null Mon 24 Dec 07:37:55 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1z82-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1z82-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1z82-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1z82-3.8-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1z82-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1z82-3.8-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:37:59 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/noncs/ArpWArp/wArpResults/WorkingDir/1z82-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1z82-3.8-parrot-noncs/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-noncs.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-noncs.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 5925 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3303 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3033 (Rfree = 0.000) for 5925 atoms. Found 32 (32 requested) and removed 84 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.60 4.12 Search for helices and strands: 0 residues in 0 chains, 5997 seeds are put forward NCS extension: 0 residues added, 5997 seeds are put forward Round 1: 145 peptides, 34 chains. Longest chain 6 peptides. Score 0.198 Round 2: 196 peptides, 41 chains. Longest chain 9 peptides. Score 0.269 Round 3: 212 peptides, 43 chains. Longest chain 7 peptides. Score 0.292 Round 4: 217 peptides, 42 chains. Longest chain 14 peptides. Score 0.319 Round 5: 224 peptides, 43 chains. Longest chain 14 peptides. Score 0.327 Taking the results from Round 5 Chains 43, Residues 181, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 6033 reflections ( 99.55 % complete ) and 11620 restraints for refining 4845 atoms. 10878 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2357 (Rfree = 0.000) for 4845 atoms. Found 14 (26 requested) and removed 40 (13 requested) atoms. Cycle 2: After refmac, R = 0.2109 (Rfree = 0.000) for 4763 atoms. Found 16 (26 requested) and removed 25 (13 requested) atoms. Cycle 3: After refmac, R = 0.2021 (Rfree = 0.000) for 4736 atoms. Found 9 (26 requested) and removed 19 (13 requested) atoms. Cycle 4: After refmac, R = 0.1976 (Rfree = 0.000) for 4711 atoms. Found 12 (25 requested) and removed 17 (12 requested) atoms. Cycle 5: After refmac, R = 0.1933 (Rfree = 0.000) for 4699 atoms. Found 3 (25 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 4.25 Search for helices and strands: 0 residues in 0 chains, 4848 seeds are put forward NCS extension: 0 residues added, 4848 seeds are put forward Round 1: 189 peptides, 41 chains. Longest chain 8 peptides. Score 0.247 Round 2: 257 peptides, 48 chains. Longest chain 12 peptides. Score 0.359 Round 3: 279 peptides, 47 chains. Longest chain 13 peptides. Score 0.428 Round 4: 288 peptides, 46 chains. Longest chain 13 peptides. Score 0.461 Round 5: 277 peptides, 46 chains. Longest chain 14 peptides. Score 0.434 Taking the results from Round 4 Chains 47, Residues 242, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 6033 reflections ( 99.55 % complete ) and 10826 restraints for refining 4581 atoms. 9865 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2013 (Rfree = 0.000) for 4581 atoms. Found 20 (25 requested) and removed 33 (12 requested) atoms. Cycle 7: After refmac, R = 0.1834 (Rfree = 0.000) for 4531 atoms. Found 7 (25 requested) and removed 22 (12 requested) atoms. Cycle 8: After refmac, R = 0.1809 (Rfree = 0.000) for 4503 atoms. Found 1 (24 requested) and removed 14 (12 requested) atoms. Cycle 9: After refmac, R = 0.1798 (Rfree = 0.000) for 4488 atoms. Found 2 (24 requested) and removed 14 (12 requested) atoms. Cycle 10: After refmac, R = 0.1790 (Rfree = 0.000) for 4475 atoms. Found 1 (24 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.67 4.20 Search for helices and strands: 0 residues in 0 chains, 4608 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4622 seeds are put forward Round 1: 215 peptides, 45 chains. Longest chain 10 peptides. Score 0.276 Round 2: 252 peptides, 43 chains. Longest chain 11 peptides. Score 0.403 Round 3: 251 peptides, 42 chains. Longest chain 10 peptides. Score 0.412 Round 4: 278 peptides, 45 chains. Longest chain 11 peptides. Score 0.448 Round 5: 261 peptides, 41 chains. Longest chain 16 peptides. Score 0.449 Taking the results from Round 5 Chains 41, Residues 220, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6033 reflections ( 99.55 % complete ) and 10905 restraints for refining 4579 atoms. 