null Tue 25 Dec 19:27:55 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 2afb-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2afb-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2afb-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2afb-3.8-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/2afb-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2afb-3.8-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 ============================================================ Tue 25 Dec 19:28:05 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/2afb-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2afb-3.8-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 479 and 0 Target number of residues in the AU: 479 Target solvent content: 0.6465 Checking the provided sequence file Detected sequence length: 351 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 702 Adjusted target solvent content: 0.48 Input MTZ file: 2afb-3.8-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: 155 Cell parameters: 120.993 120.993 260.300 90.000 90.000 120.000 Input sequence file: 2afb-3.8-parrot-hancs.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: 97.203 3.800 Wilson plot Bfac: 75.97 7461 reflections ( 99.35 % complete ) and 0 restraints for refining 6264 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3293 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3304 (Rfree = 0.000) for 6264 atoms. Found 34 (34 requested) and removed 41 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 6379 seeds are put forward NCS extension: 0 residues added, 6379 seeds are put forward Round 1: 233 peptides, 49 chains. Longest chain 9 peptides. Score 0.265 Round 2: 314 peptides, 56 chains. Longest chain 13 peptides. Score 0.386 Round 3: 335 peptides, 55 chains. Longest chain 13 peptides. Score 0.441 Round 4: 343 peptides, 49 chains. Longest chain 19 peptides. Score 0.509 Round 5: 343 peptides, 45 chains. Longest chain 16 peptides. Score 0.542 Taking the results from Round 5 Chains 47, Residues 298, Estimated correctness of the model 0.0 % 6 chains (39 residues) have been docked in sequence ------------------------------------------------------ 7461 reflections ( 99.35 % complete ) and 11576 restraints for refining 5080 atoms. 10326 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2736 (Rfree = 0.000) for 5080 atoms. Found 27 (27 requested) and removed 30 (13 requested) atoms. Cycle 2: After refmac, R = 0.2722 (Rfree = 0.000) for 4996 atoms. Found 27 (27 requested) and removed 43 (13 requested) atoms. Cycle 3: After refmac, R = 0.2150 (Rfree = 0.000) for 4923 atoms. Found 20 (27 requested) and removed 28 (13 requested) atoms. Cycle 4: After refmac, R = 0.2046 (Rfree = 0.000) for 4886 atoms. Found 16 (26 requested) and removed 21 (13 requested) atoms. Cycle 5: After refmac, R = 0.2493 (Rfree = 0.000) for 4867 atoms. Found 26 (26 requested) and removed 27 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.55 3.65 Search for helices and strands: 0 residues in 0 chains, 5082 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 5098 seeds are put forward Round 1: 312 peptides, 57 chains. Longest chain 15 peptides. Score 0.373 Round 2: 343 peptides, 53 chains. Longest chain 16 peptides. Score 0.475 Round 3: 356 peptides, 51 chains. Longest chain 17 peptides. Score 0.517 Round 4: 351 peptides, 52 chains. Longest chain 17 peptides. Score 0.499 Round 5: 358 peptides, 51 chains. Longest chain 18 peptides. Score 0.521 Taking the results from Round 5 Chains 51, Residues 307, Estimated correctness of the model 0.0 % 7 chains (31 residues) have been docked in sequence ------------------------------------------------------ 7461 reflections ( 99.35 % complete ) and 11583 restraints for refining 5080 atoms. 