Mon 24 Dec 00:54:12 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 1vp7-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vp7-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vp7-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp7-3.6-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/1vp7-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp7-3.6-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 00:54:17 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/1vp7-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp7-3.6-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: 0.5698 Checking the provided sequence file Detected sequence length: 100 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 600 Adjusted target solvent content: 0.53 Input MTZ file: 1vp7-3.6-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: 177 Cell parameters: 106.979 106.979 207.138 90.000 90.000 120.000 Input sequence file: 1vp7-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4800 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: 207.138 3.600 Wilson plot Bfac: 41.56 8705 reflections ( 99.61 % complete ) and 0 restraints for refining 5338 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3044 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3203 (Rfree = 0.000) for 5338 atoms. Found 34 (34 requested) and removed 48 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.12 3.00 Search for helices and strands: 0 residues in 0 chains, 5422 seeds are put forward NCS extension: 0 residues added, 5422 seeds are put forward Round 1: 188 peptides, 36 chains. Longest chain 13 peptides. Score 0.297 Round 2: 246 peptides, 36 chains. Longest chain 15 peptides. Score 0.443 Round 3: 272 peptides, 37 chains. Longest chain 17 peptides. Score 0.490 Round 4: 279 peptides, 42 chains. Longest chain 14 peptides. Score 0.457 Round 5: 293 peptides, 40 chains. Longest chain 17 peptides. Score 0.506 Taking the results from Round 5 Chains 40, Residues 253, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8705 reflections ( 99.61 % complete ) and 9075 restraints for refining 3950 atoms. 8103 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2886 (Rfree = 0.000) for 3950 atoms. Found 25 (25 requested) and removed 54 (12 requested) atoms. Cycle 2: After refmac, R = 0.2673 (Rfree = 0.000) for 3807 atoms. Found 24 (25 requested) and removed 39 (12 requested) atoms. Cycle 3: After refmac, R = 0.2537 (Rfree = 0.000) for 3746 atoms. Found 24 (24 requested) and removed 42 (12 requested) atoms. Cycle 4: After refmac, R = 0.2411 (Rfree = 0.000) for 3700 atoms. Found 23 (23 requested) and removed 23 (11 requested) atoms. Cycle 5: After refmac, R = 0.2460 (Rfree = 0.000) for 3692 atoms. Found 23 (23 requested) and removed 29 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.10 2.98 Search for helices and strands: 0 residues in 0 chains, 3879 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 3892 seeds are put forward Round 1: 245 peptides, 43 chains. Longest chain 13 peptides. Score 0.367 Round 2: 288 peptides, 39 chains. Longest chain 18 peptides. Score 0.505 Round 3: 281 peptides, 40 chains. Longest chain 18 peptides. Score 0.480 Round 4: 299 peptides, 40 chains. Longest chain 14 peptides. Score 0.518 Round 5: 289 peptides, 41 chains. Longest chain 15 peptides. Score 0.488 Taking the results from Round 4 Chains 42, Residues 259, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 8705 reflections ( 99.61 % complete ) and 8348 restraints for refining 3792 atoms. 