Sun 23 Dec 22:23:10 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-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2iiu-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2iiu-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2iiu-4.0-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-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2iiu-4.0-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 22:23:20 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-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2iiu-4.0-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 487 and 0 Target number of residues in the AU: 487 Target solvent content: 0.6546 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-4.0-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-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 5448 target number of atoms Had to go as low as 0.80 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 4.000 Wilson plot Bfac: 80.80 6724 reflections ( 98.74 % complete ) and 0 restraints for refining 6020 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3755 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3031 (Rfree = 0.000) for 6020 atoms. Found 23 (28 requested) and removed 53 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.75 3.65 Search for helices and strands: 0 residues in 0 chains, 6100 seeds are put forward NCS extension: 0 residues added, 6100 seeds are put forward Round 1: 138 peptides, 30 chains. Longest chain 9 peptides. Score 0.222 Round 2: 196 peptides, 38 chains. Longest chain 11 peptides. Score 0.286 Round 3: 207 peptides, 37 chains. Longest chain 12 peptides. Score 0.324 Round 4: 202 peptides, 35 chains. Longest chain 17 peptides. Score 0.333 Round 5: 205 peptides, 36 chains. Longest chain 19 peptides. Score 0.330 Taking the results from Round 4 Chains 35, Residues 167, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6724 reflections ( 98.74 % complete ) and 12374 restraints for refining 4920 atoms. 11741 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2894 (Rfree = 0.000) for 4920 atoms. Found 16 (23 requested) and removed 16 (11 requested) atoms. Cycle 2: After refmac, R = 0.2744 (Rfree = 0.000) for 4902 atoms. Found 9 (23 requested) and removed 12 (11 requested) atoms. Cycle 3: After refmac, R = 0.2712 (Rfree = 0.000) for 4892 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. Cycle 4: After refmac, R = 0.2781 (Rfree = 0.000) for 4879 atoms. Found 3 (23 requested) and removed 12 (11 requested) atoms. Cycle 5: After refmac, R = 0.2756 (Rfree = 0.000) for 4867 atoms. Found 4 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 4996 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 5014 seeds are put forward Round 1: 196 peptides, 36 chains. Longest chain 12 peptides. Score 0.308 Round 2: 214 peptides, 34 chains. Longest chain 16 peptides. Score 0.372 Round 3: 205 peptides, 32 chains. Longest chain 15 peptides. Score 0.372 Round 4: 211 peptides, 31 chains. Longest chain 13 peptides. Score 0.396 Round 5: 206 peptides, 33 chains. Longest chain 11 peptides. Score 0.364 Taking the results from Round 4 Chains 32, Residues 180, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 6724 reflections ( 98.74 % complete ) and 11980 restraints for refining 4846 atoms. 11235 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2674 (Rfree = 0.000) for 4846 atoms. Found 14 (23 requested) and removed 37 (11 requested) atoms. Cycle 7: After refmac, R = 0.2592 (Rfree = 0.000) for 4800 atoms. Found 4 (22 requested) and removed 16 (11 requested) atoms. Cycle 8: After refmac, R = 0.2475 (Rfree = 0.000) for 4779 atoms. Found 6 (22 requested) and removed 15 (11 requested) atoms. Cycle 9: After refmac, R = 0.2462 (Rfree = 0.000) for 4765 atoms. Found 0 (22 requested) and removed 12 (11 requested) atoms. Cycle 10: After refmac, R = 0.2505 (Rfree = 0.000) for 4748 atoms. Found 8 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.69 3.59 Search for helices and strands: 0 residues in 0 chains, 4905 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 4920 seeds are put forward Round 1: 211 peptides, 40 chains. Longest chain 11 peptides. Score 0.302 Round 2: 244 peptides, 40 chains. Longest chain 13 peptides. Score 0.379 Round 3: 219 peptides, 37 chains. Longest chain 13 peptides. Score 0.352 Round 4: 242 peptides, 37 chains. Longest chain 17 peptides. Score 0.404 Round 5: 233 peptides, 35 chains. Longest chain 14 peptides. Score 0.404 Taking the results from Round 5 Chains 35, Residues 198, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6724 reflections ( 98.74 % complete ) and 12065 restraints for refining 4920 atoms. 