Mon 24 Dec 00:54:56 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 1vqs-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vqs-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vqs-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqs-4.0-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/1vqs-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqs-4.0-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 00:55:01 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/1vqs-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqs-4.0-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 449 and 0 Target number of residues in the AU: 449 Target solvent content: 0.6429 Checking the provided sequence file Detected sequence length: 116 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 5 Adjusted target number of residues: 580 Adjusted target solvent content: 0.54 Input MTZ file: 1vqs-4.0-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: 97 Cell parameters: 94.778 94.778 303.043 90.000 90.000 90.000 Input sequence file: 1vqs-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4640 target number of atoms Had to go as low as 0.85 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: 29.971 4.000 Wilson plot Bfac: 73.36 6209 reflections ( 99.41 % complete ) and 0 restraints for refining 5121 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3472 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3302 (Rfree = 0.000) for 5121 atoms. Found 24 (24 requested) and removed 25 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.59 3.40 Search for helices and strands: 0 residues in 0 chains, 5208 seeds are put forward NCS extension: 0 residues added, 5208 seeds are put forward Round 1: 185 peptides, 36 chains. Longest chain 10 peptides. Score 0.289 Round 2: 271 peptides, 43 chains. Longest chain 12 peptides. Score 0.430 Round 3: 299 peptides, 43 chains. Longest chain 20 peptides. Score 0.491 Round 4: 318 peptides, 39 chains. Longest chain 23 peptides. Score 0.566 Round 5: 324 peptides, 43 chains. Longest chain 22 peptides. Score 0.542 Taking the results from Round 4 Chains 39, Residues 279, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6209 reflections ( 99.41 % complete ) and 9742 restraints for refining 4189 atoms. 8665 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2856 (Rfree = 0.000) for 4189 atoms. Found 12 (19 requested) and removed 31 (9 requested) atoms. Cycle 2: After refmac, R = 0.2754 (Rfree = 0.000) for 4064 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. Cycle 3: After refmac, R = 0.2650 (Rfree = 0.000) for 3992 atoms. Found 19 (19 requested) and removed 32 (9 requested) atoms. Cycle 4: After refmac, R = 0.2630 (Rfree = 0.000) for 3935 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 5: After refmac, R = 0.2589 (Rfree = 0.000) for 3916 atoms. Found 18 (18 requested) and removed 22 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.62 3.43 Search for helices and strands: 0 residues in 0 chains, 4054 seeds are put forward NCS extension: 32 residues added (8 deleted due to clashes), 4086 seeds are put forward Round 1: 250 peptides, 46 chains. Longest chain 12 peptides. Score 0.348 Round 2: 284 peptides, 42 chains. Longest chain 18 peptides. Score 0.469 Round 3: 275 peptides, 38 chains. Longest chain 17 peptides. Score 0.488 Round 4: 280 peptides, 36 chains. Longest chain 22 peptides. Score 0.518 Round 5: 292 peptides, 43 chains. Longest chain 14 peptides. Score 0.476 Taking the results from Round 4 Chains 36, Residues 244, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6209 reflections ( 99.41 % complete ) and 9478 restraints for refining 4073 atoms. 8538 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2477 (Rfree = 0.000) for 4073 atoms. Found 19 (19 requested) and removed 45 (9 requested) atoms. Cycle 7: After refmac, R = 0.2478 (Rfree = 0.000) for 3999 atoms. Found 19 (19 requested) and removed 33 (9 requested) atoms. Cycle 8: After refmac, R = 0.2355 (Rfree = 0.000) for 3964 atoms. Found 18 (18 requested) and removed 23 (9 requested) atoms. Cycle 9: After refmac, R = 0.2395 (Rfree = 0.000) for 3918 atoms. Found 18 (18 requested) and removed 26 (9 requested) atoms. Cycle 10: After refmac, R = 0.1938 (Rfree = 0.000) for 3889 atoms. Found 9 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.67 3.48 Search for helices and strands: 0 residues in 0 chains, 4047 seeds are put forward NCS extension: 26 residues added (3 deleted due to clashes), 4073 seeds are put forward Round 1: 262 peptides, 50 chains. Longest chain 9 peptides. Score 0.335 Round 2: 285 peptides, 45 chains. Longest chain 12 peptides. Score 0.441 Round 3: 296 peptides, 46 chains. Longest chain 14 peptides. Score 0.456 Round 4: 307 peptides, 43 chains. Longest chain 23 peptides. Score 0.508 Round 5: 290 peptides, 41 chains. Longest chain 14 peptides. Score 0.491 Taking the results from Round 4 Chains 44, Residues 264, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6209 reflections ( 99.41 % complete ) and 8894 restraints for refining 4062 atoms. 