Mon 24 Dec 00:35:02 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 2fna-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fna-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fna-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fna-3.4-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/2fna-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fna-3.4-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 ============================================================ Mon 24 Dec 00:35:07 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/2fna-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fna-3.4-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 544 and 0 Target number of residues in the AU: 544 Target solvent content: 0.6469 Checking the provided sequence file Detected sequence length: 357 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 714 Adjusted target solvent content: 0.54 Input MTZ file: 2fna-3.4-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: 55.380 108.390 70.600 90.000 100.307 90.000 Input sequence file: 2fna-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5712 target number of atoms Had to go as low as 0.80 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: 69.461 3.400 Wilson plot Bfac: 75.99 11204 reflections ( 98.52 % complete ) and 0 restraints for refining 6366 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3181 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2756 (Rfree = 0.000) for 6366 atoms. Found 48 (48 requested) and removed 43 (24 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.40 3.22 Search for helices and strands: 0 residues in 0 chains, 6544 seeds are put forward NCS extension: 0 residues added, 6544 seeds are put forward Round 1: 344 peptides, 61 chains. Longest chain 14 peptides. Score 0.383 Round 2: 397 peptides, 60 chains. Longest chain 15 peptides. Score 0.488 Round 3: 423 peptides, 56 chains. Longest chain 20 peptides. Score 0.560 Round 4: 420 peptides, 55 chains. Longest chain 19 peptides. Score 0.562 Round 5: 422 peptides, 55 chains. Longest chain 20 peptides. Score 0.565 Taking the results from Round 5 Chains 57, Residues 367, Estimated correctness of the model 16.8 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 11204 reflections ( 98.52 % complete ) and 11460 restraints for refining 5193 atoms. 9969 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2225 (Rfree = 0.000) for 5193 atoms. Found 20 (39 requested) and removed 33 (19 requested) atoms. Cycle 2: After refmac, R = 0.2090 (Rfree = 0.000) for 5129 atoms. Found 12 (39 requested) and removed 30 (19 requested) atoms. Cycle 3: After refmac, R = 0.2052 (Rfree = 0.000) for 5090 atoms. Found 11 (38 requested) and removed 20 (19 requested) atoms. Cycle 4: After refmac, R = 0.2003 (Rfree = 0.000) for 5066 atoms. Found 5 (38 requested) and removed 21 (19 requested) atoms. Cycle 5: After refmac, R = 0.1979 (Rfree = 0.000) for 5044 atoms. Found 6 (38 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 3.19 Search for helices and strands: 0 residues in 0 chains, 5278 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 5303 seeds are put forward Round 1: 361 peptides, 58 chains. Longest chain 13 peptides. Score 0.440 Round 2: 422 peptides, 59 chains. Longest chain 20 peptides. Score 0.537 Round 3: 425 peptides, 53 chains. Longest chain 21 peptides. Score 0.583 Round 4: 424 peptides, 51 chains. Longest chain 22 peptides. Score 0.595 Round 5: 420 peptides, 52 chains. Longest chain 26 peptides. Score 0.583 Taking the results from Round 4 Chains 51, Residues 373, Estimated correctness of the model 27.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 11204 reflections ( 98.52 % complete ) and 11617 restraints for refining 5192 atoms. 