null Sun 23 Dec 22:23:01 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 1z82-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1z82-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1z82-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z82-3.4-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/1z82-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z82-3.4-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 22:23:11 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/1z82-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z82-3.4-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 410 and 0 Target number of residues in the AU: 410 Target solvent content: 0.6357 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: 1z82-3.4-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: 1z82-3.4-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 3.400 Wilson plot Bfac: 69.58 8387 reflections ( 99.63 % complete ) and 0 restraints for refining 5979 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3009 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2920 (Rfree = 0.000) for 5979 atoms. Found 45 (45 requested) and removed 38 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 3.86 Search for helices and strands: 0 residues in 0 chains, 6107 seeds are put forward NCS extension: 0 residues added, 6107 seeds are put forward Round 1: 200 peptides, 45 chains. Longest chain 6 peptides. Score 0.230 Round 2: 280 peptides, 54 chains. Longest chain 10 peptides. Score 0.353 Round 3: 310 peptides, 52 chains. Longest chain 14 peptides. Score 0.452 Round 4: 331 peptides, 52 chains. Longest chain 15 peptides. Score 0.501 Round 5: 347 peptides, 49 chains. Longest chain 20 peptides. Score 0.565 Taking the results from Round 5 Chains 51, Residues 298, Estimated correctness of the model 16.8 % 7 chains (59 residues) have been docked in sequence ------------------------------------------------------ 8387 reflections ( 99.63 % complete ) and 10643 restraints for refining 4869 atoms. 9302 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2541 (Rfree = 0.000) for 4869 atoms. Found 28 (36 requested) and removed 40 (18 requested) atoms. Cycle 2: After refmac, R = 0.2441 (Rfree = 0.000) for 4782 atoms. Found 35 (36 requested) and removed 35 (18 requested) atoms. Cycle 3: After refmac, R = 0.2432 (Rfree = 0.000) for 4744 atoms. Found 36 (36 requested) and removed 36 (18 requested) atoms. Cycle 4: After refmac, R = 0.2372 (Rfree = 0.000) for 4712 atoms. Found 31 (35 requested) and removed 27 (17 requested) atoms. Cycle 5: After refmac, R = 0.2333 (Rfree = 0.000) for 4692 atoms. Found 32 (35 requested) and removed 26 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.35 3.83 Search for helices and strands: 0 residues in 0 chains, 4910 seeds are put forward NCS extension: 20 residues added (4 deleted due to clashes), 4930 seeds are put forward Round 1: 259 peptides, 50 chains. Longest chain 15 peptides. Score 0.342 Round 2: 321 peptides, 52 chains. Longest chain 15 peptides. Score 0.478 Round 3: 310 peptides, 52 chains. Longest chain 13 peptides. Score 0.452 Round 4: 318 peptides, 50 chains. Longest chain 18 peptides. Score 0.491 Round 5: 333 peptides, 49 chains. Longest chain 22 peptides. Score 0.535 Taking the results from Round 5 Chains 52, Residues 284, Estimated correctness of the model 6.0 % 6 chains (60 residues) have been docked in sequence ------------------------------------------------------ 8387 reflections ( 99.63 % complete ) and 10107 restraints for refining 4592 atoms. 