Sun 23 Dec 23:44:11 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 1z82-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1z82-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1z82-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z82-3.8-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/1z82-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z82-3.8-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 23:44:15 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/1z82-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z82-3.8-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 388 and 0 Target number of residues in the AU: 388 Target solvent content: 0.6552 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: 1z82-3.8-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: 4 Cell parameters: 65.170 67.461 75.617 90.000 113.643 90.000 Input sequence file: 1z82-3.8-parrot-mrncs.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 3.801 Wilson plot Bfac: 81.37 6033 reflections ( 99.55 % complete ) and 0 restraints for refining 5942 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3126 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3041 (Rfree = 0.000) for 5942 atoms. Found 32 (32 requested) and removed 35 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.64 4.17 Search for helices and strands: 0 residues in 0 chains, 6071 seeds are put forward NCS extension: 0 residues added, 6071 seeds are put forward Round 1: 192 peptides, 43 chains. Longest chain 8 peptides. Score 0.231 Round 2: 275 peptides, 52 chains. Longest chain 12 peptides. Score 0.362 Round 3: 287 peptides, 52 chains. Longest chain 16 peptides. Score 0.394 Round 4: 306 peptides, 48 chains. Longest chain 23 peptides. Score 0.484 Round 5: 297 peptides, 50 chains. Longest chain 18 peptides. Score 0.441 Taking the results from Round 4 Chains 51, Residues 258, Estimated correctness of the model 0.0 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 6033 reflections ( 99.55 % complete ) and 11304 restraints for refining 4845 atoms. 10214 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2362 (Rfree = 0.000) for 4845 atoms. Found 14 (26 requested) and removed 45 (13 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2235 (Rfree = 0.000) for 4738 atoms. Found 14 (26 requested) and removed 36 (13 requested) atoms. Cycle 3: After refmac, R = 0.2267 (Rfree = 0.000) for 4674 atoms. Found 16 (25 requested) and removed 34 (12 requested) atoms. Cycle 4: After refmac, R = 0.2289 (Rfree = 0.000) for 4633 atoms. Found 25 (25 requested) and removed 34 (12 requested) atoms. Cycle 5: After refmac, R = 0.2104 (Rfree = 0.000) for 4585 atoms. Found 12 (25 requested) and removed 23 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.61 4.13 Search for helices and strands: 0 residues in 0 chains, 4791 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 4819 seeds are put forward Round 1: 211 peptides, 46 chains. Longest chain 9 peptides. Score 0.251 Round 2: 258 peptides, 45 chains. Longest chain 16 peptides. Score 0.396 Round 3: 279 peptides, 46 chains. Longest chain 14 peptides. Score 0.439 Round 4: 287 peptides, 47 chains. Longest chain 16 peptides. Score 0.448 Round 5: 297 peptides, 46 chains. Longest chain 21 peptides. Score 0.483 Taking the results from Round 5 Chains 47, Residues 251, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 6033 reflections ( 99.55 % complete ) and 10353 restraints for refining 4526 atoms. 9314 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2000 (Rfree = 0.000) for 4526 atoms. Found 22 (24 requested) and removed 42 (12 requested) atoms. Cycle 7: After refmac, R = 0.1809 (Rfree = 0.000) for 4471 atoms. Found 13 (24 requested) and removed 21 (12 requested) atoms. Cycle 8: After refmac, R = 0.1720 (Rfree = 0.000) for 4444 atoms. Found 12 (24 requested) and removed 19 (12 requested) atoms. Cycle 9: After refmac, R = 0.1748 (Rfree = 0.000) for 4428 atoms. Found 19 (24 requested) and removed 25 (12 requested) atoms. Cycle 10: After refmac, R = 0.1393 (Rfree = 0.000) for 4408 atoms. Found 4 (24 requested) and removed 20 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.64 4.17 Search for helices and strands: 0 residues in 0 chains, 4582 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4602 seeds are put forward Round 1: 274 peptides, 56 chains. Longest chain 10 peptides. Score 0.314 Round 2: 312 peptides, 50 chains. Longest chain 17 peptides. Score 0.477 Round 3: 310 peptides, 47 chains. Longest chain 19 peptides. Score 0.503 Round 4: 325 peptides, 51 chains. Longest chain 17 peptides. Score 0.498 Round 5: 318 peptides, 51 chains. Longest chain 15 peptides. Score 0.481 Taking the results from Round 3 Chains 47, Residues 263, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6033 reflections ( 99.55 % complete ) and 10212 restraints for refining 4432 atoms. 