null Mon 24 Dec 01:05:39 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 2h1q-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2h1q-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2h1q-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2h1q-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/2h1q-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2h1q-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 01:05:44 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/2h1q-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2h1q-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 405 and 0 Target number of residues in the AU: 405 Target solvent content: 0.6538 Checking the provided sequence file Detected sequence length: 270 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 540 Adjusted target solvent content: 0.54 Input MTZ file: 2h1q-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: 169 Cell parameters: 120.720 120.720 75.240 90.000 90.000 120.000 Input sequence file: 2h1q-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4320 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: 28.996 3.400 Wilson plot Bfac: 80.39 8694 reflections ( 99.63 % complete ) and 0 restraints for refining 4783 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3333 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3174 (Rfree = 0.000) for 4783 atoms. Found 36 (36 requested) and removed 33 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 3.34 Search for helices and strands: 0 residues in 0 chains, 4858 seeds are put forward NCS extension: 0 residues added, 4858 seeds are put forward Round 1: 176 peptides, 37 chains. Longest chain 9 peptides. Score 0.256 Round 2: 235 peptides, 37 chains. Longest chain 21 peptides. Score 0.420 Round 3: 254 peptides, 35 chains. Longest chain 21 peptides. Score 0.487 Round 4: 281 peptides, 38 chains. Longest chain 19 peptides. Score 0.518 Round 5: 278 peptides, 34 chains. Longest chain 31 peptides. Score 0.550 Taking the results from Round 5 Chains 35, Residues 244, Estimated correctness of the model 11.5 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8694 reflections ( 99.63 % complete ) and 8385 restraints for refining 3705 atoms. 7407 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2874 (Rfree = 0.000) for 3705 atoms. Found 26 (27 requested) and removed 53 (13 requested) atoms. Cycle 2: After refmac, R = 0.2591 (Rfree = 0.000) for 3616 atoms. Found 27 (27 requested) and removed 18 (13 requested) atoms. Cycle 3: After refmac, R = 0.2510 (Rfree = 0.000) for 3591 atoms. Found 24 (27 requested) and removed 23 (13 requested) atoms. Cycle 4: After refmac, R = 0.2347 (Rfree = 0.000) for 3572 atoms. Found 13 (27 requested) and removed 23 (13 requested) atoms. Cycle 5: After refmac, R = 0.2381 (Rfree = 0.000) for 3547 atoms. Found 13 (26 requested) and removed 22 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.41 3.23 Search for helices and strands: 0 residues in 0 chains, 3671 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3687 seeds are put forward Round 1: 242 peptides, 43 chains. Longest chain 13 peptides. Score 0.370 Round 2: 281 peptides, 41 chains. Longest chain 15 peptides. Score 0.488 Round 3: 270 peptides, 35 chains. Longest chain 21 peptides. Score 0.523 Round 4: 303 peptides, 40 chains. Longest chain 21 peptides. Score 0.546 Round 5: 304 peptides, 42 chains. Longest chain 24 peptides. Score 0.529 Taking the results from Round 4 Chains 41, Residues 263, Estimated correctness of the model 10.1 % 3 chains (36 residues) have been docked in sequence ------------------------------------------------------ 8694 reflections ( 99.63 % complete ) and 8178 restraints for refining 3739 atoms. 