Sun 23 Dec 22:22:43 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 2iiu-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2iiu-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2iiu-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2iiu-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/2iiu-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2iiu-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 22:22:53 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/2iiu-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2iiu-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 543 and 0 Target number of residues in the AU: 543 Target solvent content: 0.6149 Checking the provided sequence file Detected sequence length: 227 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 681 Adjusted target solvent content: 0.52 Input MTZ file: 2iiu-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: 155 Cell parameters: 99.900 99.900 397.311 90.000 90.000 120.000 Input sequence file: 2iiu-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 5448 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: 132.437 3.200 Wilson plot Bfac: 58.76 12997 reflections ( 99.27 % complete ) and 0 restraints for refining 6015 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3355 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2789 (Rfree = 0.000) for 6015 atoms. Found 53 (53 requested) and removed 78 (26 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.07 2.99 Search for helices and strands: 0 residues in 0 chains, 6151 seeds are put forward NCS extension: 0 residues added, 6151 seeds are put forward Round 1: 309 peptides, 63 chains. Longest chain 11 peptides. Score 0.304 Round 2: 373 peptides, 62 chains. Longest chain 16 peptides. Score 0.448 Round 3: 405 peptides, 65 chains. Longest chain 15 peptides. Score 0.484 Round 4: 388 peptides, 59 chains. Longest chain 24 peptides. Score 0.501 Round 5: 414 peptides, 58 chains. Longest chain 23 peptides. Score 0.555 Taking the results from Round 5 Chains 58, Residues 356, Estimated correctness of the model 28.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12997 reflections ( 99.27 % complete ) and 10947 restraints for refining 4973 atoms. 9581 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2694 (Rfree = 0.000) for 4973 atoms. Found 44 (44 requested) and removed 43 (22 requested) atoms. Cycle 2: After refmac, R = 0.2396 (Rfree = 0.000) for 4937 atoms. Found 25 (44 requested) and removed 27 (22 requested) atoms. Cycle 3: After refmac, R = 0.2342 (Rfree = 0.000) for 4909 atoms. Found 21 (44 requested) and removed 34 (22 requested) atoms. Cycle 4: After refmac, R = 0.2277 (Rfree = 0.000) for 4876 atoms. Found 22 (43 requested) and removed 30 (21 requested) atoms. Cycle 5: After refmac, R = 0.2202 (Rfree = 0.000) for 4857 atoms. Found 22 (43 requested) and removed 26 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.05 2.97 Search for helices and strands: 0 residues in 0 chains, 5115 seeds are put forward NCS extension: 32 residues added (3 deleted due to clashes), 5147 seeds are put forward Round 1: 356 peptides, 56 chains. Longest chain 20 peptides. Score 0.466 Round 2: 387 peptides, 54 chains. Longest chain 17 peptides. Score 0.539 Round 3: 410 peptides, 55 chains. Longest chain 21 peptides. Score 0.570 Round 4: 413 peptides, 55 chains. Longest chain 29 peptides. Score 0.575 Round 5: 403 peptides, 48 chains. Longest chain 24 peptides. Score 0.609 Taking the results from Round 5 Chains 52, Residues 355, Estimated correctness of the model 43.5 % 7 chains (89 residues) have been docked in sequence ------------------------------------------------------ 12997 reflections ( 99.27 % complete ) and 9999 restraints for refining 4974 atoms. 