Mon 24 Dec 07:33:25 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 2op5-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2op5-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2op5-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2op5-4.0-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/2op5-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2op5-4.0-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 07:33:30 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/2op5-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2op5-4.0-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 458 and 0 Target number of residues in the AU: 458 Target solvent content: 0.6428 Checking the provided sequence file Detected sequence length: 117 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 702 Adjusted target solvent content: 0.45 Input MTZ file: 2op5-4.0-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: 19 Cell parameters: 56.562 84.634 144.950 90.000 90.000 90.000 Input sequence file: 2op5-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 5616 target number of atoms Had to go as low as 0.75 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: 73.087 4.000 Wilson plot Bfac: 73.49 6261 reflections ( 99.73 % complete ) and 0 restraints for refining 6226 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3485 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3466 (Rfree = 0.000) for 6226 atoms. Found 28 (29 requested) and removed 59 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.67 3.92 Search for helices and strands: 0 residues in 0 chains, 6289 seeds are put forward NCS extension: 0 residues added, 6289 seeds are put forward Round 1: 134 peptides, 30 chains. Longest chain 7 peptides. Score 0.213 Round 2: 200 peptides, 40 chains. Longest chain 13 peptides. Score 0.282 Round 3: 233 peptides, 46 chains. Longest chain 11 peptides. Score 0.302 Round 4: 270 peptides, 50 chains. Longest chain 12 peptides. Score 0.352 Round 5: 262 peptides, 47 chains. Longest chain 12 peptides. Score 0.364 Taking the results from Round 5 Chains 47, Residues 215, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6261 reflections ( 99.73 % complete ) and 12494 restraints for refining 5070 atoms. 11681 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2951 (Rfree = 0.000) for 5070 atoms. Found 19 (24 requested) and removed 45 (12 requested) atoms. Cycle 2: After refmac, R = 0.2556 (Rfree = 0.000) for 4946 atoms. Found 9 (23 requested) and removed 29 (11 requested) atoms. Cycle 3: After refmac, R = 0.2461 (Rfree = 0.000) for 4898 atoms. Found 3 (23 requested) and removed 26 (11 requested) atoms. Cycle 4: After refmac, R = 0.2435 (Rfree = 0.000) for 4866 atoms. Found 9 (23 requested) and removed 16 (11 requested) atoms. Cycle 5: After refmac, R = 0.2397 (Rfree = 0.000) for 4851 atoms. Found 6 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.63 3.88 Search for helices and strands: 0 residues in 0 chains, 4986 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 5002 seeds are put forward Round 1: 242 peptides, 51 chains. Longest chain 8 peptides. Score 0.271 Round 2: 284 peptides, 50 chains. Longest chain 11 peptides. Score 0.386 Round 3: 271 peptides, 48 chains. Longest chain 11 peptides. Score 0.375 Round 4: 284 peptides, 49 chains. Longest chain 13 peptides. Score 0.396 Round 5: 284 peptides, 46 chains. Longest chain 13 peptides. Score 0.426 Taking the results from Round 5 Chains 46, Residues 238, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6261 reflections ( 99.73 % complete ) and 11457 restraints for refining 4737 atoms. 10551 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2630 (Rfree = 0.000) for 4737 atoms. Found 10 (22 requested) and removed 47 (11 requested) atoms. Cycle 7: After refmac, R = 0.2446 (Rfree = 0.000) for 4666 atoms. Found 9 (22 requested) and removed 15 (11 requested) atoms. Cycle 8: After refmac, R = 0.2398 (Rfree = 0.000) for 4643 atoms. Found 3 (22 requested) and removed 15 (11 requested) atoms. Cycle 9: After refmac, R = 0.2377 (Rfree = 0.000) for 4622 atoms. Found 4 (22 requested) and removed 11 (11 requested) atoms. Cycle 10: After refmac, R = 0.2360 (Rfree = 0.000) for 4610 atoms. Found 3 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.57 3.82 Search for helices and strands: 0 residues in 0 chains, 4731 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 4746 seeds are put forward Round 1: 228 peptides, 48 chains. Longest chain 8 peptides. Score 0.267 Round 2: 278 peptides, 49 chains. Longest chain 15 peptides. Score 0.382 Round 3: 281 peptides, 50 chains. Longest chain 14 peptides. Score 0.379 Round 4: 284 peptides, 51 chains. Longest chain 14 peptides. Score 0.376 Round 5: 280 peptides, 48 chains. Longest chain 13 peptides. Score 0.397 Taking the results from Round 5 Chains 48, Residues 232, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6261 reflections ( 99.73 % complete ) and 11093 restraints for refining 4685 atoms. 