9188 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1907 (Rfree = 0.000) for 4432 atoms. Found 21 (24 requested) and removed 32 (12 requested) atoms. Cycle 12: After refmac, R = 0.1868 (Rfree = 0.000) for 4393 atoms. Found 24 (24 requested) and removed 22 (12 requested) atoms. Cycle 13: After refmac, R = 0.1448 (Rfree = 0.000) for 4379 atoms. Found 8 (24 requested) and removed 13 (12 requested) atoms. Cycle 14: After refmac, R = 0.1428 (Rfree = 0.000) for 4368 atoms. Found 2 (24 requested) and removed 13 (12 requested) atoms. Cycle 15: After refmac, R = 0.1379 (Rfree = 0.000) for 4352 atoms. Found 3 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.62 4.14 Search for helices and strands: 0 residues in 0 chains, 4555 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4572 seeds are put forward Round 1: 286 peptides, 60 chains. Longest chain 11 peptides. Score 0.301 Round 2: 311 peptides, 52 chains. Longest chain 18 peptides. Score 0.454 Round 3: 333 peptides, 53 chains. Longest chain 22 peptides. Score 0.496 Round 4: 317 peptides, 49 chains. Longest chain 22 peptides. Score 0.499 Round 5: 321 peptides, 53 chains. Longest chain 14 peptides. Score 0.468 Taking the results from Round 4 Chains 49, Residues 268, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6033 reflections ( 99.55 % complete ) and 10542 restraints for refining 4569 atoms. 9519 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1873 (Rfree = 0.000) for 4569 atoms. Found 23 (25 requested) and removed 36 (12 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.1714 (Rfree = 0.000) for 4529 atoms. Found 17 (25 requested) and removed 20 (12 requested) atoms. Cycle 18: After refmac, R = 0.1676 (Rfree = 0.000) for 4510 atoms. Found 11 (24 requested) and removed 22 (12 requested) atoms. Cycle 19: After refmac, R = 0.1452 (Rfree = 0.000) for 4495 atoms. Found 7 (24 requested) and removed 13 (12 requested) atoms. Cycle 20: After refmac, R = 0.1461 (Rfree = 0.000) for 4480 atoms. Found 5 (24 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.59 4.11 Search for helices and strands: 0 residues in 0 chains, 4646 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4666 seeds are put forward Round 1: 249 peptides, 55 chains. Longest chain 7 peptides. Score 0.254 Round 2: 277 peptides, 55 chains. Longest chain 10 peptides. Score 0.333 Round 3: 294 peptides, 52 chains. Longest chain 11 peptides. Score 0.412 Round 4: 300 peptides, 53 chains. Longest chain 11 peptides. Score 0.416 Round 5: 310 peptides, 54 chains. Longest chain 13 peptides. Score 0.431 Taking the results from Round 5 Chains 54, Residues 256, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 6033 reflections ( 99.55 % complete ) and 10866 restraints for refining 4712 atoms. 9882 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1916 (Rfree = 0.000) for 4712 atoms. Found 23 (25 requested) and removed 38 (12 requested) atoms. Cycle 22: After refmac, R = 0.1877 (Rfree = 0.000) for 4675 atoms. Found 18 (25 requested) and removed 24 (12 requested) atoms. Cycle 23: After refmac, R = 0.1762 (Rfree = 0.000) for 4660 atoms. Found 13 (25 requested) and removed 17 (12 requested) atoms. Cycle 24: After refmac, R = 0.1686 (Rfree = 0.000) for 4648 atoms. Found 13 (25 requested) and removed 17 (12 requested) atoms. Cycle 25: After refmac, R = 0.1618 (Rfree = 0.000) for 4637 atoms. Found 6 (25 requested) and removed 22 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.64 4.17 Search for helices and strands: 0 residues in 0 chains, 4810 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4825 seeds are put forward Round 1: 248 peptides, 55 chains. Longest chain 8 peptides. Score 0.251 Round 2: 264 peptides, 49 chains. Longest chain 12 peptides. Score 0.367 Round 3: 262 peptides, 46 chains. Longest chain 16 peptides. Score 0.396 Round 4: 265 peptides, 47 chains. Longest chain 18 peptides. Score 0.392 Round 5: 277 peptides, 49 chains. Longest chain 14 peptides. Score 0.401 Taking the results from Round 5 Chains 49, Residues 228, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6033 reflections ( 99.55 % complete ) and 11446 restraints for refining 4807 atoms. 10562 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1934 (Rfree = 0.000) for 4807 atoms. Found 21 (26 requested) and removed 61 (13 requested) atoms. Cycle 27: After refmac, R = 0.1891 (Rfree = 0.000) for 4742 atoms. Found 26 (26 requested) and removed 30 (13 requested) atoms. Cycle 28: After refmac, R = 0.2128 (Rfree = 0.000) for 4728 atoms. Found 26 (26 requested) and removed 36 (13 requested) atoms. Cycle 29: After refmac, R = 0.1903 (Rfree = 0.000) for 4697 atoms. Found 25 (25 requested) and removed 20 (12 requested) atoms. Cycle 30: After refmac, R = 0.1947 (Rfree = 0.000) for 4693 atoms. Found 25 (25 requested) and removed 31 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.67 4.20 Search for helices and strands: 0 residues in 0 chains, 4902 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 4913 seeds are put forward Round 1: 221 peptides, 48 chains. Longest chain 10 peptides. Score 0.257 Round 2: 248 peptides, 49 chains. Longest chain 13 peptides. Score 0.323 Round 3: 253 peptides, 45 chains. Longest chain 12 peptides. Score 0.383 Round 4: 256 peptides, 45 chains. Longest chain 10 peptides. Score 0.391 Round 5: 247 peptides, 44 chains. Longest chain 10 peptides. Score 0.378 Taking the results from Round 4 Chains 45, Residues 211, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6033 reflections ( 99.55 % complete ) and 11422 restraints for refining 4801 atoms. 