11280 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2671 (Rfree = 0.000) for 4920 atoms. Found 13 (23 requested) and removed 22 (11 requested) atoms. Cycle 12: After refmac, R = 0.2514 (Rfree = 0.000) for 4892 atoms. Found 6 (23 requested) and removed 20 (11 requested) atoms. Cycle 13: After refmac, R = 0.2445 (Rfree = 0.000) for 4869 atoms. Found 5 (23 requested) and removed 12 (11 requested) atoms. Cycle 14: After refmac, R = 0.2428 (Rfree = 0.000) for 4858 atoms. Found 3 (23 requested) and removed 14 (11 requested) atoms. Cycle 15: After refmac, R = 0.2373 (Rfree = 0.000) for 4842 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.70 3.60 Search for helices and strands: 0 residues in 0 chains, 5004 seeds are put forward NCS extension: 4 residues added (0 deleted due to clashes), 5008 seeds are put forward Round 1: 231 peptides, 48 chains. Longest chain 7 peptides. Score 0.268 Round 2: 246 peptides, 44 chains. Longest chain 12 peptides. Score 0.344 Round 3: 243 peptides, 44 chains. Longest chain 12 peptides. Score 0.337 Round 4: 257 peptides, 45 chains. Longest chain 12 peptides. Score 0.359 Round 5: 267 peptides, 46 chains. Longest chain 12 peptides. Score 0.372 Taking the results from Round 5 Chains 46, Residues 221, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6724 reflections ( 98.74 % complete ) and 12015 restraints for refining 4920 atoms. 11164 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2761 (Rfree = 0.000) for 4920 atoms. Found 14 (23 requested) and removed 21 (11 requested) atoms. Cycle 17: After refmac, R = 0.2603 (Rfree = 0.000) for 4904 atoms. Found 3 (23 requested) and removed 13 (11 requested) atoms. Cycle 18: After refmac, R = 0.2497 (Rfree = 0.000) for 4885 atoms. Found 2 (23 requested) and removed 13 (11 requested) atoms. Cycle 19: After refmac, R = 0.2493 (Rfree = 0.000) for 4864 atoms. Found 7 (23 requested) and removed 13 (11 requested) atoms. Cycle 20: After refmac, R = 0.2367 (Rfree = 0.000) for 4851 atoms. Found 2 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.70 3.60 Search for helices and strands: 0 residues in 0 chains, 5018 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 5030 seeds are put forward Round 1: 222 peptides, 44 chains. Longest chain 8 peptides. Score 0.287 Round 2: 237 peptides, 44 chains. Longest chain 11 peptides. Score 0.323 Round 3: 236 peptides, 43 chains. Longest chain 11 peptides. Score 0.331 Round 4: 243 peptides, 43 chains. Longest chain 11 peptides. Score 0.347 Round 5: 265 peptides, 47 chains. Longest chain 15 peptides. Score 0.357 Taking the results from Round 5 Chains 47, Residues 218, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6724 reflections ( 98.74 % complete ) and 11904 restraints for refining 4919 atoms. 11079 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2642 (Rfree = 0.000) for 4919 atoms. Found 21 (23 requested) and removed 17 (11 requested) atoms. Cycle 22: After refmac, R = 0.2549 (Rfree = 0.000) for 4910 atoms. Found 3 (23 requested) and removed 14 (11 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2545 (Rfree = 0.000) for 4898 atoms. Found 3 (23 requested) and removed 14 (11 requested) atoms. Cycle 24: After refmac, R = 0.2466 (Rfree = 0.000) for 4883 atoms. Found 2 (23 requested) and removed 12 (11 requested) atoms. Cycle 25: After refmac, R = 0.2451 (Rfree = 0.000) for 4872 atoms. Found 1 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 5028 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 5047 seeds are put forward Round 1: 215 peptides, 44 chains. Longest chain 9 peptides. Score 0.270 Round 2: 238 peptides, 42 chains. Longest chain 13 peptides. Score 0.345 Round 3: 250 peptides, 42 chains. Longest chain 13 peptides. Score 0.373 Round 4: 252 peptides, 43 chains. Longest chain 13 peptides. Score 0.367 Round 5: 245 peptides, 44 chains. Longest chain 13 peptides. Score 0.342 Taking the results from Round 3 Chains 42, Residues 208, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6724 reflections ( 98.74 % complete ) and 11892 restraints for refining 4919 atoms. 11102 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2784 (Rfree = 0.000) for 4919 atoms. Found 20 (23 requested) and removed 14 (11 requested) atoms. Cycle 27: After refmac, R = 0.2607 (Rfree = 0.000) for 4920 atoms. Found 2 (23 requested) and removed 14 (11 requested) atoms. Cycle 28: After refmac, R = 0.2543 (Rfree = 0.000) for 4908 atoms. Found 2 (23 requested) and removed 12 (11 requested) atoms. Cycle 29: After refmac, R = 0.2490 (Rfree = 0.000) for 4897 atoms. Found 5 (23 requested) and removed 11 (11 requested) atoms. Cycle 30: After refmac, R = 0.2459 (Rfree = 0.000) for 4888 atoms. Found 1 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.66 3.56 Search for helices and strands: 0 residues in 0 chains, 5047 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 5058 seeds are put forward Round 1: 203 peptides, 41 chains. Longest chain 9 peptides. Score 0.272 Round 2: 230 peptides, 42 chains. Longest chain 10 peptides. Score 0.327 Round 3: 230 peptides, 39 chains. Longest chain 12 peptides. Score 0.357 Round 4: 236 peptides, 41 chains. Longest chain 11 peptides. Score 0.351 Round 5: 234 peptides, 38 chains. Longest chain 13 peptides. Score 0.376 Taking the results from Round 5 Chains 38, Residues 196, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6724 reflections ( 98.74 % complete ) and 12012 restraints for refining 4915 atoms. 