10213 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2592 (Rfree = 0.000) for 4685 atoms. Found 16 (22 requested) and removed 31 (11 requested) atoms. Cycle 12: After refmac, R = 0.2408 (Rfree = 0.000) for 4656 atoms. Found 2 (22 requested) and removed 28 (11 requested) atoms. Cycle 13: After refmac, R = 0.2287 (Rfree = 0.000) for 4624 atoms. Found 6 (21 requested) and removed 17 (10 requested) atoms. Cycle 14: After refmac, R = 0.2132 (Rfree = 0.000) for 4608 atoms. Found 3 (21 requested) and removed 13 (10 requested) atoms. Cycle 15: After refmac, R = 0.2098 (Rfree = 0.000) for 4591 atoms. Found 2 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 3.78 Search for helices and strands: 0 residues in 0 chains, 4741 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4757 seeds are put forward Round 1: 201 peptides, 42 chains. Longest chain 8 peptides. Score 0.262 Round 2: 236 peptides, 44 chains. Longest chain 10 peptides. Score 0.332 Round 3: 248 peptides, 42 chains. Longest chain 13 peptides. Score 0.383 Round 4: 269 peptides, 43 chains. Longest chain 15 peptides. Score 0.421 Round 5: 261 peptides, 45 chains. Longest chain 12 peptides. Score 0.382 Taking the results from Round 4 Chains 44, Residues 226, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6261 reflections ( 99.73 % complete ) and 11254 restraints for refining 4781 atoms. 10364 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2510 (Rfree = 0.000) for 4781 atoms. Found 21 (22 requested) and removed 52 (11 requested) atoms. Cycle 17: After refmac, R = 0.2428 (Rfree = 0.000) for 4710 atoms. Found 14 (22 requested) and removed 41 (11 requested) atoms. Cycle 18: After refmac, R = 0.2525 (Rfree = 0.000) for 4640 atoms. Found 18 (22 requested) and removed 43 (11 requested) atoms. Cycle 19: After refmac, R = 0.1786 (Rfree = 0.000) for 4585 atoms. Found 5 (21 requested) and removed 21 (10 requested) atoms. Cycle 20: After refmac, R = 0.1675 (Rfree = 0.000) for 4554 atoms. Found 1 (21 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.61 3.86 Search for helices and strands: 0 residues in 0 chains, 4642 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 4664 seeds are put forward Round 1: 191 peptides, 42 chains. Longest chain 10 peptides. Score 0.234 Round 2: 231 peptides, 45 chains. Longest chain 12 peptides. Score 0.308 Round 3: 228 peptides, 44 chains. Longest chain 10 peptides. Score 0.311 Round 4: 238 peptides, 43 chains. Longest chain 13 peptides. Score 0.347 Round 5: 237 peptides, 45 chains. Longest chain 12 peptides. Score 0.323 Taking the results from Round 4 Chains 43, Residues 195, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6261 reflections ( 99.73 % complete ) and 11047 restraints for refining 4674 atoms. 10310 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2359 (Rfree = 0.000) for 4674 atoms. Found 21 (22 requested) and removed 41 (11 requested) atoms. Cycle 22: After refmac, R = 0.2083 (Rfree = 0.000) for 4617 atoms. Found 19 (22 requested) and removed 26 (11 requested) atoms. Cycle 23: After refmac, R = 0.2026 (Rfree = 0.000) for 4591 atoms. Found 12 (21 requested) and removed 24 (10 requested) atoms. Cycle 24: After refmac, R = 0.2092 (Rfree = 0.000) for 4561 atoms. Found 17 (21 requested) and removed 17 (10 requested) atoms. Cycle 25: After refmac, R = 0.1916 (Rfree = 0.000) for 4551 atoms. Found 7 (21 requested) and removed 19 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.62 3.87 Search for helices and strands: 0 residues in 0 chains, 4672 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 4687 seeds are put forward Round 1: 195 peptides, 42 chains. Longest chain 11 peptides. Score 0.245 Round 2: 236 peptides, 46 chains. Longest chain 9 peptides. Score 0.310 Round 3: 256 peptides, 50 chains. Longest chain 9 peptides. Score 0.318 Round 4: 258 peptides, 46 chains. Longest chain 13 peptides. Score 0.365 Round 5: 263 peptides, 49 chains. Longest chain 11 peptides. Score 0.346 Taking the results from Round 4 Chains 46, Residues 212, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6261 reflections ( 99.73 % complete ) and 11072 restraints for refining 4703 atoms. 10270 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2363 (Rfree = 0.000) for 4703 atoms. Found 21 (22 requested) and removed 39 (11 requested) atoms. Cycle 27: After refmac, R = 0.1961 (Rfree = 0.000) for 4654 atoms. Found 16 (22 requested) and removed 25 (11 requested) atoms. Cycle 28: After refmac, R = 0.1985 (Rfree = 0.000) for 4624 atoms. Found 16 (22 requested) and removed 31 (11 requested) atoms. Cycle 29: After refmac, R = 0.1881 (Rfree = 0.000) for 4600 atoms. Found 11 (21 requested) and removed 16 (10 requested) atoms. Cycle 30: After refmac, R = 0.1932 (Rfree = 0.000) for 4580 atoms. Found 20 (21 requested) and removed 21 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.58 3.83 Search for helices and strands: 0 residues in 0 chains, 4720 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 4734 seeds are put forward Round 1: 179 peptides, 41 chains. Longest chain 7 peptides. Score 0.212 Round 2: 221 peptides, 43 chains. Longest chain 10 peptides. Score 0.304 Round 3: 236 peptides, 44 chains. Longest chain 10 peptides. Score 0.332 Round 4: 229 peptides, 41 chains. Longest chain 11 peptides. Score 0.347 Round 5: 240 peptides, 42 chains. Longest chain 18 peptides. Score 0.363 Taking the results from Round 5 Chains 42, Residues 198, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6261 reflections ( 99.73 % complete ) and 11263 restraints for refining 4765 atoms. 