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 1z82-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1z82-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1z82-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z82-3.6-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/1z82-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z82-3.6-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 22:23:18 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/1z82-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z82-3.6-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 400 and 0 Target number of residues in the AU: 400 Target solvent content: 0.6446 Checking the provided sequence file Detected sequence length: 335 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 670 Adjusted target solvent content: 0.40 Input MTZ file: 1z82-3.6-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: 4 Cell parameters: 65.170 67.461 75.617 90.000 113.643 90.000 Input sequence file: 1z82-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 5360 target number of atoms Had to go as low as 0.65 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: 29.850 3.600 Wilson plot Bfac: 74.45 7073 reflections ( 99.58 % complete ) and 0 restraints for refining 5966 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3124 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2802 (Rfree = 0.000) for 5966 atoms. Found 38 (38 requested) and removed 43 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.47 3.97 Search for helices and strands: 0 residues in 0 chains, 6096 seeds are put forward NCS extension: 0 residues added, 6096 seeds are put forward Round 1: 219 peptides, 46 chains. Longest chain 9 peptides. Score 0.275 Round 2: 280 peptides, 52 chains. Longest chain 11 peptides. Score 0.376 Round 3: 310 peptides, 54 chains. Longest chain 12 peptides. Score 0.431 Round 4: 343 peptides, 53 chains. Longest chain 13 peptides. Score 0.519 Round 5: 337 peptides, 52 chains. Longest chain 14 peptides. Score 0.515 Taking the results from Round 4 Chains 54, Residues 290, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 7073 reflections ( 99.58 % complete ) and 11375 restraints for refining 4857 atoms. 10224 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2236 (Rfree = 0.000) for 4857 atoms. Found 21 (31 requested) and removed 35 (15 requested) atoms. Cycle 2: After refmac, R = 0.2114 (Rfree = 0.000) for 4783 atoms. Found 23 (31 requested) and removed 34 (15 requested) atoms. Cycle 3: After refmac, R = 0.2004 (Rfree = 0.000) for 4745 atoms. Found 15 (30 requested) and removed 27 (15 requested) atoms. Cycle 4: After refmac, R = 0.1899 (Rfree = 0.000) for 4710 atoms. Found 17 (30 requested) and removed 22 (15 requested) atoms. Cycle 5: After refmac, R = 0.1908 (Rfree = 0.000) for 4690 atoms. Found 15 (30 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.95 Search for helices and strands: 0 residues in 0 chains, 4890 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4904 seeds are put forward Round 1: 285 peptides, 55 chains. Longest chain 9 peptides. Score 0.355 Round 2: 313 peptides, 52 chains. Longest chain 14 peptides. Score 0.459 Round 3: 330 peptides, 50 chains. Longest chain 25 peptides. Score 0.519 Round 4: 343 peptides, 52 chains. Longest chain 16 peptides. Score 0.528 Round 5: 333 peptides, 45 chains. Longest chain 22 peptides. Score 0.572 Taking the results from Round 5 Chains 47, Residues 288, Estimated correctness of the model 3.4 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 7073 reflections ( 99.58 % complete ) and 10912 restraints for refining 4735 atoms. 