Mon 24 Dec 00:03:46 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 1vp7-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vp7-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vp7-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp7-4.0-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/1vp7-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp7-4.0-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 00:03:50 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/1vp7-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp7-4.0-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 482 and 0 Target number of residues in the AU: 482 Target solvent content: 0.6188 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: 1vp7-4.0-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: 177 Cell parameters: 106.979 106.979 207.138 90.000 90.000 120.000 Input sequence file: 1vp7-4.0-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 4.000 Wilson plot Bfac: 60.71 6430 reflections ( 99.47 % complete ) and 0 restraints for refining 5325 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3159 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3381 (Rfree = 0.000) for 5325 atoms. Found 25 (25 requested) and removed 44 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 3.37 Search for helices and strands: 0 residues in 0 chains, 5421 seeds are put forward NCS extension: 0 residues added, 5421 seeds are put forward Round 1: 172 peptides, 33 chains. Longest chain 10 peptides. Score 0.289 Round 2: 242 peptides, 38 chains. Longest chain 14 peptides. Score 0.412 Round 3: 241 peptides, 30 chains. Longest chain 21 peptides. Score 0.492 Round 4: 256 peptides, 32 chains. Longest chain 19 peptides. Score 0.505 Round 5: 262 peptides, 32 chains. Longest chain 25 peptides. Score 0.517 Taking the results from Round 5 Chains 34, Residues 230, Estimated correctness of the model 0.0 % 3 chains (37 residues) have been docked in sequence ------------------------------------------------------ 6430 reflections ( 99.47 % complete ) and 8993 restraints for refining 4045 atoms. 7974 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2718 (Rfree = 0.000) for 4045 atoms. Found 19 (19 requested) and removed 53 (9 requested) atoms. Cycle 2: After refmac, R = 0.2409 (Rfree = 0.000) for 3867 atoms. Found 19 (19 requested) and removed 47 (9 requested) atoms. Cycle 3: After refmac, R = 0.2316 (Rfree = 0.000) for 3763 atoms. Found 18 (18 requested) and removed 41 (9 requested) atoms. Cycle 4: After refmac, R = 0.2165 (Rfree = 0.000) for 3694 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Cycle 5: After refmac, R = 0.2142 (Rfree = 0.000) for 3651 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.48 3.34 Search for helices and strands: 0 residues in 0 chains, 3858 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3870 seeds are put forward Round 1: 196 peptides, 34 chains. Longest chain 9 peptides. Score 0.342 Round 2: 240 peptides, 35 chains. Longest chain 18 peptides. Score 0.439 Round 3: 220 peptides, 31 chains. Longest chain 16 peptides. Score 0.435 Round 4: 228 peptides, 30 chains. Longest chain 17 peptides. Score 0.464 Round 5: 236 peptides, 31 chains. Longest chain 18 peptides. Score 0.471 Taking the results from Round 5 Chains 31, Residues 205, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6430 reflections ( 99.47 % complete ) and 8494 restraints for refining 3684 atoms. 7705 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2647 (Rfree = 0.000) for 3684 atoms. Found 17 (17 requested) and removed 35 (8 requested) atoms. Cycle 7: After refmac, R = 0.2486 (Rfree = 0.000) for 3585 atoms. Found 17 (17 requested) and removed 28 (8 requested) atoms. Cycle 8: After refmac, R = 0.2524 (Rfree = 0.000) for 3526 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 9: After refmac, R = 0.2299 (Rfree = 0.000) for 3479 atoms. Found 16 (16 requested) and removed 27 (8 requested) atoms. Cycle 10: After refmac, R = 0.2275 (Rfree = 0.000) for 3448 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.45 3.31 Search for helices and strands: 0 residues in 0 chains, 3647 seeds are put forward NCS extension: 23 residues added (5 deleted due to clashes), 3670 seeds are put forward Round 1: 215 peptides, 37 chains. Longest chain 11 peptides. Score 0.357 Round 2: 236 peptides, 34 chains. Longest chain 20 peptides. Score 0.440 Round 3: 241 peptides, 35 chains. Longest chain 14 peptides. Score 0.441 Round 4: 231 peptides, 33 chains. Longest chain 14 peptides. Score 0.439 Round 5: 232 peptides, 29 chains. Longest chain 27 peptides. Score 0.483 Taking the results from Round 5 Chains 31, Residues 203, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 6430 reflections ( 99.47 % complete ) and 7967 restraints for refining 3640 atoms. 