10331 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2623 (Rfree = 0.000) for 5080 atoms. Found 27 (27 requested) and removed 56 (13 requested) atoms. Cycle 7: After refmac, R = 0.2541 (Rfree = 0.000) for 4985 atoms. Found 27 (27 requested) and removed 45 (13 requested) atoms. Cycle 8: After refmac, R = 0.2428 (Rfree = 0.000) for 4933 atoms. Found 27 (27 requested) and removed 42 (13 requested) atoms. Cycle 9: After refmac, R = 0.1899 (Rfree = 0.000) for 4887 atoms. Found 10 (27 requested) and removed 26 (13 requested) atoms. Cycle 10: After refmac, R = 0.1827 (Rfree = 0.000) for 4858 atoms. Found 12 (26 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 5040 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 5057 seeds are put forward Round 1: 300 peptides, 56 chains. Longest chain 13 peptides. Score 0.355 Round 2: 346 peptides, 56 chains. Longest chain 15 peptides. Score 0.454 Round 3: 347 peptides, 54 chains. Longest chain 23 peptides. Score 0.474 Round 4: 364 peptides, 55 chains. Longest chain 17 peptides. Score 0.499 Round 5: 372 peptides, 54 chains. Longest chain 16 peptides. Score 0.522 Taking the results from Round 5 Chains 54, Residues 318, Estimated correctness of the model 0.0 % 8 chains (60 residues) have been docked in sequence ------------------------------------------------------ 7461 reflections ( 99.35 % complete ) and 11136 restraints for refining 5076 atoms. 9699 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2632 (Rfree = 0.000) for 5076 atoms. Found 26 (27 requested) and removed 37 (13 requested) atoms. Cycle 12: After refmac, R = 0.2452 (Rfree = 0.000) for 5016 atoms. Found 27 (27 requested) and removed 38 (13 requested) atoms. Cycle 13: After refmac, R = 0.2331 (Rfree = 0.000) for 4962 atoms. Found 27 (27 requested) and removed 32 (13 requested) atoms. Cycle 14: After refmac, R = 0.2324 (Rfree = 0.000) for 4917 atoms. Found 27 (27 requested) and removed 29 (13 requested) atoms. Cycle 15: After refmac, R = 0.1785 (Rfree = 0.000) for 4897 atoms. Found 16 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.55 3.65 Search for helices and strands: 0 residues in 0 chains, 5084 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 5099 seeds are put forward Round 1: 288 peptides, 55 chains. Longest chain 13 peptides. Score 0.337 Round 2: 343 peptides, 55 chains. Longest chain 17 peptides. Score 0.457 Round 3: 339 peptides, 52 chains. Longest chain 20 peptides. Score 0.475 Round 4: 351 peptides, 53 chains. Longest chain 20 peptides. Score 0.490 Round 5: 357 peptides, 51 chains. Longest chain 21 peptides. Score 0.519 Taking the results from Round 5 Chains 51, Residues 306, Estimated correctness of the model 0.0 % 7 chains (62 residues) have been docked in sequence ------------------------------------------------------ 7461 reflections ( 99.35 % complete ) and 11336 restraints for refining 5078 atoms. 9976 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2497 (Rfree = 0.000) for 5078 atoms. Found 27 (27 requested) and removed 45 (13 requested) atoms. Cycle 17: After refmac, R = 0.2145 (Rfree = 0.000) for 5016 atoms. Found 27 (27 requested) and removed 28 (13 requested) atoms. Cycle 18: After refmac, R = 0.2474 (Rfree = 0.000) for 4981 atoms. Found 27 (27 requested) and removed 40 (13 requested) atoms. Cycle 19: After refmac, R = 0.2171 (Rfree = 0.000) for 4943 atoms. Found 27 (27 requested) and removed 23 (13 requested) atoms. Cycle 20: After refmac, R = 0.2221 (Rfree = 0.000) for 4927 atoms. Found 27 (27 requested) and removed 31 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.55 3.65 Search for helices and strands: 0 residues in 0 chains, 5159 seeds are put forward NCS extension: 34 residues added (3 deleted due to clashes), 5193 seeds are put forward Round 1: 256 peptides, 51 chains. Longest chain 11 peptides. Score 0.301 Round 2: 316 peptides, 55 chains. Longest chain 12 peptides. Score 0.400 Round 3: 325 peptides, 51 chains. Longest chain 22 peptides. Score 0.456 Round 4: 321 peptides, 53 chains. Longest chain 16 peptides. Score 0.429 Round 5: 320 peptides, 50 chains. Longest chain 20 peptides. Score 0.455 Taking the results from Round 3 Chains 51, Residues 274, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7461 reflections ( 99.35 % complete ) and 11870 restraints for refining 5078 atoms. 