null Mon 24 Dec 00:18:27 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 1vkh-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkh-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkh-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkh-3.2-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/1vkh-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkh-3.2-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 00:18:31 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/1vkh-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkh-3.2-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 395 and 0 Target number of residues in the AU: 395 Target solvent content: 0.5757 Checking the provided sequence file Detected sequence length: 273 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 546 Adjusted target solvent content: 0.41 Input MTZ file: 1vkh-3.2-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: 41.965 85.956 70.476 90.000 97.713 90.000 Input sequence file: 1vkh-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4368 target number of atoms Had to go as low as 0.60 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: 19.289 3.200 Wilson plot Bfac: 43.34 8219 reflections ( 99.49 % complete ) and 0 restraints for refining 4809 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3194 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2809 (Rfree = 0.000) for 4809 atoms. Found 43 (43 requested) and removed 80 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.84 3.21 Search for helices and strands: 0 residues in 0 chains, 4917 seeds are put forward NCS extension: 0 residues added, 4917 seeds are put forward Round 1: 231 peptides, 42 chains. Longest chain 12 peptides. Score 0.387 Round 2: 314 peptides, 54 chains. Longest chain 11 peptides. Score 0.482 Round 3: 308 peptides, 47 chains. Longest chain 15 peptides. Score 0.546 Round 4: 331 peptides, 47 chains. Longest chain 22 peptides. Score 0.601 Round 5: 349 peptides, 43 chains. Longest chain 23 peptides. Score 0.677 Taking the results from Round 5 Chains 44, Residues 306, Estimated correctness of the model 60.1 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 8219 reflections ( 99.49 % complete ) and 8338 restraints for refining 3987 atoms. 7065 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2568 (Rfree = 0.000) for 3987 atoms. Found 27 (35 requested) and removed 35 (17 requested) atoms. Cycle 2: After refmac, R = 0.2271 (Rfree = 0.000) for 3936 atoms. Found 16 (35 requested) and removed 21 (17 requested) atoms. Cycle 3: After refmac, R = 0.2138 (Rfree = 0.000) for 3917 atoms. Found 10 (35 requested) and removed 21 (17 requested) atoms. Cycle 4: After refmac, R = 0.2066 (Rfree = 0.000) for 3903 atoms. Found 7 (35 requested) and removed 18 (17 requested) atoms. Cycle 5: After refmac, R = 0.2059 (Rfree = 0.000) for 3890 atoms. Found 8 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.86 3.23 Search for helices and strands: 0 residues in 0 chains, 4015 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 4027 seeds are put forward Round 1: 294 peptides, 49 chains. Longest chain 15 peptides. Score 0.486 Round 2: 329 peptides, 46 chains. Longest chain 17 peptides. Score 0.607 Round 3: 339 peptides, 39 chains. Longest chain 21 peptides. Score 0.692 Round 4: 329 peptides, 38 chains. Longest chain 25 peptides. Score 0.682 Round 5: 333 peptides, 46 chains. Longest chain 16 peptides. Score 0.616 Taking the results from Round 3 Chains 41, Residues 300, Estimated correctness of the model 63.5 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 8219 reflections ( 99.49 % complete ) and 8599 restraints for refining 3987 atoms. 