10176 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2148 (Rfree = 0.000) for 5192 atoms. Found 19 (39 requested) and removed 20 (19 requested) atoms. Cycle 7: After refmac, R = 0.2003 (Rfree = 0.000) for 5179 atoms. Found 8 (39 requested) and removed 20 (19 requested) atoms. Cycle 8: After refmac, R = 0.1950 (Rfree = 0.000) for 5157 atoms. Found 3 (39 requested) and removed 19 (19 requested) atoms. Cycle 9: After refmac, R = 0.1970 (Rfree = 0.000) for 5137 atoms. Found 6 (38 requested) and removed 19 (19 requested) atoms. Cycle 10: After refmac, R = 0.1961 (Rfree = 0.000) for 5120 atoms. Found 9 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.19 Search for helices and strands: 0 residues in 0 chains, 5308 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 5326 seeds are put forward Round 1: 390 peptides, 59 chains. Longest chain 29 peptides. Score 0.484 Round 2: 421 peptides, 57 chains. Longest chain 18 peptides. Score 0.550 Round 3: 418 peptides, 55 chains. Longest chain 23 peptides. Score 0.559 Round 4: 440 peptides, 49 chains. Longest chain 25 peptides. Score 0.631 Round 5: 433 peptides, 55 chains. Longest chain 22 peptides. Score 0.582 Taking the results from Round 4 Chains 50, Residues 391, Estimated correctness of the model 38.5 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 11204 reflections ( 98.52 % complete ) and 11486 restraints for refining 5193 atoms. 9937 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2219 (Rfree = 0.000) for 5193 atoms. Found 24 (39 requested) and removed 23 (19 requested) atoms. Cycle 12: After refmac, R = 0.2093 (Rfree = 0.000) for 5181 atoms. Found 7 (39 requested) and removed 27 (19 requested) atoms. Cycle 13: After refmac, R = 0.2015 (Rfree = 0.000) for 5151 atoms. Found 8 (38 requested) and removed 19 (19 requested) atoms. Cycle 14: After refmac, R = 0.1987 (Rfree = 0.000) for 5132 atoms. Found 8 (38 requested) and removed 19 (19 requested) atoms. Cycle 15: After refmac, R = 0.1919 (Rfree = 0.000) for 5119 atoms. Found 6 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.40 3.22 Search for helices and strands: 0 residues in 0 chains, 5299 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 5323 seeds are put forward Round 1: 387 peptides, 67 chains. Longest chain 18 peptides. Score 0.416 Round 2: 387 peptides, 55 chains. Longest chain 17 peptides. Score 0.509 Round 3: 422 peptides, 57 chains. Longest chain 23 peptides. Score 0.551 Round 4: 414 peptides, 55 chains. Longest chain 20 peptides. Score 0.553 Round 5: 411 peptides, 54 chains. Longest chain 20 peptides. Score 0.555 Taking the results from Round 5 Chains 54, Residues 357, Estimated correctness of the model 13.3 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 11204 reflections ( 98.52 % complete ) and 11769 restraints for refining 5192 atoms. 10367 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2167 (Rfree = 0.000) for 5192 atoms. Found 18 (39 requested) and removed 22 (19 requested) atoms. Cycle 17: After refmac, R = 0.1998 (Rfree = 0.000) for 5175 atoms. Found 12 (39 requested) and removed 21 (19 requested) atoms. Cycle 18: After refmac, R = 0.1968 (Rfree = 0.000) for 5156 atoms. Found 5 (39 requested) and removed 21 (19 requested) atoms. Cycle 19: After refmac, R = 0.1962 (Rfree = 0.000) for 5136 atoms. Found 7 (38 requested) and removed 20 (19 requested) atoms. Cycle 20: After refmac, R = 0.1889 (Rfree = 0.000) for 5117 atoms. Found 6 (38 requested) and removed 22 (19 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.36 3.19 Search for helices and strands: 0 residues in 0 chains, 5305 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 5324 seeds are put forward Round 1: 366 peptides, 66 chains. Longest chain 11 peptides. Score 0.384 Round 2: 404 peptides, 63 chains. Longest chain 14 peptides. Score 0.478 Round 3: 388 peptides, 60 chains. Longest chain 17 peptides. Score 0.473 Round 4: 410 peptides, 59 chains. Longest chain 16 peptides. Score 0.518 Round 5: 397 peptides, 51 chains. Longest chain 21 peptides. Score 0.554 Taking the results from Round 5 Chains 53, Residues 346, Estimated correctness of the model 13.