7034 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2529 (Rfree = 0.000) for 3739 atoms. Found 22 (28 requested) and removed 47 (14 requested) atoms. Cycle 7: After refmac, R = 0.2373 (Rfree = 0.000) for 3702 atoms. Found 12 (28 requested) and removed 29 (14 requested) atoms. Cycle 8: After refmac, R = 0.2292 (Rfree = 0.000) for 3678 atoms. Found 7 (27 requested) and removed 23 (13 requested) atoms. Cycle 9: After refmac, R = 0.2241 (Rfree = 0.000) for 3655 atoms. Found 5 (27 requested) and removed 21 (13 requested) atoms. Cycle 10: After refmac, R = 0.2216 (Rfree = 0.000) for 3636 atoms. Found 5 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.44 3.26 Search for helices and strands: 0 residues in 0 chains, 3729 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3743 seeds are put forward Round 1: 260 peptides, 42 chains. Longest chain 22 peptides. Score 0.427 Round 2: 285 peptides, 39 chains. Longest chain 22 peptides. Score 0.517 Round 3: 283 peptides, 36 chains. Longest chain 20 peptides. Score 0.542 Round 4: 291 peptides, 39 chains. Longest chain 22 peptides. Score 0.530 Round 5: 298 peptides, 37 chains. Longest chain 22 peptides. Score 0.564 Taking the results from Round 5 Chains 38, Residues 261, Estimated correctness of the model 16.5 % 3 chains (42 residues) have been docked in sequence ------------------------------------------------------ 8694 reflections ( 99.63 % complete ) and 8119 restraints for refining 3810 atoms. 6951 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2466 (Rfree = 0.000) for 3810 atoms. Found 25 (28 requested) and removed 47 (14 requested) atoms. Cycle 12: After refmac, R = 0.2308 (Rfree = 0.000) for 3774 atoms. Found 9 (28 requested) and removed 26 (14 requested) atoms. Cycle 13: After refmac, R = 0.2387 (Rfree = 0.000) for 3750 atoms. Found 13 (28 requested) and removed 28 (14 requested) atoms. Cycle 14: After refmac, R = 0.2283 (Rfree = 0.000) for 3722 atoms. Found 19 (28 requested) and removed 24 (14 requested) atoms. Cycle 15: After refmac, R = 0.2434 (Rfree = 0.000) for 3703 atoms. Found 28 (28 requested) and removed 31 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 3.24 Search for helices and strands: 0 residues in 0 chains, 3826 seeds are put forward NCS extension: 17 residues added (5 deleted due to clashes), 3843 seeds are put forward Round 1: 257 peptides, 41 chains. Longest chain 15 peptides. Score 0.431 Round 2: 279 peptides, 38 chains. Longest chain 17 peptides. Score 0.513 Round 3: 271 peptides, 40 chains. Longest chain 17 peptides. Score 0.475 Round 4: 286 peptides, 37 chains. Longest chain 26 peptides. Score 0.538 Round 5: 290 peptides, 42 chains. Longest chain 16 peptides. Score 0.498 Taking the results from Round 4 Chains 37, Residues 249, Estimated correctness of the model 7.2 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8694 reflections ( 99.63 % complete ) and 8702 restraints for refining 3849 atoms. 7722 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2261 (Rfree = 0.000) for 3849 atoms. Found 27 (29 requested) and removed 43 (14 requested) atoms. Cycle 17: After refmac, R = 0.2194 (Rfree = 0.000) for 3815 atoms. Found 17 (28 requested) and removed 38 (14 requested) atoms. Cycle 18: After refmac, R = 0.2135 (Rfree = 0.000) for 3783 atoms. Found 7 (28 requested) and removed 26 (14 requested) atoms. Cycle 19: After refmac, R = 0.2278 (Rfree = 0.000) for 3753 atoms. Found 24 (28 requested) and removed 29 (14 requested) atoms. Cycle 20: After refmac, R = 0.2355 (Rfree = 0.000) for 3734 atoms. Found 23 (28 requested) and removed 30 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.44 3.26 Search for helices and strands: 0 residues in 0 chains, 3874 seeds are put forward NCS extension: 34 residues added (3 deleted due to clashes), 3908 seeds are put forward Round 1: 213 peptides, 40 chains. Longest chain 12 peptides. Score 0.327 Round 2: 244 peptides, 36 chains. Longest chain 18 peptides. Score 0.453 Round 3: 267 peptides, 36 chains. Longest chain 20 peptides. Score 0.507 Round 4: 258 peptides, 41 chains. Longest chain 14 peptides. Score 0.433 Round 5: 265 peptides, 36 chains. Longest chain 20 peptides. Score 0.502 Taking the results from Round 3 Chains 36, Residues 231, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8694 reflections ( 99.63 % complete ) and 8861 restraints for refining 3837 atoms. 