7110 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2585 (Rfree = 0.000) for 3640 atoms. Found 17 (17 requested) and removed 46 (8 requested) atoms. Cycle 12: After refmac, R = 0.2417 (Rfree = 0.000) for 3562 atoms. Found 17 (17 requested) and removed 47 (8 requested) atoms. Cycle 13: After refmac, R = 0.2244 (Rfree = 0.000) for 3493 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 14: After refmac, R = 0.2023 (Rfree = 0.000) for 3465 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 15: After refmac, R = 0.2016 (Rfree = 0.000) for 3455 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 3.40 Search for helices and strands: 0 residues in 0 chains, 3682 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 3706 seeds are put forward Round 1: 210 peptides, 33 chains. Longest chain 17 peptides. Score 0.389 Round 2: 235 peptides, 37 chains. Longest chain 13 peptides. Score 0.406 Round 3: 226 peptides, 31 chains. Longest chain 19 peptides. Score 0.449 Round 4: 231 peptides, 31 chains. Longest chain 20 peptides. Score 0.460 Round 5: 235 peptides, 32 chains. Longest chain 19 peptides. Score 0.459 Taking the results from Round 4 Chains 32, Residues 200, Estimated correctness of the model 0.0 % 2 chains (33 residues) have been docked in sequence ------------------------------------------------------ 6430 reflections ( 99.47 % complete ) and 7993 restraints for refining 3710 atoms. 7092 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2638 (Rfree = 0.000) for 3710 atoms. Found 17 (17 requested) and removed 48 (8 requested) atoms. Cycle 17: After refmac, R = 0.2411 (Rfree = 0.000) for 3615 atoms. Found 17 (17 requested) and removed 29 (8 requested) atoms. Cycle 18: After refmac, R = 0.2408 (Rfree = 0.000) for 3560 atoms. Found 17 (17 requested) and removed 35 (8 requested) atoms. Cycle 19: After refmac, R = 0.1950 (Rfree = 0.000) for 3508 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 20: After refmac, R = 0.2057 (Rfree = 0.000) for 3495 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 3.37 Search for helices and strands: 0 residues in 0 chains, 3710 seeds are put forward NCS extension: 0 residues added, 3710 seeds are put forward Round 1: 212 peptides, 35 chains. Longest chain 14 peptides. Score 0.372 Round 2: 216 peptides, 28 chains. Longest chain 16 peptides. Score 0.458 Round 3: 224 peptides, 28 chains. Longest chain 17 peptides. Score 0.476 Round 4: 223 peptides, 28 chains. Longest chain 19 peptides. Score 0.473 Round 5: 236 peptides, 28 chains. Longest chain 19 peptides. Score 0.502 Taking the results from Round 5 Chains 28, Residues 208, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6430 reflections ( 99.47 % complete ) and 8301 restraints for refining 3671 atoms. 7497 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2606 (Rfree = 0.000) for 3671 atoms. Found 17 (17 requested) and removed 48 (8 requested) atoms. Cycle 22: After refmac, R = 0.2251 (Rfree = 0.000) for 3614 atoms. Found 17 (17 requested) and removed 32 (8 requested) atoms. Cycle 23: After refmac, R = 0.2294 (Rfree = 0.000) for 3568 atoms. Found 17 (17 requested) and removed 24 (8 requested) atoms. Cycle 24: After refmac, R = 0.2177 (Rfree = 0.000) for 3543 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. Cycle 25: After refmac, R = 0.2180 (Rfree = 0.000) for 3513 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 3.30 Search for helices and strands: 0 residues in 0 chains, 3704 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3724 seeds are put forward Round 1: 203 peptides, 36 chains. Longest chain 10 peptides. Score 0.337 Round 2: 229 peptides, 32 chains. Longest chain 18 peptides. Score 0.445 Round 3: 224 peptides, 33 chains. Longest chain 18 peptides. Score 0.423 Round 4: 231 peptides, 33 chains. Longest chain 15 peptides. Score 0.439 Round 5: 236 peptides, 35 chains. Longest chain 20 peptides. Score 0.430 Taking the results from Round 2 Chains 32, Residues 197, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6430 reflections ( 99.47 % complete ) and 8000 restraints for refining 3574 atoms. 7244 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2367 (Rfree = 0.000) for 3574 atoms. Found 16 (16 requested) and removed 32 (8 requested) atoms. Cycle 27: After refmac, R = 0.2284 (Rfree = 0.000) for 3527 atoms. Found 16 (16 requested) and removed 28 (8 requested) atoms. Cycle 28: After refmac, R = 0.2260 (Rfree = 0.000) for 3506 atoms. Found 16 (16 requested) and removed 30 (8 requested) atoms. Cycle 29: After refmac, R = 0.2231 (Rfree = 0.000) for 3484 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. Cycle 30: After refmac, R = 0.2211 (Rfree = 0.000) for 3472 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 3.34 Search for helices and strands: 0 residues in 0 chains, 3677 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 3702 seeds are put forward Round 1: 191 peptides, 33 chains. Longest chain 12 peptides. Score 0.340 Round 2: 221 peptides, 32 chains. Longest chain 13 peptides. Score 0.426 Round 3: 222 peptides, 31 chains. Longest chain 17 peptides. Score 0.439 Round 4: 214 peptides, 32 chains. Longest chain 13 peptides. Score 0.410 Round 5: 201 peptides, 30 chains. Longest chain 13 peptides. Score 0.400 Taking the results from Round 3 Chains 31, Residues 191, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6430 reflections ( 99.47 % complete ) and 8167 restraints for refining 3598 atoms. 