Sun 23 Dec 23:44:44 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 2op5-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2op5-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2op5-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2op5-3.8-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/2op5-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2op5-3.8-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 23:44:49 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/2op5-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2op5-3.8-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 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-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: 19 Cell parameters: 56.562 84.634 144.950 90.000 90.000 90.000 Input sequence file: 2op5-3.8-parrot-mrncs.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 6233 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3306 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3021 (Rfree = 0.000) for 6233 atoms. Found 34 (34 requested) and removed 40 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 3.76 Search for helices and strands: 0 residues in 0 chains, 6345 seeds are put forward NCS extension: 0 residues added, 6345 seeds are put forward Round 1: 220 peptides, 45 chains. Longest chain 10 peptides. Score 0.279 Round 2: 315 peptides, 54 chains. Longest chain 14 peptides. Score 0.417 Round 3: 351 peptides, 57 chains. Longest chain 15 peptides. Score 0.468 Round 4: 362 peptides, 53 chains. Longest chain 16 peptides. Score 0.525 Round 5: 379 peptides, 51 chains. Longest chain 24 peptides. Score 0.574 Taking the results from Round 5 Chains 51, Residues 328, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7266 reflections ( 99.77 % complete ) and 11764 restraints for refining 5074 atoms. 10484 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2715 (Rfree = 0.000) for 5074 atoms. Found 12 (27 requested) and removed 51 (13 requested) atoms. Cycle 2: After refmac, R = 0.2568 (Rfree = 0.000) for 4924 atoms. Found 10 (27 requested) and removed 35 (13 requested) atoms. Cycle 3: After refmac, R = 0.2110 (Rfree = 0.000) for 4855 atoms. Found 4 (26 requested) and removed 33 (13 requested) atoms. Cycle 4: After refmac, R = 0.2345 (Rfree = 0.000) for 4791 atoms. Found 8 (26 requested) and removed 29 (13 requested) atoms. Cycle 5: After refmac, R = 0.2369 (Rfree = 0.000) for 4739 atoms. Found 10 (26 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.44 3.68 Search for helices and strands: 0 residues in 0 chains, 4912 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 4941 seeds are put forward Round 1: 287 peptides, 49 chains. Longest chain 13 peptides. Score 0.403 Round 2: 337 peptides, 50 chains. Longest chain 16 peptides. Score 0.502 Round 3: 337 peptides, 49 chains. Longest chain 18 peptides. Score 0.511 Round 4: 330 peptides, 46 chains. Longest chain 19 peptides. Score 0.523 Round 5: 323 peptides, 46 chains. Longest chain 20 peptides. Score 0.509 Taking the results from Round 4 Chains 46, Residues 284, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7266 reflections ( 99.77 % complete ) and 10950 restraints for refining 4857 atoms. 9837 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2436 (Rfree = 0.000) for 4857 atoms. Found 15 (26 requested) and removed 43 (13 requested) atoms. Cycle 7: After refmac, R = 0.2401 (Rfree = 0.000) for 4791 atoms. Found 23 (26 requested) and removed 37 (13 requested) atoms. Cycle 8: After refmac, R = 0.2406 (Rfree = 0.000) for 4731 atoms. Found 15 (26 requested) and removed 29 (13 requested) atoms. Cycle 9: After refmac, R = 0.2308 (Rfree = 0.000) for 4688 atoms. Found 16 (25 requested) and removed 25 (12 requested) atoms. Cycle 10: After refmac, R = 0.1841 (Rfree = 0.000) for 4659 atoms. Found 3 (25 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.49 3.73 Search for helices and strands: 0 residues in 0 chains, 4816 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 4843 seeds are put forward Round 1: 280 peptides, 56 chains. Longest chain 13 peptides. Score 0.315 Round 2: 340 peptides, 57 chains. Longest chain 13 peptides. Score 0.444 Round 3: 341 peptides, 56 chains. Longest chain 14 peptides. Score 0.456 Round 4: 341 peptides, 55 chains. Longest chain 14 peptides. Score 0.465 Round 5: 338 peptides, 48 chains. Longest chain 18 peptides. Score 0.521 Taking the results from Round 5 Chains 49, Residues 290, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7266 reflections ( 99.77 % complete ) and 10927 restraints for refining 4862 atoms. 