7316 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2730 (Rfree = 0.000) for 3792 atoms. Found 24 (24 requested) and removed 35 (12 requested) atoms. Cycle 7: After refmac, R = 0.2555 (Rfree = 0.000) for 3731 atoms. Found 24 (24 requested) and removed 26 (12 requested) atoms. Cycle 8: After refmac, R = 0.2441 (Rfree = 0.000) for 3709 atoms. Found 22 (23 requested) and removed 21 (11 requested) atoms. Cycle 9: After refmac, R = 0.2360 (Rfree = 0.000) for 3700 atoms. Found 13 (23 requested) and removed 24 (11 requested) atoms. Cycle 10: After refmac, R = 0.2304 (Rfree = 0.000) for 3687 atoms. Found 6 (23 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.03 2.91 Search for helices and strands: 0 residues in 0 chains, 3852 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3865 seeds are put forward Round 1: 257 peptides, 39 chains. Longest chain 14 peptides. Score 0.437 Round 2: 279 peptides, 36 chains. Longest chain 18 peptides. Score 0.514 Round 3: 275 peptides, 36 chains. Longest chain 15 peptides. Score 0.506 Round 4: 268 peptides, 37 chains. Longest chain 15 peptides. Score 0.482 Round 5: 296 peptides, 39 chains. Longest chain 20 peptides. Score 0.521 Taking the results from Round 5 Chains 40, Residues 257, Estimated correctness of the model 0.0 % 2 chains (32 residues) have been docked in sequence ------------------------------------------------------ 8705 reflections ( 99.61 % complete ) and 8301 restraints for refining 3903 atoms. 7188 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2799 (Rfree = 0.000) for 3903 atoms. Found 25 (25 requested) and removed 51 (12 requested) atoms. Cycle 12: After refmac, R = 0.2682 (Rfree = 0.000) for 3819 atoms. Found 24 (24 requested) and removed 27 (12 requested) atoms. Cycle 13: After refmac, R = 0.2631 (Rfree = 0.000) for 3799 atoms. Found 24 (24 requested) and removed 22 (12 requested) atoms. Cycle 14: After refmac, R = 0.2537 (Rfree = 0.000) for 3787 atoms. Found 23 (24 requested) and removed 26 (12 requested) atoms. Cycle 15: After refmac, R = 0.2432 (Rfree = 0.000) for 3775 atoms. Found 11 (24 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.05 2.93 Search for helices and strands: 0 residues in 0 chains, 3977 seeds are put forward NCS extension: 5 residues added (2 deleted due to clashes), 3982 seeds are put forward Round 1: 231 peptides, 42 chains. Longest chain 11 peptides. Score 0.343 Round 2: 251 peptides, 38 chains. Longest chain 19 peptides. Score 0.433 Round 3: 249 peptides, 33 chains. Longest chain 20 peptides. Score 0.480 Round 4: 271 peptides, 37 chains. Longest chain 23 peptides. Score 0.488 Round 5: 271 peptides, 40 chains. Longest chain 17 peptides. Score 0.459 Taking the results from Round 4 Chains 37, Residues 234, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8705 reflections ( 99.61 % complete ) and 8675 restraints for refining 3861 atoms. 7776 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2743 (Rfree = 0.000) for 3861 atoms. Found 24 (24 requested) and removed 40 (12 requested) atoms. Cycle 17: After refmac, R = 0.2612 (Rfree = 0.000) for 3823 atoms. Found 24 (24 requested) and removed 30 (12 requested) atoms. Cycle 18: After refmac, R = 0.2575 (Rfree = 0.000) for 3798 atoms. Found 24 (24 requested) and removed 30 (12 requested) atoms. Cycle 19: After refmac, R = 0.2530 (Rfree = 0.000) for 3771 atoms. Found 24 (24 requested) and removed 27 (12 requested) atoms. Cycle 20: After refmac, R = 0.2416 (Rfree = 0.000) for 3757 atoms. Found 19 (24 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.98 2.86 Search for helices and strands: 0 residues in 0 chains, 3922 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 3944 seeds are put forward Round 1: 224 peptides, 45 chains. Longest chain 10 peptides. Score 0.291 Round 2: 244 peptides, 38 chains. Longest chain 15 peptides. Score 0.417 Round 3: 259 peptides, 40 chains. Longest chain 16 peptides. Score 0.431 Round 4: 268 peptides, 43 chains. Longest chain 15 peptides. Score 0.422 Round 5: 273 peptides, 41 chains. Longest chain 16 peptides. Score 0.453 Taking the results from Round 5 Chains 41, Residues 232, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 8705 reflections ( 99.61 % complete ) and 8814 restraints for refining 3906 atoms. 