10513 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2043 (Rfree = 0.000) for 4765 atoms. Found 11 (22 requested) and removed 32 (11 requested) atoms. Cycle 32: After refmac, R = 0.1968 (Rfree = 0.000) for 4719 atoms. Found 17 (22 requested) and removed 32 (11 requested) atoms. Cycle 33: After refmac, R = 0.1861 (Rfree = 0.000) for 4690 atoms. Found 12 (22 requested) and removed 20 (11 requested) atoms. Cycle 34: After refmac, R = 0.1924 (Rfree = 0.000) for 4671 atoms. Found 15 (22 requested) and removed 32 (11 requested) atoms. Cycle 35: After refmac, R = 0.1474 (Rfree = 0.000) for 4645 atoms. Found 2 (22 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 3.83 Search for helices and strands: 0 residues in 0 chains, 4745 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4763 seeds are put forward Round 1: 168 peptides, 38 chains. Longest chain 7 peptides. Score 0.216 Round 2: 193 peptides, 38 chains. Longest chain 9 peptides. Score 0.286 Round 3: 200 peptides, 35 chains. Longest chain 17 peptides. Score 0.339 Round 4: 205 peptides, 35 chains. Longest chain 12 peptides. Score 0.352 Round 5: 207 peptides, 34 chains. Longest chain 16 peptides. Score 0.368 Taking the results from Round 5 Chains 34, Residues 173, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6261 reflections ( 99.73 % complete ) and 11129 restraints for refining 4697 atoms. 10471 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2062 (Rfree = 0.000) for 4697 atoms. Found 22 (22 requested) and removed 30 (11 requested) atoms. Cycle 37: After refmac, R = 0.2134 (Rfree = 0.000) for 4668 atoms. Found 22 (22 requested) and removed 28 (11 requested) atoms. Cycle 38: After refmac, R = 0.1928 (Rfree = 0.000) for 4641 atoms. Found 15 (22 requested) and removed 23 (11 requested) atoms. Cycle 39: After refmac, R = 0.1458 (Rfree = 0.000) for 4621 atoms. Found 2 (22 requested) and removed 17 (11 requested) atoms. Cycle 40: After refmac, R = 0.1588 (Rfree = 0.000) for 4598 atoms. Found 16 (21 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.78 Search for helices and strands: 0 residues in 0 chains, 4734 seeds are put forward NCS extension: 0 residues added, 4734 seeds are put forward Round 1: 149 peptides, 33 chains. Longest chain 7 peptides. Score 0.221 Round 2: 181 peptides, 36 chains. Longest chain 10 peptides. Score 0.277 Round 3: 177 peptides, 34 chains. Longest chain 10 peptides. Score 0.290 Round 4: 164 peptides, 31 chains. Longest chain 9 peptides. Score 0.290 Round 5: 165 peptides, 30 chains. Longest chain 11 peptides. Score 0.305 Taking the results from Round 5 Chains 30, Residues 135, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6261 reflections ( 99.73 % complete ) and 10631 restraints for refining 4559 atoms. 10121 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2016 (Rfree = 0.000) for 4559 atoms. Found 21 (21 requested) and removed 29 (10 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2107 (Rfree = 0.000) for 4529 atoms. Found 20 (21 requested) and removed 28 (10 requested) atoms. Cycle 43: After refmac, R = 0.1916 (Rfree = 0.000) for 4507 atoms. Found 19 (21 requested) and removed 16 (10 requested) atoms. Cycle 44: After refmac, R = 0.1496 (Rfree = 0.000) for 4501 atoms. Found 5 (21 requested) and removed 15 (10 requested) atoms. Cycle 45: After refmac, R = 0.1433 (Rfree = 0.000) for 4481 atoms. Found 2 (21 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.57 3.82 Search for helices and strands: 0 residues in 0 chains, 4574 seeds are put forward NCS extension: 11 residues added (0 deleted due to clashes), 4585 seeds are put forward Round 1: 168 peptides, 38 chains. Longest chain 8 peptides. Score 0.216 Round 2: 202 peptides, 43 chains. Longest chain 9 peptides. Score 0.253 Round 3: 200 peptides, 41 chains. Longest chain 8 peptides. Score 0.271 Round 4: 184 peptides, 36 chains. Longest chain 11 peptides. Score 0.285 Round 5: 184 peptides, 37 chains. Longest chain 9 peptides. Score 0.273 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 148, 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 2op5-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6261 reflections ( 99.73 % complete ) and 10526 restraints for refining 4467 atoms. 9970 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2093 (Rfree = 0.000) for 4467 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2047 (Rfree = 0.000) for 4440 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2056 (Rfree = 0.000) for 4416 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.1797 (Rfree = 0.000) for 4399 atoms. TimeTaking 45.77