7381 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2367 (Rfree = 0.000) for 3987 atoms. Found 35 (35 requested) and removed 31 (17 requested) atoms. Cycle 7: After refmac, R = 0.2126 (Rfree = 0.000) for 3985 atoms. Found 13 (35 requested) and removed 21 (17 requested) atoms. Cycle 8: After refmac, R = 0.2052 (Rfree = 0.000) for 3969 atoms. Found 9 (35 requested) and removed 25 (17 requested) atoms. Cycle 9: After refmac, R = 0.1992 (Rfree = 0.000) for 3949 atoms. Found 5 (35 requested) and removed 17 (17 requested) atoms. Cycle 10: After refmac, R = 0.1964 (Rfree = 0.000) for 3935 atoms. Found 5 (35 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.87 3.24 Search for helices and strands: 0 residues in 0 chains, 4054 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 4075 seeds are put forward Round 1: 309 peptides, 45 chains. Longest chain 23 peptides. Score 0.570 Round 2: 343 peptides, 42 chains. Longest chain 20 peptides. Score 0.674 Round 3: 337 peptides, 40 chains. Longest chain 22 peptides. Score 0.680 Round 4: 345 peptides, 41 chains. Longest chain 30 peptides. Score 0.686 Round 5: 340 peptides, 39 chains. Longest chain 27 peptides. Score 0.694 Taking the results from Round 5 Chains 39, Residues 301, Estimated correctness of the model 63.9 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 8219 reflections ( 99.49 % complete ) and 8678 restraints for refining 3987 atoms. 7467 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2403 (Rfree = 0.000) for 3987 atoms. Found 26 (35 requested) and removed 25 (17 requested) atoms. Cycle 12: After refmac, R = 0.2127 (Rfree = 0.000) for 3979 atoms. Found 14 (35 requested) and removed 21 (17 requested) atoms. Cycle 13: After refmac, R = 0.2063 (Rfree = 0.000) for 3969 atoms. Found 5 (35 requested) and removed 20 (17 requested) atoms. Cycle 14: After refmac, R = 0.2045 (Rfree = 0.000) for 3954 atoms. Found 10 (35 requested) and removed 19 (17 requested) atoms. Cycle 15: After refmac, R = 0.2092 (Rfree = 0.000) for 3942 atoms. Found 17 (35 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.85 3.22 Search for helices and strands: 0 residues in 0 chains, 4096 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 4124 seeds are put forward Round 1: 294 peptides, 42 chains. Longest chain 25 peptides. Score 0.565 Round 2: 331 peptides, 41 chains. Longest chain 25 peptides. Score 0.659 Round 3: 317 peptides, 35 chains. Longest chain 25 peptides. Score 0.685 Round 4: 345 peptides, 39 chains. Longest chain 25 peptides. Score 0.703 Round 5: 350 peptides, 37 chains. Longest chain 23 peptides. Score 0.728 Taking the results from Round 5 Chains 37, Residues 313, Estimated correctness of the model 70.9 % 2 chains (30 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 137 A and 148 A 35 chains (316 residues) following loop building 1 chains (40 residues) in sequence following loop building ------------------------------------------------------ 8219 reflections ( 99.49 % complete ) and 8177 restraints for refining 3986 atoms. 6785 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2316 (Rfree = 0.000) for 3986 atoms. Found 35 (35 requested) and removed 25 (17 requested) atoms. Cycle 17: After refmac, R = 0.2108 (Rfree = 0.000) for 3990 atoms. Found 11 (34 requested) and removed 18 (17 requested) atoms. Cycle 18: After refmac, R = 0.2055 (Rfree = 0.000) for 3977 atoms. Found 14 (34 requested) and removed 18 (17 requested) atoms. Cycle 19: After refmac, R = 0.2008 (Rfree = 0.000) for 3971 atoms. Found 7 (33 requested) and removed 18 (17 requested) atoms. Cycle 20: After refmac, R = 0.1973 (Rfree = 0.000) for 3957 atoms. Found 8 (32 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.87 3.24 Search for helices and strands: 0 residues in 0 chains, 4073 seeds are put forward NCS extension: 41 residues added (4 deleted due to clashes), 4114 seeds are put forward Round 1: 287 peptides, 46 chains. Longest chain 16 peptides. Score 0.502 Round 2: 324 peptides, 39 chains. Longest chain 25 peptides. Score 0.663 Round 3: 316 peptides, 40 chains. Longest chain 19 peptides. Score 0.637 Round 4: 321 peptides, 41 chains. Longest chain 19 peptides. Score 0.638 Round 5: 312 peptides, 41 chains. Longest chain 26 peptides. Score 0.618 Taking the results from Round 2 Chains 39, Residues 285, Estimated correctness of the model 56.9 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 8219 reflections ( 99.49 % complete ) and 8586 restraints for refining 3987 atoms. 