7434 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2604 (Rfree = 0.000) for 3598 atoms. Found 17 (17 requested) and removed 35 (8 requested) atoms. Cycle 32: After refmac, R = 0.2219 (Rfree = 0.000) for 3539 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Cycle 33: After refmac, R = 0.2171 (Rfree = 0.000) for 3512 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 34: After refmac, R = 0.2155 (Rfree = 0.000) for 3493 atoms. Found 16 (16 requested) and removed 28 (8 requested) atoms. Cycle 35: After refmac, R = 0.2159 (Rfree = 0.000) for 3472 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 3.27 Search for helices and strands: 0 residues in 0 chains, 3683 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 3696 seeds are put forward Round 1: 189 peptides, 35 chains. Longest chain 9 peptides. Score 0.312 Round 2: 218 peptides, 34 chains. Longest chain 15 peptides. Score 0.398 Round 3: 230 peptides, 38 chains. Longest chain 14 peptides. Score 0.384 Round 4: 234 peptides, 35 chains. Longest chain 18 peptides. Score 0.425 Round 5: 227 peptides, 40 chains. Longest chain 10 peptides. Score 0.354 Taking the results from Round 4 Chains 37, Residues 199, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6430 reflections ( 99.47 % complete ) and 8066 restraints for refining 3669 atoms. 7255 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2656 (Rfree = 0.000) for 3669 atoms. Found 17 (17 requested) and removed 39 (8 requested) atoms. Cycle 37: After refmac, R = 0.2463 (Rfree = 0.000) for 3610 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 38: After refmac, R = 0.2251 (Rfree = 0.000) for 3578 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. Cycle 39: After refmac, R = 0.2114 (Rfree = 0.000) for 3550 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 40: After refmac, R = 0.2222 (Rfree = 0.000) for 3539 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.50 3.36 Search for helices and strands: 0 residues in 0 chains, 3744 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 3757 seeds are put forward Round 1: 185 peptides, 37 chains. Longest chain 9 peptides. Score 0.277 Round 2: 213 peptides, 38 chains. Longest chain 13 peptides. Score 0.341 Round 3: 217 peptides, 35 chains. Longest chain 12 peptides. Score 0.384 Round 4: 222 peptides, 37 chains. Longest chain 20 peptides. Score 0.375 Round 5: 216 peptides, 35 chains. Longest chain 14 peptides. Score 0.382 Taking the results from Round 3 Chains 35, Residues 182, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6430 reflections ( 99.47 % complete ) and 8145 restraints for refining 3591 atoms. 7452 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2498 (Rfree = 0.000) for 3591 atoms. Found 17 (17 requested) and removed 33 (8 requested) atoms. Cycle 42: After refmac, R = 0.2293 (Rfree = 0.000) for 3539 atoms. Found 16 (16 requested) and removed 26 (8 requested) atoms. Cycle 43: After refmac, R = 0.2403 (Rfree = 0.000) for 3500 atoms. Found 16 (16 requested) and removed 25 (8 requested) atoms. Cycle 44: After refmac, R = 0.2273 (Rfree = 0.000) for 3471 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 45: After refmac, R = 0.2355 (Rfree = 0.000) for 3451 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.46 3.32 Search for helices and strands: 0 residues in 0 chains, 3618 seeds are put forward NCS extension: 12 residues added (4 deleted due to clashes), 3630 seeds are put forward Round 1: 156 peptides, 32 chains. Longest chain 9 peptides. Score 0.255 Round 2: 193 peptides, 34 chains. Longest chain 10 peptides. Score 0.334 Round 3: 203 peptides, 36 chains. Longest chain 12 peptides. Score 0.337 Round 4: 190 peptides, 33 chains. Longest chain 13 peptides. Score 0.338 Round 5: 200 peptides, 36 chains. Longest chain 10 peptides. Score 0.330 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 157, 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 1vp7-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6430 reflections ( 99.47 % complete ) and 7914 restraints for refining 3453 atoms. 7319 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2912 (Rfree = 0.000) for 3453 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2278 (Rfree = 0.000) for 3418 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2500 (Rfree = 0.000) for 3388 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2076 (Rfree = 0.000) for 3369 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... TimeTaking 54.52