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 11204 reflections ( 98.52 % complete ) and 11704 restraints for refining 5192 atoms. 10332 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2063 (Rfree = 0.000) for 5192 atoms. Found 21 (39 requested) and removed 24 (19 requested) atoms. Cycle 22: After refmac, R = 0.1931 (Rfree = 0.000) for 5173 atoms. Found 6 (39 requested) and removed 19 (19 requested) atoms. Cycle 23: After refmac, R = 0.1936 (Rfree = 0.000) for 5150 atoms. Found 9 (38 requested) and removed 19 (19 requested) atoms. Cycle 24: After refmac, R = 0.1887 (Rfree = 0.000) for 5137 atoms. Found 5 (38 requested) and removed 19 (19 requested) atoms. Cycle 25: After refmac, R = 0.1758 (Rfree = 0.000) for 5119 atoms. Found 1 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.37 3.19 Search for helices and strands: 0 residues in 0 chains, 5277 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 5297 seeds are put forward Round 1: 382 peptides, 68 chains. Longest chain 15 peptides. Score 0.399 Round 2: 419 peptides, 61 chains. Longest chain 18 peptides. Score 0.518 Round 3: 410 peptides, 60 chains. Longest chain 26 peptides. Score 0.511 Round 4: 380 peptides, 55 chains. Longest chain 19 peptides. Score 0.497 Round 5: 395 peptides, 52 chains. Longest chain 23 peptides. Score 0.544 Taking the results from Round 5 Chains 57, Residues 343, Estimated correctness of the model 9.3 % 4 chains (44 residues) have been docked in sequence ------------------------------------------------------ 11204 reflections ( 98.52 % complete ) and 11333 restraints for refining 5191 atoms. 9835 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2179 (Rfree = 0.000) for 5191 atoms. Found 36 (39 requested) and removed 22 (19 requested) atoms. Cycle 27: After refmac, R = 0.1969 (Rfree = 0.000) for 5183 atoms. Found 12 (39 requested) and removed 21 (19 requested) atoms. Cycle 28: After refmac, R = 0.1945 (Rfree = 0.000) for 5163 atoms. Found 6 (39 requested) and removed 19 (19 requested) atoms. Cycle 29: After refmac, R = 0.1948 (Rfree = 0.000) for 5144 atoms. Found 12 (38 requested) and removed 19 (19 requested) atoms. Cycle 30: After refmac, R = 0.1883 (Rfree = 0.000) for 5123 atoms. Found 9 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.22 Search for helices and strands: 0 residues in 0 chains, 5290 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 5308 seeds are put forward Round 1: 337 peptides, 60 chains. Longest chain 17 peptides. Score 0.378 Round 2: 380 peptides, 57 chains. Longest chain 22 peptides. Score 0.482 Round 3: 394 peptides, 60 chains. Longest chain 23 peptides. Score 0.483 Round 4: 390 peptides, 57 chains. Longest chain 22 peptides. Score 0.499 Round 5: 405 peptides, 57 chains. Longest chain 20 peptides. Score 0.524 Taking the results from Round 5 Chains 58, Residues 348, Estimated correctness of the model 1.9 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 11204 reflections ( 98.52 % complete ) and 11515 restraints for refining 5192 atoms. 10113 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2062 (Rfree = 0.000) for 5192 atoms. Found 28 (39 requested) and removed 21 (19 requested) atoms. Cycle 32: After refmac, R = 0.1901 (Rfree = 0.000) for 5188 atoms. Found 7 (39 requested) and removed 19 (19 requested) atoms. Cycle 33: After refmac, R = 0.1920 (Rfree = 0.000) for 5164 atoms. Found 9 (39 requested) and removed 19 (19 requested) atoms. Cycle 34: After refmac, R = 0.1869 (Rfree = 0.000) for 5149 atoms. Found 12 (38 requested) and removed 19 (19 requested) atoms. Cycle 35: After refmac, R = 0.1803 (Rfree = 0.000) for 5137 atoms. Found 7 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 3.22 Search for helices and strands: 0 residues in 0 chains, 5291 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 5320 seeds are put forward Round 1: 313 peptides, 54 chains. Longest chain 11 peptides. Score 0.382 Round 2: 357 peptides, 52 chains. Longest chain 17 peptides. Score 0.480 Round 3: 345 peptides, 50 chains. Longest chain 14 peptides. Score 0.475 Round 4: 348 peptides, 51 chains. Longest chain 15 peptides. Score 0.472 Round 5: 365 peptides, 53 chains. Longest chain 14 peptides. Score 0.487 Taking the results from Round 5 Chains 53, Residues 312, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 11204 reflections ( 98.52 % complete ) and 12072 restraints for refining 5192 atoms. 