10027 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1889 (Rfree = 0.000) for 4579 atoms. Found 16 (25 requested) and removed 38 (12 requested) atoms. Cycle 12: After refmac, R = 0.1745 (Rfree = 0.000) for 4532 atoms. Found 7 (25 requested) and removed 17 (12 requested) atoms. Cycle 13: After refmac, R = 0.1704 (Rfree = 0.000) for 4511 atoms. Found 5 (24 requested) and removed 19 (12 requested) atoms. Cycle 14: After refmac, R = 0.1740 (Rfree = 0.000) for 4490 atoms. Found 7 (24 requested) and removed 18 (12 requested) atoms. Cycle 15: After refmac, R = 0.1679 (Rfree = 0.000) for 4471 atoms. Found 6 (24 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.67 4.20 Search for helices and strands: 0 residues in 0 chains, 4640 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4654 seeds are put forward Round 1: 254 peptides, 50 chains. Longest chain 13 peptides. Score 0.328 Round 2: 271 peptides, 48 chains. Longest chain 15 peptides. Score 0.397 Round 3: 280 peptides, 48 chains. Longest chain 14 peptides. Score 0.420 Round 4: 276 peptides, 46 chains. Longest chain 12 peptides. Score 0.432 Round 5: 286 peptides, 46 chains. Longest chain 14 peptides. Score 0.456 Taking the results from Round 5 Chains 47, Residues 240, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 6033 reflections ( 99.55 % complete ) and 10963 restraints for refining 4669 atoms. 9976 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1921 (Rfree = 0.000) for 4669 atoms. Found 21 (25 requested) and removed 55 (12 requested) atoms. Cycle 17: After refmac, R = 0.1652 (Rfree = 0.000) for 4616 atoms. Found 10 (25 requested) and removed 30 (12 requested) atoms. Cycle 18: After refmac, R = 0.1631 (Rfree = 0.000) for 4586 atoms. Found 7 (25 requested) and removed 31 (12 requested) atoms. Cycle 19: After refmac, R = 0.1532 (Rfree = 0.000) for 4559 atoms. Found 3 (25 requested) and removed 25 (12 requested) atoms. Cycle 20: After refmac, R = 0.1540 (Rfree = 0.000) for 4534 atoms. Found 2 (24 requested) and removed 19 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 4.14 Search for helices and strands: 0 residues in 0 chains, 4716 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 4736 seeds are put forward Round 1: 225 peptides, 47 chains. Longest chain 8 peptides. Score 0.281 Round 2: 280 peptides, 51 chains. Longest chain 12 peptides. Score 0.387 Round 3: 271 peptides, 48 chains. Longest chain 12 peptides. Score 0.397 Round 4: 274 peptides, 44 chains. Longest chain 13 peptides. Score 0.448 Round 5: 276 peptides, 46 chains. Longest chain 12 peptides. Score 0.432 Taking the results from Round 4 Chains 46, Residues 230, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6033 reflections ( 99.55 % complete ) and 10864 restraints for refining 4649 atoms. 9950 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1747 (Rfree = 0.000) for 4649 atoms. Found 16 (25 requested) and removed 44 (12 requested) atoms. Cycle 22: After refmac, R = 0.1705 (Rfree = 0.000) for 4606 atoms. Found 25 (25 requested) and removed 31 (12 requested) atoms. Cycle 23: After refmac, R = 0.1707 (Rfree = 0.000) for 4593 atoms. Found 25 (25 requested) and removed 20 (12 requested) atoms. Cycle 24: After refmac, R = 0.1249 (Rfree = 0.000) for 4588 atoms. Found 9 (25 requested) and removed 15 (12 requested) atoms. Cycle 25: After refmac, R = 0.1145 (Rfree = 0.000) for 4572 atoms. Found 2 (25 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.65 4.18 Search for helices and strands: 0 residues in 0 chains, 4741 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4755 seeds are put forward Round 1: 220 peptides, 48 chains. Longest chain 10 peptides. Score 0.254 Round 2: 253 peptides, 50 chains. Longest chain 12 peptides. Score 0.325 Round 3: 250 peptides, 46 chains. Longest chain 12 peptides. Score 0.363 Round 4: 264 peptides, 46 chains. Longest chain 16 peptides. Score 0.401 Round 5: 256 peptides, 43 chains. Longest chain 12 peptides. Score 0.414 Taking the results from Round 5 Chains 43, Residues 213, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 6033 reflections ( 99.55 % complete ) and 11359 restraints for refining 4764 atoms. 10490 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1795 (Rfree = 0.000) for 4764 atoms. Found 18 (26 requested) and removed 39 (13 requested) atoms. Cycle 27: After refmac, R = 0.1748 (Rfree = 0.000) for 4720 atoms. Found 25 (26 requested) and removed 21 (13 requested) atoms. Cycle 28: After refmac, R = 0.1783 (Rfree = 0.000) for 4715 atoms. Found 25 (25 requested) and removed 28 (12 requested) atoms. Cycle 29: After refmac, R = 0.1791 (Rfree = 0.000) for 4700 atoms. Found 25 (25 requested) and removed 27 (12 requested) atoms. Cycle 30: After refmac, R = 0.1250 (Rfree = 0.000) for 4690 atoms. Found 2 (25 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.61 4.13 Search for helices and strands: 0 residues in 0 chains, 4828 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 4845 seeds are put forward Round 1: 220 peptides, 48 chains. Longest chain 11 peptides. Score 0.254 Round 2: 239 peptides, 49 chains. Longest chain 12 peptides. Score 0.297 Round 3: 226 peptides, 43 chains. Longest chain 16 peptides. Score 0.332 Round 4: 222 peptides, 45 chains. Longest chain 9 peptides. Score 0.296 Round 5: 234 peptides, 43 chains. Longest chain 12 peptides. Score 0.355 Taking the results from Round 5 Chains 43, Residues 191, Estimated correctness of the model 0.0 % 3 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6033 reflections ( 99.55 % complete ) and 11280 restraints for refining 4664 atoms. 