8305 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2567 (Rfree = 0.000) for 4974 atoms. Found 44 (44 requested) and removed 49 (22 requested) atoms. Cycle 7: After refmac, R = 0.2368 (Rfree = 0.000) for 4944 atoms. Found 33 (44 requested) and removed 33 (22 requested) atoms. Cycle 8: After refmac, R = 0.2286 (Rfree = 0.000) for 4927 atoms. Found 15 (44 requested) and removed 26 (22 requested) atoms. Cycle 9: After refmac, R = 0.2254 (Rfree = 0.000) for 4909 atoms. Found 16 (44 requested) and removed 22 (22 requested) atoms. Cycle 10: After refmac, R = 0.2213 (Rfree = 0.000) for 4903 atoms. Found 6 (43 requested) and removed 22 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.08 3.00 Search for helices and strands: 0 residues in 0 chains, 5115 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 5126 seeds are put forward Round 1: 359 peptides, 59 chains. Longest chain 17 peptides. Score 0.446 Round 2: 390 peptides, 50 chains. Longest chain 24 peptides. Score 0.574 Round 3: 415 peptides, 60 chains. Longest chain 20 peptides. Score 0.541 Round 4: 417 peptides, 56 chains. Longest chain 23 peptides. Score 0.574 Round 5: 412 peptides, 57 chains. Longest chain 24 peptides. Score 0.559 Taking the results from Round 4 Chains 56, Residues 361, Estimated correctness of the model 33.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12997 reflections ( 99.27 % complete ) and 10935 restraints for refining 4974 atoms. 9547 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2387 (Rfree = 0.000) for 4974 atoms. Found 36 (44 requested) and removed 29 (22 requested) atoms. Cycle 12: After refmac, R = 0.2190 (Rfree = 0.000) for 4966 atoms. Found 12 (44 requested) and removed 23 (22 requested) atoms. Cycle 13: After refmac, R = 0.2101 (Rfree = 0.000) for 4950 atoms. Found 7 (44 requested) and removed 22 (22 requested) atoms. Cycle 14: After refmac, R = 0.2059 (Rfree = 0.000) for 4930 atoms. Found 9 (44 requested) and removed 22 (22 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2027 (Rfree = 0.000) for 4914 atoms. Found 8 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.07 2.99 Search for helices and strands: 0 residues in 0 chains, 5123 seeds are put forward NCS extension: 23 residues added (5 deleted due to clashes), 5146 seeds are put forward Round 1: 355 peptides, 65 chains. Longest chain 18 peptides. Score 0.386 Round 2: 381 peptides, 55 chains. Longest chain 24 peptides. Score 0.520 Round 3: 373 peptides, 59 chains. Longest chain 17 peptides. Score 0.473 Round 4: 382 peptides, 55 chains. Longest chain 17 peptides. Score 0.522 Round 5: 382 peptides, 59 chains. Longest chain 21 peptides. Score 0.490 Taking the results from Round 4 Chains 57, Residues 327, Estimated correctness of the model 18.3 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 12997 reflections ( 99.27 % complete ) and 10988 restraints for refining 4974 atoms. 9642 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2464 (Rfree = 0.000) for 4974 atoms. Found 36 (44 requested) and removed 35 (22 requested) atoms. Cycle 17: After refmac, R = 0.2298 (Rfree = 0.000) for 4959 atoms. Found 14 (44 requested) and removed 23 (22 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2278 (Rfree = 0.000) for 4945 atoms. Found 16 (44 requested) and removed 23 (22 requested) atoms. Cycle 19: After refmac, R = 0.2262 (Rfree = 0.000) for 4932 atoms. Found 20 (44 requested) and removed 22 (22 requested) atoms. Cycle 20: After refmac, R = 0.2196 (Rfree = 0.000) for 4921 atoms. Found 13 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.07 2.99 Search for helices and strands: 0 residues in 0 chains, 5147 seeds are put forward NCS extension: 0 residues added, 5147 seeds are put forward Round 1: 310 peptides, 55 chains. Longest chain 17 peptides. Score 0.381 Round 2: 354 peptides, 54 chains. Longest chain 17 peptides. Score 0.478 Round 3: 362 peptides, 56 chains. Longest chain 18 peptides. Score 0.477 Round 4: 369 peptides, 57 chains. Longest chain 18 peptides. Score 0.482 Round 5: 373 peptides, 56 chains. Longest chain 15 peptides. Score 0.498 Taking the results from Round 5 Chains 57, Residues 317, Estimated correctness of the model 10.7 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 12997 reflections ( 99.27 % complete ) and 11366 restraints for refining 4974 atoms. 