9782 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2489 (Rfree = 0.000) for 4862 atoms. Found 22 (26 requested) and removed 56 (13 requested) atoms. Cycle 12: After refmac, R = 0.2159 (Rfree = 0.000) for 4781 atoms. Found 13 (26 requested) and removed 38 (13 requested) atoms. Cycle 13: After refmac, R = 0.1980 (Rfree = 0.000) for 4722 atoms. Found 14 (26 requested) and removed 28 (13 requested) atoms. Cycle 14: After refmac, R = 0.1627 (Rfree = 0.000) for 4696 atoms. Found 8 (25 requested) and removed 23 (12 requested) atoms. Cycle 15: After refmac, R = 0.1546 (Rfree = 0.000) for 4665 atoms. Found 6 (25 requested) and removed 23 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.46 3.70 Search for helices and strands: 0 residues in 0 chains, 4806 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4826 seeds are put forward Round 1: 280 peptides, 57 chains. Longest chain 9 peptides. Score 0.304 Round 2: 323 peptides, 55 chains. Longest chain 12 peptides. Score 0.426 Round 3: 338 peptides, 57 chains. Longest chain 15 peptides. Score 0.440 Round 4: 311 peptides, 50 chains. Longest chain 15 peptides. Score 0.447 Round 5: 332 peptides, 52 chains. Longest chain 16 peptides. Score 0.473 Taking the results from Round 5 Chains 52, Residues 280, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7266 reflections ( 99.77 % complete ) and 11272 restraints for refining 4923 atoms. 10204 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2203 (Rfree = 0.000) for 4923 atoms. Found 20 (27 requested) and removed 50 (13 requested) atoms. Cycle 17: After refmac, R = 0.2011 (Rfree = 0.000) for 4858 atoms. Found 18 (26 requested) and removed 31 (13 requested) atoms. Cycle 18: After refmac, R = 0.1997 (Rfree = 0.000) for 4813 atoms. Found 12 (26 requested) and removed 29 (13 requested) atoms. Cycle 19: After refmac, R = 0.1892 (Rfree = 0.000) for 4778 atoms. Found 16 (26 requested) and removed 21 (13 requested) atoms. Cycle 20: After refmac, R = 0.1445 (Rfree = 0.000) for 4755 atoms. Found 9 (26 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 3.69 Search for helices and strands: 0 residues in 0 chains, 4927 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 4951 seeds are put forward Round 1: 256 peptides, 55 chains. Longest chain 7 peptides. Score 0.264 Round 2: 292 peptides, 52 chains. Longest chain 14 peptides. Score 0.384 Round 3: 299 peptides, 55 chains. Longest chain 11 peptides. Score 0.371 Round 4: 308 peptides, 51 chains. Longest chain 14 peptides. Score 0.431 Round 5: 313 peptides, 52 chains. Longest chain 14 peptides. Score 0.432 Taking the results from Round 5 Chains 52, Residues 261, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7266 reflections ( 99.77 % complete ) and 11650 restraints for refining 5005 atoms. 10658 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1939 (Rfree = 0.000) for 5005 atoms. Found 11 (27 requested) and removed 35 (13 requested) atoms. Cycle 22: After refmac, R = 0.1984 (Rfree = 0.000) for 4951 atoms. Found 18 (27 requested) and removed 22 (13 requested) atoms. Cycle 23: After refmac, R = 0.1903 (Rfree = 0.000) for 4925 atoms. Found 14 (27 requested) and removed 24 (13 requested) atoms. Cycle 24: After refmac, R = 0.1800 (Rfree = 0.000) for 4899 atoms. Found 13 (27 requested) and removed 20 (13 requested) atoms. Cycle 25: After refmac, R = 0.1704 (Rfree = 0.000) for 4884 atoms. Found 16 (26 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.39 3.62 Search for helices and strands: 0 residues in 0 chains, 5026 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 5046 seeds are put forward Round 1: 230 peptides, 50 chains. Longest chain 8 peptides. Score 0.250 Round 2: 299 peptides, 52 chains. Longest chain 12 peptides. Score 0.401 Round 3: 309 peptides, 54 chains. Longest chain 14 peptides. Score 0.404 Round 4: 309 peptides, 49 chains. Longest chain 21 peptides. Score 0.452 Round 5: 295 peptides, 49 chains. Longest chain 16 peptides. Score 0.421 Taking the results from Round 4 Chains 49, Residues 260, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7266 reflections ( 99.77 % complete ) and 11450 restraints for refining 5029 atoms. 10459 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1979 (Rfree = 0.000) for 5029 atoms. Found 16 (27 requested) and removed 26 (13 requested) atoms. Cycle 27: After refmac, R = 0.1819 (Rfree = 0.000) for 4983 atoms. Found 6 (27 requested) and removed 28 (13 requested) atoms. Cycle 28: After refmac, R = 0.1931 (Rfree = 0.000) for 4936 atoms. Found 11 (27 requested) and removed 27 (13 requested) atoms. Cycle 29: After refmac, R = 0.1852 (Rfree = 0.000) for 4901 atoms. Found 15 (27 requested) and removed 19 (13 requested) atoms. Cycle 30: After refmac, R = 0.1769 (Rfree = 0.000) for 4894 atoms. Found 8 (26 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.45 3.69 Search for helices and strands: 0 residues in 0 chains, 5044 seeds are put forward NCS extension: 38 residues added (1 deleted due to clashes), 5082 seeds are put forward Round 1: 204 peptides, 44 chains. Longest chain 8 peptides. Score 0.247 Round 2: 263 peptides, 50 chains. Longest chain 10 peptides. Score 0.335 Round 3: 252 peptides, 47 chains. Longest chain 12 peptides. Score 0.340 Round 4: 254 peptides, 48 chains. Longest chain 12 peptides. Score 0.334 Round 5: 241 peptides, 41 chains. Longest chain 10 peptides. Score 0.376 Taking the results from Round 5 Chains 41, Residues 200, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7266 reflections ( 99.77 % complete ) and 11540 restraints for refining 4938 atoms. 