10543 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1742 (Rfree = 0.000) for 4664 atoms. Found 25 (25 requested) and removed 38 (12 requested) atoms. Cycle 32: After refmac, R = 0.1828 (Rfree = 0.000) for 4625 atoms. Found 25 (25 requested) and removed 28 (12 requested) atoms. Cycle 33: After refmac, R = 0.1894 (Rfree = 0.000) for 4617 atoms. Found 25 (25 requested) and removed 21 (12 requested) atoms. Cycle 34: After refmac, R = 0.1706 (Rfree = 0.000) for 4607 atoms. Found 25 (25 requested) and removed 26 (12 requested) atoms. Cycle 35: After refmac, R = 0.1674 (Rfree = 0.000) for 4596 atoms. Found 25 (25 requested) and removed 20 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.63 4.15 Search for helices and strands: 0 residues in 0 chains, 4769 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 4783 seeds are put forward Round 1: 147 peptides, 32 chains. Longest chain 7 peptides. Score 0.233 Round 2: 188 peptides, 38 chains. Longest chain 7 peptides. Score 0.283 Round 3: 193 peptides, 37 chains. Longest chain 9 peptides. Score 0.311 Round 4: 204 peptides, 38 chains. Longest chain 11 peptides. Score 0.330 Round 5: 198 peptides, 34 chains. Longest chain 13 peptides. Score 0.363 Taking the results from Round 5 Chains 36, Residues 164, Estimated correctness of the model 0.0 % 5 chains (26 residues) have been docked in sequence ------------------------------------------------------ 6033 reflections ( 99.55 % complete ) and 10973 restraints for refining 4633 atoms. 10268 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1706 (Rfree = 0.000) for 4633 atoms. Found 24 (25 requested) and removed 36 (12 requested) atoms. Cycle 37: After refmac, R = 0.1755 (Rfree = 0.000) for 4606 atoms. Found 25 (25 requested) and removed 26 (12 requested) atoms. Cycle 38: After refmac, R = 0.1760 (Rfree = 0.000) for 4596 atoms. Found 25 (25 requested) and removed 21 (12 requested) atoms. Cycle 39: After refmac, R = 0.1620 (Rfree = 0.000) for 4588 atoms. Found 20 (25 requested) and removed 21 (12 requested) atoms. Cycle 40: After refmac, R = 0.1556 (Rfree = 0.000) for 4582 atoms. Found 25 (25 requested) and removed 20 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.65 4.18 Search for helices and strands: 0 residues in 0 chains, 4735 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 4749 seeds are put forward Round 1: 151 peptides, 34 chains. Longest chain 8 peptides. Score 0.219 Round 2: 183 peptides, 36 chains. Longest chain 9 peptides. Score 0.293 Round 3: 184 peptides, 37 chains. Longest chain 9 peptides. Score 0.284 Round 4: 193 peptides, 36 chains. Longest chain 10 peptides. Score 0.323 Round 5: 197 peptides, 36 chains. Longest chain 10 peptides. Score 0.335 Taking the results from Round 5 Chains 36, Residues 161, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6033 reflections ( 99.55 % complete ) and 11235 restraints for refining 4622 atoms. 10614 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1881 (Rfree = 0.000) for 4622 atoms. Found 25 (25 requested) and removed 28 (12 requested) atoms. Cycle 42: After refmac, R = 0.1732 (Rfree = 0.000) for 4596 atoms. Found 25 (25 requested) and removed 28 (12 requested) atoms. Cycle 43: After refmac, R = 0.1561 (Rfree = 0.000) for 4576 atoms. Found 16 (25 requested) and removed 17 (12 requested) atoms. Cycle 44: After refmac, R = 0.1218 (Rfree = 0.000) for 4566 atoms. Found 7 (25 requested) and removed 15 (12 requested) atoms. Cycle 45: After refmac, R = 0.1161 (Rfree = 0.000) for 4550 atoms. Found 4 (25 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 4.19 Search for helices and strands: 0 residues in 0 chains, 4690 seeds are put forward NCS extension: 0 residues added, 4690 seeds are put forward Round 1: 113 peptides, 26 chains. Longest chain 7 peptides. Score 0.201 Round 2: 121 peptides, 25 chains. Longest chain 9 peptides. Score 0.245 Round 3: 118 peptides, 24 chains. Longest chain 8 peptides. Score 0.249 Round 4: 125 peptides, 26 chains. Longest chain 8 peptides. Score 0.244 Round 5: 123 peptides, 24 chains. Longest chain 10 peptides. Score 0.267 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 99, 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 10895 restraints for refining 4449 atoms. 10523 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1733 (Rfree = 0.000) for 4449 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.1329 (Rfree = 0.000) for 4432 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.1225 (Rfree = 0.000) for 4417 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.1182 (Rfree = 0.000) for 4402 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:24:45 GMT 2018 Job finished. TimeTaking 46.85 Used memory is bytes: 14736752