9741 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1911 (Rfree = 0.000) for 4735 atoms. Found 17 (30 requested) and removed 42 (15 requested) atoms. Cycle 7: After refmac, R = 0.1750 (Rfree = 0.000) for 4675 atoms. Found 6 (30 requested) and removed 20 (15 requested) atoms. Cycle 8: After refmac, R = 0.1773 (Rfree = 0.000) for 4651 atoms. Found 6 (29 requested) and removed 21 (14 requested) atoms. Cycle 9: After refmac, R = 0.1756 (Rfree = 0.000) for 4624 atoms. Found 15 (29 requested) and removed 21 (14 requested) atoms. Cycle 10: After refmac, R = 0.1675 (Rfree = 0.000) for 4606 atoms. Found 11 (29 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.44 3.94 Search for helices and strands: 0 residues in 0 chains, 4784 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 4801 seeds are put forward Round 1: 293 peptides, 55 chains. Longest chain 10 peptides. Score 0.376 Round 2: 330 peptides, 55 chains. Longest chain 16 peptides. Score 0.469 Round 3: 336 peptides, 53 chains. Longest chain 13 peptides. Score 0.503 Round 4: 341 peptides, 55 chains. Longest chain 15 peptides. Score 0.495 Round 5: 344 peptides, 54 chains. Longest chain 15 peptides. Score 0.511 Taking the results from Round 5 Chains 54, Residues 290, Estimated correctness of the model 0.0 % 4 chains (19 residues) have been docked in sequence ------------------------------------------------------ 7073 reflections ( 99.58 % complete ) and 11416 restraints for refining 4817 atoms. 10261 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2047 (Rfree = 0.000) for 4817 atoms. Found 20 (30 requested) and removed 51 (15 requested) atoms. Cycle 12: After refmac, R = 0.1814 (Rfree = 0.000) for 4756 atoms. Found 7 (30 requested) and removed 29 (15 requested) atoms. Cycle 13: After refmac, R = 0.1859 (Rfree = 0.000) for 4716 atoms. Found 8 (30 requested) and removed 31 (15 requested) atoms. Cycle 14: After refmac, R = 0.1902 (Rfree = 0.000) for 4681 atoms. Found 23 (30 requested) and removed 24 (15 requested) atoms. Cycle 15: After refmac, R = 0.1603 (Rfree = 0.000) for 4670 atoms. Found 4 (30 requested) and removed 23 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 3.94 Search for helices and strands: 0 residues in 0 chains, 4832 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 4845 seeds are put forward Round 1: 294 peptides, 57 chains. Longest chain 10 peptides. Score 0.357 Round 2: 346 peptides, 55 chains. Longest chain 19 peptides. Score 0.506 Round 3: 356 peptides, 53 chains. Longest chain 18 peptides. Score 0.547 Round 4: 364 peptides, 58 chains. Longest chain 15 peptides. Score 0.517 Round 5: 341 peptides, 51 chains. Longest chain 22 peptides. Score 0.533 Taking the results from Round 3 Chains 54, Residues 303, Estimated correctness of the model 0.0 % 5 chains (35 residues) have been docked in sequence ------------------------------------------------------ 7073 reflections ( 99.58 % complete ) and 10565 restraints for refining 4763 atoms. 9300 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1915 (Rfree = 0.000) for 4763 atoms. Found 19 (30 requested) and removed 37 (15 requested) atoms. Cycle 17: After refmac, R = 0.1895 (Rfree = 0.000) for 4711 atoms. Found 24 (30 requested) and removed 29 (15 requested) atoms. Cycle 18: After refmac, R = 0.1959 (Rfree = 0.000) for 4686 atoms. Found 30 (30 requested) and removed 21 (15 requested) atoms. Cycle 19: After refmac, R = 0.1535 (Rfree = 0.000) for 4680 atoms. Found 7 (30 requested) and removed 23 (15 requested) atoms. Cycle 20: After refmac, R = 0.1446 (Rfree = 0.000) for 4656 atoms. Found 3 (29 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 3.95 Search for helices and strands: 0 residues in 0 chains, 4843 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 4865 seeds are put forward Round 1: 238 peptides, 50 chains. Longest chain 8 peptides. Score 0.282 Round 2: 295 peptides, 44 chains. Longest chain 22 peptides. Score 0.499 Round 3: 318 peptides, 44 chains. Longest chain 17 peptides. Score 0.550 Round 4: 326 peptides, 49 chains. Longest chain 18 peptides. Score 0.520 Round 5: 327 peptides, 47 chains. Longest chain 16 peptides. Score 0.541 Taking the results from Round 3 Chains 44, Residues 274, Estimated correctness of the model 0.0 % 5 chains (25 residues) have been docked in sequence ------------------------------------------------------ 7073 reflections ( 99.58 % complete ) and 10948 restraints for refining 4729 atoms. 