10781 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1919 (Rfree = 0.000) for 4938 atoms. Found 11 (27 requested) and removed 26 (13 requested) atoms. Cycle 32: After refmac, R = 0.1707 (Rfree = 0.000) for 4899 atoms. Found 18 (27 requested) and removed 25 (13 requested) atoms. Cycle 33: After refmac, R = 0.1694 (Rfree = 0.000) for 4877 atoms. Found 24 (26 requested) and removed 23 (13 requested) atoms. Cycle 34: After refmac, R = 0.1809 (Rfree = 0.000) for 4869 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. Cycle 35: After refmac, R = 0.1705 (Rfree = 0.000) for 4861 atoms. Found 26 (26 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 3.59 Search for helices and strands: 0 residues in 0 chains, 5005 seeds are put forward NCS extension: 6 residues added (3 deleted due to clashes), 5011 seeds are put forward Round 1: 209 peptides, 47 chains. Longest chain 7 peptides. Score 0.227 Round 2: 247 peptides, 46 chains. Longest chain 14 peptides. Score 0.338 Round 3: 233 peptides, 45 chains. Longest chain 8 peptides. Score 0.313 Round 4: 250 peptides, 41 chains. Longest chain 14 peptides. Score 0.398 Round 5: 238 peptides, 41 chains. Longest chain 12 peptides. Score 0.369 Taking the results from Round 4 Chains 41, Residues 209, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7266 reflections ( 99.77 % complete ) and 11627 restraints for refining 5004 atoms. 10813 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1892 (Rfree = 0.000) for 5004 atoms. Found 21 (27 requested) and removed 27 (13 requested) atoms. Cycle 37: After refmac, R = 0.1865 (Rfree = 0.000) for 4981 atoms. Found 15 (27 requested) and removed 18 (13 requested) atoms. Cycle 38: After refmac, R = 0.1780 (Rfree = 0.000) for 4969 atoms. Found 10 (27 requested) and removed 23 (13 requested) atoms. Cycle 39: After refmac, R = 0.1623 (Rfree = 0.000) for 4946 atoms. Found 6 (27 requested) and removed 21 (13 requested) atoms. Cycle 40: After refmac, R = 0.1606 (Rfree = 0.000) for 4925 atoms. Found 11 (27 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.42 3.66 Search for helices and strands: 0 residues in 0 chains, 5044 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 5056 seeds are put forward Round 1: 203 peptides, 44 chains. Longest chain 7 peptides. Score 0.245 Round 2: 251 peptides, 50 chains. Longest chain 10 peptides. Score 0.305 Round 3: 255 peptides, 46 chains. Longest chain 12 peptides. Score 0.358 Round 4: 242 peptides, 42 chains. Longest chain 13 peptides. Score 0.368 Round 5: 242 peptides, 42 chains. Longest chain 12 peptides. Score 0.368 Taking the results from Round 5 Chains 42, Residues 200, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7266 reflections ( 99.77 % complete ) and 11947 restraints for refining 5071 atoms. 11189 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1709 (Rfree = 0.000) for 5071 atoms. Found 23 (27 requested) and removed 31 (13 requested) atoms. Cycle 42: After refmac, R = 0.1745 (Rfree = 0.000) for 5047 atoms. Found 27 (27 requested) and removed 19 (13 requested) atoms. Cycle 43: After refmac, R = 0.1616 (Rfree = 0.000) for 5043 atoms. Found 26 (27 requested) and removed 24 (13 requested) atoms. Cycle 44: After refmac, R = 0.1669 (Rfree = 0.000) for 5036 atoms. Found 27 (27 requested) and removed 22 (13 requested) atoms. Cycle 45: After refmac, R = 0.1654 (Rfree = 0.000) for 5027 atoms. Found 27 (27 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.45 3.69 Search for helices and strands: 0 residues in 0 chains, 5170 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 5183 seeds are put forward Round 1: 180 peptides, 43 chains. Longest chain 7 peptides. Score 0.191 Round 2: 233 peptides, 48 chains. Longest chain 11 peptides. Score 0.280 Round 3: 240 peptides, 46 chains. Longest chain 11 peptides. Score 0.320 Round 4: 250 peptides, 46 chains. Longest chain 12 peptides. Score 0.345 Round 5: 242 peptides, 42 chains. Longest chain 12 peptides. Score 0.368 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 42, Residues 200, 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 11847 restraints for refining 5079 atoms. 11089 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1895 (Rfree = 0.000) for 5079 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.1818 (Rfree = 0.000) for 5044 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.1785 (Rfree = 0.000) for 5018 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.1687 (Rfree = 0.000) for 4993 atoms. TimeTaking 49.3