10877 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1982 (Rfree = 0.000) for 5192 atoms. Found 20 (39 requested) and removed 19 (19 requested) atoms. Cycle 37: After refmac, R = 0.1914 (Rfree = 0.000) for 5180 atoms. Found 11 (39 requested) and removed 20 (19 requested) atoms. Cycle 38: After refmac, R = 0.1841 (Rfree = 0.000) for 5167 atoms. Found 12 (39 requested) and removed 19 (19 requested) atoms. Cycle 39: After refmac, R = 0.1783 (Rfree = 0.000) for 5159 atoms. Found 4 (38 requested) and removed 19 (19 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1757 (Rfree = 0.000) for 5142 atoms. Found 8 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 3.21 Search for helices and strands: 0 residues in 0 chains, 5288 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 5301 seeds are put forward Round 1: 281 peptides, 51 chains. Longest chain 12 peptides. Score 0.343 Round 2: 339 peptides, 51 chains. Longest chain 16 peptides. Score 0.456 Round 3: 335 peptides, 49 chains. Longest chain 16 peptides. Score 0.465 Round 4: 331 peptides, 50 chains. Longest chain 15 peptides. Score 0.450 Round 5: 345 peptides, 55 chains. Longest chain 14 peptides. Score 0.435 Taking the results from Round 3 Chains 49, Residues 286, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 11204 reflections ( 98.52 % complete ) and 12193 restraints for refining 5193 atoms. 11098 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2006 (Rfree = 0.000) for 5193 atoms. Found 25 (39 requested) and removed 19 (19 requested) atoms. Cycle 42: After refmac, R = 0.1907 (Rfree = 0.000) for 5196 atoms. Found 6 (39 requested) and removed 19 (19 requested) atoms. Cycle 43: After refmac, R = 0.1873 (Rfree = 0.000) for 5178 atoms. Found 9 (39 requested) and removed 19 (19 requested) atoms. Cycle 44: After refmac, R = 0.1817 (Rfree = 0.000) for 5164 atoms. Found 9 (39 requested) and removed 19 (19 requested) atoms. Cycle 45: After refmac, R = 0.1796 (Rfree = 0.000) for 5153 atoms. Found 7 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.41 3.23 Search for helices and strands: 0 residues in 0 chains, 5293 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 5306 seeds are put forward Round 1: 278 peptides, 50 chains. Longest chain 12 peptides. Score 0.346 Round 2: 315 peptides, 49 chains. Longest chain 12 peptides. Score 0.428 Round 3: 313 peptides, 50 chains. Longest chain 12 peptides. Score 0.416 Round 4: 304 peptides, 48 chains. Longest chain 15 peptides. Score 0.415 Round 5: 307 peptides, 48 chains. Longest chain 17 peptides. Score 0.421 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 49, Residues 266, 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 2fna-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11204 reflections ( 98.52 % complete ) and 12236 restraints for refining 5193 atoms. 11221 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1859 (Rfree = 0.000) for 5193 atoms. Found 0 (39 requested) and removed 12 (19 requested) atoms. Cycle 47: After refmac, R = 0.1802 (Rfree = 0.000) for 5178 atoms. Found 0 (39 requested) and removed 6 (19 requested) atoms. Cycle 48: After refmac, R = 0.1766 (Rfree = 0.000) for 5169 atoms. Found 0 (39 requested) and removed 4 (19 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1756 (Rfree = 0.000) for 5164 atoms. Found 0 (38 requested) and removed 5 (19 requested) atoms. Writing output files ... TimeTaking 62.07