8836 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2283 (Rfree = 0.000) for 4592 atoms. Found 20 (34 requested) and removed 43 (17 requested) atoms. Cycle 7: After refmac, R = 0.2253 (Rfree = 0.000) for 4543 atoms. Found 30 (34 requested) and removed 27 (17 requested) atoms. Cycle 8: After refmac, R = 0.1892 (Rfree = 0.000) for 4527 atoms. Found 4 (34 requested) and removed 19 (17 requested) atoms. Cycle 9: After refmac, R = 0.1797 (Rfree = 0.000) for 4502 atoms. Found 8 (34 requested) and removed 20 (17 requested) atoms. Cycle 10: After refmac, R = 0.1766 (Rfree = 0.000) for 4479 atoms. Found 5 (33 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.35 3.83 Search for helices and strands: 0 residues in 0 chains, 4660 seeds are put forward NCS extension: 24 residues added (4 deleted due to clashes), 4684 seeds are put forward Round 1: 288 peptides, 52 chains. Longest chain 12 peptides. Score 0.397 Round 2: 342 peptides, 50 chains. Longest chain 18 peptides. Score 0.545 Round 3: 334 peptides, 50 chains. Longest chain 18 peptides. Score 0.528 Round 4: 336 peptides, 50 chains. Longest chain 15 peptides. Score 0.532 Round 5: 329 peptides, 46 chains. Longest chain 21 peptides. Score 0.555 Taking the results from Round 5 Chains 46, Residues 283, Estimated correctness of the model 13.3 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 8387 reflections ( 99.63 % complete ) and 10472 restraints for refining 4613 atoms. 9346 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2209 (Rfree = 0.000) for 4613 atoms. Found 28 (34 requested) and removed 29 (17 requested) atoms. Cycle 12: After refmac, R = 0.2242 (Rfree = 0.000) for 4582 atoms. Found 34 (34 requested) and removed 24 (17 requested) atoms. Cycle 13: After refmac, R = 0.2188 (Rfree = 0.000) for 4575 atoms. Found 34 (34 requested) and removed 24 (17 requested) atoms. Cycle 14: After refmac, R = 0.1716 (Rfree = 0.000) for 4571 atoms. Found 9 (34 requested) and removed 24 (17 requested) atoms. Cycle 15: After refmac, R = 0.1658 (Rfree = 0.000) for 4545 atoms. Found 6 (34 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.33 3.81 Search for helices and strands: 0 residues in 0 chains, 4710 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 4739 seeds are put forward Round 1: 279 peptides, 56 chains. Longest chain 10 peptides. Score 0.327 Round 2: 322 peptides, 55 chains. Longest chain 15 peptides. Score 0.450 Round 3: 318 peptides, 52 chains. Longest chain 14 peptides. Score 0.471 Round 4: 321 peptides, 55 chains. Longest chain 14 peptides. Score 0.447 Round 5: 324 peptides, 50 chains. Longest chain 17 peptides. Score 0.505 Taking the results from Round 5 Chains 51, Residues 274, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 8387 reflections ( 99.63 % complete ) and 10575 restraints for refining 4592 atoms. 9476 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2170 (Rfree = 0.000) for 4592 atoms. Found 34 (34 requested) and removed 40 (17 requested) atoms. Cycle 17: After refmac, R = 0.2132 (Rfree = 0.000) for 4570 atoms. Found 34 (34 requested) and removed 26 (17 requested) atoms. Cycle 18: After refmac, R = 0.2092 (Rfree = 0.000) for 4568 atoms. Found 34 (34 requested) and removed 19 (17 requested) atoms. Cycle 19: After refmac, R = 0.2030 (Rfree = 0.000) for 4575 atoms. Found 34 (34 requested) and removed 29 (17 requested) atoms. Cycle 20: After refmac, R = 0.1618 (Rfree = 0.000) for 4576 atoms. Found 6 (34 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 3.80 Search for helices and strands: 0 residues in 0 chains, 4757 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4771 seeds are put forward Round 1: 295 peptides, 57 chains. Longest chain 14 peptides. Score 0.359 Round 2: 325 peptides, 50 chains. Longest chain 18 peptides. Score 0.507 Round 3: 318 peptides, 49 chains. Longest chain 18 peptides. Score 0.501 Round 4: 322 peptides, 48 chains. Longest chain 19 peptides. Score 0.520 Round 5: 302 peptides, 49 chains. Longest chain 17 peptides. Score 0.464 Taking the results from Round 4 Chains 48, Residues 274, Estimated correctness of the model 0.4 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 8387 reflections ( 99.63 % complete ) and 10569 restraints for refining 4604 atoms. 