10623 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2098 (Rfree = 0.000) for 4801 atoms. Found 26 (26 requested) and removed 37 (13 requested) atoms. Cycle 32: After refmac, R = 0.1904 (Rfree = 0.000) for 4758 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. Cycle 33: After refmac, R = 0.2050 (Rfree = 0.000) for 4752 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. Cycle 34: After refmac, R = 0.1402 (Rfree = 0.000) for 4733 atoms. Found 7 (26 requested) and removed 19 (13 requested) atoms. Cycle 35: After refmac, R = 0.1319 (Rfree = 0.000) for 4713 atoms. Found 10 (25 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.66 4.19 Search for helices and strands: 0 residues in 0 chains, 4877 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 4883 seeds are put forward Round 1: 196 peptides, 41 chains. Longest chain 8 peptides. Score 0.269 Round 2: 222 peptides, 41 chains. Longest chain 10 peptides. Score 0.345 Round 3: 230 peptides, 44 chains. Longest chain 9 peptides. Score 0.331 Round 4: 231 peptides, 40 chains. Longest chain 11 peptides. Score 0.382 Round 5: 227 peptides, 42 chains. Longest chain 11 peptides. Score 0.347 Taking the results from Round 4 Chains 40, Residues 191, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6033 reflections ( 99.55 % complete ) and 11301 restraints for refining 4735 atoms. 10566 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1673 (Rfree = 0.000) for 4735 atoms. Found 26 (26 requested) and removed 33 (13 requested) atoms. Cycle 37: After refmac, R = 0.1785 (Rfree = 0.000) for 4708 atoms. Found 25 (25 requested) and removed 22 (12 requested) atoms. Cycle 38: After refmac, R = 0.1942 (Rfree = 0.000) for 4697 atoms. Found 25 (25 requested) and removed 26 (12 requested) atoms. Cycle 39: After refmac, R = 0.1849 (Rfree = 0.000) for 4681 atoms. Found 25 (25 requested) and removed 22 (12 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1816 (Rfree = 0.000) for 4670 atoms. Found 25 (25 requested) and removed 25 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.62 4.14 Search for helices and strands: 0 residues in 0 chains, 4850 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 4862 seeds are put forward Round 1: 163 peptides, 36 chains. Longest chain 9 peptides. Score 0.231 Round 2: 215 peptides, 42 chains. Longest chain 10 peptides. Score 0.313 Round 3: 229 peptides, 40 chains. Longest chain 13 peptides. Score 0.376 Round 4: 225 peptides, 43 chains. Longest chain 9 peptides. Score 0.329 Round 5: 228 peptides, 42 chains. Longest chain 13 peptides. Score 0.350 Taking the results from Round 3 Chains 41, Residues 189, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6033 reflections ( 99.55 % complete ) and 10646 restraints for refining 4579 atoms. 9903 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1654 (Rfree = 0.000) for 4579 atoms. Found 22 (25 requested) and removed 23 (12 requested) atoms. Cycle 42: After refmac, R = 0.1729 (Rfree = 0.000) for 4553 atoms. Found 25 (25 requested) and removed 26 (12 requested) atoms. Cycle 43: After refmac, R = 0.1995 (Rfree = 0.000) for 4544 atoms. Found 25 (25 requested) and removed 21 (12 requested) atoms. Cycle 44: After refmac, R = 0.1629 (Rfree = 0.000) for 4530 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. Cycle 45: After refmac, R = 0.1159 (Rfree = 0.000) for 4529 atoms. Found 6 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.63 4.15 Search for helices and strands: 0 residues in 0 chains, 4697 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 4709 seeds are put forward Round 1: 148 peptides, 35 chains. Longest chain 6 peptides. Score 0.195 Round 2: 180 peptides, 39 chains. Longest chain 8 peptides. Score 0.245 Round 3: 198 peptides, 41 chains. Longest chain 10 peptides. Score 0.275 Round 4: 195 peptides, 41 chains. Longest chain 7 peptides. Score 0.266 Round 5: 197 peptides, 37 chains. Longest chain 11 peptides. Score 0.322 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 37, Residues 160, 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 1z82-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6033 reflections ( 99.55 % complete ) and 10543 restraints for refining 4449 atoms. 9940 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1541 (Rfree = 0.000) for 4449 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.1737 (Rfree = 0.000) for 4416 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.1245 (Rfree = 0.000) for 4397 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.1191 (Rfree = 0.000) for 4381 atoms. TimeTaking 47.53