7426 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2153 (Rfree = 0.000) for 3987 atoms. Found 25 (31 requested) and removed 20 (17 requested) atoms. Cycle 22: After refmac, R = 0.2011 (Rfree = 0.000) for 3988 atoms. Found 12 (31 requested) and removed 20 (17 requested) atoms. Cycle 23: After refmac, R = 0.1997 (Rfree = 0.000) for 3979 atoms. Found 5 (31 requested) and removed 18 (17 requested) atoms. Cycle 24: After refmac, R = 0.1949 (Rfree = 0.000) for 3966 atoms. Found 10 (31 requested) and removed 18 (17 requested) atoms. Cycle 25: After refmac, R = 0.1962 (Rfree = 0.000) for 3957 atoms. Found 10 (31 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.89 3.26 Search for helices and strands: 0 residues in 0 chains, 4047 seeds are put forward NCS extension: 24 residues added (4 deleted due to clashes), 4071 seeds are put forward Round 1: 289 peptides, 47 chains. Longest chain 12 peptides. Score 0.495 Round 2: 318 peptides, 40 chains. Longest chain 18 peptides. Score 0.641 Round 3: 322 peptides, 42 chains. Longest chain 16 peptides. Score 0.631 Round 4: 301 peptides, 38 chains. Longest chain 27 peptides. Score 0.624 Round 5: 315 peptides, 39 chains. Longest chain 16 peptides. Score 0.644 Taking the results from Round 5 Chains 39, Residues 276, Estimated correctness of the model 52.4 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 8219 reflections ( 99.49 % complete ) and 8833 restraints for refining 3987 atoms. 7721 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2281 (Rfree = 0.000) for 3987 atoms. Found 27 (31 requested) and removed 23 (17 requested) atoms. Cycle 27: After refmac, R = 0.2072 (Rfree = 0.000) for 3987 atoms. Found 14 (31 requested) and removed 18 (17 requested) atoms. Cycle 28: After refmac, R = 0.1990 (Rfree = 0.000) for 3977 atoms. Found 16 (31 requested) and removed 19 (17 requested) atoms. Cycle 29: After refmac, R = 0.1909 (Rfree = 0.000) for 3970 atoms. Found 9 (31 requested) and removed 18 (17 requested) atoms. Cycle 30: After refmac, R = 0.1865 (Rfree = 0.000) for 3958 atoms. Found 10 (31 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.88 3.25 Search for helices and strands: 0 residues in 0 chains, 4073 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 4088 seeds are put forward Round 1: 265 peptides, 41 chains. Longest chain 16 peptides. Score 0.501 Round 2: 286 peptides, 36 chains. Longest chain 26 peptides. Score 0.610 Round 3: 294 peptides, 40 chains. Longest chain 17 peptides. Score 0.587 Round 4: 294 peptides, 42 chains. Longest chain 18 peptides. Score 0.565 Round 5: 293 peptides, 38 chains. Longest chain 26 peptides. Score 0.606 Taking the results from Round 2 Chains 36, Residues 250, Estimated correctness of the model 43.7 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 8219 reflections ( 99.49 % complete ) and 8910 restraints for refining 3987 atoms. 7925 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1951 (Rfree = 0.000) for 3987 atoms. Found 24 (31 requested) and removed 19 (17 requested) atoms. Cycle 32: After refmac, R = 0.1819 (Rfree = 0.000) for 3991 atoms. Found 9 (31 requested) and removed 18 (17 requested) atoms. Cycle 33: After refmac, R = 0.1757 (Rfree = 0.000) for 3978 atoms. Found 8 (31 requested) and removed 18 (17 requested) atoms. Cycle 34: After refmac, R = 0.1714 (Rfree = 0.000) for 3968 atoms. Found 5 (31 requested) and removed 17 (17 requested) atoms. Cycle 35: After refmac, R = 0.1712 (Rfree = 0.000) for 3955 atoms. Found 5 (31 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.88 3.25 Search for helices and strands: 0 residues in 0 chains, 4055 seeds are put forward NCS extension: 35 residues added (2 deleted due to clashes), 4090 seeds are put forward Round 1: 252 peptides, 38 chains. Longest chain 13 peptides. Score 0.501 Round 2: 270 peptides, 36 chains. Longest chain 18 peptides. Score 0.572 Round 3: 267 peptides, 38 chains. Longest chain 14 peptides. Score 0.541 Round 4: 281 peptides, 39 chains. Longest chain 17 peptides. Score 0.566 Round 5: 282 peptides, 36 chains. Longest chain 17 peptides. Score 0.601 Taking the results from Round 5 Chains 36, Residues 246, Estimated correctness of the model 41.