7825 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2390 (Rfree = 0.000) for 4062 atoms. Found 17 (19 requested) and removed 35 (9 requested) atoms. Cycle 12: After refmac, R = 0.2324 (Rfree = 0.000) for 3993 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 13: After refmac, R = 0.2111 (Rfree = 0.000) for 3963 atoms. Found 18 (18 requested) and removed 21 (9 requested) atoms. Cycle 14: After refmac, R = 0.2143 (Rfree = 0.000) for 3919 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. Cycle 15: After refmac, R = 0.2043 (Rfree = 0.000) for 3901 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 3.38 Search for helices and strands: 0 residues in 0 chains, 4050 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 4062 seeds are put forward Round 1: 255 peptides, 48 chains. Longest chain 12 peptides. Score 0.339 Round 2: 280 peptides, 44 chains. Longest chain 14 peptides. Score 0.440 Round 3: 267 peptides, 40 chains. Longest chain 18 peptides. Score 0.451 Round 4: 267 peptides, 44 chains. Longest chain 12 peptides. Score 0.410 Round 5: 267 peptides, 43 chains. Longest chain 13 peptides. Score 0.420 Taking the results from Round 3 Chains 40, Residues 227, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6209 reflections ( 99.41 % complete ) and 9103 restraints for refining 3989 atoms. 8235 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2197 (Rfree = 0.000) for 3989 atoms. Found 18 (18 requested) and removed 24 (9 requested) atoms. Cycle 17: After refmac, R = 0.2287 (Rfree = 0.000) for 3941 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 18: After refmac, R = 0.1836 (Rfree = 0.000) for 3919 atoms. Found 8 (18 requested) and removed 16 (9 requested) atoms. Cycle 19: After refmac, R = 0.1723 (Rfree = 0.000) for 3891 atoms. Found 6 (18 requested) and removed 14 (9 requested) atoms. Cycle 20: After refmac, R = 0.1728 (Rfree = 0.000) for 3868 atoms. Found 10 (18 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.63 3.44 Search for helices and strands: 0 residues in 0 chains, 3990 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4007 seeds are put forward Round 1: 237 peptides, 48 chains. Longest chain 10 peptides. Score 0.292 Round 2: 276 peptides, 52 chains. Longest chain 12 peptides. Score 0.349 Round 3: 279 peptides, 46 chains. Longest chain 15 peptides. Score 0.418 Round 4: 288 peptides, 44 chains. Longest chain 30 peptides. Score 0.458 Round 5: 275 peptides, 39 chains. Longest chain 23 peptides. Score 0.478 Taking the results from Round 5 Chains 39, Residues 236, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6209 reflections ( 99.41 % complete ) and 9527 restraints for refining 4108 atoms. 8622 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2612 (Rfree = 0.000) for 4108 atoms. Found 19 (19 requested) and removed 43 (9 requested) atoms. Cycle 22: After refmac, R = 0.2505 (Rfree = 0.000) for 4051 atoms. Found 19 (19 requested) and removed 37 (9 requested) atoms. Cycle 23: After refmac, R = 0.1952 (Rfree = 0.000) for 3991 atoms. Found 8 (19 requested) and removed 26 (9 requested) atoms. Cycle 24: After refmac, R = 0.2322 (Rfree = 0.000) for 3953 atoms. Found 18 (18 requested) and removed 22 (9 requested) atoms. Cycle 25: After refmac, R = 0.2449 (Rfree = 0.000) for 3931 atoms. Found 18 (18 requested) and removed 26 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.53 3.35 Search for helices and strands: 0 residues in 0 chains, 4052 seeds are put forward NCS extension: 35 residues added (1 deleted due to clashes), 4087 seeds are put forward Round 1: 238 peptides, 49 chains. Longest chain 9 peptides. Score 0.284 Round 2: 272 peptides, 49 chains. Longest chain 13 peptides. Score 0.370 Round 3: 253 peptides, 43 chains. Longest chain 13 peptides. Score 0.387 Round 4: 279 peptides, 51 chains. Longest chain 13 peptides. Score 0.367 Round 5: 288 peptides, 45 chains. Longest chain 16 peptides. Score 0.448 Taking the results from Round 5 Chains 45, Residues 243, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6209 reflections ( 99.41 % complete ) and 9341 restraints for refining 4099 atoms. 8400 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2413 (Rfree = 0.000) for 4099 atoms. Found 19 (19 requested) and removed 40 (9 requested) atoms. Cycle 27: After refmac, R = 0.2373 (Rfree = 0.000) for 4035 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. Cycle 28: After refmac, R = 0.2314 (Rfree = 0.000) for 4000 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 29: After refmac, R = 0.2383 (Rfree = 0.000) for 3973 atoms. Found 18 (18 requested) and removed 21 (9 requested) atoms. Cycle 30: After refmac, R = 0.2353 (Rfree = 0.000) for 3950 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.52 3.34 Search for helices and strands: 0 residues in 0 chains, 4088 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4105 seeds are put forward Round 1: 198 peptides, 43 chains. Longest chain 9 peptides. Score 0.243 Round 2: 247 peptides, 46 chains. Longest chain 14 peptides. Score 0.340 Round 3: 258 peptides, 46 chains. Longest chain 15 peptides. Score 0.368 Round 4: 265 peptides, 44 chains. Longest chain 14 peptides. Score 0.405 Round 5: 266 peptides, 47 chains. Longest chain 13 peptides. Score 0.377 Taking the results from Round 4 Chains 44, Residues 221, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6209 reflections ( 99.41 % complete ) and 9479 restraints for refining 4108 atoms. 