. Score 0.375 Taking the results from Round 5 Chains 64, Residues 305, Estimated correctness of the model 0.0 % 6 chains (38 residues) have been docked in sequence ------------------------------------------------------ 8486 reflections ( 98.79 % complete ) and 15369 restraints for refining 6856 atoms. 14085 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2882 (Rfree = 0.000) for 6856 atoms. Found 32 (32 requested) and removed 66 (16 requested) atoms. Cycle 32: After refmac, R = 0.2879 (Rfree = 0.000) for 6748 atoms. Found 32 (32 requested) and removed 39 (16 requested) atoms. Cycle 33: After refmac, R = 0.2797 (Rfree = 0.000) for 6688 atoms. Found 32 (32 requested) and removed 28 (16 requested) atoms. Cycle 34: After refmac, R = 0.2735 (Rfree = 0.000) for 6651 atoms. Found 31 (31 requested) and removed 33 (15 requested) atoms. Cycle 35: After refmac, R = 0.2773 (Rfree = 0.000) for 6616 atoms. Found 31 (31 requested) and removed 26 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.69 4.00 Search for helices and strands: 0 residues in 0 chains, 6817 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 6838 seeds are put forward Round 1: 289 peptides, 64 chains. Longest chain 8 peptides. Score 0.233 Round 2: 347 peptides, 67 chains. Longest chain 10 peptides. Score 0.316 Round 3: 337 peptides, 66 chains. Longest chain 10 peptides. Score 0.306 Round 4: 356 peptides, 67 chains. Longest chain 11 peptides. Score 0.331 Round 5: 349 peptides, 65 chains. Longest chain 13 peptides. Score 0.334 Taking the results from Round 5 Chains 66, Residues 284, Estimated correctness of the model 0.0 % 7 chains (51 residues) have been docked in sequence ------------------------------------------------------ 8486 reflections ( 98.79 % complete ) and 15175 restraints for refining 6759 atoms. 13942 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3181 (Rfree = 0.000) for 6759 atoms. Found 32 (32 requested) and removed 69 (16 requested) atoms. Cycle 37: After refmac, R = 0.3059 (Rfree = 0.000) for 6629 atoms. Found 31 (31 requested) and removed 32 (15 requested) atoms. Cycle 38: After refmac, R = 0.3022 (Rfree = 0.000) for 6563 atoms. Found 31 (31 requested) and removed 37 (15 requested) atoms. Cycle 39: After refmac, R = 0.3019 (Rfree = 0.000) for 6511 atoms. Found 31 (31 requested) and removed 28 (15 requested) atoms. Cycle 40: After refmac, R = 0.2287 (Rfree = 0.000) for 6484 atoms. Found 30 (30 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.73 4.04 Search for helices and strands: 0 residues in 0 chains, 6663 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 6676 seeds are put forward Round 1: 259 peptides, 59 chains. Longest chain 8 peptides. Score 0.214 Round 2: 321 peptides, 66 chains. Longest chain 14 peptides. Score 0.277 Round 3: 324 peptides, 63 chains. Longest chain 12 peptides. Score 0.305 Round 4: 342 peptides, 65 chains. Longest chain 14 peptides. Score 0.322 Round 5: 339 peptides, 67 chains. Longest chain 10 peptides. Score 0.302 Taking the results from Round 4 Chains 66, Residues 277, Estimated correctness of the model 0.0 % 5 chains (28 residues) have been docked in sequence ------------------------------------------------------ 8486 reflections ( 98.79 % complete ) and 14276 restraints for refining 6395 atoms. 13155 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2950 (Rfree = 0.000) for 6395 atoms. Found 30 (30 requested) and removed 50 (15 requested) atoms. Cycle 42: After refmac, R = 0.2968 (Rfree = 0.000) for 6328 atoms. Found 30 (30 requested) and removed 37 (15 requested) atoms. Cycle 43: After refmac, R = 0.2911 (Rfree = 0.000) for 6299 atoms. Found 30 (30 requested) and removed 32 (15 requested) atoms. Cycle 44: After refmac, R = 0.2168 (Rfree = 0.000) for 6259 atoms. Found 29 (29 requested) and removed 16 (14 requested) atoms. Cycle 45: After refmac, R = 0.1944 (Rfree = 0.000) for 6261 atoms. Found 29 (29 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 3.99 Search for helices and strands: 0 residues in 0 chains, 6453 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 6465 seeds are put forward Round 1: 253 peptides, 56 chains. Longest chain 8 peptides. Score 0.227 Round 2: 273 peptides, 54 chains. Longest chain 9 peptides. Score 0.282 Round 3: 277 peptides, 56 chains. Longest chain 9 peptides. Score 0.274 Round 4: 290 peptides, 56 chains. Longest chain 9 peptides. Score 0.298 Round 5: 294 peptides, 54 chains. Longest chain 10 peptides. Score 0.321 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 54, Residues 240, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2pbl-4_warpNtrace.pdb as input Building loops using Loopy2018 54 chains (240 residues) following loop building 3 chains (17 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8486 reflections ( 98.79 % complete ) and 13685 restraints for refining 6226 atoms. 12719 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2970 (Rfree = 0.000) for 6226 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.3015 (Rfree = 0.000) for 6186 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.2971 (Rfree = 0.000) for 6137 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.2189 (Rfree = 0.000) for 6096 atoms. TimeTaking 77.12