7973 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2253 (Rfree = 0.000) for 3837 atoms. Found 28 (28 requested) and removed 43 (14 requested) atoms. Cycle 22: After refmac, R = 0.2144 (Rfree = 0.000) for 3814 atoms. Found 24 (28 requested) and removed 24 (14 requested) atoms. Cycle 23: After refmac, R = 0.2619 (Rfree = 0.000) for 3807 atoms. Found 28 (28 requested) and removed 32 (14 requested) atoms. Cycle 24: After refmac, R = 0.2107 (Rfree = 0.000) for 3796 atoms. Found 22 (28 requested) and removed 25 (14 requested) atoms. Cycle 25: After refmac, R = 0.2600 (Rfree = 0.000) for 3783 atoms. Found 28 (28 requested) and removed 23 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.39 3.21 Search for helices and strands: 0 residues in 0 chains, 3893 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3913 seeds are put forward Round 1: 220 peptides, 40 chains. Longest chain 19 peptides. Score 0.346 Round 2: 244 peptides, 38 chains. Longest chain 14 peptides. Score 0.431 Round 3: 253 peptides, 37 chains. Longest chain 17 peptides. Score 0.464 Round 4: 267 peptides, 41 chains. Longest chain 24 peptides. Score 0.455 Round 5: 275 peptides, 40 chains. Longest chain 18 peptides. Score 0.484 Taking the results from Round 5 Chains 42, Residues 235, Estimated correctness of the model 0.0 % 4 chains (26 residues) have been docked in sequence ------------------------------------------------------ 8694 reflections ( 99.63 % complete ) and 8858 restraints for refining 3928 atoms. 7887 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2220 (Rfree = 0.000) for 3928 atoms. Found 23 (29 requested) and removed 44 (14 requested) atoms. Cycle 27: After refmac, R = 0.2089 (Rfree = 0.000) for 3889 atoms. Found 9 (29 requested) and removed 26 (14 requested) atoms. Cycle 28: After refmac, R = 0.2030 (Rfree = 0.000) for 3864 atoms. Found 9 (29 requested) and removed 21 (14 requested) atoms. Cycle 29: After refmac, R = 0.1988 (Rfree = 0.000) for 3848 atoms. Found 8 (29 requested) and removed 15 (14 requested) atoms. Cycle 30: After refmac, R = 0.2049 (Rfree = 0.000) for 3834 atoms. Found 11 (29 requested) and removed 25 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 3.25 Search for helices and strands: 0 residues in 0 chains, 3949 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3967 seeds are put forward Round 1: 215 peptides, 40 chains. Longest chain 16 peptides. Score 0.332 Round 2: 249 peptides, 38 chains. Longest chain 21 peptides. Score 0.444 Round 3: 255 peptides, 38 chains. Longest chain 23 peptides. Score 0.458 Round 4: 236 peptides, 36 chains. Longest chain 19 peptides. Score 0.433 Round 5: 244 peptides, 38 chains. Longest chain 21 peptides. Score 0.431 Taking the results from Round 3 Chains 39, Residues 217, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8694 reflections ( 99.63 % complete ) and 9015 restraints for refining 3928 atoms. 8150 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2112 (Rfree = 0.000) for 3928 atoms. Found 22 (29 requested) and removed 27 (14 requested) atoms. Cycle 32: After refmac, R = 0.2010 (Rfree = 0.000) for 3911 atoms. Found 13 (29 requested) and removed 22 (14 requested) atoms. Cycle 33: After refmac, R = 0.1957 (Rfree = 0.000) for 3893 atoms. Found 8 (29 requested) and removed 19 (14 requested) atoms. Cycle 34: After refmac, R = 0.1990 (Rfree = 0.000) for 3881 atoms. Found 21 (29 requested) and removed 19 (14 requested) atoms. Cycle 35: After refmac, R = 0.2331 (Rfree = 0.000) for 3875 atoms. Found 29 (29 requested) and removed 22 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.41 3.23 Search for helices and strands: 0 residues in 0 chains, 3985 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 4003 seeds are put forward Round 1: 178 peptides, 34 chains. Longest chain 17 peptides. Score 0.300 Round 2: 230 peptides, 39 chains. Longest chain 14 peptides. Score 0.384 Round 3: 230 peptides, 41 chains. Longest chain 12 peptides. Score 0.361 Round 4: 240 peptides, 40 chains. Longest chain 14 peptides. Score 0.399 Round 5: 248 peptides, 40 chains. Longest chain 14 peptides. Score 0.419 Taking the results from Round 5 Chains 40, Residues 208, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8694 reflections ( 99.63 % complete ) and 9294 restraints for refining 3927 atoms. 