8639 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2351 (Rfree = 0.000) for 4108 atoms. Found 19 (19 requested) and removed 36 (9 requested) atoms. Cycle 32: After refmac, R = 0.2326 (Rfree = 0.000) for 4056 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. Cycle 33: After refmac, R = 0.2407 (Rfree = 0.000) for 4030 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 34: After refmac, R = 0.2361 (Rfree = 0.000) for 3996 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 35: After refmac, R = 0.1933 (Rfree = 0.000) for 3982 atoms. Found 14 (18 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 3.40 Search for helices and strands: 0 residues in 0 chains, 4096 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4112 seeds are put forward Round 1: 202 peptides, 43 chains. Longest chain 11 peptides. Score 0.254 Round 2: 245 peptides, 47 chains. Longest chain 12 peptides. Score 0.324 Round 3: 247 peptides, 46 chains. Longest chain 9 peptides. Score 0.340 Round 4: 238 peptides, 40 chains. Longest chain 12 peptides. Score 0.382 Round 5: 241 peptides, 42 chains. Longest chain 12 peptides. Score 0.368 Taking the results from Round 4 Chains 40, Residues 198, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6209 reflections ( 99.41 % complete ) and 9478 restraints for refining 4037 atoms. 8726 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2645 (Rfree = 0.000) for 4037 atoms. Found 19 (19 requested) and removed 34 (9 requested) atoms. Cycle 37: After refmac, R = 0.2620 (Rfree = 0.000) for 3988 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. Cycle 38: After refmac, R = 0.2528 (Rfree = 0.000) for 3960 atoms. Found 18 (18 requested) and removed 24 (9 requested) atoms. Cycle 39: After refmac, R = 0.2353 (Rfree = 0.000) for 3934 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Cycle 40: After refmac, R = 0.2402 (Rfree = 0.000) for 3917 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 3.34 Search for helices and strands: 0 residues in 0 chains, 4019 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 4035 seeds are put forward Round 1: 156 peptides, 31 chains. Longest chain 11 peptides. Score 0.268 Round 2: 197 peptides, 39 chains. Longest chain 13 peptides. Score 0.287 Round 3: 203 peptides, 37 chains. Longest chain 12 peptides. Score 0.326 Round 4: 197 peptides, 36 chains. Longest chain 11 peptides. Score 0.322 Round 5: 187 peptides, 31 chains. Longest chain 16 peptides. Score 0.354 Taking the results from Round 5 Chains 31, Residues 156, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6209 reflections ( 99.41 % complete ) and 8989 restraints for refining 3879 atoms. 8396 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2565 (Rfree = 0.000) for 3879 atoms. Found 18 (18 requested) and removed 27 (9 requested) atoms. Cycle 42: After refmac, R = 0.2550 (Rfree = 0.000) for 3842 atoms. Found 18 (18 requested) and removed 22 (9 requested) atoms. Cycle 43: After refmac, R = 0.1957 (Rfree = 0.000) for 3823 atoms. Found 13 (18 requested) and removed 14 (9 requested) atoms. Cycle 44: After refmac, R = 0.1905 (Rfree = 0.000) for 3807 atoms. Found 9 (18 requested) and removed 15 (9 requested) atoms. Cycle 45: After refmac, R = 0.1837 (Rfree = 0.000) for 3793 atoms. Found 18 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.51 3.33 Search for helices and strands: 0 residues in 0 chains, 3874 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3895 seeds are put forward Round 1: 162 peptides, 34 chains. Longest chain 8 peptides. Score 0.248 Round 2: 187 peptides, 34 chains. Longest chain 10 peptides. Score 0.319 Round 3: 200 peptides, 34 chains. Longest chain 13 peptides. Score 0.353 Round 4: 180 peptides, 34 chains. Longest chain 8 peptides. Score 0.299 Round 5: 212 peptides, 35 chains. Longest chain 13 peptides. Score 0.372 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 177, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1vqs-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6209 reflections ( 99.41 % complete ) and 8622 restraints for refining 3851 atoms. 7917 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2632 (Rfree = 0.000) for 3851 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2632 (Rfree = 0.000) for 3816 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2041 (Rfree = 0.000) for 3786 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1980 (Rfree = 0.000) for 3770 atoms. TimeTaking 57.2