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8219 reflections ( 99.49 % complete ) and 9012 restraints for refining 3987 atoms. 8064 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1988 (Rfree = 0.000) for 3987 atoms. Found 24 (31 requested) and removed 20 (17 requested) atoms. Cycle 37: After refmac, R = 0.1837 (Rfree = 0.000) for 3989 atoms. Found 10 (31 requested) and removed 18 (17 requested) atoms. Cycle 38: After refmac, R = 0.1784 (Rfree = 0.000) for 3976 atoms. Found 7 (31 requested) and removed 17 (17 requested) atoms. Cycle 39: After refmac, R = 0.1746 (Rfree = 0.000) for 3964 atoms. Found 7 (31 requested) and removed 20 (17 requested) atoms. Cycle 40: After refmac, R = 0.1742 (Rfree = 0.000) for 3951 atoms. Found 14 (31 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.89 3.26 Search for helices and strands: 0 residues in 0 chains, 4053 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 4077 seeds are put forward Round 1: 213 peptides, 36 chains. Longest chain 13 peptides. Score 0.411 Round 2: 249 peptides, 34 chains. Longest chain 27 peptides. Score 0.541 Round 3: 251 peptides, 39 chains. Longest chain 15 peptides. Score 0.486 Round 4: 245 peptides, 35 chains. Longest chain 16 peptides. Score 0.518 Round 5: 243 peptides, 35 chains. Longest chain 17 peptides. Score 0.513 Taking the results from Round 2 Chains 34, Residues 215, Estimated correctness of the model 24.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8219 reflections ( 99.49 % complete ) and 9248 restraints for refining 3971 atoms. 8422 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1885 (Rfree = 0.000) for 3971 atoms. Found 13 (31 requested) and removed 19 (17 requested) atoms. Cycle 42: After refmac, R = 0.1985 (Rfree = 0.000) for 3963 atoms. Found 18 (31 requested) and removed 19 (17 requested) atoms. Cycle 43: After refmac, R = 0.1815 (Rfree = 0.000) for 3961 atoms. Found 11 (31 requested) and removed 17 (17 requested) atoms. Cycle 44: After refmac, R = 0.1774 (Rfree = 0.000) for 3954 atoms. Found 8 (31 requested) and removed 17 (17 requested) atoms. Cycle 45: After refmac, R = 0.1752 (Rfree = 0.000) for 3945 atoms. Found 5 (31 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.90 3.27 Search for helices and strands: 0 residues in 0 chains, 4040 seeds are put forward NCS extension: 38 residues added (1 deleted due to clashes), 4078 seeds are put forward Round 1: 205 peptides, 35 chains. Longest chain 15 peptides. Score 0.400 Round 2: 244 peptides, 36 chains. Longest chain 17 peptides. Score 0.503 Round 3: 227 peptides, 32 chains. Longest chain 16 peptides. Score 0.505 Round 4: 215 peptides, 34 chains. Longest chain 17 peptides. Score 0.444 Round 5: 225 peptides, 35 chains. Longest chain 13 peptides. Score 0.461 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 195, Estimated correctness of the model 12.9 % 1 chains (11 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1vkh-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8219 reflections ( 99.49 % complete ) and 9142 restraints for refining 3970 atoms. 8348 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1861 (Rfree = 0.000) for 3970 atoms. Found 0 (31 requested) and removed 9 (17 requested) atoms. Cycle 47: After refmac, R = 0.1855 (Rfree = 0.000) for 3958 atoms. Found 0 (31 requested) and removed 4 (17 requested) atoms. Cycle 48: After refmac, R = 0.1861 (Rfree = 0.000) for 3954 atoms. Found 0 (31 requested) and removed 5 (17 requested) atoms. Cycle 49: After refmac, R = 0.1874 (Rfree = 0.000) for 3948 atoms. Found 0 (31 requested) and removed 7 (17 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:00:21 GMT 2018 Job finished. TimeTaking 41.9 Used memory is bytes: 7056664