10126 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2373 (Rfree = 0.000) for 4974 atoms. Found 44 (44 requested) and removed 34 (22 requested) atoms. Cycle 22: After refmac, R = 0.2168 (Rfree = 0.000) for 4969 atoms. Found 22 (44 requested) and removed 23 (22 requested) atoms. Cycle 23: After refmac, R = 0.2112 (Rfree = 0.000) for 4962 atoms. Found 6 (44 requested) and removed 22 (22 requested) atoms. Cycle 24: After refmac, R = 0.2068 (Rfree = 0.000) for 4944 atoms. Found 8 (44 requested) and removed 22 (22 requested) atoms. Cycle 25: After refmac, R = 0.2027 (Rfree = 0.000) for 4921 atoms. Found 15 (44 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.08 3.00 Search for helices and strands: 0 residues in 0 chains, 5144 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 5157 seeds are put forward Round 1: 354 peptides, 62 chains. Longest chain 15 peptides. Score 0.410 Round 2: 387 peptides, 57 chains. Longest chain 17 peptides. Score 0.515 Round 3: 393 peptides, 57 chains. Longest chain 16 peptides. Score 0.526 Round 4: 385 peptides, 57 chains. Longest chain 19 peptides. Score 0.512 Round 5: 389 peptides, 54 chains. Longest chain 26 peptides. Score 0.542 Taking the results from Round 5 Chains 55, Residues 335, Estimated correctness of the model 24.5 % 2 chains (35 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 12997 reflections ( 99.27 % complete ) and 10840 restraints for refining 4973 atoms. 9421 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2380 (Rfree = 0.000) for 4973 atoms. Found 44 (44 requested) and removed 28 (22 requested) atoms. Cycle 27: After refmac, R = 0.2166 (Rfree = 0.000) for 4973 atoms. Found 21 (44 requested) and removed 25 (22 requested) atoms. Cycle 28: After refmac, R = 0.2053 (Rfree = 0.000) for 4956 atoms. Found 13 (44 requested) and removed 22 (22 requested) atoms. Cycle 29: After refmac, R = 0.1992 (Rfree = 0.000) for 4941 atoms. Found 12 (44 requested) and removed 22 (22 requested) atoms. Cycle 30: After refmac, R = 0.1921 (Rfree = 0.000) for 4930 atoms. Found 7 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.11 3.03 Search for helices and strands: 0 residues in 0 chains, 5155 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 5173 seeds are put forward Round 1: 329 peptides, 58 chains. Longest chain 17 peptides. Score 0.394 Round 2: 355 peptides, 57 chains. Longest chain 13 peptides. Score 0.455 Round 3: 374 peptides, 57 chains. Longest chain 22 peptides. Score 0.491 Round 4: 382 peptides, 59 chains. Longest chain 17 peptides. Score 0.490 Round 5: 388 peptides, 54 chains. Longest chain 18 peptides. Score 0.540 Taking the results from Round 5 Chains 54, Residues 334, Estimated correctness of the model 23.9 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 12997 reflections ( 99.27 % complete ) and 10906 restraints for refining 4973 atoms. 9595 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2274 (Rfree = 0.000) for 4973 atoms. Found 44 (44 requested) and removed 26 (22 requested) atoms. Cycle 32: After refmac, R = 0.2055 (Rfree = 0.000) for 4976 atoms. Found 13 (44 requested) and removed 27 (22 requested) atoms. Cycle 33: After refmac, R = 0.1991 (Rfree = 0.000) for 4955 atoms. Found 12 (44 requested) and removed 22 (22 requested) atoms. Cycle 34: After refmac, R = 0.1966 (Rfree = 0.000) for 4944 atoms. Found 7 (44 requested) and removed 22 (22 requested) atoms. Cycle 35: After refmac, R = 0.1951 (Rfree = 0.000) for 4928 atoms. Found 9 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.11 3.03 Search for helices and strands: 0 residues in 0 chains, 5166 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 5184 seeds are put forward Round 1: 331 peptides, 65 chains. Longest chain 14 peptides. Score 0.334 Round 2: 366 peptides, 65 chains. Longest chain 16 peptides. Score 0.408 Round 3: 382 peptides, 64 chains. Longest chain 16 peptides. Score 0.449 Round 4: 360 peptides, 56 chains. Longest chain 14 peptides. Score 0.473 Round 5: 354 peptides, 53 chains. Longest chain 14 peptides. Score 0.487 Taking the results from Round 5 Chains 53, Residues 301, Estimated correctness of the model 7.