7902 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2705 (Rfree = 0.000) for 3906 atoms. Found 25 (25 requested) and removed 35 (12 requested) atoms. Cycle 22: After refmac, R = 0.2624 (Rfree = 0.000) for 3870 atoms. Found 24 (24 requested) and removed 32 (12 requested) atoms. Cycle 23: After refmac, R = 0.2492 (Rfree = 0.000) for 3852 atoms. Found 24 (24 requested) and removed 24 (12 requested) atoms. Cycle 24: After refmac, R = 0.2363 (Rfree = 0.000) for 3843 atoms. Found 19 (24 requested) and removed 17 (12 requested) atoms. Cycle 25: After refmac, R = 0.2477 (Rfree = 0.000) for 3830 atoms. Found 24 (24 requested) and removed 21 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.00 2.88 Search for helices and strands: 0 residues in 0 chains, 4001 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 4016 seeds are put forward Round 1: 234 peptides, 45 chains. Longest chain 12 peptides. Score 0.317 Round 2: 274 peptides, 47 chains. Longest chain 13 peptides. Score 0.395 Round 3: 276 peptides, 41 chains. Longest chain 14 peptides. Score 0.460 Round 4: 272 peptides, 44 chains. Longest chain 15 peptides. Score 0.421 Round 5: 283 peptides, 45 chains. Longest chain 13 peptides. Score 0.436 Taking the results from Round 3 Chains 41, Residues 235, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8705 reflections ( 99.61 % complete ) and 8872 restraints for refining 3935 atoms. 7973 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2685 (Rfree = 0.000) for 3935 atoms. Found 25 (25 requested) and removed 31 (12 requested) atoms. Cycle 27: After refmac, R = 0.2664 (Rfree = 0.000) for 3907 atoms. Found 25 (25 requested) and removed 25 (12 requested) atoms. Cycle 28: After refmac, R = 0.2568 (Rfree = 0.000) for 3899 atoms. Found 25 (25 requested) and removed 25 (12 requested) atoms. Cycle 29: After refmac, R = 0.2616 (Rfree = 0.000) for 3890 atoms. Found 25 (25 requested) and removed 30 (12 requested) atoms. Cycle 30: After refmac, R = 0.2272 (Rfree = 0.000) for 3878 atoms. Found 22 (24 requested) and removed 19 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.93 2.82 Search for helices and strands: 0 residues in 0 chains, 4084 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 4095 seeds are put forward Round 1: 242 peptides, 45 chains. Longest chain 16 peptides. Score 0.338 Round 2: 274 peptides, 39 chains. Longest chain 22 peptides. Score 0.475 Round 3: 285 peptides, 41 chains. Longest chain 20 peptides. Score 0.479 Round 4: 282 peptides, 42 chains. Longest chain 22 peptides. Score 0.463 Round 5: 281 peptides, 37 chains. Longest chain 20 peptides. Score 0.509 Taking the results from Round 5 Chains 37, Residues 244, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8705 reflections ( 99.61 % complete ) and 8957 restraints for refining 4005 atoms. 8018 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2743 (Rfree = 0.000) for 4005 atoms. Found 25 (25 requested) and removed 27 (12 requested) atoms. Cycle 32: After refmac, R = 0.2565 (Rfree = 0.000) for 3982 atoms. Found 19 (25 requested) and removed 24 (12 requested) atoms. Cycle 33: After refmac, R = 0.2431 (Rfree = 0.000) for 3966 atoms. Found 15 (25 requested) and removed 17 (12 requested) atoms. Cycle 34: After refmac, R = 0.2351 (Rfree = 0.000) for 3950 atoms. Found 11 (25 requested) and removed 16 (12 requested) atoms. Cycle 35: After refmac, R = 0.2386 (Rfree = 0.000) for 3937 atoms. Found 17 (25 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.98 2.86 Search for helices and strands: 0 residues in 0 chains, 4109 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 4138 seeds are put forward Round 1: 230 peptides, 46 chains. Longest chain 13 peptides. Score 0.296 Round 2: 251 peptides, 44 chains. Longest chain 14 peptides. Score 0.371 Round 3: 254 peptides, 46 chains. Longest chain 14 peptides. Score 0.357 Round 4: 254 peptides, 43 chains. Longest chain 17 peptides. Score 0.389 Round 5: 255 peptides, 42 chains. Longest chain 21 peptides. Score 0.402 Taking the results from Round 5 Chains 42, Residues 213, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8705 reflections ( 99.61 % complete ) and 9294 restraints for refining 4011 atoms. 