11266 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2605 (Rfree = 0.000) for 4915 atoms. Found 18 (23 requested) and removed 15 (11 requested) atoms. Cycle 32: After refmac, R = 0.2465 (Rfree = 0.000) for 4912 atoms. Found 2 (23 requested) and removed 13 (11 requested) atoms. Cycle 33: After refmac, R = 0.2414 (Rfree = 0.000) for 4899 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 34: After refmac, R = 0.2452 (Rfree = 0.000) for 4887 atoms. Found 3 (23 requested) and removed 13 (11 requested) atoms. Cycle 35: After refmac, R = 0.2374 (Rfree = 0.000) for 4875 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.68 3.58 Search for helices and strands: 0 residues in 0 chains, 5022 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 5036 seeds are put forward Round 1: 201 peptides, 41 chains. Longest chain 11 peptides. Score 0.267 Round 2: 218 peptides, 37 chains. Longest chain 13 peptides. Score 0.350 Round 3: 214 peptides, 39 chains. Longest chain 12 peptides. Score 0.320 Round 4: 224 peptides, 39 chains. Longest chain 13 peptides. Score 0.343 Round 5: 225 peptides, 40 chains. Longest chain 10 peptides. Score 0.336 Taking the results from Round 2 Chains 37, Residues 181, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6724 reflections ( 98.74 % complete ) and 12126 restraints for refining 4918 atoms. 11439 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2516 (Rfree = 0.000) for 4918 atoms. Found 14 (23 requested) and removed 12 (11 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2453 (Rfree = 0.000) for 4918 atoms. Found 6 (23 requested) and removed 11 (11 requested) atoms. Cycle 38: After refmac, R = 0.2407 (Rfree = 0.000) for 4911 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. Cycle 39: After refmac, R = 0.2342 (Rfree = 0.000) for 4901 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 40: After refmac, R = 0.2331 (Rfree = 0.000) for 4889 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.73 3.63 Search for helices and strands: 0 residues in 0 chains, 5057 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 5074 seeds are put forward Round 1: 173 peptides, 35 chains. Longest chain 11 peptides. Score 0.260 Round 2: 190 peptides, 35 chains. Longest chain 14 peptides. Score 0.304 Round 3: 188 peptides, 33 chains. Longest chain 15 peptides. Score 0.321 Round 4: 206 peptides, 34 chains. Longest chain 14 peptides. Score 0.353 Round 5: 179 peptides, 31 chains. Longest chain 15 peptides. Score 0.320 Taking the results from Round 4 Chains 34, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6724 reflections ( 98.74 % complete ) and 12235 restraints for refining 4919 atoms. 11581 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2652 (Rfree = 0.000) for 4919 atoms. Found 20 (23 requested) and removed 12 (11 requested) atoms. Cycle 42: After refmac, R = 0.2523 (Rfree = 0.000) for 4926 atoms. Found 4 (23 requested) and removed 11 (11 requested) atoms. Cycle 43: After refmac, R = 0.2488 (Rfree = 0.000) for 4919 atoms. Found 1 (23 requested) and removed 11 (11 requested) atoms. Cycle 44: After refmac, R = 0.2414 (Rfree = 0.000) for 4908 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 45: After refmac, R = 0.2404 (Rfree = 0.000) for 4894 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.74 3.64 Search for helices and strands: 0 residues in 0 chains, 5027 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 5044 seeds are put forward Round 1: 172 peptides, 33 chains. Longest chain 11 peptides. Score 0.280 Round 2: 164 peptides, 31 chains. Longest chain 11 peptides. Score 0.282 Round 3: 165 peptides, 29 chains. Longest chain 17 peptides. Score 0.308 Round 4: 160 peptides, 28 chains. Longest chain 17 peptides. Score 0.306 Round 5: 172 peptides, 28 chains. Longest chain 11 peptides. Score 0.336 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 144, 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 2iiu-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6724 reflections ( 98.74 % complete ) and 12515 restraints for refining 4919 atoms. 11967 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2539 (Rfree = 0.000) for 4919 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2494 (Rfree = 0.000) for 4907 atoms. Found 0 (23 requested) and removed 8 (11 requested) atoms. Cycle 48: After refmac, R = 0.2452 (Rfree = 0.000) for 4898 atoms. Found 0 (23 requested) and removed 2 (11 requested) atoms. Cycle 49: After refmac, R = 0.2425 (Rfree = 0.000) for 4896 atoms. Found 0 (23 requested) and removed 2 (11 requested) atoms. Writing output files ... TimeTaking 72.55