9838 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1952 (Rfree = 0.000) for 4729 atoms. Found 28 (30 requested) and removed 35 (15 requested) atoms. Cycle 22: After refmac, R = 0.1788 (Rfree = 0.000) for 4701 atoms. Found 17 (30 requested) and removed 34 (15 requested) atoms. Cycle 23: After refmac, R = 0.1801 (Rfree = 0.000) for 4668 atoms. Found 26 (30 requested) and removed 23 (15 requested) atoms. Cycle 24: After refmac, R = 0.1655 (Rfree = 0.000) for 4667 atoms. Found 11 (29 requested) and removed 22 (14 requested) atoms. Cycle 25: After refmac, R = 0.1764 (Rfree = 0.000) for 4650 atoms. Found 29 (29 requested) and removed 25 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.48 3.98 Search for helices and strands: 0 residues in 0 chains, 4829 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 4853 seeds are put forward Round 1: 227 peptides, 45 chains. Longest chain 11 peptides. Score 0.311 Round 2: 266 peptides, 46 chains. Longest chain 15 peptides. Score 0.406 Round 3: 286 peptides, 46 chains. Longest chain 15 peptides. Score 0.456 Round 4: 256 peptides, 38 chains. Longest chain 14 peptides. Score 0.469 Round 5: 277 peptides, 45 chains. Longest chain 15 peptides. Score 0.445 Taking the results from Round 4 Chains 38, Residues 218, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 7073 reflections ( 99.58 % complete ) and 11410 restraints for refining 4734 atoms. 10536 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1715 (Rfree = 0.000) for 4734 atoms. Found 18 (30 requested) and removed 29 (15 requested) atoms. Cycle 27: After refmac, R = 0.1750 (Rfree = 0.000) for 4709 atoms. Found 20 (30 requested) and removed 29 (15 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1738 (Rfree = 0.000) for 4697 atoms. Found 30 (30 requested) and removed 19 (15 requested) atoms. Cycle 29: After refmac, R = 0.1846 (Rfree = 0.000) for 4702 atoms. Found 30 (30 requested) and removed 22 (15 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1724 (Rfree = 0.000) for 4701 atoms. Found 27 (30 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.49 3.99 Search for helices and strands: 0 residues in 0 chains, 4916 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 4932 seeds are put forward Round 1: 224 peptides, 46 chains. Longest chain 12 peptides. Score 0.290 Round 2: 278 peptides, 51 chains. Longest chain 12 peptides. Score 0.381 Round 3: 279 peptides, 50 chains. Longest chain 12 peptides. Score 0.395 Round 4: 302 peptides, 51 chains. Longest chain 13 peptides. Score 0.443 Round 5: 287 peptides, 49 chains. Longest chain 12 peptides. Score 0.427 Taking the results from Round 4 Chains 52, Residues 251, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7073 reflections ( 99.58 % complete ) and 11428 restraints for refining 4807 atoms. 10453 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1805 (Rfree = 0.000) for 4807 atoms. Found 22 (30 requested) and removed 35 (15 requested) atoms. Cycle 32: After refmac, R = 0.1685 (Rfree = 0.000) for 4771 atoms. Found 23 (30 requested) and removed 26 (15 requested) atoms. Cycle 33: After refmac, R = 0.1768 (Rfree = 0.000) for 4753 atoms. Found 23 (30 requested) and removed 24 (15 requested) atoms. Cycle 34: After refmac, R = 0.1327 (Rfree = 0.000) for 4743 atoms. Found 7 (30 requested) and removed 17 (15 requested) atoms. Cycle 35: After refmac, R = 0.1240 (Rfree = 0.000) for 4730 atoms. Found 5 (30 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.50 4.01 Search for helices and strands: 0 residues in 0 chains, 4868 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4884 