10818 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2211 (Rfree = 0.000) for 5078 atoms. Found 27 (27 requested) and removed 43 (13 requested) atoms. Cycle 22: After refmac, R = 0.2422 (Rfree = 0.000) for 5031 atoms. Found 27 (27 requested) and removed 31 (13 requested) atoms. Cycle 23: After refmac, R = 0.2000 (Rfree = 0.000) for 4995 atoms. Found 27 (27 requested) and removed 19 (13 requested) atoms. Cycle 24: After refmac, R = 0.2359 (Rfree = 0.000) for 4977 atoms. Found 27 (27 requested) and removed 28 (13 requested) atoms. Cycle 25: After refmac, R = 0.2085 (Rfree = 0.000) for 4964 atoms. Found 27 (27 requested) and removed 23 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 5176 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 5199 seeds are put forward Round 1: 244 peptides, 48 chains. Longest chain 10 peptides. Score 0.303 Round 2: 305 peptides, 51 chains. Longest chain 17 peptides. Score 0.414 Round 3: 305 peptides, 50 chains. Longest chain 17 peptides. Score 0.423 Round 4: 323 peptides, 53 chains. Longest chain 18 peptides. Score 0.434 Round 5: 324 peptides, 53 chains. Longest chain 15 peptides. Score 0.436 Taking the results from Round 5 Chains 53, Residues 271, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7461 reflections ( 99.35 % complete ) and 11888 restraints for refining 5080 atoms. 10842 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2544 (Rfree = 0.000) for 5080 atoms. Found 27 (27 requested) and removed 33 (13 requested) atoms. Cycle 27: After refmac, R = 0.2410 (Rfree = 0.000) for 5025 atoms. Found 27 (27 requested) and removed 27 (13 requested) atoms. Cycle 28: After refmac, R = 0.2229 (Rfree = 0.000) for 4978 atoms. Found 27 (27 requested) and removed 25 (13 requested) atoms. Cycle 29: After refmac, R = 0.1713 (Rfree = 0.000) for 4959 atoms. Found 22 (27 requested) and removed 20 (13 requested) atoms. Cycle 30: After refmac, R = 0.1638 (Rfree = 0.000) for 4943 atoms. Found 11 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.57 3.67 Search for helices and strands: 0 residues in 0 chains, 5099 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5114 seeds are put forward Round 1: 230 peptides, 50 chains. Longest chain 9 peptides. Score 0.247 Round 2: 282 peptides, 50 chains. Longest chain 14 peptides. Score 0.372 Round 3: 294 peptides, 50 chains. Longest chain 12 peptides. Score 0.399 Round 4: 329 peptides, 54 chains. Longest chain 20 peptides. Score 0.437 Round 5: 312 peptides, 50 chains. Longest chain 12 peptides. Score 0.438 Taking the results from Round 5 Chains 50, Residues 262, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 7461 reflections ( 99.35 % complete ) and 12020 restraints for refining 5058 atoms. 10997 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2544 (Rfree = 0.000) for 5058 atoms. Found 27 (27 requested) and removed 34 (13 requested) atoms. Cycle 32: After refmac, R = 0.2235 (Rfree = 0.000) for 5018 atoms. Found 27 (27 requested) and removed 33 (13 requested) atoms. Cycle 33: After refmac, R = 0.2112 (Rfree = 0.000) for 4977 atoms. Found 27 (27 requested) and removed 30 (13 requested) atoms. Cycle 34: After refmac, R = 0.2055 (Rfree = 0.000) for 4953 atoms. Found 27 (27 requested) and removed 20 (13 requested) atoms. Cycle 35: After refmac, R = 0.1950 (Rfree = 0.000) for 4951 atoms. Found 27 (27 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.56 3.66 Search for helices and strands: 0 residues in 0 chains, 5136 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 5155 seeds are put forward Round 1: 249 peptides, 55 chains. Longest chain 7 peptides. Score 0.243 Round 2: 298 peptides, 56 chains. Longest chain 14 peptides. Score 0.351 Round 3: 287 peptides, 50 chains. Longest chain 14 peptides. Score 0.384 Round 4: 294 peptides, 48 chains. Longest chain 14 peptides. Score 0.418 Round 5: 311 peptides, 52 chains. Longest chain 15 peptides. Score 0.417 Taking the results from Round 4 Chains 48, Residues 246, Estimated correctness of the model 0.0 % 3 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7461 reflections ( 99.35 % complete ) and 11749 restraints for refining 4995 atoms. 