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12997 reflections ( 99.27 % complete ) and 11337 restraints for refining 4974 atoms. 10186 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2280 (Rfree = 0.000) for 4974 atoms. Found 44 (44 requested) and removed 26 (22 requested) atoms. Cycle 37: After refmac, R = 0.2146 (Rfree = 0.000) for 4983 atoms. Found 17 (44 requested) and removed 24 (22 requested) atoms. Cycle 38: After refmac, R = 0.2088 (Rfree = 0.000) for 4967 atoms. Found 16 (44 requested) and removed 23 (22 requested) atoms. Cycle 39: After refmac, R = 0.2050 (Rfree = 0.000) for 4957 atoms. Found 13 (44 requested) and removed 22 (22 requested) atoms. Cycle 40: After refmac, R = 0.2014 (Rfree = 0.000) for 4943 atoms. Found 11 (44 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.09 3.01 Search for helices and strands: 0 residues in 0 chains, 5167 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 5185 seeds are put forward Round 1: 279 peptides, 54 chains. Longest chain 13 peptides. Score 0.321 Round 2: 329 peptides, 48 chains. Longest chain 16 peptides. Score 0.481 Round 3: 325 peptides, 50 chains. Longest chain 14 peptides. Score 0.456 Round 4: 328 peptides, 49 chains. Longest chain 16 peptides. Score 0.471 Round 5: 342 peptides, 55 chains. Longest chain 16 peptides. Score 0.447 Taking the results from Round 2 Chains 48, Residues 281, Estimated correctness of the model 5.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12997 reflections ( 99.27 % complete ) and 11369 restraints for refining 4973 atoms. 10293 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2128 (Rfree = 0.000) for 4973 atoms. Found 37 (44 requested) and removed 23 (22 requested) atoms. Cycle 42: After refmac, R = 0.1996 (Rfree = 0.000) for 4976 atoms. Found 18 (44 requested) and removed 22 (22 requested) atoms. Cycle 43: After refmac, R = 0.1939 (Rfree = 0.000) for 4969 atoms. Found 15 (44 requested) and removed 22 (22 requested) atoms. Cycle 44: After refmac, R = 0.1908 (Rfree = 0.000) for 4958 atoms. Found 12 (44 requested) and removed 22 (22 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1873 (Rfree = 0.000) for 4944 atoms. Found 9 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.09 3.01 Search for helices and strands: 0 residues in 0 chains, 5127 seeds are put forward NCS extension: 10 residues added (3 deleted due to clashes), 5137 seeds are put forward Round 1: 285 peptides, 53 chains. Longest chain 11 peptides. Score 0.345 Round 2: 327 peptides, 54 chains. Longest chain 11 peptides. Score 0.425 Round 3: 326 peptides, 52 chains. Longest chain 12 peptides. Score 0.441 Round 4: 349 peptides, 54 chains. Longest chain 23 peptides. Score 0.469 Round 5: 335 peptides, 52 chains. Longest chain 16 peptides. Score 0.459 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 54, Residues 295, Estimated correctness of the model 1.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2iiu-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12997 reflections ( 99.27 % complete ) and 11467 restraints for refining 4974 atoms. 10341 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2150 (Rfree = 0.000) for 4974 atoms. Found 0 (44 requested) and removed 19 (22 requested) atoms. Cycle 47: After refmac, R = 0.2088 (Rfree = 0.000) for 4950 atoms. Found 0 (44 requested) and removed 6 (22 requested) atoms. Cycle 48: After refmac, R = 0.2039 (Rfree = 0.000) for 4940 atoms. Found 0 (44 requested) and removed 3 (22 requested) atoms. Cycle 49: After refmac, R = 0.2010 (Rfree = 0.000) for 4936 atoms. TimeTaking 82.02