seeds are put forward Round 1: 217 peptides, 44 chains. Longest chain 11 peptides. Score 0.294 Round 2: 253 peptides, 47 chains. Longest chain 16 peptides. Score 0.360 Round 3: 252 peptides, 41 chains. Longest chain 13 peptides. Score 0.426 Round 4: 241 peptides, 41 chains. Longest chain 15 peptides. Score 0.397 Round 5: 248 peptides, 41 chains. Longest chain 13 peptides. Score 0.415 Taking the results from Round 3 Chains 41, Residues 211, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 7073 reflections ( 99.58 % complete ) and 11133 restraints for refining 4743 atoms. 10269 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1642 (Rfree = 0.000) for 4743 atoms. Found 21 (30 requested) and removed 26 (15 requested) atoms. Cycle 37: After refmac, R = 0.1743 (Rfree = 0.000) for 4724 atoms. Found 30 (30 requested) and removed 24 (15 requested) atoms. Cycle 38: After refmac, R = 0.1698 (Rfree = 0.000) for 4719 atoms. Found 30 (30 requested) and removed 23 (15 requested) atoms. Cycle 39: After refmac, R = 0.1244 (Rfree = 0.000) for 4720 atoms. Found 5 (30 requested) and removed 19 (15 requested) atoms. Cycle 40: After refmac, R = 0.1155 (Rfree = 0.000) for 4705 atoms. Found 6 (30 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.50 4.01 Search for helices and strands: 0 residues in 0 chains, 4888 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4905 seeds are put forward Round 1: 214 peptides, 44 chains. Longest chain 11 peptides. Score 0.285 Round 2: 252 peptides, 47 chains. Longest chain 13 peptides. Score 0.357 Round 3: 257 peptides, 43 chains. Longest chain 14 peptides. Score 0.416 Round 4: 231 peptides, 41 chains. Longest chain 13 peptides. Score 0.370 Round 5: 226 peptides, 38 chains. Longest chain 12 peptides. Score 0.392 Taking the results from Round 3 Chains 43, Residues 214, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 7073 reflections ( 99.58 % complete ) and 11277 restraints for refining 4798 atoms. 10393 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1681 (Rfree = 0.000) for 4798 atoms. Found 30 (30 requested) and removed 35 (15 requested) atoms. Cycle 42: After refmac, R = 0.1665 (Rfree = 0.000) for 4768 atoms. Found 25 (30 requested) and removed 26 (15 requested) atoms. Cycle 43: After refmac, R = 0.1703 (Rfree = 0.000) for 4761 atoms. Found 28 (30 requested) and removed 20 (15 requested) atoms. Cycle 44: After refmac, R = 0.1280 (Rfree = 0.000) for 4756 atoms. Found 8 (30 requested) and removed 17 (15 requested) atoms. Cycle 45: After refmac, R = 0.1226 (Rfree = 0.000) for 4742 atoms. Found 8 (30 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.50 4.01 Search for helices and strands: 0 residues in 0 chains, 4922 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 4941 seeds are put forward Round 1: 199 peptides, 44 chains. Longest chain 10 peptides. Score 0.240 Round 2: 229 peptides, 43 chains. Longest chain 13 peptides. Score 0.341 Round 3: 231 peptides, 40 chains. Longest chain 15 peptides. Score 0.382 Round 4: 230 peptides, 39 chains. Longest chain 13 peptides. Score 0.391 Round 5: 232 peptides, 39 chains. Longest chain 13 peptides. Score 0.396 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 39, Residues 193, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1z82-3_warpNtrace.pdb as input Building loops using Loopy2018 39 chains (193 residues) following loop building 2 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7073 reflections ( 99.58 % complete ) and 11521 restraints for refining 4783 atoms. 10773 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1643 (Rfree = 0.000) for 4783 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.1422 (Rfree = 0.000) for 4758 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.1369 (Rfree = 0.000) for 4740 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.1451 (Rfree = 0.000) for 4723 atoms. TimeTaking 69.1