10805 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2568 (Rfree = 0.000) for 4995 atoms. Found 27 (27 requested) and removed 38 (13 requested) atoms. Cycle 37: After refmac, R = 0.2314 (Rfree = 0.000) for 4953 atoms. Found 27 (27 requested) and removed 31 (13 requested) atoms. Cycle 38: After refmac, R = 0.2115 (Rfree = 0.000) for 4921 atoms. Found 27 (27 requested) and removed 23 (13 requested) atoms. Cycle 39: After refmac, R = 0.2277 (Rfree = 0.000) for 4905 atoms. Found 27 (27 requested) and removed 22 (13 requested) atoms. Cycle 40: After refmac, R = 0.2031 (Rfree = 0.000) for 4898 atoms. Found 26 (26 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 5064 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5080 seeds are put forward Round 1: 221 peptides, 48 chains. Longest chain 11 peptides. Score 0.245 Round 2: 247 peptides, 46 chains. Longest chain 11 peptides. Score 0.331 Round 3: 255 peptides, 45 chains. Longest chain 12 peptides. Score 0.360 Round 4: 243 peptides, 44 chains. Longest chain 12 peptides. Score 0.342 Round 5: 255 peptides, 47 chains. Longest chain 11 peptides. Score 0.340 Taking the results from Round 3 Chains 45, Residues 210, Estimated correctness of the model 0.0 % 5 chains (21 residues) have been docked in sequence ------------------------------------------------------ 7461 reflections ( 99.35 % complete ) and 11519 restraints for refining 4876 atoms. 10687 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2558 (Rfree = 0.000) for 4876 atoms. Found 26 (26 requested) and removed 34 (13 requested) atoms. Cycle 42: After refmac, R = 0.2469 (Rfree = 0.000) for 4843 atoms. Found 26 (26 requested) and removed 27 (13 requested) atoms. Cycle 43: After refmac, R = 0.1856 (Rfree = 0.000) for 4815 atoms. Found 21 (26 requested) and removed 16 (13 requested) atoms. Cycle 44: After refmac, R = 0.1784 (Rfree = 0.000) for 4809 atoms. Found 16 (26 requested) and removed 15 (13 requested) atoms. Cycle 45: After refmac, R = 0.1671 (Rfree = 0.000) for 4798 atoms. Found 24 (26 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.57 3.67 Search for helices and strands: 0 residues in 0 chains, 4961 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 4976 seeds are put forward Round 1: 234 peptides, 50 chains. Longest chain 9 peptides. Score 0.257 Round 2: 275 peptides, 57 chains. Longest chain 9 peptides. Score 0.287 Round 3: 246 peptides, 47 chains. Longest chain 10 peptides. Score 0.318 Round 4: 265 peptides, 43 chains. Longest chain 14 peptides. Score 0.403 Round 5: 251 peptides, 45 chains. Longest chain 12 peptides. Score 0.351 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 43, Residues 222, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2afb-3_warpNtrace.pdb as input Building loops using Loopy2018 43 chains (222 residues) following loop building 2 chains (13 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7461 reflections ( 99.35 % complete ) and 11468 restraints for refining 4877 atoms. 10591 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2448 (Rfree = 0.000) for 4877 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2291 (Rfree = 0.000) for 4828 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2115 (Rfree = 0.000) for 4787 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2102 (Rfree = 0.000) for 4756 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:55:53 GMT 2018 Job finished. TimeTaking 87.96 Used memory is bytes: 20901968