8502 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2175 (Rfree = 0.000) for 3927 atoms. Found 23 (29 requested) and removed 25 (14 requested) atoms. Cycle 37: After refmac, R = 0.2079 (Rfree = 0.000) for 3910 atoms. Found 19 (29 requested) and removed 19 (14 requested) atoms. Cycle 38: After refmac, R = 0.1992 (Rfree = 0.000) for 3902 atoms. Found 16 (29 requested) and removed 16 (14 requested) atoms. Cycle 39: After refmac, R = 0.1974 (Rfree = 0.000) for 3898 atoms. Found 17 (29 requested) and removed 18 (14 requested) atoms. Cycle 40: After refmac, R = 0.1932 (Rfree = 0.000) for 3893 atoms. Found 13 (29 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.43 3.25 Search for helices and strands: 0 residues in 0 chains, 4016 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 4027 seeds are put forward Round 1: 196 peptides, 40 chains. Longest chain 12 peptides. Score 0.278 Round 2: 216 peptides, 38 chains. Longest chain 11 peptides. Score 0.359 Round 3: 216 peptides, 35 chains. Longest chain 16 peptides. Score 0.394 Round 4: 213 peptides, 37 chains. Longest chain 12 peptides. Score 0.362 Round 5: 218 peptides, 33 chains. Longest chain 17 peptides. Score 0.422 Taking the results from Round 5 Chains 34, Residues 185, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 8694 reflections ( 99.63 % complete ) and 9002 restraints for refining 3927 atoms. 8234 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2183 (Rfree = 0.000) for 3927 atoms. Found 29 (29 requested) and removed 25 (14 requested) atoms. Cycle 42: After refmac, R = 0.2016 (Rfree = 0.000) for 3920 atoms. Found 14 (29 requested) and removed 18 (14 requested) atoms. Cycle 43: After refmac, R = 0.1918 (Rfree = 0.000) for 3908 atoms. Found 9 (29 requested) and removed 14 (14 requested) atoms. Cycle 44: After refmac, R = 0.1897 (Rfree = 0.000) for 3898 atoms. Found 14 (29 requested) and removed 17 (14 requested) atoms. Cycle 45: After refmac, R = 0.1803 (Rfree = 0.000) for 3889 atoms. Found 7 (29 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 3.24 Search for helices and strands: 0 residues in 0 chains, 4003 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 4023 seeds are put forward Round 1: 196 peptides, 42 chains. Longest chain 9 peptides. Score 0.254 Round 2: 218 peptides, 41 chains. Longest chain 11 peptides. Score 0.329 Round 3: 220 peptides, 38 chains. Longest chain 15 peptides. Score 0.369 Round 4: 212 peptides, 36 chains. Longest chain 13 peptides. Score 0.371 Round 5: 224 peptides, 38 chains. Longest chain 15 peptides. Score 0.380 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 38, Residues 186, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2h1q-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8694 reflections ( 99.63 % complete ) and 9153 restraints for refining 3927 atoms. 8433 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2062 (Rfree = 0.000) for 3927 atoms. Found 0 (29 requested) and removed 10 (14 requested) atoms. Cycle 47: After refmac, R = 0.1918 (Rfree = 0.000) for 3909 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.1866 (Rfree = 0.000) for 3890 atoms. Found 0 (29 requested) and removed 13 (14 requested) atoms. Cycle 49: After refmac, R = 0.1795 (Rfree = 0.000) for 3873 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:58:57 GMT 2018 Job finished. TimeTaking 53.31 Used memory is bytes: 18091800