8484 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2630 (Rfree = 0.000) for 4011 atoms. Found 25 (25 requested) and removed 39 (12 requested) atoms. Cycle 37: After refmac, R = 0.2486 (Rfree = 0.000) for 3989 atoms. Found 25 (25 requested) and removed 16 (12 requested) atoms. Cycle 38: After refmac, R = 0.2609 (Rfree = 0.000) for 3987 atoms. Found 25 (25 requested) and removed 23 (12 requested) atoms. Cycle 39: After refmac, R = 0.2500 (Rfree = 0.000) for 3979 atoms. Found 19 (25 requested) and removed 17 (12 requested) atoms. Cycle 40: After refmac, R = 0.2382 (Rfree = 0.000) for 3974 atoms. Found 17 (25 requested) and removed 19 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.94 2.82 Search for helices and strands: 0 residues in 0 chains, 4100 seeds are put forward NCS extension: 30 residues added (3 deleted due to clashes), 4130 seeds are put forward Round 1: 214 peptides, 45 chains. Longest chain 10 peptides. Score 0.264 Round 2: 226 peptides, 38 chains. Longest chain 25 peptides. Score 0.374 Round 3: 258 peptides, 46 chains. Longest chain 10 peptides. Score 0.367 Round 4: 257 peptides, 44 chains. Longest chain 15 peptides. Score 0.385 Round 5: 247 peptides, 41 chains. Longest chain 18 peptides. Score 0.393 Taking the results from Round 5 Chains 41, Residues 206, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 8705 reflections ( 99.61 % complete ) and 9124 restraints for refining 4051 atoms. 8243 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2502 (Rfree = 0.000) for 4051 atoms. Found 25 (25 requested) and removed 35 (12 requested) atoms. Cycle 42: After refmac, R = 0.2354 (Rfree = 0.000) for 4028 atoms. Found 18 (25 requested) and removed 23 (12 requested) atoms. Cycle 43: After refmac, R = 0.2315 (Rfree = 0.000) for 4017 atoms. Found 10 (25 requested) and removed 20 (12 requested) atoms. Cycle 44: After refmac, R = 0.2280 (Rfree = 0.000) for 4004 atoms. Found 6 (25 requested) and removed 18 (12 requested) atoms. Cycle 45: After refmac, R = 0.2283 (Rfree = 0.000) for 3990 atoms. Found 7 (25 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.01 2.89 Search for helices and strands: 0 residues in 0 chains, 4142 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 4153 seeds are put forward Round 1: 189 peptides, 38 chains. Longest chain 12 peptides. Score 0.277 Round 2: 241 peptides, 42 chains. Longest chain 12 peptides. Score 0.368 Round 3: 229 peptides, 37 chains. Longest chain 12 peptides. Score 0.392 Round 4: 228 peptides, 39 chains. Longest chain 12 peptides. Score 0.368 Round 5: 223 peptides, 38 chains. Longest chain 12 peptides. Score 0.366 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 37, Residues 192, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1vp7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8705 reflections ( 99.61 % complete ) and 9312 restraints for refining 4038 atoms. 8542 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2613 (Rfree = 0.000) for 4038 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2502 (Rfree = 0.000) for 4020 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.2484 (Rfree = 0.000) for 4005 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.2450 (Rfree = 0.000) for 3990 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Writing output files ... TimeTaking 73.65