9462 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2070 (Rfree = 0.000) for 4604 atoms. Found 32 (34 requested) and removed 33 (17 requested) atoms. Cycle 22: After refmac, R = 0.1889 (Rfree = 0.000) for 4586 atoms. Found 28 (34 requested) and removed 26 (17 requested) atoms. Cycle 23: After refmac, R = 0.1791 (Rfree = 0.000) for 4579 atoms. Found 23 (34 requested) and removed 24 (17 requested) atoms. Cycle 24: After refmac, R = 0.1739 (Rfree = 0.000) for 4571 atoms. Found 21 (34 requested) and removed 22 (17 requested) atoms. Cycle 25: After refmac, R = 0.1716 (Rfree = 0.000) for 4565 atoms. Found 19 (34 requested) and removed 23 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 3.78 Search for helices and strands: 0 residues in 0 chains, 4722 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 4742 seeds are put forward Round 1: 248 peptides, 46 chains. Longest chain 12 peptides. Score 0.358 Round 2: 281 peptides, 43 chains. Longest chain 19 peptides. Score 0.476 Round 3: 304 peptides, 47 chains. Longest chain 19 peptides. Score 0.489 Round 4: 308 peptides, 45 chains. Longest chain 19 peptides. Score 0.518 Round 5: 276 peptides, 43 chains. Longest chain 23 peptides. Score 0.464 Taking the results from Round 4 Chains 46, Residues 263, Estimated correctness of the model 0.0 % 3 chains (33 residues) have been docked in sequence ------------------------------------------------------ 8387 reflections ( 99.63 % complete ) and 10232 restraints for refining 4646 atoms. 9106 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1929 (Rfree = 0.000) for 4646 atoms. Found 28 (35 requested) and removed 34 (17 requested) atoms. Cycle 27: After refmac, R = 0.1940 (Rfree = 0.000) for 4624 atoms. Found 33 (35 requested) and removed 27 (17 requested) atoms. Cycle 28: After refmac, R = 0.1912 (Rfree = 0.000) for 4614 atoms. Found 34 (34 requested) and removed 24 (17 requested) atoms. Cycle 29: After refmac, R = 0.1853 (Rfree = 0.000) for 4609 atoms. Found 29 (34 requested) and removed 21 (17 requested) atoms. Cycle 30: After refmac, R = 0.1819 (Rfree = 0.000) for 4611 atoms. Found 34 (34 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.32 3.80 Search for helices and strands: 0 residues in 0 chains, 4797 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 4822 seeds are put forward Round 1: 211 peptides, 41 chains. Longest chain 13 peptides. Score 0.314 Round 2: 265 peptides, 46 chains. Longest chain 18 peptides. Score 0.403 Round 3: 275 peptides, 41 chains. Longest chain 19 peptides. Score 0.483 Round 4: 284 peptides, 46 chains. Longest chain 14 peptides. Score 0.452 Round 5: 270 peptides, 42 chains. Longest chain 19 peptides. Score 0.460 Taking the results from Round 3 Chains 41, Residues 234, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 8387 reflections ( 99.63 % complete ) and 10713 restraints for refining 4624 atoms. 9805 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1836 (Rfree = 0.000) for 4624 atoms. Found 33 (34 requested) and removed 24 (17 requested) atoms. Cycle 32: After refmac, R = 0.1811 (Rfree = 0.000) for 4624 atoms. Found 34 (34 requested) and removed 22 (17 requested) atoms. Cycle 33: After refmac, R = 0.1770 (Rfree = 0.000) for 4626 atoms. Found 26 (35 requested) and removed 21 (17 requested) atoms. Cycle 34: After refmac, R = 0.1675 (Rfree = 0.000) for 4620 atoms. Found 27 (34 requested) and removed 19 (17 requested) atoms. Cycle 35: After refmac, R = 0.1626 (Rfree = 0.000) for 4625 atoms. Found 15 (34 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 3.77 Search for helices and strands: 0 residues in 0 chains, 4796 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 4812 seeds are put forward Round 1: 217 peptides, 45 chains. Longest chain 9 peptides. Score 0.282 Round 2: 241 peptides, 42 chains. Longest chain 14 peptides. Score 0.385 Round 3: 256 peptides, 42 chains. Longest chain 16 peptides. Score 0.425 Round 4: 257 peptides, 42 chains. Longest chain 15 peptides. Score 0.427 Round 5: 258 peptides, 44 chains. Longest chain 12 peptides. Score 0.408 Taking the results from Round 4 Chains 42, Residues 215, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 8387 reflections ( 99.63 % complete ) and 10926 restraints for refining 4633 atoms. 10074 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1735 (Rfree = 0.000) for 4633 atoms. Found 25 (34 requested) and removed 29 (17 requested) atoms. Cycle 37: After refmac, R = 0.1574 (Rfree = 0.000) for 4622 atoms. Found 19 (34 requested) and removed 20 (17 requested) atoms. Cycle 38: After refmac, R = 0.1524 (Rfree = 0.000) for 4615 atoms. Found 4 (34 requested) and removed 19 (17 requested) atoms. Cycle 39: After refmac, R = 0.1435 (Rfree = 0.000) for 4596 atoms. Found 5 (34 requested) and removed 19 (17 requested) atoms. Cycle 40: After refmac, R = 0.1440 (Rfree = 0.000) for 4577 atoms. Found 9 (34 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.34 3.82 Search for helices and strands: 0 residues in 0 chains, 4748 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 4773 seeds are put forward Round 1: 219 peptides, 44 chains. Longest chain 10 peptides. Score 0.300 Round 2: 242 peptides, 41 chains. Longest chain 14 peptides. Score 0.400 Round 3: 243 peptides, 40 chains. Longest chain 15 peptides. Score 0.414 Round 4: 252 peptides, 43 chains. Longest chain 10 peptides. Score 0.403 Round 5: 245 peptides, 37 chains. Longest chain 25 peptides. Score 0.453 Taking the results from Round 5 Chains 39, Residues 208, Estimated correctness of the model 0.0 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 8387 reflections ( 99.63 % complete ) and 10766 restraints for refining 4681 atoms. 9885 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1746 (Rfree = 0.000) for 4681 atoms. Found 17 (35 requested) and removed 37 (17 requested) atoms. Cycle 42: After refmac, R = 0.1839 (Rfree = 0.000) for 4645 atoms. Found 22 (35 requested) and removed 25 (17 requested) atoms. Cycle 43: After refmac, R = 0.1483 (Rfree = 0.000) for 4632 atoms. Found 10 (35 requested) and removed 23 (17 requested) atoms. Cycle 44: After refmac, R = 0.1442 (Rfree = 0.000) for 4610 atoms. Found 7 (34 requested) and removed 18 (17 requested) atoms. Cycle 45: After refmac, R = 0.1424 (Rfree = 0.000) for 4598 atoms. Found 7 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.29 3.77 Search for helices and strands: 0 residues in 0 chains, 4774 seeds are put forward NCS extension: 0 residues added, 4774 seeds are put forward Round 1: 225 peptides, 45 chains. Longest chain 11 peptides. Score 0.305 Round 2: 259 peptides, 43 chains. Longest chain 18 peptides. Score 0.421 Round 3: 250 peptides, 41 chains. Longest chain 15 peptides. Score 0.421 Round 4: 233 peptides, 39 chains. Longest chain 13 peptides. Score 0.399 Round 5: 233 peptides, 37 chains. Longest chain 15 peptides. Score 0.422 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 37, Residues 196, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 1z82-3_warpNtrace.pdb as input Building loops using Loopy2018 37 chains (196 residues) following loop building 3 chains (15 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8387 reflections ( 99.63 % complete ) and 11080 restraints for refining 4696 atoms. 10295 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1741 (Rfree = 0.000) for 4696 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.2136 (Rfree = 0.000) for 4665 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.1601 (Rfree = 0.000) for 4641 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.1511 (Rfree = 0.000) for 4623 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:30:26 GMT 2018 Job finished. TimeTaking 67.42 Used memory is bytes: 2923584